---
_id: '8788'
abstract:
- lang: eng
text: 'We consider a real-time setting where an environment releases sequences of
firm-deadline tasks, and an online scheduler chooses on-the-fly the ones to execute
on a single processor so as to maximize cumulated utility. The competitive ratio
is a well-known performance measure for the scheduler: it gives the worst-case
ratio, among all possible choices for the environment, of the cumulated utility
of the online scheduler versus an offline scheduler that knows these choices in
advance. Traditionally, competitive analysis is performed by hand, while automated
techniques are rare and only handle static environments with independent tasks.
We present a quantitative-verification framework for precedence-aware competitive
analysis, where task releases may depend on preceding scheduling choices, i.e.,
the environment can respond to scheduling decisions dynamically . We consider
two general classes of precedences: 1) follower precedences force the release
of a dependent task upon the completion of a set of precursor tasks, while and
2) pairing precedences modify the characteristics of a dependent task provided
the completion of a set of precursor tasks. Precedences make competitive analysis
challenging, as the online and offline schedulers operate on diverging sequences.
We make a formal presentation of our framework, and use a GPU-based implementation
to analyze ten well-known schedulers on precedence-based application examples
taken from the existing literature: 1) a handshake protocol (HP); 2) network packet-switching;
3) query scheduling (QS); and 4) a sporadic-interrupt setting. Our experimental
results show that precedences and task parameters can vary drastically the best
scheduler. Our framework thus supports application designers in choosing the best
scheduler among a given set automatically.'
acknowledgement: 'This work was supported by the Austrian Science Foundation (FWF)
under the NFN RiSE/SHiNE under Grant S11405 and Grant S11407. This article was presented
in the International Conference on Embedded Software 2020 and appears as part of
the ESWEEK-TCAD special issue. '
article_processing_charge: No
article_type: original
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Nico
full_name: Schaumberger, Nico
last_name: Schaumberger
- first_name: Ulrich
full_name: Schmid, Ulrich
last_name: Schmid
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Pavlogiannis A, Schaumberger N, Schmid U, Chatterjee K. Precedence-aware automated
competitive analysis of real-time scheduling. IEEE Transactions on Computer-Aided
Design of Integrated Circuits and Systems. 2020;39(11):3981-3992. doi:10.1109/TCAD.2020.3012803
apa: Pavlogiannis, A., Schaumberger, N., Schmid, U., & Chatterjee, K. (2020).
Precedence-aware automated competitive analysis of real-time scheduling. IEEE
Transactions on Computer-Aided Design of Integrated Circuits and Systems.
IEEE. https://doi.org/10.1109/TCAD.2020.3012803
chicago: Pavlogiannis, Andreas, Nico Schaumberger, Ulrich Schmid, and Krishnendu
Chatterjee. “Precedence-Aware Automated Competitive Analysis of Real-Time Scheduling.”
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems.
IEEE, 2020. https://doi.org/10.1109/TCAD.2020.3012803.
ieee: A. Pavlogiannis, N. Schaumberger, U. Schmid, and K. Chatterjee, “Precedence-aware
automated competitive analysis of real-time scheduling,” IEEE Transactions
on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no.
11. IEEE, pp. 3981–3992, 2020.
ista: Pavlogiannis A, Schaumberger N, Schmid U, Chatterjee K. 2020. Precedence-aware
automated competitive analysis of real-time scheduling. IEEE Transactions on Computer-Aided
Design of Integrated Circuits and Systems. 39(11), 3981–3992.
mla: Pavlogiannis, Andreas, et al. “Precedence-Aware Automated Competitive Analysis
of Real-Time Scheduling.” IEEE Transactions on Computer-Aided Design of Integrated
Circuits and Systems, vol. 39, no. 11, IEEE, 2020, pp. 3981–92, doi:10.1109/TCAD.2020.3012803.
short: A. Pavlogiannis, N. Schaumberger, U. Schmid, K. Chatterjee, IEEE Transactions
on Computer-Aided Design of Integrated Circuits and Systems 39 (2020) 3981–3992.
date_created: 2020-11-22T23:01:24Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2023-08-22T13:27:05Z
day: '01'
department:
- _id: KrCh
doi: 10.1109/TCAD.2020.3012803
external_id:
isi:
- '000587712700069'
intvolume: ' 39'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 3981-3992
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: IEEE Transactions on Computer-Aided Design of Integrated Circuits and
Systems
publication_identifier:
eissn:
- '19374151'
issn:
- '02780070'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Precedence-aware automated competitive analysis of real-time scheduling
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 39
year: '2020'
...
---
_id: '8789'
abstract:
- lang: eng
text: Cooperation is a ubiquitous and beneficial behavioural trait despite being
prone to exploitation by free-riders. Hence, cooperative populations are prone
to invasions by selfish individuals. However, a population consisting of only
free-riders typically does not survive. Thus, cooperators and free-riders often
coexist in some proportion. An evolutionary version of a Snowdrift Game proved
its efficiency in analysing this phenomenon. However, what if the system has already
reached its stable state but was perturbed due to a change in environmental conditions?
Then, individuals may have to re-learn their effective strategies. To address
this, we consider behavioural mistakes in strategic choice execution, which we
refer to as incompetence. Parametrising the propensity to make such mistakes allows
for a mathematical description of learning. We compare strategies based on their
relative strategic advantage relying on both fitness and learning factors. When
strategies are learned at distinct rates, allowing learning according to a prescribed
order is optimal. Interestingly, the strategy with the lowest strategic advantage
should be learnt first if we are to optimise fitness over the learning path. Then,
the differences between strategies are balanced out in order to minimise the effect
of behavioural uncertainty.
acknowledgement: "This work was supported by the European Union’s Horizon 2020 research
and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411,
the Australian Research Council Discovery Grants DP160101236 and DP150100618, and
the European Research Council Consolidator Grant 863818 (FoRM-SMArt).\r\nAuthors
would like to thank Patrick McKinlay for his work on the preliminary results for
this paper."
article_number: '1945'
article_processing_charge: No
article_type: original
author:
- first_name: Maria
full_name: Kleshnina, Maria
id: 4E21749C-F248-11E8-B48F-1D18A9856A87
last_name: Kleshnina
- first_name: Sabrina
full_name: Streipert, Sabrina
last_name: Streipert
- first_name: Jerzy
full_name: Filar, Jerzy
last_name: Filar
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Kleshnina M, Streipert S, Filar J, Chatterjee K. Prioritised learning in snowdrift-type
games. Mathematics. 2020;8(11). doi:10.3390/math8111945
apa: Kleshnina, M., Streipert, S., Filar, J., & Chatterjee, K. (2020). Prioritised
learning in snowdrift-type games. Mathematics. MDPI. https://doi.org/10.3390/math8111945
chicago: Kleshnina, Maria, Sabrina Streipert, Jerzy Filar, and Krishnendu Chatterjee.
“Prioritised Learning in Snowdrift-Type Games.” Mathematics. MDPI, 2020.
https://doi.org/10.3390/math8111945.
ieee: M. Kleshnina, S. Streipert, J. Filar, and K. Chatterjee, “Prioritised learning
in snowdrift-type games,” Mathematics, vol. 8, no. 11. MDPI, 2020.
ista: Kleshnina M, Streipert S, Filar J, Chatterjee K. 2020. Prioritised learning
in snowdrift-type games. Mathematics. 8(11), 1945.
mla: Kleshnina, Maria, et al. “Prioritised Learning in Snowdrift-Type Games.” Mathematics,
vol. 8, no. 11, 1945, MDPI, 2020, doi:10.3390/math8111945.
short: M. Kleshnina, S. Streipert, J. Filar, K. Chatterjee, Mathematics 8 (2020).
date_created: 2020-11-22T23:01:24Z
date_published: 2020-11-04T00:00:00Z
date_updated: 2025-07-14T09:09:49Z
day: '04'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.3390/math8111945
ec_funded: 1
external_id:
isi:
- '000593962100001'
file:
- access_level: open_access
checksum: 61cfcc3b35760656ce7a9385a4ace5d2
content_type: application/pdf
creator: dernst
date_created: 2020-11-23T13:06:30Z
date_updated: 2020-11-23T13:06:30Z
file_id: '8797'
file_name: 2020_Mathematics_Kleshnina.pdf
file_size: 565191
relation: main_file
success: 1
file_date_updated: 2020-11-23T13:06:30Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Mathematics
publication_identifier:
eissn:
- '22277390'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Prioritised learning in snowdrift-type games
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: 8
year: '2020'
...
---
_id: '8790'
abstract:
- lang: eng
text: Reachability analysis aims at identifying states reachable by a system within
a given time horizon. This task is known to be computationally expensive for linear
hybrid systems. Reachability analysis works by iteratively applying continuous
and discrete post operators to compute states reachable according to continuous
and discrete dynamics, respectively. In this article, we enhance both of these
operators and make sure that most of the involved computations are performed in
low-dimensional state space. In particular, we improve the continuous-post operator
by performing computations in high-dimensional state space only for time intervals
relevant for the subsequent application of the discrete-post operator. Furthermore,
the new discrete-post operator performs low-dimensional computations by leveraging
the structure of the guard and assignment of a considered transition. We illustrate
the potential of our approach on a number of challenging benchmarks.
acknowledgement: 'This research was supported in part by the Austrian Science Fund
(FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), the
European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curie grant agreement No. 754411, and the Air Force Office of Scientific
Research under award number FA2386-17-1-4065. Any opinions, findings, and conclusions
or recommendations expressed in this material are those of the authors and do not
necessarily reflect the views of the United States Air Force. '
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Marcelo
full_name: Forets, Marcelo
last_name: Forets
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Kostiantyn
full_name: Potomkin, Kostiantyn
last_name: Potomkin
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
citation:
ama: Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis
of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided
Design of Integrated Circuits and Systems. 2020;39(11):4018-4029. doi:10.1109/TCAD.2020.3012859
apa: Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2020).
Reachability analysis of linear hybrid systems via block decomposition. IEEE
Transactions on Computer-Aided Design of Integrated Circuits and Systems.
IEEE. https://doi.org/10.1109/TCAD.2020.3012859
chicago: Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and
Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block
Decomposition.” IEEE Transactions on Computer-Aided Design of Integrated Circuits
and Systems. IEEE, 2020. https://doi.org/10.1109/TCAD.2020.3012859.
ieee: S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability
analysis of linear hybrid systems via block decomposition,” IEEE Transactions
on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no.
