---
_id: '9230'
abstract:
- lang: eng
text: "We consider a model of the Riemann zeta function on the critical axis and
study its maximum over intervals of length (log T)θ, where θ is either fixed or
tends to zero at a suitable rate.\r\nIt is shown that the deterministic level
of the maximum interpolates smoothly between the ones\r\nof log-correlated variables
and of i.i.d. random variables, exhibiting a smooth transition ‘from\r\n3/4 to
1/4’ in the second order. This provides a natural context where extreme value
statistics of\r\nlog-correlated variables with time-dependent variance and rate
occur. A key ingredient of the\r\nproof is a precise upper tail tightness estimate
for the maximum of the model on intervals of\r\nsize one, that includes a Gaussian
correction. This correction is expected to be present for the\r\nRiemann zeta
function and pertains to the question of the correct order of the maximum of\r\nthe
zeta function in large intervals."
acknowledgement: The research of L.-P. A. is supported in part by the grant NSF CAREER
DMS-1653602. G. D. gratefully acknowledges support from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
No. 754411. The research of L. H. is supported in part by the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation) through Project-ID 233630050 -TRR 146, Project-ID
443891315 within SPP 2265 and Project-ID 446173099.
article_number: '2103.04817'
article_processing_charge: No
arxiv: 1
author:
- first_name: Louis-Pierre
full_name: Arguin, Louis-Pierre
last_name: Arguin
- first_name: Guillaume
full_name: Dubach, Guillaume
id: D5C6A458-10C4-11EA-ABF4-A4B43DDC885E
last_name: Dubach
orcid: 0000-0001-6892-8137
- first_name: Lisa
full_name: Hartung, Lisa
last_name: Hartung
citation:
ama: Arguin L-P, Dubach G, Hartung L. Maxima of a random model of the Riemann zeta
function over intervals of varying length. arXiv. doi:10.48550/arXiv.2103.04817
apa: Arguin, L.-P., Dubach, G., & Hartung, L. (n.d.). Maxima of a random model
of the Riemann zeta function over intervals of varying length. arXiv. https://doi.org/10.48550/arXiv.2103.04817
chicago: Arguin, Louis-Pierre, Guillaume Dubach, and Lisa Hartung. “Maxima of a
Random Model of the Riemann Zeta Function over Intervals of Varying Length.” ArXiv,
n.d. https://doi.org/10.48550/arXiv.2103.04817.
ieee: L.-P. Arguin, G. Dubach, and L. Hartung, “Maxima of a random model of the
Riemann zeta function over intervals of varying length,” arXiv. .
ista: Arguin L-P, Dubach G, Hartung L. Maxima of a random model of the Riemann zeta
function over intervals of varying length. arXiv, 2103.04817.
mla: Arguin, Louis-Pierre, et al. “Maxima of a Random Model of the Riemann Zeta
Function over Intervals of Varying Length.” ArXiv, 2103.04817, doi:10.48550/arXiv.2103.04817.
short: L.-P. Arguin, G. Dubach, L. Hartung, ArXiv (n.d.).
date_created: 2021-03-09T11:08:15Z
date_published: 2021-03-08T00:00:00Z
date_updated: 2025-04-14T07:43:51Z
day: '08'
department:
- _id: LaEr
doi: 10.48550/arXiv.2103.04817
ec_funded: 1
external_id:
arxiv:
- '2103.04817'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2103.04817
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: arXiv
publication_status: submitted
status: public
title: Maxima of a random model of the Riemann zeta function over intervals of varying
length
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9234'
abstract:
- lang: eng
text: In this paper, we present two new inertial projection-type methods for solving
multivalued variational inequality problems in finite-dimensional spaces. We establish
the convergence of the sequence generated by these methods when the multivalued
mapping associated with the problem is only required to be locally bounded without
any monotonicity assumption. Furthermore, the inertial techniques that we employ
in this paper are quite different from the ones used in most papers. Moreover,
based on the weaker assumptions on the inertial factor in our methods, we derive
several special cases of our methods. Finally, we present some experimental results
to illustrate the profits that we gain by introducing the inertial extrapolation
steps.
acknowledgement: 'The authors sincerely thank the Editor-in-Chief and anonymous referees
for their careful reading, constructive comments and fruitful suggestions that help
improve the manuscript. The research of the first author is supported by the National
Research Foundation (NRF) South Africa (S& F-DSI/NRF Free Standing Postdoctoral
Fellowship; Grant Number: 120784). The first author also acknowledges the financial
support from DSI/NRF, South Africa Center of Excellence in Mathematical and Statistical
Sciences (CoE-MaSS) Postdoctoral Fellowship. The second author has received funding
from the European Research Council (ERC) under the European Union’s Seventh Framework
Program (FP7 - 2007-2013) (Grant agreement No. 616160). Open Access funding provided
by Institute of Science and Technology (IST Austria).'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Chinedu
full_name: Izuchukwu, Chinedu
last_name: Izuchukwu
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
citation:
ama: Izuchukwu C, Shehu Y. New inertial projection methods for solving multivalued
variational inequality problems beyond monotonicity. Networks and Spatial Economics.
2021;21(2):291-323. doi:10.1007/s11067-021-09517-w
apa: Izuchukwu, C., & Shehu, Y. (2021). New inertial projection methods for
solving multivalued variational inequality problems beyond monotonicity. Networks
and Spatial Economics. Springer Nature. https://doi.org/10.1007/s11067-021-09517-w
chicago: Izuchukwu, Chinedu, and Yekini Shehu. “New Inertial Projection Methods
for Solving Multivalued Variational Inequality Problems beyond Monotonicity.”
Networks and Spatial Economics. Springer Nature, 2021. https://doi.org/10.1007/s11067-021-09517-w.
ieee: C. Izuchukwu and Y. Shehu, “New inertial projection methods for solving multivalued
variational inequality problems beyond monotonicity,” Networks and Spatial
Economics, vol. 21, no. 2. Springer Nature, pp. 291–323, 2021.
ista: Izuchukwu C, Shehu Y. 2021. New inertial projection methods for solving multivalued
variational inequality problems beyond monotonicity. Networks and Spatial Economics.
21(2), 291–323.
mla: Izuchukwu, Chinedu, and Yekini Shehu. “New Inertial Projection Methods for
Solving Multivalued Variational Inequality Problems beyond Monotonicity.” Networks
and Spatial Economics, vol. 21, no. 2, Springer Nature, 2021, pp. 291–323,
doi:10.1007/s11067-021-09517-w.
short: C. Izuchukwu, Y. Shehu, Networks and Spatial Economics 21 (2021) 291–323.
date_created: 2021-03-10T12:18:47Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2024-11-04T13:52:33Z
day: '01'
ddc:
- '510'
department:
- _id: VlKo
doi: 10.1007/s11067-021-09517-w
ec_funded: 1
external_id:
isi:
- '000625002100001'
file:
- access_level: open_access
checksum: 22b4253a2e5da843622a2df713784b4c
content_type: application/pdf
creator: kschuh
date_created: 2021-08-11T12:44:16Z
date_updated: 2021-08-11T12:44:16Z
file_id: '9884'
file_name: 2021_NetworksSpatialEconomics_Shehu.pdf
file_size: 834964
relation: main_file
success: 1
file_date_updated: 2021-08-11T12:44:16Z
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '2'
keyword:
- Computer Networks and Communications
- Software
- Artificial Intelligence
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 291-323
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Networks and Spatial Economics
publication_identifier:
eissn:
- 1572-9427
issn:
- 1566-113X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: New inertial projection methods for solving multivalued variational inequality
problems beyond monotonicity
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 21
year: '2021'
...
---
_id: '9239'
abstract:
- lang: eng
text: 'A graph game proceeds as follows: two players move a token through a graph
to produce a finite or infinite path, which determines the payoff of the game.
We study bidding games in which in each turn, an auction determines which player
moves the token. Bidding games were largely studied in combination with two variants
of first-price auctions called “Richman” and “poorman” bidding. We study taxman
bidding, which span the spectrum between the two. The game is parameterized by
a constant : portion τ of the winning bid is paid to the other player, and portion to
the bank. While finite-duration (reachability) taxman games have been studied
before, we present, for the first time, results on infinite-duration taxman games:
we unify, generalize, and simplify previous equivalences between bidding games
and a class of stochastic games called random-turn games.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Đorđe
full_name: Žikelić, Đorđe
last_name: Žikelić
citation:
ama: Avni G, Henzinger TA, Žikelić Đ. Bidding mechanisms in graph games. Journal
of Computer and System Sciences. 2021;119(8):133-144. doi:10.1016/j.jcss.2021.02.008
apa: Avni, G., Henzinger, T. A., & Žikelić, Đ. (2021). Bidding mechanisms in
graph games. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2021.02.008
chicago: Avni, Guy, Thomas A Henzinger, and Đorđe Žikelić. “Bidding Mechanisms in
Graph Games.” Journal of Computer and System Sciences. Elsevier, 2021.
https://doi.org/10.1016/j.jcss.2021.02.008.
ieee: G. Avni, T. A. Henzinger, and Đ. Žikelić, “Bidding mechanisms in graph games,”
Journal of Computer and System Sciences, vol. 119, no. 8. Elsevier, pp.
133–144, 2021.
ista: Avni G, Henzinger TA, Žikelić Đ. 2021. Bidding mechanisms in graph games.
Journal of Computer and System Sciences. 119(8), 133–144.
mla: Avni, Guy, et al. “Bidding Mechanisms in Graph Games.” Journal of Computer
and System Sciences, vol. 119, no. 8, Elsevier, 2021, pp. 133–44, doi:10.1016/j.jcss.2021.02.008.
short: G. Avni, T.A. Henzinger, Đ. Žikelić, Journal of Computer and System Sciences
119 (2021) 133–144.
date_created: 2021-03-14T23:01:32Z
date_published: 2021-03-03T00:00:00Z
date_updated: 2025-07-10T11:53:57Z
day: '03'
department:
- _id: ToHe
doi: 10.1016/j.jcss.2021.02.008
external_id:
arxiv:
- '1905.03835'
isi:
- '000634149800009'
intvolume: ' 119'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1905.03835
month: '03'
oa: 1
oa_version: Preprint
page: 133-144
publication: Journal of Computer and System Sciences
publication_identifier:
eissn:
- 1090-2724
issn:
- 0022-0000
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '6884'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Bidding mechanisms in graph games
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 119
year: '2021'
...
