---
_id: '15267'
abstract:
- lang: eng
text: "We study two fundamental communication primitives: broadcasting and leader
election in the classical model of multi-hop radio networks with unknown topology
and without collision detection mechanisms. It has been known for almost 20 years
that in undirected networks with n nodes and diameter D, randomized broadcasting
requires Ω(D log n/D + log2 n) rounds, assuming that uninformed nodes are not
allowed to communicate (until they are informed). Only very recently, Haeupler
and Wajc (PODC'2016) showed that this bound can be improved for the model with
spontaneous transmissions, providing an O(D log n log log n/log D + logO(1) n)-time
broadcasting algorithm. In this article, we give a new and faster algorithm that
completes broadcasting in O(D log n/log D + logO(1) n) time, succeeding with high
probability. This yields the first optimal O(D)-time broadcasting algorithm whenever
n is polynomial in D.\r\n\r\nFurthermore, our approach can be applied to design
a new leader election algorithm that matches the performance of our broadcasting
algorithm. Previously, all fast randomized leader election algorithms have used
broadcasting as a subroutine and their complexity has been asymptotically strictly
larger than the complexity of broadcasting. In particular, the fastest previously
known randomized leader election algorithm of Ghaffari and Haeupler (SODA'2013)
requires O(D log n/D min {log log n, log n/D} + logO(1) n)-time, succeeding with
high probability. Our new algorithm again requires O(D log n/log D + logO(1) n)
time, also succeeding with high probability."
article_number: '13'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Artur
full_name: Czumaj, Artur
last_name: Czumaj
- first_name: Peter
full_name: Davies, Peter
id: 11396234-BB50-11E9-B24C-90FCE5697425
last_name: Davies
orcid: 0000-0002-5646-9524
citation:
ama: Czumaj A, Davies P. Exploiting spontaneous transmissions for broadcasting and
leader election in radio networks. Journal of the ACM. 2021;68(2). doi:10.1145/3446383
apa: Czumaj, A., & Davies, P. (2021). Exploiting spontaneous transmissions for
broadcasting and leader election in radio networks. Journal of the ACM.
ACM. https://doi.org/10.1145/3446383
chicago: Czumaj, Artur, and Peter Davies. “Exploiting Spontaneous Transmissions
for Broadcasting and Leader Election in Radio Networks.” Journal of the ACM.
ACM, 2021. https://doi.org/10.1145/3446383.
ieee: A. Czumaj and P. Davies, “Exploiting spontaneous transmissions for broadcasting
and leader election in radio networks,” Journal of the ACM, vol. 68, no.
2. ACM, 2021.
ista: Czumaj A, Davies P. 2021. Exploiting spontaneous transmissions for broadcasting
and leader election in radio networks. Journal of the ACM. 68(2), 13.
mla: Czumaj, Artur, and Peter Davies. “Exploiting Spontaneous Transmissions for
Broadcasting and Leader Election in Radio Networks.” Journal of the ACM,
vol. 68, no. 2, 13, ACM, 2021, doi:10.1145/3446383.
short: A. Czumaj, P. Davies, Journal of the ACM 68 (2021).
date_created: 2024-04-03T07:41:46Z
date_published: 2021-01-28T00:00:00Z
date_updated: 2026-08-12T14:03:54Z
day: '28'
department:
- _id: DaAl
doi: 10.1145/3446383
external_id:
arxiv:
- '1703.01859'
intvolume: ' 68'
issue: '2'
keyword:
- Artificial Intelligence
- Hardware and Architecture
- Information Systems
- Control and Systems Engineering
- Software
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1703.01859
month: '01'
oa: 1
oa_version: Preprint
publication: Journal of the ACM
publication_identifier:
eissn:
- 1557-735X
issn:
- 0004-5411
publication_status: published
publisher: ACM
quality_controlled: '1'
status: public
title: Exploiting spontaneous transmissions for broadcasting and leader election in
radio networks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 68
year: '2021'
...
---
_id: '10575'
abstract:
- lang: eng
text: The choice of the boundary conditions in mechanical problems has to reflect
the interaction of the considered material with the surface. Still the assumption
of the no-slip condition is preferred in order to avoid boundary terms in the
analysis and slipping effects are usually overlooked. Besides the “static slip
models”, there are phenomena that are not accurately described by them, e.g. at
the moment when the slip changes rapidly, the wall shear stress and the slip can
exhibit a sudden overshoot and subsequent relaxation. When these effects become
significant, the so-called dynamic slip phenomenon occurs. We develop a mathematical
analysis of Navier–Stokes-like problems with a dynamic slip boundary condition,
which requires a proper generalization of the Gelfand triplet and the corresponding
function space setting.
acknowledgement: The research of A. Abbatiello is supported by Einstein Foundation,
Berlin. A. Abbatiello is also member of the Italian National Group for the Mathematical
Physics (GNFM) of INdAM. M. Bulíček acknowledges the support of the project No.
20-11027X financed by Czech Science Foundation (GACR). M. Bulíček is member of the
Jindřich Nečas Center for Mathematical Modelling. E. Maringová acknowledges support
from Charles University Research program UNCE/SCI/023, the grant SVV-2020-260583
by the Ministry of Education, Youth and Sports, Czech Republic and from the Austrian
Science Fund (FWF), grants P30000, W1245, and F65.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Anna
full_name: Abbatiello, Anna
last_name: Abbatiello
- first_name: Miroslav
full_name: Bulíček, Miroslav
last_name: Bulíček
- first_name: Erika
full_name: Maringová, Erika
id: dbabca31-66eb-11eb-963a-fb9c22c880b4
last_name: Maringová
citation:
ama: Abbatiello A, Bulíček M, Maringová E. On the dynamic slip boundary condition
for Navier-Stokes-like problems. Mathematical Models and Methods in Applied
Sciences. 2021;31(11):2165-2212. doi:10.1142/S0218202521500470
apa: Abbatiello, A., Bulíček, M., & Maringová, E. (2021). On the dynamic slip
boundary condition for Navier-Stokes-like problems. Mathematical Models and
Methods in Applied Sciences. World Scientific Publishing. https://doi.org/10.1142/S0218202521500470
chicago: Abbatiello, Anna, Miroslav Bulíček, and Erika Maringová. “On the Dynamic
Slip Boundary Condition for Navier-Stokes-like Problems.” Mathematical Models
and Methods in Applied Sciences. World Scientific Publishing, 2021. https://doi.org/10.1142/S0218202521500470.
ieee: A. Abbatiello, M. Bulíček, and E. Maringová, “On the dynamic slip boundary
condition for Navier-Stokes-like problems,” Mathematical Models and Methods
in Applied Sciences, vol. 31, no. 11. World Scientific Publishing, pp. 2165–2212,
2021.
ista: Abbatiello A, Bulíček M, Maringová E. 2021. On the dynamic slip boundary condition
for Navier-Stokes-like problems. Mathematical Models and Methods in Applied Sciences.
31(11), 2165–2212.
mla: Abbatiello, Anna, et al. “On the Dynamic Slip Boundary Condition for Navier-Stokes-like
Problems.” Mathematical Models and Methods in Applied Sciences, vol. 31,
no. 11, World Scientific Publishing, 2021, pp. 2165–212, doi:10.1142/S0218202521500470.
short: A. Abbatiello, M. Bulíček, E. Maringová, Mathematical Models and Methods
in Applied Sciences 31 (2021) 2165–2212.
date_created: 2021-12-26T23:01:27Z
date_published: 2021-10-13T00:00:00Z
date_updated: 2025-04-15T08:31:30Z
day: '13'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1142/S0218202521500470
external_id:
arxiv:
- '2009.09057'
isi:
- '000722309400001'
file:
- access_level: open_access
checksum: 8c0a9396335f0b70e1f5cbfe450a987a
content_type: application/pdf
creator: dernst
date_created: 2022-05-16T10:55:45Z
date_updated: 2022-05-16T10:55:45Z
file_id: '11385'
file_name: 2021_MathModelsMethods_Abbatiello.pdf
file_size: 795483
relation: main_file
success: 1
file_date_updated: 2022-05-16T10:55:45Z
has_accepted_license: '1'
intvolume: ' 31'
isi: 1
issue: '11'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: 2165-2212
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 260788DE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1245
name: Dissipation and dispersion in nonlinear partial differential equations
publication: Mathematical Models and Methods in Applied Sciences
publication_identifier:
eissn:
- 1793-6314
issn:
- 0218-2025
publication_status: published
publisher: World Scientific Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the dynamic slip boundary condition for Navier-Stokes-like problems
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 31
year: '2021'
...
---
_id: '10005'
abstract:
- lang: eng
text: We study systems of nonlinear partial differential equations of parabolic
type, in which the elliptic operator is replaced by the first-order divergence
operator acting on a flux function, which is related to the spatial gradient of
the unknown through an additional implicit equation. This setting, broad enough
in terms of applications, significantly expands the paradigm of nonlinear parabolic
problems. Formulating four conditions concerning the form of the implicit equation,
we first show that these conditions describe a maximal monotone p-coercive graph.
We then establish the global-in-time and large-data existence of a (weak) solution
and its uniqueness. To this end, we adopt and significantly generalize Minty’s
method of monotone mappings. A unified theory, containing several novel tools,
is developed in a way to be tractable from the point of view of numerical approximations.
acknowledgement: "M. Bulíček and J. Málek acknowledge the support of the project No.
18-12719S financed by the Czech\r\nScience foundation (GAČR). E. Maringová acknowledges
support from Charles University Research program \r\nUNCE/SCI/023, the grant SVV-2020-260583
by the Ministry of Education, Youth and Sports, Czech Republic\r\nand from the Austrian
Science Fund (FWF), grants P30000, W1245, and F65. M. Bulíček and J. Málek are\r\nmembers
of the Nečas Center for Mathematical Modelling.\r\n"
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Miroslav
full_name: Bulíček, Miroslav
last_name: Bulíček
- first_name: Erika
full_name: Maringová, Erika
id: dbabca31-66eb-11eb-963a-fb9c22c880b4
last_name: Maringová
- first_name: Josef
full_name: Málek, Josef
last_name: Málek
citation:
ama: Bulíček M, Maringová E, Málek J. On nonlinear problems of parabolic type with
implicit constitutive equations involving flux. Mathematical Models and Methods
in Applied Sciences. 2021;31(09). doi:10.1142/S0218202521500457
apa: Bulíček, M., Maringová, E., & Málek, J. (2021). On nonlinear problems of
parabolic type with implicit constitutive equations involving flux. Mathematical
Models and Methods in Applied Sciences. World Scientific Publishing. https://doi.org/10.1142/S0218202521500457
chicago: Bulíček, Miroslav, Erika Maringová, and Josef Málek. “On Nonlinear Problems
of Parabolic Type with Implicit Constitutive Equations Involving Flux.” Mathematical
Models and Methods in Applied Sciences. World Scientific Publishing, 2021.
https://doi.org/10.1142/S0218202521500457.
ieee: M. Bulíček, E. Maringová, and J. Málek, “On nonlinear problems of parabolic
type with implicit constitutive equations involving flux,” Mathematical Models
and Methods in Applied Sciences, vol. 31, no. 09. World Scientific Publishing,
2021.
ista: Bulíček M, Maringová E, Málek J. 2021. On nonlinear problems of parabolic
type with implicit constitutive equations involving flux. Mathematical Models
and Methods in Applied Sciences. 31(09).
mla: Bulíček, Miroslav, et al. “On Nonlinear Problems of Parabolic Type with Implicit
Constitutive Equations Involving Flux.” Mathematical Models and Methods in
Applied Sciences, vol. 31, no. 09, World Scientific Publishing, 2021, doi:10.1142/S0218202521500457.
short: M. Bulíček, E. Maringová, J. Málek, Mathematical Models and Methods in Applied
Sciences 31 (2021).
date_created: 2021-09-12T22:01:25Z
date_published: 2021-08-25T00:00:00Z
date_updated: 2026-08-18T07:47:39Z
day: '25'
department:
- _id: JuFi
doi: 10.1142/S0218202521500457
external_id:
arxiv:
- '2009.06917'
isi:
- '000722222900004'
intvolume: ' 31'
isi: 1
issue: '09'
keyword:
- Nonlinear parabolic systems
- implicit constitutive theory
- weak solutions
- existence
- uniqueness
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2009.06917
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: Mathematical Models and Methods in Applied Sciences
publication_identifier:
eissn:
- 1793-6314
issn:
- 0218-2025
publication_status: published
publisher: World Scientific Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: On nonlinear problems of parabolic type with implicit constitutive equations
involving flux
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2021'
...