11. IEEE, pp. 4018–4029, 2020.
ista: Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability
analysis of linear hybrid systems via block decomposition. IEEE Transactions on
Computer-Aided Design of Integrated Circuits and Systems. 39(11), 4018–4029.
mla: Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via
Block Decomposition.” IEEE Transactions on Computer-Aided Design of Integrated
Circuits and Systems, vol. 39, no. 11, IEEE, 2020, pp. 4018–29, doi:10.1109/TCAD.2020.3012859.
short: S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, IEEE Transactions
on Computer-Aided Design of Integrated Circuits and Systems 39 (2020) 4018–4029.
date_created: 2020-11-22T23:01:25Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2023-08-22T13:27:33Z
day: '01'
department:
- _id: ToHe
doi: 10.1109/TCAD.2020.3012859
ec_funded: 1
external_id:
arxiv:
- '1905.02458'
isi:
- '000587712700072'
intvolume: ' 39'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1905.02458
month: '11'
oa: 1
oa_version: Preprint
page: 4018-4029
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: IEEE Transactions on Computer-Aided Design of Integrated Circuits and
Systems
publication_identifier:
eissn:
- '19374151'
issn:
- '02780070'
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '8287'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Reachability analysis of linear hybrid systems via block decomposition
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 39
year: '2020'
...
---
_id: '8809'
abstract:
- lang: eng
text: When divergent populations are connected by gene flow, the establishment of
complete reproductive isolation usually requires the joint action of multiple
barrier effects. One example where multiple barrier effects are coupled consists
of a single trait that is under divergent natural selection and also mediates
assortative mating. Such multiple-effect traits can strongly reduce gene flow.
However, there are few cases where patterns of assortative mating have been described
quantitatively and their impact on gene flow has been determined. Two ecotypes
of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore
habitats dominated by either crab predation or wave action. There is evidence
for divergent natural selection acting on size, and size-assortative mating has
previously been documented. Here, we analyze the mating pattern in L. saxatilis
with respect to size in intensively-sampled transects across boundaries between
the habitats. We show that the mating pattern is mostly conserved between ecotypes
and that it generates both assortment and directional sexual selection for small
male size. Using simulations, we show that the mating pattern can contribute to
reproductive isolation between ecotypes but the barrier to gene flow is likely
strengthened more by sexual selection than by assortment.
article_processing_charge: No
author:
- first_name: Samuel
full_name: Perini, Samuel
last_name: Perini
- first_name: Marina
full_name: Rafajlovic, Marina
last_name: Rafajlovic
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: 'Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative
mating, sexual selection and their consequences for gene flow in Littorina. 2020.
doi:10.5061/dryad.qrfj6q5cn'
apa: 'Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., & Butlin,
R. (2020). Data from: Assortative mating, sexual selection and their consequences
for gene flow in Littorina. Dryad. https://doi.org/10.5061/dryad.qrfj6q5cn'
chicago: 'Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson,
and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences
for Gene Flow in Littorina.” Dryad, 2020. https://doi.org/10.5061/dryad.qrfj6q5cn.'
ieee: 'S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data
from: Assortative mating, sexual selection and their consequences for gene flow
in Littorina.” Dryad, 2020.'
ista: 'Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from:
Assortative mating, sexual selection and their consequences for gene flow in Littorina,
Dryad, 10.5061/dryad.qrfj6q5cn.'
mla: 'Perini, Samuel, et al. Data from: Assortative Mating, Sexual Selection
and Their Consequences for Gene Flow in Littorina. Dryad, 2020, doi:10.5061/dryad.qrfj6q5cn.'
short: S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020).
date_created: 2020-11-25T11:07:25Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2023-08-22T07:13:37Z
day: '01'
department:
- _id: NiBa
doi: 10.5061/dryad.qrfj6q5cn
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.qrfj6q5cn
month: '07'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '7995'
relation: used_in_publication
status: public
status: public
title: 'Data from: Assortative mating, sexual selection and their consequences for
gene flow in Littorina'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '8813'
abstract:
- lang: eng
text: 'In mammals, chromatin marks at imprinted genes are asymmetrically inherited
to control parentally-biased gene expression. This control is thought predominantly
to involve parent-specific differentially methylated regions (DMR) in genomic
DNA. However, neither parent-of-origin-specific transcription nor DMRs have been
comprehensively mapped. We here address this by integrating transcriptomic and
epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis
identified 71 genes expressed with previously unknown parent-of-origin-specific
expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental
expression of nBiX genes disappeared soon after implantation. Micro-whole-genome
bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859
DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated
with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated
imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted
gene, and five novel clusters contained exclusively nBiX-genes. These data suggest
a complex program of stage-specific imprinting involving different tiers of regulation.'
article_processing_charge: No
author:
- first_name: Laura
full_name: Santini, Laura
last_name: Santini
- first_name: Florian
full_name: Halbritter, Florian
last_name: Halbritter
- first_name: Fabian
full_name: Titz-Teixeira, Fabian
last_name: Titz-Teixeira
- first_name: Toru
full_name: Suzuki, Toru
last_name: Suzuki
- first_name: Maki
full_name: Asami, Maki
last_name: Asami
- first_name: Julia
full_name: Ramesmayer, Julia
last_name: Ramesmayer
- first_name: Xiaoyan
full_name: Ma, Xiaoyan
last_name: Ma
- first_name: Andreas
full_name: Lackner, Andreas
last_name: Lackner
- first_name: Nick
full_name: Warr, Nick
last_name: Warr
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Ernest
full_name: Laue, Ernest
last_name: Laue
- first_name: Matthias
full_name: Farlik, Matthias
last_name: Farlik
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Andreas
full_name: Beyer, Andreas
last_name: Beyer
- first_name: Anthony C. F.
full_name: Perry, Anthony C. F.
last_name: Perry
- first_name: Martin
full_name: Leeb, Martin
last_name: Leeb
citation:
ama: Santini L, Halbritter F, Titz-Teixeira F, et al. Novel imprints in mouse blastocysts
are predominantly DNA methylation independent. bioRxiv. doi:10.1101/2020.11.03.366948
apa: Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ramesmayer,
J., … Leeb, M. (n.d.). Novel imprints in mouse blastocysts are predominantly DNA
methylation independent. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.03.366948
chicago: Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki,
Maki Asami, Julia Ramesmayer, Xiaoyan Ma, et al. “Novel Imprints in Mouse Blastocysts
Are Predominantly DNA Methylation Independent.” BioRxiv. Cold Spring Harbor
Laboratory, n.d. https://doi.org/10.1101/2020.11.03.366948.
ieee: L. Santini et al., “Novel imprints in mouse blastocysts are predominantly
DNA methylation independent,” bioRxiv. Cold Spring Harbor Laboratory.
ista: Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J,
Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer
A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA
methylation independent. bioRxiv, 10.1101/2020.11.03.366948.
mla: Santini, Laura, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly
DNA Methylation Independent.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.11.03.366948.
short: L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, J. Ramesmayer,
X. Ma, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C.
Bock, A. Beyer, A.C.F. Perry, M. Leeb, BioRxiv (n.d.).
date_created: 2020-11-26T07:17:19Z
date_published: 2020-11-05T00:00:00Z
date_updated: 2023-09-12T11:05:28Z
day: '05'
department:
- _id: SiHi
doi: 10.1101/2020.11.03.366948
external_id:
pmid:
- 'PPR234457 '
language:
- iso: eng
main_file_link:
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url: https://doi.org/10.1101/2020.11.03.366948
month: '11'
oa: 1
oa_version: Preprint
pmid: 1
publication: bioRxiv
publication_status: submitted
publisher: Cold Spring Harbor Laboratory
status: public
title: Novel imprints in mouse blastocysts are predominantly DNA methylation independent
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8822'
abstract:
- lang: eng
text: "Self-organization is a hallmark of plant development manifested e.g. by intricate
leaf vein patterns, flexible formation of vasculature during organogenesis or
its regeneration following wounding. Spontaneously arising channels transporting
the phytohormone auxin, created by coordinated polar localizations of PIN-FORMED
1 (PIN1) auxin exporter, provide positional cues for these as well as other plant
patterning processes. To find regulators acting downstream of auxin and the TIR1/AFB
auxin signaling pathway essential for PIN1 coordinated polarization during auxin
canalization, we performed microarray experiments. Besides the known components
of general PIN polarity maintenance, such as PID and PIP5K kinases, we identified
and characterized a new regulator of auxin canalization, the transcription factor
WRKY DNA-BINDING PROTEIN 23 (WRKY23).\r\nNext, we designed a subsequent microarray
experiment to further uncover other molecular players, downstream of auxin-TIR1/AFB-WRKY23
involved in the regulation of auxin-mediated PIN repolarization. We identified
a novel and crucial part of the molecular machinery underlying auxin canalization.
The auxin-regulated malectin-type receptor-like kinase CAMEL and the associated
leucine-rich repeat receptor-like kinase CANAR target and directly phosphorylate
PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular
trafficking and auxin-mediated repolarization leading to defects in auxin transport,
ultimately to leaf venation and vasculature regeneration defects. Our results
describe the CAMEL-CANAR receptor complex, which is required for auxin feed-back
on its own transport and thus for coordinated tissue polarization during auxin
canalization."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
citation:
ama: Hajny J. Identification and characterization of the molecular machinery of
auxin-dependent canalization during vasculature formation and regeneration. 2020.
doi:10.15479/AT:ISTA:8822
apa: Hajny, J. (2020). Identification and characterization of the molecular machinery
of auxin-dependent canalization during vasculature formation and regeneration.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8822
chicago: Hajny, Jakub. “Identification and Characterization of the Molecular Machinery
of Auxin-Dependent Canalization during Vasculature Formation and Regeneration.”
Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8822.
ieee: J. Hajny, “Identification and characterization of the molecular machinery
of auxin-dependent canalization during vasculature formation and regeneration,”
Institute of Science and Technology Austria, 2020.
ista: Hajny J. 2020. Identification and characterization of the molecular machinery
of auxin-dependent canalization during vasculature formation and regeneration.
