---
OA_place: publisher
_id: '9962'
abstract:
- lang: eng
text: The brain is one of the largest and most complex organs and it is composed
of billions of neurons that communicate together enabling e.g. consciousness.
The cerebral cortex is the largest site of neural integration in the central nervous
system. Concerted radial migration of newly born cortical projection neurons,
from their birthplace to their final position, is a key step in the assembly of
the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal
migration in vivo are however still unclear. Recent evidence suggests that distinct
signaling cues act cell-autonomously but differentially at certain steps during
the overall migration process. Moreover, functional analysis of genetic mosaics
(mutant neurons present in wild-type/heterozygote environment) using the MADM
(Mosaic Analysis with Double Markers) analyses in comparison to global knockout
also indicate a significant degree of non-cell-autonomous and/or community effects
in the control of cortical neuron migration. The interactions of cell-intrinsic
(cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely
unknown. In part of this thesis work we established a MADM-based experimental
strategy for the quantitative analysis of cell-autonomous gene function versus
non-cell-autonomous and/or community effects. The direct comparison of mutant
neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional
and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively
analyze non-cell-autonomous effects. Such analysis enable the high-resolution
analysis of projection neuron migration dynamics in distinct environments with
concomitant isolation of genomic and proteomic profiles. Using these experimental
paradigms and in combination with computational modeling we show and characterize
the nature of non-cell-autonomous effects to coordinate radial neuron migration.
Furthermore, this thesis discusses recent developments in neurodevelopment with
focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal
migration.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
citation:
ama: Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in
radial projection neuron migration. 2021. doi:10.15479/at:ista:9962
apa: Hansen, A. H. (2021). Cell-autonomous gene function and non-cell-autonomous
effects in radial projection neuron migration. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:9962
chicago: Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous
Effects in Radial Projection Neuron Migration.” Institute of Science and Technology
Austria, 2021. https://doi.org/10.15479/at:ista:9962.
ieee: A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects
in radial projection neuron migration,” Institute of Science and Technology Austria,
2021.
ista: Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects
in radial projection neuron migration. Institute of Science and Technology Austria.
mla: Hansen, Andi H. Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects
in Radial Projection Neuron Migration. Institute of Science and Technology
Austria, 2021, doi:10.15479/at:ista:9962.
short: A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects
in Radial Projection Neuron Migration, Institute of Science and Technology Austria,
2021.
corr_author: '1'
date_created: 2021-08-29T12:36:50Z
date_published: 2021-09-02T00:00:00Z
date_updated: 2026-04-08T07:19:09Z
day: '02'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SiHi
doi: 10.15479/at:ista:9962
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date_updated: 2022-09-03T22:30:04Z
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file_name: Thesis_Hansen_PDFA-1a.pdf
file_size: 13457469
relation: main_file
file_date_updated: 2022-09-03T22:30:04Z
has_accepted_license: '1'
keyword:
- Neuronal migration
- Non-cell-autonomous
- Cell-autonomous
- Neurodevelopmental disease
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '182'
project:
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
grant_number: '24812'
name: Molecular mechanisms of radial neuronal migration
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8569'
relation: part_of_dissertation
status: public
- id: '960'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
title: Cell-autonomous gene function and non-cell-autonomous effects in radial projection
neuron migration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2021'
...
---
OA_place: repository
OA_type: green
_id: '10816'
abstract:
- lang: eng
text: Pattern separation is a fundamental brain computation that converts small
differences in input patterns into large differences in output patterns. Several
synaptic mechanisms of pattern separation have been proposed, including code expansion,
inhibition and plasticity; however, which of these mechanisms play a role in the
entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation
circuit, remains unclear. Here we show that a biologically realistic, full-scale
EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive
inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator.
Both external gamma-modulated inhibition and internal lateral inhibition mediated
by PV+-INs substantially contributed to pattern separation. Both local connectivity
and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness.
Similarly, mossy fiber synapses with conditional detonator properties contributed
to pattern separation. By contrast, perforant path synapses with Hebbian synaptic
plasticity and direct EC–CA3 connection shifted the network towards pattern completion.
Our results demonstrate that the specific properties of cells and synapses optimize
higher-order computations in biological networks and might be useful to improve
the deep learning capabilities of technical networks.
acknowledged_ssus:
- _id: SSU
acknowledgement: We thank A. Aertsen, N. Kopell, W. Maass, A. Roth, F. Stella and
T. Vogels for critically reading earlier versions of the manuscript. We are grateful
to F. Marr and C. Altmutter for excellent technical assistance, E. Kralli-Beller
for manuscript editing, and the Scientific Service Units of IST Austria for efficient
support. Finally, we thank T. Carnevale, L. Erdös, M. Hines, D. Nykamp and D. Schröder
for useful discussions, and R. Friedrich and S. Wiechert for sharing unpublished
data. This project received funding from the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (grant agreement
no. 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z
312-B27, Wittgenstein award to P.J. and P 31815 to S.J.G.).
article_processing_charge: No
article_type: original
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: 'Claudia '
full_name: 'Espinoza Martinez, Claudia '
id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87
last_name: Espinoza Martinez
orcid: 0000-0003-4710-2082
- first_name: Xiaomin
full_name: Zhang, Xiaomin
id: 423EC9C2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-0256-6529
- first_name: Benjamin
full_name: Suter, Benjamin
id: 4952F31E-F248-11E8-B48F-1D18A9856A87
last_name: Suter
orcid: 0000-0002-9885-6936
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
biorxivid: 1
citation:
ama: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity
rules and synaptic properties shape the efficacy of pattern separation in the
entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science.
2021;1(12):830-842. doi:10.1038/s43588-021-00157-1
apa: Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &
Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the
efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.
Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-021-00157-1
chicago: Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang,
Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties
Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3
Network.” Nature Computational Science. Springer Nature, 2021. https://doi.org/10.1038/s43588-021-00157-1.
ieee: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M.
Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern
separation in the entorhinal cortex–dentate gyrus–CA3 network,” Nature Computational
Science, vol. 1, no. 12. Springer Nature, pp. 830–842, 2021.
ista: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021.
How connectivity rules and synaptic properties shape the efficacy of pattern separation
in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science.
1(12), 830–842.
mla: Guzmán, José, et al. “How Connectivity Rules and Synaptic Properties Shape
the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3
Network.” Nature Computational Science, vol. 1, no. 12, Springer Nature,
2021, pp. 830–42, doi:10.1038/s43588-021-00157-1.
short: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas,
Nature Computational Science 1 (2021) 830–842.
corr_author: '1'
date_created: 2022-03-04T08:32:36Z
date_published: 2021-12-16T00:00:00Z
date_updated: 2026-07-28T12:15:17Z
day: '16'
ddc:
- '610'
department:
- _id: PeJo
doi: 10.1038/s43588-021-00157-1
ec_funded: 1
external_id:
biorxivid:
- 10.1101/647800
isi:
- '000888567500015'
file:
- access_level: open_access
checksum: 9fec5b667909ef52be96d502e4f8c2ae
content_type: application/pdf
creator: patrickd
date_created: 2022-06-02T12:51:07Z
date_updated: 2022-06-18T22:30:03Z
embargo: 2022-06-17
file_id: '11430'
file_name: Guzmanetal2021.pdf
file_size: 1699466
relation: main_file
- access_level: open_access
checksum: 52a005b13a114e3c3a28fa6bbe8b1a8d
content_type: application/pdf
creator: patrickd
date_created: 2022-06-02T12:53:47Z
date_updated: 2022-06-18T22:30:03Z
embargo: 2022-06-17
file_id: '11431'
file_name: Guzmanetal2021Suppl.pdf
file_size: 3005651
relation: supplementary_material
title: Supplementary Material
file_date_updated: 2022-06-18T22:30:03Z
has_accepted_license: '1'
intvolume: ' 1'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
page: 830-842
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
publication: Nature Computational Science
publication_identifier:
issn:
- 2662-8457
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/spot-the-difference/
record:
- id: '10110'
relation: software
status: public
scopus_import: '1'
status: public
title: How connectivity rules and synaptic properties shape the efficacy of pattern
separation in the entorhinal cortex–dentate gyrus–CA3 network
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2021'
...
---
_id: '9437'
abstract:
- lang: eng
text: The synaptic connection from medial habenula (MHb) to interpeduncular nucleus
(IPN) is critical for emotion-related behaviors and uniquely expresses R-type
Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel
tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates
or inhibits transmitter release from MHb terminals depending on the IPN subnucleus,
but the role of KCTDs is unknown. We therefore examined the localization and function
of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells
that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3
currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3
co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional
modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase
of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3
with KCTDs therefore scales synaptic strength independent of GBR activation.
acknowledgement: We are grateful to Akari Hagiwara and Toshihisa Ohtsuka for CAST
antibody, and Masahiko Watanabe for neurexin antibody. We thank David Adams for
kindly providing the stable Cav2.3 cell line. Cav2.3 KO mice were kindly provided
by Tsutomu Tanabe. This project has received funding from the European Research
Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020
research and innovation programme (ERC grant agreement no. 694539 to Ryuichi Shigemoto,
no. 692692 to Peter Jonas, and the Marie Skłodowska-Curie grant agreement no. 665385
to Cihan Önal), the Swiss National Science Foundation Grant 31003A-172881 to Bernhard
Bettler and Deutsche Forschungsgemeinschaft (For 2143) and BIOSS-2 to Akos Kulik.
article_number: e68274
article_processing_charge: No
article_type: original
author:
- first_name: Pradeep
full_name: Bhandari, Pradeep
id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87
last_name: Bhandari
orcid: 0000-0003-0863-4481
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Diego
full_name: Fernández-Fernández, Diego
last_name: Fernández-Fernández
- first_name: Thorsten
full_name: Fritzius, Thorsten
last_name: Fritzius
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
- first_name: Hüseyin C
full_name: Önal, Hüseyin C
id: 4659D740-F248-11E8-B48F-1D18A9856A87
last_name: Önal
orcid: 0000-0002-2771-2011
- first_name: Jacqueline-Claire
full_name: Montanaro-Punzengruber, Jacqueline-Claire
id: 3786AB44-F248-11E8-B48F-1D18A9856A87
last_name: Montanaro-Punzengruber
- first_name: Martin
full_name: Gassmann, Martin
last_name: Gassmann
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Akos
full_name: Kulik, Akos
last_name: Kulik
- first_name: Bernhard
full_name: Bettler, Bernhard
last_name: Bettler
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
citation:
ama: Bhandari P, Vandael DH, Fernández-Fernández D, et al. GABAB receptor auxiliary
subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife.