---
_id: '10665'
abstract:
- lang: eng
text: "Formal verification of neural networks is an active topic of research, and
recent advances have significantly increased the size of the networks that verification
tools can handle. However, most methods are designed for verification of an idealized
model of the actual network which works over real arithmetic and ignores rounding
imprecisions. This idealization is in stark contrast to network quantization,
which is a technique that trades numerical precision for computational efficiency
and is, therefore, often applied in practice. Neglecting rounding errors of such
low-bit quantized neural networks has been shown to lead to wrong conclusions
about the network’s correctness. Thus, the desired approach for verifying quantized
neural networks would be one that takes these rounding errors\r\ninto account.
In this paper, we show that verifying the bitexact implementation of quantized
neural networks with bitvector specifications is PSPACE-hard, even though verifying
idealized real-valued networks and satisfiability of bit-vector specifications
alone are each in NP. Furthermore, we explore several practical heuristics toward
closing the complexity gap between idealized and bit-exact verification. In particular,
we propose three techniques for making SMT-based verification of quantized neural
networks more scalable. Our experiments demonstrate that our proposed methods
allow a speedup of up to three orders of magnitude over existing approaches."
acknowledgement: "This research was supported in part by the Austrian Science Fund
(FWF) under grant Z211-N23 (Wittgenstein\r\nAward), ERC CoG 863818 (FoRM-SMArt),
and the European Union’s Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n"
alternative_title:
- Technical Tracks
article_processing_charge: No
arxiv: 1
author:
- 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: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Henzinger TA, Lechner M, Zikelic D. Scalable verification of quantized neural
networks. In: Proceedings of the AAAI Conference on Artificial Intelligence.
Vol 35. AAAI Press; 2021:3787-3795. doi:10.1609/aaai.v35i5.16496'
apa: 'Henzinger, T. A., Lechner, M., & Zikelic, D. (2021). Scalable verification
of quantized neural networks. In Proceedings of the AAAI Conference on Artificial
Intelligence (Vol. 35, pp. 3787–3795). Virtual: AAAI Press. https://doi.org/10.1609/aaai.v35i5.16496'
chicago: Henzinger, Thomas A, Mathias Lechner, and Dorde Zikelic. “Scalable Verification
of Quantized Neural Networks.” In Proceedings of the AAAI Conference on Artificial
Intelligence, 35:3787–95. AAAI Press, 2021. https://doi.org/10.1609/aaai.v35i5.16496.
ieee: T. A. Henzinger, M. Lechner, and D. Zikelic, “Scalable verification of quantized
neural networks,” in Proceedings of the AAAI Conference on Artificial Intelligence,
Virtual, 2021, vol. 35, no. 5A, pp. 3787–3795.
ista: 'Henzinger TA, Lechner M, Zikelic D. 2021. Scalable verification of quantized
neural networks. Proceedings of the AAAI Conference on Artificial Intelligence.
AAAI: Association for the Advancement of Artificial Intelligence, Technical Tracks,
vol. 35, 3787–3795.'
mla: Henzinger, Thomas A., et al. “Scalable Verification of Quantized Neural Networks.”
Proceedings of the AAAI Conference on Artificial Intelligence, vol. 35,
no. 5A, AAAI Press, 2021, pp. 3787–95, doi:10.1609/aaai.v35i5.16496.
short: T.A. Henzinger, M. Lechner, D. Zikelic, in:, Proceedings of the AAAI Conference
on Artificial Intelligence, AAAI Press, 2021, pp. 3787–3795.
conference:
end_date: 2021-02-09
location: Virtual
name: 'AAAI: Association for the Advancement of Artificial Intelligence'
start_date: 2021-02-02
corr_author: '1'
date_created: 2022-01-25T15:15:02Z
date_published: 2021-05-28T00:00:00Z
date_updated: 2026-08-19T09:28:05Z
day: '28'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.1609/aaai.v35i5.16496
ec_funded: 1
external_id:
arxiv:
- '2012.08185'
file:
- access_level: open_access
checksum: 2bc8155b2526a70fba5b7301bc89dbd1
content_type: application/pdf
creator: mlechner
date_created: 2022-01-26T07:41:16Z
date_updated: 2022-01-26T07:41:16Z
file_id: '10684'
file_name: 16496-Article Text-19990-1-2-20210518 (1).pdf
file_size: 137235
relation: main_file
success: 1
file_date_updated: 2022-01-26T07:41:16Z
has_accepted_license: '1'
intvolume: ' 35'
issue: 5A
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://ojs.aaai.org/index.php/AAAI/article/view/16496
month: '05'
oa: 1
oa_version: Published Version
page: 3787-3795
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the AAAI Conference on Artificial Intelligence
publication_identifier:
eissn:
- 2374-3468
isbn:
- 978-1-57735-866-4
issn:
- 2159-5399
publication_status: published
publisher: AAAI Press
quality_controlled: '1'
related_material:
record:
- id: '11362'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Scalable verification of quantized neural networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2021'
...
---
_id: '10671'
abstract:
- lang: eng
text: We introduce a new class of time-continuous recurrent neural network models.
Instead of declaring a learning system’s dynamics by implicit nonlinearities,
we construct networks of linear first-order dynamical systems modulated via nonlinear
interlinked gates. The resulting models represent dynamical systems with varying
(i.e., liquid) time-constants coupled to their hidden state, with outputs being
computed by numerical differential equation solvers. These neural networks exhibit
stable and bounded behavior, yield superior expressivity within the family of
neural ordinary differential equations, and give rise to improved performance
on time-series prediction tasks. To demonstrate these properties, we first take
a theoretical approach to find bounds over their dynamics, and compute their expressive
power by the trajectory length measure in a latent trajectory space. We then conduct
a series of time-series prediction experiments to manifest the approximation capability
of Liquid Time-Constant Networks (LTCs) compared to classical and modern RNNs.
acknowledgement: "R.H. and D.R. are partially supported by Boeing. R.H. and R.G. were
partially supported by the Horizon-2020 ECSEL\r\nProject grant No. 783163 (iDev40).
M.L. was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23
(Wittgenstein Award). A.A. is supported by the National Science Foundation (NSF)
Graduate Research Fellowship Program. This research work is partially drawn from
the PhD dissertation of R.H."
alternative_title:
- Technical Tracks
article_processing_charge: No
arxiv: 1
author:
- first_name: Ramin
full_name: Hasani, Ramin
last_name: Hasani
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Alexander
full_name: Amini, Alexander
last_name: Amini
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: 'Hasani R, Lechner M, Amini A, Rus D, Grosu R. Liquid time-constant networks.
In: Proceedings of the AAAI Conference on Artificial Intelligence. Vol
35. AAAI Press; 2021:7657-7666. doi:10.1609/aaai.v35i9.16936'
apa: 'Hasani, R., Lechner, M., Amini, A., Rus, D., & Grosu, R. (2021). Liquid
time-constant networks. In Proceedings of the AAAI Conference on Artificial
Intelligence (Vol. 35, pp. 7657–7666). Virtual: AAAI Press. https://doi.org/10.1609/aaai.v35i9.16936'
chicago: Hasani, Ramin, Mathias Lechner, Alexander Amini, Daniela Rus, and Radu
Grosu. “Liquid Time-Constant Networks.” In Proceedings of the AAAI Conference
on Artificial Intelligence, 35:7657–66. AAAI Press, 2021. https://doi.org/10.1609/aaai.v35i9.16936.
ieee: R. Hasani, M. Lechner, A. Amini, D. Rus, and R. Grosu, “Liquid time-constant
networks,” in Proceedings of the AAAI Conference on Artificial Intelligence,
Virtual, 2021, vol. 35, no. 9, pp. 7657–7666.
ista: 'Hasani R, Lechner M, Amini A, Rus D, Grosu R. 2021. Liquid time-constant
networks. Proceedings of the AAAI Conference on Artificial Intelligence. AAAI:
Association for the Advancement of Artificial Intelligence, Technical Tracks,
vol. 35, 7657–7666.'
mla: Hasani, Ramin, et al. “Liquid Time-Constant Networks.” Proceedings of the
AAAI Conference on Artificial Intelligence, vol. 35, no. 9, AAAI Press, 2021,
pp. 7657–66, doi:10.1609/aaai.v35i9.16936.
short: R. Hasani, M. Lechner, A. Amini, D. Rus, R. Grosu, in:, Proceedings of the
AAAI Conference on Artificial Intelligence, AAAI Press, 2021, pp. 7657–7666.
conference:
end_date: 2021-02-09
location: Virtual
name: 'AAAI: Association for the Advancement of Artificial Intelligence'
start_date: 2021-02-02
corr_author: '1'
date_created: 2022-01-25T15:48:36Z
date_published: 2021-05-28T00:00:00Z
date_updated: 2026-08-19T09:24:30Z
day: '28'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.1609/aaai.v35i9.16936
external_id:
arxiv:
- '2006.04439'
file:
- access_level: open_access
checksum: 0f06995fba06dbcfa7ed965fc66027ff
content_type: application/pdf
creator: mlechner
date_created: 2022-01-26T07:36:03Z
date_updated: 2022-01-26T07:36:03Z
file_id: '10678'
file_name: 16936-Article Text-20430-1-2-20210518 (1).pdf
file_size: 4302669
relation: main_file
success: 1
file_date_updated: 2022-01-26T07:36:03Z
has_accepted_license: '1'
intvolume: ' 35'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://ojs.aaai.org/index.php/AAAI/article/view/16936
month: '05'
oa: 1
oa_version: Published Version
page: 7657-7666
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication: Proceedings of the AAAI Conference on Artificial Intelligence
publication_identifier:
eissn:
- 2374-3468
isbn:
- 978-1-57735-866-4
issn:
- 2159-5399
publication_status: published
publisher: AAAI Press
quality_controlled: '1'
status: public
title: Liquid time-constant networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2021'
...
---
_id: '11436'
abstract:
- lang: eng
text: Asynchronous distributed algorithms are a popular way to reduce synchronization
costs in large-scale optimization, and in particular for neural network training.
