---
OA_place: publisher
_id: '18225'
abstract:
- lang: eng
text: "Isometric feature mapping is an established time-honored algorithm in manifold
learning and non-linear dimensionality reduction. Its prominence can be attributed
to the output of a coherent global low-dimensional representation of data by preserving
intrinsic distances. In order to enable an efficient and more applicable isometric
feature mapping, a diverse set of sophisticated advancements have been proposed
to the original algorithm to incorporate important factors like sparsity of computation,
conformality, topological constraints and spectral geometry. However, a significant
shortcoming of most approaches is the dependence on large-scale dense-spectral
decompositions and the inability to generalize to points far away from the sampling
of the manifold.\r\nIn this paper, we explore an unsupervised deep learning approach
for computing distance-preserving maps for non-linear dimensionality reduction.
We demonstrate that our framework is general enough to incorporate all previous
advancements and show a significantly improved local and non-local generalization
of the isometric mapping. Our approach involves training with only a few landmark
points and avoids the need for population of dense matrices as well as computing
their spectral decomposition."
article_number: '104461'
article_processing_charge: No
article_type: original
author:
- first_name: Gautam
full_name: Pai, Gautam
last_name: Pai
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Ronen
full_name: Talmon, Ronen
last_name: Talmon
- first_name: Ron
full_name: Kimmel, Ron
last_name: Kimmel
citation:
ama: Pai G, Bronstein AM, Talmon R, Kimmel R. Deep isometric maps. Image and
Vision Computing. 2022;123. doi:10.1016/j.imavis.2022.104461
apa: Pai, G., Bronstein, A. M., Talmon, R., & Kimmel, R. (2022). Deep isometric
maps. Image and Vision Computing. Elsevier. https://doi.org/10.1016/j.imavis.2022.104461
chicago: Pai, Gautam, Alex M. Bronstein, Ronen Talmon, and Ron Kimmel. “Deep Isometric
Maps.” Image and Vision Computing. Elsevier, 2022. https://doi.org/10.1016/j.imavis.2022.104461.
ieee: G. Pai, A. M. Bronstein, R. Talmon, and R. Kimmel, “Deep isometric maps,”
Image and Vision Computing, vol. 123. Elsevier, 2022.
ista: Pai G, Bronstein AM, Talmon R, Kimmel R. 2022. Deep isometric maps. Image
and Vision Computing. 123, 104461.
mla: Pai, Gautam, et al. “Deep Isometric Maps.” Image and Vision Computing,
vol. 123, 104461, Elsevier, 2022, doi:10.1016/j.imavis.2022.104461.
short: G. Pai, A.M. Bronstein, R. Talmon, R. Kimmel, Image and Vision Computing
123 (2022).
date_created: 2024-10-08T12:54:22Z
date_published: 2022-07-01T00:00:00Z
date_updated: 2024-10-14T11:03:26Z
day: '01'
doi: 10.1016/j.imavis.2022.104461
extern: '1'
intvolume: ' 123'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.imavis.2022.104461
month: '07'
oa: 1
oa_version: Published Version
publication: Image and Vision Computing
publication_identifier:
issn:
- 0262-8856
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Deep isometric maps
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 123
year: '2022'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18226'
abstract:
- lang: eng
text: Spontaneous parametric downconversion (SPDC) in quantum optics is an invaluable
resource for the realization of high-dimensional qudits with spatial modes of
light. One of the main open challenges is how to directly generate a desirable
qudit state in the SPDC process. This problem can be addressed through advanced
computational learning methods; however, due to difficulties in modeling the SPDC
process by a fully differentiable algorithm, progress has been limited. Here,
we overcome these limitations and introduce a physically constrained and differentiable
model, validated against experimental results for shaped pump beams and structured
crystals, capable of learning the relevant interaction parameters in the process.
We avoid any restrictions induced by the stochastic nature of our physical model
and integrate the dynamic equations governing the evolution under the SPDC Hamiltonian.
We solve the inverse problem of designing a nonlinear quantum optical system that
achieves the desired quantum state of downconverted photon pairs. The desired
states are defined using either the second-order correlations between different
spatial modes or by specifying the required density matrix. By learning nonlinear
photonic crystal structures as well as different pump shapes, we successfully
show how to generate maximally entangled states. Furthermore, we simulate all-optical
coherent control over the generated quantum state by actively changing the profile
of the pump beam. Our work can be useful for applications such as novel designs
of high-dimensional quantum key distribution and quantum information processing
protocols. In addition, our method can be readily applied for controlling other
degrees of freedom of light in the SPDC process, such as spectral and temporal
properties, and may even be used in condensed-matter systems having a similar
interaction Hamiltonian.
article_processing_charge: No
article_type: original
author:
- first_name: Eyal
full_name: Rozenberg, Eyal
last_name: Rozenberg
- first_name: Aviv
full_name: Karnieli, Aviv
last_name: Karnieli
- first_name: Ofir
full_name: Yesharim, Ofir
last_name: Yesharim
- first_name: Joshua
full_name: Foley-Comer, Joshua
last_name: Foley-Comer
- first_name: Sivan
full_name: Trajtenberg-Mills, Sivan
last_name: Trajtenberg-Mills
- first_name: Daniel
full_name: Freedman, Daniel
last_name: Freedman
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Ady
full_name: Arie, Ady
last_name: Arie
citation:
ama: Rozenberg E, Karnieli A, Yesharim O, et al. Inverse design of spontaneous parametric
downconversion for generation of high-dimensional qudits. Optica. 2022;9(6):602-615.
doi:10.1364/optica.451115
apa: Rozenberg, E., Karnieli, A., Yesharim, O., Foley-Comer, J., Trajtenberg-Mills,
S., Freedman, D., … Arie, A. (2022). Inverse design of spontaneous parametric
downconversion for generation of high-dimensional qudits. Optica. Optica
Publishing Group. https://doi.org/10.1364/optica.451115
chicago: Rozenberg, Eyal, Aviv Karnieli, Ofir Yesharim, Joshua Foley-Comer, Sivan
Trajtenberg-Mills, Daniel Freedman, Alex M. Bronstein, and Ady Arie. “Inverse
Design of Spontaneous Parametric Downconversion for Generation of High-Dimensional
Qudits.” Optica. Optica Publishing Group, 2022. https://doi.org/10.1364/optica.451115.
ieee: E. Rozenberg et al., “Inverse design of spontaneous parametric downconversion
for generation of high-dimensional qudits,” Optica, vol. 9, no. 6. Optica
Publishing Group, pp. 602–615, 2022.
ista: Rozenberg E, Karnieli A, Yesharim O, Foley-Comer J, Trajtenberg-Mills S, Freedman
D, Bronstein AM, Arie A. 2022. Inverse design of spontaneous parametric downconversion
for generation of high-dimensional qudits. Optica. 9(6), 602–615.
mla: Rozenberg, Eyal, et al. “Inverse Design of Spontaneous Parametric Downconversion
for Generation of High-Dimensional Qudits.” Optica, vol. 9, no. 6, Optica
Publishing Group, 2022, pp. 602–15, doi:10.1364/optica.451115.
short: E. Rozenberg, A. Karnieli, O. Yesharim, J. Foley-Comer, S. Trajtenberg-Mills,
D. Freedman, A.M. Bronstein, A. Arie, Optica 9 (2022) 602–615.
date_created: 2024-10-08T12:54:43Z
date_published: 2022-06-06T00:00:00Z
date_updated: 2024-10-14T11:07:29Z
day: '06'
doi: 10.1364/optica.451115
extern: '1'
intvolume: ' 9'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1364/OPTICA.451115
month: '06'
oa: 1
oa_version: Published Version
page: 602-615
publication: Optica
publication_identifier:
issn:
- 2334-2536
publication_status: published
publisher: Optica Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inverse design of spontaneous parametric downconversion for generation of high-dimensional
qudits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2022'
...
---
_id: '18229'
abstract:
- lang: eng
text: We present Self-Classifier – a novel self-supervised end-to-end classification
learning approach. Self-Classifier learns labels and representations simultaneously
in a single-stage end-to-end manner by optimizing for same-class prediction of
two augmented views of the same sample. To guarantee non-degenerate solutions
(i.e., solutions where all labels are assigned to the same class) we propose a
mathematically motivated variant of the cross-entropy loss that has a uniform
prior asserted on the predicted labels. In our theoretical analysis, we prove
that degenerate solutions are not in the set of optimal solutions of our approach.
Self-Classifier is simple to implement and scalable. Unlike other popular unsupervised
classification and contrastive representation learning approaches, it does not
require any form of pre-training, expectation-maximization, pseudo-labeling, external
clustering, a second network, stop-gradient operation, or negative pairs. Despite
its simplicity, our approach sets a new state of the art for unsupervised classification
of ImageNet; and even achieves comparable to state-of-the-art results for unsupervised
representation learning. Code is available at https://github.com/elad-amrani/self-classifier.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Elad
full_name: Amrani, Elad
last_name: Amrani
- first_name: Leonid
full_name: Karlinsky, Leonid
last_name: Karlinsky
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
citation:
ama: 'Amrani E, Karlinsky L, Bronstein AM. Self-supervised classification network.
In: 17th European Conference on Computer Vision. Vol 13691. Springer Nature;
2022:116-132. doi:10.1007/978-3-031-19821-2_7'
apa: 'Amrani, E., Karlinsky, L., & Bronstein, A. M. (2022). Self-supervised
classification network. In 17th European Conference on Computer Vision
(Vol. 13691, pp. 116–132). Tel Aviv, Israel: Springer Nature. https://doi.org/10.1007/978-3-031-19821-2_7'
chicago: Amrani, Elad, Leonid Karlinsky, and Alex M. Bronstein. “Self-Supervised
Classification Network.” In 17th European Conference on Computer Vision,
13691:116–32. Springer Nature, 2022. https://doi.org/10.1007/978-3-031-19821-2_7.
ieee: E. Amrani, L. Karlinsky, and A. M. Bronstein, “Self-supervised classification
network,” in 17th European Conference on Computer Vision, Tel Aviv, Israel,
2022, vol. 13691, pp. 116–132.
ista: 'Amrani E, Karlinsky L, Bronstein AM. 2022. Self-supervised classification
network. 17th European Conference on Computer Vision. ECCV: European Conference
on Computer Vision, LNCS, vol. 13691, 116–132.'
mla: Amrani, Elad, et al. “Self-Supervised Classification Network.” 17th European
Conference on Computer Vision, vol. 13691, Springer Nature, 2022, pp. 116–32,
doi:10.1007/978-3-031-19821-2_7.
short: E. Amrani, L. Karlinsky, A.M. Bronstein, in:, 17th European Conference on
Computer Vision, Springer Nature, 2022, pp. 116–132.
conference:
end_date: 2022-10-27
location: Tel Aviv, Israel
name: 'ECCV: European Conference on Computer Vision'
start_date: 2022-10-23
date_created: 2024-10-08T12:55:44Z
date_published: 2022-10-23T00:00:00Z
date_updated: 2024-10-15T07:04:39Z
day: '23'
doi: 10.1007/978-3-031-19821-2_7
extern: '1'
external_id:
arxiv:
- '2103.10994'
intvolume: ' 13691'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2103.10994
month: '10'
oa: 1
oa_version: None
page: 116-132
publication: 17th European Conference on Computer Vision
publication_identifier:
eisbn:
- '9783031198212'
eissn:
- 1611-3349
isbn:
- '9783031198205'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/elad-amrani/self-classifier
scopus_import: '1'
status: public
title: Self-supervised classification network
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13691
year: '2022'
...