2021;10. doi:10.7554/ELIFE.68274
apa: Bhandari, P., Vandael, D. H., Fernández-Fernández, D., Fritzius, T., Kleindienst,
D., Önal, C., … Koppensteiner, P. (2021). GABAB receptor auxiliary subunits modulate
Cav2.3-mediated release from medial habenula terminals. ELife. eLife Sciences
Publications. https://doi.org/10.7554/ELIFE.68274
chicago: Bhandari, Pradeep, David H Vandael, Diego Fernández-Fernández, Thorsten
Fritzius, David Kleindienst, Cihan Önal, Jacqueline-Claire Montanaro-Punzengruber,
et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from
Medial Habenula Terminals.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/ELIFE.68274.
ieee: P. Bhandari et al., “GABAB receptor auxiliary subunits modulate Cav2.3-mediated
release from medial habenula terminals,” eLife, vol. 10. eLife Sciences
Publications, 2021.
ista: Bhandari P, Vandael DH, Fernández-Fernández D, Fritzius T, Kleindienst D,
Önal C, Montanaro-Punzengruber J-C, Gassmann M, Jonas PM, Kulik A, Bettler B,
Shigemoto R, Koppensteiner P. 2021. GABAB receptor auxiliary subunits modulate
Cav2.3-mediated release from medial habenula terminals. eLife. 10, e68274.
mla: Bhandari, Pradeep, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated
Release from Medial Habenula Terminals.” ELife, vol. 10, e68274, eLife
Sciences Publications, 2021, doi:10.7554/ELIFE.68274.
short: P. Bhandari, D.H. Vandael, D. Fernández-Fernández, T. Fritzius, D. Kleindienst,
C. Önal, J.-C. Montanaro-Punzengruber, M. Gassmann, P.M. Jonas, A. Kulik, B. Bettler,
R. Shigemoto, P. Koppensteiner, ELife 10 (2021).
date_created: 2021-05-30T22:01:23Z
date_published: 2021-04-29T00:00:00Z
date_updated: 2026-09-03T22:31:07Z
day: '29'
ddc:
- '570'
department:
- _id: RySh
- _id: PeJo
doi: 10.7554/ELIFE.68274
ec_funded: 1
external_id:
isi:
- '000651761700001'
pmid:
- '33913808'
file:
- access_level: open_access
checksum: 6ebcb79999f889766f7cd79ee134ad28
content_type: application/pdf
creator: cziletti
date_created: 2021-05-31T09:43:09Z
date_updated: 2021-05-31T09:43:09Z
file_id: '9440'
file_name: 2021_eLife_Bhandari.pdf
file_size: 8174719
relation: main_file
success: 1
file_date_updated: 2021-05-31T09:43:09Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: https://doi.org/10.1101/2020.04.16.045112
record:
- id: '19271'
relation: dissertation_contains
status: public
- id: '9562'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial
habenula terminals
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2021'
...
---
OA_place: publisher
_id: '9562'
abstract:
- lang: eng
text: Left-right asymmetries can be considered a fundamental organizational principle
of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell
synaptic connection shows an input-side dependent asymmetry where the hemispheric
location of the presynaptic CA3 neuron determines the synaptic properties. Left-input
synapses terminating on apical dendrites in stratum radiatum have a higher density
of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1
and smaller areas with less often perforated PSDs. On the other hand, left-input
synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities
than right-input ones. Apical and basal synapses further employ different signaling
pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize
synaptic membrane proteins with high sensitivity and resolution, and has been
used to reveal the asymmetry at the electron microscopic level. However, it requires
time-consuming manual demarcation of the synaptic surface for quantitative measurements.
To facilitate the analysis of replica labeling, I first developed a software named
Darea, which utilizes deep-learning to automatize this demarcation. With Darea
I characterized the synaptic distribution of NMDA and AMPA receptors as well as
the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I
explored the role of GluN2B and its carboxy-terminus in the establishment of input-side
dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B
expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged
to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were
detected. We further discovered a previously unknown functional asymmetry of GluN2A,
which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus
plays a critical role in normal formation of input-side dependent asymmetry.
acknowledged_ssus:
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
citation:
ama: 'Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor
subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning.
2021. doi:10.15479/at:ista:9562'
apa: 'Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated
by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis
by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562'
chicago: 'Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by
NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by
Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562.'
ieee: 'D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor
subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,”
Institute of Science and Technology Austria, 2021.'
ista: 'Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA
receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning.
Institute of Science and Technology Austria.'
mla: 'Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA
Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.'
short: 'D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor
Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning,
Institute of Science and Technology Austria, 2021.'
corr_author: '1'
date_created: 2021-06-17T14:10:47Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2026-07-06T13:11:44Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RySh
doi: 10.15479/at:ista:9562
file:
- access_level: open_access
checksum: 659df5518db495f679cb1df9e9bd1d94
content_type: application/pdf
creator: dkleindienst
date_created: 2021-06-17T14:03:14Z
date_updated: 2022-07-02T22:30:04Z
embargo: 2022-07-01
file_id: '9563'
file_name: Thesis.pdf
file_size: 77299142
relation: main_file
- access_level: closed
checksum: 3bcf63a2b19e5b6663be051bea332748
content_type: application/zip
creator: dkleindienst
date_created: 2021-06-17T14:04:30Z
date_updated: 2022-07-02T22:30:04Z
embargo_to: open_access
file_id: '9564'
file_name: Thesis_source.zip
file_size: 369804895
relation: source_file
file_date_updated: 2022-07-02T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '124'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9437'
relation: part_of_dissertation
status: public
- id: '612'
relation: part_of_dissertation
status: public
- id: '8532'
relation: part_of_dissertation
status: public
- id: '9756'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
title: '2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B
C-terminus and high-throughput image analysis by Deep-Learning'
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2021'
...
---
_id: '9756'
abstract:
- lang: eng
text: High-resolution visualization and quantification of membrane proteins contribute
to the understanding of their functions and the roles they play in physiological
and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica
labeling (SDS-FRL) is a powerful electron microscopy method to study quantitatively
the two-dimensional distribution of transmembrane proteins and their tightly associated
proteins. During treatment with SDS, intracellular organelles and proteins not
anchored to the replica are dissolved, whereas integral membrane proteins captured
and stabilized by carbon/platinum deposition remain on the replica. Their intra-
and extracellular domains become exposed on the surface of the replica, facilitating
the accessibility of antibodies and, therefore, providing higher labeling efficiency
than those obtained with other immunoelectron microscopy techniques. In this chapter,
we describe the protocols of SDS-FRL adapted for mammalian brain samples, and
optimization of the SDS treatment to increase the labeling efficiency for quantification
of Cav2.1, the alpha subunit of P/Q-type voltage-dependent calcium channels utilizing
deep learning algorithms.
acknowledgement: This work was supported by the European Union (European Research
Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.)
and the Austrian Academy of Sciences (DOC fellowship to D.K.).
alternative_title:
- Neuromethods
article_processing_charge: No
author:
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
- first_name: Harumi
full_name: Harada, Harumi
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: 'Kaufmann W, Kleindienst D, Harada H, Shigemoto R. High-Resolution localization
and quantitation of membrane proteins by SDS-digested freeze-fracture replica
labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain.
Vol 169. Neuromethods. New York: Humana Press; 2021:267-283. doi:10.1007/978-1-0716-1522-5_19'
apa: 'Kaufmann, W., Kleindienst, D., Harada, H., & Shigemoto, R. (2021). High-Resolution
localization and quantitation of membrane proteins by SDS-digested freeze-fracture
replica labeling (SDS-FRL). In Receptor and Ion Channel Detection in the Brain
(Vol. 169, pp. 267–283). New York: Humana Press. https://doi.org/10.1007/978-1-0716-1522-5_19'
chicago: 'Kaufmann, Walter, David Kleindienst, Harumi Harada, and Ryuichi Shigemoto.
“High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested
Freeze-Fracture Replica Labeling (SDS-FRL).” In Receptor and Ion Channel Detection
in the Brain, 169:267–83. Neuromethods. New York: Humana Press, 2021. https://doi.org/10.1007/978-1-0716-1522-5_19.'
ieee: 'W. Kaufmann, D. Kleindienst, H. Harada, and R. Shigemoto, “High-Resolution
localization and quantitation of membrane proteins by SDS-digested freeze-fracture
replica labeling (SDS-FRL),” in Receptor and Ion Channel Detection in the Brain,
vol. 169, New York: Humana Press, 2021, pp. 267–283.'
ista: 'Kaufmann W, Kleindienst D, Harada H, Shigemoto R. 2021.High-Resolution localization
and quantitation of membrane proteins by SDS-digested freeze-fracture replica
labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. Neuromethods,
vol. 169, 267–283.'
mla: Kaufmann, Walter, et al. “High-Resolution Localization and Quantitation of
Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).”
Receptor and Ion Channel Detection in the Brain, vol. 169, Humana Press,
2021, pp. 267–83, doi:10.1007/978-1-0716-1522-5_19.
short: W. Kaufmann, D. Kleindienst, H. Harada, R. Shigemoto, in:, Receptor and Ion
Channel Detection in the Brain, Humana Press, New York, 2021, pp. 267–283.
corr_author: '1'
das_tickbox: '1'
date_created: 2021-07-30T09:34:56Z
date_published: 2021-07-27T00:00:00Z
date_updated: 2026-09-03T22:31:07Z
day: '27'
ddc:
- '573'
department:
- _id: RySh
- _id: EM-Fac
doi: 10.1007/978-1-0716-1522-5_19
ec_funded: 1
has_accepted_license: '1'
intvolume: ' 169'
keyword:
- 'Freeze-fracture replica: Deep learning'
- Immunogold labeling
- Integral membrane protein
- Electron microscopy
language:
- iso: eng
month: '07'
oa_version: None
page: 267-283
place: New York
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
- _id: 25CBA828-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '720270'
name: Human Brain Project Specific Grant Agreement 1
publication: Receptor and Ion Channel Detection in the Brain
publication_identifier:
eisbn:
- '9781071615225'
isbn:
- '9781071615218'
publication_status: published
publisher: Humana Press
quality_controlled: '1'
related_material:
record:
- id: '9562'
relation: dissertation_contains
status: public
scopus_import: '1'
series_title: Neuromethods
status: public
title: High-Resolution localization and quantitation of membrane proteins by SDS-digested
freeze-fracture replica labeling (SDS-FRL)
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 169
year: '2021'
...
---
_id: '10110'
abstract:
- lang: eng
text: Pattern separation is a fundamental brain computation that converts small
differences in input patterns into large differences in output patterns. Several
synaptic mechanisms of pattern separation have been proposed, including code expansion,
inhibition and plasticity; however, which of these mechanisms play a role in the
entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation
circuit, remains unclear. Here we show that a biologically realistic, full-scale
EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive
inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator.
Both external gamma-modulated inhibition and internal lateral inhibition mediated
by PV+-INs substantially contributed to pattern separation. Both local connectivity
and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness.
Similarly, mossy fiber synapses with conditional detonator properties contributed
to pattern separation. By contrast, perforant path synapses with Hebbian synaptic
plasticity and direct EC–CA3 connection shifted the network towards pattern completion.
Our results demonstrate that the specific properties of cells and synapses optimize
higher-order computations in biological networks and might be useful to improve
the deep learning capabilities of technical networks.
