--- _id: '9048' abstract: - lang: eng text: The analogy between an equilibrium partition function and the return probability in many-body unitary dynamics has led to the concept of dynamical quantum phase transition (DQPT). DQPTs are defined by nonanalyticities in the return amplitude and are present in many models. In some cases, DQPTs can be related to equilibrium concepts, such as order parameters, yet their universal description is an open question. In this Letter, we provide first steps toward a classification of DQPTs by using a matrix product state description of unitary dynamics in the thermodynamic limit. This allows us to distinguish the two limiting cases of “precession” and “entanglement” DQPTs, which are illustrated using an analytical description in the quantum Ising model. While precession DQPTs are characterized by a large entanglement gap and are semiclassical in their nature, entanglement DQPTs occur near avoided crossings in the entanglement spectrum and can be distinguished by a complex pattern of nonlocal correlations. We demonstrate the existence of precession and entanglement DQPTs beyond Ising models, discuss observables that can distinguish them, and relate their interplay to complex DQPT phenomenology. acknowledgement: "S. D. N. acknowledges funding from the Institute of Science and Technology (IST) Austria and from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. A. M. and M. S. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 Research and\r\nInnovation Programme (Grant Agreement No. 850899)." article_number: '040602' article_processing_charge: Yes article_type: original author: - first_name: Stefano full_name: De Nicola, Stefano id: 42832B76-F248-11E8-B48F-1D18A9856A87 last_name: De Nicola orcid: 0000-0002-4842-6671 - first_name: Alexios full_name: Michailidis, Alexios id: 36EBAD38-F248-11E8-B48F-1D18A9856A87 last_name: Michailidis orcid: 0000-0002-8443-1064 - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: De Nicola S, Michailidis A, Serbyn M. Entanglement view of dynamical quantum phase transitions. Physical Review Letters. 2021;126(4). doi:10.1103/physrevlett.126.040602 apa: De Nicola, S., Michailidis, A., & Serbyn, M. (2021). Entanglement view of dynamical quantum phase transitions. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.126.040602 chicago: De Nicola, Stefano, Alexios Michailidis, and Maksym Serbyn. “Entanglement View of Dynamical Quantum Phase Transitions.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/physrevlett.126.040602. ieee: S. De Nicola, A. Michailidis, and M. Serbyn, “Entanglement view of dynamical quantum phase transitions,” Physical Review Letters, vol. 126, no. 4. American Physical Society, 2021. ista: De Nicola S, Michailidis A, Serbyn M. 2021. Entanglement view of dynamical quantum phase transitions. Physical Review Letters. 126(4), 040602. mla: De Nicola, Stefano, et al. “Entanglement View of Dynamical Quantum Phase Transitions.” Physical Review Letters, vol. 126, no. 4, 040602, American Physical Society, 2021, doi:10.1103/physrevlett.126.040602. short: S. De Nicola, A. Michailidis, M. Serbyn, Physical Review Letters 126 (2021). date_created: 2021-02-01T09:20:00Z date_published: 2021-01-29T00:00:00Z date_updated: 2023-09-05T12:08:58Z day: '29' ddc: - '530' department: - _id: MaSe doi: 10.1103/physrevlett.126.040602 ec_funded: 1 external_id: arxiv: - '2008.04894' isi: - '000613148200001' file: - access_level: open_access checksum: d9acbc502390ed7a97e631d23ae19ecd content_type: application/pdf creator: dernst date_created: 2021-02-03T12:47:04Z date_updated: 2021-02-03T12:47:04Z file_id: '9074' file_name: 2021_PhysicalRevLett_DeNicola.pdf file_size: 398075 relation: main_file success: 1 file_date_updated: 2021-02-03T12:47:04Z has_accepted_license: '1' intvolume: ' 126' isi: 1 issue: '4' keyword: - General Physics and Astronomy language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Entanglement view of dynamical quantum phase transitions 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 126 year: '2021' ... --- _id: '9368' abstract: - lang: eng text: The quality control system for messenger RNA (mRNA) is fundamental for cellular activities in eukaryotes. To elucidate the molecular mechanism of 3'-Phosphoinositide-Dependent Protein Kinase1 (PDK1), a master regulator that is essential throughout eukaryotic growth and development, we employed a forward genetic approach to screen for suppressors of the loss-of-function T-DNA insertion double mutant pdk1.1 pdk1.2 in Arabidopsis thaliana. Notably, the severe growth attenuation of pdk1.1 pdk1.2 was rescued by sop21 (suppressor of pdk1.1 pdk1.2), which harbours a loss-of-function mutation in PELOTA1 (PEL1). PEL1 is a homologue of mammalian PELOTA and yeast (Saccharomyces cerevisiae) DOM34p, which each form a heterodimeric complex with the GTPase HBS1 (HSP70 SUBFAMILY B SUPPRESSOR1, also called SUPERKILLER PROTEIN7, SKI7), a protein that is responsible for ribosomal rescue and thereby assures the quality and fidelity of mRNA molecules during translation. Genetic analysis further revealed that a dysfunctional PEL1-HBS1 complex failed to degrade the T-DNA-disrupted PDK1 transcripts, which were truncated but functional, and thus rescued the growth and developmental defects of pdk1.1 pdk1.2. Our studies demonstrated the functionality of a homologous PELOTA-HBS1 complex and identified its essential regulatory role in plants, providing insights into the mechanism of mRNA quality control. acknowledgement: 'We gratefully acknowledge the Arabidopsis Biological Resource Centre (ABRC) for providing T-DNA insertional mutants, and Prof. Remko Offringa for sharing published seeds. We thank Yuchuan Liu (Shanghai OE Biotech Co., Ltd) for help with proteomics data analysis, Xixi Zhang (IST Austria) for providing the pDONR-P4P1r-mCherry plasmid, and Yao Xiao (Technical University of Munich), Alexander Johnson (IST Austria) and Hana Semeradova (IST Austria) for helpful discussions. The study was supported by National Natural Science Foundation of China (NSFC, 31721001, 91954206, to H.