---
_id: '12010'
abstract:
- lang: eng
text: World models learn behaviors in a latent imagination space to enhance the
sample-efficiency of deep reinforcement learning (RL) algorithms. While learning
world models for high-dimensional observations (e.g., pixel inputs) has become
practicable on standard RL benchmarks and some games, their effectiveness in real-world
robotics applications has not been explored. In this paper, we investigate how
such agents generalize to real-world autonomous vehicle control tasks, where advanced
model-free deep RL algorithms fail. In particular, we set up a series of time-lap
tasks for an F1TENTH racing robot, equipped with a high-dimensional LiDAR sensor,
on a set of test tracks with a gradual increase in their complexity. In this continuous-control
setting, we show that model-based agents capable of learning in imagination substantially
outperform model-free agents with respect to performance, sample efficiency, successful
task completion, and generalization. Moreover, we show that the generalization
ability of model-based agents strongly depends on the choice of their observation
model. We provide extensive empirical evidence for the effectiveness of world
models provided with long enough memory horizons in sim2real tasks.
acknowledgement: L.B. was supported by the Doctoral College Resilient Embedded Systems.
M.L. was supported in part by the ERC2020-AdG 101020093 and the Austrian Science
Fund (FWF) under grant Z211-N23 (Wittgenstein Award). R.H. and D.R. were supported
by The Boeing Company and the Office of Naval Research (ONR) Grant N00014-18-1-2830.
R.G. was partially supported by the Horizon-2020 ECSEL Project grant No. 783163
(iDev40) and A.B. by FFG Project ADEX.
article_processing_charge: No
arxiv: 1
author:
- first_name: Axel
full_name: Brunnbauer, Axel
last_name: Brunnbauer
- first_name: Luigi
full_name: Berducci, Luigi
last_name: Berducci
- first_name: Andreas
full_name: Brandstatter, Andreas
last_name: Brandstatter
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Ramin
full_name: Hasani, Ramin
last_name: Hasani
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: 'Brunnbauer A, Berducci L, Brandstatter A, et al. Latent imagination facilitates
zero-shot transfer in autonomous racing. In: 2022 International Conference
on Robotics and Automation. IEEE; 2022:7513-7520. doi:10.1109/ICRA46639.2022.9811650'
apa: 'Brunnbauer, A., Berducci, L., Brandstatter, A., Lechner, M., Hasani, R., Rus,
D., & Grosu, R. (2022). Latent imagination facilitates zero-shot transfer
in autonomous racing. In 2022 International Conference on Robotics and Automation
(pp. 7513–7520). Philadelphia, PA, United States: IEEE. https://doi.org/10.1109/ICRA46639.2022.9811650'
chicago: Brunnbauer, Axel, Luigi Berducci, Andreas Brandstatter, Mathias Lechner,
Ramin Hasani, Daniela Rus, and Radu Grosu. “Latent Imagination Facilitates Zero-Shot
Transfer in Autonomous Racing.” In 2022 International Conference on Robotics
and Automation, 7513–20. IEEE, 2022. https://doi.org/10.1109/ICRA46639.2022.9811650.
ieee: A. Brunnbauer et al., “Latent imagination facilitates zero-shot transfer
in autonomous racing,” in 2022 International Conference on Robotics and Automation,
Philadelphia, PA, United States, 2022, pp. 7513–7520.
ista: 'Brunnbauer A, Berducci L, Brandstatter A, Lechner M, Hasani R, Rus D, Grosu
R. 2022. Latent imagination facilitates zero-shot transfer in autonomous racing.
2022 International Conference on Robotics and Automation. ICRA: International
Conference on Robotics and Automation, 7513–7520.'
mla: Brunnbauer, Axel, et al. “Latent Imagination Facilitates Zero-Shot Transfer
in Autonomous Racing.” 2022 International Conference on Robotics and Automation,
IEEE, 2022, pp. 7513–20, doi:10.1109/ICRA46639.2022.9811650.
short: A. Brunnbauer, L. Berducci, A. Brandstatter, M. Lechner, R. Hasani, D. Rus,
R. Grosu, in:, 2022 International Conference on Robotics and Automation, IEEE,
2022, pp. 7513–7520.
conference:
end_date: 2022-05-27
location: Philadelphia, PA, United States
name: 'ICRA: International Conference on Robotics and Automation'
start_date: 2022-05-23
date_created: 2022-09-04T22:02:02Z
date_published: 2022-07-12T00:00:00Z
date_updated: 2022-09-05T08:46:12Z
day: '12'
department:
- _id: ToHe
doi: 10.1109/ICRA46639.2022.9811650
ec_funded: 1
external_id:
arxiv:
- '2103.04909'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2103.04909
month: '07'
oa: 1
oa_version: Preprint
page: 7513-7520
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 2022 International Conference on Robotics and Automation
publication_identifier:
isbn:
- '9781728196817'
issn:
- 1050-4729
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Latent imagination facilitates zero-shot transfer in autonomous racing
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '12011'
abstract:
- lang: eng
text: We characterize the capacity for the discrete-time arbitrarily varying channel
with discrete inputs, outputs, and states when (a) the encoder and decoder do
not share common randomness, (b) the input and state are subject to cost constraints,
(c) the transition matrix of the channel is deterministic given the state, and
(d) at each time step the adversary can only observe the current and past channel
inputs when choosing the state at that time. The achievable strategy involves
stochastic encoding together with list decoding and a disambiguation step. The
converse uses a two-phase "babble-and-push" strategy where the adversary chooses
the state randomly in the first phase, list decodes the output, and then chooses
state inputs to symmetrize the channel in the second phase. These results generalize
prior work on specific channels models (additive, erasure) to general discrete
alphabets and models.
acknowledgement: The work of ADS and ML was supported in part by the US National Science
Foundation under awards CCF-1909468 and CCF-1909451.
article_processing_charge: No
arxiv: 1
author:
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
- first_name: Sidharth
full_name: Jaggi, Sidharth
last_name: Jaggi
- first_name: Michael
full_name: Langberg, Michael
last_name: Langberg
- first_name: Anand D.
full_name: Sarwate, Anand D.
last_name: Sarwate
citation:
ama: 'Zhang Y, Jaggi S, Langberg M, Sarwate AD. The capacity of causal adversarial
channels. In: 2022 IEEE International Symposium on Information Theory.
Vol 2022. IEEE; 2022:2523-2528. doi:10.1109/ISIT50566.2022.9834709'
apa: 'Zhang, Y., Jaggi, S., Langberg, M., & Sarwate, A. D. (2022). The capacity
of causal adversarial channels. In 2022 IEEE International Symposium on Information
Theory (Vol. 2022, pp. 2523–2528). Espoo, Finland: IEEE. https://doi.org/10.1109/ISIT50566.2022.9834709'
chicago: Zhang, Yihan, Sidharth Jaggi, Michael Langberg, and Anand D. Sarwate. “The
Capacity of Causal Adversarial Channels.” In 2022 IEEE International Symposium
on Information Theory, 2022:2523–28. IEEE, 2022. https://doi.org/10.1109/ISIT50566.2022.9834709.
ieee: Y. Zhang, S. Jaggi, M. Langberg, and A. D. Sarwate, “The capacity of causal
adversarial channels,” in 2022 IEEE International Symposium on Information
Theory, Espoo, Finland, 2022, vol. 2022, pp. 2523–2528.
ista: 'Zhang Y, Jaggi S, Langberg M, Sarwate AD. 2022. The capacity of causal adversarial
channels. 2022 IEEE International Symposium on Information Theory. ISIT: Internation
Symposium on Information Theory vol. 2022, 2523–2528.'
mla: Zhang, Yihan, et al. “The Capacity of Causal Adversarial Channels.” 2022
IEEE International Symposium on Information Theory, vol. 2022, IEEE, 2022,
pp. 2523–28, doi:10.1109/ISIT50566.2022.9834709.
short: Y. Zhang, S. Jaggi, M. Langberg, A.D. Sarwate, in:, 2022 IEEE International
Symposium on Information Theory, IEEE, 2022, pp. 2523–2528.
conference:
end_date: 2022-07-01
location: Espoo, Finland
name: 'ISIT: Internation Symposium on Information Theory'
start_date: 2022-06-26
date_created: 2022-09-04T22:02:03Z
date_published: 2022-08-03T00:00:00Z
date_updated: 2022-09-05T09:09:15Z
day: '03'
department:
- _id: MaMo
doi: 10.1109/ISIT50566.2022.9834709
external_id:
arxiv:
- '2205.06708'
intvolume: ' 2022'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2205.06708'
month: '08'
oa: 1
oa_version: Preprint
page: 2523-2528
publication: 2022 IEEE International Symposium on Information Theory
publication_identifier:
isbn:
- '9781665421591'
issn:
- 2157-8095
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: The capacity of causal adversarial channels
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2022
year: '2022'
...
---
_id: '12012'
abstract:
- lang: eng
text: This paper is eligible for the Jack Keil Wolf ISIT Student Paper Award. We
generalize a previous framework for designing utility-optimal differentially private
(DP) mechanisms via graphs, where datasets are vertices in the graph and edges
represent dataset neighborhood. The boundary set contains datasets where an individual’s
response changes the binary-valued query compared to its neighbors. Previous work
was limited to the homogeneous case where the privacy parameter ε across all datasets
was the same and the mechanism at boundary datasets was identical. In our work,
the mechanism can take different distributions at the boundary and the privacy
parameter ε is a function of neighboring datasets, which recovers an earlier definition
of personalized DP as special case. The problem is how to extend the mechanism,
which is only defined at the boundary set, to other datasets in the graph in a
computationally efficient and utility optimal manner. Using the concept of strongest
induced DP condition we solve this problem efficiently in polynomial time (in
the size of the graph).
article_processing_charge: No
arxiv: 1
author:
- first_name: Sahel
full_name: Torkamani, Sahel
id: 0503e7f8-2d05-11ed-aa17-db0640c720fc
last_name: Torkamani
- first_name: Javad B.
full_name: Ebrahimi, Javad B.
last_name: Ebrahimi
- first_name: Parastoo
full_name: Sadeghi, Parastoo
last_name: Sadeghi
- first_name: Rafael G.L.
full_name: D'Oliveira, Rafael G.L.
last_name: D'Oliveira
- first_name: Muriel
full_name: Médard, Muriel
last_name: Médard
citation:
ama: 'Torkamani S, Ebrahimi JB, Sadeghi P, D’Oliveira RGL, Médard M. Heterogeneous
differential privacy via graphs. In: 2022 IEEE International Symposium on Information
Theory. Vol 2022. IEEE; 2022:1623-1628. doi:10.1109/ISIT50566.2022.9834711'
apa: 'Torkamani, S., Ebrahimi, J. B., Sadeghi, P., D’Oliveira, R. G. L., & Médard,
M. (2022). Heterogeneous differential privacy via graphs. In 2022 IEEE International
Symposium on Information Theory (Vol. 2022, pp. 1623–1628). Espoo, Finland:
IEEE. https://doi.org/10.1109/ISIT50566.2022.9834711'
chicago: Torkamani, Sahel, Javad B. Ebrahimi, Parastoo Sadeghi, Rafael G.L. D’Oliveira,
and Muriel Médard. “Heterogeneous Differential Privacy via Graphs.” In 2022
IEEE International Symposium on Information Theory, 2022:1623–28. IEEE, 2022.
https://doi.org/10.1109/ISIT50566.2022.9834711.
ieee: S. Torkamani, J. B. Ebrahimi, P. Sadeghi, R. G. L. D’Oliveira, and M. Médard,
“Heterogeneous differential privacy via graphs,” in 2022 IEEE International
Symposium on Information Theory, Espoo, Finland, 2022, vol. 2022, pp. 1623–1628.
ista: 'Torkamani S, Ebrahimi JB, Sadeghi P, D’Oliveira RGL, Médard M. 2022. Heterogeneous
differential privacy via graphs. 2022 IEEE International Symposium on Information
Theory. ISIT: Internation Symposium on Information Theory vol. 2022, 1623–1628.'
mla: Torkamani, Sahel, et al. “Heterogeneous Differential Privacy via Graphs.” 2022
IEEE International Symposium on Information Theory, vol. 2022, IEEE, 2022,
pp. 1623–28, doi:10.1109/ISIT50566.2022.9834711.
short: S. Torkamani, J.B. Ebrahimi, P. Sadeghi, R.G.L. D’Oliveira, M. Médard, in:,
2022 IEEE International Symposium on Information Theory, IEEE, 2022, pp. 1623–1628.
conference:
end_date: 2022-07-01
location: Espoo, Finland
name: 'ISIT: Internation Symposium on Information Theory'
start_date: 2022-06-26
date_created: 2022-09-04T22:02:04Z
date_published: 2022-08-03T00:00:00Z
date_updated: 2022-09-05T10:28:35Z
day: '03'
department:
- _id: MaMo
doi: 10.1109/ISIT50566.2022.9834711
external_id:
arxiv:
- '2203.15429'
intvolume: ' 2022'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2203.15429
month: '08'
oa: 1
oa_version: Preprint
page: 1623-1628
publication: 2022 IEEE International Symposium on Information Theory
publication_identifier:
isbn:
- '9781665421591'
issn:
- 2157-8095
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Heterogeneous differential privacy via graphs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2022
year: '2022'
...