Institute of Science and Technology Austria.
mla: Hajny, Jakub. Identification and Characterization of the Molecular Machinery
of Auxin-Dependent Canalization during Vasculature Formation and Regeneration.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8822.
short: J. Hajny, Identification and Characterization of the Molecular Machinery
of Auxin-Dependent Canalization during Vasculature Formation and Regeneration,
Institute of Science and Technology Austria, 2020.
date_created: 2020-12-01T12:38:18Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2025-05-07T11:12:31Z
day: '01'
ddc:
- '580'
degree_awarded: PhD
department:
- _id: JiFr
doi: 10.15479/AT:ISTA:8822
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language:
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month: '12'
oa: 1
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page: '249'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
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relation: part_of_dissertation
status: public
- id: '6260'
relation: part_of_dissertation
status: public
- id: '7500'
relation: part_of_dissertation
status: public
- id: '449'
relation: part_of_dissertation
status: public
- id: '191'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Identification and characterization of the molecular machinery of auxin-dependent
canalization during vasculature formation and regeneration
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8831'
abstract:
- lang: eng
text: Holes in planar Ge have high mobilities, strong spin-orbit interaction and
electrically tunable g-factors, and are therefore emerging as a promising candidate
for hybrid superconductorsemiconductor devices. This is further motivated by the
observation of supercurrent transport in planar Ge Josephson Field effect transistors
(JoFETs). A key challenge towards hybrid germanium quantum technology is the design
of high quality interfaces and superconducting contacts that are robust against
magnetic fields. By combining the assets of Al, which has a long superconducting
coherence, and Nb, which has a significant superconducting gap, we form low-disordered
JoFETs with large ICRN products that are capable of withstanding high magnetic
fields. We furthermore demonstrate the ability of phase-biasing individual JoFETs
opening up an avenue to explore topological superconductivity in planar Ge. The
persistence of superconductivity in the reported hybrid devices beyond 1.8 T paves
the way towards integrating spin qubits and proximity-induced superconductivity
on the same chip.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: "This research and related results were made possible with the support
of the NOMIS Foundation. This research was supported by the Scientific Service Units
of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication
facility, the European Union’s Horizon 2020 research and innovation program under
the Marie Sklodowska-Curie grant agreement #844511 and the Grant Agreement #862046.
ICN2 acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported
by the Severo Ochoa\r\nprogram from Spanish MINECO (Grant No. SEV2017-0706) and
is funded by the CERCA Programme / Generalitat de Catalunya. Part of the present
work has been performed in the framework of Universitat Aut`onoma de Barcelona Materials
Science PhD program. The HAADF-STEM microscopy was conducted in the Laboratorio
de Microscopias Avanzadas at Instituto de Nanociencia de Aragon-Universidad de Zaragoza.
Authors acknowledge the LMA-INA for offering access to their instruments and expertise.
We acknowledge support from CSIC Research Platform on Quantum Technologies PTI-001.
This project has received funding from\r\nthe European Union’s Horizon 2020 research
and innovation programme under grant agreement No 823717 – ESTEEM3. M.B. acknowledges
support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020
FI 00103. GS and MV acknowledge support through a projectruimte grant associated
with the Netherlands Organization of Scientific Research (NWO)."
article_number: '2012.00322'
article_processing_charge: No
arxiv: 1
author:
- first_name: Kushagra
full_name: Aggarwal, Kushagra
id: b22ab905-3539-11eb-84c3-fc159dcd79cb
last_name: Aggarwal
orcid: 0000-0001-9985-9293
- first_name: Andrea C
full_name: Hofmann, Andrea C
id: 340F461A-F248-11E8-B48F-1D18A9856A87
last_name: Hofmann
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
- first_name: Ivan
full_name: Prieto Gonzalez, Ivan
id: 2A307FE2-F248-11E8-B48F-1D18A9856A87
last_name: Prieto Gonzalez
orcid: 0000-0002-7370-5357
- first_name: Amir
full_name: Sammak, Amir
last_name: Sammak
- first_name: Marc
full_name: Botifoll, Marc
last_name: Botifoll
- first_name: Sara
full_name: Marti-Sanchez, Sara
last_name: Marti-Sanchez
- first_name: Menno
full_name: Veldhorst, Menno
last_name: Veldhorst
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Giordano
full_name: Scappucci, Giordano
last_name: Scappucci
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Aggarwal K, Hofmann AC, Jirovec D, et al. Enhancement of proximity induced
superconductivity in planar Germanium. arXiv.
apa: Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A.,
Botifoll, M., … Katsaros, G. (n.d.). Enhancement of proximity induced superconductivity
in planar Germanium. arXiv.
chicago: Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez,
Amir Sammak, Marc Botifoll, Sara Marti-Sanchez, et al. “Enhancement of Proximity
Induced Superconductivity in Planar Germanium.” ArXiv, n.d.
ieee: K. Aggarwal et al., “Enhancement of proximity induced superconductivity
in planar Germanium,” arXiv. .
ista: Aggarwal K, Hofmann AC, Jirovec D, Prieto Gonzalez I, Sammak A, Botifoll M,
Marti-Sanchez S, Veldhorst M, Arbiol J, Scappucci G, Katsaros G. Enhancement of
proximity induced superconductivity in planar Germanium. arXiv, 2012.00322.
mla: Aggarwal, Kushagra, et al. “Enhancement of Proximity Induced Superconductivity
in Planar Germanium.” ArXiv, 2012.00322.
short: K. Aggarwal, A.C. Hofmann, D. Jirovec, I. Prieto Gonzalez, A. Sammak, M.
Botifoll, S. Marti-Sanchez, M. Veldhorst, J. Arbiol, G. Scappucci, G. Katsaros,
ArXiv (n.d.).
date_created: 2020-12-02T10:42:53Z
date_published: 2020-12-02T00:00:00Z
date_updated: 2024-03-25T23:30:14Z
day: '02'
ddc:
- '530'
department:
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ec_funded: 1
external_id:
arxiv:
- '2012.00322'
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file_date_updated: 2020-12-02T10:42:31Z
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language:
- iso: eng
month: '12'
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oa_version: Submitted Version
project:
- _id: 262116AA-B435-11E9-9278-68D0E5697425
name: Hybrid Semiconductor - Superconductor Quantum Devices
- _id: 26A151DA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '844511'
name: Majorana bound states in Ge/SiGe heterostructures
- _id: 237E5020-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862046'
name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS
publication: arXiv
publication_status: submitted
related_material:
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- id: '10559'
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- id: '8834'
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- id: '10058'
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status: public
status: public
title: Enhancement of proximity induced superconductivity in planar Germanium
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8834'
abstract:
- lang: eng
text: "This data collection contains the transport data for figures presented in
the supplementary material of \"Enhancement of Proximity Induced Superconductivity
in Planar Germanium\" by K. Aggarwal, et. al. \r\nThe measurements were done using
Labber Software and the data is stored in the hdf5 file format. The files can
be opened using either the Labber Log Browser (https://labber.org/overview/) or
Labber Python API (http://labber.org/online-doc/api/LogFile.html).\r\n"
article_processing_charge: No
author:
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full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium.
2020. doi:10.15479/AT:ISTA:8834
apa: Katsaros, G. (2020). Enhancement of proximity induced superconductivity in
planar Germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8834
chicago: Katsaros, Georgios. “Enhancement of Proximity Induced Superconductivity
in Planar Germanium.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8834.
ieee: G. Katsaros, “Enhancement of proximity induced superconductivity in planar
Germanium.” Institute of Science and Technology Austria, 2020.
ista: Katsaros G. 2020. Enhancement of proximity induced superconductivity in planar
Germanium, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8834.
mla: Katsaros, Georgios. Enhancement of Proximity Induced Superconductivity in
Planar Germanium. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8834.
short: G. Katsaros, (2020).
contributor:
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last_name: Aggarwal
- contributor_type: project_member
first_name: Andrea C
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last_name: Hofmann
- contributor_type: project_member
first_name: Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
- contributor_type: project_member
first_name: Ivan
id: 2A307FE2-F248-11E8-B48F-1D18A9856A87
last_name: Prieto Gonzalez
- contributor_type: project_member
first_name: Amir
last_name: Sammak
- contributor_type: project_member
first_name: Marc
last_name: Botifoll
- contributor_type: project_member
first_name: Sara
last_name: Marti-Sanchez
- contributor_type: project_member
first_name: Menno
last_name: Veldhorst
- contributor_type: project_member
first_name: Jordi
last_name: Arbiol
- contributor_type: project_member
first_name: Giordano
last_name: Scappucci
- contributor_type: project_leader
first_name: Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
date_created: 2020-12-02T10:49:30Z
date_published: 2020-12-02T00:00:00Z
date_updated: 2024-02-21T12:41:26Z
day: '02'
ddc:
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relation: used_in_publication
status: public
status: public
title: Enhancement of proximity induced superconductivity in planar Germanium
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8914'
abstract:
- lang: eng
text: Amyotrophic lateral sclerosis (ALS) leads to a loss of specific motor neuron
populations in the spinal cord and cortex. Emerging evidence suggests that interneurons
may also be affected, but a detailed characterization of interneuron loss and
its potential impacts on motor neuron loss and disease progression is lacking.
To examine this issue, the fate of V1 inhibitory neurons during ALS was assessed
in the ventral spinal cord using the SODG93A mouse model. The V1 population makes
up ∼30% of all ventral inhibitory neurons, ∼50% of direct inhibitory synaptic
contacts onto motor neuron cell bodies, and is thought to play a key role in modulating
motor output, in part through recurrent and reciprocal inhibitory circuits. We
find that approximately half of V1 inhibitory neurons are lost in SODG93A mice
at late disease stages, but that this loss is delayed relative to the loss of
motor neurons and V2a excitatory neurons. We further identify V1 subpopulations
based on transcription factor expression that are differentially susceptible to
degeneration in SODG93A mice. At an early disease stage, we show that V1 synaptic
contacts with motor neuron cell bodies increase, suggesting an upregulation of
inhibition before V1 neurons are lost in substantial numbers. These data support
a model in which progressive changes in V1 synaptic contacts early in disease,
and in select V1 subpopulations at later stages, represent a compensatory upregulation
and then deleterious breakdown of specific interneuron circuits within the spinal
cord.
acknowledgement: This work was made possible by the generous support of Project ALS.
