---
_id: '10738'
abstract:
- lang: eng
text: We prove an adiabatic theorem for the Landau–Pekar equations. This allows
us to derive new results on the accuracy of their use as effective equations for
the time evolution generated by the Fröhlich Hamiltonian with large coupling constant
α. In particular, we show that the time evolution of Pekar product states with
coherent phonon field and the electron being trapped by the phonons is well approximated
by the Landau–Pekar equations until times short compared to α2.
acknowledgement: "N. L. and R. S. gratefully acknowledge financial support by the
European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research
and innovation programme (grant\r\nagreement No 694227). B. S. acknowledges support
from the Swiss National Science Foundation (grant 200020_172623) and from the NCCR
SwissMAP. N. L. would like to thank\r\nAndreas Deuchert and David Mitrouskas for
interesting discussions. B. S. and R. S. would\r\nlike to thank Rupert Frank for
stimulating discussions about the time-evolution of a polaron.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: Simone Anna Elvira
full_name: Rademacher, Simone Anna Elvira
id: 856966FE-A408-11E9-977E-802DE6697425
last_name: Rademacher
orcid: 0000-0001-5059-4466
- 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: 'Leopold NK, Rademacher SAE, Schlein B, Seiringer R. The Landau–Pekar equations:
Adiabatic theorem and accuracy. Analysis and PDE. 2021;14(7):2079-2100.
doi:10.2140/APDE.2021.14.2079'
apa: 'Leopold, N. K., Rademacher, S. A. E., Schlein, B., & Seiringer, R. (2021). The
Landau–Pekar equations: Adiabatic theorem and accuracy. Analysis and PDE.
Mathematical Sciences Publishers. https://doi.org/10.2140/APDE.2021.14.2079'
chicago: 'Leopold, Nikolai K, Simone Anna Elvira Rademacher, Benjamin Schlein, and
Robert Seiringer. “ The Landau–Pekar Equations: Adiabatic Theorem and Accuracy.”
Analysis and PDE. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/APDE.2021.14.2079.'
ieee: 'N. K. Leopold, S. A. E. Rademacher, B. Schlein, and R. Seiringer, “ The Landau–Pekar
equations: Adiabatic theorem and accuracy,” Analysis and PDE, vol. 14,
no. 7. Mathematical Sciences Publishers, pp. 2079–2100, 2021.'
ista: 'Leopold NK, Rademacher SAE, Schlein B, Seiringer R. 2021. The Landau–Pekar
equations: Adiabatic theorem and accuracy. Analysis and PDE. 14(7), 2079–2100.'
mla: 'Leopold, Nikolai K., et al. “ The Landau–Pekar Equations: Adiabatic Theorem
and Accuracy.” Analysis and PDE, vol. 14, no. 7, Mathematical Sciences
Publishers, 2021, pp. 2079–100, doi:10.2140/APDE.2021.14.2079.'
short: N.K. Leopold, S.A.E. Rademacher, B. Schlein, R. Seiringer, Analysis and PDE
14 (2021) 2079–2100.
date_created: 2022-02-06T23:01:33Z
date_published: 2021-11-10T00:00:00Z
date_updated: 2023-10-17T11:26:45Z
day: '10'
department:
- _id: RoSe
doi: 10.2140/APDE.2021.14.2079
ec_funded: 1
external_id:
arxiv:
- '1904.12532'
isi:
- '000733976600004'
intvolume: ' 14'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1904.12532
month: '11'
oa: 1
oa_version: Preprint
page: 2079-2100
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Analysis and PDE
publication_identifier:
eissn:
- 1948-206X
issn:
- 2157-5045
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: ' The Landau–Pekar equations: Adiabatic theorem and accuracy'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
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: '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
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: '10593'
abstract:
- lang: eng
text: 'We study the problem of estimating a rank-$1$ signal in the presence of rotationally
invariant noise-a class of perturbations more general than Gaussian noise. Principal
Component Analysis (PCA) provides a natural estimator, and sharp results on its
performance have been obtained in the high-dimensional regime. Recently, an Approximate
Message Passing (AMP) algorithm has been proposed as an alternative estimator
with the potential to improve the accuracy of PCA. However, the existing analysis
of AMP requires an initialization that is both correlated with the signal and
independent of the noise, which is often unrealistic in practice. In this work,
we combine the two methods, and propose to initialize AMP with PCA. Our main result
is a rigorous asymptotic characterization of the performance of this estimator.
Both the AMP algorithm and its analysis differ from those previously derived in
the Gaussian setting: at every iteration, our AMP algorithm requires a specific
term to account for PCA initialization, while in the Gaussian case, PCA initialization
affects only the first iteration of AMP. The proof is based on a two-phase artificial
AMP that first approximates the PCA estimator and then mimics the true AMP. Our
numerical simulations show an excellent agreement between AMP results and theoretical
predictions, and suggest an interesting open direction on achieving Bayes-optimal
performance.'
acknowledgement: "M. Mondelli would like to thank László Erdős for helpful discussions.
M. Mondelli was partially supported by the 2019 Lopez-Loreta Prize. R. Venkataramanan
was partially supported by the Alan Turing Institute under the EPSRC grant EP/N510129/1.\r\n"
article_processing_charge: No
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Ramji
full_name: Venkataramanan, Ramji
last_name: Venkataramanan
citation:
ama: 'Mondelli M, Venkataramanan R. PCA initialization for approximate message passing
in rotationally invariant models. In: 35th Conference on Neural Information
Processing Systems. Vol 35. Neural Information Processing Systems Foundation;
2021:29616-29629.'
apa: 'Mondelli, M., & Venkataramanan, R. (2021). PCA initialization for approximate
message passing in rotationally invariant models. In 35th Conference on Neural
Information Processing Systems (Vol. 35, pp. 29616–29629). Virtual: Neural
Information Processing Systems Foundation.'
chicago: Mondelli, Marco, and Ramji Venkataramanan. “PCA Initialization for Approximate
Message Passing in Rotationally Invariant Models.” In 35th Conference on Neural
Information Processing Systems, 35:29616–29. Neural Information Processing
Systems Foundation, 2021.
ieee: M. Mondelli and R. Venkataramanan, “PCA initialization for approximate message
passing in rotationally invariant models,” in 35th Conference on Neural Information
Processing Systems, Virtual, 2021, vol. 35, pp. 29616–29629.
ista: 'Mondelli M, Venkataramanan R. 2021. PCA initialization for approximate message
passing in rotationally invariant models. 35th Conference on Neural Information
Processing Systems. NeurIPS: Neural Information Processing Systems vol. 35, 29616–29629.'
mla: Mondelli, Marco, and Ramji Venkataramanan. “PCA Initialization for Approximate
Message Passing in Rotationally Invariant Models.” 35th Conference on Neural
Information Processing Systems, vol. 35, Neural Information Processing Systems
Foundation, 2021, pp. 29616–29.
short: M. Mondelli, R. Venkataramanan, in:, 35th Conference on Neural Information
Processing Systems, Neural Information Processing Systems Foundation, 2021, pp.
29616–29629.
conference:
end_date: 2021-12-14
location: Virtual
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2021-12-06
date_created: 2022-01-03T10:50:02Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2023-10-17T11:48:23Z
day: '01'
department:
- _id: MaMo
external_id:
arxiv:
- '2106.02356'
intvolume: ' 35'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2106.02356
month: '12'
oa: 1
oa_version: Preprint
page: 29616-29629
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: 35th Conference on Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713845393'
issn:
- 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: PCA initialization for approximate message passing in rotationally invariant
models
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2021'
...
---
_id: '10594'
abstract:
- lang: eng
text: 'The question of how and why the phenomenon of mode connectivity occurs in
training deep neural networks has gained remarkable attention in the research
community. From a theoretical perspective, two possible explanations have been
proposed: (i) the loss function has connected sublevel sets, and (ii) the solutions
found by stochastic gradient descent are dropout stable. While these explanations
provide insights into the phenomenon, their assumptions are not always satisfied
in practice. In particular, the first approach requires the network to have one
layer with order of N neurons (N being the number of training samples), while
the second one requires the loss to be almost invariant after removing half of
the neurons at each layer (up to some rescaling of the remaining ones). In this
work, we improve both conditions by exploiting the quality of the features at
every intermediate layer together with a milder over-parameterization condition.
More specifically, we show that: (i) under generic assumptions on the features
of intermediate layers, it suffices that the last two hidden layers have order
of N−−√ neurons, and (ii) if subsets of features at each layer are linearly separable,
then no over-parameterization is needed to show the connectivity. Our experiments
confirm that the proposed condition ensures the connectivity of solutions found
by stochastic gradient descent, even in settings where the previous requirements
do not hold.'
acknowledgement: MM was partially supported by the 2019 Lopez-Loreta Prize. QN and
PB acknowledge support from the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (grant agreement no 757983).
article_processing_charge: No
author:
- first_name: Quynh
full_name: Nguyen, Quynh
last_name: Nguyen
- first_name: Pierre
full_name: Bréchet, Pierre
last_name: Bréchet
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: 'Nguyen Q, Bréchet P, Mondelli M. When are solutions connected in deep networks?
In: 35th Conference on Neural Information Processing Systems. Vol 35. Neural
Information Processing Systems Foundation; 2021.'
apa: 'Nguyen, Q., Bréchet, P., & Mondelli, M. (2021). When are solutions connected
in deep networks? In 35th Conference on Neural Information Processing Systems
(Vol. 35). Virtual: Neural Information Processing Systems Foundation.'
chicago: Nguyen, Quynh, Pierre Bréchet, and Marco Mondelli. “When Are Solutions
Connected in Deep Networks?” In 35th Conference on Neural Information Processing
Systems, Vol. 35. Neural Information Processing Systems Foundation, 2021.
ieee: Q. Nguyen, P. Bréchet, and M. Mondelli, “When are solutions connected in deep
networks?,” in 35th Conference on Neural Information Processing Systems,
Virtual, 2021, vol. 35.
ista: Nguyen Q, Bréchet P, Mondelli M. 2021. When are solutions connected in deep
networks? 35th Conference on Neural Information Processing Systems. 35th Conference
on Neural Information Processing Systems vol. 35.
mla: Nguyen, Quynh, et al. “When Are Solutions Connected in Deep Networks?” 35th
Conference on Neural Information Processing Systems, vol. 35, Neural Information
Processing Systems Foundation, 2021.
short: Q. Nguyen, P. Bréchet, M. Mondelli, in:, 35th Conference on Neural Information
Processing Systems, Neural Information Processing Systems Foundation, 2021.
conference:
end_date: 2021-12-14
location: Virtual
name: 35th Conference on Neural Information Processing Systems
start_date: 2021-12-06
date_created: 2022-01-03T10:56:20Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2023-10-17T11:48:40Z
day: '01'
department:
- _id: MaMo
external_id:
arxiv:
- '2102.09671'
intvolume: ' 35'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2102.09671
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: 35th Conference on Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713845393'
issn:
- 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
status: public
title: When are solutions connected in deep networks?
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2021'
...
---
_id: '9815'
abstract:
- lang: eng
text: The quantum bits (qubits) on which superconducting quantum computers are based
have energy scales corresponding to photons with GHz frequencies. The energy of
photons in the gigahertz domain is too low to allow transmission through the noisy
room-temperature environment, where the signal would be lost in thermal noise.
Optical photons, on the other hand, have much higher energies, and signals can
be detected using highly efficient single-photon detectors. Transduction from
microwave to optical frequencies is therefore a potential enabling technology
for quantum devices. However, in such a device the optical pump can be a source
of thermal noise and thus degrade the fidelity; the similarity of input microwave
state to the output optical state. In order to investigate the magnitude of this
effect we model the sub-Kelvin thermal behavior of an electro-optic transducer
based on a lithium niobate whispering gallery mode resonator. We find that there
is an optimum power level for a continuous pump, whilst pulsed operation of the
pump increases the fidelity of the conversion.
acknowledgement: NJL is supported by the MBIE Endeavour Fund (UOOX1805) and GL is
by the Julius von Haast Fellowship of New Zealand. SM acknowledges stimulating discussions
with T M Jensen.
article_number: '045005'
article_processing_charge: Yes
article_type: original
author:
- first_name: Sonia
full_name: Mobassem, Sonia
last_name: Mobassem
- first_name: Nicholas J.
full_name: Lambert, Nicholas J.
last_name: Lambert
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Gerd
full_name: Leuchs, Gerd
last_name: Leuchs
- first_name: Harald G.L.
full_name: Schwefel, Harald G.L.
last_name: Schwefel
citation:
ama: Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL.
Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science
and Technology. 2021;6(4). doi:10.1088/2058-9565/ac0f36
apa: Mobassem, S., Lambert, N. J., Rueda Sanchez, A. R., Fink, J. M., Leuchs, G.,
& Schwefel, H. G. L. (2021). Thermal noise in electro-optic devices at cryogenic
temperatures. Quantum Science and Technology. IOP Publishing. https://doi.org/10.1088/2058-9565/ac0f36
chicago: Mobassem, Sonia, Nicholas J. Lambert, Alfredo R Rueda Sanchez, Johannes
M Fink, Gerd Leuchs, and Harald G.L. Schwefel. “Thermal Noise in Electro-Optic
Devices at Cryogenic Temperatures.” Quantum Science and Technology. IOP
Publishing, 2021. https://doi.org/10.1088/2058-9565/ac0f36.
ieee: S. Mobassem, N. J. Lambert, A. R. Rueda Sanchez, J. M. Fink, G. Leuchs, and
H. G. L. Schwefel, “Thermal noise in electro-optic devices at cryogenic temperatures,”
Quantum Science and Technology, vol. 6, no. 4. IOP Publishing, 2021.
ista: Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL.
2021. Thermal noise in electro-optic devices at cryogenic temperatures. Quantum
Science and Technology. 6(4), 045005.
mla: Mobassem, Sonia, et al. “Thermal Noise in Electro-Optic Devices at Cryogenic
Temperatures.” Quantum Science and Technology, vol. 6, no. 4, 045005, IOP
Publishing, 2021, doi:10.1088/2058-9565/ac0f36.
short: S. Mobassem, N.J. Lambert, A.R. Rueda Sanchez, J.M. Fink, G. Leuchs, H.G.L.
Schwefel, Quantum Science and Technology 6 (2021).
date_created: 2021-08-08T22:01:25Z
date_published: 2021-07-15T00:00:00Z
date_updated: 2023-10-17T12:54:54Z
day: '15'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1088/2058-9565/ac0f36
external_id:
arxiv:
- '2008.08764'
isi:
- '000673081500001'
file:
- access_level: open_access
checksum: b15c2c228487a75002c3b52d56f23d5c
content_type: application/pdf
creator: cchlebak
date_created: 2021-08-09T12:23:13Z
date_updated: 2021-08-09T12:23:13Z
file_id: '9836'
file_name: 2021_QuantumScienceTechnology_Mobassem.pdf
file_size: 2366118
relation: main_file
file_date_updated: 2021-08-09T12:23:13Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Quantum Science and Technology
publication_identifier:
eissn:
- 2058-9565
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thermal noise in electro-optic devices at cryogenic temperatures
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: 6
year: '2021'
...
---
_id: '9978'
abstract:
- lang: eng
text: Redox mediators could catalyse otherwise slow and energy-inefficient cycling
of Li-S and Li-O 2 batteries by shuttling electrons/holes between the electrode
and the solid insulating storage materials. For mediators to work efficiently
they need to oxidize the solid with fast kinetics yet the lowest possible overpotential.
Here, we found that when the redox potentials of mediators are tuned via, e.g.,
Li + concentration in the electrolyte, they exhibit distinct threshold potentials,
where the kinetics accelerate several-fold within a range as small as 10 mV. This
phenomenon is independent of types of mediators and electrolyte. The acceleration
originates from the overpotentials required to activate fast Li + /e – extraction
and the following chemical step at specific abundant surface facets. Efficient
redox catalysis at insulating solids requires therefore carefully considering
the surface conditions of the storage materials and electrolyte-dependent redox
potentials, which may be tuned by salt concentrations or solvents.
acknowledgement: 'This work was financially supported by the National Natural Science
Foundation of China (51773092, 21975124, 11874254, 51802187, U2030206). S.A.F. is
indebted to IST Austria for support. '
article_processing_charge: No
author:
- first_name: Deqing
full_name: Cao, Deqing
last_name: Cao
- first_name: Xiaoxiao
full_name: Shen, Xiaoxiao
last_name: Shen
- first_name: Aiping
full_name: Wang, Aiping
last_name: Wang
- first_name: Fengjiao
full_name: Yu, Fengjiao
last_name: Yu
- first_name: Yuping
full_name: Wu, Yuping
last_name: Wu
- first_name: Siqi
full_name: Shi, Siqi
last_name: Shi
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Yuhui
full_name: Chen, Yuhui
last_name: Chen
citation:
ama: Cao D, Shen X, Wang A, et al. Sharp kinetic acceleration potentials during
mediated redox catalysis of insulators. Research Square. doi:10.21203/rs.3.rs-750965/v1
apa: Cao, D., Shen, X., Wang, A., Yu, F., Wu, Y., Shi, S., … Chen, Y. (n.d.). Sharp
kinetic acceleration potentials during mediated redox catalysis of insulators.
Research Square. Research Square. https://doi.org/10.21203/rs.3.rs-750965/v1
chicago: Cao, Deqing, Xiaoxiao Shen, Aiping Wang, Fengjiao Yu, Yuping Wu, Siqi Shi,
Stefan Alexander Freunberger, and Yuhui Chen. “Sharp Kinetic Acceleration Potentials
during Mediated Redox Catalysis of Insulators.” Research Square. Research
Square, n.d. https://doi.org/10.21203/rs.3.rs-750965/v1.
ieee: D. Cao et al., “Sharp kinetic acceleration potentials during mediated
redox catalysis of insulators,” Research Square. Research Square.
ista: Cao D, Shen X, Wang A, Yu F, Wu Y, Shi S, Freunberger SA, Chen Y. Sharp kinetic
acceleration potentials during mediated redox catalysis of insulators. Research
Square, 10.21203/rs.3.rs-750965/v1.
mla: Cao, Deqing, et al. “Sharp Kinetic Acceleration Potentials during Mediated
Redox Catalysis of Insulators.” Research Square, Research Square, doi:10.21203/rs.3.rs-750965/v1.
short: D. Cao, X. Shen, A. Wang, F. Yu, Y. Wu, S. Shi, S.A. Freunberger, Y. Chen,
Research Square (n.d.).
date_created: 2021-08-31T12:54:16Z
date_published: 2021-08-18T00:00:00Z
date_updated: 2023-10-17T13:06:29Z
day: '18'
ddc:
- '541'
department:
- _id: StFr
doi: 10.21203/rs.3.rs-750965/v1
file:
- access_level: open_access
checksum: 1878e91c29d5769ed5a827b0b7addf00
content_type: application/pdf
creator: cchlebak
date_created: 2021-08-31T14:02:19Z
date_updated: 2021-08-31T14:02:19Z
file_id: '9979'
file_name: 2021_ResearchSquare_Cao.pdf
file_size: 1019662
relation: main_file
success: 1
file_date_updated: 2021-08-31T14:02:19Z
has_accepted_license: '1'
keyword:
- Catalysis
- Energy engineering
- Materials theory and modeling
language:
- iso: eng
month: '08'
oa: 1
oa_version: Preprint
page: '21'
publication: Research Square
publication_identifier:
eissn:
- 2693-5015
publication_status: submitted
publisher: Research Square
related_material:
record:
- id: '10813'
relation: later_version
status: public
status: public
title: Sharp kinetic acceleration potentials during mediated redox catalysis of insulators
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '8730'
abstract:
- lang: eng
text: P-glycoprotein (ABCB1) and breast cancer resistance protein (ABCG2) restrict
at the blood–brain barrier (BBB) the brain distribution of the majority of currently
known molecularly targeted anticancer drugs. To improve brain delivery of dual
ABCB1/ABCG2 substrates, both ABCB1 and ABCG2 need to be inhibited simultaneously
at the BBB. We examined the feasibility of simultaneous ABCB1/ABCG2 inhibition
with i.v. co-infusion of erlotinib and tariquidar by studying brain distribution
of the model ABCB1/ABCG2 substrate [11C]erlotinib in mice and rhesus macaques
with PET. Tolerability of the erlotinib/tariquidar combination was assessed in
human embryonic stem cell-derived cerebral organoids. In mice and macaques, baseline
brain distribution of [11C]erlotinib was low (brain distribution volume, VT,brain < 0.3 mL/cm3).
Co-infusion of erlotinib and tariquidar increased VT,brain in mice by 3.0-fold
and in macaques by 3.4- to 5.0-fold, while infusion of erlotinib alone or tariquidar
alone led to less pronounced VT,brain increases in both species. Treatment of
cerebral organoids with erlotinib/tariquidar led to an induction of Caspase-3-dependent
apoptosis. Co-infusion of erlotinib/tariquidar may potentially allow for complete
ABCB1/ABCG2 inhibition at the BBB, while simultaneously achieving brain-targeted
EGFR inhibition. Our protocol may be applicable to enhance brain delivery of molecularly
targeted anticancer drugs for a more effective treatment of brain tumors.
article_processing_charge: No
article_type: original
author:
- first_name: N
full_name: Tournier, N
last_name: Tournier
- first_name: S
full_name: Goutal, S
last_name: Goutal
- first_name: S
full_name: Mairinger, S
last_name: Mairinger
- first_name: IH
full_name: Lozano, IH
last_name: Lozano
- first_name: T
full_name: Filip, T
last_name: Filip
- first_name: M
full_name: Sauberer, M
last_name: Sauberer
- first_name: F
full_name: Caillé, F
last_name: Caillé
- first_name: L
full_name: Breuil, L
last_name: Breuil
- first_name: J
full_name: Stanek, J
last_name: Stanek
- first_name: AF
full_name: Freeman, AF
last_name: Freeman
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: C
full_name: Truillet, C
last_name: Truillet
- first_name: T
full_name: Wanek, T
last_name: Wanek
- first_name: O
full_name: Langer, O
last_name: Langer
citation:
ama: Tournier N, Goutal S, Mairinger S, et al. Complete inhibition of ABCB1 and
ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to
improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Journal
of Cerebral Blood Flow and Metabolism. 2021;41(7):1634-1646. doi:10.1177/0271678X20965500
apa: Tournier, N., Goutal, S., Mairinger, S., Lozano, I., Filip, T., Sauberer, M.,
… Langer, O. (2021). Complete inhibition of ABCB1 and ABCG2 at the blood-brain
barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of
the model ABCB1/ABCG2 substrate [11C]erlotinib. Journal of Cerebral Blood Flow
and Metabolism. SAGE Publications. https://doi.org/10.1177/0271678X20965500
chicago: Tournier, N, S Goutal, S Mairinger, IH Lozano, T Filip, M Sauberer, F Caillé,
et al. “Complete Inhibition of ABCB1 and ABCG2 at the Blood-Brain Barrier by Co-Infusion
of Erlotinib and Tariquidar to Improve Brain Delivery of the Model ABCB1/ABCG2
Substrate [11C]Erlotinib.” Journal of Cerebral Blood Flow and Metabolism.
