---
_id: '13136'
abstract:
- lang: eng
text: Despite its fundamental importance for development, the question of how organs
achieve their correct size and shape is poorly understood. This complex process
requires coordination between the generation of cell mass and the morphogenetic
mechanisms that sculpt tissues. These processes are regulated by morphogen signalling
pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical
and mechanical signalling are quantitatively interpreted to determine the behaviours
of individual cells and how they contribute to growth and morphogenesis at the
tissue scale. In this review, we discuss the development of the vertebrate neural
tube and somites as an example of the state of knowledge, as well as the challenges
in understanding the mechanisms of tissue size control in vertebrate organogenesis.
We highlight how the recent advances in stem cell differentiation and organoid
approaches can be harnessed to provide new insights into this question.
acknowledgement: 'We thank J. Briscoe for comments on the manuscript. Work in the
AK lab is supported by ISTA, the European Research Council under Horizon Europe:
grant 101044579, and Austrian Science Fund (FWF): F78 (Stem Cell Modulation). SR
is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship
SC19-011.'
article_number: '100459'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Thomas
full_name: Minchington, Thomas
id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f
last_name: Minchington
- first_name: Stefanie
full_name: Rus, Stefanie
id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87
last_name: Rus
orcid: 0000-0001-8703-1093
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: Minchington T, Rus S, Kicheva A. Control of tissue dimensions in the developing
neural tube and somites. Current Opinion in Systems Biology. 2023;35. doi:10.1016/j.coisb.2023.100459
apa: Minchington, T., Rus, S., & Kicheva, A. (2023). Control of tissue dimensions
in the developing neural tube and somites. Current Opinion in Systems Biology.
Elsevier. https://doi.org/10.1016/j.coisb.2023.100459
chicago: Minchington, Thomas, Stefanie Rus, and Anna Kicheva. “Control of Tissue
Dimensions in the Developing Neural Tube and Somites.” Current Opinion in Systems
Biology. Elsevier, 2023. https://doi.org/10.1016/j.coisb.2023.100459.
ieee: T. Minchington, S. Rus, and A. Kicheva, “Control of tissue dimensions in the
developing neural tube and somites,” Current Opinion in Systems Biology,
vol. 35. Elsevier, 2023.
ista: Minchington T, Rus S, Kicheva A. 2023. Control of tissue dimensions in the
developing neural tube and somites. Current Opinion in Systems Biology. 35, 100459.
mla: Minchington, Thomas, et al. “Control of Tissue Dimensions in the Developing
Neural Tube and Somites.” Current Opinion in Systems Biology, vol. 35,
100459, Elsevier, 2023, doi:10.1016/j.coisb.2023.100459.
short: T. Minchington, S. Rus, A. Kicheva, Current Opinion in Systems Biology 35
(2023).
corr_author: '1'
date_created: 2023-06-18T22:00:46Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2026-10-30T23:31:11Z
day: '01'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1016/j.coisb.2023.100459
file:
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checksum: 8a75c4e29fd9b62e3c50663c2265b173
content_type: application/pdf
creator: dernst
date_created: 2024-01-29T11:06:45Z
date_updated: 2024-01-29T11:06:45Z
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file_size: 598842
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file_date_updated: 2024-01-29T11:06:45Z
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has_accepted_license: '1'
intvolume: ' 35'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa
grant_number: '101044579'
name: Mechanisms of tissue size regulation in spinal cord development
- _id: 059DF620-7A3F-11EA-A408-12923DDC885E
grant_number: F7802
name: Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen
control of growth and pattern in the spinal cord
- _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A
grant_number: SC19-011
name: The regulatory logic of pattern formation in the vertebrate dorsal neural
tube
publication: Current Opinion in Systems Biology
publication_identifier:
eissn:
- 2452-3100
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Control of tissue dimensions in the developing neural tube and somites
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: 35
year: '2023'
...
---
_id: '12159'
abstract:
- lang: eng
text: The term “haplotype block” is commonly used in the developing field of haplotype-based
inference methods. We argue that the term should be defined based on the structure
of the Ancestral Recombination Graph (ARG), which contains complete information
on the ancestry of a sample. We use simulated examples to demonstrate key features
of the relationship between haplotype blocks and ancestral structure, emphasizing
the stochasticity of the processes that generate them. Even the simplest cases
of neutrality or of a “hard” selective sweep produce a rich structure, often missed
by commonly used statistics. We highlight a number of novel methods for inferring
haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate
how they can be used to define haplotype blocks using an empirical data set. While
the advent of new, computationally efficient methods makes it possible to apply
these concepts broadly, they (and additional new methods) could benefit from adding
features to explore haplotype blocks, as we define them. Understanding and applying
the concept of the haplotype block will be essential to fully exploit long and
linked-read sequencing technologies.
acknowledgement: 'We thank the Barton group for useful discussion and feedback during
the writing of this article. Comments from Roger Butlin, Molly Schumer''s Group,
the tskit development team, editors and three reviewers greatly improved the manuscript.
Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg
Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant
P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society
and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Daria
full_name: Shipilina, Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure
of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793
apa: Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023).
On the origin and structure of haplotype blocks. Molecular Ecology. Wiley.
https://doi.org/10.1111/mec.16793
chicago: Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and
Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular
Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.
ieee: D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the
origin and structure of haplotype blocks,” Molecular Ecology, vol. 32,
no. 6. Wiley, pp. 1441–1457, 2023.
ista: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin
and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.
mla: Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.”
Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.
short: D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology
32 (2023) 1441–1457.
corr_author: '1'
date_created: 2023-01-12T12:09:17Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2026-10-30T23:31:12Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.16793
external_id:
isi:
- '000900762000001'
pmid:
- '36433653'
file:
- access_level: open_access
checksum: b10e0f8fa3dc4d72aaf77a557200978a
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T08:15:41Z
date_updated: 2023-08-16T08:15:41Z
file_id: '14062'
file_name: 2023_MolecularEcology_Shipilina.pdf
file_size: 7144607
relation: main_file
success: 1
file_date_updated: 2023-08-16T08:15:41Z
fulldoi: https://doi.org/10.1111/mec.16793
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '6'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 1441-1457
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '20694'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: On the origin and structure of haplotype blocks
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: 32
year: '2023'
...
---
_id: '13212'
abstract:
- lang: eng
text: Auxin is the major plant hormone regulating growth and development (Friml,
2022). Forward genetic approaches in the model plant Arabidopsis thaliana have
identified major components of auxin signalling and established the canonical
mechanism mediating transcriptional and thus developmental reprogramming. In this
textbook view, TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFBs)
are auxin receptors, which act as F-box subunits determining the substrate specificity
of the Skp1-Cullin1-F box protein (SCF) type E3 ubiquitin ligase complex. Auxin
acts as a “molecular glue” increasing the affinity between TIR1/AFBs and the Aux/IAA
repressors. Subsequently, Aux/IAAs are ubiquitinated and degraded, thus releasing
auxin transcription factors from their repression making them free to mediate
transcription of auxin response genes (Yu et al., 2022). Nonetheless, accumulating
evidence suggests existence of rapid, non-transcriptional responses downstream
of TIR1/AFBs such as auxin-induced cytosolic calcium (Ca2+) transients, plasma
membrane depolarization and apoplast alkalinisation, all converging on the process
of root growth inhibition and root gravitropism (Li et al., 2022). Particularly,
these rapid responses are mostly contributed by predominantly cytosolic AFB1,
while the long-term growth responses are mediated by mainly nuclear TIR1 and AFB2-AFB5
(Li et al., 2021; Prigge et al., 2020; Serre et al., 2021). How AFB1 conducts
auxin-triggered rapid responses and how it is different from TIR1 and AFB2-AFB5
remains elusive. Here, we compare the roles of TIR1 and AFB1 in transcriptional
and rapid responses by modulating their subcellular localization in Arabidopsis
and by testing their ability to mediate transcriptional responses when part of
the minimal auxin circuit reconstituted in yeast.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: We thank all the authors for sharing the published materials. This
research was supported by the Lab Support Facility and the Imaging and Optics Facility
of ISTA. We thank Lukáš Fiedler (ISTA) for critical reading of the manuscript. This
project was funded by the European Research Council Advanced Grant (ETAP-742985).
article_processing_charge: Yes (via OA deal)
article_type: letter_note
author:
- first_name: Huihuang
full_name: Chen, Huihuang
id: 83c96512-15b2-11ec-abd3-b7eede36184f
last_name: Chen
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Minxia
full_name: Zou, Minxia
id: 5c243f41-03f3-11ec-841c-96faf48a7ef9
last_name: Zou
- first_name: Linlin
full_name: Qi, Linlin
id: 44B04502-A9ED-11E9-B6FC-583AE6697425
last_name: Qi
orcid: 0000-0001-5187-8401
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Chen H, Li L, Zou M, Qi L, Friml J. Distinct functions of TIR1 and AFB1 receptors
in auxin signalling. Molecular Plant. 2023;16(7):1117-1119. doi:10.1016/j.molp.2023.06.007
apa: Chen, H., Li, L., Zou, M., Qi, L., & Friml, J. (2023). Distinct functions
of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. Elsevier.
https://doi.org/10.1016/j.molp.2023.06.007
chicago: Chen, Huihuang, Lanxin Li, Minxia Zou, Linlin Qi, and Jiří Friml. “Distinct
Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” Molecular Plant.
Elsevier, 2023. https://doi.org/10.1016/j.molp.2023.06.007.
ieee: H. Chen, L. Li, M. Zou, L. Qi, and J. Friml, “Distinct functions of TIR1 and
AFB1 receptors in auxin signalling.,” Molecular Plant, vol. 16, no. 7.
Elsevier, pp. 1117–1119, 2023.
ista: Chen H, Li L, Zou M, Qi L, Friml J. 2023. Distinct functions of TIR1 and AFB1
receptors in auxin signalling. Molecular Plant. 16(7), 1117–1119.
mla: Chen, Huihuang, et al. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin
Signalling.” Molecular Plant, vol. 16, no. 7, Elsevier, 2023, pp. 1117–19,
doi:10.1016/j.molp.2023.06.007.
short: H. Chen, L. Li, M. Zou, L. Qi, J. Friml, Molecular Plant 16 (2023) 1117–1119.
corr_author: '1'
das_tickbox: '1'
date_created: 2023-07-12T07:32:46Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2026-10-30T23:31:14Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.molp.2023.06.007
ec_funded: 1
external_id:
isi:
- '001044410900001'
pmid:
- '37393433'
file:
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checksum: 6012b7e4a2f680ee6c1f84001e2b945f
content_type: application/pdf
creator: dernst
date_created: 2024-01-29T10:37:05Z
date_updated: 2024-01-29T10:37:05Z
file_id: '14894'
file_name: 2023_MolecularPlant_Chen.pdf
file_size: 1000871
relation: main_file
success: 1
file_date_updated: 2024-01-29T10:37:05Z
fulldoi: https://doi.org/10.1016/j.molp.2023.06.007
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1117-1119
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Molecular Plant
publication_identifier:
eissn:
- 1674-2052
issn:
- 1752-9867
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '19478'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Distinct functions of TIR1 and AFB1 receptors in auxin signalling.
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: 16
year: '2023'
...