Imaging and related analyses were facilitated by The Waitt Advanced Biophotonics
Center Core at the Salk Institute, supported by grants from NIH-NCI CCSG (P30 014195)
and NINDS Neuroscience Center (NS072031). The authors would like to additionally
thank Drs. Jane Dodd, Robert Brownstone, and Laskaro Zagoraiou for helpful comments
on the manuscript. This manuscript is dedicated to Tom Jessell, an inspirational
scientist, friend and mentor.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Alina
full_name: Salamatina, Alina
last_name: Salamatina
- first_name: Jerry H
full_name: Yang, Jerry H
last_name: Yang
- first_name: Susan
full_name: Brenner-Morton, Susan
last_name: Brenner-Morton
- first_name: 'Jay B '
full_name: 'Bikoff, Jay B '
last_name: Bikoff
- first_name: Linjing
full_name: Fang, Linjing
last_name: Fang
- first_name: Christopher R
full_name: Kintner, Christopher R
last_name: Kintner
- first_name: Thomas M
full_name: Jessell, Thomas M
last_name: Jessell
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
citation:
ama: Salamatina A, Yang JH, Brenner-Morton S, et al. Differential loss of spinal
interneurons in a mouse model of ALS. Neuroscience. 2020;450:81-95. doi:10.1016/j.neuroscience.2020.08.011
apa: Salamatina, A., Yang, J. H., Brenner-Morton, S., Bikoff, J. B., Fang, L., Kintner,
C. R., … Sweeney, L. B. (2020). Differential loss of spinal interneurons in a
mouse model of ALS. Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2020.08.011
chicago: Salamatina, Alina, Jerry H Yang, Susan Brenner-Morton, Jay B Bikoff, Linjing
Fang, Christopher R Kintner, Thomas M Jessell, and Lora B. Sweeney. “Differential
Loss of Spinal Interneurons in a Mouse Model of ALS.” Neuroscience. Elsevier,
2020. https://doi.org/10.1016/j.neuroscience.2020.08.011.
ieee: A. Salamatina et al., “Differential loss of spinal interneurons in
a mouse model of ALS,” Neuroscience, vol. 450. Elsevier, pp. 81–95, 2020.
ista: Salamatina A, Yang JH, Brenner-Morton S, Bikoff JB, Fang L, Kintner CR, Jessell
TM, Sweeney LB. 2020. Differential loss of spinal interneurons in a mouse model
of ALS. Neuroscience. 450, 81–95.
mla: Salamatina, Alina, et al. “Differential Loss of Spinal Interneurons in a Mouse
Model of ALS.” Neuroscience, vol. 450, Elsevier, 2020, pp. 81–95, doi:10.1016/j.neuroscience.2020.08.011.
short: A. Salamatina, J.H. Yang, S. Brenner-Morton, J.B. Bikoff, L. Fang, C.R. Kintner,
T.M. Jessell, L.B. Sweeney, Neuroscience 450 (2020) 81–95.
date_created: 2020-12-03T11:47:31Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2024-01-31T10:15:34Z
day: '01'
ddc:
- '570'
department:
- _id: LoSw
doi: 10.1016/j.neuroscience.2020.08.011
external_id:
isi:
- '000595588700008'
pmid:
- '32858144'
file:
- access_level: open_access
checksum: da7413c819e079720669c82451b49294
content_type: application/pdf
creator: dernst
date_created: 2020-12-03T11:45:26Z
date_updated: 2020-12-03T11:45:26Z
file_id: '8915'
file_name: 2020_Neuroscience_Salamatina.pdf
file_size: 4071247
relation: main_file
success: 1
file_date_updated: 2020-12-03T11:45:26Z
has_accepted_license: '1'
intvolume: ' 450'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 81-95
pmid: 1
publication: Neuroscience
publication_identifier:
issn:
- 0306-4522
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Differential loss of spinal interneurons in a mouse model of ALS
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 450
year: '2020'
...
---
_id: '8924'
abstract:
- lang: eng
text: 'Maintaining fertility in a fluctuating environment is key to the reproductive
success of flowering plants. Meiosis and pollen formation are particularly sensitive
to changes in growing conditions, especially temperature. We have previously identified
cyclin-dependent kinase G1 (CDKG1) as a master regulator of temperature-dependent
meiosis and this may involve the regulation of alternative splicing (AS), including
of its own transcript. CDKG1 mRNA can undergo several AS events, potentially producing
two protein variants: CDKG1L and CDKG1S, differing in their N-terminal domain
which may be involved in co-factor interaction. In leaves, both isoforms have
distinct temperature-dependent functions on target mRNA processing, but their
role in pollen development is unknown. In the present study, we characterize the
role of CDKG1L and CDKG1S in maintaining Arabidopsis fertility. We show that the
long (L) form is necessary and sufficient to rescue the fertility defects of the
cdkg1-1 mutant, while the short (S) form is unable to rescue fertility. On the
other hand, an extra copy of CDKG1L reduces fertility. In addition, mutation of
the ATP binding pocket of the kinase indicates that kinase activity is necessary
for the function of CDKG1. Kinase mutants of CDKG1L and CDKG1S correctly localize
to the cell nucleus and nucleus and cytoplasm, respectively, but are unable to
rescue either the fertility or the splicing defects of the cdkg1-1 mutant. Furthermore,
we show that there is partial functional overlap between CDKG1 and its paralog
CDKG2 that could in part be explained by overlapping gene expression.'
acknowledgement: CN, DD, NF-F, and JD were funded by the BBSRC (grant number BB/M009459/1).
NK and AM were funded through the ERASMUS+Program. NC was funded by the VIPS Program
of the Austrian Federal Ministry of Science and Research and the City of Vienna.
article_number: '586870'
article_processing_charge: No
article_type: original
author:
- first_name: Candida
full_name: Nibau, Candida
last_name: Nibau
- first_name: Despoina
full_name: Dadarou, Despoina
last_name: Dadarou
- first_name: Nestoras
full_name: Kargios, Nestoras
last_name: Kargios
- first_name: Areti
full_name: Mallioura, Areti
last_name: Mallioura
- first_name: Narcis
full_name: Fernandez-Fuentes, Narcis
last_name: Fernandez-Fuentes
- first_name: Nicola
full_name: Cavallari, Nicola
id: 457160E6-F248-11E8-B48F-1D18A9856A87
last_name: Cavallari
- first_name: John H.
full_name: Doonan, John H.
last_name: Doonan
citation:
ama: Nibau C, Dadarou D, Kargios N, et al. A functional kinase is necessary for
cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature
in Arabidopsis. Frontiers in Plant Science. 2020;11. doi:10.3389/fpls.2020.586870
apa: Nibau, C., Dadarou, D., Kargios, N., Mallioura, A., Fernandez-Fuentes, N.,
Cavallari, N., & Doonan, J. H. (2020). A functional kinase is necessary for
cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature
in Arabidopsis. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2020.586870
chicago: Nibau, Candida, Despoina Dadarou, Nestoras Kargios, Areti Mallioura, Narcis
Fernandez-Fuentes, Nicola Cavallari, and John H. Doonan. “A Functional Kinase
Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High
Ambient Temperature in Arabidopsis.” Frontiers in Plant Science. Frontiers,
2020. https://doi.org/10.3389/fpls.2020.586870.
ieee: C. Nibau et al., “A functional kinase is necessary for cyclin-dependent
kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis,”
Frontiers in Plant Science, vol. 11. Frontiers, 2020.
ista: Nibau C, Dadarou D, Kargios N, Mallioura A, Fernandez-Fuentes N, Cavallari
N, Doonan JH. 2020. A functional kinase is necessary for cyclin-dependent kinase
G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. Frontiers
in Plant Science. 11, 586870.
mla: Nibau, Candida, et al. “A Functional Kinase Is Necessary for Cyclin-Dependent
Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.”
Frontiers in Plant Science, vol. 11, 586870, Frontiers, 2020, doi:10.3389/fpls.2020.586870.
short: C. Nibau, D. Dadarou, N. Kargios, A. Mallioura, N. Fernandez-Fuentes, N.
Cavallari, J.H. Doonan, Frontiers in Plant Science 11 (2020).
date_created: 2020-12-06T23:01:14Z
date_published: 2020-11-10T00:00:00Z
date_updated: 2023-08-24T10:50:00Z
day: '10'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.3389/fpls.2020.586870
external_id:
isi:
- '000591637000001'
file:
- access_level: open_access
checksum: 1c0ee6ce9950aa665d6a5cc64aa6b752
content_type: application/pdf
creator: dernst
date_created: 2020-12-09T09:14:19Z
date_updated: 2020-12-09T09:14:19Z
file_id: '8929'
file_name: 2020_Frontiers_Nibau.pdf
file_size: 1833244
relation: main_file
success: 1
file_date_updated: 2020-12-09T09:14:19Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Frontiers in Plant Science
publication_identifier:
eissn:
- 1664-462X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to
maintain fertility at high ambient temperature in Arabidopsis
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: 11
year: '2020'
...
---
_id: '8926'
abstract:
- lang: eng
text: 'Bimetallic nanoparticles with tailored size and specific composition have
shown promise as stable and selective catalysts for electrochemical reduction
of CO2 (CO2R) in batch systems. Yet, limited effort was devoted to understand
the effect of ligand coverage and postsynthesis treatments on CO2 reduction, especially
under industrially applicable conditions, such as at high currents (>100 mA/cm2)
using gas diffusion electrodes (GDE) and flow reactors. In this work, Cu–Ag core–shell
nanoparticles (11 ± 2 nm) were prepared with three different surface modes: (i)
capped with oleylamine, (ii) capped with monoisopropylamine, and (iii) surfactant-free
with a reducing borohydride agent; Cu–Ag (OAm), Cu–Ag (MIPA), and Cu–Ag (NaBH4),
respectively. The ligand exchange and removal was evidenced by infrared spectroscopy
(ATR-FTIR) analysis, whereas high-resolution scanning transmission electron microscopy
(HAADF-STEM) showed their effect on the interparticle distance and nanoparticle
rearrangement. Later on, we developed a process-on-substrate method to track these
effects on CO2R. Cu–Ag (OAm) gave a lower on-set potential for hydrocarbon production,
whereas Cu–Ag (MIPA) and Cu–Ag (NaBH4) promoted syngas production. The electrochemical
impedance and surface area analysis on the well-controlled electrodes showed gradual
increases in the electrical conductivity and active surface area after each surface
treatment. We found that the increasing amount of the triple phase boundaries
(the meeting point for the electron–electrolyte–CO2 reactant) affect the required
electrode potential and eventually the C+2e̅/C2e̅ product ratio. This study highlights
the importance of the electron transfer to those active sites affected by the
capping agents—particularly on larger substrates that are crucial for their industrial
application.'
acknowledgement: The authors also acknowledge financial support from the University
Research Fund (BOF-GOA-PS ID No. 33928). S.L. has received funding from the European
Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie
Grant Agreement No. 665385.
article_processing_charge: No
article_type: original
author:
- first_name: Erdem
full_name: Irtem, Erdem
last_name: Irtem
- first_name: Daniel
full_name: Arenas Esteban, Daniel
last_name: Arenas Esteban
- first_name: Miguel
full_name: Duarte, Miguel
last_name: Duarte
- first_name: Daniel
full_name: Choukroun, Daniel
last_name: Choukroun
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Sara
full_name: Bals, Sara
last_name: Bals
- first_name: Tom
full_name: Breugelmans, Tom
last_name: Breugelmans
citation:
ama: Irtem E, Arenas Esteban D, Duarte M, et al. Ligand-mode directed selectivity
in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. ACS
Catalysis. 2020;10(22):13468-13478. doi:10.1021/acscatal.0c03210
apa: Irtem, E., Arenas Esteban, D., Duarte, M., Choukroun, D., Lee, S., Ibáñez,
M., … Breugelmans, T. (2020). Ligand-mode directed selectivity in Cu-Ag core-shell
based gas diffusion electrodes for CO2 electroreduction. ACS Catalysis.