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: 'Claudia '
full_name: 'Espinoza Martinez, Claudia '
id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87
last_name: Espinoza Martinez
orcid: 0000-0003-4710-2082
- first_name: Xiaomin
full_name: Zhang, Xiaomin
id: 423EC9C2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-0256-6529
- first_name: Benjamin
full_name: Suter, Benjamin
id: 4952F31E-F248-11E8-B48F-1D18A9856A87
last_name: Suter
orcid: 0000-0002-9885-6936
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity
rules and synaptic properties shape the efficacy of pattern separation in the
entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:10.15479/AT:ISTA:10110
apa: Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &
Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the
efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.
IST Austria. https://doi.org/10.15479/AT:ISTA:10110
chicago: Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang,
Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties
Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3
Network.” IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:10110.
ieee: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M.
Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern
separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.
ista: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021.
How connectivity rules and synaptic properties shape the efficacy of pattern separation
in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, 10.15479/AT:ISTA:10110.
mla: Guzmán, José, et al. How Connectivity Rules and Synaptic Properties Shape
the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3
Network. IST Austria, 2021, doi:10.15479/AT:ISTA:10110.
short: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas,
(2021).
date_created: 2021-10-08T06:44:22Z
date_published: 2021-12-16T00:00:00Z
date_updated: 2026-09-03T22:31:07Z
day: '16'
ddc:
- '005'
department:
- _id: PeJo
- _id: ScienComp
doi: 10.15479/AT:ISTA:10110
file:
- access_level: open_access
checksum: f92f8931cad0aa7e411c1715337bf408
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2021-10-08T08:46:04Z
date_updated: 2021-10-08T08:46:04Z
file_id: '10114'
file_name: patternseparation-main (1).zip
file_size: 332990101
relation: main_file
success: 1
file_date_updated: 2021-10-08T08:46:04Z
has_accepted_license: '1'
license: https://opensource.org/licenses/GPL-3.0
month: '12'
oa: 1
publisher: IST Austria
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/spot-the-difference/
record:
- id: '10816'
relation: used_for_analysis_in
status: public
status: public
title: How connectivity rules and synaptic properties shape the efficacy of pattern
separation in the entorhinal cortex–dentate gyrus–CA3 network
tmp:
legal_code_url: https://www.gnu.org/licenses/gpl-3.0.en.html
name: GNU General Public License 3.0
short: GPL 3.0
type: software
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '9760'
abstract:
- lang: eng
text: "The quantum approximate optimization algorithm (QAOA) is a prospective near-term
quantum algorithm due to its modest circuit depth and promising benchmarks. However,
an external parameter optimization required in the QAOA could become a performance
bottleneck. This motivates studies of the optimization landscape and search for
heuristic ways of parameter initialization. In this work we visualize the optimization
landscape of the QAOA applied to the MaxCut problem on random graphs, demonstrating
that random initialization of the QAOA is prone to converging to local minima
with suboptimal performance. We introduce the initialization of QAOA parameters
based on the Trotterized quantum annealing (TQA) protocol, parameterized by the
Trotter time step. We find that the TQA initialization allows to circumvent\r\nthe
issue of false minima for a broad range of time steps, yielding the same performance
as the best result out of an exponentially scaling number of random initializations.
Moreover, we demonstrate that the optimal value of the time step coincides with
the point of proliferation of Trotter errors in quantum annealing. Our results
suggest practical ways of initializing QAOA protocols on near-term quantum devices
and reveal new connections between QAOA and quantum annealing."
acknowledgement: We would like to thank D. Abanin and R. Medina for fruitful discussions
and A. Smith and I. Kim for valuable feedback on the manuscript. We acknowledge
support by the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation program (Grant Agreement No. 850899).
article_number: '491'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Stefan
full_name: Sack, Stefan
id: dd622248-f6e0-11ea-865d-ce382a1c81a5
last_name: Sack
orcid: 0000-0001-5400-8508
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Sack S, Serbyn M. Quantum annealing initialization of the quantum approximate
optimization algorithm. Quantum. 2021;5. doi:10.22331/Q-2021-07-01-491
apa: Sack, S., & Serbyn, M. (2021). Quantum annealing initialization of the
quantum approximate optimization algorithm. Quantum. Verein zur Förderung
des Open Access Publizierens in den Quantenwissenschaften. https://doi.org/10.22331/Q-2021-07-01-491
chicago: Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the
Quantum Approximate Optimization Algorithm.” Quantum. Verein zur Förderung
des Open Access Publizierens in den Quantenwissenschaften, 2021. https://doi.org/10.22331/Q-2021-07-01-491.
ieee: S. Sack and M. Serbyn, “Quantum annealing initialization of the quantum approximate
optimization algorithm,” Quantum, vol. 5. Verein zur Förderung des Open
Access Publizierens in den Quantenwissenschaften, 2021.
ista: Sack S, Serbyn M. 2021. Quantum annealing initialization of the quantum approximate
optimization algorithm. Quantum. 5, 491.
mla: Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum
Approximate Optimization Algorithm.” Quantum, vol. 5, 491, Verein zur Förderung
des Open Access Publizierens in den Quantenwissenschaften, 2021, doi:10.22331/Q-2021-07-01-491.
short: S. Sack, M. Serbyn, Quantum 5 (2021).
corr_author: '1'
date_created: 2021-08-01T22:01:21Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2026-09-03T22:31:11Z
day: '01'
ddc:
- '530'
department:
- _id: GradSch
- _id: MaSe
doi: 10.22331/Q-2021-07-01-491
ec_funded: 1
external_id:
arxiv:
- '2101.05742'
isi:
- '000669830600001'
file:
- access_level: open_access
checksum: 9706c2bb8e748e9b5b138381995a7f6f
content_type: application/pdf
creator: cchlebak
date_created: 2021-08-06T06:44:31Z
date_updated: 2021-08-06T06:44:31Z
file_id: '9774'
file_name: 2021_Quantum_Sack.pdf
file_size: 2312482
relation: main_file
file_date_updated: 2021-08-06T06:44:31Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Quantum
publication_identifier:
eissn:
- 2521-327X
publication_status: published
publisher: Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften
quality_controlled: '1'
related_material:
record:
- id: '14622'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Quantum annealing initialization of the quantum approximate optimization algorithm
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2021'
...
---
_id: '10299'
abstract:
- lang: eng
text: Turbulence generally arises in shear flows if velocities and hence, inertial
forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit
disordered motion even at vanishing inertia. Intermediate between these cases,
a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed
in a narrow Reynolds number interval. We here determine the origin of EIT in experiments
and show that characteristic EIT structures can be detected across an unexpectedly
wide range of parameters. Close to onset, a pattern of chevron-shaped streaks
emerges in qualitative agreement with linear and weakly nonlinear theory. However,
in experiments, the dynamics remain weakly chaotic, and the instability can be
traced to far lower Reynolds numbers than permitted by theory. For increasing
inertia, the flow undergoes a transformation to a wall mode composed of inclined
near-wall streaks and shear layers. This mode persists to what is known as the
“maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic
flows across more than three orders of magnitude in Reynolds number.
acknowledgement: We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg,
and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge
funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft
research unit FOR 2688.
article_number: e2102350118
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: George H
full_name: Choueiri, George H
id: 448BD5BC-F248-11E8-B48F-1D18A9856A87
last_name: Choueiri
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Sarath
full_name: Sankar, Sarath
last_name: Sankar
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation
of the origin and structure of elastoinertial turbulence. Proceedings of the
National Academy of Sciences of the United States of America. 2021;118(45).
doi:10.1073/pnas.2102350118
apa: Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., & Hof,
B. (2021). Experimental observation of the origin and structure of elastoinertial
turbulence. Proceedings of the National Academy of Sciences of the United States
of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2102350118
chicago: Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar,
and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial
Turbulence.” Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2102350118.
ieee: G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental
observation of the origin and structure of elastoinertial turbulence,” Proceedings
of the National Academy of Sciences of the United States of America, vol.
118, no. 45. National Academy of Sciences, 2021.
ista: Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental
observation of the origin and structure of elastoinertial turbulence. Proceedings
of the National Academy of Sciences of the United States of America. 118(45),
e2102350118.
mla: Choueiri, George H., et al. “Experimental Observation of the Origin and Structure
of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences
of the United States of America, vol. 118, no. 45, e2102350118, National Academy
of Sciences, 2021, doi:10.1073/pnas.2102350118.
short: G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings
of the National Academy of Sciences of the United States of America 118 (2021).
corr_author: '1'
date_created: 2021-11-17T13:24:24Z
date_published: 2021-11-03T00:00:00Z
date_updated: 2026-09-03T22:31:10Z
day: '03'
department:
- _id: BjHo
doi: 10.1073/pnas.2102350118
external_id:
arxiv:
- '2103.00023'
isi:
- '000720926900019'
pmid:
- ' 34732570'
intvolume: ' 118'
isi: 1
issue: '45'
keyword:
- multidisciplinary
- elastoinertial turbulence
- viscoelastic flows
- elastic instability
- drag reduction
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2103.00023
month: '11'
oa: 1
oa_version: Preprint
pmid: 1
project:
- _id: 238B8092-32DE-11EA-91FC-C7463DDC885E
call_identifier: FWF
grant_number: I04188
name: Instabilities in pulsating pipe flow in complex fluids
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '19906'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Experimental observation of the origin and structure of elastoinertial turbulence
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2021'
...
---
_id: '10861'
abstract:
- lang: eng
text: We introduce in this paper AMT2.0, a tool for qualitative and quantitative
analysis of hybrid continuous and Boolean signals that combine numerical values
and discrete events. The evaluation of the signals is based on rich temporal specifications
expressed in extended signal temporal logic, which integrates timed regular expressions
within signal temporal logic. The tool features qualitative monitoring (property
satisfaction checking), trace diagnostics for explaining and justifying property
violations and specification-driven measurement of quantitative features of the
signal. We demonstrate the tool functionality on several running examples and
case studies, and evaluate its performance.
article_processing_charge: No
article_type: original
author:
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Olivier
full_name: Lebeltel, Olivier
last_name: Lebeltel
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Dogan
full_name: Ulus, Dogan
last_name: Ulus
citation:
ama: 'Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. AMT 2.0: Qualitative and
quantitative trace analysis with extended signal temporal logic. International
Journal on Software Tools for Technology Transfer. 2020;22(6):741-758. doi:10.1007/s10009-020-00582-z'
apa: 'Nickovic, D., Lebeltel, O., Maler, O., Ferrere, T., & Ulus, D. (2020).
AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal
logic. International Journal on Software Tools for Technology Transfer.
Springer Nature. https://doi.org/10.1007/s10009-020-00582-z'
chicago: 'Nickovic, Dejan, Olivier Lebeltel, Oded Maler, Thomas Ferrere, and Dogan
Ulus. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal
Temporal Logic.” International Journal on Software Tools for Technology Transfer.