SAGE Publications, 2021. https://doi.org/10.1177/0271678X20965500.
ieee: N. Tournier et al., “Complete inhibition of ABCB1 and ABCG2 at the
blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain
delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib,” Journal of Cerebral
Blood Flow and Metabolism, vol. 41, no. 7. SAGE Publications, pp. 1634–1646,
2021.
ista: Tournier N, Goutal S, Mairinger S, Lozano I, Filip T, Sauberer M, Caillé F,
Breuil L, Stanek J, Freeman A, Novarino G, Truillet C, Wanek T, Langer O. 2021.
Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion
of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2
substrate [11C]erlotinib. Journal of Cerebral Blood Flow and Metabolism. 41(7),
1634–1646.
mla: Tournier, N., et al. “Complete Inhibition of ABCB1 and ABCG2 at the Blood-Brain
Barrier by Co-Infusion of Erlotinib and Tariquidar to Improve Brain Delivery of
the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Journal of Cerebral Blood
Flow and Metabolism, vol. 41, no. 7, SAGE Publications, 2021, pp. 1634–46,
doi:10.1177/0271678X20965500.
short: N. Tournier, S. Goutal, S. Mairinger, I. Lozano, T. Filip, M. Sauberer, F.
Caillé, L. Breuil, J. Stanek, A. Freeman, G. Novarino, C. Truillet, T. Wanek,
O. Langer, Journal of Cerebral Blood Flow and Metabolism 41 (2021) 1634–1646.
date_created: 2020-11-06T08:39:01Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-10-18T06:45:30Z
day: '01'
department:
- _id: GaNo
doi: 10.1177/0271678X20965500
external_id:
isi:
- '000664214100012'
pmid:
- '33081568'
intvolume: ' 41'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8221757/
month: '07'
oa: 1
oa_version: Published Version
page: 1634-1646
pmid: 1
publication: Journal of Cerebral Blood Flow and Metabolism
publication_identifier:
eissn:
- 1559-7016
issn:
- 0271-678x
publication_status: published
publisher: SAGE Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion
of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate
[11C]erlotinib
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 41
year: '2021'
...
---
_id: '9383'
abstract:
- lang: eng
text: A primary roadblock to our understanding of speciation is that it usually
occurs over a timeframe that is too long to study from start to finish. The idea
of a speciation continuum provides something of a solution to this problem; rather
than observing the entire process, we can simply reconstruct it from the multitude
of speciation events that surround us. But what do we really mean when we talk
about the speciation continuum, and can it really help us understand speciation?
We explored these questions using a literature review and online survey of speciation
researchers. Although most researchers were familiar with the concept and thought
it was useful, our survey revealed extensive disagreement about what the speciation
continuum actually tells us. This is due partly to the lack of a clear definition.
Here, we provide an explicit definition that is compatible with the Biological
Species Concept. That is, the speciation continuum is a continuum of reproductive
isolation. After outlining the logic of the definition in light of alternatives,
we explain why attempts to reconstruct the speciation process from present‐day
populations will ultimately fail. We then outline how we think the speciation
continuum concept can continue to act as a foundation for understanding the continuum
of reproductive isolation that surrounds us.
acknowledgement: We thank M. Garlovsky, S. Martin, C. Cooney, C. Roux, J. Larson,
and J. Mallet for critical feedback and for discussion. K. Lohse, M. de la Cámara,
J. Cerca, M. A. Chase, C. Baskett, A. M. Westram, and N. H. Barton gave feedback
on a draft of the manuscript. O. Seehausen, two anonymous reviewers, and the AE
(Michael Kopp) provided comments that greatly improved the manuscript. V. Holzmann
made many corrections to the proofs. G. Bisschop and K. Lohse kindly contributed
the simulations and analyses presented in Box 3. We would also like to extend our
thanks to everyone who took part in the speciation survey, which received ethical
approval through the University of Sheffield Ethics Review Procedure (Application
029768). We are especially grateful to R. K. Butlin for stimulating discussion throughout
the writing of the manuscript and for feedback on an earlier draft.
article_processing_charge: No
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
citation:
ama: Stankowski S, Ravinet M. Defining the speciation continuum. Evolution.
2021;75(6):1256-1273. doi:10.1111/evo.14215
apa: Stankowski, S., & Ravinet, M. (2021). Defining the speciation continuum.
Evolution. Oxford University Press. https://doi.org/10.1111/evo.14215
chicago: Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.”
Evolution. Oxford University Press, 2021. https://doi.org/10.1111/evo.14215.
ieee: S. Stankowski and M. Ravinet, “Defining the speciation continuum,” Evolution,
vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021.
ista: Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution.
75(6), 1256–1273.
mla: Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution,
vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:10.1111/evo.14215.
short: S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273.
date_created: 2021-05-09T22:01:39Z
date_published: 2021-03-22T00:00:00Z
date_updated: 2023-10-18T08:16:01Z
day: '22'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.14215
external_id:
isi:
- '000647226400001'
file:
- access_level: open_access
checksum: 96f6ccf15d95a4e9f7c0b27eee570fa6
content_type: application/pdf
creator: kschuh
date_created: 2022-03-25T12:02:04Z
date_updated: 2022-03-25T12:02:04Z
file_id: '10921'
file_name: 2021_Evolution_Stankowski.pdf
file_size: 719991
relation: main_file
success: 1
file_date_updated: 2022-03-25T12:02:04Z
has_accepted_license: '1'
intvolume: ' 75'
isi: 1
issue: '6'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 1256-1273
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Defining the speciation continuum
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 75
year: '2021'
...
---
_id: '10223'
abstract:
- lang: eng
text: Growth regulation tailors development in plants to their environment. A prominent
example of this is the response to gravity, in which shoots bend up and roots
bend down1. This paradox is based on opposite effects of the phytohormone auxin,
which promotes cell expansion in shoots while inhibiting it in roots via a yet
unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic
engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding
of how auxin inhibits root growth. We show that auxin activates two distinct,
antagonistically acting signalling pathways that converge on rapid regulation
of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE
KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma
membrane H+-ATPases for apoplast acidification, while intracellular canonical
auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization.
Simultaneous activation of these two counteracting mechanisms poises roots for
rapid, fine-tuned growth modulation in navigating complex soil environments.
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
- _id: Bio
acknowledgement: We thank N. Gnyliukh and L. Hörmayer for technical assistance and
N. Paris for sharing PM-Cyto seeds. We gratefully acknowledge the Life Science,
Machine Shop and Bioimaging Facilities of IST Austria. This project has received
funding from the European Research Council Advanced Grant (ETAP-742985) and the
Austrian Science Fund (FWF) under I 3630-B25 to J.F., the National Institutes of
Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research
(NWO; VIDI-864.13.001), Research Foundation-Flanders (FWO; Odysseus II G0D0515N)
and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R.,
the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research
to M.R. and D.W., the Australian Research Council and China National Distinguished
Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685)
and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and
innovation programme under Marie Skłodowska-Curie grant agreement no. 665385 and
the DOC Fellowship of the Austrian Academy of Sciences to L.L., and the China Scholarship
Council to J.C.
article_processing_charge: No
article_type: original
author:
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Mark
full_name: Roosjen, Mark
last_name: Roosjen
- first_name: Koji
full_name: Takahashi, Koji
last_name: Takahashi
- first_name: Lesia
full_name: Rodriguez Solovey, Lesia
id: 3922B506-F248-11E8-B48F-1D18A9856A87
last_name: Rodriguez Solovey
orcid: 0000-0002-7244-7237
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Jian
full_name: Chen, Jian
last_name: Chen
- first_name: Lana
full_name: Shabala, Lana
last_name: Shabala
- first_name: Wouter
full_name: Smet, Wouter
last_name: Smet
- first_name: Hong
full_name: Ren, Hong
last_name: Ren
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Sergey
full_name: Shabala, Sergey
last_name: Shabala
- first_name: Bert
full_name: De Rybel, Bert
last_name: De Rybel
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Toshinori
full_name: Kinoshita, Toshinori
last_name: Kinoshita
- first_name: William M.
full_name: Gray, William M.
last_name: Gray
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin
signalling for H+ fluxes in root growth. Nature. 2021;599(7884):273-277.
doi:10.1038/s41586-021-04037-6
apa: Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L.,
Merrin, J., … Friml, J. (2021). Cell surface and intracellular auxin signalling
for H+ fluxes in root growth. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-04037-6
chicago: Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez
Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin
Signalling for H+ Fluxes in Root Growth.” Nature. Springer Nature,
2021. https://doi.org/10.1038/s41586-021-04037-6.
ieee: L. Li et al., “Cell surface and intracellular auxin signalling for
H+ fluxes in root growth,” Nature, vol. 599, no. 7884. Springer
Nature, pp. 273–277, 2021.
ista: Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J,
Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D,
Kinoshita T, Gray WM, Friml J. 2021. Cell surface and intracellular auxin signalling
for H+ fluxes in root growth. Nature. 599(7884), 273–277.
mla: Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+
Fluxes in Root Growth.” Nature, vol. 599, no. 7884, Springer Nature, 2021,
pp. 273–77, doi:10.1038/s41586-021-04037-6.
short: L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J.
Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel,
D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Nature 599 (2021) 273–277.
date_created: 2021-11-07T23:01:25Z
date_published: 2021-11-11T00:00:00Z
date_updated: 2023-10-18T08:30:53Z
day: '11'
department:
- _id: JiFr
- _id: NanoFab
doi: 10.1038/s41586-021-04037-6
ec_funded: 1
external_id:
isi:
- '000713338100006'
pmid:
- '34707283'
intvolume: ' 599'
isi: 1
issue: '7884'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.doi.org/10.21203/rs.3.rs-266395/v3
month: '11'
oa: 1
oa_version: Preprint
page: 273-277
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 26B4D67E-B435-11E9-9278-68D0E5697425
grant_number: '25351'
name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated
Rapid Growth Inhibition in Arabidopsis Root'
publication: Nature
publication_identifier:
eissn:
- '14764687'
issn:
- '00280836'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/stop-and-grow/
record:
- id: '10095'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Cell surface and intracellular auxin signalling for H+ fluxes in
root growth
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 599
year: '2021'
...
---
_id: '9379'
abstract:
- lang: eng
text: When B cells encounter membrane-bound antigens, the formation and coalescence
of B cell antigen receptor (BCR) microclusters amplifies BCR signaling. The ability
of B cells to probe the surface of antigen-presenting cells (APCs) and respond
to APC-bound antigens requires remodeling of the actin cytoskeleton. Initial BCR
signaling stimulates actin-related protein (Arp) 2/3 complex-dependent actin polymerization,
which drives B cell spreading as well as the centripetal movement and coalescence
of BCR microclusters at the B cell-APC synapse. Sustained actin polymerization
depends on concomitant actin filament depolymerization, which enables the recycling
of actin monomers and Arp2/3 complexes. Cofilin-mediated severing of actin filaments
is a rate-limiting step in the morphological changes that occur during immune
synapse formation. Hence, regulators of cofilin activity such as WD repeat-containing
protein 1 (Wdr1), LIM domain kinase (LIMK), and coactosin-like 1 (Cotl1) may also
be essential for actin-dependent processes in B cells. Wdr1 enhances cofilin-mediated
actin disassembly. Conversely, Cotl1 competes with cofilin for binding to actin
and LIMK phosphorylates cofilin and prevents it from binding to actin filaments.
We now show that Wdr1 and LIMK have distinct roles in BCR-induced assembly of
the peripheral actin structures that drive B cell spreading, and that cofilin,
Wdr1, and LIMK all contribute to the actin-dependent amplification of BCR signaling
at the immune synapse. Depleting Cotl1 had no effect on these processes. Thus,
the Wdr1-LIMK-cofilin axis is critical for BCR-induced actin remodeling and for
B cell responses to APC-bound antigens.
acknowledgement: We thank the UBC Life Sciences Institute Imaging Facility andthe
UBC Flow Cytometry Facility.
article_number: '649433'
article_processing_charge: No
article_type: original
author:
- first_name: Madison
full_name: Bolger-Munro, Madison
id: 516F03FA-93A3-11EA-A7C5-D6BE3DDC885E
last_name: Bolger-Munro
orcid: 0000-0002-8176-4824
- first_name: Kate
full_name: Choi, Kate
last_name: Choi
- first_name: Faith
full_name: Cheung, Faith
last_name: Cheung
- first_name: Yi Tian
full_name: Liu, Yi Tian
last_name: Liu
- first_name: May
full_name: Dang-Lawson, May
last_name: Dang-Lawson
- first_name: Nikola
full_name: Deretic, Nikola
last_name: Deretic
- first_name: Connor
full_name: Keane, Connor
last_name: Keane
- first_name: Michael R.
full_name: Gold, Michael R.
last_name: Gold
citation:
ama: Bolger-Munro M, Choi K, Cheung F, et al. The Wdr1-LIMK-Cofilin axis controls
B cell antigen receptor-induced actin remodeling and signaling at the immune synapse.
Frontiers in Cell and Developmental Biology. 2021;9. doi:10.3389/fcell.2021.649433
apa: Bolger-Munro, M., Choi, K., Cheung, F., Liu, Y. T., Dang-Lawson, M., Deretic,
N., … Gold, M. R. (2021). The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced
actin remodeling and signaling at the immune synapse. Frontiers in Cell and
Developmental Biology. Frontiers Media. https://doi.org/10.3389/fcell.2021.649433
chicago: Bolger-Munro, Madison, Kate Choi, Faith Cheung, Yi Tian Liu, May Dang-Lawson,
Nikola Deretic, Connor Keane, and Michael R. Gold. “The Wdr1-LIMK-Cofilin Axis
Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the
Immune Synapse.” Frontiers in Cell and Developmental Biology. Frontiers
Media, 2021. https://doi.org/10.3389/fcell.2021.649433.
ieee: M. Bolger-Munro et al., “The Wdr1-LIMK-Cofilin axis controls B cell
antigen receptor-induced actin remodeling and signaling at the immune synapse,”
Frontiers in Cell and Developmental Biology, vol. 9. Frontiers Media, 2021.
ista: Bolger-Munro M, Choi K, Cheung F, Liu YT, Dang-Lawson M, Deretic N, Keane
C, Gold MR. 2021. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced
actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental
Biology. 9, 649433.
mla: Bolger-Munro, Madison, et al. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen
Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” Frontiers
in Cell and Developmental Biology, vol. 9, 649433, Frontiers Media, 2021,
doi:10.3389/fcell.2021.649433.
short: M. Bolger-Munro, K. Choi, F. Cheung, Y.T. Liu, M. Dang-Lawson, N. Deretic,
C. Keane, M.R. Gold, Frontiers in Cell and Developmental Biology 9 (2021).
date_created: 2021-05-09T22:01:37Z
date_published: 2021-04-13T00:00:00Z
date_updated: 2023-10-18T08:19:49Z
day: '13'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.3389/fcell.2021.649433
external_id:
isi:
- '000644419500001'
pmid:
- '33928084'
file:
- access_level: open_access
checksum: 8c8a03575d2f7583f88dc3b658b0976b
content_type: application/pdf
creator: kschuh
date_created: 2021-05-11T15:09:23Z
date_updated: 2021-05-11T15:09:23Z
file_id: '9386'
file_name: 2021_Frontiers_Cell_Bolger-Munro.pdf
file_size: 4076024
relation: main_file
success: 1
file_date_updated: 2021-05-11T15:09:23Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
keyword:
- B cell
- actin
- immune synapse
- cell spreading
- cofilin
- WDR1 (AIP1)
- LIM domain kinase
- B cell receptor (BCR)
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Cell and Developmental Biology
publication_identifier:
eissn:
- 2296-634X
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling
and signaling at the immune synapse
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2021'
...
---
_id: '9362'
abstract:
- lang: eng
text: A central goal in systems neuroscience is to understand the functions performed
by neural circuits. Previous top-down models addressed this question by comparing
the behaviour of an ideal model circuit, optimised to perform a given function,
with neural recordings. However, this requires guessing in advance what function
is being performed, which may not be possible for many neural systems. To address
this, we propose an inverse reinforcement learning (RL) framework for inferring
the function performed by a neural network from data. We assume that the responses
of each neuron in a network are optimised so as to drive the network towards ‘rewarded’
states, that are desirable for performing a given function. We then show how one
can use inverse RL to infer the reward function optimised by the network from
observing its responses. This inferred reward function can be used to predict
how the neural network should adapt its dynamics to perform the same function
when the external environment or network structure changes. This could lead to
theoretical predictions about how neural network dynamics adapt to deal with cell
death and/or varying sensory stimulus statistics.
acknowledgement: The authors would like to thank Ulisse Ferrari for useful discussions
and feedback.
article_number: e0248940
article_processing_charge: No
article_type: original
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
citation:
ama: Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent
neural network. PLoS ONE. 2021;16(4). doi:10.1371/journal.pone.0248940
apa: Chalk, M. J., Tkačik, G., & Marre, O. (2021). Inferring the function performed
by a recurrent neural network. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0248940
chicago: Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function
Performed by a Recurrent Neural Network.” PLoS ONE. Public Library of Science,
2021. https://doi.org/10.1371/journal.pone.0248940.
ieee: M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by
a recurrent neural network,” PLoS ONE, vol. 16, no. 4. Public Library of
Science, 2021.
ista: Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent
neural network. PLoS ONE. 16(4), e0248940.
mla: Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent
Neural Network.” PLoS ONE, vol. 16, no. 4, e0248940, Public Library of
Science, 2021, doi:10.1371/journal.pone.0248940.
short: M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).
date_created: 2021-05-02T22:01:28Z
date_published: 2021-04-15T00:00:00Z
date_updated: 2023-10-18T08:17:42Z
day: '15'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0248940
external_id:
isi:
- '000641474900072'
pmid:
- '33857170'
file:
- access_level: open_access
checksum: c52da133850307d2031f552d998f00e8
content_type: application/pdf
creator: kschuh
date_created: 2021-05-04T13:22:19Z
date_updated: 2021-05-04T13:22:19Z
file_id: '9371'
file_name: 2021_pone_Chalk.pdf
file_size: 2768282
relation: main_file
success: 1
file_date_updated: 2021-05-04T13:22:19Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS ONE
publication_identifier:
eissn:
- '19326203'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inferring the function performed by a recurrent neural network
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2021'
...
---
_id: '9986'
abstract:
- lang: eng
text: Size control is a fundamental question in biology, showing incremental complexity
in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a
vital growth regulator with central importance for differential growth control.
Our results indicate that auxin-reliant growth programs affect the molecular complexity
of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent
induction and repression of growth coincide with reduced and enhanced molecular
complexity of xyloglucans, respectively. In agreement with a proposed function
in growth control, genetic interference with xyloglucan side decorations distinctly
modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent
growth programs have a spatially defined effect on xyloglucan’s molecular structure,
which in turn affects cell wall mechanics and specifies differential, gravitropic
hypocotyl growth.
acknowledgement: "We are grateful to Paul Knox, Markus Pauly, Malcom O’Neill, and
Ignacio Zarra for providing published material; the BOKU-VIBT Imaging Center for
access and M. Debreczeny for expertise; J.I. Thaker and Georg Seifert for critical
reading.\r\n"
article_number: '9222'
article_processing_charge: Yes
article_type: original
author:
- first_name: Silvia Melina
full_name: Velasquez, Silvia Melina
last_name: Velasquez
- first_name: Xiaoyuan
full_name: Guo, Xiaoyuan
last_name: Guo
- first_name: Marçal
full_name: Gallemi, Marçal
id: 460C6802-F248-11E8-B48F-1D18A9856A87
last_name: Gallemi
orcid: 0000-0003-4675-6893
- first_name: Bibek
full_name: Aryal, Bibek
last_name: Aryal
- first_name: Peter
full_name: Venhuizen, Peter
last_name: Venhuizen
- first_name: Elke
full_name: Barbez, Elke
last_name: Barbez
- first_name: Kai Alexander
full_name: Dünser, Kai Alexander
last_name: Dünser
- first_name: Martin
full_name: Darino, Martin
last_name: Darino
- first_name: Aleš
full_name: Pӗnčík, Aleš
last_name: Pӗnčík
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Maria
full_name: Kalyna, Maria
last_name: Kalyna
- first_name: Gregory
full_name: Mouille, Gregory
last_name: Mouille
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Rishikesh P.
full_name: Bhalerao, Rishikesh P.
last_name: Bhalerao
- first_name: Jozef
full_name: Mravec, Jozef
last_name: Mravec
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine-Vehn
citation:
ama: Velasquez SM, Guo X, Gallemi M, et al. Xyloglucan remodeling defines auxin-dependent
differential tissue expansion in plants. International Journal of Molecular
Sciences. 2021;22(17). doi:10.3390/ijms22179222
apa: Velasquez, S. M., Guo, X., Gallemi, M., Aryal, B., Venhuizen, P., Barbez, E.,
… Kleine-Vehn, J. (2021). Xyloglucan remodeling defines auxin-dependent differential
tissue expansion in plants. International Journal of Molecular Sciences.
