---
_id: '14757'
abstract:
- lang: eng
text: The cerebral cortex is comprised of a vast cell-type diversity sequentially
generated by cortical progenitor cells. Faithful progenitor lineage progression
requires the tight orchestration of distinct molecular and cellular mechanisms
regulating proper progenitor proliferation behavior and differentiation. Correct
execution of developmental programs involves a complex interplay of cell intrinsic
and tissue-wide mechanisms. Many studies over the past decades have been able
to determine a plethora of genes critically involved in cortical development.
However, only a few made use of genetic paradigms with sparse and global gene
deletion to probe cell-autonomous vs. tissue-wide contribution. In this chapter,
we will elaborate on the importance of dissecting the cell-autonomous and tissue-wide
mechanisms to gain a precise understanding of gene function during radial glial
progenitor lineage progression.
article_processing_charge: No
author:
- first_name: Ana
full_name: Villalba Requena, Ana
id: 68cb85a0-39f7-11eb-9559-9aaab4f6a247
last_name: Villalba Requena
orcid: 0000-0002-5615-5277
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: 'Villalba Requena A, Amberg N, Hippenmeyer S. Interplay of Cell‐autonomous
Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage
Progression. In: Huttner W, ed. Neocortical Neurogenesis in Development and
Evolution. Wiley; 2023:169-191. doi:10.1002/9781119860914.ch10'
apa: Villalba Requena, A., Amberg, N., & Hippenmeyer, S. (2023). Interplay of
Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial
Progenitor Lineage Progression. In W. Huttner (Ed.), Neocortical Neurogenesis
in Development and Evolution (pp. 169–191). Wiley. https://doi.org/10.1002/9781119860914.ch10
chicago: Villalba Requena, Ana, Nicole Amberg, and Simon Hippenmeyer. “Interplay
of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial
Glial Progenitor Lineage Progression.” In Neocortical Neurogenesis in Development
and Evolution, edited by Wieland Huttner, 169–91. Wiley, 2023. https://doi.org/10.1002/9781119860914.ch10.
ieee: A. Villalba Requena, N. Amberg, and S. Hippenmeyer, “Interplay of Cell‐autonomous
Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage
Progression,” in Neocortical Neurogenesis in Development and Evolution,
W. Huttner, Ed. Wiley, 2023, pp. 169–191.
ista: 'Villalba Requena A, Amberg N, Hippenmeyer S. 2023.Interplay of Cell‐autonomous
Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage
Progression. In: Neocortical Neurogenesis in Development and Evolution. , 169–191.'
mla: Villalba Requena, Ana, et al. “Interplay of Cell‐autonomous Gene Function and
Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression.”
Neocortical Neurogenesis in Development and Evolution, edited by Wieland
Huttner, Wiley, 2023, pp. 169–91, doi:10.1002/9781119860914.ch10.
short: A. Villalba Requena, N. Amberg, S. Hippenmeyer, in:, W. Huttner (Ed.), Neocortical
Neurogenesis in Development and Evolution, Wiley, 2023, pp. 169–191.
corr_author: '1'
date_created: 2024-01-08T13:16:36Z
date_published: 2023-08-08T00:00:00Z
date_updated: 2024-10-09T21:07:46Z
day: '08'
department:
- _id: SiHi
doi: 10.1002/9781119860914.ch10
editor:
- first_name: Wieland
full_name: Huttner, Wieland
last_name: Huttner
language:
- iso: eng
month: '08'
oa_version: None
page: 169-191
publication: Neocortical Neurogenesis in Development and Evolution
publication_identifier:
eisbn:
- '9781119860914'
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating
Radial Glial Progenitor Lineage Progression
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14758'
abstract:
- lang: eng
text: 'We present a flexible and efficient toolchain to symbolically solve (standard)
Rabin games, fair-adversarial Rabin games, and 2 1/2 license type-player Rabin
games. To our best knowledge, our tools are the first ones to be able to solve
these problems. Furthermore, using these flexible game solvers as a back-end,
we implemented a tool for computing correct-by-construction controllers for stochastic
dynamical systems under LTL specifications. Our implementations use the recent
theoretical result that all of these games can be solved using the same symbolic
fixpoint algorithm but utilizing different, domain specific calculations of the
involved predecessor operators. The main feature of our toolchain is the utilization
of two programming abstractions: one to separate the symbolic fixpoint computations
from the predecessor calculations, and another one to allow the integration of
different BDD libraries as back-ends. In particular, we employ a multi-threaded
execution of the fixpoint algorithm by using the multi-threaded BDD library Sylvan,
which leads to enormous computational savings.'
acknowledgement: 'Authors ordered alphabetically. R. Majumdar and A.-K. Schmuck are
partially supported by DFG project 389792660 TRR 248-CPEC. A.-K. Schmuck is additionally
funded through DFG project (SCHM 3541/1-1). K. Mallik is supported by the ERC project
ERC-2020-AdG 101020093. M. Rychlicki is supported by the EPSRC project EP/V00252X/1.
S. Soudjani is supported by the following projects: EPSRC EP/V043676/1, EIC 101070802,
and ERC 101089047.'
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
- first_name: Mateusz
full_name: Rychlicki, Mateusz
last_name: Rychlicki
- first_name: Anne-Kathrin
full_name: Schmuck, Anne-Kathrin
last_name: Schmuck
- first_name: Sadegh
full_name: Soudjani, Sadegh
last_name: Soudjani
citation:
ama: 'Majumdar R, Mallik K, Rychlicki M, Schmuck A-K, Soudjani S. A flexible toolchain
for symbolic rabin games under fair and stochastic uncertainties. In: 35th
International Conference on Computer Aided Verification. Vol 13966. Springer
Nature; 2023:3-15. doi:10.1007/978-3-031-37709-9_1'
apa: 'Majumdar, R., Mallik, K., Rychlicki, M., Schmuck, A.-K., & Soudjani, S.
(2023). A flexible toolchain for symbolic rabin games under fair and stochastic
uncertainties. In 35th International Conference on Computer Aided Verification
(Vol. 13966, pp. 3–15). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_1'
chicago: Majumdar, Rupak, Kaushik Mallik, Mateusz Rychlicki, Anne-Kathrin Schmuck,
and Sadegh Soudjani. “A Flexible Toolchain for Symbolic Rabin Games under Fair
and Stochastic Uncertainties.” In 35th International Conference on Computer
Aided Verification, 13966:3–15. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_1.
ieee: R. Majumdar, K. Mallik, M. Rychlicki, A.-K. Schmuck, and S. Soudjani, “A flexible
toolchain for symbolic rabin games under fair and stochastic uncertainties,” in
35th International Conference on Computer Aided Verification, Paris, France,
2023, vol. 13966, pp. 3–15.
ista: 'Majumdar R, Mallik K, Rychlicki M, Schmuck A-K, Soudjani S. 2023. A flexible
toolchain for symbolic rabin games under fair and stochastic uncertainties. 35th
International Conference on Computer Aided Verification. CAV: Computer Aided Verification,
LNCS, vol. 13966, 3–15.'
mla: Majumdar, Rupak, et al. “A Flexible Toolchain for Symbolic Rabin Games under
Fair and Stochastic Uncertainties.” 35th International Conference on Computer
Aided Verification, vol. 13966, Springer Nature, 2023, pp. 3–15, doi:10.1007/978-3-031-37709-9_1.
short: R. Majumdar, K. Mallik, M. Rychlicki, A.-K. Schmuck, S. Soudjani, in:, 35th
International Conference on Computer Aided Verification, Springer Nature, 2023,
pp. 3–15.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
corr_author: '1'
date_created: 2024-01-08T13:18:00Z
date_published: 2023-07-16T00:00:00Z
date_updated: 2025-09-09T14:16:49Z
day: '16'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-031-37709-9_1
ec_funded: 1
external_id:
isi:
- '001310805600001'
file:
- access_level: open_access
checksum: 1a361d83db0244fd32c03b544c294b5a
content_type: application/pdf
creator: dernst
date_created: 2024-01-09T10:01:07Z
date_updated: 2024-01-09T10:01:07Z
file_id: '14765'
file_name: 2023_LNCSCAV_Majumdar.pdf
file_size: 405147
relation: main_file
success: 1
file_date_updated: 2024-01-09T10:01:07Z
has_accepted_license: '1'
intvolume: ' 13966'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 3-15
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 35th International Conference on Computer Aided Verification
publication_identifier:
eisbn:
- '9783031377099'
eissn:
- 1611-3349
isbn:
- '9783031377082'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '14994'
relation: research_data
status: public
scopus_import: '1'
status: public
title: A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties
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: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13966
year: '2023'
...
---
_id: '14768'
abstract:
- lang: eng
text: 'In all state-of-the-art sketching and coreset techniques for clustering,
as well as in the best known fixed-parameter tractable approximation algorithms,
randomness plays a key role. For the classic k-median and k-means problems, there
are no known deterministic dimensionality reduction procedure or coreset construction
that avoid an exponential dependency on the input dimension d, the precision parameter
$\varepsilon^{-1}$ or k. Furthermore, there is no coreset construction that succeeds
with probability $1-1/n$ and whose size does not depend on the number of input
points, n. This has led researchers in the area to ask what is the power of randomness
for clustering sketches [Feldman WIREs Data Mining Knowl. Discov’20].Similarly,
the best approximation ratio achievable deterministically without a complexity
exponential in the dimension are $1+\sqrt{2}$ for k-median [Cohen-Addad, Esfandiari,
Mirrokni, Narayanan, STOC’22] and 6.12903 for k-means [Grandoni, Ostrovsky, Rabani,
Schulman, Venkat, Inf. Process. Lett.’22]. Those are the best results, even when
allowing a complexity FPT in the number of clusters k: this stands in sharp contrast
with the $(1+\varepsilon)$-approximation achievable in that case, when allowing
randomization.In this paper, we provide deterministic sketches constructions for
clustering, whose size bounds are close to the best-known randomized ones. We
show how to compute a dimension reduction onto $\varepsilon^{-O(1)} \log k$ dimensions
in time $k^{O\left(\varepsilon^{-O(1)}+\log \log k\right)}$ poly $(n d)$, and
how to build a coreset of size $O\left(k^{2} \log ^{3} k \varepsilon^{-O(1)}\right)$
in time $2^{\varepsilon^{O(1)} k \log ^{3} k}+k^{O\left(\varepsilon^{-O(1)}+\log
\log k\right)}$ poly $(n d)$. In the case where k is small, this answers an open
question of [Feldman WIDM’20] and [Munteanu and Schwiegelshohn, Künstliche Intell.
’18] on whether it is possible to efficiently compute coresets deterministically.We
also construct a deterministic algorithm for computing $(1+$ $\varepsilon)$-approximation
to k-median and k-means in high dimensional Euclidean spaces in time $2^{k^{2}
\log ^{3} k / \varepsilon^{O(1)}}$ poly $(n d)$, close to the best randomized
complexity of $2^{(k / \varepsilon)^{O(1)}}$ nd (see [Kumar, Sabharwal, Sen, JACM
10] and [Bhattacharya, Jaiswal, Kumar, TCS’18]).Furthermore, our new insights
on sketches also yield a randomized coreset construction that uses uniform sampling,
that immediately improves over the recent results of [Braverman et al. FOCS ’22]
by a factor k.'
acknowledgement: "D. Sauplic has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
No 101034413, and Grant agreement No. 101019564 “The Design of Modern Fully Dynamic
Data Structures (MoDynStruct)”.\r\nC. Schwiegelshohn acknowledges the support of
the Independent Research Fund Denmark (DFF) under a Sapere Aude Research Leader
grant No 1051-00106B."
article_processing_charge: No
arxiv: 1
author:
- first_name: Vincent
full_name: Cohen-Addad, Vincent
last_name: Cohen-Addad
- first_name: David
full_name: Saulpic, David
id: f8e48cf0-b0ff-11ed-b0e9-b4c35598f964
last_name: Saulpic
- first_name: Chris
full_name: Schwiegelshohn, Chris
last_name: Schwiegelshohn
citation:
ama: 'Cohen-Addad V, Saulpic D, Schwiegelshohn C. Deterministic clustering in high
dimensional spaces: Sketches and approximation. In: 2023 IEEE 64th Annual Symposium
on Foundations of Computer Science. IEEE; 2023:1105-1130. doi:10.1109/focs57990.2023.00066'
apa: 'Cohen-Addad, V., Saulpic, D., & Schwiegelshohn, C. (2023). Deterministic
clustering in high dimensional spaces: Sketches and approximation. In 2023
IEEE 64th Annual Symposium on Foundations of Computer Science (pp. 1105–1130).