-W. X.), “Ten-Thousand Talent Program” (to H.-W. X.) and Collaborative Innovation Center of Crop Stress Biology, Henan Province, and Austrian Science Fund (FWF): I 3630-B25 (to J. F.). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015).' article_processing_charge: No article_type: original author: - first_name: W full_name: Kong, W last_name: Kong - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Q full_name: Zhao, Q last_name: Zhao - first_name: DL full_name: Lin, DL last_name: Lin - first_name: ZH full_name: Xu, ZH last_name: Xu - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: HW full_name: Xue, HW last_name: Xue citation: ama: Kong W, Tan S, Zhao Q, et al. mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. Plant Physiology. 2021;186(4):2003-2020. doi:10.1093/plphys/kiab199 apa: Kong, W., Tan, S., Zhao, Q., Lin, D., Xu, Z., Friml, J., & Xue, H. (2021). mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1093/plphys/kiab199 chicago: Kong, W, Shutang Tan, Q Zhao, DL Lin, ZH Xu, Jiří Friml, and HW Xue. “MRNA Surveillance Complex PELOTA-HBS1 Eegulates Phosphoinositide-Sependent Protein Kinase1 and Plant Growth.” Plant Physiology. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plphys/kiab199. ieee: W. Kong et al., “mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth,” Plant Physiology, vol. 186, no. 4. American Society of Plant Biologists, pp. 2003–2020, 2021. ista: Kong W, Tan S, Zhao Q, Lin D, Xu Z, Friml J, Xue H. 2021. mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. Plant Physiology. 186(4), 2003–2020. mla: Kong, W., et al. “MRNA Surveillance Complex PELOTA-HBS1 Eegulates Phosphoinositide-Sependent Protein Kinase1 and Plant Growth.” Plant Physiology, vol. 186, no. 4, American Society of Plant Biologists, 2021, pp. 2003–20, doi:10.1093/plphys/kiab199. short: W. Kong, S. Tan, Q. Zhao, D. Lin, Z. Xu, J. Friml, H. Xue, Plant Physiology 186 (2021) 2003–2020. date_created: 2021-05-03T13:28:20Z date_published: 2021-04-30T00:00:00Z date_updated: 2023-09-05T12:20:27Z day: '30' department: - _id: JiFr doi: 10.1093/plphys/kiab199 external_id: isi: - '000703922000025' pmid: - '33930167' intvolume: ' 186' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/plphys/kiab199 month: '04' oa: 1 oa_version: Published Version page: 2003-2020 pmid: 1 project: - _id: 256FEF10-B435-11E9-9278-68D0E5697425 grant_number: 723-2015 name: Long Term Fellowship - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants publication: Plant Physiology publication_identifier: eissn: - 1532-2548 issn: - 0032-0889 publication_status: published publisher: American Society of Plant Biologists quality_controlled: '1' status: public title: mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 186 year: '2021' ... --- _id: '10860' abstract: - lang: eng text: A tight frame is the orthogonal projection of some orthonormal basis of Rn onto Rk. We show that a set of vectors is a tight frame if and only if the set of all cross products of these vectors is a tight frame. We reformulate a range of problems on the volume of projections (or sections) of regular polytopes in terms of tight frames and write a first-order necessary condition for local extrema of these problems. As applications, we prove new results for the problem of maximization of the volume of zonotopes. acknowledgement: The author was supported by the Swiss National Science Foundation grant 200021_179133. The author acknowledges the financial support from the Ministry of Education and Science of the Russian Federation in the framework of MegaGrant no. 075-15-2019-1926. article_processing_charge: No article_type: original author: - first_name: Grigory full_name: Ivanov, Grigory id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E last_name: Ivanov citation: ama: Ivanov G. Tight frames and related geometric problems. Canadian Mathematical Bulletin. 2021;64(4):942-963. doi:10.4153/s000843952000096x apa: Ivanov, G. (2021). Tight frames and related geometric problems. Canadian Mathematical Bulletin. Canadian Mathematical Society. https://doi.org/10.4153/s000843952000096x chicago: Ivanov, Grigory. “Tight Frames and Related Geometric Problems.” Canadian Mathematical Bulletin. Canadian Mathematical Society, 2021. https://doi.org/10.4153/s000843952000096x. ieee: G. Ivanov, “Tight frames and related geometric problems,” Canadian Mathematical Bulletin, vol. 64, no. 4. Canadian Mathematical Society, pp. 942–963, 2021. ista: Ivanov G. 2021. Tight frames and related geometric problems. Canadian Mathematical Bulletin. 64(4), 942–963. mla: Ivanov, Grigory. “Tight Frames and Related Geometric Problems.” Canadian Mathematical Bulletin, vol. 64, no. 4, Canadian Mathematical Society, 2021, pp. 942–63, doi:10.4153/s000843952000096x. short: G. Ivanov, Canadian Mathematical Bulletin 64 (2021) 942–963. date_created: 2022-03-18T09:55:59Z date_published: 2021-12-18T00:00:00Z date_updated: 2023-09-05T12:43:09Z day: '18' department: - _id: UlWa doi: 10.4153/s000843952000096x external_id: arxiv: - '1804.10055' isi: - '000730165300021' intvolume: ' 64' isi: 1 issue: '4' keyword: - General Mathematics - Tight frame - Grassmannian - zonotope language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.10055 month: '12' oa: 1 oa_version: Preprint page: 942-963 publication: Canadian Mathematical Bulletin publication_identifier: eissn: - 1496-4287 issn: - 0008-4395 publication_status: published publisher: Canadian Mathematical Society quality_controlled: '1' scopus_import: '1' status: public title: Tight frames and related geometric problems type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 64 year: '2021' ... --- _id: '9290' abstract: - lang: eng text: Polar subcellular localization of the PIN exporters of the phytohormone