---
_id: '12013'
abstract:
- lang: eng
text: We consider the problem of communication over adversarial channels with feedback.
Two parties comprising sender Alice and receiver Bob seek to communicate reliably.
An adversary James observes Alice's channel transmission entirely and chooses,
maliciously, its additive channel input or jamming state thereby corrupting Bob's
observation. Bob can communicate over a one-way reverse link with Alice; we assume
that transmissions over this feedback link cannot be corrupted by James. Our goal
in this work is to study the optimum throughput or capacity over such channels
with feedback. We first present results for the quadratically-constrained additive
channel where communication is known to be impossible when the noise-to-signal
(power) ratio (NSR) is at least 1. We present a novel achievability scheme to
establish that positive rate communication is possible even when the NSR is as
high as 8/9. We also present new converse upper bounds on the capacity of this
channel under potentially stochastic encoders and decoders. We also study feedback
communication over the more widely studied q-ary alphabet channel under additive
noise. For the q -ary channel, where q > 2, it is well known that capacity is
positive under full feedback if and only if the adversary can corrupt strictly
less than half the transmitted symbols. We generalize this result and show that
the same threshold holds for positive rate communication when the noiseless feedback
may only be partial; our scheme employs a stochastic decoder. We extend this characterization,
albeit partially, to fully deterministic schemes under partial noiseless feedback.
We also present new converse upper bounds for q-ary channels under full feedback,
where the encoder and/or decoder may privately randomize. Our converse results
bring to the fore an interesting alternate expression for the well known converse
bound for the q—ary channel under full feedback which, when specialized to the
binary channel, also equals its known capacity.
article_processing_charge: No
author:
- first_name: Pranav
full_name: Joshi, Pranav
last_name: Joshi
- first_name: Amritakshya
full_name: Purkayastha, Amritakshya
last_name: Purkayastha
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
- first_name: Amitalok J.
full_name: Budkuley, Amitalok J.
last_name: Budkuley
- first_name: Sidharth
full_name: Jaggi, Sidharth
last_name: Jaggi
citation:
ama: 'Joshi P, Purkayastha A, Zhang Y, Budkuley AJ, Jaggi S. On the capacity of
additive AVCs with feedback. In: 2022 IEEE International Symposium on Information
Theory. Vol 2022. IEEE; 2022:504-509. doi:10.1109/ISIT50566.2022.9834850'
apa: 'Joshi, P., Purkayastha, A., Zhang, Y., Budkuley, A. J., & Jaggi, S. (2022).
On the capacity of additive AVCs with feedback. In 2022 IEEE International
Symposium on Information Theory (Vol. 2022, pp. 504–509). Espoo, Finland:
IEEE. https://doi.org/10.1109/ISIT50566.2022.9834850'
chicago: Joshi, Pranav, Amritakshya Purkayastha, Yihan Zhang, Amitalok J. Budkuley,
and Sidharth Jaggi. “On the Capacity of Additive AVCs with Feedback.” In 2022
IEEE International Symposium on Information Theory, 2022:504–9. IEEE, 2022.
https://doi.org/10.1109/ISIT50566.2022.9834850.
ieee: P. Joshi, A. Purkayastha, Y. Zhang, A. J. Budkuley, and S. Jaggi, “On the
capacity of additive AVCs with feedback,” in 2022 IEEE International Symposium
on Information Theory, Espoo, Finland, 2022, vol. 2022, pp. 504–509.
ista: 'Joshi P, Purkayastha A, Zhang Y, Budkuley AJ, Jaggi S. 2022. On the capacity
of additive AVCs with feedback. 2022 IEEE International Symposium on Information
Theory. ISIT: Internation Symposium on Information Theory vol. 2022, 504–509.'
mla: Joshi, Pranav, et al. “On the Capacity of Additive AVCs with Feedback.” 2022
IEEE International Symposium on Information Theory, vol. 2022, IEEE, 2022,
pp. 504–09, doi:10.1109/ISIT50566.2022.9834850.
short: P. Joshi, A. Purkayastha, Y. Zhang, A.J. Budkuley, S. Jaggi, in:, 2022 IEEE
International Symposium on Information Theory, IEEE, 2022, pp. 504–509.
conference:
end_date: 2022-07-01
location: Espoo, Finland
name: 'ISIT: Internation Symposium on Information Theory'
start_date: 2022-06-26
date_created: 2022-09-04T22:02:04Z
date_published: 2022-08-03T00:00:00Z
date_updated: 2022-09-05T10:23:35Z
day: '03'
department:
- _id: MaMo
doi: 10.1109/ISIT50566.2022.9834850
intvolume: ' 2022'
language:
- iso: eng
month: '08'
oa_version: None
page: 504-509
publication: 2022 IEEE International Symposium on Information Theory
publication_identifier:
isbn:
- '9781665421591'
issn:
- 2157-8095
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the capacity of additive AVCs with feedback
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2022
year: '2022'
...
---
_id: '12014'
abstract:
- lang: eng
text: We study the problem of high-dimensional multiple packing in Euclidean space.
Multiple packing is a natural generalization of sphere packing and is defined
as follows. Let N > 0 and L∈Z≥2. A multiple packing is a set C of points in Rn
such that any point in Rn lies in the intersection of at most L – 1 balls of radius
nN−−−√ around points in C. Given a well-known connection with coding theory, multiple
packings can be viewed as the Euclidean analog of list-decodable codes, which
are well-studied for finite fields. In this paper, we exactly pin down the asymptotic
density of (expurgated) Poisson Point Processes under a stronger notion called
average-radius multiple packing. To this end, we apply tools from high-dimensional
geometry and large deviation theory. This gives rise to the best known lower bound
on the largest multiple packing density. Our result corrects a mistake in a previous
paper by Blinovsky [Bli05].
article_processing_charge: No
author:
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
- first_name: Shashank
full_name: Vatedka, Shashank
last_name: Vatedka
citation:
ama: 'Zhang Y, Vatedka S. List-decodability of Poisson Point Processes. In: 2022
IEEE International Symposium on Information Theory. Vol 2022. IEEE; 2022:2559-2564.
doi:10.1109/ISIT50566.2022.9834512'
apa: 'Zhang, Y., & Vatedka, S. (2022). List-decodability of Poisson Point Processes.
In 2022 IEEE International Symposium on Information Theory (Vol. 2022,
pp. 2559–2564). Espoo, Finland: IEEE. https://doi.org/10.1109/ISIT50566.2022.9834512'
chicago: Zhang, Yihan, and Shashank Vatedka. “List-Decodability of Poisson Point
Processes.” In 2022 IEEE International Symposium on Information Theory,
2022:2559–64. IEEE, 2022. https://doi.org/10.1109/ISIT50566.2022.9834512.
ieee: Y. Zhang and S. Vatedka, “List-decodability of Poisson Point Processes,” in
2022 IEEE International Symposium on Information Theory, Espoo, Finland,
2022, vol. 2022, pp. 2559–2564.
ista: 'Zhang Y, Vatedka S. 2022. List-decodability of Poisson Point Processes. 2022
IEEE International Symposium on Information Theory. ISIT: Internation Symposium
on Information Theory vol. 2022, 2559–2564.'
mla: Zhang, Yihan, and Shashank Vatedka. “List-Decodability of Poisson Point Processes.”
2022 IEEE International Symposium on Information Theory, vol. 2022, IEEE,
2022, pp. 2559–64, doi:10.1109/ISIT50566.2022.9834512.
short: Y. Zhang, S. Vatedka, in:, 2022 IEEE International Symposium on Information
Theory, IEEE, 2022, pp. 2559–2564.
conference:
end_date: 2022-07-01
location: Espoo, Finland
name: 'ISIT: Internation Symposium on Information Theory'
start_date: 2022-06-26
date_created: 2022-09-04T22:02:04Z
date_published: 2022-08-03T00:00:00Z
date_updated: 2022-09-05T09:23:04Z
day: '03'
department:
- _id: MaMo
doi: 10.1109/ISIT50566.2022.9834512
intvolume: ' 2022'
language:
- iso: eng
month: '08'
oa_version: None
page: 2559-2564
publication: 2022 IEEE International Symposium on Information Theory
publication_identifier:
isbn:
- '9781665421591'
issn:
- 2157-8095
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: List-decodability of Poisson Point Processes
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2022
year: '2022'
...
---
_id: '12015'
abstract:
- lang: eng
text: We study the problem of high-dimensional multiple packing in Euclidean space.
Multiple packing is a natural generalization of sphere packing and is defined
as follows. Let P, N > 0 and L∈Z≥2. A multiple packing is a set C of points in
Bn(0–,nP−−−√) such that any point in ℝ n lies in the intersection of at most L
– 1 balls of radius nN−−−√ around points in C. 1 In this paper, we derive two
lower bounds on the largest possible density of a multiple packing. These bounds
are obtained through a stronger notion called average-radius multiple packing.
Specifically, we exactly pin down the asymptotics of (expurgated) Gaussian codes
and (expurgated) spherical codes under average-radius multiple packing. To this
end, we apply tools from high-dimensional geometry and large deviation theory.
The bound for spherical codes matches the previous best known bound which was
obtained for the standard (weaker) notion of multiple packing through a curious
connection with error exponents [Bli99], [ZV21]. The bound for Gaussian codes
suggests that they are strictly inferior to spherical codes.
article_processing_charge: No
author:
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
- first_name: Shashank
full_name: Vatedka, Shashank
last_name: Vatedka
citation:
ama: 'Zhang Y, Vatedka S. Lower bounds for multiple packing. In: 2022 IEEE International
Symposium on Information Theory. Vol 2022. IEEE; 2022:3085-3090. doi:10.1109/ISIT50566.2022.9834443'
apa: 'Zhang, Y., & Vatedka, S. (2022). Lower bounds for multiple packing. In
2022 IEEE International Symposium on Information Theory (Vol. 2022, pp.
3085–3090). Espoo, Finland: IEEE. https://doi.org/10.1109/ISIT50566.2022.9834443'
chicago: Zhang, Yihan, and Shashank Vatedka. “Lower Bounds for Multiple Packing.”
In 2022 IEEE International Symposium on Information Theory, 2022:3085–90.