---
_id: '18291'
article_processing_charge: No
author:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
citation:
ama: "Katsaros G, Jirovec D. Dynamics of Hole Singlet-Triplet Qubits with Large
\U0001D454-Factor Differences. 2022. doi:10.15479/AT:ISTA:18291"
apa: "Katsaros, G., & Jirovec, D. (2022). Dynamics of Hole Singlet-Triplet Qubits
with Large \U0001D454-Factor Differences. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:18291"
chicago: "Katsaros, Georgios, and Daniel Jirovec. “Dynamics of Hole Singlet-Triplet
Qubits with Large \U0001D454-Factor Differences.” Institute of Science and Technology
Austria, 2022. https://doi.org/10.15479/AT:ISTA:18291."
ieee: "G. Katsaros and D. Jirovec, “Dynamics of Hole Singlet-Triplet Qubits with
Large \U0001D454-Factor Differences.” Institute of Science and Technology Austria,
2022."
ista: "Katsaros G, Jirovec D. 2022. Dynamics of Hole Singlet-Triplet Qubits with
Large \U0001D454-Factor Differences, Institute of Science and Technology Austria,
10.15479/AT:ISTA:18291."
mla: "Katsaros, Georgios, and Daniel Jirovec. Dynamics of Hole Singlet-Triplet
Qubits with Large \U0001D454-Factor Differences. Institute of Science and
Technology Austria, 2022, doi:10.15479/AT:ISTA:18291."
short: G. Katsaros, D. Jirovec, (2022).
corr_author: '1'
date_created: 2024-10-09T19:35:03Z
date_published: 2022-03-01T00:00:00Z
date_updated: 2025-04-15T07:15:24Z
day: '01'
department:
- _id: GeKa
doi: 10.15479/AT:ISTA:18291
file:
- access_level: open_access
checksum: 3128dffbd09267b93c2d0b1425fd3ba2
content_type: application/x-zip-compressed
creator: gkatsaro
date_created: 2024-10-09T19:31:35Z
date_updated: 2024-10-09T19:31:35Z
file_id: '18292'
file_name: SOIPaper.zip
file_size: 25566516
relation: main_file
success: 1
- access_level: open_access
checksum: df077d2f4652afeb3bf100068e88aa48
content_type: text/plain
creator: gkatsaro
date_created: 2024-10-14T18:11:45Z
date_updated: 2024-10-14T18:11:45Z
file_id: '18442'
file_name: Readme.txt
file_size: 6776
relation: main_file
success: 1
file_date_updated: 2024-10-14T18:11:45Z
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: None
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10920'
relation: research_paper
status: public
status: public
title: "Dynamics of Hole Singlet-Triplet Qubits with Large \U0001D454-Factor Differences"
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: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2022'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18606'
abstract:
- lang: eng
text: "Shear thickening is an intriguing rheological behaviour which consists in
a brutal increase in the viscosity above a critical shear rate. It is famously
encountered in suspensions of corn starch in water. Despite having been discovered
in the early 1930's, its underlying mechanisms remained a mystery for a long time.
In 2013–14, numerical and theoretical works [[1], [2], [3]] put forward a frictional
transition scenario to explain this phenomenon.\r\nIn this talk, I will present
experimental work investigating this frictional transition scenario. In order
to test the ideas of this model, one has to go further than standard rheological
techniques, since they do not provide access to the frictional state of the measured
suspension. I will thus focus on the techniques that we developed in order to
evidence the frictional transition and link it to the presence of a shear-thickening
behaviour."
acknowledgement: "This talk presents parts of my PhD work, conducted at IUSTI in Marseille
under the supervision of Yoël Forterre and Bloen Metzger. It aslo benefited from
contributions from Antoine Bérut, and some of the data was acquired by Pauline Dame
as part of a summer internship.\r\nThis work was supported by the European Research
Council (ERC) under the European Union Horizon 2020 Research and Innovation program
(ERC Grant 647384) and by the Labex MEC (ANR-10-LABX-0092) under the 647384) and
by the A*MIDEX project (ANR-11-IDEX-0001-02) funded by the French government program
Investissements d'Avenir, and by ANR ScienceFriction (No. ANR-18-CE30-0024)."
article_number: '100038'
article_processing_charge: No
article_type: original
author:
- first_name: Cécile
full_name: Clavaud, Cécile
id: 5f654c5d-04a1-11eb-ab36-ba9ffec58bd8
last_name: Clavaud
orcid: 0000-0002-1843-3803
citation:
ama: 'Clavaud C. Shear thickening in dense suspensions: an experimental study. Science
Talks. 2022;3. doi:10.1016/j.sctalk.2022.100038'
apa: 'Clavaud, C. (2022). Shear thickening in dense suspensions: an experimental
study. Science Talks. Elsevier. https://doi.org/10.1016/j.sctalk.2022.100038'
chicago: 'Clavaud, Cécile. “Shear Thickening in Dense Suspensions: An Experimental
Study.” Science Talks. Elsevier, 2022. https://doi.org/10.1016/j.sctalk.2022.100038.'
ieee: 'C. Clavaud, “Shear thickening in dense suspensions: an experimental study,”
Science Talks, vol. 3. Elsevier, 2022.'
ista: 'Clavaud C. 2022. Shear thickening in dense suspensions: an experimental study.
Science Talks. 3, 100038.'
mla: 'Clavaud, Cécile. “Shear Thickening in Dense Suspensions: An Experimental Study.”
Science Talks, vol. 3, 100038, Elsevier, 2022, doi:10.1016/j.sctalk.2022.100038.'
short: C. Clavaud, Science Talks 3 (2022).
corr_author: '1'
date_created: 2024-12-01T23:01:55Z
date_published: 2022-08-01T00:00:00Z
date_updated: 2024-12-11T09:24:57Z
day: '01'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1016/j.sctalk.2022.100038
file:
- access_level: open_access
checksum: 379a5f0b2684cd5393a23be374591484
content_type: application/pdf
creator: dernst
date_created: 2024-12-03T08:41:48Z
date_updated: 2024-12-03T08:41:48Z
file_id: '18607'
file_name: 2022_ScienceTalks_Clavaud.pdf
file_size: 1128564
relation: main_file
success: 1
- access_level: open_access
checksum: 666c0bd9af8432437554d0c75c540809
content_type: video/mp4
creator: dernst
date_created: 2024-12-11T09:22:13Z
date_updated: 2024-12-11T09:22:13Z
file_id: '18646'
file_name: 2024_ScienceTalk_Clavaud_Video.mp4
file_size: 93265727
relation: main_file
success: 1
- access_level: open_access
checksum: 8fd0d6224d7a0125fcf7d9ca0d80d700
content_type: video/mp4
creator: dernst
date_created: 2024-12-11T09:22:19Z
date_updated: 2024-12-11T09:22:19Z
file_id: '18647'
file_name: 2024_ScienceTalk__Clavaud_QA.mp4
file_size: 58282147
relation: supplementary_material
file_date_updated: 2024-12-11T09:22:19Z
has_accepted_license: '1'
intvolume: ' 3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '08'
oa: 1
oa_version: Published Version
publication: Science Talks
publication_identifier:
eissn:
- 2772-5693
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Shear thickening in dense suspensions: an experimental study'
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: 3
year: '2022'
...
---
_id: '12261'
abstract:
- lang: eng
text: 'Dose–response relationships are a general concept for quantitatively describing
biological systems across multiple scales, from the molecular to the whole-cell
level. A clinically relevant example is the bacterial growth response to antibiotics,
which is routinely characterized by dose–response curves. The shape of the dose–response
curve varies drastically between antibiotics and plays a key role in treatment,
drug interactions, and resistance evolution. However, the mechanisms shaping the
dose–response curve remain largely unclear. Here, we show in Escherichia coli
that the distinctively shallow dose–response curve of the antibiotic trimethoprim
is caused by a negative growth-mediated feedback loop: Trimethoprim slows growth,
which in turn weakens the effect of this antibiotic. At the molecular level, this
feedback is caused by the upregulation of the drug target dihydrofolate reductase
(FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim
but follows a universal trend line that depends primarily on the growth rate,
irrespective of its cause. Rewiring the feedback loop alters the dose–response
curve in a predictable manner, which we corroborate using a mathematical model
of cellular resource allocation and growth. Our results indicate that growth-mediated
feedback loops may shape drug responses more generally and could be exploited
to design evolutionary traps that enable selection against drug resistance.'
acknowledged_ssus:
- _id: M-Shop
acknowledgement: This work was in part supported by Human Frontier Science Program
GrantRGP0042/2013, Marie Curie Career Integration Grant303507, AustrianScience Fund
(FWF) Grant P27201-B22, and German Research Foundation(DFG) Collaborative Research
Center (SFB)1310to TB. SAA was supportedby the European Union’s Horizon2020Research
and Innovation Programunder the Marie Skłodowska-Curie Grant agreement No707352.
We wouldlike to thank the Bollenbach group for regular fruitful discussions. We
areparticularly thankful for the technical assistance of Booshini Fernando andfor
discussions of the theoretical aspects with Gerrit Ansmann. We areindebted to Bor
Kavˇciˇc for invaluable advice, help with setting up theluciferase-based growth
monitoring system, and for sharing plasmids. Weacknowledge the IST Austria Miba
Machine Shop for their support inbuilding a housing for the stacker of the plate
reader, which enabled thehigh-throughput luciferase-based experiments. We are grateful
to RosalindAllen, Bor Kavˇciˇc and Dor Russ for feedback on the manuscript. Open
Accessfunding enabled and organized by Projekt DEAL.
article_number: e10490
article_processing_charge: No
article_type: original
author:
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Tin Yau
full_name: Pang, Tin Yau
last_name: Pang
- first_name: Guillaume
full_name: Chevereau, Guillaume
last_name: Chevereau
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
- first_name: Martin J
full_name: Lercher, Martin J
last_name: Lercher
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. Growth‐mediated
negative feedback shapes quantitative antibiotic response. Molecular Systems
Biology. 2022;18(9). doi:10.15252/msb.202110490
apa: Angermayr, A., Pang, T. Y., Chevereau, G., Mitosch, K., Lercher, M. J., &
Bollenbach, M. T. (2022). Growth‐mediated negative feedback shapes quantitative
antibiotic response. Molecular Systems Biology. Embo Press. https://doi.org/10.15252/msb.202110490
chicago: Angermayr, Andreas, Tin Yau Pang, Guillaume Chevereau, Karin Mitosch, Martin
J Lercher, and Mark Tobias Bollenbach. “Growth‐mediated Negative Feedback Shapes
Quantitative Antibiotic Response.” Molecular Systems Biology. Embo Press,
2022. https://doi.org/10.15252/msb.202110490.
ieee: A. Angermayr, T. Y. Pang, G. Chevereau, K. Mitosch, M. J. Lercher, and M.