---
_id: '10818'
abstract:
- lang: eng
text: Microglia cells are active players in regulating synaptic development and
plasticity in the brain. However, how they influence the normal functioning of
synapses is largely unknown. In this study, we characterized the effects of pharmacological
microglia depletion, achieved by administration of PLX5622, on hippocampal CA3-CA1
synapses of adult wild type mice. Following microglial depletion, we observed
a reduction of spontaneous and evoked glutamatergic activity associated with a
decrease of dendritic spine density. We also observed the appearance of immature
synaptic features and higher levels of plasticity. Microglia depleted mice showed
a deficit in the acquisition of the Novel Object Recognition task. These events
were accompanied by hippocampal astrogliosis, although in the absence ofneuroinflammatory
condition. PLX-induced synaptic changes were absent in Cx3cr1−/− mice, highlighting
the role of CX3CL1/CX3CR1 axis in microglia control of synaptic functioning. Remarkably,
microglia repopulation after PLX5622 withdrawal was associated with the recovery
of hippocampal synapses and learning functions. Altogether, these data demonstrate
that microglia contribute to normal synaptic functioning in the adult brain and
that their removal induces reversible changes in organization and activity of
glutamatergic synapses.
acknowledgement: The work was supported by a grant from MIUR (PRIN 2017HPTFFC_003)
to Davide Ragozzino and in part by funds to Silvia Di Angelantonio (CrestOptics-IIT
JointLab for Advanced Microscopy) and Daniele Caprioli (Istituto Pasteur-Fondazione
Cenci Bolognetti). Bernadette Basilico, and Laura Ferrucci were supported by the
PhD program in Clinical-Experimental Neuroscience and Psychiatry, Sapienza University,
Rome; Caterina Sanchini was supported by the PhD program in Life Science, Sapienza
University, Rome and by the Italian Institute of Technology, Rome. The authors thank
Alessandro Felici, Claudia Valeri, Arsenio Armagno, and Senthilkumar Deivasigamani
for help with animal husbandry and transgenic colonies management. They also wish
to thank Piotr Bregestovski and Michal Schwartz for helpful discussions and criticism.
PLX5622 was provided under Materials Transfer Agreement by Plexxikon Inc. (Berkeley,
CA). Open Access Funding provided by Universita degli Studi di Roma La Sapienza
within the CRUI-CARE Agreement.
article_processing_charge: No
article_type: original
author:
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Laura
full_name: Ferrucci, Laura
last_name: Ferrucci
- first_name: Patrizia
full_name: Ratano, Patrizia
last_name: Ratano
- first_name: Maria T.
full_name: Golia, Maria T.
last_name: Golia
- first_name: Alfonso
full_name: Grimaldi, Alfonso
last_name: Grimaldi
- first_name: Maria
full_name: Rosito, Maria
last_name: Rosito
- first_name: Valentina
full_name: Ferretti, Valentina
last_name: Ferretti
- first_name: Ingrid
full_name: Reverte, Ingrid
last_name: Reverte
- first_name: Caterina
full_name: Sanchini, Caterina
last_name: Sanchini
- first_name: Maria C.
full_name: Marrone, Maria C.
last_name: Marrone
- first_name: Maria
full_name: Giubettini, Maria
last_name: Giubettini
- first_name: Valeria
full_name: De Turris, Valeria
last_name: De Turris
- first_name: Debora
full_name: Salerno, Debora
last_name: Salerno
- first_name: Stefano
full_name: Garofalo, Stefano
last_name: Garofalo
- first_name: Marie‐Kim
full_name: St‐Pierre, Marie‐Kim
last_name: St‐Pierre
- first_name: Micael
full_name: Carrier, Micael
last_name: Carrier
- first_name: Massimiliano
full_name: Renzi, Massimiliano
last_name: Renzi
- first_name: Francesca
full_name: Pagani, Francesca
last_name: Pagani
- first_name: Brijesh
full_name: Modi, Brijesh
last_name: Modi
- first_name: Marcello
full_name: Raspa, Marcello
last_name: Raspa
- first_name: Ferdinando
full_name: Scavizzi, Ferdinando
last_name: Scavizzi
- first_name: Cornelius T.
full_name: Gross, Cornelius T.
last_name: Gross
- first_name: Silvia
full_name: Marinelli, Silvia
last_name: Marinelli
- first_name: Marie‐Ève
full_name: Tremblay, Marie‐Ève
last_name: Tremblay
- first_name: Daniele
full_name: Caprioli, Daniele
last_name: Caprioli
- first_name: Laura
full_name: Maggi, Laura
last_name: Maggi
- first_name: Cristina
full_name: Limatola, Cristina
last_name: Limatola
- first_name: Silvia
full_name: Di Angelantonio, Silvia
last_name: Di Angelantonio
- first_name: Davide
full_name: Ragozzino, Davide
last_name: Ragozzino
citation:
ama: Basilico B, Ferrucci L, Ratano P, et al. Microglia control glutamatergic synapses
in the adult mouse hippocampus. Glia. 2022;70(1):173-195. doi:10.1002/glia.24101
apa: Basilico, B., Ferrucci, L., Ratano, P., Golia, M. T., Grimaldi, A., Rosito,
M., … Ragozzino, D. (2022). Microglia control glutamatergic synapses in the adult
mouse hippocampus. Glia. Wiley. https://doi.org/10.1002/glia.24101
chicago: Basilico, Bernadette, Laura Ferrucci, Patrizia Ratano, Maria T. Golia,
Alfonso Grimaldi, Maria Rosito, Valentina Ferretti, et al. “Microglia Control
Glutamatergic Synapses in the Adult Mouse Hippocampus.” Glia. Wiley, 2022.
https://doi.org/10.1002/glia.24101.
ieee: B. Basilico et al., “Microglia control glutamatergic synapses in the
adult mouse hippocampus,” Glia, vol. 70, no. 1. Wiley, pp. 173–195, 2022.
ista: Basilico B, Ferrucci L, Ratano P, Golia MT, Grimaldi A, Rosito M, Ferretti
V, Reverte I, Sanchini C, Marrone MC, Giubettini M, De Turris V, Salerno D, Garofalo
S, St‐Pierre M, Carrier M, Renzi M, Pagani F, Modi B, Raspa M, Scavizzi F, Gross
CT, Marinelli S, Tremblay M, Caprioli D, Maggi L, Limatola C, Di Angelantonio
S, Ragozzino D. 2022. Microglia control glutamatergic synapses in the adult mouse
hippocampus. Glia. 70(1), 173–195.
mla: Basilico, Bernadette, et al. “Microglia Control Glutamatergic Synapses in the
Adult Mouse Hippocampus.” Glia, vol. 70, no. 1, Wiley, 2022, pp. 173–95,
doi:10.1002/glia.24101.
short: B. Basilico, L. Ferrucci, P. Ratano, M.T. Golia, A. Grimaldi, M. Rosito,
V. Ferretti, I. Reverte, C. Sanchini, M.C. Marrone, M. Giubettini, V. De Turris,
D. Salerno, S. Garofalo, M. St‐Pierre, M. Carrier, M. Renzi, F. Pagani, B. Modi,
M. Raspa, F. Scavizzi, C.T. Gross, S. Marinelli, M. Tremblay, D. Caprioli, L.
Maggi, C. Limatola, S. Di Angelantonio, D. Ragozzino, Glia 70 (2022) 173–195.
corr_author: '1'
date_created: 2022-03-04T08:53:37Z
date_published: 2022-01-01T00:00:00Z
date_updated: 2024-10-09T21:04:02Z
day: '01'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1002/glia.24101
external_id:
isi:
- '000708025800001'
pmid:
- '34661306'
file:
- access_level: open_access
checksum: f10a897290e66c0a062e04ba91db6c17
content_type: application/pdf
creator: dernst
date_created: 2022-03-04T08:55:27Z
date_updated: 2022-03-04T08:55:27Z
file_id: '10819'
file_name: 2021_Glia_Basilico.pdf
file_size: 5340294
relation: main_file
success: 1
file_date_updated: 2022-03-04T08:55:27Z
fulldoi: https://doi.org/10.1002/glia.24101
has_accepted_license: '1'
intvolume: ' 70'
isi: 1
issue: '1'
keyword:
- Cellular and Molecular Neuroscience
- Neurology
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 173-195
pmid: 1
publication: Glia
publication_identifier:
eissn:
- 1098-1136
issn:
- 0894-1491
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Microglia control glutamatergic synapses in the adult mouse hippocampus
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 70
year: '2022'
...
---
OA_type: closed access
_id: '10820'
abstract:
- lang: eng
text: Streaky structures in the boundary layers are often generated by surface roughness
elements and/or free-stream turbulence, and are known to have significant effects
on boundary-layer instability. In this paper, we investigate the impact of two
forms of streaks on the instability of supersonic boundary layers. The first concerns
the streaks generated by an array of spanwise periodic and streamwise elongated
surface roughness elements, and our interest is how these streaks influence the
lower-branch viscous first modes, whose characteristic wavelength and frequency
are on the classical triple-deck scales. By adapting the triple-deck theory in
the incompressible regime to the supersonic one, we first derived a simplified
system which allows for efficient calculation of the streaks. The asymptotic analysis
simplifies a bi-global eigenvalue problem to a one-dimensional problem in the
spanwise direction, showing that the instability is controlled at leading order
solely by the spanwise-dependent wall shear. In the fundamental configuration,
the streaks stabilize first modes at low frequencies but destabilize the high-frequency
ones. In the subharmonic configuration, the streaks generally destabilize the
first mode across the entire frequency band. Importantly, the spanwise even modes
are of radiating nature, i.e. they emit acoustic waves spontaneously to the far
field. Streaks of the second form are generated by low-frequency vortical disturbances
representing free-stream turbulence. They alter the flow in the entire layer and
their effects on instability are investigated by solving the inviscid bi-global
eigenvalue problem. Different from the incompressible case, a multitude of compressible
instability modes exists, of which the dominant mode is an inviscid instability
associated with the spanwise shear. In addition, there exists a separate branch
of instability modes that have smaller growth rates but are spontaneously radiating.
acknowledgement: The work is supported by the National Key Research and Development
Program of China (No. 2016YFA0401200), the National Natural Science Foundation of
China (Grant Nos. 91952202 and 11402167).
alternative_title:
- IUTAM
article_processing_charge: No
author:
- first_name: Jianxin
full_name: Liu, Jianxin
last_name: Liu
- first_name: Elena
full_name: Marensi, Elena
id: 0BE7553A-1004-11EA-B805-18983DDC885E
last_name: Marensi
orcid: 0000-0001-7173-4923
- first_name: Xuesong
full_name: Wu, Xuesong
last_name: Wu
citation:
ama: 'Liu J, Marensi E, Wu X. Effects of streaky structures on the instability of
supersonic boundary layers. In: IUTAM Laminar-Turbulent Transition. Vol
38. Springer Nature; 2022:587-598. doi:10.1007/978-3-030-67902-6_51'
apa: 'Liu, J., Marensi, E., & Wu, X. (2022). Effects of streaky structures on
the instability of supersonic boundary layers. In IUTAM Laminar-Turbulent Transition
(Vol. 38, pp. 587–598). London, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-030-67902-6_51'
chicago: Liu, Jianxin, Elena Marensi, and Xuesong Wu. “Effects of Streaky Structures
on the Instability of Supersonic Boundary Layers.” In IUTAM Laminar-Turbulent
Transition, 38:587–98. Springer Nature, 2022. https://doi.org/10.1007/978-3-030-67902-6_51.