However, for nonsmooth and nonconvex objectives, few convergence guarantees exist
beyond cases where closed-form proximal operator solutions are available. As training
most popular deep neural networks corresponds to optimizing nonsmooth and nonconvex
objectives, there is a pressing need for such convergence guarantees. In this
paper, we analyze for the first time the convergence of stochastic asynchronous
optimization for this general class of objectives. In particular, we focus on
stochastic subgradient methods allowing for block variable partitioning, where
the shared model is asynchronously updated by concurrent processes. To this end,
we use a probabilistic model which captures key features of real asynchronous
scheduling between concurrent processes. Under this model, we establish convergence
with probability one to an invariant set for stochastic subgradient methods with
momentum. From a practical perspective, one issue with the family of algorithms
that we consider is that they are not efficiently supported by machine learning
frameworks, which mostly focus on distributed data-parallel strategies. To address
this, we propose a new implementation strategy for shared-memory based training
of deep neural networks for a partitioned but shared model in single- and multi-GPU
settings. Based on this implementation, we achieve on average1.2x speed-up in
comparison to state-of-the-art training methods for popular image classification
tasks, without compromising accuracy.
acknowledgement: Vyacheslav Kungurtsev was supported by the OP VVV project CZ.02.1.01/0.0/0.0/16
019/0000765 “Research Center for Informatics. Bapi Chatterjee was supported by the
European Union’s Horizon 2020 research and innovation programme under the Marie
Sklodowska-Curie grant agreement No. 754411 (ISTPlus). Dan Alistarh has received
funding from the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation programme (grant agreement No 805223 ScaleML).
article_processing_charge: No
arxiv: 1
author:
- first_name: Vyacheslav
full_name: Kungurtsev, Vyacheslav
last_name: Kungurtsev
- first_name: Malcolm
full_name: Egan, Malcolm
last_name: Egan
- first_name: Bapi
full_name: Chatterjee, Bapi
id: 3C41A08A-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-2742-4028
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Kungurtsev V, Egan M, Chatterjee B, Alistarh D-A. Asynchronous optimization
methods for efficient training of deep neural networks with guarantees. In: 35th
AAAI Conference on Artificial Intelligence, AAAI 2021. Vol 35. AAAI Press;
2021:8209-8216. doi:10.1609/aaai.v35i9.16999'
apa: 'Kungurtsev, V., Egan, M., Chatterjee, B., & Alistarh, D.-A. (2021). Asynchronous
optimization methods for efficient training of deep neural networks with guarantees.
In 35th AAAI Conference on Artificial Intelligence, AAAI 2021 (Vol. 35,
pp. 8209–8216). Virtual, Online: AAAI Press. https://doi.org/10.1609/aaai.v35i9.16999'
chicago: Kungurtsev, Vyacheslav, Malcolm Egan, Bapi Chatterjee, and Dan-Adrian Alistarh.
“Asynchronous Optimization Methods for Efficient Training of Deep Neural Networks
with Guarantees.” In 35th AAAI Conference on Artificial Intelligence, AAAI
2021, 35:8209–16. AAAI Press, 2021. https://doi.org/10.1609/aaai.v35i9.16999.
ieee: V. Kungurtsev, M. Egan, B. Chatterjee, and D.-A. Alistarh, “Asynchronous optimization
methods for efficient training of deep neural networks with guarantees,” in 35th
AAAI Conference on Artificial Intelligence, AAAI 2021, Virtual, Online, 2021,
vol. 35, no. 9B, pp. 8209–8216.
ista: 'Kungurtsev V, Egan M, Chatterjee B, Alistarh D-A. 2021. Asynchronous optimization
methods for efficient training of deep neural networks with guarantees. 35th AAAI
Conference on Artificial Intelligence, AAAI 2021. AAAI: Conference on Artificial
Intelligence vol. 35, 8209–8216.'
mla: Kungurtsev, Vyacheslav, et al. “Asynchronous Optimization Methods for Efficient
Training of Deep Neural Networks with Guarantees.” 35th AAAI Conference on
Artificial Intelligence, AAAI 2021, vol. 35, no. 9B, AAAI Press, 2021, pp.
8209–16, doi:10.1609/aaai.v35i9.16999.
short: V. Kungurtsev, M. Egan, B. Chatterjee, D.-A. Alistarh, in:, 35th AAAI Conference
on Artificial Intelligence, AAAI 2021, AAAI Press, 2021, pp. 8209–8216.
conference:
end_date: 2021-02-09
location: Virtual, Online
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2021-02-02
date_created: 2022-06-05T22:01:52Z
date_published: 2021-05-18T00:00:00Z
date_updated: 2026-08-19T09:25:06Z
day: '18'
department:
- _id: DaAl
doi: 10.1609/aaai.v35i9.16999
ec_funded: 1
external_id:
arxiv:
- '1905.11845'
intvolume: ' 35'
issue: 9B
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1905.11845'
month: '05'
oa: 1
oa_version: Preprint
page: 8209-8216
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: 35th AAAI Conference on Artificial Intelligence, AAAI 2021
publication_identifier:
eissn:
- 2374-3468
isbn:
- '9781713835974'
issn:
- 2159-5399
publication_status: published
publisher: AAAI Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Asynchronous optimization methods for efficient training of deep neural networks
with guarantees
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2021'
...
---
_id: '10669'
abstract:
- lang: eng
text: "We show that Neural ODEs, an emerging class of timecontinuous neural networks,
can be verified by solving a set of global-optimization problems. For this purpose,
we introduce Stochastic Lagrangian Reachability (SLR), an\r\nabstraction-based
technique for constructing a tight Reachtube (an over-approximation of the set
of reachable states\r\nover a given time-horizon), and provide stochastic guarantees
in the form of confidence intervals for the Reachtube bounds. SLR inherently avoids
the infamous wrapping effect (accumulation of over-approximation errors) by performing
local optimization steps to expand safe regions instead of repeatedly forward-propagating
them as is done by deterministic reachability methods. To enable fast local optimizations,
we introduce a novel forward-mode adjoint sensitivity method to compute gradients
without the need for backpropagation. Finally, we establish asymptotic and non-asymptotic
convergence rates for SLR."
acknowledgement: "The authors would like to thank the reviewers for their insightful
comments. RH and RG were partially supported by\r\nHorizon-2020 ECSEL Project grant
No. 783163 (iDev40). RH was partially supported by Boeing. ML was supported\r\nin
part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).
SG was funded by FWF\r\nproject W1255-N23. JC was partially supported by NAWA Polish
Returns grant PPN/PPO/2018/1/00029. SS was supported by NSF awards DCL-2040599,
CCF-1918225, and CPS-1446832.\r\n"
alternative_title:
- Technical Tracks
article_processing_charge: No
arxiv: 1
author:
- first_name: Sophie
full_name: Grunbacher, Sophie
last_name: Grunbacher
- first_name: Ramin
full_name: Hasani, Ramin
last_name: Hasani
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Jacek
full_name: Cyranka, Jacek
last_name: Cyranka
- first_name: Scott A
full_name: Smolka, Scott A
last_name: Smolka
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: 'Grunbacher S, Hasani R, Lechner M, Cyranka J, Smolka SA, Grosu R. On the verification
of neural ODEs with stochastic guarantees. In: Proceedings of the AAAI Conference
on Artificial Intelligence. Vol 35. AAAI Press; 2021:11525-11535. doi:10.1609/aaai.v35i13.17372'
apa: 'Grunbacher, S., Hasani, R., Lechner, M., Cyranka, J., Smolka, S. A., &
Grosu, R. (2021). On the verification of neural ODEs with stochastic guarantees.
In Proceedings of the AAAI Conference on Artificial Intelligence (Vol.
35, pp. 11525–11535). Virtual: AAAI Press. https://doi.org/10.1609/aaai.v35i13.17372'
chicago: Grunbacher, Sophie, Ramin Hasani, Mathias Lechner, Jacek Cyranka, Scott
A Smolka, and Radu Grosu. “On the Verification of Neural ODEs with Stochastic
Guarantees.” In Proceedings of the AAAI Conference on Artificial Intelligence,
35:11525–35. AAAI Press, 2021. https://doi.org/10.1609/aaai.v35i13.17372.
ieee: S. Grunbacher, R. Hasani, M. Lechner, J. Cyranka, S. A. Smolka, and R. Grosu,
“On the verification of neural ODEs with stochastic guarantees,” in Proceedings
of the AAAI Conference on Artificial Intelligence, Virtual, 2021, vol. 35,
no. 13, pp. 11525–11535.
ista: 'Grunbacher S, Hasani R, Lechner M, Cyranka J, Smolka SA, Grosu R. 2021. On
the verification of neural ODEs with stochastic guarantees. Proceedings of the
AAAI Conference on Artificial Intelligence. AAAI: Association for the Advancement
of Artificial Intelligence, Technical Tracks, vol. 35, 11525–11535.'
mla: Grunbacher, Sophie, et al. “On the Verification of Neural ODEs with Stochastic
Guarantees.” Proceedings of the AAAI Conference on Artificial Intelligence,
vol. 35, no. 13, AAAI Press, 2021, pp. 11525–35, doi:10.1609/aaai.v35i13.17372.
short: S. Grunbacher, R. Hasani, M. Lechner, J. Cyranka, S.A. Smolka, R. Grosu,
in:, Proceedings of the AAAI Conference on Artificial Intelligence, AAAI Press,
2021, pp. 11525–11535.
conference:
end_date: 2021-02-09
location: Virtual
name: 'AAAI: Association for the Advancement of Artificial Intelligence'
start_date: 2021-02-02
corr_author: '1'
date_created: 2022-01-25T15:47:20Z
date_published: 2021-05-28T00:00:00Z
date_updated: 2026-08-19T09:29:48Z
day: '28'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.1609/aaai.v35i13.17372
external_id:
arxiv:
- '2012.08863'
file:
- access_level: open_access
checksum: 468d07041e282a1d46ffdae92f709630
content_type: application/pdf
creator: mlechner
date_created: 2022-01-26T07:38:08Z
date_updated: 2022-01-26T07:38:08Z
file_id: '10680'
file_name: 17372-Article Text-20866-1-2-20210518.pdf
file_size: 286906
relation: main_file
success: 1
file_date_updated: 2022-01-26T07:38:08Z
has_accepted_license: '1'
intvolume: ' 35'
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://ojs.aaai.org/index.php/AAAI/article/view/17372
month: '05'
oa: 1
oa_version: Published Version
page: 11525-11535
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication: Proceedings of the AAAI Conference on Artificial Intelligence
publication_identifier:
eissn:
- 2374-3468
isbn:
- 978-1-57735-866-4
issn:
- 2159-5399
publication_status: published
publisher: AAAI Press
quality_controlled: '1'
status: public
title: On the verification of neural ODEs with stochastic guarantees
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2021'
...