Santa Cruz, CA, United States: IEEE. https://doi.org/10.1109/focs57990.2023.00066'
chicago: 'Cohen-Addad, Vincent, David Saulpic, and Chris Schwiegelshohn. “Deterministic
Clustering in High Dimensional Spaces: Sketches and Approximation.” In 2023
IEEE 64th Annual Symposium on Foundations of Computer Science, 1105–30. IEEE,
2023. https://doi.org/10.1109/focs57990.2023.00066.'
ieee: 'V. Cohen-Addad, D. Saulpic, and C. Schwiegelshohn, “Deterministic clustering
in high dimensional spaces: Sketches and approximation,” in 2023 IEEE 64th
Annual Symposium on Foundations of Computer Science, Santa Cruz, CA, United
States, 2023, pp. 1105–1130.'
ista: 'Cohen-Addad V, Saulpic D, Schwiegelshohn C. 2023. Deterministic clustering
in high dimensional spaces: Sketches and approximation. 2023 IEEE 64th Annual
Symposium on Foundations of Computer Science. FOCS: Foundations of Computer Science,
1105–1130.'
mla: 'Cohen-Addad, Vincent, et al. “Deterministic Clustering in High Dimensional
Spaces: Sketches and Approximation.” 2023 IEEE 64th Annual Symposium on Foundations
of Computer Science, IEEE, 2023, pp. 1105–30, doi:10.1109/focs57990.2023.00066.'
short: V. Cohen-Addad, D. Saulpic, C. Schwiegelshohn, in:, 2023 IEEE 64th Annual
Symposium on Foundations of Computer Science, IEEE, 2023, pp. 1105–1130.
conference:
end_date: 2023-11-09
location: Santa Cruz, CA, United States
name: 'FOCS: Foundations of Computer Science'
start_date: 2023-11-06
date_created: 2024-01-09T16:20:09Z
date_published: 2023-12-22T00:00:00Z
date_updated: 2025-09-09T14:17:59Z
day: '22'
department:
- _id: MoHe
doi: 10.1109/focs57990.2023.00066
ec_funded: 1
external_id:
arxiv:
- '2310.04076'
isi:
- '001137125900060'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2310.04076
month: '12'
oa: 1
oa_version: Preprint
page: 1105-1130
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
publication: 2023 IEEE 64th Annual Symposium on Foundations of Computer Science
publication_identifier:
eisbn:
- '9798350318944'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Deterministic clustering in high dimensional spaces: Sketches and approximation'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2023'
...
---
_id: '14771'
abstract:
- lang: eng
text: Pruning—that is, setting a significant subset of the parameters of a neural
network to zero—is one of the most popular methods of model compression. Yet,
several recent works have raised the issue that pruning may induce or exacerbate
bias in the output of the compressed model. Despite existing evidence for this
phenomenon, the relationship between neural network pruning and induced bias is
not well-understood. In this work, we systematically investigate and characterize
this phenomenon in Convolutional Neural Networks for computer vision. First, we
show that it is in fact possible to obtain highly-sparse models, e.g. with less
than 10% remaining weights, which do not decrease in accuracy nor substantially
increase in bias when compared to dense models. At the same time, we also find
that, at higher sparsities, pruned models exhibit higher uncertainty in their
outputs, as well as increased correlations, which we directly link to increased
bias. We propose easy-to-use criteria which, based only on the uncompressed model,
establish whether bias will increase with pruning, and identify the samples most
susceptible to biased predictions post-compression. Our code can be found at https://github.com/IST-DASLab/pruned-vision-model-bias.
acknowledgement: The authors would like to sincerely thank Sara Hooker for her feedback
during the development of this work. EI was supported in part by the FWF DK VGSCO,
grant agreement number W1260-N35. AP and DA acknowledge generous ERC support, via
Starting Grant 805223 ScaleML.
article_processing_charge: No
arxiv: 1
author:
- first_name: Eugenia B
full_name: Iofinova, Eugenia B
id: f9a17499-f6e0-11ea-865d-fdf9a3f77117
last_name: Iofinova
orcid: 0000-0002-7778-3221
- first_name: Elena-Alexandra
full_name: Peste, Elena-Alexandra
id: 32D78294-F248-11E8-B48F-1D18A9856A87
last_name: Peste
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Iofinova EB, Krumes A, Alistarh D-A. Bias in pruned vision models: In-depth
analysis and countermeasures. In: 2023 IEEE/CVF Conference on Computer Vision
and Pattern Recognition. IEEE; 2023:24364-24373. doi:10.1109/cvpr52729.2023.02334'
apa: 'Iofinova, E. B., Krumes, A., & Alistarh, D.-A. (2023). Bias in pruned
vision models: In-depth analysis and countermeasures. In 2023 IEEE/CVF Conference
on Computer Vision and Pattern Recognition (pp. 24364–24373). Vancouver, BC,
Canada: IEEE. https://doi.org/10.1109/cvpr52729.2023.02334'
chicago: 'Iofinova, Eugenia B, Alexandra Krumes, and Dan-Adrian Alistarh. “Bias
in Pruned Vision Models: In-Depth Analysis and Countermeasures.” In 2023 IEEE/CVF
Conference on Computer Vision and Pattern Recognition, 24364–73. IEEE, 2023.
https://doi.org/10.1109/cvpr52729.2023.02334.'
ieee: 'E. B. Iofinova, A. Krumes, and D.-A. Alistarh, “Bias in pruned vision models:
In-depth analysis and countermeasures,” in 2023 IEEE/CVF Conference on Computer
Vision and Pattern Recognition, Vancouver, BC, Canada, 2023, pp. 24364–24373.'
ista: 'Iofinova EB, Krumes A, Alistarh D-A. 2023. Bias in pruned vision models:
In-depth analysis and countermeasures. 2023 IEEE/CVF Conference on Computer Vision
and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition,
24364–24373.'
mla: 'Iofinova, Eugenia B., et al. “Bias in Pruned Vision Models: In-Depth Analysis
and Countermeasures.” 2023 IEEE/CVF Conference on Computer Vision and Pattern
Recognition, IEEE, 2023, pp. 24364–73, doi:10.1109/cvpr52729.2023.02334.'
short: E.B. Iofinova, A. Krumes, D.-A. Alistarh, in:, 2023 IEEE/CVF Conference on
Computer Vision and Pattern Recognition, IEEE, 2023, pp. 24364–24373.
conference:
end_date: 2023-06-24
location: Vancouver, BC, Canada
name: 'CVPR: Conference on Computer Vision and Pattern Recognition'
start_date: 2023-06-17
corr_author: '1'
date_created: 2024-01-10T08:42:40Z
date_published: 2023-08-22T00:00:00Z
date_updated: 2025-04-25T10:32:05Z
day: '22'
department:
- _id: DaAl
- _id: ChLa
doi: 10.1109/cvpr52729.2023.02334
ec_funded: 1
external_id:
arxiv:
- '2304.12622'
isi:
- '001062531308068'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2304.12622
month: '08'
oa: 1
oa_version: Preprint
page: 24364-24373
project:
- _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A
grant_number: W1260-N35
name: Vienna Graduate School on Computational Optimization
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition
publication_identifier:
eisbn:
- '9798350301298'
eissn:
- 2575-7075
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/IST-DASLab/pruned-vision-model-bias
status: public
title: 'Bias in pruned vision models: In-depth analysis and countermeasures'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14772'
abstract:
- lang: eng
text: "Many coupled evolution equations can be described via 2×2-block operator
matrices of the form A=[ \r\nA\tB\r\nC\tD\r\n ] in a product space X=X1×X2 with
possibly unbounded entries. Here, the case of diagonally dominant block operator
matrices is considered, that is, the case where the full operator A can be seen
as a relatively bounded perturbation of its diagonal part with D(A)=D(A)×D(D)
though with possibly large relative bound. For such operators the properties of
sectoriality, R-sectoriality and the boundedness of the H∞-calculus are studied,
and for these properties perturbation results for possibly large but structured
perturbations are derived. Thereby, the time dependent parabolic problem associated
with A can be analyzed in maximal Lpt\r\n-regularity spaces, and this is applied
to a wide range of problems such as different theories for liquid crystals, an
artificial Stokes system, strongly damped wave and plate equations, and a Keller-Segel
model."
acknowledgement: "We would like to thank Tim Binz, Emiel Lorist and Mark Veraar for
valuable discussions. We also thank the anonymous referees for their helpful comments
and suggestions, and for the very accurate reading of the manuscript.\r\nThe first
author has been supported partially by the Nachwuchsring – Network for the promotion
of young scientists – at TU Kaiserslautern. Both authors have been supported by
MathApp – Mathematics Applied to Real-World Problems - part of the Research Initiative
of the Federal State of Rhineland-Palatinate, Germany."
article_number: '110146'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Antonio
full_name: Agresti, Antonio
id: 673cd0cc-9b9a-11eb-b144-88f30e1fbb72
last_name: Agresti
orcid: 0000-0002-9573-2962
- first_name: Amru
full_name: Hussein, Amru
last_name: Hussein
citation:
ama: Agresti A, Hussein A. Maximal Lp-regularity and H∞-calculus for block operator
matrices and applications. Journal of Functional Analysis. 2023;285(11).
doi:10.1016/j.jfa.2023.110146
apa: Agresti, A., & Hussein, A. (2023). Maximal Lp-regularity and H∞-calculus
for block operator matrices and applications. Journal of Functional Analysis.
Elsevier. https://doi.org/10.1016/j.jfa.2023.110146
chicago: Agresti, Antonio, and Amru Hussein. “Maximal Lp-Regularity and H∞-Calculus
for Block Operator Matrices and Applications.” Journal of Functional Analysis.
Elsevier, 2023. https://doi.org/10.1016/j.jfa.2023.110146.
ieee: A. Agresti and A. Hussein, “Maximal Lp-regularity and H∞-calculus for block
operator matrices and applications,” Journal of Functional Analysis, vol.
285, no. 11. Elsevier, 2023.
ista: Agresti A, Hussein A. 2023. Maximal Lp-regularity and H∞-calculus for block
operator matrices and applications. Journal of Functional Analysis. 285(11), 110146.
mla: Agresti, Antonio, and Amru Hussein. “Maximal Lp-Regularity and H∞-Calculus
for Block Operator Matrices and Applications.” Journal of Functional Analysis,
vol. 285, no. 11, 110146, Elsevier, 2023, doi:10.1016/j.jfa.2023.110146.
short: A. Agresti, A. Hussein, Journal of Functional Analysis 285 (2023).
corr_author: '1'
date_created: 2024-01-10T09:15:18Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-10-09T21:07:48Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1016/j.jfa.2023.110146
external_id:
arxiv:
- '2108.01962'
isi:
- '001081809000001'
file:
- access_level: open_access
checksum: eda98ca2aa73da91bd074baed34c2b3c
content_type: application/pdf
creator: dernst
date_created: 2024-01-10T11:23:57Z
date_updated: 2024-01-10T11:23:57Z
file_id: '14789'
file_name: 2023_JourFunctionalAnalysis_Agresti.pdf
file_size: 1120592
relation: main_file
success: 1
file_date_updated: 2024-01-10T11:23:57Z
has_accepted_license: '1'
intvolume: ' 285'
isi: 1
issue: '11'
keyword:
- Analysis
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Journal of Functional Analysis
publication_identifier:
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Maximal Lp-regularity and H∞-calculus for block operator matrices and applications
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: 285
year: '2023'
...
