---
_id: '9647'
abstract:
- lang: eng
text: 'Gene expression is regulated by the set of transcription factors (TFs) that
bind to the promoter. The ensuing regulating function is often represented as
a combinational logic circuit, where output (gene expression) is determined by
current input values (promoter bound TFs) only. However, the simultaneous arrival
of TFs is a strong assumption, since transcription and translation of genes introduce
intrinsic time delays and there is no global synchronisation among the arrival
times of different molecular species at their targets. We present an experimentally
implementable genetic circuit with two inputs and one output, which in the presence
of small delays in input arrival, exhibits qualitatively distinct population-level
phenotypes, over timescales that are longer than typical cell doubling times.
From a dynamical systems point of view, these phenotypes represent long-lived
transients: although they converge to the same value eventually, they do so after
a very long time span. The key feature of this toy model genetic circuit is that,
despite having only two inputs and one output, it is regulated by twenty-three
distinct DNA-TF configurations, two of which are more stable than others (DNA
looped states), one promoting and another blocking the expression of the output
gene. Small delays in input arrival time result in a majority of cells in the
population quickly reaching the stable state associated with the first input,
while exiting of this stable state occurs at a slow timescale. In order to mechanistically
model the behaviour of this genetic circuit, we used a rule-based modelling language,
and implemented a grid-search to find parameter combinations giving rise to long-lived
transients. Our analysis shows that in the absence of feedback, there exist path-dependent
gene regulatory mechanisms based on the long timescale of transients. The behaviour
of this toy model circuit suggests that gene regulatory networks can exploit event
timing to create phenotypes, and it opens the possibility that they could use
event timing to memorise events, without regulatory feedback. The model reveals
the importance of (i) mechanistically modelling the transitions between the different
DNA-TF states, and (ii) employing transient analysis thereof.'
acknowledgement: 'Tatjana Petrov’s research was supported in part by SNSF Advanced
Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science,
Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence
2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia
Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences.
Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund
(FWF) under grant Z211-N23 (Wittgenstein Award).'
article_processing_charge: No
article_type: original
author:
- first_name: Tatjana
full_name: Petrov, Tatjana
last_name: Petrov
- first_name: Claudia
full_name: Igler, Claudia
id: 46613666-F248-11E8-B48F-1D18A9856A87
last_name: Igler
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in
gene regulation. Theoretical Computer Science. 2021;893:1-16. doi:10.1016/j.tcs.2021.05.023
apa: Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., & Guet, C. C. (2021).
Long lived transients in gene regulation. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2021.05.023
chicago: Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin
C Guet. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science.
Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.05.023.
ieee: T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived
transients in gene regulation,” Theoretical Computer Science, vol. 893.
Elsevier, pp. 1–16, 2021.
ista: Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients
in gene regulation. Theoretical Computer Science. 893, 1–16.
mla: Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” Theoretical
Computer Science, vol. 893, Elsevier, 2021, pp. 1–16, doi:10.1016/j.tcs.2021.05.023.
short: T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer
Science 893 (2021) 1–16.
date_created: 2021-07-11T22:01:18Z
date_published: 2021-06-04T00:00:00Z
date_updated: 2023-08-10T14:11:19Z
day: '04'
ddc:
- '004'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1016/j.tcs.2021.05.023
external_id:
isi:
- '000710180500002'
file:
- access_level: open_access
checksum: d3aef34cfb13e53bba4cf44d01680793
content_type: application/pdf
creator: dernst
date_created: 2022-05-12T12:13:27Z
date_updated: 2022-05-12T12:13:27Z
file_id: '11364'
file_name: 2021_TheoreticalComputerScience_Petrov.pdf
file_size: 2566504
relation: main_file
success: 1
file_date_updated: 2022-05-12T12:13:27Z
has_accepted_license: '1'
intvolume: ' 893'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1-16
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long lived transients in gene regulation
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: 893
year: '2021'
...
---
_id: '9761'
abstract:
- lang: eng
text: 'The important roles of mitochondrial function and dysfunction in the process
of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear
to be a highly vulnerable neuronal cell type in the central nervous system with
respect to mitochondrial dysfunction but the actual reasons for this are still
incompletely understood. These cells have a unique circumstance where unmyelinated
axons must bend nearly 90° to exit the eye and then cross a translaminar pressure
gradient before becoming myelinated in the optic nerve. This region, the optic
nerve head, contains some of the highest density of mitochondria present in these
cells. Glaucoma represents a perfect storm of events occurring at this location,
with a combination of changes in the translaminar pressure gradient and reassignment
of the metabolic support functions of supporting glia, which appears to apply
increased metabolic stress to the RGC axons leading to a failure of axonal transport
mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations,
particularly in genes affecting mitochondrial dynamics and mitochondrial clearance.
These mutations, which systemically affect the mitochondria in every cell, often
lead to an optic neuropathy as the sole pathologic defect in affected patients.
This review summarizes knowledge of mitochondrial structure and function, the
known energy demands of neurons in general, and places these in the context of
normal and pathological characteristics of mitochondria attributed to RGCs. '
acknowledgement: The authors are grateful to Kazuya Oikawa and Gillian McLellan for
generously sharing some of their data for this review, and to Janis Eells for helpful
comments on the manuscript.
article_number: '1593'
article_processing_charge: Yes
article_type: original
author:
- first_name: Nicole A.
full_name: Muench, Nicole A.
last_name: Muench
- first_name: Sonia
full_name: Patel, Sonia
last_name: Patel
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Ryan J.
full_name: Donahue, Ryan J.
last_name: Donahue
- first_name: Akihiro
full_name: Ikeda, Akihiro
last_name: Ikeda
- first_name: Robert W.
full_name: Nickells, Robert W.
last_name: Nickells
citation:
ama: Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence
of mitochondrial dynamics and function on retinal ganglion cell susceptibility
in optic nerve disease. Cells. 2021;10(7). doi:10.3390/cells10071593
apa: Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., & Nickells,
R. W. (2021). The influence of mitochondrial dynamics and function on retinal
ganglion cell susceptibility in optic nerve disease. Cells. MDPI. https://doi.org/10.3390/cells10071593
chicago: Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro
Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function
on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells.
MDPI, 2021. https://doi.org/10.3390/cells10071593.
ieee: N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells,
“The influence of mitochondrial dynamics and function on retinal ganglion cell
susceptibility in optic nerve disease,” Cells, vol. 10, no. 7. MDPI, 2021.
ista: Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence
of mitochondrial dynamics and function on retinal ganglion cell susceptibility
in optic nerve disease. Cells. 10(7), 1593.
mla: Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function
on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells,
vol. 10, no. 7, 1593, MDPI, 2021, doi:10.3390/cells10071593.
short: N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells,
Cells 10 (2021).
date_created: 2021-08-01T22:01:22Z
date_published: 2021-06-25T00:00:00Z
date_updated: 2023-08-10T14:14:53Z
day: '25'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.3390/cells10071593
external_id:
isi:
- '000678193300001'
pmid:
- '34201955'
file:
- access_level: open_access
checksum: e0497ce5c77fa3b65a538c7d6e0f6c66
content_type: application/pdf
creator: cziletti
date_created: 2021-08-04T14:01:30Z
date_updated: 2021-08-04T14:01:30Z
file_id: '9768'
file_name: 2021_Cells_Muench.pdf
file_size: 4555611
relation: main_file
success: 1
file_date_updated: 2021-08-04T14:01:30Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '7'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cells
publication_identifier:
eissn:
- '20734409'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: The influence of mitochondrial dynamics and function on retinal ganglion cell
susceptibility in optic nerve disease
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '9641'
abstract:
- lang: eng
text: At the encounter with a novel environment, contextual memory formation is
greatly enhanced, accompanied with increased arousal and active exploration. Although
this phenomenon has been widely observed in animal and human daily life, how the
novelty in the environment is detected and contributes to contextual memory formation
has lately started to be unveiled. The hippocampus has been studied for many decades
for its largely known roles in encoding spatial memory, and a growing body of
evidence indicates a differential involvement of dorsal and ventral hippocampal
divisions in novelty detection. In this brief review article, we discuss the recent
findings of the role of mossy cells in the ventral hippocampal moiety in novelty
detection and put them in perspective with other novelty-related pathways in the
hippocampus. We propose a mechanism for novelty-driven memory acquisition in the
dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate
granule cells. By this projection, the ventral hippocampus sends novelty signals
to the dorsal hippocampus, opening a gate for memory encoding in dentate granule
cells based on information coming from the entorhinal cortex. We conclude that,
contrary to the presently accepted functional independence, the dorsal and ventral
hippocampi cooperate to link the novelty and contextual information, and this
dorso-ventral interaction is crucial for the novelty-dependent memory formation.
acknowledgement: This work was supported by a European Research Council Advanced Grant
694539 to Ryuichi Shigemoto.
article_number: '107486'
article_processing_charge: No
article_type: original
author:
- first_name: Felipe
full_name: Fredes, Felipe
last_name: Fredes
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Fredes F, Shigemoto R. The role of hippocampal mossy cells in novelty detection.
Neurobiology of Learning and Memory. 2021;183. doi:10.1016/j.nlm.2021.107486
apa: Fredes, F., & Shigemoto, R. (2021). The role of hippocampal mossy cells
in novelty detection. Neurobiology of Learning and Memory. Elsevier. https://doi.org/10.1016/j.nlm.2021.107486
chicago: Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells
in Novelty Detection.” Neurobiology of Learning and Memory. Elsevier, 2021.
https://doi.org/10.1016/j.nlm.2021.107486.
ieee: F. Fredes and R. Shigemoto, “The role of hippocampal mossy cells in novelty
detection,” Neurobiology of Learning and Memory, vol. 183. Elsevier, 2021.
ista: Fredes F, Shigemoto R. 2021. The role of hippocampal mossy cells in novelty
detection. Neurobiology of Learning and Memory. 183, 107486.
mla: Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells
in Novelty Detection.” Neurobiology of Learning and Memory, vol. 183, 107486,
Elsevier, 2021, doi:10.1016/j.nlm.2021.107486.
short: F. Fredes, R. Shigemoto, Neurobiology of Learning and Memory 183 (2021).
date_created: 2021-07-11T22:01:16Z
date_published: 2021-06-30T00:00:00Z
date_updated: 2023-08-10T14:10:37Z
day: '30'
ddc:
- '610'
department:
- _id: RySh
doi: 10.1016/j.nlm.2021.107486
ec_funded: 1
external_id:
isi:
- '000677694900004'
pmid:
- '34214666'
file:
- access_level: open_access
checksum: 8e8298a9e8c7df146ad23f32c2a63929
content_type: application/pdf
creator: cziletti
date_created: 2021-07-19T13:46:06Z
date_updated: 2021-07-19T13:46:06Z
file_id: '9694'
file_name: 2021_NeurobLearnMemory_Fredes.pdf
file_size: 1994793
relation: main_file
success: 1
file_date_updated: 2021-07-19T13:46:06Z
has_accepted_license: '1'
intvolume: ' 183'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
publication: Neurobiology of Learning and Memory
publication_identifier:
eissn:
- '10959564'
issn:
- '10747427'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The role of hippocampal mossy cells in novelty detection
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: 183
year: '2021'
...
---
_id: '9646'
abstract:
- lang: eng
text: We consider the fundamental problem of deriving quantitative bounds on the
probability that a given assertion is violated in a probabilistic program. We
provide automated algorithms that obtain both lower and upper bounds on the assertion
violation probability. The main novelty of our approach is that we prove new and
dedicated fixed-point theorems which serve as the theoretical basis of our algorithms
and enable us to reason about assertion violation bounds in terms of pre and post
fixed-point functions. To synthesize such fixed-points, we devise algorithms that
utilize a wide range of mathematical tools, including repulsing ranking supermartingales,
Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization.
On the theoretical side, we provide (i) the first automated algorithm for lower-bounds
on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds
of exponential form in affine programs, and (iii) provably and significantly tighter
upper-bounds than the previous approaches. On the practical side, we show our
algorithms can handle a wide variety of programs from the literature and synthesize
bounds that are remarkably tighter than previous results, in some cases by thousands
of orders of magnitude.
acknowledgement: 'We are very thankful to the anonymous reviewers for the helpful
and valuable comments. The work was partially supported by the National Natural
Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research
Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and
DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW).'
article_processing_charge: No
author:
- first_name: Jinyi
full_name: Wang, Jinyi
last_name: Wang
- first_name: Yican
full_name: Sun, Yican
last_name: Sun
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: 'Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of
assertion violations in probabilistic programs. In: Proceedings of the 42nd
ACM SIGPLAN International Conference on Programming Language Design and Implementation.
Association for Computing Machinery; 2021:1171-1186. doi:10.1145/3453483.3454102'
apa: 'Wang, J., Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2021).
Quantitative analysis of assertion violations in probabilistic programs. In Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation (pp. 1171–1186). Online: Association for Computing Machinery.
https://doi.org/10.1145/3453483.3454102'
chicago: Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar
Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.”
In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, 1171–86. Association for Computing Machinery,
2021. https://doi.org/10.1145/3453483.3454102.
ieee: J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative
analysis of assertion violations in probabilistic programs,” in Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Online, 2021, pp. 1171–1186.
ista: 'Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis
of assertion violations in probabilistic programs. Proceedings of the 42nd ACM
SIGPLAN International Conference on Programming Language Design and Implementation.
PLDI: Programming Language Design and Implementation, 1171–1186.'
mla: Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic
Programs.” Proceedings of the 42nd ACM SIGPLAN International Conference on
Programming Language Design and Implementation, Association for Computing
Machinery, 2021, pp. 1171–86, doi:10.1145/3453483.3454102.
short: J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186.
conference:
end_date: 2021-06-26
location: Online
name: 'PLDI: Programming Language Design and Implementation'
start_date: 2021-06-20
date_created: 2021-07-11T22:01:18Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-10T14:14:08Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3453483.3454102
ec_funded: 1
external_id:
arxiv:
- '2011.14617'
isi:
- '000723661700076'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2011.14617
month: '06'
oa: 1
oa_version: Preprint
page: 1171-1186
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450383912'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantitative analysis of assertion violations in probabilistic programs
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9645'
abstract:
- lang: eng
text: "We consider the fundamental problem of reachability analysis over imperative
programs with real variables. Previous works that tackle reachability are either
unable to handle programs consisting of general loops (e.g. symbolic execution),
or lack completeness guarantees (e.g. abstract interpretation), or are not automated
(e.g. incorrectness logic). In contrast, we propose a novel approach for reachability
analysis that can handle general and complex loops, is complete, and can be entirely
automated for a wide family of programs. Through the notion of Inductive Reachability
Witnesses (IRWs), our approach extends ideas from both invariant generation and
termination to reachability analysis.\r\n\r\nWe first show that our IRW-based
approach is sound and complete for reachability analysis of imperative programs.
Then, we focus on linear and polynomial programs and develop automated methods
for synthesizing linear and polynomial IRWs. In the linear case, we follow the
well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial
case, where we present a push-button semi-complete algorithm. We achieve this
using a novel combination of classical theorems in real algebraic geometry, such
as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally,
our experimental results show we can prove complex reachability objectives over
various benchmarks that were beyond the reach of previous methods."
acknowledgement: This research was partially supported by the ERC CoG 863818 (ForM-SMArt),
the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the
Huawei Innovation Research Program, the Facebook PhD Fellowship Program, and DOC
Fellowship No. 24956 of the Austrian Academy of Sciences (ÖAW).
article_processing_charge: No
author:
- first_name: Ali
full_name: Asadi, Ali
last_name: Asadi
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Mohammad
full_name: Mahdavi, Mohammad
last_name: Mahdavi
citation:
ama: 'Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability
witnesses via Stellensätze. In: Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation. Association
for Computing Machinery; 2021:772-787. doi:10.1145/3453483.3454076'
apa: 'Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., & Mahdavi, M. (2021).
Polynomial reachability witnesses via Stellensätze. In Proceedings of the 42nd
ACM SIGPLAN International Conference on Programming Language Design and Implementation
(pp. 772–787). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454076'
chicago: Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady,
and Mohammad Mahdavi. “Polynomial Reachability Witnesses via Stellensätze.” In
Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, 772–87. Association for Computing Machinery,
2021. https://doi.org/10.1145/3453483.3454076.
ieee: A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial
reachability witnesses via Stellensätze,” in Proceedings of the 42nd ACM SIGPLAN
International Conference on Programming Language Design and Implementation,
Online, 2021, pp. 772–787.
ista: 'Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability
witnesses via Stellensätze. Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation. PLDI: Programming
Language Design and Implementation, 772–787.'
mla: Asadi, Ali, et al. “Polynomial Reachability Witnesses via Stellensätze.” Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 772–87,
doi:10.1145/3453483.3454076.
short: A. Asadi, K. Chatterjee, H. Fu, A.K. Goharshady, M. Mahdavi, in:, Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 772–787.
conference:
end_date: 2021-06-26
location: Online
name: ' PLDI: Programming Language Design and Implementation'
start_date: 2021-06-20
date_created: 2021-07-11T22:01:17Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-10T14:13:39Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3453483.3454076
ec_funded: 1
external_id:
isi:
- '000723661700050'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-03183862/
month: '06'
oa: 1
oa_version: Submitted Version
page: 772-787
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450383912'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Polynomial reachability witnesses via Stellensätze
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9759'
acknowledgement: The authors thank Inez Lam of Johns Hopkins University for valuable
comments on an earlier version of the manuscript. We also thank the facilitators
of the 2019–2020 eLife Community Ambassador program.
article_number: e1009124
article_processing_charge: Yes
article_type: letter_note
author:
- first_name: Michael John
full_name: Bartlett, Michael John
last_name: Bartlett
- first_name: Feyza N
full_name: Arslan, Feyza N
id: 49DA7910-F248-11E8-B48F-1D18A9856A87
last_name: Arslan
orcid: 0000-0001-5809-9566
- first_name: Adriana
full_name: Bankston, Adriana
last_name: Bankston
- first_name: Sarvenaz
full_name: Sarabipour, Sarvenaz
last_name: Sarabipour
citation:
ama: Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve
academic work- life balance. PLoS Computational Biology. 2021;17(7). doi:10.1371/journal.pcbi.1009124
apa: Bartlett, M. J., Arslan, F. N., Bankston, A., & Sarabipour, S. (2021).
Ten simple rules to improve academic work- life balance. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009124
chicago: Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz
Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS
Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009124.
ieee: M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple
rules to improve academic work- life balance,” PLoS Computational Biology,
vol. 17, no. 7. Public Library of Science, 2021.
ista: Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to
improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124.
mla: Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work-
Life Balance.” PLoS Computational Biology, vol. 17, no. 7, e1009124, Public
Library of Science, 2021, doi:10.1371/journal.pcbi.1009124.
short: M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational
Biology 17 (2021).
date_created: 2021-08-01T22:01:21Z
date_published: 2021-07-15T00:00:00Z
date_updated: 2023-08-10T14:16:46Z
day: '15'
ddc:
- '613'
department:
- _id: CaHe
doi: 10.1371/journal.pcbi.1009124
external_id:
isi:
- '000677713500008'
pmid:
- '34264932'
file:
- access_level: open_access
checksum: e56d91f0eeadb36f143a90e2c1b3ab63
content_type: application/pdf
creator: cchlebak
date_created: 2021-08-05T12:06:49Z
date_updated: 2021-08-05T12:06:49Z
file_id: '9771'
file_name: 2021_PlosCompBio_Bartlett.pdf
file_size: 693633
relation: main_file
file_date_updated: 2021-08-05T12:06:49Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Computational Biology
publication_identifier:
eissn:
- '15537358'
issn:
- 1553734X
publication_status: published
publisher: Public Library of Science
scopus_import: '1'
status: public
title: Ten simple rules to improve academic work- life balance
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2021'
...
---
_id: '9822'
abstract:
- lang: eng
text: Attachment of adhesive molecules on cell culture surfaces to restrict cell
adhesion to defined areas and shapes has been vital for the progress of in vitro
research. In currently existing patterning methods, a combination of pattern properties
such as stability, precision, specificity, high-throughput outcome, and spatiotemporal
control is highly desirable but challenging to achieve. Here, we introduce a versatile
and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent
patterning step and a subsequent functionalization of the pattern via click chemistry.
This two-step process is feasible on arbitrary surfaces and allows for generation
of sustainable patterns and gradients. The method is validated in different biological
systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining
the growth and migration of cells to the designated areas. We then implement a
sequential photopatterning approach by adding a second switchable patterning step,
allowing for spatiotemporal control over two distinct surface patterns. As a proof
of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis.
Our results show that the spatiotemporal control provided by our “sequential photopatterning”
system is essential for mimicking dynamic biological processes and that our innovative
approach has great potential for further applications in cell science.
acknowledgement: We would like to thank Charlott Leu for the production of our chromium
wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh
Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim
Rädler for his valuable scientific guidance.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Themistoklis
full_name: Zisis, Themistoklis
last_name: Zisis
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Miriam
full_name: Balles, Miriam
last_name: Balles
- first_name: Maibritt
full_name: Kretschmer, Maibritt
last_name: Kretschmer
- first_name: Maria
full_name: Nemethova, Maria
id: 34E27F1C-F248-11E8-B48F-1D18A9856A87
last_name: Nemethova
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Janina
full_name: Lange, Janina
last_name: Lange
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-4561-241X
- first_name: Stefan
full_name: Zahler, Stefan
last_name: Zahler
citation:
ama: Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for
studying cellular processes under spatiotemporal control. ACS Applied Materials
and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850
apa: Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R.
P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular
processes under spatiotemporal control. ACS Applied Materials and Interfaces.
American Chemical Society. https://doi.org/10.1021/acsami.1c09850
chicago: Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria
Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning
for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied
Materials and Interfaces. American Chemical Society, 2021. https://doi.org/10.1021/acsami.1c09850.
ieee: T. Zisis et al., “Sequential and switchable patterning for studying
cellular processes under spatiotemporal control,” ACS Applied Materials and
Interfaces, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.
ista: Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild
R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning
for studying cellular processes under spatiotemporal control. ACS Applied Materials
and Interfaces. 13(30), 35545–35560.
mla: Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying
Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and
Interfaces, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560,
doi:10.1021/acsami.1c09850.
short: T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait,
R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials
and Interfaces 13 (2021) 35545–35560.
date_created: 2021-08-08T22:01:28Z
date_published: 2021-08-04T00:00:00Z
date_updated: 2023-08-10T14:22:48Z
day: '04'
ddc:
- '620'
- '570'
department:
- _id: MiSi
- _id: GaTk
- _id: Bio
- _id: CaGu
doi: 10.1021/acsami.1c09850
ec_funded: 1
external_id:
isi:
- '000683741400026'
pmid:
- '34283577'
file:
- access_level: open_access
checksum: b043a91d9f9200e467b970b692687ed3
content_type: application/pdf
creator: asandaue
date_created: 2021-08-09T09:44:03Z
date_updated: 2021-08-09T09:44:03Z
file_id: '9833'
file_name: 2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf
file_size: 7123293
relation: main_file
success: 1
file_date_updated: 2021-08-09T09:44:03Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '30'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 35545–35560
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
publication: ACS Applied Materials and Interfaces
publication_identifier:
eissn:
- '19448252'
issn:
- '19448244'
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sequential and switchable patterning for studying cellular processes under
spatiotemporal control
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: 13
year: '2021'
...
---
_id: '9819'
abstract:
- lang: eng
text: Photorealistic editing of head portraits is a challenging task as humans are
very sensitive to inconsistencies in faces. We present an approach for high-quality
intuitive editing of the camera viewpoint and scene illumination (parameterised
with an environment map) in a portrait image. This requires our method to capture
and control the full reflectance field of the person in the image. Most editing
approaches rely on supervised learning using training data captured with setups
such as light and camera stages. Such datasets are expensive to acquire, not readily
available and do not capture all the rich variations of in-the-wild portrait images.
In addition, most supervised approaches only focus on relighting, and do not allow
camera viewpoint editing. Thus, they only capture and control a subset of the
reflectance field. Recently, portrait editing has been demonstrated by operating
in the generative model space of StyleGAN. While such approaches do not require
direct supervision, there is a significant loss of quality when compared to the
supervised approaches. In this paper, we present a method which learns from limited
supervised training data. The training images only include people in a fixed neutral
expression with eyes closed, without much hair or background variations. Each
person is captured under 150 one-light-at-a-time conditions and under 8 camera
poses. Instead of training directly in the image space, we design a supervised
problem which learns transformations in the latent space of StyleGAN. This combines
the best of supervised learning and generative adversarial modeling. We show that
the StyleGAN prior allows for generalisation to different expressions, hairstyles
and backgrounds. This produces high-quality photorealistic results for in-the-wild
images and significantly outperforms existing methods. Our approach can edit the
illumination and pose simultaneously, and runs at interactive rates.
acknowledgement: This work was supported by the ERC Consolidator Grant 4DReply (770784).
We also acknowledge support from Technicolor and InterDigital. We thank Tiancheng
Sun for kindly helping us with the comparisons with Sun et al. [2019].
article_number: '44'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: B. R.
full_name: Mallikarjun, B. R.
last_name: Mallikarjun
- first_name: Ayush
full_name: Tewari, Ayush
last_name: Tewari
- first_name: Abdallah
full_name: Dib, Abdallah
last_name: Dib
- first_name: Tim
full_name: Weyrich, Tim
last_name: Weyrich
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Hans Peter
full_name: Seidel, Hans Peter
last_name: Seidel
- first_name: Hanspeter
full_name: Pfister, Hanspeter
last_name: Pfister
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
- first_name: Louis
full_name: Chevallier, Louis
last_name: Chevallier
- first_name: Mohamed A.
full_name: Elgharib, Mohamed A.
last_name: Elgharib
- first_name: Christian
full_name: Theobalt, Christian
last_name: Theobalt
citation:
ama: 'Mallikarjun BR, Tewari A, Dib A, et al. PhotoApp: Photorealistic appearance
editing of head portraits. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459765'
apa: 'Mallikarjun, B. R., Tewari, A., Dib, A., Weyrich, T., Bickel, B., Seidel,
H. P., … Theobalt, C. (2021). PhotoApp: Photorealistic appearance editing of head
portraits. ACM Transactions on Graphics. Association for Computing Machinery.
https://doi.org/10.1145/3450626.3459765'
chicago: 'Mallikarjun, B. R., Ayush Tewari, Abdallah Dib, Tim Weyrich, Bernd Bickel,
Hans Peter Seidel, Hanspeter Pfister, et al. “PhotoApp: Photorealistic Appearance
Editing of Head Portraits.” ACM Transactions on Graphics. Association for
Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459765.'
ieee: 'B. R. Mallikarjun et al., “PhotoApp: Photorealistic appearance editing
of head portraits,” ACM Transactions on Graphics, vol. 40, no. 4. Association
for Computing Machinery, 2021.'
ista: 'Mallikarjun BR, Tewari A, Dib A, Weyrich T, Bickel B, Seidel HP, Pfister
H, Matusik W, Chevallier L, Elgharib MA, Theobalt C. 2021. PhotoApp: Photorealistic
appearance editing of head portraits. ACM Transactions on Graphics. 40(4), 44.'
mla: 'Mallikarjun, B. R., et al. “PhotoApp: Photorealistic Appearance Editing of
Head Portraits.” ACM Transactions on Graphics, vol. 40, no. 4, 44, Association
for Computing Machinery, 2021, doi:10.1145/3450626.3459765.'
short: B.R. Mallikarjun, A. Tewari, A. Dib, T. Weyrich, B. Bickel, H.P. Seidel,
H. Pfister, W. Matusik, L. Chevallier, M.A. Elgharib, C. Theobalt, ACM Transactions
on Graphics 40 (2021).
date_created: 2021-08-08T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-10T14:25:08Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3450626.3459765
external_id:
arxiv:
- '2103.07658'
isi:
- '000674930900011'
file:
- access_level: open_access
checksum: 51b61b7e5c175e2d7ed8fa3b35f7525a
content_type: application/pdf
creator: asandaue
date_created: 2021-08-09T11:41:50Z
date_updated: 2021-08-09T11:41:50Z
file_id: '9834'
file_name: 2021_ACMTransactionsOnGraphics_Mallikarjun.pdf
file_size: 49840741
relation: main_file
success: 1
file_date_updated: 2021-08-09T11:41:50Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'PhotoApp: Photorealistic appearance editing of head portraits'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2021'
...
---
_id: '9816'
abstract:
- lang: eng
text: "Aims: Mass antigen testing programs have been challenged because of an alleged
insufficient specificity, leading to a large number of false positives. The objective
of this study is to derive a lower bound of the specificity of the SD Biosensor
Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data
from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020
we calculate a lower confidence bound for the specificity. As positive test results
were not systematically verified by PCR tests, we base the lower bound on a worst
case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332
persons from 79 counties were tested. The lowest positivity rate was observed
in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This
implies a test specificity of at least 99.6% (97.5% one-sided lower confidence
bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests
a higher specificity compared to earlier studies in spite of the underlying worst
case assumption and the application in a mass testing setting. The actual specificity
is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible
at the time of testing. To our knowledge, this estimate constitutes the first
bound obtained from large scale practical use of an antigen test."
acknowledgement: We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová
for very helpful comments. We also thank Matej Mišík for discussion and information
regarding the Slovak testing data and Ag-Test used.
article_number: e0255267
article_processing_charge: Yes
article_type: original
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: Mathias
full_name: Beiglböck, Mathias
last_name: Beiglböck
- first_name: Anna Nele
full_name: Herdina, Anna Nele
last_name: Herdina
- first_name: Robert
full_name: Strassl, Robert
last_name: Strassl
- first_name: Martin
full_name: Posch, Martin
last_name: Posch
citation:
ama: Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis
of the specificity of a COVID-19 antigen test in the Slovak mass testing program.
PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0255267
apa: Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., &
Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the
Slovak mass testing program. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0255267
chicago: Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina,
Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen
Test in the Slovak Mass Testing Program.” PLoS ONE. Public Library of Science,
2021. https://doi.org/10.1371/journal.pone.0255267.
ieee: M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch,
“Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing
program,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021.
ista: Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021.
Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing
program. PLoS ONE. 16(7), e0255267.
mla: Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test
in the Slovak Mass Testing Program.” PLoS ONE, vol. 16, no. 7, e0255267,
Public Library of Science, 2021, doi:10.1371/journal.pone.0255267.
short: M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch,
PLoS ONE 16 (2021).
date_created: 2021-08-08T22:01:26Z
date_published: 2021-07-29T00:00:00Z
date_updated: 2023-08-10T14:26:32Z
day: '29'
ddc:
- '610'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0255267
external_id:
isi:
- '000685248200095'
pmid:
- '34324553'
file:
- access_level: open_access
checksum: ae4df60eb62f4491278588548d0c1f93
content_type: application/pdf
creator: asandaue
date_created: 2021-08-09T11:52:14Z
date_updated: 2021-08-09T11:52:14Z
file_id: '9835'
file_name: 2021_PLoSONE_Hledík.pdf
file_size: 773921
relation: main_file
success: 1
file_date_updated: 2021-08-09T11:52:14Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS ONE
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing
program
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: 16
year: '2021'
...
---
_id: '9821'
abstract:
- lang: eng
text: Heart rate variability (hrv) is a physiological phenomenon of the variation
in the length of the time interval between consecutive heartbeats. In many cases
it could be an indicator of the development of pathological states. The classical
approach to the analysis of hrv includes time domain methods and frequency domain
methods. However, attempts are still being made to define new and more effective
hrv assessment tools. Persistent homology is a novel data analysis tool developed
in the recent decades that is rooted at algebraic topology. The Topological Data
Analysis (TDA) approach focuses on examining the shape of the data in terms of
connectedness and holes, and has recently proved to be very effective in various
fields of research. In this paper we propose the use of persistent homology to
the hrv analysis. We recall selected topological descriptors used in the literature
and we introduce some new topological descriptors that reflect the specificity
of hrv, and we discuss their relation to the standard hrv measures. In particular,
we show that this novel approach provides a collection of indices that might be
at least as useful as the classical parameters in differentiating between series
of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering
from a stroke episode.
acknowledgement: We express our gratitude to the anonymous referees who provided constructive
comments that helped us improve the quality of the paper.
article_number: e0253851
article_processing_charge: Yes
article_type: original
author:
- first_name: Grzegorz
full_name: Graff, Grzegorz
last_name: Graff
- first_name: Beata
full_name: Graff, Beata
last_name: Graff
- first_name: Pawel
full_name: Pilarczyk, Pawel
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
- first_name: Grzegorz
full_name: Jablonski, Grzegorz
id: 4483EF78-F248-11E8-B48F-1D18A9856A87
last_name: Jablonski
orcid: 0000-0002-3536-9866
- first_name: Dariusz
full_name: Gąsecki, Dariusz
last_name: Gąsecki
- first_name: Krzysztof
full_name: Narkiewicz, Krzysztof
last_name: Narkiewicz
citation:
ama: Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. Persistent
homology as a new method of the assessment of heart rate variability. PLoS
ONE. 2021;16(7). doi:10.1371/journal.pone.0253851
apa: Graff, G., Graff, B., Pilarczyk, P., Jablonski, G., Gąsecki, D., & Narkiewicz,
K. (2021). Persistent homology as a new method of the assessment of heart rate
variability. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0253851
chicago: Graff, Grzegorz, Beata Graff, Pawel Pilarczyk, Grzegorz Jablonski, Dariusz
Gąsecki, and Krzysztof Narkiewicz. “Persistent Homology as a New Method of the
Assessment of Heart Rate Variability.” PLoS ONE. Public Library of Science,
2021. https://doi.org/10.1371/journal.pone.0253851.
ieee: G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, and K. Narkiewicz,
“Persistent homology as a new method of the assessment of heart rate variability,”
PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021.
ista: Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. 2021.
Persistent homology as a new method of the assessment of heart rate variability.
PLoS ONE. 16(7), e0253851.
mla: Graff, Grzegorz, et al. “Persistent Homology as a New Method of the Assessment
of Heart Rate Variability.” PLoS ONE, vol. 16, no. 7, e0253851, Public
Library of Science, 2021, doi:10.1371/journal.pone.0253851.
short: G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz,
PLoS ONE 16 (2021).
date_created: 2021-08-08T22:01:28Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-10T14:21:42Z
day: '01'
ddc:
- '006'
department:
- _id: HeEd
doi: 10.1371/journal.pone.0253851
external_id:
isi:
- '000678124900050'
pmid:
- '34292957'
file:
- access_level: open_access
checksum: 0277aa155d5db1febd2cb384768bba5f
content_type: application/pdf
creator: asandaue
date_created: 2021-08-09T09:25:41Z
date_updated: 2021-08-09T09:25:41Z
file_id: '9832'
file_name: 2021_PLoSONE_Graff.pdf
file_size: 2706919
relation: main_file
success: 1
file_date_updated: 2021-08-09T09:25:41Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS ONE
publication_identifier:
eissn:
- '19326203'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Persistent homology as a new method of the assessment of heart rate variability
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: 16
year: '2021'
...
---
_id: '9820'
abstract:
- lang: eng
text: Material appearance hinges on material reflectance properties but also surface
geometry and illumination. The unlimited number of potential combinations between
these factors makes understanding and predicting material appearance a very challenging
task. In this work, we collect a large-scale dataset of perceptual ratings of
appearance attributes with more than 215,680 responses for 42,120 distinct combinations
of material, shape, and illumination. The goal of this dataset is twofold. First,
we analyze for the first time the effects of illumination and geometry in material
perception across such a large collection of varied appearances. We connect our
findings to those of the literature, discussing how previous knowledge generalizes
across very diverse materials, shapes, and illuminations. Second, we use the collected
dataset to train a deep learning architecture for predicting perceptual attributes
that correlate with human judgments. We demonstrate the consistent and robust
behavior of our predictor in various challenging scenarios, which, for the first
time, enables estimating perceived material attributes from general 2D images.
Since our predictor relies on the final appearance in an image, it can compare
appearance properties across different geometries and illumination conditions.
Finally, we demonstrate several applications that use our predictor, including
appearance reproduction using 3D printing, BRDF editing by integrating our predictor
in a differentiable renderer, illumination design, or material recommendations
for scene design.
acknowledgement: This project has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie, grant agreement
Nº 765911 (RealVision) and from the European Research Council (ERC), grant agreement
Nº 804226 (PERDY).
article_number: '125'
article_processing_charge: No
article_type: original
author:
- first_name: Ana
full_name: Serrano, Ana
last_name: Serrano
- first_name: Bin
full_name: Chen, Bin
last_name: Chen
- first_name: Chao
full_name: Wang, Chao
last_name: Wang
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
orcid: 0000-0002-5062-4474
- first_name: Hans Peter
full_name: Seidel, Hans Peter
last_name: Seidel
- first_name: Piotr
full_name: Didyk, Piotr
last_name: Didyk
- first_name: Karol
full_name: Myszkowski, Karol
last_name: Myszkowski
citation:
ama: 'Serrano A, Chen B, Wang C, et al. The effect of shape and illumination on
material perception: Model and applications. ACM Transactions on Graphics.
2021;40(4). doi:10.1145/3450626.3459813'
apa: 'Serrano, A., Chen, B., Wang, C., Piovarci, M., Seidel, H. P., Didyk, P., &
Myszkowski, K. (2021). The effect of shape and illumination on material perception:
Model and applications. ACM Transactions on Graphics. Association for Computing
Machinery. https://doi.org/10.1145/3450626.3459813'
chicago: 'Serrano, Ana, Bin Chen, Chao Wang, Michael Piovarci, Hans Peter Seidel,
Piotr Didyk, and Karol Myszkowski. “The Effect of Shape and Illumination on Material
Perception: Model and Applications.” ACM Transactions on Graphics. Association
for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459813.'
ieee: 'A. Serrano et al., “The effect of shape and illumination on material
perception: Model and applications,” ACM Transactions on Graphics, vol.
40, no. 4. Association for Computing Machinery, 2021.'
ista: 'Serrano A, Chen B, Wang C, Piovarci M, Seidel HP, Didyk P, Myszkowski K.
2021. The effect of shape and illumination on material perception: Model and applications.
ACM Transactions on Graphics. 40(4), 125.'
mla: 'Serrano, Ana, et al. “The Effect of Shape and Illumination on Material Perception:
Model and Applications.” ACM Transactions on Graphics, vol. 40, no. 4,
125, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459813.'
short: A. Serrano, B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski,
ACM Transactions on Graphics 40 (2021).
date_created: 2021-08-08T22:01:28Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-10T14:20:10Z
day: '01'
department:
- _id: BeBi
doi: 10.1145/3450626.3459813
external_id:
isi:
- '000674930900090'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://zaguan.unizar.es/record/110704/files/texto_completo.pdf
month: '08'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The effect of shape and illumination on material perception: Model and applications'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2021'
...
---
_id: '9818'
abstract:
- lang: eng
text: Triangle mesh-based simulations are able to produce satisfying animations
of knitted and woven cloth; however, they lack the rich geometric detail of yarn-level
simulations. Naive texturing approaches do not consider yarn-level physics, while
full yarn-level simulations may become prohibitively expensive for large garments.
We propose a method to animate yarn-level cloth geometry on top of an underlying
deforming mesh in a mechanics-aware fashion. Using triangle strains to interpolate
precomputed yarn geometry, we are able to reproduce effects such as knit loops
tightening under stretching. In combination with precomputed mesh animation or
real-time mesh simulation, our method is able to animate yarn-level cloth in real-time
at large scales.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We wish to thank the anonymous reviewers and the members of the
Visual Computing Group at IST Austria for their valuable feedback. We also thank
Seddi Labs for providing the garment model with fold-over seams.\r\nThis research
was supported by the Scientific Service Units (SSU) of IST Austria through resources
provided by Scientific\r\nComputing. This project has received funding from the
European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation programme under grant agreement No. 638176. Rahul Narain is supported
by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc."
article_number: '168'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
- first_name: Rahul
full_name: Narain, Rahul
last_name: Narain
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Sperl G, Narain R, Wojtan C. Mechanics-aware deformation of yarn pattern geometry.
ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459816
apa: Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-aware deformation
of yarn pattern geometry. ACM Transactions on Graphics. Association for
Computing Machinery. https://doi.org/10.1145/3450626.3459816
chicago: Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation
of Yarn Pattern Geometry.” ACM Transactions on Graphics. Association for
Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459816.
ieee: G. Sperl, R. Narain, and C. Wojtan, “Mechanics-aware deformation of yarn pattern
geometry,” ACM Transactions on Graphics, vol. 40, no. 4. Association for
Computing Machinery, 2021.
ista: Sperl G, Narain R, Wojtan C. 2021. Mechanics-aware deformation of yarn pattern
geometry. ACM Transactions on Graphics. 40(4), 168.
mla: Sperl, Georg, et al. “Mechanics-Aware Deformation of Yarn Pattern Geometry.”
ACM Transactions on Graphics, vol. 40, no. 4, 168, Association for Computing
Machinery, 2021, doi:10.1145/3450626.3459816.
short: G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 40 (2021).
date_created: 2021-08-08T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-10T14:24:36Z
day: '01'
department:
- _id: GradSch
- _id: ChWo
doi: 10.1145/3450626.3459816
ec_funded: 1
external_id:
isi:
- '000674930900132'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/3450626.3459816
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/knitting-virtual-yarn/
record:
- id: '12358'
relation: dissertation_contains
status: public
- id: '9327'
relation: software
status: public
scopus_import: '1'
status: public
title: Mechanics-aware deformation of yarn pattern geometry
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2021'
...
---
_id: '9828'
abstract:
- lang: eng
text: Amplitude demodulation is a classical operation used in signal processing.
For a long time, its effective applications in practice have been limited to narrowband
signals. In this work, we generalize amplitude demodulation to wideband signals.
We pose demodulation as a recovery problem of an oversampled corrupted signal
and introduce special iterative schemes belonging to the family of alternating
projection algorithms to solve it. Sensibly chosen structural assumptions on the
demodulation outputs allow us to reveal the high inferential accuracy of the method
over a rich set of relevant signals. This new approach surpasses current state-of-the-art
demodulation techniques apt to wideband signals in computational efficiency by
up to many orders of magnitude with no sacrifice in quality. Such performance
opens the door for applications of the amplitude demodulation procedure in new
contexts. In particular, the new method makes online and large-scale offline data
processing feasible, including the calculation of modulator-carrier pairs in higher
dimensions and poor sampling conditions, independent of the signal bandwidth.
We illustrate the utility and specifics of applications of the new method in practice
by using natural speech and synthetic signals.
acknowledgement: The author thanks his colleagues K. Huszár and G. Tkačik for valuable
discussions and comments on the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Mantas
full_name: Gabrielaitis, Mantas
id: 4D5B0CBC-F248-11E8-B48F-1D18A9856A87
last_name: Gabrielaitis
orcid: 0000-0002-7758-2016
citation:
ama: Gabrielaitis M. Fast and accurate amplitude demodulation of wideband signals.
IEEE Transactions on Signal Processing. 2021;69:4039-4054. doi:10.1109/TSP.2021.3087899
apa: Gabrielaitis, M. (2021). Fast and accurate amplitude demodulation of wideband
signals. IEEE Transactions on Signal Processing. Institute of Electrical
and Electronics Engineers. https://doi.org/10.1109/TSP.2021.3087899
chicago: Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband
Signals.” IEEE Transactions on Signal Processing. Institute of Electrical
and Electronics Engineers, 2021. https://doi.org/10.1109/TSP.2021.3087899.
ieee: M. Gabrielaitis, “Fast and accurate amplitude demodulation of wideband signals,”
IEEE Transactions on Signal Processing, vol. 69. Institute of Electrical
and Electronics Engineers, pp. 4039–4054, 2021.
ista: Gabrielaitis M. 2021. Fast and accurate amplitude demodulation of wideband
signals. IEEE Transactions on Signal Processing. 69, 4039–4054.
mla: Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband
Signals.” IEEE Transactions on Signal Processing, vol. 69, Institute of
Electrical and Electronics Engineers, 2021, pp. 4039–54, doi:10.1109/TSP.2021.3087899.
short: M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054.
date_created: 2021-08-08T22:01:31Z
date_published: 2021-06-09T00:00:00Z
date_updated: 2023-08-10T14:19:33Z
day: '09'
department:
- _id: GaTk
doi: 10.1109/TSP.2021.3087899
external_id:
arxiv:
- '2102.04832'
isi:
- '000682123900002'
intvolume: ' 69'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2102.04832
month: '06'
oa: 1
oa_version: Preprint
page: 4039 - 4054
publication: IEEE Transactions on Signal Processing
publication_identifier:
eissn:
- 1941-0476
issn:
- 1053-587X
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast and accurate amplitude demodulation of wideband signals
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 69
year: '2021'
...
---
_id: '9327'
abstract:
- lang: eng
text: "This archive contains the missing sweater mesh animations and displacement
models for the code of \"Mechanics-Aware Deformation of Yarn Pattern Geometry\"\r\n\r\nCode
Repository: https://git.ist.ac.at/gsperl/MADYPG"
author:
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
- first_name: Rahul
full_name: Narain, Rahul
last_name: Narain
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Sperl G, Narain R, Wojtan C. Mechanics-Aware Deformation of Yarn Pattern Geometry
(Additional Animation/Model Data). 2021. doi:10.15479/AT:ISTA:9327
apa: Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-Aware Deformation
of Yarn Pattern Geometry (Additional Animation/Model Data). IST Austria. https://doi.org/10.15479/AT:ISTA:9327
chicago: Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation
of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021.
https://doi.org/10.15479/AT:ISTA:9327.
ieee: G. Sperl, R. Narain, and C. Wojtan, “Mechanics-Aware Deformation of Yarn Pattern
Geometry (Additional Animation/Model Data).” IST Austria, 2021.
ista: Sperl G, Narain R, Wojtan C. 2021. Mechanics-Aware Deformation of Yarn Pattern
Geometry (Additional Animation/Model Data), IST Austria, 10.15479/AT:ISTA:9327.
mla: Sperl, Georg, et al. Mechanics-Aware Deformation of Yarn Pattern Geometry
(Additional Animation/Model Data). IST Austria, 2021, doi:10.15479/AT:ISTA:9327.
short: G. Sperl, R. Narain, C. Wojtan, (2021).
date_created: 2021-04-16T14:26:19Z
date_published: 2021-05-01T00:00:00Z
date_updated: 2023-08-10T14:24:36Z
ddc:
- '005'
department:
- _id: GradSch
- _id: ChWo
doi: 10.15479/AT:ISTA:9327
file:
- access_level: open_access
checksum: 0324cb519273371708743f3282e7c081
content_type: application/zip
creator: gsperl
date_created: 2021-04-16T14:15:12Z
date_updated: 2021-04-16T14:15:12Z
file_id: '9328'
file_name: MADYPG_extra_data.zip
file_size: 802586232
relation: main_file
success: 1
- access_level: open_access
checksum: 4c224551adf852b136ec21a4e13f0c1b
content_type: application/gzip
creator: pub-gitlab-bot
date_created: 2021-04-26T09:33:44Z
date_updated: 2021-04-26T09:33:44Z
file_id: '9353'
file_name: MADYPG.zip
file_size: 64962865
relation: main_file
file_date_updated: 2021-04-26T09:33:44Z
gitlab_commit_id: 6a77e7e22769230ae5f5edaa090fb4b828e57573
gitlab_url: https://git.ist.ac.at/gsperl/MADYPG
has_accepted_license: '1'
license: https://opensource.org/licenses/MIT
month: '05'
oa: 1
publisher: IST Austria
related_material:
record:
- id: '9818'
relation: used_for_analysis_in
status: public
status: public
title: Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model
Data)
tmp:
legal_code_url: https://opensource.org/licenses/MIT
name: The MIT License
short: MIT
type: software
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '9770'
abstract:
- lang: eng
text: We study an effective one-dimensional quantum model that includes friction
and spin-orbit coupling (SOC), and show that the model exhibits spin polarization
when both terms are finite. Most important, strong spin polarization can be observed
even for moderate SOC, provided that the friction is strong. Our findings might
help to explain the pronounced effect of chirality on spin distribution and transport
in chiral molecules. In particular, our model implies static magnetic properties
of a chiral molecule, which lead to Shiba-like states when a molecule is placed
on a superconductor, in accordance with recent experimental data.
acknowledgement: "We thank Rafael Barfknecht for useful discussions. This work has
received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.\r\nand
A.G.V.). M.L. acknowledges support by the European Research Council (ERC) Starting
Grant No. 801770 (ANGULON). Y.P. and O.M. acknowledge funding from the Nidersachsen
Ministry of Science and Culture, and from the\r\nAcademia Sinica Research Program.
O.M. is thankful for support through the Harry de Jur Chair in Applied Science."
article_number: '024430'
article_processing_charge: No
article_type: original
author:
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Hen
full_name: Alpern, Hen
last_name: Alpern
- first_name: Yossi
full_name: Paltiel, Yossi
last_name: Paltiel
- first_name: Oded
full_name: Millo, Oded
last_name: Millo
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
citation:
ama: Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. Interplay
between friction and spin-orbit coupling as a source of spin polarization. Physical
Review B. 2021;104(2). doi:10.1103/physrevb.104.024430
apa: Volosniev, A., Alpern, H., Paltiel, Y., Millo, O., Lemeshko, M., & Ghazaryan,
A. (2021). Interplay between friction and spin-orbit coupling as a source of spin
polarization. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.104.024430
chicago: Volosniev, Artem, Hen Alpern, Yossi Paltiel, Oded Millo, Mikhail Lemeshko,
and Areg Ghazaryan. “Interplay between Friction and Spin-Orbit Coupling as a Source
of Spin Polarization.” Physical Review B. American Physical Society, 2021.
https://doi.org/10.1103/physrevb.104.024430.
ieee: A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, and A. Ghazaryan,
“Interplay between friction and spin-orbit coupling as a source of spin polarization,”
Physical Review B, vol. 104, no. 2. American Physical Society, 2021.
ista: Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. 2021.
Interplay between friction and spin-orbit coupling as a source of spin polarization.
Physical Review B. 104(2), 024430.
mla: Volosniev, Artem, et al. “Interplay between Friction and Spin-Orbit Coupling
as a Source of Spin Polarization.” Physical Review B, vol. 104, no. 2,
024430, American Physical Society, 2021, doi:10.1103/physrevb.104.024430.
short: A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, A. Ghazaryan,
Physical Review B 104 (2021).
date_created: 2021-08-04T15:05:32Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-10T14:27:07Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/physrevb.104.024430
ec_funded: 1
external_id:
arxiv:
- '2101.05173'
isi:
- '000678780800003'
intvolume: ' 104'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2101.05173
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interplay between friction and spin-orbit coupling as a source of spin polarization
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 104
year: '2021'
...
---
_id: '9827'
abstract:
- lang: eng
text: 'The Nearest neighbour search (NNS) is a fundamental problem in many application
domains dealing with multidimensional data. In a concurrent setting, where dynamic
modifications are allowed, a linearizable implementation of the NNS is highly
desirable.This paper introduces the LockFree-kD-tree (LFkD-tree ): a lock-free
concurrent kD-tree, which implements an abstract data type (ADT) that provides
the operations Add, Remove, Contains, and NNS. Our implementation is linearizable.
The operations in the LFkD-tree use single-word read and compare-and-swap (Image
1 ) atomic primitives, which are readily supported on available multi-core processors.
We experimentally evaluate the LFkD-tree using several benchmarks comprising real-world
and synthetic datasets. The experiments show that the presented design is scalable
and achieves significant speed-up compared to the implementations of an existing
sequential kD-tree and a recently proposed multidimensional indexing structure,
PH-tree.'
article_processing_charge: No
article_type: original
author:
- first_name: Bapi
full_name: Chatterjee, Bapi
id: 3C41A08A-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-2742-4028
- first_name: Ivan
full_name: Walulya, Ivan
last_name: Walulya
- first_name: Philippas
full_name: Tsigas, Philippas
last_name: Tsigas
citation:
ama: Chatterjee B, Walulya I, Tsigas P. Concurrent linearizable nearest neighbour
search in LockFree-kD-tree. Theoretical Computer Science. 2021;886:27-48.
doi:10.1016/j.tcs.2021.06.041
apa: Chatterjee, B., Walulya, I., & Tsigas, P. (2021). Concurrent linearizable
nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2021.06.041
chicago: Chatterjee, Bapi, Ivan Walulya, and Philippas Tsigas. “Concurrent Linearizable
Nearest Neighbour Search in LockFree-KD-Tree.” Theoretical Computer Science.
Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.06.041.
ieee: B. Chatterjee, I. Walulya, and P. Tsigas, “Concurrent linearizable nearest
neighbour search in LockFree-kD-tree,” Theoretical Computer Science, vol.
