---
_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'
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creator: dernst
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file_name: 2021_JourNeuroscience_Hanganu.pdf
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isi: 1
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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'
...