auxin is a key determinant of directional, intercellular auxin transport and thus a central topic of both plant cell and developmental biology. Arabidopsis mutants lacking PID, a kinase that phosphorylates PINs, or the MAB4/MEL proteins of unknown molecular function display PIN polarity defects and phenocopy pin mutants, but mechanistic insights into how these factors convey PIN polarity are missing. Here, by combining protein biochemistry with quantitative live-cell imaging, we demonstrate that PINs, MAB4/MELs, and AGC kinases interact in the same complex at the plasma membrane. MAB4/MELs are recruited to the plasma membrane by the PINs and in concert with the AGC kinases maintain PIN polarity through limiting lateral diffusion-based escape of PINs from the polar domain. The PIN-MAB4/MEL-PID protein complex has self-reinforcing properties thanks to positive feedback between AGC kinase-mediated PIN phosphorylation and MAB4/MEL recruitment. We thus uncover the molecular mechanism by which AGC kinases and MAB4/MEL proteins regulate PIN localization and plant development. acknowledged_ssus: - _id: Bio acknowledgement: We acknowledge Ben Scheres, Christian Luschnig, and Claus Schwechheimer for sharing published material. We thank Monika Hrtyan and Dorota Jaworska at IST Austria and Gerda Lamers and Ward de Winter at IBL Netherlands for technical assistance; Corinna Hartinger, Jakub Hajný, Lesia Rodriguez, Mingyue Li, and Lindy Abas for experimental support; and the Bioimaging Facility at IST Austria and the Bioimaging Core at VIB for imaging support. We are grateful to Christian Luschnig, Lindy Abas, and Roman Pleskot for valuable discussions. We also acknowledge the EMBO for supporting M.G. with a long-term fellowship ( ALTF 1005-2019 ) during the finalization and revision of this manuscript in the laboratory of B.D.R., and we thank R. Pierik for allowing K.V.G. to work on this manuscript during a postdoc in his laboratory at Utrecht University. This work was supported by grants from the European Research Council under the European Union’s Seventh Framework Programme (ERC grant agreements 742985 to J.F., 714055 to B.D.R., and 803048 to M.F.), the Austrian Science Fund (FWF; I 3630-B25 to J.F.), Chemical Sciences (partly) financed by the Dutch Research Council (NWO-CW TOP 700.58.301 to R.O.), the Dutch Research Council (NWO-VICI 865.17.002 to R. Pierik), Grants-in-Aid from the Ministry of Education, Culture, Sports, Science and Technology, Japan (KAKENHI grant 17K17595 to S.N.), the Ministry of Education, Youth and Sports of the Czech Republic (MŠMT project NPUI-LO1417 ), and a China Scholarship Council (to X.W.). article_processing_charge: No article_type: original author: - first_name: Matous full_name: Glanc, Matous id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2 last_name: Glanc orcid: 0000-0003-0619-7783 - first_name: K full_name: Van Gelderen, K last_name: Van Gelderen - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer orcid: 0000-0001-8295-2926 - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: S full_name: Naramoto, S last_name: Naramoto - first_name: Xixi full_name: Zhang, Xixi id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A last_name: Zhang orcid: 0000-0001-7048-4627 - first_name: David full_name: Domjan, David id: C684CD7A-257E-11EA-9B6F-D8588B4F947F last_name: Domjan orcid: 0000-0003-2267-106X - first_name: L full_name: Vcelarova, L last_name: Vcelarova - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Alexander J full_name: Johnson, Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 - first_name: E full_name: de Koning, E last_name: de Koning - first_name: M full_name: van Dop, M last_name: van Dop - first_name: E full_name: Rademacher, E last_name: Rademacher - first_name: S full_name: Janson, S last_name: Janson - first_name: X full_name: Wei, X last_name: Wei - first_name: Gergely full_name: Molnar, Gergely id: 34F1AF46-F248-11E8-B48F-1D18A9856A87 last_name: Molnar - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: B full_name: De Rybel, B last_name: De Rybel - first_name: R full_name: Offringa, R last_name: Offringa - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Glanc M, Van Gelderen K, Hörmayer L, et al. AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. Current Biology. 2021;31(9):1918-1930. doi:10.1016/j.cub.2021.02.028 apa: Glanc, M., Van Gelderen, K., Hörmayer, L., Tan, S., Naramoto, S., Zhang, X., … Friml, J. (2021). AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2021.02.028 chicago: Glanc, Matous, K Van Gelderen, Lukas Hörmayer, Shutang Tan, S Naramoto, Xixi Zhang, David Domjan, et al. “AGC Kinases and MAB4/MEL Proteins Maintain PIN Polarity by Limiting Lateral Diffusion in Plant Cells.” Current Biology. Elsevier, 2021. https://doi.org/10.1016/j.cub.2021.02.028. ieee: M. Glanc et al., “AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells,” Current Biology, vol. 31, no. 9. Elsevier, pp. 1918–1930, 2021. ista: Glanc M, Van Gelderen K, Hörmayer L, Tan S, Naramoto S, Zhang X, Domjan D, Vcelarova L, Hauschild R, Johnson AJ, de Koning E, van Dop M, Rademacher E, Janson S, Wei X, Molnar G, Fendrych M, De Rybel B, Offringa R, Friml J. 2021. AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. Current Biology. 