886. Elsevier, pp. 27–48, 2021.
ista: Chatterjee B, Walulya I, Tsigas P. 2021. Concurrent linearizable nearest neighbour
search in LockFree-kD-tree. Theoretical Computer Science. 886, 27–48.
mla: Chatterjee, Bapi, et al. “Concurrent Linearizable Nearest Neighbour Search
in LockFree-KD-Tree.” Theoretical Computer Science, vol. 886, Elsevier,
2021, pp. 27–48, doi:10.1016/j.tcs.2021.06.041.
short: B. Chatterjee, I. Walulya, P. Tsigas, Theoretical Computer Science 886 (2021)
27–48.
date_created: 2021-08-08T22:01:31Z
date_published: 2021-09-13T00:00:00Z
date_updated: 2023-08-10T14:27:43Z
day: '13'
department:
- _id: DaAl
doi: 10.1016/j.tcs.2021.06.041
external_id:
isi:
- '000694718900004'
intvolume: ' 886'
isi: 1
keyword:
- Concurrent data structure
- kD-tree
- Nearest neighbor search
- Similarity search
- Lock-free
- Linearizability
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://publications.lib.chalmers.se/records/fulltext/232185/232185.pdf
month: '09'
oa: 1
oa_version: Submitted Version
page: 27-48
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Concurrent linearizable nearest neighbour search in LockFree-kD-tree
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 886
year: '2021'
...
---
_id: '9877'
abstract:
- lang: eng
text: 'Parent-of-origin–dependent gene expression in mammals and flowering plants
results from differing chromatin imprints (genomic imprinting) between maternally
and paternally inherited alleles. Imprinted gene expression in the endosperm of
seeds is associated with localized hypomethylation of maternally but not paternally
inherited DNA, with certain small RNAs also displaying parent-of-origin–specific
expression. To understand the evolution of imprinting mechanisms in Oryza sativa
(rice), we analyzed imprinting divergence among four cultivars that span both
japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted
genes are imprinted across cultivars and enriched for functions in chromatin and
transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted
genes display divergent imprinting. Analyses of DNA methylation and small RNAs
revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed
DNA methylation, frequently overlap genes, and are imprinted four times more often
than genes. However, imprinting divergence most often correlated with local DNA
methylation epimutations (9 of 17 assessable loci), which were largely stable
within subspecies. Small insertion/deletion events and transposable element insertions
accompanied 4 of the 9 locally epimutated loci and associated with imprinting
divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic
variation occurred at key regulatory regions—the promoter and transcription start
site of maternally biased genes, and the promoter and gene body of paternally
biased genes. Our results reinforce models for the role of maternal-specific DNA
hypomethylation in imprinting of both maternally and paternally biased genes,
and highlight the role of transposition and epimutation in rice imprinting evolution.'
acknowledgement: We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing
team for generating the IR64 genome sequence and initial analysis; L. Bartley and
E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University
of California (UC), Berkeley Sanger sequencing team for technical advice and service.
This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH
Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator
Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright
Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying
Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing
Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.
article_number: e2104445118
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Deling
full_name: Ruan, Deling
last_name: Ruan
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Manoj K.
full_name: Sharma, Manoj K.
last_name: Sharma
- first_name: Rita
full_name: Sharma, Rita
last_name: Sharma
- first_name: XinYi
full_name: Ye, XinYi
last_name: Ye
- first_name: Nicholas D.
full_name: Nguyen, Nicholas D.
last_name: Nguyen
- first_name: Sukhranjan
full_name: Nijjar, Sukhranjan
last_name: Nijjar
- first_name: Pamela C.
full_name: Ronald, Pamela C.
last_name: Ronald
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals
roles for transposition and epimutation in ongoing evolution of genomic imprinting.
Proceedings of the National Academy of Sciences. 2021;118(29). doi:10.1073/pnas.2104445118
apa: Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma,
R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for
transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2104445118
chicago: Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura,
Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars
Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic
Imprinting.” Proceedings of the National Academy of Sciences. National
Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2104445118.
ieee: J. A. Rodrigues et al., “Divergence among rice cultivars reveals roles
for transposition and epimutation in ongoing evolution of genomic imprinting,”
Proceedings of the National Academy of Sciences, vol. 118, no. 29. National
Academy of Sciences, 2021.
ista: Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen
ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice
cultivars reveals roles for transposition and epimutation in ongoing evolution
of genomic imprinting. Proceedings of the National Academy of Sciences. 118(29),
e2104445118.
mla: Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles
for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.”
Proceedings of the National Academy of Sciences, vol. 118, no. 29, e2104445118,
National Academy of Sciences, 2021, doi:10.1073/pnas.2104445118.
short: J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma,
X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings
of the National Academy of Sciences 118 (2021).
date_created: 2021-08-10T19:30:41Z
date_published: 2021-07-16T00:00:00Z
date_updated: 2023-08-11T10:28:10Z
day: '16'
ddc:
- '580'
- '570'
department:
- _id: DaZi
doi: 10.1073/pnas.2104445118
external_id:
isi:
- '000685037700012'
pmid:
- '34272287'
file:
- access_level: open_access
checksum: 19e84ad8c03c60222744ee8e16cd6998
content_type: application/pdf
creator: asandaue
date_created: 2021-08-11T09:31:41Z
date_updated: 2021-08-11T09:31:41Z
file_id: '9879'
file_name: 2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf
file_size: 1898360
relation: main_file
success: 1
file_date_updated: 2021-08-11T09:31:41Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '29'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divergence among rice cultivars reveals roles for transposition and epimutation
in ongoing evolution of genomic imprinting
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: 118
year: '2021'
...
---
_id: '9874'
abstract:
- lang: eng
text: Myocardial regeneration is restricted to early postnatal life, when mammalian
cardiomyocytes still retain the ability to proliferate. The molecular cues that
induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated
adult heart muscle cells remain obscure. Here we report that the miR-106b~25 cluster
is higher expressed in the early postnatal myocardium and decreases in expression
towards adulthood, especially under conditions of overload, and orchestrates the
transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy
by virtue of its targetome. In line, gene delivery of miR-106b~25 to the mouse
heart provokes cardiomyocyte proliferation by targeting a network of negative
cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted
miR-106b~25 null mice display spontaneous hypertrophic remodeling and exaggerated
remodeling to overload by derepression of the prohypertrophic transcription factors
Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b~25 on
cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b~25
provokes nearly complete regeneration of the adult myocardium after ischemic injury.
Our data demonstrate that exploitation of conserved molecular programs can enhance
the regenerative capacity of the injured heart.
acknowledgement: E.D. is supported by a VENI award 916-150-16 from the Netherlands
Organization for Health Research and Development (ZonMW), an EMBO Long-term Fellowship
(EMBO ALTF 848-2013) and a FP7 Marie Curie Intra-European Fellowship (Project number
627539). V.S.P. was funded by a fellowship from the FCT/ Ministério da Ciência,
Tecnologia e Inovação SFRH/BD/111799/2015. P.D.C.M. is an Established Investigator
of the Dutch Heart Foundation. L.D.W. acknowledges support from the Dutch CardioVascular
Alliance (ARENA-PRIME). L.D.W. was further supported by grant 311549 from the European
Research Council (ERC), a VICI award 918-156-47 from the Dutch Research Council
and Marie Sklodowska-Curie grant agreement no. 813716 (TRAIN-HEART).
article_number: '4808'
article_processing_charge: Yes
article_type: original
author:
- first_name: Andrea
full_name: Raso, Andrea
last_name: Raso
- first_name: Ellen
full_name: Dirkx, Ellen
last_name: Dirkx
- first_name: Vasco
full_name: Sampaio-Pinto, Vasco
last_name: Sampaio-Pinto
- first_name: Hamid
full_name: el Azzouzi, Hamid
last_name: el Azzouzi
- first_name: Ryan J
full_name: Cubero, Ryan J
id: 850B2E12-9CD4-11E9-837F-E719E6697425
last_name: Cubero
orcid: 0000-0003-0002-1867
- first_name: Daniel W.
full_name: Sorensen, Daniel W.
last_name: Sorensen
- first_name: Lara
full_name: Ottaviani, Lara
last_name: Ottaviani
- first_name: Servé
full_name: Olieslagers, Servé
last_name: Olieslagers
- first_name: Manon M.
full_name: Huibers, Manon M.
last_name: Huibers
- first_name: Roel
full_name: de Weger, Roel
last_name: de Weger
- first_name: Sailay
full_name: Siddiqi, Sailay
last_name: Siddiqi
- first_name: Silvia
full_name: Moimas, Silvia
last_name: Moimas
- first_name: Consuelo
full_name: Torrini, Consuelo
last_name: Torrini
- first_name: Lorena
full_name: Zentillin, Lorena
last_name: Zentillin
- first_name: Luca
full_name: Braga, Luca
last_name: Braga
- first_name: Diana S.
full_name: Nascimento, Diana S.
last_name: Nascimento
- first_name: Paula A.
full_name: da Costa Martins, Paula A.
last_name: da Costa Martins
- first_name: Jop H.
full_name: van Berlo, Jop H.
last_name: van Berlo
- first_name: Serena
full_name: Zacchigna, Serena
last_name: Zacchigna
- first_name: Mauro
full_name: Giacca, Mauro
last_name: Giacca
- first_name: Leon J.
full_name: De Windt, Leon J.
last_name: De Windt
citation:
ama: Raso A, Dirkx E, Sampaio-Pinto V, et al. A microRNA program regulates the balance
between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration.
Nature Communications. 2021;12. doi:10.1038/s41467-021-25211-4
apa: Raso, A., Dirkx, E., Sampaio-Pinto, V., el Azzouzi, H., Cubero, R. J., Sorensen,
D. W., … De Windt, L. J. (2021). A microRNA program regulates the balance between
cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-25211-4
chicago: Raso, Andrea, Ellen Dirkx, Vasco Sampaio-Pinto, Hamid el Azzouzi, Ryan
J Cubero, Daniel W. Sorensen, Lara Ottaviani, et al. “A MicroRNA Program Regulates
the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac
Regeneration.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-25211-4.
ieee: A. Raso et al., “A microRNA program regulates the balance between cardiomyocyte
hyperplasia and hypertrophy and stimulates cardiac regeneration,” Nature Communications,
vol. 12. Springer Nature, 2021.
ista: Raso A, Dirkx E, Sampaio-Pinto V, el Azzouzi H, Cubero RJ, Sorensen DW, Ottaviani
L, Olieslagers S, Huibers MM, de Weger R, Siddiqi S, Moimas S, Torrini C, Zentillin
L, Braga L, Nascimento DS, da Costa Martins PA, van Berlo JH, Zacchigna S, Giacca
M, De Windt LJ. 2021. A microRNA program regulates the balance between cardiomyocyte
hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications.
12, 4808.
mla: Raso, Andrea, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte
Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” Nature Communications,
vol. 12, 4808, Springer Nature, 2021, doi:10.1038/s41467-021-25211-4.
short: A. Raso, E. Dirkx, V. Sampaio-Pinto, H. el Azzouzi, R.J. Cubero, D.W. Sorensen,
L. Ottaviani, S. Olieslagers, M.M. Huibers, R. de Weger, S. Siddiqi, S. Moimas,
C. Torrini, L. Zentillin, L. Braga, D.S. Nascimento, P.A. da Costa Martins, J.H.
van Berlo, S. Zacchigna, M. Giacca, L.J. De Windt, Nature Communications 12 (2021).
date_created: 2021-08-10T11:49:20Z
date_published: 2021-08-10T00:00:00Z
date_updated: 2023-08-11T10:27:03Z
day: '10'
ddc:
- '610'
- '570'
department:
- _id: SaSi
doi: 10.1038/s41467-021-25211-4
external_id:
isi:
- '000683910200042'
pmid:
- '34376683'
file:
- access_level: open_access
checksum: 48d8562e8229e4282f3f354b329722c5
content_type: application/pdf
creator: asandaue
date_created: 2021-08-10T12:29:59Z
date_updated: 2021-08-10T12:29:59Z
file_id: '9876'
file_name: 2021_NatureCommunications_Raso.pdf
file_size: 4364333
relation: main_file
success: 1
file_date_updated: 2021-08-10T12:29:59Z
genbank:
- GSE178867
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-022-32785-0
scopus_import: '1'
status: public
title: A microRNA program regulates the balance between cardiomyocyte hyperplasia
and hypertrophy and stimulates cardiac regeneration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9769'
abstract:
- lang: eng
text: A few years ago, flow equations were introduced as a technique for calculating
the ground-state energies of cold Bose gases with and without impurities. In this
paper, we extend this approach to compute observables other than the energy. As
an example, we calculate the densities, and phase fluctuations of one-dimensional
Bose gases with one and two impurities. For a single mobile impurity, we use flow
equations to validate the mean-field results obtained upon the Lee-Low-Pines transformation.
We show that the mean-field approximation is accurate for all values of the boson-impurity
interaction strength as long as the phase coherence length is much larger than
the healing length of the condensate. For two static impurities, we calculate
impurity-impurity interactions induced by the Bose gas. We find that leading order
perturbation theory fails when boson-impurity interactions are stronger than boson-boson
interactions. The mean-field approximation reproduces the flow equation results
for all values of the boson-impurity interaction strength as long as boson-boson
interactions are weak.
acknowledgement: We thank Matthias Heinz and Volker Karle for helpful comments on
the manuscript; Zoran Ristivojevic for useful correspondence regarding mean-field
calculations of induced impurity-impurity interactions; Fabian Grusdt for sharing
with us the data for the densities presented in Ref. [14]. This work has received
funding from the DFG Project No. 413495248 [VO 2437/1-1] (F. B., H.-W. H., A. G.
V.) and European Union’s Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 754411 (A. G. V.). M. L. acknowledges
support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).
H.-W.H. thanks the ECT* for hospitality during the workshop “Universal physics in
Many-Body Quantum Systems – From Atoms to Quarks". This infrastructure is part of
a project that has received funding from the European Union’s Horizon 2020 research
and innovation programme under grant agreement No 824093. H.-W.H. was supported
by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID
279384907 - SFB 1245.
article_number: '008'
article_processing_charge: Yes
article_type: original
author:
- first_name: Fabian
full_name: Brauneis, Fabian
last_name: Brauneis
- first_name: Hans-Werner
full_name: Hammer, Hans-Werner
last_name: Hammer
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: 'Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. Impurities in a one-dimensional
Bose gas: The flow equation approach. SciPost Physics. 2021;11(1). doi:10.21468/scipostphys.11.1.008'
apa: 'Brauneis, F., Hammer, H.-W., Lemeshko, M., & Volosniev, A. (2021). Impurities
in a one-dimensional Bose gas: The flow equation approach. SciPost Physics.
SciPost. https://doi.org/10.21468/scipostphys.11.1.008'
chicago: 'Brauneis, Fabian, Hans-Werner Hammer, Mikhail Lemeshko, and Artem Volosniev.
“Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” SciPost
Physics. SciPost, 2021. https://doi.org/10.21468/scipostphys.11.1.008.'
ieee: 'F. Brauneis, H.-W. Hammer, M. Lemeshko, and A. Volosniev, “Impurities in
a one-dimensional Bose gas: The flow equation approach,” SciPost Physics,
vol. 11, no. 1. SciPost, 2021.'
ista: 'Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. 2021. Impurities in a one-dimensional
Bose gas: The flow equation approach. SciPost Physics. 11(1), 008.'
mla: 'Brauneis, Fabian, et al. “Impurities in a One-Dimensional Bose Gas: The Flow
Equation Approach.” SciPost Physics, vol. 11, no. 1, 008, SciPost, 2021,
doi:10.21468/scipostphys.11.1.008.'
short: F. Brauneis, H.-W. Hammer, M. Lemeshko, A. Volosniev, SciPost Physics 11
(2021).
date_created: 2021-08-04T15:00:55Z
date_published: 2021-07-13T00:00:00Z
date_updated: 2023-08-11T10:25:44Z
day: '13'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.21468/scipostphys.11.1.008
ec_funded: 1
external_id:
arxiv:
- '2101.10958'
isi:
- '000680039500013'
file:
- access_level: open_access
checksum: eaa847346b1a023d97bbb291779610ed
content_type: application/pdf
creator: asandaue
date_created: 2021-08-10T11:44:59Z
date_updated: 2021-08-10T11:44:59Z
file_id: '9875'
file_name: 2021_SciPostPhysics_Brauneis.pdf
file_size: 1085300
relation: main_file
success: 1
file_date_updated: 2021-08-10T11:44:59Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: SciPost Physics
publication_identifier:
eissn:
- 2542-4653
publication_status: published
publisher: SciPost
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Impurities in a one-dimensional Bose gas: The flow equation approach'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2021'
...
---
_id: '9746'
abstract:
- lang: eng
text: Evolutionary adaptation is a major source of antibiotic resistance in bacterial
pathogens. Evolution-informed therapy aims to constrain resistance by accounting
for bacterial evolvability. Sequential treatments with antibiotics that target
different bacterial processes were previously shown to limit adaptation through
genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous
sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly
lead to cross-resistance. We here challenged this assumption by determining the
evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments
involving both heterogenous and homogeneous antibiotic sets. To our surprise,
we found that fast switching between only β-lactam antibiotics resulted in increased
extinction of bacterial populations. We demonstrate that extinction is favored
by low rates of spontaneous resistance emergence and low levels of spontaneous
cross-resistance among the antibiotics in sequence. The uncovered principles may
help to guide the optimized use of available antibiotics in highly potent, evolution-informed
treatment designs.
acknowledgement: We would like to thank Leif Tueffers and João Botelho for discussions
and suggestions as well as Kira Haas and Julia Bunk for technical support. We acknowledge
financial support from the German Science Foundation (grant SCHU 1415/12-2 to HS,
and funding under Germany’s Excellence Strategy EXC 2167–390884018 as well as the
Research Training Group 2501 TransEvo to HS and SN), the Max Planck Society (IMPRS
scholarship to AB; Max-Planck fellowship to HS), and the Leibniz Science Campus
Evolutionary Medicine of the Lung (EvoLUNG, to HS and SN). This work was further
supported by the German Science Foundation Research Infrastructure NGS_CC (project
407495230) as part of the Next Generation Sequencing Competence Network (project
423957469). NGS analyses were carried out at the Competence Centre for Genomic Analysis
Kiel (CCGA Kiel).
article_number: e68876
article_processing_charge: No
article_type: original
author:
- first_name: Aditi
full_name: Batra, Aditi
last_name: Batra
- first_name: Roderich
full_name: Römhild, Roderich
id: 68E56E44-62B0-11EA-B963-444F3DDC885E
last_name: Römhild
orcid: 0000-0001-9480-5261
- first_name: Emilie
full_name: Rousseau, Emilie
last_name: Rousseau
- first_name: Sören
full_name: Franzenburg, Sören
last_name: Franzenburg
- first_name: Stefan
full_name: Niemann, Stefan
last_name: Niemann
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
citation:
ama: Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. High
potency of sequential therapy with only beta-lactam antibiotics. eLife.
2021;10. doi:10.7554/elife.68876
apa: Batra, A., Römhild, R., Rousseau, E., Franzenburg, S., Niemann, S., & Schulenburg,
H. (2021). High potency of sequential therapy with only beta-lactam antibiotics.
ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68876
chicago: Batra, Aditi, Roderich Römhild, Emilie Rousseau, Sören Franzenburg, Stefan
Niemann, and Hinrich Schulenburg. “High Potency of Sequential Therapy with Only
Beta-Lactam Antibiotics.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.68876.
ieee: A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, and H. Schulenburg,
“High potency of sequential therapy with only beta-lactam antibiotics,” eLife,
vol. 10. eLife Sciences Publications, 2021.
ista: Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. 2021.
High potency of sequential therapy with only beta-lactam antibiotics. eLife. 10,
e68876.
mla: Batra, Aditi, et al. “High Potency of Sequential Therapy with Only Beta-Lactam
Antibiotics.” ELife, vol. 10, e68876, eLife Sciences Publications, 2021,
doi:10.7554/elife.68876.
short: A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, H. Schulenburg,
ELife 10 (2021).
date_created: 2021-07-28T13:36:57Z
date_published: 2021-07-28T00:00:00Z
date_updated: 2023-08-11T10:26:29Z
day: '28'
department:
- _id: CaGu
doi: 10.7554/elife.68876
external_id:
isi:
- '000692027800001'
pmid:
- '34318749'
intvolume: ' 10'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.7554/eLife.68876
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: High potency of sequential therapy with only beta-lactam antibiotics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '9911'
abstract:
- lang: eng
text: A modern day light microscope has evolved from a tool devoted to making primarily
empirical observations to what is now a sophisticated , quantitative device that
is an integral part of both physical and life science research. Nowadays, microscopes
are found in nearly every experimental laboratory. However, despite their prevalent
use in capturing and quantifying scientific phenomena, neither a thorough understanding
of the principles underlying quantitative imaging techniques nor appropriate knowledge
of how to calibrate, operate and maintain microscopes can be taken for granted.
This is clearly demonstrated by the well-documented and widespread difficulties
that are routinely encountered in evaluating acquired data and reproducing scientific
experiments. Indeed, studies have shown that more than 70% of researchers have
tried and failed to repeat another scientist's experiments, while more than half
have even failed to reproduce their own experiments. One factor behind the reproducibility
crisis of experiments published in scientific journals is the frequent underreporting
of imaging methods caused by a lack of awareness and/or a lack of knowledge of
the applied technique. Whereas quality control procedures for some methods used
in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry,
have been introduced (e.g. ENCODE), this issue has not been tackled for optical
microscopy instrumentation and images. Although many calibration standards and
protocols have been published, there is a lack of awareness and agreement on common
standards and guidelines for quality assessment and reproducibility. In April
2020, the QUality Assessment and REProducibility for instruments and images in
Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises
imaging scientists from academia and industry who share a common interest in achieving
a better understanding of the performance and limitations of microscopes and improved
quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi
initiative is to establish a set of common QC standards, guidelines, metadata
models and tools, including detailed protocols, with the ultimate aim of improving
reproducible advances in scientific research. This White Paper (1) summarizes
the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi
initiative; (2) identifies the urgent need to address these obstacles in a grassroots
manner, through a community of stakeholders including, researchers, imaging scientists,
bioimage analysts, bioimage informatics developers, corporate partners, funding
agencies, standards organizations, scientific publishers and observers of such;
(3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes
future steps that can be taken to improve the dissemination and acceptance of
the proposed guidelines to manage QC. To summarize, the principal goal of the
QUAREP-LiMi initiative is to improve the overall quality and reproducibility of
light microscope image data by introducing broadly accepted standard practices
and accurately captured image data metrics.
acknowledgement: We thank https://www.somersault1824.com/somersault18:24 BV (Leuven,
Belgium) for help with Figure 1. E. C.-S. was supported by the project PPBI-POCI-01-0145-FEDER-022122,
in the scope of Fundação para a Ciência e Tecnologia, Portugal (FCT) National Roadmap
of Research Infrastructures. R.N. was funded by the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation) Grant number Ni 451/9-1 - MIAP-Freiburg.
article_processing_charge: Yes
article_type: original
author:
- first_name: Glyn
full_name: Nelson, Glyn
last_name: Nelson
- first_name: Ulrike
full_name: Boehm, Ulrike
last_name: Boehm
- first_name: Steve
full_name: Bagley, Steve
last_name: Bagley
- first_name: Peter
full_name: Bajcsy, Peter
last_name: Bajcsy
- first_name: Johanna
full_name: Bischof, Johanna
last_name: Bischof
- first_name: Claire M.
full_name: Brown, Claire M.
last_name: Brown
- first_name: Aurélien
full_name: Dauphin, Aurélien
last_name: Dauphin
- first_name: Ian M.
full_name: Dobbie, Ian M.
last_name: Dobbie
- first_name: John E.
full_name: Eriksson, John E.
last_name: Eriksson
- first_name: Orestis
full_name: Faklaris, Orestis
last_name: Faklaris
- first_name: Julia
full_name: Fernandez-Rodriguez, Julia
last_name: Fernandez-Rodriguez
- first_name: Alexia
full_name: Ferrand, Alexia
last_name: Ferrand
- first_name: Laurent
full_name: Gelman, Laurent
last_name: Gelman
- first_name: Ali
full_name: Gheisari, Ali
last_name: Gheisari
- first_name: Hella
full_name: Hartmann, Hella
last_name: Hartmann
- first_name: Christian
full_name: Kukat, Christian
last_name: Kukat
- first_name: Alex
full_name: Laude, Alex
last_name: Laude
- first_name: Miso
full_name: Mitkovski, Miso
last_name: Mitkovski
- first_name: Sebastian
full_name: Munck, Sebastian
last_name: Munck
- first_name: Alison J.
full_name: North, Alison J.
last_name: North
- first_name: Tobias M.
full_name: Rasse, Tobias M.
last_name: Rasse
- first_name: Ute
full_name: Resch-Genger, Ute
last_name: Resch-Genger
- first_name: Lucas C.
full_name: Schuetz, Lucas C.
last_name: Schuetz
- first_name: Arne
full_name: Seitz, Arne
last_name: Seitz
- first_name: Caterina
full_name: Strambio-De-Castillia, Caterina
last_name: Strambio-De-Castillia
- first_name: Jason R.
full_name: Swedlow, Jason R.
last_name: Swedlow
- first_name: Ioannis
full_name: Alexopoulos, Ioannis
last_name: Alexopoulos
- first_name: Karin
full_name: Aumayr, Karin
last_name: Aumayr
- first_name: Sergiy
full_name: Avilov, Sergiy
last_name: Avilov
- first_name: Gert Jan
full_name: Bakker, Gert Jan
last_name: Bakker
- first_name: Rodrigo R.
full_name: Bammann, Rodrigo R.
last_name: Bammann
- first_name: Andrea
full_name: Bassi, Andrea
last_name: Bassi
- first_name: Hannes
full_name: Beckert, Hannes
last_name: Beckert
- first_name: Sebastian
full_name: Beer, Sebastian
last_name: Beer
- first_name: Yury
full_name: Belyaev, Yury
last_name: Belyaev
- first_name: Jakob
full_name: Bierwagen, Jakob
last_name: Bierwagen
- first_name: Konstantin A.
full_name: Birngruber, Konstantin A.
last_name: Birngruber
- first_name: Manel
full_name: Bosch, Manel
last_name: Bosch
- first_name: Juergen
full_name: Breitlow, Juergen
last_name: Breitlow
- first_name: Lisa A.
full_name: Cameron, Lisa A.
last_name: Cameron
- first_name: Joe
full_name: Chalfoun, Joe
last_name: Chalfoun
- first_name: James J.
full_name: Chambers, James J.
last_name: Chambers
- first_name: Chieh Li
full_name: Chen, Chieh Li
last_name: Chen
- first_name: Eduardo
full_name: Conde-Sousa, Eduardo
last_name: Conde-Sousa
- first_name: Alexander D.
full_name: Corbett, Alexander D.
last_name: Corbett
- first_name: Fabrice P.
full_name: Cordelieres, Fabrice P.
last_name: Cordelieres
- first_name: Elaine Del
full_name: Nery, Elaine Del
last_name: Nery
- first_name: Ralf
full_name: Dietzel, Ralf
last_name: Dietzel
- first_name: Frank
full_name: Eismann, Frank
last_name: Eismann
- first_name: Elnaz
full_name: Fazeli, Elnaz
last_name: Fazeli
- first_name: Andreas
full_name: Felscher, Andreas
last_name: Felscher
- first_name: Hans
full_name: Fried, Hans
last_name: Fried
- first_name: Nathalie
full_name: Gaudreault, Nathalie
last_name: Gaudreault
- first_name: Wah Ing
full_name: Goh, Wah Ing
last_name: Goh
- first_name: Thomas
full_name: Guilbert, Thomas
last_name: Guilbert
- first_name: Roland
full_name: Hadleigh, Roland
last_name: Hadleigh
- first_name: Peter
full_name: Hemmerich, Peter
last_name: Hemmerich
- first_name: Gerhard A.
full_name: Holst, Gerhard A.
last_name: Holst
- first_name: Michelle S.
full_name: Itano, Michelle S.
last_name: Itano
- first_name: Claudia B.
full_name: Jaffe, Claudia B.
last_name: Jaffe
- first_name: Helena K.
full_name: Jambor, Helena K.
last_name: Jambor
- first_name: Stuart C.
full_name: Jarvis, Stuart C.
last_name: Jarvis
- first_name: Antje
full_name: Keppler, Antje
last_name: Keppler
- first_name: David
full_name: Kirchenbuechler, David
last_name: Kirchenbuechler
- first_name: Marcel
full_name: Kirchner, Marcel
last_name: Kirchner
- first_name: Norio
full_name: Kobayashi, Norio
last_name: Kobayashi
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Susanne
full_name: Kunis, Susanne
last_name: Kunis
- first_name: Judith
full_name: Lacoste, Judith
last_name: Lacoste
- first_name: Marco
full_name: Marcello, Marco
last_name: Marcello
- first_name: Gabriel G.
full_name: Martins, Gabriel G.
last_name: Martins
- first_name: Daniel J.
full_name: Metcalf, Daniel J.
last_name: Metcalf
- first_name: Claire A.
full_name: Mitchell, Claire A.
last_name: Mitchell
- first_name: Joshua
full_name: Moore, Joshua
last_name: Moore
- first_name: Tobias
full_name: Mueller, Tobias
last_name: Mueller
- first_name: Michael S.
full_name: Nelson, Michael S.
last_name: Nelson
- first_name: Stephen
full_name: Ogg, Stephen
last_name: Ogg
- first_name: Shuichi
full_name: Onami, Shuichi
last_name: Onami
- first_name: Alexandra L.
full_name: Palmer, Alexandra L.
last_name: Palmer
- first_name: Perrine
full_name: Paul-Gilloteaux, Perrine
last_name: Paul-Gilloteaux
- first_name: Jaime A.
full_name: Pimentel, Jaime A.
last_name: Pimentel
- first_name: Laure
full_name: Plantard, Laure
last_name: Plantard
- first_name: Santosh
full_name: Podder, Santosh
last_name: Podder
- first_name: Elton
full_name: Rexhepaj, Elton
last_name: Rexhepaj
- first_name: Arnaud
full_name: Royon, Arnaud
last_name: Royon
- first_name: Markku A.
full_name: Saari, Markku A.
last_name: Saari
- first_name: Damien
full_name: Schapman, Damien
last_name: Schapman
- first_name: Vincent
full_name: Schoonderwoert, Vincent
last_name: Schoonderwoert
- first_name: Britta
full_name: Schroth-Diez, Britta
last_name: Schroth-Diez
- first_name: Stanley
full_name: Schwartz, Stanley
last_name: Schwartz
- first_name: Michael
full_name: Shaw, Michael
last_name: Shaw
- first_name: Martin
full_name: Spitaler, Martin
last_name: Spitaler
- first_name: Martin T.
full_name: Stoeckl, Martin T.
last_name: Stoeckl
- first_name: Damir
full_name: Sudar, Damir
last_name: Sudar
- first_name: Jeremie
full_name: Teillon, Jeremie
last_name: Teillon
- first_name: Stefan
full_name: Terjung, Stefan
last_name: Terjung
- first_name: Roland
full_name: Thuenauer, Roland
last_name: Thuenauer
- first_name: Christian D.
full_name: Wilms, Christian D.
last_name: Wilms
- first_name: Graham D.
full_name: Wright, Graham D.
last_name: Wright
- first_name: Roland
full_name: Nitschke, Roland
last_name: Nitschke
citation:
ama: 'Nelson G, Boehm U, Bagley S, et al. QUAREP-LiMi: A community-driven initiative
to establish guidelines for quality assessment and reproducibility for instruments
and images in light microscopy. Journal of Microscopy. 2021;284(1):56-73.
doi:10.1111/jmi.13041'
apa: 'Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M.,
… Nitschke, R. (2021). QUAREP-LiMi: A community-driven initiative to establish
guidelines for quality assessment and reproducibility for instruments and images
in light microscopy. Journal of Microscopy. Wiley. https://doi.org/10.1111/jmi.13041'
chicago: 'Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof,
Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative
to Establish Guidelines for Quality Assessment and Reproducibility for Instruments
and Images in Light Microscopy.” Journal of Microscopy. Wiley, 2021. https://doi.org/10.1111/jmi.13041.'
ieee: 'G. Nelson et al., “QUAREP-LiMi: A community-driven initiative to establish
guidelines for quality assessment and reproducibility for instruments and images
in light microscopy,” Journal of Microscopy, vol. 284, no. 1. Wiley, pp.
56–73, 2021.'
ista: 'Nelson G et al. 2021. QUAREP-LiMi: A community-driven initiative to establish
guidelines for quality assessment and reproducibility for instruments and images
in light microscopy. Journal of Microscopy. 284(1), 56–73.'
mla: 'Nelson, Glyn, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish
Guidelines for Quality Assessment and Reproducibility for Instruments and Images
in Light Microscopy.” Journal of Microscopy, vol. 284, no. 1, Wiley, 2021,
pp. 56–73, doi:10.1111/jmi.13041.'
short: G. Nelson, U. Boehm, S. Bagley, P. Bajcsy, J. Bischof, C.M. Brown, A. Dauphin,
I.M. Dobbie, J.E. Eriksson, O. Faklaris, J. Fernandez-Rodriguez, A. Ferrand, L.
Gelman, A. Gheisari, H. Hartmann, C. Kukat, A. Laude, M. Mitkovski, S. Munck,
A.J. North, T.M. Rasse, U. Resch-Genger, L.C. Schuetz, A. Seitz, C. Strambio-De-Castillia,
J.R. Swedlow, I. Alexopoulos, K. Aumayr, S. Avilov, G.J. Bakker, R.R. Bammann,
A. Bassi, H. Beckert, S. Beer, Y. Belyaev, J. Bierwagen, K.A. Birngruber, M. Bosch,
J. Breitlow, L.A. Cameron, J. Chalfoun, J.J. Chambers, C.L. Chen, E. Conde-Sousa,
A.D. Corbett, F.P. Cordelieres, E.D. Nery, R. Dietzel, F. Eismann, E. Fazeli,
A. Felscher, H. Fried, N. Gaudreault, W.I. Goh, T. Guilbert, R. Hadleigh, P. Hemmerich,
G.A. Holst, M.S. Itano, C.B. Jaffe, H.K. Jambor, S.C. Jarvis, A. Keppler, D. Kirchenbuechler,
M. Kirchner, N. Kobayashi, G. Krens, S. Kunis, J. Lacoste, M. Marcello, G.G. Martins,
D.J. Metcalf, C.A. Mitchell, J. Moore, T. Mueller, M.S. Nelson, S. Ogg, S. Onami,
A.L. Palmer, P. Paul-Gilloteaux, J.A. Pimentel, L. Plantard, S. Podder, E. Rexhepaj,
A. Royon, M.A. Saari, D. Schapman, V. Schoonderwoert, B. Schroth-Diez, S. Schwartz,
M. Shaw, M. Spitaler, M.T. Stoeckl, D. Sudar, J. Teillon, S. Terjung, R. Thuenauer,
C.D. Wilms, G.D. Wright, R. Nitschke, Journal of Microscopy 284 (2021) 56–73.
date_created: 2021-08-15T22:01:29Z
date_published: 2021-08-11T00:00:00Z
date_updated: 2023-08-11T10:30:40Z
day: '11'
department:
- _id: Bio
doi: 10.1111/jmi.13041
external_id:
isi:
- '000683702700001'
intvolume: ' 284'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jmi.13041
month: '08'
oa: 1
oa_version: Published Version
page: 56-73
publication: Journal of Microscopy
publication_identifier:
eissn:
- 1365-2818
issn:
- 0022-2720
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'QUAREP-LiMi: A community-driven initiative to establish guidelines for quality
assessment and reproducibility for instruments and images in light microscopy'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 284
year: '2021'
...
---
_id: '9906'
abstract:
- lang: eng
text: Endometriosis is a common gynecological disorder characterized by ectopic
growth of endometrium outside the uterus and is associated with chronic pain and
infertility. We investigated the role of the long intergenic noncoding RNA 01133
(LINC01133) in endometriosis, an lncRNA that has been implicated in several types
of cancer. We found that LINC01133 is upregulated in ectopic endometriotic lesions.
As expression appeared higher in the epithelial endometrial layer, we performed
a siRNA knockdown of LINC01133 in an endometriosis epithelial cell line. Phenotypic
assays indicated that LINC01133 may promote proliferation and suppress cellular
migration, and affect the cytoskeleton and morphology of the cells. Gene ontology
analysis of differentially expressed genes indicated that cell proliferation and
migration pathways were affected in line with the observed phenotype. We validated
upregulation of p21 and downregulation of Cyclin A at the protein level, which
together with the quantification of the DNA content using fluorescence-activated
cell sorting (FACS) analysis indicated that the observed effects on cellular proliferation
may be due to changes in cell cycle. Further, we found testis-specific protein
kinase 1 (TESK1) kinase upregulation corresponding with phosphorylation and inactivation
of actin severing protein Cofilin, which could explain changes in the cytoskeleton
and cellular migration. These results indicate that endometriosis is associated
with LINC01133 upregulation, which may affect pathogenesis via the cellular proliferation
and migration pathways.
acknowledgement: "Open access funding provided by Medical University of Vienna. The
authors would like to thank all the participants and health professionals involved
in the present study. We want to thank our technical assistants Barbara Widmar and
Matthias Witzmann-Stern for their diligent work and constant assistance. We would
like to thank Simon Hippenmeyer for access to\r\nbioinformatic infrastructure and
resources."
article_number: '8385'
article_processing_charge: Yes
article_type: original
author:
- first_name: Iveta
full_name: Yotova, Iveta
last_name: Yotova
- first_name: Quanah J.
full_name: Hudson, Quanah J.
last_name: Hudson
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Katharina
full_name: Proestling, Katharina
last_name: Proestling
- first_name: Isabella
full_name: Haslinger, Isabella
last_name: Haslinger
- first_name: Lorenz
full_name: Kuessel, Lorenz
last_name: Kuessel
- first_name: Alexandra
full_name: Perricos, Alexandra
last_name: Perricos
- first_name: Heinrich
full_name: Husslein, Heinrich
last_name: Husslein
- first_name: René
full_name: Wenzl, René
last_name: Wenzl
citation:
ama: Yotova I, Hudson QJ, Pauler F, et al. LINC01133 inhibits invasion and promotes
proliferation in an endometriosis epithelial cell line. International Journal
of Molecular Sciences. 2021;22(16). doi:10.3390/ijms22168385
apa: Yotova, I., Hudson, Q. J., Pauler, F., Proestling, K., Haslinger, I., Kuessel,
L., … Wenzl, R. (2021). LINC01133 inhibits invasion and promotes proliferation
in an endometriosis epithelial cell line. International Journal of Molecular
Sciences. MDPI. https://doi.org/10.3390/ijms22168385
chicago: Yotova, Iveta, Quanah J. Hudson, Florian Pauler, Katharina Proestling,
Isabella Haslinger, Lorenz Kuessel, Alexandra Perricos, Heinrich Husslein, and
René Wenzl. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis
Epithelial Cell Line.” International Journal of Molecular Sciences. MDPI,
2021. https://doi.org/10.3390/ijms22168385.
ieee: I. Yotova et al., “LINC01133 inhibits invasion and promotes proliferation
in an endometriosis epithelial cell line,” International Journal of Molecular
Sciences, vol. 22, no. 16. MDPI, 2021.
ista: Yotova I, Hudson QJ, Pauler F, Proestling K, Haslinger I, Kuessel L, Perricos
A, Husslein H, Wenzl R. 2021. LINC01133 inhibits invasion and promotes proliferation
in an endometriosis epithelial cell line. International Journal of Molecular Sciences.
22(16), 8385.
mla: Yotova, Iveta, et al. “LINC01133 Inhibits Invasion and Promotes Proliferation
in an Endometriosis Epithelial Cell Line.” International Journal of Molecular
Sciences, vol. 22, no. 16, 8385, MDPI, 2021, doi:10.3390/ijms22168385.
short: I. Yotova, Q.J. Hudson, F. Pauler, K. Proestling, I. Haslinger, L. Kuessel,
A. Perricos, H. Husslein, R. Wenzl, International Journal of Molecular Sciences
22 (2021).
date_created: 2021-08-15T22:01:27Z
date_published: 2021-08-04T00:00:00Z
date_updated: 2023-08-11T10:34:13Z
day: '04'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.3390/ijms22168385
external_id:
isi:
- '000689147400001'
file:
- access_level: open_access
checksum: be7f0042607ca60549cb27513c19c6af
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:29:17Z
date_updated: 2021-08-16T09:29:17Z
file_id: '9922'
file_name: 2021_InternationalJournalOfMolecularSciences_Yotova.pdf
file_size: 2646018
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:29:17Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '16'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- '14220067'
issn:
- '16616596'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: LINC01133 inhibits invasion and promotes proliferation in an endometriosis
epithelial cell line
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: 22
year: '2021'
...
---
_id: '9910'
abstract:
- lang: eng
text: Adult height inspired the first biometrical and quantitative genetic studies
and is a test-case trait for understanding heritability. The studies of height
led to formulation of the classical polygenic model, that has a profound influence
on the way we view and analyse complex traits. An essential part of the classical
model is an assumption of additivity of effects and normality of the distribution
of the residuals. However, it may be expected that the normal approximation will
become insufficient in bigger studies. Here, we demonstrate that when the height
of hundreds of thousands of individuals is analysed, the model complexity needs
to be increased to include non-additive interactions between sex, environment
and genes. Alternatively, the use of log-normal approximation allowed us to still
use the additive effects model. These findings are important for future genetic
and methodologic studies that make use of adult height as an exemplar trait.
acknowledgement: "We are grateful to Marianna Bevova and Pavel Borodin for fruitful
discussion and help with conceptualising our findings and to Lennart C. Karssen
for help with handling the UK Biobank data.\r\n\r\nFunding\r\nThis research has
been conducted using the UK Biobank Resource (project # 41601, “Non-additive effects
in control of complex human traits”). The work of SAS, IAK, and TIS were supported
by Russian Ministry of Science and Education under the 5–100 Excellence Programme.
The work of YSA and TIA was supported by the Ministry of Education and Science of
the RF via the Institute of Cytology and Genetics SB RAS (project number 0324-2019-0040-C-01/AAAA-A17-117092070032-4).
FAK is supported by the ERC Consolidator Grant (ChrFL: 771209)."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Sergei A.
full_name: Slavskii, Sergei A.
last_name: Slavskii
- first_name: Ivan A.
full_name: Kuznetsov, Ivan A.
last_name: Kuznetsov
- first_name: Tatiana I.
full_name: Shashkova, Tatiana I.
last_name: Shashkova
- first_name: Georgii A.
full_name: Bazykin, Georgii A.
last_name: Bazykin
- first_name: Tatiana I.
full_name: Axenovich, Tatiana I.
last_name: Axenovich
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Yurii S.
full_name: Aulchenko, Yurii S.
last_name: Aulchenko
citation:
ama: Slavskii SA, Kuznetsov IA, Shashkova TI, et al. The limits of normal approximation
for adult height. European Journal of Human Genetics. 2021;29(7):1082-1091.
doi:10.1038/s41431-021-00836-7
apa: Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich,
T. I., Kondrashov, F., & Aulchenko, Y. S. (2021). The limits of normal approximation
for adult height. European Journal of Human Genetics. Springer Nature.
https://doi.org/10.1038/s41431-021-00836-7
chicago: Slavskii, Sergei A., Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A.
Bazykin, Tatiana I. Axenovich, Fyodor Kondrashov, and Yurii S. Aulchenko. “The
Limits of Normal Approximation for Adult Height.” European Journal of Human
Genetics. Springer Nature, 2021. https://doi.org/10.1038/s41431-021-00836-7.
ieee: S. A. Slavskii et al., “The limits of normal approximation for adult
height,” European Journal of Human Genetics, vol. 29, no. 7. Springer Nature,
pp. 1082–1091, 2021.
ista: Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov
F, Aulchenko YS. 2021. The limits of normal approximation for adult height. European
Journal of Human Genetics. 29(7), 1082–1091.
mla: Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.”
European Journal of Human Genetics, vol. 29, no. 7, Springer Nature, 2021,
pp. 1082–91, doi:10.1038/s41431-021-00836-7.
short: S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich,
F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091.
date_created: 2021-08-15T22:01:28Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-11T10:33:42Z
day: '01'
ddc:
- '576'
department:
- _id: FyKo
doi: 10.1038/s41431-021-00836-7
ec_funded: 1
external_id:
isi:
- '000625853200001'
pmid:
- '33664501'
file:
- access_level: open_access
checksum: a676d76f91b0dbe0504c63e469129c2a
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:14:36Z
date_updated: 2021-08-16T09:14:36Z
file_id: '9921'
file_name: 2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf
file_size: 1079395
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:14:36Z
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1082-1091
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: European Journal of Human Genetics
publication_identifier:
eissn:
- '14765438'
issn:
- '10184813'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The limits of normal approximation for adult height
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: 29
year: '2021'
...
---
_id: '9912'
abstract:
- lang: eng
text: "In the customary random matrix model for transport in quantum dots with M
internal degrees of freedom coupled to a chaotic environment via \U0001D441≪\U0001D440
channels, the density \U0001D70C of transmission eigenvalues is computed from
a specific invariant ensemble for which explicit formula for the joint probability
density of all eigenvalues is available. We revisit this problem in the large
N regime allowing for (i) arbitrary ratio \U0001D719:=\U0001D441/\U0001D440≤1;
and (ii) general distributions for the matrix elements of the Hamiltonian of the
quantum dot. In the limit \U0001D719→0, we recover the formula for the density
\U0001D70C that Beenakker (Rev Mod Phys 69:731–808, 1997) has derived for a special
matrix ensemble. We also prove that the inverse square root singularity of the
density at zero and full transmission in Beenakker’s formula persists for any
\U0001D719<1 but in the borderline case \U0001D719=1 an anomalous \U0001D706−2/3
singularity arises at zero. To access this level of generality, we develop the
theory of global and local laws on the spectral density of a large class of noncommutative
rational expressions in large random matrices with i.i.d. entries."
acknowledgement: The authors are very grateful to Yan Fyodorov for discussions on
the physical background and for providing references, and to the anonymous referee
for numerous valuable remarks.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
- first_name: Yuriy
full_name: Nemish, Yuriy
id: 4D902E6A-F248-11E8-B48F-1D18A9856A87
last_name: Nemish
orcid: 0000-0002-7327-856X
citation:
ama: Erdös L, Krüger TH, Nemish Y. Scattering in quantum dots via noncommutative
rational functions. Annales Henri Poincaré . 2021;22:4205–4269. doi:10.1007/s00023-021-01085-6
apa: Erdös, L., Krüger, T. H., & Nemish, Y. (2021). Scattering in quantum dots
via noncommutative rational functions. Annales Henri Poincaré . Springer
Nature. https://doi.org/10.1007/s00023-021-01085-6
chicago: Erdös, László, Torben H Krüger, and Yuriy Nemish. “Scattering in Quantum
Dots via Noncommutative Rational Functions.” Annales Henri Poincaré . Springer
Nature, 2021. https://doi.org/10.1007/s00023-021-01085-6.
ieee: L. Erdös, T. H. Krüger, and Y. Nemish, “Scattering in quantum dots via noncommutative
rational functions,” Annales Henri Poincaré , vol. 22. Springer Nature,
pp. 4205–4269, 2021.
ista: Erdös L, Krüger TH, Nemish Y. 2021. Scattering in quantum dots via noncommutative
rational functions. Annales Henri Poincaré . 22, 4205–4269.
mla: Erdös, László, et al. “Scattering in Quantum Dots via Noncommutative Rational
Functions.” Annales Henri Poincaré , vol. 22, Springer Nature, 2021, pp.
4205–4269, doi:10.1007/s00023-021-01085-6.
short: L. Erdös, T.H. Krüger, Y. Nemish, Annales Henri Poincaré 22 (2021) 4205–4269.
date_created: 2021-08-15T22:01:29Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2023-08-11T10:31:48Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00023-021-01085-6
ec_funded: 1
external_id:
arxiv:
- '1911.05112'
isi:
- '000681531500001'
file:
- access_level: open_access
checksum: 8d6bac0e2b0a28539608b0538a8e3b38
content_type: application/pdf
creator: dernst
date_created: 2022-05-12T12:50:27Z
date_updated: 2022-05-12T12:50:27Z
file_id: '11365'
file_name: 2021_AnnHenriPoincare_Erdoes.pdf
file_size: 1162454
relation: main_file
success: 1
file_date_updated: 2022-05-12T12:50:27Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 4205–4269
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: 'Annales Henri Poincaré '
publication_identifier:
eissn:
- 1424-0661
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scattering in quantum dots via noncommutative rational functions
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: 22
year: '2021'
...
---
_id: '9891'
abstract:
- lang: eng
text: 'Extending on ideas of Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127
(2019)], we present a modified “floating crystal” trial state for jellium (also
known as the classical homogeneous electron gas) with density equal to a characteristic
function. This allows us to show that three definitions of the jellium energy
coincide in dimensions d ≥ 2, thus extending the result of Cotar and Petrache
[“Equality of the Jellium and uniform electron gas next-order asymptotic terms
for Coulomb and Riesz potentials,” arXiv: 1707.07664 (2019)] and Lewin, Lieb,
and Seiringer [Phys. Rev. B 100, 035127 (2019)] that the three definitions coincide
in dimension d ≥ 3. We show that the jellium energy is also equivalent to a “renormalized
energy” studied in a series of papers by Serfaty and others, and thus, by the
work of Bétermin and Sandier [Constr. Approximation 47, 39–74 (2018)], we relate
the jellium energy to the order n term in the logarithmic energy of n points on
the unit 2-sphere. We improve upon known lower bounds for this renormalized energy.
Additionally, we derive formulas for the jellium energy of periodic configurations.'
acknowledgement: The author would like to thank Robert Seiringer for guidance and
many helpful comments on this project. The author would also like to thank Mathieu
Lewin for his comments on the manuscript and Lorenzo Portinale for providing his
lecture notes for the course “Mathematics of quantum many-body systems” in spring
2020, taught by Robert Seiringer. The Proof of Theorem III.1 is inspired by these
lecture notes.
article_number: '083305'
article_processing_charge: No
article_type: original
author:
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
citation:
ama: Lauritsen AB. Floating Wigner crystal and periodic jellium configurations.
Journal of Mathematical Physics. 2021;62(8). doi:10.1063/5.0053494
apa: Lauritsen, A. B. (2021). Floating Wigner crystal and periodic jellium configurations.
Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0053494
chicago: Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium
Configurations.” Journal of Mathematical Physics. AIP Publishing, 2021.
https://doi.org/10.1063/5.0053494.
ieee: A. B. Lauritsen, “Floating Wigner crystal and periodic jellium configurations,”
Journal of Mathematical Physics, vol. 62, no. 8. AIP Publishing, 2021.
ista: Lauritsen AB. 2021. Floating Wigner crystal and periodic jellium configurations.
Journal of Mathematical Physics. 62(8), 083305.
mla: Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium
Configurations.” Journal of Mathematical Physics, vol. 62, no. 8, 083305,
AIP Publishing, 2021, doi:10.1063/5.0053494.
short: A.B. Lauritsen, Journal of Mathematical Physics 62 (2021).
date_created: 2021-08-12T07:08:36Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-11T10:29:48Z
day: '01'
ddc:
- '530'
department:
- _id: GradSch
- _id: RoSe
doi: 10.1063/5.0053494
external_id:
arxiv:
- '2103.07975'
isi:
- '000683960800003'
file:
- access_level: open_access
checksum: d035be2b894c4d50d90ac5ce252e27cd
content_type: application/pdf
creator: cziletti
date_created: 2021-10-27T12:57:06Z
date_updated: 2021-10-27T12:57:06Z
file_id: '10188'
file_name: 2021_JMathPhy_Lauritsen.pdf
file_size: 4352640
relation: main_file
success: 1
file_date_updated: 2021-10-27T12:57:06Z
has_accepted_license: '1'
intvolume: ' 62'
isi: 1
issue: '8'
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Journal of Mathematical Physics
publication_identifier:
eissn:
- 1089-7658
issn:
- 0022-2488
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Floating Wigner crystal and periodic jellium configurations
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: 62
year: '2021'
...