ieee: J. Liu, E. Marensi, and X. Wu, “Effects of streaky structures on the instability
of supersonic boundary layers,” in IUTAM Laminar-Turbulent Transition,
London, United Kingdom, 2022, vol. 38, pp. 587–598.
ista: Liu J, Marensi E, Wu X. 2022. Effects of streaky structures on the instability
of supersonic boundary layers. IUTAM Laminar-Turbulent Transition. IUTAM Symposium,
IUTAM, vol. 38, 587–598.
mla: Liu, Jianxin, et al. “Effects of Streaky Structures on the Instability of Supersonic
Boundary Layers.” IUTAM Laminar-Turbulent Transition, vol. 38, Springer
Nature, 2022, pp. 587–98, doi:10.1007/978-3-030-67902-6_51.
short: J. Liu, E. Marensi, X. Wu, in:, IUTAM Laminar-Turbulent Transition, Springer
Nature, 2022, pp. 587–598.
conference:
end_date: 2019-09-06
location: London, United Kingdom
name: IUTAM Symposium
start_date: 2019-09-02
date_created: 2022-03-04T09:14:34Z
date_published: 2022-01-01T00:00:00Z
date_updated: 2025-05-20T06:08:26Z
day: '01'
department:
- _id: BjHo
doi: 10.1007/978-3-030-67902-6_51
external_id:
isi:
- '000709087600051'
fulldoi: https://doi.org/10.1007/978-3-030-67902-6_51
intvolume: ' 38'
isi: 1
language:
- iso: eng
month: '01'
oa_version: None
page: 587-598
publication: IUTAM Laminar-Turbulent Transition
publication_identifier:
eisbn:
- '9783030679026'
eissn:
- 1875-3493
isbn:
- '9783030679019'
issn:
- 1875-3507
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effects of streaky structures on the instability of supersonic boundary layers
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2022'
...
---
_id: '10825'
abstract:
- lang: eng
text: In development, lineage segregation is coordinated in time and space. An important
example is the mammalian inner cell mass, in which the primitive endoderm (PrE,
founder of the yolk sac) physically segregates from the epiblast (EPI, founder
of the fetus). While the molecular requirements have been well studied, the physical
mechanisms determining spatial segregation between EPI and PrE remain elusive.
Here, we investigate the mechanical basis of EPI and PrE sorting. We find that
rather than the differences in static cell surface mechanical parameters as in
classical sorting models, it is the differences in surface fluctuations that robustly
ensure physical lineage sorting. These differential surface fluctuations systematically
correlate with differential cellular fluidity, which we propose together constitute
a non-equilibrium sorting mechanism for EPI and PrE lineages. By combining experiments
and modeling, we identify cell surface dynamics as a key factor orchestrating
the correct spatial segregation of the founder embryonic lineages.
acknowledgement: We are grateful to H. Niwa for Dox regulatable PB vector; G. Charras
for EzrinT567D cDNA; K. Jones for tdTomato ESCs, R26-Confetti ESCs, and laboratory
assistance; M. Kinoshita for pPB-CAG-H2B-BFP plasmid; P. Humphreys and D. Clements
for imaging support; G. Chu, P. Attlesey, and staff for animal husbandry; S. Pallett
for laboratory assistance; C. Mulas for critical feedback on the project; T. Boroviak
for single-cell RNA-seq; the EMBL Genomics Core Facility for sequencing; and M.
Merkel for developing and sharing the original version of the 3D Voronoi code. This
work was financially supported by BBSRC ( BB/Moo4023/1 and BB/T007044/1 to K.J.C.
and J.N., Alert16 grant BB/R000042 to E.K.P.), Leverhulme Trust ( RPG-2014-080 to
K.J.C. and J.N.), European Research Council ( 772798 -CellFateTech to K.J.C., 311637
-MorphoCorDiv and 820188 -NanoMechShape to E.K.P., Starting Grant 851288 to E.H.,
and 772426 -MeChemGui to K.F.), the Isaac Newton Trust (to E.K.P.), Medical Research
Council UK (MRC program award MC_UU_00012/5 to E.K.P.), the European Union’s Horizon
2020 research and innovation program under the Marie Sklodowska-Curie grant agreement
no. 641639 ( ITN Biopol , H.D.B. and E.K.P.), the Alexander von Humboldt Foundation
(Alexander von Humboldt Professorship to K.F.), EMBO ALTF 522-2021 (to P.S.), Centre
for Trophoblast Research (Next Generation fellowship to S.A.), and JSPS Overseas
Research Fellowships (to A.Y.). The Wellcome-MRC Cambridge Stem Cell Institute receives
core funding from Wellcome Trust ( 203151/Z/16/Z ) and MRC ( MC_PC_17230 ). For
the purpose of open access, the author has applied a CC BY public copyright licence
to any Author Accepted Manuscript version arising from this submission.
article_processing_charge: No
article_type: original
author:
- first_name: Ayaka
full_name: Yanagida, Ayaka
last_name: Yanagida
- first_name: Elena
full_name: Corujo-Simon, Elena
last_name: Corujo-Simon
- first_name: Christopher K.
full_name: Revell, Christopher K.
last_name: Revell
- first_name: Preeti
full_name: Sahu, Preeti
id: 55BA52EE-A185-11EA-88FD-18AD3DDC885E
last_name: Sahu
- first_name: Giuliano G.
full_name: Stirparo, Giuliano G.
last_name: Stirparo
- first_name: Irene M.
full_name: Aspalter, Irene M.
last_name: Aspalter
- first_name: Alex K.
full_name: Winkel, Alex K.
last_name: Winkel
- first_name: Ruby
full_name: Peters, Ruby
last_name: Peters
- first_name: Henry
full_name: De Belly, Henry
last_name: De Belly
- first_name: Davide A.D.
full_name: Cassani, Davide A.D.
last_name: Cassani
- first_name: Sarra
full_name: Achouri, Sarra
last_name: Achouri
- first_name: Raphael
full_name: Blumenfeld, Raphael
last_name: Blumenfeld
- first_name: Kristian
full_name: Franze, Kristian
last_name: Franze
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Ewa K.
full_name: Paluch, Ewa K.
last_name: Paluch
- first_name: Jennifer
full_name: Nichols, Jennifer
last_name: Nichols
- first_name: Kevin J.
full_name: Chalut, Kevin J.
last_name: Chalut
citation:
ama: Yanagida A, Corujo-Simon E, Revell CK, et al. Cell surface fluctuations regulate
early embryonic lineage sorting. Cell. 2022;185(5):777-793.e20. doi:10.1016/j.cell.2022.01.022
apa: Yanagida, A., Corujo-Simon, E., Revell, C. K., Sahu, P., Stirparo, G. G., Aspalter,
I. M., … Chalut, K. J. (2022). Cell surface fluctuations regulate early embryonic
lineage sorting. Cell. Cell Press. https://doi.org/10.1016/j.cell.2022.01.022
chicago: Yanagida, Ayaka, Elena Corujo-Simon, Christopher K. Revell, Preeti Sahu,
Giuliano G. Stirparo, Irene M. Aspalter, Alex K. Winkel, et al. “Cell Surface
Fluctuations Regulate Early Embryonic Lineage Sorting.” Cell. Cell Press,
2022. https://doi.org/10.1016/j.cell.2022.01.022.
ieee: A. Yanagida et al., “Cell surface fluctuations regulate early embryonic
lineage sorting,” Cell, vol. 185, no. 5. Cell Press, p. 777–793.e20, 2022.
ista: Yanagida A, Corujo-Simon E, Revell CK, Sahu P, Stirparo GG, Aspalter IM, Winkel
AK, Peters R, De Belly H, Cassani DAD, Achouri S, Blumenfeld R, Franze K, Hannezo
EB, Paluch EK, Nichols J, Chalut KJ. 2022. Cell surface fluctuations regulate
early embryonic lineage sorting. Cell. 185(5), 777–793.e20.
mla: Yanagida, Ayaka, et al. “Cell Surface Fluctuations Regulate Early Embryonic
Lineage Sorting.” Cell, vol. 185, no. 5, Cell Press, 2022, p. 777–793.e20,
doi:10.1016/j.cell.2022.01.022.
short: A. Yanagida, E. Corujo-Simon, C.K. Revell, P. Sahu, G.G. Stirparo, I.M. Aspalter,
A.K. Winkel, R. Peters, H. De Belly, D.A.D. Cassani, S. Achouri, R. Blumenfeld,
K. Franze, E.B. Hannezo, E.K. Paluch, J. Nichols, K.J. Chalut, Cell 185 (2022)
777–793.e20.
date_created: 2022-03-06T23:01:52Z
date_published: 2022-02-22T00:00:00Z
date_updated: 2025-07-10T11:50:00Z
day: '22'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1016/j.cell.2022.01.022
ec_funded: 1
external_id:
isi:
- '000796293700007'
pmid:
- '35196500'
file:
- access_level: open_access
checksum: ae305060e8031297771b89dae9e36a29
content_type: application/pdf
creator: dernst
date_created: 2022-03-07T07:55:23Z
date_updated: 2022-03-07T07:55:23Z
file_id: '10831'
file_name: 2022_Cell_Yanagida.pdf
file_size: 8478995
relation: main_file
success: 1
file_date_updated: 2022-03-07T07:55:23Z
fulldoi: https://doi.org/10.1016/j.cell.2022.01.022
has_accepted_license: '1'
intvolume: ' 185'
isi: 1
issue: '5'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 777-793.e20
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell surface fluctuations regulate early embryonic lineage sorting
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: 185
year: '2022'
...