Springer Nature, 2020. https://doi.org/10.1007/s10009-020-00582-z.'
ieee: 'D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, and D. Ulus, “AMT 2.0: Qualitative
and quantitative trace analysis with extended signal temporal logic,” International
Journal on Software Tools for Technology Transfer, vol. 22, no. 6. Springer
Nature, pp. 741–758, 2020.'
ista: 'Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. 2020. AMT 2.0: Qualitative
and quantitative trace analysis with extended signal temporal logic. International
Journal on Software Tools for Technology Transfer. 22(6), 741–758.'
mla: 'Nickovic, Dejan, et al. “AMT 2.0: Qualitative and Quantitative Trace Analysis
with Extended Signal Temporal Logic.” International Journal on Software Tools
for Technology Transfer, vol. 22, no. 6, Springer Nature, 2020, pp. 741–58,
doi:10.1007/s10009-020-00582-z.'
short: D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, D. Ulus, International Journal
on Software Tools for Technology Transfer 22 (2020) 741–758.
date_created: 2022-03-18T10:10:53Z
date_published: 2020-08-03T00:00:00Z
date_updated: 2024-10-09T20:58:18Z
day: '03'
department:
- _id: ToHe
doi: 10.1007/s10009-020-00582-z
external_id:
isi:
- '000555398600001'
intvolume: ' 22'
isi: 1
issue: '6'
keyword:
- Information Systems
- Software
language:
- iso: eng
month: '08'
oa_version: None
page: 741-758
publication: International Journal on Software Tools for Technology Transfer
publication_identifier:
eissn:
- 1433-2787
issn:
- 1433-2779
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '299'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'AMT 2.0: Qualitative and quantitative trace analysis with extended signal
temporal logic'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 22
year: '2020'
...
---
_id: '10862'
abstract:
- lang: eng
text: We consider the sum of two large Hermitian matrices A and B with a Haar unitary
conjugation bringing them into a general relative position. We prove that the
eigenvalue density on the scale slightly above the local eigenvalue spacing is
asymptotically given by the free additive convolution of the laws of A and B as
the dimension of the matrix increases. This implies optimal rigidity of the eigenvalues
and optimal rate of convergence in Voiculescu's theorem. Our previous works [4],
[5] established these results in the bulk spectrum, the current paper completely
settles the problem at the spectral edges provided they have the typical square-root
behavior. The key element of our proof is to compensate the deterioration of the
stability of the subordination equations by sharp error estimates that properly
account for the local density near the edge. Our results also hold if the Haar
unitary matrix is replaced by the Haar orthogonal matrix.
acknowledgement: Partially supported by ERC Advanced Grant RANMAT No. 338804.
article_number: '108639'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Kevin
full_name: Schnelli, Kevin
last_name: Schnelli
citation:
ama: Bao Z, Erdös L, Schnelli K. Spectral rigidity for addition of random matrices
at the regular edge. Journal of Functional Analysis. 2020;279(7). doi:10.1016/j.jfa.2020.108639
apa: Bao, Z., Erdös, L., & Schnelli, K. (2020). Spectral rigidity for addition
of random matrices at the regular edge. Journal of Functional Analysis.
Elsevier. https://doi.org/10.1016/j.jfa.2020.108639
chicago: Bao, Zhigang, László Erdös, and Kevin Schnelli. “Spectral Rigidity for
Addition of Random Matrices at the Regular Edge.” Journal of Functional Analysis.
Elsevier, 2020. https://doi.org/10.1016/j.jfa.2020.108639.
ieee: Z. Bao, L. Erdös, and K. Schnelli, “Spectral rigidity for addition of random
matrices at the regular edge,” Journal of Functional Analysis, vol. 279,
no. 7. Elsevier, 2020.
ista: Bao Z, Erdös L, Schnelli K. 2020. Spectral rigidity for addition of random
matrices at the regular edge. Journal of Functional Analysis. 279(7), 108639.
mla: Bao, Zhigang, et al. “Spectral Rigidity for Addition of Random Matrices at
the Regular Edge.” Journal of Functional Analysis, vol. 279, no. 7, 108639,
Elsevier, 2020, doi:10.1016/j.jfa.2020.108639.
short: Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 279 (2020).
corr_author: '1'
date_created: 2022-03-18T10:18:59Z
date_published: 2020-10-15T00:00:00Z
date_updated: 2025-04-15T08:05:01Z
day: '15'
department:
- _id: LaEr
doi: 10.1016/j.jfa.2020.108639
ec_funded: 1
external_id:
arxiv:
- '1708.01597'
isi:
- '000559623200009'
intvolume: ' 279'
isi: 1
issue: '7'
keyword:
- Analysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.01597
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Journal of Functional Analysis
publication_identifier:
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spectral rigidity for addition of random matrices at the regular edge
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 279
year: '2020'
...
---
_id: '10865'
abstract:
- lang: eng
text: "We introduce the notion of Witness Maps as a cryptographic notion of a proof
system. A Unique Witness Map (UWM) deterministically maps all witnesses for an
\ NP statement to a single representative witness, resulting in a computationally
sound, deterministic-prover, non-interactive witness independent proof system.
A relaxation of UWM, called Compact Witness Map (CWM), maps all the witnesses
to a small number of witnesses, resulting in a “lossy” deterministic-prover, non-interactive
proof-system. We also define a Dual Mode Witness Map (DMWM) which adds an “extractable”
mode to a CWM.\r\nOur main construction is a DMWM for all NP relations, assuming
sub-exponentially secure indistinguishability obfuscation ( iO ), along with
standard cryptographic assumptions. The DMWM construction relies on a CWM and
a new primitive called Cumulative All-Lossy-But-One Trapdoor Functions (C-ALBO-TDF),
both of which are in turn instantiated based on iO and other primitives. Our
instantiation of a CWM is in fact a UWM; in turn, we show that a UWM implies Witness
Encryption. Along the way to constructing UWM and C-ALBO-TDF, we also construct,
from standard assumptions, Puncturable Digital Signatures and a new primitive
called Cumulative Lossy Trapdoor Functions (C-LTDF). The former improves up on
a construction of Bellare et al. (Eurocrypt 2016), who relied on sub-exponentially
secure iO and sub-exponentially secure OWF.\r\nAs an application of our constructions,
we show how to use a DMWM to construct the first leakage and tamper-resilient
signatures with a deterministic signer, thereby solving a decade old open problem
posed by Katz and Vaikunthanathan (Asiacrypt 2009), by Boyle, Segev and Wichs
(Eurocrypt 2011), as well as by Faonio and Venturi (Asiacrypt 2016). Our construction
achieves the optimal leakage rate of 1−o(1) ."
acknowledgement: We would like to thank the anonymous reviewers of PKC 2019 for their
useful comments and suggestions. We thank Omer Paneth for pointing out to us the
connection between Unique Witness Maps (UWM) and Witness encryption (WE). The first
author would like to acknowledge Pandu Rangan for his involvement during the initial
discussion phase of the project.
article_processing_charge: No
author:
- first_name: Suvradip
full_name: Chakraborty, Suvradip
id: B9CD0494-D033-11E9-B219-A439E6697425
last_name: Chakraborty
- first_name: Manoj
full_name: Prabhakaran, Manoj
last_name: Prabhakaran
- first_name: Daniel
full_name: Wichs, Daniel
last_name: Wichs
citation:
ama: 'Chakraborty S, Prabhakaran M, Wichs D. Witness maps and applications. In:
Kiayias A, ed. Public-Key Cryptography. Vol 12110. LNCS. Cham: Springer
Nature; 2020:220-246. doi:10.1007/978-3-030-45374-9_8'
apa: 'Chakraborty, S., Prabhakaran, M., & Wichs, D. (2020). Witness maps and
applications. In A. Kiayias (Ed.), Public-Key Cryptography (Vol. 12110,
pp. 220–246). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-45374-9_8'
chicago: 'Chakraborty, Suvradip, Manoj Prabhakaran, and Daniel Wichs. “Witness Maps
and Applications.” In Public-Key Cryptography, edited by A Kiayias, 12110:220–46.
LNCS. Cham: Springer Nature, 2020. https://doi.org/10.1007/978-3-030-45374-9_8.'
ieee: 'S. Chakraborty, M. Prabhakaran, and D. Wichs, “Witness maps and applications,”
in Public-Key Cryptography, vol. 12110, A. Kiayias, Ed. Cham: Springer
Nature, 2020, pp. 220–246.'
ista: 'Chakraborty S, Prabhakaran M, Wichs D. 2020.Witness maps and applications.
In: Public-Key Cryptography. vol. 12110, 220–246.'
mla: Chakraborty, Suvradip, et al. “Witness Maps and Applications.” Public-Key
Cryptography, edited by A Kiayias, vol. 12110, Springer Nature, 2020, pp.
220–46, doi:10.1007/978-3-030-45374-9_8.
short: S. Chakraborty, M. Prabhakaran, D. Wichs, in:, A. Kiayias (Ed.), Public-Key
Cryptography, Springer Nature, Cham, 2020, pp. 220–246.
corr_author: '1'
date_created: 2022-03-18T11:35:51Z
date_published: 2020-04-29T00:00:00Z
date_updated: 2026-04-16T10:21:31Z
day: '29'
doi: 10.1007/978-3-030-45374-9_8
editor:
- first_name: A
full_name: Kiayias, A
last_name: Kiayias
external_id:
isi:
- '001299210200008'
intvolume: ' 12110'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2020/090
month: '04'
oa: 1
oa_version: Preprint
page: 220-246
place: Cham
publication: Public-Key Cryptography
publication_identifier:
eisbn:
- '9783030453749'
eissn:
- 1611-3349
isbn:
- '9783030453732'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: Witness maps and applications
type: book_chapter
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 12110
year: '2020'
...
---
_id: '10866'
abstract:
- lang: eng
text: Recent discoveries have shown that, when two layers of van der Waals (vdW)
materials are superimposed with a relative twist angle between them, the electronic
properties of the coupled system can be dramatically altered. Here, we demonstrate
that a similar concept can be extended to the optics realm, particularly to propagating
phonon polaritons–hybrid light-matter interactions. To do this, we fabricate stacks
composed of two twisted slabs of a vdW crystal (α-MoO3) supporting anisotropic
phonon polaritons (PhPs), and image the propagation of the latter when launched
by localized sources. Our images reveal that, under a critical angle, the PhPs
isofrequency curve undergoes a topological transition, in which the propagation
of PhPs is strongly guided (canalization regime) along predetermined directions
without geometric spreading. These results demonstrate a new degree of freedom
(twist angle) for controlling the propagation of polaritons at the nanoscale with
potential for nanoimaging, (bio)-sensing, or heat management.
acknowledgement: "J.T.-G. and G.Á.-P. acknowledge support through the Severo Ochoa
Program from the\r\nGovernment of the Principality of Asturias (nos. PA-18-PF-BP17-126
and PA20-PF-BP19-053,\r\nrespectively). J. M-S acknowledges financial support through
the Ramón y Cajal Program from\r\nthe Government of Spain (RYC2018-026196-I). A.Y.N.
