---
_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
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'
...
---
OA_place: repository
OA_type: green
_id: '11552'
abstract:
- lang: eng
text: Rotational dynamics of D2 molecules inside helium nanodroplets is induced
by a moderately intense femtosecond pump pulse and measured as a function of time
by recording the yield of HeD+ ions, created through strong-field dissociative
ionization with a delayed femtosecond probe pulse. The yield oscillates with a
period of 185 fs, reflecting field-free rotational wave packet dynamics, and the
oscillation persists for more than 500 periods. Within the experimental uncertainty,
the rotational constant BHe of the in-droplet D2 molecule, determined by Fourier
analysis, is the same as Bgas for an isolated D2 molecule. Our observations show
that the D2 molecules inside helium nanodroplets essentially rotate as free D2
molecules.
article_number: '243201'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Junjie
full_name: Qiang, Junjie
last_name: Qiang
- first_name: Lianrong
full_name: Zhou, Lianrong
last_name: Zhou
- first_name: Peifen
full_name: Lu, Peifen
last_name: Lu
- first_name: Kang
full_name: Lin, Kang
last_name: Lin
- first_name: Yongzhe
full_name: Ma, Yongzhe
last_name: Ma
- first_name: Shengzhe
full_name: Pan, Shengzhe
last_name: Pan
- first_name: Chenxu
full_name: Lu, Chenxu
last_name: Lu
- first_name: Wenyu
full_name: Jiang, Wenyu
last_name: Jiang
- first_name: Fenghao
full_name: Sun, Fenghao
last_name: Sun
- first_name: Wenbin
full_name: Zhang, Wenbin
last_name: Zhang
- first_name: Hui
full_name: Li, Hui
last_name: Li
- first_name: Xiaochun
full_name: Gong, Xiaochun
last_name: Gong
- first_name: Ilya Sh
full_name: Averbukh, Ilya Sh
last_name: Averbukh
- first_name: Yehiam
full_name: Prior, Yehiam
last_name: Prior
- first_name: Constant A.
full_name: Schouder, Constant A.
last_name: Schouder
- first_name: Henrik
full_name: Stapelfeldt, Henrik
last_name: Stapelfeldt
- first_name: Igor
full_name: Cherepanov, Igor
id: 339C7E5A-F248-11E8-B48F-1D18A9856A87
last_name: Cherepanov
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Wolfgang
full_name: Jäger, Wolfgang
last_name: Jäger
- first_name: Jian
full_name: Wu, Jian
last_name: Wu
citation:
ama: Qiang J, Zhou L, Lu P, et al. Femtosecond rotational dynamics of D2 molecules
in superfluid helium nanodroplets. Physical Review Letters. 2022;128(24).
doi:10.1103/PhysRevLett.128.243201
apa: Qiang, J., Zhou, L., Lu, P., Lin, K., Ma, Y., Pan, S., … Wu, J. (2022). Femtosecond
rotational dynamics of D2 molecules in superfluid helium nanodroplets. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.128.243201
chicago: Qiang, Junjie, Lianrong Zhou, Peifen Lu, Kang Lin, Yongzhe Ma, Shengzhe
Pan, Chenxu Lu, et al. “Femtosecond Rotational Dynamics of D2 Molecules in Superfluid
Helium Nanodroplets.” Physical Review Letters. American Physical Society,
2022. https://doi.org/10.1103/PhysRevLett.128.243201.
ieee: J. Qiang et al., “Femtosecond rotational dynamics of D2 molecules in
superfluid helium nanodroplets,” Physical Review Letters, vol. 128, no.
24. American Physical Society, 2022.
ista: Qiang J, Zhou L, Lu P, Lin K, Ma Y, Pan S, Lu C, Jiang W, Sun F, Zhang W,
Li H, Gong X, Averbukh IS, Prior Y, Schouder CA, Stapelfeldt H, Cherepanov I,
Lemeshko M, Jäger W, Wu J. 2022. Femtosecond rotational dynamics of D2 molecules
in superfluid helium nanodroplets. Physical Review Letters. 128(24), 243201.
mla: Qiang, Junjie, et al. “Femtosecond Rotational Dynamics of D2 Molecules in Superfluid
Helium Nanodroplets.” Physical Review Letters, vol. 128, no. 24, 243201,
American Physical Society, 2022, doi:10.1103/PhysRevLett.128.243201.
short: J. Qiang, L. Zhou, P. Lu, K. Lin, Y. Ma, S. Pan, C. Lu, W. Jiang, F. Sun,
W. Zhang, H. Li, X. Gong, I.S. Averbukh, Y. Prior, C.A. Schouder, H. Stapelfeldt,
I. Cherepanov, M. Lemeshko, W. Jäger, J. Wu, Physical Review Letters 128 (2022).
date_created: 2022-07-10T22:01:52Z
date_published: 2022-06-16T00:00:00Z
date_updated: 2026-04-16T08:18:26Z
day: '16'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.128.243201
ec_funded: 1
external_id:
arxiv:
- '2201.09281'
isi:
- '000820659700002'
pmid:
- '35776471'
intvolume: ' 128'
isi: 1
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2201.09281
month: '06'
oa: 1
oa_version: Preprint
pmid: 1
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 128
year: '2022'
...
---
OA_place: publisher
_id: '12358'
abstract:
- lang: eng
text: "The complex yarn structure of knitted and woven fabrics gives rise to both
a mechanical and\r\nvisual complexity. The small-scale interactions of yarns colliding
with and pulling on each\r\nother result in drastically different large-scale
stretching and bending behavior, introducing\r\nanisotropy, curling, and more.
While simulating cloth as individual yarns can reproduce this\r\ncomplexity and
match the quality of real fabric, it may be too computationally expensive for\r\nlarge
fabrics. On the other hand, continuum-based approaches do not need to discretize
the\r\ncloth at a stitch-level, but it is non-trivial to find a material model
that would replicate the\r\nlarge-scale behavior of yarn fabrics, and they discard
the intricate visual detail. In this thesis,\r\nwe discuss three methods to try
and bridge the gap between small-scale and large-scale yarn\r\nmechanics using
numerical homogenization: fitting a continuum model to periodic yarn simulations,
adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively\r\nfitting
yarn parameters to physical measurements of real fabric.\r\nTo start, we present
a method for animating yarn-level cloth effects using a thin-shell solver.\r\nWe
first use a large number of periodic yarn-level simulations to build a model of
the potential\r\nenergy density of the cloth, and then use it to compute forces
in a thin-shell simulator. The\r\nresulting simulations faithfully reproduce expected
effects like the stiffening of woven fabrics\r\nand the highly deformable nature
and anisotropy of knitted fabrics at a fraction of the cost of\r\nfull yarn-level
simulation.\r\nWhile our thin-shell simulations are able to capture large-scale
yarn mechanics, they lack\r\nthe rich visual detail of yarn-level simulations.
Therefore, we propose a method to animate\r\nyarn-level cloth geometry on top
of an underlying deforming mesh in a mechanics-aware\r\nfashion in real time.
Using triangle strains to interpolate precomputed yarn geometry, we are\r\nable
to reproduce effects such as knit loops tightening under stretching at negligible
cost.\r\nFinally, we introduce a methodology for inverse-modeling of yarn-level
mechanics of cloth,\r\nbased on the mechanical response of fabrics in the real
world. We compile a database from\r\nphysical tests of several knitted fabrics
used in the textile industry spanning diverse physical\r\nproperties like stiffness,
nonlinearity, and anisotropy. We then develop a system for approximating these
mechanical responses with yarn-level cloth simulation, using homogenized\r\nshell
models to speed up computation and adding some small-but-necessary extensions
to\r\nyarn-level models used in computer graphics.\r\n"
acknowledged_ssus:
- _id: SSU
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
citation:
ama: 'Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale
detail, and quantitative fitting. 2022. doi:10.15479/at:ista:12103'
apa: 'Sperl, G. (2022). Homogenizing yarn simulations: Large-scale mechanics,
small-scale detail, and quantitative fitting. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:12103'
chicago: 'Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale
Detail, and Quantitative Fitting.” Institute of Science and Technology Austria,
2022. https://doi.org/10.15479/at:ista:12103.'
ieee: 'G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale
detail, and quantitative fitting,” Institute of Science and Technology Austria,
2022.'
ista: 'Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale
detail, and quantitative fitting. Institute of Science and Technology Austria.'
mla: 'Sperl, Georg. Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale
Detail, and Quantitative Fitting. Institute of Science and Technology Austria,
2022, doi:10.15479/at:ista:12103.'
short: 'G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale
Detail, and Quantitative Fitting, Institute of Science and Technology Austria,
2022.'
corr_author: '1'
date_created: 2023-01-24T10:49:46Z
date_published: 2022-09-22T00:00:00Z
date_updated: 2026-04-16T08:31:54Z
day: '22'
ddc:
- '000'
- '620'
degree_awarded: PhD
department:
- _id: GradSch
- _id: ChWo
doi: 10.15479/at:ista:12103
ec_funded: 1
file:
- access_level: open_access
checksum: 083722acbb8115e52e3b0fdec6226769
content_type: application/pdf
creator: cchlebak
date_created: 2023-01-25T12:04:41Z
date_updated: 2023-02-02T09:29:57Z
description: 'This is the main PDF file of the thesis. File size: 105 MB'
file_id: '12371'
file_name: thesis_gsperl.pdf
file_size: 104497530
relation: main_file
title: Thesis
- access_level: open_access
checksum: 511f82025e5fcb70bff4731d6896ca07
content_type: application/pdf
creator: cchlebak
date_created: 2023-02-02T09:33:37Z
date_updated: 2023-02-02T09:33:37Z
description: This version of the thesis uses stronger image compression for a smaller
file size of 23MB.
file_id: '12483'
file_name: thesis_gsperl_compressed.pdf
file_size: 23183710
relation: main_file
title: Thesis (compressed 23MB)
- access_level: open_access
checksum: ed4cb85225eedff761c25bddfc37a2ed
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2023-02-02T09:39:25Z
date_updated: 2023-02-02T09:39:25Z
file_id: '12484'
file_name: thesis-source.zip
file_size: 98382247
relation: source_file
file_date_updated: 2023-02-02T09:39:25Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '138'
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: 'Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large
Scales'
publication_identifier:
isbn:
- 978-3-99078-020-6
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11736'
relation: part_of_dissertation
status: public
- id: '9818'
relation: part_of_dissertation
status: public
- id: '8385'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
title: 'Homogenizing yarn simulations: Large-scale mechanics, small-scale detail,
and quantitative fitting'
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2022'
...