T. Bollenbach, “Growth‐mediated negative feedback shapes quantitative antibiotic
response,” Molecular Systems Biology, vol. 18, no. 9. Embo Press, 2022.
ista: Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. 2022.
Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular
Systems Biology. 18(9), e10490.
mla: Angermayr, Andreas, et al. “Growth‐mediated Negative Feedback Shapes Quantitative
Antibiotic Response.” Molecular Systems Biology, vol. 18, no. 9, e10490,
Embo Press, 2022, doi:10.15252/msb.202110490.
short: A. Angermayr, T.Y. Pang, G. Chevereau, K. Mitosch, M.J. Lercher, M.T. Bollenbach,
Molecular Systems Biology 18 (2022).
date_created: 2023-01-16T09:58:34Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2025-06-11T14:10:18Z
day: '01'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.15252/msb.202110490
external_id:
isi:
- '000856482800001'
pmid:
- '36124745'
file:
- access_level: open_access
checksum: 8b1d8f5ea20c8408acf466435fb6ae01
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:49:55Z
date_updated: 2023-01-30T09:49:55Z
file_id: '12446'
file_name: 2022_MolecularSystemsBio_Angermayr.pdf
file_size: 1098812
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:49:55Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '9'
keyword:
- Applied Mathematics
- Computational Theory and Mathematics
- General Agricultural and Biological Sciences
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- Information Systems
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Systems Biology
publication_identifier:
eissn:
- 1744-4292
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Growth‐mediated negative feedback shapes quantitative antibiotic response
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2022'
...
---
_id: '12262'
abstract:
- lang: eng
text: The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that
initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases
the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear
export, a strict requirement for downstream maturation. The molecular mechanism
of release remained elusive. Here, we report a series of cryo-EM structures that
captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae
Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion
segment ES27 form a joint docking platform that positions Drg1 for efficient extraction
of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the
Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction
by a hand-over-hand translocation mechanism. Our results uncover substrate recognition
and processing by Drg1 step by step and provide a comprehensive mechanistic picture
of the conserved modus operandi of AAA-ATPases.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "We thank M. Fromont-Racine, A. Johnson, J. Woolford, S. Rospert,
J. P. G. Ballesta and\r\nE. Hurt for supplying antibodies. The work was supported
by Boehringer Ingelheim (to\r\nD. H.), the Austrian Science Foundation FWF (grants
32536 and 32977 to H. B.), the\r\nUK Medical Research Council (MR/T012412/1 to A.
J. W.) and the German Research\r\nFoundation (Emmy Noether Programme STE 2517/1-1
and STE 2517/5-1 to F.S.). We\r\nthank Norberto Escudero-Urquijo, Pablo Castro-Hartmann
and K. Dent, Cambridge\r\nInstitute for Medical Research, for their help in cryo-EM
during early phases of this\r\nproject. This research was supported by the Scientific
Service Units of IST Austria through\r\nresources provided by the Electron Microscopy
Facility. We thank S. Keller, Institute of\r\nMolecular Biosciences (Biophysics),
University Graz for support with the quantification of\r\nthe SPR particle release
assay. We thank I. Schaffner, University of Natural Resources and\r\nLife Sciences,
Vienna for her help in early stages of the SPR experiments."
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Prattes, Michael
last_name: Prattes
- first_name: Irina
full_name: Grishkovskaya, Irina
last_name: Grishkovskaya
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Christina
full_name: Hetzmannseder, Christina
last_name: Hetzmannseder
- first_name: Gertrude
full_name: Zisser, Gertrude
last_name: Zisser
- first_name: Carolin
full_name: Sailer, Carolin
last_name: Sailer
- first_name: Vasileios
full_name: Kargas, Vasileios
last_name: Kargas
- first_name: Mathias
full_name: Loibl, Mathias
last_name: Loibl
- first_name: Magdalena
full_name: Gerhalter, Magdalena
last_name: Gerhalter
- first_name: Lisa
full_name: Kofler, Lisa
last_name: Kofler
- first_name: Alan J.
full_name: Warren, Alan J.
last_name: Warren
- first_name: Florian
full_name: Stengel, Florian
last_name: Stengel
- first_name: David
full_name: Haselbach, David
last_name: Haselbach
- first_name: Helmut
full_name: Bergler, Helmut
last_name: Bergler
citation:
ama: Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Visualizing maturation factor
extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural
& Molecular Biology. 2022;29(9):942-953. doi:10.1038/s41594-022-00832-5
apa: Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Hetzmannseder, C., Zisser,
G., Sailer, C., … Bergler, H. (2022). Visualizing maturation factor extraction
from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural & Molecular
Biology. Springer Nature. https://doi.org/10.1038/s41594-022-00832-5
chicago: Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Christina
Hetzmannseder, Gertrude Zisser, Carolin Sailer, Vasileios Kargas, et al. “Visualizing
Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.”
Nature Structural & Molecular Biology. Springer Nature, 2022. https://doi.org/10.1038/s41594-022-00832-5.
ieee: M. Prattes et al., “Visualizing maturation factor extraction from the
nascent ribosome by the AAA-ATPase Drg1,” Nature Structural & Molecular
Biology, vol. 29, no. 9. Springer Nature, pp. 942–953, 2022.
ista: Prattes M, Grishkovskaya I, Hodirnau V-V, Hetzmannseder C, Zisser G, Sailer
C, Kargas V, Loibl M, Gerhalter M, Kofler L, Warren AJ, Stengel F, Haselbach D,
Bergler H. 2022. Visualizing maturation factor extraction from the nascent ribosome
by the AAA-ATPase Drg1. Nature Structural & Molecular Biology. 29(9), 942–953.
mla: Prattes, Michael, et al. “Visualizing Maturation Factor Extraction from the
Nascent Ribosome by the AAA-ATPase Drg1.” Nature Structural & Molecular
Biology, vol. 29, no. 9, Springer Nature, 2022, pp. 942–53, doi:10.1038/s41594-022-00832-5.
short: M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, C. Hetzmannseder, G. Zisser,
C. Sailer, V. Kargas, M. Loibl, M. Gerhalter, L. Kofler, A.J. Warren, F. Stengel,
D. Haselbach, H. Bergler, Nature Structural & Molecular Biology 29 (2022)
942–953.
date_created: 2023-01-16T09:59:06Z
date_published: 2022-09-12T00:00:00Z
date_updated: 2023-08-04T09:52:20Z
day: '12'
ddc:
- '570'
department:
- _id: EM-Fac
doi: 10.1038/s41594-022-00832-5
external_id:
isi:
- '000852942100004'
pmid:
- '36097293'
file:
- access_level: open_access
checksum: 2d5c3ec01718fefd7553052b0b8a0793
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:00:04Z
date_updated: 2023-01-30T10:00:04Z
file_id: '12447'
file_name: 2022_NatureStrucMolecBio_Prattes.pdf
file_size: 9935057
relation: main_file
success: 1
file_date_updated: 2023-01-30T10:00:04Z
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
issue: '9'
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 942-953
pmid: 1
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase
Drg1
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: 29
year: '2022'
...
---
_id: '12264'
abstract:
- lang: eng
text: Reproductive isolation (RI) is a core concept in evolutionary biology. It
has been the central focus of speciation research since the modern synthesis and
is the basis by which biological species are defined. Despite this, the term is
used in seemingly different ways, and attempts to quantify RI have used very different
approaches. After showing that the field lacks a clear definition of the term,
we attempt to clarify key issues, including what RI is, how it can be quantified
in principle, and how it can be measured in practice. Following other definitions
with a genetic focus, we propose that RI is a quantitative measure of the effect
that genetic differences between populations have on gene flow. Specifically,
RI compares the flow of neutral alleles in the presence of these genetic differences
to the flow without any such differences. RI is thus greater than zero when genetic
differences between populations reduce the flow of neutral alleles between populations.
We show how RI can be quantified in a range of scenarios. A key conclusion is
that RI depends strongly on circumstances—including the spatial, temporal and
genomic context—making it difficult to compare across systems. After reviewing
methods for estimating RI from data, we conclude that it is difficult to measure
in practice. We discuss our findings in light of the goals of speciation research
and encourage the use of methods for estimating RI that integrate organismal and
genetic approaches.
acknowledgement: 'We are grateful to the participants of the ESEB satellite symposium
‘Understanding reproductive isolation: bridging conceptual barriers in speciation research’ in 2021 for the interesting discussions that helped us clarify the thoughts presented in this article. We thank Roger
Butlin, Michael Turelli and two anonymous reviewers for their thoughtful comments
on this manuscript. We are also very grateful to Roger Butlin and the Barton Group
for the continued conversa-tions about RI. In addition, we thank all participants
of the speciation survey. Part of this work was funded by the Austrian Science Fund
FWF (grant P 32166)'
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- 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: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
orcid: 0000-0001-6395-386X
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Westram AM, Stankowski S, Surendranadh P, Barton NH. What is reproductive isolation?
Journal of Evolutionary Biology. 2022;35(9):1143-1164. doi:10.1111/jeb.14005
apa: Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022).
What is reproductive isolation? Journal of Evolutionary Biology. Wiley.
https://doi.org/10.1111/jeb.14005
chicago: Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H
Barton. “What Is Reproductive Isolation?” Journal of Evolutionary Biology.
Wiley, 2022. https://doi.org/10.1111/jeb.14005.
ieee: A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “What is
reproductive isolation?,” Journal of Evolutionary Biology, vol. 35, no.
9. Wiley, pp. 1143–1164, 2022.
ista: Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. What is reproductive
isolation? Journal of Evolutionary Biology. 35(9), 1143–1164.
mla: Westram, Anja M., et al. “What Is Reproductive Isolation?” Journal of Evolutionary
Biology, vol. 35, no. 9, Wiley, 2022, pp. 1143–64, doi:10.1111/jeb.14005.
short: A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary
Biology 35 (2022) 1143–1164.
corr_author: '1'
date_created: 2023-01-16T09:59:24Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2025-04-15T08:20:40Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.14005
external_id:
isi:
- '000849851100002'
pmid:
- '36063156'
file:
- access_level: open_access
checksum: f08de57112330a7ee88d2e1b20576a1e
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:05:31Z
date_updated: 2023-01-30T10:05:31Z
file_id: '12448'
file_name: 2022_JourEvoBiology_Westram.pdf
file_size: 3146793
relation: main_file
success: 1
file_date_updated: 2023-01-30T10:05:31Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '9'
keyword:
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1143-1164
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '12265'
relation: other
status: public
scopus_import: '1'
status: public
title: What is reproductive isolation?