acknowledges the Spanish Ministry of\r\nScience, Innovation and Universities (national
project no. MAT201788358-C3-3-R). P.A.-G.\r\nacknowledges support from the European
Research Council under starting grant no. 715496,\r\n2DNANOPTICA."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jiahua
full_name: Duan, Jiahua
last_name: Duan
- first_name: Nathaniel
full_name: Capote-Robayna, Nathaniel
last_name: Capote-Robayna
- first_name: Javier
full_name: Taboada-Gutiérrez, Javier
last_name: Taboada-Gutiérrez
- first_name: Gonzalo
full_name: Álvarez-Pérez, Gonzalo
last_name: Álvarez-Pérez
- first_name: Ivan
full_name: Prieto Gonzalez, Ivan
id: 2A307FE2-F248-11E8-B48F-1D18A9856A87
last_name: Prieto Gonzalez
orcid: 0000-0002-7370-5357
- first_name: Javier
full_name: Martín-Sánchez, Javier
last_name: Martín-Sánchez
- first_name: Alexey Y.
full_name: Nikitin, Alexey Y.
last_name: Nikitin
- first_name: Pablo
full_name: Alonso-González, Pablo
last_name: Alonso-González
citation:
ama: 'Duan J, Capote-Robayna N, Taboada-Gutiérrez J, et al. Twisted nano-optics:
Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano
Letters. 2020;20(7):5323-5329. doi:10.1021/acs.nanolett.0c01673'
apa: 'Duan, J., Capote-Robayna, N., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Prieto
Gonzalez, I., Martín-Sánchez, J., … Alonso-González, P. (2020). Twisted nano-optics:
Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano
Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.0c01673'
chicago: 'Duan, Jiahua, Nathaniel Capote-Robayna, Javier Taboada-Gutiérrez, Gonzalo
Álvarez-Pérez, Ivan Prieto Gonzalez, Javier Martín-Sánchez, Alexey Y. Nikitin,
and Pablo Alonso-González. “Twisted Nano-Optics: Manipulating Light at the Nanoscale
with Twisted Phonon Polaritonic Slabs.” Nano Letters. American Chemical
Society, 2020. https://doi.org/10.1021/acs.nanolett.0c01673.'
ieee: 'J. Duan et al., “Twisted nano-optics: Manipulating light at the nanoscale
with twisted phonon polaritonic slabs,” Nano Letters, vol. 20, no. 7. American
Chemical Society, pp. 5323–5329, 2020.'
ista: 'Duan J, Capote-Robayna N, Taboada-Gutiérrez J, Álvarez-Pérez G, Prieto Gonzalez
I, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2020. Twisted nano-optics:
Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano
Letters. 20(7), 5323–5329.'
mla: 'Duan, Jiahua, et al. “Twisted Nano-Optics: Manipulating Light at the Nanoscale
with Twisted Phonon Polaritonic Slabs.” Nano Letters, vol. 20, no. 7, American
Chemical Society, 2020, pp. 5323–29, doi:10.1021/acs.nanolett.0c01673.'
short: J. Duan, N. Capote-Robayna, J. Taboada-Gutiérrez, G. Álvarez-Pérez, I. Prieto
Gonzalez, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Nano Letters 20
(2020) 5323–5329.
date_created: 2022-03-18T11:37:38Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2023-09-05T12:05:58Z
day: '01'
department:
- _id: NanoFab
doi: 10.1021/acs.nanolett.0c01673
external_id:
arxiv:
- '2004.14599'
isi:
- '000548893200082'
pmid:
- '32530634'
intvolume: ' 20'
isi: 1
issue: '7'
keyword:
- Mechanical Engineering
- Condensed Matter Physics
- General Materials Science
- General Chemistry
- Bioengineering
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2004.14599
month: '07'
oa: 1
oa_version: Preprint
page: 5323-5329
pmid: 1
publication: Nano Letters
publication_identifier:
eissn:
- 1530-6992
issn:
- 1530-6984
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon
polaritonic slabs'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 20
year: '2020'
...
---
_id: '10867'
abstract:
- lang: eng
text: In this paper we find a tight estimate for Gromov’s waist of the balls in
spaces of constant curvature, deduce the estimates for the balls in Riemannian
manifolds with upper bounds on the curvature (CAT(ϰ)-spaces), and establish similar
result for normed spaces.
acknowledgement: ' Supported by the Russian Foundation for Basic Research grant 18-01-00036.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Roman
full_name: Karasev, Roman
last_name: Karasev
citation:
ama: Akopyan A, Karasev R. Waist of balls in hyperbolic and spherical spaces. International
Mathematics Research Notices. 2020;2020(3):669-697. doi:10.1093/imrn/rny037
apa: Akopyan, A., & Karasev, R. (2020). Waist of balls in hyperbolic and spherical
spaces. International Mathematics Research Notices. Oxford University Press.
https://doi.org/10.1093/imrn/rny037
chicago: Akopyan, Arseniy, and Roman Karasev. “Waist of Balls in Hyperbolic and
Spherical Spaces.” International Mathematics Research Notices. Oxford University
Press, 2020. https://doi.org/10.1093/imrn/rny037.
ieee: A. Akopyan and R. Karasev, “Waist of balls in hyperbolic and spherical spaces,”
International Mathematics Research Notices, vol. 2020, no. 3. Oxford University
Press, pp. 669–697, 2020.
ista: Akopyan A, Karasev R. 2020. Waist of balls in hyperbolic and spherical spaces.
International Mathematics Research Notices. 2020(3), 669–697.
mla: Akopyan, Arseniy, and Roman Karasev. “Waist of Balls in Hyperbolic and Spherical
Spaces.” International Mathematics Research Notices, vol. 2020, no. 3,
Oxford University Press, 2020, pp. 669–97, doi:10.1093/imrn/rny037.
short: A. Akopyan, R. Karasev, International Mathematics Research Notices 2020 (2020)
669–697.
date_created: 2022-03-18T11:39:30Z
date_published: 2020-02-01T00:00:00Z
date_updated: 2023-08-24T14:19:55Z
day: '01'
department:
- _id: HeEd
doi: 10.1093/imrn/rny037
external_id:
arxiv:
- '1702.07513'
isi:
- '000522852700002'
intvolume: ' 2020'
isi: 1
issue: '3'
keyword:
- General Mathematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.07513
month: '02'
oa: 1
oa_version: Preprint
page: 669-697
publication: International Mathematics Research Notices
publication_identifier:
eissn:
- 1687-0247
issn:
- 1073-7928
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Waist of balls in hyperbolic and spherical spaces
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 2020
year: '2020'
...
---
_id: '11054'
abstract:
- lang: eng
text: In recent years, the nuclear pore complex (NPC) has emerged as a key player
in genome regulation and cellular homeostasis. New discoveries have revealed that
the NPC has multiple cellular functions besides mediating the molecular exchange
between the nucleus and the cytoplasm. In this review, we discuss non-transport
aspects of the NPC focusing on the NPC-genome interaction, the extreme longevity
of the NPC proteins, and NPC dysfunction in age-related diseases. The examples
summarized herein demonstrate that the NPC, which first evolved to enable the
biochemical communication between the nucleus and the cytoplasm, now doubles as
the gatekeeper of cellular identity and aging.
article_processing_charge: No
article_type: review
author:
- first_name: Ukrae H.
full_name: Cho, Ukrae H.
last_name: Cho
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: 'Cho UH, Hetzer M. Nuclear periphery takes center stage: The role of nuclear
pore complexes in cell identity and aging. Neuron. 2020;106(6):899-911.
doi:10.1016/j.neuron.2020.05.031'
apa: 'Cho, U. H., & Hetzer, M. (2020). Nuclear periphery takes center stage:
The role of nuclear pore complexes in cell identity and aging. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2020.05.031'
chicago: 'Cho, Ukrae H., and Martin Hetzer. “Nuclear Periphery Takes Center Stage:
The Role of Nuclear Pore Complexes in Cell Identity and Aging.” Neuron.
Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.05.031.'
ieee: 'U. H. Cho and M. Hetzer, “Nuclear periphery takes center stage: The role
of nuclear pore complexes in cell identity and aging,” Neuron, vol. 106,
no. 6. Elsevier, pp. 899–911, 2020.'
ista: 'Cho UH, Hetzer M. 2020. Nuclear periphery takes center stage: The role of
nuclear pore complexes in cell identity and aging. Neuron. 106(6), 899–911.'
mla: 'Cho, Ukrae H., and Martin Hetzer. “Nuclear Periphery Takes Center Stage: The
Role of Nuclear Pore Complexes in Cell Identity and Aging.” Neuron, vol.
106, no. 6, Elsevier, 2020, pp. 899–911, doi:10.1016/j.neuron.2020.05.031.'
short: U.H. Cho, M. Hetzer, Neuron 106 (2020) 899–911.
date_created: 2022-04-07T07:43:36Z
date_published: 2020-06-17T00:00:00Z
date_updated: 2024-10-14T11:15:26Z
day: '17'
doi: 10.1016/j.neuron.2020.05.031
extern: '1'
external_id:
pmid:
- '32553207'
intvolume: ' 106'
issue: '6'
keyword:
- General Neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.neuron.2020.05.031
month: '06'
oa: 1
oa_version: Published Version
page: 899-911
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Nuclear periphery takes center stage: The role of nuclear pore complexes in
cell identity and aging'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 106
year: '2020'
...
---
_id: '11055'
abstract:
- lang: eng
text: Vascular dysfunctions are a common feature of multiple age-related diseases.
However, modeling healthy and pathological aging of the human vasculature represents
an unresolved experimental challenge. Here, we generated induced vascular endothelial
cells (iVECs) and smooth muscle cells (iSMCs) by direct reprogramming of healthy
human fibroblasts from donors of different ages and Hutchinson-Gilford Progeria
Syndrome (HGPS) patients. iVECs induced from old donors revealed upregulation
of GSTM1 and PALD1, genes linked to oxidative stress, inflammation and endothelial
junction stability, as vascular aging markers. A functional assay performed on
PALD1 KD VECs demonstrated a recovery in vascular permeability. We found that
iSMCs from HGPS donors overexpressed bone morphogenetic protein (BMP)−4, which
plays a key role in both vascular calcification and endothelial barrier damage
observed in HGPS. Strikingly, BMP4 concentrations are higher in serum from HGPS
vs. age-matched mice. Furthermore, targeting BMP4 with blocking antibody recovered
the functionality of the vascular barrier in vitro, hence representing a potential
future therapeutic strategy to limit cardiovascular dysfunction in HGPS. These
results show that iVECs and iSMCs retain disease-related signatures, allowing
modeling of vascular aging and HGPS in vitro.
article_number: e54383
article_processing_charge: No
article_type: original
author:
- first_name: Simone
full_name: Bersini, Simone
last_name: Bersini
- first_name: Roberta
full_name: Schulte, Roberta
last_name: Schulte
- first_name: Ling
full_name: Huang, Ling
last_name: Huang
- first_name: Hannah
full_name: Tsai, Hannah
last_name: Tsai
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. Direct reprogramming of human
smooth muscle and vascular endothelial cells reveals defects associated with aging
and Hutchinson-Gilford progeria syndrome. eLife. 2020;9. doi:10.7554/elife.54383
apa: Bersini, S., Schulte, R., Huang, L., Tsai, H., & Hetzer, M. (2020). Direct
reprogramming of human smooth muscle and vascular endothelial cells reveals defects
associated with aging and Hutchinson-Gilford progeria syndrome. ELife.
eLife Sciences Publications. https://doi.org/10.7554/elife.54383
chicago: Bersini, Simone, Roberta Schulte, Ling Huang, Hannah Tsai, and Martin Hetzer.
“Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals
Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” ELife.
eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.54383.
ieee: S. Bersini, R. Schulte, L. Huang, H. Tsai, and M. Hetzer, “Direct reprogramming
of human smooth muscle and vascular endothelial cells reveals defects associated
with aging and Hutchinson-Gilford progeria syndrome,” eLife, vol. 9. eLife
Sciences Publications, 2020.
ista: Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. 2020. Direct reprogramming
of human smooth muscle and vascular endothelial cells reveals defects associated
with aging and Hutchinson-Gilford progeria syndrome. eLife. 9, e54383.
mla: Bersini, Simone, et al. “Direct Reprogramming of Human Smooth Muscle and Vascular
Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford
Progeria Syndrome.” ELife, vol. 9, e54383, eLife Sciences Publications,
2020, doi:10.7554/elife.54383.
short: S. Bersini, R. Schulte, L. Huang, H. Tsai, M. Hetzer, ELife 9 (2020).
date_created: 2022-04-07T07:43:48Z
date_published: 2020-09-08T00:00:00Z
date_updated: 2024-10-14T11:17:02Z
day: '08'
ddc:
- '570'
doi: 10.7554/elife.54383
extern: '1'
external_id:
pmid:
- '32896271'
file:
- access_level: open_access
checksum: f8b3821349a194050be02570d8fe7d4b
content_type: application/pdf
creator: dernst
date_created: 2022-04-08T06:53:10Z
date_updated: 2022-04-08T06:53:10Z
file_id: '11132'
file_name: 2020_eLife_Bersini.pdf
file_size: 4399825
relation: main_file
success: 1
file_date_updated: 2022-04-08T06:53:10Z
has_accepted_license: '1'
intvolume: ' 9'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Direct reprogramming of human smooth muscle and vascular endothelial cells
reveals defects associated with aging and Hutchinson-Gilford progeria syndrome
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2020'
...
---
_id: '11056'
abstract:
- lang: eng
text: Aging of the circulatory system correlates with the pathogenesis of a large
spectrum of diseases. However, it is largely unknown which factors drive the age-dependent
or pathological decline of the vasculature and how vascular defects relate to
tissue aging. The goal of the study is to design a multianalytical approach to
identify how the cellular microenvironment (i.e., fibroblasts) and serum from
healthy donors of different ages or Alzheimer disease (AD) patients can modulate
the functionality of organ-specific vascular endothelial cells (VECs). Long-living
human microvascular networks embedding VECs and fibroblasts from skin biopsies
are generated. RNA-seq, secretome analyses, and microfluidic assays demonstrate
that fibroblasts from young donors restore the functionality of aged endothelial
cells, an effect also achieved by serum from young donors. New biomarkers of vascular
aging are validated in human biopsies and it is shown that young serum induces
angiopoietin-like-4, which can restore compromised vascular barriers. This strategy
is then employed to characterize transcriptional/functional changes induced on
the blood–brain barrier by AD serum, demonstrating the importance of PTP4A3 in
the regulation of permeability. Features of vascular degeneration during aging
and AD are recapitulated, and a tool to identify novel biomarkers that can be
exploited to develop future therapeutics modulating vascular function is established.
article_number: '2000044'
article_processing_charge: No
article_type: original
author:
- first_name: Simone
full_name: Bersini, Simone
last_name: Bersini
- first_name: Rafael
full_name: Arrojo e Drigo, Rafael
last_name: Arrojo e Drigo
- first_name: Ling
full_name: Huang, Ling
last_name: Huang
- first_name: Maxim N.
full_name: Shokhirev, Maxim N.
last_name: Shokhirev
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. Transcriptional
and functional changes of the human microvasculature during physiological aging
and Alzheimer disease. Advanced Biosystems. 2020;4(5). doi:10.1002/adbi.202000044
apa: Bersini, S., Arrojo e Drigo, R., Huang, L., Shokhirev, M. N., & Hetzer,
M. (2020). Transcriptional and functional changes of the human microvasculature
during physiological aging and Alzheimer disease. Advanced Biosystems.
Wiley. https://doi.org/10.1002/adbi.202000044
chicago: Bersini, Simone, Rafael Arrojo e Drigo, Ling Huang, Maxim N. Shokhirev,
and Martin Hetzer. “Transcriptional and Functional Changes of the Human Microvasculature
during Physiological Aging and Alzheimer Disease.” Advanced Biosystems.
Wiley, 2020. https://doi.org/10.1002/adbi.202000044.
ieee: S. Bersini, R. Arrojo e Drigo, L. Huang, M. N. Shokhirev, and M. Hetzer, “Transcriptional
and functional changes of the human microvasculature during physiological aging
and Alzheimer disease,” Advanced Biosystems, vol. 4, no. 5. Wiley, 2020.
ista: Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. 2020. Transcriptional
and functional changes of the human microvasculature during physiological aging
and Alzheimer disease. Advanced Biosystems. 4(5), 2000044.
mla: Bersini, Simone, et al. “Transcriptional and Functional Changes of the Human
Microvasculature during Physiological Aging and Alzheimer Disease.” Advanced
Biosystems, vol. 4, no. 5, 2000044, Wiley, 2020, doi:10.1002/adbi.202000044.
short: S. Bersini, R. Arrojo e Drigo, L. Huang, M.N. Shokhirev, M. Hetzer, Advanced
Biosystems 4 (2020).
date_created: 2022-04-07T07:43:57Z
date_published: 2020-05-01T00:00:00Z
date_updated: 2024-10-14T11:18:07Z
day: '01'
ddc:
- '570'
doi: 10.1002/adbi.202000044
extern: '1'
external_id:
pmid:
- '32402127'
file:
- access_level: open_access
checksum: 5584d9a1609812dc75c02ce1e35d2ec0
content_type: application/pdf
creator: dernst
date_created: 2022-04-08T07:06:05Z
date_updated: 2022-04-08T07:06:05Z
file_id: '11134'
file_name: 2020_AdvancedBiosystems_Bersini.pdf
file_size: 2490829
relation: main_file
success: 1
file_date_updated: 2022-04-08T07:06:05Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '5'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- Biomedical Engineering
- Biomaterials
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Advanced Biosystems
publication_identifier:
issn:
- 2366-7478
- 2366-7478
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transcriptional and functional changes of the human microvasculature during
physiological aging and Alzheimer disease
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2020'
...
---
_id: '11057'
abstract:
- lang: eng
text: During mitosis, transcription of genomic DNA is dramatically reduced, before
it is reactivated during nuclear reformation in anaphase/telophase. Many aspects
of the underlying principles that mediate transcriptional memory and reactivation
in the daughter cells remain unclear. Here, we used ChIP-seq on synchronized cells
at different stages after mitosis to generate genome-wide maps of histone modifications.
Combined with EU-RNA-seq and Hi-C analyses, we found that during prometaphase,
promoters, enhancers, and insulators retain H3K4me3 and H3K4me1, while losing
H3K27ac. Enhancers globally retaining mitotic H3K4me1 or locally retaining mitotic
H3K27ac are associated with cell type-specific genes and their transcription factors
for rapid transcriptional activation. As cells exit mitosis, promoters regain
H3K27ac, which correlates with transcriptional reactivation. Insulators also gain
H3K27ac and CCCTC-binding factor (CTCF) in anaphase/telophase. This increase of
H3K27ac in anaphase/telophase is required for posttranscriptional activation and
may play a role in the establishment of topologically associating domains (TADs).
Together, our results suggest that the genome is reorganized in a sequential order,
in which histone methylations occur first in prometaphase, histone acetylation,
and CTCF in anaphase/telophase, transcription in cytokinesis, and long-range chromatin
interactions in early G1. We thus provide insights into the histone modification
landscape that allows faithful reestablishment of the transcriptional program
and TADs during cell division.
article_processing_charge: No
article_type: original
author:
- first_name: Hyeseon
full_name: Kang, Hyeseon
last_name: Kang
- first_name: Maxim N.
full_name: Shokhirev, Maxim N.
last_name: Shokhirev
- first_name: Zhichao
full_name: Xu, Zhichao
last_name: Xu
- first_name: Sahaana
full_name: Chandran, Sahaana
last_name: Chandran
- first_name: Jesse R.
full_name: Dixon, Jesse R.
last_name: Dixon
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer M. Dynamic regulation
of histone modifications and long-range chromosomal interactions during postmitotic
transcriptional reactivation. Genes & Development. 2020;34(13-14):913-930.
doi:10.1101/gad.335794.119
apa: Kang, H., Shokhirev, M. N., Xu, Z., Chandran, S., Dixon, J. R., & Hetzer,
M. (2020). Dynamic regulation of histone modifications and long-range chromosomal
interactions during postmitotic transcriptional reactivation. Genes & Development.
Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.335794.119
chicago: Kang, Hyeseon, Maxim N. Shokhirev, Zhichao Xu, Sahaana Chandran, Jesse
R. Dixon, and Martin Hetzer. “Dynamic Regulation of Histone Modifications and
Long-Range Chromosomal Interactions during Postmitotic Transcriptional Reactivation.”
Genes & Development. Cold Spring Harbor Laboratory Press, 2020. https://doi.org/10.1101/gad.335794.119.
ieee: H. Kang, M. N. Shokhirev, Z. Xu, S. Chandran, J. R. Dixon, and M. Hetzer,
“Dynamic regulation of histone modifications and long-range chromosomal interactions
during postmitotic transcriptional reactivation,” Genes & Development,
vol. 34, no. 13–14. Cold Spring Harbor Laboratory Press, pp. 913–930, 2020.
ista: Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer M. 2020. Dynamic
regulation of histone modifications and long-range chromosomal interactions during
postmitotic transcriptional reactivation. Genes & Development. 34(13–14),
913–930.
mla: Kang, Hyeseon, et al. “Dynamic Regulation of Histone Modifications and Long-Range
Chromosomal Interactions during Postmitotic Transcriptional Reactivation.” Genes
& Development, vol. 34, no. 13–14, Cold Spring Harbor Laboratory Press,
2020, pp. 913–30, doi:10.1101/gad.335794.119.
short: H. Kang, M.N. Shokhirev, Z. Xu, S. Chandran, J.R. Dixon, M. Hetzer, Genes
& Development 34 (2020) 913–930.
date_created: 2022-04-07T07:44:09Z
date_published: 2020-04-28T00:00:00Z
date_updated: 2024-10-14T11:18:25Z
day: '28'
ddc:
- '570'
doi: 10.1101/gad.335794.119
extern: '1'
external_id:
pmid:
- '32499403'
file:
- access_level: open_access
checksum: 84e92d40e67936c739628315c238daf9
content_type: application/pdf
creator: dernst
date_created: 2022-04-08T07:12:33Z
date_updated: 2022-04-08T07:12:33Z
file_id: '11136'
file_name: 2020_GenesDevelopment_Kang.pdf
file_size: 4406772
relation: main_file
success: 1
file_date_updated: 2022-04-08T07:12:33Z
has_accepted_license: '1'
intvolume: ' 34'
issue: 13-14
keyword:
- Developmental Biology
- Genetics
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 913-930
pmid: 1
publication: Genes & Development
publication_identifier:
issn:
- 0890-9369
- 1549-5477
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic regulation of histone modifications and long-range chromosomal interactions
during postmitotic transcriptional reactivation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2020'
...