---
_id: '9909'
abstract:
- lang: eng
text: Roots are composed of different root types and, in the dicotyledonous Arabidopsis,
typically consist of a primary root that branches into lateral roots. Adventitious
roots emerge from non-root tissue and are formed upon wounding or other types
of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis
hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously
applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was
less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a
more potent inhibitor at concentrations above 1 µM, suggesting that it was more
selective in triggering a root inhibition response. Analysis of a series of phosphonamide
and phosphonate pyrabactin analogs suggested that adventitious root formation
and lateral root branching are differentially regulated by ABA signaling. ABA
biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and
point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition.
acknowledgement: We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis
mutants and ABA signaling mutants.
article_number: '1141'
article_processing_charge: Yes
article_type: original
author:
- first_name: Yinwei
full_name: Zeng, Yinwei
last_name: Zeng
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Hoang Khai
full_name: Trinh, Hoang Khai
last_name: Trinh
- first_name: Thomas
full_name: Heugebaert, Thomas
last_name: Heugebaert
- first_name: Christian V.
full_name: Stevens, Christian V.
last_name: Stevens
- first_name: Irene
full_name: Garcia-Maquilon, Irene
last_name: Garcia-Maquilon
- first_name: Pedro L.
full_name: Rodriguez, Pedro L.
last_name: Rodriguez
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Danny
full_name: Geelen, Danny
last_name: Geelen
citation:
ama: Zeng Y, Verstraeten I, Trinh HK, et al. Arabidopsis hypocotyl adventitious
root formation is suppressed by ABA signaling. Genes. 2021;12(8). doi:10.3390/genes12081141
apa: Zeng, Y., Verstraeten, I., Trinh, H. K., Heugebaert, T., Stevens, C. V., Garcia-Maquilon,
I., … Geelen, D. (2021). Arabidopsis hypocotyl adventitious root formation is
suppressed by ABA signaling. Genes. MDPI. https://doi.org/10.3390/genes12081141
chicago: Zeng, Yinwei, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian
V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste, and Danny
Geelen. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA
Signaling.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12081141.
ieee: Y. Zeng et al., “Arabidopsis hypocotyl adventitious root formation
is suppressed by ABA signaling,” Genes, vol. 12, no. 8. MDPI, 2021.
ista: Zeng Y, Verstraeten I, Trinh HK, Heugebaert T, Stevens CV, Garcia-Maquilon
I, Rodriguez PL, Vanneste S, Geelen D. 2021. Arabidopsis hypocotyl adventitious
root formation is suppressed by ABA signaling. Genes. 12(8), 1141.
mla: Zeng, Yinwei, et al. “Arabidopsis Hypocotyl Adventitious Root Formation Is
Suppressed by ABA Signaling.” Genes, vol. 12, no. 8, 1141, MDPI, 2021,
doi:10.3390/genes12081141.
short: Y. Zeng, I. Verstraeten, H.K. Trinh, T. Heugebaert, C.V. Stevens, I. Garcia-Maquilon,
P.L. Rodriguez, S. Vanneste, D. Geelen, Genes 12 (2021).
date_created: 2021-08-15T22:01:28Z
date_published: 2021-07-27T00:00:00Z
date_updated: 2023-08-11T10:32:21Z
day: '27'
ddc:
- '580'
- '570'
department:
- _id: JiFr
doi: 10.3390/genes12081141
external_id:
isi:
- '000690558000001'
file:
- access_level: open_access
checksum: 3d99535618cf9a5b14d264408fa52e97
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:02:40Z
date_updated: 2021-08-16T09:02:40Z
file_id: '9919'
file_name: 2021_Genes_Zeng.pdf
file_size: 1340305
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:02:40Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '8'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Genes
publication_identifier:
eissn:
- '20734425'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9907'
abstract:
- lang: eng
text: 'DivIVA is a protein initially identified as a spatial regulator of cell division
in the model organism Bacillus subtilis, but its homologues are present in many
other Gram-positive bacteria, including Clostridia species. Besides its role as
topological regulator of the Min system during bacterial cell division, DivIVA
is involved in chromosome segregation during sporulation, genetic competence,
and cell wall synthesis. DivIVA localizes to regions of high membrane curvature,
such as the cell poles and cell division site, where it recruits distinct binding
partners. Previously, it was suggested that negative curvature sensing is the
main mechanism by which DivIVA binds to these specific regions. Here, we show
that Clostridioides difficile DivIVA binds preferably to membranes containing
negatively charged phospholipids, especially cardiolipin. Strikingly, we observed
that upon binding, DivIVA modifies the lipid distribution and induces changes
to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA
might play a more complex and so far unknown active role during the formation
of the cell division septal membrane. '
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "We thank Daniela Krajˇcíkova, Katarína Muchová, Zuzana Chromíkova
and other members of Barák’s laboratory for useful discussions, suggestions and
help. Special thanks also to Emília Chovancová for technical support. We are grateful
to Juraj Labaj for drawing the model and for help with graphics. Many thanks to
all members of Loose’s laboratory: Maria del Mar\r\nLópez, Paulo Caldas, Philipp
Radler, and other members of the Loose’s laboratory for sharing their knowledge
of SLB preparation and TIRF experiment chambers, for sharing coverslips and for
help with the TIRF microscope and data analysis. We also thank the members of the
Dept. of Biochemistry of Biomembranes at the Institute of Animal Biochemistry and
Genetics, CBs SAS for their help with preparing the lipid mixtures. We thank J.
Bauer for critically reading the manuscript."
article_number: '8350'
article_processing_charge: Yes
article_type: original
author:
- first_name: Naďa
full_name: Labajová, Naďa
last_name: Labajová
- first_name: Natalia S.
full_name: Baranova, Natalia S.
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Miroslav
full_name: Jurásek, Miroslav
last_name: Jurásek
- first_name: Robert
full_name: Vácha, Robert
last_name: Vácha
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Imrich
full_name: Barák, Imrich
last_name: Barák
citation:
ama: Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. Cardiolipin-containing
lipid membranes attract the bacterial cell division protein diviva. International
Journal of Molecular Sciences. 2021;22(15). doi:10.3390/ijms22158350
apa: Labajová, N., Baranova, N. S., Jurásek, M., Vácha, R., Loose, M., & Barák,
I. (2021). Cardiolipin-containing lipid membranes attract the bacterial cell division
protein diviva. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22158350
chicago: Labajová, Naďa, Natalia S. Baranova, Miroslav Jurásek, Robert Vácha, Martin
Loose, and Imrich Barák. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial
Cell Division Protein Diviva.” International Journal of Molecular Sciences.
MDPI, 2021. https://doi.org/10.3390/ijms22158350.
ieee: N. Labajová, N. S. Baranova, M. Jurásek, R. Vácha, M. Loose, and I. Barák,
“Cardiolipin-containing lipid membranes attract the bacterial cell division protein
diviva,” International Journal of Molecular Sciences, vol. 22, no. 15.
MDPI, 2021.
ista: Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. 2021. Cardiolipin-containing
lipid membranes attract the bacterial cell division protein diviva. International
Journal of Molecular Sciences. 22(15), 8350.
mla: Labajová, Naďa, et al. “Cardiolipin-Containing Lipid Membranes Attract the
Bacterial Cell Division Protein Diviva.” International Journal of Molecular
Sciences, vol. 22, no. 15, 8350, MDPI, 2021, doi:10.3390/ijms22158350.
short: N. Labajová, N.S. Baranova, M. Jurásek, R. Vácha, M. Loose, I. Barák, International
Journal of Molecular Sciences 22 (2021).
date_created: 2021-08-15T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-11T10:34:44Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.3390/ijms22158350
ec_funded: 1
external_id:
isi:
- '000681815400001'
pmid:
- '34361115'
file:
- access_level: open_access
checksum: a4bc06e9a2c803ceff5a91f10b174054
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:35:56Z
date_updated: 2021-08-16T09:35:56Z
file_id: '9923'
file_name: 2021_InternationalJournalOfMolecularSciences_Labajová .pdf
file_size: 6132410
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:35:56Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '15'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- '14220067'
issn:
- '16616596'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cardiolipin-containing lipid membranes attract the bacterial cell division
protein diviva
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: 22
year: '2021'
...
---
_id: '9905'
abstract:
- lang: eng
text: Vaccines are thought to be the best available solution for controlling the
ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains
may come too rapidly for current vaccine developments to alleviate the health,
economic and social consequences of the pandemic. To quantify and characterize
the risk of such a scenario, we created a SIR-derived model with initial stochastic
dynamics of the vaccine-resistant strain to study the probability of its emergence
and establishment. Using parameters realistically resembling SARS-CoV-2 transmission,
we model a wave-like pattern of the pandemic and consider the impact of the rate
of vaccination and the strength of non-pharmaceutical intervention measures on
the probability of emergence of a resistant strain. As expected, we found that
a fast rate of vaccination decreases the probability of emergence of a resistant
strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions
happened at a time when most individuals of the population have already been vaccinated
the probability of emergence of a resistant strain was greatly increased. Consequently,
we show that a period of transmission reduction close to the end of the vaccination
campaign can substantially reduce the probability of resistant strain establishment.
Our results suggest that policymakers and individuals should consider maintaining
non-pharmaceutical interventions and transmission-reducing behaviours throughout
the entire vaccination period.
acknowledgement: We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta,
Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants
of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España
for useful comments. The opinions expressed in this document are exclusively of
the authors and, therefore, do not necessarily coincide with those of the Banco
de España or the Eurosystem. ETD is supported by the Swiss National Science and
Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator
Grant (771209-CharFL).
article_number: '15729'
article_processing_charge: Yes
article_type: original
author:
- first_name: Simon
full_name: Rella, Simon
id: B4765ACA-AA38-11E9-AC9A-0930E6697425
last_name: Rella
- first_name: Yuliya A.
full_name: Kulikova, Yuliya A.
last_name: Kulikova
- first_name: Emmanouil T.
full_name: Dermitzakis, Emmanouil T.
last_name: Dermitzakis
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission
and vaccination impact the fate of vaccine-resistant strains. Scientific Reports.
2021;11(1). doi:10.1038/s41598-021-95025-3
apa: Rella, S., Kulikova, Y. A., Dermitzakis, E. T., & Kondrashov, F. (2021).
Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant
strains. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-95025-3
chicago: Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor
Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate
of Vaccine-Resistant Strains.” Scientific Reports. Springer Nature, 2021.
https://doi.org/10.1038/s41598-021-95025-3.
ieee: S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of
SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,”
Scientific Reports, vol. 11, no. 1. Springer Nature, 2021.
ista: Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2
transmission and vaccination impact the fate of vaccine-resistant strains. Scientific
Reports. 11(1), 15729.
mla: Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact
the Fate of Vaccine-Resistant Strains.” Scientific Reports, vol. 11, no.
1, 15729, Springer Nature, 2021, doi:10.1038/s41598-021-95025-3.
short: S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports
11 (2021).
date_created: 2021-08-15T22:01:26Z
date_published: 2021-07-30T00:00:00Z
date_updated: 2023-08-11T10:42:58Z
day: '30'
ddc:
- '570'
- '610'
department:
- _id: FyKo
doi: 10.1038/s41598-021-95025-3
ec_funded: 1
external_id:
isi:
- '000683329100001'
pmid:
- '34330988'
file:
- access_level: open_access
checksum: ac86892ed17e6724c7251844da5cef5c
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T11:36:49Z
date_updated: 2021-08-16T11:36:49Z
file_id: '9927'
file_name: 2021_ScientificReports_Rella.pdf
file_size: 3432001
relation: main_file
success: 1
file_date_updated: 2021-08-16T11:36:49Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: Scientific Reports
publication_identifier:
eissn:
- '20452322'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/
scopus_import: '1'
status: public
title: Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant
strains
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2021'
...
---
_id: '9903'
abstract:
- lang: eng
text: Eigenstate thermalization in quantum many-body systems implies that eigenstates
at high energy are similar to random vectors. Identifying systems where at least
some eigenstates are nonthermal is an outstanding question. In this Letter we
show that interacting quantum models that have a nullspace—a degenerate subspace
of eigenstates at zero energy (zero modes), which corresponds to infinite temperature,
provide a route to nonthermal eigenstates. We analytically show the existence
of a zero mode which can be represented as a matrix product state for a certain
class of local Hamiltonians. In the more general case we use a subspace disentangling
algorithm to generate an orthogonal basis of zero modes characterized by increasing
entanglement entropy. We show evidence for an area-law entanglement scaling of
the least-entangled zero mode in the broad parameter regime, leading to a conjecture
that all local Hamiltonians with the nullspace feature zero modes with area-law
entanglement scaling and, as such, break the strong thermalization hypothesis.
Finally, we find zero modes in constrained models and propose a setup for observing
their experimental signatures.
acknowledgement: "We acknowledge useful discussions with V. Gritsev and A. Garkun
and suggestions on implementation of the\r\nPPXPP model by D. Bluvstein. A. M. and
M. S. were supported by the European Research Council (ERC) under\r\nthe European
Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899)"
article_number: '060602'
article_processing_charge: Yes (in subscription journal)
article_type: letter_note
author:
- first_name: Volker
full_name: Karle, Volker
id: D7C012AE-D7ED-11E9-95E8-1EC5E5697425
last_name: Karle
orcid: 0000-0002-6963-0129
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
citation:
ama: Karle V, Serbyn M, Michailidis A. Area-law entangled eigenstates from nullspaces
of local Hamiltonians. Physical Review Letters. 2021;127(6). doi:10.1103/physrevlett.127.060602
apa: Karle, V., Serbyn, M., & Michailidis, A. (2021). Area-law entangled eigenstates
from nullspaces of local Hamiltonians. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/physrevlett.127.060602
chicago: Karle, Volker, Maksym Serbyn, and Alexios Michailidis. “Area-Law Entangled
Eigenstates from Nullspaces of Local Hamiltonians.” Physical Review Letters.
American Physical Society, 2021. https://doi.org/10.1103/physrevlett.127.060602.
ieee: V. Karle, M. Serbyn, and A. Michailidis, “Area-law entangled eigenstates from
nullspaces of local Hamiltonians,” Physical Review Letters, vol. 127, no.
6. American Physical Society, 2021.
ista: Karle V, Serbyn M, Michailidis A. 2021. Area-law entangled eigenstates from
nullspaces of local Hamiltonians. Physical Review Letters. 127(6), 060602.
mla: Karle, Volker, et al. “Area-Law Entangled Eigenstates from Nullspaces of Local
Hamiltonians.” Physical Review Letters, vol. 127, no. 6, 060602, American
Physical Society, 2021, doi:10.1103/physrevlett.127.060602.
short: V. Karle, M. Serbyn, A. Michailidis, Physical Review Letters 127 (2021).
date_created: 2021-08-13T09:27:39Z
date_published: 2021-08-06T00:00:00Z
date_updated: 2023-08-11T10:43:27Z
day: '06'
ddc:
- '539'
department:
- _id: MaSe
- _id: GradSch
- _id: MiLe
doi: 10.1103/physrevlett.127.060602
ec_funded: 1
external_id:
arxiv:
- '2102.13633'
isi:
- '000684276000002'
file:
- access_level: open_access
checksum: 51218f302dcef99d90d1209809fcc874
content_type: application/pdf
creator: mserbyn
date_created: 2021-08-13T09:28:08Z
date_updated: 2021-08-13T09:28:08Z
file_id: '9904'
file_name: PhysRevLett.127.060602_SOM.pdf
file_size: 5064231
relation: main_file
success: 1
file_date_updated: 2021-08-13T09:28:08Z
has_accepted_license: '1'
intvolume: ' 127'
isi: 1
issue: '6'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Area-law entangled eigenstates from nullspaces of local Hamiltonians
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: 127
year: '2021'
...
---
_id: '9952'
abstract:
- lang: eng
text: Proper control of division orientation and symmetry, largely determined by
spindle positioning, is essential to development and homeostasis. Spindle positioning
has been extensively studied in cells dividing in two-dimensional (2D) environments
and in epithelial tissues, where proteins such as NuMA (also known as NUMA1) orient
division along the interphase long axis of the cell. However, little is known
about how cells control spindle positioning in three-dimensional (3D) environments,
such as early mammalian embryos and a variety of adult tissues. Here, we use mouse
embryonic stem cells (ESCs), which grow in 3D colonies, as a model to investigate
division in 3D. We observe that, at the periphery of 3D colonies, ESCs display
high spindle mobility and divide asymmetrically. Our data suggest that enhanced
spindle movements are due to unequal distribution of the cell–cell junction protein
E-cadherin between future daughter cells. Interestingly, when cells progress towards
differentiation, division becomes more symmetric, with more elongated shapes in
metaphase and enhanced cortical NuMA recruitment in anaphase. Altogether, this
study suggests that in 3D contexts, the geometry of the cell and its contacts
with neighbors control division orientation and symmetry.
acknowledgement: We would like to thank the entire Paluch and Baum laboratories at
the MRC-LMCB and the Chalut lab at the Cambridge SCI for discussions and feedback
throughout the project, and the MRC-LMCB microscopy platform, in particular Andrew
Vaughan, for technical support.
article_number: jcs255018
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Agathe
full_name: Chaigne, Agathe
last_name: Chaigne
- first_name: Matthew B.
full_name: Smith, Matthew B.
last_name: Smith
- first_name: R. L.
full_name: Cavestany, R. L.
last_name: Cavestany
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Kevin J.
full_name: Chalut, Kevin J.
last_name: Chalut
- first_name: Ewa K.
full_name: Paluch, Ewa K.
last_name: Paluch
citation:
ama: Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. Three-dimensional
geometry controls division symmetry in stem cell colonies. Journal of Cell
Science. 2021;134(14). doi:10.1242/jcs.255018
apa: Chaigne, A., Smith, M. B., Cavestany, R. L., Hannezo, E. B., Chalut, K. J.,
& Paluch, E. K. (2021). Three-dimensional geometry controls division symmetry
in stem cell colonies. Journal of Cell Science. The Company of Biologists.
https://doi.org/10.1242/jcs.255018
chicago: Chaigne, Agathe, Matthew B. Smith, R. L. Cavestany, Edouard B Hannezo,
Kevin J. Chalut, and Ewa K. Paluch. “Three-Dimensional Geometry Controls Division
Symmetry in Stem Cell Colonies.” Journal of Cell Science. The Company of
Biologists, 2021. https://doi.org/10.1242/jcs.255018.
ieee: A. Chaigne, M. B. Smith, R. L. Cavestany, E. B. Hannezo, K. J. Chalut, and
E. K. Paluch, “Three-dimensional geometry controls division symmetry in stem cell
colonies,” Journal of Cell Science, vol. 134, no. 14. The Company of Biologists,
2021.
ista: Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. 2021.
Three-dimensional geometry controls division symmetry in stem cell colonies. Journal
of Cell Science. 134(14), jcs255018.
mla: Chaigne, Agathe, et al. “Three-Dimensional Geometry Controls Division Symmetry
in Stem Cell Colonies.” Journal of Cell Science, vol. 134, no. 14, jcs255018,
The Company of Biologists, 2021, doi:10.1242/jcs.255018.
short: A. Chaigne, M.B. Smith, R.L. Cavestany, E.B. Hannezo, K.J. Chalut, E.K. Paluch,
Journal of Cell Science 134 (2021).
date_created: 2021-08-22T22:01:20Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-11T10:55:36Z
day: '01'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1242/jcs.255018
external_id:
isi:
- '000681395800008'
file:
- access_level: open_access
checksum: f086f9d7cb63b2474c01921cb060c513
content_type: application/pdf
creator: asandaue
date_created: 2021-08-23T07:32:20Z
date_updated: 2021-08-23T07:32:20Z
file_id: '9954'
file_name: 2021_JournalOfCellScience_Chaigne.pdf
file_size: 8651724
relation: main_file
success: 1
file_date_updated: 2021-08-23T07:32:20Z
has_accepted_license: '1'
intvolume: ' 134'
isi: 1
issue: '14'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Journal of Cell Science
publication_identifier:
eissn:
- '14779137'
issn:
- '00219533'
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Three-dimensional geometry controls division symmetry in stem cell colonies
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: 134
year: '2021'
...
---
_id: '9908'
abstract:
- lang: eng
text: About eight million animal species are estimated to live on Earth, and all
except those belonging to one subphylum are invertebrates. Invertebrates are incredibly
diverse in their morphologies, life histories, and in the range of the ecological
niches that they occupy. A great variety of modes of reproduction and sex determination
systems is also observed among them, and their mosaic-distribution across the
phylogeny shows that transitions between them occur frequently and rapidly. Genetic
conflict in its various forms is a long-standing theory to explain what drives
those evolutionary transitions. Here, we review (1) the different modes of reproduction
among invertebrate species, highlighting sexual reproduction as the probable ancestral
state; (2) the paradoxical diversity of sex determination systems; (3) the different
types of genetic conflicts that could drive the evolution of such different systems.
article_number: '1136'
article_processing_charge: Yes
article_type: review
author:
- first_name: Marion A L
full_name: Picard, Marion A L
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Stéphanie
full_name: Bertrand, Stéphanie
last_name: Bertrand
- first_name: Hector
full_name: Escriva, Hector
last_name: Escriva
citation:
ama: Picard MAL, Vicoso B, Bertrand S, Escriva H. Diversity of modes of reproduction
and sex determination systems in invertebrates, and the putative contribution
of genetic conflict. Genes. 2021;12(8). doi:10.3390/genes12081136
apa: Picard, M. A. L., Vicoso, B., Bertrand, S., & Escriva, H. (2021). Diversity
of modes of reproduction and sex determination systems in invertebrates, and the
putative contribution of genetic conflict. Genes. MDPI. https://doi.org/10.3390/genes12081136
chicago: Picard, Marion A L, Beatriz Vicoso, Stéphanie Bertrand, and Hector Escriva.
“Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates,
and the Putative Contribution of Genetic Conflict.” Genes. MDPI, 2021.
https://doi.org/10.3390/genes12081136.
ieee: M. A. L. Picard, B. Vicoso, S. Bertrand, and H. Escriva, “Diversity of modes
of reproduction and sex determination systems in invertebrates, and the putative
contribution of genetic conflict,” Genes, vol. 12, no. 8. MDPI, 2021.
ista: Picard MAL, Vicoso B, Bertrand S, Escriva H. 2021. Diversity of modes of reproduction
and sex determination systems in invertebrates, and the putative contribution
of genetic conflict. Genes. 12(8), 1136.
mla: Picard, Marion A. L., et al. “Diversity of Modes of Reproduction and Sex Determination
Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.”
Genes, vol. 12, no. 8, 1136, MDPI, 2021, doi:10.3390/genes12081136.
short: M.A.L. Picard, B. Vicoso, S. Bertrand, H. Escriva, Genes 12 (2021).
date_created: 2021-08-15T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-11T10:42:32Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.3390/genes12081136
ec_funded: 1
external_id:
isi:
- '000690475900001'
file:
- access_level: open_access
checksum: 744e60e56d290a96da3c91a9779f886f
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:49:35Z
date_updated: 2021-08-16T09:49:35Z
file_id: '9926'
file_name: 2021_Genes_Picard.pdf
file_size: 2297655
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:49:35Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Genes
publication_identifier:
eissn:
- '20734425'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diversity of modes of reproduction and sex determination systems in invertebrates,
and the putative contribution of genetic conflict
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9829'
abstract:
- lang: eng
text: In 2020, many in-person scientific events were canceled due to the COVID-19
pandemic, creating a vacuum in networking and knowledge exchange between scientists.
To fill this void in scientific communication, a group of early career nanocrystal
enthusiasts launched the virtual seminar series, News in Nanocrystals, in the
summer of 2020. By the end of the year, the series had attracted over 850 participants
from 46 countries. In this Nano Focus, we describe the process of organizing the
News in Nanocrystals seminar series; discuss its growth, emphasizing what the
organizers have learned in terms of diversity and accessibility; and provide an
outlook for the next steps and future opportunities. This summary and analysis
of experiences and learned lessons are intended to inform the broader scientific
community, especially those who are looking for avenues to continue fostering
discussion and scientific engagement virtually, both during the pandemic and after.
acknowledgement: K. E. Shulenberger, M. D. Klein, T. Šverko, and H. R. Keller would
like to thank Professors Moungi Bawendi (MIT) and Gordana Dukovic (CU Boulder) for
their feedback and support of the News in Nanocrystals initiative. The authors thank
Madison Jilek (CU Boulder) and Dhananjeya Kumaar (ETH Zurich) for their help in
the organization of the seminar, and Professors Brandi Cossairt (University of Washington)
and Gordana Dukovic for their feedback on an earlier version of this manuscript.
The authors thank all the seminar speakers and attendees for their interest and
continuing participation in the seminar series.
article_processing_charge: No
article_type: original
author:
- first_name: Dmitry
full_name: Baranov, Dmitry
last_name: Baranov
- first_name: Tara
full_name: Šverko, Tara
last_name: Šverko
- first_name: Taylor
full_name: Moot, Taylor
last_name: Moot
- first_name: Helena R.
full_name: Keller, Helena R.
last_name: Keller
- first_name: Megan D.
full_name: Klein, Megan D.
last_name: Klein
- first_name: E. K.
full_name: Vishnu, E. K.
last_name: Vishnu
- first_name: Daniel
full_name: Balazs, Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- first_name: Katherine E.
full_name: Shulenberger, Katherine E.
last_name: Shulenberger
citation:
ama: 'Baranov D, Šverko T, Moot T, et al. News in Nanocrystals seminar: Self-assembly
of early career researchers toward globally accessible nanoscience. ACS Nano.
2021;15(7):10743–10747. doi:10.1021/acsnano.1c03276'
apa: 'Baranov, D., Šverko, T., Moot, T., Keller, H. R., Klein, M. D., Vishnu, E.
K., … Shulenberger, K. E. (2021). News in Nanocrystals seminar: Self-assembly
of early career researchers toward globally accessible nanoscience. ACS Nano.
American Chemical Society. https://doi.org/10.1021/acsnano.1c03276'
chicago: 'Baranov, Dmitry, Tara Šverko, Taylor Moot, Helena R. Keller, Megan D.
Klein, E. K. Vishnu, Daniel Balazs, and Katherine E. Shulenberger. “News in Nanocrystals
Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible
Nanoscience.” ACS Nano. American Chemical Society, 2021. https://doi.org/10.1021/acsnano.1c03276.'
ieee: 'D. Baranov et al., “News in Nanocrystals seminar: Self-assembly of
early career researchers toward globally accessible nanoscience,” ACS Nano,
vol. 15, no. 7. American Chemical Society, pp. 10743–10747, 2021.'
ista: 'Baranov D, Šverko T, Moot T, Keller HR, Klein MD, Vishnu EK, Balazs D, Shulenberger
KE. 2021. News in Nanocrystals seminar: Self-assembly of early career researchers
toward globally accessible nanoscience. ACS Nano. 15(7), 10743–10747.'
mla: 'Baranov, Dmitry, et al. “News in Nanocrystals Seminar: Self-Assembly of Early
Career Researchers toward Globally Accessible Nanoscience.” ACS Nano, vol.
15, no. 7, American Chemical Society, 2021, pp. 10743–10747, doi:10.1021/acsnano.1c03276.'
short: D. Baranov, T. Šverko, T. Moot, H.R. Keller, M.D. Klein, E.K. Vishnu, D.
Balazs, K.E. Shulenberger, ACS Nano 15 (2021) 10743–10747.
date_created: 2021-08-08T22:01:31Z
date_published: 2021-07-06T00:00:00Z
date_updated: 2023-08-11T10:55:08Z
day: '06'
department:
- _id: MaIb
doi: 10.1021/acsnano.1c03276
external_id:
isi:
- '000679406500002'
pmid:
- '34228432'
intvolume: ' 15'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/acsnano.1c03276
month: '07'
oa: 1
oa_version: Published Version
page: 10743–10747
pmid: 1
publication: ACS Nano
publication_identifier:
eissn:
- 1936086X
issn:
- '19360851'
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'News in Nanocrystals seminar: Self-assembly of early career researchers toward
globally accessible nanoscience'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2021'
...
---
_id: '13057'
abstract:
- lang: eng
text: 'This dataset comprises all data shown in the figures of the submitted article
"Geometric superinductance qubits: Controlling phase delocalization across a single
Josephson junction". Additional raw data are available from the corresponding
author on reasonable request.'
article_processing_charge: No
author:
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Grisha
full_name: Szep, Grisha
last_name: Szep
- first_name: Andrea
full_name: Trioni, Andrea
id: 42F71B44-F248-11E8-B48F-1D18A9856A87
last_name: Trioni
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: 'Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling
phase delocalization across a single Josephson junction. 2021. doi:10.5281/ZENODO.5592103'
apa: 'Peruzzo, M., Hassani, F., Szep, G., Trioni, A., Redchenko, E., Zemlicka, M.,
& Fink, J. M. (2021). Geometric superinductance qubits: Controlling phase
delocalization across a single Josephson junction. Zenodo. https://doi.org/10.5281/ZENODO.5592103'
chicago: 'Peruzzo, Matilda, Farid Hassani, Grisha Szep, Andrea Trioni, Elena Redchenko,
Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling
Phase Delocalization across a Single Josephson Junction.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5592103.'
ieee: 'M. Peruzzo et al., “Geometric superinductance qubits: Controlling
phase delocalization across a single Josephson junction.” Zenodo, 2021.'
ista: 'Peruzzo M, Hassani F, Szep G, Trioni A, Redchenko E, Zemlicka M, Fink JM.
2021. Geometric superinductance qubits: Controlling phase delocalization across
a single Josephson junction, Zenodo, 10.5281/ZENODO.5592103.'
mla: 'Peruzzo, Matilda, et al. Geometric Superinductance Qubits: Controlling
Phase Delocalization across a Single Josephson Junction. Zenodo, 2021, doi:10.5281/ZENODO.5592103.'
short: M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M.
Fink, (2021).
date_created: 2023-05-23T13:42:27Z
date_published: 2021-10-22T00:00:00Z
date_updated: 2023-08-11T10:44:21Z
day: '22'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.5281/ZENODO.5592103
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5592104
month: '10'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '9928'
relation: used_in_publication
status: public
status: public
title: 'Geometric superinductance qubits: Controlling phase delocalization across
a single Josephson junction'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9985'
abstract:
- lang: eng
text: AMPA receptor (AMPAR) abundance and positioning at excitatory synapses regulates
the strength of transmission. Changes in AMPAR localisation can enact synaptic
plasticity, allowing long-term information storage, and is therefore tightly controlled.
Multiple mechanisms regulating AMPAR synaptic anchoring have been described, but
with limited coherence or comparison between reports, our understanding of this
process is unclear. Here, combining synaptic recordings from mouse hippocampal
slices and super-resolution imaging in dissociated cultures, we compare the contributions
of three AMPAR interaction domains controlling transmission at hippocampal CA1
synapses. We show that the AMPAR C-termini play only a modulatory role, whereas
the extracellular N-terminal domain (NTD) and PDZ interactions of the auxiliary
subunit TARP γ8 are both crucial, and each is sufficient to maintain transmission.
Our data support a model in which γ8 accumulates AMPARs at the postsynaptic density,
where the NTD further tunes their positioning. This interplay between cytosolic
(TARP γ8) and synaptic cleft (NTD) interactions provides versatility to regulate
synaptic transmission and plasticity.
acknowledgement: The authors are very grateful to Andrew Penn for advice and discussions
on surface receptor labelling in slice tissue, dissociated culture transfection,
and for providing tdTomato and BirAER expression plasmids. This work would not have
been possible without support from the Biological Services teams at both the Laboratory
of Molecular Biology and Ares facilities. We are also very grateful to Nick Barry
and Jerome Boulanger of the LMB Light Microscopy facility for support with confocal
and STORM imaging and analysis, Junichi Takagi for providing scFv-Clasp expression
constructs, Veronica Chang for assistance with scFv-Clasp protein production, and
Nejc Kejzar for assistance with cluster analysis. We would like to thank Teru Nakagawa
and Ole Paulsen for critical reading of the manuscript and constructive feedback.
This work was supported by grants from the Medical Research Council (MC_U105174197)
and BBSRC (BB/N002113/1).
article_number: '5083'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Alexandra
full_name: Pinggera, Alexandra
last_name: Pinggera
- first_name: Hinze
full_name: Ho, Hinze
last_name: Ho
- first_name: Ingo H.
full_name: Greger, Ingo H.
last_name: Greger
citation:
ama: Watson J, Pinggera A, Ho H, Greger IH. AMPA receptor anchoring at CA1 synapses
is determined by N-terminal domain and TARP γ8 interactions. Nature Communications.
2021;12(1). doi:10.1038/s41467-021-25281-4
apa: Watson, J., Pinggera, A., Ho, H., & Greger, I. H. (2021). AMPA receptor
anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions.
Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-021-25281-4
chicago: Watson, Jake, Alexandra Pinggera, Hinze Ho, and Ingo H. Greger. “AMPA Receptor
Anchoring at CA1 Synapses Is Determined by N-Terminal Domain and TARP Γ8 Interactions.”
Nature Communications. Nature Publishing Group, 2021. https://doi.org/10.1038/s41467-021-25281-4.
ieee: J. Watson, A. Pinggera, H. Ho, and I. H. Greger, “AMPA receptor anchoring
at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions,”
Nature Communications, vol. 12, no. 1. Nature Publishing Group, 2021.
ista: Watson J, Pinggera A, Ho H, Greger IH. 2021. AMPA receptor anchoring at CA1
synapses is determined by N-terminal domain and TARP γ8 interactions. Nature Communications.
12(1), 5083.
mla: Watson, Jake, et al. “AMPA Receptor Anchoring at CA1 Synapses Is Determined
by N-Terminal Domain and TARP Γ8 Interactions.” Nature Communications,
vol. 12, no. 1, 5083, Nature Publishing Group, 2021, doi:10.1038/s41467-021-25281-4.
short: J. Watson, A. Pinggera, H. Ho, I.H. Greger, Nature Communications 12 (2021).
date_created: 2021-09-05T22:01:23Z
date_published: 2021-08-23T00:00:00Z
date_updated: 2023-08-11T11:07:51Z
day: '23'
ddc:
- '612'
department:
- _id: PeJo
doi: 10.1038/s41467-021-25281-4
external_id:
isi:
- '000687672000006'
pmid:
- '34426577 '
file:
- access_level: open_access
checksum: 1bf4f6a561f96bc426d754de9cb57710
content_type: application/pdf
creator: cchlebak
date_created: 2021-09-08T12:57:06Z
date_updated: 2021-09-08T12:57:06Z
file_id: '9991'
file_name: 2021_NatureCommunications_Watson.pdf
file_size: 18310502
relation: main_file
success: 1
file_date_updated: 2021-09-08T12:57:06Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain
and TARP γ8 interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9981'
abstract:
- lang: eng
text: "The numerical simulation of dynamical phenomena in interacting quantum systems
is a notoriously hard problem. Although a number of promising numerical methods
exist, they often have limited applicability due to the growth of entanglement
or the presence of the so-called sign problem. In this work, we develop an importance
sampling scheme for the simulation of quantum spin dynamics, building on a recent
approach mapping quantum spin systems to classical stochastic processes. The importance
sampling scheme is based on identifying the classical trajectory that yields the
largest contribution to a given quantum observable. An exact transformation is
then carried out to preferentially sample trajectories that are close to the dominant
one. We demonstrate that this approach is capable of reducing the temporal growth
of fluctuations in the stochastic quantities, thus extending the range of accessible
times and system sizes compared to direct sampling. We discuss advantages and
limitations of the proposed approach, outlining directions\r\nfor further developments."
article_number: '048'
article_processing_charge: No
article_type: original
author:
- first_name: Stefano
full_name: De Nicola, Stefano
id: 42832B76-F248-11E8-B48F-1D18A9856A87
last_name: De Nicola
orcid: 0000-0002-4842-6671
citation:
ama: De Nicola S. Importance sampling scheme for the stochastic simulation of quantum
spin dynamics. SciPost Physics. 2021;11(3). doi:10.21468/scipostphys.11.3.048
apa: De Nicola, S. (2021). Importance sampling scheme for the stochastic simulation
of quantum spin dynamics. SciPost Physics. SciPost. https://doi.org/10.21468/scipostphys.11.3.048
chicago: De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation
of Quantum Spin Dynamics.” SciPost Physics. SciPost, 2021. https://doi.org/10.21468/scipostphys.11.3.048.
ieee: S. De Nicola, “Importance sampling scheme for the stochastic simulation of
quantum spin dynamics,” SciPost Physics, vol. 11, no. 3. SciPost, 2021.
ista: De Nicola S. 2021. Importance sampling scheme for the stochastic simulation
of quantum spin dynamics. SciPost Physics. 11(3), 048.
mla: De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation
of Quantum Spin Dynamics.” SciPost Physics, vol. 11, no. 3, 048, SciPost,
2021, doi:10.21468/scipostphys.11.3.048.
short: S. De Nicola, SciPost Physics 11 (2021).
date_created: 2021-09-02T11:49:47Z
date_published: 2021-09-02T00:00:00Z
date_updated: 2023-08-11T10:59:29Z
day: '02'
ddc:
- '519'
department:
- _id: MaSe
doi: 10.21468/scipostphys.11.3.048
ec_funded: 1
external_id:
arxiv:
- '2103.16468'
isi:
- '000692534200001'
file:
- access_level: open_access
checksum: e4ec69d893e31811efc6093cb6ea8eb7
content_type: application/pdf
creator: cchlebak
date_created: 2021-09-02T14:05:43Z
date_updated: 2021-09-02T14:05:43Z
file_id: '9984'
file_name: 2021_SciPostPhys_DeNicola.pdf
file_size: 373833
relation: main_file
success: 1
file_date_updated: 2021-09-02T14:05:43Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '3'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: SciPost Physics
publication_identifier:
eissn:
- 2666-9366
issn:
- 2542-4653
publication_status: published
publisher: SciPost
quality_controlled: '1'
status: public
title: Importance sampling scheme for the stochastic simulation of quantum spin dynamics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2021'
...
---
_id: '9951'
abstract:
- lang: eng
text: "There has recently been a surge of interest in the computational and complexity
properties of the population model, which assumes n anonymous, computationally-bounded
nodes, interacting at random, with the goal of jointly computing global predicates.
Significant work has gone towards investigating majority or consensus dynamics
in this model: that is, assuming that every node is initially in one of two states
X or Y, determine which state had higher initial count.\r\n\r\nIn this paper,
we consider a natural generalization of majority/consensus, which we call comparison
: in its simplest formulation, we are given two baseline states, X and Y, present
in any initial configuration in fixed, but possibly small counts. One of these
states has higher count than the other: we will assume |X_0| > C |Y_0| for some
constant C > 1. The challenge is to design a protocol by which nodes can quickly
and reliably decide on which of the baseline states X_0 and Y_0 has higher initial
count. We begin by analyzing a simple and general dynamics solving the above comparison
problem, which uses O( log n ) states per node, and converges in O(log n) (parallel)
time, with high probability, to a state where the whole population votes on opinions
X or Y at rates proportional to the initial concentrations of |X_0| vs. |Y_0|.
We then describe how this procedure can be bootstrapped to solve comparison, i.e.
have every node in the population reach the \"correct'' decision, with probability
1 - o(1), at the cost of O (log log n) additional states. Further, we prove that
this dynamics is self-stabilizing, in the sense that it converges to the correct
decision from arbitrary initial states, and leak-robust, in the sense that it
can withstand spurious faulty reactions, which are known to occur in practical
implementations of population protocols. Our analysis is based on a new martingale
concentration result relating the discrete-time evolution of a population protocol
to its expected (steady-state) analysis, which should be a useful tool when analyzing
opinion dynamics and epidemic dissemination in the population model."
acknowledgement: We would like to thank Rati Gelashvili for very useful discussions,
and the PODC anonymous reviewers for their careful reading of our paper, and for
their useful remarks. This work is partially supported by the Polish National Science
Center (NCN) grant UMO2017/25/B/ST6/02010.
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Martin
full_name: Töpfer, Martin
id: 4B865388-F248-11E8-B48F-1D18A9856A87
last_name: Töpfer
- first_name: Przemysław
full_name: Uznański, Przemysław
last_name: Uznański
citation:
ama: 'Alistarh D-A, Töpfer M, Uznański P. Comparison dynamics in population protocols.
In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing.
Association for Computing Machinery; 2021:55-65. doi:10.1145/3465084.3467915'
apa: 'Alistarh, D.-A., Töpfer, M., & Uznański, P. (2021). Comparison dynamics
in population protocols. In Proceedings of the 2021 ACM Symposium on Principles
of Distributed Computing (pp. 55–65). Virtual, Italy: Association for Computing
Machinery. https://doi.org/10.1145/3465084.3467915'
chicago: Alistarh, Dan-Adrian, Martin Töpfer, and Przemysław Uznański. “Comparison
Dynamics in Population Protocols.” In Proceedings of the 2021 ACM Symposium
on Principles of Distributed Computing, 55–65. Association for Computing Machinery,
2021. https://doi.org/10.1145/3465084.3467915.
ieee: D.-A. Alistarh, M. Töpfer, and P. Uznański, “Comparison dynamics in population
protocols,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed
Computing, Virtual, Italy, 2021, pp. 55–65.
ista: 'Alistarh D-A, Töpfer M, Uznański P. 2021. Comparison dynamics in population
protocols. Proceedings of the 2021 ACM Symposium on Principles of Distributed
Computing. PODC: Symposium on Principles of Distributed Computing, 55–65.'
mla: Alistarh, Dan-Adrian, et al. “Comparison Dynamics in Population Protocols.”
Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing,
Association for Computing Machinery, 2021, pp. 55–65, doi:10.1145/3465084.3467915.
short: D.-A. Alistarh, M. Töpfer, P. Uznański, in:, Proceedings of the 2021 ACM
Symposium on Principles of Distributed Computing, Association for Computing Machinery,
2021, pp. 55–65.
conference:
end_date: 2021-07-30
location: Virtual, Italy
name: 'PODC: Symposium on Principles of Distributed Computing'
start_date: 2021-07-26
date_created: 2021-08-22T22:01:20Z
date_published: 2021-07-21T00:00:00Z
date_updated: 2023-08-11T10:56:04Z
day: '21'
department:
- _id: DaAl
doi: 10.1145/3465084.3467915
external_id:
isi:
- '000744439800005'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 55-65
publication: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing
publication_identifier:
isbn:
- '9781450385480'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Comparison dynamics in population protocols
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9960'
abstract:
- lang: eng
text: The control of many-body quantum dynamics in complex systems is a key challenge
in the quest to reliably produce and manipulate large-scale quantum entangled
states. Recently, quench experiments in Rydberg atom arrays [Bluvstein et al.
Science 371, 1355 (2021)] demonstrated that coherent revivals associated with
quantum many-body scars can be stabilized by periodic driving, generating stable
subharmonic responses over a wide parameter regime. We analyze a simple, related
model where these phenomena originate from spatiotemporal ordering in an effective
Floquet unitary, corresponding to discrete time-crystalline behavior in a prethermal
regime. Unlike conventional discrete time crystals, the subharmonic response exists
only for Néel-like initial states, associated with quantum scars. We predict robustness
to perturbations and identify emergent timescales that could be observed in future
experiments. Our results suggest a route to controlling entanglement in interacting
quantum systems by combining periodic driving with many-body scars.
acknowledgement: We thank Dmitry Abanin, Ehud Altman, Iris Cong, Sepehr Ebadi, Alex
Keesling, Harry Levine, Ahmed Omran, Hannes Pichler, Rhine Samajdar, Guilia Semeghini,
Tout Wang, Norman Yao, and Harry Zhou or stimulating discussions. We acknowledge
support from the Center for Ultracold Atoms, the National Science Foundation, the
Vannevar Bush Faculty Fellowship, the U.S. Department of Energy, the Army Research
Office MURI, and the DARPA ONISQ program (M. L., N. M, W. W. H., D. B.); the European
Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation
Programme Grant Agreement No. 850899 (A. M. and M. S.); the Department of Energy
Computational Science Graduate Fellowship under Awards No. DESC0021110 (N. M.);
the Moore Foundation EPiQS initiative Grant No. GBMF4306, the National University
of Singapore (NUS) Development Grant AY2019/2020 and the Stanford Institute for
Theoretical Physics (W. W. H.); the NSF Graduate Research Fellowship Program (Grant
No. DGE1745303) and The Fannie and John Hertz Foundation (D. B.); the Miller Institute
for Basic Research in Science (S. C.); DOE Quantum Systems Accelerator – Contract
No. 7568717; and DOE Programmable Quantum Simulators for Lattice Gauge Theories
and Gauge-Gravity Correspondence – Grant No. DE-SC0021013.
article_number: '090602'
article_processing_charge: No
article_type: letter_note
author:
- first_name: N.
full_name: Maskara, N.
last_name: Maskara
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: W. W.
full_name: Ho, W. W.
last_name: Ho
- first_name: D.
full_name: Bluvstein, D.
last_name: Bluvstein
- first_name: S.
full_name: Choi, S.
last_name: Choi
- first_name: M. D.
full_name: Lukin, M. D.
last_name: Lukin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: 'Maskara N, Michailidis A, Ho WW, et al. Discrete time-crystalline order enabled
by quantum many-body scars: Entanglement steering via periodic driving. Physical
Review Letters. 2021;127(9). doi:10.1103/PhysRevLett.127.090602'
apa: 'Maskara, N., Michailidis, A., Ho, W. W., Bluvstein, D., Choi, S., Lukin, M.
D., & Serbyn, M. (2021). Discrete time-crystalline order enabled by quantum
many-body scars: Entanglement steering via periodic driving. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.127.090602'
chicago: 'Maskara, N., Alexios Michailidis, W. W. Ho, D. Bluvstein, S. Choi, M.
D. Lukin, and Maksym Serbyn. “Discrete Time-Crystalline Order Enabled by Quantum
Many-Body Scars: Entanglement Steering via Periodic Driving.” Physical Review
Letters. American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.127.090602.'
ieee: 'N. Maskara et al., “Discrete time-crystalline order enabled by quantum
many-body scars: Entanglement steering via periodic driving,” Physical Review
Letters, vol. 127, no. 9. American Physical Society, 2021.'
ista: 'Maskara N, Michailidis A, Ho WW, Bluvstein D, Choi S, Lukin MD, Serbyn M.
2021. Discrete time-crystalline order enabled by quantum many-body scars: Entanglement
steering via periodic driving. Physical Review Letters. 127(9), 090602.'
mla: 'Maskara, N., et al. “Discrete Time-Crystalline Order Enabled by Quantum Many-Body
Scars: Entanglement Steering via Periodic Driving.” Physical Review Letters,
vol. 127, no. 9, 090602, American Physical Society, 2021, doi:10.1103/PhysRevLett.127.090602.'
short: N. Maskara, A. Michailidis, W.W. Ho, D. Bluvstein, S. Choi, M.D. Lukin, M.
Serbyn, Physical Review Letters 127 (2021).
date_created: 2021-08-28T08:08:58Z
date_published: 2021-08-27T00:00:00Z
date_updated: 2023-08-11T10:57:51Z
day: '27'
department:
- _id: MaSe
doi: 10.1103/PhysRevLett.127.090602
ec_funded: 1
external_id:
arxiv:
- '2102.13160'
isi:
- '000692200100002'
intvolume: ' 127'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2102.13160
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'Discrete time-crystalline order enabled by quantum many-body scars: Entanglement
steering via periodic driving'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 127
year: '2021'
...
---
_id: '9961'
abstract:
- lang: eng
text: The notion of Thouless energy plays a central role in the theory of Anderson
localization. We investigate and compare the scaling of Thouless energy across
the many-body localization (MBL) transition in a Floquet model. We use a combination
of methods that are reliable on the ergodic side of the transition (e.g., spectral
form factor) and methods that work on the MBL side (e.g., typical matrix elements
of local operators) to obtain a complete picture of the Thouless energy behavior
across the transition. On the ergodic side, Thouless energy decreases slowly with
the system size, while at the transition it becomes comparable to the level spacing.
Different probes yield consistent estimates of Thouless energy in their overlapping
regime of applicability, giving the location of the transition point nearly free
of finite-size drift. This work establishes a connection between different definitions
of Thouless energy in a many-body setting and yields insights into the MBL transition
in Floquet systems.
acknowledgement: "We thank S. Garratt for useful comments on the manuscript. This
work was supported by the Swiss National Science Foundation (M. Sonner and D.A.A.)
and by the European Research Council (ERC) under the European Union’s Horizon 2020
research and innovation program (M. Serbyn, Grant Agreement No. 850899, and D.A.A.,
Grant Agreement No. 864597). Z.P. acknowledges support from EPSRC Grant No. EP/R020612/1
and from Leverhulme Trust Research Leadership Award No. RL-2019-015. The computations
were performed on the Baobab cluster of the University\r\nof Geneva."
article_number: L081112
article_processing_charge: No
article_type: letter_note
author:
- first_name: Michael
full_name: Sonner, Michael
last_name: Sonner
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
citation:
ama: Sonner M, Serbyn M, Papić Z, Abanin DA. Thouless energy across the many-body
localization transition in Floquet systems. Physical Review B. 2021;104(8).
doi:10.1103/PhysRevB.104.L081112
apa: Sonner, M., Serbyn, M., Papić, Z., & Abanin, D. A. (2021). Thouless energy
across the many-body localization transition in Floquet systems. Physical Review
B. American Physical Society. https://doi.org/10.1103/PhysRevB.104.L081112
chicago: Sonner, Michael, Maksym Serbyn, Zlatko Papić, and Dmitry A. Abanin. “Thouless
Energy across the Many-Body Localization Transition in Floquet Systems.” Physical
Review B. American Physical Society, 2021. https://doi.org/10.1103/PhysRevB.104.L081112.
ieee: M. Sonner, M. Serbyn, Z. Papić, and D. A. Abanin, “Thouless energy across
the many-body localization transition in Floquet systems,” Physical Review
B, vol. 104, no. 8. American Physical Society, 2021.
ista: Sonner M, Serbyn M, Papić Z, Abanin DA. 2021. Thouless energy across the many-body
localization transition in Floquet systems. Physical Review B. 104(8), L081112.
mla: Sonner, Michael, et al. “Thouless Energy across the Many-Body Localization
Transition in Floquet Systems.” Physical Review B, vol. 104, no. 8, L081112,
American Physical Society, 2021, doi:10.1103/PhysRevB.104.L081112.
short: M. Sonner, M. Serbyn, Z. Papić, D.A. Abanin, Physical Review B 104 (2021).
date_created: 2021-08-28T16:44:55Z
date_published: 2021-08-15T00:00:00Z
date_updated: 2023-08-11T10:57:09Z
day: '15'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.104.L081112
ec_funded: 1
external_id:
arxiv:
- '2012.15676'
isi:
- '000689734500009'
intvolume: ' 104'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2012.15676
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Thouless energy across the many-body localization transition in Floquet systems
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 104
year: '2021'
...
---
_id: '9957'
abstract:
- lang: eng
text: The reflectance field of a face describes the reflectance properties responsible
for complex lighting effects including diffuse, specular, inter-reflection and
self shadowing. Most existing methods for estimating the face reflectance from
a monocular image assume faces to be diffuse with very few approaches adding a
specular component. This still leaves out important perceptual aspects of reflectance
as higher-order global illumination effects and self-shadowing are not modeled.
We present a new neural representation for face reflectance where we can estimate
all components of the reflectance responsible for the final appearance from a
single monocular image. Instead of modeling each component of the reflectance
separately using parametric models, our neural representation allows us to generate
a basis set of faces in a geometric deformation-invariant space, parameterized
by the input light direction, viewpoint and face geometry. We learn to reconstruct
this reflectance field of a face just from a monocular image, which can be used
to render the face from any viewpoint in any light condition. Our method is trained
on a light-stage training dataset, which captures 300 people illuminated with
150 light conditions from 8 viewpoints. We show that our method outperforms existing
monocular reflectance reconstruction methods, in terms of photorealism due to
better capturing of physical premitives, such as sub-surface scattering, specularities,
self-shadows and other higher-order effects.
acknowledgement: "We thank Tarun Yenamandra and Duarte David for helping us with the
comparisons. This work was supported by the\r\nERC Consolidator Grant 4DReply (770784).
We also acknowledge support from InterDigital."
article_processing_charge: No
author:
- first_name: Mallikarjun
full_name: B R, Mallikarjun
last_name: B R
- first_name: Ayush
full_name: Tewari, Ayush
last_name: Tewari
- first_name: Tae-Hyun
full_name: Oh, Tae-Hyun
last_name: Oh
- first_name: Tim
full_name: Weyrich, Tim
last_name: Weyrich
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Hans-Peter
full_name: Seidel, Hans-Peter
last_name: Seidel
- first_name: Hanspeter
full_name: Pfister, Hanspeter
last_name: Pfister
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
- first_name: Mohamed
full_name: Elgharib, Mohamed
last_name: Elgharib
- first_name: Christian
full_name: Theobalt, Christian
last_name: Theobalt
citation:
ama: 'B R M, Tewari A, Oh T-H, et al. Monocular reconstruction of neural face reflectance
fields. In: Proceedings of the IEEE Computer Society Conference on Computer
Vision and Pattern Recognition. IEEE; 2021:4791-4800. doi:10.1109/CVPR46437.2021.00476'
apa: 'B R, M., Tewari, A., Oh, T.-H., Weyrich, T., Bickel, B., Seidel, H.-P., …
Theobalt, C. (2021). Monocular reconstruction of neural face reflectance fields.