31(9), 1918–1930. mla: Glanc, Matous, et al. “AGC Kinases and MAB4/MEL Proteins Maintain PIN Polarity by Limiting Lateral Diffusion in Plant Cells.” Current Biology, vol. 31, no. 9, Elsevier, 2021, pp. 1918–30, doi:10.1016/j.cub.2021.02.028. short: M. Glanc, K. Van Gelderen, L. Hörmayer, S. Tan, S. Naramoto, X. Zhang, D. Domjan, L. Vcelarova, R. Hauschild, A.J. Johnson, E. de Koning, M. van Dop, E. Rademacher, S. Janson, X. Wei, G. Molnar, M. Fendrych, B. De Rybel, R. Offringa, J. Friml, Current Biology 31 (2021) 1918–1930. date_created: 2021-03-26T12:09:33Z date_published: 2021-03-10T00:00:00Z date_updated: 2023-09-05T13:03:34Z day: '10' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.cub.2021.02.028 ec_funded: 1 external_id: isi: - '000653077800004' pmid: - '33705718' file: - access_level: open_access checksum: b1723040ecfd8c81194185472eb62546 content_type: application/pdf creator: dernst date_created: 2021-04-01T10:53:42Z date_updated: 2021-04-01T10:53:42Z file_id: '9303' file_name: 2021_CurrentBiology_Glanc.pdf file_size: 4324371 relation: main_file success: 1 file_date_updated: 2021-04-01T10:53:42Z has_accepted_license: '1' intvolume: ' 31' isi: 1 issue: '9' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 1918-1930 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants publication: Current Biology publication_identifier: eissn: - 1879-0445 issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 31 year: '2021' ... --- _id: '8824' abstract: - lang: eng text: Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture.1 Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation.1, 2, 3 Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers.1, 2, 3, 4 In particular, the timing of this dynamic response is regulated by PIN2,5,6 but the underlying molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response. We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by acting as a negative regulator of the cell-surface signaling mediated by the receptor-like kinase TRANSMEMBRANE KINASE1 (TMK1).2,7, 8, 9, 10 Furthermore, we show that the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our findings suggest that the timing of the root gravitropic response is orchestrated by the reversible inhibition of the TMK1 signaling pathway at the cell surface. acknowledgement: "We thank the SiCE group for discussions and comments; S. Yalovsky, B. Scheres, and the NASC/ABRC collection for providing transgenic Arabidopsis lines and plasmids; L. Kalmbach and M. Barberon for the gift of pLOK180_pFR7m34GW; A. Lacroix, J. Berger, and P. Bolland for plant care; and M. Fendrych for help with microfluidics in the J.F. lab. We acknowledge\r\nthe contribution of the SFR Biosciences (UMS3444/CNRS, US8/Inser m, ENS de Lyon, UCBL) facilities: C. Lionet, E. Chatre, and J. Brocard at LBIPLATIM-MICROSCOPY for assistance with imaging, and V. GuegenChaignon and A. Page at the Protein Science Facility (PSF) for assistance with protein purification and mass spectrometry. Y.J. was funded by ERC\r\ngrant 3363360-APPL under FP/2007–2013. Y.J. and Z.L.N. were funded by an ANR- and NSF-supported ERA-CAPS project (SICOPID: ANR-17-CAPS0003-01/NSF PGRP IOS-1841917). A.I.C.-D. is funded by an ERC consolidator grant (ERC-2015-CoG–683163) and BIO2016-78955 grant from the Spanish Ministry of Economy and Competitiveness. Exchanges between the Y.J. and T.B. laboratories were funded by Tournesol grant 35656NB. B.K.M. was\r\nfunded by the Omics@vib Marie Curie COFUND and Research Foundation Flanders for a postdoctoral fellowship." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: MM full_name: Marquès-Bueno, MM last_name: Marquès-Bueno - first_name: L full_name: Armengot, L last_name: Armengot - first_name: LC full_name: Noack, LC last_name: Noack - first_name: J full_name: Bareille, J last_name: Bareille - first_name: Lesia full_name: Rodriguez Solovey, Lesia id: 3922B506-F248-11E8-B48F-1D18A9856A87 last_name: Rodriguez Solovey orcid: 0000-0002-7244-7237 - first_name: MP full_name: Platre, MP last_name: Platre - first_name: V full_name: Bayle, V last_name: Bayle - first_name: M full_name: Liu, M last_name: Liu - first_name: D full_name: Opdenacker, D last_name: Opdenacker - first_name: S full_name: Vanneste, S last_name: Vanneste - first_name: BK full_name: Möller, BK last_name: Möller - first_name: ZL full_name: Nimchuk, ZL last_name: Nimchuk - first_name: T full_name: Beeckman, T last_name: Beeckman - first_name: AI full_name: Caño-Delgado, AI last_name: Caño-Delgado - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Y full_name: Jaillais, Y last_name: Jaillais citation: ama: Marquès-Bueno M, Armengot L, Noack L, et al. Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current Biology. 2021;31(1). doi:10.1016/j.cub.2020.10.011 apa: Marquès-Bueno, M., Armengot, L., Noack, L., Bareille, J., Rodriguez Solovey, L., Platre, M., … Jaillais, Y. (2021). Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2020.10.011 chicago: Marquès-Bueno, MM, L Armengot, LC Noack, J Bareille, Lesia Rodriguez Solovey, MP Platre, V Bayle, et al. “Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism.” Current Biology. Elsevier, 2021. https://doi.org/10.1016/j.cub.2020.10.011. ieee: M. Marquès-Bueno et al., “Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism,” Current Biology, vol. 31, no. 1. Elsevier, 2021. ista: Marquès-Bueno M, Armengot L, Noack L, Bareille J, Rodriguez Solovey L, Platre M, Bayle V, Liu M, Opdenacker D, Vanneste S, Möller B, Nimchuk Z, Beeckman T, Caño-Delgado A, Friml J, Jaillais Y. 2021. Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current Biology. 31(1). mla: Marquès-Bueno, MM, et al. “Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism.” Current Biology, vol. 31, no. 1, Elsevier, 2021, doi:10.1016/j.cub.2020.10.011. short: M. Marquès-Bueno, L. Armengot, L. Noack, J. Bareille, L. Rodriguez Solovey, M. Platre, V. Bayle, M. Liu, D. Opdenacker, S. Vanneste, B. Möller, Z. Nimchuk, T. Beeckman, A. Caño-Delgado, J. Friml, Y. Jaillais, Current Biology 31 (2021). date_created: 2020-12-01T13:39:46Z date_published: 2021-01-11T00:00:00Z date_updated: 2023-09-05T13:03:15Z day: '11' ddc: - '570' department: - _id: JiFr doi: 10.1016/j.cub.2020.10.011 external_id: isi: - '000614361000039' pmid: - '33157019' file: - access_level: open_access checksum: 30b3393d841fb2b1e2b22fb42b5c8fff content_type: application/pdf creator: dernst date_created: 2021-02-04T11:37:50Z date_updated: 2021-02-04T11:37:50Z file_id: '9090' file_name: 2021_CurrentBiology_MarquesBueno.pdf file_size: 3458646 