---
_id: '14773'
abstract:
- lang: eng
text: Through a combination of idealized simulations and real-world data, researchers
are uncovering how internal feedbacks and large-scale motions influence cloud
dynamics.
article_number: '28'
article_processing_charge: No
article_type: original
author:
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Sophie
full_name: Abramian, Sophie
last_name: Abramian
citation:
ama: Muller CJ, Abramian S. The cloud dynamics of convective storm systems. Physics
Today. 2023;76(5). doi:10.1063/pt.3.5234
apa: Muller, C. J., & Abramian, S. (2023). The cloud dynamics of convective
storm systems. Physics Today. AIP Publishing. https://doi.org/10.1063/pt.3.5234
chicago: Muller, Caroline J, and Sophie Abramian. “The Cloud Dynamics of Convective
Storm Systems.” Physics Today. AIP Publishing, 2023. https://doi.org/10.1063/pt.3.5234.
ieee: C. J. Muller and S. Abramian, “The cloud dynamics of convective storm systems,”
Physics Today, vol. 76, no. 5. AIP Publishing, 2023.
ista: Muller CJ, Abramian S. 2023. The cloud dynamics of convective storm systems.
Physics Today. 76(5), 28.
mla: Muller, Caroline J., and Sophie Abramian. “The Cloud Dynamics of Convective
Storm Systems.” Physics Today, vol. 76, no. 5, 28, AIP Publishing, 2023,
doi:10.1063/pt.3.5234.
short: C.J. Muller, S. Abramian, Physics Today 76 (2023).
corr_author: '1'
date_created: 2024-01-10T09:18:04Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2024-10-09T21:07:48Z
day: '01'
department:
- _id: CaMu
doi: 10.1063/pt.3.5234
external_id:
isi:
- '000984516100007'
intvolume: ' 76'
isi: 1
issue: '5'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.lmd.ens.fr/muller/Pubs/2023-MullerAbramianPhysToday.pdf
month: '05'
oa: 1
oa_version: Published Version
publication: Physics Today
publication_identifier:
eissn:
- 1945-0699
issn:
- 0031-9228
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
status: public
title: The cloud dynamics of convective storm systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 76
year: '2023'
...
---
_id: '14774'
abstract:
- lang: eng
text: Morphogen gradients impart positional information to cells in a homogenous
tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act
as a morphogen during zebrafish gastrulation. However, technical limitations have
so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation
of its morphogenic activity. Here, we monitor Fgf8a propagation in the developing
neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a
locus. By combining sensitive imaging with single-molecule fluorescence correlation
spectroscopy, we demonstrate that Fgf8a, which is produced at the embryonic margin,
propagates by diffusion through the extracellular space and forms a graded distribution
towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles
of its downstream targets determines the precise input-output relationship of
Fgf8a-mediated patterning. Manipulation of the extracellular Fgf8a levels alters
the signaling outcome, thus establishing Fgf8a as a bona fide morphogen during
zebrafish gastrulation. Furthermore, by hindering Fgf8a diffusion, we demonstrate
that extracellular diffusion of the protein from the source is crucial for it
to achieve its morphogenic potential.
acknowledgement: "We thank members of the Brand lab, as well as Justina Stark (Ivo
Sbalzarini group, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden,
Germany) for project-related discussions; Darren Gilmour (University of Zurich),
Karuna Sampath (University of Warwick) and Gokul Kesavan (Vowels Lifesciences Private
Limited, Bangalore) for comments on the manuscript; personnel of the CMCB technology
platform, TU Dresden for imaging and image analysis-related support; and Maurizio
Abbate (Technical support, Arivis) for help with image analysis. We are also grateful
to Stapornwongkul and Briscoe for commenting on a preprint version of our work (Stapornwongkul
and Briscoe, 2022).\r\nThis work was supported by the Deutsche Forschungsgemeinschaft
(BR 1746/6-2, BR 1746/11-1 and BR 1746/3 to M.B.), by a Cluster of Excellence ‘Physics
of Life’ seed grant and by institutional funds from Technische Universitat Dresden
(to M.B.). Open Access funding provided by Technische Universitat Dresden. Deposited
in PMC for immediate release."
article_number: dev201559
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Rohit K
full_name: Harish, Rohit K
id: 1bae78aa-ee0e-11ec-9b76-bc42990f409d
last_name: Harish
- first_name: Mansi
full_name: Gupta, Mansi
last_name: Gupta
- first_name: Daniela
full_name: Zöller, Daniela
last_name: Zöller
- first_name: Hella
full_name: Hartmann, Hella
last_name: Hartmann
- first_name: Ali
full_name: Gheisari, Ali
last_name: Gheisari
- first_name: Anja
full_name: Machate, Anja
last_name: Machate
- first_name: Stefan
full_name: Hans, Stefan
last_name: Hans
- first_name: Michael
full_name: Brand, Michael
last_name: Brand
citation:
ama: Harish RK, Gupta M, Zöller D, et al. Real-time monitoring of an endogenous
Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation.
Development. 2023;150(19). doi:10.1242/dev.201559
apa: Harish, R. K., Gupta, M., Zöller, D., Hartmann, H., Gheisari, A., Machate,
A., … Brand, M. (2023). Real-time monitoring of an endogenous Fgf8a gradient attests
to its role as a morphogen during zebrafish gastrulation. Development.
The Company of Biologists. https://doi.org/10.1242/dev.201559
chicago: Harish, Rohit K, Mansi Gupta, Daniela Zöller, Hella Hartmann, Ali Gheisari,
Anja Machate, Stefan Hans, and Michael Brand. “Real-Time Monitoring of an Endogenous
Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.”
Development. The Company of Biologists, 2023. https://doi.org/10.1242/dev.201559.
ieee: R. K. Harish et al., “Real-time monitoring of an endogenous Fgf8a gradient
attests to its role as a morphogen during zebrafish gastrulation,” Development,
vol. 150, no. 19. The Company of Biologists, 2023.
ista: Harish RK, Gupta M, Zöller D, Hartmann H, Gheisari A, Machate A, Hans S, Brand
M. 2023. Real-time monitoring of an endogenous Fgf8a gradient attests to its role
as a morphogen during zebrafish gastrulation. Development. 150(19), dev201559.
mla: Harish, Rohit K., et al. “Real-Time Monitoring of an Endogenous Fgf8a Gradient
Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” Development,
vol. 150, no. 19, dev201559, The Company of Biologists, 2023, doi:10.1242/dev.201559.
short: R.K. Harish, M. Gupta, D. Zöller, H. Hartmann, A. Gheisari, A. Machate, S.
Hans, M. Brand, Development 150 (2023).
date_created: 2024-01-10T09:18:54Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-01-10T12:45:25Z
day: '01'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1242/dev.201559
external_id:
isi:
- '001097449100002'
pmid:
- '37665167'
file:
- access_level: open_access
checksum: 2d6f52dc33260a9b2352b8f28374ba5f
content_type: application/pdf
creator: dernst
date_created: 2024-01-10T12:41:13Z
date_updated: 2024-01-10T12:41:13Z
file_id: '14790'
file_name: 2023_Development_Harish.pdf
file_size: 12836306
relation: main_file
success: 1
file_date_updated: 2024-01-10T12:41:13Z
has_accepted_license: '1'
intvolume: ' 150'
isi: 1
issue: '19'
keyword:
- Developmental Biology
- Molecular Biology
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Development
publication_identifier:
eissn:
- 1477-9129
issn:
- 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
status: public
title: Real-time monitoring of an endogenous Fgf8a gradient attests to its role as
a morphogen during zebrafish gastrulation
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: 150
year: '2023'
...
---
_id: '14775'
abstract:
- lang: eng
text: We establish a quantitative version of the Tracy–Widom law for the largest
eigenvalue of high-dimensional sample covariance matrices. To be precise, we show
that the fluctuations of the largest eigenvalue of a sample covariance matrix
X∗X converge to its Tracy–Widom limit at a rate nearly N−1/3, where X is an M×N
random matrix whose entries are independent real or complex random variables,
assuming that both M and N tend to infinity at a constant rate. This result improves
the previous estimate N−2/9 obtained by Wang (2019). Our proof relies on a Green
function comparison method (Adv. Math. 229 (2012) 1435–1515) using iterative cumulant
expansions, the local laws for the Green function and asymptotic properties of
the correlation kernel of the white Wishart ensemble.
acknowledgement: K. Schnelli was supported by the Swedish Research Council Grants
VR-2017-05195, and the Knut and Alice Wallenberg Foundation. Y. Xu was supported
by the Swedish Research Council Grant VR-2017-05195 and the ERC Advanced Grant “RMTBeyond”
No. 101020331.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
- first_name: Yuanyuan
full_name: Xu, Yuanyuan
id: 7902bdb1-a2a4-11eb-a164-c9216f71aea3
last_name: Xu
orcid: 0000-0003-1559-1205
citation:
ama: Schnelli K, Xu Y. Convergence rate to the Tracy–Widom laws for the largest
eigenvalue of sample covariance matrices. The Annals of Applied Probability.
2023;33(1):677-725. doi:10.1214/22-aap1826
apa: Schnelli, K., & Xu, Y. (2023). Convergence rate to the Tracy–Widom laws
for the largest eigenvalue of sample covariance matrices. The Annals of Applied
Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/22-aap1826
chicago: Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom
Laws for the Largest Eigenvalue of Sample Covariance Matrices.” The Annals
of Applied Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/22-aap1826.
ieee: K. Schnelli and Y. Xu, “Convergence rate to the Tracy–Widom laws for the largest
eigenvalue of sample covariance matrices,” The Annals of Applied Probability,
vol. 33, no. 1. Institute of Mathematical Statistics, pp. 677–725, 2023.
ista: Schnelli K, Xu Y. 2023. Convergence rate to the Tracy–Widom laws for the largest
eigenvalue of sample covariance matrices. The Annals of Applied Probability. 33(1),
677–725.
mla: Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws
for the Largest Eigenvalue of Sample Covariance Matrices.” The Annals of Applied
Probability, vol. 33, no. 1, Institute of Mathematical Statistics, 2023, pp.
677–725, doi:10.1214/22-aap1826.
short: K. Schnelli, Y. Xu, The Annals of Applied Probability 33 (2023) 677–725.
corr_author: '1'
date_created: 2024-01-10T09:23:31Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2025-04-14T07:57:19Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/22-aap1826
ec_funded: 1
external_id:
arxiv:
- '2108.02728'
isi:
- '000946432400021'
intvolume: ' 33'
isi: 1
issue: '1'
keyword:
- Statistics
- Probability and Uncertainty
- Statistics and Probability
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2108.02728
month: '02'
oa: 1
oa_version: Preprint
page: 677-725
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: The Annals of Applied Probability
publication_identifier:
issn:
- 1050-5164
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample
covariance matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2023'
...