In Proceedings of the IEEE Computer Society Conference on Computer Vision and
Pattern Recognition (pp. 4791–4800). Nashville, TN, United States; Virtual:
IEEE. https://doi.org/10.1109/CVPR46437.2021.00476'
chicago: B R, Mallikarjun, Ayush Tewari, Tae-Hyun Oh, Tim Weyrich, Bernd Bickel,
Hans-Peter Seidel, Hanspeter Pfister, Wojciech Matusik, Mohamed Elgharib, and
Christian Theobalt. “Monocular Reconstruction of Neural Face Reflectance Fields.”
In Proceedings of the IEEE Computer Society Conference on Computer Vision and
Pattern Recognition, 4791–4800. IEEE, 2021. https://doi.org/10.1109/CVPR46437.2021.00476.
ieee: M. B R et al., “Monocular reconstruction of neural face reflectance
fields,” in Proceedings of the IEEE Computer Society Conference on Computer
Vision and Pattern Recognition, Nashville, TN, United States; Virtual, 2021,
pp. 4791–4800.
ista: 'B R M, Tewari A, Oh T-H, Weyrich T, Bickel B, Seidel H-P, Pfister H, Matusik
W, Elgharib M, Theobalt C. 2021. Monocular reconstruction of neural face reflectance
fields. Proceedings of the IEEE Computer Society Conference on Computer Vision
and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition,
4791–4800.'
mla: B R, Mallikarjun, et al. “Monocular Reconstruction of Neural Face Reflectance
Fields.” Proceedings of the IEEE Computer Society Conference on Computer Vision
and Pattern Recognition, IEEE, 2021, pp. 4791–800, doi:10.1109/CVPR46437.2021.00476.
short: M. B R, A. Tewari, T.-H. Oh, T. Weyrich, B. Bickel, H.-P. Seidel, H. Pfister,
W. Matusik, M. Elgharib, C. Theobalt, in:, Proceedings of the IEEE Computer Society
Conference on Computer Vision and Pattern Recognition, IEEE, 2021, pp. 4791–4800.
conference:
end_date: 2021-06-25
location: Nashville, TN, United States; Virtual
name: 'CVPR: Conference on Computer Vision and Pattern Recognition'
start_date: 2021-06-20
date_created: 2021-08-24T06:03:00Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2023-08-11T11:08:35Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1109/CVPR46437.2021.00476
external_id:
arxiv:
- '2008.10247'
isi:
- '000739917304096'
file:
- access_level: open_access
checksum: 961db0bde76dd87cf833930080bb9f38
content_type: application/pdf
creator: bbickel
date_created: 2021-08-24T06:02:15Z
date_updated: 2021-08-24T06:02:15Z
file_id: '9958'
file_name: R_Monocular_Reconstruction_of_Neural_Face_Reflectance_Fields_CVPR_2021_paper[1].pdf
file_size: 4746649
relation: main_file
file_date_updated: 2021-08-24T06:02:15Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Preprint
page: 4791-4800
publication: Proceedings of the IEEE Computer Society Conference on Computer Vision
and Pattern Recognition
publication_identifier:
isbn:
- 978-166544509-2
issn:
- 1063-6919
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monocular reconstruction of neural face reflectance fields
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9973'
abstract:
- lang: eng
text: In this article we introduce a complete gradient estimate for symmetric quantum
Markov semigroups on von Neumann algebras equipped with a normal faithful tracial
state, which implies semi-convexity of the entropy with respect to the recently
introduced noncommutative 2-Wasserstein distance. We show that this complete gradient
estimate is stable under tensor products and free products and establish its validity
for a number of examples. As an application we prove a complete modified logarithmic
Sobolev inequality with optimal constant for Poisson-type semigroups on free group
factors.
acknowledgement: Both authors would like to thank Jan Maas for fruitful discussions
and helpful comments.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
- first_name: Haonan
full_name: Zhang, Haonan
id: D8F41E38-9E66-11E9-A9E2-65C2E5697425
last_name: Zhang
citation:
ama: Wirth M, Zhang H. Complete gradient estimates of quantum Markov semigroups.
Communications in Mathematical Physics. 2021;387:761–791. doi:10.1007/s00220-021-04199-4
apa: Wirth, M., & Zhang, H. (2021). Complete gradient estimates of quantum Markov
semigroups. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-021-04199-4
chicago: Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum
Markov Semigroups.” Communications in Mathematical Physics. Springer Nature,
2021. https://doi.org/10.1007/s00220-021-04199-4.
ieee: M. Wirth and H. Zhang, “Complete gradient estimates of quantum Markov semigroups,”
Communications in Mathematical Physics, vol. 387. Springer Nature, pp.
761–791, 2021.
ista: Wirth M, Zhang H. 2021. Complete gradient estimates of quantum Markov semigroups.
Communications in Mathematical Physics. 387, 761–791.
mla: Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum
Markov Semigroups.” Communications in Mathematical Physics, vol. 387, Springer
Nature, 2021, pp. 761–791, doi:10.1007/s00220-021-04199-4.
short: M. Wirth, H. Zhang, Communications in Mathematical Physics 387 (2021) 761–791.
date_created: 2021-08-30T10:07:44Z
date_published: 2021-08-30T00:00:00Z
date_updated: 2023-08-11T11:09:07Z
day: '30'
ddc:
- '621'
department:
- _id: JaMa
doi: 10.1007/s00220-021-04199-4
ec_funded: 1
external_id:
arxiv:
- '2007.13506'
isi:
- '000691214200001'
file:
- access_level: open_access
checksum: 8a602f916b1c2b0dc1159708b7cb204b
content_type: application/pdf
creator: cchlebak
date_created: 2021-09-08T07:34:24Z
date_updated: 2021-09-08T09:46:34Z
file_id: '9990'
file_name: 2021_CommunMathPhys_Wirth.pdf
file_size: 505971
relation: main_file
file_date_updated: 2021-09-08T09:46:34Z
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intvolume: ' 387'
isi: 1
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 761–791
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- 1432-0916
issn:
- 0010-3616
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Complete gradient estimates of quantum Markov semigroups
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: 387
year: '2021'
...
---
_id: '10000'
abstract:
- lang: eng
text: Inhibition or targeted deletion of histone deacetylase 3 (HDAC3) is neuroprotective
in a variety neurodegenerative conditions, including retinal ganglion cells (RGCs)
after acute optic nerve damage. Consistent with this, induced HDAC3 expression
in cultured cells shows selective toxicity to neurons. Despite an established
role for HDAC3 in neuronal pathology, little is known regarding the mechanism
of this pathology.
acknowledgement: 'The authors thank Joel Dietz for maintaining the mice used in this
study, Satoshi Kinoshita and the Translational Research Initiative in Pathology
Laboratory at the University of Wisconsin-Madison for cutting retinal sections analyzed
in this study, and Mark Banghart for statistical review of the data analysis. Supported
by National Eye Institute Grants R01 EY012223 (RWN), R01 EY030123 (RWN), R01 EY029809
(LWG), R01 EY029809 (LWG) and a Vision Research CORE grant P30 EY016665, NRSA grant
T32 GM081061, by an unrestricted research grant from Research to Prevent Blindness,
Inc., and by a University of Wisconsin-Madison Vilas Life Cycle award and the Frederick
A. Davis Research Chair (RWN). '
article_number: '14'
article_processing_charge: Yes
article_type: original
author:
- first_name: Heather M.
full_name: Schmitt, Heather M.
last_name: Schmitt
- first_name: Rachel L.
full_name: Fehrman, Rachel L.
last_name: Fehrman
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Huan
full_name: Yang, Huan
last_name: Yang
- first_name: Lian Wang
full_name: Guo, Lian Wang
last_name: Guo
- first_name: Cassandra L.
full_name: Schlamp, Cassandra L.
last_name: Schlamp
- first_name: Heather R.
full_name: Pelzel, Heather R.
last_name: Pelzel
- first_name: Robert W.
full_name: Nickells, Robert W.
last_name: Nickells
citation:
ama: Schmitt HM, Fehrman RL, Maes ME, et al. Increased susceptibility and intrinsic
apoptotic signaling in neurons by induced HDAC3 expression. Investigative Ophthalmology
and Visual Science. 2021;62(10). doi:10.1167/IOVS.62.10.14
apa: Schmitt, H. M., Fehrman, R. L., Maes, M. E., Yang, H., Guo, L. W., Schlamp,
C. L., … Nickells, R. W. (2021). Increased susceptibility and intrinsic apoptotic
signaling in neurons by induced HDAC3 expression. Investigative Ophthalmology
and Visual Science. Association for Research in Vision and Ophthalmology.
https://doi.org/10.1167/IOVS.62.10.14
chicago: Schmitt, Heather M., Rachel L. Fehrman, Margaret E Maes, Huan Yang, Lian
Wang Guo, Cassandra L. Schlamp, Heather R. Pelzel, and Robert W. Nickells. “Increased
Susceptibility and Intrinsic Apoptotic Signaling in Neurons by Induced HDAC3 Expression.”
Investigative Ophthalmology and Visual Science. Association for Research
in Vision and Ophthalmology, 2021. https://doi.org/10.1167/IOVS.62.10.14.
ieee: H. M. Schmitt et al., “Increased susceptibility and intrinsic apoptotic
signaling in neurons by induced HDAC3 expression,” Investigative Ophthalmology
and Visual Science, vol. 62, no. 10. Association for Research in Vision and
Ophthalmology, 2021.
ista: Schmitt HM, Fehrman RL, Maes ME, Yang H, Guo LW, Schlamp CL, Pelzel HR, Nickells
RW. 2021. Increased susceptibility and intrinsic apoptotic signaling in neurons
by induced HDAC3 expression. Investigative Ophthalmology and Visual Science. 62(10),
14.
mla: Schmitt, Heather M., et al. “Increased Susceptibility and Intrinsic Apoptotic
Signaling in Neurons by Induced HDAC3 Expression.” Investigative Ophthalmology
and Visual Science, vol. 62, no. 10, 14, Association for Research in Vision
and Ophthalmology, 2021, doi:10.1167/IOVS.62.10.14.
short: H.M. Schmitt, R.L. Fehrman, M.E. Maes, H. Yang, L.W. Guo, C.L. Schlamp, H.R.
Pelzel, R.W. Nickells, Investigative Ophthalmology and Visual Science 62 (2021).
date_created: 2021-09-12T22:01:23Z
date_published: 2021-08-16T00:00:00Z
date_updated: 2023-08-14T06:35:17Z
day: '16'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1167/IOVS.62.10.14
external_id:
isi:
- '000695230000014'
pmid:
- '34398198'
file:
- access_level: open_access
checksum: c430967746f653aa1ae84ee617f62b73
content_type: application/pdf
creator: dernst
date_created: 2022-05-13T07:40:15Z
date_updated: 2022-05-13T07:40:15Z
file_id: '11369'
file_name: 2021_IOVS_Schmitt.pdf
file_size: 19707796
relation: main_file
success: 1
file_date_updated: 2022-05-13T07:40:15Z
has_accepted_license: '1'
intvolume: ' 62'
isi: 1
issue: '10'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Investigative Ophthalmology and Visual Science
publication_identifier:
eissn:
- 1552-5783
issn:
- 0146-0404
publication_status: published
publisher: Association for Research in Vision and Ophthalmology
quality_controlled: '1'
scopus_import: '1'
status: public
title: Increased susceptibility and intrinsic apoptotic signaling in neurons by induced
HDAC3 expression
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: 62
year: '2021'
...
---
_id: '9998'
abstract:
- lang: eng
text: We define quantum equivariant K-theory of Nakajima quiver varieties. We discuss
type A in detail as well as its connections with quantum XXZ spin chains and trigonometric
Ruijsenaars-Schneider models. Finally we study a limit which produces a K-theoretic
version of results of Givental and Kim, connecting quantum geometry of flag varieties
and Toda lattice.
acknowledgement: 'First of all we would like to thank Andrei Okounkov for invaluable
discussions, advises and sharing with us his fantastic viewpoint on modern quantum
geometry. We are also grateful to D. Korb and Z. Zhou for their interest and comments.
The work of A. Smirnov was supported in part by RFBR Grants under Numbers 15-02-04175
and 15-01-04217 and in part by NSF Grant DMS–2054527. The work of P. Koroteev, A.M.
Zeitlin and A. Smirnov is supported in part by AMS Simons travel Grant. A. M. Zeitlin
is partially supported by Simons Collaboration Grant, Award ID: 578501. Open access
funding provided by Institute of Science and Technology (IST Austria).'
article_number: '87'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Peter
full_name: Koroteev, Peter
last_name: Koroteev
- first_name: Petr
full_name: Pushkar, Petr
id: 151DCEB6-9EC3-11E9-8480-ABECE5697425
last_name: Pushkar
- first_name: Andrey V.
full_name: Smirnov, Andrey V.
last_name: Smirnov
- first_name: Anton M.
full_name: Zeitlin, Anton M.
last_name: Zeitlin
citation:
ama: Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. Quantum K-theory of quiver varieties
and many-body systems. Selecta Mathematica. 2021;27(5). doi:10.1007/s00029-021-00698-3
apa: Koroteev, P., Pushkar, P., Smirnov, A. V., & Zeitlin, A. M. (2021). Quantum
K-theory of quiver varieties and many-body systems. Selecta Mathematica.
Springer Nature. https://doi.org/10.1007/s00029-021-00698-3
chicago: Koroteev, Peter, Petr Pushkar, Andrey V. Smirnov, and Anton M. Zeitlin.
“Quantum K-Theory of Quiver Varieties and Many-Body Systems.” Selecta Mathematica.
Springer Nature, 2021. https://doi.org/10.1007/s00029-021-00698-3.
ieee: P. Koroteev, P. Pushkar, A. V. Smirnov, and A. M. Zeitlin, “Quantum K-theory
of quiver varieties and many-body systems,” Selecta Mathematica, vol. 27,
no. 5. Springer Nature, 2021.
ista: Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. 2021. Quantum K-theory of quiver
varieties and many-body systems. Selecta Mathematica. 27(5), 87.
mla: Koroteev, Peter, et al. “Quantum K-Theory of Quiver Varieties and Many-Body
Systems.” Selecta Mathematica, vol. 27, no. 5, 87, Springer Nature, 2021,
doi:10.1007/s00029-021-00698-3.
short: P. Koroteev, P. Pushkar, A.V. Smirnov, A.M. Zeitlin, Selecta Mathematica
27 (2021).
date_created: 2021-09-12T22:01:22Z
date_published: 2021-08-30T00:00:00Z
date_updated: 2023-08-14T06:34:14Z
day: '30'
ddc:
- '530'
department:
- _id: TaHa
doi: 10.1007/s00029-021-00698-3
external_id:
isi:
- '000692795200001'
file:
- access_level: open_access
checksum: beadc5a722ffb48190e1e63ee2dbfee5
content_type: application/pdf
creator: cchlebak
date_created: 2021-09-13T11:31:34Z
date_updated: 2021-09-13T11:31:34Z
file_id: '10010'
file_name: 2021_SelectaMath_Koroteev.pdf
file_size: 584648
relation: main_file
success: 1
file_date_updated: 2021-09-13T11:31:34Z
has_accepted_license: '1'
intvolume: ' 27'
isi: 1
issue: '5'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Selecta Mathematica
publication_identifier:
eissn:
- 1420-9020
issn:
- 1022-1824
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum K-theory of quiver varieties and many-body systems
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 27
year: '2021'
...
---
_id: '9999'
abstract:
- lang: eng
text: 'The developmental strategies used by progenitor cells to endure a safe journey
from their induction place towards the site of terminal differentiation are still
poorly understood. Here we uncovered a progenitor cell allocation mechanism that
stems from an incomplete process of epithelial delamination that allows progenitors
to coordinate their movement with adjacent extra-embryonic tissues. Progenitors
of the zebrafish laterality organ originate from the surface epithelial enveloping
layer by an apical constriction process of cell delamination. During this process,
progenitors retain long-term apical contacts that enable the epithelial layer
to pull a subset of progenitors along their way towards the vegetal pole. The
remaining delaminated progenitors follow apically-attached progenitors’ movement
by a co-attraction mechanism, avoiding sequestration by the adjacent endoderm,
ensuring their fate and collective allocation at the differentiation site. Thus,
we reveal that incomplete delamination serves as a cellular platform for coordinated
tissue movements during development. Impact Statement: Incomplete delamination
serves as a cellular platform for coordinated tissue movements during development,
guiding newly formed progenitor cell groups to the differentiation site.'
article_number: e66483
article_processing_charge: Yes
article_type: original
author:
- first_name: Eduardo
full_name: Pulgar, Eduardo
last_name: Pulgar
- first_name: Cornelia
full_name: Schwayer, Cornelia
id: 3436488C-F248-11E8-B48F-1D18A9856A87
last_name: Schwayer
orcid: 0000-0001-5130-2226
- first_name: Néstor
full_name: Guerrero, Néstor
last_name: Guerrero
- first_name: Loreto
full_name: López, Loreto
last_name: López
- first_name: Susana
full_name: Márquez, Susana
last_name: Márquez
- first_name: Steffen
full_name: Härtel, Steffen
last_name: Härtel
- first_name: Rodrigo
full_name: Soto, Rodrigo
last_name: Soto
- first_name: Carl Philipp
full_name: Heisenberg, Carl Philipp
last_name: Heisenberg
- first_name: Miguel L.
full_name: Concha, Miguel L.
last_name: Concha
citation:
ama: Pulgar E, Schwayer C, Guerrero N, et al. Apical contacts stemming from incomplete
delamination guide progenitor cell allocation through a dragging mechanism. eLife.
2021;10. doi:10.7554/eLife.66483
apa: Pulgar, E., Schwayer, C., Guerrero, N., López, L., Márquez, S., Härtel, S.,
… Concha, M. L. (2021). Apical contacts stemming from incomplete delamination
guide progenitor cell allocation through a dragging mechanism. ELife. eLife
Sciences Publications. https://doi.org/10.7554/eLife.66483
chicago: Pulgar, Eduardo, Cornelia Schwayer, Néstor Guerrero, Loreto López, Susana
Márquez, Steffen Härtel, Rodrigo Soto, Carl Philipp Heisenberg, and Miguel L.
Concha. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor
Cell Allocation through a Dragging Mechanism.” ELife. eLife Sciences Publications,
2021. https://doi.org/10.7554/eLife.66483.
ieee: E. Pulgar et al., “Apical contacts stemming from incomplete delamination
guide progenitor cell allocation through a dragging mechanism,” eLife,
vol. 10. eLife Sciences Publications, 2021.
ista: Pulgar E, Schwayer C, Guerrero N, López L, Márquez S, Härtel S, Soto R, Heisenberg
CP, Concha ML. 2021. Apical contacts stemming from incomplete delamination guide
progenitor cell allocation through a dragging mechanism. eLife. 10, e66483.
mla: Pulgar, Eduardo, et al. “Apical Contacts Stemming from Incomplete Delamination
Guide Progenitor Cell Allocation through a Dragging Mechanism.” ELife,
vol. 10, e66483, eLife Sciences Publications, 2021, doi:10.7554/eLife.66483.
short: E. Pulgar, C. Schwayer, N. Guerrero, L. López, S. Márquez, S. Härtel, R.
Soto, C.P. Heisenberg, M.L. Concha, ELife 10 (2021).
date_created: 2021-09-12T22:01:23Z
date_published: 2021-08-27T00:00:00Z
date_updated: 2023-08-14T06:53:33Z
day: '27'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.7554/eLife.66483
ec_funded: 1
external_id:
isi:
- '000700428500001'
pmid:
- '34448451'
file:
- access_level: open_access
checksum: a3f82b0499cc822ac1eab48a01f3f57e
content_type: application/pdf
creator: dernst
date_created: 2022-05-13T08:03:37Z
date_updated: 2022-05-13T08:03:37Z
file_id: '11371'
file_name: 2021_eLife_Pulgar.pdf
file_size: 9010446
relation: main_file
success: 1
file_date_updated: 2022-05-13T08:03:37Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
keyword:
- cell delamination
- apical constriction
- dragging
- mechanical forces
- collective 18 locomotion
- dorsal forerunner cells
- zebrafish
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Apical contacts stemming from incomplete delamination guide progenitor cell
allocation through a dragging mechanism
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '10002'
abstract:
- lang: eng
text: 'We present a faster symbolic algorithm for the following central problem
in probabilistic verification: Compute the maximal end-component (MEC) decomposition
of Markov decision processes (MDPs). This problem generalizes the SCC decomposition
problem of graphs and closed recurrent sets of Markov chains. The model of symbolic
algorithms is widely used in formal verification and model-checking, where access
to the input model is restricted to only symbolic operations (e.g., basic set
operations and computation of one-step neighborhood). For an input MDP with n vertices
and m edges, the classical symbolic algorithm from the 1990s for the MEC decomposition
requires O(n2) symbolic operations and O(1) symbolic space. The only other
symbolic algorithm for the MEC decomposition requires O(nm−−√) symbolic operations
and O(m−−√) symbolic space. A main open question is whether the worst-case O(n2) bound
for symbolic operations can be beaten. We present a symbolic algorithm that requires O˜(n1.5) symbolic
operations and O˜(n−−√) symbolic space. Moreover, the parametrization of our
algorithm provides a trade-off between symbolic operations and symbolic space:
for all 0<ϵ≤1/2 the symbolic algorithm requires O˜(n2−ϵ) symbolic operations
and O˜(nϵ) symbolic space ( O˜ hides poly-logarithmic factors). Using our techniques
we present faster algorithms for computing the almost-sure winning regions of ω
-regular objectives for MDPs. We consider the canonical parity objectives for ω
-regular objectives, and for parity objectives with d -priorities we present
an algorithm that computes the almost-sure winning region with O˜(n2−ϵ) symbolic
operations and O˜(nϵ) symbolic space, for all 0<ϵ≤1/2 .'
acknowledgement: The authors are grateful to the anonymous referees for their valuable
comments. A. S. is fully supported by the Vienna Science and Technology Fund (WWTF)
through project ICT15–003. K. C. is supported by the Austrian Science Fund (FWF)
NFN Grant No S11407-N23 (RiSE/SHiNE) and by the ERC CoG 863818 (ForM-SMArt). For
M. H. the research leading to these results has received funding from the European
Research Council under the European Unions Seventh Framework Programme (FP/2007–2013)
/ ERC Grant Agreement no. 340506.
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Wolfgang
full_name: Dvorak, Wolfgang
last_name: Dvorak
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Alexander
full_name: Svozil, Alexander
last_name: Svozil
citation:
ama: 'Chatterjee K, Dvorak W, Henzinger MH, Svozil A. Symbolic time and space tradeoffs
for probabilistic verification. In: Proceedings of the 36th Annual ACM/IEEE
Symposium on Logic in Computer Science. Institute of Electrical and Electronics
Engineers; 2021:1-13. doi:10.1109/LICS52264.2021.9470739'
apa: 'Chatterjee, K., Dvorak, W., Henzinger, M. H., & Svozil, A. (2021). Symbolic
time and space tradeoffs for probabilistic verification. In Proceedings of
the 36th Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 1–13).
Rome, Italy: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS52264.2021.9470739'
chicago: Chatterjee, Krishnendu, Wolfgang Dvorak, Monika H Henzinger, and Alexander
Svozil. “Symbolic Time and Space Tradeoffs for Probabilistic Verification.” In
Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science,
1–13. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/LICS52264.2021.9470739.
ieee: K. Chatterjee, W. Dvorak, M. H. Henzinger, and A. Svozil, “Symbolic time and
space tradeoffs for probabilistic verification,” in Proceedings of the 36th
Annual ACM/IEEE Symposium on Logic in Computer Science, Rome, Italy, 2021,
pp. 1–13.
ista: 'Chatterjee K, Dvorak W, Henzinger MH, Svozil A. 2021. Symbolic time and space
tradeoffs for probabilistic verification. Proceedings of the 36th Annual ACM/IEEE
Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science,
1–13.'
mla: Chatterjee, Krishnendu, et al. “Symbolic Time and Space Tradeoffs for Probabilistic
Verification.” Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in
Computer Science, Institute of Electrical and Electronics Engineers, 2021,
pp. 1–13, doi:10.1109/LICS52264.2021.9470739.
short: K. Chatterjee, W. Dvorak, M.H. Henzinger, A. Svozil, in:, Proceedings of
the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of
Electrical and Electronics Engineers, 2021, pp. 1–13.
conference:
end_date: 2021-07-02
location: Rome, Italy
name: 'LICS: Symposium on Logic in Computer Science'
start_date: 2021-06-29
date_created: 2021-09-12T22:01:24Z
date_published: 2021-07-07T00:00:00Z
date_updated: 2023-08-14T06:51:33Z
day: '07'
department:
- _id: KrCh
doi: 10.1109/LICS52264.2021.9470739
ec_funded: 1
external_id:
arxiv:
- '2104.07466'
isi:
- '000947350400089'
isi: 1
keyword:
- Computer science
- Computational modeling
- Markov processes
- Probabilistic logic
- Formal verification
- Game Theory
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2104.07466
month: '07'
oa: 1
oa_version: Preprint
page: 1-13
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer
Science
publication_identifier:
eisbn:
- 978-1-6654-4895-6
isbn:
- 978-1-6654-4896-3
issn:
- 1043-6871
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Symbolic time and space tradeoffs for probabilistic verification
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '10024'
abstract:
- lang: eng
text: In this paper, we introduce a random environment for the exclusion process
in obtained by assigning a maximal occupancy to each site. This maximal occupancy
is allowed to randomly vary among sites, and partial exclusion occurs. Under the
assumption of ergodicity under translation and uniform ellipticity of the environment,
we derive a quenched hydrodynamic limit in path space by strengthening the mild
solution approach initiated in Nagy (2002) and Faggionato (2007). To this purpose,
we prove, employing the technology developed for the random conductance model,
a homogenization result in the form of an arbitrary starting point quenched invariance
principle for a single particle in the same environment, which is a result of
independent interest. The self-duality property of the partial exclusion process
allows us to transfer this homogenization result to the particle system and, then,
apply the tightness criterion in Redig et al. (2020).
acknowledgement: The authors would like to thank Marek Biskup and Alberto Chiarini
for useful suggestions and Cristian Giardina, Frank den Hollander and Shubhamoy Nandan for inspiring discussions. S.F. acknowledges Simona Villa for her help in creating the picture. Furthermore,
the authors thank two anonymous referees for the careful reading of the manuscript. S.F.
acknowledges financial support from NWO, The Netherlands via the grant TOP1.17.019.
F.S. acknowledges financial support from NWO via the TOP1 grant 613.001.552 as well as
funding from the European Union’s Horizon 2020 research and innovation programme
under the Marie-Skłodowska-Curie grant agreement No. 754411.
article_processing_charge: Yes
article_type: original
author:
- first_name: Simone
full_name: Floreani, Simone
last_name: Floreani
- first_name: Frank
full_name: Redig, Frank
last_name: Redig
- first_name: Federico
full_name: Sau, Federico
id: E1836206-9F16-11E9-8814-AEFDE5697425
last_name: Sau
citation:
ama: Floreani S, Redig F, Sau F. Hydrodynamics for the partial exclusion process
in random environment. Stochastic Processes and their Applications. 2021;142:124-158.
doi:10.1016/j.spa.2021.08.006
apa: Floreani, S., Redig, F., & Sau, F. (2021). Hydrodynamics for the partial
exclusion process in random environment. Stochastic Processes and Their Applications.
Elsevier. https://doi.org/10.1016/j.spa.2021.08.006
chicago: Floreani, Simone, Frank Redig, and Federico Sau. “Hydrodynamics for the
Partial Exclusion Process in Random Environment.” Stochastic Processes and
Their Applications. Elsevier, 2021. https://doi.org/10.1016/j.spa.2021.08.006.
ieee: S. Floreani, F. Redig, and F. Sau, “Hydrodynamics for the partial exclusion
process in random environment,” Stochastic Processes and their Applications,
vol. 142. Elsevier, pp. 124–158, 2021.
ista: Floreani S, Redig F, Sau F. 2021. Hydrodynamics for the partial exclusion
process in random environment. Stochastic Processes and their Applications. 142,
124–158.
mla: Floreani, Simone, et al. “Hydrodynamics for the Partial Exclusion Process in
Random Environment.” Stochastic Processes and Their Applications, vol.
142, Elsevier, 2021, pp. 124–58, doi:10.1016/j.spa.2021.08.006.
short: S. Floreani, F. Redig, F. Sau, Stochastic Processes and Their Applications
142 (2021) 124–158.
date_created: 2021-09-19T22:01:25Z
date_published: 2021-08-27T00:00:00Z
date_updated: 2023-08-14T06:52:43Z
day: '27'
ddc:
- '519'
department:
- _id: JaMa
doi: 10.1016/j.spa.2021.08.006
ec_funded: 1
external_id:
arxiv:
- '1911.12564'
isi:
- '000697748500005'
file:
- access_level: open_access
checksum: 56768c553d7218ee5714902ffec90ec4
content_type: application/pdf
creator: dernst
date_created: 2022-05-13T07:55:50Z
date_updated: 2022-05-13T07:55:50Z
file_id: '11370'
file_name: 2021_StochasticProcessesAppl_Floreani.pdf
file_size: 2115791
relation: main_file
success: 1
file_date_updated: 2022-05-13T07:55:50Z
has_accepted_license: '1'
intvolume: ' 142'
isi: 1
keyword:
- hydrodynamic limit
- random environment
- random conductance model
- arbitrary starting point quenched invariance principle
- duality
- mild solution
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 124-158
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Stochastic Processes and their Applications
publication_identifier:
issn:
- 0304-4149
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hydrodynamics for the partial exclusion process in random environment
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 142
year: '2021'
...
---
_id: '10004'
abstract:
- lang: eng
text: 'Markov chains are the de facto finite-state model for stochastic dynamical
systems, and Markov decision processes (MDPs) extend Markov chains by incorporating
non-deterministic behaviors. Given an MDP and rewards on states, a classical optimization
criterion is the maximal expected total reward where the MDP stops after T steps,
which can be computed by a simple dynamic programming algorithm. We consider a
natural generalization of the problem where the stopping times can be chosen according
to a probability distribution, such that the expected stopping time is T, to optimize
the expected total reward. Quite surprisingly we establish inter-reducibility
of the expected stopping-time problem for Markov chains with the Positivity problem
(which is related to the well-known Skolem problem), for which establishing either
decidability or undecidability would be a major breakthrough. Given the hardness
of the exact problem, we consider the approximate version of the problem: we show
that it can be solved in exponential time for Markov chains and in exponential
space for MDPs.'
acknowledgement: We are grateful to the anonymous reviewers of LICS 2021 and of a
previous version of this paper for insightful comments that helped improving the
presentation. This research was partially supported by the grant ERC CoG 863818
(ForM-SMArt).
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: 'Chatterjee K, Doyen L. Stochastic processes with expected stopping time. In:
Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science.
Institute of Electrical and Electronics Engineers; 2021:1-13. doi:10.1109/LICS52264.2021.9470595'
apa: 'Chatterjee, K., & Doyen, L. (2021). Stochastic processes with expected
stopping time. In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic
in Computer Science (pp. 1–13). Rome, Italy: Institute of Electrical and Electronics
Engineers. https://doi.org/10.1109/LICS52264.2021.9470595'
chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected
Stopping Time.” In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic
in Computer Science, 1–13. Institute of Electrical and Electronics Engineers,
2021. https://doi.org/10.1109/LICS52264.2021.9470595.
ieee: K. Chatterjee and L. Doyen, “Stochastic processes with expected stopping time,”
in Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science,
Rome, Italy, 2021, pp. 1–13.
ista: 'Chatterjee K, Doyen L. 2021. Stochastic processes with expected stopping
time. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science.
LICS: Symposium on Logic in Computer Science, 1–13.'
mla: Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected
Stopping Time.” Proceedings of the 36th Annual ACM/IEEE Symposium on Logic
in Computer Science, Institute of Electrical and Electronics Engineers, 2021,
pp. 1–13, doi:10.1109/LICS52264.2021.9470595.
short: K. Chatterjee, L. Doyen, in:, Proceedings of the 36th Annual ACM/IEEE Symposium
on Logic in Computer Science, Institute of Electrical and Electronics Engineers,
2021, pp. 1–13.
conference:
end_date: 2021-07-02
location: Rome, Italy
name: 'LICS: Symposium on Logic in Computer Science'
start_date: 2021-06-29
date_created: 2021-09-12T22:01:25Z
date_published: 2021-07-07T00:00:00Z
date_updated: 2023-08-14T06:52:07Z
day: '07'
department:
- _id: KrCh
doi: 10.1109/LICS52264.2021.9470595
ec_funded: 1
external_id:
arxiv:
- '2104.07278'
isi:
- '000947350400036'
isi: 1
keyword:
- Computer science
- Heuristic algorithms
- Memory management
- Automata
- Markov processes
- Probability distribution
- Complexity theory
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2104.07278
month: '07'
oa: 1
oa_version: Preprint
page: 1-13
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer
Science
publication_identifier:
eisbn:
- 978-1-6654-4895-6
isbn:
- 978-1-6654-4896-3
issn:
- 1043-6871
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stochastic processes with expected stopping time
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '10053'
abstract:
- lang: eng
text: 'This paper characterizes the latency of the simplified successive-cancellation
(SSC) decoding scheme for polar codes under hardware resource constraints. In
particular, when the number of processing elements P that can perform SSC decoding
operations in parallel is limited, as is the case in practice, the latency of
SSC decoding is O(N1−1 μ+NPlog2log2NP), where N is the block length of the code
and μ is the scaling exponent of polar codes for the channel. Three direct consequences
of this bound are presented. First, in a fully-parallel implementation where P=N2
, the latency of SSC decoding is O(N1−1/μ) , which is sublinear in the block length.
This recovers a result from an earlier work. Second, in a fully-serial implementation
where P=1 , the latency of SSC decoding scales as O(Nlog2log2N) . The multiplicative
constant is also calculated: we show that the latency of SSC decoding when P=1
is given by (2+o(1))Nlog2log2N . Third, in a semi-parallel implementation, the
smallest P that gives the same latency as that of the fully-parallel implementation
is P=N1/μ . The tightness of our bound on SSC decoding latency and the applicability
of the foregoing results is validated through extensive simulations.'
acknowledgement: "S. A. Hashemi is supported by a Postdoctoral Fellowship from the
Natural Sciences and Engineering Research Council\r\nof Canada (NSERC) and by Huawei.
M. Mondelli is partially supported by the 2019 Lopez-Loreta Prize. A. Fazeli and
A. Vardy were supported in part by the National Science Foundation under Grant CCF-1764104."
article_processing_charge: No
author:
- first_name: Seyyed Ali
full_name: Hashemi, Seyyed Ali
last_name: Hashemi
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Arman
full_name: Fazeli, Arman
last_name: Fazeli
- first_name: Alexander
full_name: Vardy, Alexander
last_name: Vardy
- first_name: John
full_name: Cioffi, John
last_name: Cioffi
- first_name: Andrea
full_name: Goldsmith, Andrea
last_name: Goldsmith
citation:
ama: 'Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. Parallelism
versus latency in simplified successive-cancellation decoding of polar codes.
In: 2021 IEEE International Symposium on Information Theory. Institute
of Electrical and Electronics Engineers; 2021:2369-2374. doi:10.1109/ISIT45174.2021.9518153'
apa: 'Hashemi, S. A., Mondelli, M., Fazeli, A., Vardy, A., Cioffi, J., & Goldsmith,
A. (2021). Parallelism versus latency in simplified successive-cancellation decoding
of polar codes. In 2021 IEEE International Symposium on Information Theory
(pp. 2369–2374). Melbourne, Australia: Institute of Electrical and Electronics
Engineers. https://doi.org/10.1109/ISIT45174.2021.9518153'
chicago: Hashemi, Seyyed Ali, Marco Mondelli, Arman Fazeli, Alexander Vardy, John
Cioffi, and Andrea Goldsmith. “Parallelism versus Latency in Simplified Successive-Cancellation
Decoding of Polar Codes.” In 2021 IEEE International Symposium on Information
Theory, 2369–74. Institute of Electrical and Electronics Engineers, 2021.
https://doi.org/10.1109/ISIT45174.2021.9518153.
ieee: S. A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, and A. Goldsmith,
“Parallelism versus latency in simplified successive-cancellation decoding of
polar codes,” in 2021 IEEE International Symposium on Information Theory,
Melbourne, Australia, 2021, pp. 2369–2374.
ista: 'Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. 2021. Parallelism
versus latency in simplified successive-cancellation decoding of polar codes.
2021 IEEE International Symposium on Information Theory. ISIT: International Symposium
on Information Theory, 2369–2374.'
mla: Hashemi, Seyyed Ali, et al. “Parallelism versus Latency in Simplified Successive-Cancellation
Decoding of Polar Codes.” 2021 IEEE International Symposium on Information
Theory, Institute of Electrical and Electronics Engineers, 2021, pp. 2369–74,
doi:10.1109/ISIT45174.2021.9518153.
short: S.A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, A. Goldsmith,
in:, 2021 IEEE International Symposium on Information Theory, Institute of Electrical
and Electronics Engineers, 2021, pp. 2369–2374.
conference:
end_date: 2021-07-20
location: Melbourne, Australia
name: 'ISIT: International Symposium on Information Theory'
start_date: 2021-07-12
date_created: 2021-09-27T14:33:14Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2023-08-14T06:55:58Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/ISIT45174.2021.9518153
external_id:
arxiv:
- '2012.13378'
isi:
- '000701502202078'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2012.13378
month: '09'
oa: 1
oa_version: Preprint
page: 2369-2374
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: 2021 IEEE International Symposium on Information Theory
publication_identifier:
eisbn:
- 978-1-5386-8209-8
isbn:
- 978-1-5386-8210-4
issn:
- 2157-8095
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
related_material:
record:
- id: '10364'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Parallelism versus latency in simplified successive-cancellation decoding of
polar codes
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '10033'
abstract:
- lang: eng
text: The ⊗*-monoidal structure on the category of sheaves on the Ran space is not
pro-nilpotent in the sense of [3]. However, under some connectivity assumptions,
we prove that Koszul duality induces an equivalence of categories and that this
equivalence behaves nicely with respect to Verdier duality on the Ran space and
integrating along the Ran space, i.e. taking factorization homology. Based on
ideas sketched in [4], we show that these results also offer a simpler alternative
to one of the two main steps in the proof of the Atiyah-Bott formula given in
[7] and [5].
acknowledgement: 'The author would like to express his gratitude to D. Gaitsgory,
without whose tireless guidance and encouragement in pursuing this problem, this
work would not have been possible. The author is grateful to his advisor B.C. Ngô
for many years of patient guidance and support. This paper is revised while the
author is a postdoc in Hausel group at IST Austria. We thank him and the group for
providing a wonderful research environment. The author also gratefully acknowledges
the support of the Lise Meitner fellowship “Algebro-Geometric Applications of Factorization
Homology,” Austrian Science Fund (FWF): M 2751.'
article_number: '107992'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Quoc P
full_name: Ho, Quoc P
id: 3DD82E3C-F248-11E8-B48F-1D18A9856A87
last_name: Ho
orcid: 0000-0001-6889-1418
citation:
ama: Ho QP. The Atiyah-Bott formula and connectivity in chiral Koszul duality. Advances
in Mathematics. 2021;392. doi:10.1016/j.aim.2021.107992
apa: Ho, Q. P. (2021). The Atiyah-Bott formula and connectivity in chiral Koszul
duality. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2021.107992
chicago: Ho, Quoc P. “The Atiyah-Bott Formula and Connectivity in Chiral Koszul
Duality.” Advances in Mathematics. Elsevier, 2021. https://doi.org/10.1016/j.aim.2021.107992.
ieee: Q. P. Ho, “The Atiyah-Bott formula and connectivity in chiral Koszul duality,”
Advances in Mathematics, vol. 392. Elsevier, 2021.
ista: Ho QP. 2021. The Atiyah-Bott formula and connectivity in chiral Koszul duality.
Advances in Mathematics. 392, 107992.
mla: Ho, Quoc P. “The Atiyah-Bott Formula and Connectivity in Chiral Koszul Duality.”
Advances in Mathematics, vol. 392, 107992, Elsevier, 2021, doi:10.1016/j.aim.2021.107992.
short: Q.P. Ho, Advances in Mathematics 392 (2021).
date_created: 2021-09-21T15:58:59Z
date_published: 2021-09-21T00:00:00Z
date_updated: 2023-08-14T06:54:35Z
day: '21'
ddc:
- '514'
department:
- _id: TaHa
doi: 10.1016/j.aim.2021.107992
external_id:
arxiv:
- '1610.00212'
isi:
- '000707040300031'
file:
- access_level: open_access
checksum: f3c0086d41af11db31c00014efb38072
content_type: application/pdf
creator: qho
date_created: 2021-09-21T15:58:52Z
date_updated: 2021-09-21T15:58:52Z
file_id: '10034'
file_name: 1-s2.0-S000187082100431X-main.pdf
file_size: 840635
relation: main_file
file_date_updated: 2021-09-21T15:58:52Z
has_accepted_license: '1'
intvolume: ' 392'
isi: 1
keyword:
- Chiral algebras
- Chiral homology
- Factorization algebras
- Koszul duality
- Ran space
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 26B96266-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02751
name: Algebro-Geometric Applications of Factorization Homology
publication: Advances in Mathematics
publication_identifier:
eissn:
- 1090-2082
issn:
- 0001-8708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Atiyah-Bott formula and connectivity in chiral Koszul duality
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: 392
year: '2021'
...
---
_id: '10051'
abstract:
- lang: eng
text: 'Rab-interacting molecule (RIM)-binding protein 2 (BP2) is a multidomain protein
of the presynaptic active zone (AZ). By binding to RIM, bassoon (Bsn), and voltage-gated
Ca2+ channels (CaV), it is considered to be a central organizer of the topography
of CaV and release sites of synaptic vesicles (SVs) at the AZ. Here, we used RIM-BP2
knock-out (KO) mice and their wild-type (WT) littermates of either sex to investigate
the role of RIM-BP2 at the endbulb of Held synapse of auditory nerve fibers (ANFs)
with bushy cells (BCs) of the cochlear nucleus, a fast relay of the auditory pathway
with high release probability. Disruption of RIM-BP2 lowered release probability
altering short-term plasticity and reduced evoked EPSCs. Analysis of SV pool dynamics
during high-frequency train stimulation indicated a reduction of SVs with high
release probability but an overall normal size of the readily releasable SV pool
(RRP). The Ca2+-dependent fast component of SV replenishment after RRP depletion
was slowed. Ultrastructural analysis by superresolution light and electron microscopy
revealed an impaired topography of presynaptic CaV and a reduction of docked and
membrane-proximal SVs at the AZ. We conclude that RIM-BP2 organizes the topography
of CaV, and promotes SV tethering and docking. This way RIM-BP2 is critical for
establishing a high initial release probability as required to reliably signal
sound onset information that we found to be degraded in BCs of RIM-BP2-deficient
mice in vivo. SIGNIFICANCE STATEMENT: Rab-interacting molecule (RIM)-binding proteins
(BPs) are key organizers of the active zone (AZ). Using a multidisciplinary approach
to the calyceal endbulb of Held synapse that transmits auditory information at
rates of up to hundreds of Hertz with submillisecond precision we demonstrate
a requirement for RIM-BP2 for normal auditory signaling. Endbulb synapses lacking
RIM-BP2 show a reduced release probability despite normal whole-terminal Ca2+
influx and abundance of the key priming protein Munc13-1, a reduced rate of SV
replenishment, as well as an altered topography of voltage-gated (CaV)2.1 Ca2+
channels, and fewer docked and membrane proximal synaptic vesicles (SVs). This
hampers transmission of sound onset information likely affecting downstream neural
computations such as of sound localization.'
acknowledgement: This work was supported by the Deutsche Forschungsgemeinschaft (DFG,
German Research Foundation) through the Collaborative Sensory Research Center 1286
[to C.W. (A4) and T.M. (B5)] and under Germany’s Excellence Strategy Grant EXC 2067/1-390729940.
We thank S. Gerke, A.J. Goldak, and C. Senger-Freitag for expert technical assistance;
G. Hoch for developing image analysis routines; and S. Chepurwar and N. Strenzke
for technical support and discussion regarding in vivo experiments. We also thank
Dr. Christian Rosenmund, Dr. Katharina Grauel, and Dr. Stephan Sigrist for providing
RIM-BP2 KO mice and Dr. Masahiko Watanabe for providing the anti-neurexin-antibody,
and Dr. Toshihisa Ohtsuka for the anti-ELKS-antibody. J. Neef for help with the
STED imaging and image analysis; E. Neher and S. Rizzoli for discussion and comments
on the manuscript; K. Eguchi for help with the statistical analysis; and C. H. Huang
and J. Neef for constant support and scientific discussion.
article_processing_charge: No
article_type: original
author:
- first_name: Tanvi
full_name: Butola, Tanvi
last_name: Butola
- first_name: Theocharis
full_name: Alvanos, Theocharis
last_name: Alvanos
- first_name: Anika
full_name: Hintze, Anika
last_name: Hintze
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Carolin
full_name: Wichmann, Carolin
last_name: Wichmann
- first_name: Tobias
full_name: Moser, Tobias
last_name: Moser
citation:
ama: Butola T, Alvanos T, Hintze A, et al. RIM-binding protein 2 organizes Ca21
channel topography and regulates release probability and vesicle replenishment
at a fast central synapse. Journal of Neuroscience. 2021;41(37):7742-7767.
doi:10.1523/JNEUROSCI.0586-21.2021
apa: Butola, T., Alvanos, T., Hintze, A., Koppensteiner, P., Kleindienst, D., Shigemoto,
R., … Moser, T. (2021). RIM-binding protein 2 organizes Ca21 channel
topography and regulates release probability and vesicle replenishment at a fast
central synapse. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0586-21.2021
chicago: Butola, Tanvi, Theocharis Alvanos, Anika Hintze, Peter Koppensteiner, David
Kleindienst, Ryuichi Shigemoto, Carolin Wichmann, and Tobias Moser. “RIM-Binding
Protein 2 Organizes Ca21 Channel Topography and Regulates Release Probability
and Vesicle Replenishment at a Fast Central Synapse.” Journal of Neuroscience.
Society for Neuroscience, 2021. https://doi.org/10.1523/JNEUROSCI.0586-21.2021.
ieee: T. Butola et al., “RIM-binding protein 2 organizes Ca21
channel topography and regulates release probability and vesicle replenishment
at a fast central synapse,” Journal of Neuroscience, vol. 41, no. 37. Society
for Neuroscience, pp. 7742–7767, 2021.
ista: Butola T, Alvanos T, Hintze A, Koppensteiner P, Kleindienst D, Shigemoto R,
Wichmann C, Moser T. 2021. RIM-binding protein 2 organizes Ca21 channel
topography and regulates release probability and vesicle replenishment at a fast
central synapse. Journal of Neuroscience. 41(37), 7742–7767.
mla: Butola, Tanvi, et al. “RIM-Binding Protein 2 Organizes Ca21 Channel
Topography and Regulates Release Probability and Vesicle Replenishment at a Fast
Central Synapse.” Journal of Neuroscience, vol. 41, no. 37, Society for
Neuroscience, 2021, pp. 7742–67, doi:10.1523/JNEUROSCI.0586-21.2021.
short: T. Butola, T. Alvanos, A. Hintze, P. Koppensteiner, D. Kleindienst, R. Shigemoto,
C. Wichmann, T. Moser, Journal of Neuroscience 41 (2021) 7742–7767.
date_created: 2021-09-27T14:33:13Z
date_published: 2021-09-15T00:00:00Z
date_updated: 2023-08-14T06:56:30Z
day: '15'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1523/JNEUROSCI.0586-21.2021
external_id:
isi:
- '000752287700005'
pmid:
- '34353898'
file:
- access_level: open_access
checksum: 769ab627c7355a50ccfd445e43a5f351
content_type: application/pdf
creator: dernst
date_created: 2022-05-31T09:10:15Z
date_updated: 2022-05-31T09:10:15Z
file_id: '11423'
file_name: 2021_JourNeuroscience_Butola.pdf
file_size: 11571961
relation: main_file
success: 1
file_date_updated: 2022-05-31T09:10:15Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '37'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 7742-7767
pmid: 1
publication: Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
issn:
- 0270-6474
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: RIM-binding protein 2 organizes Ca21 channel topography and regulates
release probability and vesicle replenishment at a fast central synapse
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 41
year: '2021'
...
---
_id: '10055'
abstract:
- lang: eng
text: "Repeated idempotent elements are commonly used to characterise iterable behaviours
in abstract models of computation. Therefore, given a monoid M, it is natural
to ask how long a sequence of elements of M needs to be to ensure the presence
of consecutive idempotent factors. This question is formalised through the notion
of the Ramsey function R_M associated to M, obtained by mapping every k ∈ ℕ to
the minimal integer R_M(k) such that every word u ∈ M^* of length R_M(k) contains
k consecutive non-empty factors that correspond to the same idempotent element
of M. In this work, we study the behaviour of the Ramsey function R_M by investigating
the regular \U0001D49F-length of M, defined as the largest size L(M) of a submonoid
of M isomorphic to the set of natural numbers {1,2, …, L(M)} equipped with the
max operation. We show that the regular \U0001D49F-length of M determines the
degree of R_M, by proving that k^L(M) ≤ R_M(k) ≤ (k|M|⁴)^L(M). To allow applications
of this result, we provide the value of the regular \U0001D49F-length of diverse
monoids. In particular, we prove that the full monoid of n × n Boolean matrices,
which is used to express transition monoids of non-deterministic automata, has
a regular \U0001D49F-length of (n²+n+2)/2."
acknowledgement: This project has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
No. 754411. I wish to thank Michaël Cadilhac, Emmanuel Filiot and Charles Paperman
for their valuable insights concerning Green’s relations.
alternative_title:
- LIPIcs
article_number: '44'
article_processing_charge: No
author:
- first_name: Ismael R
full_name: Jecker, Ismael R
id: 85D7C63E-7D5D-11E9-9C0F-98C4E5697425
last_name: Jecker
citation:
ama: 'Jecker IR. A Ramsey theorem for finite monoids. In: 38th International
Symposium on Theoretical Aspects of Computer Science. Vol 187. Schloss Dagstuhl
- Leibniz Zentrum für Informatik; 2021. doi:10.4230/LIPIcs.STACS.2021.44'
apa: 'Jecker, I. R. (2021). A Ramsey theorem for finite monoids. In 38th International
Symposium on Theoretical Aspects of Computer Science (Vol. 187). Saarbrücken,
Germany: Schloss Dagstuhl - Leibniz Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2021.44'
chicago: Jecker, Ismael R. “A Ramsey Theorem for Finite Monoids.” In 38th International
Symposium on Theoretical Aspects of Computer Science, Vol. 187. Schloss Dagstuhl
- Leibniz Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.STACS.2021.44.
ieee: I. R. Jecker, “A Ramsey theorem for finite monoids,” in 38th International
Symposium on Theoretical Aspects of Computer Science, Saarbrücken, Germany,
2021, vol. 187.
ista: 'Jecker IR. 2021. A Ramsey theorem for finite monoids. 38th International
Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical
Aspects of Computer Science, LIPIcs, vol. 187, 44.'
mla: Jecker, Ismael R. “A Ramsey Theorem for Finite Monoids.” 38th International
Symposium on Theoretical Aspects of Computer Science, vol. 187, 44, Schloss
Dagstuhl - Leibniz Zentrum für Informatik, 2021, doi:10.4230/LIPIcs.STACS.2021.44.
short: I.R. Jecker, in:, 38th International Symposium on Theoretical Aspects of
Computer Science, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021.
conference:
end_date: 2021-03-19
location: Saarbrücken, Germany
name: 'STACS: Symposium on Theoretical Aspects of Computer Science'
start_date: 2021-03-16
date_created: 2021-09-27T14:33:15Z
date_published: 2021-03-10T00:00:00Z
date_updated: 2023-08-14T07:03:23Z
day: '10'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.STACS.2021.44
ec_funded: 1
external_id:
isi:
- '000635691700044'
file:
- access_level: open_access
checksum: 17432a05733f408de300e17e390a90e4
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-01T09:55:00Z
date_updated: 2021-10-01T09:55:00Z
file_id: '10063'
file_name: 2021_LIPIcs_Jecker.pdf
file_size: 720250
relation: main_file
success: 1
file_date_updated: 2021-10-01T09:55:00Z
has_accepted_license: '1'
intvolume: ' 187'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 38th International Symposium on Theoretical Aspects of Computer Science
publication_identifier:
isbn:
- 978-3-9597-7180-1
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: A Ramsey theorem for finite monoids
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: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 187
year: '2021'
...