MDPI. https://doi.org/10.3390/ijms22179222
chicago: Velasquez, Silvia Melina, Xiaoyuan Guo, Marçal Gallemi, Bibek Aryal, Peter
Venhuizen, Elke Barbez, Kai Alexander Dünser, et al. “Xyloglucan Remodeling Defines
Auxin-Dependent Differential Tissue Expansion in Plants.” International Journal
of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22179222.
ieee: S. M. Velasquez et al., “Xyloglucan remodeling defines auxin-dependent
differential tissue expansion in plants,” International Journal of Molecular
Sciences, vol. 22, no. 17. MDPI, 2021.
ista: Velasquez SM, Guo X, Gallemi M, Aryal B, Venhuizen P, Barbez E, Dünser KA,
Darino M, Pӗnčík A, Novák O, Kalyna M, Mouille G, Benková E, Bhalerao RP, Mravec
J, Kleine-Vehn J. 2021. Xyloglucan remodeling defines auxin-dependent differential
tissue expansion in plants. International Journal of Molecular Sciences. 22(17),
9222.
mla: Velasquez, Silvia Melina, et al. “Xyloglucan Remodeling Defines Auxin-Dependent
Differential Tissue Expansion in Plants.” International Journal of Molecular
Sciences, vol. 22, no. 17, 9222, MDPI, 2021, doi:10.3390/ijms22179222.
short: S.M. Velasquez, X. Guo, M. Gallemi, B. Aryal, P. Venhuizen, E. Barbez, K.A.
Dünser, M. Darino, A. Pӗnčík, O. Novák, M. Kalyna, G. Mouille, E. Benková, R.P.
Bhalerao, J. Mravec, J. Kleine-Vehn, International Journal of Molecular Sciences
22 (2021).
date_created: 2021-09-05T22:01:24Z
date_published: 2021-08-26T00:00:00Z
date_updated: 2023-10-31T19:29:38Z
day: '26'
ddc:
- '575'
department:
- _id: EvBe
doi: 10.3390/ijms22179222
external_id:
isi:
- '000694347100001'
pmid:
- '34502129'
file:
- access_level: open_access
checksum: 6b7055cf89f1b7ed8594c3fdf56f000b
content_type: application/pdf
creator: cchlebak
date_created: 2021-09-06T12:50:19Z
date_updated: 2021-09-07T09:04:53Z
file_id: '9988'
file_name: 2021_IntJMolecularSciences_Velasquez.pdf
file_size: 2162247
relation: main_file
file_date_updated: 2021-09-07T09:04:53Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '17'
keyword:
- auxin
- growth
- cell wall
- xyloglucans
- hypocotyls
- gravitropism
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- 1422-0067
issn:
- 1661-6596
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Xyloglucan remodeling defines auxin-dependent differential tissue expansion
in plants
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: 22
year: '2021'
...
---
_id: '9189'
abstract:
- lang: eng
text: Transposable elements exist widely throughout plant genomes and play important
roles in plant evolution. Auxin is an important regulator that is traditionally
associated with root development and drought stress adaptation. The DEEPER ROOTING
1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified
a transposon that acts as an autonomous auxin‐responsive promoter and its presence
at specific genome positions conveys physiological adaptations related to drought
avoidance. Rice varieties with high and auxin‐mediated transcription of DRO1 in
the root tip show deeper and longer root phenotypes and are thus better adapted
to drought. The INDITTO2 transposon contains an auxin response element and displays
auxin‐responsive promoter activity; it is thus able to convey auxin regulation
of transcription to genes in its proximity. In the rice Acuce, which displays
DRO1‐mediated drought adaptation, the INDITTO2 transposon was found to be inserted
at the promoter region of the DRO1 locus. Transgenesis‐based insertion of the
INDITTO2 transposon into the DRO1 promoter of the non‐adapted rice variety Nipponbare
was sufficient to promote its drought avoidance. Our data identify an example
of how transposons can act as promoters and convey hormonal regulation to nearby
loci, improving plant fitness in response to different abiotic stresses.
article_processing_charge: No
article_type: original
author:
- first_name: Y
full_name: Zhao, Y
last_name: Zhao
- first_name: L
full_name: Wu, L
last_name: Wu
- first_name: Q
full_name: Fu, Q
last_name: Fu
- first_name: D
full_name: Wang, D
last_name: Wang
- first_name: J
full_name: Li, J
last_name: Li
- first_name: B
full_name: Yao, B
last_name: Yao
- first_name: S
full_name: Yu, S
last_name: Yu
- first_name: L
full_name: Jiang, L
last_name: Jiang
- first_name: J
full_name: Qian, J
last_name: Qian
- first_name: X
full_name: Zhou, X
last_name: Zhou
- first_name: L
full_name: Han, L
last_name: Han
- first_name: S
full_name: Zhao, S
last_name: Zhao
- first_name: C
full_name: Ma, C
last_name: Ma
- first_name: Y
full_name: Zhang, Y
last_name: Zhang
- first_name: C
full_name: Luo, C
last_name: Luo
- first_name: Q
full_name: Dong, Q
last_name: Dong
- first_name: S
full_name: Li, S
last_name: Li
- first_name: L
full_name: Zhang, L
last_name: Zhang
- first_name: X
full_name: Jiang, X
last_name: Jiang
- first_name: Y
full_name: Li, Y
last_name: Li
- first_name: H
full_name: Luo, H
last_name: Luo
- first_name: K
full_name: Li, K
last_name: Li
- first_name: J
full_name: Yang, J
last_name: Yang
- first_name: Q
full_name: Luo, Q
last_name: Luo
- first_name: L
full_name: Li, L
last_name: Li
- first_name: S
full_name: Peng, S
last_name: Peng
- first_name: H
full_name: Huang, H
last_name: Huang
- first_name: Z
full_name: Zuo, Z
last_name: Zuo
- first_name: C
full_name: Liu, C
last_name: Liu
- first_name: L
full_name: Wang, L
last_name: Wang
- first_name: C
full_name: Li, C
last_name: Li
- first_name: X
full_name: He, X
last_name: He
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Y
full_name: Du, Y
last_name: Du
citation:
ama: Zhao Y, Wu L, Fu Q, et al. INDITTO2 transposon conveys auxin-mediated DRO1
transcription for rice drought avoidance. Plant, Cell & Environment.
2021;44(6):1846-1857. doi:10.1111/pce.14029
apa: Zhao, Y., Wu, L., Fu, Q., Wang, D., Li, J., Yao, B., … Du, Y. (2021). INDITTO2
transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance.
Plant, Cell & Environment. Wiley. https://doi.org/10.1111/pce.14029
chicago: Zhao, Y, L Wu, Q Fu, D Wang, J Li, B Yao, S Yu, et al. “INDITTO2 Transposon
Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” Plant,
Cell & Environment. Wiley, 2021. https://doi.org/10.1111/pce.14029.
ieee: Y. Zhao et al., “INDITTO2 transposon conveys auxin-mediated DRO1 transcription
for rice drought avoidance,” Plant, Cell & Environment, vol. 44, no.
6. Wiley, pp. 1846–1857, 2021.
ista: Zhao Y, Wu L, Fu Q, Wang D, Li J, Yao B, Yu S, Jiang L, Qian J, Zhou X, Han
L, Zhao S, Ma C, Zhang Y, Luo C, Dong Q, Li S, Zhang L, Jiang X, Li Y, Luo H,
Li K, Yang J, Luo Q, Li L, Peng S, Huang H, Zuo Z, Liu C, Wang L, Li C, He X,
Friml J, Du Y. 2021. INDITTO2 transposon conveys auxin-mediated DRO1 transcription
for rice drought avoidance. Plant, Cell & Environment. 44(6), 1846–1857.
mla: Zhao, Y., et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription
for Rice Drought Avoidance.” Plant, Cell & Environment, vol. 44, no.
6, Wiley, 2021, pp. 1846–57, doi:10.1111/pce.14029.
short: Y. Zhao, L. Wu, Q. Fu, D. Wang, J. Li, B. Yao, S. Yu, L. Jiang, J. Qian,
X. Zhou, L. Han, S. Zhao, C. Ma, Y. Zhang, C. Luo, Q. Dong, S. Li, L. Zhang, X.
Jiang, Y. Li, H. Luo, K. Li, J. Yang, Q. Luo, L. Li, S. Peng, H. Huang, Z. Zuo,
C. Liu, L. Wang, C. Li, X. He, J. Friml, Y. Du, Plant, Cell & Environment
44 (2021) 1846–1857.
date_created: 2021-02-24T10:07:21Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-11-07T08:18:36Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/pce.14029
external_id:
isi:
- '000625398600001'
pmid:
- '33576018'
file:
- access_level: open_access
checksum: a812418fede076741c9c4dc07f317068
content_type: application/pdf
creator: amally
date_created: 2023-11-02T17:02:11Z
date_updated: 2023-11-02T17:02:11Z
file_id: '14481'
file_name: Zhao PlantCellEnv 2021_accepted.pdf
file_size: 8437528
relation: main_file
success: 1
file_date_updated: 2023-11-02T17:02:11Z
has_accepted_license: '1'
intvolume: ' 44'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 1846-1857
pmid: 1
publication: Plant, Cell & Environment
publication_identifier:
eissn:
- 1365-3040
issn:
- 0140-7791
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought
avoidance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2021'
...
---
_id: '9792'
abstract:
- lang: eng
text: 'This paper establishes new connections between many-body quantum systems,
One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport
(OT), by interpreting the problem of computing the ground-state energy of a finite
dimensional composite quantum system at positive temperature as a non-commutative
entropy regularized Optimal Transport problem. We develop a new approach to fully
characterize the dual-primal solutions in such non-commutative setting. The mathematical
formalism is particularly relevant in quantum chemistry: numerical realizations
of the many-electron ground state energy can be computed via a non-commutative
version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness
of this algorithm, which, to our best knowledge, were unknown even in the two
marginal case. Our methods are based on careful a priori estimates in the dual
problem, which we believe to be of independent interest. Finally, the above results
are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions
are enforced on the problem.'
acknowledgement: 'This work started when A.G. was visiting the Erwin Schrödinger Institute
and then continued when D.F. and L.P visited the Theoretical Chemistry Department
of the Vrije Universiteit Amsterdam. The authors thanks the hospitality of both
places and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions
and literature suggestions in the early state of the project. Finally, the authors
also thanks J. Maas and R. Seiringer for their feedback and useful comments to a
first draft of the article. L.P. acknowledges support by the Austrian Science Fund
(FWF), grants No W1245 and NoF65. D.F acknowledges support by the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreements No 716117 and No 694227). A.G. acknowledges funding by the European
Research Council under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942].'
article_number: '2106.11217'
article_processing_charge: No
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
- first_name: Augusto
full_name: Gerolin, Augusto
last_name: Gerolin
- first_name: Lorenzo
full_name: Portinale, Lorenzo
id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
last_name: Portinale
citation:
ama: Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal
transport approach to quantum composite systems at positive temperature. arXiv.
doi:10.48550/arXiv.2106.11217
apa: Feliciangeli, D., Gerolin, A., & Portinale, L. (n.d.). A non-commutative
entropic optimal transport approach to quantum composite systems at positive temperature.
arXiv. https://doi.org/10.48550/arXiv.2106.11217
chicago: Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative
Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.”
ArXiv, n.d. https://doi.org/10.48550/arXiv.2106.11217.
ieee: D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic
optimal transport approach to quantum composite systems at positive temperature,”
arXiv. .
ista: Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal
transport approach to quantum composite systems at positive temperature. arXiv,
2106.11217.
mla: Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach
to Quantum Composite Systems at Positive Temperature.” ArXiv, 2106.11217,
doi:10.48550/arXiv.2106.11217.
short: D. Feliciangeli, A. Gerolin, L. Portinale, ArXiv (n.d.).
date_created: 2021-08-06T09:07:12Z
date_published: 2021-07-21T00:00:00Z
date_updated: 2023-11-14T13:21:01Z
day: '21'
ddc:
- '510'
department:
- _id: RoSe
- _id: JaMa
doi: 10.48550/arXiv.2106.11217
ec_funded: 1
external_id:
arxiv:
- '2106.11217'
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2106.11217
month: '07'
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
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '9733'
relation: dissertation_contains
status: public
- id: '10030'
relation: dissertation_contains
status: public
- id: '12911'
relation: later_version
status: public
status: public
title: A non-commutative entropic optimal transport approach to quantum composite
systems at positive temperature
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10655'
abstract:
- lang: eng
text: "Adeno-associated viruses (AAVs) are widely used to deliver genetic material
in vivo to distinct cell types such as neurons or glial cells, allowing for targeted
manipulation. Transduction of microglia is mostly excluded from this strategy,
likely due to the cells’ heterogeneous state upon environmental changes, which
makes AAV design challenging. Here, we established the retina as a model system
for microglial AAV validation and optimization. First, we show that AAV2/6 transduced
microglia in both synaptic layers, where layer preference corresponds to the intravitreal
or subretinal delivery method. Surprisingly, we observed significantly enhanced
microglial transduction during photoreceptor degeneration. Thus, we modified the
AAV6 capsid to reduce heparin binding by introducing four point mutations (K531E,
R576Q, K493S, and K459S), resulting in increased microglial transduction in the
outer plexiform layer. Finally, to improve microglial-specific transduction, we
validated a Cre-dependent transgene delivery cassette for use in combination with
the Cx3cr1CreERT2 mouse line. Together, our results provide a foundation for future
studies optimizing AAV-mediated microglia transduction and highlight that environmental
conditions influence microglial transduction efficiency.\r\n"
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement no. 715571). The research was supported by the Scientific Service
Units (SSU) of IST Austria through resources provided by the Bioimaging Facility,
the Life Science Facility, and the Pre-Clinical Facility, namely Sonja Haslinger
and Michael Schunn for their animal colony management and support. We would also
like to thank Chakrabarty Lab for sharing the plasmids for AAV2/6 production. Finally,
we would like to thank the Siegert team members for discussion about the manuscript.
article_processing_charge: Yes
article_type: original
author:
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Gabriele M.
full_name: Wögenstein, Gabriele M.
last_name: Wögenstein
- first_name: Gloria
full_name: Colombo, Gloria
id: 3483CF6C-F248-11E8-B48F-1D18A9856A87
last_name: Colombo
orcid: 0000-0001-9434-8902
- first_name: Raquel
full_name: Casado Polanco, Raquel
id: 15240fc1-dbcd-11ea-9d1d-ac5a786425fd
last_name: Casado Polanco
orcid: 0000-0001-8293-4568
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. Optimizing
AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor
degenerative environment. Molecular Therapy - Methods and Clinical Development.
2021;23:210-224. doi:10.1016/j.omtm.2021.09.006
apa: Maes, M. E., Wögenstein, G. M., Colombo, G., Casado Polanco, R., & Siegert,
S. (2021). Optimizing AAV2/6 microglial targeting identified enhanced efficiency
in the photoreceptor degenerative environment. Molecular Therapy - Methods
and Clinical Development. Elsevier. https://doi.org/10.1016/j.omtm.2021.09.006
chicago: Maes, Margaret E, Gabriele M. Wögenstein, Gloria Colombo, Raquel Casado
Polanco, and Sandra Siegert. “Optimizing AAV2/6 Microglial Targeting Identified
Enhanced Efficiency in the Photoreceptor Degenerative Environment.” Molecular
Therapy - Methods and Clinical Development. Elsevier, 2021. https://doi.org/10.1016/j.omtm.2021.09.006.
ieee: M. E. Maes, G. M. Wögenstein, G. Colombo, R. Casado Polanco, and S. Siegert,
“Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the
photoreceptor degenerative environment,” Molecular Therapy - Methods and Clinical
Development, vol. 23. Elsevier, pp. 210–224, 2021.
ista: Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. 2021. Optimizing
AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor
degenerative environment. Molecular Therapy - Methods and Clinical Development.
23, 210–224.
mla: Maes, Margaret E., et al. “Optimizing AAV2/6 Microglial Targeting Identified
Enhanced Efficiency in the Photoreceptor Degenerative Environment.” Molecular
Therapy - Methods and Clinical Development, vol. 23, Elsevier, 2021, pp. 210–24,
doi:10.1016/j.omtm.2021.09.006.
short: M.E. Maes, G.M. Wögenstein, G. Colombo, R. Casado Polanco, S. Siegert, Molecular
Therapy - Methods and Clinical Development 23 (2021) 210–224.
date_created: 2022-01-23T23:01:28Z
date_published: 2021-12-10T00:00:00Z
date_updated: 2023-11-16T13:12:03Z
day: '10'
ddc:
- '570'
department:
- _id: SaSi
- _id: SiHi
doi: 10.1016/j.omtm.2021.09.006
ec_funded: 1
external_id:
isi:
- '000748748500019'
file:
- access_level: open_access
checksum: 77dc540e8011c5475031bdf6ccef20a6
content_type: application/pdf
creator: cchlebak
date_created: 2022-01-24T07:43:09Z
date_updated: 2022-01-24T07:43:09Z
file_id: '10657'
file_name: 2021_MolTherMethodsClinDev_Maes.pdf
file_size: 4794147
relation: main_file
success: 1
file_date_updated: 2022-01-24T07:43:09Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 210-224
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: Molecular Therapy - Methods and Clinical Development
publication_identifier:
eissn:
- 2329-0501
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the
photoreceptor degenerative environment
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: 23
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: '10321'
abstract:
- lang: eng
text: Mosaic analysis with double markers (MADM) technology enables the generation
of genetic mosaic tissue in mice. MADM enables concomitant fluorescent cell labeling
and introduction of a mutation of a gene of interest with single-cell resolution.
This protocol highlights major steps for the generation of genetic mosaic tissue
and the isolation and processing of respective tissues for downstream histological
analysis. For complete details on the use and execution of this protocol, please
refer to Contreras et al. (2021).
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: This research was supported by the Scientific Service Units (SSU)
at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical
Facilities (PCF). We particularly thank Mohammad Goudarzi for assistance with photography
of mouse perfusion and dissection. N.A. received support from FWF Firnberg-Programm
(T 1031). This work was also supported by IST Austria institutional funds; FWF SFB
F78 to S.H.; and the European Research Council (ERC) under the European Union’s
Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro)
to S.H.
article_number: '100939'
article_processing_charge: Yes
article_type: original
author:
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Amberg N, Hippenmeyer S. Genetic mosaic dissection of candidate genes in mice
using mosaic analysis with double markers. STAR Protocols. 2021;2(4). doi:10.1016/j.xpro.2021.100939
apa: Amberg, N., & Hippenmeyer, S. (2021). Genetic mosaic dissection of candidate
genes in mice using mosaic analysis with double markers. STAR Protocols.
Cell Press. https://doi.org/10.1016/j.xpro.2021.100939
chicago: Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate
Genes in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols.
Cell Press, 2021. https://doi.org/10.1016/j.xpro.2021.100939.
ieee: N. Amberg and S. Hippenmeyer, “Genetic mosaic dissection of candidate genes
in mice using mosaic analysis with double markers,” STAR Protocols, vol.
2, no. 4. Cell Press, 2021.
ista: Amberg N, Hippenmeyer S. 2021. Genetic mosaic dissection of candidate genes
in mice using mosaic analysis with double markers. STAR Protocols. 2(4), 100939.
mla: Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate
Genes in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols,
vol. 2, no. 4, 100939, Cell Press, 2021, doi:10.1016/j.xpro.2021.100939.
short: N. Amberg, S. Hippenmeyer, STAR Protocols 2 (2021).
date_created: 2021-11-21T23:01:28Z
date_published: 2021-11-10T00:00:00Z
date_updated: 2023-11-16T13:08:03Z
day: '10'
ddc:
- '573'
department:
- _id: SiHi
doi: 10.1016/j.xpro.2021.100939
ec_funded: 1
file:
- access_level: open_access
checksum: 9e3f6d06bf583e7a8b6a9e9a60500a28
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-22T08:23:58Z
date_updated: 2021-11-22T08:23:58Z
file_id: '10329'
file_name: 2021_STARProtocols_Amberg.pdf
file_size: 7309464
relation: main_file
success: 1
file_date_updated: 2021-11-22T08:23:58Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '4'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 268F8446-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T0101031
name: Role of Eed in neural stem cell lineage progression
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F07805
name: Molecular Mechanisms of Neural Stem Cell Lineage Progression
publication: STAR Protocols
publication_identifier:
eissn:
- 2666-1667
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic mosaic dissection of candidate genes in mice using mosaic analysis
with double markers
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: '10290'
abstract:
- lang: eng
text: A precise quantitative description of the ultrastructural characteristics
underlying biological mechanisms is often key to their understanding. This is
particularly true for dynamic extra- and intracellular filamentous assemblies,
playing a role in cell motility, cell integrity, cytokinesis, tissue formation
and maintenance. For example, genetic manipulation or modulation of actin regulatory
proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural
architecture of actin filament-rich cell peripheral structures, such as lamellipodia
or filopodia. However, the observed ultrastructural effects often remain subtle
and require sufficiently large datasets for appropriate quantitative analysis.
The acquisition of such large datasets has been enabled by recent advances in
high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates
the development of complementary approaches to maximize the extraction of relevant
biological information. We have developed a computational toolbox for the semi-automatic
quantification of segmented and vectorized filamentous networks from pre-processed
cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple
experimental conditions. GUI-based components simplify the processing of data
and allow users to obtain a large number of ultrastructural parameters describing
filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing
cryo-ET data of untreated and chemically perturbed branched actin filament networks
and that of parallel actin filament arrays. In principle, the computational toolbox
presented here is applicable for data analysis comprising any type of filaments
in regular (i.e. parallel) or random arrangement. We show that it can ease the
identification of key differences between experimental groups and facilitate the
in-depth analysis of ultrastructural data in a time-efficient manner.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
acknowledgement: 'This research was supported by the Scientific Service Units (SSUs)
of IST Austria through resources provided by Scientific Computing (SciComp), the
Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy
Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data
acquisition. The authors acknowledge support from IST Austria and from the Austrian
Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.'
article_number: '107808'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Behnam
full_name: Amiri, Behnam
last_name: Amiri
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Martin
full_name: Falcke, Martin
last_name: Falcke
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for
ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal
of Structural Biology. 2021;213(4). doi:10.1016/j.jsb.2021.107808
apa: Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2021).