American Chemical Society. https://doi.org/10.1021/acscatal.0c03210
chicago: Irtem, Erdem, Daniel Arenas Esteban, Miguel Duarte, Daniel Choukroun, Seungho
Lee, Maria Ibáñez, Sara Bals, and Tom Breugelmans. “Ligand-Mode Directed Selectivity
in Cu-Ag Core-Shell Based Gas Diffusion Electrodes for CO2 Electroreduction.”
ACS Catalysis. American Chemical Society, 2020. https://doi.org/10.1021/acscatal.0c03210.
ieee: E. Irtem et al., “Ligand-mode directed selectivity in Cu-Ag core-shell
based gas diffusion electrodes for CO2 electroreduction,” ACS Catalysis,
vol. 10, no. 22. American Chemical Society, pp. 13468–13478, 2020.
ista: Irtem E, Arenas Esteban D, Duarte M, Choukroun D, Lee S, Ibáñez M, Bals S,
Breugelmans T. 2020. Ligand-mode directed selectivity in Cu-Ag core-shell based
gas diffusion electrodes for CO2 electroreduction. ACS Catalysis. 10(22), 13468–13478.
mla: Irtem, Erdem, et al. “Ligand-Mode Directed Selectivity in Cu-Ag Core-Shell
Based Gas Diffusion Electrodes for CO2 Electroreduction.” ACS Catalysis,
vol. 10, no. 22, American Chemical Society, 2020, pp. 13468–78, doi:10.1021/acscatal.0c03210.
short: E. Irtem, D. Arenas Esteban, M. Duarte, D. Choukroun, S. Lee, M. Ibáñez,
S. Bals, T. Breugelmans, ACS Catalysis 10 (2020) 13468–13478.
date_created: 2020-12-06T23:01:15Z
date_published: 2020-11-20T00:00:00Z
date_updated: 2023-08-24T10:52:32Z
day: '20'
department:
- _id: MaIb
doi: 10.1021/acscatal.0c03210
ec_funded: 1
external_id:
isi:
- '000592978900031'
intvolume: ' 10'
isi: 1
issue: '22'
language:
- iso: eng
month: '11'
oa_version: None
page: 13468-13478
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: ACS Catalysis
publication_identifier:
eissn:
- '21555435'
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes
for CO2 electroreduction
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2020'
...
---
_id: '8930'
abstract:
- lang: eng
text: Phenomenological relations such as Ohm’s or Fourier’s law have a venerable
history in physics but are still scarce in biology. This situation restrains predictive
theory. Here, we build on bacterial “growth laws,” which capture physiological
feedback between translation and cell growth, to construct a minimal biophysical
model for the combined action of ribosome-targeting antibiotics. Our model predicts
drug interactions like antagonism or synergy solely from responses to individual
drugs. We provide analytical results for limiting cases, which agree well with
numerical results. We systematically refine the model by including direct physical
interactions of different antibiotics on the ribosome. In a limiting case, our
model provides a mechanistic underpinning for recent predictions of higher-order
interactions that were derived using entropy maximization. We further refine the
model to include the effects of antibiotics that mimic starvation and the presence
of resistance genes. We describe the impact of a starvation-mimicking antibiotic
on drug interactions analytically and verify it experimentally. Our extended model
suggests a change in the type of drug interaction that depends on the strength
of resistance, which challenges established rescaling paradigms. We experimentally
show that the presence of unregulated resistance genes can lead to altered drug
interaction, which agrees with the prediction of the model. While minimal, the
model is readily adaptable and opens the door to predicting interactions of second
and higher-order in a broad range of biological systems.
article_processing_charge: No
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
citation:
ama: Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical
model of combined antibiotic action.” 2020. doi:10.15479/AT:ISTA:8930
apa: Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal
biophysical model of combined antibiotic action.” Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:8930
chicago: Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal
Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology
Austria, 2020. https://doi.org/10.15479/AT:ISTA:8930.
ieee: B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical
model of combined antibiotic action.’” Institute of Science and Technology Austria,
2020.
ista: Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal
biophysical model of combined antibiotic action’, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:8930.
mla: Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Minimal Biophysical
Model of Combined Antibiotic Action.” Institute of Science and Technology
Austria, 2020, doi:10.15479/AT:ISTA:8930.
short: B. Kavcic, (2020).
contributor:
- contributor_type: supervisor
first_name: Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- contributor_type: supervisor
first_name: Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
date_created: 2020-12-09T15:04:02Z
date_published: 2020-12-10T00:00:00Z
date_updated: 2024-02-21T12:41:42Z
day: '10'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.15479/AT:ISTA:8930
file:
- access_level: open_access
checksum: 60a818edeffaa7da1ebf5f8fbea9ba18
content_type: application/zip
creator: bkavcic
date_created: 2020-12-09T15:00:19Z
date_updated: 2020-12-09T15:00:19Z
file_id: '8932'
file_name: PLoSCompBiol2020_datarep.zip
file_size: 315494370
relation: main_file
success: 1
file_date_updated: 2020-12-09T15:00:19Z
has_accepted_license: '1'
keyword:
- Escherichia coli
- antibiotic combinations
- translation
- growth laws
- drug interactions
- bacterial physiology
- translation inhibitors
month: '12'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8997'
relation: used_in_publication
status: public
status: public
title: Analysis scripts and research data for the paper "Minimal biophysical model
of combined antibiotic action"
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: '2020'
...
---
_id: '8943'
abstract:
- lang: eng
text: The widely used non-steroidal anti-inflammatory drugs (NSAIDs) are derivatives
of the phytohormone salicylic acid (SA). SA is well known to regulate plant immunity
and development, whereas there have been few reports focusing on the effects of
NSAIDs in plants. Our studies here reveal that NSAIDs exhibit largely overlapping
physiological activities to SA in the model plant Arabidopsis. NSAID treatments
lead to shorter and agravitropic primary roots and inhibited lateral root organogenesis.
Notably, in addition to the SA-like action, which in roots involves binding to
the protein phosphatase 2A (PP2A), NSAIDs also exhibit PP2A-independent effects.
Cell biological and biochemical analyses reveal that many NSAIDs bind directly
to and inhibit the chaperone activity of TWISTED DWARF1, thereby regulating actin
cytoskeleton dynamics and subsequent endosomal trafficking. Our findings uncover
an unexpected bioactivity of human pharmaceuticals in plants and provide insights
into the molecular mechanism underlying the cellular action of this class of anti-inflammatory
compounds.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: "We thank Drs. Sebastian Bednarek (University of Wisconsin-Madison),
Niko Geldner (University of Lausanne), and Karin Schumacher (Heidelberg University)
for kindly sharing published Arabidopsis lines; Dr. Satoshi Naramoto for the pPIN2::PIN2-GFP;
pVHA-a1::VHA-a1-mRFP reporter; the staff at the Life Science Facility and Bioimaging
Facility, Monika Hrtyan, and Dorota Jaworska at IST Austria for technical support;
and Drs. Su Tang (Texas A&M University),\r\nMelinda Abas (BOKU), Eva Benkova´ (IST
Austria), Christian Luschnig (BOKU), Bartel Vanholme (Gent University), and the
Friml group for valuable discussions. The research leading to these findings was
funded by the European Union’s Horizon 2020 program (ERC grant agreement no. 742985,
to J.F.), the People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme (FP7/2007-2013) under REA grant agreement no.\r\n291734, the
Swiss National Funds (31003A_165877, to M.G.), the Ministry of Education, Youth,
and Sports of the Czech Republic (project no. CZ.02.1.01/0.0/0.0/16_019/0000738,
EU Operational Programme ‘‘Research, development and education and Centre for Plant
Experimental Biology’’), and the EU Operational Programme Prague - Competitiveness
(project no. CZ.2.16/3.1.00/21519). S.T. was funded by a European Molecular Biology
Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). X.Z. was
partly supported by a PhD scholarship from the China Scholarship Council."
article_number: '108463'
article_processing_charge: Yes
article_type: original
author:
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Martin
full_name: Di Donato, Martin
last_name: Di Donato
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Xixi
full_name: Zhang, Xixi
id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A
last_name: Zhang
orcid: 0000-0001-7048-4627
- first_name: Petr
full_name: Klíma, Petr
last_name: Klíma
- first_name: Jie
full_name: Liu, Jie
last_name: Liu
- first_name: Aurélien
full_name: Bailly, Aurélien
last_name: Bailly
- first_name: Noel
full_name: Ferro, Noel
last_name: Ferro
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Tan S, Di Donato M, Glanc M, et al. Non-steroidal anti-inflammatory drugs target
TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development.
Cell Reports. 2020;33(9). doi:10.1016/j.celrep.2020.108463
apa: Tan, S., Di Donato, M., Glanc, M., Zhang, X., Klíma, P., Liu, J., … Friml,
J. (2020). Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated
actin dynamics and auxin transport-mediated plant development. Cell Reports.
Elsevier. https://doi.org/10.1016/j.celrep.2020.108463
chicago: Tan, Shutang, Martin Di Donato, Matous Glanc, Xixi Zhang, Petr Klíma, Jie
Liu, Aurélien Bailly, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED
DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.”
Cell Reports. Elsevier, 2020. https://doi.org/10.1016/j.celrep.2020.108463.
ieee: S. Tan et al., “Non-steroidal anti-inflammatory drugs target TWISTED
DWARF1-regulated actin dynamics and auxin transport-mediated plant development,”
Cell Reports, vol. 33, no. 9. Elsevier, 2020.
ista: Tan S, Di Donato M, Glanc M, Zhang X, Klíma P, Liu J, Bailly A, Ferro N, Petrášek
J, Geisler M, Friml J. 2020. Non-steroidal anti-inflammatory drugs target TWISTED
DWARF1-regulated actin dynamics and auxin transport-mediated plant development.