---
_id: '9240'
abstract:
- lang: eng
text: A stochastic PDE, describing mesoscopic fluctuations in systems of weakly
interacting inertial particles of finite volume, is proposed and analysed in any
finite dimension . It is a regularised and inertial version of the Dean–Kawasaki
model. A high-probability well-posedness theory for this model is developed. This
theory improves significantly on the spatial scaling restrictions imposed in an
earlier work of the same authors, which applied only to significantly larger particles
in one dimension. The well-posedness theory now applies in d-dimensions when the
particle-width ϵ is proportional to for and N is the number of particles. This
scaling is optimal in a certain Sobolev norm. Key tools of the analysis are fractional
Sobolev spaces, sharp bounds on Bessel functions, separability of the regularisation
in the d-spatial dimensions, and use of the Faà di Bruno's formula.
acknowledgement: All authors thank the anonymous referee for his/her careful reading
of the manuscript and valuable suggestions. This paper was motivated by stimulating
discussions at the First Berlin–Leipzig Workshop on Fluctuating Hydrodynamics in
August 2019 with Ana Djurdjevac, Rupert Klein and Ralf Kornhuber. JZ gratefully
acknowledges funding by a Royal Society Wolfson Research Merit Award. FC gratefully
acknowledges funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement No. 754411.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Federico
full_name: Cornalba, Federico
id: 2CEB641C-A400-11E9-A717-D712E6697425
last_name: Cornalba
orcid: 0000-0002-6269-5149
- first_name: Tony
full_name: Shardlow, Tony
last_name: Shardlow
- first_name: Johannes
full_name: Zimmer, Johannes
last_name: Zimmer
citation:
ama: Cornalba F, Shardlow T, Zimmer J. Well-posedness for a regularised inertial
Dean–Kawasaki model for slender particles in several space dimensions. Journal
of Differential Equations. 2021;284(5):253-283. doi:10.1016/j.jde.2021.02.048
apa: Cornalba, F., Shardlow, T., & Zimmer, J. (2021). Well-posedness for a regularised
inertial Dean–Kawasaki model for slender particles in several space dimensions.
Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2021.02.048
chicago: Cornalba, Federico, Tony Shardlow, and Johannes Zimmer. “Well-Posedness
for a Regularised Inertial Dean–Kawasaki Model for Slender Particles in Several
Space Dimensions.” Journal of Differential Equations. Elsevier, 2021. https://doi.org/10.1016/j.jde.2021.02.048.
ieee: F. Cornalba, T. Shardlow, and J. Zimmer, “Well-posedness for a regularised
inertial Dean–Kawasaki model for slender particles in several space dimensions,”
Journal of Differential Equations, vol. 284, no. 5. Elsevier, pp. 253–283,
2021.
ista: Cornalba F, Shardlow T, Zimmer J. 2021. Well-posedness for a regularised inertial
Dean–Kawasaki model for slender particles in several space dimensions. Journal
of Differential Equations. 284(5), 253–283.
mla: Cornalba, Federico, et al. “Well-Posedness for a Regularised Inertial Dean–Kawasaki
Model for Slender Particles in Several Space Dimensions.” Journal of Differential
Equations, vol. 284, no. 5, Elsevier, 2021, pp. 253–83, doi:10.1016/j.jde.2021.02.048.
short: F. Cornalba, T. Shardlow, J. Zimmer, Journal of Differential Equations 284
(2021) 253–283.
date_created: 2021-03-14T23:01:32Z
date_published: 2021-05-25T00:00:00Z
date_updated: 2025-04-14T07:43:51Z
day: '25'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1016/j.jde.2021.02.048
ec_funded: 1
external_id:
isi:
- '000634823300010'
file:
- access_level: open_access
checksum: c630b691fb9e716b02aa6103a9794ec8
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T07:18:01Z
date_updated: 2021-03-22T07:18:01Z
file_id: '9267'
file_name: 2021_JourDiffEquations_Cornalba.pdf
file_size: 473310
relation: main_file
success: 1
file_date_updated: 2021-03-22T07:18:01Z
has_accepted_license: '1'
intvolume: ' 284'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 253-283
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Differential Equations
publication_identifier:
eissn:
- 1090-2732
issn:
- 0022-0396
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles
in several space dimensions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 284
year: '2021'
...
---
_id: '9242'
abstract:
- lang: eng
text: In the recent years important experimental advances in resonant electro-optic
modulators as high-efficiency sources for coherent frequency combs and as devices
for quantum information transfer have been realized, where strong optical and
microwave mode coupling were achieved. These features suggest electro-optic-based
devices as candidates for entangled optical frequency comb sources. In the present
work, I study the generation of entangled optical frequency combs in millimeter-sized
resonant electro-optic modulators. These devices profit from the experimentally
proven advantages such as nearly constant optical free spectral ranges over several
gigahertz, and high optical and microwave quality factors. The generation of frequency
multiplexed quantum channels with spectral bandwidth in the MHz range for conservative
parameter values paves the way towards novel uses in long-distance hybrid quantum
networks, quantum key distribution, enhanced optical metrology, and quantum computing.
acknowledgement: "I thank Prof. Shabir Barzanjeh and Dr. Ulrich Vogl for the fruitful
discussions.\r\n"
article_number: '023708'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
citation:
ama: Rueda Sanchez AR. Frequency-multiplexed hybrid optical entangled source based
on the Pockels effect. Physical Review A. 2021;103(2). doi:10.1103/PhysRevA.103.023708
apa: Rueda Sanchez, A. R. (2021). Frequency-multiplexed hybrid optical entangled
source based on the Pockels effect. Physical Review A. American Physical
Society. https://doi.org/10.1103/PhysRevA.103.023708
chicago: Rueda Sanchez, Alfredo R. “Frequency-Multiplexed Hybrid Optical Entangled
Source Based on the Pockels Effect.” Physical Review A. American Physical
Society, 2021. https://doi.org/10.1103/PhysRevA.103.023708.
ieee: A. R. Rueda Sanchez, “Frequency-multiplexed hybrid optical entangled source
based on the Pockels effect,” Physical Review A, vol. 103, no. 2. American
Physical Society, 2021.
ista: Rueda Sanchez AR. 2021. Frequency-multiplexed hybrid optical entangled source
based on the Pockels effect. Physical Review A. 103(2), 023708.
mla: Rueda Sanchez, Alfredo R. “Frequency-Multiplexed Hybrid Optical Entangled Source
Based on the Pockels Effect.” Physical Review A, vol. 103, no. 2, 023708,
American Physical Society, 2021, doi:10.1103/PhysRevA.103.023708.
short: A.R. Rueda Sanchez, Physical Review A 103 (2021).
date_created: 2021-03-14T23:01:33Z
date_published: 2021-02-11T00:00:00Z
date_updated: 2023-08-07T14:11:18Z
day: '11'
department:
- _id: JoFi
doi: 10.1103/PhysRevA.103.023708
external_id:
arxiv:
- '2010.05356'
isi:
- '000617037900013'
intvolume: ' 103'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2010.05356
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Frequency-multiplexed hybrid optical entangled source based on the Pockels
effect
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 103
year: '2021'
...
---
_id: '9243'
abstract:
- lang: eng
text: Peptidoglycan is an essential component of the bacterial cell envelope that
surrounds the cytoplasmic membrane to protect the cell from osmotic lysis. Important
antibiotics such as β-lactams and glycopeptides target peptidoglycan biosynthesis.
Class A penicillin-binding proteins (PBPs) are bifunctional membrane-bound peptidoglycan
synthases that polymerize glycan chains and connect adjacent stem peptides by
transpeptidation. How these enzymes work in their physiological membrane environment
is poorly understood. Here, we developed a novel Förster resonance energy transfer-based
assay to follow in real time both reactions of class A PBPs reconstituted in liposomes
or supported lipid bilayers and applied this assay with PBP1B homologues from
Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii in the presence
or absence of their cognate lipoprotein activator. Our assay will allow unravelling
the mechanisms of peptidoglycan synthesis in a lipid-bilayer environment and can
be further developed to be used for high-throughput screening for new antimicrobials.
acknowledgement: 'We thank Alexander Egan (Newcastle University) for purified proteins
LpoB(sol) and LpoPPa(sol), Federico Corona (Newcastle University) for purified MepM,
and Oliver Birkholz and Jacob Piehler (Department of Biology and Center of Cellular
Nanoanalytics, University of Osnabru¨ ck) for their help with PBP1B reconstitution
into polymer-SLBs and initial guidance on single particle tracking. We also acknowledge
Christian P Richter and Changjiang You (Department of Biology and Center of Cellular
Nanoanalytics, University of Osnabru¨ ck) for providing SLIMfast software and tris-DODA-NTA
reagent, respectively. This work was funded by the BBSRC grant BB/R017409/1 (to
WV), the European Research Council through grant ERC-2015-StG-679239 (to ML), and
long-term fellowships HFSP LT 000824/2016-L4 and EMBO ALTF 1163–2015 (to NB). '
article_number: 1-32
article_processing_charge: No
article_type: original
author:
- first_name: Víctor M.
full_name: Hernández-Rocamora, Víctor M.
last_name: Hernández-Rocamora
- first_name: Natalia S.
full_name: Baranova, Natalia S.
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Katharina
full_name: Peters, Katharina
last_name: Peters
- first_name: Eefjan
full_name: Breukink, Eefjan
last_name: Breukink
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Waldemar
full_name: Vollmer, Waldemar
last_name: Vollmer
citation:
ama: Hernández-Rocamora VM, Baranova NS, Peters K, Breukink E, Loose M, Vollmer
W. Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin
binding proteins. eLife. 2021;10. doi:10.7554/eLife.61525
apa: Hernández-Rocamora, V. M., Baranova, N. S., Peters, K., Breukink, E., Loose,
M., & Vollmer, W. (2021). Real time monitoring of peptidoglycan synthesis
by membrane-reconstituted penicillin binding proteins. ELife. eLife Sciences
Publications. https://doi.org/10.7554/eLife.61525
chicago: Hernández-Rocamora, Víctor M., Natalia S. Baranova, Katharina Peters, Eefjan
Breukink, Martin Loose, and Waldemar Vollmer. “Real Time Monitoring of Peptidoglycan
Synthesis by Membrane-Reconstituted Penicillin Binding Proteins.” ELife.
eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.61525.
ieee: V. M. Hernández-Rocamora, N. S. Baranova, K. Peters, E. Breukink, M. Loose,
and W. Vollmer, “Real time monitoring of peptidoglycan synthesis by membrane-reconstituted
penicillin binding proteins,” eLife, vol. 10. eLife Sciences Publications,
2021.
ista: Hernández-Rocamora VM, Baranova NS, Peters K, Breukink E, Loose M, Vollmer
W. 2021. Real time monitoring of peptidoglycan synthesis by membrane-reconstituted
penicillin binding proteins. eLife. 10, 1–32.
mla: Hernández-Rocamora, Víctor M., et al. “Real Time Monitoring of Peptidoglycan
Synthesis by Membrane-Reconstituted Penicillin Binding Proteins.” ELife,
vol. 10, 1–32, eLife Sciences Publications, 2021, doi:10.7554/eLife.61525.