---
_id: '14776'
abstract:
- lang: eng
text: Soluble chaperones residing in the endoplasmic reticulum (ER) play vitally
important roles in folding and quality control of newly synthesized proteins that
transiently pass through the ER en route to their final destinations. These soluble
residents of the ER are themselves endowed with an ER retrieval signal that enables
the cell to bring the escaped residents back from the Golgi. Here, by using purified
proteins, we showed that Nicotiana tabacum phytaspase, a plant aspartate-specific
protease, introduces two breaks at the C-terminus of the N. tabacum ER resident
calreticulin-3. These cleavages resulted in removal of either a dipeptide or a
hexapeptide from the C-terminus of calreticulin-3 encompassing part or all of
the ER retrieval signal. Consistently, expression of the calreticulin-3 derivative
mimicking the phytaspase cleavage product in Nicotiana benthamiana cells demonstrated
loss of the ER accumulation of the protein. Notably, upon its escape from the
ER, calreticulin-3 was further processed by an unknown protease(s) to generate
the free N-terminal (N) domain of calreticulin-3, which was ultimately secreted
into the apoplast. Our study thus identified a specific proteolytic enzyme capable
of precise detachment of the ER retrieval signal from a plant ER resident protein,
with implications for the further fate of the escaped resident.
acknowledgement: "We thank C.U.T. Hellen for critically reading the manuscript. The
MALDI MS facility and CLSM became available to us in the framework of Moscow State
University Development Programs PNG 5.13 and PNR 5.13.\r\nThis work was funded by
the Russian Science Foundation, grant numbers 19-14-00010 and 22-14-00071."
article_number: '16527'
article_processing_charge: Yes
article_type: original
author:
- first_name: Anastasiia
full_name: Teplova, Anastasiia
id: e3736151-106c-11ec-b916-c2558e2762c6
last_name: Teplova
- first_name: Artemii A.
full_name: Pigidanov, Artemii A.
last_name: Pigidanov
- first_name: Marina V.
full_name: Serebryakova, Marina V.
last_name: Serebryakova
- first_name: Sergei A.
full_name: Golyshev, Sergei A.
last_name: Golyshev
- first_name: Raisa A.
full_name: Galiullina, Raisa A.
last_name: Galiullina
- first_name: Nina V.
full_name: Chichkova, Nina V.
last_name: Chichkova
- first_name: Andrey B.
full_name: Vartapetian, Andrey B.
last_name: Vartapetian
citation:
ama: Teplova A, Pigidanov AA, Serebryakova MV, et al. Phytaspase Is capable of detaching
the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International
Journal of Molecular Sciences. 2023;24(22). doi:10.3390/ijms242216527
apa: Teplova, A., Pigidanov, A. A., Serebryakova, M. V., Golyshev, S. A., Galiullina,
R. A., Chichkova, N. V., & Vartapetian, A. B. (2023). Phytaspase Is capable
of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3.
International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms242216527
chicago: Teplova, Anastasiia, Artemii A. Pigidanov, Marina V. Serebryakova, Sergei
A. Golyshev, Raisa A. Galiullina, Nina V. Chichkova, and Andrey B. Vartapetian.
“Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal
from Tobacco Calreticulin-3.” International Journal of Molecular Sciences.
MDPI, 2023. https://doi.org/10.3390/ijms242216527.
ieee: A. Teplova et al., “Phytaspase Is capable of detaching the endoplasmic
reticulum retrieval signal from tobacco calreticulin-3,” International Journal
of Molecular Sciences, vol. 24, no. 22. MDPI, 2023.
ista: Teplova A, Pigidanov AA, Serebryakova MV, Golyshev SA, Galiullina RA, Chichkova
NV, Vartapetian AB. 2023. Phytaspase Is capable of detaching the endoplasmic reticulum
retrieval signal from tobacco calreticulin-3. International Journal of Molecular
Sciences. 24(22), 16527.
mla: Teplova, Anastasiia, et al. “Phytaspase Is Capable of Detaching the Endoplasmic
Reticulum Retrieval Signal from Tobacco Calreticulin-3.” International Journal
of Molecular Sciences, vol. 24, no. 22, 16527, MDPI, 2023, doi:10.3390/ijms242216527.
short: A. Teplova, A.A. Pigidanov, M.V. Serebryakova, S.A. Golyshev, R.A. Galiullina,
N.V. Chichkova, A.B. Vartapetian, International Journal of Molecular Sciences
24 (2023).
corr_author: '1'
date_created: 2024-01-10T09:24:35Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2024-10-09T21:07:49Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3390/ijms242216527
external_id:
isi:
- '001113792600001'
pmid:
- '38003717'
file:
- access_level: open_access
checksum: 4df7d206ba022b7f54eff1f0aec1659a
content_type: application/pdf
creator: dernst
date_created: 2024-01-10T13:39:42Z
date_updated: 2024-01-10T13:39:42Z
file_id: '14791'
file_name: 2023_IJMS_Teplova.pdf
file_size: 2637784
relation: main_file
success: 1
file_date_updated: 2024-01-10T13:39:42Z
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
issue: '22'
keyword:
- Inorganic Chemistry
- Organic Chemistry
- Physical and Theoretical Chemistry
- Computer Science Applications
- Spectroscopy
- Molecular Biology
- General Medicine
- Catalysis
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: International Journal of Molecular Sciences
publication_identifier:
issn:
- 1422-0067
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal
from tobacco calreticulin-3
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: 24
year: '2023'
...
---
_id: '14777'
abstract:
- lang: eng
text: The effects of the partial V-substitution for Ag on the thermoelectric (TE)
properties are investigated for a flexible semiconducting compound Ag2S0.55Se0.45.
Density functional theory calculations predict that such a partial V-substitution
constructively modifies the electronic structure near the bottom of the conduction
band to improve the TE performance. The synthesized Ag1.97V0.03S0.55Se0.45 is
found to possess a TE dimensionless figure-of-merit (ZT) of 0.71 at 350 K with
maintaining its flexible nature. This ZT value is relatively high in comparison
with those reported for flexible TE materials below 360 K. The increase in the
ZT value is caused by the enhanced absolute value of the Seebeck coefficient with
less significant variation in electrical resistivity. The high ZT value with the
flexible nature naturally allows us to employ the Ag1.97V0.03S0.55Se0.45 as a
component of flexible TE generators.
acknowledgement: This work received financial support partially from Japan Science
and Technology Agency (JST) CREST Grant No. JPMJCR18I2, Japan. The powder-XRD experiments
were conducted at BL5S2 of Aichi Synchrotron Radiation Center, Aichi Science & Technology
Foundation, Aichi, Japan (Proposal No. 202301057).
article_number: '125206'
article_processing_charge: Yes
article_type: original
author:
- first_name: Kosuke
full_name: Sato, Kosuke
last_name: Sato
- first_name: Saurabh
full_name: Singh, Saurabh
id: 12d625da-9cb3-11ed-9667-af09d37d3f0a
last_name: Singh
orcid: 0000-0003-2209-5269
- first_name: Itsuki
full_name: Yamazaki, Itsuki
last_name: Yamazaki
- first_name: Keisuke
full_name: Hirata, Keisuke
last_name: Hirata
- first_name: Artoni Kevin R.
full_name: Ang, Artoni Kevin R.
last_name: Ang
- first_name: Masaharu
full_name: Matsunami, Masaharu
last_name: Matsunami
- first_name: Tsunehiro
full_name: Takeuchi, Tsunehiro
last_name: Takeuchi
citation:
ama: Sato K, Singh S, Yamazaki I, et al. Improvement of thermoelectric performance
of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag.
AIP Advances. 2023;13(12). doi:10.1063/5.0171888
apa: Sato, K., Singh, S., Yamazaki, I., Hirata, K., Ang, A. K. R., Matsunami, M.,
& Takeuchi, T. (2023). Improvement of thermoelectric performance of flexible
compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag. AIP Advances.
AIP Publishing. https://doi.org/10.1063/5.0171888
chicago: Sato, Kosuke, Saurabh Singh, Itsuki Yamazaki, Keisuke Hirata, Artoni Kevin
R. Ang, Masaharu Matsunami, and Tsunehiro Takeuchi. “Improvement of Thermoelectric
Performance of Flexible Compound Ag2S0.55Se0.45 by Means of Partial V-Substitution
for Ag.” AIP Advances. AIP Publishing, 2023. https://doi.org/10.1063/5.0171888.
ieee: K. Sato et al., “Improvement of thermoelectric performance of flexible
compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag,” AIP Advances,
vol. 13, no. 12. AIP Publishing, 2023.
ista: Sato K, Singh S, Yamazaki I, Hirata K, Ang AKR, Matsunami M, Takeuchi T. 2023.
Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45
by means of partial V-substitution for Ag. AIP Advances. 13(12), 125206.
mla: Sato, Kosuke, et al. “Improvement of Thermoelectric Performance of Flexible
Compound Ag2S0.55Se0.45 by Means of Partial V-Substitution for Ag.” AIP Advances,
vol. 13, no. 12, 125206, AIP Publishing, 2023, doi:10.1063/5.0171888.
short: K. Sato, S. Singh, I. Yamazaki, K. Hirata, A.K.R. Ang, M. Matsunami, T. Takeuchi,
AIP Advances 13 (2023).
corr_author: '1'
date_created: 2024-01-10T09:26:08Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-10-09T21:07:49Z
day: '01'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1063/5.0171888
external_id:
isi:
- '001114917200005'
file:
- access_level: open_access
checksum: a7098388b8ff822b47f5ddd37ed3bdbc
content_type: application/pdf
creator: dernst
date_created: 2024-01-10T13:47:31Z
date_updated: 2024-01-10T13:47:31Z
file_id: '14792'
file_name: 2023_AIPAdvances_Sato.pdf
file_size: 9676071
relation: main_file
success: 1
file_date_updated: 2024-01-10T13:47:31Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '12'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: AIP Advances
publication_identifier:
eissn:
- 2158-3226
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
status: public
title: Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45
by means of partial V-substitution for Ag
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: 13
year: '2023'
...
---
_id: '14778'
abstract:
- lang: eng
text: 'We consider the almost-sure (a.s.) termination problem for probabilistic
programs, which are a stochastic extension of classical imperative programs. Lexicographic
ranking functions provide a sound and practical approach for termination of non-probabilistic
programs, and their extension to probabilistic programs is achieved via lexicographic
ranking supermartingales (LexRSMs). However, LexRSMs introduced in the previous
work have a limitation that impedes their automation: all of their components
have to be non-negative in all reachable states. This might result in a LexRSM
not existing even for simple terminating programs. Our contributions are twofold.
First, we introduce a generalization of LexRSMs that allows for some components
to be negative. This standard feature of non-probabilistic termination proofs
was hitherto not known to be sound in the probabilistic setting, as the soundness
proof requires a careful analysis of the underlying stochastic process. Second,
we present polynomial-time algorithms using our generalized LexRSMs for proving
a.s. termination in broad classes of linear-arithmetic programs.'
acknowledgement: This research was partially supported by the ERC CoG (grant no. 863818;
ForM-SMArt), the Czech Science Foundation (grant no. GA21-24711S), and the European
Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie
Grant Agreement No. 665385.
article_number: '11'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ehsan
full_name: Kafshdar Goharshady, Ehsan
last_name: Kafshdar Goharshady
- first_name: Petr
full_name: Novotný, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotný
- first_name: Jiří
full_name: Zárevúcky, Jiří
last_name: Zárevúcky
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: Chatterjee K, Kafshdar Goharshady E, Novotný P, Zárevúcky J, Zikelic D. On
lexicographic proof rules for probabilistic termination. Formal Aspects of
Computing. 2023;35(2). doi:10.1145/3585391
apa: Chatterjee, K., Kafshdar Goharshady, E., Novotný, P., Zárevúcky, J., &
Zikelic, D. (2023). On lexicographic proof rules for probabilistic termination.
Formal Aspects of Computing. Association for Computing Machinery. https://doi.org/10.1145/3585391
chicago: Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, Jiří Zárevúcky,
and Dorde Zikelic. “On Lexicographic Proof Rules for Probabilistic Termination.”
Formal Aspects of Computing. Association for Computing Machinery, 2023.
https://doi.org/10.1145/3585391.
ieee: K. Chatterjee, E. Kafshdar Goharshady, P. Novotný, J. Zárevúcky, and D. Zikelic,
“On lexicographic proof rules for probabilistic termination,” Formal Aspects
of Computing, vol. 35, no. 2. Association for Computing Machinery, 2023.
ista: Chatterjee K, Kafshdar Goharshady E, Novotný P, Zárevúcky J, Zikelic D. 2023.