---
_id: '10826'
abstract:
- lang: eng
text: Animals that lose one sensory modality often show augmented responses to other
sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly
understood. We probe such mechanisms by performing a forward genetic screen for
mutants with enhanced O2 perception in Caenorhabditis elegans. Multiple mutants
exhibiting increased O2 responsiveness concomitantly show defects in other sensory
responses. One mutant, qui-1, defective in a conserved NACHT/WD40 protein, abolishes
pheromone-evoked Ca2+ responses in the ADL pheromone-sensing neurons. At the same
time, ADL responsiveness to pre-synaptic input from O2-sensing neurons is heightened
in qui-1, and other sensory defective mutants, resulting in enhanced neurosecretion
although not increased Ca2+ responses. Expressing qui-1 selectively in ADL rescues
both the qui-1 ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling
ADL neurons in qui-1 mutants highlights extensive changes in gene expression,
notably of many neuropeptide receptors. We show that elevated ADL expression of
the conserved neuropeptide receptor NPR-22 is necessary for enhanced ADL neurosecretion
in qui-1 mutants, and is sufficient to confer increased ADL neurosecretion in
control animals. Sensory loss can thus confer cross-modal plasticity by changing
the peptidergic connectome.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: ScienComp
acknowledgement: "We would like to thank Gemma Chandratillake and Merav Cohen for
identifying mutants and José David Moñino Sánchez for his help on neurosecretion
assays. We are grateful to Kaveh Ashrafi (UCSF), Piali Sengupta (Brandeis), and
the Caenorhabditis Genetic Center (funded by National Institutes of Health Infrastructure
Program P40 OD010440) for strains and reagents ... and Rebecca Butcher (Univ. Florida)
for C9 pheromone. We thank Tim Stevens, Paula Freire-Pritchett, Alastair Crisp,
GurpreetGhattaoraya, and Fabian Amman for help with bioinformatic analysis, Ekaterina
Lashmanova for help with injections, Iris Hardege for strains, and Isabel Beets
(KU Leuven) and members of the de Bono Lab for comments on the manuscript. We thank
the CRUK Cambridge Research Institute Genomics Core for next generation sequencing
and the Flow Cytometry Facility at LMB for FACS. This research was supported by
the Scientific Service Units (SSU) of IST Austria through resources provided by
the Bioimaging Facility (BIF), the Life Science Facility (LSF) and Scientific Computing
(SciCo-p– Bioinformatics).\r\nThis work was supported by the Medical Research Council
UK (Studentship to GV), an\r\nAdvanced ERC grant (269,058 ACMO to MdB), and a Wellcome
Investigator Award (209504/Z/17/Z to MdB)."
article_number: e68040
article_processing_charge: No
article_type: original
author:
- first_name: Giulio
full_name: Valperga, Giulio
id: 67F289DE-0D8F-11EA-9BDD-54AE3DDC885E
last_name: Valperga
orcid: 0000-0001-6726-3890
- first_name: Mario
full_name: De Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: De Bono
orcid: 0000-0001-8347-0443
citation:
ama: Valperga G, de Bono M. Impairing one sensory modality enhances another by reconfiguring
peptidergic signalling in Caenorhabditis elegans. eLife. 2022;11. doi:10.7554/eLife.68040
apa: Valperga, G., & de Bono, M. (2022). Impairing one sensory modality enhances
another by reconfiguring peptidergic signalling in Caenorhabditis elegans. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.68040
chicago: Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances
Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” ELife.
eLife Sciences Publications, 2022. https://doi.org/10.7554/eLife.68040.
ieee: G. Valperga and M. de Bono, “Impairing one sensory modality enhances another
by reconfiguring peptidergic signalling in Caenorhabditis elegans,” eLife,
vol. 11. eLife Sciences Publications, 2022.
ista: Valperga G, de Bono M. 2022. Impairing one sensory modality enhances another
by reconfiguring peptidergic signalling in Caenorhabditis elegans. eLife. 11,
e68040.
mla: Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances
Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” ELife,
vol. 11, e68040, eLife Sciences Publications, 2022, doi:10.7554/eLife.68040.
short: G. Valperga, M. de Bono, ELife 11 (2022).
corr_author: '1'
date_created: 2022-03-06T23:01:52Z
date_published: 2022-02-24T00:00:00Z
date_updated: 2026-04-02T12:45:39Z
day: '24'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.7554/eLife.68040
external_id:
isi:
- '000763432300001'
pmid:
- '35201977'
file:
- access_level: open_access
checksum: cc1b9bf866d0f61f965556e0dd03d3ac
content_type: application/pdf
creator: dernst
date_created: 2022-03-07T07:39:25Z
date_updated: 2022-03-07T07:39:25Z
file_id: '10830'
file_name: 2022_eLife_Valperga.pdf
file_size: 4095591
relation: main_file
success: 1
file_date_updated: 2022-03-07T07:39:25Z
fulldoi: https://doi.org/10.7554/eLife.68040
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 23870BE8-32DE-11EA-91FC-C7463DDC885E
grant_number: 209504/A/17/Z
name: Molecular mechanisms of neural circuit function
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Impairing one sensory modality enhances another by reconfiguring peptidergic
signalling in Caenorhabditis elegans
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 11
year: '2022'
...
---
_id: '10829'
abstract:
- lang: eng
text: A novel multivariable system, combining a transistor with fiber optic-based
surface plasmon resonance spectroscopy with the gate electrode simultaneously
acting as the fiber optic sensor surface, is reported. The dual-mode sensor allows
for discrimination of mass and charge contributions for binding assays on the
same sensor surface. Furthermore, we optimize the sensor geometry by investigating
the influence of the fiber area to transistor channel area ratio and distance.
We show that larger fiber optic tip diameters are favorable for electronic and
optical signals and demonstrate the reversibility of plasmon resonance wavelength
shifts after electric field application. As a proof of principle, a layer-by-layer
assembly of polyelectrolytes is performed to benchmark the system against multivariable
sensing platforms with planar surface plasmon resonance configurations. Furthermore,
the biosensing performance is assessed using a thrombin binding assay with surface-immobilized
aptamers as receptors, allowing for the detection of medically relevant thrombin
concentrations.
acknowledgement: "This project has received funding from the European Union’s Horizon
2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement
No. 813863-\r\nBORGES. Additionally, we gratefully acknowledge the financial support
from the Austrian Research Promotion Agency (FFG; 870025 and 873541) for this research.
The data that support the findings of this study are openly available in Zenodo
(DOI: 10.5281/zenodo.5500360)"
article_processing_charge: No
article_type: original
author:
- first_name: Roger
full_name: Hasler, Roger
last_name: Hasler
- first_name: Ciril
full_name: Reiner-Rozman, Ciril
last_name: Reiner-Rozman
- first_name: Stefan
full_name: Fossati, Stefan
last_name: Fossati
- first_name: Patrik
full_name: Aspermair, Patrik
last_name: Aspermair
- first_name: Jakub
full_name: Dostalek, Jakub
last_name: Dostalek
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Johannes
full_name: Bintinger, Johannes
last_name: Bintinger
- first_name: Wolfgang
full_name: Knoll, Wolfgang
last_name: Knoll
citation:
ama: Hasler R, Reiner-Rozman C, Fossati S, et al. Field-effect transistor with a
plasmonic fiber optic gate electrode as a multivariable biosensor device. ACS
Sensors. 2022;7(2):504-512. doi:10.1021/acssensors.1c02313
apa: Hasler, R., Reiner-Rozman, C., Fossati, S., Aspermair, P., Dostalek, J., Lee,
S., … Knoll, W. (2022). Field-effect transistor with a plasmonic fiber optic gate
electrode as a multivariable biosensor device. ACS Sensors. American Chemical
Society. https://doi.org/10.1021/acssensors.1c02313
chicago: Hasler, Roger, Ciril Reiner-Rozman, Stefan Fossati, Patrik Aspermair, Jakub
Dostalek, Seungho Lee, Maria Ibáñez, Johannes Bintinger, and Wolfgang Knoll. “Field-Effect
Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor
Device.” ACS Sensors. American Chemical Society, 2022. https://doi.org/10.1021/acssensors.1c02313.
ieee: R. Hasler et al., “Field-effect transistor with a plasmonic fiber optic
gate electrode as a multivariable biosensor device,” ACS Sensors, vol.
7, no. 2. American Chemical Society, pp. 504–512, 2022.
ista: Hasler R, Reiner-Rozman C, Fossati S, Aspermair P, Dostalek J, Lee S, Ibáñez
M, Bintinger J, Knoll W. 2022. Field-effect transistor with a plasmonic fiber
optic gate electrode as a multivariable biosensor device. ACS Sensors. 7(2), 504–512.
mla: Hasler, Roger, et al. “Field-Effect Transistor with a Plasmonic Fiber Optic
Gate Electrode as a Multivariable Biosensor Device.” ACS Sensors, vol.
7, no. 2, American Chemical Society, 2022, pp. 504–12, doi:10.1021/acssensors.1c02313.
short: R. Hasler, C. Reiner-Rozman, S. Fossati, P. Aspermair, J. Dostalek, S. Lee,
M. Ibáñez, J. Bintinger, W. Knoll, ACS Sensors 7 (2022) 504–512.
date_created: 2022-03-06T23:01:54Z
date_published: 2022-02-08T00:00:00Z
date_updated: 2026-04-02T12:33:46Z
day: '08'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1021/acssensors.1c02313
external_id:
isi:
- '000765113000016'
pmid:
- '35134289'
file:
- access_level: open_access
checksum: d704af7262cd484da9bb84b7d84e2b09
content_type: application/pdf
creator: dernst
date_created: 2022-03-07T08:15:01Z
date_updated: 2022-03-07T08:15:01Z
file_id: '10832'
file_name: 2022_ACSSensors_Hasler.pdf
file_size: 2969415
relation: main_file
success: 1
file_date_updated: 2022-03-07T08:15:01Z
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intvolume: ' 7'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 504-512
pmid: 1
publication: ACS Sensors
publication_identifier:
eissn:
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publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
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relation: research_data
status: public
scopus_import: '1'
status: public
title: Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable
biosensor device
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 7
year: '2022'
...
---
_id: '10833'
abstract:
- lang: eng
text: Detailed information about the data set see "dataset description.txt" file.
article_processing_charge: No
author:
- first_name: Roger
full_name: Hasler, Roger
last_name: Hasler
- first_name: Ciril
full_name: Reiner-Rozman, Ciril
last_name: Reiner-Rozman
- first_name: Stefan
full_name: Fossati, Stefan
last_name: Fossati
- first_name: Patrik
full_name: Aspermair, Patrik
last_name: Aspermair
- first_name: Jakub
full_name: Dostalek, Jakub
last_name: Dostalek
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Johannes
full_name: Bintinger, Johannes
last_name: Bintinger
- first_name: Wolfgang
full_name: Knoll, Wolfgang
last_name: Knoll
citation:
ama: Hasler R, Reiner-Rozman C, Fossati S, et al. Field-effect transistor with a
plasmonic fiber optic gate electrode as a multivariable biosensor device. 2022.
doi:10.5281/ZENODO.5500360
apa: Hasler, R., Reiner-Rozman, C., Fossati, S., Aspermair, P., Dostalek, J., Lee,
S., … Knoll, W. (2022). Field-effect transistor with a plasmonic fiber optic gate
electrode as a multivariable biosensor device. Zenodo. https://doi.org/10.5281/ZENODO.5500360
chicago: Hasler, Roger, Ciril Reiner-Rozman, Stefan Fossati, Patrik Aspermair, Jakub
Dostalek, Seungho Lee, Maria Ibáñez, Johannes Bintinger, and Wolfgang Knoll. “Field-Effect
Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor
Device.” Zenodo, 2022. https://doi.org/10.5281/ZENODO.5500360.
ieee: R. Hasler et al., “Field-effect transistor with a plasmonic fiber optic
gate electrode as a multivariable biosensor device.” Zenodo, 2022.
ista: Hasler R, Reiner-Rozman C, Fossati S, Aspermair P, Dostalek J, Lee S, Ibáñez
M, Bintinger J, Knoll W. 2022. Field-effect transistor with a plasmonic fiber
optic gate electrode as a multivariable biosensor device, Zenodo, 10.5281/ZENODO.5500360.
mla: Hasler, Roger, et al. Field-Effect Transistor with a Plasmonic Fiber Optic
Gate Electrode as a Multivariable Biosensor Device. Zenodo, 2022, doi:10.5281/ZENODO.5500360.
short: R. Hasler, C. Reiner-Rozman, S. Fossati, P. Aspermair, J. Dostalek, S. Lee,
M. Ibáñez, J. Bintinger, W. Knoll, (2022).
date_created: 2022-03-07T08:19:11Z
date_published: 2022-02-08T00:00:00Z
date_updated: 2026-04-02T12:33:44Z
day: '08'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.5281/ZENODO.5500360
fulldoi: https://doi.org/10.5281/ZENODO.5500360
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5500360
month: '02'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '10829'
relation: used_in_publication
status: public
status: public
title: Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable
biosensor device
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2022'
...