Computational toolbox for ultrastructural quantitative analysis of filament networks
in cryo-ET data. Journal of Structural Biology. Elsevier . https://doi.org/10.1016/j.jsb.2021.107808
chicago: Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian
KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of
Filament Networks in Cryo-ET Data.” Journal of Structural Biology. Elsevier
, 2021. https://doi.org/10.1016/j.jsb.2021.107808.
ieee: G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational
toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET
data,” Journal of Structural Biology, vol. 213, no. 4. Elsevier , 2021.
ista: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox
for ultrastructural quantitative analysis of filament networks in cryo-ET data.
Journal of Structural Biology. 213(4), 107808.
mla: Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative
Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology,
vol. 213, no. 4, 107808, Elsevier , 2021, doi:10.1016/j.jsb.2021.107808.
short: G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural
Biology 213 (2021).
date_created: 2021-11-15T12:21:42Z
date_published: 2021-11-03T00:00:00Z
date_updated: 2023-11-21T08:36:02Z
day: '03'
ddc:
- '572'
department:
- _id: FlSc
doi: 10.1016/j.jsb.2021.107808
external_id:
isi:
- '000720259500002'
file:
- access_level: open_access
checksum: 6b209e4d44775d4e02b50f78982c15fa
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-15T13:11:27Z
date_updated: 2021-11-15T13:11:27Z
file_id: '10291'
file_name: 2021_JournalStructBiol_Dimchev.pdf
file_size: 16818304
relation: main_file
success: 1
file_date_updated: 2021-11-15T13:11:27Z
has_accepted_license: '1'
intvolume: ' 213'
isi: 1
issue: '4'
keyword:
- Structural Biology
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
- _id: 2674F658-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02495
name: Protein structure and function in filopodia across scales
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: 'Elsevier '
quality_controlled: '1'
related_material:
record:
- id: '14502'
relation: software
status: public
scopus_import: '1'
status: public
title: Computational toolbox for ultrastructural quantitative analysis of filament
networks in cryo-ET data
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: 213
year: '2021'
...
---
_id: '9969'
abstract:
- lang: eng
text: 'Payment channel networks are a promising approach to improve the scalability
of cryptocurrencies: they allow to perform transactions in a peer-to-peer fashion,
along multihop routes in the network, without requiring consensus on the blockchain.
However, during the discovery of cost-efficient routes for the transaction, critical
information may be revealed about the transacting entities. This paper initiates
the study of privacy-preserving route discovery mechanisms for payment channel
networks. In particular, we present LightPIR, an approach which allows a client
to learn the shortest (or cheapest in terms of fees) path between two nodes without
revealing any information about the endpoints of the transaction to the servers.
The two main observations which allow for an efficient solution in LightPIR are
that: (1) surprisingly, hub labelling algorithms – which were developed to preprocess
“street network like” graphs so one can later efficiently compute shortest paths
– also perform well for the graphs underlying payment channel networks, and that
(2) hub labelling algorithms can be conveniently combined with private information
retrieval. LightPIR relies on a simple hub labeling heuristic on top of existing
hub labeling algorithms which leverages the specific topological features of cryptocurrency
networks to further minimize storage and bandwidth overheads. In a case study
considering the Lightning network, we show that our approach is an order of magnitude
more efficient compared to a privacy-preserving baseline based on using private
information retrieval on a database that stores all pairs shortest paths.'
article_processing_charge: No
author:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Iosif
full_name: Salem, Iosif
last_name: Salem
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
citation:
ama: 'Pietrzak KZ, Salem I, Schmid S, Yeo MX. LightPIR: Privacy-preserving route
discovery for payment channel networks. In: IEEE; 2021. doi:10.23919/IFIPNetworking52078.2021.9472205'
apa: 'Pietrzak, K. Z., Salem, I., Schmid, S., & Yeo, M. X. (2021). LightPIR:
Privacy-preserving route discovery for payment channel networks. Presented at
the 2021 IFIP Networking Conference (IFIP Networking), Espoo and Helsinki, Finland:
IEEE. https://doi.org/10.23919/IFIPNetworking52078.2021.9472205'
chicago: 'Pietrzak, Krzysztof Z, Iosif Salem, Stefan Schmid, and Michelle X Yeo.
“LightPIR: Privacy-Preserving Route Discovery for Payment Channel Networks.” IEEE,
2021. https://doi.org/10.23919/IFIPNetworking52078.2021.9472205.'
ieee: 'K. Z. Pietrzak, I. Salem, S. Schmid, and M. X. Yeo, “LightPIR: Privacy-preserving
route discovery for payment channel networks,” presented at the 2021 IFIP Networking
Conference (IFIP Networking), Espoo and Helsinki, Finland, 2021.'
ista: 'Pietrzak KZ, Salem I, Schmid S, Yeo MX. 2021. LightPIR: Privacy-preserving
route discovery for payment channel networks. 2021 IFIP Networking Conference
(IFIP Networking).'
mla: 'Pietrzak, Krzysztof Z., et al. LightPIR: Privacy-Preserving Route Discovery
for Payment Channel Networks. IEEE, 2021, doi:10.23919/IFIPNetworking52078.2021.9472205.'
short: K.Z. Pietrzak, I. Salem, S. Schmid, M.X. Yeo, in:, IEEE, 2021.
conference:
end_date: 2021-06-24
location: Espoo and Helsinki, Finland
name: 2021 IFIP Networking Conference (IFIP Networking)
start_date: 2021-06-21
date_created: 2021-08-29T22:01:16Z
date_published: 2021-06-21T00:00:00Z
date_updated: 2023-11-30T10:54:50Z
day: '21'
department:
- _id: KrPi
doi: 10.23919/IFIPNetworking52078.2021.9472205
ec_funded: 1
external_id:
arxiv:
- '2104.04293'
isi:
- '000853016800008'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2104.04293
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
eisbn:
- 978-3-9031-7639-3
eissn:
- 1861-2288
isbn:
- 978-1-6654-4501-6
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '14506'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'LightPIR: Privacy-preserving route discovery for payment channel networks'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9644'
abstract:
- lang: eng
text: 'We present a new approach to proving non-termination of non-deterministic
integer programs. Our technique is rather simple but efficient. It relies on a
purely syntactic reversal of the program''s transition system followed by a constraint-based
invariant synthesis with constraints coming from both the original and the reversed
transition system. The latter task is performed by a simple call to an off-the-shelf
SMT-solver, which allows us to leverage the latest advances in SMT-solving. Moreover,
our method offers a combination of features not present (as a whole) in previous
approaches: it handles programs with non-determinism, provides relative completeness
guarantees and supports programs with polynomial arithmetic. The experiments performed
with our prototype tool RevTerm show that our approach, despite its simplicity
and stronger theoretical guarantees, is at least on par with the state-of-the-art
tools, often achieving a non-trivial improvement under a proper configuration
of its parameters.'
acknowledgement: We thank the anonymous reviewers for their helpful comments. This
research was partially supported by the ERCCoG 863818 (ForM-SMArt) and the Czech
Science Foundation grant No. GJ19-15134Y.
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ehsan Kafshdar
full_name: Goharshady, Ehsan Kafshdar
last_name: Goharshady
- first_name: Petr
full_name: Novotný, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotný
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Chatterjee K, Goharshady EK, Novotný P, Zikelic D. Proving non-termination
by program reversal. In: Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation. Association
for Computing Machinery; 2021:1033-1048. doi:10.1145/3453483.3454093'
apa: 'Chatterjee, K., Goharshady, E. K., Novotný, P., & Zikelic, D. (2021).
Proving non-termination by program reversal. In Proceedings of the 42nd ACM
SIGPLAN International Conference on Programming Language Design and Implementation
(pp. 1033–1048). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454093'
chicago: Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, and Dorde
Zikelic. “Proving Non-Termination by Program Reversal.” In Proceedings of the
42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation,
1033–48. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454093.
ieee: K. Chatterjee, E. K. Goharshady, P. Novotný, and D. Zikelic, “Proving non-termination
by program reversal,” in Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation, Online, 2021,
pp. 1033–1048.
ista: 'Chatterjee K, Goharshady EK, Novotný P, Zikelic D. 2021. Proving non-termination
by program reversal. Proceedings of the 42nd ACM SIGPLAN International Conference
on Programming Language Design and Implementation. PLDI: Programming Language
Design and Implementation, 1033–1048.'
mla: Chatterjee, Krishnendu, et al. “Proving Non-Termination by Program Reversal.”
Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, Association for Computing Machinery, 2021,
pp. 1033–48, doi:10.1145/3453483.3454093.
short: K. Chatterjee, E.K. Goharshady, P. Novotný, D. Zikelic, in:, Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 1033–1048.
conference:
end_date: 2021-06-26
location: Online
name: 'PLDI: Programming Language Design and Implementation'
start_date: 2021-06-20
date_created: 2021-07-11T22:01:17Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-11-30T10:55:37Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3453483.3454093
ec_funded: 1
external_id:
arxiv:
- '2104.01189'
isi:
- '000723661700067'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2104.01189
month: '06'
oa: 1
oa_version: Preprint
page: 1033-1048
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450383912'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '14539'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Proving non-termination by program reversal
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9760'
abstract:
- lang: eng
text: "The quantum approximate optimization algorithm (QAOA) is a prospective near-term
quantum algorithm due to its modest circuit depth and promising benchmarks. However,
an external parameter optimization required in the QAOA could become a performance
bottleneck. This motivates studies of the optimization landscape and search for
heuristic ways of parameter initialization. In this work we visualize the optimization
landscape of the QAOA applied to the MaxCut problem on random graphs, demonstrating
that random initialization of the QAOA is prone to converging to local minima
with suboptimal performance. We introduce the initialization of QAOA parameters
based on the Trotterized quantum annealing (TQA) protocol, parameterized by the
Trotter time step. We find that the TQA initialization allows to circumvent\r\nthe
issue of false minima for a broad range of time steps, yielding the same performance
as the best result out of an exponentially scaling number of random initializations.
Moreover, we demonstrate that the optimal value of the time step coincides with
the point of proliferation of Trotter errors in quantum annealing. Our results
suggest practical ways of initializing QAOA protocols on near-term quantum devices
and reveal new connections between QAOA and quantum annealing."
acknowledgement: We would like to thank D. Abanin and R. Medina for fruitful discussions
and A. Smith and I. Kim for valuable feedback on the manuscript. We acknowledge
support by the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation program (Grant Agreement No. 850899).
article_number: '491'
article_processing_charge: Yes
article_type: original
author:
- first_name: Stefan
full_name: Sack, Stefan
id: dd622248-f6e0-11ea-865d-ce382a1c81a5
last_name: Sack
orcid: 0000-0001-5400-8508
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Sack S, Serbyn M. Quantum annealing initialization of the quantum approximate
optimization algorithm. Quantum. 2021;5. doi:10.22331/Q-2021-07-01-491
apa: Sack, S., & Serbyn, M. (2021). Quantum annealing initialization of the
quantum approximate optimization algorithm. Quantum. Verein zur Förderung
des Open Access Publizierens in den Quantenwissenschaften. https://doi.org/10.22331/Q-2021-07-01-491
chicago: Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the
Quantum Approximate Optimization Algorithm.” Quantum. Verein zur Förderung
des Open Access Publizierens in den Quantenwissenschaften, 2021. https://doi.org/10.22331/Q-2021-07-01-491.
ieee: S. Sack and M. Serbyn, “Quantum annealing initialization of the quantum approximate
optimization algorithm,” Quantum, vol. 5. Verein zur Förderung des Open
Access Publizierens in den Quantenwissenschaften, 2021.
ista: Sack S, Serbyn M. 2021. Quantum annealing initialization of the quantum approximate
optimization algorithm. Quantum. 5, 491.
mla: Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum
Approximate Optimization Algorithm.” Quantum, vol. 5, 491, Verein zur Förderung
des Open Access Publizierens in den Quantenwissenschaften, 2021, doi:10.22331/Q-2021-07-01-491.
short: S. Sack, M. Serbyn, Quantum 5 (2021).
date_created: 2021-08-01T22:01:21Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-12-13T14:47:25Z
day: '01'
ddc:
- '530'
department:
- _id: GradSch
- _id: MaSe
doi: 10.22331/Q-2021-07-01-491
ec_funded: 1
external_id:
arxiv:
- '2101.05742'
isi:
- '000669830600001'
file:
- access_level: open_access
checksum: 9706c2bb8e748e9b5b138381995a7f6f
content_type: application/pdf
creator: cchlebak
date_created: 2021-08-06T06:44:31Z
date_updated: 2021-08-06T06:44:31Z
file_id: '9774'
file_name: 2021_Quantum_Sack.pdf
file_size: 2312482
relation: main_file
file_date_updated: 2021-08-06T06:44:31Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Quantum
publication_identifier:
eissn:
- 2521-327X
publication_status: published
publisher: Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften
quality_controlled: '1'
related_material:
record:
- id: '14622'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Quantum annealing initialization of the quantum approximate optimization algorithm
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: 5
year: '2021'
...
---
_id: '10414'
abstract:
- lang: eng
text: 'We consider the almost-sure (a.s.) termination problem for probabilistic
programs, which are a stochastic extension of classical imperative programs. Lexicographic
ranking functions provide a sound and practical approach for termination of non-probabilistic
programs, and their extension to probabilistic programs is achieved via lexicographic
ranking supermartingales (LexRSMs). However, LexRSMs introduced in the previous
work have a limitation that impedes their automation: all of their components
have to be non-negative in all reachable states. This might result in LexRSM not
existing even for simple terminating programs. Our contributions are twofold:
First, we introduce a generalization of LexRSMs which allows for some components
to be negative. This standard feature of non-probabilistic termination proofs
was hitherto not known to be sound in the probabilistic setting, as the soundness
proof requires a careful analysis of the underlying stochastic process. Second,
we present polynomial-time algorithms using our generalized LexRSMs for proving
a.s. termination in broad classes of linear-arithmetic programs.'
acknowledgement: This research was partially supported by the ERC CoG 863818 (ForM-SMArt),
the Czech Science Foundation grant No. GJ19-15134Y, and the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
No. 665385.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ehsan Kafshdar
full_name: Goharshady, Ehsan Kafshdar
last_name: Goharshady
- first_name: Petr
full_name: Novotný, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotný
- first_name: Jiří
full_name: Zárevúcky, Jiří
last_name: Zárevúcky
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Chatterjee K, Goharshady EK, Novotný P, Zárevúcky J, Zikelic D. On lexicographic
proof rules for probabilistic termination. In: 24th International Symposium
on Formal Methods. Vol 13047. Springer Nature; 2021:619-639. doi:10.1007/978-3-030-90870-6_33'
apa: 'Chatterjee, K., Goharshady, E. K., Novotný, P., Zárevúcky, J., & Zikelic,
D. (2021). On lexicographic proof rules for probabilistic termination. In 24th
International Symposium on Formal Methods (Vol. 13047, pp. 619–639). Virtual:
Springer Nature. https://doi.org/10.1007/978-3-030-90870-6_33'
chicago: Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, Jiří Zárevúcky,
and Dorde Zikelic. “On Lexicographic Proof Rules for Probabilistic Termination.”
In 24th International Symposium on Formal Methods, 13047:619–39. Springer
Nature, 2021. https://doi.org/10.1007/978-3-030-90870-6_33.
ieee: K. Chatterjee, E. K. Goharshady, P. Novotný, J. Zárevúcky, and D. Zikelic,
“On lexicographic proof rules for probabilistic termination,” in 24th International
Symposium on Formal Methods, Virtual, 2021, vol. 13047, pp. 619–639.
ista: 'Chatterjee K, Goharshady EK, Novotný P, Zárevúcky J, Zikelic D. 2021. On
lexicographic proof rules for probabilistic termination. 24th International Symposium
on Formal Methods. FM: Formal Methods, LNCS, vol. 13047, 619–639.'
mla: Chatterjee, Krishnendu, et al. “On Lexicographic Proof Rules for Probabilistic
Termination.” 24th International Symposium on Formal Methods, vol. 13047,
Springer Nature, 2021, pp. 619–39, doi:10.1007/978-3-030-90870-6_33.
short: K. Chatterjee, E.K. Goharshady, P. Novotný, J. Zárevúcky, D. Zikelic, in:,
24th International Symposium on Formal Methods, Springer Nature, 2021, pp. 619–639.
conference:
end_date: 2021-11-26
location: Virtual
name: 'FM: Formal Methods'
start_date: 2021-11-20
date_created: 2021-12-05T23:01:45Z
date_published: 2021-11-10T00:00:00Z
date_updated: 2024-01-17T08:19:41Z
day: '10'
department:
- _id: KrCh
doi: 10.1007/978-3-030-90870-6_33
ec_funded: 1
external_id:
arxiv:
- '2108.02188'
isi:
- '000758218600033'
intvolume: ' 13047'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2108.02188
month: '11'
oa: 1
oa_version: Preprint
page: 619-639
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: 24th International Symposium on Formal Methods
publication_identifier:
eisbn:
- 978-3-030-90870-6
eissn:
- 1611-3349
isbn:
- 9-783-0309-0869-0
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '14539'
relation: dissertation_contains
status: public
- id: '14778'
relation: later_version
status: public
scopus_import: '1'
status: public
title: On lexicographic proof rules for probabilistic termination
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13047
year: '2021'
...
---
_id: '14800'
abstract:
- lang: eng
text: 'Research on two-dimensional (2D) materials has been explosively increasing
in last seventeen years in varying subjects including condensed matter physics,
electronic engineering, materials science, and chemistry since the mechanical
exfoliation of graphene in 2004. Starting from graphene, 2D materials now have
become a big family with numerous members and diverse categories. The unique structural
features and physicochemical properties of 2D materials make them one class of
the most appealing candidates for a wide range of potential applications. In particular,
we have seen some major breakthroughs made in the field of 2D materials in last
five years not only in developing novel synthetic methods and exploring new structures/properties
but also in identifying innovative applications and pushing forward commercialisation.
In this review, we provide a critical summary on the recent progress made in the
field of 2D materials with a particular focus on last five years. After a brief
background introduction, we first discuss the major synthetic methods for 2D materials,
including the mechanical exfoliation, liquid exfoliation, vapor phase deposition,
and wet-chemical synthesis as well as phase engineering of 2D materials belonging
to the field of phase engineering of nanomaterials (PEN). We then introduce the
superconducting/optical/magnetic properties and chirality of 2D materials along
with newly emerging magic angle 2D superlattices. Following that, the promising
applications of 2D materials in electronics, optoelectronics, catalysis, energy
storage, solar cells, biomedicine, sensors, environments, etc. are described sequentially.
Thereafter, we present the theoretic calculations and simulations of 2D materials.
Finally, after concluding the current progress, we provide some personal discussions
on the existing challenges and future outlooks in this rapidly developing field. '
article_number: '2108017'
article_processing_charge: No
article_type: review
author:
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Wei
full_name: Chen, Wei
last_name: Chen
- first_name: Ye
full_name: Chen, Ye
last_name: Chen
- first_name: Yonghua
full_name: Chen, Yonghua
last_name: Chen
- first_name: Yu
full_name: Chen, Yu
last_name: Chen
- first_name: Feng
full_name: Ding, Feng
last_name: Ding
- first_name: Chunhai
full_name: Fan, Chunhai
last_name: Fan
- first_name: Hong Jin
full_name: Fan, Hong Jin
last_name: Fan
- first_name: Zhanxi
full_name: Fan, Zhanxi
last_name: Fan
- first_name: Cheng
full_name: Gong, Cheng
last_name: Gong
- first_name: Yongji
full_name: Gong, Yongji
last_name: Gong
- first_name: Qiyuan
full_name: He, Qiyuan
last_name: He
- first_name: Xun
full_name: Hong, Xun
last_name: Hong
- first_name: Sheng
full_name: Hu, Sheng
last_name: Hu
- first_name: Weida
full_name: Hu, Weida
last_name: Hu
- first_name: Wei
full_name: Huang, Wei
last_name: Huang
- first_name: Yuan
full_name: Huang, Yuan
last_name: Huang
- first_name: Wei
full_name: Ji, Wei
last_name: Ji
- first_name: Dehui
full_name: Li, Dehui
last_name: Li
- first_name: Lain Jong
full_name: Li, Lain Jong
last_name: Li
- first_name: Qiang
full_name: Li, Qiang
last_name: Li
- first_name: Li
full_name: Lin, Li
last_name: Lin
- first_name: Chongyi
full_name: Ling, Chongyi
last_name: Ling
- first_name: Minghua
full_name: Liu, Minghua
last_name: Liu
- first_name: 'Nan'
full_name: Liu, Nan
last_name: Liu
- first_name: Zhuang
full_name: Liu, Zhuang
last_name: Liu
- first_name: Kian Ping
full_name: Loh, Kian Ping
last_name: Loh
- first_name: Jianmin
full_name: Ma, Jianmin
last_name: Ma
- first_name: Feng
full_name: Miao, Feng
last_name: Miao
- first_name: Hailin
full_name: Peng, Hailin
last_name: Peng
- first_name: Mingfei
full_name: Shao, Mingfei
last_name: Shao
- first_name: Li
full_name: Song, Li
last_name: Song
- first_name: Shao
full_name: Su, Shao
last_name: Su
- first_name: Shuo
full_name: Sun, Shuo
last_name: Sun
- first_name: Chaoliang
full_name: Tan, Chaoliang
last_name: Tan
- first_name: Zhiyong
full_name: Tang, Zhiyong
last_name: Tang
- first_name: Dingsheng
full_name: Wang, Dingsheng
last_name: Wang
- first_name: Huan
full_name: Wang, Huan
last_name: Wang
- first_name: Jinlan
full_name: Wang, Jinlan
last_name: Wang
- first_name: Xin
full_name: Wang, Xin
last_name: Wang
- first_name: Xinran
full_name: Wang, Xinran
last_name: Wang
- first_name: Andrew T.S.
full_name: Wee, Andrew T.S.
last_name: Wee
- first_name: Zhongming
full_name: Wei, Zhongming
last_name: Wei
- first_name: Yuen
full_name: Wu, Yuen
last_name: Wu
- first_name: Zhong Shuai
full_name: Wu, Zhong Shuai
last_name: Wu
- first_name: Jie
full_name: Xiong, Jie
last_name: Xiong
- first_name: Qihua
full_name: Xiong, Qihua
last_name: Xiong
- first_name: Weigao
full_name: Xu, Weigao
last_name: Xu
- first_name: Peng
full_name: Yin, Peng
last_name: Yin
- first_name: Haibo
full_name: Zeng, Haibo
last_name: Zeng
- first_name: Zhiyuan
full_name: Zeng, Zhiyuan
last_name: Zeng
- first_name: Tianyou
full_name: Zhai, Tianyou
last_name: Zhai
- first_name: Han
full_name: Zhang, Han
last_name: Zhang
- first_name: Hui
full_name: Zhang, Hui
last_name: Zhang
- first_name: Qichun
full_name: Zhang, Qichun
last_name: Zhang
- first_name: Tierui
full_name: Zhang, Tierui
last_name: Zhang
- first_name: Xiang
full_name: Zhang, Xiang
last_name: Zhang
- first_name: Li Dong
full_name: Zhao, Li Dong
last_name: Zhao
- first_name: Meiting
full_name: Zhao, Meiting
last_name: Zhao
- first_name: Weijie
full_name: Zhao, Weijie
last_name: Zhao
- first_name: Yunxuan
full_name: Zhao, Yunxuan
last_name: Zhao
- first_name: Kai Ge
full_name: Zhou, Kai Ge
last_name: Zhou
- first_name: Xing
full_name: Zhou, Xing
last_name: Zhou
- first_name: Yu
full_name: Zhou, Yu
last_name: Zhou
- first_name: Hongwei
full_name: Zhu, Hongwei
last_name: Zhu
- first_name: Hua
full_name: Zhang, Hua
last_name: Zhang
- first_name: Zhongfan
full_name: Liu, Zhongfan
last_name: Liu
citation:
ama: Chang C, Chen W, Chen Y, et al. Recent progress on two-dimensional materials.