On lexicographic proof rules for probabilistic termination. Formal Aspects of
Computing. 35(2), 11.
mla: Chatterjee, Krishnendu, et al. “On Lexicographic Proof Rules for Probabilistic
Termination.” Formal Aspects of Computing, vol. 35, no. 2, 11, Association
for Computing Machinery, 2023, doi:10.1145/3585391.
short: K. Chatterjee, E. Kafshdar Goharshady, P. Novotný, J. Zárevúcky, D. Zikelic,
Formal Aspects of Computing 35 (2023).
corr_author: '1'
date_created: 2024-01-10T09:27:43Z
date_published: 2023-06-23T00:00:00Z
date_updated: 2025-09-09T14:19:27Z
day: '23'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3585391
ec_funded: 1
external_id:
arxiv:
- '2108.02188'
isi:
- '001035915800006'
file:
- access_level: open_access
checksum: 3bb133eeb27ec01649a9a36445d952d9
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T08:11:24Z
date_updated: 2024-01-16T08:11:24Z
file_id: '14804'
file_name: 2023_FormalAspectsComputing_Chatterjee.pdf
file_size: 502522
relation: main_file
success: 1
file_date_updated: 2024-01-16T08:11:24Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '2'
keyword:
- Theoretical Computer Science
- Software
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Formal Aspects of Computing
publication_identifier:
eissn:
- 1433-299X
issn:
- 0934-5043
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '10414'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: On lexicographic proof rules for probabilistic termination
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 35
year: '2023'
...
---
_id: '14779'
abstract:
- lang: eng
text: The presence of a developed boundary layer decouples a glacier's response
from ambient conditions, suggesting that sensitivity to climate change is increased
by glacier retreat. To test this hypothesis, we explore six years of distributed
meteorological data on a small Swiss glacier in the period 2001–2022. Large glacier
fragmentation has occurred since 2001 (−35% area change up to 2022) coinciding
with notable frontal retreat, an observed switch from down‐glacier katabatic to
up‐glacier valley winds and an increased sensitivity (ratio) of on‐glacier to
off‐glacier temperature. As the glacier ceases to develop density‐driven katabatic
winds, sensible heat fluxes on the glacier are increasingly determined by the
conditions occurring outside the boundary layer of the glacier, sealing the glacier's
demise as the climate continues to warm and experience an increased frequency
of extreme summers.
acknowledgement: This work was funded by the EU Horizon 2020 Marie Skłodowska-Curie
Actions Grant 101026058. The authors acknowl-edge the dedicated collection of field
data by many parties since 2001, including those acknowledged for the cited works
on Arolla Glacier. The authors would like to thank Fabienne Meier, Alice Zaugg,
Raphael Willi, Maria Grundmann, and Marta Corrà for assistance in the field for
the summers of 2021 and 2022. Off-glacier data provided by Grand Dixence SA (Arolla)
and MeteoSwiss are kindly acknowledged. Simone Fatichi is thanked for the provision
and support in the use of the Tethys-Chloris model. We thank Editor Mathieu Morlighem
and two anonymous reviewers whose comments have helped to improve the quality of
the manuscript.
article_number: e2023GL103043
article_processing_charge: No
article_type: original
author:
- first_name: Thomas E.
full_name: Shaw, Thomas E.
last_name: Shaw
- first_name: Pascal
full_name: Buri, Pascal
last_name: Buri
- first_name: Michael
full_name: McCarthy, Michael
last_name: McCarthy
- first_name: Evan S.
full_name: Miles, Evan S.
last_name: Miles
- first_name: Álvaro
full_name: Ayala, Álvaro
last_name: Ayala
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
orcid: 0000-0002-5554-8087
citation:
ama: Shaw TE, Buri P, McCarthy M, Miles ES, Ayala Á, Pellicciotti F. The decaying
near‐surface boundary layer of a retreating alpine glacier. Geophysical Research
Letters. 2023;50(11). doi:10.1029/2023gl103043
apa: Shaw, T. E., Buri, P., McCarthy, M., Miles, E. S., Ayala, Á., & Pellicciotti,
F. (2023). The decaying near‐surface boundary layer of a retreating alpine glacier.
Geophysical Research Letters. American Geophysical Union. https://doi.org/10.1029/2023gl103043
chicago: Shaw, Thomas E., Pascal Buri, Michael McCarthy, Evan S. Miles, Álvaro Ayala,
and Francesca Pellicciotti. “The Decaying Near‐surface Boundary Layer of a Retreating
Alpine Glacier.” Geophysical Research Letters. American Geophysical Union,
2023. https://doi.org/10.1029/2023gl103043.
ieee: T. E. Shaw, P. Buri, M. McCarthy, E. S. Miles, Á. Ayala, and F. Pellicciotti,
“The decaying near‐surface boundary layer of a retreating alpine glacier,” Geophysical
Research Letters, vol. 50, no. 11. American Geophysical Union, 2023.
ista: Shaw TE, Buri P, McCarthy M, Miles ES, Ayala Á, Pellicciotti F. 2023. The
decaying near‐surface boundary layer of a retreating alpine glacier. Geophysical
Research Letters. 50(11), e2023GL103043.
mla: Shaw, Thomas E., et al. “The Decaying Near‐surface Boundary Layer of a Retreating
Alpine Glacier.” Geophysical Research Letters, vol. 50, no. 11, e2023GL103043,
American Geophysical Union, 2023, doi:10.1029/2023gl103043.
short: T.E. Shaw, P. Buri, M. McCarthy, E.S. Miles, Á. Ayala, F. Pellicciotti, Geophysical
Research Letters 50 (2023).
date_created: 2024-01-10T09:28:34Z
date_published: 2023-06-16T00:00:00Z
date_updated: 2024-10-21T06:01:34Z
day: '16'
ddc:
- '550'
department:
- _id: FrPe
doi: 10.1029/2023gl103043
external_id:
isi:
- '000999436400001'
file:
- access_level: open_access
checksum: 391a3005c95340a0ae129ce4fbdf2bae
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T08:35:02Z
date_updated: 2024-01-16T08:35:02Z
file_id: '14805'
file_name: 2023_GeophysicalResearchLetter_Shaw.pdf
file_size: 2529327
relation: main_file
success: 1
file_date_updated: 2024-01-16T08:35:02Z
has_accepted_license: '1'
intvolume: ' 50'
isi: 1
issue: '11'
keyword:
- General Earth and Planetary Sciences
- Geophysics
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Geophysical Research Letters
publication_identifier:
eissn:
- 1944-8007
issn:
- 0094-8276
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: The decaying near‐surface boundary layer of a retreating alpine glacier
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: 50
year: '2023'
...
---
_id: '14780'
abstract:
- lang: eng
text: In this paper, we study the eigenvalues and eigenvectors of the spiked invariant
multiplicative models when the randomness is from Haar matrices. We establish
the limits of the outlier eigenvalues λˆi and the generalized components (⟨v,uˆi⟩
for any deterministic vector v) of the outlier eigenvectors uˆi with optimal convergence
rates. Moreover, we prove that the non-outlier eigenvalues stick with those of
the unspiked matrices and the non-outlier eigenvectors are delocalized. The results
also hold near the so-called BBP transition and for degenerate spikes. On one
hand, our results can be regarded as a refinement of the counterparts of [12]
under additional regularity conditions. On the other hand, they can be viewed
as an analog of [34] by replacing the random matrix with i.i.d. entries with Haar
random matrix.
acknowledgement: The authors would like to thank the editor, the associated editor
and two anonymous referees for their many critical suggestions which have significantly
improved the paper. The authors are also grateful to Zhigang Bao and Ji Oon Lee
for many helpful discussions. The first author also wants to thank Hari Bercovici
for many useful comments. The first author is partially supported by National Science
Foundation DMS-2113489 and the second author is supported by ERC Advanced Grant
“RMTBeyond” No. 101020331.
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Xiucai
full_name: Ding, Xiucai
last_name: Ding
- first_name: Hong Chang
full_name: Ji, Hong Chang
id: dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d
last_name: Ji
citation:
ama: Ding X, Ji HC. Spiked multiplicative random matrices and principal components.
Stochastic Processes and their Applications. 2023;163:25-60. doi:10.1016/j.spa.2023.05.009
apa: Ding, X., & Ji, H. C. (2023). Spiked multiplicative random matrices and
principal components. Stochastic Processes and Their Applications. Elsevier.
https://doi.org/10.1016/j.spa.2023.05.009
chicago: Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices
and Principal Components.” Stochastic Processes and Their Applications.
Elsevier, 2023. https://doi.org/10.1016/j.spa.2023.05.009.
ieee: X. Ding and H. C. Ji, “Spiked multiplicative random matrices and principal
components,” Stochastic Processes and their Applications, vol. 163. Elsevier,
pp. 25–60, 2023.
ista: Ding X, Ji HC. 2023. Spiked multiplicative random matrices and principal components.
Stochastic Processes and their Applications. 163, 25–60.
mla: Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices and
Principal Components.” Stochastic Processes and Their Applications, vol.
163, Elsevier, 2023, pp. 25–60, doi:10.1016/j.spa.2023.05.009.
short: X. Ding, H.C. Ji, Stochastic Processes and Their Applications 163 (2023)
25–60.
date_created: 2024-01-10T09:29:25Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2025-07-16T08:01:03Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1016/j.spa.2023.05.009
ec_funded: 1
external_id:
arxiv:
- '2302.13502'
isi:
- '001113615900001'
file:
- access_level: open_access
checksum: 46a708b0cd5569a73d0f3d6c3e0a44dc
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T08:47:31Z
date_updated: 2024-01-16T08:47:31Z
file_id: '14806'
file_name: 2023_StochasticProcAppl_Ding.pdf
file_size: 1870349
relation: main_file
success: 1
file_date_updated: 2024-01-16T08:47:31Z
has_accepted_license: '1'
intvolume: ' 163'
isi: 1
keyword:
- Applied Mathematics
- Modeling and Simulation
- Statistics and Probability
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 25-60
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Stochastic Processes and their Applications
publication_identifier:
eissn:
- 1879-209X
issn:
- 0304-4149
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spiked multiplicative random matrices and principal components
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 163
year: '2023'
...
---
_id: '14782'
abstract:
- lang: eng
text: The actin cortex is a complex cytoskeletal machinery that drives and responds
to changes in cell shape. It must generate or adapt to plasma membrane curvature
to facilitate diverse functions such as cell division, migration, and phagocytosis.
Due to the complex molecular makeup of the actin cortex, it remains unclear whether
actin networks are inherently able to sense and generate membrane curvature, or
whether they rely on their diverse binding partners to accomplish this. Here,
we show that curvature sensing is an inherent capability of branched actin networks
nucleated by Arp2/3 and VCA. We develop a robust method to encapsulate actin inside
giant unilamellar vesicles (GUVs) and assemble an actin cortex at the inner surface
of the GUV membrane. We show that actin forms a uniform and thin cortical layer
when present at high concentration and distinct patches associated with negative
membrane curvature at low concentration. Serendipitously, we find that the GUV
production method also produces dumbbell-shaped GUVs, which we explain using mathematical
modeling in terms of membrane hemifusion of nested GUVs. We find that branched
actin networks preferentially assemble at the neck of the dumbbells, which possess
a micrometer-range convex curvature comparable with the curvature of the actin
patches found in spherical GUVs. Minimal branched actin networks can thus sense
membrane curvature, which may help mammalian cells to robustly recruit actin to
curved membranes to facilitate diverse cellular functions such as cytokinesis
and migration.
acknowledgement: We thank Jeffrey den Haan for protein purification, Kristina Ganzinger
(AMOLF) for providing the 10xHis VCA construct, David Kovar (University of Chicago)
for the CP constructs, and Michael Way (Crick Institute) for providing purified
human Arp2/3 proteins. We are grateful to Iris Lambert for early actin encapsulation
experiments that formed the basis for establishing the eDICE method, to Federico
Fanalista for acquiring images of dumbbell-shaped GUVs in samples produced by cDICE,
and to Tom Aarts for images of dumbbell-shaped GUVs produced by gel-assisted swelling.
Lennard van Buren is thanked for his help with image analysis to quantify actin
concentrations in GUVs. We thank Kristina Ganzinger (AMOLF) for hosting us to perform
pyrene assays in her lab, and Balász Antalicz (AMOLF) for technical assistance with
the spectrophotometer. The authors also thank Matthieu Piel and Daniel Fletcher
for insightful and inspiring discussions. We acknowledge financial support from
The Netherlands Organization of Scientific Research (NWO/OCW) Gravitation program
Building a Synthetic Cell (BaSyC) (024.003.019). F.F. gratefully acknowledges funding
from the Kavli Synergy program of the Kavli Institute of Nanoscience Delft.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Lucia
full_name: Baldauf, Lucia
last_name: Baldauf
- first_name: Felix F
full_name: Frey, Felix F
id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3
last_name: Frey
- first_name: Marcos
full_name: Arribas Perez, Marcos
last_name: Arribas Perez
- first_name: Timon
full_name: Idema, Timon
last_name: Idema
- first_name: Gijsje H.
full_name: Koenderink, Gijsje H.
last_name: Koenderink
citation:
ama: Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. Branched actin
cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal.