short: V.M. Hernández-Rocamora, N.S. Baranova, K. Peters, E. Breukink, M. Loose,
W. Vollmer, ELife 10 (2021).
date_created: 2021-03-14T23:01:33Z
date_published: 2021-02-24T00:00:00Z
date_updated: 2024-10-22T10:04:21Z
day: '24'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.7554/eLife.61525
ec_funded: 1
external_id:
isi:
- '000627596400001'
file:
- access_level: open_access
checksum: 79897a09bfecd9914d39c4aea2841855
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T07:36:08Z
date_updated: 2021-03-22T07:36:08Z
file_id: '9268'
file_name: 2021_eLife_HernandezRocamora.pdf
file_size: 2314698
relation: main_file
success: 1
file_date_updated: 2021-03-22T07:36:08Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: 2596EAB6-B435-11E9-9278-68D0E5697425
grant_number: ALTF 2015-1163
name: Synthesis of bacterial cell wall
- _id: 259B655A-B435-11E9-9278-68D0E5697425
grant_number: LT000824/2016
name: Reconstitution of bacterial cell wall synthesis
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin
binding proteins
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '9244'
abstract:
- lang: eng
text: 'Organ function depends on tissues adopting the correct architecture. However,
insights into organ architecture are currently hampered by an absence of standardized
quantitative 3D analysis. We aimed to develop a robust technology to visualize,
digitalize, and segment the architecture of two tubular systems in 3D: double
resin casting micro computed tomography (DUCT). As proof of principle, we applied
DUCT to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), characterized
by intrahepatic bile duct paucity, that can spontaneously generate a biliary system
in adulthood. DUCT identified increased central biliary branching and peripheral
bile duct tortuosity as two compensatory processes occurring in distinct regions
of Jag1Ndr/Ndr liver, leading to full reconstitution of wild-type biliary volume
and phenotypic recovery. DUCT is thus a powerful new technology for 3D analysis,
which can reveal novel phenotypes and provide a standardized method of defining
liver architecture in mouse models.'
acknowledgement: "Work in ERA lab is supported by the Swedish Research Council, the
Center of Innovative Medicine (CIMED) Grant, Karolinska Institutet, and the Heart
and Lung Foundation, and\r\nthe Daniel Alagille Award from the European Association
for the Study of the Liver. One project in ERA lab is funded by ModeRNA, unrelated
to this project. The funders have no role in the design or interpretation of the
work. SH has been supported by a KI-MU PhD student program, and by a Wera Ekstro¨m
Foundation Scholarship. We are grateful for support from Tornspiran foundation to
NVH. JK: This research was carried out under the project CEITEC 2020 (LQ1601) with
financial support from the Ministry of Education, Youth and Sports of the Czech
Republic under the National Sustainability Programme II and CzechNanoLab Research
Infrastructure supported by MEYS CR (LM2018110) . UL: The financial support from
the Swedish Research Council and ICMC (Integrated CardioMetabolic Center) is acknowledged.
JJ: The work was supported by the Grant Agency of Masaryk University (project no.
MUNI/A/1565/2018). We thank Kari Huppert and Stacey Huppert for their expertise
and help regarding bile duct cannulation and their laboratory hospitality. We also
thank Nadja Schultz and Charlotte L Mattsson for their help with common bile duct
cannulation. We thank Daniel Holl for his help with trachea cannulation. We thank
Nikos Papadogiannakis for his assistance with mild Alagille biopsy samples and discussion.
We thank Karolinska Biomedicum Imaging Core, especially Shigeaki Kanatani for his
help with image analysis. We thank Jan Masek and Carolina Gutierrez for their scientific
input in manuscript writing. We thank Peter Ranefall and the BioImage Informatics
(SciLife national facility) for their help writing parts of the MATLAB pipeline.\r\nThe
TROMA-III antibody developed by Rolf Kemler was obtained from the Developmental
Studies Hybridoma (DSHB) Bank developed under the auspices of NICHD and maintained
by The University of Iowa, Department of Biological Sciences, Iowa City, IA52242.
We thank Goncalo M Brito for all illustrations. This work was supported by the European
Union (European Research Council Starting grant 851288 to E.H.)."
article_number: e60916
article_processing_charge: No
article_type: original
author:
- first_name: Simona
full_name: Hankeova, Simona
last_name: Hankeova
- first_name: Jakub
full_name: Salplachta, Jakub
last_name: Salplachta
- first_name: Tomas
full_name: Zikmund, Tomas
last_name: Zikmund
- first_name: Michaela
full_name: Kavkova, Michaela
last_name: Kavkova
- first_name: Noémi
full_name: Van Hul, Noémi
last_name: Van Hul
- first_name: Adam
full_name: Brinek, Adam
last_name: Brinek
- first_name: Veronika
full_name: Smekalova, Veronika
last_name: Smekalova
- first_name: Jakub
full_name: Laznovsky, Jakub
last_name: Laznovsky
- first_name: Feven
full_name: Dawit, Feven
last_name: Dawit
- first_name: Josef
full_name: Jaros, Josef
last_name: Jaros
- first_name: Vítězslav
full_name: Bryja, Vítězslav
last_name: Bryja
- first_name: Urban
full_name: Lendahl, Urban
last_name: Lendahl
- first_name: Ewa
full_name: Ellis, Ewa
last_name: Ellis
- first_name: Antal
full_name: Nemeth, Antal
last_name: Nemeth
- first_name: Björn
full_name: Fischler, Björn
last_name: Fischler
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Jozef
full_name: Kaiser, Jozef
last_name: Kaiser
- first_name: Emma Rachel
full_name: Andersson, Emma Rachel
last_name: Andersson
citation:
ama: Hankeova S, Salplachta J, Zikmund T, et al. DUCT reveals architectural mechanisms
contributing to bile duct recovery in a mouse model for alagille syndrome. eLife.
2021;10. doi:10.7554/eLife.60916
apa: Hankeova, S., Salplachta, J., Zikmund, T., Kavkova, M., Van Hul, N., Brinek,
A., … Andersson, E. R. (2021). DUCT reveals architectural mechanisms contributing
to bile duct recovery in a mouse model for alagille syndrome. ELife. eLife
Sciences Publications. https://doi.org/10.7554/eLife.60916
chicago: Hankeova, Simona, Jakub Salplachta, Tomas Zikmund, Michaela Kavkova, Noémi
Van Hul, Adam Brinek, Veronika Smekalova, et al. “DUCT Reveals Architectural Mechanisms
Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” ELife.
eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.60916.
ieee: S. Hankeova et al., “DUCT reveals architectural mechanisms contributing
to bile duct recovery in a mouse model for alagille syndrome,” eLife, vol.
10. eLife Sciences Publications, 2021.
ista: Hankeova S, Salplachta J, Zikmund T, Kavkova M, Van Hul N, Brinek A, Smekalova
V, Laznovsky J, Dawit F, Jaros J, Bryja V, Lendahl U, Ellis E, Nemeth A, Fischler
B, Hannezo EB, Kaiser J, Andersson ER. 2021. DUCT reveals architectural mechanisms
contributing to bile duct recovery in a mouse model for alagille syndrome. eLife.
10, e60916.
mla: Hankeova, Simona, et al. “DUCT Reveals Architectural Mechanisms Contributing
to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” ELife, vol.
10, e60916, eLife Sciences Publications, 2021, doi:10.7554/eLife.60916.
short: S. Hankeova, J. Salplachta, T. Zikmund, M. Kavkova, N. Van Hul, A. Brinek,
V. Smekalova, J. Laznovsky, F. Dawit, J. Jaros, V. Bryja, U. Lendahl, E. Ellis,
A. Nemeth, B. Fischler, E.B. Hannezo, J. Kaiser, E.R. Andersson, ELife 10 (2021).
date_created: 2021-03-14T23:01:34Z
date_published: 2021-02-26T00:00:00Z
date_updated: 2026-04-02T14:00:00Z
day: '26'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.7554/eLife.60916
ec_funded: 1
external_id:
isi:
- '000625357100001'
pmid:
- '33635272'
file:
- access_level: open_access
checksum: 20ccf4dfe46c48cf986794c8bf4fd1cb
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T08:50:33Z
date_updated: 2021-03-22T08:50:33Z
file_id: '9271'
file_name: 2021_eLife_Hankeova.pdf
file_size: 9259690
relation: main_file
success: 1
file_date_updated: 2021-03-22T08:50:33Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: DUCT reveals architectural mechanisms contributing to bile duct recovery in
a mouse model for alagille syndrome
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 10
year: '2021'
...
---
_id: '9246'
abstract:
- lang: eng
text: We consider the Fröhlich Hamiltonian in a mean-field limit where many bosonic
particles weakly couple to the quantized phonon field. For large particle numbers
and a suitably small coupling, we show that the dynamics of the system is approximately
described by the Landau–Pekar equations. These describe a Bose–Einstein condensate
interacting with a classical polarization field, whose dynamics is effected by
the condensate, i.e., the back-reaction of the phonons that are created by the
particles during the time evolution is of leading order.
acknowledgement: "Financial support by the European Research Council (ERC) under the\r\nEuropean
Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo 694227;
N.L and R.S.), the SNSF Eccellenza Project PCEFP2 181153 (N.L) and the\r\nDeutsche
Forschungsgemeinschaft (DFG) through the Research TrainingGroup 1838: Spectral\r\nTheory
and Dynamics of Quantum Systems (D.M.) is gratefully acknowledged. N.L.\r\ngratefully
acknowledges support from the NCCRSwissMAP and would like to thank Simone\r\nRademacher
and Benjamin Schlein for interesting discussions about the time-evolution of\r\nthe
polaron at strong coupling. D.M. thanks Marcel Griesemer and Andreas Wünsch for\r\nextensive
discussions about the Fröhlich polaron."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Leopold NK, Mitrouskas DJ, Seiringer R. Derivation of the Landau–Pekar equations
in a many-body mean-field limit. Archive for Rational Mechanics and Analysis.
2021;240:383-417. doi:10.1007/s00205-021-01616-9
apa: Leopold, N. K., Mitrouskas, D. J., & Seiringer, R. (2021). Derivation of
the Landau–Pekar equations in a many-body mean-field limit. Archive for Rational
Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01616-9
chicago: Leopold, Nikolai K, David Johannes Mitrouskas, and Robert Seiringer. “Derivation
of the Landau–Pekar Equations in a Many-Body Mean-Field Limit.” Archive for
Rational Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01616-9.
ieee: N. K. Leopold, D. J. Mitrouskas, and R. Seiringer, “Derivation of the Landau–Pekar
equations in a many-body mean-field limit,” Archive for Rational Mechanics
and Analysis, vol. 240. Springer Nature, pp. 383–417, 2021.
ista: Leopold NK, Mitrouskas DJ, Seiringer R. 2021. Derivation of the Landau–Pekar
equations in a many-body mean-field limit. Archive for Rational Mechanics and
Analysis. 240, 383–417.
mla: Leopold, Nikolai K., et al. “Derivation of the Landau–Pekar Equations in a
Many-Body Mean-Field Limit.” Archive for Rational Mechanics and Analysis,
vol. 240, Springer Nature, 2021, pp. 383–417, doi:10.1007/s00205-021-01616-9.
short: N.K. Leopold, D.J. Mitrouskas, R. Seiringer, Archive for Rational Mechanics
and Analysis 240 (2021) 383–417.
date_created: 2021-03-14T23:01:34Z
date_published: 2021-02-26T00:00:00Z
date_updated: 2025-06-12T06:35:22Z
day: '26'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s00205-021-01616-9
ec_funded: 1
external_id:
arxiv:
- '2001.03993'
isi:
- '000622226200001'
pmid:
- '33785964'
file:
- access_level: open_access
checksum: 23449e44dc5132501a5c86e70638800f
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T08:31:29Z
date_updated: 2021-03-22T08:31:29Z
file_id: '9270'
file_name: 2021_ArchRationalMechAnal_Leopold.pdf
file_size: 558006
relation: main_file
success: 1
file_date_updated: 2021-03-22T08:31:29Z
has_accepted_license: '1'
intvolume: ' 240'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 383-417
pmid: 1
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Archive for Rational Mechanics and Analysis
publication_identifier:
eissn:
- 1432-0673
issn:
- 0003-9527
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Derivation of the Landau–Pekar equations in a many-body mean-field limit
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: 240
year: '2021'
...