relation: main_file success: 1 file_date_updated: 2021-02-04T11:37:50Z has_accepted_license: '1' intvolume: ' 31' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Current Biology publication_identifier: eissn: - 1879-0445 issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 31 year: '2021' ... --- _id: '9301' abstract: - lang: eng text: Electrodepositing insulating lithium peroxide (Li2O2) is the key process during discharge of aprotic Li–O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and dissolved lithium superoxide governs whether Li2O2 grows as a conformal surface film or larger particles, leading to low or high capacities, respectively. However, better understanding governing factors for Li2O2 packing density and capacity requires structural sensitive in situ metrologies. Here, we establish in situ small- and wide-angle X-ray scattering (SAXS/WAXS) as a suitable method to record the Li2O2 phase evolution with atomic to submicrometer resolution during cycling a custom-built in situ Li–O2 cell. Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative structural information from complex multiphase systems. Surprisingly, we find that features are absent that would point at a Li2O2 surface film formed via two consecutive electron transfers, even in poorly solvating electrolytes thought to be prototypical for surface growth. All scattering data can be modeled by stacks of thin Li2O2 platelets potentially forming large toroidal particles. Li2O2 solution growth is further justified by rotating ring-disk electrode measurements and electron microscopy. Higher discharge overpotentials lead to smaller Li2O2 particles, but there is no transition to an electronically passivating, conformal Li2O2 coating. Hence, mass transport of reactive species rather than electronic transport through a Li2O2 film limits the discharge capacity. Provided that species mobilities and carbon surface areas are high, this allows for high discharge capacities even in weakly solvating electrolytes. The currently accepted Li–O2 reaction mechanism ought to be reconsidered. acknowledged_ssus: - _id: EM-Fac acknowledgement: S.A.F. and C.P. are indebted to the European Research Council under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 636069), the Austrian Federal Ministry of Science, Research and Economy, and the Austrian Research Promotion Agency (Grant No. 845364). We acknowledge A. Zankel and H. Schroettner for support with SEM measurements. C.P. thanks N. Kostoglou, C. Koczwara, M. Hartmann, and M. Burian for discussions on gas sorption analysis, C++ programming, Monte Carlo modeling, and in situ SAXS experiments, respectively. We thank S. Stadlbauer for help with Karl Fischer titration, R. Riccò for gas sorption measurements, and acknowledge Graz University of Technology for support through the Lead Project LP-03. Likewise, the use of SOMAPP Lab, a core facility supported by the Austrian Federal Ministry of Education, Science and Research, the Graz University of Technology, the University of Graz, and Anton Paar GmbH is acknowledged. S.A.F. is indebted to Institute of Science and Technology Austria (IST Austria) for support. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility. article_number: e2021893118 article_processing_charge: No article_type: original author: - first_name: Christian full_name: Prehal, Christian last_name: Prehal - first_name: Aleksej full_name: Samojlov, Aleksej last_name: Samojlov - first_name: Manfred full_name: Nachtnebel, Manfred last_name: Nachtnebel - first_name: Ludek full_name: Lovicar, Ludek id: 36DB3A20-F248-11E8-B48F-1D18A9856A87 last_name: Lovicar orcid: 0000-0001-6206-4200 - first_name: Manfred full_name: Kriechbaum, Manfred last_name: Kriechbaum - first_name: Heinz full_name: Amenitsch, Heinz last_name: Amenitsch - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Prehal C, Samojlov A, Nachtnebel M, et al. In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. 2021;118(14). doi:10.1073/pnas.2021893118 apa: Prehal, C., Samojlov, A., Nachtnebel, M., Lovicar, L., Kriechbaum, M., Amenitsch, H., & Freunberger, S. A. (2021). In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2021893118 chicago: Prehal, Christian, Aleksej Samojlov, Manfred Nachtnebel, Ludek Lovicar, Manfred Kriechbaum, Heinz Amenitsch, and Stefan Alexander Freunberger. “In Situ Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2021893118. ieee: C. Prehal et al., “In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes,” Proceedings of the National Academy of Sciences, vol. 118, no. 14. National Academy of Sciences, 2021. ista: Prehal C, Samojlov A, Nachtnebel M, Lovicar L, Kriechbaum M, Amenitsch H, Freunberger SA. 2021. In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. 118(14), e2021893118. mla: Prehal, Christian, et al. “In Situ Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” Proceedings of the National Academy of Sciences, vol. 118, no. 14, e2021893118, National Academy of Sciences, 2021, doi:10.1073/pnas.2021893118. short: C. Prehal, A. Samojlov, M. Nachtnebel, L. Lovicar, M. Kriechbaum, H. Amenitsch, S.A. Freunberger, Proceedings of the National Academy of Sciences 118 (2021). date_created: 2021-03-31T07:00:01Z date_published: 2021-04-06T00:00:00Z date_updated: 2023-09-05T13:27:18Z day: '06' department: - _id: StFr - _id: EM-Fac doi: 10.1073/pnas.2021893118 external_id: isi: - '000637398300050' intvolume: ' 118' isi: 1 issue: '14' keyword: - small-angle X-ray scattering - oxygen reduction - disproportionation - Li-air battery language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.26434/chemrxiv.11447775 month: '04' oa: 1 oa_version: Preprint publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' status: public title: In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 118 year: '2021' ... --- _id: '9094' abstract: - lang: eng text: Dendritic cells (DCs) are crucial for the priming of naive