---
_id: '10841'
abstract:
- lang: eng
text: In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization
of material from the cell surface as well as the movement of cargo in post-Golgi
trafficking pathways. This diversity of functions is partially provided by multiple
monomeric and multimeric clathrin adaptor complexes that provide compartment and
cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates
as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2
complex and the TPLATE complex jointly operate at the plasma membrane to execute
clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated
trafficking in plants will be the comprehensive identification and characterization
of the network of evolutionarily conserved and plant-specific core and accessory
machinery involved in the formation and targeting of CCVs. To facilitate these
studies, we have analyzed the proteome of enriched TGN/early endosome-derived
and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis
(Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated
by differential chemical labeling experiments to identify proteins co-enriching
with CCVs. Proteins enriched in CCVs included previously characterized CCV components
and cargos such as the vacuolar sorting receptors in addition to conserved and
plant-specific components whose function in clathrin-mediated trafficking has
not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits
of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance
in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis
CCVs is further supported via additional biochemical data.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: 'The authors would like to acknowledge the VIB Proteomics Core Facility
(VIB-UGent Center for Medical Biotechnology in Ghent, Belgium) and the Research
Technology Support Facility Proteomics Core (Michigan State University in East Lansing,
Michigan) for sample analysis, as well as the University of Wisconsin Biotechnology
Center Mass Spectrometry Core Facility (Madison, WI) for help with data processing.
Additionally, we are grateful to Sue Weintraub (UT Health San Antonio) and Sydney
Thomas (UW- Madison) for assistance with data analysis. This research was supported
by grants to S.Y.B. from the National Science Foundation (Nos. 1121998 and 1614915)
and a Vilas Associate Award (University of Wisconsin, Madison, Graduate School);
to J.P. from the National Natural Science Foundation of China (Nos. 91754104, 31820103008,
and 31670283); to I.H. from the National Research Foundation of Korea (No. 2019R1A2B5B03099982).
This research was also supported by the Scientific Service Units (SSU) of IST Austria
through resources provided by the Electron microscopy Facility (EMF). A.J. is supported
by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. A.H. is supported
by funding from the National Science Foundation (NSF IOS Nos. 1025837 and 1147032).'
article_processing_charge: No
article_type: original
author:
- first_name: DA
full_name: Dahhan, DA
last_name: Dahhan
- first_name: GD
full_name: Reynolds, GD
last_name: Reynolds
- first_name: JJ
full_name: Cárdenas, JJ
last_name: Cárdenas
- first_name: D
full_name: Eeckhout, D
last_name: Eeckhout
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: K
full_name: Yperman, K
last_name: Yperman
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: N
full_name: Vang, N
last_name: Vang
- first_name: X
full_name: Yan, X
last_name: Yan
- first_name: I
full_name: Hwang, I
last_name: Hwang
- first_name: A
full_name: Heese, A
last_name: Heese
- first_name: G
full_name: De Jaeger, G
last_name: De Jaeger
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: D
full_name: Van Damme, D
last_name: Van Damme
- first_name: J
full_name: Pan, J
last_name: Pan
- first_name: SY
full_name: Bednarek, SY
last_name: Bednarek
citation:
ama: Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated
Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific
components. Plant Cell. 2022;34(6):2150-2173. doi:10.1093/plcell/koac071
apa: Dahhan, D., Reynolds, G., Cárdenas, J., Eeckhout, D., Johnson, A. J., Yperman,
K., … Bednarek, S. (2022). Proteomic characterization of isolated Arabidopsis
clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components.
Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koac071
chicago: Dahhan, DA, GD Reynolds, JJ Cárdenas, D Eeckhout, Alexander J Johnson,
K Yperman, Walter Kaufmann, et al. “Proteomic Characterization of Isolated Arabidopsis
Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.”
Plant Cell. Oxford University Press, 2022. https://doi.org/10.1093/plcell/koac071.
ieee: D. Dahhan et al., “Proteomic characterization of isolated Arabidopsis
clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,”
Plant Cell, vol. 34, no. 6. Oxford University Press, pp. 2150–2173, 2022.
ista: Dahhan D, Reynolds G, Cárdenas J, Eeckhout D, Johnson AJ, Yperman K, Kaufmann
W, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J,
Bednarek S. 2022. Proteomic characterization of isolated Arabidopsis clathrin-coated
vesicles reveals evolutionarily conserved and plant-specific components. Plant
Cell. 34(6), 2150–2173.
mla: Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated
Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” Plant
Cell, vol. 34, no. 6, Oxford University Press, 2022, pp. 2150–73, doi:10.1093/plcell/koac071.
short: D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman,
W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van
Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173.
date_created: 2022-03-08T13:47:51Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2025-05-14T11:06:15Z
day: '01'
department:
- _id: JiFr
- _id: EM-Fac
doi: 10.1093/plcell/koac071
external_id:
isi:
- '000767438800001'
pmid:
- '35218346'
fulldoi: https://doi.org/10.1093/plcell/koac071
intvolume: ' 34'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2021.09.16.460678
month: '06'
oa: 1
oa_version: Preprint
page: 2150-2173
pmid: 1
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: Plant Cell
publication_identifier:
eissn:
- 1532-298x
issn:
- 1040-4651
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles
reveals evolutionarily conserved and plant-specific components
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2022'
...
---
_id: '10842'
abstract:
- lang: eng
text: We determine the unique factorization of some polynomials over a finite local
commutative ring with identity explicitly. This solves and generalizes the main
conjecture of Qian, Shi and Solé in [13]. We also give some applications to enumeration
of certain generalized double circulant self-dual and linear complementary dual
(LCD) codes over some finite rings together with an application in asymptotic
coding theory.
acknowledgement: The authors would like to thank Prof. Dr. Minjia Shi for bringing
[13, Conjecture 3.5] to our attention. We would also like to thank the associate
editor and anonymous reviewers for their valuable comments and suggestions which
improved and clarified the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Seyda
full_name: Köse, Seyda
id: 8ba3170d-dc85-11ea-9058-c4251c96a6eb
last_name: Köse
- first_name: Ferruh
full_name: Özbudak, Ferruh
last_name: Özbudak
citation:
ama: Köse S, Özbudak F. Factorization of some polynomials over finite local commutative
rings and applications to certain self-dual and LCD codes. Cryptography and
Communications. 2022;14(4):933-948. doi:10.1007/s12095-022-00557-8
apa: Köse, S., & Özbudak, F. (2022). Factorization of some polynomials over
finite local commutative rings and applications to certain self-dual and LCD codes.
Cryptography and Communications. Springer Nature. https://doi.org/10.1007/s12095-022-00557-8
chicago: Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over
Finite Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.”
Cryptography and Communications. Springer Nature, 2022. https://doi.org/10.1007/s12095-022-00557-8.
ieee: S. Köse and F. Özbudak, “Factorization of some polynomials over finite local
commutative rings and applications to certain self-dual and LCD codes,” Cryptography
and Communications, vol. 14, no. 4. Springer Nature, pp. 933–948, 2022.
ista: Köse S, Özbudak F. 2022. Factorization of some polynomials over finite local
commutative rings and applications to certain self-dual and LCD codes. Cryptography
and Communications. 14(4), 933–948.
mla: Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over Finite
Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.”
Cryptography and Communications, vol. 14, no. 4, Springer Nature, 2022,
pp. 933–48, doi:10.1007/s12095-022-00557-8.
short: S. Köse, F. Özbudak, Cryptography and Communications 14 (2022) 933–948.
date_created: 2022-03-10T12:16:19Z
date_published: 2022-07-01T00:00:00Z
date_updated: 2023-09-05T15:35:55Z
day: '01'
department:
- _id: GradSch
doi: 10.1007/s12095-022-00557-8
external_id:
isi:
- '000766422000002'
fulldoi: https://doi.org/10.1007/s12095-022-00557-8
intvolume: ' 14'
isi: 1
issue: '4'
keyword:
- Applied Mathematics
- Computational Theory and Mathematics
- Computer Networks and Communications
language:
- iso: eng
month: '07'
oa_version: None
page: 933-948
publication: Cryptography and Communications
publication_identifier:
eissn:
- 1936-2455
issn:
- 1936-2447
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Factorization of some polynomials over finite local commutative rings and applications
to certain self-dual and LCD codes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2022'
...
---
_id: '10845'
abstract:
- lang: eng
text: We study an impurity with a resonance level whose position coincides with
the Fermi energy of the surrounding Fermi gas. An impurity causes a rapid variation
of the scattering phase shift for fermions at the Fermi surface, introducing a
new characteristic length scale into the problem. We investigate manifestations
of this length scale in the self-energy of the impurity and in the density of
the bath. Our calculations reveal a model-independent deformation of the density
of the Fermi gas, which is determined by the width of the resonance. To provide
a broader picture, we investigate time evolution of the density in quench dynamics,
and study the behavior of the system at finite temperatures. Finally, we briefly
discuss implications of our findings for the Fermi-polaron problem.
acknowledgement: M.L. acknowledges support by the Austrian Science Fund (FWF), under
Project No. P29902-N27, and by the European Research Council (ERC) starting Grant
No. 801770 (ANGULON). A.G.V. acknowledges support by European Union’s Horizon 2020
research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
No. 754411.
article_number: '013160'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Mikhail
full_name: Maslov, Mikhail
id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87
last_name: Maslov
orcid: 0000-0003-4074-2570
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Maslov M, Lemeshko M, Volosniev A. Impurity with a resonance in the vicinity
of the Fermi energy. Physical Review Research. 2022;4. doi:10.1103/PhysRevResearch.4.013160
apa: Maslov, M., Lemeshko, M., & Volosniev, A. (2022). Impurity with a resonance
in the vicinity of the Fermi energy. Physical Review Research. American
Physical Society. https://doi.org/10.1103/PhysRevResearch.4.013160
chicago: Maslov, Mikhail, Mikhail Lemeshko, and Artem Volosniev. “Impurity with
a Resonance in the Vicinity of the Fermi Energy.” Physical Review Research.
