---
_id: '10422'
abstract:
- lang: eng
text: Those who aim to devise new materials with desirable properties usually examine
present methods first. However, they will find out that some approaches can exist
only conceptually without high chances to become practically useful. It seems
that a numerical technique called automatic differentiation together with increasing
supply of computational accelerators will soon shift many methods of the material
design from the category ”unimaginable” to the category ”expensive but possible”.
Approach we suggest is not an exception. Our overall goal is to have an efficient
and generalizable approach allowing to solve inverse design problems. In this
thesis we scratch its surface. We consider jammed systems of identical particles.
And ask ourselves how the shape of those particles (or the parameters codifying
it) may affect mechanical properties of the system. An indispensable part of reaching
the answer is an appropriate particle parametrization. We come up with a simple,
yet generalizable and purposeful scheme for it. Using our generalizable shape
parameterization, we simulate the formation of a solid composed of pentagonal-like
particles and measure anisotropy in the resulting elastic response. Through automatic
differentiation techniques, we directly connect the shape parameters with the
elastic response. Interestingly, for our system we find that less isotropic particles
lead to a more isotropic elastic response. Together with other results known about
our method it seems that it can be successfully generalized for different inverse
design problems.
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Anton
full_name: Piankov, Anton
id: 865E3C26-AA8C-11E9-A409-C4C4E5697425
last_name: Piankov
citation:
ama: Piankov A. Towards designer materials using customizable particle shape. 2021.
doi:10.15479/at:ista:10422
apa: Piankov, A. (2021). Towards designer materials using customizable particle
shape. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10422
chicago: Piankov, Anton. “Towards Designer Materials Using Customizable Particle
Shape.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10422.
ieee: A. Piankov, “Towards designer materials using customizable particle shape,”
Institute of Science and Technology Austria, 2021.
ista: Piankov A. 2021. Towards designer materials using customizable particle shape.
Institute of Science and Technology Austria.
mla: Piankov, Anton. Towards Designer Materials Using Customizable Particle Shape.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10422.
short: A. Piankov, Towards Designer Materials Using Customizable Particle Shape,
Institute of Science and Technology Austria, 2021.
date_created: 2021-12-07T10:48:06Z
date_published: 2021-12-07T00:00:00Z
date_updated: 2023-09-07T13:34:12Z
day: '07'
ddc:
- '530'
degree_awarded: MS
department:
- _id: GradSch
- _id: CaGo
doi: 10.15479/at:ista:10422
file:
- access_level: closed
checksum: 114e8f4b2c002c6c352416c12de2c695
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2021-12-07T11:13:52Z
date_updated: 2022-03-10T12:10:25Z
file_id: '10424'
file_name: Thesis.zip
file_size: 394018
relation: source_file
- access_level: closed
checksum: cd15ae991ced352a9959815f794e657c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cchlebak
date_created: 2021-12-07T11:14:01Z
date_updated: 2022-03-10T12:10:25Z
file_id: '10425'
file_name: Preliminary_pages_Piankov.docx
file_size: 47638
relation: source_file
- access_level: open_access
checksum: e6899c798b75ba42fab9822bce309050
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-07T11:20:35Z
date_updated: 2021-12-07T11:20:35Z
file_id: '10426'
file_name: 2021_Piankov_combined.pdf
file_size: 484965
relation: main_file
success: 1
file_date_updated: 2022-03-10T12:10:25Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
title: Towards designer materials using customizable particle shape
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_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.
date_created: 2021-12-08T21:52:28Z
date_published: 2021-12-09T00:00:00Z
date_updated: 2023-10-17T11:48:55Z
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: '10432'
relation: part_of_dissertation
status: public
- id: '6673'
relation: part_of_dissertation
status: public
- id: '5965'
relation: part_of_dissertation
status: public
- id: '10435'
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
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.'
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.'
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.'
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.'
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: 2023-09-07T13:31:39Z
day: '18'
department:
- _id: DaAl
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 35
year: '2021'
...
---
_id: '10435'
abstract:
- lang: eng
text: Decentralized optimization is emerging as a viable alternative for scalable
distributed machine learning, but also introduces new challenges in terms of synchronization
costs. To this end, several communication-reduction techniques, such as non-blocking
communication, quantization, and local steps, have been explored in the decentralized
setting. Due to the complexity of analyzing optimization in such a relaxed setting,
this line of work often assumes \emph{global} communication rounds, which require
additional synchronization. In this paper, we consider decentralized optimization
in the simpler, but harder to analyze, \emph{asynchronous gossip} model, in which
communication occurs in discrete, randomly chosen pairings among nodes. Perhaps
surprisingly, we show that a variant of SGD called \emph{SwarmSGD} still converges
in this setting, even if \emph{non-blocking communication}, \emph{quantization},
and \emph{local steps} are all applied \emph{in conjunction}, and even if the
node data distributions and underlying graph topology are both \emph{heterogenous}.
Our analysis is based on a new connection with multi-dimensional load-balancing
processes. We implement this algorithm and deploy it in a super-computing environment,
showing that it can outperform previous decentralized methods in terms of end-to-end
training time, and that it can even rival carefully-tuned large-batch SGD for
certain tasks.
acknowledgement: "We gratefully acknowledge funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No 805223 ScaleML). PD partly conducted this work while at IST
Austria and was supported by the European Union’s Horizon 2020 programme under the
Marie Skłodowska-Curie grant agreement No. 754411. SL was funded in part by European
Research Council (ERC) under the European Union’s Horizon 2020 programme (grant
agreement DAPP, No. 678880, and EPiGRAM-HS, No. 801039).\r\n"
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: Amirmojtaba
full_name: Sabour, Amirmojtaba
id: bcc145fd-e77f-11ea-ae8b-80d661dbff67
last_name: Sabour
- first_name: Peter
full_name: Davies, Peter
id: 11396234-BB50-11E9-B24C-90FCE5697425
last_name: Davies
orcid: 0000-0002-5646-9524
- first_name: Shigang
full_name: Li, Shigang
last_name: Li
- 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, Sabour A, Davies P, Li S, Alistarh D-A. Asynchronous decentralized
SGD with quantized and local updates. In: 35th Conference on Neural Information
Processing Systems. Neural Information Processing Systems Foundation; 2021.'
apa: 'Nadiradze, G., Sabour, A., Davies, P., Li, S., & Alistarh, D.-A. (2021).
Asynchronous decentralized SGD with quantized and local updates. In 35th Conference
on Neural Information Processing Systems. Sydney, Australia: Neural Information
Processing Systems Foundation.'
chicago: Nadiradze, Giorgi, Amirmojtaba Sabour, Peter Davies, Shigang Li, and Dan-Adrian
Alistarh. “Asynchronous Decentralized SGD with Quantized and Local Updates.” In
35th Conference on Neural Information Processing Systems. Neural Information
Processing Systems Foundation, 2021.
ieee: G. Nadiradze, A. Sabour, P. Davies, S. Li, and D.-A. Alistarh, “Asynchronous
decentralized SGD with quantized and local updates,” in 35th Conference on
Neural Information Processing Systems, Sydney, Australia, 2021.
ista: 'Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. 2021. Asynchronous decentralized
SGD with quantized and local updates. 35th Conference on Neural Information Processing
Systems. NeurIPS: Neural Information Processing Systems.'
mla: Nadiradze, Giorgi, et al. “Asynchronous Decentralized SGD with Quantized and
Local Updates.” 35th Conference on Neural Information Processing Systems,
Neural Information Processing Systems Foundation, 2021.
short: G. Nadiradze, A. Sabour, P. Davies, S. Li, D.-A. Alistarh, in:, 35th Conference
on Neural Information Processing Systems, Neural Information Processing Systems
Foundation, 2021.
conference:
end_date: 2021-12-14
location: Sydney, Australia
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2021-12-06
date_created: 2021-12-09T10:59:12Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2023-10-17T11:48:56Z
day: '01'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '1910.12308'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://papers.nips.cc/paper/2021/hash/362c99307cdc3f2d8b410652386a9dd1-Abstract.html
month: '12'
oa: 1
oa_version: Published Version
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 Conference on Neural Information Processing Systems
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
related_material:
record:
- id: '10429'
relation: dissertation_contains
status: public
status: public
title: Asynchronous decentralized SGD with quantized and local updates
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10527'
abstract:
- lang: eng
text: We show that in a two-dimensional electron gas with an annular Fermi surface,
long-range Coulomb interactions can lead to unconventional superconductivity by
the Kohn-Luttinger mechanism. Superconductivity is strongly enhanced when the
inner and outer Fermi surfaces are close to each other. The most prevalent state
has chiral p-wave symmetry, but d-wave and extended s-wave pairing are also possible.
We discuss these results in the context of rhombohedral trilayer graphene, where
superconductivity was recently discovered in regimes where the normal state has
an annular Fermi surface. Using realistic parameters, our mechanism can account
for the order of magnitude of Tc, as well as its trends as a function of electron
density and perpendicular displacement field. Moreover, it naturally explains
some of the outstanding puzzles in this material, that include the weak temperature
dependence of the resistivity above Tc, and the proximity of spin singlet superconductivity
to the ferromagnetic phase.
acknowledgement: We thank Yang-Zhi Chou, Andrey Chubukov, Johannes Hofmann, Steve
Kivelson, Sri Raghu, and Sankar das Sarma, Jay Sau, Fengcheng Wu, and Andrea Young
for many stimulating discussions and for their comments on the manuscript. E.B.
thanks S. Chatterjee, T. Wang, and M. Zaletel for a collaboration on a related topic.
A.G. acknowledges support by the European Unions Horizon 2020 research and innovation
program under the Marie Sklodowska-Curie Grant Agreement No. 754411. E.B. and T.H.
were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement
No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research
grant from Irving and Cherna Moskowitz.
article_number: '247001'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Tobias
full_name: Holder, Tobias
last_name: Holder
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Erez
full_name: Berg, Erez
last_name: Berg
citation:
ama: 'Ghazaryan A, Holder T, Serbyn M, Berg E. Unconventional superconductivity
in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene.