---
_id: '10774'
abstract:
- lang: eng
text: We study the problem of specifying sequential information-flow properties
of systems. Information-flow properties are hyperproperties, as they compare different
traces of a system. Sequential information-flow properties can express changes,
over time, in the information-flow constraints. For example, information-flow
constraints during an initialization phase of a system may be different from information-flow
constraints that are required during the operation phase. We formalize several
variants of interpreting sequential information-flow constraints, which arise
from different assumptions about what can be observed of the system. For this
purpose, we introduce a first-order logic, called Hypertrace Logic, with both
trace and time quantifiers for specifying linear-time hyperproperties. We prove
that HyperLTL, which corresponds to a fragment of Hypertrace Logic with restricted
quantifier prefixes, cannot specify the majority of the studied variants of sequential
information flow, including all variants in which the transition between sequential
phases (such as initialization and operation) happens asynchronously. Our results
rely on new equivalences between sets of traces that cannot be distinguished by
certain classes of formulas from Hypertrace Logic. This presents a new approach
to proving inexpressiveness results for HyperLTL.
acknowledgement: This work was funded in part by the Wittgenstein Award Z211-N23 of
the Austrian Science Fund (FWF) and by the FWF project W1255-N23.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Ana Oliveira
full_name: Da Costa, Ana Oliveira
last_name: Da Costa
citation:
ama: 'Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. Flavors of sequential
information flow. In: Lecture Notes in Computer Science (Including Subseries
Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).
Vol 13182. Springer Nature; 2022:1-19. doi:10.1007/978-3-030-94583-1_1'
apa: 'Bartocci, E., Ferrere, T., Henzinger, T. A., Nickovic, D., & Da Costa,
A. O. (2022). Flavors of sequential information flow. In Lecture Notes in Computer
Science (including subseries Lecture Notes in Artificial Intelligence and Lecture
Notes in Bioinformatics) (Vol. 13182, pp. 1–19). Philadelphia, PA, United
States: Springer Nature. https://doi.org/10.1007/978-3-030-94583-1_1'
chicago: Bartocci, Ezio, Thomas Ferrere, Thomas A Henzinger, Dejan Nickovic, and
Ana Oliveira Da Costa. “Flavors of Sequential Information Flow.” In Lecture
Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence
and Lecture Notes in Bioinformatics), 13182:1–19. Springer Nature, 2022. https://doi.org/10.1007/978-3-030-94583-1_1.
ieee: E. Bartocci, T. Ferrere, T. A. Henzinger, D. Nickovic, and A. O. Da Costa,
“Flavors of sequential information flow,” in Lecture Notes in Computer Science
(including subseries Lecture Notes in Artificial Intelligence and Lecture Notes
in Bioinformatics), Philadelphia, PA, United States, 2022, vol. 13182, pp.
1–19.
ista: 'Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. 2022. Flavors
of sequential information flow. Lecture Notes in Computer Science (including subseries
Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).
VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 13182,
1–19.'
mla: Bartocci, Ezio, et al. “Flavors of Sequential Information Flow.” Lecture
Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence
and Lecture Notes in Bioinformatics), vol. 13182, Springer Nature, 2022, pp.
1–19, doi:10.1007/978-3-030-94583-1_1.
short: E. Bartocci, T. Ferrere, T.A. Henzinger, D. Nickovic, A.O. Da Costa, in:,
Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial
Intelligence and Lecture Notes in Bioinformatics), Springer Nature, 2022, pp.
1–19.
conference:
end_date: 2022-01-18
location: Philadelphia, PA, United States
name: 'VMCAI: Verifcation, Model Checking, and Abstract Interpretation'
start_date: 2022-01-16
date_created: 2022-02-20T23:01:34Z
date_published: 2022-01-14T00:00:00Z
date_updated: 2026-04-16T09:13:43Z
day: '14'
department:
- _id: ToHe
doi: 10.1007/978-3-030-94583-1_1
external_id:
arxiv:
- '2105.02013'
isi:
- '001059208500001'
intvolume: ' 13182'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2105.02013'
month: '01'
oa: 1
oa_version: Preprint
page: 1-19
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: Lecture Notes in Computer Science (including subseries Lecture Notes
in Artificial Intelligence and Lecture Notes in Bioinformatics)
publication_identifier:
eisbn:
- '9783030945831'
eissn:
- 1611-3349
isbn:
- '9783030945824'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Flavors of sequential information flow
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 13182
year: '2022'
...
---
_id: '11938'
abstract:
- lang: eng
text: A matching is compatible to two or more labeled point sets of size n with
labels {1, . . . , n} if its straight-line drawing on each of these point sets
is crossing-free. We study the maximum number of edges in a matching compatible
to two or more labeled point sets in general position in the plane. We show that
for any two labeled sets of n points in convex position there exists a compatible
matching with ⌊√2n + 1 − 1⌋ edges. More generally, for any ℓ labeled point sets
we construct compatible matchings of size Ω(n1/ℓ). As a corresponding upper bound,
we use probabilistic arguments to show that for any ℓ given sets of n points there
exists a labeling of each set such that the largest compatible matching has O(n2/(ℓ+1))
edges. Finally, we show that Θ(log n) copies of any set of n points are necessary
and sufficient for the existence of labelings of these point sets such that any
compatible matching consists only of a single edge.
acknowledgement: 'A.A. funded by the Marie Sklodowska-Curie grant agreement No 754411.
Z.M. partially funded by Wittgenstein Prize, Austrian Science Fund (FWF), grant
no. Z 342-N31. I.P., D.P., and B.V. partially supported by FWF within the collaborative
DACH project Arrangements and Drawings as FWF project I 3340-N35. A.P. supported
by a Schrödinger fellowship of the FWF: J-3847-N35. J.T. partially supported by
ERC Start grant no. (279307: Graph Games), FWF grant no. P23499-N23 and S11407-N23
(RiSE).'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Oswin
full_name: Aichholzer, Oswin
last_name: Aichholzer
- first_name: Alan M
full_name: Arroyo Guevara, Alan M
id: 3207FDC6-F248-11E8-B48F-1D18A9856A87
last_name: Arroyo Guevara
orcid: 0000-0003-2401-8670
- first_name: Zuzana
full_name: Masárová, Zuzana
id: 45CFE238-F248-11E8-B48F-1D18A9856A87
last_name: Masárová
orcid: 0000-0002-6660-1322
- first_name: Irene
full_name: Parada, Irene
last_name: Parada
- first_name: Daniel
full_name: Perz, Daniel
last_name: Perz
- first_name: Alexander
full_name: Pilz, Alexander
last_name: Pilz
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Birgit
full_name: Vogtenhuber, Birgit
last_name: Vogtenhuber
citation:
ama: Aichholzer O, Arroyo Guevara AM, Masárová Z, et al. On compatible matchings.
Journal of Graph Algorithms and Applications. 2022;26(2):225-240. doi:10.7155/jgaa.00591
apa: Aichholzer, O., Arroyo Guevara, A. M., Masárová, Z., Parada, I., Perz, D.,
Pilz, A., … Vogtenhuber, B. (2022). On compatible matchings. Journal of Graph
Algorithms and Applications. Brown University. https://doi.org/10.7155/jgaa.00591
chicago: Aichholzer, Oswin, Alan M Arroyo Guevara, Zuzana Masárová, Irene Parada,
Daniel Perz, Alexander Pilz, Josef Tkadlec, and Birgit Vogtenhuber. “On Compatible
Matchings.” Journal of Graph Algorithms and Applications. Brown University,
2022. https://doi.org/10.7155/jgaa.00591.
ieee: O. Aichholzer et al., “On compatible matchings,” Journal of Graph
Algorithms and Applications, vol. 26, no. 2. Brown University, pp. 225–240,
2022.
ista: Aichholzer O, Arroyo Guevara AM, Masárová Z, Parada I, Perz D, Pilz A, Tkadlec
J, Vogtenhuber B. 2022. On compatible matchings. Journal of Graph Algorithms and
Applications. 26(2), 225–240.
mla: Aichholzer, Oswin, et al. “On Compatible Matchings.” Journal of Graph Algorithms
and Applications, vol. 26, no. 2, Brown University, 2022, pp. 225–40, doi:10.7155/jgaa.00591.
short: O. Aichholzer, A.M. Arroyo Guevara, Z. Masárová, I. Parada, D. Perz, A. Pilz,
J. Tkadlec, B. Vogtenhuber, Journal of Graph Algorithms and Applications 26 (2022)
225–240.
corr_author: '1'
date_created: 2022-08-21T22:01:56Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2026-04-16T09:18:20Z
day: '01'
ddc:
- '000'
department:
- _id: UlWa
- _id: HeEd
- _id: KrCh
doi: 10.7155/jgaa.00591
ec_funded: 1
external_id:
arxiv:
- '2101.03928'
file:
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intvolume: ' 26'
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language:
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month: '06'
oa: 1
oa_version: Published Version
page: 225-240
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: Mathematics, Computer Science
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: Journal of Graph Algorithms and Applications
publication_identifier:
issn:
- 1526-1719
publication_status: published
publisher: Brown University
quality_controlled: '1'
related_material:
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relation: earlier_version
status: public
scopus_import: '1'
status: public
title: On compatible matchings
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: 26
year: '2022'
...
---
OA_place: publisher
_id: '11362'
abstract:
- lang: eng
text: "Deep learning has enabled breakthroughs in challenging computing problems
and has emerged as the standard problem-solving tool for computer vision and natural
language processing tasks.\r\nOne exception to this trend is safety-critical tasks
where robustness and resilience requirements contradict the black-box nature of
neural networks. \r\nTo deploy deep learning methods for these tasks, it is vital
to provide guarantees on neural network agents' safety and robustness criteria.