---
OA_place: publisher
_id: '10429'
abstract:
- lang: eng
text: "The scalability of concurrent data structures and distributed algorithms
strongly depends on\r\nreducing the contention for shared resources and the costs
of synchronization and communication. We show how such cost reductions can be
attained by relaxing the strict consistency conditions required by sequential
implementations. In the first part of the thesis, we consider relaxation in the
context of concurrent data structures. Specifically, in data structures \r\nsuch
as priority queues, imposing strong semantics renders scalability impossible,
since a correct implementation of the remove operation should return only the
element with highest priority. Intuitively, attempting to invoke remove operations
concurrently creates a race condition. This bottleneck can be circumvented by
relaxing semantics of the affected data structure, thus allowing removal of the
elements which are no longer required to have the highest priority. We prove that
the randomized implementations of relaxed data structures provide provable guarantees
on the priority of the removed elements even under concurrency. Additionally,
we show that in some cases the relaxed data structures can be used to scale the
classical algorithms which are usually implemented with the exact ones. In the
second part, we study parallel variants of the stochastic gradient descent (SGD)
algorithm, which distribute computation among the multiple processors, thus reducing
the running time. Unfortunately, in order for standard parallel SGD to succeed,
each processor has to maintain a local copy of the necessary model parameter,
which is identical to the local copies of other processors; the overheads from
this perfect consistency in terms of communication and synchronization can negate
the speedup gained by distributing the computation. We show that the consistency
conditions required by SGD can be relaxed, allowing the algorithm to be more
flexible in terms of tolerating quantized communication, asynchrony, or even crash
faults, while its convergence remains asymptotically the same."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
orcid: 0000-0001-5634-0731
citation:
ama: Nadiradze G. On achieving scalability through relaxation. 2021. doi:10.15479/at:ista:10429
apa: Nadiradze, G. (2021). On achieving scalability through relaxation. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:10429
chicago: Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute
of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10429.
ieee: G. Nadiradze, “On achieving scalability through relaxation,” Institute of
Science and Technology Austria, 2021.
ista: Nadiradze G. 2021. On achieving scalability through relaxation. Institute
of Science and Technology Austria.
mla: Nadiradze, Giorgi. On Achieving Scalability through Relaxation. Institute
of Science and Technology Austria, 2021, doi:10.15479/at:ista:10429.
short: G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science
and Technology Austria, 2021.
corr_author: '1'
date_created: 2021-12-08T21:52:28Z
date_published: 2021-12-09T00:00:00Z
date_updated: 2026-08-19T09:30:23Z
day: '09'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: DaAl
doi: 10.15479/at:ista:10429
ec_funded: 1
file:
- access_level: open_access
checksum: 6bf14e9a523387328f016c0689f5e10e
content_type: application/pdf
creator: gnadirad
date_created: 2021-12-09T17:47:49Z
date_updated: 2021-12-09T17:47:49Z
file_id: '10436'
file_name: Thesis_Final_09_12_2021.pdf
file_size: 2370859
relation: main_file
success: 1
- access_level: closed
checksum: 914d6c5ca86bd0add471971a8f4c4341
content_type: application/zip
creator: gnadirad
date_created: 2021-12-09T17:47:49Z
date_updated: 2022-03-28T12:55:12Z
file_id: '10437'
file_name: Thesis_Final_09_12_2021.zip
file_size: 2596924
relation: source_file
file_date_updated: 2022-03-28T12:55:12Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '132'
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6673'
relation: part_of_dissertation
status: public
- id: '5965'
relation: part_of_dissertation
status: public
- id: '10435'
relation: part_of_dissertation
status: public
- id: '10432'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
title: On achieving scalability through relaxation
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2021'
...
---
_id: '10432'
abstract:
- lang: eng
text: One key element behind the recent progress of machine learning has been the
ability to train machine learning models in large-scale distributed shared-memory
and message-passing environments. Most of these models are trained employing variants
of stochastic gradient descent (SGD) based optimization, but most methods involve
some type of consistency relaxation relative to sequential SGD, to mitigate its
large communication or synchronization costs at scale. In this paper, we introduce
a general consistency condition covering communication-reduced and asynchronous
distributed SGD implementations. Our framework, called elastic consistency, decouples
the system-specific aspects of the implementation from the SGD convergence requirements,
giving a general way to obtain convergence bounds for a wide variety of distributed
SGD methods used in practice. Elastic consistency can be used to re-derive or
improve several previous convergence bounds in message-passing and shared-memory
settings, but also to analyze new models and distribution schemes. As a direct
application, we propose and analyze a new synchronization-avoiding scheduling
scheme for distributed SGD, and show that it can be used to efficiently train
deep convolutional models for image classification.
acknowledgement: "We would like to thank Christopher De Sa for his feedback on an
earlier draft of this paper, as well as the anonymous AAAI reviewers for their useful
comments. This project has received\r\nfunding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No 805223 ScaleML). Bapi\r\nChatterjee was supported by the European
Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie
grant agreement No. 754411 (ISTPlus)."
article_processing_charge: No
arxiv: 1
author:
- first_name: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
orcid: 0000-0001-5634-0731
- first_name: Ilia
full_name: Markov, Ilia
id: D0CF4148-C985-11E9-8066-0BDEE5697425
last_name: Markov
- first_name: Bapi
full_name: Chatterjee, Bapi
id: 3C41A08A-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-2742-4028
- first_name: 'Vyacheslav '
full_name: 'Kungurtsev, Vyacheslav '
last_name: Kungurtsev
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Nadiradze G, Markov I, Chatterjee B, Kungurtsev V, Alistarh D-A. Elastic consistency:
A practical consistency model for distributed stochastic gradient descent. In:
Proceedings of the AAAI Conference on Artificial Intelligence. Vol 35.
; 2021:9037-9045. doi:10.1609/aaai.v35i10.17092'
apa: 'Nadiradze, G., Markov, I., Chatterjee, B., Kungurtsev, V., & Alistarh,
D.-A. (2021). Elastic consistency: A practical consistency model for distributed
stochastic gradient descent. In Proceedings of the AAAI Conference on Artificial
Intelligence (Vol. 35, pp. 9037–9045). Virtual. https://doi.org/10.1609/aaai.v35i10.17092'
chicago: 'Nadiradze, Giorgi, Ilia Markov, Bapi Chatterjee, Vyacheslav Kungurtsev,
and Dan-Adrian Alistarh. “Elastic Consistency: A Practical Consistency Model for
Distributed Stochastic Gradient Descent.” In Proceedings of the AAAI Conference
on Artificial Intelligence, 35:9037–45, 2021. https://doi.org/10.1609/aaai.v35i10.17092.'
ieee: 'G. Nadiradze, I. Markov, B. Chatterjee, V. Kungurtsev, and D.-A. Alistarh,
“Elastic consistency: A practical consistency model for distributed stochastic
gradient descent,” in Proceedings of the AAAI Conference on Artificial Intelligence,
Virtual, 2021, vol. 35, no. 10, pp. 9037–9045.'
ista: 'Nadiradze G, Markov I, Chatterjee B, Kungurtsev V, Alistarh D-A. 2021. Elastic
consistency: A practical consistency model for distributed stochastic gradient
descent. Proceedings of the AAAI Conference on Artificial Intelligence. AAAI:
Association for the Advancement of Artificial Intelligence vol. 35, 9037–9045.'
mla: 'Nadiradze, Giorgi, et al. “Elastic Consistency: A Practical Consistency Model
for Distributed Stochastic Gradient Descent.” Proceedings of the AAAI Conference
on Artificial Intelligence, vol. 35, no. 10, 2021, pp. 9037–45, doi:10.1609/aaai.v35i10.17092.'
short: G. Nadiradze, I. Markov, B. Chatterjee, V. Kungurtsev, D.-A. Alistarh, in:,
Proceedings of the AAAI Conference on Artificial Intelligence, 2021, pp. 9037–9045.
conference:
end_date: 2021-02-09
location: Virtual
name: 'AAAI: Association for the Advancement of Artificial Intelligence'
start_date: 2021-02-02
date_created: 2021-12-09T09:21:35Z
date_published: 2021-05-18T00:00:00Z
date_updated: 2026-08-19T09:30:23Z
day: '18'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1609/aaai.v35i10.17092
ec_funded: 1
external_id:
arxiv:
- '2001.05918'
intvolume: ' 35'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://ojs.aaai.org/index.php/AAAI/article/view/17092
month: '05'
oa: 1
oa_version: Published Version
page: 9037-9045
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Proceedings of the AAAI Conference on Artificial Intelligence
publication_status: published
quality_controlled: '1'
related_material:
record:
- id: '10429'
relation: dissertation_contains
status: public
status: public
title: 'Elastic consistency: A practical consistency model for distributed stochastic
gradient descent'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2021'
...
---
_id: '12077'
abstract:
- lang: eng
text: "We compare the Manin-type conjecture for Campana points recently formulated\r\nby
Pieropan, Smeets, Tanimoto and V\\'{a}rilly-Alvarado with an alternative\r\nprediction
of Browning and Van Valckenborgh in the special case of the orbifold\r\n$(\\mathbb{P}^1,D)$,
where $D =\\frac{1}{2}[0]+\\frac{1}{2}[1]+\\frac{1}{2}[\\infty]$. We find that
the two predicted leading constants do not agree, and we discuss whether thin
sets\r\ncould explain this discrepancy. Motivated by this, we provide a counterexample\r\nto
the Manin-type conjecture for Campana points, by considering orbifolds\r\ncorresponding
to squareful values of binary quadratic forms."
acknowledgement: The author would like to thank Damaris Schindler and Florian Wilsch
for their helpful comments on the heights and Tamagawa measures used in Section
3, together with Marta Pieropan, Sho Tanimoto and Sam Streeter for providing valuable
feedback on an earlier version of this paper, and Tim Browning for many useful comments
and discussions during the development of this work. The author is also grateful
to the anonymous referee for providing many valuable comments and suggestions that
improved the quality of the paper.
article_number: '2104.14946'
article_processing_charge: No
arxiv: 1
author:
- first_name: Alec L
full_name: Shute, Alec L
id: 440EB050-F248-11E8-B48F-1D18A9856A87
last_name: Shute
orcid: 0000-0002-1812-2810
citation:
ama: Shute AL. On the leading constant in the Manin-type conjecture for Campana
points. arXiv. doi:10.48550/arXiv.2104.14946
apa: Shute, A. L. (n.d.). On the leading constant in the Manin-type conjecture for
Campana points. arXiv. https://doi.org/10.48550/arXiv.2104.14946
chicago: Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for
Campana Points.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2104.14946.
ieee: A. L. Shute, “On the leading constant in the Manin-type conjecture for Campana
points,” arXiv. .
ista: Shute AL. On the leading constant in the Manin-type conjecture for Campana
points. arXiv, 2104.14946.
mla: Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana
Points.” ArXiv, 2104.14946, doi:10.48550/arXiv.2104.14946.
short: A.L. Shute, ArXiv (n.d.).
corr_author: '1'
das_tickbox: '0'
date_created: 2022-09-09T10:43:17Z
date_published: 2021-04-30T00:00:00Z
date_updated: 2026-08-19T12:54:58Z
day: '30'
department:
- _id: TiBr
doi: 10.48550/arXiv.2104.14946
external_id:
arxiv:
- '2104.14946'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2104.14946
month: '04'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: draft
related_material:
record:
- id: '12072'
relation: dissertation_contains
status: public
- id: '17058'
relation: later_version
status: public
researchdata_availability: no
status: public
supplementarymaterial: no
title: On the leading constant in the Manin-type conjecture for Campana points
type: preprint
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2021'
...
---
_id: '9558'
abstract:
- lang: eng
text: "We show that turbulent dynamics that arise in simulations of the three-dimensional
Navier--Stokes equations in a triply-periodic domain under sinusoidal forcing
can be described as transient visits to the neighborhoods of unstable time-periodic
solutions. Based on this description, we reduce the original system with more
than 10^5 degrees of freedom to a 17-node Markov chain where each node corresponds
to the neighborhood of a periodic orbit. The model accurately reproduces long-term
averages of the system's observables as weighted sums over the periodic orbits.\r\n"
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank the referees for improving this Letter with their comments.