---
_id: '10069'
abstract:
- lang: eng
text: 'The extent to which women differ in the course of blood cell counts throughout
pregnancy, and the importance of these changes to pregnancy outcomes has not been
well defined. Here, we develop a series of statistical analyses of repeated measures
data to reveal the degree to which women differ in the course of pregnancy, predict
the changes that occur, and determine the importance of these changes for post-partum
hemorrhage (PPH) which is one of the leading causes of maternal mortality. We
present a prospective cohort of 4082 births recorded at the University Hospital,
Lausanne, Switzerland between 2009 and 2014 where full labour records could be
obtained, along with complete blood count data taken at hospital admission. We
find significant differences, at a [Formula: see text] level, among women in how
blood count values change through pregnancy for mean corpuscular hemoglobin, mean
corpuscular volume, mean platelet volume, platelet count and red cell distribution
width. We find evidence that almost all complete blood count values show trimester-specific
associations with PPH. For example, high platelet count (OR 1.20, 95% CI 1.01-1.53),
high mean platelet volume (OR 1.58, 95% CI 1.04-2.08), and high erythrocyte levels
(OR 1.36, 95% CI 1.01-1.57) in trimester 1 increased PPH, but high values in trimester
3 decreased PPH risk (OR 0.85, 0.79, 0.67 respectively). We show that differences
among women in the course of blood cell counts throughout pregnancy have an important
role in shaping pregnancy outcome and tracking blood count value changes through
pregnancy improves identification of women at increased risk of postpartum hemorrhage.
This study provides greater understanding of the complex changes in blood count
values that occur through pregnancy and provides indicators to guide the stratification
of patients into risk groups.'
acknowledgement: This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181),
and by core funding from the Institute of Science and Technology Austria. We would
like to thank the participants of the study and all the midwives and doctors for
the computerized obstetrical data.
article_number: '19238'
article_processing_charge: Yes
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Marion
full_name: Patxot, Marion
last_name: Patxot
- first_name: Miloš
full_name: Stojanov, Miloš
last_name: Stojanov
- first_name: Sabine
full_name: Blum, Sabine
last_name: Blum
- first_name: David
full_name: Baud, David
last_name: Baud
citation:
ama: Robinson MR, Patxot M, Stojanov M, Blum S, Baud D. Postpartum hemorrhage risk
is driven by changes in blood composition through pregnancy. Scientific Reports.
2021;11. doi:10.1038/s41598-021-98411-z
apa: Robinson, M. R., Patxot, M., Stojanov, M., Blum, S., & Baud, D. (2021).
Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy.
Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-98411-z
chicago: Robinson, Matthew Richard, Marion Patxot, Miloš Stojanov, Sabine Blum,
and David Baud. “Postpartum Hemorrhage Risk Is Driven by Changes in Blood Composition
through Pregnancy.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-98411-z.
ieee: M. R. Robinson, M. Patxot, M. Stojanov, S. Blum, and D. Baud, “Postpartum
hemorrhage risk is driven by changes in blood composition through pregnancy,”
Scientific Reports, vol. 11. Springer Nature, 2021.
ista: Robinson MR, Patxot M, Stojanov M, Blum S, Baud D. 2021. Postpartum hemorrhage
risk is driven by changes in blood composition through pregnancy. Scientific Reports.
11, 19238.
mla: Robinson, Matthew Richard, et al. “Postpartum Hemorrhage Risk Is Driven by
Changes in Blood Composition through Pregnancy.” Scientific Reports, vol.
11, 19238, Springer Nature, 2021, doi:10.1038/s41598-021-98411-z.
short: M.R. Robinson, M. Patxot, M. Stojanov, S. Blum, D. Baud, Scientific Reports
11 (2021).
date_created: 2021-10-03T22:01:21Z
date_published: 2021-09-28T00:00:00Z
date_updated: 2023-08-14T07:05:15Z
day: '28'
ddc:
- '618'
department:
- _id: MaRo
doi: 10.1038/s41598-021-98411-z
external_id:
isi:
- '000701575500083'
pmid:
- '34584125'
file:
- access_level: open_access
checksum: f002ec22f609f58e1263b79e7f79601e
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-05T14:56:48Z
date_updated: 2021-10-05T14:56:48Z
file_id: '10091'
file_name: 2021_ScientificReports_Robinson.pdf
file_size: 6970368
relation: main_file
success: 1
file_date_updated: 2021-10-05T14:56:48Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
eissn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Postpartum hemorrhage risk is driven by changes in blood composition through
pregnancy
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2021'
...
---
_id: '10025'
abstract:
- lang: eng
text: Ferromagnetism is most common in transition metal compounds but may also arise
in low-density two-dimensional electron systems, with signatures observed in silicon,
III-V semiconductor systems, and graphene moiré heterostructures. Here we show
that gate-tuned van Hove singularities in rhombohedral trilayer graphene drive
the spontaneous ferromagnetic polarization of the electron system into one or
more spin- and valley flavors. Using capacitance measurements on graphite-gated
van der Waals heterostructures, we find a cascade of density- and electronic displacement
field tuned phase transitions marked by negative electronic compressibility. The
transitions define the boundaries between phases where quantum oscillations have
either four-fold, two-fold, or one-fold degeneracy, associated with a spin and
valley degenerate normal metal, spin-polarized `half-metal', and spin and valley
polarized `quarter metal', respectively. For electron doping, the salient features
are well captured by a phenomenological Stoner model with a valley-anisotropic
Hund's coupling, likely arising from interactions at the lattice scale. For hole
filling, we observe a richer phase diagram featuring a delicate interplay of broken
symmetries and transitions in the Fermi surface topology. Finally, by rotational
alignment of a hexagonal boron nitride substrate to induce a moiré superlattice,
we find that the superlattice perturbs the preexisting isospin order only weakly,
leaving the basic phase diagram intact while catalyzing the formation of topologically
nontrivial gapped states whenever itinerant half- or quarter metal states occur
at half- or quarter superlattice band filling. Our results show that rhombohedral
trilayer graphene is an ideal platform for well-controlled tests of many-body
theory and reveal magnetism in moiré materials to be fundamentally itinerant in
nature.
acknowledgement: "The authors acknowledge discussions with A. Macdonald, L. Fu, F.
Wang and M. Zaletel. AFY acknowledges support of the National Science Foundation
under DMR1654186, and the Gordon and Betty Moore Foundation under award GBMF9471.
The authors acknowledge the use of the research facilities within the California
NanoSystems Institute, supported by the University of California, Santa Barbara
and the University of California, Office of the President.\r\nK.W. and T.T. acknowledge
support from the Elemental Strategy Initiative conducted by the MEXT, Japan, Grant
Number JPMXP0112101001 and JSPS KAKENHI, Grant Number JP20H00354. EB and TH were
supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement
No. 817799). A.G. acknowledges support by the European Unions Horizon 2020 research
and innovation program under the Marie Sklodowska-Curie Grant Agreement\r\nNo. 754411.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Haoxin
full_name: Zhou, Haoxin
last_name: Zhou
- first_name: Tian
full_name: Xie, Tian
last_name: Xie
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Tobias
full_name: Holder, Tobias
last_name: Holder
- first_name: James R.
full_name: Ehrets, James R.
last_name: Ehrets
- first_name: Eric M.
full_name: Spanton, Eric M.
last_name: Spanton
- first_name: Takashi
full_name: Taniguchi, Takashi
last_name: Taniguchi
- first_name: Kenji
full_name: Watanabe, Kenji
last_name: Watanabe
- first_name: Erez
full_name: Berg, Erez
last_name: Berg
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Andrea F.
full_name: Young, Andrea F.
last_name: Young
citation:
ama: Zhou H, Xie T, Ghazaryan A, et al. Half and quarter metals in rhombohedral
trilayer graphene. Nature. 2021. doi:10.1038/s41586-021-03938-w
apa: Zhou, H., Xie, T., Ghazaryan, A., Holder, T., Ehrets, J. R., Spanton, E. M.,
… Young, A. F. (2021). Half and quarter metals in rhombohedral trilayer graphene.
Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03938-w
chicago: Zhou, Haoxin, Tian Xie, Areg Ghazaryan, Tobias Holder, James R. Ehrets,
Eric M. Spanton, Takashi Taniguchi, et al. “Half and Quarter Metals in Rhombohedral
Trilayer Graphene.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03938-w.
ieee: H. Zhou et al., “Half and quarter metals in rhombohedral trilayer graphene,”
Nature. Springer Nature, 2021.
ista: Zhou H, Xie T, Ghazaryan A, Holder T, Ehrets JR, Spanton EM, Taniguchi T,
Watanabe K, Berg E, Serbyn M, Young AF. 2021. Half and quarter metals in rhombohedral
trilayer graphene. Nature.
mla: Zhou, Haoxin, et al. “Half and Quarter Metals in Rhombohedral Trilayer Graphene.”
Nature, Springer Nature, 2021, doi:10.1038/s41586-021-03938-w.
short: H. Zhou, T. Xie, A. Ghazaryan, T. Holder, J.R. Ehrets, E.M. Spanton, T. Taniguchi,
K. Watanabe, E. Berg, M. Serbyn, A.F. Young, Nature (2021).
date_created: 2021-09-19T22:01:25Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2023-08-14T07:04:06Z
day: '01'
department:
- _id: MaSe
- _id: MiLe
doi: 10.1038/s41586-021-03938-w
ec_funded: 1
external_id:
arxiv:
- '2104.00653'
isi:
- '000706977400002'
isi: 1
keyword:
- condensed matter - mesoscale and nanoscale physics
- condensed matter - strongly correlated electrons
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2104.00653
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-021-04181-z
scopus_import: '1'
status: public
title: Half and quarter metals in rhombohedral trilayer graphene
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '10076'
abstract:
- lang: eng
text: We present a novel approach for blockchain asset owners to reclaim their funds
in case of accidental private-key loss or transfer to a mistyped address. Our
solution can be deployed upon failure or absence of proactively implemented backup
mechanisms, such as secret sharing and cold storage. The main advantages against
previous proposals is it does not require any prior action from users and works
with both single-key and multi-sig accounts. We achieve this by a 3-phase Commit()→Reveal()→Claim()−or−Challenge() smart
contract that enables accessing funds of addresses for which the spending key
is not available. We provide an analysis of the threat and incentive models and
formalize the concept of reactive KEy-Loss Protection (KELP).
acknowledgement: The authors would like to thank all anonymous reviewers of FC21 WTSC
workshop for comments and suggestions that greatly improved the quality of this
paper.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sam
full_name: Blackshear, Sam
last_name: Blackshear
- first_name: Konstantinos
full_name: Chalkias, Konstantinos
last_name: Chalkias
- first_name: Panagiotis
full_name: Chatzigiannis, Panagiotis
last_name: Chatzigiannis
- first_name: Riyaz
full_name: Faizullabhoy, Riyaz
last_name: Faizullabhoy
- first_name: Irakliy
full_name: Khaburzaniya, Irakliy
last_name: Khaburzaniya
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Joshua
full_name: Lind, Joshua
last_name: Lind
- first_name: David
full_name: Wong, David
last_name: Wong
- first_name: Tim
full_name: Zakian, Tim
last_name: Zakian
citation:
ama: 'Blackshear S, Chalkias K, Chatzigiannis P, et al. Reactive key-loss protection
in blockchains. In: FC 2021 Workshops. Vol 12676. Springer Nature; 2021:431-450.
doi:10.1007/978-3-662-63958-0_34'
apa: 'Blackshear, S., Chalkias, K., Chatzigiannis, P., Faizullabhoy, R., Khaburzaniya,
I., Kokoris Kogias, E., … Zakian, T. (2021). Reactive key-loss protection in blockchains.
In FC 2021 Workshops (Vol. 12676, pp. 431–450). Virtual: Springer Nature.
https://doi.org/10.1007/978-3-662-63958-0_34'
chicago: Blackshear, Sam, Konstantinos Chalkias, Panagiotis Chatzigiannis, Riyaz
Faizullabhoy, Irakliy Khaburzaniya, Eleftherios Kokoris Kogias, Joshua Lind, David
Wong, and Tim Zakian. “Reactive Key-Loss Protection in Blockchains.” In FC
2021 Workshops, 12676:431–50. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-63958-0_34.
ieee: S. Blackshear et al., “Reactive key-loss protection in blockchains,”
in FC 2021 Workshops, Virtual, 2021, vol. 12676, pp. 431–450.
ista: 'Blackshear S, Chalkias K, Chatzigiannis P, Faizullabhoy R, Khaburzaniya I,
Kokoris Kogias E, Lind J, Wong D, Zakian T. 2021. Reactive key-loss protection
in blockchains. FC 2021 Workshops. FC: International Conference on Financial Cryptography
and Data Security, LNCS, vol. 12676, 431–450.'
mla: Blackshear, Sam, et al. “Reactive Key-Loss Protection in Blockchains.” FC
2021 Workshops, vol. 12676, Springer Nature, 2021, pp. 431–50, doi:10.1007/978-3-662-63958-0_34.
short: S. Blackshear, K. Chalkias, P. Chatzigiannis, R. Faizullabhoy, I. Khaburzaniya,
E. Kokoris Kogias, J. Lind, D. Wong, T. Zakian, in:, FC 2021 Workshops, Springer
Nature, 2021, pp. 431–450.
conference:
end_date: 2021-03-05
location: Virtual
name: 'FC: International Conference on Financial Cryptography and Data Security'
start_date: 2021-03-01
date_created: 2021-10-03T22:01:24Z
date_published: 2021-09-17T00:00:00Z
date_updated: 2023-08-14T07:06:16Z
day: '17'
department:
- _id: ElKo
doi: 10.1007/978-3-662-63958-0_34
external_id:
isi:
- '000713005000034'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://research.fb.com/publications/reactive-key-loss-protection-in-blockchains/
month: '09'
oa: 1
oa_version: Preprint
page: 431-450
publication: FC 2021 Workshops
publication_identifier:
eisbn:
- 978-3-662-63958-0
eissn:
- 1611-3349
isbn:
- 978-3-6626-3957-3
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reactive key-loss protection in blockchains
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: '12676 '
year: '2021'
...
---
_id: '10070'
abstract:
- lang: eng
text: We extensively discuss the Rademacher and Sobolev-to-Lipschitz properties
for generalized intrinsic distances on strongly local Dirichlet spaces possibly
without square field operator. We present many non-smooth and infinite-dimensional
examples. As an application, we prove the integral Varadhan short-time asymptotic
with respect to a given distance function for a large class of strongly local
Dirichlet forms.
acknowledgement: 'The authors are grateful to Professor Kazuhiro Kuwae for kindly
providing a copy of [49]. They are also grateful to Dr. Bang-Xian Han for helpful
discussions on the Sobolev-to-Lipschitz property on metric measure spaces. They
wish to express their deepest gratitude to an anonymous Reviewer, whose punctual
remarks and comments greatly improved the accessibility and overall quality of the
initial submission. This work was completed while L.D.S. was a member of the Institut
für Angewandte Mathematik of the University of Bonn. He acknowledges funding of
his position at that time by the Deutsche Forschungsgemeinschaft (DFG, German Research
Foundation) through the Sonderforschungsbereich (Sfb, Collaborative Research Center)
1060 - project number 211504053. He also acknowledges funding of his current position
by the Austrian Science Fund (FWF) grant F65, and by the European Research Council
(ERC, grant No. 716117, awarded to Prof. Dr. Jan Maas). K.S. gratefully acknowledges
funding by: the JSPS Overseas Research Fellowships, Grant Nr. 290142; World Premier
International Research Center Initiative (WPI), MEXT, Japan; and JSPS Grant-in-Aid
for Scientific Research on Innovative Areas “Discrete Geometric Analysis for Materials
Design”, Grant Number 17H06465.'
article_number: '109234'
article_processing_charge: No
article_type: original
author:
- first_name: Lorenzo
full_name: Dello Schiavo, Lorenzo
id: ECEBF480-9E4F-11EA-B557-B0823DDC885E
last_name: Dello Schiavo
orcid: 0000-0002-9881-6870
- first_name: Kohei
full_name: Suzuki, Kohei
last_name: Suzuki
citation:
ama: Dello Schiavo L, Suzuki K. Rademacher-type theorems and Sobolev-to-Lipschitz
properties for strongly local Dirichlet spaces. Journal of Functional Analysis.
2021;281(11). doi:10.1016/j.jfa.2021.109234
apa: Dello Schiavo, L., & Suzuki, K. (2021). Rademacher-type theorems and Sobolev-to-Lipschitz
properties for strongly local Dirichlet spaces. Journal of Functional Analysis.
Elsevier. https://doi.org/10.1016/j.jfa.2021.109234
chicago: Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and
Sobolev-to-Lipschitz Properties for Strongly Local Dirichlet Spaces.” Journal
of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109234.
ieee: L. Dello Schiavo and K. Suzuki, “Rademacher-type theorems and Sobolev-to-Lipschitz
properties for strongly local Dirichlet spaces,” Journal of Functional Analysis,
vol. 281, no. 11. Elsevier, 2021.
ista: Dello Schiavo L, Suzuki K. 2021. Rademacher-type theorems and Sobolev-to-Lipschitz
properties for strongly local Dirichlet spaces. Journal of Functional Analysis.
281(11), 109234.
mla: Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and Sobolev-to-Lipschitz
Properties for Strongly Local Dirichlet Spaces.” Journal of Functional Analysis,
vol. 281, no. 11, 109234, Elsevier, 2021, doi:10.1016/j.jfa.2021.109234.
short: L. Dello Schiavo, K. Suzuki, Journal of Functional Analysis 281 (2021).
date_created: 2021-10-03T22:01:21Z
date_published: 2021-09-15T00:00:00Z
date_updated: 2023-08-14T07:05:44Z
day: '15'
department:
- _id: JaMa
doi: 10.1016/j.jfa.2021.109234
ec_funded: 1
external_id:
arxiv:
- '2008.01492'
isi:
- '000703896600005'
intvolume: ' 281'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2008.01492
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local
Dirichlet spaces
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 281
year: '2021'
...
---
_id: '10123'
abstract:
- lang: eng
text: Solution synthesis of particles emerged as an alternative to prepare thermoelectric
materials with less demanding processing conditions than conventional solid-state
synthetic methods. However, solution synthesis generally involves the presence
of additional molecules or ions belonging to the precursors or added to enable
solubility and/or regulate nucleation and growth. These molecules or ions can
end up in the particles as surface adsorbates and interfere in the material properties.
This work demonstrates that ionic adsorbates, in particular Na⁺ ions, are electrostatically
adsorbed in SnSe particles synthesized in water and play a crucial role not only
in directing the material nano/microstructure but also in determining the transport
properties of the consolidated material. In dense pellets prepared by sintering
SnSe particles, Na remains within the crystal lattice as dopant, in dislocations,
precipitates, and forming grain boundary complexions. These results highlight
the importance of considering all the possible unintentional impurities to establish
proper structure-property relationships and control material properties in solution-processed
thermoelectric materials.
acknowledged_ssus:
- _id: EM-Fac
- _id: NanoFab
acknowledgement: 'Y.L. and M.C. contributed equally to this work. This research was
supported by the Scientific Service Units (SSU) of IST Austria through resources
provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility
(NNF). This work was financially supported by IST Austria and the Werner Siemens
Foundation. Y.L. acknowledges funding from the European Union''s Horizon 2020 research
and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411.
M.C. has received funding from the European Union''s Horizon 2020 research and innovation
program under the Marie Skłodowska-Curie Grant Agreement No. 665385. Y.Y. and O.C.-M.
acknowledge the financial support from DFG within the project SFB 917: Nanoswitches.
J.L. is a Serra Húnter Fellow and is grateful to ICREA Academia program. C.C. acknowledges
funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N.'
article_number: '2106858'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Mariano
full_name: Calcabrini, Mariano
id: 45D7531A-F248-11E8-B48F-1D18A9856A87
last_name: Calcabrini
orcid: 0000-0003-4566-5877
- first_name: Yuan
full_name: Yu, Yuan
last_name: Yu
- first_name: Aziz
full_name: Genç, Aziz
last_name: Genç
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Tobias
full_name: Kleinhanns, Tobias
id: 8BD9DE16-AB3C-11E9-9C8C-2A03E6697425
last_name: Kleinhanns
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Jordi
full_name: Llorca, Jordi
last_name: Llorca
- first_name: Oana
full_name: Cojocaru‐Mirédin, Oana
last_name: Cojocaru‐Mirédin
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: 'Liu Y, Calcabrini M, Yu Y, et al. The importance of surface adsorbates in
solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials.
2021;33(52). doi:10.1002/adma.202106858'
apa: 'Liu, Y., Calcabrini, M., Yu, Y., Genç, A., Chang, C., Costanzo, T., … Ibáñez,
M. (2021). The importance of surface adsorbates in solution‐processed thermoelectric
materials: The case of SnSe. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202106858'
chicago: 'Liu, Yu, Mariano Calcabrini, Yuan Yu, Aziz Genç, Cheng Chang, Tommaso
Costanzo, Tobias Kleinhanns, et al. “The Importance of Surface Adsorbates in Solution‐processed
Thermoelectric Materials: The Case of SnSe.” Advanced Materials. Wiley,
2021. https://doi.org/10.1002/adma.202106858.'
ieee: 'Y. Liu et al., “The importance of surface adsorbates in solution‐processed
thermoelectric materials: The case of SnSe,” Advanced Materials, vol. 33,
no. 52. Wiley, 2021.'
ista: 'Liu Y, Calcabrini M, Yu Y, Genç A, Chang C, Costanzo T, Kleinhanns T, Lee
S, Llorca J, Cojocaru‐Mirédin O, Ibáñez M. 2021. The importance of surface adsorbates
in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials.
33(52), 2106858.'
mla: 'Liu, Yu, et al. “The Importance of Surface Adsorbates in Solution‐processed
Thermoelectric Materials: The Case of SnSe.” Advanced Materials, vol. 33,
no. 52, 2106858, Wiley, 2021, doi:10.1002/adma.202106858.'
short: Y. Liu, M. Calcabrini, Y. Yu, A. Genç, C. Chang, T. Costanzo, T. Kleinhanns,
S. Lee, J. Llorca, O. Cojocaru‐Mirédin, M. Ibáñez, Advanced Materials 33 (2021).
date_created: 2021-10-11T20:07:24Z
date_published: 2021-12-29T00:00:00Z
date_updated: 2023-08-14T07:25:27Z
day: '29'
ddc:
- '620'
department:
- _id: EM-Fac
- _id: MaIb
doi: 10.1002/adma.202106858
ec_funded: 1
external_id:
isi:
- '000709899300001'
pmid:
- '34626034'
file:
- access_level: open_access
checksum: 990bccc527c64d85cf1c97885110b5f4
content_type: application/pdf
creator: cchlebak
date_created: 2022-02-03T13:16:14Z
date_updated: 2022-02-03T13:16:14Z
file_id: '10720'
file_name: 2021_AdvancedMaterials_Liu.pdf
file_size: 5595666
relation: main_file
success: 1
file_date_updated: 2022-02-03T13:16:14Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '52'
keyword:
- mechanical engineering
- mechanics of materials
- general materials science
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
publication: Advanced Materials
publication_identifier:
eissn:
- 1521-4095
issn:
- 0935-9648
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '12885'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'The importance of surface adsorbates in solution‐processed thermoelectric
materials: The case of SnSe'
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: 33
year: '2021'
...
---
_id: '10117'
abstract:
- lang: eng
text: Proximity labeling provides a powerful in vivo tool to characterize the proteome
of subcellular structures and the interactome of specific proteins. The nematode
Caenorhabditis elegans is one of the most intensely studied organisms in biology,
offering many advantages for biochemistry. Using the highly active biotin ligase
TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage
of TurboID is that biotin's high affinity for streptavidin means biotin-labeled
proteins can be affinity-purified under harsh denaturing conditions. By combining
extensive sonication with aggressive denaturation using SDS and urea, we achieved
near-complete solubilization of worm proteins. We then used this protocol to characterize
the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among
the smallest C. elegans cells. To probe the method's sensitivity, we expressed
TurboID exclusively in the two AFD neurons and showed that the protocol could
identify known and previously unknown proteins expressed selectively in AFD. The
active zones of synapses are composed of a protein matrix that is difficult to
solubilize and purify. To test if our protocol could solubilize active zone proteins,
we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic
active zone protein. We identified many known ELKS-1-interacting active zone proteins,
as well as previously uncharacterized synaptic proteins. Versatile vectors and
the inherent advantages of using C. elegans, including fast growth and the ability
to rapidly make and functionally test knock-ins, make proximity labeling a valuable
addition to the armory of this model organism.
acknowledgement: We thank de Bono lab members for helpful comments on the manuscript,
IST Austria and University of Vienna Mass Spec Facilities for invaluable discussions
and comments for the optimization of mass spec analyses of worm samples. The biotin
auxotropic E. coli strain MG1655bioB:kan was gift from John Cronan (University of
Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford
University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54
3′UTR entry vector were kindly shared by Dr Dominique Glauser (University of Fribourg).
Codon-optimized mScarlet vector was a generous gift from Dr Manuel Zimmer (University
of Vienna).
article_number: '101094'
article_processing_charge: Yes
article_type: original
author:
- first_name: Murat
full_name: Artan, Murat
id: C407B586-6052-11E9-B3AE-7006E6697425
last_name: Artan
orcid: 0000-0001-8945-6992
- first_name: Stephen
full_name: Barratt, Stephen
id: 57740d2b-2a88-11ec-97cf-d9e6d1b39677
last_name: Barratt
- first_name: Sean M.
full_name: Flynn, Sean M.
last_name: Flynn
- first_name: Farida
full_name: Begum, Farida
last_name: Begum
- first_name: Mark
full_name: Skehel, Mark
last_name: Skehel
- first_name: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- 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, Barratt S, Flynn SM, et al. Interactome analysis of Caenorhabditis
elegans synapses by TurboID-based proximity labeling. Journal of Biological
Chemistry. 2021;297(3). doi:10.1016/J.JBC.2021.101094
apa: Artan, M., Barratt, S., Flynn, S. M., Begum, F., Skehel, M., Nicolas, A., &
de Bono, M. (2021). Interactome analysis of Caenorhabditis elegans synapses by
TurboID-based proximity labeling. Journal of Biological Chemistry. Elsevier.
https://doi.org/10.1016/J.JBC.2021.101094
chicago: Artan, Murat, Stephen Barratt, Sean M. Flynn, Farida Begum, Mark Skehel,
Armel Nicolas, and Mario de Bono. “Interactome Analysis of Caenorhabditis Elegans
Synapses by TurboID-Based Proximity Labeling.” Journal of Biological Chemistry.
Elsevier, 2021. https://doi.org/10.1016/J.JBC.2021.101094.
ieee: M. Artan et al., “Interactome analysis of Caenorhabditis elegans synapses
by TurboID-based proximity labeling,” Journal of Biological Chemistry,
vol. 297, no. 3. Elsevier, 2021.
ista: Artan M, Barratt S, Flynn SM, Begum F, Skehel M, Nicolas A, de Bono M. 2021.
Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity
labeling. Journal of Biological Chemistry. 297(3), 101094.
mla: Artan, Murat, et al. “Interactome Analysis of Caenorhabditis Elegans Synapses
by TurboID-Based Proximity Labeling.” Journal of Biological Chemistry,
vol. 297, no. 3, 101094, Elsevier, 2021, doi:10.1016/J.JBC.2021.101094.
short: M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de
Bono, Journal of Biological Chemistry 297 (2021).
date_created: 2021-10-10T22:01:23Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2023-08-14T07:24:09Z
day: '01'
ddc:
- '612'
department:
- _id: MaDe
- _id: LifeSc
doi: 10.1016/J.JBC.2021.101094
ec_funded: 1
external_id:
isi:
- '000706409200006'
file:
- access_level: open_access
checksum: 19e39d36c5b9387c6dc0e89c9ae856ab
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-11T12:20:58Z
date_updated: 2021-10-11T12:20:58Z
file_id: '10121'
file_name: 2021_JBC_Artan.pdf
file_size: 1680010
relation: main_file
success: 1
file_date_updated: 2021-10-11T12:20:58Z
has_accepted_license: '1'
intvolume: ' 297'
isi: 1
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _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: Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity
labeling
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: 297
year: '2021'
...
---
_id: '10108'
abstract:
- lang: eng
text: We argue that the time is ripe to investigate differential monitoring, in
which the specification of a program's behavior is implicitly given by a second
program implementing the same informal specification. Similar ideas have been
proposed before, and are currently implemented in restricted form for testing
and specialized run-time analyses, aspects of which we combine. We discuss the
challenges of implementing differential monitoring as a general-purpose, black-box
run-time monitoring framework, and present promising results of a preliminary
implementation, showing low monitoring overheads for diverse programs.
acknowledgement: The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer,
Adrian Francalanza, Owolabi Legunsen, Mae Milano, Manuel Rigger, Cesar Sanchez,
and the members of the IST Verification Seminar for their helpful comments and insights
on various stages of this work, as well as the reviewers of RV’21 for their helpful
suggestions on the actual paper.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Fabian
full_name: Mühlböck, Fabian
id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425
last_name: Mühlböck
orcid: 0000-0003-1548-0177
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Mühlböck F, Henzinger TA. Differential monitoring. In: International Conference
on Runtime Verification. Vol 12974. Cham: Springer Nature; 2021:231-243. doi:10.1007/978-3-030-88494-9_12'
apa: 'Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring. In International
Conference on Runtime Verification (Vol. 12974, pp. 231–243). Cham: Springer
Nature. https://doi.org/10.1007/978-3-030-88494-9_12'
chicago: 'Mühlböck, Fabian, and Thomas A Henzinger. “Differential Monitoring.” In
International Conference on Runtime Verification, 12974:231–43. Cham: Springer
Nature, 2021. https://doi.org/10.1007/978-3-030-88494-9_12.'
ieee: F. Mühlböck and T. A. Henzinger, “Differential monitoring,” in International
Conference on Runtime Verification, Virtual, 2021, vol. 12974, pp. 231–243.
ista: 'Mühlböck F, Henzinger TA. 2021. Differential monitoring. International Conference
on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 231–243.'
mla: Mühlböck, Fabian, and Thomas A. Henzinger. “Differential Monitoring.” International
Conference on Runtime Verification, vol. 12974, Springer Nature, 2021, pp.
231–43, doi:10.1007/978-3-030-88494-9_12.
short: F. Mühlböck, T.A. Henzinger, in:, International Conference on Runtime Verification,
Springer Nature, Cham, 2021, pp. 231–243.
conference:
end_date: 2021-10-14
location: Virtual
name: 'RV: Runtime Verification'
start_date: 2021-10-11
date_created: 2021-10-07T23:30:10Z
date_published: 2021-10-06T00:00:00Z
date_updated: 2023-08-14T07:20:30Z
day: '06'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-030-88494-9_12
external_id:
isi:
- '000719383800012'
file:
- access_level: open_access
checksum: 554c7fdb259eda703a8b6328a6dad55a
content_type: application/pdf
creator: fmuehlbo
date_created: 2021-10-07T23:32:18Z
date_updated: 2021-10-07T23:32:18Z
file_id: '10109'
file_name: differentialmonitoring-cameraready-openaccess.pdf
file_size: 350632
relation: main_file
success: 1
file_date_updated: 2021-10-07T23:32:18Z
has_accepted_license: '1'
intvolume: ' 12974'
isi: 1
keyword:
- run-time verification
- software engineering
- implicit specification
language:
- iso: eng
month: '10'
oa: 1
oa_version: Preprint
page: 231-243
place: Cham
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: International Conference on Runtime Verification
publication_identifier:
eisbn:
- 978-3-030-88494-9
eissn:
- 1611-3349
isbn:
- 978-3-030-88493-2
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '9946'
relation: extended_version
status: public
scopus_import: '1'
status: public
title: Differential monitoring
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12974
year: '2021'
...
---
_id: '10116'
abstract:
- lang: eng
text: The ubiquitous Ca2+ sensor calmodulin (CaM) binds and regulates many proteins,
including ion channels, CaM kinases, and calcineurin, according to Ca2+-CaM levels.
What regulates neuronal CaM levels, is, however, unclear. CaM-binding transcription
activators (CAMTAs) are ancient proteins expressed broadly in nervous systems
and whose loss confers pleiotropic behavioral defects in flies, mice, and humans.
Using Caenorhabditis elegans and Drosophila, we show that CAMTAs control neuronal
CaM levels. The behavioral and neuronal Ca2+ signaling defects in mutants lacking
camt-1, the sole C. elegans CAMTA, can be rescued by supplementing neuronal CaM.
CAMT-1 binds multiple sites in the CaM promoter and deleting these sites phenocopies
camt-1. Our data suggest CAMTAs mediate a conserved and general mechanism that
controls neuronal CaM levels, thereby regulating Ca2+ signaling, physiology, and
behavior.
acknowledgement: The authors thank the MRC-LMB Flow Cytometry facility and Imaging
Service for support, the Cancer Research UK Cambridge Institute Genomics Core for
Next Generation Sequencing, Julie Ahringer and Alex Appert for advice and technical
help for ChIP-seq experiments, Paula Freire-Pritchett, Tim Stevens, and Gurpreet
Ghattaoraya for RNA-seq and ChIP-seq analyses, Nikos Chronis for the TN-XL plasmid,
Hong-Sheng Li and Daisuke Yamamoto for generously sending the tes2 and cro mutants,
Daria Siekhaus for hosting the fly work, Michaela Misova for technical assistance.
The authors are very grateful to Salihah Ece Sönmez for teaching us how to dissect,
mount and stain Drosophila retinae. This work was supported by an Advanced ERC grant
(269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB, and an IST
Plus Fellowship to TV-B (Marie Sklodowska-Curie Agreement no 754411).
article_number: e68238
article_processing_charge: No
article_type: original
author:
- first_name: Thanh
full_name: Vuong-Brender, Thanh
id: D389312E-10C4-11EA-ABF4-A4B43DDC885E
last_name: Vuong-Brender
- first_name: Sean
full_name: Flynn, Sean
last_name: Flynn
- first_name: Yvonne
full_name: Vallis, Yvonne
id: 05A2795C-31B5-11EA-83A7-7DA23DDC885E
last_name: Vallis
- 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: Vuong-Brender T, Flynn S, Vallis Y, de Bono M. Neuronal calmodulin levels are
controlled by CAMTA transcription factors. eLife. 2021;10. doi:10.7554/eLife.68238
apa: Vuong-Brender, T., Flynn, S., Vallis, Y., & de Bono, M. (2021). Neuronal
calmodulin levels are controlled by CAMTA transcription factors. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.68238
chicago: Vuong-Brender, Thanh, Sean Flynn, Yvonne Vallis, and Mario de Bono. “Neuronal
Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” ELife.
eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.68238.
ieee: T. Vuong-Brender, S. Flynn, Y. Vallis, and M. de Bono, “Neuronal calmodulin
levels are controlled by CAMTA transcription factors,” eLife, vol. 10.
eLife Sciences Publications, 2021.
ista: Vuong-Brender T, Flynn S, Vallis Y, de Bono M. 2021. Neuronal calmodulin levels
are controlled by CAMTA transcription factors. eLife. 10, e68238.
mla: Vuong-Brender, Thanh, et al. “Neuronal Calmodulin Levels Are Controlled by
CAMTA Transcription Factors.” ELife, vol. 10, e68238, eLife Sciences Publications,
2021, doi:10.7554/eLife.68238.
short: T. Vuong-Brender, S. Flynn, Y. Vallis, M. de Bono, ELife 10 (2021).
date_created: 2021-10-10T22:01:22Z
date_published: 2021-09-17T00:00:00Z
date_updated: 2023-08-14T07:23:39Z
day: '17'
ddc:
- '610'
department:
- _id: MaDe
doi: 10.7554/eLife.68238
ec_funded: 1
external_id:
isi:
- '000695716100001'
pmid:
- '34499028'
file:
- access_level: open_access
checksum: b465e172d2b1f57aa26a2571a085d052
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-11T14:15:07Z
date_updated: 2021-10-11T14:15:07Z
file_id: '10122'
file_name: 2021_eLife_VuongBrender.pdf
file_size: 1774624
relation: main_file
success: 1
file_date_updated: 2021-10-11T14:15:07Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neuronal calmodulin levels are controlled by CAMTA transcription factors
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '10103'
abstract:
- lang: eng
text: The small cellular molecule inositol hexakisphosphate (IP6) has been known
for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like
particles. However, the molecular details underlying this effect have been determined
only recently, with the identification of the IP6 binding site in the immature
Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice
via a second IP6 binding site, and enhances core stability, creating a favorable
environment for reverse transcription. IP6 also enhances assembly of other retroviruses,
from both the Lentivirus and the Alpharetrovirus genera. These findings suggest
that IP6 may have a conserved function throughout the family Retroviridae. Here,
we discuss the different steps in the viral life cycle that are influenced by
IP6, and describe in detail how IP6 interacts with the immature and mature lattices
of different retroviruses.
acknowledgement: We thank Volker M. Vogt for his critical comments in preparation
of the review.
article_number: '1853'
article_processing_charge: Yes
article_type: original
author:
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Robert A.
full_name: Dick, Robert A.
last_name: Dick
citation:
ama: Obr M, Schur FK, Dick RA. A structural perspective of the role of IP6 in immature
and mature retroviral assembly. Viruses. 2021;13(9). doi:10.3390/v13091853
apa: Obr, M., Schur, F. K., & Dick, R. A. (2021). A structural perspective of
the role of IP6 in immature and mature retroviral assembly. Viruses. MDPI.
https://doi.org/10.3390/v13091853
chicago: Obr, Martin, Florian KM Schur, and Robert A. Dick. “A Structural Perspective
of the Role of IP6 in Immature and Mature Retroviral Assembly.” Viruses.
MDPI, 2021. https://doi.org/10.3390/v13091853.
ieee: M. Obr, F. K. Schur, and R. A. Dick, “A structural perspective of the role
of IP6 in immature and mature retroviral assembly,” Viruses, vol. 13, no.
9. MDPI, 2021.
ista: Obr M, Schur FK, Dick RA. 2021. A structural perspective of the role of IP6
in immature and mature retroviral assembly. Viruses. 13(9), 1853.
mla: Obr, Martin, et al. “A Structural Perspective of the Role of IP6 in Immature
and Mature Retroviral Assembly.” Viruses, vol. 13, no. 9, 1853, MDPI, 2021,
doi:10.3390/v13091853.
short: M. Obr, F.K. Schur, R.A. Dick, Viruses 13 (2021).
date_created: 2021-10-07T09:13:29Z
date_published: 2021-09-17T00:00:00Z
date_updated: 2023-08-14T07:21:51Z
day: '17'
ddc:
- '616'
department:
- _id: FlSc
doi: 10.3390/v13091853
external_id:
isi:
- '000699841100001'
pmid:
- '34578434'
file:
- access_level: open_access
checksum: bcfd72a12977d48e22df3d0cc55aacf1
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-08T10:38:15Z
date_updated: 2021-10-08T10:38:15Z
file_id: '10115'
file_name: 2021_Viruses_Obr.pdf
file_size: 4146796
relation: main_file
success: 1
file_date_updated: 2021-10-08T10:38:15Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '9'
keyword:
- virology
- infectious diseases
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: Viruses
publication_identifier:
issn:
- 1999-4915
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: A structural perspective of the role of IP6 in immature and mature retroviral
assembly
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: '2021'
...
---
_id: '10067'
abstract:
- lang: eng
text: The search for novel entangled phases of matter has lead to the recent discovery
of a new class of “entanglement transitions,” exemplified by random tensor networks
and monitored quantum circuits. Most known examples can be understood as some
classical ordering transitions in an underlying statistical mechanics model, where
entanglement maps onto the free-energy cost of inserting a domain wall. In this
paper we study the possibility of entanglement transitions driven by physics beyond
such statistical mechanics mappings. Motivated by recent applications of neural-network-inspired
variational Ansätze, we investigate under what conditions on the variational parameters
these Ansätze can capture an entanglement transition. We study the entanglement
scaling of short-range restricted Boltzmann machine (RBM) quantum states with
random phases. For uncorrelated random phases, we analytically demonstrate the
absence of an entanglement transition and reveal subtle finite-size effects in
finite-size numerical simulations. Introducing phases with correlations decaying
as 1/r^α in real space, we observe three regions with a different scaling of entanglement
entropy depending on the exponent α. We study the nature of the transition between
these regions, finding numerical evidence for critical behavior. Our work establishes
the presence of long-range correlated phases in RBM-based wave functions as a
required ingredient for entanglement transitions.
acknowledgement: We would like to thank S. De Nicola, P. Brighi, and V. Karle for
fruitful discussions and valuable feedback on the manuscript. R.M. and M.S. acknowledge
support by the European Research Council (ERC) under the European Union's Horizon
2020 research and innovation program (Grant Agreement No. 850899). R.V. acknowledges
support from the US Department of Energy, Office of Science, Basic Energy Sciences,
under Early Career Award No. DE-SC0019168, and the Alfred P. Sloan Foundation through
a Sloan Research Fellowship.
article_number: '104205'
article_processing_charge: No
article_type: original
author:
- first_name: Raimel A
full_name: Medina Ramos, Raimel A
id: CE680B90-D85A-11E9-B684-C920E6697425
last_name: Medina Ramos
orcid: 0000-0002-5383-2869
- first_name: Romain
full_name: Vasseur, Romain
last_name: Vasseur
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Medina Ramos RA, Vasseur R, Serbyn M. Entanglement transitions from restricted
Boltzmann machines. Physical Review B. 2021;104(10). doi:10.1103/physrevb.104.104205
apa: Medina Ramos, R. A., Vasseur, R., & Serbyn, M. (2021). Entanglement transitions
from restricted Boltzmann machines. Physical Review B. American Physical
Society. https://doi.org/10.1103/physrevb.104.104205
chicago: Medina Ramos, Raimel A, Romain Vasseur, and Maksym Serbyn. “Entanglement
Transitions from Restricted Boltzmann Machines.” Physical Review B. American
Physical Society, 2021. https://doi.org/10.1103/physrevb.104.104205.
ieee: R. A. Medina Ramos, R. Vasseur, and M. Serbyn, “Entanglement transitions from
restricted Boltzmann machines,” Physical Review B, vol. 104, no. 10. American
Physical Society, 2021.
ista: Medina Ramos RA, Vasseur R, Serbyn M. 2021. Entanglement transitions from
restricted Boltzmann machines. Physical Review B. 104(10), 104205.
mla: Medina Ramos, Raimel A., et al. “Entanglement Transitions from Restricted Boltzmann
Machines.” Physical Review B, vol. 104, no. 10, 104205, American Physical
Society, 2021, doi:10.1103/physrevb.104.104205.
short: R.A. Medina Ramos, R. Vasseur, M. Serbyn, Physical Review B 104 (2021).
date_created: 2021-10-02T09:03:42Z
date_published: 2021-09-30T00:00:00Z
date_updated: 2023-08-14T07:24:47Z
day: '30'
department:
- _id: MaSe
doi: 10.1103/physrevb.104.104205
ec_funded: 1
external_id:
arxiv:
- '2107.05735'
isi:
- '000704414400002'
intvolume: ' 104'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2107.05735
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Entanglement transitions from restricted Boltzmann machines
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 104
year: '2021'
...
---
_id: '9946'
abstract:
- lang: eng
text: We argue that the time is ripe to investigate differential monitoring, in
which the specification of a program's behavior is implicitly given by a second
program implementing the same informal specification. Similar ideas have been
proposed before, and are currently implemented in restricted form for testing
and specialized run-time analyses, aspects of which we combine. We discuss the
challenges of implementing differential monitoring as a general-purpose, black-box
run-time monitoring framework, and present promising results of a preliminary
implementation, showing low monitoring overheads for diverse programs.
acknowledgement: The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer,
Adrian Francalanza, Owolabi Legunsen, Matthew Milano, Manuel Rigger, Cesar Sanchez,
and the members of the IST Verification Seminar for their helpful comments and insights
on various stages of this work, as well as the reviewers of RV’21 for their helpful
suggestions on the actual paper.
alternative_title:
- IST Austria Technical Report
article_processing_charge: No
author:
- first_name: Fabian
full_name: Mühlböck, Fabian
id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425
last_name: Mühlböck
orcid: 0000-0003-1548-0177
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: Mühlböck F, Henzinger TA. Differential Monitoring. IST Austria; 2021.
doi:10.15479/AT:ISTA:9946
apa: Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring.
IST Austria. https://doi.org/10.15479/AT:ISTA:9946
chicago: Mühlböck, Fabian, and Thomas A Henzinger. Differential Monitoring.
IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9946.
ieee: F. Mühlböck and T. A. Henzinger, Differential monitoring. IST Austria,
2021.
ista: Mühlböck F, Henzinger TA. 2021. Differential monitoring, IST Austria, 17p.
mla: Mühlböck, Fabian, and Thomas A. Henzinger. Differential Monitoring.
IST Austria, 2021, doi:10.15479/AT:ISTA:9946.
short: F. Mühlböck, T.A. Henzinger, Differential Monitoring, IST Austria, 2021.
date_created: 2021-08-20T20:00:37Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2023-08-14T07:20:29Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.15479/AT:ISTA:9946
file:
- access_level: open_access
checksum: 0f9aafd59444cb6bdca6925d163ab946
content_type: application/pdf
creator: fmuehlbo
date_created: 2021-08-20T19:59:44Z
date_updated: 2021-09-03T12:34:28Z
file_id: '9948'
file_name: differentialmonitoring-techreport.pdf
file_size: '320453'
relation: main_file
file_date_updated: 2021-09-03T12:34:28Z
has_accepted_license: '1'
keyword:
- run-time verification
- software engineering
- implicit specification
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '17'
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
related_material:
record:
- id: '9281'
relation: other
status: public
- id: '10108'
relation: shorter_version
status: public
status: public
title: Differential monitoring
type: technical_report
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '10073'
abstract:
- lang: eng
text: Thermoelectric materials enable the direct conversion between heat and electricity.
SnTe is a promising candidate due to its high charge transport performance. Here,
we prepared SnTe nanocomposites by employing an aqueous method to synthetize SnTe
nanoparticles (NP), followed by a unique surface treatment prior NP consolidation.
This synthetic approach allowed optimizing the charge and phonon transport synergistically.
The novelty of this strategy was the use of a soluble PbS molecular complex prepared
using a thiol-amine solvent mixture that upon blending is adsorbed on the SnTe
NP surface. Upon consolidation with spark plasma sintering, SnTe-PbS nanocomposite
is formed. The presence of PbS complexes significantly compensates for the Sn
vacancy and increases the average grain size of the nanocomposite, thus improving
the carrier mobility. Moreover, lattice thermal conductivity is also reduced by
the Pb and S-induced mass and strain fluctuation. As a result, an enhanced ZT
of ca. 0.8 is reached at 873 K. Our finding provides a novel strategy to conduct
rational surface treatment on NP-based thermoelectrics.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "The authors thank the EMF facility in IST Austria for providing
SEM and EDX measurements.\r\n"
article_number: '5416'
article_processing_charge: Yes
article_type: original
author:
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: Chang C, Ibáñez M. Enhanced thermoelectric performance by surface engineering
in SnTe-PbS nanocomposites. Materials. 2021;14(18). doi:10.3390/ma14185416
apa: Chang, C., & Ibáñez, M. (2021). Enhanced thermoelectric performance by
surface engineering in SnTe-PbS nanocomposites. Materials. MDPI. https://doi.org/10.3390/ma14185416
chicago: Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by
Surface Engineering in SnTe-PbS Nanocomposites.” Materials. MDPI, 2021.
https://doi.org/10.3390/ma14185416.
ieee: C. Chang and M. Ibáñez, “Enhanced thermoelectric performance by surface engineering
in SnTe-PbS nanocomposites,” Materials, vol. 14, no. 18. MDPI, 2021.
ista: Chang C, Ibáñez M. 2021. Enhanced thermoelectric performance by surface engineering
in SnTe-PbS nanocomposites. Materials. 14(18), 5416.
mla: Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface
Engineering in SnTe-PbS Nanocomposites.” Materials, vol. 14, no. 18, 5416,
MDPI, 2021, doi:10.3390/ma14185416.
short: C. Chang, M. Ibáñez, Materials 14 (2021).
date_created: 2021-10-03T22:01:23Z
date_published: 2021-09-19T00:00:00Z
date_updated: 2023-08-14T08:00:01Z
day: '19'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.3390/ma14185416
external_id:
isi:
- '000700689400001'
pmid:
- '34576640'
file:
- access_level: open_access
checksum: 4929dfc673a3ae77c010b6174279cc1d
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-14T11:56:39Z
date_updated: 2021-10-14T11:56:39Z
file_id: '10140'
file_name: 2021_Materials_Chang.pdf
file_size: 4404141
relation: main_file
success: 1
file_date_updated: 2021-10-14T11:56:39Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '18'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
publication: Materials
publication_identifier:
eissn:
- 1996-1944
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites
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: 14
year: '2021'
...
---
_id: '10167'
abstract:
- lang: eng
text: Schistosomes, the human parasites responsible for snail fever, are female-heterogametic.
Different parts of their ZW sex chromosomes have stopped recombining in distinct
lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome
is well characterized at the genomic and molecular level, the W-chromosome has
remained largely unstudied from an evolutionary perspective, as only a few W-linked
genes have been detected outside of the model species Schistosoma mansoni. Here,
we characterize the gene content and evolution of the W-chromosomes of S. mansoni
and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based
pipeline to assemble around 100 candidate W-specific transcripts in each of the
species. About half of them map to known protein coding genes, the majority homologous
to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary
strata present in the two species (including characterizing a previously undetected
young stratum in S. japonicum) to infer patterns of sequence and expression evolution
of W-linked genes at different time points after recombination was lost. W-linked
genes show evidence of degeneration, including high rates of protein evolution
and reduced expression. Most are found in young lineage-specific strata, with
only a few high expression ancestral W-genes remaining, consistent with the progressive
erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands
out as a promising candidate for primary sex determination, opening new avenues
for understanding the molecular basis of the reproductive biology of this group.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: The authors thank IT support at IST Austria for providing an optimal
environment for bioinformatic analyses. This work was supported by an Austrian Science
Foundation FWF grant (Project P28842) to B.V.
article_processing_charge: No
article_type: original
author:
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Mikhail A.
full_name: Moldovan, Mikhail A.
id: c8bb7f32-3315-11ec-b58b-e5950e6c14a0
last_name: Moldovan
orcid: 0000-0002-8876-6494
- first_name: Marion A L
full_name: Picard, Marion A L
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-Linked genes inform
temporal dynamics of sex chromosome evolution and suggest candidate for sex determination.
Molecular Biology and Evolution. 2021. doi:10.1093/molbev/msab178
apa: Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., & Vicoso, B. (2021).
Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution
and suggest candidate for sex determination. Molecular Biology and Evolution.
Oxford University Press . https://doi.org/10.1093/molbev/msab178
chicago: Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz
Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome
Evolution and Suggest Candidate for Sex Determination.” Molecular Biology and
Evolution. Oxford University Press , 2021. https://doi.org/10.1093/molbev/msab178.
ieee: M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome
W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest
candidate for sex determination,” Molecular Biology and Evolution. Oxford
University Press , 2021.
ista: Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-Linked
genes inform temporal dynamics of sex chromosome evolution and suggest candidate
for sex determination. Molecular Biology and Evolution.
mla: Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics
of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” Molecular
Biology and Evolution, Oxford University Press , 2021, doi:10.1093/molbev/msab178.
short: M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology
and Evolution (2021).
date_created: 2021-10-21T07:49:12Z
date_published: 2021-06-19T00:00:00Z
date_updated: 2023-08-14T08:03:06Z
day: '19'
ddc:
- '610'
department:
- _id: BeVi
doi: 10.1093/molbev/msab178
external_id:
isi:
- '000741368600009'
pmid:
- '34146097'
file:
- access_level: open_access
checksum: 1b096702fb356d9c0eb88e1b3fcff5f8
content_type: application/pdf
creator: dernst
date_created: 2022-05-06T09:47:18Z
date_updated: 2022-05-06T09:47:18Z
file_id: '11352'
file_name: 2021_MolecularBiolEvolution_Elkrewi.pdf
file_size: 1008594
relation: main_file
success: 1
file_date_updated: 2022-05-06T09:47:18Z
has_accepted_license: '1'
isi: 1
keyword:
- sex chromosomes
- evolutionary strata
- W-linked gene
- sex determining gene
- schistosome parasites
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: Molecular Biology and Evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: 'Oxford University Press '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution
and suggest candidate for sex determination
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '10163'
abstract:
- lang: eng
text: The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol
II) is a regulatory hub for transcription and RNA processing. Here, we identify
PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability
that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a
CTD reader domain that preferentially binds two phosphorylated Serine-2 marks
in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated
Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length
of genes. PHF3 knock-out or SPOC deletion in human cells results in increased
Pol II stalling, reduced elongation rate and an increase in mRNA stability, with
marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed
in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation.
Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation
by bridging transcription with mRNA decay.
acknowledgement: 'D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz
Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help
with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase;
Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for
design of the arrest assay sequences; Petra van der Lelij for help with generating
mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan
Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing
reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski
for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility
for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing;
Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich
Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for
sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne
Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis;
staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support;
Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for
critical comments on the manuscript; Life Science Editors for editing assistance.