IEEE, 2022. https://doi.org/10.1109/ISIT50566.2022.9834443.
ieee: Y. Zhang and S. Vatedka, “Lower bounds for multiple packing,” in 2022 IEEE
International Symposium on Information Theory, Espoo, Finland, 2022, vol.
2022, pp. 3085–3090.
ista: 'Zhang Y, Vatedka S. 2022. Lower bounds for multiple packing. 2022 IEEE International
Symposium on Information Theory. ISIT: Internation Symposium on Information Theory
vol. 2022, 3085–3090.'
mla: Zhang, Yihan, and Shashank Vatedka. “Lower Bounds for Multiple Packing.” 2022
IEEE International Symposium on Information Theory, vol. 2022, IEEE, 2022,
pp. 3085–90, doi:10.1109/ISIT50566.2022.9834443.
short: Y. Zhang, S. Vatedka, in:, 2022 IEEE International Symposium on Information
Theory, IEEE, 2022, pp. 3085–3090.
conference:
end_date: 2022-07-01
location: Espoo, Finland
name: 'ISIT: Internation Symposium on Information Theory'
start_date: 2022-06-26
date_created: 2022-09-04T22:02:05Z
date_published: 2022-08-03T00:00:00Z
date_updated: 2022-09-05T10:39:04Z
day: '03'
department:
- _id: MaMo
doi: 10.1109/ISIT50566.2022.9834443
intvolume: ' 2022'
language:
- iso: eng
month: '08'
oa_version: None
page: 3085-3090
publication: 2022 IEEE International Symposium on Information Theory
publication_identifier:
isbn:
- '9781665421591'
issn:
- 2157-8095
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lower bounds for multiple packing
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2022
year: '2022'
...
---
_id: '12016'
abstract:
- lang: eng
text: We consider the problem of coded distributed computing using polar codes.
The average execution time of a coded computing system is related to the error
probability for transmission over the binary erasure channel in recent work by
Soleymani, Jamali and Mahdavifar, where the performance of binary linear codes
is investigated. In this paper, we focus on polar codes and unveil a connection
between the average execution time and the scaling exponent μ of the family of
codes. In the finite-length characterization of polar codes, the scaling exponent
is a key object capturing the speed of convergence to capacity. In particular,
we show that (i) the gap between the normalized average execution time of polar
codes and that of optimal MDS codes is O(n –1/μ ), and (ii) this upper bound can
be improved to roughly O(n –1/2 ) by considering polar codes with large kernels.
We conjecture that these bounds could be improved to O(n –2/μ ) and O(n –1 ),
respectively, and provide a heuristic argument as well as numerical evidence supporting
this view.
acknowledgement: D. Fathollahi and M. Mondelli were partially supported by the 2019
Lopez-Loreta Prize. The authors thank Hamed Hassani and Hessam Mahdavifar for helpful
discussions.
article_processing_charge: No
arxiv: 1
author:
- first_name: Dorsa
full_name: Fathollahi, Dorsa
last_name: Fathollahi
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: 'Fathollahi D, Mondelli M. Polar coded computing: The role of the scaling exponent.
In: 2022 IEEE International Symposium on Information Theory. Vol 2022.
IEEE; 2022:2154-2159. doi:10.1109/ISIT50566.2022.9834712'
apa: 'Fathollahi, D., & Mondelli, M. (2022). Polar coded computing: The role
of the scaling exponent. In 2022 IEEE International Symposium on Information
Theory (Vol. 2022, pp. 2154–2159). Espoo, Finland: IEEE. https://doi.org/10.1109/ISIT50566.2022.9834712'
chicago: 'Fathollahi, Dorsa, and Marco Mondelli. “Polar Coded Computing: The Role
of the Scaling Exponent.” In 2022 IEEE International Symposium on Information
Theory, 2022:2154–59. IEEE, 2022. https://doi.org/10.1109/ISIT50566.2022.9834712.'
ieee: 'D. Fathollahi and M. Mondelli, “Polar coded computing: The role of the scaling
exponent,” in 2022 IEEE International Symposium on Information Theory,
Espoo, Finland, 2022, vol. 2022, pp. 2154–2159.'
ista: 'Fathollahi D, Mondelli M. 2022. Polar coded computing: The role of the scaling
exponent. 2022 IEEE International Symposium on Information Theory. ISIT: Internation
Symposium on Information Theory vol. 2022, 2154–2159.'
mla: 'Fathollahi, Dorsa, and Marco Mondelli. “Polar Coded Computing: The Role of
the Scaling Exponent.” 2022 IEEE International Symposium on Information Theory,
vol. 2022, IEEE, 2022, pp. 2154–59, doi:10.1109/ISIT50566.2022.9834712.'
short: D. Fathollahi, M. Mondelli, in:, 2022 IEEE International Symposium on Information
Theory, IEEE, 2022, pp. 2154–2159.
conference:
end_date: 2022-07-01
location: Espoo, Finland
name: 'ISIT: Internation Symposium on Information Theory'
start_date: 2022-06-26
date_created: 2022-09-04T22:02:05Z
date_published: 2022-08-03T00:00:00Z
date_updated: 2024-09-10T13:03:17Z
day: '03'
department:
- _id: MaMo
doi: 10.1109/ISIT50566.2022.9834712
external_id:
arxiv:
- '2201.10082'
intvolume: ' 2022'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2201.10082
month: '08'
oa: 1
oa_version: Preprint
page: 2154-2159
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: 2022 IEEE International Symposium on Information Theory
publication_identifier:
isbn:
- '9781665421591'
issn:
- 2157-8095
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Polar coded computing: The role of the scaling exponent'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2022
year: '2022'
...
---
_id: '12017'
abstract:
- lang: eng
text: 'In the classic adversarial communication problem, two parties communicate
over a noisy channel in the presence of a malicious jamming adversary. The arbitrarily
varying channels (AVCs) offer an elegant framework to study a wide range of interesting
adversary models. The optimal throughput or capacity over such AVCs is intimately
tied to the underlying adversary model; in some cases, capacity is unknown and
the problem is known to be notoriously hard. The omniscient adversary, one which
knows the sender’s entire channel transmission a priori, is one of such classic
models of interest; the capacity under such an adversary remains an exciting open
problem. The myopic adversary is a generalization of that model where the adversary’s
observation may be corrupted over a noisy discrete memoryless channel. Through
the adversary’s myopicity, one can unify the slew of different adversary models,
ranging from the omniscient adversary to one that is completely blind to the transmission
(the latter is the well known oblivious model where the capacity is fully characterized).In
this work, we present new results on the capacity under both the omniscient and
myopic adversary models. We completely characterize the positive capacity threshold
over general AVCs with omniscient adversaries. The characterization is in terms
of two key combinatorial objects: the set of completely positive distributions
and the CP-confusability set. For omniscient AVCs with positive capacity, we present
non-trivial lower and upper bounds on the capacity; unlike some of the previous
bounds, our bounds hold under fairly general input and jamming constraints. Our
lower bound improves upon the generalized Gilbert-Varshamov bound for general
AVCs while the upper bound generalizes the well known Elias-Bassalygo bound (known
for binary and q-ary alphabets). For the myopic AVCs, we build on prior results
known for the so-called sufficiently myopic model, and present new results on
the positive rate communication threshold over the so-called insufficiently myopic
regime (a completely insufficient myopic adversary specializes to an omniscient
adversary). We present interesting examples for the widely studied models of adversarial
bit-flip and bit-erasure channels. In fact, for the bit-flip AVC with additive
adversarial noise as well as random noise, we completely characterize the omniscient
model capacity when the random noise is sufficiently large vis-a-vis the adversary’s
budget.'
article_processing_charge: No
author:
- first_name: Anuj Kumar
full_name: Yadav, Anuj Kumar
last_name: Yadav
- first_name: Mohammadreza
full_name: Alimohammadi, Mohammadreza
last_name: Alimohammadi
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
- first_name: Amitalok J.
full_name: Budkuley, Amitalok J.
last_name: Budkuley
- first_name: Sidharth
full_name: Jaggi, Sidharth
last_name: Jaggi
citation:
ama: 'Yadav AK, Alimohammadi M, Zhang Y, Budkuley AJ, Jaggi S. New results on AVCs
with omniscient and myopic adversaries. In: 2022 IEEE International Symposium
on Information Theory. Vol 2022. Institute of Electrical and Electronics Engineers;
2022:2535-2540. doi:10.1109/ISIT50566.2022.9834632'
apa: 'Yadav, A. K., Alimohammadi, M., Zhang, Y., Budkuley, A. J., & Jaggi, S.
(2022). New results on AVCs with omniscient and myopic adversaries. In 2022
IEEE International Symposium on Information Theory (Vol. 2022, pp. 2535–2540).
Espoo, Finland: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/ISIT50566.2022.9834632'
chicago: Yadav, Anuj Kumar, Mohammadreza Alimohammadi, Yihan Zhang, Amitalok J.
Budkuley, and Sidharth Jaggi. “New Results on AVCs with Omniscient and Myopic
Adversaries.” In 2022 IEEE International Symposium on Information Theory,
2022:2535–40. Institute of Electrical and Electronics Engineers, 2022. https://doi.org/10.1109/ISIT50566.2022.9834632.
ieee: A. K. Yadav, M. Alimohammadi, Y. Zhang, A. J. Budkuley, and S. Jaggi, “New
results on AVCs with omniscient and myopic adversaries,” in 2022 IEEE International
Symposium on Information Theory, Espoo, Finland, 2022, vol. 2022, pp. 2535–2540.
ista: 'Yadav AK, Alimohammadi M, Zhang Y, Budkuley AJ, Jaggi S. 2022. New results
on AVCs with omniscient and myopic adversaries. 2022 IEEE International Symposium
on Information Theory. ISIT: Internation Symposium on Information Theory vol.
2022, 2535–2540.'
mla: Yadav, Anuj Kumar, et al. “New Results on AVCs with Omniscient and Myopic Adversaries.”
2022 IEEE International Symposium on Information Theory, vol. 2022, Institute
of Electrical and Electronics Engineers, 2022, pp. 2535–40, doi:10.1109/ISIT50566.2022.9834632.
short: A.K. Yadav, M. Alimohammadi, Y. Zhang, A.J. Budkuley, S. Jaggi, in:, 2022
IEEE International Symposium on Information Theory, Institute of Electrical and
Electronics Engineers, 2022, pp. 2535–2540.
conference:
end_date: 2022-07-01
location: Espoo, Finland
name: 'ISIT: Internation Symposium on Information Theory'
start_date: 2022-06-26
date_created: 2022-09-04T22:02:06Z
date_published: 2022-08-03T00:00:00Z
date_updated: 2023-02-13T09:00:14Z
day: '03'
department:
- _id: MaMo
doi: 10.1109/ISIT50566.2022.9834632
intvolume: ' 2022'
language:
- iso: eng
month: '08'
oa_version: None
page: 2535-2540
publication: 2022 IEEE International Symposium on Information Theory
publication_identifier:
isbn:
- '9781665421591'
issn:
- 2157-8095
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: New results on AVCs with omniscient and myopic adversaries
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2022
year: '2022'
...
---
_id: '12018'
abstract:
- lang: eng
text: We study the problem of characterizing the maximal rates of list decoding
in Euclidean spaces for finite list sizes. For any positive integer L ≥ 2 and
real N > 0, we say that a subset C⊂Rn is an (N,L – 1)-multiple packing or an (N,L–
1)-list decodable code if every Euclidean ball of radius nN−−−√ in ℝ n contains
no more than L − 1 points of C. We study this problem with and without ℓ 2 norm
constraints on C, and derive the best-known lower bounds on the maximal rate for
(N,L−1) multiple packing. Our bounds are obtained via error exponents for list
decoding over Additive White Gaussian Noise (AWGN) channels. We establish a curious
inequality which relates the error exponent, a quantity of average-case nature,
to the list-decoding radius, a quantity of worst-case nature. We derive various
bounds on the error exponent for list decoding in both bounded and unbounded settings
which could be of independent interest beyond multiple packing.
article_processing_charge: No
author:
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
- first_name: Shashank
full_name: Vatedka, Shashank
last_name: Vatedka
citation:
ama: 'Zhang Y, Vatedka S. Lower bounds on list decoding capacity using error exponents.