---
_id: '9252'
abstract:
- lang: eng
text: 'This paper analyses the conditions for local adaptation in a metapopulation
with infinitely many islands under a model of hard selection, where population
size depends on local fitness. Each island belongs to one of two distinct ecological
niches or habitats. Fitness is influenced by an additive trait which is under
habitat‐dependent directional selection. Our analysis is based on the diffusion
approximation and accounts for both genetic drift and demographic stochasticity.
By neglecting linkage disequilibria, it yields the joint distribution of allele
frequencies and population size on each island. We find that under hard selection,
the conditions for local adaptation in a rare habitat are more restrictive for
more polygenic traits: even moderate migration load per locus at very many loci
is sufficient for population sizes to decline. This further reduces the efficacy
of selection at individual loci due to increased drift and because smaller populations
are more prone to swamping due to migration, causing a positive feedback between
increasing maladaptation and declining population sizes. Our analysis also highlights
the importance of demographic stochasticity, which exacerbates the decline in
numbers of maladapted populations, leading to population collapse in the rare
habitat at significantly lower migration than predicted by deterministic arguments.'
acknowledgement: We thank the reviewers for their helpful comments, and also our colleagues,
for illuminating discussions over the long gestation of this paper.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Eniko
full_name: Szep, Eniko
id: 485BB5A4-F248-11E8-B48F-1D18A9856A87
last_name: Szep
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Szep E, Sachdeva H, Barton NH. Polygenic local adaptation in metapopulations:
A stochastic eco‐evolutionary model. Evolution. 2021;75(5):1030-1045. doi:10.1111/evo.14210'
apa: 'Szep, E., Sachdeva, H., & Barton, N. H. (2021). Polygenic local adaptation
in metapopulations: A stochastic eco‐evolutionary model. Evolution. Wiley.
https://doi.org/10.1111/evo.14210'
chicago: 'Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Polygenic Local
Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” Evolution.
Wiley, 2021. https://doi.org/10.1111/evo.14210.'
ieee: 'E. Szep, H. Sachdeva, and N. H. Barton, “Polygenic local adaptation in metapopulations:
A stochastic eco‐evolutionary model,” Evolution, vol. 75, no. 5. Wiley,
pp. 1030–1045, 2021.'
ista: 'Szep E, Sachdeva H, Barton NH. 2021. Polygenic local adaptation in metapopulations:
A stochastic eco‐evolutionary model. Evolution. 75(5), 1030–1045.'
mla: 'Szep, Eniko, et al. “Polygenic Local Adaptation in Metapopulations: A Stochastic
Eco‐evolutionary Model.” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 1030–45,
doi:10.1111/evo.14210.'
short: E. Szep, H. Sachdeva, N.H. Barton, Evolution 75 (2021) 1030–1045.
corr_author: '1'
date_created: 2021-03-20T08:22:10Z
date_published: 2021-05-01T00:00:00Z
date_updated: 2025-06-12T06:35:39Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.14210
external_id:
isi:
- '000636966300001'
pmid:
- '33742441'
file:
- access_level: open_access
checksum: b90fb5767d623602046fed03725e16ca
content_type: application/pdf
creator: kschuh
date_created: 2021-08-11T13:39:19Z
date_updated: 2021-08-11T13:39:19Z
file_id: '9886'
file_name: 2021_Evolution_Szep.pdf
file_size: 734102
relation: main_file
success: 1
file_date_updated: 2021-08-11T13:39:19Z
has_accepted_license: '1'
intvolume: ' 75'
isi: 1
issue: '5'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
- General Agricultural and Biological Sciences
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: 1030-1045
pmid: 1
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '13062'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary
model'
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: 75
year: '2021'
...
---
_id: '9253'
abstract:
- lang: eng
text: In March 2020, the Austrian government introduced a widespread lock-down in
response to the COVID-19 pandemic. Based on subjective impressions and anecdotal
evidence, Austrian public and private life came to a sudden halt. Here we assess
the effect of the lock-down quantitatively for all regions in Austria and present
an analysis of daily changes of human mobility throughout Austria using near-real-time
anonymized mobile phone data. We describe an efficient data aggregation pipeline
and analyze the mobility by quantifying mobile-phone traffic at specific point
of interests (POIs), analyzing individual trajectories and investigating the cluster
structure of the origin-destination graph. We found a reduction of commuters at
Viennese metro stations of over 80% and the number of devices with a radius of
gyration of less than 500 m almost doubled. The results of studying crowd-movement
behavior highlight considerable changes in the structure of mobility networks,
revealed by a higher modularity and an increase from 12 to 20 detected communities.
We demonstrate the relevance of mobility data for epidemiological studies by showing
a significant correlation of the outflow from the town of Ischgl (an early COVID-19
hotspot) and the reported COVID-19 cases with an 8-day time lag. This research
indicates that mobile phone usage data permits the moment-by-moment quantification
of mobility behavior for a whole country. We emphasize the need to improve the
availability of such data in anonymized form to empower rapid response to combat
COVID-19 and future pandemics.
article_processing_charge: No
arxiv: 1
author:
- first_name: Georg
full_name: Heiler, Georg
last_name: Heiler
- first_name: Tobias
full_name: Reisch, Tobias
last_name: Reisch
- first_name: Jan
full_name: Hurt, Jan
last_name: Hurt
- first_name: Mohammad
full_name: Forghani, Mohammad
last_name: Forghani
- first_name: Aida
full_name: Omani, Aida
last_name: Omani
- first_name: Allan
full_name: Hanbury, Allan
last_name: Hanbury
- first_name: Farid
full_name: Karimipour, Farid
id: 2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425
last_name: Karimipour
orcid: 0000-0001-6746-4174
citation:
ama: 'Heiler G, Reisch T, Hurt J, et al. Country-wide mobility changes observed
using mobile phone data during COVID-19 pandemic. In: 2020 IEEE International
Conference on Big Data. IEEE; 2021:3123-3132. doi:10.1109/bigdata50022.2020.9378374'
apa: 'Heiler, G., Reisch, T., Hurt, J., Forghani, M., Omani, A., Hanbury, A., &
Karimipour, F. (2021). Country-wide mobility changes observed using mobile phone
data during COVID-19 pandemic. In 2020 IEEE International Conference on Big
Data (pp. 3123–3132). Atlanta, GA, United States: IEEE. https://doi.org/10.1109/bigdata50022.2020.9378374'
chicago: Heiler, Georg, Tobias Reisch, Jan Hurt, Mohammad Forghani, Aida Omani,
Allan Hanbury, and Farid Karimipour. “Country-Wide Mobility Changes Observed Using
Mobile Phone Data during COVID-19 Pandemic.” In 2020 IEEE International Conference
on Big Data, 3123–32. IEEE, 2021. https://doi.org/10.1109/bigdata50022.2020.9378374.
ieee: G. Heiler et al., “Country-wide mobility changes observed using mobile
phone data during COVID-19 pandemic,” in 2020 IEEE International Conference
on Big Data, Atlanta, GA, United States, 2021, pp. 3123–3132.
ista: 'Heiler G, Reisch T, Hurt J, Forghani M, Omani A, Hanbury A, Karimipour F.
2021. Country-wide mobility changes observed using mobile phone data during COVID-19
pandemic. 2020 IEEE International Conference on Big Data. Big Data: International
Conference on Big Data, 3123–3132.'
mla: Heiler, Georg, et al. “Country-Wide Mobility Changes Observed Using Mobile
Phone Data during COVID-19 Pandemic.” 2020 IEEE International Conference on
Big Data, IEEE, 2021, pp. 3123–32, doi:10.1109/bigdata50022.2020.9378374.
short: G. Heiler, T. Reisch, J. Hurt, M. Forghani, A. Omani, A. Hanbury, F. Karimipour,
in:, 2020 IEEE International Conference on Big Data, IEEE, 2021, pp. 3123–3132.
conference:
end_date: 2020-12-13
location: Atlanta, GA, United States
name: 'Big Data: International Conference on Big Data'
start_date: 2020-12-10
date_created: 2021-03-21T11:34:07Z
date_published: 2021-03-19T00:00:00Z
date_updated: 2023-08-07T14:00:13Z
day: '19'
department:
- _id: HeEd
doi: 10.1109/bigdata50022.2020.9378374
external_id:
arxiv:
- '2008.10064'
isi:
- '000662554703032'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2008.10064
month: '03'
oa: 1
oa_version: Preprint
page: 3123-3132
publication: 2020 IEEE International Conference on Big Data
publication_identifier:
isbn:
- '9781728162515'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Country-wide mobility changes observed using mobile phone data during COVID-19
pandemic
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9254'
abstract:
- lang: eng
text: 'Auxin is a key regulator of plant growth and development. Local auxin biosynthesis
and intercellular transport generates regional gradients in the root that are
instructive for processes such as specification of developmental zones that maintain
root growth and tropic responses. Here we present a toolbox to study auxin-mediated
root development that features: (i) the ability to control auxin synthesis with
high spatio-temporal resolution and (ii) single-cell nucleus tracking and morphokinetic
analysis infrastructure. Integration of these two features enables cutting-edge
analysis of root development at single-cell resolution based on morphokinetic
parameters under normal growth conditions and during cell-type-specific induction
of auxin biosynthesis. We show directional auxin flow in the root and refine the
contributions of key players in this process. In addition, we determine the quantitative
kinetics of Arabidopsis root meristem skewing, which depends on local auxin gradients
but does not require PIN2 and AUX1 auxin transporter activities. Beyond the mechanistic
insights into root development, the tools developed here will enable biologists
to study kinetics and morphology of various critical processes at the single cell-level
in whole organisms.'
acknowledgement: This work was supported by grants from the Israel Science Foundation
(2378/19 to E.S.), the Joint NSFC-ISF Research Grant (3419/20 to E.S. and Z.D.),
the Human Frontier Science Program (HFSP—LIY000540/2020 to E.S.), the European Research
Council Starting Grant (757683- RobustHormoneTrans to E.S.), PBC postdoctoral fellowships
(to Y.H. and M.O.), NIH (GM114660 to Y.Z.), Breast Cancer Research Foundation (BCRF
to I.T.).
article_number: '1657'
article_processing_charge: No
article_type: original
author:
- first_name: Yangjie
full_name: Hu, Yangjie
last_name: Hu
- first_name: Moutasem
full_name: Omary, Moutasem
last_name: Omary
- first_name: Yun
full_name: Hu, Yun
last_name: Hu
- first_name: Ohad
full_name: Doron, Ohad
last_name: Doron
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Qingguo
full_name: Chen, Qingguo
last_name: Chen
- first_name: Or
full_name: Megides, Or
last_name: Megides
- first_name: Ori
full_name: Chekli, Ori
last_name: Chekli
- first_name: Zhaojun
full_name: Ding, Zhaojun
last_name: Ding
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Yunde
full_name: Zhao, Yunde
last_name: Zhao
- first_name: Ilan
full_name: Tsarfaty, Ilan
last_name: Tsarfaty
- first_name: Eilon
full_name: Shani, Eilon
last_name: Shani
citation:
ama: Hu Y, Omary M, Hu Y, et al. Cell kinetics of auxin transport and activity in
Arabidopsis root growth and skewing. Nature Communications. 2021;12. doi:10.1038/s41467-021-21802-3
apa: Hu, Y., Omary, M., Hu, Y., Doron, O., Hörmayer, L., Chen, Q., … Shani, E. (2021).
Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-21802-3
chicago: Hu, Yangjie, Moutasem Omary, Yun Hu, Ohad Doron, Lukas Hörmayer, Qingguo
Chen, Or Megides, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis
Root Growth and Skewing.” Nature Communications. Springer Nature, 2021.
https://doi.org/10.1038/s41467-021-21802-3.
ieee: Y. Hu et al., “Cell kinetics of auxin transport and activity in Arabidopsis
root growth and skewing,” Nature Communications, vol. 12. Springer Nature,
2021.
ista: Hu Y, Omary M, Hu Y, Doron O, Hörmayer L, Chen Q, Megides O, Chekli O, Ding
Z, Friml J, Zhao Y, Tsarfaty I, Shani E. 2021. Cell kinetics of auxin transport
and activity in Arabidopsis root growth and skewing. Nature Communications. 12,
1657.
mla: Hu, Yangjie, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis
Root Growth and Skewing.” Nature Communications, vol. 12, 1657, Springer
Nature, 2021, doi:10.1038/s41467-021-21802-3.
short: Y. Hu, M. Omary, Y. Hu, O. Doron, L. Hörmayer, Q. Chen, O. Megides, O. Chekli,
Z. Ding, J. Friml, Y. Zhao, I. Tsarfaty, E. Shani, Nature Communications 12 (2021).
date_created: 2021-03-21T23:01:19Z
date_published: 2021-03-12T00:00:00Z
date_updated: 2026-04-02T13:57:40Z
day: '12'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41467-021-21802-3
external_id:
isi:
- '000630419400048'
pmid:
- '33712581'
file:
- access_level: open_access
checksum: e1022f3aee349853ded2b2b3e092362d
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T11:18:58Z
date_updated: 2021-03-22T11:18:58Z
file_id: '9275'
file_name: 2021_NatureComm_Hu.pdf
file_size: 8602096
relation: main_file
success: 1
file_date_updated: 2021-03-22T11:18:58Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell kinetics of auxin transport and activity in Arabidopsis root growth and
skewing
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 12
year: '2021'
...
---
_id: '9255'
abstract:
- lang: eng
text: Our ability to trust that a random number is truly random is essential for
fields as diverse as cryptography and fundamental tests of quantum mechanics.
Existing solutions both come with drawbacks—device-independent quantum random
number generators (QRNGs) are highly impractical and standard semi-device-independent
QRNGs are limited to a specific physical implementation and level of trust. Here
we propose a framework for semi-device-independent randomness certification, using
a source of trusted vacuum in the form of a signal shutter. It employs a flexible
set of assumptions and levels of trust, allowing it to be applied in a wide range
of physical scenarios involving both quantum and classical entropy sources. We
experimentally demonstrate our protocol with a photonic setup and generate secure
random bits under three different assumptions with varying degrees of security
and resulting data rates.
acknowledgement: We would like to thank Robert Fickler for discussions about the experimental
realization and Marek Sýs for running the NIST randomness test on the data we acquired
in the experiment. We would like to thank Ugo Zanforlin, Gerald Buller, Daniel White,
and Cristian Bonato for their help with the experiment. M. Pivoluska, M. Plesch,
and M.M. acknowledge Czech-Austrian project MultiQUEST (I3053-N27 and GF17-33780L).
M. Pivoluska and M. Plesch additionally acknowledge the support of VEGA project
2/0136/19. M.F. acknowledges support from the Polish NCN grant Sonata UMO-2014/14/E/ST2/00020,
the European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation program ERC AdG CERQUTE (grant agreement No 834266), the State Research
Agency (AEI) TRANQI (PID2019-106888GB-I00/10.13039/501100011033), the Government
of Spain (FIS2020-TRANQI; Severo Ochoa CEX2019-000910-S), Fundació Cellex, Fundació
Mir-Puig, and Generalitat de Catalunya (CERCA, AGAUR). M.M., W.M., N.H.V., and C.F.
acknowledge support from the QuantERA ERA-NET Co-fund (FWF Project I3773-N36) and
the UK Engineering and Physical Sciences Research Council (EPSRC) (EP/P024114/1).
article_number: '50'
article_processing_charge: No
article_type: original
author:
- first_name: Matej
full_name: Pivoluska, Matej
last_name: Pivoluska
- first_name: Martin
full_name: Plesch, Martin
last_name: Plesch
- first_name: Máté
full_name: Farkas, Máté
last_name: Farkas
- first_name: Natalia
full_name: Ruzickova, Natalia
id: D2761128-D73D-11E9-A1BF-BA0DE6697425
last_name: Ruzickova
- first_name: Clara
full_name: Flegel, Clara
last_name: Flegel
- first_name: Natalia Herrera
full_name: Valencia, Natalia Herrera
last_name: Valencia
- first_name: Will
full_name: Mccutcheon, Will
last_name: Mccutcheon
- first_name: Mehul
full_name: Malik, Mehul
last_name: Malik
- first_name: Edgar A.
full_name: Aguilar, Edgar A.
last_name: Aguilar
citation:
ama: Pivoluska M, Plesch M, Farkas M, et al. Semi-device-independent random number
generation with flexible assumptions. npj Quantum Information. 2021;7.
doi:10.1038/s41534-021-00387-1
apa: Pivoluska, M., Plesch, M., Farkas, M., Ruzickova, N., Flegel, C., Valencia,
N. H., … Aguilar, E. A. (2021). Semi-device-independent random number generation
with flexible assumptions. Npj Quantum Information. Springer Nature. https://doi.org/10.1038/s41534-021-00387-1
chicago: Pivoluska, Matej, Martin Plesch, Máté Farkas, Natalia Ruzickova, Clara
Flegel, Natalia Herrera Valencia, Will Mccutcheon, Mehul Malik, and Edgar A. Aguilar.
“Semi-Device-Independent Random Number Generation with Flexible Assumptions.”
Npj Quantum Information. Springer Nature, 2021. https://doi.org/10.1038/s41534-021-00387-1.
ieee: M. Pivoluska et al., “Semi-device-independent random number generation
with flexible assumptions,” npj Quantum Information, vol. 7. Springer Nature,
2021.
ista: Pivoluska M, Plesch M, Farkas M, Ruzickova N, Flegel C, Valencia NH, Mccutcheon
W, Malik M, Aguilar EA. 2021. Semi-device-independent random number generation
with flexible assumptions. npj Quantum Information. 7, 50.
mla: Pivoluska, Matej, et al. “Semi-Device-Independent Random Number Generation
with Flexible Assumptions.” Npj Quantum Information, vol. 7, 50, Springer
Nature, 2021, doi:10.1038/s41534-021-00387-1.
short: M. Pivoluska, M. Plesch, M. Farkas, N. Ruzickova, C. Flegel, N.H. Valencia,
W. Mccutcheon, M. Malik, E.A. Aguilar, Npj Quantum Information 7 (2021).
date_created: 2021-03-21T23:01:19Z
date_published: 2021-03-15T00:00:00Z
date_updated: 2023-08-07T14:17:26Z
day: '15'
ddc:
- '530'
department:
- _id: FyKo
doi: 10.1038/s41534-021-00387-1
external_id:
isi:
- '000629173100001'
file:
- access_level: open_access
checksum: 26d3f2a2c8c8fa8c1002028326b45f64
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T11:09:34Z
date_updated: 2021-03-22T11:09:34Z
file_id: '9274'
file_name: 2021_NPJQuantumInformation_Pivoluska.pdf
file_size: 1360271
relation: main_file
success: 1
file_date_updated: 2021-03-22T11:09:34Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: npj Quantum Information
publication_identifier:
eissn:
- 2056-6387
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Semi-device-independent random number generation with flexible assumptions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 7
year: '2021'
...
---
_id: '9256'
abstract:
- lang: eng
text: We consider the ferromagnetic quantum Heisenberg model in one dimension, for
any spin S≥1/2. We give upper and lower bounds on the free energy, proving that
at low temperature it is asymptotically equal to the one of an ideal Bose gas
of magnons, as predicted by the spin-wave approximation. The trial state used
in the upper bound yields an analogous estimate also in the case of two spatial
dimensions, which is believed to be sharp at low temperature.
acknowledgement: "The work of MN was supported by the National Science Centre (NCN)
Project Nr. 2016/21/D/ST1/02430. The work of RS was supported by the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
(Grant Agreement No. 694227).\r\nOpen access funding provided by Institute of Science
and Technology (IST Austria)."
article_number: '31'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Marcin M
full_name: Napiórkowski, Marcin M
id: 4197AD04-F248-11E8-B48F-1D18A9856A87
last_name: Napiórkowski
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Napiórkowski MM, Seiringer R. Free energy asymptotics of the quantum Heisenberg
spin chain. Letters in Mathematical Physics. 2021;111(2). doi:10.1007/s11005-021-01375-4
apa: Napiórkowski, M. M., & Seiringer, R. (2021). Free energy asymptotics of
the quantum Heisenberg spin chain. Letters in Mathematical Physics. Springer
Nature. https://doi.org/10.1007/s11005-021-01375-4
chicago: Napiórkowski, Marcin M, and Robert Seiringer. “Free Energy Asymptotics
of the Quantum Heisenberg Spin Chain.” Letters in Mathematical Physics.
Springer Nature, 2021. https://doi.org/10.1007/s11005-021-01375-4.
ieee: M. M. Napiórkowski and R. Seiringer, “Free energy asymptotics of the quantum
Heisenberg spin chain,” Letters in Mathematical Physics, vol. 111, no.
2. Springer Nature, 2021.
ista: Napiórkowski MM, Seiringer R. 2021. Free energy asymptotics of the quantum
Heisenberg spin chain. Letters in Mathematical Physics. 111(2), 31.
mla: Napiórkowski, Marcin M., and Robert Seiringer. “Free Energy Asymptotics of
the Quantum Heisenberg Spin Chain.” Letters in Mathematical Physics, vol.
111, no. 2, 31, Springer Nature, 2021, doi:10.1007/s11005-021-01375-4.
short: M.M. Napiórkowski, R. Seiringer, Letters in Mathematical Physics 111 (2021).
date_created: 2021-03-21T23:01:19Z
date_published: 2021-03-09T00:00:00Z
date_updated: 2026-04-02T14:06:48Z
day: '09'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s11005-021-01375-4
external_id:
isi:
- '000626837400001'
pmid:
- '33785980'
file:
- access_level: open_access
checksum: 687fef1525789c0950de90468dd81604
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T11:01:09Z
date_updated: 2021-03-22T11:01:09Z
file_id: '9273'
file_name: 2021_LettersMathPhysics_Napiorkowski.pdf
file_size: 397962
relation: main_file
success: 1
file_date_updated: 2021-03-22T11:01:09Z
has_accepted_license: '1'
intvolume: ' 111'
isi: 1
issue: '2'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Letters in Mathematical Physics
publication_identifier:
eissn:
- 1573-0530
issn:
- 0377-9017
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Free energy asymptotics of the quantum Heisenberg spin chain
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 111
year: '2021'
...