We acknowledge stimulating discussions with\r\nH. Edelsbrunner. This work was supported
by Grant No. 662960 from the Simons Foundation (B. H.). The numerical calculations
were performed at TUBITAK ULAKBIM High Performance and Grid Computing Center (TRUBA
resources) and IST Austria High Performance Computing cluster."
article_number: '244502'
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Gökhan
full_name: Yalniz, Gökhan
id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425
last_name: Yalniz
orcid: 0000-0002-8490-9312
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
citation:
ama: Yalniz G, Hof B, Budanur NB. Coarse graining the state space of a turbulent
flow using periodic orbits. Physical Review Letters. 2021;126(24). doi:10.1103/PhysRevLett.126.244502
apa: Yalniz, G., Hof, B., & Budanur, N. B. (2021). Coarse graining the state
space of a turbulent flow using periodic orbits. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.126.244502
chicago: Yalniz, Gökhan, Björn Hof, and Nazmi B Budanur. “Coarse Graining the State
Space of a Turbulent Flow Using Periodic Orbits.” Physical Review Letters.
American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.126.244502.
ieee: G. Yalniz, B. Hof, and N. B. Budanur, “Coarse graining the state space of
a turbulent flow using periodic orbits,” Physical Review Letters, vol.
126, no. 24. American Physical Society, 2021.
ista: Yalniz G, Hof B, Budanur NB. 2021. Coarse graining the state space of a turbulent
flow using periodic orbits. Physical Review Letters. 126(24), 244502.
mla: Yalniz, Gökhan, et al. “Coarse Graining the State Space of a Turbulent Flow
Using Periodic Orbits.” Physical Review Letters, vol. 126, no. 24, 244502,
American Physical Society, 2021, doi:10.1103/PhysRevLett.126.244502.
short: G. Yalniz, B. Hof, N.B. Budanur, Physical Review Letters 126 (2021).
corr_author: '1'
date_created: 2021-06-16T15:45:36Z
date_published: 2021-06-18T00:00:00Z
date_updated: 2026-09-02T08:16:31Z
day: '18'
department:
- _id: GradSch
- _id: BjHo
doi: 10.1103/PhysRevLett.126.244502
external_id:
arxiv:
- '2007.02584'
isi:
- '000663310100008'
intvolume: ' 126'
isi: 1
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2007.02584
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 238598C6-32DE-11EA-91FC-C7463DDC885E
grant_number: '662960'
name: Revisiting the Turbulence Problem Using Statistical Mechanics
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/turbulent-flow-simplified/
record:
- id: '19591'
relation: popular_science
status: returned
- id: '19684'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Coarse graining the state space of a turbulent flow using periodic orbits
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 126
year: '2021'
...
---
_id: '8602'
abstract:
- lang: eng
text: Collective cell migration offers a rich field of study for non-equilibrium
physics and cellular biology, revealing phenomena such as glassy dynamics, pattern
formation and active turbulence. However, how mechanical and chemical signalling
are integrated at the cellular level to give rise to such collective behaviours
remains unclear. We address this by focusing on the highly conserved phenomenon
of spatiotemporal waves of density and extracellular signal-regulated kinase (ERK)
activation, which appear both in vitro and in vivo during collective cell migration
and wound healing. First, we propose a biophysical theory, backed by mechanical
and optogenetic perturbation experiments, showing that patterns can be quantitatively
explained by a mechanochemical coupling between active cellular tensions and the
mechanosensitive ERK pathway. Next, we demonstrate how this biophysical mechanism
can robustly induce long-ranged order and migration in a desired orientation,
and we determine the theoretically optimal wavelength and period for inducing
maximal migration towards free edges, which fits well with experimentally observed
dynamics. We thereby provide a bridge between the biophysical origin of spatiotemporal
instabilities and the design principles of robust and efficient long-ranged migration.
acknowledgement: We would like to thank G. Tkacik and all of the members of the Hannezo
and Hirashima groups for useful discussions, X. Trepat for help on traction force
microscopy and M. Matsuda for use of the lab facility. E.H. acknowledges grants
from the Austrian Science Fund (FWF) (P 31639) and the European Research Council
(851288). T.H. acknowledges a grant from JST, PRESTO (JPMJPR1949). This project
has received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement no. 665385 (to D.B.),
from JSPS KAKENHI grant no. 17J02107 (to N.H.) and from the SPIRITS 2018 of Kyoto
University (to E.H. and T.H.).
article_processing_charge: No
article_type: original
author:
- first_name: Daniel R
full_name: Boocock, Daniel R
id: 453AF628-F248-11E8-B48F-1D18A9856A87
last_name: Boocock
orcid: 0000-0002-1585-2631
- first_name: Naoya
full_name: Hino, Naoya
last_name: Hino
- first_name: Natalia
full_name: Ruzickova, Natalia
id: D2761128-D73D-11E9-A1BF-BA0DE6697425
last_name: Ruzickova
- first_name: Tsuyoshi
full_name: Hirashima, Tsuyoshi
last_name: Hirashima
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. Theory of mechanochemical
patterning and optimal migration in cell monolayers. Nature Physics. 2021;17:267-274.
doi:10.1038/s41567-020-01037-7
apa: Boocock, D. R., Hino, N., Ruzickova, N., Hirashima, T., & Hannezo, E. B.
(2021). Theory of mechanochemical patterning and optimal migration in cell monolayers.
Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-020-01037-7
chicago: Boocock, Daniel R, Naoya Hino, Natalia Ruzickova, Tsuyoshi Hirashima, and
Edouard B Hannezo. “Theory of Mechanochemical Patterning and Optimal Migration
in Cell Monolayers.” Nature Physics. Springer Nature, 2021. https://doi.org/10.1038/s41567-020-01037-7.
ieee: D. R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, and E. B. Hannezo, “Theory
of mechanochemical patterning and optimal migration in cell monolayers,” Nature
Physics, vol. 17. Springer Nature, pp. 267–274, 2021.
ista: Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. 2021. Theory of
mechanochemical patterning and optimal migration in cell monolayers. Nature Physics.
17, 267–274.
mla: Boocock, Daniel R., et al. “Theory of Mechanochemical Patterning and Optimal
Migration in Cell Monolayers.” Nature Physics, vol. 17, Springer Nature,
2021, pp. 267–74, doi:10.1038/s41567-020-01037-7.
short: D.R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, E.B. Hannezo, Nature Physics
17 (2021) 267–274.
corr_author: '1'
date_created: 2020-10-04T22:01:37Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2026-09-02T22:30:04Z
day: '01'
department:
- _id: EdHa
doi: 10.1038/s41567-020-01037-7
ec_funded: 1
external_id:
isi:
- '000573519500002'
intvolume: ' 17'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.05.15.096479
month: '02'
oa: 1
oa_version: Preprint
page: 267-274
project:
- _id: 268294B6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31639
name: Active mechano-chemical description of the cell cytoskeleton
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/wound-healing-waves/
record:
- id: '12964'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Theory of mechanochemical patterning and optimal migration in cell monolayers
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2021'
...
---
_id: '9817'
abstract:
- lang: eng
text: Elastic bending of initially flat slender elements allows the realization
and economic fabrication of intriguing curved shapes. In this work, we derive
an intuitive but rigorous geometric characterization of the design space of plane
elastic rods with variable stiffness. It enables designers to determine which
shapes are physically viable with active bending by visual inspection alone. Building
on these insights, we propose a method for efficiently designing the geometry
of a flat elastic rod that realizes a target equilibrium curve, which only requires
solving a linear program. We implement this method in an interactive computational
design tool that gives feedback about the feasibility of a design, and computes
the geometry of the structural elements necessary to realize it within an instant.
The tool also offers an iterative optimization routine that improves the fabricability
of a model while modifying it as little as possible. In addition, we use our geometric
characterization to derive an algorithm for analyzing and recovering the stability
of elastic curves that would otherwise snap out of their unstable equilibrium
shapes by buckling. We show the efficacy of our approach by designing and manufacturing
several physical models that are assembled from flat elements.
acknowledgement: "We thank the anonymous reviewers for their generous feedback, and
Michal Piovarči for his help in producing the supplemental video. This project has
received funding from the European Research Council (ERC) under the European Union’s
Horizon 2020 research and innovation programme (grant agreement No 715767).\r\n"
article_number: '126'
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: Hafner C, Bickel B. The design space of plane elastic curves. ACM Transactions
on Graphics. 2021;40(4). doi:10.1145/3450626.3459800
apa: 'Hafner, C., & Bickel, B. (2021). The design space of plane elastic curves.
ACM Transactions on Graphics. Virtual: Association for Computing Machinery.
https://doi.org/10.1145/3450626.3459800'
chicago: Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic
Curves.” ACM Transactions on Graphics. Association for Computing Machinery,
2021. https://doi.org/10.1145/3450626.3459800.
ieee: C. Hafner and B. Bickel, “The design space of plane elastic curves,” ACM
Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery,
2021.
ista: Hafner C, Bickel B. 2021. The design space of plane elastic curves. ACM Transactions
on Graphics. 40(4), 126.
mla: Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.”
ACM Transactions on Graphics, vol. 40, no. 4, 126, Association for Computing
Machinery, 2021, doi:10.1145/3450626.3459800.
short: C. Hafner, B. Bickel, ACM Transactions on Graphics 40 (2021).
conference:
end_date: 2021-08-13
location: Virtual
name: 'SIGGRAF: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2021-08-09
date_created: 2021-08-08T22:01:26Z
date_published: 2021-07-19T00:00:00Z
date_updated: 2026-09-02T22:30:05Z
day: '19'
ddc:
- '516'
department:
- _id: BeBi
doi: 10.1145/3450626.3459800
ec_funded: 1
external_id:
isi:
- '000674930900091'
file:
- access_level: open_access
checksum: 7e5d08ce46b0451b3102eacd3d00f85f
content_type: application/pdf
creator: chafner
date_created: 2021-10-18T10:42:15Z
date_updated: 2021-10-18T10:42:15Z
file_id: '10150'
file_name: elastic-curves-paper.pdf
file_size: 17064290
relation: main_file
success: 1
- access_level: open_access
checksum: 0088643478be7c01a703b5b10767348f
content_type: application/pdf
creator: chafner
date_created: 2021-10-18T10:42:22Z
date_updated: 2021-10-18T10:42:22Z
file_id: '10151'
file_name: elastic-curves-supp.pdf
file_size: 547156
relation: supplementary_material
file_date_updated: 2021-10-18T10:42:22Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '4'
keyword:
- Computing methodologies
- shape modeling
- modeling and simulation
- theory of computation
- computational geometry
- mathematics of computing
- mathematical optimization
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/designing-with-elastic-structures/
record:
- id: '12897'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The design space of plane elastic curves
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: 40
year: '2021'
...
---
_id: '9429'
abstract:
- lang: eng
text: De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3
lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency
leads to motor coordination deficits as well as ASD-relevant social and cognitive
impairments. However, induction of Cul3 haploinsufficiency later in life does
not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during
a critical developmental window. Here we show that Cul3 is essential to regulate
neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice
display cortical lamination abnormalities. At the molecular level, we found that
Cul3 controls neuronal migration by tightly regulating the amount of Plastin3
(Pls3), a previously unrecognized player of neural migration. Furthermore, we
found that Pls3 cell-autonomously regulates cell migration by regulating actin
cytoskeleton organization, and its levels are inversely proportional to neural
migration speed. Finally, we provide evidence that cellular phenotypes associated
with autism-linked gene haploinsufficiency can be rescued by transcriptional activation
of the intact allele in vitro, offering a proof of concept for a potential therapeutic
approach for ASDs.
acknowledged_ssus:
- _id: PreCl
acknowledgement: We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A.
Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the
management of our animal colony, as well as M. Schunn and the Preclinical Facility
team for technical assistance. We thank K. Heesom and her team at the University
of Bristol Proteomics Facility for the proteomics sample preparation, data generation,
and analysis support. We thank Y. B. Simon for kindly providing the plasmid for
lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration
and the fruitful discussions. This work was supported by the ISTPlus postdoctoral
fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon
2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by
the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D
(I3600-B27).
article_number: '3058'
article_processing_charge: No
article_type: original
author:
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
- first_name: Lena A
full_name: Schwarz, Lena A
id: 29A8453C-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Saren
full_name: Tasciyan, Saren
id: 4323B49C-F248-11E8-B48F-1D18A9856A87
last_name: Tasciyan
orcid: 0000-0003-1671-393X
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Lisa
full_name: Knaus, Lisa
id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87
last_name: Knaus
- first_name: Zoe
full_name: Dobler, Zoe
id: D23090A2-9057-11EA-883A-A8396FC7A38F
last_name: Dobler
- first_name: Emanuele
full_name: Cacci, Emanuele
last_name: Cacci
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein
homeostasis and cell migration during a critical window of brain development.
Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23123-x
apa: Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A.,
Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis
and cell migration during a critical window of brain development. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-021-23123-x
chicago: Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan,
Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton
Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.”
Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23123-x.
ieee: J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis
and cell migration during a critical window of brain development,” Nature Communications,
vol. 12, no. 1. Springer Nature, 2021.
ista: Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer
CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino
G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during
a critical window of brain development. Nature Communications. 12(1), 3058.
mla: Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis
and Cell Migration during a Critical Window of Brain Development.” Nature Communications,
vol. 12, no. 1, 3058, Springer Nature, 2021, doi:10.1038/s41467-021-23123-x.
short: J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas,
C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur,
J.G. Danzl, G. Novarino, Nature Communications 12 (2021).
corr_author: '1'
date_created: 2021-05-28T11:49:46Z
date_published: 2021-05-24T00:00:00Z
date_updated: 2026-09-02T22:30:09Z
day: '24'
ddc:
- '572'
department:
- _id: GaNo
- _id: JoDa
- _id: FlSc
- _id: MiSi
- _id: LifeSc
- _id: Bio
doi: 10.1038/s41467-021-23123-x
ec_funded: 1
external_id:
isi:
- '000658769900010'
file:
- access_level: open_access
checksum: 337e0f7959c35ec959984cacdcb472ba
content_type: application/pdf
creator: kschuh
date_created: 2021-05-28T12:39:43Z
date_updated: 2021-05-28T12:39:43Z
file_id: '9430'
file_name: 2021_NatureCommunications_Morandell.pdf
file_size: 9358599
relation: main_file
success: 1
file_date_updated: 2021-05-28T12:39:43Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232
name: Molecular Drug Targets
- _id: 05A0D778-7A3F-11EA-A408-12923DDC885E
grant_number: F7807
name: Stem Cell Modulation in Neural Development and Regeneration/ P07-Neural stem
cells in autism and epilepsy
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: press_release
url: https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/
record:
- id: '19557'
relation: dissertation_contains
status: public
- id: '7800'
relation: earlier_version
status: public
- id: '12401'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Cul3 regulates cytoskeleton protein homeostasis and cell migration during a
critical window of brain development
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '8966'
abstract:
- lang: eng
text: During development, a single cell is transformed into a highly complex organism
through progressive cell division, specification and rearrangement. An important
prerequisite for the emergence of patterns within the developing organism is to
establish asymmetries at various scales, ranging from individual cells to the
entire embryo, eventually giving rise to the different body structures. This becomes
especially apparent during gastrulation, when the earliest major lineage restriction
events lead to the formation of the different germ layers. Traditionally, the
unfolding of the developmental program from symmetry breaking to germ layer formation
has been studied by dissecting the contributions of different signaling pathways
and cellular rearrangements in the in vivo context of intact embryos. Recent efforts,
using the intrinsic capacity of embryonic stem cells to self-assemble and generate
embryo-like structures de novo, have opened new avenues for understanding the
many ways by which an embryo can be built and the influence of extrinsic factors
therein. Here, we discuss and compare divergent and conserved strategies leading
to germ layer formation in embryos as compared to in vitro systems, their upstream
molecular cascades and the role of extrinsic factors in this process.
acknowledgement: We thank Nicoletta Petridou, Diana Pinheiro, Cornelia Schwayer and
Stefania Tavano for feedback on the manuscript. Research in the Heisenberg lab is
supported by an ERC Advanced Grant (MECSPEC 742573) to C.-P.H. A.S. is a recipient
of a DOC Fellowship of the Austrian Academy of Science.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Schauer A, Heisenberg C-PJ. Reassembling gastrulation. Developmental Biology.
2021;474:71-81. doi:10.1016/j.ydbio.2020.12.014
apa: Schauer, A., & Heisenberg, C.-P. J. (2021). Reassembling gastrulation.
Developmental Biology. Elsevier. https://doi.org/10.1016/j.ydbio.2020.12.014
chicago: Schauer, Alexandra, and Carl-Philipp J Heisenberg. “Reassembling Gastrulation.”
Developmental Biology. Elsevier, 2021. https://doi.org/10.1016/j.ydbio.2020.12.014.
ieee: A. Schauer and C.-P. J. Heisenberg, “Reassembling gastrulation,” Developmental
Biology, vol. 474. Elsevier, pp. 71–81, 2021.
ista: Schauer A, Heisenberg C-PJ. 2021. Reassembling gastrulation. Developmental
Biology. 474, 71–81.
mla: Schauer, Alexandra, and Carl-Philipp J. Heisenberg. “Reassembling Gastrulation.”
Developmental Biology, vol. 474, Elsevier, 2021, pp. 71–81, doi:10.1016/j.ydbio.2020.12.014.
short: A. Schauer, C.-P.J. Heisenberg, Developmental Biology 474 (2021) 71–81.
date_created: 2020-12-22T09:53:34Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2026-09-02T22:30:13Z
day: '01'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1016/j.ydbio.2020.12.014
ec_funded: 1
external_id:
isi:
- '000639461800008'
pmid:
- '33352181'
file:
- access_level: open_access
checksum: fa2a5731fd16ab171b029f32f031c440
content_type: application/pdf
creator: kschuh
date_created: 2021-08-11T10:28:06Z
date_updated: 2021-08-11T10:28:06Z
file_id: '9880'
file_name: 2021_DevBiology_Schauer.pdf
file_size: 1440321
relation: main_file
success: 1
file_date_updated: 2021-08-11T10:28:06Z
has_accepted_license: '1'
intvolume: ' 474'
isi: 1
keyword:
- Developmental Biology
- Cell Biology
- Molecular Biology
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 71-81
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 26B1E39C-B435-11E9-9278-68D0E5697425
grant_number: '25239'
name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues'
publication: Developmental Biology
publication_identifier:
issn:
- 0012-1606
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '12891'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Reassembling gastrulation
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: 474
year: '2021'
...
---
_id: '9349'
abstract:
- lang: eng
text: 'The way in which interactions between mechanics and biochemistry lead to
the emergence of complex cell and tissue organization is an old question that
has recently attracted renewed interest from biologists, physicists, mathematicians
and computer scientists. Rapid advances in optical physics, microscopy and computational
image analysis have greatly enhanced our ability to observe and quantify spatiotemporal
patterns of signalling, force generation, deformation, and flow in living cells
and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation
are allowing us to perturb the underlying machinery that generates these patterns
in increasingly sophisticated ways. Rapid advances in theory and computing have
made it possible to construct predictive models that describe how cell and tissue
organization and dynamics emerge from the local coupling of biochemistry and mechanics.
Together, these advances have opened up a wealth of new opportunities to explore
how mechanochemical patterning shapes organismal development. In this roadmap,
we present a series of forward-looking case studies on mechanochemical patterning
in development, written by scientists working at the interface between the physical
and biological sciences, and covering a wide range of spatial and temporal scales,
organisms, and modes of development. Together, these contributions highlight the
many ways in which the dynamic coupling of mechanics and biochemistry shapes biological
dynamics: from mechanoenzymes that sense force to tune their activity and motor
output, to collectives of cells in tissues that flow and redistribute biochemical
signals during development.'
acknowledgement: The AK group is supported by IST Austria and by the ERC under European
Union Horizon 2020 research and innovation programme Grant 680037. Apologies to
those whose work could not be mentioned due to limited space. We thank all my lab
members, both past and present, for stimulating discussion. This work was funded
by a Singapore Ministry of Education Tier 3 Grant, MOE2016-T3-1-005. We thank Francis
Corson for continuous discussion and collaboration contributing to these views and
for figure 4(A). PC is sponsored by the Institut Pasteur and the European Union's
Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie
Grant Agreement No. 665807. Research in JG's laboratory is funded by the European
Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC
Grant Agreement No. 337635, Institut Pasteur, CNRS, Cercle FSER, Fondation pour
la Recherche Medicale, the Vallee Foundation and the ANR-19-CE-13-0024 Grant. We
thank Erez Braun and Alex Mogilner for comments on the manuscript and Niv Ierushalmi
for help with figure 5. This project has received funding from the European Union's
Horizon 2020 research and innovation programme under Grant Agreement No. ERC-2018-COG
Grant 819174-HydraMechanics awarded to KK. EH thanks all lab members, as well as
Pierre Recho, Tsuyoshi Hirashima, Diana Pinheiro and Carl-Philip Heisenberg, for
fruitful discussions on these topics—and apologize for not being able to cite many
very relevant publications due to the strict 10-reference limit. EH acknowledges
the support of Austrian Science Fund (FWF) (P 31639) and the European Research Council
under the European Union's Horizon 2020 Research and Innovation Programme Grant
Agreements (851288). The authors acknowledge the inspiring scientists whose work
could not be cited in this perspective due to space constraints; the members of
the Gartner Lab for helpful discussions; the Barbara and Gerson Bakar Foundation,
the Chan Zuckerberg Biohub Investigators Programme, the National Institute of Health,
and the Centre for Cellular Construction, an NSF Science and Technology Centre.
The Minc laboratory is currently funded by the CNRS and the European Research Council
(CoG Forcaster No. 647073). Research in the lab of J-LM is supported by the Institut
Curie, the Centre National de la Recherche Scientifique (CNRS), the Institut National
de la Santé Et de la Recherche Médicale (INSERM), and is funded by grants from the
ATIP-Avenir programme, the Fondation Schlumberger pour l'Éducation et la Recherche
via the Fondation pour la Recherche Médicale, the European Research Council Starting
Grant ERC-2017-StG 757557, the European Molecular Biology Organization Young Investigator
programme (EMBO YIP), the INSERM transversal programme Human Development Cell Atlas
(HuDeCA), Paris Sciences Lettres (PSL) 'nouvelle équipe' and QLife (17-CONV-0005)
grants and Labex DEEP (ANR-11-LABX-0044) which are part of the IDEX PSL (ANR-10-IDEX-0001-02).