In: 2022 IEEE International Symposium on Information Theory. Vol 2022.
Institute of Electrical and Electronics Engineers; 2022:1324-1329. doi:10.1109/ISIT50566.2022.9834815'
apa: 'Zhang, Y., & Vatedka, S. (2022). Lower bounds on list decoding capacity
using error exponents. In 2022 IEEE International Symposium on Information
Theory (Vol. 2022, pp. 1324–1329). Espoo, Finland: Institute of Electrical
and Electronics Engineers. https://doi.org/10.1109/ISIT50566.2022.9834815'
chicago: Zhang, Yihan, and Shashank Vatedka. “Lower Bounds on List Decoding Capacity
Using Error Exponents.” In 2022 IEEE International Symposium on Information
Theory, 2022:1324–29. Institute of Electrical and Electronics Engineers, 2022.
https://doi.org/10.1109/ISIT50566.2022.9834815.
ieee: Y. Zhang and S. Vatedka, “Lower bounds on list decoding capacity using error
exponents,” in 2022 IEEE International Symposium on Information Theory,
Espoo, Finland, 2022, vol. 2022, pp. 1324–1329.
ista: 'Zhang Y, Vatedka S. 2022. Lower bounds on list decoding capacity using error
exponents. 2022 IEEE International Symposium on Information Theory. ISIT: Internation
Symposium on Information Theory vol. 2022, 1324–1329.'
mla: Zhang, Yihan, and Shashank Vatedka. “Lower Bounds on List Decoding Capacity
Using Error Exponents.” 2022 IEEE International Symposium on Information Theory,
vol. 2022, Institute of Electrical and Electronics Engineers, 2022, pp. 1324–29,
doi:10.1109/ISIT50566.2022.9834815.
short: Y. Zhang, S. Vatedka, in:, 2022 IEEE International Symposium on Information
Theory, Institute of Electrical and Electronics Engineers, 2022, pp. 1324–1329.
conference:
end_date: 2022-07-01
location: Espoo, Finland
name: 'ISIT: Internation Symposium on Information Theory'
start_date: 2022-06-26
date_created: 2022-09-04T22:02:06Z
date_published: 2022-08-03T00:00:00Z
date_updated: 2023-02-13T09:02:06Z
day: '03'
department:
- _id: MaMo
doi: 10.1109/ISIT50566.2022.9834815
intvolume: ' 2022'
language:
- iso: eng
month: '08'
oa_version: None
page: 1324-1329
publication: 2022 IEEE International Symposium on Information Theory
publication_identifier:
isbn:
- '9781665421591'
issn:
- 2157-8095
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lower bounds on list decoding capacity using error exponents
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2022
year: '2022'
...
---
_id: '12019'
abstract:
- lang: eng
text: This paper studies combinatorial properties of codes for the Z-channel. A
Z-channel with error fraction τ takes as input a length-n binary codeword and
injects in an adversarial manner up to nτ asymmetric errors, i.e., errors that
only zero out bits but do not flip 0’s to 1’s. It is known that the largest (L
− 1)-list-decodable code for the Z-channel with error fraction τ has exponential
(in n) size if τ is less than a critical value that we call the Plotkin point
and has constant size if τ is larger than the threshold. The (L−1)-list-decoding
Plotkin point is known to be L−1L−1−L−LL−1. In this paper, we show that the largest
(L−1)-list-decodable code ε-above the Plotkin point has size Θ L (ε −3/2 ) for
any L − 1 ≥ 1.
article_processing_charge: No
author:
- first_name: Nikita
full_name: Polyanskii, Nikita
last_name: Polyanskii
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
citation:
ama: 'Polyanskii N, Zhang Y. List-decodable zero-rate codes for the Z-channel. In:
2022 IEEE International Symposium on Information Theory. Vol 2022. Institute
of Electrical and Electronics Engineers; 2022:2553-2558. doi:10.1109/ISIT50566.2022.9834829'
apa: 'Polyanskii, N., & Zhang, Y. (2022). List-decodable zero-rate codes for
the Z-channel. In 2022 IEEE International Symposium on Information Theory
(Vol. 2022, pp. 2553–2558). Espoo, Finland: Institute of Electrical and Electronics
Engineers. https://doi.org/10.1109/ISIT50566.2022.9834829'
chicago: Polyanskii, Nikita, and Yihan Zhang. “List-Decodable Zero-Rate Codes for
the Z-Channel.” In 2022 IEEE International Symposium on Information Theory,
2022:2553–58. Institute of Electrical and Electronics Engineers, 2022. https://doi.org/10.1109/ISIT50566.2022.9834829.
ieee: N. Polyanskii and Y. Zhang, “List-decodable zero-rate codes for the Z-channel,”
in 2022 IEEE International Symposium on Information Theory, Espoo, Finland,
2022, vol. 2022, pp. 2553–2558.
ista: 'Polyanskii N, Zhang Y. 2022. List-decodable zero-rate codes for the Z-channel.
2022 IEEE International Symposium on Information Theory. ISIT: Internation Symposium
on Information Theory vol. 2022, 2553–2558.'
mla: Polyanskii, Nikita, and Yihan Zhang. “List-Decodable Zero-Rate Codes for the
Z-Channel.” 2022 IEEE International Symposium on Information Theory, vol.
2022, Institute of Electrical and Electronics Engineers, 2022, pp. 2553–58, doi:10.1109/ISIT50566.2022.9834829.
short: N. Polyanskii, Y. Zhang, in:, 2022 IEEE International Symposium on Information
Theory, Institute of Electrical and Electronics Engineers, 2022, pp. 2553–2558.
conference:
end_date: 2022-07-01
location: Espoo, Finland
name: 'ISIT: Internation Symposium on Information Theory'
start_date: 2022-06-26
date_created: 2022-09-04T22:02:07Z
date_published: 2022-08-03T00:00:00Z
date_updated: 2023-02-13T09:02:18Z
day: '03'
department:
- _id: MaMo
doi: 10.1109/ISIT50566.2022.9834829
intvolume: ' 2022'
language:
- iso: eng
month: '08'
oa_version: None
page: 2553-2558
publication: 2022 IEEE International Symposium on Information Theory
publication_identifier:
isbn:
- '9781665421591'
issn:
- 2157-8095
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: List-decodable zero-rate codes for the Z-channel
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2022
year: '2022'
...
---
_id: '12051'
abstract:
- lang: eng
text: Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is
a major determinant of cellular growth, and dysregulation is observed in many
cancer types. Here, we present the purification of human Pol I from cells carrying
a genomic GFP fusion on the largest subunit allowing the structural and functional
analysis of the enzyme across species. In contrast to yeast, human Pol I carries
a single-subunit stalk, and in vitro transcription indicates a reduced proofreading
activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native
state rationalizes the effects of disease-associated mutations and uncovers an
additional domain that is built into the sequence of Pol I subunit RPA1. This
“dock II” domain resembles a truncated HMG box incapable of DNA binding which
may serve as a downstream transcription factor–binding platform in metazoans.
Biochemical analysis, in situ modelling, and ChIP data indicate that Topoisomerase
2a can be recruited to Pol I via the domain and cooperates with the HMG box domain–containing
factor UBF. These adaptations of the metazoan Pol I transcription system may allow
efficient release of positive DNA supercoils accumulating downstream of the transcription
bubble.
acknowledgement: "The authors especially thank Philip Gunkel for his contribution.
We thank all\r\npast and present members of the Engel lab, Achim Griesenbeck, Colyn
Crane-\r\nRobinson, Christophe Lotz, Marlene Vayssieres, Klaus Grasser, Herbert
Tschochner, and Philipp Milkereit for help and discussion; Gerhard Lehmann and Nobert
Eichner for IT support; Joost Zomerdijk for UBF-constructs, Volker Cordes for the
Hela P2 cell line; Remco Sprangers for shared cell culture; Dina Grohmann and the
Archaea Center for fermentation; and Thomas\r\nDresselhaus for access to fluorescence
microscopes. This work was in part supported by the Emmy-Noether Programm (DFG grant
no. EN 1204/1-1 to C Engel) of the German Research Council and Collaborative Research
Center 960 (TP-A8 to C Engel)."
article_number: e202201568
article_processing_charge: No
article_type: original
author:
- first_name: Julia L
full_name: Daiß, Julia L
last_name: Daiß
- first_name: Michael
full_name: Pilsl, Michael
last_name: Pilsl
- first_name: Kristina
full_name: Straub, Kristina
last_name: Straub
- first_name: Andrea
full_name: Bleckmann, Andrea
last_name: Bleckmann
- first_name: Mona
full_name: Höcherl, Mona
last_name: Höcherl
- first_name: Florian B
full_name: Heiss, Florian B
last_name: Heiss
- first_name: Guillermo
full_name: Abascal-Palacios, Guillermo
last_name: Abascal-Palacios
- first_name: Ewan P
full_name: Ramsay, Ewan P
last_name: Ramsay
- first_name: Katarina
full_name: Tluckova, Katarina
id: 4AC7D980-F248-11E8-B48F-1D18A9856A87
last_name: Tluckova
- first_name: Jean-Clement
full_name: Mars, Jean-Clement
last_name: Mars
- first_name: Torben
full_name: Fürtges, Torben
last_name: Fürtges
- first_name: Astrid
full_name: Bruckmann, Astrid
last_name: Bruckmann
- first_name: Till
full_name: Rudack, Till
last_name: Rudack
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Valérie
full_name: Lamour, Valérie
last_name: Lamour
- first_name: Konstantin
full_name: Panov, Konstantin
last_name: Panov
- first_name: Alessandro
full_name: Vannini, Alessandro
last_name: Vannini
- first_name: Tom
full_name: Moss, Tom
last_name: Moss
- first_name: Christoph
full_name: Engel, Christoph
last_name: Engel
citation:
ama: Daiß JL, Pilsl M, Straub K, et al. The human RNA polymerase I structure reveals
an HMG-like docking domain specific to metazoans. Life Science Alliance.
2022;5(11). doi:10.26508/lsa.202201568
apa: Daiß, J. L., Pilsl, M., Straub, K., Bleckmann, A., Höcherl, M., Heiss, F. B.,
… Engel, C. (2022). The human RNA polymerase I structure reveals an HMG-like docking
domain specific to metazoans. Life Science Alliance. Life Science Alliance.
https://doi.org/10.26508/lsa.202201568
chicago: Daiß, Julia L, Michael Pilsl, Kristina Straub, Andrea Bleckmann, Mona Höcherl,
Florian B Heiss, Guillermo Abascal-Palacios, et al. “The Human RNA Polymerase
I Structure Reveals an HMG-like Docking Domain Specific to Metazoans.” Life
Science Alliance. Life Science Alliance, 2022. https://doi.org/10.26508/lsa.202201568.
ieee: J. L. Daiß et al., “The human RNA polymerase I structure reveals an
HMG-like docking domain specific to metazoans,” Life Science Alliance,
vol. 5, no. 11. Life Science Alliance, 2022.
ista: Daiß JL, Pilsl M, Straub K, Bleckmann A, Höcherl M, Heiss FB, Abascal-Palacios
G, Ramsay EP, Tluckova K, Mars J-C, Fürtges T, Bruckmann A, Rudack T, Bernecky
C, Lamour V, Panov K, Vannini A, Moss T, Engel C. 2022. The human RNA polymerase
I structure reveals an HMG-like docking domain specific to metazoans. Life Science
Alliance. 5(11), e202201568.
mla: Daiß, Julia L., et al. “The Human RNA Polymerase I Structure Reveals an HMG-like
Docking Domain Specific to Metazoans.” Life Science Alliance, vol. 5, no.