Physical Review Letters. 2021;127(24). doi:10.1103/physrevlett.127.247001'
apa: 'Ghazaryan, A., Holder, T., Serbyn, M., & Berg, E. (2021). Unconventional
superconductivity in systems with annular Fermi surfaces: Application to rhombohedral
trilayer graphene. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/physrevlett.127.247001'
chicago: 'Ghazaryan, Areg, Tobias Holder, Maksym Serbyn, and Erez Berg. “Unconventional
Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral
Trilayer Graphene.” Physical Review Letters. American Physical Society,
2021. https://doi.org/10.1103/physrevlett.127.247001.'
ieee: 'A. Ghazaryan, T. Holder, M. Serbyn, and E. Berg, “Unconventional superconductivity
in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene,”
Physical Review Letters, vol. 127, no. 24. American Physical Society, 2021.'
ista: 'Ghazaryan A, Holder T, Serbyn M, Berg E. 2021. Unconventional superconductivity
in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene.
Physical Review Letters. 127(24), 247001.'
mla: 'Ghazaryan, Areg, et al. “Unconventional Superconductivity in Systems with
Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” Physical
Review Letters, vol. 127, no. 24, 247001, American Physical Society, 2021,
doi:10.1103/physrevlett.127.247001.'
short: A. Ghazaryan, T. Holder, M. Serbyn, E. Berg, Physical Review Letters 127
(2021).
date_created: 2021-12-10T07:51:33Z
date_published: 2021-12-09T00:00:00Z
date_updated: 2023-08-14T13:19:13Z
day: '09'
department:
- _id: MaSe
doi: 10.1103/physrevlett.127.247001
ec_funded: 1
external_id:
arxiv:
- '2109.00011'
isi:
- '000923819400004'
intvolume: ' 127'
isi: 1
issue: '24'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2109.00011
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
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 Webpage
relation: press_release
url: https://ist.ac.at/en/news/resolving-the-puzzles-of-graphene-superconductivity/
scopus_import: '1'
status: public
title: 'Unconventional superconductivity in systems with annular Fermi surfaces: Application
to rhombohedral trilayer graphene'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 127
year: '2021'
...
---
_id: '10533'
abstract:
- lang: eng
text: Flowering plants utilize small RNA molecules to guide DNA methyltransferases
to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially
targets euchromatic transposable elements. However, RdDM is thought to be recruited
by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin.
How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear.
Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially
at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component
that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation.
Instead, we find that non-CG methylation is specifically associated with small
RNA biogenesis, and without H1 small RNA production quantitatively expands to
non-CG methylated loci. Our results demonstrate that H1 enforces the separation
of euchromatic and heterochromatic DNA methylation pathways by excluding the small
RNA-generating branch of RdDM from non-CG methylated heterochromatin.
acknowledgement: We thank X Feng for helpful comments on the manuscript. This work
was supported by a European Research Council grant MaintainMeth (725746) to DZ.
article_number: e72676
article_processing_charge: No
article_type: original
author:
- first_name: Jaemyung
full_name: Choi, Jaemyung
last_name: Choi
- first_name: David B
full_name: Lyons, David B
last_name: Lyons
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated
small RNA biogenesis in Arabidopsis heterochromatin. eLife. 2021;10. doi:10.7554/elife.72676
apa: Choi, J., Lyons, D. B., & Zilberman, D. (2021). Histone H1 prevents non-CG
methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. ELife.
eLife Sciences Publications. https://doi.org/10.7554/elife.72676
chicago: Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histone H1 Prevents
Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.”
ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72676.
ieee: J. Choi, D. B. Lyons, and D. Zilberman, “Histone H1 prevents non-CG methylation-mediated
small RNA biogenesis in Arabidopsis heterochromatin,” eLife, vol. 10. eLife
Sciences Publications, 2021.
ista: Choi J, Lyons DB, Zilberman D. 2021. Histone H1 prevents non-CG methylation-mediated
small RNA biogenesis in Arabidopsis heterochromatin. eLife. 10, e72676.
mla: Choi, Jaemyung, et al. “Histone H1 Prevents Non-CG Methylation-Mediated Small
RNA Biogenesis in Arabidopsis Heterochromatin.” ELife, vol. 10, e72676,
eLife Sciences Publications, 2021, doi:10.7554/elife.72676.
short: J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021).
date_created: 2021-12-10T13:12:08Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2023-08-17T06:21:08Z
day: '01'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.7554/elife.72676
ec_funded: 1
external_id:
isi:
- '000754832000001'
pmid:
- '34850679'
file:
- access_level: open_access
checksum: 22ed4c55fb550f6da02ae55c359be651
content_type: application/pdf
creator: dernst
date_created: 2022-05-16T10:42:22Z
date_updated: 2022-05-16T10:42:22Z
file_id: '11384'
file_name: 2021_eLife_Choi.pdf
file_size: 2715200
relation: main_file
success: 1
file_date_updated: 2022-05-16T10:42:22Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
keyword:
- genetics and molecular biology
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 62935a00-2b32-11ec-9570-eff30fa39068
call_identifier: H2020
grant_number: '725746'
name: Quantitative analysis of DNA methylation maintenance with chromatin
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis
heterochromatin
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '10534'
abstract:
- lang: eng
text: For many years, fullerene derivatives have been the main n-type material of
organic electronics and optoelectronics. Recently, fullerene derivatives functionalized
with ethylene glycol (EG) side chains have been showing important properties such
as enhanced dielectric constants, facile doping and enhanced self-assembly capabilities.
Here, we have prepared field-effect transistors using a series of these fullerene
derivatives equipped with EG side chains of different lengths. Transport data
show the beneficial effect of increasing the EG side chain. In order to understand
the material properties, full structural determination of these fullerene derivatives
has been achieved by coupling the X-ray data with molecular dynamics (MD) simulations.
The increase in transport properties is paired with the formation of extended
layered structures, efficient molecular packing and an increase in the crystallite
alignment. The layer-like structure is composed of conducting layers, containing
of closely packed C60 balls approaching the inter-distance of 1 nm, that are separated
by well-defined EG layers, where the EG chains are rather splayed with the chain
direction almost perpendicular to the layer normal. Such a layered structure appears
highly ordered and highly aligned with the C60 planes oriented parallel to the
substrate in the thin film configuration. The order inside the thin film increases
with the EG chain length, allowing the systems to achieve mobilities as high as
0.053 cm2 V−1 s−1. Our work elucidates the structure of these interesting semiconducting
organic molecules and shows that the synergistic use of X-ray structural analysis
and MD simulations is a powerful tool to identify the structure of thin organic
films for optoelectronic applications.
acknowledgement: J. D. gratefully acknowledges the China Scholarship Council (CSC
No. 201606340158) for supporting his PhD studies. S. S. thanks J. Antoja-Lleonart
for insightful discussions on simulating the X-ray diffraction patterns. Part of
the work was sponsored by NWO Exact and Natural Sciences for the use of supercomputer
facilities (Contract no. 17197 7095). Regarding S. S., R. A., R. W. A. H., J. C.
H., and M. A. L., this is a publication by the FOM Focus Group “Next Generation
Organic Photovoltaics”, participating in the Dutch Institute for Fundamental Energy
Research (DIFFER). The ESRF is acknowledged for providing the beamtime. J. D. and
G. P. are grateful to the BM26B staff for their great support during the beamtime.
M. A. L., D. M. B. are grateful for the financial support of the European Research
Council via a Starting Grant (HySPOD, No. 306983).
article_processing_charge: No
article_type: original
author:
- first_name: Jingjin
full_name: Dong, Jingjin
last_name: Dong
- first_name: Selim
full_name: Sami, Selim
last_name: Sami
- first_name: Daniel
full_name: Balazs, Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- first_name: Riccardo
full_name: Alessandri, Riccardo
last_name: Alessandri
- first_name: Fatimeh
full_name: Jahani, Fatimeh
last_name: Jahani
- first_name: Li
full_name: Qiu, Li
last_name: Qiu
- first_name: Siewert J.
full_name: Marrink, Siewert J.
last_name: Marrink
- first_name: Remco W.A.
full_name: Havenith, Remco W.A.
last_name: Havenith
- first_name: Jan C.
full_name: Hummelen, Jan C.
last_name: Hummelen
- first_name: Maria A.
full_name: Loi, Maria A.
last_name: Loi
- first_name: Giuseppe
full_name: Portale, Giuseppe
last_name: Portale
citation:
ama: 'Dong J, Sami S, Balazs D, et al. Fullerene derivatives with oligoethylene-glycol
side chains: An investigation on the origin of their outstanding transport properties.
Journal of Materials Chemistry C. 2021;9(45):16217-16225. doi:10.1039/d1tc02753k'
apa: 'Dong, J., Sami, S., Balazs, D., Alessandri, R., Jahani, F., Qiu, L., … Portale,
G. (2021). Fullerene derivatives with oligoethylene-glycol side chains: An investigation
on the origin of their outstanding transport properties. Journal of Materials
Chemistry C. Royal Society of Chemistry. https://doi.org/10.1039/d1tc02753k'
chicago: 'Dong, Jingjin, Selim Sami, Daniel Balazs, Riccardo Alessandri, Fatimeh
Jahani, Li Qiu, Siewert J. Marrink, et al. “Fullerene Derivatives with Oligoethylene-Glycol
Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.”