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: 35
year: '2022'
...
---
_id: '12265'
acknowledgement: We are very grateful to the authors of the commentaries for the interesting
discussion and to Luke Holman for handling this set of manuscripts. Part of this
work was funded by the Austrian Science Fund FWF (grant P 32166).
article_processing_charge: Yes (via OA deal)
article_type: letter_note
author:
- 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: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
orcid: 0000-0001-6395-386X
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Westram AM, Stankowski S, Surendranadh P, Barton NH. Reproductive isolation,
speciation, and the value of disagreement: A reply to the commentaries on ‘What
is reproductive isolation?’ Journal of Evolutionary Biology. 2022;35(9):1200-1205.
doi:10.1111/jeb.14082'
apa: 'Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022).
Reproductive isolation, speciation, and the value of disagreement: A reply to
the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary
Biology. Wiley. https://doi.org/10.1111/jeb.14082'
chicago: 'Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas
H Barton. “Reproductive Isolation, Speciation, and the Value of Disagreement:
A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of
Evolutionary Biology. Wiley, 2022. https://doi.org/10.1111/jeb.14082.'
ieee: 'A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “Reproductive
isolation, speciation, and the value of disagreement: A reply to the commentaries
on ‘What is reproductive isolation?,’” Journal of Evolutionary Biology,
vol. 35, no. 9. Wiley, pp. 1200–1205, 2022.'
ista: 'Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. Reproductive isolation,
speciation, and the value of disagreement: A reply to the commentaries on ‘What
is reproductive isolation?’ Journal of Evolutionary Biology. 35(9), 1200–1205.'
mla: 'Westram, Anja M., et al. “Reproductive Isolation, Speciation, and the Value
of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’”
Journal of Evolutionary Biology, vol. 35, no. 9, Wiley, 2022, pp. 1200–05,
doi:10.1111/jeb.14082.'
short: A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary
Biology 35 (2022) 1200–1205.
corr_author: '1'
date_created: 2023-01-16T09:59:37Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2025-04-15T08:20:40Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.14082
external_id:
isi:
- '000849851100009'
file:
- access_level: open_access
checksum: 27268009e5eec030bc10667a4ac5ed4c
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:14:09Z
date_updated: 2023-01-30T10:14:09Z
file_id: '12449'
file_name: 2022_JourEvoBiology_Westram_Response.pdf
file_size: 349603
relation: main_file
success: 1
file_date_updated: 2023-01-30T10:14:09Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '9'
keyword:
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1200-1205
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '12264'
relation: other
status: public
scopus_import: '1'
status: public
title: 'Reproductive isolation, speciation, and the value of disagreement: A reply
to the commentaries on ‘What is reproductive isolation?’'
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: 35
year: '2022'
...
---
_id: '12268'
abstract:
- lang: eng
text: The complexity of the microenvironment effects on cell response, show accumulating
evidence that glioblastoma (GBM) migration and invasiveness are influenced by
the mechanical rigidity of their surroundings. The epithelial–mesenchymal transition
(EMT) is a well-recognized driving force of the invasive behavior of cancer. However,
the primary mechanisms of EMT initiation and progression remain unclear. We have
previously showed that certain substrate stiffness can selectively stimulate human
GBM U251-MG and GL15 glioblastoma cell lines motility. The present study unifies
several known EMT mediators to uncover the reason of the regulation and response
to these stiffnesses. Our results revealed that changing the rigidity of the mechanical
environment tuned the response of both cell lines through change in morphological
features, epithelial-mesenchymal markers (E-, N-Cadherin), EGFR and ROS expressions
in an interrelated manner. Specifically, a stiffer microenvironment induced a
mesenchymal cell shape, a more fragmented morphology, higher intracellular cytosolic
ROS expression and lower mitochondrial ROS. Finally, we observed that cells more
motile showed a more depolarized mitochondrial membrane potential. Unravelling
the process that regulates GBM cells’ infiltrative behavior could provide new
opportunities for identification of new targets and less invasive approaches for
treatment.
acknowledgement: "The research leading to these results has received funding from
AIRC under IG 2021 - ID. 26328 project – P.I. Cortese Barbara and AIRC under MFAG
2015 - ID. 16803 project – “P.I. Cortese Barbara”. The authors are also grateful
to the ”Tecnopolo per la medicina di precisione” (TecnoMed Puglia) - Regione Puglia:
DGR n.2117 del 21/11/2018, CUP: B84I18000540002 and “Tecnopolo di Nanotecnologia
e Fotonica per la medicina di precisione” (TECNOMED) - FISR/MIUR-CNR: delibera CIPE
n.3449 del 7-08-2017, CUP: B83B17000010001.\r\nWe thank Dr. Francesca Pagani for
useful technical support. We thank also Irene Iacuitto, Giovanna Loffredo and Manuela
Marchetti for practical administrative support."
article_number: '983507'
article_processing_charge: No
article_type: original
author:
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Ilaria Elena
full_name: Palamà, Ilaria Elena
last_name: Palamà
- first_name: Stefania
full_name: D’Amone, Stefania
last_name: D’Amone
- first_name: Clotilde
full_name: Lauro, Clotilde
last_name: Lauro
- first_name: Maria
full_name: Rosito, Maria
last_name: Rosito
- first_name: Maddalena
full_name: Grieco, Maddalena
last_name: Grieco
- first_name: Patrizia
full_name: Ratano, Patrizia
last_name: Ratano
- first_name: Federica
full_name: Cordella, Federica
last_name: Cordella
- first_name: Caterina
full_name: Sanchini, Caterina
last_name: Sanchini
- first_name: Silvia
full_name: Di Angelantonio, Silvia
last_name: Di Angelantonio
- first_name: Davide
full_name: Ragozzino, Davide
last_name: Ragozzino
- first_name: Mariafrancesca
full_name: Cascione, Mariafrancesca
last_name: Cascione
- first_name: Giuseppe
full_name: Gigli, Giuseppe
last_name: Gigli
- first_name: Barbara
full_name: Cortese, Barbara
last_name: Cortese
citation:
ama: Basilico B, Palamà IE, D’Amone S, et al. Substrate stiffness effect on molecular
crosstalk of epithelial-mesenchymal transition mediators of human glioblastoma
cells. Frontiers in Oncology. 2022;12. doi:10.3389/fonc.2022.983507
apa: Basilico, B., Palamà, I. E., D’Amone, S., Lauro, C., Rosito, M., Grieco, M.,
… Cortese, B. (2022). Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal
transition mediators of human glioblastoma cells. Frontiers in Oncology.
Frontiers Media. https://doi.org/10.3389/fonc.2022.983507
chicago: Basilico, Bernadette, Ilaria Elena Palamà, Stefania D’Amone, Clotilde Lauro,
Maria Rosito, Maddalena Grieco, Patrizia Ratano, et al. “Substrate Stiffness Effect
on Molecular Crosstalk of Epithelial-Mesenchymal Transition Mediators of Human
Glioblastoma Cells.” Frontiers in Oncology. Frontiers Media, 2022. https://doi.org/10.3389/fonc.2022.983507.
ieee: B. Basilico et al., “Substrate stiffness effect on molecular crosstalk
of epithelial-mesenchymal transition mediators of human glioblastoma cells,” Frontiers
in Oncology, vol. 12. Frontiers Media, 2022.
ista: Basilico B, Palamà IE, D’Amone S, Lauro C, Rosito M, Grieco M, Ratano P, Cordella
F, Sanchini C, Di Angelantonio S, Ragozzino D, Cascione M, Gigli G, Cortese B.
2022. Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal
transition mediators of human glioblastoma cells. Frontiers in Oncology. 12, 983507.
mla: Basilico, Bernadette, et al. “Substrate Stiffness Effect on Molecular Crosstalk
of Epithelial-Mesenchymal Transition Mediators of Human Glioblastoma Cells.” Frontiers
in Oncology, vol. 12, 983507, Frontiers Media, 2022, doi:10.3389/fonc.2022.983507.
short: B. Basilico, I.E. Palamà, S. D’Amone, C. Lauro, M. Rosito, M. Grieco, P.
Ratano, F. Cordella, C. Sanchini, S. Di Angelantonio, D. Ragozzino, M. Cascione,
G. Gigli, B. Cortese, Frontiers in Oncology 12 (2022).
date_created: 2023-01-16T10:00:28Z
date_published: 2022-08-25T00:00:00Z
date_updated: 2023-08-04T09:54:16Z
day: '25'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.3389/fonc.2022.983507
external_id:
isi:
- '000856524900001'
pmid:
- '36091138'
file:
- access_level: open_access
checksum: efc7edf9f626af31853790c5b598a68c
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:25:21Z
date_updated: 2023-01-30T10:25:21Z
file_id: '12450'
file_name: 2022_FrontiersOntology_Basilico.pdf
file_size: 13588502
relation: main_file
success: 1
file_date_updated: 2023-01-30T10:25:21Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
keyword:
- Cancer Research
- Oncology
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Oncology
publication_identifier:
issn:
- 2234-943X
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal
transition mediators of human glioblastoma cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2022'
...
---
_id: '12269'
abstract:
- lang: eng
text: We study the thermalization of a small XX chain coupled to long, gapped XXZ
leads at either side by observing the relaxation dynamics of the whole system.
Using extensive tensor network simulations, we show that such systems, although
not integrable, appear to show either extremely slow thermalization or even lack
thereof since the two cannot be distinguished within the accuracy of our numerics.
We show that the persistent oscillations observed in the spin current in the middle
of the XX chain are related to eigenstates of the entire system located within
the gap of the boundary chains. We find from exact diagonalization that some of
these states remain strictly localized within the XX chain and do not hybridize
with the rest of the system. The frequencies of the persistent oscillations determined
by numerical simulations of dynamics match the energy differences between these
states exactly. This has important implications for open systems, where the strongly
interacting leads are often assumed to thermalize the central system. Our results
suggest that, if we employ gapped systems for the leads, this assumption does
not hold.
acknowledgement: "M.L. and T.P. acknowledge support from the European Research Council
(ERC) through the advanced grant 694544 – OMNES and the grant P1-0402 of Slovenian
Research Agency (ARRS). M.L. acknowledges support from the European Research Council
(ERC) through the starting grant 850899 – NEQuM. D.R. acknowledges support from
the Ministry of Electronics & Information Technology (MeitY), India under the grant
for “Centre for Excellence in Quantum\r\nTechnologies” with Ref. No. 4(7)/2020-ITEA. "
article_number: '054314'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
orcid: 0000-0003-0038-7068
- first_name: Dibyendu
full_name: Roy, Dibyendu
last_name: Roy
- first_name: Tomaž
full_name: Prosen, Tomaž
last_name: Prosen
citation:
ama: Ljubotina M, Roy D, Prosen T. Absence of thermalization of free systems coupled
to gapped interacting reservoirs. Physical Review B. 2022;106(5). doi:10.1103/physrevb.106.054314
apa: Ljubotina, M., Roy, D., & Prosen, T. (2022). Absence of thermalization
of free systems coupled to gapped interacting reservoirs. Physical Review B.