2023;122(11):2311-2324. doi:10.1016/j.bpj.2023.02.018
apa: Baldauf, L., Frey, F. F., Arribas Perez, M., Idema, T., & Koenderink, G.
H. (2023). Branched actin cortices reconstituted in vesicles sense membrane curvature.
Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2023.02.018
chicago: Baldauf, Lucia, Felix F Frey, Marcos Arribas Perez, Timon Idema, and Gijsje
H. Koenderink. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane
Curvature.” Biophysical Journal. Elsevier, 2023. https://doi.org/10.1016/j.bpj.2023.02.018.
ieee: L. Baldauf, F. F. Frey, M. Arribas Perez, T. Idema, and G. H. Koenderink,
“Branched actin cortices reconstituted in vesicles sense membrane curvature,”
Biophysical Journal, vol. 122, no. 11. Elsevier, pp. 2311–2324, 2023.
ista: Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. 2023. Branched
actin cortices reconstituted in vesicles sense membrane curvature. Biophysical
Journal. 122(11), 2311–2324.
mla: Baldauf, Lucia, et al. “Branched Actin Cortices Reconstituted in Vesicles Sense
Membrane Curvature.” Biophysical Journal, vol. 122, no. 11, Elsevier, 2023,
pp. 2311–24, doi:10.1016/j.bpj.2023.02.018.
short: L. Baldauf, F.F. Frey, M. Arribas Perez, T. Idema, G.H. Koenderink, Biophysical
Journal 122 (2023) 2311–2324.
date_created: 2024-01-10T09:45:48Z
date_published: 2023-06-06T00:00:00Z
date_updated: 2024-01-16T09:20:03Z
day: '06'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1016/j.bpj.2023.02.018
external_id:
isi:
- '001016792600001'
pmid:
- '36806830'
file:
- access_level: open_access
checksum: 70566e54cd95ea6df340909ad44c5cd5
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T09:09:29Z
date_updated: 2024-01-16T09:09:29Z
file_id: '14807'
file_name: 2023_BiophysicalJournal_Baldauf.pdf
file_size: 3285810
relation: main_file
success: 1
file_date_updated: 2024-01-16T09:09:29Z
has_accepted_license: '1'
intvolume: ' 122'
isi: 1
issue: '11'
keyword:
- Biophysics
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 2311-2324
pmid: 1
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/BioSoftMatterGroup/actin-curvature-sensing
status: public
title: Branched actin cortices reconstituted in vesicles sense membrane curvature
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: 122
year: '2023'
...
---
_id: '14783'
abstract:
- lang: eng
text: Connexin 43, an astroglial gap junction protein, is enriched in perisynaptic
astroglial processes and plays major roles in synaptic transmission. We have previously
found that astroglial Cx43 controls synaptic glutamate levels and allows for activity-dependent
glutamine release to sustain physiological synaptic transmissions and cognitiogns.
However, whether Cx43 is important for the release of synaptic vesicles, which
is a critical component of synaptic efficacy, remains unanswered. Here, using
transgenic mice with a glial conditional knockout of Cx43 (Cx43−/−), we investigate
whether and how astrocytes regulate the release of synaptic vesicles from hippocampal
synapses. We report that CA1 pyramidal neurons and their synapses develop normally
in the absence of astroglial Cx43. However, a significant impairment in synaptic
vesicle distribution and release dynamics were observed. In particular, the FM1-43
assays performed using two-photon live imaging and combined with multi-electrode
array stimulation in acute hippocampal slices, revealed a slower rate of synaptic
vesicle release in Cx43−/− mice. Furthermore, paired-pulse recordings showed that
synaptic vesicle release probability was also reduced and is dependent on glutamine
supply via Cx43 hemichannel (HC). Taken together, we have uncovered a role for
Cx43 in regulating presynaptic functions by controlling the rate and probability
of synaptic vesicle release. Our findings further highlight the significance of
astroglial Cx43 in synaptic transmission and efficacy.
acknowledgement: 'This research was funded by grants from the European Research Council
(Consolidator grant #683154) and European Union’s Horizon 2020 research and innovation
program (Marie Sklodowska-Curie Innovative Training Networks, grant #722053, EU-GliaPhD)
to N.R., as well as from FP7-PEOPLE Marie Curie Intra-European Fellowship for career
development (grant #622289) to G.C. We thank Elena Dossi, Grégory Ghézali, and Jérémie
Teillon for support with setting up the MEA system for the two-photon microscope.
We would also like to thank Tayfun Palaz for their technical assistance with the
EM preparations.'
article_number: '1133'
article_processing_charge: Yes
article_type: original
author:
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Oana
full_name: Chever, Oana
last_name: Chever
- first_name: Astrid
full_name: Rollenhagen, Astrid
last_name: Rollenhagen
- first_name: Nicole
full_name: Quenech’du, Nicole
last_name: Quenech’du
- first_name: Pascal
full_name: Ezan, Pascal
last_name: Ezan
- first_name: Joachim H. R.
full_name: Lübke, Joachim H. R.
last_name: Lübke
- first_name: Nathalie
full_name: Rouach, Nathalie
last_name: Rouach
citation:
ama: Cheung GT, Chever O, Rollenhagen A, et al. Astroglial connexin 43 regulates
synaptic vesicle release at hippocampal synapses. Cells. 2023;12(8). doi:10.3390/cells12081133
apa: Cheung, G. T., Chever, O., Rollenhagen, A., Quenech’du, N., Ezan, P., Lübke,
J. H. R., & Rouach, N. (2023). Astroglial connexin 43 regulates synaptic vesicle
release at hippocampal synapses. Cells. MDPI. https://doi.org/10.3390/cells12081133
chicago: Cheung, Giselle T, Oana Chever, Astrid Rollenhagen, Nicole Quenech’du,
Pascal Ezan, Joachim H. R. Lübke, and Nathalie Rouach. “Astroglial Connexin 43
Regulates Synaptic Vesicle Release at Hippocampal Synapses.” Cells. MDPI,
2023. https://doi.org/10.3390/cells12081133.
ieee: G. T. Cheung et al., “Astroglial connexin 43 regulates synaptic vesicle
release at hippocampal synapses,” Cells, vol. 12, no. 8. MDPI, 2023.
ista: Cheung GT, Chever O, Rollenhagen A, Quenech’du N, Ezan P, Lübke JHR, Rouach
N. 2023. Astroglial connexin 43 regulates synaptic vesicle release at hippocampal
synapses. Cells. 12(8), 1133.
mla: Cheung, Giselle T., et al. “Astroglial Connexin 43 Regulates Synaptic Vesicle
Release at Hippocampal Synapses.” Cells, vol. 12, no. 8, 1133, MDPI, 2023,
doi:10.3390/cells12081133.
short: G.T. Cheung, O. Chever, A. Rollenhagen, N. Quenech’du, P. Ezan, J.H.R. Lübke,
N. Rouach, Cells 12 (2023).
date_created: 2024-01-10T09:46:35Z
date_published: 2023-04-11T00:00:00Z
date_updated: 2024-01-16T09:29:35Z
day: '11'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.3390/cells12081133
external_id:
isi:
- '000977445700001'
pmid:
- '37190042'
file:
- access_level: open_access
checksum: 6798cd75d8857976fbc58a43fd173d68
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T09:26:52Z
date_updated: 2024-01-16T09:26:52Z
file_id: '14808'
file_name: 2023_Cells_Cheung.pdf
file_size: 7931643
relation: main_file
success: 1
file_date_updated: 2024-01-16T09:26:52Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '8'
keyword:
- General Medicine
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cells
publication_identifier:
issn:
- 2073-4409
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses
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: '2023'
...
---
_id: '14784'
abstract:
- lang: eng
text: The next steps of deep space exploration are manned missions to Moon and Mars.
For safe space missions for crew members, it is important to understand the impact
of space flight on the immune system. We studied the effects of 21 days dry immersion
(DI) exposure on the transcriptomes of T cells isolated from blood samples of
eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14,
and 21 during DI, and 7 days after DI. RNA sequencing of CD3+T cells revealed
transcriptional alterations across all time points, with most changes occurring
14 days after DI exposure. At day 21, T cells showed evidence of adaptation with
a transcriptional profile resembling that of 7 days before DI. At 7 days after
DI, T cells again changed their transcriptional profile. These data suggest that
T cells adapt by rewiring their transcriptomes in response to simulated weightlessness
and that remodeling cues persist when reexposed to normal gravity.
acknowledgement: This work was supported by a postdoctoral fellowship from the Swedish
Society for Medical Research to J.R., a CAPES-STINT joint grant to R.G.G. and L.S.W.,
a PhD fellowship from Karolinska Institutet (KID) to E.D., a PhD fellowship from
Fundação para a Ciência e a Tecnologia and European Social Fund to M.M.S.O., the
program of fundamental research (theme 65.1) of the Institute for Biomedical Problems
of the Russian Academy of Sciences (IBMP RAS) to A.A.S., S.M.S., V.A.S., O.V.K.,
D.D.V., K.D.O., M.P.R., and S.A.P., the Tamkeen under the NYU Abu Dhabi Research
Institute Award to the NYUAD Center for Genomics and Systems Biology (ADHPG-CGSB)
to P.P., the Knut and Alice Wallenberg foundation to C.K., the Swedish National
Space Agency to N.V.K. and L.S.W., Swedish Research Council, Gösta Fraenckel Foundation,
and Karolinska Institutet to L.S.W.
article_number: adg1610
article_processing_charge: Yes
article_type: original
author:
- first_name: Carlos J.
full_name: Gallardo-Dodd, Carlos J.
last_name: Gallardo-Dodd
- first_name: Christian
full_name: Oertlin, Christian
last_name: Oertlin
- first_name: Julien
full_name: Record, Julien
last_name: Record
- first_name: Rômulo G.
full_name: Galvani, Rômulo G.
last_name: Galvani
- first_name: Christian
full_name: Sommerauer, Christian
last_name: Sommerauer
- first_name: Nikolai V.
full_name: Kuznetsov, Nikolai V.
last_name: Kuznetsov
- first_name: Evangelos
full_name: Doukoumopoulos, Evangelos
last_name: Doukoumopoulos
- first_name: Liaqat
full_name: Ali, Liaqat
last_name: Ali
- first_name: Mariana M. S.
full_name: Oliveira, Mariana M. S.
last_name: Oliveira
- first_name: Christina
full_name: Seitz, Christina
last_name: Seitz
- first_name: Mathias
full_name: Percipalle, Mathias
id: 4986e21c-eb97-11eb-a6c2-a4ef0b629971
last_name: Percipalle
- first_name: Tijana
full_name: Nikić, Tijana
last_name: Nikić
- first_name: Anastasia A.
full_name: Sadova, Anastasia A.
last_name: Sadova
- first_name: Sofia M.
full_name: Shulgina, Sofia M.
last_name: Shulgina
- first_name: Vjacheslav A.
full_name: Shmarov, Vjacheslav A.
last_name: Shmarov
- first_name: Olga V.
full_name: Kutko, Olga V.
last_name: Kutko
- first_name: Daria D.
full_name: Vlasova, Daria D.
last_name: Vlasova
- first_name: Kseniya D.
full_name: Orlova, Kseniya D.
last_name: Orlova
- first_name: Marina P.
full_name: Rykova, Marina P.
last_name: Rykova
- first_name: John
full_name: Andersson, John
last_name: Andersson
- first_name: Piergiorgio
full_name: Percipalle, Piergiorgio
last_name: Percipalle
- first_name: Claudia
full_name: Kutter, Claudia
last_name: Kutter
- first_name: Sergey A.
full_name: Ponomarev, Sergey A.