Cell Reports. 33(9), 108463.
mla: Tan, Shutang, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED
DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.”
Cell Reports, vol. 33, no. 9, 108463, Elsevier, 2020, doi:10.1016/j.celrep.2020.108463.
short: S. Tan, M. Di Donato, M. Glanc, X. Zhang, P. Klíma, J. Liu, A. Bailly, N.
Ferro, J. Petrášek, M. Geisler, J. Friml, Cell Reports 33 (2020).
date_created: 2020-12-13T23:01:21Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2023-11-16T13:03:31Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.celrep.2020.108463
ec_funded: 1
external_id:
isi:
- '000595658100018'
pmid:
- '33264621'
file:
- access_level: open_access
checksum: ed18cba0fb48ed2e789381a54cc21904
content_type: application/pdf
creator: dernst
date_created: 2020-12-14T07:33:39Z
date_updated: 2020-12-14T07:33:39Z
file_id: '8948'
file_name: 2020_CellReports_Tan.pdf
file_size: 8056434
relation: main_file
success: 1
file_date_updated: 2020-12-14T07:33:39Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '9'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 256FEF10-B435-11E9-9278-68D0E5697425
grant_number: 723-2015
name: Long Term Fellowship
publication: Cell Reports
publication_identifier:
eissn:
- '22111247'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/plants-on-aspirin/
scopus_import: '1'
status: public
title: Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin
dynamics and auxin transport-mediated plant development
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: 33
year: '2020'
...
---
_id: '8944'
abstract:
- lang: eng
text: "Superconductor insulator transition in transverse magnetic field is studied
in the highly disordered MoC film with the product of the Fermi momentum and the
mean free path kF*l close to unity. Surprisingly, the Zeeman paramagnetic effects
dominate over orbital coupling on both sides of the transition. In superconducting
state it is evidenced by a high upper critical magnetic field \U0001D435\U0001D4502,
by its square root dependence on temperature, as well as by the Zeeman splitting
of the quasiparticle density of states (DOS) measured by scanning tunneling microscopy.
At \U0001D435\U0001D4502 a logarithmic anomaly in DOS is observed. This anomaly
is further enhanced in increasing magnetic field, which is explained by the Zeeman
splitting of the Altshuler-Aronov DOS driving\r\nthe system into a more insulating
or resistive state. Spin dependent Altshuler-Aronov correction is also needed
to explain the transport behavior above \U0001D435\U0001D4502."
acknowledgement: 'We gratefully acknowledge helpful conversations with B.L. Altshuler
and R. Hlubina. The work was supported by the projects APVV-18-0358, VEGA 2/0058/20,
VEGA 1/0743/19 the European Microkelvin Platform, the COST action CA16218 (Nanocohybri)
and by U.S. Steel Košice. '
article_number: '180508'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
- first_name: M.
full_name: Kopčík, M.
last_name: Kopčík
- first_name: P.
full_name: Szabó, P.
last_name: Szabó
- first_name: T.
full_name: Samuely, T.
last_name: Samuely
- first_name: J.
full_name: Kačmarčík, J.
last_name: Kačmarčík
- first_name: P.
full_name: Neilinger, P.
last_name: Neilinger
- first_name: M.
full_name: Grajcar, M.
last_name: Grajcar
- first_name: P.
full_name: Samuely, P.
last_name: Samuely
citation:
ama: 'Zemlicka M, Kopčík M, Szabó P, et al. Zeeman-driven superconductor-insulator
transition in strongly disordered MoC films: Scanning tunneling microscopy and
transport studies in a transverse magnetic field. Physical Review B. 2020;102(18).
doi:10.1103/PhysRevB.102.180508'
apa: 'Zemlicka, M., Kopčík, M., Szabó, P., Samuely, T., Kačmarčík, J., Neilinger,
P., … Samuely, P. (2020). Zeeman-driven superconductor-insulator transition in
strongly disordered MoC films: Scanning tunneling microscopy and transport studies
in a transverse magnetic field. Physical Review B. American Physical Society.
https://doi.org/10.1103/PhysRevB.102.180508'
chicago: 'Zemlicka, Martin, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger,
M. Grajcar, and P. Samuely. “Zeeman-Driven Superconductor-Insulator Transition
in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport
Studies in a Transverse Magnetic Field.” Physical Review B. American Physical
Society, 2020. https://doi.org/10.1103/PhysRevB.102.180508.'
ieee: 'M. Zemlicka et al., “Zeeman-driven superconductor-insulator transition
in strongly disordered MoC films: Scanning tunneling microscopy and transport
studies in a transverse magnetic field,” Physical Review B, vol. 102, no.
18. American Physical Society, 2020.'
ista: 'Zemlicka M, Kopčík M, Szabó P, Samuely T, Kačmarčík J, Neilinger P, Grajcar
M, Samuely P. 2020. Zeeman-driven superconductor-insulator transition in strongly
disordered MoC films: Scanning tunneling microscopy and transport studies in a
transverse magnetic field. Physical Review B. 102(18), 180508.'
mla: 'Zemlicka, Martin, et al. “Zeeman-Driven Superconductor-Insulator Transition
in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport
Studies in a Transverse Magnetic Field.” Physical Review B, vol. 102, no.
18, 180508, American Physical Society, 2020, doi:10.1103/PhysRevB.102.180508.'
short: M. Zemlicka, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger,
M. Grajcar, P. Samuely, Physical Review B 102 (2020).
date_created: 2020-12-13T23:01:21Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2023-08-24T10:53:36Z
day: '01'
department:
- _id: JoFi
doi: 10.1103/PhysRevB.102.180508
external_id:
arxiv:
- '2011.04329'
isi:
- '000591509900003'
intvolume: ' 102'
isi: 1
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2011.04329
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- '24699969'
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Zeeman-driven superconductor-insulator transition in strongly disordered MoC
films: Scanning tunneling microscopy and transport studies in a transverse magnetic
field'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 102
year: '2020'
...
---
_id: '8949'
abstract:
- lang: eng
text: Development of the nervous system undergoes important transitions,
including one from neurogenesis to gliogenesis which occurs late during embryonic
gestation. Here we report on clonal analysis of gliogenesis in mice using Mosaic
Analysis with Double Markers (MADM) with quantitative and computational methods.
Results reveal that developmental gliogenesis in the cerebral cortex occurs in
a fraction of earlier neurogenic clones, accelerating around E16.5, and giving
rise to both astrocytes and oligodendrocytes. Moreover, MADM-based genetic deletion
of the epidermal growth factor receptor (Egfr) in gliogenic clones revealed that
Egfr is cell autonomously required for gliogenesis in the mouse dorsolateral cortices.
A broad range in the proliferation capacity, symmetry of clones, and competitive
advantage of MADM cells was evident in clones that contained one cellular lineage
with double dosage of Egfr relative to their environment, while their sibling
Egfr-null cells failed to generate glia. Remarkably, the total numbers of glia
in MADM clones balance out regardless of significant alterations in clonal symmetries.
The variability in glial clones shows stochastic patterns that we define mathematically,
which are different from the deterministic patterns in neuronal clones. This study
sets a foundation for studying the biological significance of stochastic and deterministic
clonal principles underlying tissue development, and identifying mechanisms that
differentiate between neurogenesis and gliogenesis.
acknowledgement: This research was funded by grants from the National Institutes of
Health to H.T.G. (R01NS098370 and R01NS089795). C.V.M. was supported by a National
Science Foundation Graduate Research Fellowship (DGE-1746939). R.B. was supported
by the FWF Lise-Meitner program (M 2416), and S.H. was supported by the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
programme (grant agreement No 725780 LinPro).The authors thank members of the Ghashghaei
lab for discussions, technical support, and help with preparation of the manuscript.
article_number: '2662'
article_processing_charge: No
article_type: original
author:
- first_name: Xuying
full_name: Zhang, Xuying
last_name: Zhang
- first_name: Christine V.
full_name: Mennicke, Christine V.
last_name: Mennicke
- first_name: Guanxi
full_name: Xiao, Guanxi
last_name: Xiao
- first_name: Robert J
full_name: Beattie, Robert J
id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
last_name: Beattie
orcid: 0000-0002-8483-8753
- first_name: Mansoor
full_name: Haider, Mansoor
last_name: Haider
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: H. Troy
full_name: Ghashghaei, H. Troy
last_name: Ghashghaei
citation:
ama: Zhang X, Mennicke CV, Xiao G, et al. Clonal analysis of gliogenesis in the
cerebral cortex reveals stochastic expansion of glia and cell autonomous responses
to Egfr dosage. Cells. 2020;9(12). doi:10.3390/cells9122662
apa: Zhang, X., Mennicke, C. V., Xiao, G., Beattie, R. J., Haider, M., Hippenmeyer,
S., & Ghashghaei, H. T. (2020). Clonal analysis of gliogenesis in the cerebral
cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr
dosage. Cells. MDPI. https://doi.org/10.3390/cells9122662
chicago: Zhang, Xuying, Christine V. Mennicke, Guanxi Xiao, Robert J Beattie, Mansoor
Haider, Simon Hippenmeyer, and H. Troy Ghashghaei. “Clonal Analysis of Gliogenesis
in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous
Responses to Egfr Dosage.” Cells. MDPI, 2020. https://doi.org/10.3390/cells9122662.
ieee: X. Zhang et al., “Clonal analysis of gliogenesis in the cerebral cortex
reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage,”
Cells, vol. 9, no. 12. MDPI, 2020.
ista: Zhang X, Mennicke CV, Xiao G, Beattie RJ, Haider M, Hippenmeyer S, Ghashghaei
HT. 2020. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic
expansion of glia and cell autonomous responses to Egfr dosage. Cells. 9(12),
2662.
mla: Zhang, Xuying, et al. “Clonal Analysis of Gliogenesis in the Cerebral Cortex
Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.”