American Physical Society. https://doi.org/10.1103/physrevb.106.054314
chicago: Ljubotina, Marko, Dibyendu Roy, and Tomaž Prosen. “Absence of Thermalization
of Free Systems Coupled to Gapped Interacting Reservoirs.” Physical Review
B. American Physical Society, 2022. https://doi.org/10.1103/physrevb.106.054314.
ieee: M. Ljubotina, D. Roy, and T. Prosen, “Absence of thermalization of free systems
coupled to gapped interacting reservoirs,” Physical Review B, vol. 106,
no. 5. American Physical Society, 2022.
ista: Ljubotina M, Roy D, Prosen T. 2022. Absence of thermalization of free systems
coupled to gapped interacting reservoirs. Physical Review B. 106(5), 054314.
mla: Ljubotina, Marko, et al. “Absence of Thermalization of Free Systems Coupled
to Gapped Interacting Reservoirs.” Physical Review B, vol. 106, no. 5,
054314, American Physical Society, 2022, doi:10.1103/physrevb.106.054314.
short: M. Ljubotina, D. Roy, T. Prosen, Physical Review B 106 (2022).
date_created: 2023-01-16T10:00:39Z
date_published: 2022-08-31T00:00:00Z
date_updated: 2025-04-14T07:52:06Z
day: '31'
department:
- _id: MaSe
doi: 10.1103/physrevb.106.054314
ec_funded: 1
external_id:
arxiv:
- '2106.08373'
isi:
- '000861332900005'
intvolume: ' 106'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2106.08373
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Absence of thermalization of free systems coupled to gapped interacting reservoirs
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 106
year: '2022'
...
---
_id: '12273'
abstract:
- lang: eng
text: We study communication in the presence of a jamming adversary where quadratic
power constraints are imposed on the transmitter and the jammer. The jamming signal
is allowed to be a function of the codebook, and a noncausal but noisy observation
of the transmitted codeword. For a certain range of the noise-to-signal ratios
(NSRs) of the transmitter and the jammer, we are able to characterize the capacity
of this channel under deterministic encoding or stochastic encoding, i.e., with
no common randomness between the encoder/decoder pair. For the remaining NSR regimes,
we determine the capacity under the assumption of a small amount of common randomness
(at most 2log(n) bits in one sub-regime, and at most Ω(n) bits in the other sub-regime)
available to the encoder-decoder pair. Our proof techniques involve a novel myopic
list-decoding result for achievability, and a Plotkin-type push attack for the
converse in a subregion of the NSRs, both of which may be of independent interest.
We also give bounds on the strong secrecy capacity of this channel assuming that
the jammer is simultaneously eavesdropping.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
orcid: 0000-0002-6465-6258
- first_name: Shashank
full_name: Vatedka, Shashank
last_name: Vatedka
- first_name: Sidharth
full_name: Jaggi, Sidharth
last_name: Jaggi
- first_name: Anand D.
full_name: Sarwate, Anand D.
last_name: Sarwate
citation:
ama: Zhang Y, Vatedka S, Jaggi S, Sarwate AD. Quadratically constrained myopic adversarial
channels. IEEE Transactions on Information Theory. 2022;68(8):4901-4948.
doi:10.1109/tit.2022.3167554
apa: Zhang, Y., Vatedka, S., Jaggi, S., & Sarwate, A. D. (2022). Quadratically
constrained myopic adversarial channels. IEEE Transactions on Information Theory.
Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/tit.2022.3167554
chicago: Zhang, Yihan, Shashank Vatedka, Sidharth Jaggi, and Anand D. Sarwate. “Quadratically
Constrained Myopic Adversarial Channels.” IEEE Transactions on Information
Theory. Institute of Electrical and Electronics Engineers, 2022. https://doi.org/10.1109/tit.2022.3167554.
ieee: Y. Zhang, S. Vatedka, S. Jaggi, and A. D. Sarwate, “Quadratically constrained
myopic adversarial channels,” IEEE Transactions on Information Theory,
vol. 68, no. 8. Institute of Electrical and Electronics Engineers, pp. 4901–4948,
2022.
ista: Zhang Y, Vatedka S, Jaggi S, Sarwate AD. 2022. Quadratically constrained myopic
adversarial channels. IEEE Transactions on Information Theory. 68(8), 4901–4948.
mla: Zhang, Yihan, et al. “Quadratically Constrained Myopic Adversarial Channels.”
IEEE Transactions on Information Theory, vol. 68, no. 8, Institute of Electrical
and Electronics Engineers, 2022, pp. 4901–48, doi:10.1109/tit.2022.3167554.
short: Y. Zhang, S. Vatedka, S. Jaggi, A.D. Sarwate, IEEE Transactions on Information
Theory 68 (2022) 4901–4948.
corr_author: '1'
date_created: 2023-01-16T10:01:19Z
date_published: 2022-08-01T00:00:00Z
date_updated: 2024-10-09T21:03:54Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/tit.2022.3167554
external_id:
arxiv:
- '1801.05951'
isi:
- '000838527100004'
intvolume: ' 68'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1801.05951
month: '08'
oa: 1
oa_version: Preprint
page: 4901-4948
publication: IEEE Transactions on Information Theory
publication_identifier:
eissn:
- 1557-9654
issn:
- 0018-9448
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quadratically constrained myopic adversarial channels
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 68
year: '2022'
...
---
_id: '12274'
abstract:
- lang: eng
text: The morphology and functionality of the epithelial lining differ along the
intestinal tract, but tissue renewal at all sites is driven by stem cells at the
base of crypts1,2,3. Whether stem cell numbers and behaviour vary at different
sites is unknown. Here we show using intravital microscopy that, despite similarities
in the number and distribution of proliferative cells with an Lgr5 signature in
mice, small intestinal crypts contain twice as many effective stem cells as large
intestinal crypts. We find that, although passively displaced by a conveyor-belt-like
upward movement, small intestinal cells positioned away from the crypt base can
function as long-term effective stem cells owing to Wnt-dependent retrograde cellular
movement. By contrast, the near absence of retrograde movement in the large intestine
restricts cell repositioning, leading to a reduction in effective stem cell number.
Moreover, after suppression of the retrograde movement in the small intestine,
the number of effective stem cells is reduced, and the rate of monoclonal conversion
of crypts is accelerated. Together, these results show that the number of effective
stem cells is determined by active retrograde movement, revealing a new channel
of stem cell regulation that can be experimentally and pharmacologically manipulated.
acknowledgement: We thank the members of the van Rheenen laboratory for reading the
manuscript, and the members of the bioimaging, FACS and animal facility of the NKI
for experimental support. We acknowledge the staff at the MedH Flow Cytometry core
facility, Karolinska Institutet, and LCI facility/Nikon Center of Excellence, Karolinska
Institutet. This work was financially supported by the Netherlands Organization
of Scientific Research NWO (Veni grant 863.15.011 to S.I.J.E. and Vici grant 09150182110004
to J.v.R.) and the CancerGenomics.nl (Netherlands Organisation for Scientific Research)
program (to J.v.R.) the Doctor Josef Steiner Foundation (to J.v.R). B.D.S. acknowledges
funding from the Royal Society E.P. Abraham Research Professorship (RP\R1\180165)
and the Wellcome Trust (098357/Z/12/Z and 219478/Z/19/Z). B.C.-M. acknowledges the
support of the field of excellence ‘Complexity of life in basic research and innovation’
of the University of Graz. O.J.S. and their laboratory acknowledge CRUK core funding
to the CRUK Beatson Institute (A17196 and A31287) and CRUK core funding to the Sansom
laboratory (A21139). P.K. and their laboratory are supported by grants from the
Swedish Research Council (2018-03078), Cancerfonden (190634), Academy of Finland
Centre of Excellence (266869, 304591 and 320185) and the Jane and Aatos Erkko Foundation.
P.L. has received funding from the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (grant agreement no. 758617).
E.H. acknowledges funding from the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (grant agreement no. 851288).
article_processing_charge: No
article_type: original
author:
- first_name: Maria
full_name: Azkanaz, Maria
last_name: Azkanaz
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Saskia I. J.
full_name: Ellenbroek, Saskia I. J.
last_name: Ellenbroek
- first_name: Lotte
full_name: Bruens, Lotte
last_name: Bruens
- first_name: Anna T.
full_name: Webb, Anna T.
last_name: Webb
- first_name: Dimitrios
full_name: Laskaris, Dimitrios
last_name: Laskaris
- first_name: Koen C.
full_name: Oost, Koen C.
last_name: Oost
- first_name: Simona J. A.
full_name: Lafirenze, Simona J. A.
last_name: Lafirenze
- first_name: Karl
full_name: Annusver, Karl
last_name: Annusver
- first_name: Hendrik A.
full_name: Messal, Hendrik A.
last_name: Messal
- first_name: Sharif
full_name: Iqbal, Sharif
last_name: Iqbal
- first_name: Dustin J.
full_name: Flanagan, Dustin J.
last_name: Flanagan
- first_name: David J.
full_name: Huels, David J.
last_name: Huels
- first_name: Felipe
full_name: Rojas-Rodríguez, Felipe
last_name: Rojas-Rodríguez
- first_name: Miguel
full_name: Vizoso, Miguel
last_name: Vizoso
- first_name: Maria
full_name: Kasper, Maria
last_name: Kasper
- first_name: Owen J.
full_name: Sansom, Owen J.
last_name: Sansom
- first_name: Hugo J.
full_name: Snippert, Hugo J.
last_name: Snippert
- first_name: Prisca
full_name: Liberali, Prisca
last_name: Liberali
- first_name: Benjamin D.
full_name: Simons, Benjamin D.
last_name: Simons
- first_name: Pekka
full_name: Katajisto, Pekka
last_name: Katajisto
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Jacco
full_name: van Rheenen, Jacco
last_name: van Rheenen
citation:
ama: Azkanaz M, Corominas-Murtra B, Ellenbroek SIJ, et al. Retrograde movements
determine effective stem cell numbers in the intestine. Nature. 2022;607(7919):548-554.
doi:10.1038/s41586-022-04962-0
apa: Azkanaz, M., Corominas-Murtra, B., Ellenbroek, S. I. J., Bruens, L., Webb,
A. T., Laskaris, D., … van Rheenen, J. (2022). Retrograde movements determine
effective stem cell numbers in the intestine. Nature. Springer Nature.
https://doi.org/10.1038/s41586-022-04962-0
chicago: Azkanaz, Maria, Bernat Corominas-Murtra, Saskia I. J. Ellenbroek, Lotte
Bruens, Anna T. Webb, Dimitrios Laskaris, Koen C. Oost, et al. “Retrograde Movements
Determine Effective Stem Cell Numbers in the Intestine.” Nature. Springer
Nature, 2022. https://doi.org/10.1038/s41586-022-04962-0.