last_name: Ponomarev
- first_name: Lisa S.
full_name: Westerberg, Lisa S.
last_name: Westerberg
citation:
ama: Gallardo-Dodd CJ, Oertlin C, Record J, et al. Exposure of volunteers to microgravity
by dry immersion bed over 21 days results in gene expression changes and adaptation
of T cells. Science Advances. 2023;9(34). doi:10.1126/sciadv.adg1610
apa: Gallardo-Dodd, C. J., Oertlin, C., Record, J., Galvani, R. G., Sommerauer,
C., Kuznetsov, N. V., … Westerberg, L. S. (2023). Exposure of volunteers to microgravity
by dry immersion bed over 21 days results in gene expression changes and adaptation
of T cells. Science Advances. American Association for the Advancement
of Science. https://doi.org/10.1126/sciadv.adg1610
chicago: Gallardo-Dodd, Carlos J., Christian Oertlin, Julien Record, Rômulo G. Galvani,
Christian Sommerauer, Nikolai V. Kuznetsov, Evangelos Doukoumopoulos, et al. “Exposure
of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene
Expression Changes and Adaptation of T Cells.” Science Advances. American
Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.adg1610.
ieee: C. J. Gallardo-Dodd et al., “Exposure of volunteers to microgravity
by dry immersion bed over 21 days results in gene expression changes and adaptation
of T cells,” Science Advances, vol. 9, no. 34. American Association for
the Advancement of Science, 2023.
ista: Gallardo-Dodd CJ, Oertlin C, Record J, Galvani RG, Sommerauer C, Kuznetsov
NV, Doukoumopoulos E, Ali L, Oliveira MMS, Seitz C, Percipalle M, Nikić T, Sadova
AA, Shulgina SM, Shmarov VA, Kutko OV, Vlasova DD, Orlova KD, Rykova MP, Andersson
J, Percipalle P, Kutter C, Ponomarev SA, Westerberg LS. 2023. Exposure of volunteers
to microgravity by dry immersion bed over 21 days results in gene expression changes
and adaptation of T cells. Science Advances. 9(34), adg1610.
mla: Gallardo-Dodd, Carlos J., et al. “Exposure of Volunteers to Microgravity by
Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation
of T Cells.” Science Advances, vol. 9, no. 34, adg1610, American Association
for the Advancement of Science, 2023, doi:10.1126/sciadv.adg1610.
short: C.J. Gallardo-Dodd, C. Oertlin, J. Record, R.G. Galvani, C. Sommerauer, N.V.
Kuznetsov, E. Doukoumopoulos, L. Ali, M.M.S. Oliveira, C. Seitz, M. Percipalle,
T. Nikić, A.A. Sadova, S.M. Shulgina, V.A. Shmarov, O.V. Kutko, D.D. Vlasova,
K.D. Orlova, M.P. Rykova, J. Andersson, P. Percipalle, C. Kutter, S.A. Ponomarev,
L.S. Westerberg, Science Advances 9 (2023).
date_created: 2024-01-10T09:48:01Z
date_published: 2023-08-25T00:00:00Z
date_updated: 2024-09-09T08:03:13Z
day: '25'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1126/sciadv.adg1610
external_id:
isi:
- '001054596800007'
pmid:
- '37624890'
file:
- access_level: open_access
checksum: b9072e20e2d5d9d34d2c53319bafee41
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T09:35:28Z
date_updated: 2024-01-16T09:35:28Z
file_id: '14809'
file_name: 2023_ScienceAdvances_GallardoDodd.pdf
file_size: 1596639
relation: main_file
success: 1
file_date_updated: 2024-01-16T09:35:28Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '34'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
status: public
title: Exposure of volunteers to microgravity by dry immersion bed over 21 days results
in gene expression changes and adaptation of T 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2023'
...
---
_id: '14785'
abstract:
- lang: eng
text: Small cryptic plasmids have no clear effect on the host fitness and their
functional repertoire remains obscure. The naturally competent cyanobacterium
Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their
evolution with this species is supported by horizontal transfer remains understudied.
Here, we show that the small cryptic plasmid DNA is transferred in the population
exclusively by natural transformation, where the transfer frequency of plasmid‐encoded
genes is similar to that of chromosome‐encoded genes. Establishing a system to
follow gene transfer, we compared the transfer frequency of genes encoded in cryptic
plasmids pCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations
of two Synechocystis sp. PCC 6803 labtypes (termed
Kiel and Sevilla). Our results reveal that plasmid gene transfer frequency depends
on the recipient labtype. Furthermore, gene transfer via whole plasmid uptake
in the Sevilla labtype ranged among the lowest detected transfer rates in our
experiments. Our study indicates that horizontal DNA transfer via natural transformation
is frequent in the evolution of small cryptic plasmids that reside in naturally
competent organisms. Furthermore, we suggest that the contribution of natural
transformation to cryptic plasmid persistence in Synechocystis is limited.
acknowledgement: "We thank the lab of Francisco Javier Florencio Bel-lido, Sevilla,
Spain for supplying theSynechocystislabtype Sevilla used in this work and the lab
of MartinHagemann, Rostock, Germany for supplying the pIGAplasmidusedinthiswork.WethankNilsHülterforfruitful
discussions. We thank Fenna Stücker forgraphical illustrations and Katrin Schumann,
FennaStücker, and Lidusha Manivannan for technicalsupport.\r\nChilean National
Agency for Research andDevelopment (ANID), Grant/Award Number:21191763; DeutscheForschungsgemeinschaft,
Grant/AwardNumbers: 456882089, RTG2501; EuropeanResearch Council (ERC), Grant/AwardNumber:
101043835"
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Fabian
full_name: Nies, Fabian
last_name: Nies
- first_name: Tanita
full_name: Wein, Tanita
last_name: Wein
- first_name: Dustin M.
full_name: Hanke, Dustin M.
last_name: Hanke
- first_name: Benjamin L
full_name: Springstein, Benjamin L
id: b4eb62ef-ac72-11ed-9503-ed3b4d66c083
last_name: Springstein
orcid: 0000-0002-3461-5391
- first_name: Jaime
full_name: Alcorta, Jaime
last_name: Alcorta
- first_name: Claudia
full_name: Taubenheim, Claudia
last_name: Taubenheim
- first_name: Tal
full_name: Dagan, Tal
last_name: Dagan
citation:
ama: Nies F, Wein T, Hanke DM, et al. Role of natural transformation in the evolution
of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology
Reports. 2023;15(6):656-668. doi:10.1111/1758-2229.13203
apa: Nies, F., Wein, T., Hanke, D. M., Springstein, B. L., Alcorta, J., Taubenheim,
C., & Dagan, T. (2023). Role of natural transformation in the evolution of
small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology
Reports. Wiley. https://doi.org/10.1111/1758-2229.13203
chicago: Nies, Fabian, Tanita Wein, Dustin M. Hanke, Benjamin L Springstein, Jaime
Alcorta, Claudia Taubenheim, and Tal Dagan. “Role of Natural Transformation in
the Evolution of Small Cryptic Plasmids in Synechocystis Sp. PCC 6803.” Environmental
Microbiology Reports. Wiley, 2023. https://doi.org/10.1111/1758-2229.13203.
ieee: F. Nies et al., “Role of natural transformation in the evolution of
small cryptic plasmids in Synechocystis sp. PCC 6803,” Environmental Microbiology
Reports, vol. 15, no. 6. Wiley, pp. 656–668, 2023.
ista: Nies F, Wein T, Hanke DM, Springstein BL, Alcorta J, Taubenheim C, Dagan T.
2023. Role of natural transformation in the evolution of small cryptic plasmids
in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. 15(6), 656–668.
mla: Nies, Fabian, et al. “Role of Natural Transformation in the Evolution of Small
Cryptic Plasmids in Synechocystis Sp. PCC 6803.” Environmental Microbiology
Reports, vol. 15, no. 6, Wiley, 2023, pp. 656–68, doi:10.1111/1758-2229.13203.
short: F. Nies, T. Wein, D.M. Hanke, B.L. Springstein, J. Alcorta, C. Taubenheim,
T. Dagan, Environmental Microbiology Reports 15 (2023) 656–668.
date_created: 2024-01-10T10:41:07Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-01-16T09:46:12Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1111/1758-2229.13203
external_id:
isi:
- '001080203100001'
pmid:
- '37794696'
file:
- access_level: open_access
checksum: d09ebb68fee61f4e2e09ec286c9cf1d3
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T09:42:10Z
date_updated: 2024-01-16T09:42:10Z
file_id: '14810'
file_name: 2023_EnvirMicroBiolReports_Nies.pdf
file_size: 1518350
relation: main_file
success: 1
file_date_updated: 2024-01-16T09:42:10Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '6'
keyword:
- Agricultural and Biological Sciences (miscellaneous)
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 656-668
pmid: 1
publication: Environmental Microbiology Reports
publication_identifier:
eissn:
- 1758-2229
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Role of natural transformation in the evolution of small cryptic plasmids in
Synechocystis sp. PCC 6803
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: 15
year: '2023'
...
---
_id: '14787'
abstract:
- lang: eng
text: Understanding the phenotypic and genetic architecture of reproductive isolation
is a long‐standing goal of speciation research. In several systems, large‐effect
loci contributing to barrier phenotypes have been characterized, but such causal
connections are rarely known for more complex genetic architectures. In this study,
we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward
an integrated understanding of speciation across a monkeyflower hybrid zone. Previous
work suggests that pollinator visitation acts as a primary barrier to gene flow
between two divergent red‐ and yellow‐flowered ecotypes ofMimulus
aurantiacus. Several candidate isolating traits and anonymous single
nucleotide polymorphism loci under divergent selection have been identified, but
their genomic positions remain unknown. Here, we report findings from demographic
analyses that indicate this hybrid zone formed by secondary contact, but that
subsequent gene flow was restricted by widespread barrier loci across the genome.
Using a novel, geographic cline‐based genome scan, we demonstrate that candidate
barrier loci are broadly distributed across the genome, rather than mapping to
one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals
that most floral traits are highly polygenic, with little evidence that QTL colocalize,
indicating that most traits are genetically independent. Finally, we find little
evidence that QTL and candidate barrier loci overlap, suggesting that some loci
contribute to other forms of reproductive isolation. Our findings highlight the
challenges of understanding the genetic architecture of reproductive isolation
and reveal that barriers to gene flow other than pollinator isolation may play
an important role in this system.
acknowledgement: We thank Julian Catchen for making modifications to Stacks to aid
this project. Peter L. Ralph, Thomas Nelson, Roger K. Butlin, Anja M. Westram and
Nicholas H. Barton provided advice, stimulating discussion and critical feedback.
The project was supported by National Science Foundation grant DEB-1258199.
article_processing_charge: No
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Madeline A.
full_name: Chase, Madeline A.
last_name: Chase
- first_name: Hanna
full_name: McIntosh, Hanna
last_name: McIntosh
- first_name: Matthew A.
full_name: Streisfeld, Matthew A.
last_name: Streisfeld
citation:
ama: Stankowski S, Chase MA, McIntosh H, Streisfeld MA. Integrating top‐down and
bottom‐up approaches to understand the genetic architecture of speciation across
a monkeyflower hybrid zone. Molecular Ecology. 2023;32(8):2041-2054. doi:10.1111/mec.16849
apa: Stankowski, S., Chase, M. A., McIntosh, H., & Streisfeld, M. A. (2023).
Integrating top‐down and bottom‐up approaches to understand the genetic architecture
of speciation across a monkeyflower hybrid zone. Molecular Ecology. Wiley.
https://doi.org/10.1111/mec.16849
chicago: Stankowski, Sean, Madeline A. Chase, Hanna McIntosh, and Matthew A. Streisfeld.
“Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture
of Speciation across a Monkeyflower Hybrid Zone.” Molecular Ecology. Wiley,
2023. https://doi.org/10.1111/mec.16849.
ieee: S. Stankowski, M. A. Chase, H. McIntosh, and M. A. Streisfeld, “Integrating
top‐down and bottom‐up approaches to understand the genetic architecture of speciation
across a monkeyflower hybrid zone,” Molecular Ecology, vol. 32, no. 8.