Journal of Materials Chemistry C. Royal Society of Chemistry, 2021. https://doi.org/10.1039/d1tc02753k.'
ieee: 'J. Dong et al., “Fullerene derivatives with oligoethylene-glycol side
chains: An investigation on the origin of their outstanding transport properties,”
Journal of Materials Chemistry C, vol. 9, no. 45. Royal Society of Chemistry,
pp. 16217–16225, 2021.'
ista: 'Dong J, Sami S, Balazs D, Alessandri R, Jahani F, Qiu L, Marrink SJ, Havenith
RWA, Hummelen JC, Loi MA, Portale G. 2021. Fullerene derivatives with oligoethylene-glycol
side chains: An investigation on the origin of their outstanding transport properties.
Journal of Materials Chemistry C. 9(45), 16217–16225.'
mla: 'Dong, Jingjin, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side
Chains: An Investigation on the Origin of Their Outstanding Transport Properties.”
Journal of Materials Chemistry C, vol. 9, no. 45, Royal Society of Chemistry,
2021, pp. 16217–25, doi:10.1039/d1tc02753k.'
short: J. Dong, S. Sami, D. Balazs, R. Alessandri, F. Jahani, L. Qiu, S.J. Marrink,
R.W.A. Havenith, J.C. Hummelen, M.A. Loi, G. Portale, Journal of Materials Chemistry
C 9 (2021) 16217–16225.
date_created: 2021-12-12T23:01:27Z
date_published: 2021-12-07T00:00:00Z
date_updated: 2023-08-17T06:18:44Z
day: '07'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1039/d1tc02753k
external_id:
isi:
- '000688135700001'
file:
- access_level: open_access
checksum: 6b73c214ce54a6894a5854b4364413d7
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-13T09:24:42Z
date_updated: 2021-12-13T09:24:42Z
file_id: '10538'
file_name: 2021_JMaterChemC_Dong.pdf
file_size: 4979390
relation: main_file
success: 1
file_date_updated: 2021-12-13T09:24:42Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '45'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 16217-16225
publication: Journal of Materials Chemistry C
publication_identifier:
eissn:
- 2050-7526
issn:
- 2050-7534
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Fullerene derivatives with oligoethylene-glycol side chains: An investigation
on the origin of their outstanding transport properties'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2021'
...
---
_id: '10535'
abstract:
- lang: eng
text: Realistic models of biological processes typically involve interacting components
on multiple scales, driven by changing environment and inherent stochasticity.
Such models are often analytically and numerically intractable. We revisit a dynamic
maximum entropy method that combines a static maximum entropy with a quasi-stationary
approximation. This allows us to reduce stochastic non-equilibrium dynamics expressed
by the Fokker-Planck equation to a simpler low-dimensional deterministic dynamics,
without the need to track microscopic details. Although the method has been previously
applied to a few (rather complicated) applications in population genetics, our
main goal here is to explain and to better understand how the method works. We
demonstrate the usefulness of the method for two widely studied stochastic problems,
highlighting its accuracy in capturing important macroscopic quantities even in
rapidly changing non-stationary conditions. For the Ornstein-Uhlenbeck process,
the method recovers the exact dynamics whilst for a stochastic island model with
migration from other habitats, the approximation retains high macroscopic accuracy
under a wide range of scenarios in a dynamic environment.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "Computational resources for the study were provided by the Institute
of Science and Technology, Austria.\r\nKB received funding from the Scientific Grant
Agency of the Slovak Republic under the Grants Nos. 1/0755/19 and 1/0521/20."
article_number: e1009661
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Katarína
full_name: Bod'ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'ová
orcid: 0000-0002-7214-0171
- first_name: Eniko
full_name: Szep, Eniko
id: 485BB5A4-F248-11E8-B48F-1D18A9856A87
last_name: Szep
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Bodova K, Szep E, Barton NH. Dynamic maximum entropy provides accurate approximation
of structured population dynamics. PLoS Computational Biology. 2021;17(12).
doi:10.1371/journal.pcbi.1009661
apa: Bodova, K., Szep, E., & Barton, N. H. (2021). Dynamic maximum entropy provides
accurate approximation of structured population dynamics. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009661
chicago: Bodova, Katarina, Eniko Szep, and Nicholas H Barton. “Dynamic Maximum Entropy
Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational
Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009661.
ieee: K. Bodova, E. Szep, and N. H. Barton, “Dynamic maximum entropy provides accurate
approximation of structured population dynamics,” PLoS Computational Biology,
vol. 17, no. 12. Public Library of Science, 2021.
ista: Bodova K, Szep E, Barton NH. 2021. Dynamic maximum entropy provides accurate
approximation of structured population dynamics. PLoS Computational Biology. 17(12),
e1009661.
mla: Bodova, Katarina, et al. “Dynamic Maximum Entropy Provides Accurate Approximation
of Structured Population Dynamics.” PLoS Computational Biology, vol. 17,
no. 12, e1009661, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009661.
short: K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).
date_created: 2021-12-12T23:01:27Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2022-08-01T10:48:04Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1371/journal.pcbi.1009661
external_id:
arxiv:
- '2102.03669'
pmid:
- '34851948'
file:
- access_level: open_access
checksum: dcd185d4f7e0acee25edf1d6537f447e
content_type: application/pdf
creator: dernst
date_created: 2022-05-16T08:53:11Z
date_updated: 2022-05-16T08:53:11Z
file_id: '11383'
file_name: 2021_PLOsComBio_Bodova.pdf
file_size: 2299486
relation: main_file
success: 1
file_date_updated: 2022-05-16T08:53:11Z
has_accepted_license: '1'
intvolume: ' 17'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
issn:
- 1553-734X
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic maximum entropy provides accurate approximation of structured population
dynamics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2021'
...
---
_id: '10536'
abstract:
- lang: eng
text: TGFβ overexpression is commonly detected in cancer patients and correlates
with poor prognosis and metastasis. Cancer progression is often associated with
an enhanced recruitment of myeloid-derived cells to the tumor microenvironment.
Here we show that functional TGFβ-signaling in myeloid cells is required for metastasis
to the lungs and the liver. Myeloid-specific deletion of Tgfbr2 resulted in reduced
spontaneous lung metastasis, which was associated with a reduction of proinflammatory
cytokines in the metastatic microenvironment. Notably, CD8+ T cell depletion in
myeloid-specific Tgfbr2-deficient mice rescued lung metastasis. Myeloid-specific
Tgfbr2-deficiency resulted in reduced liver metastasis with an almost complete
absence of myeloid cells within metastatic foci. On contrary, an accumulation
of Tgfβ-responsive myeloid cells was associated with an increased recruitment
of monocytes and granulocytes and higher proinflammatory cytokine levels in control
mice. Monocytic cells isolated from metastatic livers of Tgfbr2-deficient mice
showed increased polarization towards the M1 phenotype, Tnfα and Il-1β expression,
reduced levels of M2 markers and reduced production of chemokines responsible
for myeloid-cell recruitment. No significant differences in Tgfβ levels were observed
at metastatic sites of any model. These data demonstrate that Tgfβ signaling in
monocytic myeloid cells suppresses CD8+ T cell activity during lung metastasis,
while these cells actively contribute to tumor growth during liver metastasis.
Thus, myeloid cells modulate metastasis through different mechanisms in a tissue-specific
manner.
acknowledgement: The authors acknowledge the assistance of the Laboratory Animal Services
Center (LASC) – UZH, Center for Microscopy and Image Analysis, and the Flow Cytometry
Center of the University of Zurich.
article_number: '765151'
article_processing_charge: No
article_type: original
author:
- first_name: Cristina
full_name: Stefanescu, Cristina
last_name: Stefanescu
- first_name: Merel
full_name: Van Gogh, Merel
last_name: Van Gogh
- first_name: Marko
full_name: Roblek, Marko
id: 3047D808-F248-11E8-B48F-1D18A9856A87
last_name: Roblek
orcid: 0000-0001-9588-1389
- first_name: Mathias
full_name: Heikenwalder, Mathias
last_name: Heikenwalder
- first_name: Lubor
full_name: Borsig, Lubor
last_name: Borsig
citation:
ama: Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. TGFβ signaling
in myeloid cells promotes lung and liver metastasis through different mechanisms.
Frontiers in Oncology. 2021;11. doi:10.3389/fonc.2021.765151
apa: Stefanescu, C., Van Gogh, M., Roblek, M., Heikenwalder, M., & Borsig, L.
(2021). TGFβ signaling in myeloid cells promotes lung and liver metastasis through
different mechanisms. Frontiers in Oncology. Frontiers. https://doi.org/10.3389/fonc.2021.765151
chicago: Stefanescu, Cristina, Merel Van Gogh, Marko Roblek, Mathias Heikenwalder,
and Lubor Borsig. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis
through Different Mechanisms.” Frontiers in Oncology. Frontiers, 2021.
https://doi.org/10.3389/fonc.2021.765151.
ieee: C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, and L. Borsig, “TGFβ
signaling in myeloid cells promotes lung and liver metastasis through different
mechanisms,” Frontiers in Oncology, vol. 11. Frontiers, 2021.
ista: Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. 2021. TGFβ signaling
in myeloid cells promotes lung and liver metastasis through different mechanisms.
Frontiers in Oncology. 11, 765151.
mla: Stefanescu, Cristina, et al. “TGFβ Signaling in Myeloid Cells Promotes Lung
and Liver Metastasis through Different Mechanisms.” Frontiers in Oncology,
vol. 11, 765151, Frontiers, 2021, doi:10.3389/fonc.2021.765151.
short: C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, L. Borsig, Frontiers
in Oncology 11 (2021).
date_created: 2021-12-12T23:01:27Z
date_published: 2021-11-18T00:00:00Z
date_updated: 2023-08-17T06:20:32Z
day: '18'
ddc:
- '610'
department:
- _id: DaSi
doi: 10.3389/fonc.2021.765151
external_id:
isi:
- '000726603400001'
pmid:
- '34868988'
file:
- access_level: open_access
checksum: 56cbac80e6891ce750511a30161b7792
content_type: application/pdf
creator: alisjak
date_created: 2021-12-13T13:32:37Z
date_updated: 2021-12-13T13:32:37Z
file_id: '10539'
file_name: 2021_Frontiers_Stefanescu.pdf
file_size: 9245199
relation: main_file
success: 1
file_date_updated: 2021-12-13T13:32:37Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Oncology
publication_identifier:
eissn:
- 2234-943X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: TGFβ signaling in myeloid cells promotes lung and liver metastasis through
different mechanisms
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2021'
...