---
_id: '11058'
abstract:
- lang: eng
text: Nucleoporin 93 (Nup93) expression inversely correlates with the survival of
triple-negative breast cancer patients. However, our knowledge of Nup93 function
in breast cancer besides its role as structural component of the nuclear pore
complex is not understood. Combination of functional assays and genetic analyses
suggested that chromatin interaction of Nup93 partially modulates the expression
of genes associated with actin cytoskeleton remodeling and epithelial to mesenchymal
transition, resulting in impaired invasion of triple-negative, claudin-low breast
cancer cells. Nup93 depletion induced stress fiber formation associated with reduced
cell migration/proliferation and impaired expression of mesenchymal-like genes.
Silencing LIMCH1, a gene responsible for actin cytoskeleton remodeling and up-regulated
upon Nup93 depletion, partially restored the invasive phenotype of cancer cells.
Loss of Nup93 led to significant defects in tumor establishment/propagation in
vivo, whereas patient samples revealed that high Nup93 and low LIMCH1 expression
correlate with late tumor stage. Our approach identified Nup93 as contributor
of triple-negative, claudin-low breast cancer cell invasion and paves the way
to study the role of nuclear envelope proteins during breast cancer tumorigenesis.
article_number: e201900623
article_processing_charge: No
article_type: original
author:
- first_name: Simone
full_name: Bersini, Simone
last_name: Bersini
- first_name: Nikki K
full_name: Lytle, Nikki K
last_name: Lytle
- first_name: Roberta
full_name: Schulte, Roberta
last_name: Schulte
- first_name: Ling
full_name: Huang, Ling
last_name: Huang
- first_name: Geoffrey M
full_name: Wahl, Geoffrey M
last_name: Wahl
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Bersini S, Lytle NK, Schulte R, Huang L, Wahl GM, Hetzer M. Nup93 regulates
breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling.
Life Science Alliance. 2020;3(1). doi:10.26508/lsa.201900623
apa: Bersini, S., Lytle, N. K., Schulte, R., Huang, L., Wahl, G. M., & Hetzer,
M. (2020). Nup93 regulates breast tumor growth by modulating cell proliferation
and actin cytoskeleton remodeling. Life Science Alliance. Life Science
Alliance. https://doi.org/10.26508/lsa.201900623
chicago: Bersini, Simone, Nikki K Lytle, Roberta Schulte, Ling Huang, Geoffrey M
Wahl, and Martin Hetzer. “Nup93 Regulates Breast Tumor Growth by Modulating Cell
Proliferation and Actin Cytoskeleton Remodeling.” Life Science Alliance.
Life Science Alliance, 2020. https://doi.org/10.26508/lsa.201900623.
ieee: S. Bersini, N. K. Lytle, R. Schulte, L. Huang, G. M. Wahl, and M. Hetzer,
“Nup93 regulates breast tumor growth by modulating cell proliferation and actin
cytoskeleton remodeling,” Life Science Alliance, vol. 3, no. 1. Life Science
Alliance, 2020.
ista: Bersini S, Lytle NK, Schulte R, Huang L, Wahl GM, Hetzer M. 2020. Nup93 regulates
breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling.
Life Science Alliance. 3(1), e201900623.
mla: Bersini, Simone, et al. “Nup93 Regulates Breast Tumor Growth by Modulating
Cell Proliferation and Actin Cytoskeleton Remodeling.” Life Science Alliance,
vol. 3, no. 1, e201900623, Life Science Alliance, 2020, doi:10.26508/lsa.201900623.
short: S. Bersini, N.K. Lytle, R. Schulte, L. Huang, G.M. Wahl, M. Hetzer, Life
Science Alliance 3 (2020).
date_created: 2022-04-07T07:44:18Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2024-10-14T11:18:41Z
day: '01'
ddc:
- '570'
doi: 10.26508/lsa.201900623
extern: '1'
external_id:
pmid:
- '31959624'
file:
- access_level: open_access
checksum: 3bf33e7e93bef7823287807206b69b38
content_type: application/pdf
creator: dernst
date_created: 2022-04-08T07:33:01Z
date_updated: 2022-04-08T07:33:01Z
file_id: '11137'
file_name: 2020_LifeScienceAlliance_Bersini.pdf
file_size: 2653960
relation: main_file
success: 1
file_date_updated: 2022-04-08T07:33:01Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '1'
keyword:
- Health
- Toxicology and Mutagenesis
- Plant Science
- Biochemistry
- Genetics and Molecular Biology (miscellaneous)
- Ecology
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Life Science Alliance
publication_identifier:
issn:
- 2575-1077
publication_status: published
publisher: Life Science Alliance
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nup93 regulates breast tumor growth by modulating cell proliferation and actin
cytoskeleton remodeling
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2020'
...
---
_id: '11501'
abstract:
- lang: eng
text: We investigated the ultraviolet (UV) spectral properties of faint Lyman-α
emitters (LAEs) in the redshift range 2.9 ≤ z ≤ 4.6, and we provide material to
prepare future observations of the faint Universe. We used data from the MUSE
Hubble Ultra Deep Survey to construct mean rest-frame spectra of continuum-faint
(median MUV of −18 and down to MUV of −16), low stellar mass (median value of
108.4 M⊙ and down to 107 M⊙) LAEs at redshift z ≳ 3. We computed various averaged
spectra of LAEs, subsampled on the basis of their observational (e.g., Lyα strength,
UV magnitude and spectral slope) and physical (e.g., stellar mass and star-formation
rate) properties. We searched for UV spectral features other than Lyα, such as
higher ionization nebular emission lines and absorption features. We successfully
observed the O III]λ1666 and [C III]λ1907+C III]λ1909 collisionally excited emission
lines and the He IIλ1640 recombination feature, as well as the resonant C IVλλ1548,1551
doublet either in emission or P-Cygni. We compared the observed spectral properties
of the different mean spectra and find the emission lines to vary with the observational
and physical properties of the LAEs. In particular, the mean spectra of LAEs with
larger Lyα equivalent widths, fainter UV magnitudes, bluer UV spectral slopes,
and lower stellar masses show the strongest nebular emission. The line ratios
of these lines are similar to those measured in the spectra of local metal-poor
galaxies, while their equivalent widths are weaker compared to the handful of
extreme values detected in individual spectra of z > 2 galaxies. This suggests
that weak UV features are likely ubiquitous in high z, low-mass, and faint LAEs.
We publicly released the stacked spectra, as they can serve as empirical templates
for the design of future observations, such as those with the James Webb Space
Telescope and the Extremely Large Telescope.
acknowledgement: 'We thank Margherita Talia, Stéphane Charlot, Adele Plat and Alba
Vidal-García for helpful discussions. This work is supported by the ERC advanced
grant 339659-MUSICOS (R. Bacon). AF acknowledges the support from grant PRIN MIUR
2017 20173ML3WW. MVM and JP would like to thank the Leiden/ESA Astrophysics Program
for Summer Students (LEAPS) for funding at the outset of this project. FL, HK, and
AV acknowledge support from the ERC starting grant ERC-757258-TRIPLE. TH was supported
by Leading Initiative for Excellent Young Researchers, MEXT, Japan. JB acknowledges
support by FCT/MCTES through national funds by the grant UID/FIS/04434/2019, UIDB/04434/2020
and UIDP/04434/2020 and through the Investigador FCT Contract No. IF/01654/2014/CP1215/CT0003.
HI acknowledges support from JSPS KAKENHI Grant Number JP19K23462. We would also
like to thank the organizers and participants of the Leiden Lorentz Center workshop:
Revolutionary Spectroscopy of Today as a Springboard to Webb. This work made use
of several open source python packages: NUMPY (van der Walt et al. 2011), MATPLOTLIB
(Hunter 2007), ASTROPY (Astropy Collaboration 2013) and MPDAF (MUSE Python Data
Analysis Framework, Piqueras et al. 2019).'
article_number: A118
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Anna
full_name: Feltre, Anna
last_name: Feltre
- first_name: Michael V.
full_name: Maseda, Michael V.
last_name: Maseda
- first_name: Roland
full_name: Bacon, Roland
last_name: Bacon
- first_name: Jayadev
full_name: Pradeep, Jayadev
last_name: Pradeep
- first_name: Floriane
full_name: Leclercq, Floriane
last_name: Leclercq
- first_name: Haruka
full_name: Kusakabe, Haruka
last_name: Kusakabe
- first_name: Lutz
full_name: Wisotzki, Lutz
last_name: Wisotzki
- first_name: Takuya
full_name: Hashimoto, Takuya
last_name: Hashimoto
- first_name: Kasper B.
full_name: Schmidt, Kasper B.
last_name: Schmidt
- first_name: Jeremy
full_name: Blaizot, Jeremy
last_name: Blaizot
- first_name: Jarle
full_name: Brinchmann, Jarle
last_name: Brinchmann
- first_name: Leindert
full_name: Boogaard, Leindert
last_name: Boogaard
- first_name: Sebastiano
full_name: Cantalupo, Sebastiano
last_name: Cantalupo
- first_name: David
full_name: Carton, David
last_name: Carton
- first_name: Hanae
full_name: Inami, Hanae
last_name: Inami
- first_name: Wolfram
full_name: Kollatschny, Wolfram
last_name: Kollatschny
- first_name: Raffaella A.
full_name: Marino, Raffaella A.
last_name: Marino
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: Themiya
full_name: Nanayakkara, Themiya
last_name: Nanayakkara
- first_name: Johan
full_name: Richard, Johan
last_name: Richard
- first_name: Joop
full_name: Schaye, Joop
last_name: Schaye
- first_name: Laurence
full_name: Tresse, Laurence
last_name: Tresse
- first_name: Tanya
full_name: Urrutia, Tanya
last_name: Urrutia
- first_name: Anne
full_name: Verhamme, Anne
last_name: Verhamme
- first_name: Peter M.
full_name: Weilbacher, Peter M.
last_name: Weilbacher
citation:
ama: 'Feltre A, Maseda MV, Bacon R, et al. The MUSE Hubble Ultra Deep Field Survey:
XV. The mean rest-UV spectra of Lyα emitters at z > 3. Astronomy &
Astrophysics. 2020;641. doi:10.1051/0004-6361/202038133'
apa: 'Feltre, A., Maseda, M. V., Bacon, R., Pradeep, J., Leclercq, F., Kusakabe,
H., … Weilbacher, P. M. (2020). The MUSE Hubble Ultra Deep Field Survey: XV. The
mean rest-UV spectra of Lyα emitters at z > 3. Astronomy & Astrophysics.