Acta Physico-Chimica Sinica. 2021;37(12). doi:10.3866/PKU.WHXB202108017
apa: Chang, C., Chen, W., Chen, Y., Chen, Y., Chen, Y., Ding, F., … Liu, Z. (2021).
Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica.
Peking University. https://doi.org/10.3866/PKU.WHXB202108017
chicago: Chang, Cheng, Wei Chen, Ye Chen, Yonghua Chen, Yu Chen, Feng Ding, Chunhai
Fan, et al. “Recent Progress on Two-Dimensional Materials.” Acta Physico-Chimica
Sinica. Peking University, 2021. https://doi.org/10.3866/PKU.WHXB202108017.
ieee: C. Chang et al., “Recent progress on two-dimensional materials,” Acta
Physico-Chimica Sinica, vol. 37, no. 12. Peking University, 2021.
ista: Chang C, Chen W, Chen Y, Chen Y, Chen Y, Ding F, Fan C, Fan HJ, Fan Z, Gong
C, Gong Y, He Q, Hong X, Hu S, Hu W, Huang W, Huang Y, Ji W, Li D, Li LJ, Li Q,
Lin L, Ling C, Liu M, Liu N, Liu Z, Loh KP, Ma J, Miao F, Peng H, Shao M, Song
L, Su S, Sun S, Tan C, Tang Z, Wang D, Wang H, Wang J, Wang X, Wang X, Wee ATS,
Wei Z, Wu Y, Wu ZS, Xiong J, Xiong Q, Xu W, Yin P, Zeng H, Zeng Z, Zhai T, Zhang
H, Zhang H, Zhang Q, Zhang T, Zhang X, Zhao LD, Zhao M, Zhao W, Zhao Y, Zhou KG,
Zhou X, Zhou Y, Zhu H, Zhang H, Liu Z. 2021. Recent progress on two-dimensional
materials. Acta Physico-Chimica Sinica. 37(12), 2108017.
mla: Chang, Cheng, et al. “Recent Progress on Two-Dimensional Materials.” Acta
Physico-Chimica Sinica, vol. 37, no. 12, 2108017, Peking University, 2021,
doi:10.3866/PKU.WHXB202108017.
short: C. Chang, W. Chen, Y. Chen, Y. Chen, Y. Chen, F. Ding, C. Fan, H.J. Fan,
Z. Fan, C. Gong, Y. Gong, Q. He, X. Hong, S. Hu, W. Hu, W. Huang, Y. Huang, W.
Ji, D. Li, L.J. Li, Q. Li, L. Lin, C. Ling, M. Liu, N. Liu, Z. Liu, K.P. Loh,
J. Ma, F. Miao, H. Peng, M. Shao, L. Song, S. Su, S. Sun, C. Tan, Z. Tang, D.
Wang, H. Wang, J. Wang, X. Wang, X. Wang, A.T.S. Wee, Z. Wei, Y. Wu, Z.S. Wu,
J. Xiong, Q. Xiong, W. Xu, P. Yin, H. Zeng, Z. Zeng, T. Zhai, H. Zhang, H. Zhang,
Q. Zhang, T. Zhang, X. Zhang, L.D. Zhao, M. Zhao, W. Zhao, Y. Zhao, K.G. Zhou,
X. Zhou, Y. Zhou, H. Zhu, H. Zhang, Z. Liu, Acta Physico-Chimica Sinica 37 (2021).
date_created: 2024-01-14T23:00:58Z
date_published: 2021-10-13T00:00:00Z
date_updated: 2024-01-17T11:29:33Z
day: '13'
department:
- _id: MaIb
doi: 10.3866/PKU.WHXB202108017
intvolume: ' 37'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3866/PKU.WHXB202108017
month: '10'
oa: 1
oa_version: Submitted Version
publication: Acta Physico-Chimica Sinica
publication_identifier:
issn:
- 1001-4861
publication_status: published
publisher: Peking University
quality_controlled: '1'
scopus_import: '1'
status: public
title: Recent progress on two-dimensional materials
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2021'
...
---
_id: '10206'
abstract:
- lang: eng
text: Neural-network classifiers achieve high accuracy when predicting the class
of an input that they were trained to identify. Maintaining this accuracy in dynamic
environments, where inputs frequently fall outside the fixed set of initially
known classes, remains a challenge. The typical approach is to detect inputs from
novel classes and retrain the classifier on an augmented dataset. However, not
only the classifier but also the detection mechanism needs to adapt in order to
distinguish between newly learned and yet unknown input classes. To address this
challenge, we introduce an algorithmic framework for active monitoring of a neural
network. A monitor wrapped in our framework operates in parallel with the neural
network and interacts with a human user via a series of interpretable labeling
queries for incremental adaptation. In addition, we propose an adaptive quantitative
monitor to improve precision. An experimental evaluation on a diverse set of benchmarks
with varying numbers of classes confirms the benefits of our active monitoring
framework in dynamic scenarios.
acknowledgement: We thank Christoph Lampert and Alex Greengold for fruitful discussions.
This research was supported in part by the Simons Institute for the Theory of Computing,
the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and the
European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curie grant agreement No. 754411.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Anna
full_name: Lukina, Anna
id: CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425
last_name: Lukina
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Lukina A, Schilling C, Henzinger TA. Into the unknown: active monitoring of neural
networks. In: 21st International Conference on Runtime Verification. Vol
12974. Cham: Springer Nature; 2021:42-61. doi:10.1007/978-3-030-88494-9_3'
apa: 'Lukina, A., Schilling, C., & Henzinger, T. A. (2021). Into the unknown:
active monitoring of neural networks. In 21st International Conference on Runtime
Verification (Vol. 12974, pp. 42–61). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-88494-9_3'
chicago: 'Lukina, Anna, Christian Schilling, and Thomas A Henzinger. “Into the Unknown:
Active Monitoring of Neural Networks.” In 21st International Conference on
Runtime Verification, 12974:42–61. Cham: Springer Nature, 2021. https://doi.org/10.1007/978-3-030-88494-9_3.'
ieee: 'A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown: active monitoring
of neural networks,” in 21st International Conference on Runtime Verification,
Virtual, 2021, vol. 12974, pp. 42–61.'
ista: 'Lukina A, Schilling C, Henzinger TA. 2021. Into the unknown: active monitoring
of neural networks. 21st International Conference on Runtime Verification. RV:
Runtime Verification, LNCS, vol. 12974, 42–61.'
mla: 'Lukina, Anna, et al. “Into the Unknown: Active Monitoring of Neural Networks.”
21st International Conference on Runtime Verification, vol. 12974, Springer
Nature, 2021, pp. 42–61, doi:10.1007/978-3-030-88494-9_3.'
short: A. Lukina, C. Schilling, T.A. Henzinger, in:, 21st International Conference
on Runtime Verification, Springer Nature, Cham, 2021, pp. 42–61.
conference:
end_date: 2021-10-14
location: Virtual
name: 'RV: Runtime Verification'
start_date: 2021-10-11
date_created: 2021-10-31T23:01:31Z
date_published: 2021-10-06T00:00:00Z
date_updated: 2024-01-30T12:06:56Z
day: '06'
department:
- _id: ToHe
doi: 10.1007/978-3-030-88494-9_3
ec_funded: 1
external_id:
arxiv:
- '2009.06429'
isi:
- '000719383800003'
isi: 1
keyword:
- monitoring
- neural networks
- novelty detection
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2009.06429
month: '10'
oa: 1
oa_version: Preprint
page: 42-61
place: Cham
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 21st International Conference on Runtime Verification
publication_identifier:
eisbn:
- 978-3-030-88494-9
eissn:
- 1611-3349
isbn:
- 9-783-0308-8493-2
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13234'
relation: extended_version
status: public
scopus_import: '1'
status: public
title: 'Into the unknown: active monitoring of neural networks'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: '12974 '
year: '2021'
...
---
_id: '14889'
abstract:
- lang: eng
text: We consider the Fröhlich Hamiltonian with large coupling constant α. For initial
data of Pekar product form with coherent phonon field and with the electron minimizing
the corresponding energy, we provide a norm approximation of the evolution, valid
up to times of order α2. The approximation is given in terms of a Pekar product
state, evolved through the Landau-Pekar equations, corrected by a Bogoliubov dynamics
taking quantum fluctuations into account. This allows us to show that the Landau-Pekar
equations approximately describe the evolution of the electron- and one-phonon
reduced density matrices under the Fröhlich dynamics up to times of order α2.
acknowledgement: "Financial support by the European Union’s Horizon 2020 research
and innovation programme\r\nunder the Marie Skłodowska-Curie grant agreement No.
754411 (S.R.) and the European\r\nResearch Council under grant agreement No. 694227
(N.L. and R.S.), as well as by the SNSF\r\nEccellenza project PCEFP2 181153 (N.L.),
the NCCR SwissMAP (N.L. and B.S.) and by the\r\nDeutsche Forschungsgemeinschaft
(DFG) through the Research Training Group 1838: Spectral\r\nTheory and Dynamics
of Quantum Systems (D.M.) is gratefully acknowledged. B.S. gratefully\r\nacknowledges
financial support from the Swiss National Science Foundation through the Grant\r\n“Dynamical
and energetic properties of Bose-Einstein condensates” and from the European\r\nResearch
Council through the ERC-AdG CLaQS (grant agreement No 834782). D.M. thanks\r\nMarcel
Griesemer for helpful discussions."
article_processing_charge: No
article_type: original
author:
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
- first_name: Simone Anna Elvira
full_name: Rademacher, Simone Anna Elvira
id: 856966FE-A408-11E9-977E-802DE6697425
last_name: Rademacher
orcid: 0000-0001-5059-4466
- 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: Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. Landau–Pekar
equations and quantum fluctuations for the dynamics of a strongly coupled polaron.
Pure and Applied Analysis. 2021;3(4):653-676. doi:10.2140/paa.2021.3.653
apa: Leopold, N. K., Mitrouskas, D. J., Rademacher, S. A. E., Schlein, B., &
Seiringer, R. (2021). Landau–Pekar equations and quantum fluctuations for the
dynamics of a strongly coupled polaron. Pure and Applied Analysis. Mathematical
Sciences Publishers. https://doi.org/10.2140/paa.2021.3.653
chicago: Leopold, Nikolai K, David Johannes Mitrouskas, Simone Anna Elvira Rademacher,
Benjamin Schlein, and Robert Seiringer. “Landau–Pekar Equations and Quantum Fluctuations
for the Dynamics of a Strongly Coupled Polaron.” Pure and Applied Analysis.
Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/paa.2021.3.653.
ieee: N. K. Leopold, D. J. Mitrouskas, S. A. E. Rademacher, B. Schlein, and R. Seiringer,
“Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly
coupled polaron,” Pure and Applied Analysis, vol. 3, no. 4. Mathematical
Sciences Publishers, pp. 653–676, 2021.
ista: Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. 2021. Landau–Pekar
equations and quantum fluctuations for the dynamics of a strongly coupled polaron.
Pure and Applied Analysis. 3(4), 653–676.
mla: Leopold, Nikolai K., et al. “Landau–Pekar Equations and Quantum Fluctuations
for the Dynamics of a Strongly Coupled Polaron.” Pure and Applied Analysis,
vol. 3, no. 4, Mathematical Sciences Publishers, 2021, pp. 653–76, doi:10.2140/paa.2021.3.653.
short: N.K. Leopold, D.J. Mitrouskas, S.A.E. Rademacher, B. Schlein, R. Seiringer,
Pure and Applied Analysis 3 (2021) 653–676.
date_created: 2024-01-28T23:01:43Z
date_published: 2021-10-01T00:00:00Z
date_updated: 2024-02-05T10:02:45Z
day: '01'
department:
- _id: RoSe
doi: 10.2140/paa.2021.3.653
ec_funded: 1
external_id:
arxiv:
- '2005.02098'
intvolume: ' 3'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2005.02098
month: '10'
oa: 1
oa_version: Preprint
page: 653-676
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Pure and Applied Analysis
publication_identifier:
eissn:
- 2578-5885
issn:
- 2578-5893
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly
coupled polaron
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2021'
...
---
_id: '14890'
abstract:
- lang: eng
text: We consider a system of N interacting bosons in the mean-field scaling regime
and construct corrections to the Bogoliubov dynamics that approximate the true
N-body dynamics in norm to arbitrary precision. The N-independent corrections
are given in terms of the solutions of the Bogoliubov and Hartree equations and
satisfy a generalized form of Wick's theorem. We determine the n-point correlation
functions of the excitations around the condensate, as well as the reduced densities
of the N-body system, to arbitrary accuracy, given only the knowledge of the two-point
functions of a quasi-free state and the solution of the Hartree equation. In this
way, the complex problem of computing all n-point correlation functions for an
interacting N-body system is essentially reduced to the problem of solving the
Hartree equation and the PDEs for the Bogoliubov two-point functions.
acknowledgement: "We are grateful for the hospitality of Central China Normal University
(CCNU),\r\nwhere parts of this work were done, and thank Phan Th`anh Nam, Simone\r\nRademacher,
Robert Seiringer and Stefan Teufel for helpful discussions. L.B. gratefully acknowledges
the support by the German Research Foundation (DFG) within the Research\r\nTraining
Group 1838 “Spectral Theory and Dynamics of Quantum Systems”, and the funding\r\nfrom
the European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSk
lodowska-Curie Grant Agreement No. 754411."
article_processing_charge: No
article_type: original
author:
- first_name: Lea
full_name: Bossmann, Lea
id: A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425
last_name: Bossmann
orcid: 0000-0002-6854-1343
- first_name: Sören P
full_name: Petrat, Sören P
id: 40AC02DC-F248-11E8-B48F-1D18A9856A87
last_name: Petrat
orcid: 0000-0002-9166-5889
- first_name: Peter
full_name: Pickl, Peter
last_name: Pickl
- first_name: Avy
full_name: Soffer, Avy
last_name: Soffer
citation:
ama: Bossmann L, Petrat SP, Pickl P, Soffer A. Beyond Bogoliubov dynamics. Pure
and Applied Analysis. 2021;3(4):677-726. doi:10.2140/paa.2021.3.677
apa: Bossmann, L., Petrat, S. P., Pickl, P., & Soffer, A. (2021). Beyond Bogoliubov
dynamics. Pure and Applied Analysis. Mathematical Sciences Publishers.
https://doi.org/10.2140/paa.2021.3.677
chicago: Bossmann, Lea, Sören P Petrat, Peter Pickl, and Avy Soffer. “Beyond Bogoliubov
Dynamics.” Pure and Applied Analysis. Mathematical Sciences Publishers,
2021. https://doi.org/10.2140/paa.2021.3.677.
ieee: L. Bossmann, S. P. Petrat, P. Pickl, and A. Soffer, “Beyond Bogoliubov dynamics,”
Pure and Applied Analysis, vol. 3, no. 4. Mathematical Sciences Publishers,
pp. 677–726, 2021.
ista: Bossmann L, Petrat SP, Pickl P, Soffer A. 2021. Beyond Bogoliubov dynamics.
Pure and Applied Analysis. 3(4), 677–726.
mla: Bossmann, Lea, et al. “Beyond Bogoliubov Dynamics.” Pure and Applied Analysis,
vol. 3, no. 4, Mathematical Sciences Publishers, 2021, pp. 677–726, doi:10.2140/paa.2021.3.677.
short: L. Bossmann, S.P. Petrat, P. Pickl, A. Soffer, Pure and Applied Analysis
3 (2021) 677–726.
date_created: 2024-01-28T23:01:43Z
date_published: 2021-10-01T00:00:00Z
date_updated: 2024-02-05T09:26:31Z
day: '01'
department:
- _id: RoSe
doi: 10.2140/paa.2021.3.677
ec_funded: 1
external_id:
arxiv:
- '1912.11004'
intvolume: ' 3'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1912.11004
month: '10'
oa: 1
oa_version: Preprint
page: 677-726
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Pure and Applied Analysis
publication_identifier:
eissn:
- 2578-5885
issn:
- 2578-5893
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Beyond Bogoliubov dynamics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2021'
...
---
_id: '15013'
abstract:
- lang: eng
text: We consider random n×n matrices X with independent and centered entries and
a general variance profile. We show that the spectral radius of X converges with
very high probability to the square root of the spectral radius of the variance
matrix of X when n tends to infinity. We also establish the optimal rate of convergence,
that is a new result even for general i.i.d. matrices beyond the explicitly solvable
Gaussian cases. The main ingredient is the proof of the local inhomogeneous circular
law [arXiv:1612.07776] at the spectral edge.
acknowledgement: Partially supported by ERC Starting Grant RandMat No. 715539 and
the SwissMap grant of Swiss National Science Foundation. Partially supported by
ERC Advanced Grant RanMat No. 338804. Partially supported by the Hausdorff Center
for Mathematics in Bonn.
article_processing_charge: No
article_type: original
author:
- first_name: Johannes
full_name: Alt, Johannes
id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87
last_name: Alt
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: Alt J, Erdös L, Krüger TH. Spectral radius of random matrices with independent
entries. Probability and Mathematical Physics. 2021;2(2):221-280. doi:10.2140/pmp.2021.2.221
apa: Alt, J., Erdös, L., & Krüger, T. H. (2021). Spectral radius of random matrices
with independent entries. Probability and Mathematical Physics. Mathematical
Sciences Publishers. https://doi.org/10.2140/pmp.2021.2.221
chicago: Alt, Johannes, László Erdös, and Torben H Krüger. “Spectral Radius of Random
Matrices with Independent Entries.” Probability and Mathematical Physics.
Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/pmp.2021.2.221.
ieee: J. Alt, L. Erdös, and T. H. Krüger, “Spectral radius of random matrices with
independent entries,” Probability and Mathematical Physics, vol. 2, no.
2. Mathematical Sciences Publishers, pp. 221–280, 2021.
ista: Alt J, Erdös L, Krüger TH. 2021. Spectral radius of random matrices with independent
entries. Probability and Mathematical Physics. 2(2), 221–280.
mla: Alt, Johannes, et al. “Spectral Radius of Random Matrices with Independent
Entries.” Probability and Mathematical Physics, vol. 2, no. 2, Mathematical
Sciences Publishers, 2021, pp. 221–80, doi:10.2140/pmp.2021.2.221.
short: J. Alt, L. Erdös, T.H. Krüger, Probability and Mathematical Physics 2 (2021)
221–280.
date_created: 2024-02-18T23:01:03Z
date_published: 2021-05-21T00:00:00Z
date_updated: 2024-02-19T08:30:00Z
day: '21'
department:
- _id: LaEr
doi: 10.2140/pmp.2021.2.221
ec_funded: 1
external_id:
arxiv:
- '1907.13631'
intvolume: ' 2'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1907.13631
month: '05'
oa: 1
oa_version: Preprint
page: 221-280
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Probability and Mathematical Physics
publication_identifier:
eissn:
- 2690-1005
issn:
- 2690-0998
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spectral radius of random matrices with independent entries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2021'
...