---
_id: '9257'
abstract:
- lang: eng
text: 'The inverse problem of designing component interactions to target emergent
structure is fundamental to numerous applications in biotechnology, materials
science, and statistical physics. Equally important is the inverse problem of
designing emergent kinetics, but this has received considerably less attention.
Using recent advances in automatic differentiation, we show how kinetic pathways
can be precisely designed by directly differentiating through statistical physics
models, namely free energy calculations and molecular dynamics simulations. We
consider two systems that are crucial to our understanding of structural self-assembly:
bulk crystallization and small nanoclusters. In each case, we are able to assemble
precise dynamical features. Using gradient information, we manipulate interactions
among constituent particles to tune the rate at which these systems yield specific
structures of interest. Moreover, we use this approach to learn nontrivial features
about the high-dimensional design space, allowing us to accurately predict when
multiple kinetic features can be simultaneously and independently controlled.
These results provide a concrete and generalizable foundation for studying nonstructural
self-assembly, including kinetic properties as well as other complex emergent
properties, in a vast array of systems.'
acknowledgement: We thank Agnese Curatolo, Megan Engel, Ofer Kimchi, Seong Ho Pahng,
and Roy Frostig for helpful discussions. This material is based on work supported
by NSF Graduate Research Fellowship Grant DGE1745303. This research was funded by
NSF Grant DMS-1715477, Materials Research Science and Engineering Centers Grant
DMR-1420570, and Office of Naval Research Grant N00014-17-1-3029. M.P.B. is an investigator
of the Simons Foundation.
article_number: e2024083118
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Ella M.
full_name: King, Ella M.
last_name: King
- first_name: Samuel S.
full_name: Schoenholz, Samuel S.
last_name: Schoenholz
- first_name: Ekin D.
full_name: Cubuk, Ekin D.
last_name: Cubuk
- first_name: Michael P.
full_name: Brenner, Michael P.
last_name: Brenner
citation:
ama: Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. Designing self-assembling
kinetics with differentiable statistical physics models. Proceedings of the
National Academy of Sciences of the United States of America. 2021;118(10).
doi:10.1073/pnas.2024083118
apa: Goodrich, C. P., King, E. M., Schoenholz, S. S., Cubuk, E. D., & Brenner,
M. P. (2021). Designing self-assembling kinetics with differentiable statistical
physics models. Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2024083118
chicago: Goodrich, Carl Peter, Ella M. King, Samuel S. Schoenholz, Ekin D. Cubuk,
and Michael P. Brenner. “Designing Self-Assembling Kinetics with Differentiable
Statistical Physics Models.” Proceedings of the National Academy of Sciences
of the United States of America. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2024083118.
ieee: C. P. Goodrich, E. M. King, S. S. Schoenholz, E. D. Cubuk, and M. P. Brenner,
“Designing self-assembling kinetics with differentiable statistical physics models,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 118, no. 10. National Academy of Sciences, 2021.
ista: Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. 2021. Designing
self-assembling kinetics with differentiable statistical physics models. Proceedings
of the National Academy of Sciences of the United States of America. 118(10),
e2024083118.
mla: Goodrich, Carl Peter, et al. “Designing Self-Assembling Kinetics with Differentiable
Statistical Physics Models.” Proceedings of the National Academy of Sciences
of the United States of America, vol. 118, no. 10, e2024083118, National Academy
of Sciences, 2021, doi:10.1073/pnas.2024083118.
short: C.P. Goodrich, E.M. King, S.S. Schoenholz, E.D. Cubuk, M.P. Brenner, Proceedings
of the National Academy of Sciences of the United States of America 118 (2021).
date_created: 2021-03-21T23:01:20Z
date_published: 2021-03-09T00:00:00Z
date_updated: 2025-05-14T10:58:42Z
day: '09'
ddc:
- '530'
department:
- _id: CaGo
doi: 10.1073/pnas.2024083118
external_id:
isi:
- '000627429100097'
pmid:
- '33653960'
file:
- access_level: open_access
checksum: 5be8da2b1c0757feb1057f1a515cf9e0
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T12:23:54Z
date_updated: 2021-03-22T12:23:54Z
file_id: '9278'
file_name: 2021_PNAS_Goodrich.pdf
file_size: 1047954
relation: main_file
success: 1
file_date_updated: 2021-03-22T12:23:54Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '10'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Designing self-assembling kinetics with differentiable statistical physics
models
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: 118
year: '2021'
...
---
_id: '9258'
acknowledgement: 'We thank S. van der Walt and K. Marchuk for discussion during development.
This project was funded by Packard Fellowship and Chan Zuckerberg Biohub Investigator
Awards to L.W.; STROBE: A NSF Science and Technology Center; an NSF Graduate Research
Fellowship awarded to H.P.; a Berkeley Institute for Data Science/UCSF Bakar Computational
Health Sciences Institute Fellowship awarded to H.P. with support from the Koret
Foundation, the Gordon and Betty Moore Foundation, and the Alfred P. Sloan Foundation
to the University of California, Berkeley. K.W.E., B.L. and M.T. were funded by
the Chan Zuckerberg Initiative and NIH grant P41GM135019.'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Henry
full_name: Pinkard, Henry
last_name: Pinkard
- first_name: Nico
full_name: Stuurman, Nico
last_name: Stuurman
- first_name: Ivan E.
full_name: Ivanov, Ivan E.
last_name: Ivanov
- first_name: Nicholas M.
full_name: Anthony, Nicholas M.
last_name: Anthony
- first_name: Wei
full_name: Ouyang, Wei
last_name: Ouyang
- first_name: Bin
full_name: Li, Bin
last_name: Li
- first_name: Bin
full_name: Yang, Bin
last_name: Yang
- first_name: Mark A.
full_name: Tsuchida, Mark A.
last_name: Tsuchida
- first_name: Bryant
full_name: Chhun, Bryant
last_name: Chhun
- first_name: Grace
full_name: Zhang, Grace
last_name: Zhang
- first_name: Ryan
full_name: Mei, Ryan
last_name: Mei
- first_name: Michael
full_name: Anderson, Michael
last_name: Anderson
- first_name: Douglas P.
full_name: Shepherd, Douglas P.
last_name: Shepherd
- first_name: Ian
full_name: Hunt-Isaak, Ian
last_name: Hunt-Isaak
- first_name: Raymond L.
full_name: Dunn, Raymond L.
last_name: Dunn
- first_name: Wiebke
full_name: Jahr, Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
orcid: 0000-0003-0201-2315
- first_name: Saul
full_name: Kato, Saul
last_name: Kato
- first_name: Loïc A.
full_name: Royer, Loïc A.
last_name: Royer
- first_name: Jay R.
full_name: Thiagarajah, Jay R.
last_name: Thiagarajah
- first_name: Kevin W.
full_name: Eliceiri, Kevin W.
last_name: Eliceiri
- first_name: Emma
full_name: Lundberg, Emma
last_name: Lundberg
- first_name: Shalin B.
full_name: Mehta, Shalin B.
last_name: Mehta
- first_name: Laura
full_name: Waller, Laura
last_name: Waller
citation:
ama: 'Pinkard H, Stuurman N, Ivanov IE, et al. Pycro-Manager: Open-source software
for customized and reproducible microscope control. Nature Methods. 2021;18(3):226-228.
doi:10.1038/s41592-021-01087-6'
apa: 'Pinkard, H., Stuurman, N., Ivanov, I. E., Anthony, N. M., Ouyang, W., Li,
B., … Waller, L. (2021). Pycro-Manager: Open-source software for customized and
reproducible microscope control. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-021-01087-6'
chicago: 'Pinkard, Henry, Nico Stuurman, Ivan E. Ivanov, Nicholas M. Anthony, Wei
Ouyang, Bin Li, Bin Yang, et al. “Pycro-Manager: Open-Source Software for Customized
and Reproducible Microscope Control.” Nature Methods. Springer Nature,
2021. https://doi.org/10.1038/s41592-021-01087-6.'
ieee: 'H. Pinkard et al., “Pycro-Manager: Open-source software for customized
and reproducible microscope control,” Nature Methods, vol. 18, no. 3. Springer
Nature, pp. 226–228, 2021.'
ista: 'Pinkard H, Stuurman N, Ivanov IE, Anthony NM, Ouyang W, Li B, Yang B, Tsuchida
MA, Chhun B, Zhang G, Mei R, Anderson M, Shepherd DP, Hunt-Isaak I, Dunn RL, Jahr
W, Kato S, Royer LA, Thiagarajah JR, Eliceiri KW, Lundberg E, Mehta SB, Waller
L. 2021. Pycro-Manager: Open-source software for customized and reproducible microscope
control. Nature Methods. 18(3), 226–228.'
mla: 'Pinkard, Henry, et al. “Pycro-Manager: Open-Source Software for Customized
and Reproducible Microscope Control.” Nature Methods, vol. 18, no. 3, Springer
Nature, 2021, pp. 226–28, doi:10.1038/s41592-021-01087-6.'
short: H. Pinkard, N. Stuurman, I.E. Ivanov, N.M. Anthony, W. Ouyang, B. Li, B.
Yang, M.A. Tsuchida, B. Chhun, G. Zhang, R. Mei, M. Anderson, D.P. Shepherd, I.
Hunt-Isaak, R.L. Dunn, W. Jahr, S. Kato, L.A. Royer, J.R. Thiagarajah, K.W. Eliceiri,
E. Lundberg, S.B. Mehta, L. Waller, Nature Methods 18 (2021) 226–228.
date_created: 2021-03-21T23:01:20Z
date_published: 2021-03-01T00:00:00Z
date_updated: 2026-06-18T19:43:50Z
day: '01'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.1038/s41592-021-01087-6
external_id:
isi:
- '000625600600007'
pmid:
- '33674797'
intvolume: ' 18'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41592-021-01087-6
month: '03'
oa: 1
oa_version: Published Version
page: 226-228
pmid: 1
publication: Nature Methods
publication_identifier:
eissn:
- 1548-7105
issn:
- 1548-7091
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Pycro-Manager: Open-source software for customized and reproducible microscope
control'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2021'
...
---
_id: '9259'
abstract:
- lang: eng
text: Gradients of chemokines and growth factors guide migrating cells and morphogenetic
processes. Migration of antigen-presenting dendritic cells from the interstitium
into the lymphatic system is dependent on chemokine CCL21, which is secreted by
endothelial cells of the lymphatic capillary, binds heparan sulfates and forms
gradients decaying into the interstitium. Despite the importance of CCL21 gradients,
and chemokine gradients in general, the mechanisms of gradient formation are unclear.