\r\nThis can be achieved by developing formal verification methods to verify the
safety and robustness properties of neural networks.\r\n\r\nOur goal is to design,
develop and assess safety verification methods for neural networks to improve
their reliability and trustworthiness in real-world applications.\r\nThis thesis
establishes techniques for the verification of compressed and adversarially trained
models as well as the design of novel neural networks for verifiably safe decision-making.\r\n\r\nFirst,
we establish the problem of verifying quantized neural networks. Quantization
is a technique that trades numerical precision for the computational efficiency
of running a neural network and is widely adopted in industry.\r\nWe show that
neglecting the reduced precision when verifying a neural network can lead to wrong
conclusions about the robustness and safety of the network, highlighting that
novel techniques for quantized network verification are necessary. We introduce
several bit-exact verification methods explicitly designed for quantized neural
networks and experimentally confirm on realistic networks that the network's robustness
and other formal properties are affected by the quantization.\r\n\r\nFurthermore,
we perform a case study providing evidence that adversarial training, a standard
technique for making neural networks more robust, has detrimental effects on the
network's performance. This robustness-accuracy tradeoff has been studied before
regarding the accuracy obtained on classification datasets where each data point
is independent of all other data points. On the other hand, we investigate the
tradeoff empirically in robot learning settings where a both, a high accuracy
and a high robustness, are desirable.\r\nOur results suggest that the negative
side-effects of adversarial training outweigh its robustness benefits in practice.\r\n\r\nFinally,
we consider the problem of verifying safety when running a Bayesian neural network
policy in a feedback loop with systems over the infinite time horizon. Bayesian
neural networks are probabilistic models for learning uncertainties in the data
and are therefore often used on robotic and healthcare applications where data
is inherently stochastic.\r\nWe introduce a method for recalibrating Bayesian
neural networks so that they yield probability distributions over safe decisions
only.\r\nOur method learns a safety certificate that guarantees safety over the
infinite time horizon to determine which decisions are safe in every possible
state of the system.\r\nWe demonstrate the effectiveness of our approach on a
series of reinforcement learning benchmarks."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
citation:
ama: Lechner M. Learning verifiable representations. 2022. doi:10.15479/at:ista:11362
apa: Lechner, M. (2022). Learning verifiable representations. Institute of
Science and Technology Austria. https://doi.org/10.15479/at:ista:11362
chicago: Lechner, Mathias. “Learning Verifiable Representations.” Institute of Science
and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11362.
ieee: M. Lechner, “Learning verifiable representations,” Institute of Science and
Technology Austria, 2022.
ista: Lechner M. 2022. Learning verifiable representations. Institute of Science
and Technology Austria.
mla: Lechner, Mathias. Learning Verifiable Representations. Institute of
Science and Technology Austria, 2022, doi:10.15479/at:ista:11362.
short: M. Lechner, Learning Verifiable Representations, Institute of Science and
Technology Austria, 2022.
corr_author: '1'
date_created: 2022-05-12T07:14:01Z
date_published: 2022-05-12T00:00:00Z
date_updated: 2026-04-16T09:46:06Z
day: '12'
ddc:
- '004'
degree_awarded: PhD
department:
- _id: GradSch
- _id: ToHe
doi: 10.15479/at:ista:11362
ec_funded: 1
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date_created: 2022-05-13T12:33:26Z
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creator: mlechner
date_created: 2022-05-16T08:02:28Z
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file_id: '11382'
file_name: thesis_main-a2.pdf
file_size: 2732536
relation: main_file
file_date_updated: 2022-05-17T15:19:39Z
has_accepted_license: '1'
keyword:
- neural networks
- verification
- machine learning
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: '124'
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication_identifier:
isbn:
- 978-3-99078-017-6
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11366'
relation: part_of_dissertation
status: public
- id: '10665'
relation: part_of_dissertation
status: public
- id: '10667'
relation: part_of_dissertation
status: public
- id: '10666'
relation: part_of_dissertation
status: public
- id: '7808'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
title: Learning verifiable representations
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2022'
...
---
_id: '11420'
abstract:
- lang: eng
text: 'Understanding the properties of neural networks trained via stochastic gradient
descent (SGD) is at the heart of the theory of deep learning. In this work, we
take a mean-field view, and consider a two-layer ReLU network trained via noisy-SGD
for a univariate regularized regression problem. Our main result is that SGD with
vanishingly small noise injected in the gradients is biased towards a simple solution:
at convergence, the ReLU network implements a piecewise linear map of the inputs,
and the number of “knot” points -- i.e., points where the tangent of the ReLU
network estimator changes -- between two consecutive training inputs is at most
three. In particular, as the number of neurons of the network grows, the SGD dynamics
is captured by the solution of a gradient flow and, at convergence, the distribution
of the weights approaches the unique minimizer of a related free energy, which
has a Gibbs form. Our key technical contribution consists in the analysis of the
estimator resulting from this minimizer: we show that its second derivative vanishes
everywhere, except at some specific locations which represent the “knot” points.
We also provide empirical evidence that knots at locations distinct from the data
points might occur, as predicted by our theory.'
acknowledgement: "We would like to thank Mert Pilanci for several exploratory discussions
in the early stage\r\nof the project, Jan Maas for clarifications about Jordan et
al. (1998), and Max Zimmer for\r\nsuggestive numerical experiments. A. Shevchenko
and M. Mondelli are partially supported\r\nby the 2019 Lopez-Loreta Prize. V. Kungurtsev
acknowledges support to the OP VVV\r\nproject CZ.02.1.01/0.0/0.0/16 019/0000765
Research Center for Informatics.\r\n"
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Aleksandr
full_name: Shevchenko, Aleksandr
id: F2B06EC2-C99E-11E9-89F0-752EE6697425
last_name: Shevchenko
- first_name: Vyacheslav
full_name: Kungurtsev, Vyacheslav
last_name: Kungurtsev
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: Shevchenko A, Kungurtsev V, Mondelli M. Mean-field analysis of piecewise linear
solutions for wide ReLU networks. Journal of Machine Learning Research.
2022;23(130):1-55.
apa: Shevchenko, A., Kungurtsev, V., & Mondelli, M. (2022). Mean-field analysis
of piecewise linear solutions for wide ReLU networks. Journal of Machine Learning
Research. Journal of Machine Learning Research.
chicago: Shevchenko, Alexander, Vyacheslav Kungurtsev, and Marco Mondelli. “Mean-Field
Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” Journal of
Machine Learning Research. Journal of Machine Learning Research, 2022.
ieee: A. Shevchenko, V. Kungurtsev, and M. Mondelli, “Mean-field analysis of piecewise
linear solutions for wide ReLU networks,” Journal of Machine Learning Research,
vol. 23, no. 130. Journal of Machine Learning Research, pp. 1–55, 2022.
ista: Shevchenko A, Kungurtsev V, Mondelli M. 2022. Mean-field analysis of piecewise
linear solutions for wide ReLU networks. Journal of Machine Learning Research.
23(130), 1–55.
mla: Shevchenko, Alexander, et al. “Mean-Field Analysis of Piecewise Linear Solutions
for Wide ReLU Networks.” Journal of Machine Learning Research, vol. 23,
no. 130, Journal of Machine Learning Research, 2022, pp. 1–55.
short: A. Shevchenko, V. Kungurtsev, M. Mondelli, Journal of Machine Learning Research
23 (2022) 1–55.
corr_author: '1'
date_created: 2022-05-29T22:01:54Z
date_published: 2022-04-01T00:00:00Z
date_updated: 2026-05-02T22:30:05Z
day: '01'
ddc:
- '000'
department:
- _id: MaMo
- _id: DaAl
external_id:
arxiv:
- '2111.02278'
file:
- access_level: open_access
checksum: d4ff5d1affb34848b5c5e4002483fc62
content_type: application/pdf
creator: cchlebak
date_created: 2022-05-30T08:22:55Z
date_updated: 2022-05-30T08:22:55Z
file_id: '11422'
file_name: 21-1365.pdf
file_size: 1521701
relation: main_file
success: 1
file_date_updated: 2022-05-30T08:22:55Z
has_accepted_license: '1'
intvolume: ' 23'
issue: '130'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1-55
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: Journal of Machine Learning Research
publication_identifier:
eissn:
- 1533-7928
issn:
- 1532-4435
publication_status: published
publisher: Journal of Machine Learning Research
quality_controlled: '1'
related_material:
link:
- relation: other
url: https://www.jmlr.org/papers/v23/21-1365.html
record:
- id: '17465'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Mean-field analysis of piecewise linear solutions for wide ReLU networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 23
year: '2022'
...
---
_id: '12080'
abstract:
- lang: eng
text: 'Endocytosis is a multistep process involving the sequential recruitment and
action of numerous proteins. This process can be divided into two phases: an early
phase, in which sites of endocytosis are formed, and a late phase in which clathrin-coated
vesicles are formed and internalized into the cytosol, but how these phases link
to each other remains unclear. In this study, we demonstrate that anchoring the
yeast Eps15-like protein Pan1p to the peroxisome triggers most of the events occurring
during the late phase at the peroxisome. At this ectopic location, Pan1p recruits
most proteins that function in the late phases—including actin nucleation promoting
factors—and then initiates actin polymerization. Pan1p also recruited Prk1 kinase
and actin depolymerizing factors, thereby triggering disassembly immediately after
actin assembly and inducing dissociation of endocytic proteins from the peroxisome.
These observations suggest that Pan1p is a key regulator for initiating, processing,
and completing the late phase of endocytosis.'
acknowledgement: 'This work was supported by JSPS KAKENHI GRANT #18K062291, and the
Takeda Science Foundation to J.Y. Toshima, as well as JSPS KAKENHI GRANT #19K065710,
the Uehara Memorial Foundation, and Life Science Foundation of JAPAN to J. Toshima.'
article_number: e202112138
article_processing_charge: No
article_type: original
author:
- first_name: Mariko
full_name: Enshoji, Mariko
last_name: Enshoji
- first_name: Yoshiko
full_name: Miyano, Yoshiko
last_name: Miyano
- first_name: Nao
full_name: Yoshida, Nao
last_name: Yoshida
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Minami
full_name: Watanabe, Minami
last_name: Watanabe
- first_name: Mayumi
full_name: Kunihiro, Mayumi
last_name: Kunihiro
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Junko Y.
full_name: Toshima, Junko Y.
last_name: Toshima
- first_name: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Enshoji M, Miyano Y, Yoshida N, et al. Eps15/Pan1p is a master regulator of
the late stages of the endocytic pathway. Journal of Cell Biology. 2022;221(10).
doi:10.1083/jcb.202112138
apa: Enshoji, M., Miyano, Y., Yoshida, N., Nagano, M., Watanabe, M., Kunihiro, M.,
… Toshima, J. (2022). Eps15/Pan1p is a master regulator of the late stages of
the endocytic pathway. Journal of Cell Biology. Rockefeller University
Press. https://doi.org/10.1083/jcb.202112138
chicago: Enshoji, Mariko, Yoshiko Miyano, Nao Yoshida, Makoto Nagano, Minami Watanabe,
Mayumi Kunihiro, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Eps15/Pan1p
Is a Master Regulator of the Late Stages of the Endocytic Pathway.” Journal
of Cell Biology. Rockefeller University Press, 2022. https://doi.org/10.1083/jcb.202112138.
ieee: M. Enshoji et al., “Eps15/Pan1p is a master regulator of the late stages
of the endocytic pathway,” Journal of Cell Biology, vol. 221, no. 10. Rockefeller
University Press, 2022.
ista: Enshoji M, Miyano Y, Yoshida N, Nagano M, Watanabe M, Kunihiro M, Siekhaus
DE, Toshima JY, Toshima J. 2022. Eps15/Pan1p is a master regulator of the late
stages of the endocytic pathway. Journal of Cell Biology. 221(10), e202112138.
mla: Enshoji, Mariko, et al. “Eps15/Pan1p Is a Master Regulator of the Late Stages
of the Endocytic Pathway.” Journal of Cell Biology, vol. 221, no. 10, e202112138,
Rockefeller University Press, 2022, doi:10.1083/jcb.202112138.
short: M. Enshoji, Y. Miyano, N. Yoshida, M. Nagano, M. Watanabe, M. Kunihiro, D.E.
Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Biology 221 (2022).
date_created: 2022-09-11T22:01:54Z
date_published: 2022-08-19T00:00:00Z
date_updated: 2023-08-03T13:49:07Z
day: '19'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.1083/jcb.202112138
external_id:
isi:
- '000932770500001'
pmid:
- '35984332'
file:
- access_level: open_access
checksum: f2e581e66b5cdab9df81b56e850b3eaa
content_type: application/pdf
creator: dernst
date_created: 2023-01-20T09:32:53Z
date_updated: 2023-02-21T23:30:39Z
embargo: 2023-02-20
file_id: '12321'
file_name: 2022_JCB_Enshoji.pdf
file_size: 7816875
relation: main_file
file_date_updated: 2023-02-21T23:30:39Z
has_accepted_license: '1'
intvolume: ' 221'
isi: 1
issue: '10'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
issn:
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 221
year: '2022'
...
---
_id: '11653'
abstract:
- lang: eng
text: Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual
lineages of parthenogenetic females, which produce rare males at low frequencies.
Although they are known to have ZW chromosomes, these are not well characterized,
and it is unclear whether they are shared across the clade. Furthermore, the underlying
genetic architecture of the transmission of asexuality, which can occur when rare
males mate with closely related sexual females, is not well understood. We produced
a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized
in detail the pair of sex chromosomes of this species. We combined this new assembly
with short-read genomic data for the sexual species A. sp. Kazakhstan and several
asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization
of sex-chromosome evolution across the genus. We identified a small differentiated
region of the ZW pair that is shared by all sexual and asexual lineages, supporting
the shared ancestry of the sex chromosomes. We also inferred that recombination
suppression has spread to larger sections of the chromosome independently in the
American and Eurasian lineages. Finally, we took advantage of a rare male, which
we backcrossed to sexual females, to explore the genetic basis of asexuality.
Our results suggest that parthenogenesis is likely partly controlled by a locus
on the Z chromosome, highlighting the interplay between sex determination and
asexuality.
article_processing_charge: No
author:
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
citation:
ama: Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome
evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:10.15479/AT:ISTA:11653
apa: Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022,
“ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:11653
chicago: Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022,
‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’”
Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:11653.
ieee: M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome
evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute
of Science and Technology Austria, 2022.
ista: Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW
sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:11653.
mla: Elkrewi, Marwan N. Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW
Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.”
Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:11653.
short: M.N. Elkrewi, (2022).
contributor:
- first_name: Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Uladzislava
last_name: Khauratovich
- first_name: Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
- first_name: Vincent K
id: 57854184-AAE0-11E9-8D04-98D6E5697425
last_name: Bett
- first_name: Andrea
id: 353FAC84-AE61-11E9-8BFC-00D3E5697425
last_name: Mrnjavac
- first_name: Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Luca
last_name: Sax
- first_name: Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
- first_name: Francisco
last_name: 'Hontoria '
- first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
corr_author: '1'
date_created: 2022-07-26T11:01:47Z
date_published: 2022-08-05T00:00:00Z
date_updated: 2025-04-15T08:34:17Z
day: '05'
ddc:
- '570'
department:
- _id: GradSch
- _id: BeVi
doi: 10.15479/AT:ISTA:11653
file:
- access_level: open_access
checksum: 5f1d7c6d7ab5375ed2564521432bed0c
content_type: application/x-zip-compressed
creator: melkrewi
date_created: 2022-07-26T12:37:52Z
date_updated: 2022-08-08T22:30:04Z
description: |
The folder contains the following datasets (fasta files, and text files):
Sup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan
male draft assembly
Sup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana
Sup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and
A. parthenogenetica females and rare male.
Sup. Dataset 4: Artemia sinica Male:female FST per 1Kb window
Sup. Dataset 5: FASTA file with candidate W scaffolds
Sup. Dataset 6: Candidate W-derived transcripts and alignments
Sup. Dataset 7: Gene expression with genomic location
Sup. Dataset 8: VCF for asexual female and rare male
Sup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)
Sup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using
A. sp. Kazakhstan as the reference), and inferred ancestry
Sup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their
locations in the Artemia sinica male genome.
embargo: 2022-08-07
file_id: '11655'
file_name: Data.zip
file_size: 2209382998
relation: main_file
title: Supplementary Datasets
file_date_updated: 2022-08-08T22:30:04Z
has_accepted_license: '1'
month: '08'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12248'
relation: used_in_publication
status: public
status: public
title: Data from Elkrewi, Khauratovich, Toups et al. 2022, "ZW sex-chromosome evolution
and contagious parthenogenesis in Artemia brine shrimp"
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: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '10208'
abstract:
- lang: eng
text: It is practical to collect a huge amount of movement data and environmental
context information along with the health signals of individuals because there
is the emergence of new generations of positioning and tracking technologies and
rapid advancements of health sensors. The study of the relations between these
datasets and their sequence similarity analysis is of interest to many applications
such as health monitoring and recommender systems. However, entering all movement
parameters and health signals can lead to the complexity of the problem and an
increase in its computational load. In this situation, dimension reduction techniques
can be used to avoid consideration of simultaneous dependent parameters in the
process of similarity measurement of the trajectories. The present study provides
a framework, named CaDRAW, to use spatial–temporal data and movement parameters
along with independent context information in the process of measuring the similarity
of trajectories. In this regard, the omission of dependent movement characteristic
signals is conducted by using an unsupervised feature selection dimension reduction
technique. To evaluate the effectiveness of the proposed framework, it was applied
to a real contextualized movement and related health signal datasets of individuals.
The results indicated the capability of the proposed framework in measuring the
similarity and in decreasing the characteristic signals in such a way that the
similarity results -before and after reduction of dependent characteristic signals-
have small differences. The mean differences between the obtained results before
and after reducing the dimension were 0.029 and 0.023 for the round path, respectively.
acknowledgement: The third author acknowledges the funding received from the Wittgenstein
Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.
article_processing_charge: No
article_type: original
author:
- first_name: Samira
full_name: Goudarzi, Samira
last_name: Goudarzi
- first_name: Mohammad
full_name: Sharif, Mohammad
last_name: Sharif
- first_name: Farid
full_name: Karimipour, Farid
id: 2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425
last_name: Karimipour
orcid: 0000-0001-6746-4174
citation:
ama: Goudarzi S, Sharif M, Karimipour F. A context-aware dimension reduction framework
for trajectory and health signal analyses. Journal of Ambient Intelligence
and Humanized Computing. 2022;13:2621–2635. doi:10.1007/s12652-021-03569-z
apa: Goudarzi, S., Sharif, M., & Karimipour, F. (2022). A context-aware dimension
reduction framework for trajectory and health signal analyses. Journal of Ambient
Intelligence and Humanized Computing. Springer Nature. https://doi.org/10.1007/s12652-021-03569-z
chicago: Goudarzi, Samira, Mohammad Sharif, and Farid Karimipour. “A Context-Aware
Dimension Reduction Framework for Trajectory and Health Signal Analyses.” Journal
of Ambient Intelligence and Humanized Computing. Springer Nature, 2022. https://doi.org/10.1007/s12652-021-03569-z.
ieee: S. Goudarzi, M. Sharif, and F. Karimipour, “A context-aware dimension reduction
framework for trajectory and health signal analyses,” Journal of Ambient Intelligence
and Humanized Computing, vol. 13. Springer Nature, pp. 2621–2635, 2022.
ista: Goudarzi S, Sharif M, Karimipour F. 2022. A context-aware dimension reduction
framework for trajectory and health signal analyses. Journal of Ambient Intelligence
and Humanized Computing. 13, 2621–2635.
mla: Goudarzi, Samira, et al. “A Context-Aware Dimension Reduction Framework for
Trajectory and Health Signal Analyses.” Journal of Ambient Intelligence and
Humanized Computing, vol. 13, Springer Nature, 2022, pp. 2621–2635, doi:10.1007/s12652-021-03569-z.
short: S. Goudarzi, M. Sharif, F. Karimipour, Journal of Ambient Intelligence and
Humanized Computing 13 (2022) 2621–2635.
date_created: 2021-11-02T09:28:55Z
date_published: 2022-05-01T00:00:00Z
date_updated: 2025-04-15T07:16:55Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/s12652-021-03569-z
external_id:
isi:
- '000712198000001'
file:
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checksum: 0a8961416a9bb2be5a1cebda65468bcf
content_type: application/pdf
creator: fkarimip
date_created: 2021-11-12T19:38:05Z
date_updated: 2022-12-20T23:30:08Z
embargo: 2022-11-12
file_id: '10279'
file_name: A Context‑aware Dimension Reduction Framework - Journal of Ambient Intelligence
2021 (Preprint version).pdf
file_size: 1634958
relation: main_file
file_date_updated: 2022-12-20T23:30:08Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
keyword:
- general computer science
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 2621–2635
project:
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: Mathematics, Computer Science
publication: Journal of Ambient Intelligence and Humanized Computing
publication_identifier:
eissn:
- 1868-5145
issn:
- 1868-5137
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A context-aware dimension reduction framework for trajectory and health signal
analyses
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2022'
...
---
_id: '7577'
abstract:
- lang: eng
text: Weak convergence of inertial iterative method for solving variational inequalities
is the focus of this paper. The cost function is assumed to be non-Lipschitz and
monotone. We propose a projection-type method with inertial terms and give weak
convergence analysis under appropriate conditions. Some test results are performed
and compared with relevant methods in the literature to show the efficiency and
advantages given by our proposed methods.
acknowledgement: The project of the first author has received funding from the European
Research Council (ERC) under the European Union's Seventh Framework Program (FP7
- 2007-2013) (Grant agreement No. 616160).
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
- first_name: Olaniyi S.
full_name: Iyiola, Olaniyi S.
last_name: Iyiola
citation:
ama: Shehu Y, Iyiola OS. Weak convergence for variational inequalities with inertial-type
method. Applicable Analysis. 2022;101(1):192-216. doi:10.1080/00036811.2020.1736287
apa: Shehu, Y., & Iyiola, O. S. (2022). Weak convergence for variational inequalities
with inertial-type method. Applicable Analysis. Taylor & Francis. https://doi.org/10.1080/00036811.2020.1736287
chicago: Shehu, Yekini, and Olaniyi S. Iyiola. “Weak Convergence for Variational
Inequalities with Inertial-Type Method.” Applicable Analysis. Taylor &
Francis, 2022. https://doi.org/10.1080/00036811.2020.1736287.
ieee: Y. Shehu and O. S. Iyiola, “Weak convergence for variational inequalities
with inertial-type method,” Applicable Analysis, vol. 101, no. 1. Taylor
& Francis, pp. 192–216, 2022.
ista: Shehu Y, Iyiola OS. 2022. Weak convergence for variational inequalities with
inertial-type method. Applicable Analysis. 101(1), 192–216.
mla: Shehu, Yekini, and Olaniyi S. Iyiola. “Weak Convergence for Variational Inequalities
with Inertial-Type Method.” Applicable Analysis, vol. 101, no. 1, Taylor
& Francis, 2022, pp. 192–216, doi:10.1080/00036811.2020.1736287.
short: Y. Shehu, O.S. Iyiola, Applicable Analysis 101 (2022) 192–216.
corr_author: '1'
date_created: 2020-03-09T07:06:52Z
date_published: 2022-01-01T00:00:00Z
date_updated: 2024-11-04T13:52:44Z
day: '01'
ddc:
- '510'
- '515'
- '518'
department:
- _id: VlKo
doi: 10.1080/00036811.2020.1736287
ec_funded: 1
external_id:
arxiv:
- '2101.08057'
isi:
- '000518364100001'
file:
- access_level: open_access
checksum: 869efe8cb09505dfa6012f67d20db63d
content_type: application/pdf
creator: dernst
date_created: 2020-10-12T10:42:54Z
date_updated: 2021-03-16T23:30:06Z
embargo: 2021-03-15
file_id: '8648'
file_name: 2020_ApplicAnalysis_Shehu.pdf
file_size: 4282586
relation: main_file
file_date_updated: 2021-03-16T23:30:06Z
has_accepted_license: '1'
intvolume: ' 101'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 192-216
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Applicable Analysis
publication_identifier:
eissn:
- 1563-504X
issn:
- 0003-6811
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Weak convergence for variational inequalities with inertial-type method
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 101
year: '2022'
...