Cells, vol. 9, no. 12, 2662, MDPI, 2020, doi:10.3390/cells9122662.
short: X. Zhang, C.V. Mennicke, G. Xiao, R.J. Beattie, M. Haider, S. Hippenmeyer,
H.T. Ghashghaei, Cells 9 (2020).
date_created: 2020-12-14T08:04:03Z
date_published: 2020-12-11T00:00:00Z
date_updated: 2023-08-24T10:57:48Z
day: '11'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.3390/cells9122662
ec_funded: 1
external_id:
isi:
- '000601787300001'
file:
- access_level: open_access
checksum: 5095cbdc728c9a510c5761cf60a8861c
content_type: application/pdf
creator: dernst
date_created: 2020-12-14T08:09:43Z
date_updated: 2020-12-14T08:09:43Z
file_id: '8950'
file_name: 2020_Cells_Zhang.pdf
file_size: 3504525
relation: main_file
success: 1
file_date_updated: 2020-12-14T08:09:43Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 264E56E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02416
name: Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Cells
publication_identifier:
issn:
- 2073-4409
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion
of glia and cell autonomous responses to Egfr dosage
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: 9
year: '2020'
...
---
_id: '8951'
abstract:
- lang: eng
text: Gene expression levels are influenced by multiple coexisting molecular mechanisms.
Some of these interactions, such as those of transcription factors and promoters
have been studied extensively. However, predicting phenotypes of gene regulatory
networks remains a major challenge. Here, we use a well-defined synthetic gene
regulatory network to study how network phenotypes depend on local genetic context,
i.e. the genetic neighborhood of a transcription factor and its relative position.
We show that one gene regulatory network with fixed topology can display not only
quantitatively but also qualitatively different phenotypes, depending solely on
the local genetic context of its components. Our results demonstrate that changes
in local genetic context can place a single transcriptional unit within two separate
regulons without the need for complex regulatory sequences. We propose that relative
order of individual transcriptional units, with its potential for combinatorial
complexity, plays an important role in shaping phenotypes of gene regulatory networks.
article_processing_charge: No
author:
- first_name: Anna A
full_name: Nagy-Staron, Anna A
id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87
last_name: Nagy-Staron
orcid: 0000-0002-1391-8377
citation:
ama: Nagy-Staron AA. Sequences of gene regulatory network permutations for the article
“Local genetic context shapes the function of a gene regulatory network.” 2020.
doi:10.15479/AT:ISTA:8951
apa: Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations
for the article “Local genetic context shapes the function of a gene regulatory
network.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8951
chicago: Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations
for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory
Network.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8951.
ieee: A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for
the article ‘Local genetic context shapes the function of a gene regulatory network.’”
Institute of Science and Technology Austria, 2020.
ista: Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for
the article ‘Local genetic context shapes the function of a gene regulatory network’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:8951.
mla: Nagy-Staron, Anna A. Sequences of Gene Regulatory Network Permutations for
the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.”
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8951.
short: A.A. Nagy-Staron, (2020).
contributor:
- contributor_type: project_member
first_name: Anna A
id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87
last_name: Nagy-Staron
- contributor_type: project_member
first_name: Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
- contributor_type: project_member
first_name: Caroline
last_name: Caruso Carter
- contributor_type: project_member
first_name: Elisabeth
last_name: Sonnleitner
- contributor_type: project_member
first_name: Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- contributor_type: project_member
first_name: Tiago
last_name: Paixão
- contributor_type: project_manager
first_name: Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
date_created: 2020-12-20T10:00:26Z
date_published: 2020-12-21T00:00:00Z
date_updated: 2024-02-21T12:41:57Z
day: '21'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:8951
file:
- access_level: open_access
checksum: f57862aeee1690c7effd2b1117d40ed1
content_type: text/plain
creator: bkavcic
date_created: 2020-12-20T09:52:52Z
date_updated: 2020-12-20T09:52:52Z
file_id: '8952'
file_name: readme.txt
file_size: 523
relation: main_file
success: 1
- access_level: open_access
checksum: f2c6d5232ec6d551b6993991e8689e9f
content_type: application/octet-stream
creator: bkavcic
date_created: 2020-12-20T22:01:44Z
date_updated: 2020-12-20T22:01:44Z
file_id: '8954'
file_name: GRNs Research depository.gb
file_size: 379228
relation: main_file
success: 1
file_date_updated: 2020-12-20T22:01:44Z
has_accepted_license: '1'
keyword:
- Gene regulatory networks
- Gene expression
- Escherichia coli
- Synthetic Biology
month: '12'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9283'
relation: used_in_publication
status: public
status: public
title: Sequences of gene regulatory network permutations for the article "Local genetic
context shapes the function of a gene regulatory network"
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: '2020'
...
---
_id: '8955'
abstract:
- lang: eng
text: Skeletal muscle activity is continuously modulated across physiologic states
to provide coordination, flexibility and responsiveness to body tasks and external
inputs. Despite the central role the muscular system plays in facilitating vital
body functions, the network of brain-muscle interactions required to control hundreds
of muscles and synchronize their activation in relation to distinct physiologic
states has not been investigated. Recent approaches have focused on general associations
between individual brain rhythms and muscle activation during movement tasks.
However, the specific forms of coupling, the functional network of cortico-muscular
coordination, and how network structure and dynamics are modulated by autonomic
regulation across physiologic states remains unknown. To identify and quantify
the cortico-muscular interaction network and uncover basic features of neuro-autonomic
control of muscle function, we investigate the coupling between synchronous bursts
in cortical rhythms and peripheral muscle activation during sleep and wake. Utilizing
the concept of time delay stability and a novel network physiology approach, we
find that the brain-muscle network exhibits complex dynamic patterns of communication
involving multiple brain rhythms across cortical locations and different electromyographic
frequency bands. Moreover, our results show that during each physiologic state
the cortico-muscular network is characterized by a specific profile of network
links strength, where particular brain rhythms play role of main mediators of
interaction and control. Further, we discover a hierarchical reorganization in
network structure across physiologic states, with high connectivity and network
link strength during wake, intermediate during REM and light sleep, and low during
deep sleep, a sleep-stage stratification that demonstrates a unique association
between physiologic states and cortico-muscular network structure. The reported
empirical observations are consistent across individual subjects, indicating universal
behavior in network structure and dynamics, and high sensitivity of cortico-muscular
control to changes in autonomic regulation, even at low levels of physical activity
and muscle tone during sleep. Our findings demonstrate previously unrecognized
basic principles of brain-muscle network communication and control, and provide
new perspectives on the regulatory mechanisms of brain dynamics and locomotor
activation, with potential clinical implications for neurodegenerative, movement
and sleep disorders, and for developing efficient treatment strategies.
acknowledgement: We acknowledge support from the W. M. Keck Foundation, National Institutes
of Health (NIH Grant 1R01-HL098437), the US-Israel Binational Science Foundation
(BSF Grant 2012219), and the Office of Naval Research (ONR Grant 000141010078).
FL acknowledges support also from the European Union's Horizon 2020 research and
innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411.
article_number: '558070'
article_processing_charge: No
article_type: original
author:
- first_name: Rossella
full_name: Rizzo, Rossella
last_name: Rizzo
- first_name: Xiyun
full_name: Zhang, Xiyun
last_name: Zhang
- first_name: Jilin W.J.L.
full_name: Wang, Jilin W.J.L.
last_name: Wang
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Plamen Ch
full_name: Ivanov, Plamen Ch
last_name: Ivanov
citation:
ama: Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. Network physiology of cortico–muscular
interactions. Frontiers in Physiology. 2020;11. doi:10.3389/fphys.2020.558070
apa: Rizzo, R., Zhang, X., Wang, J. W. J. L., Lombardi, F., & Ivanov, P. C.
(2020). Network physiology of cortico–muscular interactions. Frontiers in Physiology.
Frontiers. https://doi.org/10.3389/fphys.2020.558070
chicago: Rizzo, Rossella, Xiyun Zhang, Jilin W.J.L. Wang, Fabrizio Lombardi, and
Plamen Ch Ivanov. “Network Physiology of Cortico–Muscular Interactions.” Frontiers
in Physiology. Frontiers, 2020. https://doi.org/10.3389/fphys.2020.558070.
ieee: R. Rizzo, X. Zhang, J. W. J. L. Wang, F. Lombardi, and P. C. Ivanov, “Network
physiology of cortico–muscular interactions,” Frontiers in Physiology,
vol. 11. Frontiers, 2020.
ista: Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. 2020. Network physiology
of cortico–muscular interactions. Frontiers in Physiology. 11, 558070.
mla: Rizzo, Rossella, et al. “Network Physiology of Cortico–Muscular Interactions.”
Frontiers in Physiology, vol. 11, 558070, Frontiers, 2020, doi:10.3389/fphys.2020.558070.
short: R. Rizzo, X. Zhang, J.W.J.L. Wang, F. Lombardi, P.C. Ivanov, Frontiers in
Physiology 11 (2020).
date_created: 2020-12-20T23:01:18Z
date_published: 2020-11-26T00:00:00Z
date_updated: 2023-08-24T11:00:45Z
day: '26'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.3389/fphys.2020.558070
ec_funded: 1
external_id:
isi:
- '000596849400001'
pmid:
- '33324233'
file:
- access_level: open_access
checksum: ef9515b28c5619b7126c0f347958bcb3
content_type: application/pdf
creator: dernst
date_created: 2020-12-21T10:37:50Z
date_updated: 2020-12-21T10:37:50Z
file_id: '8961'
file_name: 2020_Frontiers_Rizzo.pdf
file_size: 13380030
relation: main_file
success: 1
file_date_updated: 2020-12-21T10:37:50Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Frontiers in Physiology
publication_identifier:
eissn:
- 1664042X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Network physiology of cortico–muscular interactions
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: 11
year: '2020'
...
---
_id: '8957'
abstract:
- lang: eng
text: Global tissue tension anisotropy has been shown to trigger stereotypical cell
division orientation by elongating mitotic cells along the main tension axis.
Yet, how tissue tension elongates mitotic cells despite those cells undergoing
mitotic rounding (MR) by globally upregulating cortical actomyosin tension remains
unclear. We addressed this question by taking advantage of ascidian embryos, consisting
of a small number of interphasic and mitotic blastomeres and displaying an invariant
division pattern. We found that blastomeres undergo MR by locally relaxing cortical
tension at their apex, thereby allowing extrinsic pulling forces from neighboring
interphasic blastomeres to polarize their shape and thus division orientation.