---
_id: '10537'
abstract:
- lang: eng
text: We consider the quantum many-body evolution of a homogeneous Fermi gas in
three dimensions in the coupled semiclassical and mean-field scaling regime. We
study a class of initial data describing collective particle–hole pair excitations
on the Fermi ball. Using a rigorous version of approximate bosonization, we prove
that the many-body evolution can be approximated in Fock space norm by a quasi-free
bosonic evolution of the collective particle–hole excitations.
acknowledgement: NB was supported by Gruppo Nazionale per la Fisica Matematica (GNFM).
RS was supported by the European Research Council (ERC) under the European Union’s
Horizon 2020 research and innovation program (Grant Agreement No. 694227). PTN was
supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)
under Germany’s Excellence Strategy (EXC-2111-390814868). MP was supported by the
European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation program (ERC StG MaMBoQ, Grant Agreement No. 802901). BS was supported
by the NCCR SwissMAP, the Swiss National Science Foundation through the Grant “Dynamical
and energetic properties of Bose-Einstein condensates,” and the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation program
through the ERC-AdG CLaQS (Grant Agreement No. 834782).
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Niels P
full_name: Benedikter, Niels P
id: 3DE6C32A-F248-11E8-B48F-1D18A9856A87
last_name: Benedikter
orcid: 0000-0002-1071-6091
- first_name: Phan Thành
full_name: Nam, Phan Thành
last_name: Nam
- first_name: Marcello
full_name: Porta, Marcello
last_name: Porta
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Bosonization of fermionic
many-body dynamics. Annales Henri Poincaré. 2021. doi:10.1007/s00023-021-01136-y
apa: Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., & Seiringer, R.
(2021). Bosonization of fermionic many-body dynamics. Annales Henri Poincaré.
Springer Nature. https://doi.org/10.1007/s00023-021-01136-y
chicago: Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein,
and Robert Seiringer. “Bosonization of Fermionic Many-Body Dynamics.” Annales
Henri Poincaré. Springer Nature, 2021. https://doi.org/10.1007/s00023-021-01136-y.
ieee: N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Bosonization
of fermionic many-body dynamics,” Annales Henri Poincaré. Springer Nature,
2021.
ista: Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2021. Bosonization
of fermionic many-body dynamics. Annales Henri Poincaré.
mla: Benedikter, Niels P., et al. “Bosonization of Fermionic Many-Body Dynamics.”
Annales Henri Poincaré, Springer Nature, 2021, doi:10.1007/s00023-021-01136-y.
short: N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Annales Henri
Poincaré (2021).
date_created: 2021-12-12T23:01:28Z
date_published: 2021-12-02T00:00:00Z
date_updated: 2023-08-17T06:19:14Z
day: '02'
department:
- _id: RoSe
doi: 10.1007/s00023-021-01136-y
ec_funded: 1
external_id:
arxiv:
- '2103.08224'
isi:
- '000725405700001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2103.08224
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Annales Henri Poincaré
publication_identifier:
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bosonization of fermionic many-body dynamics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '10545'
abstract:
- lang: eng
text: Classical models with complex energy landscapes represent a perspective avenue
for the near-term application of quantum simulators. Until now, many theoretical
works studied the performance of quantum algorithms for models with a unique ground
state. However, when the classical problem is in a so-called clustering phase,
the ground state manifold is highly degenerate. As an example, we consider a 3-XORSAT
model defined on simple hypergraphs. The degeneracy of classical ground state
manifold translates into the emergence of an extensive number of Z2 symmetries,
which remain intact even in the presence of a quantum transverse magnetic field.
We establish a general duality approach that restricts the quantum problem to
a given sector of conserved Z2 charges and use it to study how the outcome of
the quantum adiabatic algorithm depends on the hypergraph geometry. We show that
the tree hypergraph which corresponds to a classically solvable instance of the
3-XORSAT problem features a constant gap, whereas the closed hypergraph encounters
a second-order phase transition with a gap vanishing as a power-law in the problem
size. The duality developed in this work provides a practical tool for studies
of quantum models with classically degenerate energy manifold and reveals potential
connections between glasses and gauge theories.
acknowledgement: We would like to thank S. De Nicola, A. Michaidilis, T. Gulden, Y.
Nez-Fernndez, P. Brighi, and S. Sack for fruitful discussions and valuable feedback
on the manuscript. M.S. acknowledges useful discussions with E. Altman, L. Cugliandolo,
and C. Laumann. We acknowledge support from the European Research Council (ERC)
under the European Union's Horizon 2020 Research and Innovation Programme Grant
Agreement No. 850899.
article_number: '062423'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Raimel A
full_name: Medina Ramos, Raimel A
id: CE680B90-D85A-11E9-B684-C920E6697425
last_name: Medina Ramos
orcid: 0000-0002-5383-2869
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Medina Ramos RA, Serbyn M. Duality approach to quantum annealing of the 3-variable
exclusive-or satisfiability problem (3-XORSAT). Physical Review A. 2021;104(6).
doi:10.1103/physreva.104.062423
apa: Medina Ramos, R. A., & Serbyn, M. (2021). Duality approach to quantum annealing
of the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical
Review A. American Physical Society. https://doi.org/10.1103/physreva.104.062423
chicago: Medina Ramos, Raimel A, and Maksym Serbyn. “Duality Approach to Quantum
Annealing of the 3-Variable Exclusive-or Satisfiability Problem (3-XORSAT).” Physical
Review A. American Physical Society, 2021. https://doi.org/10.1103/physreva.104.062423.
ieee: R. A. Medina Ramos and M. Serbyn, “Duality approach to quantum annealing of
the 3-variable exclusive-or satisfiability problem (3-XORSAT),” Physical Review
A, vol. 104, no. 6. American Physical Society, 2021.
ista: Medina Ramos RA, Serbyn M. 2021. Duality approach to quantum annealing of
the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review
A. 104(6), 062423.
mla: Medina Ramos, Raimel A., and Maksym Serbyn. “Duality Approach to Quantum Annealing
of the 3-Variable Exclusive-or Satisfiability Problem (3-XORSAT).” Physical
Review A, vol. 104, no. 6, 062423, American Physical Society, 2021, doi:10.1103/physreva.104.062423.
short: R.A. Medina Ramos, M. Serbyn, Physical Review A 104 (2021).
date_created: 2021-12-14T20:46:07Z
date_published: 2021-12-14T00:00:00Z
date_updated: 2023-08-17T06:22:49Z
day: '14'
department:
- _id: MaSe
doi: 10.1103/physreva.104.062423
ec_funded: 1
external_id:
arxiv:
- '2106.06344'
isi:
- '000753659200004'
intvolume: ' 104'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2106.06344
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability
problem (3-XORSAT)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 104
year: '2021'
...
---
_id: '10549'
abstract:
- lang: eng
text: We derive optimal-order homogenization rates for random nonlinear elliptic
PDEs with monotone nonlinearity in the uniformly elliptic case. More precisely,
for a random monotone operator on \mathbb {R}^d with stationary law (that is spatially
homogeneous statistics) and fast decay of correlations on scales larger than the
microscale \varepsilon >0, we establish homogenization error estimates of the
order \varepsilon in case d\geqq 3, and of the order \varepsilon |\log \varepsilon
|^{1/2} in case d=2. Previous results in nonlinear stochastic homogenization have
been limited to a small algebraic rate of convergence \varepsilon ^\delta . We
also establish error estimates for the approximation of the homogenized operator
by the method of representative volumes of the order (L/\varepsilon )^{-d/2} for
a representative volume of size L. Our results also hold in the case of systems
for which a (small-scale) C^{1,\alpha } regularity theory is available.
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria). SN acknowledges partial support by the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation) – project number 405009441.
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Stefan
full_name: Neukamm, Stefan
last_name: Neukamm
citation:
ama: Fischer JL, Neukamm S. Optimal homogenization rates in stochastic homogenization
of nonlinear uniformly elliptic equations and systems. Archive for Rational
Mechanics and Analysis. 2021;242(1):343-452. doi:10.1007/s00205-021-01686-9
apa: Fischer, J. L., & Neukamm, S. (2021). Optimal homogenization rates in stochastic
homogenization of nonlinear uniformly elliptic equations and systems. Archive
for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01686-9
chicago: Fischer, Julian L, and Stefan Neukamm. “Optimal Homogenization Rates in
Stochastic Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.”
Archive for Rational Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01686-9.
ieee: J. L. Fischer and S. Neukamm, “Optimal homogenization rates in stochastic
homogenization of nonlinear uniformly elliptic equations and systems,” Archive
for Rational Mechanics and Analysis, vol. 242, no. 1. Springer Nature, pp.