American Physical Society, 2022. https://doi.org/10.1103/PhysRevResearch.4.013160.
ieee: M. Maslov, M. Lemeshko, and A. Volosniev, “Impurity with a resonance in the
vicinity of the Fermi energy,” Physical Review Research, vol. 4. American
Physical Society, 2022.
ista: Maslov M, Lemeshko M, Volosniev A. 2022. Impurity with a resonance in the
vicinity of the Fermi energy. Physical Review Research. 4, 013160.
mla: Maslov, Mikhail, et al. “Impurity with a Resonance in the Vicinity of the Fermi
Energy.” Physical Review Research, vol. 4, 013160, American Physical Society,
2022, doi:10.1103/PhysRevResearch.4.013160.
short: M. Maslov, M. Lemeshko, A. Volosniev, Physical Review Research 4 (2022).
corr_author: '1'
date_created: 2022-03-13T23:01:46Z
date_published: 2022-03-01T00:00:00Z
date_updated: 2026-04-07T11:52:53Z
day: '01'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/PhysRevResearch.4.013160
ec_funded: 1
external_id:
arxiv:
- '2111.13570'
file:
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checksum: 62f64b3421a969656ebf52467fa7b6e8
content_type: application/pdf
creator: dernst
date_created: 2022-03-14T08:38:49Z
date_updated: 2022-03-14T08:38:49Z
file_id: '10848'
file_name: 2022_PhysicalReviewResearch_Maslov.pdf
file_size: 1258324
relation: main_file
success: 1
file_date_updated: 2022-03-14T08:38:49Z
fulldoi: https://doi.org/10.1103/PhysRevResearch.4.013160
has_accepted_license: '1'
intvolume: ' 4'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '19048'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Impurity with a resonance in the vicinity of the Fermi energy
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: 4
year: '2022'
...
---
_id: '10850'
abstract:
- lang: eng
text: "We study two interacting quantum particles forming a bound state in d-dimensional
free\r\nspace, and constrain the particles in k directions to (0, ∞)k ×Rd−k, with
Neumann boundary\r\nconditions. First, we prove that the ground state energy strictly
decreases upon going from k\r\nto k+1. This shows that the particles stick to
the corner where all boundary planes intersect.\r\nSecond, we show that for all
k the resulting Hamiltonian, after removing the free part of the\r\nkinetic energy,
has only finitely many eigenvalues below the essential spectrum. This paper\r\ngeneralizes
the work of Egger, Kerner and Pankrashkin (J. Spectr. Theory 10(4):1413–1444,\r\n2020)
to dimensions d > 1."
acknowledgement: We thank Rupert Frank for contributing Appendix B. Funding from the
European Union's Horizon 2020 research and innovation programme under the ERC grant
agreement No. 694227 is gratefully acknowledged.
article_number: '109455'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Barbara
full_name: Roos, Barbara
id: 5DA90512-D80F-11E9-8994-2E2EE6697425
last_name: Roos
orcid: 0000-0002-9071-5880
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Roos B, Seiringer R. Two-particle bound states at interfaces and corners. Journal
of Functional Analysis. 2022;282(12). doi:10.1016/j.jfa.2022.109455
apa: Roos, B., & Seiringer, R. (2022). Two-particle bound states at interfaces
and corners. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2022.109455
chicago: Roos, Barbara, and Robert Seiringer. “Two-Particle Bound States at Interfaces
and Corners.” Journal of Functional Analysis. Elsevier, 2022. https://doi.org/10.1016/j.jfa.2022.109455.
ieee: B. Roos and R. Seiringer, “Two-particle bound states at interfaces and corners,”
Journal of Functional Analysis, vol. 282, no. 12. Elsevier, 2022.
ista: Roos B, Seiringer R. 2022. Two-particle bound states at interfaces and corners.
Journal of Functional Analysis. 282(12), 109455.
mla: Roos, Barbara, and Robert Seiringer. “Two-Particle Bound States at Interfaces
and Corners.” Journal of Functional Analysis, vol. 282, no. 12, 109455,
Elsevier, 2022, doi:10.1016/j.jfa.2022.109455.
short: B. Roos, R. Seiringer, Journal of Functional Analysis 282 (2022).
corr_author: '1'
date_created: 2022-03-16T08:41:53Z
date_published: 2022-06-15T00:00:00Z
date_updated: 2026-04-07T13:27:39Z
day: '15'
ddc:
- '510'
department:
- _id: GradSch
- _id: RoSe
doi: 10.1016/j.jfa.2022.109455
ec_funded: 1
external_id:
arxiv:
- '2105.04874'
isi:
- '000795160200009'
file:
- access_level: open_access
checksum: 63efcefaa1f2717244ef5407bd564426
content_type: application/pdf
creator: dernst
date_created: 2022-08-02T10:37:55Z
date_updated: 2022-08-02T10:37:55Z
file_id: '11720'
file_name: 2022_JourFunctionalAnalysis_Roos.pdf
file_size: 631391
relation: main_file
success: 1
file_date_updated: 2022-08-02T10:37:55Z
fulldoi: https://doi.org/10.1016/j.jfa.2022.109455
has_accepted_license: '1'
intvolume: ' 282'
isi: 1
issue: '12'
keyword:
- Analysis
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Journal of Functional Analysis
publication_identifier:
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '14374'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Two-particle bound states at interfaces and corners
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 282
year: '2022'
...
---
_id: '10851'
abstract:
- lang: eng
text: Superconductor-semiconductor hybrid devices are at the heart of several proposed
approaches to quantum information processing, but their basic properties remain
to be understood. We embed a twodimensional Al-InAs hybrid system in a resonant
microwave circuit, probing the breakdown of superconductivity due to an applied
magnetic field. We find a fingerprint from the two-component nature of the hybrid
system, and quantitatively compare with a theory that includes the contribution
of intraband p±ip pairing in the InAs, as well as the emergence of Bogoliubov-Fermi
surfaces due to magnetic field. Separately resolving the Al and InAs contributions
allows us to determine the carrier density and mobility in the InAs.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: M. S. acknowledges useful discussions with A. Levchenko and P. A.
Lee, and E. Berg. This research was supported by the Scientific Service Units of
IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication
facility. J. S. and A. G. acknowledge funding from the European Union’s Horizon
2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement
No. 754411.W. M. Hatefipour, W. M. Strickland and J. Shabani acknowledge funding
from Office of Naval Research Award No. N00014-21-1-2450.
article_number: '107701'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Duc T
full_name: Phan, Duc T
id: 29C8C0B4-F248-11E8-B48F-1D18A9856A87
last_name: Phan
- first_name: Jorden L
full_name: Senior, Jorden L
id: 5479D234-2D30-11EA-89CC-40953DDC885E
last_name: Senior
orcid: 0000-0002-0672-9295
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: M.
full_name: Hatefipour, M.
last_name: Hatefipour
- first_name: W. M.
full_name: Strickland, W. M.
last_name: Strickland
- first_name: J.
full_name: Shabani, J.
last_name: Shabani
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Phan DT, Senior JL, Ghazaryan A, et al. Detecting induced p±ip pairing at the
Al-InAs interface with a quantum microwave circuit. Physical Review Letters.
2022;128(10). doi:10.1103/physrevlett.128.107701
apa: Phan, D. T., Senior, J. L., Ghazaryan, A., Hatefipour, M., Strickland, W. M.,
Shabani, J., … Higginbotham, A. P. (2022). Detecting induced p±ip pairing at the
Al-InAs interface with a quantum microwave circuit. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/physrevlett.128.107701
chicago: Phan, Duc T, Jorden L Senior, Areg Ghazaryan, M. Hatefipour, W. M. Strickland,
J. Shabani, Maksym Serbyn, and Andrew P Higginbotham. “Detecting Induced P±ip
Pairing at the Al-InAs Interface with a Quantum Microwave Circuit.” Physical
Review Letters. American Physical Society, 2022. https://doi.org/10.1103/physrevlett.128.107701.
ieee: D. T. Phan et al., “Detecting induced p±ip pairing at the Al-InAs interface
with a quantum microwave circuit,” Physical Review Letters, vol. 128, no.
10. American Physical Society, 2022.
ista: Phan DT, Senior JL, Ghazaryan A, Hatefipour M, Strickland WM, Shabani J, Serbyn
M, Higginbotham AP. 2022. Detecting induced p±ip pairing at the Al-InAs interface
with a quantum microwave circuit. Physical Review Letters. 128(10), 107701.
mla: Phan, Duc T., et al. “Detecting Induced P±ip Pairing at the Al-InAs Interface
with a Quantum Microwave Circuit.” Physical Review Letters, vol. 128, no.
10, 107701, American Physical Society, 2022, doi:10.1103/physrevlett.128.107701.
short: D.T. Phan, J.L. Senior, A. Ghazaryan, M. Hatefipour, W.M. Strickland, J.
Shabani, M. Serbyn, A.P. Higginbotham, Physical Review Letters 128 (2022).
corr_author: '1'
date_created: 2022-03-17T11:37:47Z
date_published: 2022-03-11T00:00:00Z
date_updated: 2026-04-07T13:25:51Z
day: '11'
department:
- _id: MaSe
- _id: AnHi
doi: 10.1103/physrevlett.128.107701
ec_funded: 1
external_id:
arxiv:
- '2107.03695'
isi:
- '000771391100002'
pmid:
- ' 35333085'
fulldoi: https://doi.org/10.1103/physrevlett.128.107701
intvolume: ' 128'
isi: 1
issue: '10'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2107.03695
month: '03'
oa: 1
oa_version: Preprint
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/characterizing-super-semi-sandwiches-for-quantum-computing/
record:
- id: '10029'
relation: earlier_version
status: public
- id: '14547'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave
circuit
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 128
year: '2022'
...
---
_id: '10863'
abstract:
- lang: eng
text: 'Nonlinear optical responses are commonly used as a probe for studying the
electronic properties of materials. For topological materials, studies thus far
focused on photogalvanic electric currents, which are forbidden in centrosymmetric
materials because they require broken inversion symmetry. In this Letter, we propose
a class of symmetry-allowed responses for inversion-symmetric topological insulators
with two doubly degenerate bands. We consider a specific example of such a response,
the orbital current, and show that the sign of the response reflects the Z2 topological
index, i.e., the orbital current changes sign at the transition between trivial
and topological insulator phases. This is illustrated in two models of topological
insulators: the Bernevig-Hughes-Zhang model and the 1T′ phase of transition metal
dichalcogenides.'
acknowledgement: "We are grateful to Takahiro Morimoto and Zhanybek Alpichshev for
fruitful discussions. MD was supported by Austrian Agency for International Cooperation
in Education and Research (OeAD-GmbH) and by the John Seo Fellowship at MIT. HI
was supported by JSPS KAKENHI Grant Numbers JP19K14649 and JP18H03676, and by UTokyo
Global Activity Support Program for\r\nYoung Researchers."
article_number: L121407
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Margarita
full_name: Davydova, Margarita
last_name: Davydova
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Hiroaki
full_name: Ishizuka, Hiroaki
last_name: Ishizuka
citation:
ama: Davydova M, Serbyn M, Ishizuka H. Symmetry-allowed nonlinear orbital response
across the topological phase transition in centrosymmetric materials. Physical
Review B. 2022;105. doi:10.1103/PhysRevB.105.L121407
apa: Davydova, M., Serbyn, M., & Ishizuka, H. (2022). Symmetry-allowed nonlinear
orbital response across the topological phase transition in centrosymmetric materials.
Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.105.L121407
chicago: Davydova, Margarita, Maksym Serbyn, and Hiroaki Ishizuka. “Symmetry-Allowed
Nonlinear Orbital Response across the Topological Phase Transition in Centrosymmetric
Materials.” Physical Review B. American Physical Society, 2022. https://doi.org/10.1103/PhysRevB.105.L121407.
ieee: M. Davydova, M. Serbyn, and H. Ishizuka, “Symmetry-allowed nonlinear orbital
response across the topological phase transition in centrosymmetric materials,”
Physical Review B, vol. 105. American Physical Society, 2022.
ista: Davydova M, Serbyn M, Ishizuka H. 2022. Symmetry-allowed nonlinear orbital
response across the topological phase transition in centrosymmetric materials.