Consistently, interfering with extrinsic forces by reducing the contractility
of interphasic blastomeres or disrupting the establishment of asynchronous mitotic
domains leads to aberrant mitotic cell division orientations. Thus, apical relaxation
during MR constitutes a key mechanism by which tissue tension anisotropy controls
stereotypical cell division orientation.
acknowledged_ssus:
- _id: Bio
- _id: NanoFab
acknowledgement: 'We thank members of the Heisenberg and McDougall groups for technical
advice and discussion, Hitoyoshi Yasuo for sharing lab equipment, Lucas Leclère
and Hitoyoshi Yasuo for their comments on a preliminary version of the manuscript,
and Philippe Dru for the Rose plots. We are grateful to the Bioimaging and Nanofabrication
facilities of IST Austria and the Imaging Platform (PIM) and animal facility (CRB)
of Institut de la Mer de Villefranche (IMEV), which is supported by EMBRC-France,
whose French state funds are managed by the ANR within the Investments of the Future
program under reference ANR-10-INBS-0, for continuous support. This work was supported
by a grant from the French Government funding agency Agence National de la Recherche
(ANR “MorCell”: ANR-17-CE 13-002 8).'
article_processing_charge: No
article_type: original
author:
- first_name: Benoit G
full_name: Godard, Benoit G
id: 33280250-F248-11E8-B48F-1D18A9856A87
last_name: Godard
- first_name: Rémi
full_name: Dumollard, Rémi
last_name: Dumollard
- first_name: Edwin
full_name: Munro, Edwin
last_name: Munro
- first_name: Janet
full_name: Chenevert, Janet
last_name: Chenevert
- first_name: Céline
full_name: Hebras, Céline
last_name: Hebras
- first_name: Alex
full_name: Mcdougall, Alex
last_name: Mcdougall
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Godard BG, Dumollard R, Munro E, et al. Apical relaxation during mitotic rounding
promotes tension-oriented cell division. Developmental Cell. 2020;55(6):695-706.
doi:10.1016/j.devcel.2020.10.016
apa: Godard, B. G., Dumollard, R., Munro, E., Chenevert, J., Hebras, C., Mcdougall,
A., & Heisenberg, C.-P. J. (2020). Apical relaxation during mitotic rounding
promotes tension-oriented cell division. Developmental Cell. Elsevier.
https://doi.org/10.1016/j.devcel.2020.10.016
chicago: Godard, Benoit G, Rémi Dumollard, Edwin Munro, Janet Chenevert, Céline
Hebras, Alex Mcdougall, and Carl-Philipp J Heisenberg. “Apical Relaxation during
Mitotic Rounding Promotes Tension-Oriented Cell Division.” Developmental Cell.
Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.10.016.
ieee: B. G. Godard et al., “Apical relaxation during mitotic rounding promotes
tension-oriented cell division,” Developmental Cell, vol. 55, no. 6. Elsevier,
pp. 695–706, 2020.
ista: Godard BG, Dumollard R, Munro E, Chenevert J, Hebras C, Mcdougall A, Heisenberg
C-PJ. 2020. Apical relaxation during mitotic rounding promotes tension-oriented
cell division. Developmental Cell. 55(6), 695–706.
mla: Godard, Benoit G., et al. “Apical Relaxation during Mitotic Rounding Promotes
Tension-Oriented Cell Division.” Developmental Cell, vol. 55, no. 6, Elsevier,
2020, pp. 695–706, doi:10.1016/j.devcel.2020.10.016.
short: B.G. Godard, R. Dumollard, E. Munro, J. Chenevert, C. Hebras, A. Mcdougall,
C.-P.J. Heisenberg, Developmental Cell 55 (2020) 695–706.
date_created: 2020-12-20T23:01:19Z
date_published: 2020-12-21T00:00:00Z
date_updated: 2023-08-24T11:01:22Z
day: '21'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2020.10.016
external_id:
isi:
- '000600665700008'
pmid:
- '33207225'
intvolume: ' 55'
isi: 1
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 695-706
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- '18781551'
issn:
- '15345807'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/relaxing-cell-divisions/
scopus_import: '1'
status: public
title: Apical relaxation during mitotic rounding promotes tension-oriented cell division
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 55
year: '2020'
...
---
_id: '8958'
abstract:
- lang: eng
text: "The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom
too many'' has been disavowed. Inspired by the possibility to experimentally manipulate
and enhance chemical reactivity in helium nanodroplets, we investigate the rotation
of coupled cold molecules in the presence of a many-body environment.\r\nIn this
thesis, we introduce new variational approaches to quantum impurities and apply
them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other
point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed
out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox,
we reveal the self-localization transition for the angulon quasiparticle. We show
that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath
coupling already at the mean-field level. The transition is accompanied by the
spherical-symmetry breaking of the angulon ground state and a discontinuity in
the first derivative of the ground-state energy. Moreover, the type of symmetry
breaking is dictated by the symmetry of the microscopic impurity-bath interaction,
which leads to a number of distinct self-localized states. \r\nFor the system
containing multiple impurities, by analogy with the bipolaron, we introduce the
biangulon quasiparticle describing two rotating molecules that align with respect
to each other due to the effective attractive interaction mediated by the excitations
of the bath. We study this system from the strong-coupling regime to the weak
molecule-bath interaction regime. We show that the molecules tend to have a strong
alignment in the ground state, the biangulon shows shifted angulon instabilities
and an additional spectral instability, where resonant angular momentum transfer
between the molecules and the bath takes place. Finally, we introduce a diagonalization
scheme that allows us to describe the transition from two separated angulons to
a biangulon as a function of the distance between the two molecules."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Xiang
full_name: Li, Xiang
id: 4B7E523C-F248-11E8-B48F-1D18A9856A87
last_name: Li
citation:
ama: Li X. Rotation of coupled cold molecules in the presence of a many-body environment.
2020. doi:10.15479/AT:ISTA:8958
apa: Li, X. (2020). Rotation of coupled cold molecules in the presence of a many-body
environment. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8958
chicago: Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body
Environment.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8958.
ieee: X. Li, “Rotation of coupled cold molecules in the presence of a many-body
environment,” Institute of Science and Technology Austria, 2020.
ista: Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body
environment. Institute of Science and Technology Austria.
mla: Li, Xiang. Rotation of Coupled Cold Molecules in the Presence of a Many-Body
Environment. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8958.
short: X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body
Environment, Institute of Science and Technology Austria, 2020.
date_created: 2020-12-21T09:44:30Z
date_published: 2020-12-21T00:00:00Z
date_updated: 2024-08-07T07:16:53Z
day: '21'
ddc:
- '539'
degree_awarded: PhD
department:
- _id: MiLe
doi: 10.15479/AT:ISTA:8958
ec_funded: 1
file:
- access_level: open_access
checksum: 3994c54a1241451d561db1d4f43bad30
content_type: application/pdf
creator: xli
date_created: 2020-12-22T10:55:56Z
date_updated: 2020-12-22T10:55:56Z
file_id: '8967'
file_name: THESIS_Xiang_Li.pdf
file_size: 3622305
relation: main_file
success: 1
- access_level: closed
checksum: 0954ecfc5554c05615c14de803341f00
content_type: application/x-zip-compressed
creator: xli
date_created: 2020-12-22T10:56:03Z
date_updated: 2020-12-30T07:18:03Z
file_id: '8968'
file_name: THESIS_Xiang_Li.zip
file_size: 4018859
relation: source_file
file_date_updated: 2020-12-30T07:18:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '125'
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '5886'
relation: part_of_dissertation
status: public
- id: '1120'
relation: part_of_dissertation
status: public
- id: '8587'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
title: Rotation of coupled cold molecules in the presence of a many-body environment
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8971'
abstract:
- lang: eng
text: The actin-related protein (Arp)2/3 complex nucleates branched actin filament
networks pivotal for cell migration, endocytosis and pathogen infection. Its activation
is tightly regulated and involves complex structural rearrangements and actin
filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution
structure of the actin filament Arp2/3 complex branch junction in cells using
cryo-electron tomography and subtomogram averaging. This allows us to generate
an accurate model of the active Arp2/3 complex in the branch junction and its
interaction with actin filaments. Notably, our model reveals a previously undescribed
set of interactions of the Arp2/3 complex with the mother filament, significantly
different to the previous branch junction model. Our structure also indicates
a central role for the ArpC3 subunit in stabilizing the active conformation.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
acknowledgement: "This research was supported by the Scientific Service Units (SSUs)
of IST Austria through resources provided by Scientific Computing (SciComp), the
Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy
Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for
helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and
Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical
reading of the manuscript. We also thank Gregory Voth (University of Chicago) for
providing us the MD-derived branch junction model for comparison. The authors acknowledge
support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D.
and Austrian Science Fund (FWF): P33367 to F.K.M.S. "
article_number: '6437'
article_processing_charge: No
article_type: original
author:
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: William
full_name: Wan, William
last_name: Wan
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography
structure of Arp2/3 complex in cells reveals new insights into the branch junction.
Nature Communications. 2020;11. doi:10.1038/s41467-020-20286-x
apa: Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., & Schur, F. K. (2020).
Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights
into the branch junction. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-20286-x
chicago: Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan,
and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in
Cells Reveals New Insights into the Branch Junction.” Nature Communications.
Springer Nature, 2020. https://doi.org/10.1038/s41467-020-20286-x.
ieee: F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron
tomography structure of Arp2/3 complex in cells reveals new insights into the
branch junction,” Nature Communications, vol. 11. Springer Nature, 2020.
ista: Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography
structure of Arp2/3 complex in cells reveals new insights into the branch junction.
Nature Communications. 11, 6437.
mla: Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex
in Cells Reveals New Insights into the Branch Junction.” Nature Communications,
vol. 11, 6437, Springer Nature, 2020, doi:10.1038/s41467-020-20286-x.
short: F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications
11 (2020).
date_created: 2020-12-23T08:25:45Z
date_published: 2020-12-22T00:00:00Z
date_updated: 2023-08-24T11:01:50Z
day: '22'
ddc:
- '570'
department:
- _id: FlSc
- _id: EM-Fac
doi: 10.1038/s41467-020-20286-x
external_id:
isi:
- '000603078000003'
file:
- access_level: open_access
checksum: 55d43ea0061cc4027ba45e966e1db8cc
content_type: application/pdf
creator: dernst
date_created: 2020-12-28T08:16:10Z
date_updated: 2020-12-28T08:16:10Z
file_id: '8975'
file_name: 2020_NatureComm_Faessler.pdf
file_size: 3958727
relation: main_file
success: 1
file_date_updated: 2020-12-28T08:16:10Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
- _id: 2674F658-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02495
name: Protein structure and function in filopodia across scales
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/
scopus_import: '1'
status: public
title: Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights
into the branch junction
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: 11
year: '2020'
...