343–452, 2021.
ista: Fischer JL, Neukamm S. 2021. Optimal homogenization rates in stochastic homogenization
of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics
and Analysis. 242(1), 343–452.
mla: Fischer, Julian L., and Stefan Neukamm. “Optimal Homogenization Rates in Stochastic
Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.” Archive
for Rational Mechanics and Analysis, vol. 242, no. 1, Springer Nature, 2021,
pp. 343–452, doi:10.1007/s00205-021-01686-9.
short: J.L. Fischer, S. Neukamm, Archive for Rational Mechanics and Analysis 242
(2021) 343–452.
date_created: 2021-12-16T12:12:33Z
date_published: 2021-06-30T00:00:00Z
date_updated: 2023-08-17T06:23:21Z
day: '30'
ddc:
- '530'
department:
- _id: JuFi
doi: 10.1007/s00205-021-01686-9
external_id:
arxiv:
- '1908.02273'
isi:
- '000668431200001'
file:
- access_level: open_access
checksum: cc830b739aed83ca2e32c4e0ce266a4c
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-16T14:58:08Z
date_updated: 2021-12-16T14:58:08Z
file_id: '10558'
file_name: 2021_ArchRatMechAnalysis_Fischer.pdf
file_size: 1640121
relation: main_file
success: 1
file_date_updated: 2021-12-16T14:58:08Z
has_accepted_license: '1'
intvolume: ' 242'
isi: 1
issue: '1'
keyword:
- Mechanical Engineering
- Mathematics (miscellaneous)
- Analysis
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 343-452
publication: Archive for Rational Mechanics and Analysis
publication_identifier:
eissn:
- 1432-0673
issn:
- 0003-9527
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimal homogenization rates in stochastic homogenization of nonlinear uniformly
elliptic equations and systems
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: 242
year: '2021'
...
---
_id: '10552'
abstract:
- lang: eng
text: We study a class of convex-concave saddle-point problems of the form minxmaxy⟨Kx,y⟩+fP(x)−h∗(y)
where K is a linear operator, fP is the sum of a convex function f with a Lipschitz-continuous
gradient and the indicator function of a bounded convex polytope P, and h∗ is
a convex (possibly nonsmooth) function. Such problem arises, for example, as a
Lagrangian relaxation of various discrete optimization problems. Our main assumptions
are the existence of an efficient linear minimization oracle (lmo) for fP and
an efficient proximal map for h∗ which motivate the solution via a blend of proximal
primal-dual algorithms and Frank-Wolfe algorithms. In case h∗ is the indicator
function of a linear constraint and function f is quadratic, we show a O(1/n2)
convergence rate on the dual objective, requiring O(nlogn) calls of lmo. If the
problem comes from the constrained optimization problem minx∈Rd{fP(x)|Ax−b=0}
then we additionally get bound O(1/n2) both on the primal gap and on the infeasibility
gap. In the most general case, we show a O(1/n) convergence rate of the primal-dual
gap again requiring O(nlogn) calls of lmo. To the best of our knowledge, this
improves on the known convergence rates for the considered class of saddle-point
problems. We show applications to labeling problems frequently appearing in machine
learning and computer vision.
acknowledgement: Vladimir Kolmogorov was supported by the European Research Council
under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant
agreement no 616160. Thomas Pock acknowledges support by an ERC grant HOMOVIS, no
640156.
article_processing_charge: No
arxiv: 1
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Thomas
full_name: Pock, Thomas
last_name: Pock
citation:
ama: 'Kolmogorov V, Pock T. One-sided Frank-Wolfe algorithms for saddle problems.
In: 38th International Conference on Machine Learning. ; 2021.'
apa: Kolmogorov, V., & Pock, T. (2021). One-sided Frank-Wolfe algorithms for
saddle problems. In 38th International Conference on Machine Learning.
Virtual.
chicago: Kolmogorov, Vladimir, and Thomas Pock. “One-Sided Frank-Wolfe Algorithms
for Saddle Problems.” In 38th International Conference on Machine Learning,
2021.
ieee: V. Kolmogorov and T. Pock, “One-sided Frank-Wolfe algorithms for saddle problems,”
in 38th International Conference on Machine Learning, Virtual, 2021.
ista: 'Kolmogorov V, Pock T. 2021. One-sided Frank-Wolfe algorithms for saddle problems.
38th International Conference on Machine Learning. ICML: International Conference
on Machine Learning.'
mla: Kolmogorov, Vladimir, and Thomas Pock. “One-Sided Frank-Wolfe Algorithms for
Saddle Problems.” 38th International Conference on Machine Learning, 2021.
short: V. Kolmogorov, T. Pock, in:, 38th International Conference on Machine Learning,
2021.
conference:
end_date: 2021-07-24
location: Virtual
name: 'ICML: International Conference on Machine Learning'
start_date: 2021-07-18
date_created: 2021-12-16T12:41:20Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2021-12-17T09:06:46Z
day: '01'
department:
- _id: VlKo
ec_funded: 1
external_id:
arxiv:
- '2101.12617'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2101.12617
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: 38th International Conference on Machine Learning
publication_status: published
quality_controlled: '1'
status: public
title: One-sided Frank-Wolfe algorithms for saddle problems
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '10553'
abstract:
- lang: eng
text: The popularity of permissioned blockchain systems demands BFT SMR protocols
that are efficient under good network conditions (synchrony) and robust under
bad network conditions (asynchrony). The state-of-the-art partially synchronous
BFT SMR protocols provide optimal linear communication cost per decision under
synchrony and good leaders, but lose liveness under asynchrony. On the other hand,
the state-of-the-art asynchronous BFT SMR protocols are live even under asynchrony,
but always pay quadratic cost even under synchrony. In this paper, we propose
a BFT SMR protocol that achieves the best of both worlds -- optimal linear cost
per decision under good networks and leaders, optimal quadratic cost per decision
under bad networks, and remains always live.
article_processing_charge: No
arxiv: 1
author:
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Alexander
full_name: Spiegelman, Alexander
last_name: Spiegelman
- first_name: Zhuolun
full_name: Xiang, Zhuolun
last_name: Xiang
citation:
ama: 'Gelashvili R, Kokoris Kogias E, Spiegelman A, Xiang Z. Brief announcement:
Be prepared when network goes bad: An asynchronous view-change protocol. In: Proceedings
of the 2021 ACM Symposium on Principles of Distributed Computing. Association
for Computing Machinery; 2021:187-190. doi:10.1145/3465084.3467941'
apa: 'Gelashvili, R., Kokoris Kogias, E., Spiegelman, A., & Xiang, Z. (2021).
Brief announcement: Be prepared when network goes bad: An asynchronous view-change
protocol. In Proceedings of the 2021 ACM Symposium on Principles of Distributed
Computing (pp. 187–190). Virtual, Italy: Association for Computing Machinery.
https://doi.org/10.1145/3465084.3467941'
chicago: 'Gelashvili, Rati, Eleftherios Kokoris Kogias, Alexander Spiegelman, and
Zhuolun Xiang. “Brief Announcement: Be Prepared When Network Goes Bad: An Asynchronous
View-Change Protocol.” In Proceedings of the 2021 ACM Symposium on Principles
of Distributed Computing, 187–90. Association for Computing Machinery, 2021.
https://doi.org/10.1145/3465084.3467941.'
ieee: 'R. Gelashvili, E. Kokoris Kogias, A. Spiegelman, and Z. Xiang, “Brief announcement:
Be prepared when network goes bad: An asynchronous view-change protocol,” in Proceedings
of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual,
Italy, 2021, pp. 187–190.'
ista: 'Gelashvili R, Kokoris Kogias E, Spiegelman A, Xiang Z. 2021. Brief announcement:
Be prepared when network goes bad: An asynchronous view-change protocol. Proceedings
of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Principles
of Distributed Computing, 187–190.'
mla: 'Gelashvili, Rati, et al. “Brief Announcement: Be Prepared When Network Goes
Bad: An Asynchronous View-Change Protocol.” Proceedings of the 2021 ACM Symposium
on Principles of Distributed Computing, Association for Computing Machinery,
2021, pp. 187–90, doi:10.1145/3465084.3467941.'
short: R. Gelashvili, E. Kokoris Kogias, A. Spiegelman, Z. Xiang, in:, Proceedings
of the 2021 ACM Symposium on Principles of Distributed Computing, Association
for Computing Machinery, 2021, pp. 187–190.
conference:
end_date: 2021-07-30
location: Virtual, Italy
name: 'PODC: Principles of Distributed Computing'
start_date: 2021-07-26
date_created: 2021-12-16T13:20:19Z
date_published: 2021-07-21T00:00:00Z
date_updated: 2023-09-04T11:42:10Z
day: '21'
department:
- _id: ElKo
doi: 10.1145/3465084.3467941
external_id:
arxiv:
- '2103.03181'
isi:
- '000744439800018'
isi: 1
keyword:
- optimal
- state machine replication
- fallback
- asynchrony
- byzantine faults
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2103.03181
month: '07'
oa: 1
oa_version: Preprint
page: 187-190
publication: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing
publication_identifier:
isbn:
- 9-781-4503-8548-0
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Brief announcement: Be prepared when network goes bad: An asynchronous view-change
protocol'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10554'
abstract:
- lang: eng
text: 'We present DAG-Rider, the first asynchronous Byzantine Atomic Broadcast protocol
that achieves optimal resilience, optimal amortized communication complexity,
and optimal time complexity. DAG-Rider is post-quantum safe and ensures that all
values proposed by correct processes eventually get delivered. We construct DAG-Rider
in two layers: In the first layer, processes reliably broadcast their proposals
and build a structured Directed Acyclic Graph (DAG) of the communication among
them. In the second layer, processes locally observe their DAGs and totally order
all proposals with no extra communication.'
acknowledgement: "Oded Naor is grateful to the Technion Hiroshi Fujiwara Cyber-Security
Research Center for providing a research grant. Part of Oded’s work was done while
at Novi Research. This work was funded by the Novi team at Facebook. We also wish
to thank the Novi Research team for valuable feedback, and in particular George
Danezis, Alberto Sonnino, and Dahlia Malkhi.\r\n"
article_processing_charge: No
arxiv: 1
author:
- first_name: Idit
full_name: Keidar, Idit
last_name: Keidar
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Oded
full_name: Naor, Oded
last_name: Naor
- first_name: Alexander
full_name: Spiegelman, Alexander
last_name: Spiegelman
citation:
ama: 'Keidar I, Kokoris Kogias E, Naor O, Spiegelman A. All You Need is DAG. In:
Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing.