M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K.
is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S.
is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian
Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology
Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S
and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic
(CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (Grant agreement
no. 649030); this publication reflects only the author’s view and the Research Executive
Agency is not responsible for any use that may be made of the information it contains.
M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research
is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276,
P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative
‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural
Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action
BM1405 Non-globular proteins - from sequence to structure, function and application
in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF
LS17-008), and by the University of Vienna. This project was funded by the MFPL
start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the
Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”)
to D.S.'
article_number: '6078'
article_processing_charge: No
article_type: original
author:
- first_name: Lisa-Marie
full_name: Appel, Lisa-Marie
last_name: Appel
- first_name: Vedran
full_name: Franke, Vedran
last_name: Franke
- first_name: Melania
full_name: Bruno, Melania
last_name: Bruno
- first_name: Irina
full_name: Grishkovskaya, Irina
last_name: Grishkovskaya
- first_name: Aiste
full_name: Kasiliauskaite, Aiste
last_name: Kasiliauskaite
- first_name: Tanja
full_name: Kaufmann, Tanja
last_name: Kaufmann
- first_name: Ursula E.
full_name: Schoeberl, Ursula E.
last_name: Schoeberl
- first_name: Martin G.
full_name: Puchinger, Martin G.
last_name: Puchinger
- first_name: Sebastian
full_name: Kostrhon, Sebastian
last_name: Kostrhon
- first_name: Carmen
full_name: Ebenwaldner, Carmen
last_name: Ebenwaldner
- first_name: Marek
full_name: Sebesta, Marek
last_name: Sebesta
- first_name: Etienne
full_name: Beltzung, Etienne
last_name: Beltzung
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Gen
full_name: Lin, Gen
last_name: Lin
- first_name: Anna
full_name: Vlasova, Anna
last_name: Vlasova
- first_name: Martin
full_name: Leeb, Martin
last_name: Leeb
- first_name: Rushad
full_name: Pavri, Rushad
last_name: Pavri
- first_name: Alexander
full_name: Stark, Alexander
last_name: Stark
- first_name: Altuna
full_name: Akalin, Altuna
last_name: Akalin
- first_name: Richard
full_name: Stefl, Richard
last_name: Stefl
- 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: Kristina
full_name: Djinovic-Carugo, Kristina
last_name: Djinovic-Carugo
- first_name: Dea
full_name: Slade, Dea
last_name: Slade
citation:
ama: Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression
through the Pol II CTD reader domain SPOC. Nature Communications. 2021;12(1).
doi:10.1038/s41467-021-26360-2
apa: Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A.,
Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through
the Pol II CTD reader domain SPOC. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-021-26360-2
chicago: Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste
Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal
Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26360-2.
ieee: L.-M. Appel et al., “PHF3 regulates neuronal gene expression through
the Pol II CTD reader domain SPOC,” Nature Communications, vol. 12, no.
1. Springer Nature, 2021.
ista: Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann
T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung
E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R,
Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression
through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.
mla: Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through
the Pol II CTD Reader Domain SPOC.” Nature Communications, vol. 12, no.
1, 6078, Springer Nature, 2021, doi:10.1038/s41467-021-26360-2.
short: L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T.
Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta,
E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A.
Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications
12 (2021).
date_created: 2021-10-20T14:40:32Z
date_published: 2021-10-19T00:00:00Z
date_updated: 2023-08-14T08:02:31Z
day: '19'
ddc:
- '610'
department:
- _id: CaBe
doi: 10.1038/s41467-021-26360-2
external_id:
isi:
- '000709050300001'
file:
- access_level: open_access
checksum: d99fcd51aebde19c21314e3de0148007
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-21T13:51:49Z
date_updated: 2021-10-21T13:51:49Z
file_id: '10169'
file_name: 2021_NatComm_Appel.pdf
file_size: 5111706
relation: main_file
success: 1
file_date_updated: 2021-10-21T13:51:49Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- general physics and astronomy
- general biochemistry
- genetics and molecular biology
- general chemistry
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: 'Preprint '
relation: earlier_version
url: https://www.biorxiv.org/content/10.1101/2020.02.11.943159
status: public
title: PHF3 regulates neuronal gene expression through the Pol II CTD reader domain
SPOC
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9547'
abstract:
- lang: eng
text: With the wider availability of full-color 3D printers, color-accurate 3D-print
preparation has received increased attention. A key challenge lies in the inherent
translucency of commonly used print materials that blurs out details of the color
texture. Previous work tries to compensate for these scattering effects through
strategic assignment of colored primary materials to printer voxels. To date,
the highest-quality approach uses iterative optimization that relies on computationally
expensive Monte Carlo light transport simulation to predict the surface appearance
from subsurface scattering within a given print material distribution; that optimization,
however, takes in the order of days on a single machine. In our work, we dramatically
speed up the process by replacing the light transport simulation with a data-driven
approach. Leveraging a deep neural network to predict the scattering within a
highly heterogeneous medium, our method performs around two orders of magnitude
faster than Monte Carlo rendering while yielding optimization results of similar
quality level. The network is based on an established method from atmospheric
cloud rendering, adapted to our domain and extended by a physically motivated
weight sharing scheme that substantially reduces the network size. We analyze
its performance in an end-to-end print preparation pipeline and compare quality
and runtime to alternative approaches, and demonstrate its generalization to unseen
geometry and material values. This for the first time enables full heterogenous
material optimization for 3D-print preparation within time frames in the order
of the actual printing time.
acknowledgement: We thank Sebastian Cucerca for processing and capturing the phys-cal
printouts. This work was supported by the Charles University grant SVV-260588 and
Czech Science Foundation grant 19-07626S. This project has received funding from
the European Union’s Horizon 2020 research and innovation programme, under the Marie
Skłodowska Curie grant agreements No 642841 (DISTRO) and No765911 (RealVision),
and under the European Research Council grant agreement No 715767 (MATERIALIZABLE).
article_processing_charge: No
article_type: original
author:
- first_name: Tobias
full_name: Rittig, Tobias
last_name: Rittig
- first_name: Denis
full_name: Sumin, Denis
last_name: Sumin
- first_name: Vahid
full_name: Babaei, Vahid
last_name: Babaei
- first_name: Piotr
full_name: Didyk, Piotr
last_name: Didyk
- first_name: Alexey
full_name: Voloboy, Alexey
last_name: Voloboy
- first_name: Alexander
full_name: Wilkie, Alexander
last_name: Wilkie
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Karol
full_name: Myszkowski, Karol
last_name: Myszkowski
- first_name: Tim
full_name: Weyrich, Tim
last_name: Weyrich
- first_name: Jaroslav
full_name: Křivánek, Jaroslav
last_name: Křivánek
citation:
ama: Rittig T, Sumin D, Babaei V, et al. Neural acceleration of scattering-aware
color 3D printing. Computer Graphics Forum. 2021;40(2):205-219. doi:10.1111/cgf.142626
apa: Rittig, T., Sumin, D., Babaei, V., Didyk, P., Voloboy, A., Wilkie, A., … Křivánek,
J. (2021). Neural acceleration of scattering-aware color 3D printing. Computer
Graphics Forum. Wiley. https://doi.org/10.1111/cgf.142626
chicago: Rittig, Tobias, Denis Sumin, Vahid Babaei, Piotr Didyk, Alexey Voloboy,
Alexander Wilkie, Bernd Bickel, Karol Myszkowski, Tim Weyrich, and Jaroslav Křivánek.
“Neural Acceleration of Scattering-Aware Color 3D Printing.” Computer Graphics
Forum. Wiley, 2021. https://doi.org/10.1111/cgf.142626.
ieee: T. Rittig et al., “Neural acceleration of scattering-aware color 3D
printing,” Computer Graphics Forum, vol. 40, no. 2. Wiley, pp. 205–219,
2021.
ista: Rittig T, Sumin D, Babaei V, Didyk P, Voloboy A, Wilkie A, Bickel B, Myszkowski
K, Weyrich T, Křivánek J. 2021. Neural acceleration of scattering-aware color
3D printing. Computer Graphics Forum. 40(2), 205–219.
mla: Rittig, Tobias, et al. “Neural Acceleration of Scattering-Aware Color 3D Printing.”
Computer Graphics Forum, vol. 40, no. 2, Wiley, 2021, pp. 205–19, doi:10.1111/cgf.142626.
short: T. Rittig, D. Sumin, V. Babaei, P. Didyk, A. Voloboy, A. Wilkie, B. Bickel,
K. Myszkowski, T. Weyrich, J. Křivánek, Computer Graphics Forum 40 (2021) 205–219.
date_created: 2021-06-13T22:01:32Z
date_published: 2021-05-01T00:00:00Z
date_updated: 2023-08-14T08:01:50Z
day: '01'
ddc:
- '004'
department:
- _id: BeBi
doi: 10.1111/cgf.142626
ec_funded: 1
external_id:
isi:
- '000657959600017'
file:
- access_level: open_access
checksum: 33271724215f54a75c39d2ed40f2c502
content_type: application/pdf
creator: bbickel
date_created: 2021-10-11T12:06:50Z
date_updated: 2021-10-11T12:06:50Z
file_id: '10120'
file_name: ScatteringAwareColor3DPrinting_authorVersion.pdf
file_size: 26026501
relation: main_file
success: 1
file_date_updated: 2021-10-11T12:06:50Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 205-219
project:
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: Computer Graphics Forum
publication_identifier:
eissn:
- 1467-8659
issn:
- 0167-7055
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neural acceleration of scattering-aware color 3D printing
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2021'
...
---
_id: '10177'
abstract:
- lang: eng
text: Phonon polaritons (PhPs)—light coupled to lattice vibrations—with in-plane
hyperbolic dispersion exhibit ray-like propagation with large wave vectors and
enhanced density of optical states along certain directions on a surface. As such,
they have raised a surge of interest, promising unprecedented manipulation of
infrared light at the nanoscale in a planar circuitry. Here, we demonstrate focusing
of in-plane hyperbolic PhPs propagating along thin slabs of α-MoO3. To that end,
we developed metallic nanoantennas of convex geometries for both efficient launching
and focusing of the polaritons. The foci obtained exhibit enhanced near-field
confinement and absorption compared to foci produced by in-plane isotropic PhPs.
Foci sizes as small as λp/4.5 = λ0/50 were achieved (λp is the polariton wavelength
and λ0 is the photon wavelength). Focusing of in-plane hyperbolic polaritons introduces
a first and most basic building block developing planar polariton optics using
in-plane anisotropic van der Waals materials.
acknowledgement: J.M.-S. acknowledges financial support from the Ramón y Cajal Program
of the Government of Spain and FSE (RYC2018-026196-I) and the Spanish Ministry of
Science and Innovation (State Plan for Scientific and Technical Research and Innovation
grant number PID2019-110308GA-I00). P.A.-G. acknowledges support from the European
Research Council under starting grant no. 715496, 2DNANOPTICA, and the Spanish Ministry
of Science and Innovation (State Plan for Scientific and Technical Research and
Innovation grant number PID2019-111156GB-I00). J.T.-G. acknowledges support through
the Severo Ochoa Program from the Government of the Principality of Asturias (PA-18-PF-BP17-126).
G.A.-P. acknowledges support through the Severo Ochoa Program from the Government
of the Principality of Asturias (PA-20-PF-BP19-053). K.V.V. and V.S.V. acknowledge
the financial support from the Ministry of Science and Higher Education of the Russian
Federation (agreement no. 075-15-2021-606). A.Y.N. acknowledges the Spanish Ministry
of Science, Innovation, and Universities (national projects MAT2017-88358-C3-3-R
and PID2020-115221GB-C42) and the Basque Department of Education (PIBA-2020-1-0014).
R.H. acknowledges financial support from the Spanish Ministry of Science, Innovation,
and Universities (national project number RTI2018-094830-B-100 and project number
MDM-2016-0618 of the Marie de Maeztu Units of Excellence Program) and the Basque
Government (grant number IT1164-19).
article_number: abj0127
article_processing_charge: Yes
article_type: original
author:
- first_name: Javier
full_name: Martín-Sánchez, Javier
last_name: Martín-Sánchez
- first_name: Jiahua
full_name: Duan, Jiahua
last_name: Duan
- first_name: Javier
full_name: Taboada-Gutiérrez, Javier
last_name: Taboada-Gutiérrez
- first_name: Gonzalo
full_name: Álvarez-Pérez, Gonzalo
last_name: Álvarez-Pérez
- first_name: Kirill V.
full_name: Voronin, Kirill V.
last_name: Voronin
- first_name: Ivan
full_name: Prieto Gonzalez, Ivan
id: 2A307FE2-F248-11E8-B48F-1D18A9856A87
last_name: Prieto Gonzalez
orcid: 0000-0002-7370-5357
- first_name: Weiliang
full_name: Ma, Weiliang
last_name: Ma
- first_name: Qiaoliang
full_name: Bao, Qiaoliang
last_name: Bao
- first_name: Valentyn S.
full_name: Volkov, Valentyn S.
last_name: Volkov
- first_name: Rainer
full_name: Hillenbrand, Rainer
last_name: Hillenbrand
- first_name: Alexey Y.
full_name: Nikitin, Alexey Y.
last_name: Nikitin
- first_name: Pablo
full_name: Alonso-González, Pablo
last_name: Alonso-González
citation:
ama: Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, et al. Focusing of in-plane
hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas.
Science Advances. 2021;7(41). doi:10.1126/sciadv.abj0127
apa: Martín-Sánchez, J., Duan, J., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Voronin,
K. V., Prieto Gonzalez, I., … Alonso-González, P. (2021). Focusing of in-plane
hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas.
Science Advances. American Association for the Advancement of Science.
https://doi.org/10.1126/sciadv.abj0127
chicago: Martín-Sánchez, Javier, Jiahua Duan, Javier Taboada-Gutiérrez, Gonzalo
Álvarez-Pérez, Kirill V. Voronin, Ivan Prieto Gonzalez, Weiliang Ma, et al. “Focusing
of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared
Nanoantennas.” Science Advances. American Association for the Advancement
of Science, 2021. https://doi.org/10.1126/sciadv.abj0127.
ieee: J. Martín-Sánchez et al., “Focusing of in-plane hyperbolic polaritons
in van der Waals crystals with tailored infrared nanoantennas,” Science Advances,
vol. 7, no. 41. American Association for the Advancement of Science, 2021.
ista: Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, Álvarez-Pérez G, Voronin KV,
Prieto Gonzalez I, Ma W, Bao Q, Volkov VS, Hillenbrand R, Nikitin AY, Alonso-González
P. 2021. Focusing of in-plane hyperbolic polaritons in van der Waals crystals
with tailored infrared nanoantennas. Science Advances. 7(41), abj0127.
mla: Martín-Sánchez, Javier, et al. “Focusing of In-Plane Hyperbolic Polaritons
in van Der Waals Crystals with Tailored Infrared Nanoantennas.” Science Advances,
vol. 7, no. 41, abj0127, American Association for the Advancement of Science,
2021, doi:10.1126/sciadv.abj0127.
short: J. Martín-Sánchez, J. Duan, J. Taboada-Gutiérrez, G. Álvarez-Pérez, K.V.
Voronin, I. Prieto Gonzalez, W. Ma, Q. Bao, V.S. Volkov, R. Hillenbrand, A.Y.
Nikitin, P. Alonso-González, Science Advances 7 (2021).
date_created: 2021-10-24T22:01:33Z
date_published: 2021-10-08T00:00:00Z
date_updated: 2023-08-14T08:04:42Z
day: '08'
ddc:
- '530'
department:
- _id: NanoFab
doi: 10.1126/sciadv.abj0127
external_id:
arxiv:
- '2103.10852'
isi:
- '000704912700024'
file:
- access_level: open_access
checksum: 0a470ef6a47d2b8a96ede4c4d28cfacd
content_type: application/pdf
creator: cziletti
date_created: 2021-10-27T14:16:06Z
date_updated: 2021-10-27T14:16:06Z
file_id: '10189'
file_name: 2021_ScienceAdv_Martin-Sanchez.pdf
file_size: 2441163
relation: main_file
success: 1
file_date_updated: 2021-10-27T14:16:06Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '41'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Science Advances
publication_identifier:
eissn:
- '23752548'
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored
infrared nanoantennas
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 7
year: '2021'
...
---
_id: '10146'
abstract:
- lang: eng
text: The enzymes of the mitochondrial electron transport chain are key players
of cell metabolism. Despite being active when isolated, in vivo they associate
into supercomplexes1, whose precise role is debated. Supercomplexes CIII2CIV1-2
(refs. 2,3), CICIII2 (ref. 4) and CICIII2CIV (respirasome)5,6,7,8,9,10 exist in
mammals, but in contrast to CICIII2 and the respirasome, to date the only known
eukaryotic structures of CIII2CIV1-2 come from Saccharomyces cerevisiae11,12 and
plants13, which have different organization. Here we present the first, to our
knowledge, structures of mammalian (mouse and ovine) CIII2CIV and its assembly
intermediates, in different conformations. We describe the assembly of CIII2CIV
from the CIII2 precursor to the final CIII2CIV conformation, driven by the insertion
of the N terminus of the assembly factor SCAF1 (ref. 14) deep into CIII2, while
its C terminus is integrated into CIV. Our structures (which include CICIII2 and
the respirasome) also confirm that SCAF1 is exclusively required for the assembly
of CIII2CIV and has no role in the assembly of the respirasome. We show that CIII2
is asymmetric due to the presence of only one copy of subunit 9, which straddles
both monomers and prevents the attachment of a second copy of SCAF1 to CIII2,
explaining the presence of one copy of CIV in CIII2CIV in mammals. Finally, we
show that CIII2 and CIV gain catalytic advantage when assembled into the supercomplex
and propose a role for CIII2CIV in fine tuning the efficiency of electron transfer
in the electron transport chain.
acknowledged_ssus:
- _id: PreCl
- _id: EM-Fac
- _id: ScienComp
acknowledgement: We thank the pre-clinical facility of the IST Austria and A. Venturino
for assistance with the animals; and V.-V. Hodirnau for assistance during the Titan
Krios data collection, performed at the IST Austria. The data processing was performed
at the IST high-performance computing cluster. This project has received funding
from the European Union’s Horizon 2020 research and innovation program under the
Marie Skłodowska-Curie grant agreement no. 754411.
article_processing_charge: No
article_type: original
author:
- first_name: Irene
full_name: Vercellino, Irene
id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87
last_name: Vercellino
orcid: 0000-0001-5618-3449
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Vercellino I, Sazanov LA. Structure and assembly of the mammalian mitochondrial
supercomplex CIII2CIV. Nature. 2021;598(7880):364-367. doi:10.1038/s41586-021-03927-z
apa: Vercellino, I., & Sazanov, L. A. (2021). Structure and assembly of the
mammalian mitochondrial supercomplex CIII2CIV. Nature. Springer
Nature. https://doi.org/10.1038/s41586-021-03927-z
chicago: Vercellino, Irene, and Leonid A Sazanov. “Structure and Assembly of the
Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature. Springer
Nature, 2021. https://doi.org/10.1038/s41586-021-03927-z.
ieee: I. Vercellino and L. A. Sazanov, “Structure and assembly of the mammalian
mitochondrial supercomplex CIII2CIV,” Nature, vol. 598, no.
7880. Springer Nature, pp. 364–367, 2021.
ista: Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial
supercomplex CIII2CIV. Nature. 598(7880), 364–367.
mla: Vercellino, Irene, and Leonid A. Sazanov. “Structure and Assembly of the Mammalian
Mitochondrial Supercomplex CIII2CIV.” Nature, vol. 598, no.
7880, Springer Nature, 2021, pp. 364–67, doi:10.1038/s41586-021-03927-z.
short: I. Vercellino, L.A. Sazanov, Nature 598 (2021) 364–367.
date_created: 2021-10-17T22:01:17Z
date_published: 2021-10-14T00:00:00Z
date_updated: 2023-08-14T08:01:21Z
day: '14'
department:
- _id: LeSa
doi: 10.1038/s41586-021-03927-z
ec_funded: 1
external_id:
isi:
- '000704581600001'
pmid:
- '34616041'
intvolume: ' 598'
isi: 1
issue: '7880'
language:
- iso: eng
month: '10'
oa_version: None
page: 364-367
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/boosting-the-cells-power-house/
scopus_import: '1'
status: public
title: Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 598
year: '2021'
...
---
_id: '10176'
abstract:
- lang: eng
text: "We give a combinatorial model for r-spin surfaces with parameterized boundary
based on Novak (“Lattice topological field theories in two dimensions,” Ph.D.
thesis, Universität Hamburg, 2015). The r-spin structure is encoded in terms of
ℤ\U0001D45F-valued indices assigned to the edges of a polygonal decomposition.
This combinatorial model is designed for our state-sum construction of two-dimensional
topological field theories on r-spin surfaces. We show that an example of such
a topological field theory computes the Arf-invariant of an r-spin surface as
introduced by Randal-Williams [J. Topol. 7, 155 (2014)] and Geiges et al. [Osaka
J. Math. 49, 449 (2012)]. This implies, in particular, that the r-spin Arf-invariant
is constant on orbits of the mapping class group, providing an alternative proof
of that fact."
acknowledgement: We would like to thank Nils Carqueville, Tobias Dyckerhoff, Jan Hesse,
Ehud Meir, Sebastian Novak, Louis-Hadrien Robert, Nick Salter, Walker Stern, and
Lukas Woike for helpful discussions and comments. L.S. was supported by the DFG
Research Training Group 1670 “Mathematics Inspired by String Theory and Quantum
Field Theory.”
article_number: '102302'
article_processing_charge: No
article_type: original
author:
- first_name: Ingo
full_name: Runkel, Ingo
last_name: Runkel
- first_name: Lorant
full_name: Szegedy, Lorant
id: 7943226E-220E-11EA-94C7-D59F3DDC885E
last_name: Szegedy
orcid: 0000-0003-2834-5054
citation:
ama: Runkel I, Szegedy L. Topological field theory on r-spin surfaces and the Arf-invariant.
Journal of Mathematical Physics. 2021;62(10). doi:10.1063/5.0037826
apa: Runkel, I., & Szegedy, L. (2021). Topological field theory on r-spin surfaces
and the Arf-invariant. Journal of Mathematical Physics. AIP Publishing.
https://doi.org/10.1063/5.0037826
chicago: Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces
and the Arf-Invariant.” Journal of Mathematical Physics. AIP Publishing,
2021. https://doi.org/10.1063/5.0037826.
ieee: I. Runkel and L. Szegedy, “Topological field theory on r-spin surfaces and
the Arf-invariant,” Journal of Mathematical Physics, vol. 62, no. 10. AIP
Publishing, 2021.
ista: Runkel I, Szegedy L. 2021. Topological field theory on r-spin surfaces and
the Arf-invariant. Journal of Mathematical Physics. 62(10), 102302.
mla: Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces
and the Arf-Invariant.” Journal of Mathematical Physics, vol. 62, no. 10,
102302, AIP Publishing, 2021, doi:10.1063/5.0037826.
short: I. Runkel, L. Szegedy, Journal of Mathematical Physics 62 (2021).
date_created: 2021-10-24T22:01:32Z
date_published: 2021-10-01T00:00:00Z
date_updated: 2023-08-14T08:04:12Z
day: '01'
department:
- _id: MiLe
doi: 10.1063/5.0037826
external_id:
arxiv:
- '1802.09978'
isi:
- '000755638500010'
intvolume: ' 62'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.09978
month: '10'
oa: 1
oa_version: Preprint
publication: Journal of Mathematical Physics
publication_identifier:
issn:
- '00222488'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Topological field theory on r-spin surfaces and the Arf-invariant
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 62
year: '2021'
...
---
_id: '10179'
abstract:
- lang: eng
text: Inhibitory GABAergic interneurons migrate over long distances from their extracortical
origin into the developing cortex. In humans, this process is uniquely slow and
prolonged, and it is unclear whether guidance cues unique to humans govern the
various phases of this complex developmental process. Here, we use fused cerebral
organoids to identify key roles of neurotransmitter signaling pathways in guiding
the migratory behavior of human cortical interneurons. We use scRNAseq to reveal
expression of GABA, glutamate, glycine, and serotonin receptors along distinct
maturation trajectories across interneuron migration. We develop an image analysis
software package, TrackPal, to simultaneously assess 48 parameters for entire
migration tracks of individual cells. By chemical screening, we show that different
modes of interneuron migration depend on distinct neurotransmitter signaling pathways,
linking transcriptional maturation of interneurons with their migratory behavior.
Altogether, our study provides a comprehensive quantitative analysis of human
interneuron migration and its functional modulation by neurotransmitter signaling.
acknowledgement: We thank all Knoblich laboratory members for continued support and
discussions. We thank the IMP/IMBA BioOptics facility, particularly Pawel Pasierbek,
Alberto Moreno Cencerrado and Gerald Schmauss, the IMP/IMBA Molecular Biology Service,
in particular Robert Heinen, the IMP Bioinformatics facility, in particular Thomas
Burkard, the Vienna Biocenter Core Facilities (VBCF) Histopathology facility, in
particular Tamara Engelmaier, and the VBCF Next Generation Sequencing Facility,
notably Volodymyr Shubchynskyy and Carmen Czepe. We would also like to thank Simon
Haendeler for advice on statistical analyses, Jose Guzman for discussions and assistance
with slice culture setups, Oliver L. Eichmueller for discussions and assistance
with microscopy, and E.H. Gustafson, S. Wolfinger, and D. Reumann for technical
assistance regarding generation of cerebral organoids. This project received funding
from the European Union’s Horizon 2020 research and innovation program under the
Marie Skłodowska-Curie fellowship agreement Nr.707109 awarded to J.A.B. Work in
J.A.K.'s laboratory is supported by the Austrian Federal Ministry of Education,
Science and Research, the Austrian Academy of Sciences, the City of Vienna, a Research
Program of the Austrian Science Fund FWF (SFBF78 Stem Cell, F 7803-B) and a European
Research Council (ERC) Advanced Grant under the European 20 Union’s Horizon 2020
program (grant agreement no. 695642).
article_number: e108714
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Sunanjay
full_name: Bajaj, Sunanjay
last_name: Bajaj
- first_name: Joshua A.
full_name: Bagley, Joshua A.
last_name: Bagley
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Abel
full_name: Vertesy, Abel
last_name: Vertesy
- first_name: Sakurako
full_name: Nagumo Wong, Sakurako
last_name: Nagumo Wong
- first_name: Veronica
full_name: Krenn, Veronica
last_name: Krenn
- first_name: Julie
full_name: Lévi-Strauss, Julie
last_name: Lévi-Strauss
- first_name: Juergen A.
full_name: Knoblich, Juergen A.
last_name: Knoblich
citation:
ama: Bajaj S, Bagley JA, Sommer CM, et al. Neurotransmitter signaling regulates
distinct phases of multimodal human interneuron migration. EMBO Journal.
2021;40(23). doi:10.15252/embj.2021108714
apa: Bajaj, S., Bagley, J. A., Sommer, C. M., Vertesy, A., Nagumo Wong, S., Krenn,
V., … Knoblich, J. A. (2021). Neurotransmitter signaling regulates distinct phases
of multimodal human interneuron migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2021108714
chicago: Bajaj, Sunanjay, Joshua A. Bagley, Christoph M Sommer, Abel Vertesy, Sakurako
Nagumo Wong, Veronica Krenn, Julie Lévi-Strauss, and Juergen A. Knoblich. “Neurotransmitter
Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.”
EMBO Journal. Embo Press, 2021. https://doi.org/10.15252/embj.2021108714.
ieee: S. Bajaj et al., “Neurotransmitter signaling regulates distinct phases
of multimodal human interneuron migration,” EMBO Journal, vol. 40, no.
23. Embo Press, 2021.
ista: Bajaj S, Bagley JA, Sommer CM, Vertesy A, Nagumo Wong S, Krenn V, Lévi-Strauss
J, Knoblich JA. 2021. Neurotransmitter signaling regulates distinct phases of
multimodal human interneuron migration. EMBO Journal. 40(23), e108714.
mla: Bajaj, Sunanjay, et al. “Neurotransmitter Signaling Regulates Distinct Phases
of Multimodal Human Interneuron Migration.” EMBO Journal, vol. 40, no.
23, e108714, Embo Press, 2021, doi:10.15252/embj.2021108714.
short: S. Bajaj, J.A. Bagley, C.M. Sommer, A. Vertesy, S. Nagumo Wong, V. Krenn,
J. Lévi-Strauss, J.A. Knoblich, EMBO Journal 40 (2021).
date_created: 2021-10-24T22:01:34Z
date_published: 2021-10-18T00:00:00Z
date_updated: 2023-08-14T08:05:23Z
day: '18'
ddc:
- '610'
department:
- _id: Bio
doi: 10.15252/embj.2021108714
external_id:
isi:
- '000708012800001'
pmid:
- '34661293'
file:
- access_level: open_access
checksum: 78d2d02e775322297e774f72810a41a4
content_type: application/pdf
creator: alisjak
date_created: 2021-12-13T14:54:14Z
date_updated: 2021-12-13T14:54:14Z
file_id: '10541'
file_name: 2021_EMBO_Bajaj.pdf
file_size: 7819881
relation: main_file
success: 1
file_date_updated: 2021-12-13T14:54:14Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '23'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: EMBO Journal
publication_identifier:
eissn:
- 1460-2075
issn:
- 0261-4189
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neurotransmitter signaling regulates distinct phases of multimodal human interneuron
migration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2021'
...
---
_id: '10203'
abstract:
- lang: eng
text: Single photon emitters in atomically-thin semiconductors can be deterministically
positioned using strain induced by underlying nano-structures. Here, we couple
monolayer WSe2 to high-refractive-index gallium phosphide dielectric nano-antennas
providing both optical enhancement and monolayer deformation. For single photon
emitters formed on such nano-antennas, we find very low (femto-Joule) saturation
pulse energies and up to 104 times brighter photoluminescence than in WSe2 placed
on low-refractive-index SiO2 pillars. We show that the key to these observations
is the increase on average by a factor of 5 of the quantum efficiency of the emitters
coupled to the nano-antennas. This further allows us to gain new insights into
their photoluminescence dynamics, revealing the roles of the dark exciton reservoir
and Auger processes. We also find that the coherence time of such emitters is
limited by intrinsic dephasing processes. Our work establishes dielectric nano-antennas
as a platform for high-efficiency quantum light generation in monolayer semiconductors.
acknowledgement: L.S., P.G.Z., and A.I.T. thank the financial support of the European
Graphene Flagship Project under grant agreements 881603 and EPSRC grant EP/S030751/1.
L.S. and A.I.T. thank the European Union’s Horizon 2020 research and innovation
programme under ITN Spin-NANO Marie Sklodowska-Curie grant agreement no. 676108.
P.G.Z. and A.I.T. thank the European Union’s Horizon 2020 research and innovation
programme under ITN 4PHOTON Marie Sklodowska-Curie grant agreement no. 721394. J.C.,
S.A.M., and R.S. acknowledge funding by EPSRC (EP/P033369 and EP/M013812). C.L.P.,
A.J.B., A.I.T., and A.M.F. acknowledge funding by EPSRC Programme Grant EP/N031776/1.
S.A.M. acknowledges the Lee-Lucas Chair in Physics, the Solar Energies go Hybrid
(SolTech) programme, and the Deutsche Forschungsgemeinschaft (DFG, German Research
Foundation) under Germany’s Excellence Strategy - EXC 2089/1 - 390776260.
article_number: '6063'
article_processing_charge: No
article_type: original
author:
- first_name: Luca
full_name: Sortino, Luca
last_name: Sortino
- first_name: Panaiot G.
full_name: Zotev, Panaiot G.
last_name: Zotev
- first_name: Catherine L.
full_name: Phillips, Catherine L.
last_name: Phillips
- first_name: Alistair J.
full_name: Brash, Alistair J.
last_name: Brash
- first_name: Javier
full_name: Cambiasso, Javier
last_name: Cambiasso
- first_name: Elena
full_name: Marensi, Elena
id: 0BE7553A-1004-11EA-B805-18983DDC885E
last_name: Marensi
orcid: 0000-0001-7173-4923
- first_name: A. Mark
full_name: Fox, A. Mark
last_name: Fox
- first_name: Stefan A.
full_name: Maier, Stefan A.
last_name: Maier
- first_name: Riccardo
full_name: Sapienza, Riccardo
last_name: Sapienza
- first_name: Alexander I.
full_name: Tartakovskii, Alexander I.
last_name: Tartakovskii
citation:
ama: Sortino L, Zotev PG, Phillips CL, et al. Bright single photon emitters with
enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric
nano-antennas. Nature Communications. 2021;12. doi:10.1038/s41467-021-26262-3
apa: Sortino, L., Zotev, P. G., Phillips, C. L., Brash, A. J., Cambiasso, J., Marensi,
E., … Tartakovskii, A. I. (2021). Bright single photon emitters with enhanced
quantum efficiency in a two-dimensional semiconductor coupled with dielectric
nano-antennas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26262-3
chicago: Sortino, Luca, Panaiot G. Zotev, Catherine L. Phillips, Alistair J. Brash,
Javier Cambiasso, Elena Marensi, A. Mark Fox, Stefan A. Maier, Riccardo Sapienza,
and Alexander I. Tartakovskii. “Bright Single Photon Emitters with Enhanced Quantum
Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.”
Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26262-3.
ieee: L. Sortino et al., “Bright single photon emitters with enhanced quantum
efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas,”
Nature Communications, vol. 12. Springer Nature, 2021.
ista: Sortino L, Zotev PG, Phillips CL, Brash AJ, Cambiasso J, Marensi E, Fox AM,
Maier SA, Sapienza R, Tartakovskii AI. 2021. Bright single photon emitters with
enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric
nano-antennas. Nature Communications. 12, 6063.
mla: Sortino, Luca, et al. “Bright Single Photon Emitters with Enhanced Quantum
Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.”
Nature Communications, vol. 12, 6063, Springer Nature, 2021, doi:10.1038/s41467-021-26262-3.
short: L. Sortino, P.G. Zotev, C.L. Phillips, A.J. Brash, J. Cambiasso, E. Marensi,
A.M. Fox, S.A. Maier, R. Sapienza, A.I. Tartakovskii, Nature Communications 12
(2021).
date_created: 2021-10-31T23:01:30Z
date_published: 2021-10-18T00:00:00Z
date_updated: 2023-08-14T08:12:12Z
day: '18'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1038/s41467-021-26262-3
external_id:
arxiv:
- '2103.16986'
isi:
- '000708601800015'
file:
- access_level: open_access
checksum: 8580d128389860f732028c521cd5949e
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-03T11:31:24Z
date_updated: 2021-11-03T11:31:24Z
file_id: '10212'
file_name: 2021_NatComm_Sortino.pdf
file_size: 1434201
relation: main_file
success: 1
file_date_updated: 2021-11-03T11:31:24Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bright single photon emitters with enhanced quantum efficiency in a two-dimensional
semiconductor coupled with dielectric nano-antennas
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '10178'
abstract:
- lang: eng
text: In dense biological tissues, cell types performing different roles remain
segregated by maintaining sharp interfaces. To better understand the mechanisms
for such sharp compartmentalization, we study the effect of an imposed heterotypic
tension at the interface between two distinct cell types in a fully 3D Voronoi
model for confluent tissues. We find that cells rapidly sort and self-organize
to generate a tissue-scale interface between cell types, and cells adjacent to
this interface exhibit signature geometric features including nematic-like ordering,
bimodal facet areas, and registration, or alignment, of cell centers on either
side of the two-tissue interface. The magnitude of these features scales directly
with the magnitude of the imposed tension, suggesting that biologists can estimate
the magnitude of tissue surface tension between two tissue types simply by segmenting
a 3D tissue. To uncover the underlying physical mechanisms driving these geometric
features, we develop two minimal, ordered models using two different underlying
lattices that identify an energetic competition between bulk cell shapes and tissue
interface area. When the interface area dominates, changes to neighbor topology
are costly and occur less frequently, which generates the observed geometric features.
acknowledgement: "We thank Paula Sanematsu, Matthias Merkel, Daniel Sussman, Cristina
Marchetti and Edouard Hannezo for helpful discussions, and M Merkel for developing
and sharing the original version of the 3D Voronoi code. This work was primarily
funded by NSF-PHY-1607416, NSF-PHY-2014192 , and are in the division of physics
at the National Science Foundation. PS and MLM acknowledge additional support from
Simons Grant No. 454947.\r\n"
article_number: '093043'
article_processing_charge: Yes
article_type: original
author:
- first_name: Preeti
full_name: Sahu, Preeti
id: 55BA52EE-A185-11EA-88FD-18AD3DDC885E
last_name: Sahu
- first_name: J. M.
full_name: Schwarz, J. M.
last_name: Schwarz
- first_name: M. Lisa
full_name: Manning, M. Lisa
last_name: Manning
citation:
ama: Sahu P, Schwarz JM, Manning ML. Geometric signatures of tissue surface tension
in a three-dimensional model of confluent tissue. New Journal of Physics.
2021;23(9). doi:10.1088/1367-2630/ac23f1
apa: Sahu, P., Schwarz, J. M., & Manning, M. L. (2021). Geometric signatures
of tissue surface tension in a three-dimensional model of confluent tissue. New
Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac23f1
chicago: Sahu, Preeti, J. M. Schwarz, and M. Lisa Manning. “Geometric Signatures
of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” New
Journal of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac23f1.
ieee: P. Sahu, J. M. Schwarz, and M. L. Manning, “Geometric signatures of tissue
surface tension in a three-dimensional model of confluent tissue,” New Journal
of Physics, vol. 23, no. 9. IOP Publishing, 2021.
ista: Sahu P, Schwarz JM, Manning ML. 2021. Geometric signatures of tissue surface
tension in a three-dimensional model of confluent tissue. New Journal of Physics.
23(9), 093043.
mla: Sahu, Preeti, et al. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional
Model of Confluent Tissue.” New Journal of Physics, vol. 23, no. 9, 093043,
IOP Publishing, 2021, doi:10.1088/1367-2630/ac23f1.
short: P. Sahu, J.M. Schwarz, M.L. Manning, New Journal of Physics 23 (2021).
date_created: 2021-10-24T22:01:34Z
date_published: 2021-09-29T00:00:00Z
date_updated: 2023-08-14T08:10:31Z
day: '29'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1088/1367-2630/ac23f1
external_id:
arxiv:
- '2102.05397'
isi:
- '000702042400001'
file:
- access_level: open_access
checksum: ace603e8f0962b3ba55f23fa34f57764
content_type: application/pdf
creator: cziletti
date_created: 2021-10-28T12:06:01Z
date_updated: 2021-10-28T12:06:01Z
file_id: '10193'
file_name: 2021_NewJPhys_Sahu.pdf
file_size: 2215016
relation: main_file
success: 1
file_date_updated: 2021-10-28T12:06:01Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: New Journal of Physics
publication_identifier:
eissn:
- '13672630'
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometric signatures of tissue surface tension in a three-dimensional model
of confluent tissue
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: 23
year: '2021'
...
---
_id: '10181'
abstract:
- lang: eng
text: In this article we study some geometric properties of proximally smooth sets.
First, we introduce a modification of the metric projection and prove its existence.
Then we provide an algorithm for constructing a rectifiable curve between two
sufficiently close points of a proximally smooth set in a uniformly convex and
uniformly smooth Banach space, with the moduli of smoothness and convexity of
power type. Our algorithm returns a reasonably short curve between two sufficiently
close points of a proximally smooth set, is iterative and uses our modification
of the metric projection. We estimate the length of the constructed curve and
its deviation from the segment with the same endpoints. These estimates coincide
up to a constant factor with those for the geodesics in a proximally smooth set
in a Hilbert space.
acknowledgement: Theorem 2 was obtained at Steklov Mathematical Institute RAS and
supported by Russian Science Foundation, grant N 19-11-00087.
article_processing_charge: No
article_type: original
author:
- first_name: Grigory
full_name: Ivanov, Grigory
id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E
last_name: Ivanov
- first_name: Mariana S.
full_name: Lopushanski, Mariana S.
last_name: Lopushanski
citation:
ama: Ivanov G, Lopushanski MS. Rectifiable curves in proximally smooth sets. Set-Valued
and Variational Analysis. 2021. doi:10.1007/s11228-021-00612-1
apa: Ivanov, G., & Lopushanski, M. S. (2021). Rectifiable curves in proximally
smooth sets. Set-Valued and Variational Analysis. Springer Nature. https://doi.org/10.1007/s11228-021-00612-1
chicago: Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally
Smooth Sets.” Set-Valued and Variational Analysis. Springer Nature, 2021.
https://doi.org/10.1007/s11228-021-00612-1.
ieee: G. Ivanov and M. S. Lopushanski, “Rectifiable curves in proximally smooth
sets,” Set-Valued and Variational Analysis. Springer Nature, 2021.
ista: Ivanov G, Lopushanski MS. 2021. Rectifiable curves in proximally smooth sets.
Set-Valued and Variational Analysis.
mla: Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally
Smooth Sets.” Set-Valued and Variational Analysis, Springer Nature, 2021,
doi:10.1007/s11228-021-00612-1.
short: G. Ivanov, M.S. Lopushanski, Set-Valued and Variational Analysis (2021).
date_created: 2021-10-24T22:01:35Z
date_published: 2021-10-09T00:00:00Z
date_updated: 2023-08-14T08:11:38Z
day: '09'
department:
- _id: UlWa
doi: 10.1007/s11228-021-00612-1
external_id:
arxiv:
- '2012.10691'
isi:
- '000705774800001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2012.10691
month: '10'
oa: 1
oa_version: Published Version
publication: Set-Valued and Variational Analysis
publication_identifier:
eissn:
- 1877-0541
issn:
- 0927-6947
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rectifiable curves in proximally smooth sets
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '10202'
abstract:
- lang: eng
text: Zygotic genome activation (ZGA) initiates regionalized transcription underlying
distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture
sculpted by conserved DNA-binding proteins. However, the direct mechanistic link
between the onset of ZGA and the tissue-specific transcription remains unclear.
Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating
both processes during zebrafish embryogenesis. Integrative analysis of transcriptome,
genome-wide occupancy and chromatin accessibility reveals contrasting molecular
activities of maternally deposited and zygotically synthesized Satb2. Maternal
Satb2 prevents premature transcription of zygotic genes by influencing the interplay
between the pluripotency factors. By contrast, zygotic Satb2 activates transcription
of the same group of genes during neural crest development and organogenesis.
Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores
how these antithetical activities are temporally coordinated and functionally
implemented highlighting the evolutionary implications of the biphasic and bimodal
regulation of landmark developmental transitions by a single determinant.
acknowledgement: 'We are grateful to the members of C.-P.H. and SG lab for discussions.
Authors thank Shubha Tole for providing embryonic mouse tissues. Authors are grateful
to Alessandro Mongera and Chetana Sachidanandan for generous help with Tg: Sox10:
GFP line. Authors would like to thank Satyajeet Khare, Vanessa Barone, Jyothish
S., Shalini Mishra, Yoshita Bhide, and Keshav Jha for assistance in experiments.
We would also like to thank Chaitanya Dingare for valuable suggestions. We thank
Diana Pinhiero and Alexandra Schauer for critical reading of early versions of the
manuscript. This work was supported by the Centre of Excellence in Epigenetics program
of the Department of Biotechnology, Government of India Phase I (BT/01/COE/09/07)
to S.G. and R.K.M., and Phase II (BT/COE/34/SP17426/2016) to S.G. and JC Bose Fellowship
(JCB/2019/000013) from Science and Engineering Research Board, Government of India
to S.G., DST-BMWF Indo-Austrian bilateral program grant to S.G. and C.-P.H. The
work using animal models was partly supported by the infrastructure support grants
from the Department of Biotechnology (National Facility for Laboratory Model Organisms:
BT/INF/22/SP17358/2016 and Establishment of a Pune Biotech Cluster, Model Organism
to Human Disease: B-2 Whole Animal Imaging & Tissue Processing FacilityBT/Pune-Biocluster/01/2015).
S.J.P. was supported by Fellowship from the Council of Scientific and Industrial
Research, India and travel fellowship from the Company of Biologists, UK. P.C.R.
was supported by the Early Career Fellowship of the Wellcome Trust-DBT India Alliance
(IA/E/16/1/503057). A.S. was supported by UGC and R.S. was supported by CSIR India.
M.S. was supported by core funding from the Tata Institute of Fundamental Research
(TIFR 12P-121).'
article_number: '6094'
article_processing_charge: Yes
article_type: original
author:
- first_name: Saurabh J.
full_name: Pradhan, Saurabh J.
last_name: Pradhan
- first_name: Puli Chandramouli
full_name: Reddy, Puli Chandramouli
last_name: Reddy
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Ankita
full_name: Sharma, Ankita
last_name: Sharma
- first_name: Keisuke
full_name: Sako, Keisuke
id: 3BED66BE-F248-11E8-B48F-1D18A9856A87
last_name: Sako
orcid: 0000-0002-6453-8075
- first_name: Meghana S.
full_name: Oak, Meghana S.
last_name: Oak
- first_name: Rini
full_name: Shah, Rini
last_name: Shah
- first_name: Mrinmoy
full_name: Pal, Mrinmoy
last_name: Pal
- first_name: Ojas
full_name: Deshpande, Ojas
last_name: Deshpande
- first_name: Greg
full_name: Dsilva, Greg
last_name: Dsilva
- first_name: Yin
full_name: Tang, Yin
last_name: Tang
- first_name: Rakesh
full_name: Mishra, Rakesh
last_name: Mishra
- first_name: Girish
full_name: Deshpande, Girish
last_name: Deshpande
- first_name: Antonio J.
full_name: Giraldez, Antonio J.
last_name: Giraldez
- first_name: Mahendra
full_name: Sonawane, Mahendra
last_name: Sonawane
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Sanjeev
full_name: Galande, Sanjeev
last_name: Galande
citation:
ama: Pradhan SJ, Reddy PC, Smutny M, et al. Satb2 acts as a gatekeeper for major
developmental transitions during early vertebrate embryogenesis. Nature Communications.
2021;12(1). doi:10.1038/s41467-021-26234-7
apa: Pradhan, S. J., Reddy, P. C., Smutny, M., Sharma, A., Sako, K., Oak, M. S.,
… Galande, S. (2021). Satb2 acts as a gatekeeper for major developmental transitions
during early vertebrate embryogenesis. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-021-26234-7
chicago: Pradhan, Saurabh J., Puli Chandramouli Reddy, Michael Smutny, Ankita Sharma,
Keisuke Sako, Meghana S. Oak, Rini Shah, et al. “Satb2 Acts as a Gatekeeper for
Major Developmental Transitions during Early Vertebrate Embryogenesis.” Nature
Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26234-7.
ieee: S. J. Pradhan et al., “Satb2 acts as a gatekeeper for major developmental
transitions during early vertebrate embryogenesis,” Nature Communications,
vol. 12, no. 1. Springer Nature, 2021.
ista: Pradhan SJ, Reddy PC, Smutny M, Sharma A, Sako K, Oak MS, Shah R, Pal M, Deshpande
O, Dsilva G, Tang Y, Mishra R, Deshpande G, Giraldez AJ, Sonawane M, Heisenberg
C-PJ, Galande S. 2021. Satb2 acts as a gatekeeper for major developmental transitions
during early vertebrate embryogenesis. Nature Communications. 12(1), 6094.
mla: Pradhan, Saurabh J., et al. “Satb2 Acts as a Gatekeeper for Major Developmental
Transitions during Early Vertebrate Embryogenesis.” Nature Communications,
vol. 12, no. 1, 6094, Springer Nature, 2021, doi:10.1038/s41467-021-26234-7.
short: S.J. Pradhan, P.C. Reddy, M. Smutny, A. Sharma, K. Sako, M.S. Oak, R. Shah,
M. Pal, O. Deshpande, G. Dsilva, Y. Tang, R. Mishra, G. Deshpande, A.J. Giraldez,
M. Sonawane, C.-P.J. Heisenberg, S. Galande, Nature Communications 12 (2021).
date_created: 2021-10-31T23:01:29Z
date_published: 2021-10-19T00:00:00Z
date_updated: 2023-08-14T10:32:48Z
day: '19'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1038/s41467-021-26234-7
external_id:
isi:
- '000709050300016'
pmid:
- '34667153'
file:
- access_level: open_access
checksum: c40a69ae94435ecd3a30c9874a11ef2b
content_type: application/pdf
creator: cziletti
date_created: 2021-11-09T13:59:26Z
date_updated: 2021-11-09T13:59:26Z
file_id: '10262'
file_name: 2021_NatureComm_Pradhan.pdf
file_size: 7144437
relation: main_file
success: 1
file_date_updated: 2021-11-09T13:59:26Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: Preprint
relation: earlier_version
url: 'https://doi.org/10.1101/2020.11.23.394171 '
scopus_import: '1'
status: public
title: Satb2 acts as a gatekeeper for major developmental transitions during early
vertebrate embryogenesis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '10271'
abstract:
- lang: eng
text: Understanding interactions between antibiotics used in combination is an important
theme in microbiology. Using the interactions between the antifolate drug trimethoprim
and the ribosome-targeting antibiotic erythromycin in Escherichia coli as a model,
we applied a transcriptomic approach for dissecting interactions between two antibiotics
with different modes of action. When trimethoprim and erythromycin were combined,
the transcriptional response of genes from the sulfate reduction pathway deviated
from the dominant effect of trimethoprim on the transcriptome. We successfully
altered the drug interaction from additivity to suppression by increasing the
sulfate level in the growth environment and identified sulfate reduction as an
important metabolic determinant that shapes the interaction between the two drugs.
Our work highlights the potential of using prioritization of gene expression patterns
as a tool for identifying key metabolic determinants that shape drug-drug interactions.
We further demonstrated that the sigma factor-binding protein gene crl shapes
the interactions between the two antibiotics, which provides a rare example of
how naturally occurring variations between strains of the same bacterial species
can sometimes generate very different drug interactions.
acknowledgement: High-throughput sequencing data were generated by the Vienna BioCenter
Core Facilities. The authors would like to thank Karin Mitosch, Bor Kavcic, and
Nadine Kraupner for their constructive feedback. The authors would also like to
thank Gertraud Stift, Julia Flor, Renate Srsek, Agnieszka Wiktor, and Booshini Fernando
for technical support.
article_number: '760017'
article_processing_charge: No
article_type: original
author:
- first_name: Qin
full_name: Qi, Qin
id: 3B22D412-F248-11E8-B48F-1D18A9856A87
last_name: Qi
orcid: 0000-0002-6148-2416
- first_name: S. Andreas
full_name: Angermayr, S. Andreas
last_name: Angermayr
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Qi Q, Angermayr SA, Bollenbach MT. Uncovering Key Metabolic Determinants of
the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli.
Frontiers in Microbiology. 2021;12. doi:10.3389/fmicb.2021.760017
apa: Qi, Q., Angermayr, S. A., & Bollenbach, M. T. (2021). Uncovering Key Metabolic
Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in
Escherichia coli. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2021.760017
chicago: Qi, Qin, S. Andreas Angermayr, and Mark Tobias Bollenbach. “Uncovering
Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin
in Escherichia Coli.” Frontiers in Microbiology. Frontiers, 2021. https://doi.org/10.3389/fmicb.2021.760017.
ieee: Q. Qi, S. A. Angermayr, and M. T. Bollenbach, “Uncovering Key Metabolic Determinants
of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia
coli,” Frontiers in Microbiology, vol. 12. Frontiers, 2021.
ista: Qi Q, Angermayr SA, Bollenbach MT. 2021. Uncovering Key Metabolic Determinants
of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia
coli. Frontiers in Microbiology. 12, 760017.
mla: Qi, Qin, et al. “Uncovering Key Metabolic Determinants of the Drug Interactions
Between Trimethoprim and Erythromycin in Escherichia Coli.” Frontiers in Microbiology,
vol. 12, 760017, Frontiers, 2021, doi:10.3389/fmicb.2021.760017.
short: Q. Qi, S.A. Angermayr, M.T. Bollenbach, Frontiers in Microbiology 12 (2021).
date_created: 2021-11-11T10:39:37Z
date_published: 2021-10-20T00:00:00Z
date_updated: 2023-08-14T11:43:23Z
day: '20'
ddc:
- '610'
doi: 10.3389/fmicb.2021.760017
ec_funded: 1
external_id:
isi:
- '000715997300001'
pmid:
- '34745067'
file:
- access_level: open_access
checksum: d41321748e9588dd3cf03e9a7222127f
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-11T10:54:40Z
date_updated: 2021-11-11T10:54:40Z
file_id: '10272'
file_name: 2021_FrontiersMicrob_Qi.pdf
file_size: 2397203
relation: main_file
success: 1
file_date_updated: 2021-11-11T10:54:40Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
keyword:
- microbiology
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
publication: Frontiers in Microbiology
publication_identifier:
eissn:
- 1664-302X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim
and Erythromycin in Escherichia coli
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '10221'
abstract:
- lang: eng
text: We prove that any deterministic matrix is approximately the identity in the
eigenbasis of a large random Wigner matrix with very high probability and with
an optimal error inversely proportional to the square root of the dimension. Our
theorem thus rigorously verifies the Eigenstate Thermalisation Hypothesis by Deutsch
(Phys Rev A 43:2046–2049, 1991) for the simplest chaotic quantum system, the Wigner
ensemble. In mathematical terms, we prove the strong form of Quantum Unique Ergodicity
(QUE) with an optimal convergence rate for all eigenvectors simultaneously, generalizing
previous probabilistic QUE results in Bourgade and Yau (Commun Math Phys 350:231–278,
2017) and Bourgade et al. (Commun Pure Appl Math 73:1526–1596, 2020).