11, e202201568, Life Science Alliance, 2022, doi:10.26508/lsa.202201568.
short: J.L. Daiß, M. Pilsl, K. Straub, A. Bleckmann, M. Höcherl, F.B. Heiss, G.
Abascal-Palacios, E.P. Ramsay, K. Tluckova, J.-C. Mars, T. Fürtges, A. Bruckmann,
T. Rudack, C. Bernecky, V. Lamour, K. Panov, A. Vannini, T. Moss, C. Engel, Life
Science Alliance 5 (2022).
date_created: 2022-09-06T18:45:23Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2023-08-03T13:39:36Z
day: '01'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.26508/lsa.202201568
external_id:
isi:
- '000972702600001'
file:
- access_level: open_access
checksum: 4201d876a3e5e8b65e319d03300014ad
content_type: application/pdf
creator: dernst
date_created: 2022-09-08T06:41:14Z
date_updated: 2022-09-08T06:41:14Z
file_id: '12062'
file_name: 2022_LifeScienceAlliance_Daiss.pdf
file_size: 3183129
relation: main_file
success: 1
file_date_updated: 2022-09-08T06:41:14Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '11'
keyword:
- Health
- Toxicology and Mutagenesis
- Plant Science
- Biochemistry
- Genetics and Molecular Biology (miscellaneous)
- Ecology
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Life Science Alliance
publication_identifier:
issn:
- 2575-1077
publication_status: published
publisher: Life Science Alliance
quality_controlled: '1'
status: public
title: The human RNA polymerase I structure reveals an HMG-like docking domain specific
to metazoans
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: 5
year: '2022'
...
---
_id: '12052'
abstract:
- lang: eng
text: Directionality in the intercellular transport of the plant hormone auxin is
determined by polar plasma membrane localization of PIN-FORMED (PIN) auxin transport
proteins. However, apart from PIN phosphorylation at conserved motifs, no further
determinants explicitly controlling polar PIN sorting decisions have been identified.
Here we present Arabidopsis WAVY GROWTH 3 (WAV3) and closely related RING-finger
E3 ubiquitin ligases, whose loss-of-function mutants show a striking apical-to-basal
polarity switch in PIN2 localization in root meristem cells. WAV3 E3 ligases function
as essential determinants for PIN polarity, acting independently from PINOID/WAG-dependent
PIN phosphorylation. They antagonize ectopic deposition of de novo synthesized
PIN proteins already immediately following completion of cell division, presumably
via preventing PIN sorting into basal, ARF GEF-mediated trafficking. Our findings
reveal an involvement of E3 ligases in the selective targeting of apically localized
PINs in higher plants.
acknowledgement: We would like to thank Tatsuo Sakai, Marcus Heisler, Toru Fujiwara,
Lucia Strader, Christian Hardtke, Malcolm Bennett, Claus Schwechheimer, Gerd Jürgens
and Remko Offringa for sharing published materials and Alba Grau Gimeno for support.
We are greatly indebted to Bert de Rybel for supporting N.K. and M.G. to work on
the final stages of manuscript preparation as postdocs in his laboratory. A full-length
SOR1 cDNA clone (J090099M14) was obtained from the National Agriculture and Food
Research Organization (NARO, Japan). Support by the Multiscale Imaging Core Facility
at the BOKU is greatly acknowledged. This work has been supported by grants from
the Austrian Science Fund (FWF P25931-B16; P31493-B25 to Christian Luschnig; I3630-B25
to Jiří Friml; P30850-B32 to Barbara Korbei) and from the Swiss National Funds (31003A-165877/1
to Markus Geisler) and the European Union’s Horizon 2020 research and innovation
program (Marie Skłodowska-Curie grant agreement No 885979 to Matouš Glanc).
article_number: '5147'
article_processing_charge: No
article_type: original
author:
- first_name: N
full_name: Konstantinova, N
last_name: Konstantinova
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: R
full_name: Keshkeih, R
last_name: Keshkeih
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: M
full_name: Di Donato, M
last_name: Di Donato
- first_name: K
full_name: Retzer, K
last_name: Retzer
- first_name: J
full_name: Moulinier-Anzola, J
last_name: Moulinier-Anzola
- first_name: M
full_name: Schwihla, M
last_name: Schwihla
- first_name: B
full_name: Korbei, B
last_name: Korbei
- first_name: M
full_name: Geisler, M
last_name: Geisler
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: C
full_name: Luschnig, C
last_name: Luschnig
citation:
ama: Konstantinova N, Hörmayer L, Glanc M, et al. WAVY GROWTH Arabidopsis E3 ubiquitin
ligases affect apical PIN sorting decisions. Nature Communications. 2022;13.
doi:10.1038/s41467-022-32888-8
apa: Konstantinova, N., Hörmayer, L., Glanc, M., Keshkeih, R., Tan, S., Di Donato,
M., … Luschnig, C. (2022). WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect
apical PIN sorting decisions. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-32888-8
chicago: Konstantinova, N, Lukas Hörmayer, Matous Glanc, R Keshkeih, Shutang Tan,
M Di Donato, K Retzer, et al. “WAVY GROWTH Arabidopsis E3 Ubiquitin Ligases Affect
Apical PIN Sorting Decisions.” Nature Communications. Springer Nature,
2022. https://doi.org/10.1038/s41467-022-32888-8.
ieee: N. Konstantinova et al., “WAVY GROWTH Arabidopsis E3 ubiquitin ligases
affect apical PIN sorting decisions,” Nature Communications, vol. 13. Springer
Nature, 2022.
ista: Konstantinova N, Hörmayer L, Glanc M, Keshkeih R, Tan S, Di Donato M, Retzer
K, Moulinier-Anzola J, Schwihla M, Korbei B, Geisler M, Friml J, Luschnig C. 2022.
WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions.
Nature Communications. 13, 5147.
mla: Konstantinova, N., et al. “WAVY GROWTH Arabidopsis E3 Ubiquitin Ligases Affect
Apical PIN Sorting Decisions.” Nature Communications, vol. 13, 5147, Springer
Nature, 2022, doi:10.1038/s41467-022-32888-8.
short: N. Konstantinova, L. Hörmayer, M. Glanc, R. Keshkeih, S. Tan, M. Di Donato,
K. Retzer, J. Moulinier-Anzola, M. Schwihla, B. Korbei, M. Geisler, J. Friml,
C. Luschnig, Nature Communications 13 (2022).
date_created: 2022-09-07T14:19:26Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2023-08-03T13:40:32Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41467-022-32888-8
external_id:
isi:
- '000848744900004'
pmid:
- '36050482'
file:
- access_level: open_access
checksum: 43336758c89cd6c045839089af070afe
content_type: application/pdf
creator: dernst
date_created: 2022-09-08T07:46:16Z
date_updated: 2022-09-08T07:46:16Z
file_id: '12063'
file_name: 2022_NatureCommunications_Konstantinova.pdf
file_size: 6678579
relation: main_file
success: 1
file_date_updated: 2022-09-08T07:46:16Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
language:
- iso: eng
month: '09'
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: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-022-33198-9
status: public
title: WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions
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: 13
year: '2022'
...
---
_id: '12053'
abstract:
- lang: eng
text: Strigolactones (SLs) are a class of phytohormones that regulate plant shoot
branching and adventitious root development. However, little is known regarding
the role of SLs in controlling the behavior of the smallest unit of the organism,
the single cell. Here, taking advantage of a classic single-cell model offered
by the cotton (Gossypium hirsutum) fiber cell, we show that SLs, whose biosynthesis
is fine-tuned by gibberellins (GAs), positively regulate cell elongation and cell
wall thickness by promoting the biosynthesis of very-long-chain fatty acids (VLCFAs)
and cellulose, respectively. Furthermore, we identified two layers of transcription
factors (TFs) involved in the hierarchical regulation of this GA-SL crosstalk.
The top-layer TF GROWTH-REGULATING FACTOR 4 (GhGRF4) directly activates expression
of the SL biosynthetic gene DWARF27 (D27) to increase SL accumulation in fiber
cells and GAs induce GhGRF4 expression. SLs induce the expression of four second-layer
TF genes (GhNAC100-2, GhBLH51, GhGT2, and GhB9SHZ1), which transmit SL signals
downstream to two ketoacyl-CoA synthase genes (KCS) and three cellulose synthase
(CesA) genes by directly activating their transcription. Finally, the KCS and
CesA enzymes catalyze the biosynthesis of very long chain fatty acids and cellulose,
respectively, to regulate development of high-grade cotton fibers. In addition
to providing a theoretical basis for cotton fiber improvement, our results shed
light on SL signaling in plant development at the single-cell level.
acknowledgement: This work was supported by the National Natural Science Foundation
of China (32070549), Shaanxi Youth Entrusted Talent Program (20190205), Fundamental
Research Funds for the Central Universities (GK202002005 and GK202201017), Young
Elite Scientists Sponsorship Program by China Association for Science and Technology
(CAST) (2019-2021QNRC001), State Key Laboratory of Cotton Biology Open Fund (CB2020A12
and CB2021A21) and FWF Stand-alone Project (P29988).
article_processing_charge: No
article_type: original
author:
- first_name: Z
full_name: Tian, Z
last_name: Tian
- first_name: Yuzhou
full_name: Zhang, Yuzhou
id: 3B6137F2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-2627-6956
- first_name: L
full_name: Zhu, L
last_name: Zhu
- first_name: B
full_name: Jiang, B
last_name: Jiang
- first_name: H
full_name: Wang, H
last_name: Wang
- first_name: R
full_name: Gao, R
last_name: Gao
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: G
full_name: Xiao, G
last_name: Xiao
citation:
ama: Tian Z, Zhang Y, Zhu L, et al. Strigolactones act downstream of gibberellins
to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium
hirsutum). The Plant Cell. 2022;34(12):4816-4839. doi:10.1093/plcell/koac270
apa: Tian, Z., Zhang, Y., Zhu, L., Jiang, B., Wang, H., Gao, R., … Xiao, G. (2022).
Strigolactones act downstream of gibberellins to regulate fiber cell elongation
and cell wall thickness in cotton (Gossypium hirsutum). The Plant Cell.
Oxford University Press. https://doi.org/10.1093/plcell/koac270
chicago: Tian, Z, Yuzhou Zhang, L Zhu, B Jiang, H Wang, R Gao, Jiří Friml, and G
Xiao. “Strigolactones Act Downstream of Gibberellins to Regulate Fiber Cell Elongation
and Cell Wall Thickness in Cotton (Gossypium Hirsutum).” The Plant Cell.
Oxford University Press, 2022. https://doi.org/10.1093/plcell/koac270.
ieee: Z. Tian et al., “Strigolactones act downstream of gibberellins to regulate
fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum),”
The Plant Cell, vol. 34, no. 12. Oxford University Press, pp. 4816–4839,
2022.
ista: Tian Z, Zhang Y, Zhu L, Jiang B, Wang H, Gao R, Friml J, Xiao G. 2022. Strigolactones
act downstream of gibberellins to regulate fiber cell elongation and cell wall
thickness in cotton (Gossypium hirsutum). The Plant Cell. 34(12), 4816–4839.
mla: Tian, Z., et al. “Strigolactones Act Downstream of Gibberellins to Regulate
Fiber Cell Elongation and Cell Wall Thickness in Cotton (Gossypium Hirsutum).”