Wiley, pp. 2041–2054, 2023.
ista: Stankowski S, Chase MA, McIntosh H, Streisfeld MA. 2023. Integrating top‐down
and bottom‐up approaches to understand the genetic architecture of speciation
across a monkeyflower hybrid zone. Molecular Ecology. 32(8), 2041–2054.
mla: Stankowski, Sean, et al. “Integrating Top‐down and Bottom‐up Approaches to
Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid
Zone.” Molecular Ecology, vol. 32, no. 8, Wiley, 2023, pp. 2041–54, doi:10.1111/mec.16849.
short: S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology
32 (2023) 2041–2054.
date_created: 2024-01-10T10:44:45Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2024-01-16T10:10:00Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/mec.16849
external_id:
isi:
- '000919244600001'
pmid:
- '36651268'
intvolume: ' 32'
isi: 1
issue: '8'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2022.01.28.478139
month: '04'
oa: 1
oa_version: Preprint
page: 2041-2054
pmid: 1
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Integrating top‐down and bottom‐up approaches to understand the genetic architecture
of speciation across a monkeyflower hybrid zone
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2023'
...
---
_id: '14788'
abstract:
- lang: eng
text: "Eukaryotic cells use clathrin-mediated endocytosis to take up a large range
of extracellular cargo. During endocytosis, a clathrin coat forms on the plasma
membrane, but it remains controversial when and how it is remodeled into a spherical
vesicle.\r\nHere, we use 3D superresolution microscopy to determine the precise
geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal
sorting, we determine the average trajectory of clathrin remodeling during endocytosis.
We find that clathrin coats assemble first on flat membranes to 50% of the coat
area before they become rapidly and continuously bent, and this mechanism is confirmed
in three cell lines. We introduce the cooperative curvature model, which is based
on positive feedback for curvature generation. It accurately describes the measured
shapes and dynamics of the clathrin coat and could represent a general mechanism
for clathrin coat remodeling on the plasma membrane."
acknowledgement: We thank the entire Ries and Kaksonen labs for fruitful discussions
and support. This work was supported by the European Research Council (ERC CoG-724489
to J. Ries), the National Institutes of Health Common Fund 4D Nucleome Program (Grant
U01 to J. Ries), the Human Frontier Science Program (RGY0065/2017 to J. Ries), the
EMBL Interdisciplinary Postdoc Programme (EIPOD) under Marie Curie Actions COFUND
(Grant 229597 to O. Avinoam), the European Molecular Biology Laboratory (M. Mund,
A. Tschanz, Y.-L. Wu and J. Ries), and the Swiss National Science Foundation (grant
310030B_182825 and NCCR Chemical Biology to M. Kaksonen). O. Avinoam is an incumbent
of the Miriam Berman Presidential Development Chair.
article_number: e202206038
article_processing_charge: No
article_type: original
author:
- first_name: Markus
full_name: Mund, Markus
last_name: Mund
- first_name: Aline
full_name: Tschanz, Aline
last_name: Tschanz
- first_name: Yu-Le
full_name: Wu, Yu-Le
last_name: Wu
- first_name: Felix F
full_name: Frey, Felix F
id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3
last_name: Frey
orcid: 0000-0001-8501-6017
- first_name: Johanna L.
full_name: Mehl, Johanna L.
last_name: Mehl
- first_name: Marko
full_name: Kaksonen, Marko
last_name: Kaksonen
- first_name: Ori
full_name: Avinoam, Ori
last_name: Avinoam
- first_name: Ulrich S.
full_name: Schwarz, Ulrich S.
last_name: Schwarz
- first_name: Jonas
full_name: Ries, Jonas
last_name: Ries
citation:
ama: Mund M, Tschanz A, Wu Y-L, et al. Clathrin coats partially preassemble and
subsequently bend during endocytosis. Journal of Cell Biology. 2023;222(3).
doi:10.1083/jcb.202206038
apa: Mund, M., Tschanz, A., Wu, Y.-L., Frey, F. F., Mehl, J. L., Kaksonen, M., …
Ries, J. (2023). Clathrin coats partially preassemble and subsequently bend during
endocytosis. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202206038
chicago: Mund, Markus, Aline Tschanz, Yu-Le Wu, Felix F Frey, Johanna L. Mehl, Marko
Kaksonen, Ori Avinoam, Ulrich S. Schwarz, and Jonas Ries. “Clathrin Coats Partially
Preassemble and Subsequently Bend during Endocytosis.” Journal of Cell Biology.
Rockefeller University Press, 2023. https://doi.org/10.1083/jcb.202206038.
ieee: M. Mund et al., “Clathrin coats partially preassemble and subsequently
bend during endocytosis,” Journal of Cell Biology, vol. 222, no. 3. Rockefeller
University Press, 2023.
ista: Mund M, Tschanz A, Wu Y-L, Frey FF, Mehl JL, Kaksonen M, Avinoam O, Schwarz
US, Ries J. 2023. Clathrin coats partially preassemble and subsequently bend during
endocytosis. Journal of Cell Biology. 222(3), e202206038.
mla: Mund, Markus, et al. “Clathrin Coats Partially Preassemble and Subsequently
Bend during Endocytosis.” Journal of Cell Biology, vol. 222, no. 3, e202206038,
Rockefeller University Press, 2023, doi:10.1083/jcb.202206038.
short: M. Mund, A. Tschanz, Y.-L. Wu, F.F. Frey, J.L. Mehl, M. Kaksonen, O. Avinoam,
U.S. Schwarz, J. Ries, Journal of Cell Biology 222 (2023).
date_created: 2024-01-10T10:45:55Z
date_published: 2023-02-03T00:00:00Z
date_updated: 2024-01-16T10:17:05Z
day: '03'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1083/jcb.202206038
external_id:
isi:
- '000978065000001'
pmid:
- '36734980'
file:
- access_level: open_access
checksum: 505d5cac36c14b073b68c7fed1a92bd3
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T10:15:09Z
date_updated: 2024-01-16T10:15:09Z
file_id: '14811'
file_name: 2023_JCB_Mund.pdf
file_size: 5678069
relation: main_file
success: 1
file_date_updated: 2024-01-16T10:15:09Z
has_accepted_license: '1'
intvolume: ' 222'
isi: 1
issue: '3'
keyword:
- Cell Biology
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
issn:
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
status: public
title: Clathrin coats partially preassemble and subsequently bend during endocytosis
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: 222
year: '2023'
...
---
_id: '14798'
abstract:
- lang: eng
text: 'A faithful reproduction of gloss is inherently difficult because of the limited
dynamic range, peak luminance, and 3D capabilities of display devices. This work
investigates how the display capabilities affect gloss appearance with respect
to a real-world reference object. To this end, we employ an accurate imaging pipeline
to achieve a perceptual gloss match between a virtual and real object presented
side-by-side on an augmented-reality high-dynamic-range (HDR) stereoscopic display,
which has not been previously attained to this extent. Based on this precise gloss
reproduction, we conduct a series of gloss matching experiments to study how gloss
perception degrades based on individual factors: object albedo, display luminance,
dynamic range, stereopsis, and tone mapping. We support the study with a detailed
analysis of individual factors, followed by an in-depth discussion on the observed
perceptual effects. Our experiments demonstrate that stereoscopic presentation
has a limited effect on the gloss matching task on our HDR display. However, both
reduced luminance and dynamic range of the display reduce the perceived gloss.
This means that the visual system cannot compensate for the changes in gloss appearance
across luminance (lack of gloss constancy), and the tone mapping operator should
be carefully selected when reproducing gloss on a low dynamic range (LDR) display.'
acknowledgement: "This work is supported by FWF Lise Meitner (Grant M 3319), Spanish
Agencia Estatal de Investigación (project PID2022-141539NBI00), European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement\r\nN◦ 725253–EyeCode), Swiss National Science Foundation (Grant
no. 200502), and academic gifts from Meta. We thank Dmitry Lubyako and Ali Özgür
Yöntem for building the turntable for our experiment."
article_number: '90'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Bin
full_name: Chen, Bin
last_name: Chen
- first_name: Akshay
full_name: Jindal, Akshay
last_name: Jindal
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
orcid: 0000-0002-5062-4474
- first_name: Chao
full_name: Wang, Chao
last_name: Wang
- first_name: Hans Peter
full_name: Seidel, Hans Peter
last_name: Seidel
- first_name: Piotr
full_name: Didyk, Piotr
last_name: Didyk
- first_name: Karol
full_name: Myszkowski, Karol
last_name: Myszkowski
- first_name: Ana
full_name: Serrano, Ana
last_name: Serrano
- first_name: Rafał K.
full_name: Mantiuk, Rafał K.
last_name: Mantiuk
citation:
ama: 'Chen B, Jindal A, Piovarci M, et al. The effect of display capabilities on
the gloss consistency between real and virtual objects. In: Proceedings of
the SIGGRAPH Asia 2023 Conference. Association for Computing Machinery; 2023.
doi:10.1145/3610548.3618226'
apa: 'Chen, B., Jindal, A., Piovarci, M., Wang, C., Seidel, H. P., Didyk, P., …
Mantiuk, R. K. (2023). The effect of display capabilities on the gloss consistency
between real and virtual objects. In Proceedings of the SIGGRAPH Asia 2023
Conference. Sydney, Australia: Association for Computing Machinery. https://doi.org/10.1145/3610548.3618226'
chicago: Chen, Bin, Akshay Jindal, Michael Piovarci, Chao Wang, Hans Peter Seidel,
Piotr Didyk, Karol Myszkowski, Ana Serrano, and Rafał K. Mantiuk. “The Effect
of Display Capabilities on the Gloss Consistency between Real and Virtual Objects.”
In Proceedings of the SIGGRAPH Asia 2023 Conference. Association for Computing
Machinery, 2023. https://doi.org/10.1145/3610548.3618226.
ieee: B. Chen et al., “The effect of display capabilities on the gloss consistency
between real and virtual objects,” in Proceedings of the SIGGRAPH Asia 2023
Conference, Sydney, Australia, 2023.
ista: 'Chen B, Jindal A, Piovarci M, Wang C, Seidel HP, Didyk P, Myszkowski K, Serrano
A, Mantiuk RK. 2023. The effect of display capabilities on the gloss consistency
between real and virtual objects. Proceedings of the SIGGRAPH Asia 2023 Conference.
SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 90.'
mla: Chen, Bin, et al. “The Effect of Display Capabilities on the Gloss Consistency
between Real and Virtual Objects.” Proceedings of the SIGGRAPH Asia 2023 Conference,
90, Association for Computing Machinery, 2023, doi:10.1145/3610548.3618226.
short: B. Chen, A. Jindal, M. Piovarci, C. Wang, H.P. Seidel, P. Didyk, K. Myszkowski,
A. Serrano, R.K. Mantiuk, in:, Proceedings of the SIGGRAPH Asia 2023 Conference,
Association for Computing Machinery, 2023.
conference:
end_date: 2023-12-15
location: Sydney, Australia
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference'
start_date: 2023-12-12
date_created: 2024-01-14T23:00:57Z
date_published: 2023-12-10T00:00:00Z
date_updated: 2025-09-09T14:20:50Z
day: '10'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3610548.3618226
external_id:
isi:
- '001278296700090'
file:
- access_level: open_access
checksum: 8abe27432ed222b50d1af9b3388db1b0
content_type: application/pdf
creator: dernst
date_created: 2024-01-17T08:33:06Z
date_updated: 2024-01-17T08:33:06Z
file_id: '14823'
file_name: 2023_SA_Chen.pdf
file_size: 95967451
relation: main_file
success: 1
file_date_updated: 2024-01-17T08:33:06Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: eb901961-77a9-11ec-83b8-f5c883a62027
grant_number: M03319
name: Perception-Aware Appearance Fabrication
publication: Proceedings of the SIGGRAPH Asia 2023 Conference
publication_identifier:
isbn:
- '9798400703157'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: The effect of display capabilities on the gloss consistency between real and
virtual objects
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: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2023'
...