ieee: M. Azkanaz et al., “Retrograde movements determine effective stem cell
numbers in the intestine,” Nature, vol. 607, no. 7919. Springer Nature,
pp. 548–554, 2022.
ista: Azkanaz M, Corominas-Murtra B, Ellenbroek SIJ, Bruens L, Webb AT, Laskaris
D, Oost KC, Lafirenze SJA, Annusver K, Messal HA, Iqbal S, Flanagan DJ, Huels
DJ, Rojas-Rodríguez F, Vizoso M, Kasper M, Sansom OJ, Snippert HJ, Liberali P,
Simons BD, Katajisto P, Hannezo EB, van Rheenen J. 2022. Retrograde movements
determine effective stem cell numbers in the intestine. Nature. 607(7919), 548–554.
mla: Azkanaz, Maria, et al. “Retrograde Movements Determine Effective Stem Cell
Numbers in the Intestine.” Nature, vol. 607, no. 7919, Springer Nature,
2022, pp. 548–54, doi:10.1038/s41586-022-04962-0.
short: M. Azkanaz, B. Corominas-Murtra, S.I.J. Ellenbroek, L. Bruens, A.T. Webb,
D. Laskaris, K.C. Oost, S.J.A. Lafirenze, K. Annusver, H.A. Messal, S. Iqbal,
D.J. Flanagan, D.J. Huels, F. Rojas-Rodríguez, M. Vizoso, M. Kasper, O.J. Sansom,
H.J. Snippert, P. Liberali, B.D. Simons, P. Katajisto, E.B. Hannezo, J. van Rheenen,
Nature 607 (2022) 548–554.
corr_author: '1'
date_created: 2023-01-16T10:01:29Z
date_published: 2022-07-13T00:00:00Z
date_updated: 2025-04-14T07:52:27Z
day: '13'
department:
- _id: EdHa
doi: 10.1038/s41586-022-04962-0
ec_funded: 1
external_id:
isi:
- '000824430000004'
pmid:
- '35831497'
intvolume: ' 607'
isi: 1
issue: '7919'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://helda.helsinki.fi/items/94433455-4854-45c0-9de8-7326caea8780
month: '07'
oa: 1
oa_version: Submitted Version
page: 548-554
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/JaccovanRheenenLab/Retrograde_movement_Azkanaz_Nature_2022
scopus_import: '1'
status: public
title: Retrograde movements determine effective stem cell numbers in the intestine
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 607
year: '2022'
...
---
_id: '12275'
abstract:
- lang: eng
text: N-glycans are molecularly diverse sugars borne by over 70% of proteins transiting
the secretory pathway and have been implicated in protein folding, stability,
and localization. Mutations in genes important for N-glycosylation result in congenital
disorders of glycosylation that are often associated with intellectual disability.
Here, we show that structurally distinct N-glycans regulate an extracellular protein
complex involved in the patterning of somatosensory dendrites in Caenorhabditis
elegans. Specifically, aman-2/Golgi alpha-mannosidase II, a conserved key enzyme
in the biosynthesis of specific N-glycans, regulates the activity of the Menorin
adhesion complex without obviously affecting the protein stability and localization
of its components. AMAN-2 functions cell-autonomously to allow for decoration
of the neuronal transmembrane receptor DMA-1/LRR-TM with the correct set of high-mannose/hybrid/paucimannose
N-glycans. Moreover, distinct types of N-glycans on specific N-glycosylation sites
regulate DMA-1/LRR-TM receptor function, which, together with three other extracellular
proteins, forms the Menorin adhesion complex. In summary, specific N-glycan structures
regulate dendrite patterning by coordinating the activity of an extracellular
adhesion complex, suggesting that the molecular diversity of N-glycans can contribute
to developmental specificity in the nervous system.
acknowledgement: 'We thank Scott Garforth, Sarah Garrett, Peri Kurshan, Yehuda Salzberg,
PamelaStanley, Robert Townley, and members of the B€ulow laboratory for commentson
the manuscript or helpful discussions during the course of this work. Wethank David
Miller, Shohei Mitani, Kang Shen, and Iain Wilson for reagents,and Yuji Kohara for
theyk11g705cDNA clone. We are grateful to MeeraTrivedi for sharing thedzIs117strain
prior to publication. Some strains wereprovided by the Caenorhabditis Genome Center
(funded by the NIH Office ofResearch Infrastructure Programs P40OD010440). This
work was supportedby grants from the National Institute of Health (NIH): R01NS096672andR21NS111145to
HEB; F31NS100370to MR; T32GM007288and F31HD066967to CADB; P30HD071593to Albert Einstein
College of Medicine. We acknowl-edge support to MR by the Department of Neuroscience.
NJRS was the recipi-ent of a Colciencias-Fulbright Fellowship and HEB of an Irma
T. Hirschl/Monique Weill-Caulier research fellowship'
article_number: e54163
article_processing_charge: No
article_type: original
author:
- first_name: Maisha
full_name: Rahman, Maisha
last_name: Rahman
- first_name: Nelson
full_name: Ramirez, Nelson
id: 39831956-E4FE-11E9-85DE-0DC7E5697425
last_name: Ramirez
- first_name: Carlos A
full_name: Diaz‐Balzac, Carlos A
last_name: Diaz‐Balzac
- first_name: Hannes E
full_name: Bülow, Hannes E
last_name: Bülow
citation:
ama: Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. Specific N-glycans regulate
an extracellular adhesion complex during somatosensory dendrite patterning. EMBO
Reports. 2022;23(7). doi:10.15252/embr.202154163
apa: Rahman, M., Ramirez, N., Diaz‐Balzac, C. A., & Bülow, H. E. (2022). Specific
N-glycans regulate an extracellular adhesion complex during somatosensory dendrite
patterning. EMBO Reports. Embo Press. https://doi.org/10.15252/embr.202154163
chicago: Rahman, Maisha, Nelson Ramirez, Carlos A Diaz‐Balzac, and Hannes E Bülow.
“Specific N-Glycans Regulate an Extracellular Adhesion Complex during Somatosensory
Dendrite Patterning.” EMBO Reports. Embo Press, 2022. https://doi.org/10.15252/embr.202154163.
ieee: M. Rahman, N. Ramirez, C. A. Diaz‐Balzac, and H. E. Bülow, “Specific N-glycans
regulate an extracellular adhesion complex during somatosensory dendrite patterning,”
EMBO Reports, vol. 23, no. 7. Embo Press, 2022.
ista: Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. 2022. Specific N-glycans regulate
an extracellular adhesion complex during somatosensory dendrite patterning. EMBO
Reports. 23(7), e54163.
mla: Rahman, Maisha, et al. “Specific N-Glycans Regulate an Extracellular Adhesion
Complex during Somatosensory Dendrite Patterning.” EMBO Reports, vol. 23,
no. 7, e54163, Embo Press, 2022, doi:10.15252/embr.202154163.
short: M. Rahman, N. Ramirez, C.A. Diaz‐Balzac, H.E. Bülow, EMBO Reports 23 (2022).
date_created: 2023-01-16T10:01:44Z
date_published: 2022-07-05T00:00:00Z
date_updated: 2023-10-03T11:25:54Z
day: '05'
department:
- _id: MaDe
doi: 10.15252/embr.202154163
external_id:
isi:
- '000797302700001'
pmid:
- '35586945'
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '7'
keyword:
- Genetics
- Molecular Biology
- Biochemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.15252/embr.202154163
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: EMBO Reports
publication_identifier:
eissn:
- 1469-3178
issn:
- 1469-221X
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Specific N-glycans regulate an extracellular adhesion complex during somatosensory
dendrite patterning
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2022'
...
---
_id: '12276'
abstract:
- lang: eng
text: Ongoing development of quantum simulators allows for a progressively finer
degree of control of quantum many-body systems. This motivates the development
of efficient approaches to facilitate the control of such systems and enable the
preparation of nontrivial quantum states. Here we formulate an approach to control
quantum systems based on matrix product states (MPSs). We compare counterdiabatic
and leakage minimization approaches to the so-called local steering problem that
consists in finding the best value of the control parameters for generating a
unitary evolution of the specific MPS in a given direction. In order to benchmark
the different approaches, we apply them to the generalization of the PXP model
known to exhibit coherent quantum dynamics due to quantum many-body scars. We
find that the leakage-based approach generally outperforms the counterdiabatic
framework and use it to construct a Floquet model with quantum scars. We perform
the first steps towards global trajectory optimization and demonstrate entanglement
steering capabilities in the generalized PXP model. Finally, we apply our leakage
minimization approach to construct quantum scars in the periodically driven nonintegrable
Ising model.
acknowledgement: We thank A. A. Michailidis for insightful discussions. M.L. and M.S.
acknowledge support from the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 850899).
D.A. is supported by the European Research Council (ERC) under the European Union’s
Horizon 2020 research and innovation programme (Grant Agreement No. 864597) and
by the Swiss National Science Foundation. The infinite TEBD simulations were performed
using the ITensor library [67].
article_number: '030343'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
orcid: 0000-0003-0038-7068
- first_name: Barbara
full_name: Roos, Barbara
id: 5DA90512-D80F-11E9-8994-2E2EE6697425
last_name: Roos
orcid: 0000-0002-9071-5880
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Ljubotina M, Roos B, Abanin DA, Serbyn M. Optimal steering of matrix product
states and quantum many-body scars. PRX Quantum. 2022;3(3). doi:10.1103/prxquantum.3.030343
apa: Ljubotina, M., Roos, B., Abanin, D. A., & Serbyn, M. (2022). Optimal steering
of matrix product states and quantum many-body scars. PRX Quantum. American
Physical Society. https://doi.org/10.1103/prxquantum.3.030343
chicago: Ljubotina, Marko, Barbara Roos, Dmitry A. Abanin, and Maksym Serbyn. “Optimal
Steering of Matrix Product States and Quantum Many-Body Scars.” PRX Quantum.
American Physical Society, 2022. https://doi.org/10.1103/prxquantum.3.030343.
ieee: M. Ljubotina, B. Roos, D. A. Abanin, and M. Serbyn, “Optimal steering of matrix
product states and quantum many-body scars,” PRX Quantum, vol. 3, no. 3.
American Physical Society, 2022.
ista: Ljubotina M, Roos B, Abanin DA, Serbyn M. 2022. Optimal steering of matrix
product states and quantum many-body scars. PRX Quantum. 3(3), 030343.
mla: Ljubotina, Marko, et al. “Optimal Steering of Matrix Product States and Quantum
Many-Body Scars.” PRX Quantum, vol. 3, no. 3, 030343, American Physical
Society, 2022, doi:10.1103/prxquantum.3.030343.
short: M. Ljubotina, B. Roos, D.A. Abanin, M. Serbyn, PRX Quantum 3 (2022).
corr_author: '1'
date_created: 2023-01-16T10:01:56Z
date_published: 2022-09-23T00:00:00Z
date_updated: 2025-04-14T07:52:07Z
day: '23'
ddc:
- '530'
department:
- _id: MaSe
- _id: RoSe
doi: 10.1103/prxquantum.3.030343
ec_funded: 1
external_id:
arxiv:
- '2204.02899'
file:
- access_level: open_access
checksum: ef8f0a1b5a019b3958009162de0fa4c3
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T11:02:50Z
date_updated: 2023-01-30T11:02:50Z
file_id: '12457'
file_name: 2022_PRXQuantum_Ljubotina.pdf
file_size: 7661905
relation: main_file
success: 1
file_date_updated: 2023-01-30T11:02:50Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '3'
keyword:
- General Medicine
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: PRX Quantum
publication_identifier:
eissn:
- 2691-3399
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimal steering of matrix product states and quantum many-body scars
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2022'
...