The Plant Cell, vol. 34, no. 12, Oxford University Press, 2022, pp. 4816–39,
doi:10.1093/plcell/koac270.
short: Z. Tian, Y. Zhang, L. Zhu, B. Jiang, H. Wang, R. Gao, J. Friml, G. Xiao,
The Plant Cell 34 (2022) 4816–4839.
date_created: 2022-09-07T14:19:39Z
date_published: 2022-12-01T00:00:00Z
date_updated: 2023-08-03T13:41:06Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1093/plcell/koac270
external_id:
isi:
- '000852753000001'
pmid:
- '36040191'
file:
- access_level: open_access
checksum: 1c606d9545f29dfca15235f69ad27b58
content_type: application/pdf
creator: dernst
date_created: 2023-01-20T08:29:12Z
date_updated: 2023-01-20T08:29:12Z
file_id: '12318'
file_name: 2022_PlantCell_Tian.pdf
file_size: 3282540
relation: main_file
success: 1
file_date_updated: 2023-01-20T08:29:12Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '12'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: 4816-4839
pmid: 1
project:
- _id: 262EF96E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29988
name: RNA-directed DNA methylation in plant development
publication: The Plant Cell
publication_identifier:
eissn:
- 1532-298X
issn:
- 1040-4651
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1093/plcell/koac342
scopus_import: '1'
status: public
title: Strigolactones act downstream of gibberellins to regulate fiber cell elongation
and cell wall thickness in cotton (Gossypium hirsutum)
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 34
year: '2022'
...
---
_id: '12054'
abstract:
- lang: eng
text: 'Polar auxin transport is unique to plants and coordinates their growth and
development1,2. The PIN-FORMED (PIN) auxin transporters exhibit highly asymmetrical
localizations at the plasma membrane and drive polar auxin transport3,4; however,
their structures and transport mechanisms remain largely unknown. Here, we report
three inward-facing conformation structures of Arabidopsis thaliana PIN1: the
apo state, bound to the natural auxin indole-3-acetic acid (IAA), and in complex
with the polar auxin transport inhibitor N-1-naphthylphthalamic acid (NPA). The
transmembrane domain of PIN1 shares a conserved NhaA fold5. In the substrate-bound
structure, IAA is coordinated by both hydrophobic stacking and hydrogen bonding.
NPA competes with IAA for the same site at the intracellular pocket, but with
a much higher affinity. These findings inform our understanding of the substrate
recognition and transport mechanisms of PINs and set up a framework for future
research on directional auxin transport, one of the most crucial processes underlying
plant development.'
acknowledgement: We thank the Cryo-EM Center of the University of Science and Technology
of China (USTC) and the Center for Biological Imaging (CBI), Institute of Biophysics,
Chinese Academy of Science, for the EM facility support; we thank B. Zhu, X. Huang
and all the other staff members for their technical support on cryo-EM data collection.
We thank J. Ren for his technical support with the transport assays and M. Seeger
for providing the sybody libraries. This work was supported by the Strategic Priority
Research Program of Chinese Academy of Sciences (XDB 37020204 to D.L. and XDB37020103
to Linfeng Sun), National Natural Science Foundation of China (82151215 and 31870726
to D.L., 31900885 to X.L., and 31870732 to Linfeng Sun), Natural Science Foundation
of Anhui Province (2008085MC90 to X.L. and 2008085J15 to Linfeng Sun), the Fundamental
Research Funds for the Central Universities (WK9100000031 to Linfeng Sun), and the
USTC Research Funds of the Double First-Class Initiative (YD9100002004 to Linfeng
Sun). Linfeng Sun is supported by an Outstanding Young Scholar Award from the Qiu
Shi Science and Technologies Foundation, and a Young Scholar Award from the Cyrus
Tang Foundation.
article_processing_charge: No
article_type: original
author:
- first_name: Z
full_name: Yang, Z
last_name: Yang
- first_name: J
full_name: Xia, J
last_name: Xia
- first_name: J
full_name: Hong, J
last_name: Hong
- first_name: C
full_name: Zhang, C
last_name: Zhang
- first_name: H
full_name: Wei, H
last_name: Wei
- first_name: W
full_name: Ying, W
last_name: Ying
- first_name: C
full_name: Sun, C
last_name: Sun
- first_name: L
full_name: Sun, L
last_name: Sun
- first_name: Y
full_name: Mao, Y
last_name: Mao
- first_name: Y
full_name: Gao, Y
last_name: Gao
- first_name: S
full_name: Tan, S
last_name: Tan
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: D
full_name: Li, D
last_name: Li
- first_name: X
full_name: Liu, X
last_name: Liu
- first_name: L
full_name: Sun, L
last_name: Sun
citation:
ama: Yang Z, Xia J, Hong J, et al. Structural insights into auxin recognition and
efflux by Arabidopsis PIN1. Nature. 2022;609(7927):611-615. doi:10.1038/s41586-022-05143-9
apa: Yang, Z., Xia, J., Hong, J., Zhang, C., Wei, H., Ying, W., … Sun, L. (2022).
Structural insights into auxin recognition and efflux by Arabidopsis PIN1. Nature.
Springer Nature. https://doi.org/10.1038/s41586-022-05143-9
chicago: Yang, Z, J Xia, J Hong, C Zhang, H Wei, W Ying, C Sun, et al. “Structural
Insights into Auxin Recognition and Efflux by Arabidopsis PIN1.” Nature.
Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05143-9.
ieee: Z. Yang et al., “Structural insights into auxin recognition and efflux
by Arabidopsis PIN1,” Nature, vol. 609, no. 7927. Springer Nature, pp.
611–615, 2022.
ista: Yang Z, Xia J, Hong J, Zhang C, Wei H, Ying W, Sun C, Sun L, Mao Y, Gao Y,
Tan S, Friml J, Li D, Liu X, Sun L. 2022. Structural insights into auxin recognition
and efflux by Arabidopsis PIN1. Nature. 609(7927), 611–615.
mla: Yang, Z., et al. “Structural Insights into Auxin Recognition and Efflux by
Arabidopsis PIN1.” Nature, vol. 609, no. 7927, Springer Nature, 2022, pp.
611–15, doi:10.1038/s41586-022-05143-9.
short: Z. Yang, J. Xia, J. Hong, C. Zhang, H. Wei, W. Ying, C. Sun, L. Sun, Y. Mao,
Y. Gao, S. Tan, J. Friml, D. Li, X. Liu, L. Sun, Nature 609 (2022) 611–615.
date_created: 2022-09-07T14:19:52Z
date_published: 2022-08-02T00:00:00Z
date_updated: 2023-08-03T13:41:44Z
day: '02'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41586-022-05143-9
external_id:
isi:
- '000848082900002'
pmid:
- '35917925'
file:
- access_level: open_access
checksum: 3136a585f8e1c7e73b5e1418b3d01898
content_type: application/pdf
creator: dernst
date_created: 2022-09-08T08:02:54Z
date_updated: 2022-09-08T08:02:54Z
file_id: '12064'
file_name: 2022_Nature_Yang.pdf
file_size: 32344580
relation: main_file
success: 1
file_date_updated: 2022-09-08T08:02:54Z
has_accepted_license: '1'
intvolume: ' 609'
isi: 1
issue: '7927'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 611-615
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural insights into auxin recognition and efflux by Arabidopsis PIN1
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: 609
year: '2022'
...
---
_id: '12065'
abstract:
- lang: eng
text: Capacity, rate performance, and cycle life of aprotic Li–O2 batteries critically
depend on reversible electrodeposition of Li2O2. Current understanding states
surface-adsorbed versus solvated LiO2 controls Li2O2 growth as surface film or
as large particles. Herein, we show that Li2O2 forms across a wide range of electrolytes,
carbons, and current densities as particles via solution-mediated LiO2 disproportionation,
bringing into question the prevalence of any surface growth under practical conditions.
We describe a unified O2 reduction mechanism, which can explain all found capacity
relations and Li2O2 morphologies with exclusive solution discharge. Determining
particle morphology and achievable capacities are species mobilities, true areal
rate, and the degree of LiO2 association in solution. Capacity is conclusively
limited by mass transport through the tortuous Li2O2 rather than electron transport
through a passivating Li2O2 film. Provided that species mobilities and surface
growth are high, high capacities are also achieved with weakly solvating electrolytes,
which were previously considered prototypical for low capacity via surface growth.
acknowledged_ssus:
- _id: EM-Fac
- _id: M-Shop
acknowledgement: S.A.F. and C.P. are indebted to the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation program (Grant Agreement
No. 636069). This project has received funding from the European Union’s Horizon
2020 research and innovation program under the Marie Skłodowska-Curie Grant NanoEvolution,
Grant Agreement No. 894042. S.A.F. and S.M. are indebted to Institute of Science
and Technology Austria (ISTA) for support. This research was supported by the Scientific
Service Units of ISTA through resources provided by the Electron Microscopy Facility
and the Miba Machine Shop. C.P. thanks Vanessa Wood (ETH Zürich) for her continuing
support.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
- first_name: Soumyadip
full_name: Mondal, Soumyadip
id: d25d21ef-dc8d-11ea-abe3-ec4576307f48
last_name: Mondal
- first_name: Ludek
full_name: Lovicar, Ludek
id: 36DB3A20-F248-11E8-B48F-1D18A9856A87
last_name: Lovicar
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Prehal C, Mondal S, Lovicar L, Freunberger SA. Exclusive solution discharge
in Li-O₂ batteries? ACS Energy Letters. 2022;7(9):3112-3119. doi:10.1021/acsenergylett.2c01711
apa: Prehal, C., Mondal, S., Lovicar, L., & Freunberger, S. A. (2022). Exclusive
solution discharge in Li-O₂ batteries? ACS Energy Letters. American Chemical
Society. https://doi.org/10.1021/acsenergylett.2c01711
chicago: Prehal, Christian, Soumyadip Mondal, Ludek Lovicar, and Stefan Alexander
Freunberger. “Exclusive Solution Discharge in Li-O₂ Batteries?” ACS Energy
Letters. American Chemical Society, 2022. https://doi.org/10.1021/acsenergylett.2c01711.
ieee: C. Prehal, S. Mondal, L. Lovicar, and S. A. Freunberger, “Exclusive solution
discharge in Li-O₂ batteries?,” ACS Energy Letters, vol. 7, no. 9. American
Chemical Society, pp. 3112–3119, 2022.
ista: Prehal C, Mondal S, Lovicar L, Freunberger SA. 2022. Exclusive solution discharge
in Li-O₂ batteries? ACS Energy Letters. 7(9), 3112–3119.
mla: Prehal, Christian, et al. “Exclusive Solution Discharge in Li-O₂ Batteries?”
ACS Energy Letters, vol. 7, no. 9, American Chemical Society, 2022, pp.
3112–19, doi:10.1021/acsenergylett.2c01711.
short: C. Prehal, S. Mondal, L. Lovicar, S.A. Freunberger, ACS Energy Letters 7
(2022) 3112–3119.
date_created: 2022-09-08T09:51:09Z
date_published: 2022-08-29T00:00:00Z
date_updated: 2023-08-03T13:47:56Z
day: '29'
ddc:
- '540'
department:
- _id: StFr
- _id: EM-Fac
doi: 10.1021/acsenergylett.2c01711
external_id:
isi:
- '000860787000001'
file:
- access_level: open_access
checksum: cf0bed3a2535c11d27244cd029dbc1d0
content_type: application/pdf
creator: dernst
date_created: 2023-01-20T08:43:51Z
date_updated: 2023-01-20T08:43:51Z
file_id: '12319'
file_name: 2022_ACSEnergyLetters_Prehal.pdf
file_size: 3827583
relation: main_file
success: 1
file_date_updated: 2023-01-20T08:43:51Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '9'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 3112-3119
publication: ACS Energy Letters
publication_identifier:
eissn:
- 2380-8195
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Exclusive solution discharge in Li-O₂ batteries?