---
_id: '9887'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis is the major route of entry of cargos into cells
and thus underpins many physiological processes. During endocytosis, an area of
flat membrane is remodeled by proteins to create a spherical vesicle against intracellular
forces. The protein machinery which mediates this membrane bending in plants is
unknown. However, it is known that plant endocytosis is actin independent, thus
indicating that plants utilize a unique mechanism to mediate membrane bending
against high-turgor pressure compared to other model systems. Here, we investigate
the TPLATE complex, a plant-specific endocytosis protein complex. It has been
thought to function as a classical adaptor functioning underneath the clathrin
coat. However, by using biochemical and advanced live microscopy approaches, we
found that TPLATE is peripherally associated with clathrin-coated vesicles and
localizes at the rim of endocytosis events. As this localization is more fitting
to the protein machinery involved in membrane bending during endocytosis, we examined
cells in which the TPLATE complex was disrupted and found that the clathrin structures
present as flat patches. This suggests a requirement of the TPLATE complex for
membrane bending during plant clathrin–mediated endocytosis. Next, we used in
vitro biophysical assays to confirm that the TPLATE complex possesses protein
domains with intrinsic membrane remodeling activity. These results redefine the
role of the TPLATE complex and implicate it as a key component of the evolutionarily
distinct plant endocytosis mechanism, which mediates endocytic membrane bending
against the high-turgor pressure in plant cells.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
acknowledgement: 'We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory
Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help
and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian
Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with
material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi
protein. This research was supported by the Scientific Service Units of Institute
of Science and Technology Austria (IST Austria) through resources provided by the
Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska),
and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of
the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry
analysis of proteins, we acknowledge the University of Natural Resources and Life
Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the
following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25
to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029
Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF
No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research
Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249
(to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051
(to J.W.).'
article_number: e2113046118
article_processing_charge: No
article_type: original
author:
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Dana A
full_name: Dahhan, Dana A
last_name: Dahhan
- first_name: Nataliia
full_name: Gnyliukh, Nataliia
id: 390C1120-F248-11E8-B48F-1D18A9856A87
last_name: Gnyliukh
orcid: 0000-0002-2198-0509
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Vanessa
full_name: Zheden, Vanessa
id: 39C5A68A-F248-11E8-B48F-1D18A9856A87
last_name: Zheden
orcid: 0000-0002-9438-4783
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Pierre
full_name: Mahou, Pierre
last_name: Mahou
- first_name: Mónika
full_name: Hrtyan, Mónika
id: 45A71A74-F248-11E8-B48F-1D18A9856A87
last_name: Hrtyan
- first_name: Jie
full_name: Wang, Jie
last_name: Wang
- first_name: Juan L
full_name: Aguilera Servin, Juan L
id: 2A67C376-F248-11E8-B48F-1D18A9856A87
last_name: Aguilera Servin
orcid: 0000-0002-2862-8372
- first_name: Daniël
full_name: van Damme, Daniël
last_name: van Damme
- first_name: Emmanuel
full_name: Beaurepaire, Emmanuel
last_name: Beaurepaire
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Sebastian Y
full_name: Bednarek, Sebastian Y
last_name: Bednarek
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane
bending during plant clathrin-mediated endocytosis. Proceedings of the National
Academy of Sciences. 2021;118(51). doi:10.1073/pnas.2113046118
apa: Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo,
T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant
clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences.
National Academy of Sciences. https://doi.org/10.1073/pnas.2113046118
chicago: Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann,
Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates
Membrane Bending during Plant Clathrin-Mediated Endocytosis.” Proceedings of
the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2113046118.
ieee: A. J. Johnson et al., “The TPLATE complex mediates membrane bending
during plant clathrin-mediated endocytosis,” Proceedings of the National Academy
of Sciences, vol. 118, no. 51. National Academy of Sciences, 2021.
ista: Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou
P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M,
Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during
plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences.
118(51), e2113046118.
mla: Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending
during Plant Clathrin-Mediated Endocytosis.” Proceedings of the National Academy
of Sciences, vol. 118, no. 51, e2113046118, National Academy of Sciences,
2021, doi:10.1073/pnas.2113046118.
short: A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo,
P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire,
M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences
118 (2021).
date_created: 2021-08-11T14:11:43Z
date_published: 2021-12-14T00:00:00Z
date_updated: 2024-02-19T11:06:09Z
day: '14'
ddc:
- '580'
department:
- _id: JiFr
- _id: MaLo
- _id: EvBe
- _id: EM-Fac
- _id: NanoFab
doi: 10.1073/pnas.2113046118
external_id:
isi:
- '000736417600043'
pmid:
- '34907016'
file:
- access_level: open_access
checksum: 8d01e72e22c4fb1584e72d8601947069
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-15T08:59:40Z
date_updated: 2021-12-15T08:59:40Z
file_id: '10546'
file_name: 2021_PNAS_Johnson.pdf
file_size: 2757340
relation: main_file
success: 1
file_date_updated: 2021-12-15T08:59:40Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '51'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: https://doi.org/10.1101/2021.04.26.441441
record:
- id: '14510'
relation: dissertation_contains
status: public
- id: '14988'
relation: research_data
status: public
status: public
title: The TPLATE complex mediates membrane bending during plant clathrin-mediated
endocytosis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 118
year: '2021'
...
---
_id: '14984'
abstract:
- lang: eng
text: Hybrid zones are narrow geographic regions where different populations, races
or interbreeding species meet and mate, producing mixed ‘hybrid’ offspring. They
are relatively common and can be found in a diverse range of organisms and environments.
The study of hybrid zones has played an important role in our understanding of
the origin of species, with hybrid zones having been described as ‘natural laboratories’.
This is because they allow us to study,in situ, the conditions and evolutionary
forces that enable divergent taxa to remain distinct despite some ongoing gene
exchange between them.
article_processing_charge: No
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Daria
full_name: Shipilina, Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
citation:
ama: 'Stankowski S, Shipilina D, Westram AM. Hybrid Zones. In: Encyclopedia of
Life Sciences. Vol 2. eLS. Wiley; 2021. doi:10.1002/9780470015902.a0029355'
apa: Stankowski, S., Shipilina, D., & Westram, A. M. (2021). Hybrid Zones. In
Encyclopedia of Life Sciences (Vol. 2). Wiley. https://doi.org/10.1002/9780470015902.a0029355
chicago: Stankowski, Sean, Daria Shipilina, and Anja M Westram. “Hybrid Zones.”
In Encyclopedia of Life Sciences, Vol. 2. ELS. Wiley, 2021. https://doi.org/10.1002/9780470015902.a0029355.
ieee: S. Stankowski, D. Shipilina, and A. M. Westram, “Hybrid Zones,” in Encyclopedia
of Life Sciences, vol. 2, Wiley, 2021.
ista: 'Stankowski S, Shipilina D, Westram AM. 2021.Hybrid Zones. In: Encyclopedia
of Life Sciences. vol. 2.'
mla: Stankowski, Sean, et al. “Hybrid Zones.” Encyclopedia of Life Sciences,
vol. 2, Wiley, 2021, doi:10.1002/9780470015902.a0029355.
short: S. Stankowski, D. Shipilina, A.M. Westram, in:, Encyclopedia of Life Sciences,
Wiley, 2021.
date_created: 2024-02-14T12:05:50Z
date_published: 2021-05-28T00:00:00Z
date_updated: 2024-02-19T09:54:18Z
day: '28'
department:
- _id: NiBa
doi: 10.1002/9780470015902.a0029355
intvolume: ' 2'
language:
- iso: eng
month: '05'
oa_version: None
publication: Encyclopedia of Life Sciences
publication_identifier:
eisbn:
- '9780470015902'
isbn:
- '9780470016176'
publication_status: published
publisher: Wiley
quality_controlled: '1'
series_title: eLS
status: public
title: Hybrid Zones
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2021'
...
---
_id: '14987'
abstract:
- lang: eng
text: "The goal of zero-shot learning is to construct a classifier that can identify
object classes for which no training examples are available. When training data
for some of the object classes is available but not for others, the name generalized
zero-shot learning is commonly used.\r\nIn a wider sense, the phrase zero-shot
is also used to describe other machine learning-based approaches that require
no training data from the problem of interest, such as zero-shot action recognition
or zero-shot machine translation."
article_processing_charge: No
author:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Lampert C. Zero-Shot Learning. In: Ikeuchi K, ed. Computer Vision.
2nd ed. Cham: Springer; 2021:1395-1397. doi:10.1007/978-3-030-63416-2_874'
apa: 'Lampert, C. (2021). Zero-Shot Learning. In K. Ikeuchi (Ed.), Computer Vision
(2nd ed., pp. 1395–1397). Cham: Springer. https://doi.org/10.1007/978-3-030-63416-2_874'
chicago: 'Lampert, Christoph. “Zero-Shot Learning.” In Computer Vision, edited
by Katsushi Ikeuchi, 2nd ed., 1395–97. Cham: Springer, 2021. https://doi.org/10.1007/978-3-030-63416-2_874.'
ieee: 'C. Lampert, “Zero-Shot Learning,” in Computer Vision, 2nd ed., K.
Ikeuchi, Ed. Cham: Springer, 2021, pp. 1395–1397.'
ista: 'Lampert C. 2021.Zero-Shot Learning. In: Computer Vision. , 1395–1397.'
mla: Lampert, Christoph. “Zero-Shot Learning.” Computer Vision, edited by
Katsushi Ikeuchi, 2nd ed., Springer, 2021, pp. 1395–97, doi:10.1007/978-3-030-63416-2_874.
short: C. Lampert, in:, K. Ikeuchi (Ed.), Computer Vision, 2nd ed., Springer, Cham,
2021, pp. 1395–1397.
date_created: 2024-02-14T14:05:32Z
date_published: 2021-10-13T00:00:00Z
date_updated: 2024-02-19T10:59:04Z
day: '13'
department:
- _id: ChLa
doi: 10.1007/978-3-030-63416-2_874
edition: '2'
editor:
- first_name: Katsushi
full_name: Ikeuchi, Katsushi
last_name: Ikeuchi
language:
- iso: eng
month: '10'
oa_version: None
page: 1395-1397
place: Cham
publication: Computer Vision
publication_identifier:
eisbn:
- '9783030634162'
isbn:
- '9783030634155'
publication_status: published
publisher: Springer
quality_controlled: '1'
status: public
title: Zero-Shot Learning
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '14988'
abstract:
- lang: eng
text: Raw data generated from the publication - The TPLATE complex mediates membrane
bending during plant clathrin-mediated endocytosis by Johnson et al., 2021 In
PNAS
article_processing_charge: No
author:
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
citation:
ama: Johnson AJ. Raw data from Johnson et al, PNAS, 2021. 2021. doi:10.5281/ZENODO.5747100
apa: Johnson, A. J. (2021). Raw data from Johnson et al, PNAS, 2021. Zenodo. https://doi.org/10.5281/ZENODO.5747100
chicago: Johnson, Alexander J. “Raw Data from Johnson et Al, PNAS, 2021.” Zenodo,
2021. https://doi.org/10.5281/ZENODO.5747100.
ieee: A. J. Johnson, “Raw data from Johnson et al, PNAS, 2021.” Zenodo, 2021.
ista: Johnson AJ. 2021. Raw data from Johnson et al, PNAS, 2021, Zenodo, 10.5281/ZENODO.5747100.
mla: Johnson, Alexander J. Raw Data from Johnson et Al, PNAS, 2021. Zenodo,
2021, doi:10.5281/ZENODO.5747100.
short: A.J. Johnson, (2021).
date_created: 2024-02-14T14:13:48Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2024-02-19T11:06:09Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.5281/ZENODO.5747100
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5747100
month: '12'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '9887'
relation: used_in_publication
status: public
status: public
title: Raw data from Johnson et al, PNAS, 2021
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10029'
abstract:
- lang: eng
text: Superconductor-semiconductor hybrids are platforms for realizing effective
p-wave superconductivity. Spin-orbit coupling, combined with the proximity effect,
causes the two-dimensional semiconductor to inherit p±ip intraband pairing, and
application of magnetic field can then result in transitions to the normal state,
partial Bogoliubov Fermi surfaces, or topological phases with Majorana modes.
Experimentally probing the hybrid superconductor-semiconductor interface is challenging
due to the shunting effect of the conventional superconductor. Consequently, the
nature of induced pairing remains an open question. Here, we use the circuit quantum
electrodynamics architecture to probe induced superconductivity in a two dimensional
Al-InAs hybrid system. We observe a strong suppression of superfluid density and
enhanced dissipation driven by magnetic field, which cannot be accounted for by
the depairing theory of an s-wave superconductor. These observations are explained
by a picture of independent intraband p±ip superconductors giving way to partial
Bogoliubov Fermi surfaces, and allow for the first characterization of key properties
of the hybrid superconducting system.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: This research was supported by the Scientific Service Units of IST
Austria through resources provided by the MIBA Machine Shop and the nanofabrication
facility. JS and AG were supported by funding from the European Union’s Horizon
2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement
No.754411.
article_number: '2107.03695'
article_processing_charge: No
author:
- first_name: Duc T
full_name: Phan, Duc T
id: 29C8C0B4-F248-11E8-B48F-1D18A9856A87
last_name: Phan
- first_name: Jorden L
full_name: Senior, Jorden L
id: 5479D234-2D30-11EA-89CC-40953DDC885E
last_name: Senior
orcid: 0000-0002-0672-9295
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: M.
full_name: Hatefipour, M.
last_name: Hatefipour
- first_name: W. M.
full_name: Strickland, W. M.
last_name: Strickland
- first_name: J.
full_name: Shabani, J.
last_name: Shabani
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Phan DT, Senior JL, Ghazaryan A, et al. Breakdown of induced p±ip pairing in
a superconductor-semiconductor hybrid. arXiv.
apa: Phan, D. T., Senior, J. L., Ghazaryan, A., Hatefipour, M., Strickland, W. M.,
Shabani, J., … Higginbotham, A. P. (n.d.). Breakdown of induced p±ip pairing in
a superconductor-semiconductor hybrid. arXiv.
chicago: Phan, Duc T, Jorden L Senior, Areg Ghazaryan, M. Hatefipour, W. M. Strickland,
J. Shabani, Maksym Serbyn, and Andrew P Higginbotham. “Breakdown of Induced P±ip
Pairing in a Superconductor-Semiconductor Hybrid.” ArXiv, n.d.
ieee: D. T. Phan et al., “Breakdown of induced p±ip pairing in a superconductor-semiconductor
hybrid,” arXiv. .
ista: Phan DT, Senior JL, Ghazaryan A, Hatefipour M, Strickland WM, Shabani J, Serbyn
M, Higginbotham AP. Breakdown of induced p±ip pairing in a superconductor-semiconductor
hybrid. arXiv, 2107.03695.
mla: Phan, Duc T., et al. “Breakdown of Induced P±ip Pairing in a Superconductor-Semiconductor
Hybrid.” ArXiv, 2107.03695.
short: D.T. Phan, J.L. Senior, A. Ghazaryan, M. Hatefipour, W.M. Strickland, J.
Shabani, M. Serbyn, A.P. Higginbotham, ArXiv (n.d.).
date_created: 2021-09-21T08:41:02Z
date_published: 2021-07-08T00:00:00Z
date_updated: 2024-02-21T12:36:52Z
day: '08'
department:
- _id: MaSe
- _id: AnHi
- _id: MiLe
ec_funded: 1
external_id:
arxiv:
- '2107.03695'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2107.03695
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '10851'
relation: later_version
status: public
- id: '9636'
relation: research_data
status: public
status: public
title: Breakdown of induced p±ip pairing in a superconductor-semiconductor hybrid
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9291'
abstract:
- lang: eng
text: "This .zip File contains the transport data for figures presented in the main
text and supplementary material of \"Enhancement of Proximity Induced Superconductivity
in Planar Germanium\" by K. Aggarwal, et. al. \r\nThe measurements were done using
Labber Software and the data is stored in the hdf5 file format. The files can
be opened using either the Labber Log Browser (https://labber.org/overview/) or
Labber Python API (http://labber.org/online-doc/api/LogFile.html)."
article_processing_charge: No
author:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: 'Katsaros G. Raw transport data for: Enhancement of proximity induced superconductivity
in planar germanium. 2021. doi:10.15479/AT:ISTA:9291'
apa: 'Katsaros, G. (2021). Raw transport data for: Enhancement of proximity induced
superconductivity in planar germanium. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:9291'
chicago: 'Katsaros, Georgios. “Raw Transport Data for: Enhancement of Proximity
Induced Superconductivity in Planar Germanium.” Institute of Science and Technology
Austria, 2021. https://doi.org/10.15479/AT:ISTA:9291.'
ieee: 'G. Katsaros, “Raw transport data for: Enhancement of proximity induced superconductivity
in planar germanium.” Institute of Science and Technology Austria, 2021.'
ista: 'Katsaros G. 2021. Raw transport data for: Enhancement of proximity induced
superconductivity in planar germanium, Institute of Science and Technology Austria,
10.15479/AT:ISTA:9291.'
mla: 'Katsaros, Georgios. Raw Transport Data for: Enhancement of Proximity Induced
Superconductivity in Planar Germanium. Institute of Science and Technology
Austria, 2021, doi:10.15479/AT:ISTA:9291.'
short: G. Katsaros, (2021).
date_created: 2021-03-27T13:47:49Z
date_published: 2021-03-29T00:00:00Z
date_updated: 2024-02-21T12:37:14Z
day: '29'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.15479/AT:ISTA:9291
file:
- access_level: open_access
checksum: 635df3c08fc13c3dac008cd421aefbe4
content_type: application/x-zip-compressed
creator: gkatsaro
date_created: 2021-03-27T13:46:17Z
date_updated: 2021-03-27T13:46:17Z
file_id: '9292'
file_name: Raw Data- Enhancement of Superconductivity in a Planar Ge hole gas.zip
file_size: 10616071
relation: main_file
success: 1
- access_level: open_access
checksum: 12b3ca69ae7509a346711baae0b02a75
content_type: text/plain
creator: dernst
date_created: 2021-04-01T07:52:56Z
date_updated: 2021-04-01T07:52:56Z
file_id: '9302'
file_name: README.txt
file_size: 470
relation: main_file
success: 1
file_date_updated: 2021-04-01T07:52:56Z
has_accepted_license: '1'
month: '03'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
status: public
title: 'Raw transport data for: Enhancement of proximity induced superconductivity
in planar germanium'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9636'
article_processing_charge: No
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Higginbotham AP. Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor
hybrid.” 2021.
apa: Higginbotham, A. P. (2021). Data for “Breakdown of induced p ± ip pairing in
a superconductor-semiconductor hybrid.” Institute of Science and Technology Austria.
chicago: Higginbotham, Andrew P. “Data for ‘Breakdown of Induced p ± Ip Pairing
in a Superconductor-Semiconductor Hybrid.’” Institute of Science and Technology
Austria, 2021.
ieee: A. P. Higginbotham, “Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor
hybrid.’” Institute of Science and Technology Austria, 2021.
ista: Higginbotham AP. 2021. Data for ‘Breakdown of induced p ± ip pairing in a
superconductor-semiconductor hybrid’, Institute of Science and Technology Austria.
mla: Higginbotham, Andrew P. Data for “Breakdown of Induced p ± Ip Pairing in
a Superconductor-Semiconductor Hybrid.” Institute of Science and Technology
Austria, 2021.
short: A.P. Higginbotham, (2021).
date_created: 2021-07-07T20:43:10Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2024-02-21T12:36:52Z
department:
- _id: AnHi
file:
- access_level: open_access
checksum: 18e90687ec7bbd75f8bfea4d8293fb30
content_type: application/zip
creator: ahigginb
date_created: 2021-07-07T20:37:28Z
date_updated: 2021-07-07T20:37:28Z
file_id: '9637'
file_name: figures_data.zip
file_size: 3345244
relation: main_file
success: 1
file_date_updated: 2021-07-07T20:37:28Z
has_accepted_license: '1'
oa: 1
oa_version: Submitted Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10029'
relation: used_in_publication
status: public
status: public
title: Data for "Breakdown of induced p ± ip pairing in a superconductor-semiconductor
hybrid"
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '8910'
abstract:
- lang: eng
text: A semiconducting nanowire fully wrapped by a superconducting shell has been
proposed as a platform for obtaining Majorana modes at small magnetic fields.
In this study, we demonstrate that the appearance of subgap states in such structures
is actually governed by the junction region in tunneling spectroscopy measurements
and not the full-shell nanowire itself. Short tunneling regions never show subgap
states, whereas longer junctions always do. This can be understood in terms of
quantum dots forming in the junction and hosting Andreev levels in the Yu-Shiba-Rusinov
regime. The intricate magnetic field dependence of the Andreev levels, through
both the Zeeman and Little-Parks effects, may result in robust zero-bias peaks—features
that could be easily misinterpreted as originating from Majorana zero modes but
are unrelated to topological superconductivity.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: The authors thank A. Higginbotham, E. J. H. Lee and F. R. Martins
for helpful discussions. 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 NOMIS Foundation and Microsoft; the European Union’s Horizon 2020
research and innovation program under the Marie SklodowskaCurie grant agreement
No 844511; the FETOPEN Grant Agreement No. 828948; the European Research Commission
through the grant agreement HEMs-DAM No 716655; the Spanish Ministry of Science
and Innovation through Grants PGC2018-097018-B-I00, PCI2018-093026, FIS2016-80434-P
(AEI/FEDER, EU), RYC2011-09345 (Ram´on y Cajal Programme), and the Mar´ıa de Maeztu
Programme for Units of Excellence in R&D (CEX2018-000805-M); the CSIC Research Platform
on Quantum Technologies PTI-001.
article_number: 82-88
article_processing_charge: No
article_type: original
author:
- first_name: Marco
full_name: Valentini, Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
- first_name: Fernando
full_name: Peñaranda, Fernando
last_name: Peñaranda
- first_name: Andrea C
full_name: Hofmann, Andrea C
id: 340F461A-F248-11E8-B48F-1D18A9856A87
last_name: Hofmann
- first_name: Matthias
full_name: Brauns, Matthias
id: 33F94E3C-F248-11E8-B48F-1D18A9856A87
last_name: Brauns
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Peter
full_name: Krogstrup, Peter
last_name: Krogstrup
- first_name: Pablo
full_name: San-Jose, Pablo
last_name: San-Jose
- first_name: Elsa
full_name: Prada, Elsa
last_name: Prada
- first_name: Ramón
full_name: Aguado, Ramón
last_name: Aguado
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Valentini M, Peñaranda F, Hofmann AC, et al. Nontopological zero-bias peaks
in full-shell nanowires induced by flux-tunable Andreev states. Science.