T cells and the initiation of adaptive immunity. Priming is initiated at a heterologous cell–cell contact, the immunological synapse (IS). While it is established that F-actin dynamics regulates signaling at the T cell side of the contact, little is known about the cytoskeletal contribution on the DC side. Here, we show that the DC actin cytoskeleton is decisive for the formation of a multifocal synaptic structure, which correlates with T cell priming efficiency. DC actin at the IS appears in transient foci that are dynamized by the WAVE regulatory complex (WRC). The absence of the WRC in DCs leads to stabilized contacts with T cells, caused by an increase in ICAM1-integrin–mediated cell–cell adhesion. This results in lower numbers of activated and proliferating T cells, demonstrating an important role for DC actin in the regulation of immune synapse functionality. article_number: e202006081 article_processing_charge: No article_type: original author: - first_name: Alexander F full_name: Leithner, Alexander F id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87 last_name: Leithner orcid: 0000-0002-1073-744X - first_name: LM full_name: Altenburger, LM last_name: Altenburger - first_name: R full_name: Hauschild, R last_name: Hauschild - first_name: Frank P full_name: Assen, Frank P id: 3A8E7F24-F248-11E8-B48F-1D18A9856A87 last_name: Assen orcid: 0000-0003-3470-6119 - first_name: K full_name: Rottner, K last_name: Rottner - first_name: Stradal full_name: TEB, Stradal last_name: TEB - first_name: A full_name: Diz-Muñoz, A last_name: Diz-Muñoz - first_name: JV full_name: Stein, JV last_name: Stein - 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: Leithner AF, Altenburger L, Hauschild R, et al. Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. Journal of Cell Biology. 2021;220(4). doi:10.1083/jcb.202006081 apa: Leithner, A. F., Altenburger, L., Hauschild, R., Assen, F. P., Rottner, K., TEB, S., … Sixt, M. K. (2021). Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202006081 chicago: Leithner, Alexander F, LM Altenburger, R Hauschild, Frank P Assen, K Rottner, Stradal TEB, A Diz-Muñoz, JV Stein, and Michael K Sixt. “Dendritic Cell Actin Dynamics Control Contact Duration and Priming Efficiency at the Immunological Synapse.” Journal of Cell Biology. Rockefeller University Press, 2021. https://doi.org/10.1083/jcb.202006081. ieee: A. F. Leithner et al., “Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse,” Journal of Cell Biology, vol. 220, no. 4. Rockefeller University Press, 2021. ista: Leithner AF, Altenburger L, Hauschild R, Assen FP, Rottner K, TEB S, Diz-Muñoz A, Stein J, Sixt MK. 2021. Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. Journal of Cell Biology. 220(4), e202006081. mla: Leithner, Alexander F., et al. “Dendritic Cell Actin Dynamics Control Contact Duration and Priming Efficiency at the Immunological Synapse.” Journal of Cell Biology, vol. 220, no. 4, e202006081, Rockefeller University Press, 2021, doi:10.1083/jcb.202006081. short: A.F. Leithner, L. Altenburger, R. Hauschild, F.P. Assen, K. Rottner, S. TEB, A. Diz-Muñoz, J. Stein, M.K. Sixt, Journal of Cell Biology 220 (2021). date_created: 2021-02-05T10:08:04Z date_published: 2021-04-05T00:00:00Z date_updated: 2023-09-05T13:57:53Z day: '05' ddc: - '570' department: - _id: MiSi doi: 10.1083/jcb.202006081 external_id: isi: - '000626365700001' pmid: - '33533935' file: - access_level: open_access checksum: 843ebc153847c8626e13c9c5ce71d533 content_type: application/pdf creator: dernst date_created: 2022-05-12T14:16:21Z date_updated: 2022-05-12T14:16:21Z file_id: '11367' file_name: 2021_JournCellBiology_Leithner.pdf file_size: 5102328 relation: main_file success: 1 file_date_updated: 2022-05-12T14:16:21Z has_accepted_license: '1' intvolume: ' 220' isi: 1 issue: '4' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '04' 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: Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 220 year: '2021' ... --- _id: '9073' abstract: - lang: eng text: The sensory and cognitive abilities of the mammalian neocortex are underpinned by intricate columnar and laminar circuits formed from an array of diverse neuronal populations. One approach to determining how interactions between these circuit components give rise to complex behavior is to investigate the rules by which cortical circuits are formed and acquire functionality during development. This review summarizes recent research on the development of the neocortex, from genetic determination in neural stem cells through to the dynamic role that specific neuronal populations play in the earliest circuits of neocortex, and how they contribute to emergent function and cognition. While many of these endeavors take advantage of model systems, consideration will also be given to advances in our understanding of activity in nascent human circuits. Such cross-species perspective is imperative when investigating the mechanisms underlying the dysfunction of early neocortical circuits in neurodevelopmental disorders, so that one can identify targets amenable to therapeutic intervention. acknowledgement: Work in the I.L.H.