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 7
year: '2022'
...
---
_id: '12072'
abstract:
- lang: eng
text: "In this thesis, we study two of the most important questions in Arithmetic
geometry: that of the existence and density of solutions to Diophantine equations.
In order for a Diophantine equation to have any solutions over the rational numbers,
it must have solutions everywhere locally, i.e., over R and over Qp for every
prime p. The converse, called the Hasse principle, is known to fail in general.
However, it is still a central question in Arithmetic geometry to determine for
which varieties the Hasse principle does hold. In this work, we establish the
Hasse principle for a wide new family of varieties of the form f(t) = NK/Q(x)
̸= 0, where f is a polynomial with integer coefficients and NK/Q denotes the norm\r\nform
associated to a number field K. Our results cover products of arbitrarily many
linear, quadratic or cubic factors, and generalise an argument of Irving [69],
which makes use of the beta sieve of Rosser and Iwaniec. We also demonstrate how
our main sieve results can be applied to treat new cases of a conjecture of Harpaz
and Wittenberg on locally split values of polynomials over number fields, and
discuss consequences for rational points in fibrations.\r\nIn the second question,
about the density of solutions, one defines a height function and seeks to estimate
asymptotically the number of points of height bounded by B as B → ∞. Traditionally,
one either counts rational points, or\r\nintegral points with respect to a suitable
model. However, in this thesis, we study an emerging area of interest in Arithmetic
geometry known as Campana points, which in some sense interpolate between rational
and integral points.\r\nMore precisely, we count the number of nonzero integers
z1, z2, z3 such that gcd(z1, z2, z3) = 1, and z1, z2, z3, z1 + z2 + z3 are all
squareful and bounded by B. Using the circle method, we obtain an asymptotic formula
which agrees in\r\nthe power of B and log B with a bold new generalisation of
Manin’s conjecture to the setting of Campana points, recently formulated by Pieropan,
Smeets, Tanimoto and Várilly-Alvarado [96]. However, in this thesis we also provide
the first known counterexamples to leading constant predicted by their conjecture. "
acknowledgement: I acknowledge the received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Sklodowska Curie Grant Agreement
No. 665385.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Alec L
full_name: Shute, Alec L
id: 440EB050-F248-11E8-B48F-1D18A9856A87
last_name: Shute
orcid: 0000-0002-1812-2810
citation:
ama: 'Shute AL. Existence and density problems in Diophantine geometry: From norm
forms to Campana points. 2022. doi:10.15479/at:ista:12072'
apa: 'Shute, A. L. (2022). Existence and density problems in Diophantine geometry:
From norm forms to Campana points. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:12072'
chicago: 'Shute, Alec L. “Existence and Density Problems in Diophantine Geometry:
From Norm Forms to Campana Points.” Institute of Science and Technology Austria,
2022. https://doi.org/10.15479/at:ista:12072.'
ieee: 'A. L. Shute, “Existence and density problems in Diophantine geometry: From
norm forms to Campana points,” Institute of Science and Technology Austria, 2022.'
ista: 'Shute AL. 2022. Existence and density problems in Diophantine geometry: From
norm forms to Campana points. Institute of Science and Technology Austria.'
mla: 'Shute, Alec L. Existence and Density Problems in Diophantine Geometry:
From Norm Forms to Campana Points. Institute of Science and Technology Austria,
2022, doi:10.15479/at:ista:12072.'
short: 'A.L. Shute, Existence and Density Problems in Diophantine Geometry: From
Norm Forms to Campana Points, Institute of Science and Technology Austria, 2022.'
date_created: 2022-09-08T21:53:03Z
date_published: 2022-09-08T00:00:00Z
date_updated: 2023-02-21T16:37:35Z
day: '08'
ddc:
- '512'
degree_awarded: PhD
department:
- _id: GradSch
- _id: TiBr
doi: 10.15479/at:ista:12072
ec_funded: 1
file:
- access_level: open_access
checksum: bf073344320e05d92c224786cec2e92d
content_type: application/pdf
creator: ashute
date_created: 2022-09-08T21:50:34Z
date_updated: 2022-09-08T21:50:34Z
file_id: '12073'
file_name: Thesis_final_draft.pdf
file_size: 1907386
relation: main_file
success: 1
- access_level: closed
checksum: b054ac6baa09f70e8235403a4abbed80
content_type: application/octet-stream
creator: ashute
date_created: 2022-09-08T21:50:42Z
date_updated: 2022-09-12T11:24:21Z
file_id: '12074'
file_name: athesis.tex
file_size: 495393
relation: source_file
- access_level: closed
checksum: 0a31e905f1cff5eb8110978cc90e1e79
content_type: application/x-zip-compressed
creator: ashute
date_created: 2022-09-09T12:05:00Z
date_updated: 2022-09-12T11:24:21Z
file_id: '12078'
file_name: qfcjsfmtvtbfrjjvhdzrnqxfvgjvxtbf.zip
file_size: 944534
relation: source_file
file_date_updated: 2022-09-12T11:24:21Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '09'
oa: 1
oa_version: Published Version
page: '208'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-023-7
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12076'
relation: part_of_dissertation
status: public
- id: '12077'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
title: 'Existence and density problems in Diophantine geometry: From norm forms to
Campana points'
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '12079'
abstract:
- lang: eng
text: We extend the recent rigorous convergence result of Abels and Moser (SIAM
J Math Anal 54(1):114–172, 2022. https://doi.org/10.1137/21M1424925) concerning
convergence rates for solutions of the Allen–Cahn equation with a nonlinear Robin
boundary condition towards evolution by mean curvature flow with constant contact
angle. More precisely, in the present work we manage to remove the perturbative
assumption on the contact angle being close to 90∘. We establish under usual double-well
type assumptions on the potential and for a certain class of boundary energy densities
the sub-optimal convergence rate of order ε12 for general contact angles α∈(0,π).
For a very specific form of the boundary energy density, we even obtain from our
methods a sharp convergence rate of order ε; again for general contact angles
α∈(0,π). Our proof deviates from the popular strategy based on rigorous asymptotic
expansions and stability estimates for the linearized Allen–Cahn operator. Instead,
we follow the recent approach by Fischer et al. (SIAM J Math Anal 52(6):6222–6233,
2020. https://doi.org/10.1137/20M1322182), thus relying on a relative entropy
technique. We develop a careful adaptation of their approach in order to encode
the constant contact angle condition. In fact, we perform this task at the level
of the notion of gradient flow calibrations. This concept was recently introduced
in the context of weak-strong uniqueness for multiphase mean curvature flow by
Fischer et al. (arXiv:2003.05478v2).
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 948819) , and from the Deutsche Forschungsgemeinschaft (DFG,
German Research Foundation) under Germany’s Excellence Strategy—EXC-2047/1 - 390685813.\r\nOpen
Access funding enabled and organized by Projekt DEAL."
article_number: '201'
article_processing_charge: No
article_type: original
author:
- first_name: Sebastian
full_name: Hensel, Sebastian
id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87
last_name: Hensel
orcid: 0000-0001-7252-8072
- first_name: Maximilian
full_name: Moser, Maximilian
id: a60047a9-da77-11eb-85b4-c4dc385ebb8c
last_name: Moser
citation:
ama: 'Hensel S, Moser M. Convergence rates for the Allen–Cahn equation with boundary
contact energy: The non-perturbative regime. Calculus of Variations and Partial
Differential Equations. 2022;61(6). doi:10.1007/s00526-022-02307-3'
apa: 'Hensel, S., & Moser, M. (2022). Convergence rates for the Allen–Cahn equation
with boundary contact energy: The non-perturbative regime. Calculus of Variations
and Partial Differential Equations. Springer Nature. https://doi.org/10.1007/s00526-022-02307-3'
chicago: 'Hensel, Sebastian, and Maximilian Moser. “Convergence Rates for the Allen–Cahn
Equation with Boundary Contact Energy: The Non-Perturbative Regime.” Calculus
of Variations and Partial Differential Equations. Springer Nature, 2022. https://doi.org/10.1007/s00526-022-02307-3.'
ieee: 'S. Hensel and M. Moser, “Convergence rates for the Allen–Cahn equation with
boundary contact energy: The non-perturbative regime,” Calculus of Variations
and Partial Differential Equations, vol. 61, no. 6. Springer Nature, 2022.'
ista: 'Hensel S, Moser M. 2022. Convergence rates for the Allen–Cahn equation with
boundary contact energy: The non-perturbative regime. Calculus of Variations and
Partial Differential Equations. 61(6), 201.'
mla: 'Hensel, Sebastian, and Maximilian Moser. “Convergence Rates for the Allen–Cahn
Equation with Boundary Contact Energy: The Non-Perturbative Regime.” Calculus
of Variations and Partial Differential Equations, vol. 61, no. 6, 201, Springer
Nature, 2022, doi:10.1007/s00526-022-02307-3.'
short: S. Hensel, M. Moser, Calculus of Variations and Partial Differential Equations
61 (2022).
date_created: 2022-09-11T22:01:54Z
date_published: 2022-08-24T00:00:00Z
date_updated: 2023-08-03T13:48:30Z
day: '24'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s00526-022-02307-3
ec_funded: 1
external_id:
isi:
- '000844247300008'
file:
- access_level: open_access
checksum: b2da020ce50440080feedabeab5b09c4
content_type: application/pdf
creator: dernst
date_created: 2023-01-20T08:56:01Z
date_updated: 2023-01-20T08:56:01Z
file_id: '12320'
file_name: 2022_Calculus_Hensel.pdf
file_size: 1278493
relation: main_file
success: 1
file_date_updated: 2023-01-20T08:56:01Z
has_accepted_license: '1'
intvolume: ' 61'
isi: 1
issue: '6'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 0aa76401-070f-11eb-9043-b5bb049fa26d
call_identifier: H2020
grant_number: '948819'
name: Bridging Scales in Random Materials
publication: Calculus of Variations and Partial Differential Equations
publication_identifier:
eissn:
- 1432-0835
issn:
- 0944-2669
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Convergence rates for the Allen–Cahn equation with boundary contact energy:
The non-perturbative regime'
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: 61
year: '2022'
...
---
_id: '12080'
abstract:
- lang: eng
text: 'Endocytosis is a multistep process involving the sequential recruitment and
action of numerous proteins. This process can be divided into two phases: an early
phase, in which sites of endocytosis are formed, and a late phase in which clathrin-coated
vesicles are formed and internalized into the cytosol, but how these phases link
to each other remains unclear. In this study, we demonstrate that anchoring the
yeast Eps15-like protein Pan1p to the peroxisome triggers most of the events occurring
during the late phase at the peroxisome. At this ectopic location, Pan1p recruits
most proteins that function in the late phases—including actin nucleation promoting
factors—and then initiates actin polymerization. Pan1p also recruited Prk1 kinase
and actin depolymerizing factors, thereby triggering disassembly immediately after
actin assembly and inducing dissociation of endocytic proteins from the peroxisome.