---
_id: '11471'
abstract:
- lang: eng
text: 'Variational quantum algorithms are promising algorithms for achieving quantum
advantage on nearterm devices. The quantum hardware is used to implement a variational
wave function and measure observables, whereas the classical computer is used
to store and update the variational parameters. The optimization landscape of
expressive variational ansätze is however dominated by large regions in parameter
space, known as barren plateaus, with vanishing gradients, which prevents efficient
optimization. In this work we propose a general algorithm to avoid barren plateaus
in the initialization and throughout the optimization. To this end we define a
notion of weak barren plateaus (WBPs) based on the entropies of local reduced
density matrices. The presence of WBPs can be efficiently quantified using recently
introduced shadow tomography of the quantum state with a classical computer. We
demonstrate that avoidance of WBPs suffices to ensure sizable gradients in the
initialization. In addition, we demonstrate that decreasing the gradient step
size, guided by the entropies allows WBPs to be avoided during the optimization
process. This paves the way for efficient barren plateau-free optimization on
near-term devices. '
acknowledgement: "We thank Marco Cerezo, Zoe Holmes, and Nicholas Hunter-Jones for
fruitful discussion and valuable feedback. We also acknowledge Adam Smith, Johannes
Jakob Meyer, and Victor V. Albert for comments on the paper. The simulations were
performed in the Julia programming\r\nlanguage [65] using the Yao module [66]. S.H.S.,
R.A.M., A.A.M. and M.S. acknowledge support by the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation program (Grant Agreement
No. 850899)."
article_number: '020365'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Stefan
full_name: Sack, Stefan
id: dd622248-f6e0-11ea-865d-ce382a1c81a5
last_name: Sack
orcid: 0000-0001-5400-8508
- first_name: Raimel A
full_name: Medina Ramos, Raimel A
id: CE680B90-D85A-11E9-B684-C920E6697425
last_name: Medina Ramos
orcid: 0000-0002-5383-2869
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: Richard
full_name: Kueng, Richard
last_name: Kueng
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. Avoiding barren
plateaus using classical shadows. PRX Quantum. 2022;3(2). doi:10.1103/prxquantum.3.020365
apa: Sack, S., Medina Ramos, R. A., Michailidis, A., Kueng, R., & Serbyn, M.
(2022). Avoiding barren plateaus using classical shadows. PRX Quantum.
American Physical Society. https://doi.org/10.1103/prxquantum.3.020365
chicago: Sack, Stefan, Raimel A Medina Ramos, Alexios Michailidis, Richard Kueng,
and Maksym Serbyn. “Avoiding Barren Plateaus Using Classical Shadows.” PRX
Quantum. American Physical Society, 2022. https://doi.org/10.1103/prxquantum.3.020365.
ieee: S. Sack, R. A. Medina Ramos, A. Michailidis, R. Kueng, and M. Serbyn, “Avoiding
barren plateaus using classical shadows,” PRX Quantum, vol. 3, no. 2. American
Physical Society, 2022.
ista: Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. 2022. Avoiding
barren plateaus using classical shadows. PRX Quantum. 3(2), 020365.
mla: Sack, Stefan, et al. “Avoiding Barren Plateaus Using Classical Shadows.” PRX
Quantum, vol. 3, no. 2, 020365, American Physical Society, 2022, doi:10.1103/prxquantum.3.020365.
short: S. Sack, R.A. Medina Ramos, A. Michailidis, R. Kueng, M. Serbyn, PRX Quantum
3 (2022).
corr_author: '1'
date_created: 2022-06-29T20:21:32Z
date_published: 2022-06-29T00:00:00Z
date_updated: 2026-05-02T22:30:23Z
day: '29'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/prxquantum.3.020365
ec_funded: 1
external_id:
arxiv:
- '2201.08194'
isi:
- '000822564300001'
file:
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checksum: a7706b28d24a0e32a55ea04b82a2df43
content_type: application/pdf
creator: dernst
date_created: 2022-06-30T07:14:48Z
date_updated: 2022-06-30T07:14:48Z
file_id: '11472'
file_name: 2022_PRXQuantum_Sack.pdf
file_size: 4231591
relation: main_file
success: 1
file_date_updated: 2022-06-30T07:14:48Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
issue: '2'
keyword:
- General Medicine
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: PRX Quantum
publication_identifier:
issn:
- 2691-3399
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '17208'
relation: dissertation_contains
status: public
- id: '14622'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Avoiding barren plateaus using classical shadows
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 3
year: '2022'
...
---
_id: '12272'
abstract:
- lang: eng
text: Reading, interpreting and crawling along gradients of chemotactic cues is
one of the most complex questions in cell biology. In this issue, Georgantzoglou
et al. (2022. J. Cell. Biol.https://doi.org/10.1083/jcb.202103207) use in vivo
models to map the temporal sequence of how neutrophils respond to an acutely arising
gradient of chemoattractant.
article_number: e202206127
article_processing_charge: No
article_type: original
author:
- first_name: Julian A
full_name: Stopp, Julian A
id: 489E3F00-F248-11E8-B48F-1D18A9856A87
last_name: Stopp
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: 'Stopp JA, Sixt MK. Plan your trip before you leave: The neutrophils’ search-and-run
journey. Journal of Cell Biology. 2022;221(8). doi:10.1083/jcb.202206127'
apa: 'Stopp, J. A., & Sixt, M. K. (2022). Plan your trip before you leave: The
neutrophils’ search-and-run journey. Journal of Cell Biology. Rockefeller
University Press. https://doi.org/10.1083/jcb.202206127'
chicago: 'Stopp, Julian A, and Michael K Sixt. “Plan Your Trip before You Leave:
The Neutrophils’ Search-and-Run Journey.” Journal of Cell Biology. Rockefeller
University Press, 2022. https://doi.org/10.1083/jcb.202206127.'
ieee: 'J. A. Stopp and M. K. Sixt, “Plan your trip before you leave: The neutrophils’
search-and-run journey,” Journal of Cell Biology, vol. 221, no. 8. Rockefeller
University Press, 2022.'
ista: 'Stopp JA, Sixt MK. 2022. Plan your trip before you leave: The neutrophils’
search-and-run journey. Journal of Cell Biology. 221(8), e202206127.'
mla: 'Stopp, Julian A., and Michael K. Sixt. “Plan Your Trip before You Leave: The
Neutrophils’ Search-and-Run Journey.” Journal of Cell Biology, vol. 221,
no. 8, e202206127, Rockefeller University Press, 2022, doi:10.1083/jcb.202206127.'
short: J.A. Stopp, M.K. Sixt, Journal of Cell Biology 221 (2022).
corr_author: '1'
date_created: 2023-01-16T10:01:08Z
date_published: 2022-07-20T00:00:00Z
date_updated: 2026-05-02T22:30:27Z
day: '20'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1083/jcb.202206127
external_id:
isi:
- '000874717200001'
pmid:
- '35856919'
file:
- access_level: open_access
checksum: 6b1620743669679b48b9389bb40f5a11
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:39:34Z
date_updated: 2023-01-30T10:39:34Z
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month: '07'
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pmid: 1
publication: Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
issn:
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
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related_material:
record:
- id: '14697'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Plan your trip before you leave: The neutrophils’ search-and-run journey'
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 221
year: '2022'
...
---
_id: '10934'
abstract:
- lang: eng
text: 'FtsA is crucial for assembly of the E. coli divisome, as it dynamically links
cytoplasmic FtsZ filaments with transmembrane cell division proteins. FtsA allegedly
initiates cell division by switching from an inactive polymeric to an active monomeric
confirmation, which recruits downstream proteins and stabilizes FtsZ filaments.
Here, we use biochemical reconstitution experiments combined with quantitative
fluorescence microscopy to study divisome activation in vitro. We compare wildtype-FtsA
with FtsA-R286W, a constantly active gain-of-function mutant and find that R286W
outperforms the wildtype protein in replicating FtsZ treadmilling dynamics, stabilizing
FtsZ filaments and recruiting FtsN. We attribute these differences to a faster
membrane exchange of FtsA-R286W and its higher packing density below FtsZ filaments. Using
FRET microscopy, we find that FtsN binding does not compete with, but promotes
FtsA self-interaction. Our findings suggest a model where FtsA always forms dynamic
polymers on the membrane, which re-organize during assembly and activation of
the divisome. '
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We acknowledge members of the Loose laboratory at IST Austria for
helpful discussions—in particular L. Lindorfer for his assistance with cloning and
purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing
unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski
(Lehigh University, Bethlehem, PA, USA) as well as S. Martin (University of Lausanne,
Switzerland) for sharing their code for FRAP analysis. We are also thankful for
the support by the Scientific Service Units (SSU) of IST Austria through resources
provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF).
This work was supported by the European Research Council through grant ERC 2015-StG-679239
and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4
to N.B. For the purpose of open access, we have applied a CC BY public copyright
licence to any Author Accepted Manuscript version arising from this submission.
article_processing_charge: No
author:
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: ' 0000-0001-9198-2182 '
citation:
ama: Radler P. In vitro reconstitution of Escherichia coli divisome activation.
2022. doi:10.15479/AT:ISTA:10934
apa: Radler, P. (2022). In vitro reconstitution of Escherichia coli divisome activation.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:10934
chicago: Radler, Philipp. “In Vitro Reconstitution of Escherichia Coli Divisome
Activation.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:10934.
ieee: P. Radler, “In vitro reconstitution of Escherichia coli divisome activation.”
Institute of Science and Technology Austria, 2022.
ista: Radler P. 2022. In vitro reconstitution of Escherichia coli divisome activation,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:10934.
mla: Radler, Philipp. In Vitro Reconstitution of Escherichia Coli Divisome Activation.
Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:10934.
short: P. Radler, (2022).
contributor:
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first_name: Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- contributor_type: researcher
first_name: Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
- contributor_type: researcher
first_name: Paulo
last_name: Caldas
- contributor_type: researcher
first_name: David
id: B9577E20-AA38-11E9-AC9A-0930E6697425
last_name: Michalik
- contributor_type: researcher
first_name: Natalia
last_name: Baranova
corr_author: '1'
date_created: 2022-03-31T11:32:32Z
date_published: 2022-04-05T00:00:00Z
date_updated: 2026-05-02T22:30:29Z
day: '05'
ddc:
- '572'
department:
- _id: GradSch
- _id: MaLo
doi: 10.15479/AT:ISTA:10934
ec_funded: 1
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has_accepted_license: '1'
keyword:
- Bacterial cell division
- in vitro reconstitution
- FtsZ
- FtsN
- FtsA
month: '04'
oa: 1
oa_version: Submitted Version
project:
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call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
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name: In vitro reconstitution of bacterial cell division
publisher: Institute of Science and Technology Austria
related_material:
link:
- description: A custom written code (FRAPdiff) to quantify the Off binding rate
and Diffusion coefficient of membrane bound proteins. Written by Christoph Sommer.
relation: software
url: https://doi.org/10.5281/zenodo.6400639
record:
- id: '11373'
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status: public
- id: '14280'
relation: used_in_publication
status: public
status: public
title: In vitro reconstitution of Escherichia coli divisome activation
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: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11373'
abstract:
- lang: eng
text: The actin-homologue FtsA is essential for E. coli cell division, as it links
FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate
cell constriction by switching from an inactive polymeric to an active monomeric
conformation, which recruits downstream proteins and stabilizes the Z-ring. However,
direct biochemical evidence for this mechanism is missing. Here, we use reconstitution
experiments and quantitative fluorescence microscopy to study divisome activation
in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive
mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament
stabilization and recruitment of FtsN. We could attribute these differences to
a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using
FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction.
We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer
that follows treadmilling filaments of FtsZ.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We acknowledge members of the Loose laboratory at IST Austria for
helpful discussions—in particular L. Lindorfer for his assistance with cloning and
purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing
unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski
(Lehigh University, Bethlehem, PA, USA) and S. Martin (University of Lausanne, Switzerland)
for sharing their code for FRAP analysis. We are also thankful for the support by
the Scientific Service Units (SSU) of IST Austria through resources provided by
the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work
was supported by the European Research Council through grant ERC 2015-StG-679239
and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4
to N.B. For the purpose of open access, we have applied a CC BY public copyright
licence to any Author Accepted Manuscript version arising from this submission.
article_number: '2635'
article_processing_charge: No
article_type: original
author:
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
- first_name: Natalia S.
full_name: Baranova, Natalia S.
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Paulo R
full_name: Dos Santos Caldas, Paulo R
id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87
last_name: Dos Santos Caldas
orcid: 0000-0001-6730-4461
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Maria D
full_name: Lopez Pelegrin, Maria D
id: 319AA9CE-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Pelegrin
- first_name: David
full_name: Michalik, David
id: B9577E20-AA38-11E9-AC9A-0930E6697425
last_name: Michalik
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Radler P, Baranova NS, Dos Santos Caldas PR, et al. In vitro reconstitution
of Escherichia coli divisome activation. Nature Communications. 2022;13.
doi:10.1038/s41467-022-30301-y
apa: Radler, P., Baranova, N. S., Dos Santos Caldas, P. R., Sommer, C. M., Lopez
Pelegrin, M. D., Michalik, D., & Loose, M. (2022). In vitro reconstitution
of Escherichia coli divisome activation. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-022-30301-y
chicago: Radler, Philipp, Natalia S. Baranova, Paulo R Dos Santos Caldas, Christoph
M Sommer, Maria D Lopez Pelegrin, David Michalik, and Martin Loose. “In Vitro
Reconstitution of Escherichia Coli Divisome Activation.” Nature Communications.
Springer Nature, 2022. https://doi.org/10.1038/s41467-022-30301-y.
ieee: P. Radler et al., “In vitro reconstitution of Escherichia coli divisome
activation,” Nature Communications, vol. 13. Springer Nature, 2022.
ista: Radler P, Baranova NS, Dos Santos Caldas PR, Sommer CM, Lopez Pelegrin MD,
Michalik D, Loose M. 2022. In vitro reconstitution of Escherichia coli divisome
activation. Nature Communications. 13, 2635.
mla: Radler, Philipp, et al. “In Vitro Reconstitution of Escherichia Coli Divisome
Activation.” Nature Communications, vol. 13, 2635, Springer Nature, 2022,
doi:10.1038/s41467-022-30301-y.
short: P. Radler, N.S. Baranova, P.R. Dos Santos Caldas, C.M. Sommer, M.D. Lopez
Pelegrin, D. Michalik, M. Loose, Nature Communications 13 (2022).
corr_author: '1'
date_created: 2022-05-13T09:06:28Z
date_published: 2022-05-12T00:00:00Z
date_updated: 2026-05-02T22:30:29Z
day: '12'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1038/s41467-022-30301-y
ec_funded: 1
external_id:
isi:
- '000795171100037'
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intvolume: ' 13'
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keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: In vitro reconstitution of bacterial cell division
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-022-34485-1
record:
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relation: research_data
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scopus_import: '1'
status: public
title: In vitro reconstitution of Escherichia coli divisome activation
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: 13
year: '2022'
...
---
OA_place: publisher
_id: '11196'
abstract:
- lang: eng
text: "One of the fundamental questions in Neuroscience is how the structure of
synapses and their physiological properties are related. While synaptic transmission
remains a dynamic process, electron microscopy provides images with comparably
low temporal resolution (Studer et al., 2014). The current work overcomes this
challenge and describes an improved “Flash and Freeze” technique (Watanabe et
al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal
mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and
organotypic slices culture. The improved method allowed for selective stimulation
of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool
dynamics at the active zones. Our results uncovered several intriguing morphological
features of mossy fiber boutons. First, the docked vesicle pool was largely depleted
(more than 70%) after stimulation, implying that the docked synaptic vesicles
pool and readily releasable pool are vastly overlapping in mossy fiber boutons.
Second, the synaptic vesicles are skewed towards larger diameters, displaying
a wide range of sizes. An increase in the mean diameter of synaptic vesicles,
after single and repetitive stimulation, suggests that smaller vesicles have a
higher release probability. Third, we observed putative endocytotic structures
after moderate light stimulation, matching the timing of previously described
ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). \r\n\tIn
addition, synaptic transmission depends on a sophisticated system of protein machinery
and calcium channels (Südhof, 2013b), which amplifies the challenge in studying
synaptic communication as these interactions can be potentially modified during
synaptic plasticity. And although recent study elucidated the potential correlation
between physiological and morphological properties of synapses during synaptic
plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown.
Thus, the presented work tries to overcome this challenge and aims to pinpoint
changes in the molecular architecture at hippocampal mossy fiber bouton synapses
during short- and long-term potentiation (STP and LTP), we combined chemical potentiation,
with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin)
and freeze-fracture replica immunolabelling. This method allowed the localization
of membrane-bound proteins with nanometer precision within the active zone, in
particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2.
First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton
active zone increased significantly during STP, but decreased to lower than the
control value during LTP. Secondly, although the distance between the calcium
channels and Munc13-1s did not change after induction of STP, it shortened during
the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during
STP and LTP. These results indicate the existence of two distinct mechanisms that
govern STP and LTP at mossy fiber bouton synapses: an increase in the readily
realizable pool in the case of STP and a potential increase in release probability
during LTP. “Flash and freeze” and functional electron microscopy, are versatile
methods that can be successfully applied to intact brain circuits to study synaptic
transmission even at the molecular level.\r\n"
acknowledged_ssus:
- _id: EM-Fac
- _id: PreCl
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Olena
full_name: Kim, Olena
id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
last_name: Kim
orcid: 0000-0003-2344-1039
citation:
ama: Kim O. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses.
2022. doi:10.15479/at:ista:11196
apa: Kim, O. (2022). Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal
neuron synapses. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11196
chicago: Kim, Olena. “Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal
Neuron Synapses.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11196.
ieee: O. Kim, “Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron
synapses,” Institute of Science and Technology Austria, 2022.
ista: Kim O. 2022. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron
synapses. Institute of Science and Technology Austria.
mla: Kim, Olena. Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron
Synapses. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11196.
short: O. Kim, Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron
Synapses, Institute of Science and Technology Austria, 2022.
corr_author: '1'
date_created: 2022-04-20T09:47:12Z
date_published: 2022-04-20T00:00:00Z
date_updated: 2026-04-07T14:22:20Z
day: '20'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: PeJo
- _id: GradSch
doi: 10.15479/at:ista:11196
ec_funded: 1
file:
- access_level: open_access
checksum: 1616a8bf6f13a57c892dac873dcd0936
content_type: application/pdf
creator: okim
date_created: 2022-04-20T14:21:56Z
date_updated: 2023-04-20T22:30:03Z
embargo: 2023-04-19
file_id: '11220'
file_name: Olena_KIM_thesis_final.pdf
file_size: 21273537
relation: main_file
- access_level: closed
checksum: 1acb433f98dc42abb0b4b0cbb0c4b918
content_type: application/x-zip-compressed
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date_created: 2022-04-20T14:22:56Z
date_updated: 2023-04-20T22:30:03Z
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file_name: KIM_thesis_final.zip
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file_date_updated: 2023-04-20T22:30:03Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: '132'
project:
- _id: 25BAF7B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '708497'
name: Presynaptic calcium channels distribution and impact on coupling at the hippocampal
mossy fiber synapse
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 25C3DBB6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01205
name: Zellkommunikation in Gesundheit und Krankheit
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7473'
relation: part_of_dissertation
status: public
- id: '11222'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
title: Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses
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: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2022'
...
---
OA_place: publisher
_id: '10727'
abstract:
- lang: eng
text: "Social insects are a common model to study disease dynamics in social animals.
Even though pathogens should thrive in social insect colonies as the hosts engage
in frequent social interactions, are closely related and live in a pathogen-rich
environment, disease outbreaks are rare. This is because social insects have evolved
mechanisms to keep pathogens at bay – and fight disease as a collective. Social
insect colonies are often viewed as “superorganisms” with division of labor between
reproductive “germ-like” queens and males and “somatic” workers, which together
form an interdependent reproductive unit that parallels a multicellular body.
Superorganisms possess a “social immune system” that comprises of collective disease
defenses performed by the workers - summarized as “social immunity”. In social
groups immunization (reduced susceptibility to a parasite upon secondary exposure
to the same parasite) can e.g. be triggered by social interactions (“social immunization”).