We acknowledge useful discussions with Massimo Vergassola, Sebastian Streichan and
my lab members. Work in my laboratory on Drosophila embryogenesis is partly supported
by NIH-R01GM122936. The authors acknowledge the support by a grant from the European
Research Council (Grant No. 682161). Lenne group is funded by a grant from the 'Investissements
d'Avenir' French Government programme managed by the French National Research Agency
(ANR-16-CONV-0001) and by the Excellence Initiative of Aix-Marseille University—A*MIDEX,
and ANR projects MechaResp (ANR-17-CE13-0032) and AdGastrulo (ANR-19-CE13-0022).
article_number: '041501'
article_processing_charge: No
article_type: original
author:
- first_name: Pierre François
full_name: Lenne, Pierre François
last_name: Lenne
- first_name: Edwin
full_name: Munro, Edwin
last_name: Munro
- first_name: Idse
full_name: Heemskerk, Idse
last_name: Heemskerk
- first_name: Aryeh
full_name: Warmflash, Aryeh
last_name: Warmflash
- first_name: Laura
full_name: Bocanegra, Laura
id: 4896F754-F248-11E8-B48F-1D18A9856A87
last_name: Bocanegra
- first_name: Kasumi
full_name: Kishi, Kasumi
id: 3065DFC4-F248-11E8-B48F-1D18A9856A87
last_name: Kishi
orcid: 0000-0001-6060-4795
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Yuchen
full_name: Long, Yuchen
last_name: Long
- first_name: Antoine
full_name: Fruleux, Antoine
last_name: Fruleux
- first_name: Arezki
full_name: Boudaoud, Arezki
last_name: Boudaoud
- first_name: Timothy E.
full_name: Saunders, Timothy E.
last_name: Saunders
- first_name: Paolo
full_name: Caldarelli, Paolo
last_name: Caldarelli
- first_name: Arthur
full_name: Michaut, Arthur
last_name: Michaut
- first_name: Jerome
full_name: Gros, Jerome
last_name: Gros
- first_name: Yonit
full_name: Maroudas-Sacks, Yonit
last_name: Maroudas-Sacks
- first_name: Kinneret
full_name: Keren, Kinneret
last_name: Keren
- 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: Zev J.
full_name: Gartner, Zev J.
last_name: Gartner
- first_name: Benjamin
full_name: Stormo, Benjamin
last_name: Stormo
- first_name: Amy
full_name: Gladfelter, Amy
last_name: Gladfelter
- first_name: Alan
full_name: Rodrigues, Alan
last_name: Rodrigues
- first_name: Amy
full_name: Shyer, Amy
last_name: Shyer
- first_name: Nicolas
full_name: Minc, Nicolas
last_name: Minc
- first_name: Jean Léon
full_name: Maître, Jean Léon
last_name: Maître
- first_name: Stefano
full_name: Di Talia, Stefano
last_name: Di Talia
- first_name: Bassma
full_name: Khamaisi, Bassma
last_name: Khamaisi
- first_name: David
full_name: Sprinzak, David
last_name: Sprinzak
- first_name: Sham
full_name: Tlili, Sham
last_name: Tlili
citation:
ama: Lenne PF, Munro E, Heemskerk I, et al. Roadmap for the multiscale coupling
of biochemical and mechanical signals during development. Physical biology.
2021;18(4). doi:10.1088/1478-3975/abd0db
apa: Lenne, P. F., Munro, E., Heemskerk, I., Warmflash, A., Bocanegra, L., Kishi,
K., … Tlili, S. (2021). Roadmap for the multiscale coupling of biochemical and
mechanical signals during development. Physical Biology. IOP Publishing.
https://doi.org/10.1088/1478-3975/abd0db
chicago: Lenne, Pierre François, Edwin Munro, Idse Heemskerk, Aryeh Warmflash, Laura
Bocanegra, Kasumi Kishi, Anna Kicheva, et al. “Roadmap for the Multiscale Coupling
of Biochemical and Mechanical Signals during Development.” Physical Biology.
IOP Publishing, 2021. https://doi.org/10.1088/1478-3975/abd0db.
ieee: P. F. Lenne et al., “Roadmap for the multiscale coupling of biochemical
and mechanical signals during development,” Physical biology, vol. 18,
no. 4. IOP Publishing, 2021.
ista: Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra L, Kishi K, Kicheva
A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J,
Maroudas-Sacks Y, Keren K, Hannezo EB, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues
A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. 2021.
Roadmap for the multiscale coupling of biochemical and mechanical signals during
development. Physical biology. 18(4), 041501.
mla: Lenne, Pierre François, et al. “Roadmap for the Multiscale Coupling of Biochemical
and Mechanical Signals during Development.” Physical Biology, vol. 18,
no. 4, 041501, IOP Publishing, 2021, doi:10.1088/1478-3975/abd0db.
short: P.F. Lenne, E. Munro, I. Heemskerk, A. Warmflash, L. Bocanegra, K. Kishi,
A. Kicheva, Y. Long, A. Fruleux, A. Boudaoud, T.E. Saunders, P. Caldarelli, A.
Michaut, J. Gros, Y. Maroudas-Sacks, K. Keren, E.B. Hannezo, Z.J. Gartner, B.
Stormo, A. Gladfelter, A. Rodrigues, A. Shyer, N. Minc, J.L. Maître, S. Di Talia,
B. Khamaisi, D. Sprinzak, S. Tlili, Physical Biology 18 (2021).
date_created: 2021-04-25T22:01:29Z
date_published: 2021-04-14T00:00:00Z
date_updated: 2026-09-02T22:30:15Z
day: '14'
ddc:
- '570'
department:
- _id: AnKi
- _id: EdHa
doi: 10.1088/1478-3975/abd0db
ec_funded: 1
external_id:
isi:
- '000640396400001'
pmid:
- '33276350'
file:
- access_level: open_access
checksum: 4f52082549d3561c4c15d4d8d84ca5d8
content_type: application/pdf
creator: cziletti
date_created: 2021-04-27T08:38:35Z
date_updated: 2021-04-27T08:38:35Z
file_id: '9355'
file_name: 2021_PhysBio_Lenne.pdf
file_size: 6296324
relation: main_file
success: 1
file_date_updated: 2021-04-27T08:38:35Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
- _id: 268294B6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31639
name: Active mechano-chemical description of the cell cytoskeleton
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Physical biology
publication_identifier:
eissn:
- 1478-3975
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
related_material:
record:
- id: '13081'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Roadmap for the multiscale coupling of biochemical and mechanical signals during
development
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2021'
...
---
OA_place: publisher
OA_type: hybrid
_id: '7883'
abstract:
- lang: eng
text: All vertebrates have a spinal cord with dimensions and shape specific to their
species. Yet how species‐specific organ size and shape are achieved is a fundamental
unresolved question in biology. The formation and sculpting of organs begins during
embryonic development. As it develops, the spinal cord extends in anterior–posterior
direction in synchrony with the overall growth of the body. The dorsoventral (DV)
and apicobasal lengths of the spinal cord neuroepithelium also change, while at
the same time a characteristic pattern of neural progenitor subtypes along the
DV axis is established and elaborated. At the basis of these changes in tissue
size and shape are biophysical determinants, such as the change in cell number,
cell size and shape, and anisotropic tissue growth. These processes are controlled
by global tissue‐scale regulators, such as morphogen signaling gradients as well
as mechanical forces. Current challenges in the field are to uncover how these
tissue‐scale regulatory mechanisms are translated to the cellular and molecular
level, and how regulation of distinct cellular processes gives rise to an overall
defined size. Addressing these questions will help not only to achieve a better
understanding of how size is controlled, but also of how tissue size is coordinated
with the specification of pattern.
acknowledgement: 'Austrian Academy of Sciences, Grant/Award Number: DOC fellowship
for Katarzyna Kuzmicz-Kowalska; Austrian Science Fund, Grant/Award Number: F78 (Stem
Cell Modulation); H2020 European Research Council, Grant/Award Number: 680037'
article_number: e383
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Katarzyna
full_name: Kuzmicz-Kowalska, Katarzyna
id: 4CED352A-F248-11E8-B48F-1D18A9856A87
last_name: Kuzmicz-Kowalska
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: 'Kuzmicz-Kowalska K, Kicheva A. Regulation of size and scale in vertebrate
spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology.
2021. doi:10.1002/wdev.383'
apa: 'Kuzmicz-Kowalska, K., & Kicheva, A. (2021). Regulation of size and scale
in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental
Biology. Wiley. https://doi.org/10.1002/wdev.383'
chicago: 'Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and
Scale in Vertebrate Spinal Cord Development.” Wiley Interdisciplinary Reviews:
Developmental Biology. Wiley, 2021. https://doi.org/10.1002/wdev.383.'
ieee: 'K. Kuzmicz-Kowalska and A. Kicheva, “Regulation of size and scale in vertebrate
spinal cord development,” Wiley Interdisciplinary Reviews: Developmental Biology.
Wiley, 2021.'
ista: 'Kuzmicz-Kowalska K, Kicheva A. 2021. Regulation of size and scale in vertebrate
spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology.,
e383.'
mla: 'Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale
in Vertebrate Spinal Cord Development.” Wiley Interdisciplinary Reviews: Developmental
Biology, e383, Wiley, 2021, doi:10.1002/wdev.383.'
short: 'K. Kuzmicz-Kowalska, A. Kicheva, Wiley Interdisciplinary Reviews: Developmental
Biology (2021).'
corr_author: '1'
date_created: 2020-05-24T22:01:00Z
date_published: 2021-04-15T00:00:00Z
date_updated: 2026-09-02T22:30:16Z
day: '15'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1002/wdev.383
ec_funded: 1
external_id:
isi:
- '000531419400001'
pmid:
- '32391980'
file:
- access_level: open_access
checksum: f0a7745d48afa09ea7025e876a0145a8
content_type: application/pdf
creator: dernst
date_created: 2020-11-24T13:11:39Z
date_updated: 2020-11-24T13:11:39Z
file_id: '8800'
file_name: 2020_WIREs_DevBio_KuzmiczKowalska.pdf
file_size: 2527276
relation: main_file
success: 1
file_date_updated: 2020-11-24T13:11:39Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
- _id: 267AF0E4-B435-11E9-9278-68D0E5697425
name: The role of morphogens in the regulation of neural tube growth
- _id: 059DF620-7A3F-11EA-A408-12923DDC885E
grant_number: F7802
name: Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen
control of growth and pattern in the spinal cord
publication: 'Wiley Interdisciplinary Reviews: Developmental Biology'
publication_identifier:
eissn:
- 1759-7692
issn:
- 1759-7684
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '14323'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Regulation of size and scale in vertebrate spinal cord development
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9250'
abstract:
- lang: eng
text: Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry
occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides
and parasitic reactions that are caused by the highly reactive singlet oxygen
(1O2). Redox mediators are recognized to be key for improving rechargeability.
However, it is unclear how they affect 1O2 formation, which hinders strategies
for their improvement. Here we clarify the mechanism of mediated peroxide and
superoxide oxidation and thus explain how redox mediators either enhance or suppress
1O2 formation. We show that charging commences with peroxide oxidation to a superoxide
intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution
from superoxide oxidation, while disproportionation always generates some 1O2.
We find that 1O2 suppression requires oxidation to be faster than the generation
of 1O2 from disproportionation. Oxidation rates decrease with growing driving
force following Marcus inverted-region behaviour, establishing a region of maximum
rate.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: S.A.F. is indebted to the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (grant agreement
No. 636069) as well as IST Austria. O.F thanks the French National Research Agency
(STORE-EX Labex Project ANR-10-LABX-76-01). We thank EL-Cell GmbH (Hamburg, Germany)
for the pressure test cell. We thank R. Saf for help with the mass spectrometry,
J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH, G. Strohmeier
and R. Fürst for HPLC measurements and S. Mondal and S. Stadlbauer for kinetic measurements.
article_processing_charge: No
article_type: original
author:
- first_name: Yann K.
full_name: Petit, Yann K.
last_name: Petit
- first_name: Eléonore
full_name: Mourad, Eléonore
last_name: Mourad
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
- first_name: Christian
full_name: Leypold, Christian
last_name: Leypold
- first_name: Andreas
full_name: Windischbacher, Andreas
last_name: Windischbacher
- first_name: Daniel
full_name: Mijailovic, Daniel
last_name: Mijailovic
- first_name: Christian
full_name: Slugovc, Christian
last_name: Slugovc
- first_name: Sergey M.
full_name: Borisov, Sergey M.
last_name: Borisov
- first_name: Egbert
full_name: Zojer, Egbert
last_name: Zojer
- first_name: Sergio
full_name: Brutti, Sergio
last_name: Brutti
- first_name: Olivier
full_name: Fontaine, Olivier
last_name: Fontaine
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide
oxidation and triplet versus singlet oxygen formation. Nature Chemistry.