---
_id: '12277'
abstract:
- lang: eng
text: Cell migration in confining physiological environments relies on the concerted
dynamics of several cellular components, including protrusions, adhesions with
the environment, and the cell nucleus. However, it remains poorly understood how
the dynamic interplay of these components and the cell polarity determine the
emergent migration behavior at the cellular scale. Here, we combine data-driven
inference with a mechanistic bottom-up approach to develop a model for protrusion
and polarity dynamics in confined cell migration, revealing how the cellular dynamics
adapt to confining geometries. Specifically, we use experimental data of joint
protrusion-nucleus migration trajectories of cells on confining micropatterns
to systematically determine a mechanistic model linking the stochastic dynamics
of cell polarity, protrusions, and nucleus. This model indicates that the cellular
dynamics adapt to confining constrictions through a switch in the polarity dynamics
from a negative to a positive self-reinforcing feedback loop. Our model further
reveals how this feedback loop leads to stereotypical cycles of protrusion-nucleus
dynamics that drive the migration of the cell through constrictions. These cycles
are disrupted upon perturbation of cytoskeletal components, indicating that the
positive feedback is controlled by cellular migration mechanisms. Our data-driven
theoretical approach therefore identifies polarity feedback adaptation as a key
mechanism in confined cell migration.
acknowledgement: "We thank Grzegorz Gradziuk, StevenRiedijk, Janni Harju, and M. R.
Schnucki for helpful discussions, and Andriy Goychuk for advice on the image segmentation.
This project\r\nwas funded by the Deutsche Forschungsgemeinschaft (DFG, German Research
Foundation), Project No. 201269156—SFB 1032 (Projects B01 and B12). D. B. B. is
supported by the NOMIS Foundation and in part by a DFG fellowship within the Graduate
School of Quantitative Biosciences Munich (QBM), as well as by the Joachim Herz
Stiftung."
article_number: '031041'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Matthew
full_name: Schmitt, Matthew
last_name: Schmitt
- first_name: Alexandra
full_name: Fink, Alexandra
last_name: Fink
- first_name: Georg
full_name: Ladurner, Georg
last_name: Ladurner
- first_name: Johannes
full_name: Flommersfeld, Johannes
last_name: Flommersfeld
- first_name: Nicolas
full_name: Arlt, Nicolas
last_name: Arlt
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Joachim O.
full_name: Rädler, Joachim O.
last_name: Rädler
- first_name: Chase P.
full_name: Broedersz, Chase P.
last_name: Broedersz
citation:
ama: Brückner D, Schmitt M, Fink A, et al. Geometry adaptation of protrusion and
polarity dynamics in confined cell migration. Physical Review X. 2022;12(3).
doi:10.1103/physrevx.12.031041
apa: Brückner, D., Schmitt, M., Fink, A., Ladurner, G., Flommersfeld, J., Arlt,
N., … Broedersz, C. P. (2022). Geometry adaptation of protrusion and polarity
dynamics in confined cell migration. Physical Review X. American Physical
Society. https://doi.org/10.1103/physrevx.12.031041
chicago: Brückner, David, Matthew Schmitt, Alexandra Fink, Georg Ladurner, Johannes
Flommersfeld, Nicolas Arlt, Edouard B Hannezo, Joachim O. Rädler, and Chase P.
Broedersz. “Geometry Adaptation of Protrusion and Polarity Dynamics in Confined
Cell Migration.” Physical Review X. American Physical Society, 2022. https://doi.org/10.1103/physrevx.12.031041.
ieee: D. Brückner et al., “Geometry adaptation of protrusion and polarity
dynamics in confined cell migration,” Physical Review X, vol. 12, no. 3.
American Physical Society, 2022.
ista: Brückner D, Schmitt M, Fink A, Ladurner G, Flommersfeld J, Arlt N, Hannezo
EB, Rädler JO, Broedersz CP. 2022. Geometry adaptation of protrusion and polarity
dynamics in confined cell migration. Physical Review X. 12(3), 031041.
mla: Brückner, David, et al. “Geometry Adaptation of Protrusion and Polarity Dynamics
in Confined Cell Migration.” Physical Review X, vol. 12, no. 3, 031041,
American Physical Society, 2022, doi:10.1103/physrevx.12.031041.
short: D. Brückner, M. Schmitt, A. Fink, G. Ladurner, J. Flommersfeld, N. Arlt,
E.B. Hannezo, J.O. Rädler, C.P. Broedersz, Physical Review X 12 (2022).
date_created: 2023-01-16T10:02:06Z
date_published: 2022-09-20T00:00:00Z
date_updated: 2023-08-04T10:25:49Z
day: '20'
ddc:
- '530'
- '570'
department:
- _id: EdHa
doi: 10.1103/physrevx.12.031041
external_id:
arxiv:
- '2106.01014'
isi:
- '000861534700001'
file:
- access_level: open_access
checksum: 40a8fbc3663bf07b37cb80020974d40d
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T11:07:27Z
date_updated: 2023-01-30T11:07:27Z
file_id: '12458'
file_name: 2022_PhysicalReviewX_Brueckner.pdf
file_size: 4686804
relation: main_file
success: 1
file_date_updated: 2023-01-30T11:07:27Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '3'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Physical Review X
publication_identifier:
issn:
- 2160-3308
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometry adaptation of protrusion and polarity dynamics in confined cell migration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2022'
...
---
_id: '12278'
abstract:
- lang: eng
text: Mercury telluride (HgTe) thin films with a critical thickness of 6.5 nm are
predicted to possess a gapless Dirac-like band structure. We report a comprehensive
study on gated and optically doped samples by magnetooptical spectroscopy in the
THz range. The quasi-classical analysis of the cyclotron resonance allowed the
mapping of the band dispersion of Dirac charge carriers in a broad range of electron
and hole doping. A smooth transition through the charge neutrality point between
Dirac holes and electrons was observed. An additional peak coming from a second
type of holes with an almost density-independent mass of around 0.04m0 was detected
in the hole-doping range and attributed to an asymmetric spin splitting of the
Dirac cone. Spectroscopic evidence for disorder-induced band energy fluctuations
could not be detected in present cyclotron resonance experiments.
acknowledgement: "This work was supported by the Austrian Science Funds (W1243, I
3456-N27, I 5539-N).\r\nOpen Access Funding by the Austrian Science Fund (FWF)."
article_number: '2492'
article_processing_charge: Yes
article_type: original
author:
- first_name: Alexey
full_name: Shuvaev, Alexey
last_name: Shuvaev
- first_name: Uladzislau
full_name: Dziom, Uladzislau
id: 6A9A37C2-8C5C-11E9-AE53-F2FDE5697425
last_name: Dziom
orcid: 0000-0002-1648-0999
- first_name: Jan
full_name: Gospodarič, Jan
last_name: Gospodarič
- first_name: Elena G.
full_name: Novik, Elena G.
last_name: Novik
- first_name: Alena A.
full_name: Dobretsova, Alena A.
last_name: Dobretsova
- first_name: Nikolay N.
full_name: Mikhailov, Nikolay N.
last_name: Mikhailov
- first_name: Ze Don
full_name: Kvon, Ze Don
last_name: Kvon
- first_name: Andrei
full_name: Pimenov, Andrei
last_name: Pimenov
citation:
ama: Shuvaev A, Dziom V, Gospodarič J, et al. Band structure near the Dirac Point
in HgTe quantum wells with critical thickness. Nanomaterials. 2022;12(14).
doi:10.3390/nano12142492
apa: Shuvaev, A., Dziom, V., Gospodarič, J., Novik, E. G., Dobretsova, A. A., Mikhailov,
N. N., … Pimenov, A. (2022). Band structure near the Dirac Point in HgTe quantum
wells with critical thickness. Nanomaterials. MDPI. https://doi.org/10.3390/nano12142492
chicago: Shuvaev, Alexey, Vlad Dziom, Jan Gospodarič, Elena G. Novik, Alena A. Dobretsova,
Nikolay N. Mikhailov, Ze Don Kvon, and Andrei Pimenov. “Band Structure near the
Dirac Point in HgTe Quantum Wells with Critical Thickness.” Nanomaterials.
MDPI, 2022. https://doi.org/10.3390/nano12142492.
ieee: A. Shuvaev et al., “Band structure near the Dirac Point in HgTe quantum
wells with critical thickness,” Nanomaterials, vol. 12, no. 14. MDPI, 2022.
ista: Shuvaev A, Dziom V, Gospodarič J, Novik EG, Dobretsova AA, Mikhailov NN, Kvon
ZD, Pimenov A. 2022. Band structure near the Dirac Point in HgTe quantum wells
with critical thickness. Nanomaterials. 12(14), 2492.
mla: Shuvaev, Alexey, et al. “Band Structure near the Dirac Point in HgTe Quantum
Wells with Critical Thickness.” Nanomaterials, vol. 12, no. 14, 2492, MDPI,
2022, doi:10.3390/nano12142492.
short: A. Shuvaev, V. Dziom, J. Gospodarič, E.G. Novik, A.A. Dobretsova, N.N. Mikhailov,
Z.D. Kvon, A. Pimenov, Nanomaterials 12 (2022).
date_created: 2023-01-16T10:02:31Z
date_published: 2022-07-20T00:00:00Z
date_updated: 2025-06-11T13:45:36Z
day: '20'
ddc:
- '530'
department:
- _id: ZhAl
doi: 10.3390/nano12142492
external_id:
isi:
- '000834401600001'
pmid:
- '35889716'
file:
- access_level: open_access
checksum: efad6742f89f39a18bec63116dd689a0
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T11:16:54Z
date_updated: 2023-01-30T11:16:54Z
file_id: '12459'
file_name: 2022_Nanomaterials_Shuvaev.pdf
file_size: 464840
relation: main_file
success: 1
file_date_updated: 2023-01-30T11:16:54Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '14'
keyword:
- General Materials Science
- General Chemical Engineering
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nanomaterials
publication_identifier:
issn:
- 2079-4991
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Band structure near the Dirac Point in HgTe quantum wells with critical thickness
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2022'
...