Physical Review B. 105, L121407.
mla: Davydova, Margarita, et al. “Symmetry-Allowed Nonlinear Orbital Response across
the Topological Phase Transition in Centrosymmetric Materials.” Physical Review
B, vol. 105, L121407, American Physical Society, 2022, doi:10.1103/PhysRevB.105.L121407.
short: M. Davydova, M. Serbyn, H. Ishizuka, Physical Review B 105 (2022).
date_created: 2022-03-18T10:20:46Z
date_published: 2022-03-17T00:00:00Z
date_updated: 2023-08-03T06:09:56Z
day: '17'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.105.L121407
external_id:
arxiv:
- '2101.08277'
isi:
- '000800752500001'
fulldoi: https://doi.org/10.1103/PhysRevB.105.L121407
intvolume: ' 105'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2101.08277
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
issn:
- 2469-9969
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Symmetry-allowed nonlinear orbital response across the topological phase transition
in centrosymmetric materials
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 105
year: '2022'
...
---
_id: '10887'
abstract:
- lang: eng
text: "We introduce a new way of representing logarithmically concave functions
on Rd. It allows us to extend the notion of the largest volume ellipsoid contained
in a convex body to the setting of logarithmically concave functions as follows.
For every s>0, we define a class of non-negative functions on Rd derived from
ellipsoids in Rd+1. For any log-concave function f on Rd , and any fixed s>0,
we consider functions belonging to this class, and find the one with the largest
integral under the condition that it is pointwise less than or equal to f, and
we call it the John s-function of f. After establishing existence and uniqueness,
we give a characterization of this function similar to the one given by John in
his fundamental theorem. We find that John s-functions converge to characteristic
functions of ellipsoids as s tends to zero and to Gaussian densities as s tends
to infinity.\r\nAs an application, we prove a quantitative Helly type result:
the integral of the pointwise minimum of any family of log-concave functions is
at least a constant cd multiple of the integral of the pointwise minimum of a
properly chosen subfamily of size 3d+2, where cd depends only on d."
acknowledgement: 'G.I. was supported by the Ministry of Education and Science of the
Russian Federation in the framework of MegaGrant no 075-15-2019-1926. M.N. was supported
by the National Research, Development and Innovation Fund (NRDI) grants K119670
and KKP-133864 as well as the Bolyai Scholarship of the Hungarian Academy of Sciences
and the New National Excellence Programme and the TKP2020-NKA-06 program provided
by the NRDI. '
article_number: '109441'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Grigory
full_name: Ivanov, Grigory
id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E
last_name: Ivanov
- first_name: Márton
full_name: Naszódi, Márton
last_name: Naszódi
citation:
ama: Ivanov G, Naszódi M. Functional John ellipsoids. Journal of Functional Analysis.
2022;282(11). doi:10.1016/j.jfa.2022.109441
apa: Ivanov, G., & Naszódi, M. (2022). Functional John ellipsoids. Journal
of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2022.109441
chicago: Ivanov, Grigory, and Márton Naszódi. “Functional John Ellipsoids.” Journal
of Functional Analysis. Elsevier, 2022. https://doi.org/10.1016/j.jfa.2022.109441.
ieee: G. Ivanov and M. Naszódi, “Functional John ellipsoids,” Journal of Functional
Analysis, vol. 282, no. 11. Elsevier, 2022.
ista: Ivanov G, Naszódi M. 2022. Functional John ellipsoids. Journal of Functional
Analysis. 282(11), 109441.
mla: Ivanov, Grigory, and Márton Naszódi. “Functional John Ellipsoids.” Journal
of Functional Analysis, vol. 282, no. 11, 109441, Elsevier, 2022, doi:10.1016/j.jfa.2022.109441.
short: G. Ivanov, M. Naszódi, Journal of Functional Analysis 282 (2022).
corr_author: '1'
date_created: 2022-03-20T23:01:38Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2024-10-09T21:01:51Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.1016/j.jfa.2022.109441
external_id:
arxiv:
- '2006.09934'
isi:
- '000781371300008'
file:
- access_level: open_access
checksum: 1cf185e264e04c87cb1ce67a00db88ab
content_type: application/pdf
creator: dernst
date_created: 2022-08-02T10:40:48Z
date_updated: 2022-08-02T10:40:48Z
file_id: '11721'
file_name: 2022_JourFunctionalAnalysis_Ivanov.pdf
file_size: 734482
relation: main_file
success: 1
file_date_updated: 2022-08-02T10:40:48Z
fulldoi: https://doi.org/10.1016/j.jfa.2022.109441
has_accepted_license: '1'
intvolume: ' 282'
isi: 1
issue: '11'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Functional John ellipsoids
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 282
year: '2022'
...
---
_id: '10888'
abstract:
- lang: eng
text: Despite the growing interest in using chemical genetics in plant research,
small molecule target identification remains a major challenge. The cellular thermal
shift assay coupled with high-resolution mass spectrometry (CETSA MS) that monitors
changes in the thermal stability of proteins caused by their interactions with
small molecules, other proteins, or posttranslational modifications, allows the
discovery of drug targets or the study of protein–metabolite and protein–protein
interactions mainly in mammalian cells. To showcase the applicability of this
method in plants, we applied CETSA MS to intact Arabidopsis thaliana cells and
identified the thermal proteome of the plant-specific glycogen synthase kinase
3 (GSK3) inhibitor, bikinin. A comparison between the thermal and the phosphoproteomes
of bikinin revealed the auxin efflux carrier PIN-FORMED1 (PIN1) as a substrate
of the Arabidopsis GSK3s that negatively regulate the brassinosteroid signaling.
We established that PIN1 phosphorylation by the GSK3s is essential for maintaining
its intracellular polarity that is required for auxin-mediated regulation of vascular
patterning in the leaf, thus revealing cross-talk between brassinosteroid and
auxin signaling.
acknowledgement: "We thank Yanhai Yin for providing the anti-BES1 antibody, Johan
Winne and Brenda Callebaut for synthesizing bikinin, Yuki Kondo and Hiroo Fukuda
for published materials, Tomasz Nodzy\x03nski for useful advice, and Martine De
Cock for help in preparing the manuscript. This\r\nwork was supported by the China
Scholarship Council for predoctoral (Q.L. and X.X.) and postdoctoral (Y.Z.) fellowships;
the Agency for Innovation by Science and Technology for a predoctoral fellowship
(W.D.); the Research Foundation-Flanders, Projects G009018N and G002121N (E.R.);
and the VIB TechWatch Fund (E.R.)."
article_number: e2118220119
article_processing_charge: No
article_type: original
author:
- first_name: Qing
full_name: Lu, Qing
last_name: Lu
- first_name: Yonghong
full_name: Zhang, Yonghong
last_name: Zhang
- first_name: Joakim
full_name: Hellner, Joakim
last_name: Hellner
- first_name: Caterina
full_name: Giannini, Caterina
id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4
last_name: Giannini
- first_name: Xiangyu
full_name: Xu, Xiangyu
last_name: Xu
- first_name: Jarne
full_name: Pauwels, Jarne
last_name: Pauwels
- first_name: Qian
full_name: Ma, Qian
last_name: Ma
- first_name: Wim
full_name: Dejonghe, Wim
last_name: Dejonghe
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Brigitte
full_name: Van De Cotte, Brigitte
last_name: Van De Cotte
- first_name: Francis
full_name: Impens, Francis
last_name: Impens
- first_name: Kris
full_name: Gevaert, Kris
last_name: Gevaert
- first_name: Ive
full_name: De Smet, Ive
last_name: De Smet
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Daniel Martinez
full_name: Molina, Daniel Martinez
last_name: Molina
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Lu Q, Zhang Y, Hellner J, et al. Proteome-wide cellular thermal shift assay
reveals unexpected cross-talk between brassinosteroid and auxin signaling. Proceedings
of the National Academy of Sciences of the United States of America. 2022;119(11).
doi:10.1073/pnas.2118220119
apa: Lu, Q., Zhang, Y., Hellner, J., Giannini, C., Xu, X., Pauwels, J., … Russinova,
E. (2022). Proteome-wide cellular thermal shift assay reveals unexpected cross-talk
between brassinosteroid and auxin signaling. Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.2118220119
chicago: Lu, Qing, Yonghong Zhang, Joakim Hellner, Caterina Giannini, Xiangyu Xu,
Jarne Pauwels, Qian Ma, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected
Cross-Talk between Brassinosteroid and Auxin Signaling.” Proceedings of the
National Academy of Sciences of the United States of America. National Academy
of Sciences, 2022. https://doi.org/10.1073/pnas.2118220119.
ieee: Q. Lu et al., “Proteome-wide cellular thermal shift assay reveals unexpected
cross-talk between brassinosteroid and auxin signaling,” Proceedings of the
National Academy of Sciences of the United States of America, vol. 119, no.
11. National Academy of Sciences, 2022.
ista: Lu Q, Zhang Y, Hellner J, Giannini C, Xu X, Pauwels J, Ma Q, Dejonghe W, Han
H, Van De Cotte B, Impens F, Gevaert K, De Smet I, Friml J, Molina DM, Russinova
E. 2022. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk
between brassinosteroid and auxin signaling. Proceedings of the National Academy
of Sciences of the United States of America. 119(11), e2118220119.
mla: Lu, Qing, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected
Cross-Talk between Brassinosteroid and Auxin Signaling.” Proceedings of the
National Academy of Sciences of the United States of America, vol. 119, no.
11, e2118220119, National Academy of Sciences, 2022, doi:10.1073/pnas.2118220119.
short: Q. Lu, Y. Zhang, J. Hellner, C. Giannini, X. Xu, J. Pauwels, Q. Ma, W. Dejonghe,
H. Han, B. Van De Cotte, F. Impens, K. Gevaert, I. De Smet, J. Friml, D.M. Molina,
E. Russinova, Proceedings of the National Academy of Sciences of the United States
of America 119 (2022).
date_created: 2022-03-20T23:01:39Z
date_published: 2022-03-07T00:00:00Z
date_updated: 2025-05-14T11:01:45Z
day: '07'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1073/pnas.2118220119
external_id:
isi:
- '000771756300008'
pmid:
- '35254915'
file:
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checksum: 83e0fea7919570d0b519b41193342571
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creator: dernst
date_created: 2022-03-21T09:19:47Z
date_updated: 2022-03-21T09:19:47Z
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file_name: 2022_PNAS_Lu.pdf
file_size: 2169534
relation: main_file
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isi: 1
issue: '11'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between
brassinosteroid and auxin signaling
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: 119
year: '2022'
...
---
_id: '10889'
abstract:
- lang: eng
text: Genetically encoded tags have introduced extensive lines of application from
purification of tagged proteins to their visualization at the single molecular,
cellular, histological and whole-body levels. Combined with other rapidly developing
technologies such as clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated
protein 9 (Cas9) system, proteomics, super-resolution microscopy and proximity
labeling, a large variety of genetically encoded tags have been developed in the
last two decades. In this review, I focus on the current status of tag development
for electron microscopic (EM) visualization of proteins with metal particle labeling.