2021;13(5):465-471. doi:10.1038/s41557-021-00643-z
apa: Petit, Y. K., Mourad, E., Prehal, C., Leypold, C., Windischbacher, A., Mijailovic,
D., … Freunberger, S. A. (2021). Mechanism of mediated alkali peroxide oxidation
and triplet versus singlet oxygen formation. Nature Chemistry. Springer
Nature. https://doi.org/10.1038/s41557-021-00643-z
chicago: Petit, Yann K., Eléonore Mourad, Christian Prehal, Christian Leypold, Andreas
Windischbacher, Daniel Mijailovic, Christian Slugovc, et al. “Mechanism of Mediated
Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” Nature
Chemistry. Springer Nature, 2021. https://doi.org/10.1038/s41557-021-00643-z.
ieee: Y. K. Petit et al., “Mechanism of mediated alkali peroxide oxidation
and triplet versus singlet oxygen formation,” Nature Chemistry, vol. 13,
no. 5. Springer Nature, pp. 465–471, 2021.
ista: Petit YK, Mourad E, Prehal C, Leypold C, Windischbacher A, Mijailovic D, Slugovc
C, Borisov SM, Zojer E, Brutti S, Fontaine O, Freunberger SA. 2021. Mechanism
of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation.
Nature Chemistry. 13(5), 465–471.
mla: Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and
Triplet versus Singlet Oxygen Formation.” Nature Chemistry, vol. 13, no.
5, Springer Nature, 2021, pp. 465–71, doi:10.1038/s41557-021-00643-z.
short: Y.K. Petit, E. Mourad, C. Prehal, C. Leypold, A. Windischbacher, D. Mijailovic,
C. Slugovc, S.M. Borisov, E. Zojer, S. Brutti, O. Fontaine, S.A. Freunberger,
Nature Chemistry 13 (2021) 465–471.
corr_author: '1'
date_created: 2021-03-16T11:12:20Z
date_published: 2021-03-15T00:00:00Z
date_updated: 2024-10-09T21:00:28Z
day: '15'
ddc:
- '540'
department:
- _id: StFr
doi: 10.1038/s41557-021-00643-z
external_id:
isi:
- '000629296400001'
pmid:
- '33723377'
file:
- access_level: open_access
checksum: 3ee3f8dd79ed1b7bb0929fce184c8012
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T11:46:00Z
date_updated: 2021-09-16T22:30:03Z
embargo: 2021-09-15
file_id: '9276'
file_name: 2021_NatureChem_Petit_acceptedVersion.pdf
file_size: 1811448
relation: main_file
file_date_updated: 2021-09-16T22:30:03Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '5'
keyword:
- General Chemistry
- General Chemical Engineering
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 465-471
pmid: 1
publication: Nature Chemistry
publication_identifier:
eissn:
- 1755-4349
issn:
- 1755-4330
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanism of mediated alkali peroxide oxidation and triplet versus singlet
oxygen formation
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13
year: '2021'
...
---
_id: '9438'
abstract:
- lang: eng
text: Rigorous investigation of synaptic transmission requires analysis of unitary
synaptic events by simultaneous recording from presynaptic terminals and postsynaptic
target neurons. However, this has been achieved at only a limited number of model
synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical
presynaptic terminals have been largely inaccessible to direct presynaptic recording,
due to their small size. Here, we describe a protocol for improved subcellular
patch-clamp recording in rat and mouse brain slices, with the synapse in a largely
intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc
morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals
are stimulated minimally invasively in the bouton-attached configuration, in which
the cytoplasmic content remains unperturbed, or in the whole-bouton configuration,
in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic
recordings can be integrated with biocytin labeling and morphological analysis,
allowing correlative investigation of synapse structure and function. Paired recordings
can be obtained from mossy fiber terminals in slices from both rats and mice,
implying applicability to genetically modified synapses. Paired recordings can
also be performed together with axon tract stimulation or optogenetic activation,
allowing comparison of unitary and compound synaptic events in the same target
cell. Finally, paired recordings can be combined with spontaneous event analysis,
permitting collection of miniature events generated at a single identified synapse.
In conclusion, the subcellular patch-clamp techniques detailed here should facilitate
analysis of biophysics, plasticity and circuit function of cortical synapses in
the mammalian central nervous system.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: This project received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement no. 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen
Forschung (Z 312-B27, Wittgenstein award to P.J., V 739-B27 to C.B.M.). We are grateful
to F. Marr and C. Altmutter for excellent technical assistance and cell reconstruction,
E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST
Austria, especially T. Asenov and Miba machine shop, for maximally efficient support.
article_processing_charge: No
article_type: original
author:
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Yuji
full_name: Okamoto, Yuji
id: 3337E116-F248-11E8-B48F-1D18A9856A87
last_name: Okamoto
orcid: 0000-0003-0408-6094
- first_name: Carolina
full_name: Borges Merjane, Carolina
id: 4305C450-F248-11E8-B48F-1D18A9856A87
last_name: Borges Merjane
orcid: 0000-0003-0005-401X
- first_name: Victor M
full_name: Vargas Barroso, Victor M
id: 2F55A9DE-F248-11E8-B48F-1D18A9856A87
last_name: Vargas Barroso
- first_name: Benjamin
full_name: Suter, Benjamin
id: 4952F31E-F248-11E8-B48F-1D18A9856A87
last_name: Suter
orcid: 0000-0002-9885-6936
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas
PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous
pre- and postsynaptic recording at cortical synapses. Nature Protocols.
2021;16(6):2947–2967. doi:10.1038/s41596-021-00526-0
apa: Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter,
B., & Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton
stimulation and simultaneous pre- and postsynaptic recording at cortical synapses.
Nature Protocols. Springer Nature. https://doi.org/10.1038/s41596-021-00526-0
chicago: Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas
Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques
for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording
at Cortical Synapses.” Nature Protocols. Springer Nature, 2021. https://doi.org/10.1038/s41596-021-00526-0.
ieee: D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter,
and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation
and simultaneous pre- and postsynaptic recording at cortical synapses,” Nature
Protocols, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021.
ista: Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas
PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and
simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols.
16(6), 2947–2967.
mla: Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton
Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.”
Nature Protocols, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967,
doi:10.1038/s41596-021-00526-0.
short: D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter,
P.M. Jonas, Nature Protocols 16 (2021) 2947–2967.
corr_author: '1'
date_created: 2021-05-30T22:01:24Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2025-04-22T22:30:43Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/s41596-021-00526-0
ec_funded: 1
external_id:
isi:
- '000650528700003'
pmid:
- '33990799'
file:
- access_level: open_access
checksum: 7eb580abd8893cdb0b410cf41bc8c263
content_type: application/pdf
creator: cziletti
date_created: 2021-07-08T12:27:55Z
date_updated: 2021-12-02T23:30:05Z
embargo: 2021-12-01
file_id: '9639'
file_name: VandaeletalAuthorVersion2021.pdf
file_size: 38574802
relation: main_file
file_date_updated: 2021-12-02T23:30:05Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 2947–2967
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
- _id: 2696E7FE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: V00739
name: Structural plasticity at mossy fiber-CA3 synapses
publication: Nature Protocols
publication_identifier:
eissn:
- 1750-2799
issn:
- 1754-2189
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous
pre- and postsynaptic recording at cortical synapses
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2021'
...
---
_id: '9428'
abstract:
- lang: eng
text: Thermalization is the inevitable fate of many complex quantum systems, whose
dynamics allow them to fully explore the vast configuration space regardless of
the initial state---the behaviour known as quantum ergodicity. In a quest for
experimental realizations of coherent long-time dynamics, efforts have focused
on ergodicity-breaking mechanisms, such as integrability and localization. The
recent discovery of persistent revivals in quantum simulators based on Rydberg
atoms have pointed to the existence of a new type of behaviour where the system
rapidly relaxes for most initial conditions, while certain initial states give
rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body
scarring’by analogy with a related form of weak ergodicity breaking that occurs
for a single particle inside a stadium billiard potential. In this Review, we
provide a pedagogical introduction to quantum many-body scars and highlight the
emerging connections with the semiclassical quantization of many-body systems.
We discuss the relation between scars and more general routes towards weak violations
of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight
possible applications of scars in quantum technology.
acknowledgement: We thank our collaborators K. Bull, S. Choi, J.-Y. Desaules, W. W.
Ho, A. Hudomal, M. Lukin, I. Martin, H. Pichler, N. Regnault, I. Vasić and in particular
A. Michailidis and C. Turner, without whom this work would not have been possible.
We also benefited from discussions with E. Altman, B. A. Bernevig, A. Chandran,
P. Fendley, V. Khemani and L. Motrunich. M.S. was supported by the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement no. 850899). D.A.A. was supported by the Swiss National Science
Foundation and by the ERC under the European Union’s Horizon 2020 research and innovation
programme (grant agreement no. 864597). Z.P. acknowledges support by the Leverhulme
Trust Research Leadership Award RL-2019-015.
article_processing_charge: No
article_type: review
arxiv: 1
author:
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
citation:
ama: Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of
ergodicity. Nature Physics. 2021;17(6):675–685. doi:10.1038/s41567-021-01230-2
apa: Serbyn, M., Abanin, D. A., & Papić, Z. (2021). Quantum many-body scars
and weak breaking of ergodicity. Nature Physics. Nature Research. https://doi.org/10.1038/s41567-021-01230-2
chicago: Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body
Scars and Weak Breaking of Ergodicity.” Nature Physics. Nature Research,
2021. https://doi.org/10.1038/s41567-021-01230-2.
ieee: M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking
of ergodicity,” Nature Physics, vol. 17, no. 6. Nature Research, pp. 675–685,
2021.
ista: Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking
of ergodicity. Nature Physics. 17(6), 675–685.
mla: Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.”
Nature Physics, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:10.1038/s41567-021-01230-2.
short: M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.
date_created: 2021-05-28T09:03:50Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2025-04-14T07:52:09Z
day: '01'
ddc:
- '539'
department:
- _id: MaSe
doi: 10.1038/s41567-021-01230-2
ec_funded: 1
external_id:
arxiv:
- '2011.09486'
isi:
- '000655563800002'
file:
- access_level: open_access
checksum: 316ed42ea1b42b0f1a3025bb476266fc
content_type: application/pdf
creator: patrickd
date_created: 2021-09-20T09:27:43Z
date_updated: 2021-12-02T23:30:03Z
embargo: 2021-12-01
file_id: '10026'
file_name: RevisedQMBSreview.pdf
file_size: 10028836
relation: main_file
file_date_updated: 2021-12-02T23:30:03Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Preprint
page: 675–685
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
publication_status: published
publisher: Nature Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum many-body scars and weak breaking of ergodicity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2021'
...