Studies on fibroblast growth factors have shown that limited diffusion is crucial
for gradient formation. Here, we used the mouse dermis as a model tissue to address
the necessity of CCL21 anchoring to lymphatic capillary heparan sulfates in the
formation of interstitial CCL21 gradients. Surprisingly, the absence of lymphatic
endothelial heparan sulfates resulted only in a modest decrease of CCL21 levels
at the lymphatic capillaries and did neither affect interstitial CCL21 gradient
shape nor dendritic cell migration toward lymphatic capillaries. Thus, heparan
sulfates at the level of the lymphatic endothelium are dispensable for the formation
of a functional CCL21 gradient.
acknowledgement: "This work was supported by Sigrid Juselius fellowship (KV), University
of Helsinki 3-year research grant (KV), Academy of Finland Research fellow funding
(315710, to KV), the European Research Council (ERC CoG 724373 to MS), and by the
Austrian Science foundation (FWF) (Y564-B12 START award to MS).\r\nTaija Mäkinen
is acknowledged for providing Prox1CreERT2 transgenic mice and Yu Yamaguchi for
providing the conditional Ext1 mouse strain."
article_number: '630002'
article_processing_charge: No
article_type: original
author:
- first_name: Kari
full_name: Vaahtomeri, Kari
id: 368EE576-F248-11E8-B48F-1D18A9856A87
last_name: Vaahtomeri
orcid: 0000-0001-7829-3518
- first_name: Christine
full_name: Moussion, Christine
id: 3356F664-F248-11E8-B48F-1D18A9856A87
last_name: Moussion
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Vaahtomeri K, Moussion C, Hauschild R, Sixt MK. Shape and function of interstitial
chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic
endothelium. Frontiers in Immunology. 2021;12. doi:10.3389/fimmu.2021.630002
apa: Vaahtomeri, K., Moussion, C., Hauschild, R., & Sixt, M. K. (2021). Shape
and function of interstitial chemokine CCL21 gradients are independent of heparan
sulfates produced by lymphatic endothelium. Frontiers in Immunology. Frontiers.
https://doi.org/10.3389/fimmu.2021.630002
chicago: Vaahtomeri, Kari, Christine Moussion, Robert Hauschild, and Michael K Sixt.
“Shape and Function of Interstitial Chemokine CCL21 Gradients Are Independent
of Heparan Sulfates Produced by Lymphatic Endothelium.” Frontiers in Immunology.
Frontiers, 2021. https://doi.org/10.3389/fimmu.2021.630002.
ieee: K. Vaahtomeri, C. Moussion, R. Hauschild, and M. K. Sixt, “Shape and function
of interstitial chemokine CCL21 gradients are independent of heparan sulfates
produced by lymphatic endothelium,” Frontiers in Immunology, vol. 12. Frontiers,
2021.
ista: Vaahtomeri K, Moussion C, Hauschild R, Sixt MK. 2021. Shape and function of
interstitial chemokine CCL21 gradients are independent of heparan sulfates produced
by lymphatic endothelium. Frontiers in Immunology. 12, 630002.
mla: Vaahtomeri, Kari, et al. “Shape and Function of Interstitial Chemokine CCL21
Gradients Are Independent of Heparan Sulfates Produced by Lymphatic Endothelium.”
Frontiers in Immunology, vol. 12, 630002, Frontiers, 2021, doi:10.3389/fimmu.2021.630002.
short: K. Vaahtomeri, C. Moussion, R. Hauschild, M.K. Sixt, Frontiers in Immunology
12 (2021).
corr_author: '1'
date_created: 2021-03-21T23:01:20Z
date_published: 2021-02-25T00:00:00Z
date_updated: 2025-04-14T07:42:07Z
day: '25'
ddc:
- '570'
department:
- _id: MiSi
- _id: Bio
doi: 10.3389/fimmu.2021.630002
ec_funded: 1
external_id:
isi:
- '000627134400001'
pmid:
- '33717158'
file:
- access_level: open_access
checksum: 663f5a48375e42afa4bfef58d42ec186
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T12:08:26Z
date_updated: 2021-03-22T12:08:26Z
file_id: '9277'
file_name: 2021_FrontiersImmumo_Vaahtomeri.pdf
file_size: 3740146
relation: main_file
success: 1
file_date_updated: 2021-03-22T12:08:26Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular Navigation Along Spatial Gradients
- _id: 25A8E5EA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 564-B12
name: Cytoskeletal force generation and force transduction of migrating leukocytes
publication: Frontiers in Immunology
publication_identifier:
eissn:
- 1664-3224
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Shape and function of interstitial chemokine CCL21 gradients are independent
of heparan sulfates produced by lymphatic endothelium
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9262'
abstract:
- lang: eng
text: Sequence-specific oligomers with predictable folding patterns, i.e., foldamers,
provide new opportunities to mimic α-helical peptides and design inhibitors of
protein-protein interactions. One major hurdle of this strategy is to retain the
correct orientation of key side chains involved in protein surface recognition.
Here, we show that the structural plasticity of a foldamer backbone may notably
contribute to the required spatial adjustment for optimal interaction with the
protein surface. By using oligoureas as α helix mimics, we designed a foldamer/peptide
hybrid inhibitor of histone chaperone ASF1, a key regulator of chromatin dynamics.
The crystal structure of its complex with ASF1 reveals a notable plasticity of
the urea backbone, which adapts to the ASF1 surface to maintain the same binding
interface. One additional benefit of generating ASF1 ligands with nonpeptide oligourea
segments is the resistance to proteolysis in human plasma, which was highly improved
compared to the cognate α-helical peptide.
acknowledgement: 'We thank the Synchrotron SOLEIL, the European Synchrotron Radiation
Facility (ESRF), and the French Infrastructure for Integrated Structural Biology
(FRISBI) ANR-10-INBS-05. We are particularly grateful to A. Clavier and A. Campalans
for help in setting up and performing the cell penetration assays. Funding: Research
was funded by the French Centre National de Recherche Scientifique (CNRS), the Commissariat
à l’Energie Atomique (CEA), University of Bordeaux, University Paris-Saclay, and
the Synchrotron Soleil. The project was supported by the ANR 2007 BREAKABOUND (JC-07-216078),
2011 BIPBIP (ANR-10-BINF-0003), 2012 CHAPINHIB (ANR-12-BSV5-0022-01), 2015 CHIPSET
(ANR-15-CE11-008-01), 2015 HIMPP2I (ANR-15-CE07-0010), and the program labeled by
the ARC foundation 2016 PGA1*20160203953). M.B. was supported by Canceropole (Paris,
France) and a grant for young researchers from La Ligue contre le Cancer. J.M. was
supported by La Ligue contre le Cancer.'
article_number: eabd9153
article_processing_charge: No
article_type: original
author:
- first_name: Johanne
full_name: Mbianda, Johanne
last_name: Mbianda
- first_name: May M
full_name: Bakail, May M
id: FB3C3F8E-522F-11EA-B186-22963DDC885E
last_name: Bakail
orcid: 0000-0002-9592-1587
- first_name: Christophe
full_name: André, Christophe
last_name: André
- first_name: Gwenaëlle
full_name: Moal, Gwenaëlle
last_name: Moal
- first_name: Marie E.
full_name: Perrin, Marie E.
last_name: Perrin
- first_name: Guillaume
full_name: Pinna, Guillaume
last_name: Pinna
- first_name: Raphaël
full_name: Guerois, Raphaël
last_name: Guerois
- first_name: Francois
full_name: Becher, Francois
last_name: Becher
- first_name: Pierre
full_name: Legrand, Pierre
last_name: Legrand
- first_name: Seydou
full_name: Traoré, Seydou
last_name: Traoré
- first_name: Céline
full_name: Douat, Céline
last_name: Douat
- first_name: Gilles
full_name: Guichard, Gilles
last_name: Guichard
- first_name: Françoise
full_name: Ochsenbein, Françoise
last_name: Ochsenbein
citation:
ama: Mbianda J, Bakail MM, André C, et al. Optimal anchoring of a foldamer inhibitor
of ASF1 histone chaperone through backbone plasticity. Science Advances.
2021;7(12). doi:10.1126/sciadv.abd9153
apa: Mbianda, J., Bakail, M. M., André, C., Moal, G., Perrin, M. E., Pinna, G.,
… Ochsenbein, F. (2021). Optimal anchoring of a foldamer inhibitor of ASF1 histone
chaperone through backbone plasticity. Science Advances. American Association
for the Advancement of Science. https://doi.org/10.1126/sciadv.abd9153
chicago: Mbianda, Johanne, May M Bakail, Christophe André, Gwenaëlle Moal, Marie
E. Perrin, Guillaume Pinna, Raphaël Guerois, et al. “Optimal Anchoring of a Foldamer
Inhibitor of ASF1 Histone Chaperone through Backbone Plasticity.” Science Advances.
American Association for the Advancement of Science, 2021. https://doi.org/10.1126/sciadv.abd9153.
ieee: J. Mbianda et al., “Optimal anchoring of a foldamer inhibitor of ASF1
histone chaperone through backbone plasticity,” Science Advances, vol.
7, no. 12. American Association for the Advancement of Science, 2021.
ista: Mbianda J, Bakail MM, André C, Moal G, Perrin ME, Pinna G, Guerois R, Becher
F, Legrand P, Traoré S, Douat C, Guichard G, Ochsenbein F. 2021. Optimal anchoring
of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity.
Science Advances. 7(12), eabd9153.
mla: Mbianda, Johanne, et al. “Optimal Anchoring of a Foldamer Inhibitor of ASF1
Histone Chaperone through Backbone Plasticity.” Science Advances, vol.
7, no. 12, eabd9153, American Association for the Advancement of Science, 2021,
doi:10.1126/sciadv.abd9153.
short: J. Mbianda, M.M. Bakail, C. André, G. Moal, M.E. Perrin, G. Pinna, R. Guerois,
F. Becher, P. Legrand, S. Traoré, C. Douat, G. Guichard, F. Ochsenbein, Science
Advances 7 (2021).
date_created: 2021-03-22T07:14:03Z
date_published: 2021-03-19T00:00:00Z
date_updated: 2023-08-07T14:20:26Z
day: '19'
ddc:
- '570'
department:
- _id: CampIT
doi: 10.1126/sciadv.abd9153
external_id:
isi:
- '000633443000011'
pmid:
- '33741589'
file:
- access_level: open_access
checksum: 737624cd0e630ffa7c52797a690500e3
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T12:49:00Z
date_updated: 2021-03-22T12:49:00Z
file_id: '9280'
file_name: 2021_ScienceAdv_Mbianda.pdf
file_size: 837156
relation: main_file
success: 1
file_date_updated: 2021-03-22T12:49:00Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '12'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '03'
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: Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through
backbone plasticity
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 7
year: '2021'
...
---
_id: '9281'
abstract:
- lang: eng
text: We comment on two formal proofs of Fermat's sum of two squares theorem, written
using the Mathematical Components libraries of the Coq proof assistant. The first
one follows Zagier's celebrated one-sentence proof; the second follows David Christopher's
recent new proof relying on partition-theoretic arguments. Both formal proofs
rely on a general property of involutions of finite sets, of independent interest.