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. Eigenstate thermalization hypothesis for
Wigner matrices. Communications in Mathematical Physics. 2021;388(2):1005–1048.
doi:10.1007/s00220-021-04239-z
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Eigenstate thermalization
hypothesis for Wigner matrices. Communications in Mathematical Physics.
Springer Nature. https://doi.org/10.1007/s00220-021-04239-z
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Eigenstate Thermalization
Hypothesis for Wigner Matrices.” Communications in Mathematical Physics.
Springer Nature, 2021. https://doi.org/10.1007/s00220-021-04239-z.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Eigenstate thermalization hypothesis
for Wigner matrices,” Communications in Mathematical Physics, vol. 388,
no. 2. Springer Nature, pp. 1005–1048, 2021.
ista: Cipolloni G, Erdös L, Schröder DJ. 2021. Eigenstate thermalization hypothesis
for Wigner matrices. Communications in Mathematical Physics. 388(2), 1005–1048.
mla: Cipolloni, Giorgio, et al. “Eigenstate Thermalization Hypothesis for Wigner
Matrices.” Communications in Mathematical Physics, vol. 388, no. 2, Springer
Nature, 2021, pp. 1005–1048, doi:10.1007/s00220-021-04239-z.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics
388 (2021) 1005–1048.
date_created: 2021-11-07T23:01:25Z
date_published: 2021-10-29T00:00:00Z
date_updated: 2023-08-14T10:29:49Z
day: '29'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00220-021-04239-z
external_id:
arxiv:
- '2012.13215'
isi:
- '000712232700001'
file:
- access_level: open_access
checksum: a2c7b6f5d23b5453cd70d1261272283b
content_type: application/pdf
creator: cchlebak
date_created: 2022-02-02T10:19:55Z
date_updated: 2022-02-02T10:19:55Z
file_id: '10715'
file_name: 2021_CommunMathPhys_Cipolloni.pdf
file_size: 841426
relation: main_file
success: 1
file_date_updated: 2022-02-02T10:19:55Z
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intvolume: ' 388'
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language:
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month: '10'
oa: 1
oa_version: Published Version
page: 1005–1048
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- 1432-0916
issn:
- 0010-3616
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Eigenstate thermalization hypothesis for Wigner matrices
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: 388
year: '2021'
...
---
_id: '10224'
abstract:
- lang: eng
text: We investigate the Fröhlich polaron model on a three-dimensional torus, and
give a proof of the second-order quantum corrections to its ground-state energy
in the strong-coupling limit. Compared to previous work in the confined case,
the translational symmetry (and its breaking in the Pekar approximation) makes
the analysis substantially more challenging.
acknowledgement: "Funding from the European Union’s Horizon 2020 research and innovation
programme under the ERC grant agreement No 694227 is gratefully acknowledged. We
would also like to thank Rupert Frank for many helpful discussions, especially related
to the Gross coordinate transformation defined in Def. 4.7.\r\nOpen access funding
provided by Institute of Science and Technology (IST Austria)."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum
corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis.
2021;242(3):1835–1906. doi:10.1007/s00205-021-01715-7'
apa: 'Feliciangeli, D., & Seiringer, R. (2021). The strongly coupled polaron
on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational
Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01715-7'
chicago: 'Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron
on the Torus: Quantum Corrections to the Pekar Asymptotics.” Archive for Rational
Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01715-7.'
ieee: 'D. Feliciangeli and R. Seiringer, “The strongly coupled polaron on the torus:
Quantum corrections to the Pekar asymptotics,” Archive for Rational Mechanics
and Analysis, vol. 242, no. 3. Springer Nature, pp. 1835–1906, 2021.'
ista: 'Feliciangeli D, Seiringer R. 2021. The strongly coupled polaron on the torus:
Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and
Analysis. 242(3), 1835–1906.'
mla: 'Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on
the Torus: Quantum Corrections to the Pekar Asymptotics.” Archive for Rational
Mechanics and Analysis, vol. 242, no. 3, Springer Nature, 2021, pp. 1835–1906,
doi:10.1007/s00205-021-01715-7.'
short: D. Feliciangeli, R. Seiringer, Archive for Rational Mechanics and Analysis
242 (2021) 1835–1906.
date_created: 2021-11-07T23:01:26Z
date_published: 2021-10-25T00:00:00Z
date_updated: 2023-08-14T10:32:19Z
day: '25'
ddc:
- '530'
department:
- _id: RoSe
doi: 10.1007/s00205-021-01715-7
ec_funded: 1
external_id:
arxiv:
- '2101.12566'
isi:
- '000710850600001'
file:
- access_level: open_access
checksum: 672e9c21b20f1a50854b7c821edbb92f
content_type: application/pdf
creator: alisjak
date_created: 2021-12-14T08:35:42Z
date_updated: 2021-12-14T08:35:42Z
file_id: '10544'
file_name: 2021_Springer_Feliciangeli.pdf
file_size: 990529
relation: main_file
success: 1
file_date_updated: 2021-12-14T08:35:42Z
has_accepted_license: '1'
intvolume: ' 242'
isi: 1
issue: '3'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1835–1906
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Archive for Rational Mechanics and Analysis
publication_identifier:
eissn:
- 1432-0673
issn:
- 0003-9527
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '9787'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'The strongly coupled polaron on the torus: Quantum corrections to the Pekar
asymptotics'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 242
year: '2021'
...
---
_id: '10281'
abstract:
- lang: eng
text: Mutations affecting mTOR or RAS signaling underlie defined syndromes (the
so-called mTORopathies and RASopathies) with high risk for Autism Spectrum Disorder
(ASD). These syndromes show a broad variety of somatic phenotypes including cancers,
skin abnormalities, heart disease and facial dysmorphisms. Less well studied are
the neuropsychiatric symptoms such as ASD. Here, we assess the relevance of these
signalopathies in ASD reviewing genetic, human cell model, rodent studies and
clinical trials. We conclude that signalopathies have an increased liability for
ASD and that, in particular, ASD individuals with dysmorphic features and intellectual
disability (ID) have a higher chance for disruptive mutations in RAS- and mTOR-related
genes. Studies on rodent and human cell models confirm aberrant neuronal development
as the underlying pathology. Human studies further suggest that multiple hits
are necessary to induce the respective phenotypes. Recent clinical trials do only
report improvements for comorbid conditions such as epilepsy or cancer but not
for behavioral aspects. Animal models show that treatment during early development
can rescue behavioral phenotypes. Taken together, we suggest investigating the
differential roles of mTOR and RAS signaling in both human and rodent models,
and to test drug treatment both during and after neuronal development in the available
model systems
acknowledgement: 'This review was funded by the IMI2 Initiative under the grant AIMS-2-TRIALS
No 777394, by the Hessian Ministry for Science and Arts; State of Hesse Ministry
for Science and Arts: LOEWE-Grant to the CePTER-Consortium (www.uni-frankfurt.de/67689811);
Research (BMBF) under the grant RAISE-genic No 779282 all to AGC. This work was
also supported by the European Union’s Horizon 2020 research and innovation program
(ERC) grant 715508 (REVERSEAUTISM) and by the Austrian Science Fund (FWF) (DK W1232-B24)
both to G.N. and both BMBF GeNeRARe 01GM1519A and CRC 1080, project B10, of the
German Research Foundation (DFG) to M.J.S, respectively. We want to thank R. Waltes
for her support in preparing this manuscript.'
alternative_title:
- Special Issue "From Genes to Therapy in Autism Spectrum Disorder"
article_number: '1746'
article_processing_charge: No
article_type: original
author:
- first_name: Verica
full_name: Vasic, Verica
last_name: Vasic
- first_name: Mattson S.O.
full_name: Jones, Mattson S.O.
last_name: Jones
- first_name: Denise
full_name: Haslinger, Denise
id: 76922BDA-3D3B-11EA-90BD-A44F3DDC885E
last_name: Haslinger
- first_name: Lisa
full_name: Knaus, Lisa
id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87
last_name: Knaus
- first_name: Michael J.
full_name: Schmeisser, Michael J.
last_name: Schmeisser
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Andreas G.
full_name: Chiocchetti, Andreas G.
last_name: Chiocchetti
citation:
ama: 'Vasic V, Jones MSO, Haslinger D, et al. Translating the role of mtor-and ras-associated
signalopathies in autism spectrum disorder: Models, mechanisms and treatment.
Genes. 2021;12(11). doi:10.3390/genes12111746'
apa: 'Vasic, V., Jones, M. S. O., Haslinger, D., Knaus, L., Schmeisser, M. J., Novarino,
G., & Chiocchetti, A. G. (2021). Translating the role of mtor-and ras-associated
signalopathies in autism spectrum disorder: Models, mechanisms and treatment.
Genes. MDPI. https://doi.org/10.3390/genes12111746'
chicago: 'Vasic, Verica, Mattson S.O. Jones, Denise Haslinger, Lisa Knaus, Michael
J. Schmeisser, Gaia Novarino, and Andreas G. Chiocchetti. “Translating the Role
of Mtor-and Ras-Associated Signalopathies in Autism Spectrum Disorder: Models,
Mechanisms and Treatment.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12111746.'
ieee: 'V. Vasic et al., “Translating the role of mtor-and ras-associated
signalopathies in autism spectrum disorder: Models, mechanisms and treatment,”
Genes, vol. 12, no. 11. MDPI, 2021.'
ista: 'Vasic V, Jones MSO, Haslinger D, Knaus L, Schmeisser MJ, Novarino G, Chiocchetti
AG. 2021. Translating the role of mtor-and ras-associated signalopathies in autism
spectrum disorder: Models, mechanisms and treatment. Genes. 12(11), 1746.'
mla: 'Vasic, Verica, et al. “Translating the Role of Mtor-and Ras-Associated Signalopathies
in Autism Spectrum Disorder: Models, Mechanisms and Treatment.” Genes,
vol. 12, no. 11, 1746, MDPI, 2021, doi:10.3390/genes12111746.'
short: V. Vasic, M.S.O. Jones, D. Haslinger, L. Knaus, M.J. Schmeisser, G. Novarino,
A.G. Chiocchetti, Genes 12 (2021).
date_created: 2021-11-14T23:01:24Z
date_published: 2021-10-30T00:00:00Z
date_updated: 2023-08-14T11:46:12Z
day: '30'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.3390/genes12111746
ec_funded: 1
external_id:
isi:
- '000834044200002'
file:
- access_level: open_access
checksum: 256cb832a9c3051c7dc741f6423b8cbd
content_type: application/pdf
creator: dernst
date_created: 2022-05-16T07:02:27Z
date_updated: 2022-05-16T07:02:27Z
file_id: '11380'
file_name: 2021_Genes_Vasic.pdf
file_size: 1335308
relation: main_file
success: 1
file_date_updated: 2022-05-16T07:02:27Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '11'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Genes
publication_identifier:
eissn:
- 2073-4425
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Translating the role of mtor-and ras-associated signalopathies in autism spectrum
disorder: Models, mechanisms and treatment'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '10282'
abstract:
- lang: eng
text: Advanced transcriptome sequencing has revealed that the majority of eukaryotic
genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated
to investigating the functional relevance of particular splicing events, even
those in the key developmental and hormonal regulators. Combining approaches of
genetics, biochemistry and advanced confocal microscopy, we describe the impact
of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana.
PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces
two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing
in a four amino acid stretch, exhibit almost identical expression patterns and
subcellular localization. We reveal that they are closely associated and mutually
influence each other's mobility within the plasma membrane. Phenotypic complementation
tests indicate that the functional contribution of PIN7b per se is minor, but
it markedly reduces the prominent PIN7a activity, which is required for correct
seedling apical hook formation and auxin-mediated tropic responses. Our results
establish alternative splicing of the PIN family as a conserved, functionally
relevant mechanism, revealing an additional regulatory level of auxin-mediated
plant development.
acknowledgement: We thank Claus Schwechheimer for the pin34 and pin347 seeds, Yuliia
Mironova for technical assistance, Ksenia Timofeyenko and Dmitry Konovalov for help
with the evolutional analysis, Konstantin Kutashev and Siarhei Dabravolski for assistance
with FRET-FLIM, Huibin Han for advice with hypocotyl imaging, Karel Müller for the
initial qRT-PCR on the tobacco cell lines, Stano Pekár for suggestions regarding
the statistical analysis of the morphodynamic measurements, and Jozef Mravec, Dolf
Weijers and Lindy Abas for their comments on the manuscript. This work was supported
by the Czech Science Foundation (projects 16-26428S and 19-23773S to IK, MH and
KRůžička, 19-18917S to JHumpolíčková and 18-26981S to JF), and the Ministry of Education,
Youth and Sports of the Czech Republic (MEYS, CZ.02.1.01/0.0/0.0/16_019/0000738)
to KRůžička and JHejátko. The imaging facilities of the Institute of Experimental
Botany and CEITEC are supported by MEYS (LM2018129 – Czech BioImaging and CZ.02.1.01/0.0/0.0/16_013/0001775).
The authors declare no competing interests.
article_processing_charge: No
article_type: original
author:
- first_name: Ivan
full_name: Kashkan, Ivan
last_name: Kashkan
- first_name: Mónika
full_name: Hrtyan, Mónika
id: 45A71A74-F248-11E8-B48F-1D18A9856A87
last_name: Hrtyan
- first_name: Katarzyna
full_name: Retzer, Katarzyna
last_name: Retzer
- first_name: Jana
full_name: Humpolíčková, Jana
last_name: Humpolíčková
- first_name: Aswathy
full_name: Jayasree, Aswathy
last_name: Jayasree
- first_name: Roberta
full_name: Filepová, Roberta
last_name: Filepová
- first_name: Zuzana
full_name: Vondráková, Zuzana
last_name: Vondráková
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Debbie
full_name: Rombaut, Debbie
last_name: Rombaut
- first_name: Thomas B.
full_name: Jacobs, Thomas B.
last_name: Jacobs
- first_name: Mikko J.
full_name: Frilander, Mikko J.
last_name: Frilander
- first_name: Jan
full_name: Hejátko, Jan
last_name: Hejátko
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Kamil
full_name: Růžička, Kamil
last_name: Růžička
citation:
ama: Kashkan I, Hrtyan M, Retzer K, et al. Mutually opposing activity of PIN7 splicing
isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana.
New Phytologist. 2021;233:329-343. doi:10.1111/nph.17792
apa: Kashkan, I., Hrtyan, M., Retzer, K., Humpolíčková, J., Jayasree, A., Filepová,
R., … Růžička, K. (2021). Mutually opposing activity of PIN7 splicing isoforms
is required for auxin-mediated tropic responses in Arabidopsis thaliana. New
Phytologist. Wiley. https://doi.org/10.1111/nph.17792
chicago: Kashkan, Ivan, Mónika Hrtyan, Katarzyna Retzer, Jana Humpolíčková, Aswathy
Jayasree, Roberta Filepová, Zuzana Vondráková, et al. “Mutually Opposing Activity
of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis
Thaliana.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17792.
ieee: I. Kashkan et al., “Mutually opposing activity of PIN7 splicing isoforms
is required for auxin-mediated tropic responses in Arabidopsis thaliana,” New
Phytologist, vol. 233. Wiley, pp. 329–343, 2021.
ista: Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková
Z, Simon S, Rombaut D, Jacobs TB, Frilander MJ, Hejátko J, Friml J, Petrášek J,
Růžička K. 2021. Mutually opposing activity of PIN7 splicing isoforms is required
for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist.
233, 329–343.
mla: Kashkan, Ivan, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms
Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” New
Phytologist, vol. 233, Wiley, 2021, pp. 329–43, doi:10.1111/nph.17792.
short: I. Kashkan, M. Hrtyan, K. Retzer, J. Humpolíčková, A. Jayasree, R. Filepová,
Z. Vondráková, S. Simon, D. Rombaut, T.B. Jacobs, M.J. Frilander, J. Hejátko,
J. Friml, J. Petrášek, K. Růžička, New Phytologist 233 (2021) 329–343.
date_created: 2021-11-14T23:01:24Z
date_published: 2021-11-05T00:00:00Z
date_updated: 2023-08-14T11:46:43Z
day: '05'
department:
- _id: JiFr
doi: 10.1111/nph.17792
external_id:
isi:
- '000714678100001'
pmid:
- '34637542'
intvolume: ' 233'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2020.05.02.074070v2
month: '11'
oa: 1
oa_version: Preprint
page: 329-343
pmid: 1
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated
tropic responses in Arabidopsis thaliana
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 233
year: '2021'
...
---
_id: '10220'
abstract:
- lang: eng
text: "We study conditions under which a finite simplicial complex K can be mapped
to ℝd without higher-multiplicity intersections. An almost r-embedding is a map
f: K → ℝd such that the images of any r pairwise disjoint simplices of K do not
have a common point. We show that if r is not a prime power and d ≥ 2r + 1, then
there is a counterexample to the topological Tverberg conjecture, i.e., there
is an almost r-embedding of the (d +1)(r − 1)-simplex in ℝd. This improves on
previous constructions of counterexamples (for d ≥ 3r) based on a series of papers
by M. Özaydin, M. Gromov, P. Blagojević, F. Frick, G. Ziegler, and the second
and fourth present authors.\r\n\r\nThe counterexamples are obtained by proving
the following algebraic criterion in codimension 2: If r ≥ 3 and if K is a finite
2(r − 1)-complex, then there exists an almost r-embedding K → ℝ2r if and only
if there exists a general position PL map f: K → ℝ2r such that the algebraic intersection
number of the f-images of any r pairwise disjoint simplices of K is zero. This
result can be restated in terms of a cohomological obstruction and extends an
analogous codimension 3 criterion by the second and fourth authors. As another
application, we classify ornaments f: S3 ⊔ S3 ⊔ S3 → ℝ5 up to ornament concordance.\r\n\r\nIt
follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous
criterion for r = 2 is false. We prove a lemma on singular higher-dimensional
Borromean rings, yielding an elementary proof of the counterexample."
acknowledgement: Research supported by the Swiss National Science Foundation (Project
SNSF-PP00P2-138948), by the Austrian Science Fund (FWF Project P31312-N35), by the
Russian Foundation for Basic Research (Grants No. 15-01-06302 and 19-01-00169),
by a Simons-IUM Fellowship, and by the D. Zimin Dynasty Foundation Grant. We would
like to thank E. Alkin, A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner
and anonymous referees for helpful comments and discussions.
article_processing_charge: No
article_type: original
author:
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
- first_name: Arkadiy B.
full_name: Skopenkov, Arkadiy B.
last_name: Skopenkov
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. Eliminating higher-multiplicity
intersections. III. Codimension 2. Israel Journal of Mathematics. 2021;245:501–534.
doi:10.1007/s11856-021-2216-z
apa: Avvakumov, S., Mabillard, I., Skopenkov, A. B., & Wagner, U. (2021). Eliminating
higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics.
Springer Nature. https://doi.org/10.1007/s11856-021-2216-z
chicago: Avvakumov, Sergey, Isaac Mabillard, Arkadiy B. Skopenkov, and Uli Wagner.
“Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” Israel
Journal of Mathematics. Springer Nature, 2021. https://doi.org/10.1007/s11856-021-2216-z.
ieee: S. Avvakumov, I. Mabillard, A. B. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity
intersections. III. Codimension 2,” Israel Journal of Mathematics, vol.
245. Springer Nature, pp. 501–534, 2021.
ista: Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. 2021. Eliminating higher-multiplicity
intersections. III. Codimension 2. Israel Journal of Mathematics. 245, 501–534.
mla: Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections. III.
Codimension 2.” Israel Journal of Mathematics, vol. 245, Springer Nature,
2021, pp. 501–534, doi:10.1007/s11856-021-2216-z.
short: S. Avvakumov, I. Mabillard, A.B. Skopenkov, U. Wagner, Israel Journal of
Mathematics 245 (2021) 501–534.
date_created: 2021-11-07T23:01:24Z
date_published: 2021-10-30T00:00:00Z
date_updated: 2023-08-14T11:43:55Z
day: '30'
department:
- _id: UlWa
doi: 10.1007/s11856-021-2216-z
external_id:
arxiv:
- '1511.03501'
isi:
- '000712942100013'
intvolume: ' 245'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.03501
month: '10'
oa: 1
oa_version: Preprint
page: '501–534 '
project:
- _id: 26611F5C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31312
name: Algorithms for Embeddings and Homotopy Theory
publication: Israel Journal of Mathematics
publication_identifier:
eissn:
- 1565-8511
issn:
- 0021-2172
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8183'
relation: earlier_version
status: public
- id: '9308'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Eliminating higher-multiplicity intersections. III. Codimension 2
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 245
year: '2021'
...
---
_id: '13061'
abstract:
- lang: eng
text: Infections early in life can have enduring effects on an organism’s development
and immunity. In this study, we show that this equally applies to developing “superorganisms”
– incipient social insect colonies. When we exposed newly mated Lasius niger ant
queens to a low pathogen dose, their colonies grew more slowly than controls before
winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation
survival improved when the ratio of pupae to workers was small. Queens that reared
fewer pupae before worker emergence exhibited lower pathogen levels, indicating
that high brood rearing efforts interfere with the ability of the queen’s immune
system to suppress pathogen proliferation. Early-life queen pathogen-exposure
also improved the immunocompetence of her worker offspring, as demonstrated by
challenging the workers to the same pathogen a year later. Transgenerational transfer
of the queen’s pathogen experience to her workforce can hence durably reduce the
disease susceptibility of the whole superorganism.
article_processing_charge: No
author:
- first_name: Barbara E
full_name: Casillas Perez, Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: Filip
full_name: Naiser, Filip
last_name: Naiser
- first_name: Elisabeth
full_name: Naderlinger, Elisabeth
last_name: Naderlinger
- first_name: Jiri
full_name: Matas, Jiri
last_name: Matas
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. Early
queen infection shapes developmental dynamics and induces long-term disease protection
in incipient ant colonies. 2021. doi:10.5061/DRYAD.7PVMCVDTJ
apa: Casillas Perez, B. E., Pull, C., Naiser, F., Naderlinger, E., Matas, J., &
Cremer, S. (2021). Early queen infection shapes developmental dynamics and induces
long-term disease protection in incipient ant colonies. Dryad. https://doi.org/10.5061/DRYAD.7PVMCVDTJ
chicago: Casillas Perez, Barbara E, Christopher Pull, Filip Naiser, Elisabeth Naderlinger,
Jiri Matas, and Sylvia Cremer. “Early Queen Infection Shapes Developmental Dynamics
and Induces Long-Term Disease Protection in Incipient Ant Colonies.” Dryad, 2021.
https://doi.org/10.5061/DRYAD.7PVMCVDTJ.
ieee: B. E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, and S.
Cremer, “Early queen infection shapes developmental dynamics and induces long-term
disease protection in incipient ant colonies.” Dryad, 2021.
ista: Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. 2021.
Early queen infection shapes developmental dynamics and induces long-term disease
protection in incipient ant colonies, Dryad, 10.5061/DRYAD.7PVMCVDTJ.
mla: Casillas Perez, Barbara E., et al. Early Queen Infection Shapes Developmental
Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.
Dryad, 2021, doi:10.5061/DRYAD.7PVMCVDTJ.
short: B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer,
(2021).
date_created: 2023-05-23T16:14:35Z
date_published: 2021-10-29T00:00:00Z
date_updated: 2023-08-14T11:45:28Z
day: '29'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.5061/DRYAD.7PVMCVDTJ
ec_funded: 1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.7pvmcvdtj
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
publisher: Dryad
related_material:
record:
- id: '10284'
relation: used_in_publication
status: public
status: public
title: Early queen infection shapes developmental dynamics and induces long-term disease
protection in incipient ant colonies
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10301'
abstract:
- lang: eng
text: De novo protein synthesis is required for synapse modifications underlying
stable memory encoding. Yet neurons are highly compartmentalized cells and how
protein synthesis can be regulated at the synapse level is unknown. Here, we characterize
neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mechanistic
target of rapamycin (mTOR) kinase, and Raptor that couple synaptic stimuli to
mTOR-dependent protein synthesis; and identify NMDA receptors containing GluN3A
subunits as key negative regulators of GIT1 binding to mTOR. Disruption of GIT1/mTOR
complexes by enhancing GluN3A expression or silencing GIT1 inhibits synaptic mTOR
activation and restricts the mTOR-dependent translation of specific activity-regulated
mRNAs. Conversely, GluN3A removal enables complex formation, potentiates mTOR-dependent
protein synthesis, and facilitates the consolidation of associative and spatial
memories in mice. The memory enhancement becomes evident with light or spaced
training, can be achieved by selectively deleting GluN3A from excitatory neurons
during adulthood, and does not compromise other aspects of cognition such as memory
flexibility or extinction. Our findings provide mechanistic insight into synaptic
translational control and reveal a potentially selective target for cognitive
enhancement.
acknowledgement: We thank Stuart Lipton and Nobuki Nakanishi for providing the Grin3a
knockout mice, Beverly Davidson for the AAV-caRheb, Jose Esteban for help with behavioral
and biochemical experiments, and Noelia Campillo, Rebeca Martínez-Turrillas, and
Ana Navarro for expert technical help. Work was funded by the UTE project CIMA;
fellowships from the Fundación Tatiana Pérez de Guzmán el Bueno, FEBS, and IBRO
(to M.J.C.D.), Generalitat Valenciana (to O.E.-Z.), Juan de la Cierva (to L.G.R.),
FPI-MINECO (to E.R.V., to S.N.) and Intertalentum postdoctoral program (to V.B.);
ANR (GluBrain3A) and ERC Advanced Grants (#693021) (to P.P.); Ramón y Cajal program
RYC2014-15784, RETOS-MINECO SAF2016-76565-R, ERANET-Neuron JTC 2019 ISCIII AC19/00077
FEDER funds (to R.A.); RETOS-MINECO SAF2017-87928-R (to A.B.); an NIH grant (NS76637)
and UTHSC College of Medicine funds (to S.J.T.); and NARSAD Independent Investigator
Award and grants from the MINECO (CSD2008-00005, SAF2013-48983R, SAF2016-80895-R),
Generalitat Valenciana (PROMETEO 2019/020)(to I.P.O.) and Severo-Ochoa Excellence
Awards (SEV-2013-0317, SEV-2017-0723).
article_number: e71575
article_processing_charge: No
article_type: original
author:
- first_name: María J
full_name: Conde-Dusman, María J
last_name: Conde-Dusman
- first_name: Partha N
full_name: Dey, Partha N
last_name: Dey
- first_name: Óscar
full_name: Elía-Zudaire, Óscar
last_name: Elía-Zudaire
- first_name: Luis E
full_name: Garcia Rabaneda, Luis E
id: 33D1B084-F248-11E8-B48F-1D18A9856A87
last_name: Garcia Rabaneda
- first_name: Carmen
full_name: García-Lira, Carmen
last_name: García-Lira
- first_name: Teddy
full_name: Grand, Teddy
last_name: Grand
- first_name: Victor
full_name: Briz, Victor
last_name: Briz
- first_name: Eric R
full_name: Velasco, Eric R
last_name: Velasco
- first_name: Raül
full_name: Andero Galí, Raül
last_name: Andero Galí
- first_name: Sergio
full_name: Niñerola, Sergio
last_name: Niñerola
- first_name: Angel
full_name: Barco, Angel
last_name: Barco
- first_name: Pierre
full_name: Paoletti, Pierre
last_name: Paoletti
- first_name: John F
full_name: Wesseling, John F
last_name: Wesseling
- first_name: Fabrizio
full_name: Gardoni, Fabrizio
last_name: Gardoni
- first_name: Steven J
full_name: Tavalin, Steven J
last_name: Tavalin
- first_name: Isabel
full_name: Perez-Otaño, Isabel
last_name: Perez-Otaño
citation:
ama: Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, et al. Control of protein synthesis
and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly.
eLife. 2021;10. doi:10.7554/elife.71575
apa: Conde-Dusman, M. J., Dey, P. N., Elía-Zudaire, Ó., Garcia Rabaneda, L. E.,
García-Lira, C., Grand, T., … Perez-Otaño, I. (2021). Control of protein synthesis
and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly.
ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.71575
chicago: Conde-Dusman, María J, Partha N Dey, Óscar Elía-Zudaire, Luis E Garcia
Rabaneda, Carmen García-Lira, Teddy Grand, Victor Briz, et al. “Control of Protein
Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1
Assembly.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.71575.
ieee: M. J. Conde-Dusman et al., “Control of protein synthesis and memory
by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly,” eLife,
vol. 10. eLife Sciences Publications, 2021.
ista: Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, Garcia Rabaneda LE, García-Lira C,
Grand T, Briz V, Velasco ER, Andero Galí R, Niñerola S, Barco A, Paoletti P, Wesseling
JF, Gardoni F, Tavalin SJ, Perez-Otaño I. 2021. Control of protein synthesis and
memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife.
10, e71575.
mla: Conde-Dusman, María J., et al. “Control of Protein Synthesis and Memory by
GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife,
vol. 10, e71575, eLife Sciences Publications, 2021, doi:10.7554/elife.71575.
short: M.J. Conde-Dusman, P.N. Dey, Ó. Elía-Zudaire, L.E. Garcia Rabaneda, C. García-Lira,
T. Grand, V. Briz, E.R. Velasco, R. Andero Galí, S. Niñerola, A. Barco, P. Paoletti,
J.F. Wesseling, F. Gardoni, S.J. Tavalin, I. Perez-Otaño, ELife 10 (2021).
date_created: 2021-11-18T06:59:45Z
date_published: 2021-11-17T00:00:00Z
date_updated: 2023-08-14T11:50:50Z
day: '17'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.7554/elife.71575
external_id:
isi:
- '000720945900001'
file:
- access_level: open_access
checksum: 59318e9e41507cec83c2f4070e6ad540
content_type: application/pdf
creator: lgarciar
date_created: 2021-11-18T07:02:02Z
date_updated: 2021-11-18T07:02:02Z
file_id: '10302'
file_name: elife-71575-v1.pdf
file_size: 2477302
relation: main_file
success: 1
file_date_updated: 2021-11-18T07:02:02Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
keyword:
- general immunology and microbiology
- general biochemistry
- genetics and molecular biology
- general medicine
- general neuroscience
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
status: public
title: Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition
of GIT1/mTORC1 assembly
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '10283'
abstract:
- lang: eng
text: 'During the past decade, the scientific community and outside observers have
noted a concerning lack of rigor and transparency in preclinical research that
led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov
& Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed
to address the problem: from better training of scientists to more oversight to
expanded publishing practices such as preregistration of studies. The recently
published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the
largest initiative that aims to establish a systematic approach for increasing
the robustness and reliability of biomedical research (Bespalov et al, 2021).
However, promoting a cultural change in research practices warrants a broad adoption
of the Quality System and its underlying philosophy. It is here that academic
Core Facilities (CF), research service providers at universities and research
institutions, can make a difference. It is fair to assume that a significant fraction
of published data originated from experiments that were designed, run, or analyzed
in CFs. These academic services play an important role in the research ecosystem
by offering access to cutting-edge equipment and by developing and testing novel
techniques and methods that impact research in the academic and private sectors
alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value:
CFs employ competent personnel with profound knowledge and practical experience
of the specific field of interest: animal behavior, imaging, crystallography,
genomics, and so on. Thus, CFs are optimally positioned to address concerns about
the quality and robustness of preclinical research.'
acknowledgement: This EQIPD project has received funding from the Innovative Medicines
Initiative 2 Joint Undertaking under grant agreement no. 777364. This Joint Undertaking
receives support from the European Union’s Horizon 2020 research and innovation
program and EFPIA. LR was supported by the Faculty of Biology and Medicine, University
of Lausanne. VV was supported by Biocenter Finland and the Jane and Aatos Erkko
Foundation. CP and IKB received funding from the Federal Ministry of Education and
Research (BMBF, grant 01PW18001). SB from the Vienna BioCenter Core Facilities (VBCF)
Preclinical Phenotyping Facility acknowledges funding from the Austrian Federal
Ministry of Education, Science & Research; and the City of Vienna. MT is an incumbent
of the Carolito Stiftung Research Fellow Chair in Neurodegenerative Diseases. We
thank Dr. Katja Kivinen (Helsinki Institute of Life Science) for discussions and
feedback.
article_number: e53824
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Leonardo
full_name: Restivo, Leonardo
last_name: Restivo
- first_name: Björn
full_name: Gerlach, Björn
last_name: Gerlach
- first_name: Michael
full_name: Tsoory, Michael
last_name: Tsoory
- first_name: Lior
full_name: Bikovski, Lior
last_name: Bikovski
- first_name: Sylvia
full_name: Badurek, Sylvia
last_name: Badurek
- first_name: Claudia
full_name: Pitzer, Claudia
last_name: Pitzer
- first_name: Isabelle C.
full_name: Kos-Braun, Isabelle C.
last_name: Kos-Braun
- first_name: Anne Laure Mj
full_name: Mausset-Bonnefont, Anne Laure Mj
last_name: Mausset-Bonnefont
- first_name: Jonathan
full_name: Ward, Jonathan
last_name: Ward
- first_name: Michael
full_name: Schunn, Michael
id: 4272DB4A-F248-11E8-B48F-1D18A9856A87
last_name: Schunn
orcid: 0000-0003-4326-5300
- first_name: Lucas P.J.J.
full_name: Noldus, Lucas P.J.J.
last_name: Noldus
- first_name: Anton
full_name: Bespalov, Anton
last_name: Bespalov
- first_name: Vootele
full_name: Voikar, Vootele
last_name: Voikar
citation:
ama: 'Restivo L, Gerlach B, Tsoory M, et al. Towards best practices in research:
Role of academic core facilities. EMBO Reports. 2021;22. doi:10.15252/embr.202153824'
apa: 'Restivo, L., Gerlach, B., Tsoory, M., Bikovski, L., Badurek, S., Pitzer, C.,
… Voikar, V. (2021). Towards best practices in research: Role of academic core
facilities. EMBO Reports. EMBO Press. https://doi.org/10.15252/embr.202153824'
chicago: 'Restivo, Leonardo, Björn Gerlach, Michael Tsoory, Lior Bikovski, Sylvia
Badurek, Claudia Pitzer, Isabelle C. Kos-Braun, et al. “Towards Best Practices
in Research: Role of Academic Core Facilities.” EMBO Reports. EMBO Press,
2021. https://doi.org/10.15252/embr.202153824.'
ieee: 'L. Restivo et al., “Towards best practices in research: Role of academic
core facilities,” EMBO Reports, vol. 22. EMBO Press, 2021.'
ista: 'Restivo L, Gerlach B, Tsoory M, Bikovski L, Badurek S, Pitzer C, Kos-Braun
IC, Mausset-Bonnefont ALM, Ward J, Schunn M, Noldus LPJJ, Bespalov A, Voikar V.
2021. Towards best practices in research: Role of academic core facilities. EMBO
Reports. 22, e53824.'
mla: 'Restivo, Leonardo, et al. “Towards Best Practices in Research: Role of Academic
Core Facilities.” EMBO Reports, vol. 22, e53824, EMBO Press, 2021, doi:10.15252/embr.202153824.'
short: L. Restivo, B. Gerlach, M. Tsoory, L. Bikovski, S. Badurek, C. Pitzer, I.C.
Kos-Braun, A.L.M. Mausset-Bonnefont, J. Ward, M. Schunn, L.P.J.J. Noldus, A. Bespalov,
V. Voikar, EMBO Reports 22 (2021).
date_created: 2021-11-14T23:01:24Z
date_published: 2021-11-04T00:00:00Z
date_updated: 2023-08-14T11:47:35Z
day: '04'
ddc:
- '570'
department:
- _id: PreCl
doi: 10.15252/embr.202153824
external_id:
isi:
- '000714350000001'
file:
- access_level: open_access
checksum: 74743baa6ef431ef60c3de3bc4da045a
content_type: application/pdf
creator: dernst
date_created: 2022-05-16T07:07:41Z
date_updated: 2022-05-16T07:07:41Z
file_id: '11381'
file_name: 2021_EmboReports_Restivo.pdf
file_size: 488583
relation: main_file
success: 1
file_date_updated: 2022-05-16T07:07:41Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: EMBO Reports
publication_identifier:
eissn:
- 1469-3178
issn:
- 1469-221X
publication_status: published
publisher: EMBO Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Towards best practices in research: Role of academic core facilities'
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: 22
year: '2021'
...
---
_id: '10310'
abstract:
- lang: eng
text: A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI)
from Thermosynechococcus elongatus was reported as the first atomic model of PSI
almost 20 years ago. However, the monomeric PSI structure has not yet been reported
despite long-standing interest in its structure and extensive spectroscopic characterization
of the loss of red chlorophylls upon monomerization. Here, we describe the structure
of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the
trimer structure gave detailed insights into monomerization-induced changes in
both the central trimerization domain and the peripheral regions of the complex.
Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls
adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization
of red chlorophylls and that lipids of the surrounding membrane present a major
source of thermal energy for uphill excitation energy transfer from red chlorophylls
to P700.
acknowledgement: We are grateful for additional support and valuable scientific input
for this project by Yuko Misumi, Jiannan Li, Hisako Kubota-Kawai, Takeshi Kawabata,
Mian Wu, Eiki Yamashita, Atsushi Nakagawa, Volker Hartmann, Melanie Völkel and Matthias
Rögner. Parts of this research were funded by the German Research Council (DFG)
within the framework of GRK 2341 (Microbial Substrate Conversion) to M.M.N., the
Platform Project for Supporting Drug Discovery and Life Science Research [Basis
for Supporting Innovative Drug Discovery and Life Science Research (BINDS)] from
AMED under grant number JP20am0101117 (K.N.), JP16K07266 to Atsunori Oshima and
C.G., a Grants-in-Aid for Scientific Research under grant number JP 25000013 (K.N.),
17H03647 (C.G.) and 16H06560 (G.K.) from MEXT-KAKENHI, the International Joint Research
Promotion Program from Osaka University to M.M.N., C.G. and G.K., and the Cyclic
Innovation for Clinical Empowerment (CiCLE) Grant Number JP17pc0101020 from AMED
to K.N. and G.K.
article_number: '304'
article_processing_charge: No
article_type: original
author:
- first_name: Mehmet Orkun
full_name: Çoruh, Mehmet Orkun
id: d25163e5-8d53-11eb-a251-e6dd8ea1b8ef
last_name: Çoruh
orcid: 0000-0002-3219-2022
- first_name: Anna
full_name: Frank, Anna
last_name: Frank
- first_name: Hideaki
full_name: Tanaka, Hideaki
last_name: Tanaka
- first_name: Akihiro
full_name: Kawamoto, Akihiro
last_name: Kawamoto
- first_name: Eithar
full_name: El-Mohsnawy, Eithar
last_name: El-Mohsnawy
- first_name: Takayuki
full_name: Kato, Takayuki
last_name: Kato
- first_name: Keiichi
full_name: Namba, Keiichi
last_name: Namba
- first_name: Christoph
full_name: Gerle, Christoph
last_name: Gerle
- first_name: Marc M.
full_name: Nowaczyk, Marc M.
last_name: Nowaczyk
- first_name: Genji
full_name: Kurisu, Genji
last_name: Kurisu
citation:
ama: Çoruh MO, Frank A, Tanaka H, et al. Cryo-EM structure of a functional monomeric
Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster.
Communications Biology. 2021;4(1). doi:10.1038/s42003-021-01808-9
apa: Çoruh, M. O., Frank, A., Tanaka, H., Kawamoto, A., El-Mohsnawy, E., Kato, T.,
… Kurisu, G. (2021). Cryo-EM structure of a functional monomeric Photosystem I
from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications
Biology. Springer . https://doi.org/10.1038/s42003-021-01808-9
chicago: Çoruh, Mehmet Orkun, Anna Frank, Hideaki Tanaka, Akihiro Kawamoto, Eithar
El-Mohsnawy, Takayuki Kato, Keiichi Namba, Christoph Gerle, Marc M. Nowaczyk,
and Genji Kurisu. “Cryo-EM Structure of a Functional Monomeric Photosystem I from
Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications
Biology. Springer , 2021. https://doi.org/10.1038/s42003-021-01808-9.
ieee: M. O. Çoruh et al., “Cryo-EM structure of a functional monomeric Photosystem
I from Thermosynechococcus elongatus reveals red chlorophyll cluster,” Communications
Biology, vol. 4, no. 1. Springer , 2021.
ista: Çoruh MO, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle
C, Nowaczyk MM, Kurisu G. 2021. Cryo-EM structure of a functional monomeric Photosystem
I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications
Biology. 4(1), 304.
mla: Çoruh, Mehmet Orkun, et al. “Cryo-EM Structure of a Functional Monomeric Photosystem
I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications
Biology, vol. 4, no. 1, 304, Springer , 2021, doi:10.1038/s42003-021-01808-9.
short: M.O. Çoruh, A. Frank, H. Tanaka, A. Kawamoto, E. El-Mohsnawy, T. Kato, K.
Namba, C. Gerle, M.M. Nowaczyk, G. Kurisu, Communications Biology 4 (2021).
date_created: 2021-11-19T11:37:29Z
date_published: 2021-03-08T00:00:00Z
date_updated: 2023-08-14T11:51:19Z
day: '08'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1038/s42003-021-01808-9
external_id:
isi:
- '000627440700001'
pmid:
- '33686186'
file:
- access_level: open_access
checksum: 8ffd39f2bba7152a2441802ff313bf0b
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-19T15:09:18Z
date_updated: 2021-11-19T15:09:18Z
file_id: '10318'
file_name: 2021_CommBio_Çoruh.pdf
file_size: 6030261
relation: main_file
success: 1
file_date_updated: 2021-11-19T15:09:18Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '1'
keyword:
- general agricultural and biological Sciences
- general biochemistry
- genetics and molecular biology
- medicine (miscellaneous)
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Communications Biology
publication_identifier:
issn:
- 2399-3642
publication_status: published
publisher: 'Springer '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus
elongatus reveals red chlorophyll cluster
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: 4
year: '2021'
...
---
_id: '10270'
abstract:
- lang: eng
text: Plants develop new organs to adjust their bodies to dynamic changes in the
environment. How independent organs achieve anisotropic shapes and polarities
is poorly understood. To address this question, we constructed a mechano-biochemical
model for Arabidopsis root meristem growth that integrates biologically plausible
principles. Computer model simulations demonstrate how differential growth of
neighboring tissues results in the initial symmetry-breaking leading to anisotropic
root growth. Furthermore, the root growth feeds back on a polar transport network
of the growth regulator auxin. Model, predictions are in close agreement with
in vivo patterns of anisotropic growth, auxin distribution, and cell polarity,
as well as several root phenotypes caused by chemical, mechanical, or genetic
perturbations. Our study demonstrates that the combination of tissue mechanics
and polar auxin transport organizes anisotropic root growth and cell polarities
during organ outgrowth. Therefore, a mobile auxin signal transported through immobile
cells drives polarity and growth mechanics to coordinate complex organ development.
acknowledgement: 'e are grateful Richard Smith, Anne-Lise Routier, Crisanto Gutierrez
and Juergen Kleine-Vehn for providing critical comments on the manuscript. Funding:
This work was supported by the Programa de Atraccion de Talento 2017 (Comunidad
de Madrid, 2017-T1/BIO-5654 to KW), Severo Ochoa (SO) Programme for Centres of Excellence
in R&D from the Agencia Estatal de Investigacion of Spain (grant SEV-2016–0672 (2017–2021)
to KW via the CBGP). In the frame of SEV-2016–0672 funding MM is supported with
a postdoctoral contract. KW was supported by Programa Estatal de Generacion del
Conocimiento y Fortalecimiento Cientıfico y Tecnologico del Sistema de I + D + I
2019 (PGC2018-093387-A-I00) from MICIU (to KW). MG is recipient of an IST Interdisciplinary
Project (IC1022IPC03).'
article_number: '72132'
article_processing_charge: Yes
article_type: original
author:
- first_name: Marco
full_name: Marconi, Marco
last_name: Marconi
- first_name: Marçal
full_name: Gallemi, Marçal
id: 460C6802-F248-11E8-B48F-1D18A9856A87
last_name: Gallemi
orcid: 0000-0003-4675-6893
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Krzysztof
full_name: Wabnik, Krzysztof
last_name: Wabnik
citation:
ama: Marconi M, Gallemi M, Benková E, Wabnik K. A coupled mechano-biochemical model
for cell polarity guided anisotropic root growth. eLife. 2021;10. doi:10.7554/elife.72132
apa: Marconi, M., Gallemi, M., Benková, E., & Wabnik, K. (2021). A coupled mechano-biochemical
model for cell polarity guided anisotropic root growth. ELife. eLife Sciences
Publications. https://doi.org/10.7554/elife.72132
chicago: Marconi, Marco, Marçal Gallemi, Eva Benková, and Krzysztof Wabnik. “A Coupled
Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” ELife.
eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72132.
ieee: M. Marconi, M. Gallemi, E. Benková, and K. Wabnik, “A coupled mechano-biochemical
model for cell polarity guided anisotropic root growth,” eLife, vol. 10.
eLife Sciences Publications, 2021.
ista: Marconi M, Gallemi M, Benková E, Wabnik K. 2021. A coupled mechano-biochemical
model for cell polarity guided anisotropic root growth. eLife. 10, 72132.
mla: Marconi, Marco, et al. “A Coupled Mechano-Biochemical Model for Cell Polarity
Guided Anisotropic Root Growth.” ELife, vol. 10, 72132, eLife Sciences
Publications, 2021, doi:10.7554/elife.72132.
short: M. Marconi, M. Gallemi, E. Benková, K. Wabnik, ELife 10 (2021).
date_created: 2021-11-11T10:05:18Z
date_published: 2021-11-01T00:00:00Z
date_updated: 2023-08-14T11:49:23Z
day: '01'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.7554/elife.72132
external_id:
isi:
- '000734671200001'
pmid:
- '34723798'
file:
- access_level: open_access
checksum: fad13c509b53bb7a2bef9c946a7ca60a
content_type: application/pdf
creator: dernst
date_created: 2022-05-13T09:00:29Z
date_updated: 2022-05-13T09:00:29Z
file_id: '11372'
file_name: 2021_eLife_Marconi.pdf
file_size: 14137503
relation: main_file
success: 1
file_date_updated: 2022-05-13T09:00:29Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: A coupled mechano-biochemical model for cell polarity guided anisotropic root
growth
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '10299'
abstract:
- lang: eng
text: Turbulence generally arises in shear flows if velocities and hence, inertial
forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit
disordered motion even at vanishing inertia. Intermediate between these cases,
a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed
in a narrow Reynolds number interval. We here determine the origin of EIT in experiments
and show that characteristic EIT structures can be detected across an unexpectedly
wide range of parameters. Close to onset, a pattern of chevron-shaped streaks
emerges in qualitative agreement with linear and weakly nonlinear theory. However,
in experiments, the dynamics remain weakly chaotic, and the instability can be
traced to far lower Reynolds numbers than permitted by theory. For increasing
inertia, the flow undergoes a transformation to a wall mode composed of inclined
near-wall streaks and shear layers. This mode persists to what is known as the
“maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic
flows across more than three orders of magnitude in Reynolds number.
acknowledgement: We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg,
and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge
funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft
research unit FOR 2688.
article_number: e2102350118
article_processing_charge: No
article_type: original
author:
- first_name: George H
full_name: Choueiri, George H
id: 448BD5BC-F248-11E8-B48F-1D18A9856A87
last_name: Choueiri
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Sarath
full_name: Sankar, Sarath
last_name: Sankar
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation
of the origin and structure of elastoinertial turbulence. Proceedings of the
National Academy of Sciences. 2021;118(45). doi:10.1073/pnas.2102350118
apa: Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., & Hof,
B. (2021). Experimental observation of the origin and structure of elastoinertial
turbulence. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.2102350118
chicago: Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar,
and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial
Turbulence.” Proceedings of the National Academy of Sciences. National
Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2102350118.
ieee: G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental
observation of the origin and structure of elastoinertial turbulence,” Proceedings
of the National Academy of Sciences, vol. 118, no. 45. National Academy of
Sciences, 2021.
ista: Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental
observation of the origin and structure of elastoinertial turbulence. Proceedings
of the National Academy of Sciences. 118(45), e2102350118.
mla: Choueiri, George H., et al. “Experimental Observation of the Origin and Structure
of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences,
vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:10.1073/pnas.2102350118.
short: G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings
of the National Academy of Sciences 118 (2021).
date_created: 2021-11-17T13:24:24Z
date_published: 2021-11-03T00:00:00Z
date_updated: 2023-08-14T11:50:10Z
day: '03'
department:
- _id: BjHo
doi: 10.1073/pnas.2102350118
external_id:
arxiv:
- '2103.00023'
isi:
- '000720926900019'
pmid:
- ' 34732570'
intvolume: ' 118'
isi: 1
issue: '45'
keyword:
- multidisciplinary
- elastoinertial turbulence
- viscoelastic flows
- elastic instability
- drag reduction
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2103.00023
month: '11'
oa: 1
oa_version: Preprint
pmid: 1
project:
- _id: 238B8092-32DE-11EA-91FC-C7463DDC885E
call_identifier: FWF
grant_number: I04188
name: Instabilities in pulsating pipe flow of Newtonian and complex fluids
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Experimental observation of the origin and structure of elastoinertial turbulence
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 118
year: '2021'
...
---
_id: '10280'
abstract:
- lang: eng
text: 'Machines enabled the Industrial Revolution and are central to modern technological
progress: A machine’s parts transmit forces, motion, and energy to one another
in a predetermined manner. Today’s engineering frontier, building artificial micromachines
that emulate the biological machinery of living organisms, requires faithful assembly
and energy consumption at the microscale. Here, we demonstrate the programmable
assembly of active particles into autonomous metamachines using optical templates.
Metamachines, or machines made of machines, are stable, mobile and autonomous
architectures, whose dynamics stems from the geometry. We use the interplay between
anisotropic force generation of the active colloids with the control of their
orientation by local geometry. This allows autonomous reprogramming of active
particles of the metamachines to achieve multiple functions. It permits the modular
assembly of metamachines by fusion, reconfiguration of metamachines and, we anticipate,
a shift in focus of self-assembly towards active matter and reprogrammable materials.'
acknowledgement: The authors thank R. Jazzar for useful advice regarding the synthesis
of heterodimers. We thank S. Sacanna for critical reading. This material is based
upon work supported by the National Science Foundation under Grant No. DMR-1554724
and Department of Army Research under grant W911NF-20-1-0112.
article_number: '6398'
article_processing_charge: Yes
article_type: original
author:
- first_name: Antoine
full_name: Aubret, Antoine
last_name: Aubret
- first_name: Quentin
full_name: Martinet, Quentin
id: b37485a8-d343-11eb-a0e9-df8c484ef8ab
last_name: Martinet
orcid: 0000-0002-2916-6632
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: Aubret A, Martinet Q, Palacci JA. Metamachines of pluripotent colloids. Nature
Communications. 2021;12(1). doi:10.1038/s41467-021-26699-6
apa: Aubret, A., Martinet, Q., & Palacci, J. A. (2021). Metamachines of pluripotent
colloids. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26699-6
chicago: Aubret, Antoine, Quentin Martinet, and Jérémie A Palacci. “Metamachines
of Pluripotent Colloids.” Nature Communications. Springer Nature, 2021.
https://doi.org/10.1038/s41467-021-26699-6.
ieee: A. Aubret, Q. Martinet, and J. A. Palacci, “Metamachines of pluripotent colloids,”
Nature Communications, vol. 12, no. 1. Springer Nature, 2021.
ista: Aubret A, Martinet Q, Palacci JA. 2021. Metamachines of pluripotent colloids.