Association for Computing Machinery; 2021:165-175. doi:10.1145/3465084.3467905'
apa: 'Keidar, I., Kokoris Kogias, E., Naor, O., & Spiegelman, A. (2021). All
You Need is DAG. In Proceedings of the 2021 ACM Symposium on Principles of
Distributed Computing (pp. 165–175). Virtual, Italy: Association for Computing
Machinery. https://doi.org/10.1145/3465084.3467905'
chicago: Keidar, Idit, Eleftherios Kokoris Kogias, Oded Naor, and Alexander Spiegelman.
“All You Need Is DAG.” In Proceedings of the 2021 ACM Symposium on Principles
of Distributed Computing, 165–75. Association for Computing Machinery, 2021.
https://doi.org/10.1145/3465084.3467905.
ieee: I. Keidar, E. Kokoris Kogias, O. Naor, and A. Spiegelman, “All You Need is
DAG,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed
Computing, Virtual, Italy, 2021, pp. 165–175.
ista: 'Keidar I, Kokoris Kogias E, Naor O, Spiegelman A. 2021. All You Need is DAG.
Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing.
PODC: Principles of Distributed Computing, 165–175.'
mla: Keidar, Idit, et al. “All You Need Is DAG.” Proceedings of the 2021 ACM
Symposium on Principles of Distributed Computing, Association for Computing
Machinery, 2021, pp. 165–75, doi:10.1145/3465084.3467905.
short: I. Keidar, E. Kokoris Kogias, O. Naor, A. Spiegelman, in:, Proceedings of
the 2021 ACM Symposium on Principles of Distributed Computing, Association for
Computing Machinery, 2021, pp. 165–175.
conference:
end_date: 2021-07-30
location: Virtual, Italy
name: 'PODC: Principles of Distributed Computing'
start_date: 2021-07-26
date_created: 2021-12-16T13:21:13Z
date_published: 2021-07-21T00:00:00Z
date_updated: 2023-08-17T06:24:44Z
day: '21'
department:
- _id: ElKo
doi: 10.1145/3465084.3467905
external_id:
arxiv:
- '2102.08325'
isi:
- '000744439800016'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2102.08325
month: '07'
oa: 1
oa_version: Preprint
page: 165-175
publication: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing
publication_identifier:
isbn:
- 978-1-4503-8548-0
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: All You Need is DAG
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '10559'
abstract:
- lang: eng
text: Hole gases in planar germanium can have high mobilities in combination with
strong spin-orbit interaction and electrically tunable g factors, and are therefore
emerging as a promising platform for creating hybrid superconductor-semiconductor
devices. A key challenge towards hybrid Ge-based quantum technologies is the design
of high-quality interfaces and superconducting contacts that are robust against
magnetic fields. In this work, by combining the assets of aluminum, which provides
good contact to the Ge, and niobium, which has a significant superconducting gap,
we demonstrate highly transparent low-disordered JoFETs with relatively large
ICRN products that are capable of withstanding high magnetic fields. We furthermore
demonstrate the ability of phase-biasing individual JoFETs, opening up an avenue
to explore topological superconductivity in planar Ge. The persistence of superconductivity
in the reported hybrid devices beyond 1.8 T paves the way towards integrating
spin qubits and proximity-induced superconductivity on the same chip.
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
acknowledgement: This research and related results were made possible with the support
of the NOMIS Foundation. This research was supported by the Scientific Service Units
of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication
facility, the European Union's Horizon 2020 research and innovation program under
the Marie Sklodowska-Curie Grant agreement No. 844511 Grant Agreement No. 862046.
ICN2 acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported
by the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706) and is
funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work
has been performed in the framework of Universitat Autnoma de Barcelona Materials
Science PhD program. The HAADF-STEM microscopy was conducted in the Laboratorio
de Microscopias Avanzadas at Instituto de Nanociencia de Aragon-Universidad de Zaragoza.
Authors acknowledge the LMA-INA for offering access to their instruments and expertise.
We acknowledge support from CSIC Research Platform on Quantum Technologies PTI-001.
This project has received funding from the European Union's Horizon 2020 research
and innovation programme under Grant Agreement No. 823717 ESTEEM3. M.B. acknowledges
support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020
FI 00103. G.S. and M.V. acknowledge support through a projectruimte grant associated
with the Netherlands Organization of Scientific Research (NWO). J.D. acknowledges
support through FRIPRO-project 274853, which is funded by the Research Council of
Norway.
article_number: L022005
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Kushagra
full_name: Aggarwal, Kushagra
id: b22ab905-3539-11eb-84c3-fc159dcd79cb
last_name: Aggarwal
orcid: 0000-0001-9985-9293
- first_name: Andrea C
full_name: Hofmann, Andrea C
id: 340F461A-F248-11E8-B48F-1D18A9856A87
last_name: Hofmann
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
- first_name: Ivan
full_name: Prieto Gonzalez, Ivan
id: 2A307FE2-F248-11E8-B48F-1D18A9856A87
last_name: Prieto Gonzalez
orcid: 0000-0002-7370-5357
- first_name: Amir
full_name: Sammak, Amir
last_name: Sammak
- first_name: Marc
full_name: Botifoll, Marc
last_name: Botifoll
- first_name: Sara
full_name: Martí-Sánchez, Sara
last_name: Martí-Sánchez
- first_name: Menno
full_name: Veldhorst, Menno
last_name: Veldhorst
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Giordano
full_name: Scappucci, Giordano
last_name: Scappucci
- first_name: Jeroen
full_name: Danon, Jeroen
last_name: Danon
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Aggarwal K, Hofmann AC, Jirovec D, et al. Enhancement of proximity-induced
superconductivity in a planar Ge hole gas. Physical Review Research. 2021;3(2).
doi:10.1103/physrevresearch.3.l022005
apa: Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A.,
Botifoll, M., … Katsaros, G. (2021). Enhancement of proximity-induced superconductivity
in a planar Ge hole gas. Physical Review Research. American Physical Society.
https://doi.org/10.1103/physrevresearch.3.l022005
chicago: Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez,
Amir Sammak, Marc Botifoll, Sara Martí-Sánchez, et al. “Enhancement of Proximity-Induced
Superconductivity in a Planar Ge Hole Gas.” Physical Review Research. American
Physical Society, 2021. https://doi.org/10.1103/physrevresearch.3.l022005.
ieee: K. Aggarwal et al., “Enhancement of proximity-induced superconductivity
in a planar Ge hole gas,” Physical Review Research, vol. 3, no. 2. American
Physical Society, 2021.
ista: Aggarwal K, Hofmann AC, Jirovec D, Prieto Gonzalez I, Sammak A, Botifoll M,
Martí-Sánchez S, Veldhorst M, Arbiol J, Scappucci G, Danon J, Katsaros G. 2021.
Enhancement of proximity-induced superconductivity in a planar Ge hole gas. Physical
Review Research. 3(2), L022005.
mla: Aggarwal, Kushagra, et al. “Enhancement of Proximity-Induced Superconductivity
in a Planar Ge Hole Gas.” Physical Review Research, vol. 3, no. 2, L022005,
American Physical Society, 2021, doi:10.1103/physrevresearch.3.l022005.
short: K. Aggarwal, A.C. Hofmann, D. Jirovec, I. Prieto Gonzalez, A. Sammak, M.
Botifoll, S. Martí-Sánchez, M. Veldhorst, J. Arbiol, G. Scappucci, J. Danon, G.
Katsaros, Physical Review Research 3 (2021).
date_created: 2021-12-16T18:50:57Z
date_published: 2021-04-15T00:00:00Z
date_updated: 2024-02-21T12:41:26Z
day: '15'
ddc:
- '620'
department:
- _id: GeKa
doi: 10.1103/physrevresearch.3.l022005
ec_funded: 1
external_id:
arxiv:
- '2012.00322'
file:
- access_level: open_access
checksum: 60a1bc9c9b616b1b155044bb8cfc6484
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-17T08:12:37Z
date_updated: 2021-12-17T08:12:37Z
file_id: '10561'
file_name: 2021_PhysRevResearch_Aggarwal.pdf
file_size: 1917512
relation: main_file
success: 1
file_date_updated: 2021-12-17T08:12:37Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '2'
keyword:
- general engineering
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 26A151DA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '844511'
name: Majorana bound states in Ge/SiGe heterostructures
- _id: 237E5020-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862046'
name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '8831'
relation: earlier_version
status: public
- id: '8834'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Enhancement of proximity-induced superconductivity in a planar Ge hole gas
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 3
year: '2021'
...
---
_id: '10565'
abstract:
- lang: eng
text: 'Enzymatic digestion of the extracellular matrix with chondroitinase-ABC reinstates
juvenile-like plasticity in the adult cortex as it also disassembles the perineuronal
nets (PNNs). The disadvantage of the enzyme is that it must be applied intracerebrally
and it degrades the ECM for several weeks. Here, we provide two minimally invasive
and transient protocols for microglia-enabled PNN disassembly in mouse cortex:
repeated treatment with ketamine-xylazine-acepromazine (KXA) anesthesia and 60-Hz
light entrainment. We also discuss how to analyze PNNs within microglial endosomes-lysosomes.
For complete details on the use and execution of this protocol, please refer to
Venturino et al. (2021).'
acknowledged_ssus:
- _id: Bio
acknowledgement: This research was supported by the European Research Council (grant
715571 to S.S.). We thank Rouven Schulz, Michael Schunn, Claudia Gold, Gabriel Krens,
Sarah Gorkiewicz, Margaret Maes, Jürgen Siegert, Marco Benevento, and Sara Oakeley
for comments on the manuscript and the IST Austria Bioimaging Facility for the technical
support.
article_number: '101012'
article_processing_charge: Yes
article_type: original
author:
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Venturino A, Siegert S. Minimally invasive protocols and quantification for
microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols.