Social immunization can be caused by (i) asymptomatic low-level infections that
are acquired during caregiving to a contagious individual that can give an immune
boost, which can induce protection upon later encounter with the same pathogen
(active immunization) or (ii) by transfer of immune effectors between individuals
(passive immunization).\r\nIn the second chapter, I built up on a study that I
co-authored that found that low-level infections can not only be protective, but
also be costly and make the host more susceptible to detrimental superinfections
after contact to a very dissimilar pathogen. I here now tested different degrees
of phylogenetically-distant fungal strains of M. brunneum and M. robertsii in
L. neglectus and can describe the occurrence of cross-protection of social immunization
if the first and second pathogen are from the same level. Interestingly, low-level
infections only provided protection when the first strain was less virulent than
the second strain and elicited higher immune gene expression.\r\nIn the third
and fourth chapters, I expanded on the role of social immunity in sexual selection,
a so far unstudied field. I used the fungus Metarhizium robertsii and the ant
Cardiocondyla obscurior as a model, as in this species mating occurs in the presence
of workers and can be studied under laboratory conditions. Before males mate with
virgin queens in the nest they engage in fierce combat over the access to their
mating partners.\r\nFirst, I focused on male-male competition in the third chapter
and found that fighting with a contagious male is costly as it can lead to contamination
of the rival, but that workers can decrease the risk of disease contraction by
performing sanitary care.\r\nIn the fourth chapter, I studied the effect of fungal
infection on survival and mating success of sexuals (freshly emerged queens and
males) and found that worker-performed sanitary care can buffer the negative effect
that a pathogenic contagion would have on sexuals by spore removal from the exposed
individuals. When social immunity was prevented and queens could contract spores
from their mating partner, very low dosages led to negative consequences: their
lifespan was reduced and they produced fewer offspring with poor immunocompetence
compared to healthy queens. Interestingly, cohabitation with a late-stage infected
male where no spore transfer was possible had a positive effect on offspring immunity
– male offspring of mothers that apparently perceived an infected partner in their
vicinity reacted more sensitively to fungal challenge than male offspring without
paternal pathogen history."
acknowledged_ssus:
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sina
full_name: Metzler, Sina
id: 48204546-F248-11E8-B48F-1D18A9856A87
last_name: Metzler
orcid: 0000-0002-9547-2494
citation:
ama: Metzler S. Pathogen-mediated sexual selection and immunization in ant colonies.
2022. doi:10.15479/AT:ISTA:10727
apa: Metzler, S. (2022). Pathogen-mediated sexual selection and immunization
in ant colonies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:10727
chicago: Metzler, Sina. “Pathogen-Mediated Sexual Selection and Immunization in
Ant Colonies.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:10727.
ieee: S. Metzler, “Pathogen-mediated sexual selection and immunization in ant colonies,”
Institute of Science and Technology Austria, 2022.
ista: Metzler S. 2022. Pathogen-mediated sexual selection and immunization in ant
colonies. Institute of Science and Technology Austria.
mla: Metzler, Sina. Pathogen-Mediated Sexual Selection and Immunization in Ant
Colonies. Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:10727.
short: S. Metzler, Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies,
Institute of Science and Technology Austria, 2022.
corr_author: '1'
date_created: 2022-02-04T15:45:12Z
date_published: 2022-02-07T00:00:00Z
date_updated: 2026-04-07T14:30:18Z
day: '07'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SyCr
doi: 10.15479/AT:ISTA:10727
ec_funded: 1
file:
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checksum: 47ba18bb270dd6cc266e0a3f7c69d0e4
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: smetzler
date_created: 2022-02-04T15:36:12Z
date_updated: 2023-02-03T23:30:03Z
embargo_to: open_access
file_id: '10728'
file_name: Thesis_Sina_Metzler.docx
file_size: 6757886
relation: source_file
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content_type: application/pdf
creator: smetzler
date_created: 2022-02-04T15:36:43Z
date_updated: 2023-02-03T23:30:03Z
embargo: 2023-02-02
file_id: '10730'
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content_type: application/pdf
creator: smetzler
date_created: 2022-02-07T10:35:02Z
date_updated: 2023-02-04T23:30:03Z
embargo: 2023-02-02
file_id: '10742'
file_name: Thesis_Sina_Metzler_print.pdf
file_size: 6882557
relation: main_file
file_date_updated: 2023-02-04T23:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: Pathogen-mediated sexual selection and immunization in ant colonies
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2022'
...
---
OA_place: publisher
_id: '11879'
abstract:
- lang: eng
text: "As the overall global mean surface temperature is increasing due to climate
change, plant\r\nadaptation to those stressful conditions is of utmost importance
for their survival. Plants are\r\nsessile organisms, thus to compensate for their
lack of mobility, they evolved a variety of\r\nmechanisms enabling them to flexibly
adjust their physiological, growth and developmental\r\nprocesses to fluctuating
temperatures and to survive in harsh environments. While these unique\r\nadaptation
abilities provide an important evolutionary advantage, overall modulation of plant\r\ngrowth
and developmental program due to non-optimal temperature negatively affects biomass\r\nproduction,
crop productivity or sensitivity to pathogens. Thus, understanding molecular\r\nprocesses
underlying plant adaptation to increased temperature can provide important\r\nresources
for breeding strategies to ensure sufficient agricultural food production.\r\nAn
increase in ambient temperature by a few degrees leads to profound changes in
organ growth\r\nincluding enhanced hypocotyl elongation, expansion of petioles,
hyponastic growth of leaves and\r\ncotyledons, collectively named thermomorphogenesis
(Casal & Balasubramanian, 2019). Auxin,\r\none of the best-studied growth hormones,
plays an essential role in this process by direct\r\nactivation of transcriptional
and non-transcriptional processes resulting in elongation growth\r\n(Majda & Robert,
2018).To modulate hypocotyl growth in response to high ambient temperature\r\n(hAT),
auxin needs to be redistributed accordingly. PINs, auxin efflux transporters,
are key\r\ncomponents of the polar auxin transport (PAT) machinery, which controls
the amount and\r\ndirection of auxin translocated in the plant tissues and organs(Adamowski
& Friml, 2015). Hence,\r\nPIN-mediated transport is tightly linked with thermo-morphogenesis,
and interference with PAT\r\nthrough either chemical or genetic means dramatically
affecting the adaptive responses to hAT.\r\nIntriguingly, despite the key role
of PIN mediated transport in growth response to hAT, whether\r\nand how PINs at
the level of expression adapt to fluctuation in temperature is scarcely\r\nunderstood.\r\nWith
genetic, molecular and advanced bio-imaging approaches, we demonstrate the role
of PIN\r\nauxin transporters in the regulation of hypocotyl growth in response
to hAT. We show that via\r\nadjustment of PIN3, PIN4 and PIN7 expression in cotyledons
and hypocotyls, auxin distribution is modulated thereby determining elongation
pattern of epidermal cells at hAT. Furthermore, we\r\nidentified three Zinc-Finger
(ZF) transcription factors as novel molecular components of the\r\nthermo-regulatory
network, which through negative regulation of PIN transcription adjust the\r\ntransport
of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of
the\r\nnegative feedback loop attenuating the activity of the thermo-sensing pathway
to restrain\r\nexaggerated growth and developmental responses to hAT."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: SSU
acknowledgement: I would like to acknowledge ISTA and all the people from the Scientific
Service Units and at ISTA, in particular Dorota Jaworska for excellent technical
and scientific support as well as ÖAW for funding my research for over 3 years (DOC
ÖAW Fellowship PR1022OEAW02).
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Christina
full_name: Artner, Christina
id: 45DF286A-F248-11E8-B48F-1D18A9856A87
last_name: Artner
citation:
ama: Artner C. Modulation of auxin transport via ZF proteins adjust plant response
to high ambient temperature. 2022. doi:10.15479/at:ista:11879
apa: Artner, C. (2022). Modulation of auxin transport via ZF proteins adjust
plant response to high ambient temperature. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:11879
chicago: Artner, Christina. “Modulation of Auxin Transport via ZF Proteins Adjust
Plant Response to High Ambient Temperature.” Institute of Science and Technology
Austria, 2022. https://doi.org/10.15479/at:ista:11879.
ieee: C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response
to high ambient temperature,” Institute of Science and Technology Austria, 2022.
ista: Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant
response to high ambient temperature. Institute of Science and Technology Austria.
mla: Artner, Christina. Modulation of Auxin Transport via ZF Proteins Adjust
Plant Response to High Ambient Temperature. Institute of Science and Technology
Austria, 2022, doi:10.15479/at:ista:11879.
short: C. Artner, Modulation of Auxin Transport via ZF Proteins Adjust Plant Response
to High Ambient Temperature, Institute of Science and Technology Austria, 2022.
corr_author: '1'
date_created: 2022-08-17T07:58:53Z
date_published: 2022-08-17T00:00:00Z
date_updated: 2026-04-07T14:30:39Z
day: '17'
ddc:
- '580'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EvBe
doi: 10.15479/at:ista:11879
file:
- access_level: open_access
checksum: a2c2fdc28002538840490bfa6a08b2cb
content_type: application/pdf
creator: cartner
date_created: 2022-08-17T12:08:49Z
date_updated: 2023-09-09T22:30:03Z
embargo: 2023-09-08
file_id: '11907'
file_name: ChristinaArtner_PhD_Thesis_2022.pdf
file_size: 11113608
relation: main_file
- access_level: closed
checksum: 66b461c074b815fbe63481b3f46a9f43
content_type: application/octet-stream
creator: cartner
date_created: 2022-08-17T12:08:59Z
date_updated: 2023-09-09T22:30:03Z
embargo_to: open_access
file_id: '11908'
file_name: ChristinaArtner_PhD_Thesis_2022.7z
file_size: 19097730
relation: source_file
file_date_updated: 2023-09-09T22:30:03Z
has_accepted_license: '1'
keyword:
- high ambient temperature
- auxin
- PINs
- Zinc-Finger proteins
- thermomorphogenesis
- stress
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '128'
project:
- _id: 2685A872-B435-11E9-9278-68D0E5697425
name: Hormonal regulation of plant adaptive responses to environmental signals
publication_identifier:
isbn:
- 978-3-99078-022-0
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
title: Modulation of auxin transport via ZF proteins adjust plant response to high
ambient temperature
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2022'
...
---
_id: '12138'
abstract:
- lang: eng
text: 'Complex I is the first enzyme in the respiratory chain, which is responsible
for energy production in mitochondria and bacteria1. Complex I couples the transfer
of two electrons from NADH to quinone and the translocation of four protons across
the membrane2, but the coupling mechanism remains contentious. Here we present
cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different
redox states, including catalytic turnover. EcCI exists mostly in the open state,
in which the quinone cavity is exposed to the cytosol, allowing access for water
molecules, which enable quinone movements. Unlike the mammalian paralogues3, EcCI
can convert to the closed state only during turnover, showing that closed and
open states are genuine turnover intermediates. The open-to-closed transition
results in the tightly engulfed quinone cavity being connected to the central
axis of the membrane arm, a source of substrate protons. Consistently, the proportion
of the closed state increases with increasing pH. We propose a detailed but straightforward
and robust mechanism comprising a ‘domino effect’ series of proton transfers and
electrostatic interactions: the forward wave (‘dominoes stacking’) primes the
pump, and the reverse wave (‘dominoes falling’) results in the ejection of all
pumped protons from the distal subunit NuoL. This mechanism explains why protons
exit exclusively from the NuoL subunit and is supported by our mutagenesis data.