These observations suggest that Pan1p is a key regulator for initiating, processing,
and completing the late phase of endocytosis.'
acknowledgement: 'This work was supported by JSPS KAKENHI GRANT #18K062291, and the
Takeda Science Foundation to J.Y. Toshima, as well as JSPS KAKENHI GRANT #19K065710,
the Uehara Memorial Foundation, and Life Science Foundation of JAPAN to J. Toshima.'
article_number: e202112138
article_processing_charge: No
article_type: original
author:
- first_name: Mariko
full_name: Enshoji, Mariko
last_name: Enshoji
- first_name: Yoshiko
full_name: Miyano, Yoshiko
last_name: Miyano
- first_name: Nao
full_name: Yoshida, Nao
last_name: Yoshida
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Minami
full_name: Watanabe, Minami
last_name: Watanabe
- first_name: Mayumi
full_name: Kunihiro, Mayumi
last_name: Kunihiro
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Junko Y.
full_name: Toshima, Junko Y.
last_name: Toshima
- first_name: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Enshoji M, Miyano Y, Yoshida N, et al. Eps15/Pan1p is a master regulator of
the late stages of the endocytic pathway. Journal of Cell Biology. 2022;221(10).
doi:10.1083/jcb.202112138
apa: Enshoji, M., Miyano, Y., Yoshida, N., Nagano, M., Watanabe, M., Kunihiro, M.,
… Toshima, J. (2022). Eps15/Pan1p is a master regulator of the late stages of
the endocytic pathway. Journal of Cell Biology. Rockefeller University
Press. https://doi.org/10.1083/jcb.202112138
chicago: Enshoji, Mariko, Yoshiko Miyano, Nao Yoshida, Makoto Nagano, Minami Watanabe,
Mayumi Kunihiro, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Eps15/Pan1p
Is a Master Regulator of the Late Stages of the Endocytic Pathway.” Journal
of Cell Biology. Rockefeller University Press, 2022. https://doi.org/10.1083/jcb.202112138.
ieee: M. Enshoji et al., “Eps15/Pan1p is a master regulator of the late stages
of the endocytic pathway,” Journal of Cell Biology, vol. 221, no. 10. Rockefeller
University Press, 2022.
ista: Enshoji M, Miyano Y, Yoshida N, Nagano M, Watanabe M, Kunihiro M, Siekhaus
DE, Toshima JY, Toshima J. 2022. Eps15/Pan1p is a master regulator of the late
stages of the endocytic pathway. Journal of Cell Biology. 221(10), e202112138.
mla: Enshoji, Mariko, et al. “Eps15/Pan1p Is a Master Regulator of the Late Stages
of the Endocytic Pathway.” Journal of Cell Biology, vol. 221, no. 10, e202112138,
Rockefeller University Press, 2022, doi:10.1083/jcb.202112138.
short: M. Enshoji, Y. Miyano, N. Yoshida, M. Nagano, M. Watanabe, M. Kunihiro, D.E.
Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Biology 221 (2022).
date_created: 2022-09-11T22:01:54Z
date_published: 2022-08-19T00:00:00Z
date_updated: 2023-08-03T13:49:07Z
day: '19'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.1083/jcb.202112138
external_id:
isi:
- '000932770500001'
pmid:
- '35984332'
file:
- access_level: open_access
checksum: f2e581e66b5cdab9df81b56e850b3eaa
content_type: application/pdf
creator: dernst
date_created: 2023-01-20T09:32:53Z
date_updated: 2023-02-21T23:30:39Z
embargo: 2023-02-20
file_id: '12321'
file_name: 2022_JCB_Enshoji.pdf
file_size: 7816875
relation: main_file
file_date_updated: 2023-02-21T23:30:39Z
has_accepted_license: '1'
intvolume: ' 221'
isi: 1
issue: '10'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
issn:
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 221
year: '2022'
...
---
_id: '12081'
abstract:
- lang: eng
text: 'Selection accumulates information in the genome—it guides stochastically
evolving populations toward states (genotype frequencies) that would be unlikely
under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence
between the actual distribution of genotype frequencies and the corresponding
neutral distribution. First, we show that this population-level information sets
an upper bound on the information at the level of genotype and phenotype, limiting
how precisely they can be specified by selection. Next, we study how the accumulation
and maintenance of information is limited by the cost of selection, measured as
the genetic load or the relative fitness variance, both of which we connect to
the control-theoretic KL cost of control. The information accumulation rate is
upper bounded by the population size times the cost of selection. This bound is
very general, and applies across models (Wright–Fisher, Moran, diffusion) and
to arbitrary forms of selection, mutation, and recombination. Finally, the cost
of maintaining information depends on how it is encoded: Specifying a single allele
out of two is expensive, but one bit encoded among many weakly specified loci
(as in a polygenic trait) is cheap.'
acknowledgement: We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and
two anonymous reviewers for discussions and comments on the manuscript. G.T. and
M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018.
N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.”
article_number: e2123152119
article_processing_charge: No
article_type: original
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: '1'
citation:
ama: Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information
in evolution. Proceedings of the National Academy of Sciences. 2022;119(36).
doi:10.1073/pnas.2123152119
apa: Hledik, M., Barton, N. H., & Tkačik, G. (2022). Accumulation and maintenance
of information in evolution. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2123152119
chicago: Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and
Maintenance of Information in Evolution.” Proceedings of the National Academy
of Sciences. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2123152119.
ieee: M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information
in evolution,” Proceedings of the National Academy of Sciences, vol. 119,
no. 36. Proceedings of the National Academy of Sciences, 2022.
ista: Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information
in evolution. Proceedings of the National Academy of Sciences. 119(36), e2123152119.
mla: Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.”
Proceedings of the National Academy of Sciences, vol. 119, no. 36, e2123152119,
Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2123152119.
short: M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of
Sciences 119 (2022).
date_created: 2022-09-11T22:01:55Z
date_published: 2022-08-29T00:00:00Z
date_updated: 2025-06-30T13:21:05Z
day: '29'
ddc:
- '570'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1073/pnas.2123152119
ec_funded: 1
external_id:
isi:
- '000889278400014'
pmid:
- '36037343'
file:
- access_level: open_access
checksum: 6dec51f6567da9039982a571508a8e4d
content_type: application/pdf
creator: dernst
date_created: 2022-09-12T08:08:12Z
date_updated: 2022-09-12T08:08:12Z
file_id: '12091'
file_name: 2022_PNAS_Hledik.pdf
file_size: 2165752
relation: main_file
success: 1
file_date_updated: 2022-09-12T08:08:12Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '36'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 2665AAFE-B435-11E9-9278-68D0E5697425
grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '15020'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Accumulation and maintenance of information in evolution
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: 119
year: '2022'
...
---
_id: '12082'
abstract:
- lang: eng
text: Proximity-dependent protein labeling provides a powerful in vivo strategy
to characterize the interactomes of specific proteins. We previously optimized
a proximity labeling protocol for Caenorhabditis elegans using the highly active
biotin ligase TurboID. A significant constraint on the sensitivity of TurboID
is the presence of abundant endogenously biotinylated proteins that take up bandwidth
in the mass spectrometer, notably carboxylases that use biotin as a cofactor.
In C. elegans, these comprise POD-2/acetyl-CoA carboxylase alpha, PCCA-1/propionyl-CoA
carboxylase alpha, PYC-1/pyruvate carboxylase, and MCCC-1/methylcrotonyl-CoA carboxylase
alpha. Here, we developed ways to remove these carboxylases prior to streptavidin
purification and mass spectrometry by engineering their corresponding genes to
add a C-terminal His10 tag. This allows us to deplete them from C. elegans lysates
using immobilized metal affinity chromatography. To demonstrate the method's efficacy,
we use it to expand the interactome map of the presynaptic active zone protein
ELKS-1. We identify many known active zone proteins, including UNC-10/RIM, SYD-2/liprin-alpha,
SAD-1/BRSK1, CLA-1/CLArinet, C16E9.2/Sentryn, as well as previously uncharacterized
potentially synaptic proteins such as the ortholog of human angiomotin, F59C12.3
and the uncharacterized protein R148.3. Our approach provides a quick and inexpensive
solution to a common contaminant problem in biotin-dependent proximity labeling.
The approach may be applicable to other model organisms and will enable deeper
and more complete analysis of interactors for proteins of interest.
acknowledged_ssus:
- _id: Bio
acknowledgement: "We thank de Bono laboratory members for helpful comments on the
article and the Mass Spec Facilities at IST Austria and Max Perutz Labs for invaluable
discussions and comments on how to optimize mass spec analyses of worm samples.
We are grateful to Ekaterina Lashmanova for designing the degron knock-in constructs
and preparing the injection mixes for CRISPR/Cas9-mediated genome editing. All LC–MS/MS
analyses were performed on instruments of the Vienna BioCenter Core Facilities instrument
pool.\r\nThis work was supported by a Wellcome Investigator Award (grant no.: 209504/Z/17/Z
) to M.d.B. and an ISTplus Fellowship to M.A. (Marie Sklodowska-Curie agreement
no.: 754411)."
article_number: '102343'
article_processing_charge: No
article_type: original
author:
- first_name: Murat
full_name: Artan, Murat
id: C407B586-6052-11E9-B3AE-7006E6697425
last_name: Artan
- first_name: Markus
full_name: Hartl, Markus
last_name: Hartl
- first_name: Weiqiang
full_name: Chen, Weiqiang
last_name: Chen
- first_name: Mario
full_name: De Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: De Bono
orcid: 0000-0001-8347-0443
citation:
ama: Artan M, Hartl M, Chen W, de Bono M. Depletion of endogenously biotinylated
carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in
Caenorhabditis elegans. Journal of Biological Chemistry. 2022;298(9). doi:10.1016/j.jbc.2022.102343
apa: Artan, M., Hartl, M., Chen, W., & de Bono, M. (2022). Depletion of endogenously
biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity
labeling in Caenorhabditis elegans. Journal of Biological Chemistry. Elsevier.
https://doi.org/10.1016/j.jbc.2022.102343
chicago: Artan, Murat, Markus Hartl, Weiqiang Chen, and Mario de Bono. “Depletion
of Endogenously Biotinylated Carboxylases Enhances the Sensitivity of TurboID-Mediated
Proximity Labeling in Caenorhabditis Elegans.” Journal of Biological Chemistry.
Elsevier, 2022. https://doi.org/10.1016/j.jbc.2022.102343.
ieee: M. Artan, M. Hartl, W. Chen, and M. de Bono, “Depletion of endogenously biotinylated
carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in
Caenorhabditis elegans,” Journal of Biological Chemistry, vol. 298, no.
9. Elsevier, 2022.
ista: Artan M, Hartl M, Chen W, de Bono M. 2022. Depletion of endogenously biotinylated
carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in
Caenorhabditis elegans. Journal of Biological Chemistry. 298(9), 102343.
mla: Artan, Murat, et al. “Depletion of Endogenously Biotinylated Carboxylases Enhances
the Sensitivity of TurboID-Mediated Proximity Labeling in Caenorhabditis Elegans.”
Journal of Biological Chemistry, vol. 298, no. 9, 102343, Elsevier, 2022,
doi:10.1016/j.jbc.2022.102343.
short: M. Artan, M. Hartl, W. Chen, M. de Bono, Journal of Biological Chemistry
298 (2022).
date_created: 2022-09-11T22:01:55Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2023-08-03T13:56:46Z
day: '01'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.1016/j.jbc.2022.102343
ec_funded: 1
external_id:
isi:
- '000884241800011'
pmid:
- '35933017'
file:
- access_level: open_access
checksum: e726c7b9315230e6710e0b1f1d1677e9
content_type: application/pdf
creator: dernst
date_created: 2022-09-12T08:14:50Z
date_updated: 2022-09-12T08:14:50Z
file_id: '12092'
file_name: 2022_JBC_Artan.pdf
file_size: 2101656
relation: main_file
success: 1
file_date_updated: 2022-09-12T08:14:50Z
has_accepted_license: '1'
intvolume: ' 298'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 23870BE8-32DE-11EA-91FC-C7463DDC885E
grant_number: 209504/A/17/Z
name: Molecular mechanisms of neural circuit function
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Biological Chemistry
publication_identifier:
eissn:
- 1083-351X
issn:
- 0021-9258
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Depletion of endogenously biotinylated carboxylases enhances the sensitivity
of TurboID-mediated proximity labeling in Caenorhabditis elegans
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: 298
year: '2022'
...