2021;373(6550). doi:10.1126/science.abf1513
apa: Valentini, M., Peñaranda, F., Hofmann, A. C., Brauns, M., Hauschild, R., Krogstrup,
P., … Katsaros, G. (2021). Nontopological zero-bias peaks in full-shell nanowires
induced by flux-tunable Andreev states. Science. American Association for
the Advancement of Science. https://doi.org/10.1126/science.abf1513
chicago: Valentini, Marco, Fernando Peñaranda, Andrea C Hofmann, Matthias Brauns,
Robert Hauschild, Peter Krogstrup, Pablo San-Jose, Elsa Prada, Ramón Aguado, and
Georgios Katsaros. “Nontopological Zero-Bias Peaks in Full-Shell Nanowires Induced
by Flux-Tunable Andreev States.” Science. American Association for the
Advancement of Science, 2021. https://doi.org/10.1126/science.abf1513.
ieee: M. Valentini et al., “Nontopological zero-bias peaks in full-shell
nanowires induced by flux-tunable Andreev states,” Science, vol. 373, no.
6550. American Association for the Advancement of Science, 2021.
ista: Valentini M, Peñaranda F, Hofmann AC, Brauns M, Hauschild R, Krogstrup P,
San-Jose P, Prada E, Aguado R, Katsaros G. 2021. Nontopological zero-bias peaks
in full-shell nanowires induced by flux-tunable Andreev states. Science. 373(6550),
82–88.
mla: Valentini, Marco, et al. “Nontopological Zero-Bias Peaks in Full-Shell Nanowires
Induced by Flux-Tunable Andreev States.” Science, vol. 373, no. 6550, 82–88,
American Association for the Advancement of Science, 2021, doi:10.1126/science.abf1513.
short: M. Valentini, F. Peñaranda, A.C. Hofmann, M. Brauns, R. Hauschild, P. Krogstrup,
P. San-Jose, E. Prada, R. Aguado, G. Katsaros, Science 373 (2021).
date_created: 2020-12-02T10:51:52Z
date_published: 2021-07-02T00:00:00Z
date_updated: 2024-02-21T12:40:09Z
day: '02'
department:
- _id: GeKa
- _id: Bio
doi: 10.1126/science.abf1513
ec_funded: 1
external_id:
arxiv:
- '2008.02348'
isi:
- '000677843100034'
intvolume: ' 373'
isi: 1
issue: '6550'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2008.02348
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 262116AA-B435-11E9-9278-68D0E5697425
name: Hybrid Semiconductor - Superconductor Quantum Devices
- _id: 26A151DA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '844511'
name: Majorana bound states in Ge/SiGe heterostructures
publication: Science
publication_identifier:
eissn:
- '10959203'
issn:
- '00368075'
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/unfinding-a-split-electron/
record:
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status: public
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relation: research_data
status: public
scopus_import: '1'
status: public
title: Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable
Andreev states
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 373
year: '2021'
...
---
_id: '9323'
abstract:
- lang: eng
text: This .zip File contains the data for figures presented in the main text and
supplementary material of "A singlet triplet hole spin qubit in planar Ge" by
D. Jirovec, et. al. The measurements were done using Labber Software and the data
is stored in the hdf5 file format. The files can be opened using either the Labber
Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html).
A single file is acquired with QCodes and features the corresponding data type.
XRD data are in .dat format and a code to open the data is provided. The code
for simulations is as well provided in Python.
article_processing_charge: No
author:
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
citation:
ama: Jirovec D. Research data for “A singlet-triplet hole spin qubit planar Ge.”
2021. doi:10.15479/AT:ISTA:9323
apa: Jirovec, D. (2021). Research data for “A singlet-triplet hole spin qubit planar
Ge.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9323
chicago: Jirovec, Daniel. “Research Data for ‘A Singlet-Triplet Hole Spin Qubit
Planar Ge.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9323.
ieee: D. Jirovec, “Research data for ‘A singlet-triplet hole spin qubit planar Ge.’”
Institute of Science and Technology Austria, 2021.
ista: Jirovec D. 2021. Research data for ‘A singlet-triplet hole spin qubit planar
Ge’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9323.
mla: Jirovec, Daniel. Research Data for “A Singlet-Triplet Hole Spin Qubit Planar
Ge.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9323.
short: D. Jirovec, (2021).
contributor:
- contributor_type: project_member
first_name: Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
date_created: 2021-04-14T09:50:22Z
date_published: 2021-04-14T00:00:00Z
date_updated: 2024-02-21T12:39:15Z
day: '14'
ddc:
- '530'
department:
- _id: GradSch
- _id: GeKa
doi: 10.15479/AT:ISTA:9323
file:
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checksum: c569d2a2ce1694445cdbca19cf8ae023
content_type: application/x-zip-compressed
creator: djirovec
date_created: 2021-04-14T09:48:47Z
date_updated: 2021-04-14T09:48:47Z
file_id: '9324'
file_name: DataRepositorySTqubit.zip
file_size: 221832287
relation: main_file
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content_type: application/octet-stream
creator: djirovec
date_created: 2021-04-14T09:49:30Z
date_updated: 2021-04-14T09:49:30Z
file_id: '9325'
file_name: ReadMe
file_size: 4323
relation: main_file
success: 1
file_date_updated: 2021-04-14T09:49:30Z
has_accepted_license: '1'
month: '04'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8909'
relation: used_in_publication
status: public
status: public
title: Research data for "A singlet-triplet hole spin qubit planar Ge"
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9389'
abstract:
- lang: eng
text: "This .zip File contains the transport data for \"Non-topological zero bias
peaks in full-shell nanowires induced by flux tunable Andreev states\" by M. Valentini,
et. al. \r\nThe measurements were done using Labber Software and the data is
stored in the hdf5 file format.\r\nInstructions of how to read the data are in
\"Notebook_Valentini.pdf\"."
acknowledged_ssus:
- _id: NanoFab
article_processing_charge: No
author:
- first_name: Marco
full_name: Valentini, Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
citation:
ama: Valentini M. Research data for “Non-topological zero bias peaks in full-shell
nanowires induced by flux tunable Andreev states.” 2021. doi:10.15479/AT:ISTA:9389
apa: Valentini, M. (2021). Research data for “Non-topological zero bias peaks in
full-shell nanowires induced by flux tunable Andreev states.” Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:9389
chicago: Valentini, Marco. “Research Data for ‘Non-Topological Zero Bias Peaks in
Full-Shell Nanowires Induced by Flux Tunable Andreev States.’” Institute of Science
and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9389.
ieee: M. Valentini, “Research data for ‘Non-topological zero bias peaks in full-shell
nanowires induced by flux tunable Andreev states.’” Institute of Science and Technology
Austria, 2021.
ista: Valentini M. 2021. Research data for ‘Non-topological zero bias peaks in full-shell
nanowires induced by flux tunable Andreev states’, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:9389.
mla: Valentini, Marco. Research Data for “Non-Topological Zero Bias Peaks in
Full-Shell Nanowires Induced by Flux Tunable Andreev States.” Institute of
Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9389.
short: M. Valentini, (2021).
contributor:
- contributor_type: contact_person
first_name: Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
date_created: 2021-05-14T12:07:53Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2024-02-21T12:40:09Z
ddc:
- '530'
department:
- _id: GradSch
- _id: GeKa
doi: 10.15479/AT:ISTA:9389
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creator: mvalenti
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oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
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relation: used_in_publication
status: public
status: public
title: Research data for "Non-topological zero bias peaks in full-shell nanowires
induced by flux tunable Andreev states"
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
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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
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'
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creator: cchlebak
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relation: main_file
success: 1
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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
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title: Enhancement of proximity-induced superconductivity in a planar Ge hole gas
tmp:
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
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type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
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year: '2021'
...
---
_id: '10166'
abstract:
- lang: eng
text: While sexual reproduction is widespread among many taxa, asexual lineages
have repeatedly evolved from sexual ancestors. Despite extensive research on the
evolution of sex, it is still unclear whether this switch represents a major transition
requiring major molecular reorganization, and how convergent the changes involved
are. In this study, we investigated the phylogenetic relationship and patterns
of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp,
to assess how gene expression patterns are affected by the transition to asexuality.
We find only a few genes that are consistently associated with the evolution of
asexuality, suggesting that this shift may not require an extensive overhauling
of the meiotic machinery. While genes with sex-biased expression have high rates
of expression divergence within Eurasian Artemia, neither female- nor male-biased
genes appear to show unusual evolutionary patterns after sexuality is lost, contrary
to theoretical expectations.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We thank the Vicoso laboratory, Thomas Lenormand and Tanja Schwander
for helpful discussions, the group of Gonzalo Gajardo, especially Cristian Gallardo-Escárate
and Margarita Parraguez Donoso, for sequencing data and advice, and the IST Scientific
Computing Group for their support. This work was supported by the European Research
Council under the European Union's Horizon 2020 research and innovation program
(grant agreement no. 715257).
article_number: '20211720'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Francisco
full_name: Hontoria, Francisco
last_name: Hontoria
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and
evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal
Society B: Biological Sciences. 2021;288(1959). doi:10.1098/rspb.2021.1720'
apa: 'Huylmans, A. K., Macon, A., Hontoria, F., & Vicoso, B. (2021). Transitions
to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings
of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2021.1720'
chicago: 'Huylmans, Ann K, Ariana Macon, Francisco Hontoria, and Beatriz Vicoso.
“Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.”
Proceedings of the Royal Society B: Biological Sciences. The Royal Society,
2021. https://doi.org/10.1098/rspb.2021.1720.'
ieee: 'A. K. Huylmans, A. Macon, F. Hontoria, and B. Vicoso, “Transitions to asexuality
and evolution of gene expression in Artemia brine shrimp,” Proceedings of the
Royal Society B: Biological Sciences, vol. 288, no. 1959. The Royal Society,
2021.'
ista: 'Huylmans AK, Macon A, Hontoria F, Vicoso B. 2021. Transitions to asexuality
and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal
Society B: Biological Sciences. 288(1959), 20211720.'
mla: 'Huylmans, Ann K., et al. “Transitions to Asexuality and Evolution of Gene
Expression in Artemia Brine Shrimp.” Proceedings of the Royal Society B: Biological
Sciences, vol. 288, no. 1959, 20211720, The Royal Society, 2021, doi:10.1098/rspb.2021.1720.'
short: 'A.K. Huylmans, A. Macon, F. Hontoria, B. Vicoso, Proceedings of the Royal
Society B: Biological Sciences 288 (2021).'
date_created: 2021-10-21T07:46:06Z
date_published: 2021-09-22T00:00:00Z
date_updated: 2024-02-21T12:40:29Z
day: '22'
ddc:
- '595'
department:
- _id: BeVi
doi: 10.1098/rspb.2021.1720
ec_funded: 1
external_id:
isi:
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pmid:
- '34547909'
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content_type: application/pdf
creator: cchlebak
date_created: 2021-10-22T11:48:02Z
date_updated: 2021-10-22T11:48:02Z
file_id: '10172'
file_name: 2021_ProRoSocBBioSci_Huylmans.pdf
file_size: 995806
relation: main_file
success: 1
file_date_updated: 2021-10-22T11:48:02Z
has_accepted_license: '1'
intvolume: ' 288'
isi: 1
issue: '1959'
keyword:
- asexual reproduction
- parthenogenesis
- sex-biased genes
- sexual conflict
- automixis
- crustaceans
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: 'Proceedings of the Royal Society B: Biological Sciences'
publication_identifier:
eissn:
- 1471-2954
issn:
- 0962-8452
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
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url: https://doi.org/10.6084/m9.figshare.c.5615488.v1
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title: Transitions to asexuality and evolution of gene expression in Artemia brine
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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)
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type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 288
year: '2021'
...
---
_id: '9192'
abstract:
- lang: eng
text: Here are the research data underlying the publication " Effects of fine-scale
population structure on inbreeding in a long-term study of snapdragons (Antirrhinum
majus)." Further information are summed up in the README document.
article_processing_charge: No
author:
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
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last_name: Arathoon
orcid: 0000-0003-1771-714X
- first_name: Carina
full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
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- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
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full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
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full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects
of fine-scale population structure on the distribution of heterozygosity in a
long-term study of Antirrhinum majus. 2021. doi:10.15479/AT:ISTA:9192
apa: Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &
Barton, N. H. (2021). Effects of fine-scale population structure on the distribution
of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:9192
chicago: Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field,
Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9192.
ieee: P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H.
Barton, “Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus.” Institute of Science and Technology
Austria, 2021.
ista: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2021.
Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:9192.
mla: Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.
Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9192.
short: P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton,
(2021).
contributor:
- contributor_type: project_member
first_name: Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- contributor_type: project_member
first_name: Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
- contributor_type: project_member
first_name: Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
- contributor_type: project_member
first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
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first_name: Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- contributor_type: project_leader
first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
date_created: 2021-02-24T17:49:21Z
date_published: 2021-02-26T00:00:00Z
date_updated: 2024-02-21T12:41:09Z
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- _id: NiBa
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title: Effects of fine-scale population structure on the distribution of heterozygosity
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---
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article_processing_charge: No
author:
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full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Vicoso B. Data from Hyulmans et al 2021, “Transitions to asexuality and evolution
of gene expression in Artemia brine shrimp.” 2021. doi:10.15479/AT:ISTA:9949
apa: Vicoso, B. (2021). Data from Hyulmans et al 2021, “Transitions to asexuality
and evolution of gene expression in Artemia brine shrimp.” Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:9949
chicago: Vicoso, Beatriz. “Data from Hyulmans et Al 2021, ‘Transitions to Asexuality
and Evolution of Gene Expression in Artemia Brine Shrimp.’” Institute of Science
and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9949.
ieee: B. Vicoso, “Data from Hyulmans et al 2021, ‘Transitions to asexuality and
evolution of gene expression in Artemia brine shrimp.’” Institute of Science and
Technology Austria, 2021.
ista: Vicoso B. 2021. Data from Hyulmans et al 2021, ‘Transitions to asexuality
and evolution of gene expression in Artemia brine shrimp’, Institute of Science
and Technology Austria, 10.15479/AT:ISTA:9949.
mla: Vicoso, Beatriz. Data from Hyulmans et Al 2021, “Transitions to Asexuality
and Evolution of Gene Expression in Artemia Brine Shrimp.” Institute of Science
and Technology Austria, 2021, doi:10.15479/AT:ISTA:9949.
short: B. Vicoso, (2021).
date_created: 2021-08-21T13:44:22Z
date_published: 2021-08-24T00:00:00Z
date_updated: 2024-02-21T12:40:30Z
day: '24'
department:
- _id: BeVi
doi: 10.15479/AT:ISTA:9949
file:
- access_level: open_access
checksum: 90461837eed66beac6fa302993cf0ca9
content_type: application/zip
creator: bvicoso
date_created: 2021-08-21T13:43:59Z
date_updated: 2021-08-21T13:43:59Z
file_id: '9950'
file_name: Data.zip
file_size: 139188306
relation: main_file
success: 1
file_date_updated: 2021-08-21T13:43:59Z
has_accepted_license: '1'
month: '08'
oa: 1
oa_version: None
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10166'
relation: used_in_publication
status: public
status: public
title: Data from Hyulmans et al 2021, "Transitions to asexuality and evolution of
gene expression in Artemia brine shrimp"
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '8997'
abstract:
- lang: eng
text: Phenomenological relations such as Ohm’s or Fourier’s law have a venerable
history in physics but are still scarce in biology. This situation restrains predictive
theory. Here, we build on bacterial “growth laws,” which capture physiological
feedback between translation and cell growth, to construct a minimal biophysical
model for the combined action of ribosome-targeting antibiotics. Our model predicts
drug interactions like antagonism or synergy solely from responses to individual
drugs. We provide analytical results for limiting cases, which agree well with
numerical results. We systematically refine the model by including direct physical
interactions of different antibiotics on the ribosome. In a limiting case, our
model provides a mechanistic underpinning for recent predictions of higher-order
interactions that were derived using entropy maximization. We further refine the
model to include the effects of antibiotics that mimic starvation and the presence
of resistance genes. We describe the impact of a starvation-mimicking antibiotic
on drug interactions analytically and verify it experimentally. Our extended model
suggests a change in the type of drug interaction that depends on the strength
of resistance, which challenges established rescaling paradigms. We experimentally
show that the presence of unregulated resistance genes can lead to altered drug
interaction, which agrees with the prediction of the model. While minimal, the
model is readily adaptable and opens the door to predicting interactions of second
and higher-order in a broad range of biological systems.
acknowledgement: 'This work was supported in part by Tum stipend of Knafelj foundation
(to B.K.), Austrian Science Fund (FWF) standalone grants P 27201-B22 (to T.B.) and
P 28844(to G.T.), HFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation
(DFG) individual grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG)
Collaborative Research Centre (SFB) 1310 (to T.B.). '
article_number: e1008529
article_processing_charge: Yes
article_type: original
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic
action. PLOS Computational Biology. 2021;17. doi:10.1371/journal.pcbi.1008529
apa: Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2021). Minimal biophysical
model of combined antibiotic action. PLOS Computational Biology. Public
Library of Science. https://doi.org/10.1371/journal.pcbi.1008529
chicago: Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical
Model of Combined Antibiotic Action.” PLOS Computational Biology. Public
Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008529.
ieee: B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of
combined antibiotic action,” PLOS Computational Biology, vol. 17. Public
Library of Science, 2021.
ista: Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined
antibiotic action. PLOS Computational Biology. 17, e1008529.
mla: Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.”
PLOS Computational Biology, vol. 17, e1008529, Public Library of Science,
2021, doi:10.1371/journal.pcbi.1008529.
short: B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).
date_created: 2021-01-08T07:16:18Z
date_published: 2021-01-07T00:00:00Z
date_updated: 2024-02-21T12:41:41Z
day: '07'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1008529
external_id:
isi:
- '000608045000010'
file:
- access_level: open_access
checksum: e29f2b42651bef8e034781de8781ffac
content_type: application/pdf
creator: dernst
date_created: 2021-02-04T12:30:48Z
date_updated: 2021-02-04T12:30:48Z
file_id: '9092'
file_name: 2021_PlosComBio_Kavcic.pdf
file_size: 3690053
relation: main_file
success: 1
file_date_updated: 2021-02-04T12:30:48Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
keyword:
- Modelling and Simulation
- Genetics
- Molecular Biology
- Antibiotics
- Drug interactions
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '7673'
relation: earlier_version
status: public
- id: '8930'
relation: research_data
status: public
status: public
title: Minimal biophysical model of combined antibiotic action
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: 17
year: '2021'
...
---
_id: '9283'
abstract:
- lang: eng
text: Gene expression levels are influenced by multiple coexisting molecular mechanisms.
Some of these interactions such as those of transcription factors and promoters
have been studied extensively. However, predicting phenotypes of gene regulatory
networks (GRNs) remains a major challenge. Here, we use a well-defined synthetic
GRN to study in Escherichia coli how network phenotypes depend on local genetic
context, i.e. the genetic neighborhood of a transcription factor and its relative
position. We show that one GRN with fixed topology can display not only quantitatively
but also qualitatively different phenotypes, depending solely on the local genetic
context of its components. Transcriptional read-through is the main molecular
mechanism that places one transcriptional unit (TU) within two separate regulons
without the need for complex regulatory sequences. We propose that relative order
of individual TUs, with its potential for combinatorial complexity, plays an important
role in shaping phenotypes of GRNs.
acknowledgement: "We thank J Bollback, L Hurst, M Lagator, C Nizak, O Rivoire, M Savageau,
G Tkacik, and B Vicozo\r\nfor helpful discussions; A Dolinar and A Greshnova for
technical assistance; T Bollenbach for supplying the strain JW0336; C Rusnac, and
members of the Guet lab for comments. The research leading to these results has
received funding from the People Programme (Marie Curie Actions) of the European
Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n˚\r\n628377
(ANS) and an Austrian Science Fund (FWF) grant n˚ I 3901-B32 (CCG)."
article_number: e65993
article_processing_charge: Yes
article_type: original
author:
- first_name: Anna A
full_name: Nagy-Staron, Anna A
id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87
last_name: Nagy-Staron
orcid: 0000-0002-1391-8377
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
- first_name: Caroline
full_name: Caruso Carter, Caroline
last_name: Caruso Carter
- first_name: Elisabeth
full_name: Sonnleitner, Elisabeth
last_name: Sonnleitner
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Tiago
full_name: Paixão, Tiago
last_name: Paixão
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Nagy-Staron AA, Tomasek K, Caruso Carter C, et al. Local genetic context shapes
the function of a gene regulatory network. eLife. 2021;10. doi:10.7554/elife.65993
apa: Nagy-Staron, A. A., Tomasek, K., Caruso Carter, C., Sonnleitner, E., Kavcic,
B., Paixão, T., & Guet, C. C. (2021). Local genetic context shapes the function
of a gene regulatory network. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.65993
chicago: Nagy-Staron, Anna A, Kathrin Tomasek, Caroline Caruso Carter, Elisabeth
Sonnleitner, Bor Kavcic, Tiago Paixão, and Calin C Guet. “Local Genetic Context
Shapes the Function of a Gene Regulatory Network.” ELife. eLife Sciences
Publications, 2021. https://doi.org/10.7554/elife.65993.
ieee: A. A. Nagy-Staron et al., “Local genetic context shapes the function
of a gene regulatory network,” eLife, vol. 10. eLife Sciences Publications,
2021.
ista: Nagy-Staron AA, Tomasek K, Caruso Carter C, Sonnleitner E, Kavcic B, Paixão
T, Guet CC. 2021. Local genetic context shapes the function of a gene regulatory
network. eLife. 10, e65993.
mla: Nagy-Staron, Anna A., et al. “Local Genetic Context Shapes the Function of
a Gene Regulatory Network.” ELife, vol. 10, e65993, eLife Sciences Publications,
2021, doi:10.7554/elife.65993.
short: A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic,
T. Paixão, C.C. Guet, ELife 10 (2021).
date_created: 2021-03-23T10:11:46Z
date_published: 2021-03-08T00:00:00Z
date_updated: 2024-02-21T12:41:57Z
day: '08'
ddc:
- '570'
department:
- _id: GaTk
- _id: CaGu
doi: 10.7554/elife.65993
ec_funded: 1
external_id:
isi:
- '000631050900001'
file:
- access_level: open_access
checksum: 3c2f44058c2dd45a5a1027f09d263f8e
content_type: application/pdf
creator: bkavcic
date_created: 2021-03-23T10:12:58Z
date_updated: 2021-03-23T10:12:58Z
file_id: '9284'
file_name: elife-65993-v2.pdf
file_size: 1390469
relation: main_file
success: 1
file_date_updated: 2021-03-23T10:12:58Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
keyword:
- Genetics and Molecular Biology
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 2517526A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '628377'
name: 'The Systems Biology of Transcriptional Read-Through in Bacteria: from Synthetic
Networks to Genomic Studies'
- _id: 268BFA92-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03901
name: 'CyberCircuits: Cybergenetic circuits to test composability of gene networks'
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
record:
- id: '8951'
relation: research_data
status: public
status: public
title: Local genetic context shapes the function of a gene regulatory network
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '10184'
abstract:
- lang: eng
text: "We introduce a novel technique to automatically decompose an input object’s
volume into a set of parts that can be represented by two opposite height fields.