The proof technique consists for the most part of automating recurrent tasks (such
as case distinctions and computations on natural numbers) via ad hoc tactics.
article_number: '2103.11389'
article_processing_charge: No
arxiv: 1
author:
- first_name: Guillaume
full_name: Dubach, Guillaume
id: D5C6A458-10C4-11EA-ABF4-A4B43DDC885E
last_name: Dubach
orcid: 0000-0001-6892-8137
- first_name: Fabian
full_name: Mühlböck, Fabian
id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425
last_name: Mühlböck
orcid: 0000-0003-1548-0177
citation:
ama: Dubach G, Mühlböck F. Formal verification of Zagier’s one-sentence proof. arXiv.
doi:10.48550/arXiv.2103.11389
apa: Dubach, G., & Mühlböck, F. (n.d.). Formal verification of Zagier’s one-sentence
proof. arXiv. https://doi.org/10.48550/arXiv.2103.11389
chicago: Dubach, Guillaume, and Fabian Mühlböck. “Formal Verification of Zagier’s
One-Sentence Proof.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2103.11389.
ieee: G. Dubach and F. Mühlböck, “Formal verification of Zagier’s one-sentence proof,”
arXiv. .
ista: Dubach G, Mühlböck F. Formal verification of Zagier’s one-sentence proof.
arXiv, 2103.11389.
mla: Dubach, Guillaume, and Fabian Mühlböck. “Formal Verification of Zagier’s One-Sentence
Proof.” ArXiv, 2103.11389, doi:10.48550/arXiv.2103.11389.
short: G. Dubach, F. Mühlböck, ArXiv (n.d.).
corr_author: '1'
date_created: 2021-03-23T05:38:48Z
date_published: 2021-03-21T00:00:00Z
date_updated: 2025-04-15T06:26:12Z
day: '21'
department:
- _id: LaEr
- _id: ToHe
doi: 10.48550/arXiv.2103.11389
ec_funded: 1
external_id:
arxiv:
- '2103.11389'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2103.11389
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '9946'
relation: other
status: public
status: public
title: Formal verification of Zagier's one-sentence proof
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9283'
abstract:
- lang: eng
text: Gene expression levels are influenced by multiple coexisting molecular mechanisms.
Some of these interactions such as those of transcription factors and promoters
have been studied extensively. However, predicting phenotypes of gene regulatory
networks (GRNs) remains a major challenge. Here, we use a well-defined synthetic
GRN to study in Escherichia coli how network phenotypes depend on local genetic
context, i.e. the genetic neighborhood of a transcription factor and its relative
position. We show that one GRN with fixed topology can display not only quantitatively
but also qualitatively different phenotypes, depending solely on the local genetic
context of its components. Transcriptional read-through is the main molecular
mechanism that places one transcriptional unit (TU) within two separate regulons
without the need for complex regulatory sequences. We propose that relative order
of individual TUs, with its potential for combinatorial complexity, plays an important
role in shaping phenotypes of GRNs.
acknowledgement: "We thank J Bollback, L Hurst, M Lagator, C Nizak, O Rivoire, M Savageau,
G Tkacik, and B Vicozo\r\nfor helpful discussions; A Dolinar and A Greshnova for
technical assistance; T Bollenbach for supplying the strain JW0336; C Rusnac, and
members of the Guet lab for comments. The research leading to these results has
received funding from the People Programme (Marie Curie Actions) of the European
Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n˚\r\n628377
(ANS) and an Austrian Science Fund (FWF) grant n˚ I 3901-B32 (CCG)."
article_number: e65993
article_processing_charge: Yes
article_type: original
author:
- first_name: Anna A
full_name: Nagy-Staron, Anna A
id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87
last_name: Nagy-Staron
orcid: 0000-0002-1391-8377
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
- first_name: Caroline
full_name: Caruso Carter, Caroline
last_name: Caruso Carter
- first_name: Elisabeth
full_name: Sonnleitner, Elisabeth
last_name: Sonnleitner
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Tiago
full_name: Paixão, Tiago
last_name: Paixão
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Nagy-Staron AA, Tomasek K, Caruso Carter C, et al. Local genetic context shapes
the function of a gene regulatory network. eLife. 2021;10. doi:10.7554/elife.65993
apa: Nagy-Staron, A. A., Tomasek, K., Caruso Carter, C., Sonnleitner, E., Kavcic,
B., Paixão, T., & Guet, C. C. (2021). Local genetic context shapes the function
of a gene regulatory network. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.65993
chicago: Nagy-Staron, Anna A, Kathrin Tomasek, Caroline Caruso Carter, Elisabeth
Sonnleitner, Bor Kavcic, Tiago Paixão, and Calin C Guet. “Local Genetic Context
Shapes the Function of a Gene Regulatory Network.” ELife. eLife Sciences
Publications, 2021. https://doi.org/10.7554/elife.65993.
ieee: A. A. Nagy-Staron et al., “Local genetic context shapes the function
of a gene regulatory network,” eLife, vol. 10. eLife Sciences Publications,
2021.
ista: Nagy-Staron AA, Tomasek K, Caruso Carter C, Sonnleitner E, Kavcic B, Paixão
T, Guet CC. 2021. Local genetic context shapes the function of a gene regulatory
network. eLife. 10, e65993.
mla: Nagy-Staron, Anna A., et al. “Local Genetic Context Shapes the Function of
a Gene Regulatory Network.” ELife, vol. 10, e65993, eLife Sciences Publications,
2021, doi:10.7554/elife.65993.
short: A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic,
T. Paixão, C.C. Guet, ELife 10 (2021).
corr_author: '1'
date_created: 2021-03-23T10:11:46Z
date_published: 2021-03-08T00:00:00Z
date_updated: 2025-06-12T06:36:17Z
day: '08'
ddc:
- '570'
department:
- _id: GaTk
- _id: CaGu
doi: 10.7554/elife.65993
ec_funded: 1
external_id:
isi:
- '000631050900001'
pmid:
- '33683203'
file:
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checksum: 3c2f44058c2dd45a5a1027f09d263f8e
content_type: application/pdf
creator: bkavcic
date_created: 2021-03-23T10:12:58Z
date_updated: 2021-03-23T10:12:58Z
file_id: '9284'
file_name: elife-65993-v2.pdf
file_size: 1390469
relation: main_file
success: 1
file_date_updated: 2021-03-23T10:12:58Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
keyword:
- Genetics and Molecular Biology
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2517526A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '628377'
name: 'The Systems Biology of Transcriptional Read-Through in Bacteria: from Synthetic
Networks to Genomic Studies'
- _id: 268BFA92-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03901
name: Cybergenetic circuits to test composability of gene networks
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
record:
- id: '8951'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Local genetic context shapes the function of a gene regulatory network
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2021'
...
---
_id: '9288'
abstract:
- lang: eng
text: "• The phenylpropanoid pathway serves a central role in plant metabolism,
providing numerous compounds involved in diverse physiological processes. Most
carbon entering the pathway is incorporated into lignin. Although several phenylpropanoid
pathway mutants show seedling growth arrest, the role for lignin in seedling growth
and development is unexplored.\r\n• We use complementary pharmacological and genetic
approaches to block CINNAMATE‐4‐HYDROXYLASE (C4H) functionality in Arabidopsis
seedlings and a set of molecular and biochemical techniques to investigate the
underlying phenotypes.\r\n• Blocking C4H resulted in reduced lateral rooting and
increased adventitious rooting apically in the hypocotyl. These phenotypes coincided
with an inhibition in auxin transport. The upstream accumulation in cis‐cinnamic
acid was found to likely cause polar auxin transport inhibition. Conversely, a
downstream depletion in lignin perturbed phloem‐mediated auxin transport. Restoring
lignin deposition effectively reestablished phloem transport and, accordingly,
auxin homeostasis.\r\n• Our results show that the accumulation of bioactive intermediates
and depletion in lignin jointly cause the aberrant phenotypes upon blocking C4H,
and demonstrate that proper deposition of lignin is essential for the establishment
of auxin distribution in seedlings. Our data position the phenylpropanoid pathway
and lignin in a new physiological framework, consolidating their importance in
plant growth and development."
article_processing_charge: No
article_type: original
author:
- first_name: I
full_name: El Houari, I
last_name: El Houari
- first_name: C
full_name: Van Beirs, C
last_name: Van Beirs
- first_name: HE
full_name: Arents, HE
last_name: Arents
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: A
full_name: Chanoca, A
last_name: Chanoca
- first_name: D
full_name: Opdenacker, D
last_name: Opdenacker
- first_name: J
full_name: Pollier, J
last_name: Pollier
- first_name: V
full_name: Storme, V
last_name: Storme
- first_name: W
full_name: Steenackers, W
last_name: Steenackers
- first_name: M
full_name: Quareshy, M
last_name: Quareshy
- first_name: R
full_name: Napier, R
last_name: Napier
- first_name: T
full_name: Beeckman, T
last_name: Beeckman
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: B
full_name: De Rybel, B
last_name: De Rybel
- first_name: W
full_name: Boerjan, W
last_name: Boerjan
- first_name: B
full_name: Vanholme, B
last_name: Vanholme
citation:
ama: El Houari I, Van Beirs C, Arents H, et al. Seedling developmental defects upon
blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport.
New Phytologist. 2021;230(6):2275-2291. doi:10.1111/nph.17349
apa: El Houari, I., Van Beirs, C., Arents, H., Han, H., Chanoca, A., Opdenacker,
D., … Vanholme, B. (2021). Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE
are caused by perturbations in auxin transport. New Phytologist. Wiley.
https://doi.org/10.1111/nph.17349
chicago: El Houari, I, C Van Beirs, HE Arents, Huibin Han, A Chanoca, D Opdenacker,
J Pollier, et al. “Seedling Developmental Defects upon Blocking CINNAMATE-4-HYDROXYLASE
Are Caused by Perturbations in Auxin Transport.” New Phytologist. Wiley,
2021. https://doi.org/10.1111/nph.17349.
ieee: I. El Houari et al., “Seedling developmental defects upon blocking
CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport,” New
Phytologist, vol. 230, no. 6. Wiley, pp. 2275–2291, 2021.
ista: El Houari I, Van Beirs C, Arents H, Han H, Chanoca A, Opdenacker D, Pollier
J, Storme V, Steenackers W, Quareshy M, Napier R, Beeckman T, Friml J, De Rybel
B, Boerjan W, Vanholme B. 2021. Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE
are caused by perturbations in auxin transport. New Phytologist. 230(6), 2275–2291.
mla: El Houari, I., et al. “Seedling Developmental Defects upon Blocking CINNAMATE-4-HYDROXYLASE
Are Caused by Perturbations in Auxin Transport.” New Phytologist, vol.
230, no. 6, Wiley, 2021, pp. 2275–91, doi:10.1111/nph.17349.
short: I. El Houari, C. Van Beirs, H. Arents, H. Han, A. Chanoca, D. Opdenacker,
J. Pollier, V. Storme, W. Steenackers, M. Quareshy, R. Napier, T. Beeckman, J.
Friml, B. De Rybel, W. Boerjan, B. Vanholme, New Phytologist 230 (2021) 2275–2291.
date_created: 2021-03-26T12:09:01Z
date_published: 2021-03-17T00:00:00Z
date_updated: 2026-06-18T19:44:45Z
day: '17'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/nph.17349
external_id:
isi:
- '000639552400001'
pmid:
- '33728703'
intvolume: ' 230'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://biblio.ugent.be/publication/8703799/file/8703800.pdf
month: '03'
oa: 1
oa_version: Published Version
page: 2275-2291
pmid: 1
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646x
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused
by perturbations in auxin transport
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 230
year: '2021'
...