2021;2(4). doi:10.1016/j.xpro.2021.101012
apa: Venturino, A., & Siegert, S. (2021). Minimally invasive protocols and quantification
for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols.
Elsevier ; Cell Press. https://doi.org/10.1016/j.xpro.2021.101012
chicago: Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols
and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse
Brain.” STAR Protocols. Elsevier ; Cell Press, 2021. https://doi.org/10.1016/j.xpro.2021.101012.
ieee: A. Venturino and S. Siegert, “Minimally invasive protocols and quantification
for microglia-mediated perineuronal net disassembly in mouse brain,” STAR Protocols,
vol. 2, no. 4. Elsevier ; Cell Press, 2021.
ista: Venturino A, Siegert S. 2021. Minimally invasive protocols and quantification
for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols.
2(4), 101012.
mla: Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and
Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.”
STAR Protocols, vol. 2, no. 4, 101012, Elsevier ; Cell Press, 2021, doi:10.1016/j.xpro.2021.101012.
short: A. Venturino, S. Siegert, STAR Protocols 2 (2021).
date_created: 2021-12-19T23:01:32Z
date_published: 2021-12-17T00:00:00Z
date_updated: 2023-11-16T13:11:04Z
day: '17'
ddc:
- '573'
department:
- _id: SaSi
doi: 10.1016/j.xpro.2021.101012
ec_funded: 1
file:
- access_level: open_access
checksum: 9ea2501056c5df99e84726b845e9b976
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-20T08:58:40Z
date_updated: 2021-12-20T08:58:40Z
file_id: '10570'
file_name: 2021_STARProt_Venturino.pdf
file_size: 6207060
relation: main_file
success: 1
file_date_updated: 2021-12-20T08:58:40Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '4'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25D4A630-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715571'
name: Microglia action towards neuronal circuit formation and function in health
and disease
publication: STAR Protocols
publication_identifier:
eissn:
- 2666-1667
publication_status: published
publisher: Elsevier ; Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Minimally invasive protocols and quantification for microglia-mediated perineuronal
net disassembly in mouse brain
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2021'
...
---
_id: '10568'
abstract:
- lang: eng
text: Genetic adaptation and phenotypic plasticity facilitate the migration into
new habitats and enable organisms to cope with a rapidly changing environment.
In contrast to genetic adaptation that spans multiple generations as an evolutionary
process, phenotypic plasticity allows acclimation within the life-time of an organism.
Genetic adaptation and phenotypic plasticity are usually studied in isolation,
however, only by including their interactive impact, we can understand acclimation
and adaptation in nature. We aimed to explore the contribution of adaptation and
plasticity in coping with an abiotic (salinity) and a biotic (Vibrio bacteria)
stressor using six different populations of the broad-nosed pipefish Syngnathus
typhle that originated from either high [14–17 Practical Salinity Unit (PSU)]
or low (7–11 PSU) saline environments along the German coastline of the Baltic
Sea. We exposed wild caught animals, to either high (15 PSU) or low (7 PSU) salinity,
representing native and novel salinity conditions and allowed animals to mate.
After male pregnancy, offspring was split and each half was exposed to one of
the two salinities and infected with Vibrio alginolyticus bacteria that were evolved
at either of the two salinities in a fully reciprocal design. We investigated
life-history traits of fathers and expression of 47 target genes in mothers and
offspring. Pregnant males originating from high salinity exposed to low salinity
were highly susceptible to opportunistic fungi infections resulting in decreased
offspring size and number. In contrast, no signs of fungal infection were identified
in fathers originating from low saline conditions suggesting that genetic adaptation
has the potential to overcome the challenges encountered at low salinity. Offspring
from parents with low saline origin survived better at low salinity suggesting
genetic adaptation to low salinity. In addition, gene expression analyses of juveniles
indicated patterns of local adaptation, trans-generational plasticity and developmental
plasticity. In conclusion, our study suggests that pipefish are locally adapted
to the low salinity in their environment, however, they are retaining phenotypic
plasticity, which allows them to also cope with ancestral salinity levels and
prevailing pathogens.
acknowledgement: We are grateful for the help of Kristina Dauven, Andreas Ebner, Janina
Röckner, and Paulina Urban for fish collection in the field and fish maintenance.
Furthermore, we thank Fabian Wendt for setting up the aquaria system and Tatjana
Liese, Paulina Urban, Jakob Gismann, and Thorsten Reusch for support with DNA extraction
and analysis of pipefish population structure. The authors acknowledge support of
Isabel Tanger, Agnes Piecyk, Jonas Müller, Grace Walls, Sebastian Albrecht, Julia
Böge, and Julia Stefanschitz for their support in preparing cDNA and running of
Fluidigm chips. A special thank goes to Diana Gill for general lab support, ordering
materials and just being the good spirit of our molecular lab, to Till Bayer for
bioinformatics support and to Melanie Heckwolf for fruitful discussion and feedback
on the manuscript. HG is very grateful for inspirational office space with ocean
view provided by Lisa Hentschel and family. This manuscript has been released as
a pre-print at BIORXIV.
article_number: '626442'
article_processing_charge: No
article_type: original
author:
- first_name: Henry
full_name: Goehlich, Henry
last_name: Goehlich
- first_name: Linda
full_name: Sartoris, Linda
id: 2B9284CA-F248-11E8-B48F-1D18A9856A87
last_name: Sartoris
- first_name: Kim-Sara
full_name: Wagner, Kim-Sara
last_name: Wagner
- first_name: Carolin C.
full_name: Wendling, Carolin C.
last_name: Wendling
- first_name: Olivia
full_name: Roth, Olivia
last_name: Roth
citation:
ama: Goehlich H, Sartoris L, Wagner K-S, Wendling CC, Roth O. Pipefish locally adapted
to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral
salinity levels. Frontiers in Ecology and Evolution. 2021;9. doi:10.3389/fevo.2021.626442
apa: Goehlich, H., Sartoris, L., Wagner, K.-S., Wendling, C. C., & Roth, O.
(2021). Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic
plasticity to cope with ancestral salinity levels. Frontiers in Ecology and
Evolution. Frontiers Media. https://doi.org/10.3389/fevo.2021.626442
chicago: Goehlich, Henry, Linda Sartoris, Kim-Sara Wagner, Carolin C. Wendling,
and Olivia Roth. “Pipefish Locally Adapted to Low Salinity in the Baltic Sea Retain
Phenotypic Plasticity to Cope with Ancestral Salinity Levels.” Frontiers in
Ecology and Evolution. Frontiers Media, 2021. https://doi.org/10.3389/fevo.2021.626442.
ieee: H. Goehlich, L. Sartoris, K.-S. Wagner, C. C. Wendling, and O. Roth, “Pipefish
locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity
to cope with ancestral salinity levels,” Frontiers in Ecology and Evolution,
vol. 9. Frontiers Media, 2021.
ista: Goehlich H, Sartoris L, Wagner K-S, Wendling CC, Roth O. 2021. Pipefish locally
adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope
with ancestral salinity levels. Frontiers in Ecology and Evolution. 9, 626442.
mla: Goehlich, Henry, et al. “Pipefish Locally Adapted to Low Salinity in the Baltic
Sea Retain Phenotypic Plasticity to Cope with Ancestral Salinity Levels.” Frontiers
in Ecology and Evolution, vol. 9, 626442, Frontiers Media, 2021, doi:10.3389/fevo.2021.626442.
short: H. Goehlich, L. Sartoris, K.-S. Wagner, C.C. Wendling, O. Roth, Frontiers
in Ecology and Evolution 9 (2021).
date_created: 2021-12-20T07:53:19Z
date_published: 2021-03-25T00:00:00Z
date_updated: 2023-08-17T06:27:22Z
day: '25'
ddc:
- '597'
department:
- _id: SyCr
doi: 10.3389/fevo.2021.626442
external_id:
isi:
- '000637736300001'
file:
- access_level: open_access
checksum: 8d6e2b767bb0240a9b5a3a3555be51fd
content_type: application/pdf
creator: alisjak
date_created: 2021-12-20T10:44:20Z
date_updated: 2021-12-20T10:44:20Z
file_id: '10572'
file_name: 2021_Frontiers_Goehlich.pdf
file_size: 3175085
relation: main_file
success: 1
file_date_updated: 2021-12-20T10:44:20Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
keyword:
- ecology
- evolution
- behavior and systematics
- trans-generational plasticity
- genetic adaptation
- local adaptation
- phenotypic plasticity
- Baltic Sea
- climate change
- salinity
- syngnathids
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Frontiers in Ecology and Evolution
publication_identifier:
issn:
- 2296-701X
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic
plasticity to cope with ancestral salinity levels
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2021'
...
---
_id: '10569'
abstract:
- lang: eng
text: 'For animals to survive until reproduction, it is crucial that juveniles successfully
detect potential predators and respond with appropriate behavior. The recognition
of cues originating from predators can be innate or learned. Cues of various modalities
might be used alone or in multi-modal combinations to detect and distinguish predators
but studies investigating multi-modal integration in predator avoidance are scarce.