We contend that this is a universal coupling mechanism of complex I and related
enzymes.'
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: ScienComp
acknowledgement: This research was supported by the Scientific Service Units (SSU)
of IST Austria through resources provided by the Electron Microscopy Facility (EMF),
the Life Science Facility (LSF) and the IST high-performance computing cluster.
We thank V.-V. Hodirnau from IST Austria EMF, M. Babiak from CEITEC for assistance
with collecting cryo-EM data and A. Charnagalov for the assistance with protein
purification. V.K. was a recipient of a DOC Fellowship of the Austrian Academy of
Sciences at the Institute of Science and Technology, Austria. V.K. and O.P. are
funded by the ERC Advanced Grant 101020697 RESPICHAIN to L.S. This work was also
supported by the Medical Research Council (UK).
article_processing_charge: No
article_type: original
author:
- first_name: Vladyslav
full_name: Kravchuk, Vladyslav
id: 4D62F2A6-F248-11E8-B48F-1D18A9856A87
last_name: Kravchuk
orcid: 0000-0001-9523-9089
- first_name: Olga
full_name: Petrova, Olga
id: 5D8C9660-5D49-11EA-8188-567B3DDC885E
last_name: Petrova
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
orcid: 0000-0002-6018-3422
- first_name: Anna
full_name: Wojciechowska-Bason, Anna
last_name: Wojciechowska-Bason
- first_name: Zara
full_name: Breese, Zara
last_name: Breese
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov
LA. A universal coupling mechanism of respiratory complex I. Nature. 2022;609(7928):808-814.
doi:10.1038/s41586-022-05199-7
apa: Kravchuk, V., Petrova, O., Kampjut, D., Wojciechowska-Bason, A., Breese, Z.,
& Sazanov, L. A. (2022). A universal coupling mechanism of respiratory complex
I. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05199-7
chicago: Kravchuk, Vladyslav, Olga Petrova, Domen Kampjut, Anna Wojciechowska-Bason,
Zara Breese, and Leonid A Sazanov. “A Universal Coupling Mechanism of Respiratory
Complex I.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05199-7.
ieee: V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, and
L. A. Sazanov, “A universal coupling mechanism of respiratory complex I,” Nature,
vol. 609, no. 7928. Springer Nature, pp. 808–814, 2022.
ista: Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov
LA. 2022. A universal coupling mechanism of respiratory complex I. Nature. 609(7928),
808–814.
mla: Kravchuk, Vladyslav, et al. “A Universal Coupling Mechanism of Respiratory
Complex I.” Nature, vol. 609, no. 7928, Springer Nature, 2022, pp. 808–14,
doi:10.1038/s41586-022-05199-7.
short: V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, L.A.
Sazanov, Nature 609 (2022) 808–814.
corr_author: '1'
date_created: 2023-01-12T12:04:33Z
date_published: 2022-09-22T00:00:00Z
date_updated: 2026-05-02T22:30:32Z
day: '22'
ddc:
- '572'
department:
- _id: LeSa
doi: 10.1038/s41586-022-05199-7
ec_funded: 1
external_id:
isi:
- '000854788200001'
pmid:
- '36104567'
file:
- access_level: open_access
checksum: d42a93e24f59e883ef0b5429832391d0
content_type: application/pdf
creator: lsazanov
date_created: 2023-05-30T17:05:31Z
date_updated: 2023-05-30T17:05:31Z
file_id: '13104'
file_name: EcCxI_manuscript_rev3_noSI_updated_withFigs_opt.pdf
file_size: 1425655
relation: main_file
success: 1
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checksum: 5422bc0a73b3daadafa262c7ea6deae3
content_type: application/pdf
creator: lsazanov
date_created: 2023-05-30T17:07:05Z
date_updated: 2023-05-30T17:07:05Z
file_id: '13105'
file_name: EcCxI_manuscript_rev3_SI_All_opt_upd.pdf
file_size: 9842513
relation: main_file
success: 1
file_date_updated: 2023-05-30T17:07:05Z
has_accepted_license: '1'
intvolume: ' 609'
isi: 1
issue: '7928'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 808-814
pmid: 1
project:
- _id: 238A0A5A-32DE-11EA-91FC-C7463DDC885E
grant_number: '25541'
name: 'Structural characterization of E. coli complex I: an important mechanistic
model'
- _id: 627abdeb-2b32-11ec-9570-ec31a97243d3
call_identifier: H2020
grant_number: '101020697'
name: Structure and mechanism of respiratory chain molecular machines
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-022-05457-8
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/proton-dominos-kick-off-life/
record:
- id: '12781'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A universal coupling mechanism of respiratory complex I
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 609
year: '2022'
...
---
_id: '11160'
abstract:
- lang: eng
text: Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent
cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses
macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency
affects neurodevelopmental is unclear. Here, employing human cerebral organoids,
we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories
with an accelerated and delayed generation of, respectively, inhibitory and excitatory
neurons that yields, at days 60 and 120, symmetrically opposite expansions in
their proportions. This imbalance is consistent with an enlargement of cerebral
organoids as an in vitro correlate of patients’ macrocephaly. Through an isogenic
design of patient-specific mutations and mosaic organoids, we define genotype-phenotype
relationships and uncover their cell-autonomous nature. Our results define cell-type-specific
CHD8-dependent molecular defects related to an abnormal program of proliferation
and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations,
our study uncovers reproducible developmental alterations that may be employed
for neurodevelopmental disease modeling.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We thank Farnaz Freeman for technical assistance. This research was
supported by the Scientific Service Units (SSU) of IST Austria through resources
provided by the Bioimaging Facility (BIF) and the Life Science Facility (LSF). This
work supported by the European Union’s Horizon 2020 research and innovation program
(ERC) grant 715508 to G.N. (REVERSEAUTISM) and grant 825759 to G.T. (ENDpoiNTs);
the Fondazione Cariplo 2017-0886 to A.L.T.; E-Rare-3 JTC 2018 IMPACT to M. Gabriele;
and the Austrian Science Fund FWF I 4205-B to G.N. Graphical abstract and figures
were created using BioRender.com.
article_number: '110615'
article_processing_charge: Yes
article_type: original
author:
- first_name: Carlo Emanuele
full_name: Villa, Carlo Emanuele
last_name: Villa
- first_name: Cristina
full_name: Cheroni, Cristina
last_name: Cheroni
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Alejandro
full_name: López-Tóbon, Alejandro
last_name: López-Tóbon
- first_name: Bárbara
full_name: Oliveira, Bárbara
id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
last_name: Oliveira
- first_name: Roberto
full_name: Sacco, Roberto
id: 42C9F57E-F248-11E8-B48F-1D18A9856A87
last_name: Sacco
- first_name: Aysan Çerağ
full_name: Yahya, Aysan Çerağ
id: 365A65F8-F248-11E8-B48F-1D18A9856A87
last_name: Yahya
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
- first_name: Michele
full_name: Gabriele, Michele
last_name: Gabriele
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Mariano
full_name: Gabitto, Mariano
last_name: Gabitto
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Giuseppe
full_name: Testa, Giuseppe
last_name: Testa
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Villa CE, Cheroni C, Dotter C, et al. CHD8 haploinsufficiency links autism
to transient alterations in excitatory and inhibitory trajectories. Cell Reports.
2022;39(1). doi:10.1016/j.celrep.2022.110615
apa: Villa, C. E., Cheroni, C., Dotter, C., López-Tóbon, A., Oliveira, B., Sacco,
R., … Novarino, G. (2022). CHD8 haploinsufficiency links autism to transient alterations
in excitatory and inhibitory trajectories. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2022.110615
chicago: Villa, Carlo Emanuele, Cristina Cheroni, Christoph Dotter, Alejandro López-Tóbon,
Bárbara Oliveira, Roberto Sacco, Aysan Çerağ Yahya, et al. “CHD8 Haploinsufficiency
Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.”
Cell Reports. Elsevier, 2022. https://doi.org/10.1016/j.celrep.2022.110615.
ieee: C. E. Villa et al., “CHD8 haploinsufficiency links autism to transient
alterations in excitatory and inhibitory trajectories,” Cell Reports, vol.
39, no. 1. Elsevier, 2022.
ista: Villa CE, Cheroni C, Dotter C, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ,
Morandell J, Gabriele M, Tavakoli M, Lyudchik J, Sommer CM, Gabitto M, Danzl JG,
Testa G, Novarino G. 2022. CHD8 haploinsufficiency links autism to transient alterations
in excitatory and inhibitory trajectories. Cell Reports. 39(1), 110615.
mla: Villa, Carlo Emanuele, et al. “CHD8 Haploinsufficiency Links Autism to Transient
Alterations in Excitatory and Inhibitory Trajectories.” Cell Reports, vol.
39, no. 1, 110615, Elsevier, 2022, doi:10.1016/j.celrep.2022.110615.
short: C.E. Villa, C. Cheroni, C. Dotter, A. López-Tóbon, B. Oliveira, R. Sacco,
A.Ç. Yahya, J. Morandell, M. Gabriele, M. Tavakoli, J. Lyudchik, C.M. Sommer,
M. Gabitto, J.G. Danzl, G. Testa, G. Novarino, Cell Reports 39 (2022).
corr_author: '1'
date_created: 2022-04-15T09:03:10Z
date_published: 2022-04-05T00:00:00Z
date_updated: 2026-05-02T22:30:33Z
day: '05'
ddc:
- '570'
department:
- _id: JoDa
- _id: GaNo
doi: 10.1016/j.celrep.2022.110615
ec_funded: 1
external_id:
isi:
- '000785983900003'
pmid:
- '35385734'
file:
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checksum: b4e8d68f0268dec499af333e6fd5d8e1
content_type: application/pdf
creator: dernst
date_created: 2022-04-15T09:06:25Z
date_updated: 2022-04-15T09:06:25Z
file_id: '11164'
file_name: 2022_CellReports_Villa.pdf
file_size: '7808644'
relation: main_file
success: 1
file_date_updated: 2022-04-15T09:06:25Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 2690FEAC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I04205
name: Identification of converging Molecular Pathways Across Chromatinopathies as
Targets for Therapy
publication: Cell Reports
publication_identifier:
issn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '18681'
relation: dissertation_contains
status: public
- id: '18674'
relation: dissertation_contains
status: public
- id: '12364'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: CHD8 haploinsufficiency links autism to transient alterations in excitatory
and inhibitory trajectories
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2022'
...