Compared with conventional immunoelectron microscopy using gold particles, tag-mediated
metal particle labeling has several advantages that could potentially improve
the sensitivity, spatial and temporal resolution, and applicability to a wide
range of proteins of interest (POIs). It may enable researchers to detect single
molecules in situ, allowing the quantitative measurement of absolute numbers and
exact localization patterns of POI in the ultrastructural context. Thus, genetically
encoded tags for EM could revolutionize the field as green fluorescence protein
did for light microscopy, although we still have many challenges to overcome before
reaching this goal.
acknowledgement: European Research Council Advanced Grant (694539 to R.S.).
article_processing_charge: No
article_type: original
author:
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Shigemoto R. Electron microscopic visualization of single molecules by tag-mediated
metal particle labeling. Microscopy. 2022;71(Supplement_1):i72-i80. doi:10.1093/jmicro/dfab048
apa: Shigemoto, R. (2022). Electron microscopic visualization of single molecules
by tag-mediated metal particle labeling. Microscopy. Oxford University
Press. https://doi.org/10.1093/jmicro/dfab048
chicago: Shigemoto, Ryuichi. “Electron Microscopic Visualization of Single Molecules
by Tag-Mediated Metal Particle Labeling.” Microscopy. Oxford University
Press, 2022. https://doi.org/10.1093/jmicro/dfab048.
ieee: R. Shigemoto, “Electron microscopic visualization of single molecules by tag-mediated
metal particle labeling,” Microscopy, vol. 71, no. Supplement_1. Oxford
University Press, pp. i72–i80, 2022.
ista: Shigemoto R. 2022. Electron microscopic visualization of single molecules
by tag-mediated metal particle labeling. Microscopy. 71(Supplement_1), i72–i80.
mla: Shigemoto, Ryuichi. “Electron Microscopic Visualization of Single Molecules
by Tag-Mediated Metal Particle Labeling.” Microscopy, vol. 71, no. Supplement_1,
Oxford University Press, 2022, pp. i72–80, doi:10.1093/jmicro/dfab048.
short: R. Shigemoto, Microscopy 71 (2022) i72–i80.
corr_author: '1'
date_created: 2022-03-20T23:01:39Z
date_published: 2022-03-01T00:00:00Z
date_updated: 2026-06-18T10:44:57Z
day: '01'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1093/jmicro/dfab048
ec_funded: 1
external_id:
isi:
- '000768384100011'
pmid:
- '35275179'
fulldoi: https://doi.org/10.1093/jmicro/dfab048
intvolume: ' 71'
isi: 1
issue: Supplement_1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/jmicro/dfab048
month: '03'
oa: 1
oa_version: Published Version
page: i72-i80
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'
publication: Microscopy
publication_identifier:
eissn:
- 2050-5701
issn:
- 2050-5698
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Electron microscopic visualization of single molecules by tag-mediated metal
particle labeling
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 71
year: '2022'
...
---
_id: '10890'
abstract:
- lang: eng
text: Upon the arrival of action potentials at nerve terminals, neurotransmitters
are released from synaptic vesicles (SVs) by exocytosis. CaV2.1, 2.2, and 2.3
are the major subunits of the voltage-gated calcium channel (VGCC) responsible
for increasing intraterminal calcium levels and triggering SV exocytosis in the
central nervous system (CNS) synapses. The two-dimensional analysis of CaV2 distributions
using sodium dodecyl sulfate (SDS)-digested freeze-fracture replica labeling (SDS-FRL)
has revealed their numbers, densities, and nanoscale clustering patterns in individual
presynaptic active zones. The variation in these properties affects the coupling
of VGCCs with calcium sensors on SVs, synaptic efficacy, and temporal precision
of transmission. In this study, we summarize how the morphological parameters
of CaV2 distribution obtained using SDS-FRL differ depending on the different
types of synapses and could correspond to functional properties in synaptic transmission.
acknowledgement: "This work was supported by the European Research Council advanced
grant No. 694539 and the joint German-Austrian DFG and FWF project SYNABS (FWF:
I-4638-B) to RS.\r\nThe authors thank Walter Kaufmann for his critical comments
on the manuscript."
article_number: '846615'
article_processing_charge: No
article_type: original
author:
- first_name: Kohgaku
full_name: Eguchi, Kohgaku
id: 2B7846DC-F248-11E8-B48F-1D18A9856A87
last_name: Eguchi
orcid: 0000-0002-6170-2546
- first_name: Jacqueline-Claire
full_name: Montanaro-Punzengruber, Jacqueline-Claire
id: 3786AB44-F248-11E8-B48F-1D18A9856A87
last_name: Montanaro-Punzengruber
- first_name: Elodie
full_name: Le Monnier, Elodie
id: 3B59276A-F248-11E8-B48F-1D18A9856A87
last_name: Le Monnier
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Eguchi K, Montanaro-Punzengruber J-C, Le Monnier E, Shigemoto R. The number
and distinct clustering patterns of voltage-gated Calcium channels in nerve terminals.
Frontiers in Neuroanatomy. 2022;16. doi:10.3389/fnana.2022.846615
apa: Eguchi, K., Montanaro-Punzengruber, J.-C., Le Monnier, E., & Shigemoto,
R. (2022). The number and distinct clustering patterns of voltage-gated Calcium
channels in nerve terminals. Frontiers in Neuroanatomy. Frontiers. https://doi.org/10.3389/fnana.2022.846615
chicago: Eguchi, Kohgaku, Jacqueline-Claire Montanaro-Punzengruber, Elodie Le Monnier,
and Ryuichi Shigemoto. “The Number and Distinct Clustering Patterns of Voltage-Gated
Calcium Channels in Nerve Terminals.” Frontiers in Neuroanatomy. Frontiers,
2022. https://doi.org/10.3389/fnana.2022.846615.
ieee: K. Eguchi, J.-C. Montanaro-Punzengruber, E. Le Monnier, and R. Shigemoto,
“The number and distinct clustering patterns of voltage-gated Calcium channels
in nerve terminals,” Frontiers in Neuroanatomy, vol. 16. Frontiers, 2022.
ista: Eguchi K, Montanaro-Punzengruber J-C, Le Monnier E, Shigemoto R. 2022. The
number and distinct clustering patterns of voltage-gated Calcium channels in nerve
terminals. Frontiers in Neuroanatomy. 16, 846615.
mla: Eguchi, Kohgaku, et al. “The Number and Distinct Clustering Patterns of Voltage-Gated
Calcium Channels in Nerve Terminals.” Frontiers in Neuroanatomy, vol. 16,
846615, Frontiers, 2022, doi:10.3389/fnana.2022.846615.
short: K. Eguchi, J.-C. Montanaro-Punzengruber, E. Le Monnier, R. Shigemoto, Frontiers
in Neuroanatomy 16 (2022).
corr_author: '1'
date_created: 2022-03-20T23:01:39Z
date_published: 2022-02-24T00:00:00Z
date_updated: 2026-04-16T08:18:54Z
day: '24'
ddc:
- '570'
department:
- _id: RySh
doi: 10.3389/fnana.2022.846615
ec_funded: 1
external_id:
isi:
- '000766662700001'
pmid:
- '35280978'
file:
- access_level: open_access
checksum: 51ec9b90e7da919e22c01a15489eaacd
content_type: application/pdf
creator: dernst
date_created: 2022-03-21T09:41:19Z
date_updated: 2022-03-21T09:41:19Z
file_id: '10911'
file_name: 2022_FrontiersNeuroanatomy_Eguchi.pdf
file_size: 2416395
relation: main_file
success: 1
file_date_updated: 2022-03-21T09:41:19Z
fulldoi: https://doi.org/10.3389/fnana.2022.846615
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
language:
- iso: eng
month: '02'
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: 05970B30-7A3F-11EA-A408-12923DDC885E
grant_number: I04638
name: LGI1 antibody-induced pathophysiology in synapses
publication: Frontiers in Neuroanatomy
publication_identifier:
eissn:
- 1662-5129
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: The number and distinct clustering patterns of voltage-gated Calcium channels
in nerve 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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 16
year: '2022'
...
---
_id: '10891'
abstract:
- lang: eng
text: We present a formal framework for the online black-box monitoring of software
using monitors with quantitative verdict functions. Quantitative verdict functions
have several advantages. First, quantitative monitors can be approximate, i.e.,
the value of the verdict function does not need to correspond exactly to the value
of the property under observation. Second, quantitative monitors can be quantified
universally, i.e., for every possible observed behavior, the monitor tries to
make the best effort to estimate the value of the property under observation.
Third, quantitative monitors can watch boolean as well as quantitative properties,
such as average response time. Fourth, quantitative monitors can use non-finite-state
resources, such as counters. As a consequence, quantitative monitors can be compared
according to how many resources they use (e.g., the number of counters) and how
precisely they approximate the property under observation. This allows for a rich
spectrum of cost-precision trade-offs in monitoring software.
acknowledgement: The formal framework for quantitative monitoring which is presented
in this invited talk was defined jointly with N. Ege Saraç at LICS 2021. This work
was supported in part by the Wittgenstein Award Z211-N23 of the Austrian Science
Fund.
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Henzinger TA. Quantitative monitoring of software. In: Software Verification.
Vol 13124. LNCS. Springer Nature; 2022:3-6. doi:10.1007/978-3-030-95561-8_1'
apa: 'Henzinger, T. A. (2022). Quantitative monitoring of software. In Software
Verification (Vol. 13124, pp. 3–6). New Haven, CT, United States: Springer
Nature. https://doi.org/10.1007/978-3-030-95561-8_1'
chicago: Henzinger, Thomas A. “Quantitative Monitoring of Software.” In Software
Verification, 13124:3–6. LNCS. Springer Nature, 2022. https://doi.org/10.1007/978-3-030-95561-8_1.
ieee: T. A. Henzinger, “Quantitative monitoring of software,” in Software Verification,
New Haven, CT, United States, 2022, vol. 13124, pp. 3–6.
ista: 'Henzinger TA. 2022. Quantitative monitoring of software. Software Verification.
NSV: Numerical Software VerificationLNCS vol. 13124, 3–6.'
mla: Henzinger, Thomas A. “Quantitative Monitoring of Software.” Software Verification,
vol. 13124, Springer Nature, 2022, pp. 3–6, doi:10.1007/978-3-030-95561-8_1.
short: T.A. Henzinger, in:, Software Verification, Springer Nature, 2022, pp. 3–6.
conference:
end_date: 2021-10-19
location: New Haven, CT, United States
name: 'NSV: Numerical Software Verification'
start_date: 2021-10-18
corr_author: '1'
date_created: 2022-03-20T23:01:40Z
date_published: 2022-02-22T00:00:00Z
date_updated: 2025-04-15T06:25:58Z
day: '22'
department:
- _id: ToHe
doi: 10.1007/978-3-030-95561-8_1
external_id:
isi:
- '000771713200001'
fulldoi: https://doi.org/10.1007/978-3-030-95561-8_1
intvolume: ' 13124'
isi: 1
language:
- iso: eng
month: '02'
oa_version: None
page: 3-6
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication: Software Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030955601'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: Quantitative monitoring of software
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13124
year: '2022'
...