EDP Sciences. https://doi.org/10.1051/0004-6361/202038133'
chicago: 'Feltre, Anna, Michael V. Maseda, Roland Bacon, Jayadev Pradeep, Floriane
Leclercq, Haruka Kusakabe, Lutz Wisotzki, et al. “The MUSE Hubble Ultra Deep Field
Survey: XV. The Mean Rest-UV Spectra of Lyα Emitters at z > 3.” Astronomy
& Astrophysics. EDP Sciences, 2020. https://doi.org/10.1051/0004-6361/202038133.'
ieee: 'A. Feltre et al., “The MUSE Hubble Ultra Deep Field Survey: XV. The
mean rest-UV spectra of Lyα emitters at z > 3,” Astronomy & Astrophysics,
vol. 641. EDP Sciences, 2020.'
ista: 'Feltre A, Maseda MV, Bacon R, Pradeep J, Leclercq F, Kusakabe H, Wisotzki
L, Hashimoto T, Schmidt KB, Blaizot J, Brinchmann J, Boogaard L, Cantalupo S,
Carton D, Inami H, Kollatschny W, Marino RA, Matthee JJ, Nanayakkara T, Richard
J, Schaye J, Tresse L, Urrutia T, Verhamme A, Weilbacher PM. 2020. The MUSE Hubble
Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z >
3. Astronomy & Astrophysics. 641, A118.'
mla: 'Feltre, Anna, et al. “The MUSE Hubble Ultra Deep Field Survey: XV. The Mean
Rest-UV Spectra of Lyα Emitters at z > 3.” Astronomy & Astrophysics,
vol. 641, A118, EDP Sciences, 2020, doi:10.1051/0004-6361/202038133.'
short: A. Feltre, M.V. Maseda, R. Bacon, J. Pradeep, F. Leclercq, H. Kusakabe, L.
Wisotzki, T. Hashimoto, K.B. Schmidt, J. Blaizot, J. Brinchmann, L. Boogaard,
S. Cantalupo, D. Carton, H. Inami, W. Kollatschny, R.A. Marino, J.J. Matthee,
T. Nanayakkara, J. Richard, J. Schaye, L. Tresse, T. Urrutia, A. Verhamme, P.M.
Weilbacher, Astronomy & Astrophysics 641 (2020).
date_created: 2022-07-06T09:38:16Z
date_published: 2020-09-18T00:00:00Z
date_updated: 2022-07-19T09:35:43Z
day: '18'
doi: 10.1051/0004-6361/202038133
extern: '1'
external_id:
arxiv:
- '2007.01878'
intvolume: ' 641'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: evolution / galaxies: high-redshift / ISM: lines and bands / ultraviolet:
ISM / ultraviolet: galaxies'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2007.01878
month: '09'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα
emitters at z > 3'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 641
year: '2020'
...
---
_id: '11503'
abstract:
- lang: eng
text: "Context. The Lyα emitter (LAE) fraction, XLAE, is a potentially powerful
probe of the evolution of the intergalactic neutral hydrogen gas fraction. However,
uncertainties in the measurement of XLAE are still under debate.\r\nAims. Thanks
to deep data obtained with the integral field spectrograph Multi Unit Spectroscopic
Explorer (MUSE), we can measure the evolution of the LAE fraction homogeneously
over a wide redshift range of z ≈ 3–6 for UV-faint galaxies (down to UV magnitudes
of M1500 ≈ −17.75). This is a significantly fainter range than in former studies
(M1500 ≤ −18.75) and it allows us to probe the bulk of the population of high-redshift
star-forming galaxies.\r\nMethods. We constructed a UV-complete photometric-redshift
sample following UV luminosity functions and measured the Lyα emission with MUSE
using the latest (second) data release from the MUSE Hubble Ultra Deep Field Survey.\r\nResults.
We derived the redshift evolution of XLAE for M1500 ∈ [ − 21.75; −17.75] for the
first time with a equivalent width range EW(Lyα) ≥ 65 Å and found low values of
XLAE ≲ 30% at z ≲ 6. The best-fit linear relation is XLAE = 0.07+0.06−0.03z −
0.22+0.12−0.24. For M1500 ∈ [ − 20.25; −18.75] and EW(Lyα) ≥ 25 Å, our XLAE values
are consistent with those in the literature within 1σ at z ≲ 5, but our median
values are systematically lower than reported values over the whole redshift range.
In addition, we do not find a significant dependence of XLAE on M1500 for EW(Lyα)
≥ 50 Å at z ≈ 3–4, in contrast with previous work. The differences in XLAE mainly
arise from selection biases for Lyman Break Galaxies (LBGs) in the literature:
UV-faint LBGs are more easily selected if they have strong Lyα emission, hence
XLAE is biased towards higher values when those samples are used.\r\nConclusions.
Our results suggest either a lower increase of XLAE towards z ≈ 6 than previously
suggested, or even a turnover of XLAE at z ≈ 5.5, which may be the signature of
a late or patchy reionization process. We compared our results with predictions
from a cosmological galaxy evolution model. We find that a model with a bursty
star formation (SF) can reproduce our observed LAE fractions much better than
models where SF is a smooth function of time."
acknowledgement: We thank the anonymous referee for constructive comments and suggestions.
We would like to express our gratitude to Stephane De Barros and Pablo Arrabal Haro
for kindly providing their data plotted in Figs. 1, 2, and 8. We are grateful to
Kazuhiro Shimasaku, Masami Ouchi, Rieko Momose, Daniel Schaerer, Hidenobu Yajima,
Taku Okamura, Makoto Ando, and Hinako Goto for giving insightful comments and suggestions.
This work is based on observations taken by VLT, which is operated by European Southern
Observatory. This research made use of Astropy (http://www.astropy.org), which is
a community-developed core Python package for Astronomy (Astropy Collaboration 2013,
2018), MARZ, MPDAF, and matplotlib (Hunter 2007). H.K. acknowledges support from
Japan Society for the Promotion of Science (JSPS) through the JSPS Research Fellowship
for Young Scientists and Overseas Challenge Program for Young Researchers. AV acknowledges
support from the ERC starting grant 757258-TRIPLE and the SNF Professorship 176808-TRIPLE.
This work was supported by the project FOGHAR (Agence Nationale de la Recherche,
ANR-13-BS05-0010-02). JB acknowledges support from the ORAGE project from the Agence
Nationale de la Recherche under grant ANR-14-CE33-0016-03. JR acknowledges support
from the ERC starting grant 336736-CALENDS. T. H. acknowledges supports by the Grant-inAid
for Scientic Research 19J01620.
article_number: A12
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Haruka
full_name: Kusakabe, Haruka
last_name: Kusakabe
- first_name: Jérémy
full_name: Blaizot, Jérémy
last_name: Blaizot
- first_name: Thibault
full_name: Garel, Thibault
last_name: Garel
- first_name: Anne
full_name: Verhamme, Anne
last_name: Verhamme
- first_name: Roland
full_name: Bacon, Roland
last_name: Bacon
- first_name: Johan
full_name: Richard, Johan
last_name: Richard
- first_name: Takuya
full_name: Hashimoto, Takuya
last_name: Hashimoto
- first_name: Hanae
full_name: Inami, Hanae
last_name: Inami
- first_name: Simon
full_name: Conseil, Simon
last_name: Conseil
- first_name: Bruno
full_name: Guiderdoni, Bruno
last_name: Guiderdoni
- first_name: Alyssa B.
full_name: Drake, Alyssa B.
last_name: Drake
- first_name: Edmund
full_name: Christian Herenz, Edmund
last_name: Christian Herenz
- first_name: Joop
full_name: Schaye, Joop
last_name: Schaye
- first_name: Pascal
full_name: Oesch, Pascal
last_name: Oesch
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: Raffaella
full_name: Anna Marino, Raffaella
last_name: Anna Marino
- first_name: Kasper
full_name: Borello Schmidt, Kasper
last_name: Borello Schmidt
- first_name: Roser
full_name: Pelló, Roser
last_name: Pelló
- first_name: Michael
full_name: Maseda, Michael
last_name: Maseda
- first_name: Floriane
full_name: Leclercq, Floriane
last_name: Leclercq
- first_name: Josephine
full_name: Kerutt, Josephine
last_name: Kerutt
- first_name: Guillaume
full_name: Mahler, Guillaume
last_name: Mahler
citation:
ama: 'Kusakabe H, Blaizot J, Garel T, et al. The MUSE Hubble Ultra Deep Field Survey:
XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6. Astronomy &
Astrophysics. 2020;638. doi:10.1051/0004-6361/201937340'
apa: 'Kusakabe, H., Blaizot, J., Garel, T., Verhamme, A., Bacon, R., Richard, J.,
… Mahler, G. (2020). The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of
the Lyα emitter fraction from z = 3 to z = 6. Astronomy & Astrophysics.
EDP Sciences. https://doi.org/10.1051/0004-6361/201937340'
chicago: 'Kusakabe, Haruka, Jérémy Blaizot, Thibault Garel, Anne Verhamme, Roland
Bacon, Johan Richard, Takuya Hashimoto, et al. “The MUSE Hubble Ultra Deep Field
Survey: XIV. Evolution of the Lyα Emitter Fraction from z = 3 to z = 6.” Astronomy
& Astrophysics. EDP Sciences, 2020. https://doi.org/10.1051/0004-6361/201937340.'
ieee: 'H. Kusakabe et al., “The MUSE Hubble Ultra Deep Field Survey: XIV.
Evolution of the Lyα emitter fraction from z = 3 to z = 6,” Astronomy &
Astrophysics, vol. 638. EDP Sciences, 2020.'
ista: 'Kusakabe H, Blaizot J, Garel T, Verhamme A, Bacon R, Richard J, Hashimoto
T, Inami H, Conseil S, Guiderdoni B, Drake AB, Christian Herenz E, Schaye J, Oesch
P, Matthee JJ, Anna Marino R, Borello Schmidt K, Pelló R, Maseda M, Leclercq F,
Kerutt J, Mahler G. 2020. The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution
of the Lyα emitter fraction from z = 3 to z = 6. Astronomy & Astrophysics.
638, A12.'
mla: 'Kusakabe, Haruka, et al. “The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution
of the Lyα Emitter Fraction from z = 3 to z = 6.” Astronomy & Astrophysics,
vol. 638, A12, EDP Sciences, 2020, doi:10.1051/0004-6361/201937340.'
short: H. Kusakabe, J. Blaizot, T. Garel, A. Verhamme, R. Bacon, J. Richard, T.
Hashimoto, H. Inami, S. Conseil, B. Guiderdoni, A.B. Drake, E. Christian Herenz,
J. Schaye, P. Oesch, J.J. Matthee, R. Anna Marino, K. Borello Schmidt, R. Pelló,
M. Maseda, F. Leclercq, J. Kerutt, G. Mahler, Astronomy & Astrophysics 638
(2020).
date_created: 2022-07-06T09:50:48Z
date_published: 2020-06-03T00:00:00Z
date_updated: 2022-07-19T09:35:20Z
day: '03'
doi: 10.1051/0004-6361/201937340
extern: '1'
external_id:
arxiv:
- '2003.12083'
intvolume: ' 638'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'dark ages / reionization / first stars / early Universe / cosmology: observations
/ galaxies: evolution / galaxies: high-redshift / intergalactic medium'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2003.12083
month: '06'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter
fraction from z = 3 to z = 6'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 638
year: '2020'
...