-O. laboratory was supported by European Research Council Grant ERC-2015-CoG 681577 and German Research Foundation Ha 4466/10-1, Ha4466/11-1, Ha4466/12-1, SPP 1665, and SFB 936B5. Work in the S.J.B.B. laboratory was supported by Biotechnology and Biological Sciences Research Council BB/P003796/1, Medical Research Council MR/K004387/1 and MR/T033320/1, Wellcome Trust 215199/Z/19/Z and 102386/Z/13/Z, and John Fell Fund. Work in the S.H. laboratory was supported by European Research Council Grants ERC-2016-CoG 725780 LinPro and FWF SFB F78. This work was supported by National Institutes of Health Grant NIMH 1R01MH110553 to N.V.D.M.G. Work in the J.A.C. laboratory was supported by the Ludwig Family Foundation, Simons Foundation SFARI Research Award, and National Institutes of Health/National Institute of Mental Health R01 MH102365 and R01MH113852. The B.V. laboratory was supported by Whitehall Foundation 2017-12-73, National Science Foundation 1736028, National Institutes of Health, National Institute of General Medical Sciences R01GM134363-01, and Halıcıoğlu Data Science Institute Fellowship. This work was supported by the University of California San Diego School of Medicine. article_processing_charge: No article_type: original author: - first_name: Ileana L. full_name: Hanganu-Opatz, Ileana L. last_name: Hanganu-Opatz - first_name: Simon J. B. full_name: Butt, Simon J. B. last_name: Butt - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Natalia V. full_name: De Marco García, Natalia V. last_name: De Marco García - first_name: Jessica A. full_name: Cardin, Jessica A. last_name: Cardin - first_name: Bradley full_name: Voytek, Bradley last_name: Voytek - first_name: Alysson R. full_name: Muotri, Alysson R. last_name: Muotri citation: ama: Hanganu-Opatz IL, Butt SJB, Hippenmeyer S, et al. The logic of developing neocortical circuits in health and disease. The Journal of Neuroscience. 2021;41(5):813-822. doi:10.1523/jneurosci.1655-20.2020 apa: Hanganu-Opatz, I. L., Butt, S. J. B., Hippenmeyer, S., De Marco García, N. V., Cardin, J. A., Voytek, B., & Muotri, A. R. (2021). The logic of developing neocortical circuits in health and disease. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/jneurosci.1655-20.2020 chicago: Hanganu-Opatz, Ileana L., Simon J. B. Butt, Simon Hippenmeyer, Natalia V. De Marco García, Jessica A. Cardin, Bradley Voytek, and Alysson R. Muotri. “The Logic of Developing Neocortical Circuits in Health and Disease.” The Journal of Neuroscience. Society for Neuroscience, 2021. https://doi.org/10.1523/jneurosci.1655-20.2020. ieee: I. L. Hanganu-Opatz et al., “The logic of developing neocortical circuits in health and disease,” The Journal of Neuroscience, vol. 41, no. 5. Society for Neuroscience, pp. 813–822, 2021. ista: Hanganu-Opatz IL, Butt SJB, Hippenmeyer S, De Marco García NV, Cardin JA, Voytek B, Muotri AR. 2021. The logic of developing neocortical circuits in health and disease. The Journal of Neuroscience. 41(5), 813–822. mla: Hanganu-Opatz, Ileana L., et al. “The Logic of Developing Neocortical Circuits in Health and Disease.” The Journal of Neuroscience, vol. 41, no. 5, Society for Neuroscience, 2021, pp. 813–22, doi:10.1523/jneurosci.1655-20.2020. short: I.L. Hanganu-Opatz, S.J.B. Butt, S. Hippenmeyer, N.V. De Marco García, J.A. Cardin, B. Voytek, A.R. Muotri, The Journal of Neuroscience 41 (2021) 813–822. date_created: 2021-02-03T12:23:51Z date_published: 2021-02-03T00:00:00Z date_updated: 2023-09-05T14:03:17Z day: '03' ddc: - '570' department: - _id: SiHi doi: 10.1523/jneurosci.1655-20.2020 ec_funded: 1 external_id: isi: - '000616763400002' pmid: - '33431633' file: - access_level: open_access checksum: 578fd7ed1a0aef74bce61bea2d987b33 content_type: application/pdf creator: dernst date_created: 2022-05-27T06:59:55Z date_updated: 2022-05-27T06:59:55Z file_id: '11414' file_name: 2021_JourNeuroscience_Hanganu.pdf file_size: 1031150 relation: main_file success: 1 file_date_updated: 2022-05-27T06:59:55Z has_accepted_license: '1' intvolume: ' 41' isi: 1 issue: '5' keyword: - General Neuroscience language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 813-822 pmid: 1 project: - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F07805 name: Molecular Mechanisms of Neural Stem Cell Lineage Progression publication: The Journal of Neuroscience publication_identifier: eissn: - 1529-2401 issn: - 0270-6474 publication_status: published publisher: Society for Neuroscience quality_controlled: '1' scopus_import: '1' status: public title: The logic of developing neocortical circuits in health and disease type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 41 year: '2021' ... --- _id: '10211' abstract: - lang: eng text: "We study the problem of recovering an unknown signal \U0001D465\U0001D465 given measurements obtained from a generalized linear model with a Gaussian sensing matrix. Two popular solutions are based on a linear estimator \U0001D465\U0001D465^L and a spectral estimator \U0001D465\U0001D465^s. The former is a data-dependent linear combination of the columns of the measurement matrix, and its analysis is quite simple. The latter is the principal eigenvector of a data-dependent matrix, and a recent line of work has studied its performance. In this paper, we show how to optimally combine \U0001D465\U0001D465^L and \U0001D465\U0001D465^s. At the heart of our analysis is the exact characterization of the empirical joint distribution of (\U0001D465\U0001D465,\U0001D465\U0001D465^L,\U0001D465\U0001D465^s) in the high-dimensional limit. This allows us to compute the Bayes-optimal combination of \U0001D465\U0001D465^L and \U0001D465\U0001D465^s, given the limiting distribution of the signal \U0001D465\U0001D465. When the distribution of the signal is Gaussian, then the Bayes-optimal combination has the form \U0001D703\U0001D465\U0001D465^L+\U0001D465\U0001D465^s and we derive the optimal combination coefficient. In order to establish the limiting distribution of (\U0001D465\U0001D465,\U0001D465\U0001D465^L,\U0001D465\U0001D465^s), we design and analyze an approximate message passing algorithm whose iterates give \U0001D465\U0001D465^L and approach \U0001D465\U0001D465^s. Numerical simulations demonstrate the improvement of the proposed combination with respect to the two methods considered separately." acknowledgement: M. Mondelli would like to thank Andrea Montanari for helpful discussions. All the authors would like to thank the anonymous reviewers for their helpful comments. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Christos full_name: Thrampoulidis, Christos last_name: Thrampoulidis - first_name: Ramji full_name: Venkataramanan, Ramji last_name: Venkataramanan citation: ama: Mondelli M, Thrampoulidis C, Venkataramanan R. Optimal combination of linear and spectral estimators for generalized linear models. Foundations of Computational Mathematics. 2021. doi:10.1007/s10208-021-09531-x apa: Mondelli, M., Thrampoulidis, C., & Venkataramanan, R. (2021). Optimal combination of linear and spectral estimators for generalized linear models. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-021-09531-x chicago: Mondelli, Marco, Christos Thrampoulidis, and Ramji Venkataramanan. “Optimal Combination of Linear and Spectral Estimators for Generalized Linear Models.” Foundations of Computational Mathematics. Springer, 2021. https://doi.org/10.1007/s10208-021-09531-x. ieee: M. Mondelli, C. Thrampoulidis, and R. Venkataramanan, “Optimal combination of linear and spectral estimators for generalized linear models,” Foundations of Computational Mathematics. Springer, 2021. ista: Mondelli M, Thrampoulidis C, Venkataramanan R. 2021. Optimal combination of linear and spectral estimators for generalized linear models. Foundations of Computational Mathematics. mla: Mondelli, Marco, et al. “Optimal Combination of Linear and Spectral Estimators for Generalized Linear Models.” Foundations of Computational Mathematics, Springer, 2021, doi:10.1007/s10208-021-09531-x. short: M. Mondelli, C. Thrampoulidis, R. Venkataramanan, Foundations of Computational Mathematics (2021). date_created: 2021-11-03T10:59:08Z date_published: 2021-08-17T00:00:00Z date_updated: 2023-09-05T14:13:57Z day: '17' ddc: - '510' department: - _id: MaMo doi: 10.1007/s10208-021-09531-x external_id: arxiv: - '2008.03326' isi: - '000685721000001' file: - access_level: open_access checksum: 9ea12dd8045a0678000a3a59295221cb content_type: application/pdf creator: alisjak date_created: 2021-12-13T15:47:54Z date_updated: 2021-12-13T15:47:54Z file_id: '10542' file_name: 2021_Springer_Mondelli.pdf file_size: 2305731 relation: main_file success: 1 file_date_updated: 2021-12-13T15:47:54Z has_accepted_license: '1' isi: 1 keyword: - Applied Mathematics - Computational Theory and Mathematics - Computational Mathematics - Analysis language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Foundations of Computational Mathematics publication_identifier: eissn: - 1615-3383 issn: - 1615-3375 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Optimal combination of linear and spectral estimators for generalized linear models 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '8940' abstract: - lang: eng text: We quantise Whitney’s construction to prove the existence of a triangulation for any C^2 manifold, so that we get an algorithm with explicit bounds. We also give a new elementary proof, which is completely geometric. acknowledgement: This work has been funded by the European Research Council under the European Union’s ERC Grant Agreement Number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). The third author also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. Open access funding provided by the Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Jean-Daniel full_name: Boissonnat, Jean-Daniel last_name: Boissonnat - first_name: Siargey full_name: Kachanovich, Siargey last_name: Kachanovich - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: ama: 'Boissonnat J-D, Kachanovich S, Wintraecken M. Triangulating submanifolds: An elementary and quantified version of Whitney’s method. Discrete & Computational Geometry. 2021;66(1):386-434. doi:10.1007/s00454-020-00250-8' apa: 'Boissonnat, J.-D., Kachanovich, S., & Wintraecken, M. (2021). Triangulating submanifolds: An elementary and quantified version of Whitney’s method. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00250-8' chicago: 'Boissonnat, Jean-Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Triangulating Submanifolds: An Elementary and Quantified Version of Whitney’s Method.” Discrete & Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00250-8.' ieee: 'J.-D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Triangulating submanifolds: An elementary and quantified version of Whitney’s method,” Discrete & Computational Geometry, vol. 66, no. 1. Springer Nature, pp. 386–434, 2021.' ista: 'Boissonnat J-D, Kachanovich S, Wintraecken M. 2021. Triangulating submanifolds: An elementary and quantified version of Whitney’s method. Discrete & Computational Geometry. 66(1), 386–434.' mla: 'Boissonnat, Jean-Daniel, et al. “Triangulating Submanifolds: An Elementary and Quantified Version of Whitney’s Method.” Discrete & Computational Geometry, vol. 66, no. 1, Springer Nature, 2021, pp. 386–434, doi:10.1007/s00454-020-00250-8.' short: J.-D. Boissonnat, S. Kachanovich, M. Wintraecken, Discrete & Computational Geometry 66 (2021) 386–434. date_created: 2020-12-12T11:07:02Z date_published: 2021-07-01T00:00:00Z date_updated: 2023-09-05T15:02:40Z day: '01' ddc: - '516' department: - _id: HeEd doi: 10.1007/s00454-020-00250-8 ec_funded: 1 external_id: isi: - '000597770300001' file: - access_level: open_access checksum: c848986091e56699dc12de85adb1e39c content_type: application/pdf creator: kschuh date_created: 2021-08-06T09:52:29Z date_updated: 2021-08-06T09:52:29Z file_id: '9795' file_name: 2021_DescreteCompGeopmetry_Boissonnat.pdf file_size: 983307 relation: main_file success: 1 file_date_updated: 2021-08-06T09:52:29Z has_accepted_license: '1' intvolume: ' 66' isi: 1 issue: '1' keyword: - Theoretical Computer Science - Computational Theory and Mathematics - Geometry and Topology - Discrete Mathematics and Combinatorics language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 386-434 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Discrete & Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: 'Triangulating submanifolds: An elementary and quantified version of Whitney’s method' 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 66 year: '2021' ...