Such decomposition enables the manufacturing of individual parts using two-piece
reusable rigid molds. Our decomposition strategy relies on a new energy formulation
that utilizes a pre-computed signal on the mesh volume representing the accessibility
for a predefined set of extraction directions. Thanks to this novel formulation,
our method allows for efficient optimization of a fabrication-aware partitioning
of volumes in a completely\r\nautomatic way. We demonstrate the efficacy of our
approach by generating valid volume partitionings for a wide range of complex
objects and physically reproducing several of them."
acknowledgement: 'The authors thank Marco Callieri for all his precious help with
the resin casts. The models used in the paper are courtesy of the Stanford 3D Scanning
Repository, the AIM@SHAPE Shape Repository, and Thingi10K Repository. The research
was partially funded by the European Research Council (ERC) MATERIALIZABLE: Intelligent
fabrication-oriented computational design and modeling (grant no. 715767).'
article_number: '272'
article_processing_charge: No
article_type: original
author:
- first_name: Thomas
full_name: Alderighi, Thomas
last_name: Alderighi
- first_name: Luigi
full_name: Malomo, Luigi
last_name: Malomo
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Paolo
full_name: Cignoni, Paolo
last_name: Cignoni
- first_name: Nico
full_name: Pietroni, Nico
last_name: Pietroni
citation:
ama: Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. Volume decomposition
for two-piece rigid casting. ACM Transactions on Graphics. 2021;40(6).
doi:10.1145/3478513.3480555
apa: Alderighi, T., Malomo, L., Bickel, B., Cignoni, P., & Pietroni, N. (2021).
Volume decomposition for two-piece rigid casting. ACM Transactions on Graphics.
Association for Computing Machinery. https://doi.org/10.1145/3478513.3480555
chicago: Alderighi, Thomas, Luigi Malomo, Bernd Bickel, Paolo Cignoni, and Nico
Pietroni. “Volume Decomposition for Two-Piece Rigid Casting.” ACM Transactions
on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3478513.3480555.
ieee: T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, and N. Pietroni, “Volume decomposition
for two-piece rigid casting,” ACM Transactions on Graphics, vol. 40, no.
6. Association for Computing Machinery, 2021.
ista: Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. 2021. Volume decomposition
for two-piece rigid casting. ACM Transactions on Graphics. 40(6), 272.
mla: Alderighi, Thomas, et al. “Volume Decomposition for Two-Piece Rigid Casting.”
ACM Transactions on Graphics, vol. 40, no. 6, 272, Association for Computing
Machinery, 2021, doi:10.1145/3478513.3480555.
short: T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions
on Graphics 40 (2021).
date_created: 2021-10-27T07:08:19Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2024-02-28T12:52:48Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3478513.3480555
ec_funded: 1
external_id:
isi:
- '000729846700077'
file:
- access_level: open_access
checksum: 384ece7a9ad1026787ba9560b04336d5
content_type: application/pdf
creator: bbickel
date_created: 2021-10-27T07:08:07Z
date_updated: 2021-10-27T07:08:07Z
file_id: '10185'
file_name: rigidmolds-authorversion.pdf
file_size: 107708317
relation: main_file
file_date_updated: 2021-10-27T07:08:07Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://vcg.isti.cnr.it/Publications/2021/AMBCP21
month: '12'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '1557-7368 '
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: Volume decomposition for two-piece rigid casting
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2021'
...
---
_id: '9541'
abstract:
- lang: eng
text: The Massively Parallel Computation (MPC) model is an emerging model that distills
core aspects of distributed and parallel computation, developed as a tool to solve
combinatorial (typically graph) problems in systems of many machines with limited
space. Recent work has focused on the regime in which machines have sublinear
(in n, the number of nodes in the input graph) space, with randomized algorithms
presented for the fundamental problems of Maximal Matching and Maximal Independent
Set. However, there have been no prior corresponding deterministic algorithms.
A major challenge underlying the sublinear space setting is that the local space
of each machine might be too small to store all edges incident to a single node.
This poses a considerable obstacle compared to classical models in which each
node is assumed to know and have easy access to its incident edges. To overcome
this barrier, we introduce a new graph sparsification technique that deterministically
computes a low-degree subgraph, with the additional property that solving the
problem on this subgraph provides significant progress towards solving the problem
for the original input graph. Using this framework to derandomize the well-known
algorithm of Luby [SICOMP’86], we obtain O(log Δ + log log n)-round deterministic
MPC algorithms for solving the problems of Maximal Matching and Maximal Independent
Set with O(nɛ) space on each machine for any constant ɛ > 0. These algorithms
also run in O(log Δ) rounds in the closely related model of CONGESTED CLIQUE,
improving upon the state-of-the-art bound of O(log 2Δ) rounds by Censor-Hillel
et al. [DISC’17].
acknowledgement: "Institute of Science and Technology Austria (IST Austria). Email:
peter.davies@ist.ac.at. Work partially\r\ndone at the Department of Computer Science
and Centre for Discrete Mathematics and its Applications (DIMAP),University of Warwick.
Research partially supported by the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement No 754411, the Centre
for Discrete Mathematics and its Applications, a Weizmann-UK Making Connections
Grant, and EPSRC award EP/N011163/1."
article_number: '16'
article_processing_charge: No
article_type: original
author:
- first_name: Artur
full_name: Czumaj, Artur
last_name: Czumaj
- first_name: Peter
full_name: Davies, Peter
id: 11396234-BB50-11E9-B24C-90FCE5697425
last_name: Davies
orcid: 0000-0002-5646-9524
- first_name: Merav
full_name: Parter, Merav
last_name: Parter
citation:
ama: Czumaj A, Davies P, Parter M. Graph sparsification for derandomizing massively
parallel computation with low space. ACM Transactions on Algorithms. 2021;17(2).
doi:10.1145/3451992
apa: Czumaj, A., Davies, P., & Parter, M. (2021). Graph sparsification for derandomizing
massively parallel computation with low space. ACM Transactions on Algorithms.
Association for Computing Machinery. https://doi.org/10.1145/3451992
chicago: Czumaj, Artur, Peter Davies, and Merav Parter. “Graph Sparsification for
Derandomizing Massively Parallel Computation with Low Space.” ACM Transactions
on Algorithms. Association for Computing Machinery, 2021. https://doi.org/10.1145/3451992.
ieee: A. Czumaj, P. Davies, and M. Parter, “Graph sparsification for derandomizing
massively parallel computation with low space,” ACM Transactions on Algorithms,
vol. 17, no. 2. Association for Computing Machinery, 2021.
ista: Czumaj A, Davies P, Parter M. 2021. Graph sparsification for derandomizing
massively parallel computation with low space. ACM Transactions on Algorithms.
17(2), 16.
mla: Czumaj, Artur, et al. “Graph Sparsification for Derandomizing Massively Parallel
Computation with Low Space.” ACM Transactions on Algorithms, vol. 17, no.
2, 16, Association for Computing Machinery, 2021, doi:10.1145/3451992.
short: A. Czumaj, P. Davies, M. Parter, ACM Transactions on Algorithms 17 (2021).
date_created: 2021-06-10T19:31:05Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2024-02-28T12:53:09Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1145/3451992
ec_funded: 1
external_id:
arxiv:
- '1912.05390'
isi:
- '000661311300006'
file:
- access_level: open_access
checksum: a21c627683890c309a68f6389302c408
content_type: application/pdf
creator: pdavies
date_created: 2021-06-10T19:33:56Z
date_updated: 2021-06-10T19:33:56Z
file_id: '9542'
file_name: MISMM-arxiv.pdf
file_size: 587404
relation: main_file
success: 1
file_date_updated: 2021-06-10T19:33:56Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1912.05390
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: ACM Transactions on Algorithms
publication_identifier:
eissn:
- 1549-6333
issn:
- 1549-6325
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '7802'
relation: earlier_version
status: public
status: public
title: Graph sparsification for derandomizing massively parallel computation with
low space
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2021'
...
---
_id: '10134'
abstract:
- lang: eng
text: We investigate the effect of coupling between translational and internal degrees
of freedom of composite quantum particles on their localization in a random potential.
We show that entanglement between the two degrees of freedom weakens localization
due to the upper bound imposed on the inverse participation ratio by purity of
a quantum state. We perform numerical calculations for a two-particle system bound
by a harmonic force in a 1D disordered lattice and a rigid rotor in a 2D disordered
lattice. We illustrate that the coupling has a dramatic effect on localization
properties, even with a small number of internal states participating in quantum
dynamics.
acknowledgement: "We acknowledge helpful discussions with W. G. Unruh and A. Rodriguez.
F. S. is supported by European Union’s\r\nHorizon 2020 research and innovation programme
under the Marie Skłodowska-Curie Grant No. 754411. M. L. acknowledges support by
the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). W. H. Z.
is\r\nsupported by Department of Energy under the Los\r\nAlamos National Laboratory
LDRD Program as well as by the U.S. Department of Energy, Office of Science, Basic\r\nEnergy
Sciences, Materials Sciences and Engineering Division, Condensed Matter Theory Program.
R. V. K. is supported by NSERC of Canada.\r\n"
article_number: '160602'
article_processing_charge: No
article_type: original
author:
- first_name: Fumika
full_name: Suzuki, Fumika
id: 650C99FC-1079-11EA-A3C0-73AE3DDC885E
last_name: Suzuki
orcid: 0000-0003-4982-5970
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Wojciech H.
full_name: Zurek, Wojciech H.
last_name: Zurek
- first_name: Roman V.
full_name: Krems, Roman V.
last_name: Krems
citation:
ama: Suzuki F, Lemeshko M, Zurek WH, Krems RV. Anderson localization of composite
particles. Physical Review Letters. 2021;127(16). doi:10.1103/physrevlett.127.160602
apa: Suzuki, F., Lemeshko, M., Zurek, W. H., & Krems, R. V. (2021). Anderson
localization of composite particles. Physical Review Letters. American
Physical Society . https://doi.org/10.1103/physrevlett.127.160602
chicago: Suzuki, Fumika, Mikhail Lemeshko, Wojciech H. Zurek, and Roman V. Krems.
“Anderson Localization of Composite Particles.” Physical Review Letters.
American Physical Society , 2021. https://doi.org/10.1103/physrevlett.127.160602.
ieee: F. Suzuki, M. Lemeshko, W. H. Zurek, and R. V. Krems, “Anderson localization
of composite particles,” Physical Review Letters, vol. 127, no. 16. American
Physical Society , 2021.
ista: Suzuki F, Lemeshko M, Zurek WH, Krems RV. 2021. Anderson localization of composite
particles. Physical Review Letters. 127(16), 160602.
mla: Suzuki, Fumika, et al. “Anderson Localization of Composite Particles.” Physical
Review Letters, vol. 127, no. 16, 160602, American Physical Society , 2021,
doi:10.1103/physrevlett.127.160602.
short: F. Suzuki, M. Lemeshko, W.H. Zurek, R.V. Krems, Physical Review Letters 127
(2021).
date_created: 2021-10-13T09:21:33Z
date_published: 2021-10-12T00:00:00Z
date_updated: 2024-02-29T12:34:10Z
day: '12'
department:
- _id: MiLe
doi: 10.1103/physrevlett.127.160602
ec_funded: 1
external_id:
arxiv:
- '2011.06279'
isi:
- '000707495700001'
intvolume: ' 127'
isi: 1
issue: '16'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2011.06279
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: 'American Physical Society '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anderson localization of composite particles
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 127
year: '2021'
...
---
_id: '9678'
abstract:
- lang: eng
text: We introduce a new graph problem, the token dropping game, and we show how
to solve it efficiently in a distributed setting. We use the token dropping game
as a tool to design an efficient distributed algorithm for stable orientations
and more generally for locally optimal semi-matchings. The prior work by Czygrinow
et al. (DISC 2012) finds a stable orientation in O(Δ^5) rounds in graphs of maximum
degree Δ, while we improve it to O(Δ^4) and also prove a lower bound of Ω(Δ).
For the more general problem of locally optimal semi-matchings, the prior upper
bound is O(S^5) and our new algorithm runs in O(C · S^4) rounds, which is an improvement
for C = o(S); here C and S are the maximum degrees of customers and servers, respectively.
acknowledgement: We thank Orr Fischer, Juho Hirvonen, and Tuomo Lempiäinen for valuable
discussions. This project has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
No. 840605.
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Brandt, Sebastian
last_name: Brandt
- first_name: Barbara
full_name: Keller, Barbara
last_name: Keller
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
- first_name: Jukka
full_name: Suomela, Jukka
last_name: Suomela
- first_name: Jara
full_name: Uitto, Jara
last_name: Uitto
citation:
ama: 'Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Efficient load-balancing
through distributed token dropping. In: Annual ACM Symposium on Parallelism
in Algorithms and Architectures. ; 2021:129-139. doi:10.1145/3409964.3461785'
apa: Brandt, S., Keller, B., Rybicki, J., Suomela, J., & Uitto, J. (2021). Efficient
load-balancing through distributed token dropping. In Annual ACM Symposium
on Parallelism in Algorithms and Architectures (pp. 129–139). Virtual Event,
United States. https://doi.org/10.1145/3409964.3461785
chicago: Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara
Uitto. “Efficient Load-Balancing through Distributed Token Dropping.” In Annual
ACM Symposium on Parallelism in Algorithms and Architectures, 129–39, 2021.
https://doi.org/10.1145/3409964.3461785.
ieee: S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Efficient load-balancing
through distributed token dropping,” in Annual ACM Symposium on Parallelism
in Algorithms and Architectures, Virtual Event, United States, 2021, pp.
129–139.
ista: 'Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2021. Efficient load-balancing
through distributed token dropping. Annual ACM Symposium on Parallelism in Algorithms
and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures
, 129–139.'
mla: Brandt, Sebastian, et al. “Efficient Load-Balancing through Distributed Token
Dropping.” Annual ACM Symposium on Parallelism in Algorithms and Architectures,
2021, pp. 129–39, doi:10.1145/3409964.3461785.
short: S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, Annual ACM Symposium
on Parallelism in Algorithms and Architectures, 2021, pp. 129–139.
conference:
end_date: 2021-07-08
location: ' Virtual Event, United States'
name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures '
start_date: 2021-07-06
date_created: 2021-07-18T22:01:22Z
date_published: 2021-07-06T00:00:00Z
date_updated: 2024-03-05T07:13:12Z
day: '06'
department:
- _id: DaAl
doi: 10.1145/3409964.3461785
ec_funded: 1
external_id:
arxiv:
- '2005.07761'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2005.07761
month: '07'
oa: 1
oa_version: Preprint
page: 129-139
project:
- _id: 26A5D39A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '840605'
name: Coordination in constrained and natural distributed systems
publication: Annual ACM Symposium on Parallelism in Algorithms and Architectures
publication_identifier:
isbn:
- '9781450380706'
publication_status: published
quality_controlled: '1'
related_material:
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relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Efficient load-balancing through distributed token dropping
type: conference
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
year: '2021'
...
---
_id: '8286'
abstract:
- lang: eng
text: "We consider the following dynamic load-balancing process: given an underlying
graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed
at a randomly chosen graph node. In the same step, the chosen node picks a random
neighbor, and the two nodes balance their loads by averaging them. We are interested
in the expected gap between the minimum and maximum loads at nodes as the process
progresses, and its dependence on n and on the graph structure. Variants of the
above graphical balanced allocation process have been studied previously by Peres,
Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and
Sun, 2015]. These authors left as open the question of characterizing the gap
in the case of cycle graphs in the dynamic case, where weights are created during
the algorithm’s execution. For this case, the only known upper bound is of \U0001D4AA(n
log n), following from a majorization argument due to [Peres et al., 2015], which
analyzes a related graphical allocation process. In this paper, we provide an
upper bound of \U0001D4AA (√n log n) on the expected gap of the above process
for cycles of length n. We introduce a new potential analysis technique, which
enables us to bound the difference in load between k-hop neighbors on the cycle,
for any k ≤ n/2. We complement this with a \"gap covering\" argument, which bounds
the maximum value of the gap by bounding its value across all possible subsets
of a certain structure, and recursively bounding the gaps within each subset.
We provide analytical and experimental evidence that our upper bound on the gap
is tight up to a logarithmic factor. "
acknowledgement: The authors sincerely thank Thomas Sauerwald and George Giakkoupis
for insightful discussions, and Mohsen Ghaffari, Yuval Peres, and Udi Wieder for
feedback on earlier versions of this draft. We also thank the ICALP anonymous reviewers
for their very useful comments. Open access funding provided by Institute of Science
and Technology (IST Austria). Funding was provided by European Research Council
(Grant No. PR1042ERC01).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- 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
citation:
ama: Alistarh D-A, Nadiradze G, Sabour A. Dynamic averaging load balancing on cycles.
Algorithmica. 2021. doi:10.1007/s00453-021-00905-9
apa: 'Alistarh, D.-A., Nadiradze, G., & Sabour, A. (2021). Dynamic averaging
load balancing on cycles. Algorithmica. Virtual, Online; Germany: Springer
Nature. https://doi.org/10.1007/s00453-021-00905-9'
chicago: Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic
Averaging Load Balancing on Cycles.” Algorithmica. Springer Nature, 2021.
https://doi.org/10.1007/s00453-021-00905-9.
ieee: D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing
on cycles,” Algorithmica. Springer Nature, 2021.
ista: Alistarh D-A, Nadiradze G, Sabour A. 2021. Dynamic averaging load balancing
on cycles. Algorithmica.
mla: Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.”
Algorithmica, Springer Nature, 2021, doi:10.1007/s00453-021-00905-9.
short: D.-A. Alistarh, G. Nadiradze, A. Sabour, Algorithmica (2021).
conference:
end_date: 2020-07-11
location: Virtual, Online; Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming '
start_date: 2020-07-08
date_created: 2020-08-24T06:24:04Z
date_published: 2021-12-24T00:00:00Z
date_updated: 2024-03-05T07:35:53Z
day: '24'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1007/s00453-021-00905-9
ec_funded: 1
external_id:
arxiv:
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isi:
- '000734004600001'
file:
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checksum: 21169b25b0c8e17b21e12af22bff9870
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file_name: 2021_Algorithmica_Alistarh.pdf
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file_date_updated: 2021-12-27T10:36:40Z
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isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Algorithmica
publication_identifier:
eissn:
- 1432-0541
issn:
- 0178-4617
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: https://doi.org/10.4230/LIPIcs.ICALP.2020.7
record:
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scopus_import: '1'
status: public
title: Dynamic averaging load balancing on cycles
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
year: '2021'
...
---
_id: '9733'
abstract:
- lang: eng
text: This thesis is the result of the research carried out by the author during
his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich
polaron model, specifically to its regime of strong coupling. This model, which
is rigorously introduced and discussed in the introduction, has been of great
interest in condensed matter physics and field theory for more than eighty years.
It is used to describe an electron interacting with the atoms of a solid material
(the strength of this interaction is modeled by the presence of a coupling constant
α in the Hamiltonian of the system). The particular regime examined here, which
is mathematically described by considering the limit α →∞, displays many interesting
features related to the emergence of classical behavior, which allows for a simplified
effective description of the system under analysis. The properties, the range
of validity and a quantitative analysis of the precision of such classical approximations
are the main object of the present work. We specify our investigation to the study
of the ground state energy of the system, its dynamics and its effective mass.
For each of these problems, we provide in the introduction an overview of the
previously known results and a detailed account of the original contributions
by the author.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
citation:
ama: Feliciangeli D. The polaron at strong coupling. 2021. doi:10.15479/at:ista:9733
apa: Feliciangeli, D. (2021). The polaron at strong coupling. Institute of
Science and Technology Austria. https://doi.org/10.15479/at:ista:9733
chicago: Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science
and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9733.
ieee: D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and
Technology Austria, 2021.
ista: Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science
and Technology Austria.
mla: Feliciangeli, Dario. The Polaron at Strong Coupling. Institute of Science
and Technology Austria, 2021, doi:10.15479/at:ista:9733.
short: D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and
Technology Austria, 2021.
date_created: 2021-07-27T15:48:30Z
date_published: 2021-08-20T00:00:00Z
date_updated: 2024-03-06T12:30:44Z
day: '20'
ddc:
- '515'
- '519'
- '539'
degree_awarded: PhD
department:
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- _id: RoSe
- _id: JaMa
doi: 10.15479/at:ista:9733
ec_funded: 1
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file_id: '9945'
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language:
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license: https://creativecommons.org/licenses/by-nd/4.0/
month: '08'
oa: 1
oa_version: Published Version
page: '180'
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9787'
relation: part_of_dissertation
status: public
- id: '9792'
relation: part_of_dissertation
status: public
- id: '9225'
relation: part_of_dissertation
status: public
- id: '9781'
relation: part_of_dissertation
status: public
- id: '9791'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
title: The polaron at strong coupling
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...