---
_id: '12279'
abstract:
- lang: eng
text: We report frictional drag reduction and a complete flow relaminarization of
elastic turbulence (ET) at vanishing inertia in a viscoelastic channel flow past
an obstacle. We show that the intensity of the observed elastic waves and wall-normal
vorticity correlate well with the measured drag above the onset of ET. Moreover,
we find that the elastic wave frequency grows with the Weissenberg number, and
at sufficiently high frequency it causes a decay of the elastic waves, resulting
in ET attenuation and drag reduction. Thus, this allows us to substantiate a physical
mechanism, involving the interaction of elastic waves with wall-normal vorticity
fluctuations, leading to the drag reduction and relaminarization phenomena at
low Reynolds number.
acknowledgement: "We thank G. Falkovich for discussion and Guy Han for technical support.
We are grateful to N. Jha for his help in µPIV measurements. This work is partially
supported by the grants from\r\nIsrael Science Foundation (ISF; grant #882/15 and
grant #784/19) and Binational USA-Israel Foundation (BSF;grant #2016145). "
article_number: L081301
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: M. Vijay
full_name: Kumar, M. Vijay
last_name: Kumar
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Dongyang
full_name: Li, Dongyang
last_name: Li
- first_name: Victor
full_name: Steinberg, Victor
last_name: Steinberg
citation:
ama: Kumar MV, Varshney A, Li D, Steinberg V. Relaminarization of elastic turbulence.
Physical Review Fluids. 2022;7(8). doi:10.1103/physrevfluids.7.l081301
apa: Kumar, M. V., Varshney, A., Li, D., & Steinberg, V. (2022). Relaminarization
of elastic turbulence. Physical Review Fluids. American Physical Society.
https://doi.org/10.1103/physrevfluids.7.l081301
chicago: Kumar, M. Vijay, Atul Varshney, Dongyang Li, and Victor Steinberg. “Relaminarization
of Elastic Turbulence.” Physical Review Fluids. American Physical Society,
2022. https://doi.org/10.1103/physrevfluids.7.l081301.
ieee: M. V. Kumar, A. Varshney, D. Li, and V. Steinberg, “Relaminarization of elastic
turbulence,” Physical Review Fluids, vol. 7, no. 8. American Physical Society,
2022.
ista: Kumar MV, Varshney A, Li D, Steinberg V. 2022. Relaminarization of elastic
turbulence. Physical Review Fluids. 7(8), L081301.
mla: Kumar, M. Vijay, et al. “Relaminarization of Elastic Turbulence.” Physical
Review Fluids, vol. 7, no. 8, L081301, American Physical Society, 2022, doi:10.1103/physrevfluids.7.l081301.
short: M.V. Kumar, A. Varshney, D. Li, V. Steinberg, Physical Review Fluids 7 (2022).
corr_author: '1'
date_created: 2023-01-16T10:02:40Z
date_published: 2022-08-03T00:00:00Z
date_updated: 2024-10-09T21:03:55Z
day: '03'
department:
- _id: BjHo
doi: 10.1103/physrevfluids.7.l081301
external_id:
arxiv:
- '2205.12871'
isi:
- '000836397000001'
intvolume: ' 7'
isi: 1
issue: '8'
keyword:
- Fluid Flow and Transfer Processes
- Modeling and Simulation
- Computational Mechanics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2205.12871'
month: '08'
oa: 1
oa_version: Preprint
publication: Physical Review Fluids
publication_identifier:
issn:
- 2469-990X
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Relaminarization of elastic turbulence
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 7
year: '2022'
...
---
_id: '12280'
abstract:
- lang: eng
text: 'In repeated interactions, players can use strategies that respond to the
outcome of previous rounds. Much of the existing literature on direct reciprocity
assumes that all competing individuals use the same strategy space. Here, we study
both learning and evolutionary dynamics of players that differ in the strategy
space they explore. We focus on the infinitely repeated donation game and compare
three natural strategy spaces: memory-1 strategies, which consider the last moves
of both players, reactive strategies, which respond to the last move of the co-player,
and unconditional strategies. These three strategy spaces differ in the memory
capacity that is needed. We compute the long term average payoff that is achieved
in a pairwise learning process. We find that smaller strategy spaces can dominate
larger ones. For weak selection, unconditional players dominate both reactive
and memory-1 players. For intermediate selection, reactive players dominate memory-1
players. Only for strong selection and low cost-to-benefit ratio, memory-1 players
dominate the others. We observe that the supergame between strategy spaces can
be a social dilemma: maximum payoff is achieved if both players explore a larger
strategy space, but smaller strategy spaces dominate.'
acknowledgement: "This work was supported by the European Research Council (https://erc.europa.eu/)\r\nCoG
863818 (ForM-SMArt) (to K.C.), and the European Research Council Starting Grant
850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection
and analysis, decision to publish, or preparation of the manuscript."
article_number: e1010149
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Schmid L, Hilbe C, Chatterjee K, Nowak M. Direct reciprocity between individuals
that use different strategy spaces. PLOS Computational Biology. 2022;18(6).
doi:10.1371/journal.pcbi.1010149
apa: Schmid, L., Hilbe, C., Chatterjee, K., & Nowak, M. (2022). Direct reciprocity
between individuals that use different strategy spaces. PLOS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010149
chicago: Schmid, Laura, Christian Hilbe, Krishnendu Chatterjee, and Martin Nowak.
“Direct Reciprocity between Individuals That Use Different Strategy Spaces.” PLOS
Computational Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pcbi.1010149.
ieee: L. Schmid, C. Hilbe, K. Chatterjee, and M. Nowak, “Direct reciprocity between
individuals that use different strategy spaces,” PLOS Computational Biology,
vol. 18, no. 6. Public Library of Science, 2022.
ista: Schmid L, Hilbe C, Chatterjee K, Nowak M. 2022. Direct reciprocity between
individuals that use different strategy spaces. PLOS Computational Biology. 18(6),
e1010149.
mla: Schmid, Laura, et al. “Direct Reciprocity between Individuals That Use Different
Strategy Spaces.” PLOS Computational Biology, vol. 18, no. 6, e1010149,
Public Library of Science, 2022, doi:10.1371/journal.pcbi.1010149.
short: L. Schmid, C. Hilbe, K. Chatterjee, M. Nowak, PLOS Computational Biology
18 (2022).
corr_author: '1'
date_created: 2023-01-16T10:02:51Z
date_published: 2022-06-14T00:00:00Z
date_updated: 2025-04-14T07:52:47Z
day: '14'
ddc:
- '000'
- '570'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1010149
ec_funded: 1
external_id:
isi:
- '000843626800031'
pmid:
- '35700167'
file:
- access_level: open_access
checksum: 31b6b311b6731f1658277a9dfff6632c
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T11:28:13Z
date_updated: 2023-01-30T11:28:13Z
file_id: '12460'
file_name: 2022_PlosCompBio_Schmid.pdf
file_size: 3143222
relation: main_file
success: 1
file_date_updated: 2023-01-30T11:28:13Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '6'
keyword:
- Computational Theory and Mathematics
- Cellular and Molecular Neuroscience
- Genetics
- Molecular Biology
- Ecology
- Modeling and Simulation
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: PLOS Computational Biology
publication_identifier:
eissn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Direct reciprocity between individuals that use different strategy spaces
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: 18
year: '2022'
...
---
_id: '12281'
abstract:
- lang: eng
text: We study the hydrodynamic and hydrostatic limits of the one-dimensional open
symmetric inclusion process with slow boundary. Depending on the value of the
parameter tuning the interaction rate of the bulk of the system with the boundary,
we obtain a linear heat equation with either Dirichlet, Robin or Neumann boundary
conditions as hydrodynamic equation. In our approach, we combine duality and first-second
class particle techniques to reduce the scaling limit of the inclusion process
to the limiting behavior of a single, non-interacting, particle.
acknowledgement: "C.F. and P.G. thank FCT/Portugal for support through the project
UID/MAT/04459/2013.\r\nThis project has received funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovative programme
(grant agreement No. 715734). F.S. was founded by the European Union’s Horizon 2020
research and innovation programme under the Marie-Skłodowska-Curie grant agreement
No. 754411.\r\nF.S. wishes to thank Joe P. Chen for some fruitful discussions at
an early stage of this work. F.S. thanks CAMGSD, IST, Lisbon, where part of this
work has been done, and the European research and innovative programme No. 715734
for the kind hospitality."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Chiara
full_name: Franceschini, Chiara
last_name: Franceschini
- first_name: Patrícia
full_name: Gonçalves, Patrícia
last_name: Gonçalves
- first_name: Federico
full_name: Sau, Federico
id: E1836206-9F16-11E9-8814-AEFDE5697425
last_name: Sau
citation:
ama: 'Franceschini C, Gonçalves P, Sau F. Symmetric inclusion process with slow
boundary: Hydrodynamics and hydrostatics. Bernoulli. 2022;28(2):1340-1381.
doi:10.3150/21-bej1390'
apa: 'Franceschini, C., Gonçalves, P., & Sau, F. (2022). Symmetric inclusion
process with slow boundary: Hydrodynamics and hydrostatics. Bernoulli.
Bernoulli Society for Mathematical Statistics and Probability. https://doi.org/10.3150/21-bej1390'
chicago: 'Franceschini, Chiara, Patrícia Gonçalves, and Federico Sau. “Symmetric
Inclusion Process with Slow Boundary: Hydrodynamics and Hydrostatics.” Bernoulli.
Bernoulli Society for Mathematical Statistics and Probability, 2022. https://doi.org/10.3150/21-bej1390.'
ieee: 'C. Franceschini, P. Gonçalves, and F. Sau, “Symmetric inclusion process with
slow boundary: Hydrodynamics and hydrostatics,” Bernoulli, vol. 28, no.
2. Bernoulli Society for Mathematical Statistics and Probability, pp. 1340–1381,
2022.'
ista: 'Franceschini C, Gonçalves P, Sau F. 2022. Symmetric inclusion process with
slow boundary: Hydrodynamics and hydrostatics. Bernoulli. 28(2), 1340–1381.'
mla: 'Franceschini, Chiara, et al. “Symmetric Inclusion Process with Slow Boundary:
Hydrodynamics and Hydrostatics.” Bernoulli, vol. 28, no. 2, Bernoulli Society
for Mathematical Statistics and Probability, 2022, pp. 1340–81, doi:10.3150/21-bej1390.'
short: C. Franceschini, P. Gonçalves, F. Sau, Bernoulli 28 (2022) 1340–1381.
date_created: 2023-01-16T10:03:04Z
date_published: 2022-05-01T00:00:00Z
date_updated: 2025-04-14T07:44:00Z
day: '01'
department:
- _id: JaMa
doi: 10.3150/21-bej1390
ec_funded: 1
external_id:
arxiv:
- '2007.11998'
isi:
- '000766619100025'
intvolume: ' 28'
isi: 1
issue: '2'
keyword:
- Statistics and Probability
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2007.11998
month: '05'
oa: 1
oa_version: Preprint
page: 1340-1381
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Bernoulli
publication_identifier:
issn:
- 1350-7265
publication_status: published
publisher: Bernoulli Society for Mathematical Statistics and Probability
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 28
year: '2022'
...