Here, we used wild, naive tadpoles of the Neotropical poison frog Allobates femoralis
( Boulenger, 1884) to test their reaction to cues with two modalities from two
different sympatrically occurring potential predators: heterospecific predatory
Dendrobates tinctorius tadpoles and dragonfly larvae. We presented A. femoralis
tadpoles with olfactory or visual cues, or a combination of the two, and compared
their reaction to a water control in a between-individual design. In our trials,
A. femoralis tadpoles reacted to multi-modal stimuli (a combination of visual
and chemical information) originating from dragonfly larvae with avoidance but
showed no reaction to uni-modal cues or cues from heterospecific tadpoles. In
addition, visual cues from conspecifics increased swimming activity while cues
from predators had no effect on tadpole activity. Our results show that A. femoralis
tadpoles can innately recognize some predators and probably need both visual and
chemical information to effectively avoid them. This is the first study looking
at anti-predator behavior in poison frog tadpoles. We discuss how parental care
might influence the expression of predator avoidance responses in tadpoles.'
acknowledgement: We are grateful to Véronique Helfer, Walter Hödl, Lisa Schretzmeyer
and Julia Wotke, who assisted with fieldwork in French Guiana. This work was supported
by the Austrian Science Fund (FWF) [P24788, T699 and P31518 to E.R.; P33728 to M.R.;
J3827 to Thomas Bugnyar, Tecumseh Fitch and Ludwig Huber]; and by the Austrian Bundesministerium
für Wissenschaft, Forschung und Wirtschaft [IS761001 to J.O. (Tecumseh Fitch, Thomas
Bugnyar and Ludwig Huber)]. A.P. was supported by the European Union's Horizon 2020
research and innovation programme under the Marie Sklodowska-Curie grant agreement
no. 835530. S.A.R. was supported by the HT faculty, Lund University. We thank the
CNRS Nouragues Ecological Research Station, which benefited from the ‘Investissement
d'Avenir’ grants managed by the Agence Nationale de la Recherche (AnaEE France ANR-11-INBS-0001;
Labex CEBA ANR-10-LABX-25-01). Open access funding provided by University of Vienna.
Deposited in PMC for immediate release.
article_number: jeb243647
article_processing_charge: No
article_type: original
author:
- first_name: B
full_name: Szabo, B
last_name: Szabo
- first_name: R
full_name: Mangione, R
last_name: Mangione
- first_name: M
full_name: Rath, M
last_name: Rath
- first_name: A
full_name: Pašukonis, A
last_name: Pašukonis
- first_name: SA
full_name: Reber, SA
last_name: Reber
- first_name: Jinook
full_name: Oh, Jinook
id: 403169A4-080F-11EA-9993-BF3F3DDC885E
last_name: Oh
orcid: 0000-0001-7425-2372
- first_name: M
full_name: Ringler, M
last_name: Ringler
- first_name: E
full_name: Ringler, E
last_name: Ringler
citation:
ama: Szabo B, Mangione R, Rath M, et al. Naïve poison frog tadpoles use bi-modal
cues to avoid insect predators but not heterospecific predatory tadpoles. Journal
of Experimental Biology. 2021;224(24). doi:10.1242/jeb.243647
apa: Szabo, B., Mangione, R., Rath, M., Pašukonis, A., Reber, S., Oh, J., … Ringler,
E. (2021). Naïve poison frog tadpoles use bi-modal cues to avoid insect predators
but not heterospecific predatory tadpoles. Journal of Experimental Biology.
The Company of Biologists. https://doi.org/10.1242/jeb.243647
chicago: Szabo, B, R Mangione, M Rath, A Pašukonis, SA Reber, Jinook Oh, M Ringler,
and E Ringler. “Naïve Poison Frog Tadpoles Use Bi-Modal Cues to Avoid Insect Predators
but Not Heterospecific Predatory Tadpoles.” Journal of Experimental Biology.
The Company of Biologists, 2021. https://doi.org/10.1242/jeb.243647.
ieee: B. Szabo et al., “Naïve poison frog tadpoles use bi-modal cues to avoid
insect predators but not heterospecific predatory tadpoles,” Journal of Experimental
Biology, vol. 224, no. 24. The Company of Biologists, 2021.
ista: Szabo B, Mangione R, Rath M, Pašukonis A, Reber S, Oh J, Ringler M, Ringler
E. 2021. Naïve poison frog tadpoles use bi-modal cues to avoid insect predators
but not heterospecific predatory tadpoles. Journal of Experimental Biology. 224(24),
jeb243647.
mla: Szabo, B., et al. “Naïve Poison Frog Tadpoles Use Bi-Modal Cues to Avoid Insect
Predators but Not Heterospecific Predatory Tadpoles.” Journal of Experimental
Biology, vol. 224, no. 24, jeb243647, The Company of Biologists, 2021, doi:10.1242/jeb.243647.
short: B. Szabo, R. Mangione, M. Rath, A. Pašukonis, S. Reber, J. Oh, M. Ringler,
E. Ringler, Journal of Experimental Biology 224 (2021).
date_created: 2021-12-20T07:54:22Z
date_published: 2021-12-16T00:00:00Z
date_updated: 2023-08-17T06:26:15Z
day: '16'
ddc:
- '573'
department:
- _id: SyCr
doi: 10.1242/jeb.243647
external_id:
isi:
- '000738259300013'
pmid:
- '34845497'
file:
- access_level: open_access
checksum: 75d13a5ec8e3b90e3bc02bd8a9c17eef
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-20T10:14:14Z
date_updated: 2021-12-20T10:14:14Z
file_id: '10571'
file_name: 2021_JExpBio_Szabo.pdf
file_size: 607096
relation: main_file
success: 1
file_date_updated: 2021-12-20T10:14:14Z
has_accepted_license: '1'
intvolume: ' 224'
isi: 1
issue: '24'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Experimental Biology
publication_identifier:
eissn:
- 1477-9145
issn:
- 0022-0949
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
status: public
title: Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but
not heterospecific predatory tadpoles
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: 224
year: '2021'
...
---
_id: '10573'
abstract:
- lang: eng
text: How tissues acquire complex shapes is a fundamental question in biology and
regenerative medicine. Zebrafish semicircular canals form from invaginations in
the otic epithelium (buds) that extend and fuse to form the hubs of each canal.
We find that conventional actomyosin-driven behaviors are not required. Instead,
local secretion of hyaluronan, made by the enzymes uridine 5′-diphosphate dehydrogenase
(ugdh) and hyaluronan synthase 3 (has3), drives canal morphogenesis. Charged hyaluronate
polymers osmotically swell with water and generate isotropic extracellular pressure
to deform the overlying epithelium into buds. The mechanical anisotropy needed
to shape buds into tubes is conferred by a polarized distribution of actomyosin
and E-cadherin-rich membrane tethers, which we term cytocinches. Most work on
tissue morphogenesis ascribes actomyosin contractility as the driving force, while
the extracellular matrix shapes tissues through differential stiffness. Our work
inverts this expectation. Hyaluronate pressure shaped by anisotropic tissue stiffness
may be a widespread mechanism for powering morphological change in organogenesis
and tissue engineering.
acknowledgement: We thank Ian Swinburne, Sandy Nandagopal, and Toru Kawanishi for
support, discussions, and reagents. We thank Vanessa Barone, Joseph Nasser, and
members of the Megason lab for useful comments on the manuscript and general feedback.
We are grateful to the Heisenberg and Knaut labs for transgenic fish. Diagrams on
the right in the graphical abstract were created using BioRender. This work was
supported by NIH R01DC015478 and NIH R01GM107733 to S.G.M. A.M. was supported by
Human Frontiers Science Program LTF and NIH K99HD098918.
article_processing_charge: No
article_type: original
author:
- first_name: Akankshi
full_name: Munjal, Akankshi
last_name: Munjal
- 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: Tony Y.C.
full_name: Tsai, Tony Y.C.
last_name: Tsai
- first_name: Timothy J.
full_name: Mitchison, Timothy J.
last_name: Mitchison
- first_name: Sean G.
full_name: Megason, Sean G.
last_name: Megason
citation:
ama: Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. Extracellular hyaluronate
pressure shaped by cellular tethers drives tissue morphogenesis. Cell.
2021;184(26):6313-6325.e18. doi:10.1016/j.cell.2021.11.025
apa: Munjal, A., Hannezo, E. B., Tsai, T. Y. C., Mitchison, T. J., & Megason,
S. G. (2021). Extracellular hyaluronate pressure shaped by cellular tethers drives
tissue morphogenesis. Cell. Elsevier ; Cell Press. https://doi.org/10.1016/j.cell.2021.11.025
chicago: Munjal, Akankshi, Edouard B Hannezo, Tony Y.C. Tsai, Timothy J. Mitchison,
and Sean G. Megason. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers
Drives Tissue Morphogenesis.” Cell. Elsevier ; Cell Press, 2021. https://doi.org/10.1016/j.cell.2021.11.025.
ieee: A. Munjal, E. B. Hannezo, T. Y. C. Tsai, T. J. Mitchison, and S. G. Megason,
“Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis,”
Cell, vol. 184, no. 26. Elsevier ; Cell Press, p. 6313–6325.e18, 2021.
ista: Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. 2021. Extracellular
hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell.
184(26), 6313–6325.e18.
mla: Munjal, Akankshi, et al. “Extracellular Hyaluronate Pressure Shaped by Cellular
Tethers Drives Tissue Morphogenesis.” Cell, vol. 184, no. 26, Elsevier ;
Cell Press, 2021, p. 6313–6325.e18, doi:10.1016/j.cell.2021.11.025.
short: A. Munjal, E.B. Hannezo, T.Y.C. Tsai, T.J. Mitchison, S.G. Megason, Cell
184 (2021) 6313–6325.e18.
date_created: 2021-12-26T23:01:26Z
date_published: 2021-12-22T00:00:00Z
date_updated: 2023-08-17T06:28:25Z
day: '22'
department:
- _id: EdHa
doi: 10.1016/j.cell.2021.11.025
external_id:
isi:
- '000735387500002'
intvolume: ' 184'
isi: 1
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2020.09.28.316042
month: '12'
oa: 1
oa_version: Preprint
page: 6313-6325.e18
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier ; Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extracellular hyaluronate pressure shaped by cellular tethers drives tissue
morphogenesis
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 184
year: '2021'
...