Nature Communications. 12(1), 6398.
mla: Aubret, Antoine, et al. “Metamachines of Pluripotent Colloids.” Nature Communications,
vol. 12, no. 1, 6398, Springer Nature, 2021, doi:10.1038/s41467-021-26699-6.
short: A. Aubret, Q. Martinet, J.A. Palacci, Nature Communications 12 (2021).
date_created: 2021-11-14T23:01:23Z
date_published: 2021-11-04T00:00:00Z
date_updated: 2023-08-14T11:48:37Z
day: '04'
ddc:
- '530'
department:
- _id: JePa
doi: 10.1038/s41467-021-26699-6
external_id:
isi:
- '000714754400010'
pmid:
- '34737315'
file:
- access_level: open_access
checksum: 1c392b12b9b7b615d422d9fabe19cdb9
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-15T13:25:52Z
date_updated: 2021-11-15T13:25:52Z
file_id: '10292'
file_name: 2021_NatComm_Aubret.pdf
file_size: 6282703
relation: main_file
success: 1
file_date_updated: 2021-11-15T13:25:52Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Metamachines of pluripotent colloids
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '10322'
abstract:
- lang: eng
text: To survive elevated temperatures, ectotherms adjust the fluidity of membranes
by fine-tuning lipid desaturation levels in a process previously described to
be cell autonomous. We have discovered that, in Caenorhabditis elegans, neuronal
heat shock factor 1 (HSF-1), the conserved master regulator of the heat shock
response (HSR), causes extensive fat remodeling in peripheral tissues. These changes
include a decrease in fat desaturase and acid lipase expression in the intestine
and a global shift in the saturation levels of plasma membrane’s phospholipids.
The observed remodeling of plasma membrane is in line with ectothermic adaptive
responses and gives worms a cumulative advantage to warm temperatures. We have
determined that at least 6 TAX-2/TAX-4 cyclic guanosine monophosphate (cGMP) gated
channel expressing sensory neurons, and transforming growth factor ß (TGF-β)/bone
morphogenetic protein (BMP) are required for signaling across tissues to modulate
fat desaturation. We also find neuronal hsf-1 is not only sufficient but also
partially necessary to control the fat remodeling response and for survival at
warm temperatures. This is the first study to show that a thermostat-based mechanism
can cell nonautonomously coordinate membrane saturation and composition across
tissues in a multicellular animal.
acknowledgement: We dedicate this work to the memory of Michael J.O. Wakelam. We would
like to acknowledge Michael Fasseas (Invermis, Magnitude Biosciences) for plasmid
injections and Sunny Biotech for transgenics; Catalina Vallejos and John Marioni
for statistical advice at the beginning of the work; Simon Walker, Imaging, Bioinformatics
and Lipidomics Facilities at Babraham Institute for technical support; and Cindy
Voisine, Michael Witting, Jon Houseley, Len Stephens, Carmen Nussbaum Krammer, Rebeca
Aldunate, Patricija van Oosten-Hawle, Jean-Louis Bessereau, and Jane Alfred for
feedback on the manuscript. We thank Andy Dillin, Atsushi Kuhara, Amy Walker, Andrew
Leifer, Yun Zhang, and Michalis Barkoulas for reagents and Julie Ahringer, Anne
Ferguson-Smith, and Anne Corcoran for support and helpful discussions. We also acknowledge
Babraham Institute Facilities.
article_number: e3001431
article_processing_charge: No
article_type: original
author:
- first_name: Laetitia
full_name: Chauve, Laetitia
last_name: Chauve
- first_name: Francesca
full_name: Hodge, Francesca
last_name: Hodge
- first_name: Sharlene
full_name: Murdoch, Sharlene
last_name: Murdoch
- first_name: Fatemah
full_name: Masoudzadeh, Fatemah
last_name: Masoudzadeh
- first_name: Harry Jack
full_name: Mann, Harry Jack
last_name: Mann
- first_name: Andrea
full_name: Lopez-Clavijo, Andrea
last_name: Lopez-Clavijo
- first_name: Hanneke
full_name: Okkenhaug, Hanneke
last_name: Okkenhaug
- first_name: Greg
full_name: West, Greg
last_name: West
- first_name: Bebiana C.
full_name: Sousa, Bebiana C.
last_name: Sousa
- first_name: Anne
full_name: Segonds-Pichon, Anne
last_name: Segonds-Pichon
- first_name: Cheryl
full_name: Li, Cheryl
last_name: Li
- first_name: Steven
full_name: Wingett, Steven
last_name: Wingett
- first_name: Hermine
full_name: Kienberger, Hermine
last_name: Kienberger
- first_name: Karin
full_name: Kleigrewe, Karin
last_name: Kleigrewe
- first_name: Mario
full_name: De Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: De Bono
orcid: 0000-0001-8347-0443
- first_name: Michael
full_name: Wakelam, Michael
last_name: Wakelam
- first_name: Olivia
full_name: Casanueva, Olivia
last_name: Casanueva
citation:
ama: Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation
of fat desaturation across tissues to enable adaptation to high temperatures in
C. elegans. PLoS Biology. 2021;19(11). doi:10.1371/journal.pbio.3001431
apa: Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H. J., Lopez-Clavijo,
A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat
desaturation across tissues to enable adaptation to high temperatures in C. elegans.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3001431
chicago: Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh,
Harry Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1
Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation
to High Temperatures in C. Elegans.” PLoS Biology. Public Library of Science,
2021. https://doi.org/10.1371/journal.pbio.3001431.
ieee: L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat
desaturation across tissues to enable adaptation to high temperatures in C. elegans,”
PLoS Biology, vol. 19, no. 11. Public Library of Science, 2021.
ista: Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann HJ, Lopez-Clavijo A, Okkenhaug
H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe
K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation
of fat desaturation across tissues to enable adaptation to high temperatures in
C. elegans. PLoS Biology. 19(11), e3001431.
mla: Chauve, Laetitia, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat
Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.”
PLoS Biology, vol. 19, no. 11, e3001431, Public Library of Science, 2021,
doi:10.1371/journal.pbio.3001431.
short: L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.J. Mann, A. Lopez-Clavijo,
H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger,
K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, PLoS Biology 19 (2021).
date_created: 2021-11-21T23:01:28Z
date_published: 2021-11-01T00:00:00Z
date_updated: 2023-08-14T11:53:27Z
day: '01'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.1371/journal.pbio.3001431
external_id:
isi:
- '000715818400001'
pmid:
- '34723964'
file:
- access_level: open_access
checksum: 0c61b667f814fd9435b3ac42036fc36d
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-22T09:34:03Z
date_updated: 2021-11-22T09:34:03Z
file_id: '10330'
file_name: 2021_PLoSBio_Chauve.pdf
file_size: 4069215
relation: main_file
success: 1
file_date_updated: 2021-11-22T09:34:03Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Biology
publication_identifier:
eissn:
- 1545-7885
issn:
- 1544-9173
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '13069'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues
to enable adaptation to high temperatures in C. 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: 19
year: '2021'
...
---
_id: '10222'
abstract:
- lang: eng
text: Consider a random set of points on the unit sphere in ℝd, which can be either
uniformly sampled or a Poisson point process. Its convex hull is a random inscribed
polytope, whose boundary approximates the sphere. We focus on the case d = 3,
for which there are elementary proofs and fascinating formulas for metric properties.
In particular, we study the fraction of acute facets, the expected intrinsic volumes,
the total edge length, and the distance to a fixed point. Finally we generalize
the results to the ellipsoid with homeoid density.
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme,
grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant
no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization
in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.\r\nWe
are grateful to Dmitry Zaporozhets and Christoph Thäle for valuable comments and
for directing us to relevant references. We also thank to Anton Mellit for a useful
discussion on Bessel functions."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Anton
full_name: Nikitenko, Anton
id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87
last_name: Nikitenko
orcid: 0000-0002-0659-3201
citation:
ama: Akopyan A, Edelsbrunner H, Nikitenko A. The beauty of random polytopes inscribed
in the 2-sphere. Experimental Mathematics. 2021:1-15. doi:10.1080/10586458.2021.1980459
apa: Akopyan, A., Edelsbrunner, H., & Nikitenko, A. (2021). The beauty of random
polytopes inscribed in the 2-sphere. Experimental Mathematics. Taylor and
Francis. https://doi.org/10.1080/10586458.2021.1980459
chicago: Akopyan, Arseniy, Herbert Edelsbrunner, and Anton Nikitenko. “The Beauty
of Random Polytopes Inscribed in the 2-Sphere.” Experimental Mathematics.
Taylor and Francis, 2021. https://doi.org/10.1080/10586458.2021.1980459.
ieee: A. Akopyan, H. Edelsbrunner, and A. Nikitenko, “The beauty of random polytopes
inscribed in the 2-sphere,” Experimental Mathematics. Taylor and Francis,
pp. 1–15, 2021.
ista: Akopyan A, Edelsbrunner H, Nikitenko A. 2021. The beauty of random polytopes
inscribed in the 2-sphere. Experimental Mathematics., 1–15.
mla: Akopyan, Arseniy, et al. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.”
Experimental Mathematics, Taylor and Francis, 2021, pp. 1–15, doi:10.1080/10586458.2021.1980459.
short: A. Akopyan, H. Edelsbrunner, A. Nikitenko, Experimental Mathematics (2021)
1–15.
date_created: 2021-11-07T23:01:25Z
date_published: 2021-10-25T00:00:00Z
date_updated: 2023-08-14T11:57:07Z
day: '25'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1080/10586458.2021.1980459
ec_funded: 1
external_id:
arxiv:
- '2007.07783'
isi:
- '000710893500001'
file:
- access_level: open_access
checksum: 3514382e3a1eb87fa6c61ad622874415
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T11:55:10Z
date_updated: 2023-08-14T11:55:10Z
file_id: '14053'
file_name: 2023_ExperimentalMath_Akopyan.pdf
file_size: 1966019
relation: main_file
success: 1
file_date_updated: 2023-08-14T11:55:10Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1-15
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
- _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316
grant_number: I4887
name: Discretization in Geometry and Dynamics
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Experimental Mathematics
publication_identifier:
eissn:
- 1944-950X
issn:
- 1058-6458
publication_status: published
publisher: Taylor and Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: The beauty of random polytopes inscribed in the 2-sphere
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10323'
abstract:
- lang: eng
text: Molecular chaperones are central to cellular protein homeostasis. Dynamic
disorder is a key feature of the complexes of molecular chaperones and their client
proteins, and it facilitates the client release towards a folded state or the
handover to downstream components. The dynamic nature also implies that a given
chaperone can interact with many different client proteins, based on physico-chemical
sequence properties rather than on structural complementarity of their (folded)
3D structure. Yet, the balance between this promiscuity and some degree of client
specificity is poorly understood. Here, we review recent atomic-level descriptions
of chaperones with client proteins, including chaperones in complex with intrinsically
disordered proteins, with membrane-protein precursors, or partially folded client
proteins. We focus hereby on chaperone-client interactions that are independent
of ATP. The picture emerging from these studies highlights the importance of dynamics
in these complexes, whereby several interaction types, not only hydrophobic ones,
contribute to the complex formation. We discuss these features of chaperone-client
complexes and possible factors that may contribute to this balance of promiscuity
and specificity.
acknowledgement: We thank Juan C. Fontecilla-Camps for insightful discussions related
to ATP-driven machineries, and Elif Karagöz for providing the structural model of
the Hsp90-Tau complex. This study was supported by the European Research Council
(StG-2012-311318-ProtDyn2Function) and the Agence Nationale de la Recherche (ANR-18-CE92-0032-MitoMemProtImp).
article_number: '762005'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Iva
full_name: Sučec, Iva
last_name: Sučec
- first_name: Beate
full_name: Bersch, Beate
last_name: Bersch
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Sučec I, Bersch B, Schanda P. How do chaperones bind (partly) unfolded client
proteins? Frontiers in Molecular Biosciences. 2021;8. doi:10.3389/fmolb.2021.762005
apa: Sučec, I., Bersch, B., & Schanda, P. (2021). How do chaperones bind (partly)
unfolded client proteins? Frontiers in Molecular Biosciences. Frontiers.
https://doi.org/10.3389/fmolb.2021.762005
chicago: Sučec, Iva, Beate Bersch, and Paul Schanda. “How Do Chaperones Bind (Partly)
Unfolded Client Proteins?” Frontiers in Molecular Biosciences. Frontiers,
2021. https://doi.org/10.3389/fmolb.2021.762005.
ieee: I. Sučec, B. Bersch, and P. Schanda, “How do chaperones bind (partly) unfolded
client proteins?,” Frontiers in Molecular Biosciences, vol. 8. Frontiers,
2021.
ista: Sučec I, Bersch B, Schanda P. 2021. How do chaperones bind (partly) unfolded
client proteins? Frontiers in Molecular Biosciences. 8, 762005.
mla: Sučec, Iva, et al. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?”
Frontiers in Molecular Biosciences, vol. 8, 762005, Frontiers, 2021, doi:10.3389/fmolb.2021.762005.
short: I. Sučec, B. Bersch, P. Schanda, Frontiers in Molecular Biosciences 8 (2021).
date_created: 2021-11-21T23:01:29Z
date_published: 2021-10-25T00:00:00Z
date_updated: 2023-08-14T11:55:04Z
day: '25'
ddc:
- '547'
department:
- _id: PaSc
doi: 10.3389/fmolb.2021.762005
external_id:
isi:
- '000717241700001'
pmid:
- '34760928'
file:
- access_level: open_access
checksum: a5c9dbf80dc2c5aaa737f456c941d964
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-23T15:06:58Z
date_updated: 2021-11-23T15:06:58Z
file_id: '10333'
file_name: 2021_FrontiersMolBioSc_Sučec.pdf
file_size: 4700798
relation: main_file
success: 1
file_date_updated: 2021-11-23T15:06:58Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Molecular Biosciences
publication_identifier:
eissn:
- 2296-889X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: How do chaperones bind (partly) unfolded client proteins?
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 8
year: '2021'
...
---
_id: '10326'
abstract:
- lang: eng
text: Strigolactones (SLs) are carotenoid-derived plant hormones that control shoot
branching and communications between host plants and symbiotic fungi or root parasitic
plants. Extensive studies have identified the key components participating in
SL biosynthesis and signalling, whereas the catabolism or deactivation of endogenous
SLs in planta remains largely unknown. Here, we report that the Arabidopsis carboxylesterase
15 (AtCXE15) and its orthologues function as efficient hydrolases of SLs. We show
that overexpression of AtCXE15 promotes shoot branching by dampening SL-inhibited
axillary bud outgrowth. We further demonstrate that AtCXE15 could bind and efficiently
hydrolyse SLs both in vitro and in planta. We also provide evidence that AtCXE15
is capable of catalysing hydrolysis of diverse SL analogues and that such CXE15-dependent
catabolism of SLs is evolutionarily conserved in seed plants. These results disclose
a catalytic mechanism underlying homoeostatic regulation of SLs in plants, which
also provides a rational approach to spatial-temporally manipulate the endogenous
SLs and thus architecture of crops and ornamental plants.
acknowledgement: We thank J. Li (Institute of Genetics and Developmental Biology,
China) for providing the at14-1, atmax2-1, atmax3-9, atmax4-1, atmax1-1, kai2-2
(Col-0 background) mutants and B. Xu for providing the complementary DNA of P. patens.
We are grateful to L. Wang for assistance with MST, B. Han for assistance with UPLC–MS,
J. Li for assistance with confocal microscopy and B. Mikael and J. Zhang for their
comments on the manuscript. This work was supported by grants from Strategic Priority
Research Program of Chinese Academy of Sciences (Y.H., XDB27030102) and the National
Natural Science Foundation of China (E.X., 31700253; Y.H., 31830055).
article_processing_charge: No
article_type: original
author:
- first_name: Enjun
full_name: Xu, Enjun
last_name: Xu
- first_name: Liang
full_name: Chai, Liang
last_name: Chai
- first_name: Shiqi
full_name: Zhang, Shiqi
last_name: Zhang
- first_name: Ruixue
full_name: Yu, Ruixue
last_name: Yu
- first_name: Xixi
full_name: Zhang, Xixi
id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A
last_name: Zhang
orcid: 0000-0001-7048-4627
- first_name: Chongyi
full_name: Xu, Chongyi
last_name: Xu
- first_name: Yuxin
full_name: Hu, Yuxin
last_name: Hu
citation:
ama: Xu E, Chai L, Zhang S, et al. Catabolism of strigolactones by a carboxylesterase.
Nature Plants. 2021;7:1495–1504. doi:10.1038/s41477-021-01011-y
apa: Xu, E., Chai, L., Zhang, S., Yu, R., Zhang, X., Xu, C., & Hu, Y. (2021).
Catabolism of strigolactones by a carboxylesterase. Nature Plants. Springer
Nature. https://doi.org/10.1038/s41477-021-01011-y
chicago: Xu, Enjun, Liang Chai, Shiqi Zhang, Ruixue Yu, Xixi Zhang, Chongyi Xu,
and Yuxin Hu. “Catabolism of Strigolactones by a Carboxylesterase.” Nature
Plants. Springer Nature, 2021. https://doi.org/10.1038/s41477-021-01011-y.
ieee: E. Xu et al., “Catabolism of strigolactones by a carboxylesterase,”
Nature Plants, vol. 7. Springer Nature, pp. 1495–1504, 2021.
ista: Xu E, Chai L, Zhang S, Yu R, Zhang X, Xu C, Hu Y. 2021. Catabolism of strigolactones
by a carboxylesterase. Nature Plants. 7, 1495–1504.
mla: Xu, Enjun, et al. “Catabolism of Strigolactones by a Carboxylesterase.” Nature
Plants, vol. 7, Springer Nature, 2021, pp. 1495–1504, doi:10.1038/s41477-021-01011-y.
short: E. Xu, L. Chai, S. Zhang, R. Yu, X. Zhang, C. Xu, Y. Hu, Nature Plants 7
(2021) 1495–1504.
date_created: 2021-11-21T23:01:30Z
date_published: 2021-11-11T00:00:00Z
date_updated: 2023-08-14T11:54:02Z
day: '11'
department:
- _id: JiFr
doi: 10.1038/s41477-021-01011-y
external_id:
isi:
- '000717408000002'
pmid:
- '34764442'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '11'
oa_version: None
page: '1495–1504 '
pmid: 1
publication: Nature Plants
publication_identifier:
eissn:
- 2055-0278
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Catabolism of strigolactones by a carboxylesterase
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 7
year: '2021'
...
---
_id: '13069'
abstract:
- lang: eng
text: To survive elevated temperatures, ectotherms adjust the fluidity of membranes
by fine-tuning lipid desaturation levels in a process previously described to
be cell-autonomous. We have discovered that, in Caenorhabditis elegans, neuronal
Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock
response (HSR)- causes extensive fat remodelling in peripheral tissues. These
changes include a decrease in fat desaturase and acid lipase expression in the
intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids.
The observed remodelling of plasma membrane is in line with ectothermic adaptive
responses and gives worms a cumulative advantage to warm temperatures. We have
determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory
neurons and TGF-β/BMP are required for signalling across tissues to modulate fat
desaturation. We also find neuronal hsf-1 is not only sufficient but also partially
necessary to control the fat remodelling response and for survival at warm temperatures.
This is the first study to show that a thermostat-based mechanism can cell non-autonomously
coordinate membrane saturation and composition across tissues in a multicellular
animal.
article_processing_charge: No
author:
- first_name: Laetitia
full_name: Chauve, Laetitia
last_name: Chauve
- first_name: Francesca
full_name: Hodge, Francesca
last_name: Hodge
- first_name: Sharlene
full_name: Murdoch, Sharlene
last_name: Murdoch
- first_name: Fatemah
full_name: Masoudzadeh, Fatemah
last_name: Masoudzadeh
- first_name: Harry-Jack
full_name: Mann, Harry-Jack
last_name: Mann
- first_name: Andrea
full_name: Lopez-Clavijo, Andrea
last_name: Lopez-Clavijo
- first_name: Hanneke
full_name: Okkenhaug, Hanneke
last_name: Okkenhaug
- first_name: Greg
full_name: West, Greg
last_name: West
- first_name: Bebiana C.
full_name: Sousa, Bebiana C.
last_name: Sousa
- first_name: Anne
full_name: Segonds-Pichon, Anne
last_name: Segonds-Pichon
- first_name: Cheryl
full_name: Li, Cheryl
last_name: Li
- first_name: Steven
full_name: Wingett, Steven
last_name: Wingett
- first_name: Hermine
full_name: Kienberger, Hermine
last_name: Kienberger
- first_name: Karin
full_name: Kleigrewe, Karin
last_name: Kleigrewe
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: Michael
full_name: Wakelam, Michael
last_name: Wakelam
- first_name: Olivia
full_name: Casanueva, Olivia
last_name: Casanueva
citation:
ama: Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation
of fat desaturation across tissues to enable adaptation to high temperatures in
C. elegans. 2021. doi:10.5281/ZENODO.5519410
apa: Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H.-J., Lopez-Clavijo,
A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat
desaturation across tissues to enable adaptation to high temperatures in C. elegans.
Zenodo. https://doi.org/10.5281/ZENODO.5519410
chicago: Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh,
Harry-Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1
Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation
to High Temperatures in C. Elegans.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5519410.
ieee: L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat
desaturation across tissues to enable adaptation to high temperatures in C. elegans.”
Zenodo, 2021.
ista: Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann H-J, Lopez-Clavijo A, Okkenhaug
H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe
K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation
of fat desaturation across tissues to enable adaptation to high temperatures in
C. elegans, Zenodo, 10.5281/ZENODO.5519410.
mla: Chauve, Laetitia, et al. Neuronal HSF-1 Coordinates the Propagation of Fat
Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.
Zenodo, 2021, doi:10.5281/ZENODO.5519410.
short: L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.-J. Mann, A. Lopez-Clavijo,
H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger,
K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, (2021).
date_created: 2023-05-23T16:40:56Z
date_published: 2021-12-25T00:00:00Z
date_updated: 2023-08-14T11:53:26Z
day: '25'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.5281/ZENODO.5519410
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5547464
month: '12'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '10322'
relation: used_in_publication
status: public
status: public
title: Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues
to enable adaptation to high temperatures in C. 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: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10325'
abstract:
- lang: eng
text: Since the inception of Bitcoin, a plethora of distributed ledgers differing
in design and purpose has been created. While by design, blockchains provide no
means to securely communicate with external systems, numerous attempts towards
trustless cross-chain communication have been proposed over the years. Today,
cross-chain communication (CCC) plays a fundamental role in cryptocurrency exchanges,
scalability efforts via sharding, extension of existing systems through sidechains,
and bootstrapping of new blockchains. Unfortunately, existing proposals are designed
ad-hoc for specific use-cases, making it hard to gain confidence in their correctness
and composability. We provide the first systematic exposition of cross-chain communication
protocols. We formalize the underlying research problem and show that CCC is impossible
without a trusted third party, contrary to common beliefs in the blockchain community.
With this result in mind, we develop a framework to design new and evaluate existing
CCC protocols, focusing on the inherent trust assumptions thereof, and derive
a classification covering the field of cross-chain communication to date. We conclude
by discussing open challenges for CCC research and the implications of interoperability
on the security and privacy of blockchains.
acknowledgement: 'We would like express our gratitude to Georgia Avarikioti, Daniel
Perez and Dominik Harz for helpful comments and feedback on earlier versions of
this manuscript. We also thank Nicholas Stifter, Aljosha Judmayer, Philipp Schindler,
Edgar Weippl, and Alistair Stewart for insightful discussions during the early stages
of this research. We also wish to thank the anonymous reviewers for their valuable
comments that helped improve the presentation of our results. This research was
funded by Bridge 1 858561 SESC; Bridge 1 864738 PR4DLT (all FFG); the Christian
Doppler Laboratory for Security and Quality Improvement in the Production System
Lifecycle (CDL-SQI); the competence center SBA-K1 funded by COMET; Chaincode Labs
through the project SLN: Scalability for the Lightning Network; and by the Austrian
Science Fund (FWF) through the Meitner program (project M-2608). Mustafa Al-Bassam
is funded by a scholarship from the Alan Turing Institute. Alexei Zamyatin conducted
the early stages of this work during his time at SBA Research, and was supported
by a Binance Research Fellowship.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Alexei
full_name: Zamyatin, Alexei
last_name: Zamyatin
- first_name: Mustafa
full_name: Al-Bassam, Mustafa
last_name: Al-Bassam
- first_name: Dionysis
full_name: Zindros, Dionysis
last_name: Zindros
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Pedro
full_name: Moreno-Sanchez, Pedro
last_name: Moreno-Sanchez
- first_name: Aggelos
full_name: Kiayias, Aggelos
last_name: Kiayias
- first_name: William J.
full_name: Knottenbelt, William J.
last_name: Knottenbelt
citation:
ama: 'Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed
ledgers. In: 25th International Conference on Financial Cryptography and Data
Security. Vol 12675. Springer Nature; 2021:3-36. doi:10.1007/978-3-662-64331-0_1'
apa: 'Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez,
P., Kiayias, A., & Knottenbelt, W. J. (2021). SoK: Communication across distributed
ledgers. In 25th International Conference on Financial Cryptography and Data
Security (Vol. 12675, pp. 3–36). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-64331-0_1'
chicago: 'Zamyatin, Alexei, Mustafa Al-Bassam, Dionysis Zindros, Eleftherios Kokoris
Kogias, Pedro Moreno-Sanchez, Aggelos Kiayias, and William J. Knottenbelt. “SoK:
Communication across Distributed Ledgers.” In 25th International Conference
on Financial Cryptography and Data Security, 12675:3–36. Springer Nature,
2021. https://doi.org/10.1007/978-3-662-64331-0_1.'
ieee: 'A. Zamyatin et al., “SoK: Communication across distributed ledgers,”
in 25th International Conference on Financial Cryptography and Data Security,
Virtual, 2021, vol. 12675, pp. 3–36.'
ista: 'Zamyatin A, Al-Bassam M, Zindros D, Kokoris Kogias E, Moreno-Sanchez P, Kiayias
A, Knottenbelt WJ. 2021. SoK: Communication across distributed ledgers. 25th International
Conference on Financial Cryptography and Data Security. FC: Financial Cryptography,
LNCS, vol. 12675, 3–36.'
mla: 'Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.”
25th International Conference on Financial Cryptography and Data Security,
vol. 12675, Springer Nature, 2021, pp. 3–36, doi:10.1007/978-3-662-64331-0_1.'
short: A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez,
A. Kiayias, W.J. Knottenbelt, in:, 25th International Conference on Financial
Cryptography and Data Security, Springer Nature, 2021, pp. 3–36.
conference:
end_date: 2021-03-05
location: Virtual
name: 'FC: Financial Cryptography'
start_date: 2021-03-01
date_created: 2021-11-21T23:01:29Z
date_published: 2021-10-23T00:00:00Z
date_updated: 2023-08-14T12:59:26Z
day: '23'
department:
- _id: ElKo
doi: 10.1007/978-3-662-64331-0_1
external_id:
isi:
- '000712016200001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2019/1128
month: '10'
oa: 1
oa_version: Preprint
page: 3-36
publication: 25th International Conference on Financial Cryptography and Data Security
publication_identifier:
eisbn:
- 978-3-662-64331-0
eissn:
- 1611-3349
isbn:
- 9-783-6626-4330-3
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'SoK: Communication across distributed ledgers'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: '12675 '
year: '2021'
...
---
_id: '10324'
abstract:
- lang: eng
text: Off-chain protocols (channels) are a promising solution to the scalability
and privacy challenges of blockchain payments. Current proposals, however, require
synchrony assumptions to preserve the safety of a channel, leaking to an adversary
the exact amount of time needed to control the network for a successful attack.
In this paper, we introduce Brick, the first payment channel that remains secure
under network asynchrony and concurrently provides correct incentives. The core
idea is to incorporate the conflict resolution process within the channel by introducing
a rational committee of external parties, called wardens. Hence, if a party wants
to close a channel unilaterally, it can only get the committee’s approval for
the last valid state. Additionally, Brick provides sub-second latency because
it does not employ heavy-weight consensus. Instead, Brick uses consistent broadcast
to announce updates and close the channel, a light-weight abstraction that is
powerful enough to preserve safety and liveness to any rational parties. We formally
define and prove for Brick the properties a payment channel construction should
fulfill. We also design incentives for Brick such that honest and rational behavior
aligns. Finally, we provide a reference implementation of the smart contracts
in Solidity.
acknowledgement: We would like to thank Kaoutar Elkhiyaoui for her valuable feedback
as well as Jakub Sliwinski for his impactful contribution to this work.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Zeta
full_name: Avarikioti, Zeta
last_name: Avarikioti
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Roger
full_name: Wattenhofer, Roger
last_name: Wattenhofer
- first_name: Dionysis
full_name: Zindros, Dionysis
last_name: Zindros
citation:
ama: 'Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous
incentive-compatible payment channels. In: 25th International Conference on
Financial Cryptography and Data Security. Vol 12675. Springer Nature; 2021:209-230.
doi:10.1007/978-3-662-64331-0_11'
apa: 'Avarikioti, Z., Kokoris Kogias, E., Wattenhofer, R., & Zindros, D. (2021).
Brick: Asynchronous incentive-compatible payment channels. In 25th International
Conference on Financial Cryptography and Data Security (Vol. 12675, pp. 209–230).
Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-64331-0_11'
chicago: 'Avarikioti, Zeta, Eleftherios Kokoris Kogias, Roger Wattenhofer, and Dionysis
Zindros. “Brick: Asynchronous Incentive-Compatible Payment Channels.” In 25th
International Conference on Financial Cryptography and Data Security, 12675:209–30.
Springer Nature, 2021. https://doi.org/10.1007/978-3-662-64331-0_11.'
ieee: 'Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick:
Asynchronous incentive-compatible payment channels,” in 25th International
Conference on Financial Cryptography and Data Security, Virtual, 2021, vol.
12675, pp. 209–230.'
ista: 'Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. 2021. Brick: Asynchronous
incentive-compatible payment channels. 25th International Conference on Financial
Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 12675,
209–230.'
mla: 'Avarikioti, Zeta, et al. “Brick: Asynchronous Incentive-Compatible Payment
Channels.” 25th International Conference on Financial Cryptography and Data
Security, vol. 12675, Springer Nature, 2021, pp. 209–30, doi:10.1007/978-3-662-64331-0_11.'
short: Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, D. Zindros, in:, 25th International
Conference on Financial Cryptography and Data Security, Springer Nature, 2021,
pp. 209–230.
conference:
end_date: 2021-03-05
location: Virtual
name: 'FC: Financial Cryptography'
start_date: 2021-03-01
date_created: 2021-11-21T23:01:29Z
date_published: 2021-10-23T00:00:00Z
date_updated: 2023-08-14T12:59:58Z
day: '23'
department:
- _id: ElKo
doi: 10.1007/978-3-662-64331-0_11
external_id:
arxiv:
- '1905.11360'
isi:
- '000712016200011'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1905.11360
month: '10'
oa: 1
oa_version: Preprint
page: 209-230
publication: 25th International Conference on Financial Cryptography and Data Security
publication_identifier:
eisbn:
- 978-3-662-64331-0
eissn:
- 1611-3349
isbn:
- 9-783-6626-4330-3
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Brick: Asynchronous incentive-compatible payment channels'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: '12675 '
year: '2021'
...
---
_id: '10363'
abstract:
- lang: eng
text: Erythropoietin enhances oxygen delivery and reduces hypoxia-induced cell death,
but its pro-thrombotic activity is problematic for use of erythropoietin in treating
hypoxia. We constructed a fusion protein that stimulates red blood cell production
and neuroprotection without triggering platelet production, a marker for thrombosis.
The protein consists of an anti-glycophorin A nanobody and an erythropoietin mutant
(L108A). The mutation reduces activation of erythropoietin receptor homodimers
that induce erythropoiesis and thrombosis, but maintains the tissue-protective
signaling. The binding of the nanobody element to glycophorin A rescues homodimeric
erythropoietin receptor activation on red blood cell precursors. In a cell proliferation
assay, the fusion protein is active at 10−14 M, allowing an estimate of the number
of receptor–ligand complexes needed for signaling. This fusion protein stimulates
erythroid cell proliferation in vitro and in mice, and shows neuroprotective activity
in vitro. Our erythropoietin fusion protein presents a novel molecule for treating
hypoxia.
acknowledgement: This work was supported by funds from the Wyss Institute for Biologically
Inspired Engineering and the Boston Biomedical Innovation Center (Pilot Award 112475;
Drive Award U54HL119145). J.L., K.M.K., D.R.B., J.C.W. and P.A.S. were supported
by the Harvard Medical School Department of Systems Biology. J.C.W. was further
supported by the Harvard Medical School Laboratory of Systems Pharmacology. A.V.,
D.R.B. and P.A.S. were further supported by the Wyss Institute for Biologically
Inspired Engineering. N.G.G. was sponsored by the Army Research Office under Grant
Number W911NF-17-2-0092. The views and conclusions contained in this document are
those of the authors and should not be interpreted as representing the official
policies, either expressed or implied, of the Army Research Office or the U.S. Government.
The U.S. Government is authorized to reproduce and distribute reprints for Government
purposes notwithstanding any copyright notation herein. We sincerely thank Amanda
Graveline and the Wyss Institute at Harvard for their scientific support.
article_number: gzab025
article_processing_charge: No
article_type: original
author:
- first_name: Jungmin
full_name: Lee, Jungmin
last_name: Lee
- first_name: Andyna
full_name: Vernet, Andyna
last_name: Vernet
- first_name: Nathalie
full_name: Gruber, Nathalie
id: 2C9C8316-AA17-11E9-B5C2-8BC2E5697425
last_name: Gruber
- first_name: Kasia M.
full_name: Kready, Kasia M.
last_name: Kready
- first_name: Devin R.
full_name: Burrill, Devin R.
last_name: Burrill
- first_name: Jeffrey C.
full_name: Way, Jeffrey C.
last_name: Way
- first_name: Pamela A.
full_name: Silver, Pamela A.
last_name: Silver
citation:
ama: Lee J, Vernet A, Gruber N, et al. Rational engineering of an erythropoietin
fusion protein to treat hypoxia. Protein Engineering, Design and Selection.
2021;34. doi:10.1093/protein/gzab025
apa: Lee, J., Vernet, A., Gruber, N., Kready, K. M., Burrill, D. R., Way, J. C.,
& Silver, P. A. (2021). Rational engineering of an erythropoietin fusion protein
to treat hypoxia. Protein Engineering, Design and Selection. Oxford University
Press. https://doi.org/10.1093/protein/gzab025
chicago: Lee, Jungmin, Andyna Vernet, Nathalie Gruber, Kasia M. Kready, Devin R.
Burrill, Jeffrey C. Way, and Pamela A. Silver. “Rational Engineering of an Erythropoietin
Fusion Protein to Treat Hypoxia.” Protein Engineering, Design and Selection.
Oxford University Press, 2021. https://doi.org/10.1093/protein/gzab025.
ieee: J. Lee et al., “Rational engineering of an erythropoietin fusion protein
to treat hypoxia,” Protein Engineering, Design and Selection, vol. 34.
Oxford University Press, 2021.
ista: Lee J, Vernet A, Gruber N, Kready KM, Burrill DR, Way JC, Silver PA. 2021.
Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein
Engineering, Design and Selection. 34, gzab025.
mla: Lee, Jungmin, et al. “Rational Engineering of an Erythropoietin Fusion Protein
to Treat Hypoxia.” Protein Engineering, Design and Selection, vol. 34,
gzab025, Oxford University Press, 2021, doi:10.1093/protein/gzab025.
short: J. Lee, A. Vernet, N. Gruber, K.M. Kready, D.R. Burrill, J.C. Way, P.A. Silver,
Protein Engineering, Design and Selection 34 (2021).
date_created: 2021-11-28T23:01:28Z
date_published: 2021-11-01T00:00:00Z
date_updated: 2023-08-14T13:01:38Z
day: '01'
department:
- _id: CaGu
doi: 10.1093/protein/gzab025
external_id:
isi:
- '000746596900001'
pmid:
- '34725710'
intvolume: ' 34'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/protein/gzab025
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Protein Engineering, Design and Selection
publication_identifier:
eissn:
- 1741-0134
issn:
- 1741-0126
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rational engineering of an erythropoietin fusion protein to treat hypoxia
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 34
year: '2021'
...
---
_id: '10366'
article_number: '203758'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Ana Maria
full_name: Lennon, Ana Maria
last_name: Lennon
- first_name: Roberto
full_name: Mayor, Roberto
last_name: Mayor
- first_name: Guillaume
full_name: Salbreux, Guillaume
last_name: Salbreux
citation:
ama: 'Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. Special rebranding issue:
“Quantitative cell and developmental biology.” Cells and Development. 2021;168(12).
doi:10.1016/j.cdev.2021.203758'
apa: 'Heisenberg, C.-P. J., Lennon, A. M., Mayor, R., & Salbreux, G. (2021).
Special rebranding issue: “Quantitative cell and developmental biology.” Cells
and Development. Elsevier. https://doi.org/10.1016/j.cdev.2021.203758'
chicago: 'Heisenberg, Carl-Philipp J, Ana Maria Lennon, Roberto Mayor, and Guillaume
Salbreux. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’”
Cells and Development. Elsevier, 2021. https://doi.org/10.1016/j.cdev.2021.203758.'
ieee: 'C.-P. J. Heisenberg, A. M. Lennon, R. Mayor, and G. Salbreux, “Special rebranding
issue: ‘Quantitative cell and developmental biology,’” Cells and Development,
vol. 168, no. 12. Elsevier, 2021.'
ista: 'Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. 2021. Special rebranding
issue: “Quantitative cell and developmental biology”. Cells and Development. 168(12),
203758.'
mla: 'Heisenberg, Carl-Philipp J., et al. “Special Rebranding Issue: ‘Quantitative
Cell and Developmental Biology.’” Cells and Development, vol. 168, no.
12, 203758, Elsevier, 2021, doi:10.1016/j.cdev.2021.203758.'
short: C.-P.J. Heisenberg, A.M. Lennon, R. Mayor, G. Salbreux, Cells and Development
168 (2021).
date_created: 2021-11-28T23:01:30Z
date_published: 2021-11-17T00:00:00Z
date_updated: 2023-08-14T13:02:40Z
day: '17'
department:
- _id: CaHe
doi: 10.1016/j.cdev.2021.203758
external_id:
isi:
- '000974771600028'
pmid:
- '34800748'
intvolume: ' 168'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cdev.2021.203758
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cells and Development
publication_identifier:
issn:
- 2667-2901
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Special rebranding issue: “Quantitative cell and developmental biology”'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 168
year: '2021'
...
---
_id: '10402'
abstract:
- lang: eng
text: Branching morphogenesis governs the formation of many organs such as lung,
kidney, and the neurovascular system. Many studies have explored system-specific
molecular and cellular regulatory mechanisms, as well as self-organizing rules
underlying branching morphogenesis. However, in addition to local cues, branched
tissue growth can also be influenced by global guidance. Here, we develop a theoretical
framework for a stochastic self-organized branching process in the presence of
external cues. Combining analytical theory with numerical simulations, we predict
differential signatures of global vs. local regulatory mechanisms on the branching
pattern, such as angle distributions, domain size, and space-filling efficiency.
We find that branch alignment follows a generic scaling law determined by the
strength of global guidance, while local interactions influence the tissue density
but not its overall territory. Finally, using zebrafish innervation as a model
system, we test these key features of the model experimentally. Our work thus
provides quantitative predictions to disentangle the role of different types of
cues in shaping branched structures across scales.
acknowledgement: We thank all members of our respective groups for helpful discussion
on the paper. The authors are also grateful to Prof. Abdel El. Manira for support
and sharing Tg(HUC:Gal4;UAS:Synaptohysin-GFP), to Haohao Wu for discussion, and
thank Elena Zabalueva for the zebrafish schematic. The authors also acknowledge
Zebrafish core facility, Genome Engineering Zebrafish and Biomedicum Imaging Core
from the Karolinska Institutet for technical support. This work received funding
from the ERC under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No. 851288 to E.H.) and under the Marie Skłodowska-Curie grant
agreement No. 754411 (to M.C.U.); Swedish Research Council (to F.L., I.A. and S.H.);
Knut and Alice Wallenberg Foundation (F.L. and I.A.); Swedish Brain Foundation (F.L.
and S.H.); Ming Wai Lau Foundation (to F.L.); StratRegen (to F.L.); ERC Consolidator
grant STEMMING-FROM-NERVE and ERC Synergy Grant KILL-OR-DIFFERENTIATE (to I.A.);
Bertil Hallsten Research Foundation (to I.A.); Cancerfonden (to I.A.); the Paradifference
Foundation (to I.A.); Austrian Science Fund (to I.A.); and StratNeuro (to S.H.).
article_number: '6830'
article_processing_charge: No
article_type: original
author:
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
- first_name: Dmitrii
full_name: Kamenev, Dmitrii
last_name: Kamenev
- first_name: Kazunori
full_name: Sunadome, Kazunori
last_name: Sunadome
- first_name: Dominik C
full_name: Fachet, Dominik C
id: 14FDD550-AA41-11E9-A0E5-1ACCE5697425
last_name: Fachet
- first_name: Francois
full_name: Lallemend, Francois
last_name: Lallemend
- first_name: Igor
full_name: Adameyko, Igor
last_name: Adameyko
- first_name: Saida
full_name: Hadjab, Saida
last_name: Hadjab
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Ucar MC, Kamenev D, Sunadome K, et al. Theory of branching morphogenesis by
local interactions and global guidance. Nature Communications. 2021;12.
doi:10.1038/s41467-021-27135-5
apa: Ucar, M. C., Kamenev, D., Sunadome, K., Fachet, D. C., Lallemend, F., Adameyko,
I., … Hannezo, E. B. (2021). Theory of branching morphogenesis by local interactions
and global guidance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-27135-5
chicago: Ucar, Mehmet C, Dmitrii Kamenev, Kazunori Sunadome, Dominik C Fachet, Francois
Lallemend, Igor Adameyko, Saida Hadjab, and Edouard B Hannezo. “Theory of Branching
Morphogenesis by Local Interactions and Global Guidance.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-27135-5.
ieee: M. C. Ucar et al., “Theory of branching morphogenesis by local interactions
and global guidance,” Nature Communications, vol. 12. Springer Nature,
2021.
ista: Ucar MC, Kamenev D, Sunadome K, Fachet DC, Lallemend F, Adameyko I, Hadjab
S, Hannezo EB. 2021. Theory of branching morphogenesis by local interactions and
global guidance. Nature Communications. 12, 6830.
mla: Ucar, Mehmet C., et al. “Theory of Branching Morphogenesis by Local Interactions
and Global Guidance.” Nature Communications, vol. 12, 6830, Springer Nature,
2021, doi:10.1038/s41467-021-27135-5.
short: M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko,
S. Hadjab, E.B. Hannezo, Nature Communications 12 (2021).
date_created: 2021-12-05T23:01:40Z
date_published: 2021-11-24T00:00:00Z
date_updated: 2023-08-14T13:18:46Z
day: '24'
ddc:
- '573'
department:
- _id: EdHa
doi: 10.1038/s41467-021-27135-5
ec_funded: 1
external_id:
isi:
- '000722322900020'
pmid:
- '34819507'
file:
- access_level: open_access
checksum: 63c56ec75314a71e63e7dd2920b3c5b5
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-10T08:54:09Z
date_updated: 2021-12-10T08:54:09Z
file_id: '10529'
file_name: 2021_NatComm_Ucar.pdf
file_size: 2303405
relation: main_file
success: 1
file_date_updated: 2021-12-10T08:54:09Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13058'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Theory of branching morphogenesis by local interactions and global guidance
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '10407'
abstract:
- lang: eng
text: Digital hardware Trojans are integrated circuits whose implementation differ
from the specification in an arbitrary and malicious way. For example, the circuit
can differ from its specified input/output behavior after some fixed number of
queries (known as “time bombs”) or on some particular input (known as “cheat codes”).
To detect such Trojans, countermeasures using multiparty computation (MPC) or
verifiable computation (VC) have been proposed. On a high level, to realize a
circuit with specification F one has more sophisticated circuits F⋄ manufactured
(where F⋄ specifies a MPC or VC of F ), and then embeds these F⋄ ’s into
a master circuit which must be trusted but is relatively simple compared to F
. Those solutions impose a significant overhead as F⋄ is much more complex
than F , also the master circuits are not exactly trivial. In this work, we
show that in restricted settings, where F has no evolving state and is queried
on independent inputs, we can achieve a relaxed security notion using very simple
constructions. In particular, we do not change the specification of the circuit
at all (i.e., F=F⋄ ). Moreover the master circuit basically just queries a subset
of its manufactured circuits and checks if they’re all the same. The security
we achieve guarantees that, if the manufactured circuits are initially tested
on up to T inputs, the master circuit will catch Trojans that try to deviate on
significantly more than a 1/T fraction of the inputs. This bound is optimal for
the type of construction considered, and we provably achieve it using a construction
where 12 instantiations of F need to be embedded into the master. We also discuss
an extremely simple construction with just 2 instantiations for which we conjecture
that it already achieves the optimal bound.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Suvradip
full_name: Chakraborty, Suvradip
id: B9CD0494-D033-11E9-B219-A439E6697425
last_name: Chakraborty
- first_name: Stefan
full_name: Dziembowski, Stefan
last_name: Dziembowski
- first_name: Małgorzata
full_name: Gałązka, Małgorzata
last_name: Gałązka
- first_name: Tomasz
full_name: Lizurej, Tomasz
last_name: Lizurej
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
citation:
ama: 'Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. Trojan-resilience
without cryptography. In: Vol 13043. Springer Nature; 2021:397-428. doi:10.1007/978-3-030-90453-1_14'
apa: 'Chakraborty, S., Dziembowski, S., Gałązka, M., Lizurej, T., Pietrzak, K. Z.,
& Yeo, M. X. (2021). Trojan-resilience without cryptography (Vol. 13043, pp.
397–428). Presented at the TCC: Theory of Cryptography Conference, Raleigh, NC,
United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_14'
chicago: Chakraborty, Suvradip, Stefan Dziembowski, Małgorzata Gałązka, Tomasz Lizurej,
Krzysztof Z Pietrzak, and Michelle X Yeo. “Trojan-Resilience without Cryptography,”
13043:397–428. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_14.
ieee: 'S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K. Z. Pietrzak, and
M. X. Yeo, “Trojan-resilience without cryptography,” presented at the TCC: Theory
of Cryptography Conference, Raleigh, NC, United States, 2021, vol. 13043, pp.
397–428.'
ista: 'Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX.
2021. Trojan-resilience without cryptography. TCC: Theory of Cryptography Conference,
LNCS, vol. 13043, 397–428.'
mla: Chakraborty, Suvradip, et al. Trojan-Resilience without Cryptography.
Vol. 13043, Springer Nature, 2021, pp. 397–428, doi:10.1007/978-3-030-90453-1_14.
short: S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K.Z. Pietrzak, M.X.
Yeo, in:, Springer Nature, 2021, pp. 397–428.
conference:
end_date: 2021-11-11
location: Raleigh, NC, United States
name: 'TCC: Theory of Cryptography Conference'
start_date: 2021-11-08
date_created: 2021-12-05T23:01:42Z
date_published: 2021-11-04T00:00:00Z
date_updated: 2023-08-14T13:07:46Z
day: '04'
department:
- _id: KrPi
doi: 10.1007/978-3-030-90453-1_14
ec_funded: 1
external_id:
isi:
- '000728364000014'
intvolume: ' 13043'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2021/1224
month: '11'
oa: 1
oa_version: Preprint
page: 397-428
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
eissn:
- 1611-3349
isbn:
- 9-783-0309-0452-4
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Trojan-resilience without cryptography
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13043
year: '2021'
...
---
_id: '10403'
abstract:
- lang: eng
text: Synaptic transmission, connectivity, and dendritic morphology mature in parallel
during brain development and are often disrupted in neurodevelopmental disorders.
Yet how these changes influence the neuronal computations necessary for normal
brain function are not well understood. To identify cellular mechanisms underlying
the maturation of synaptic integration in interneurons, we combined patch-clamp
recordings of excitatory inputs in mouse cerebellar stellate cells (SCs), three-dimensional
reconstruction of SC morphology with excitatory synapse location, and biophysical
modeling. We found that postnatal maturation of postsynaptic strength was homogeneously
reduced along the somatodendritic axis, but dendritic integration was always sublinear.
However, dendritic branching increased without changes in synapse density, leading
to a substantial gain in distal inputs. Thus, changes in synapse distribution,
rather than dendrite cable properties, are the dominant mechanism underlying the
maturation of neuronal computation. These mechanisms favor the emergence of a
spatially compartmentalized two-stage integration model promoting location-dependent
integration within dendritic subunits.
acknowledgement: This study was supported by the Centre National de la Recherche Scientifique
and the Agence Nationale de la Recherche (ANR-13-BSV4-00166, to LC and DAD). TA
was supported by fellowships from the Fondation pour la Recherche Medicale and the
Swedish Research Council. We thank Dmitry Ershov from the Image Analysis Hub of
the Institut Pasteur, Elodie Le Monnier, Elena Hollergschwandtner, Vanessa Zheden,
and Corinne Nantet for technical support and Haining Zhong for providing the Venus-tagged
PSD95 mouse line. We would like to thank Alberto Bacci, Ann Lohof, and Nelson Rebola
for comments on the manuscript.
article_number: e65954
article_processing_charge: No
article_type: original
author:
- first_name: Celia
full_name: Biane, Celia
last_name: Biane
- first_name: Florian
full_name: Rückerl, Florian
last_name: Rückerl
- first_name: Therese
full_name: Abrahamsson, Therese
last_name: Abrahamsson
- first_name: Cécile
full_name: Saint-Cloment, Cécile
last_name: Saint-Cloment
- first_name: Jean
full_name: Mariani, Jean
last_name: Mariani
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: David A.
full_name: Digregorio, David A.
last_name: Digregorio
- first_name: Rachel M.
full_name: Sherrard, Rachel M.
last_name: Sherrard
- first_name: Laurence
full_name: Cathala, Laurence
last_name: Cathala
citation:
ama: Biane C, Rückerl F, Abrahamsson T, et al. Developmental emergence of two-stage
nonlinear synaptic integration in cerebellar interneurons. eLife. 2021;10.
doi:10.7554/eLife.65954
apa: Biane, C., Rückerl, F., Abrahamsson, T., Saint-Cloment, C., Mariani, J., Shigemoto,
R., … Cathala, L. (2021). Developmental emergence of two-stage nonlinear synaptic
integration in cerebellar interneurons. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.65954
chicago: Biane, Celia, Florian Rückerl, Therese Abrahamsson, Cécile Saint-Cloment,
Jean Mariani, Ryuichi Shigemoto, David A. Digregorio, Rachel M. Sherrard, and
Laurence Cathala. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration
in Cerebellar Interneurons.” ELife. eLife Sciences Publications, 2021.
https://doi.org/10.7554/eLife.65954.
ieee: C. Biane et al., “Developmental emergence of two-stage nonlinear synaptic
integration in cerebellar interneurons,” eLife, vol. 10. eLife Sciences
Publications, 2021.
ista: Biane C, Rückerl F, Abrahamsson T, Saint-Cloment C, Mariani J, Shigemoto R,
Digregorio DA, Sherrard RM, Cathala L. 2021. Developmental emergence of two-stage
nonlinear synaptic integration in cerebellar interneurons. eLife. 10, e65954.
mla: Biane, Celia, et al. “Developmental Emergence of Two-Stage Nonlinear Synaptic
Integration in Cerebellar Interneurons.” ELife, vol. 10, e65954, eLife
Sciences Publications, 2021, doi:10.7554/eLife.65954.
short: C. Biane, F. Rückerl, T. Abrahamsson, C. Saint-Cloment, J. Mariani, R. Shigemoto,
D.A. Digregorio, R.M. Sherrard, L. Cathala, ELife 10 (2021).
date_created: 2021-12-05T23:01:40Z
date_published: 2021-11-03T00:00:00Z
date_updated: 2023-08-14T13:12:07Z
day: '03'
ddc:
- '570'
department:
- _id: RySh
doi: 10.7554/eLife.65954
external_id:
isi:
- '000715789500001'
file:
- access_level: open_access
checksum: c7c33c3319428d56e332e22349c50ed3
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-10T08:31:41Z
date_updated: 2021-12-10T08:31:41Z
file_id: '10528'
file_name: 2021_eLife_Biane.pdf
file_size: 13131322
relation: main_file
success: 1
file_date_updated: 2021-12-10T08:31:41Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Developmental emergence of two-stage nonlinear synaptic integration in cerebellar
interneurons
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '10401'
abstract:
- lang: eng
text: Theoretical and experimental studies of the interaction between spins and
temperature are vital for the development of spin caloritronics, as they dictate
the design of future devices. In this work, we propose a two-terminal cold-atom
simulator to study that interaction. The proposed quantum simulator consists of
strongly interacting atoms that occupy two temperature reservoirs connected by
a one-dimensional link. First, we argue that the dynamics in the link can be described
using an inhomogeneous Heisenberg spin chain whose couplings are defined by the
local temperature. Second, we show the existence of a spin current in a system
with a temperature difference by studying the dynamics that follows the spin-flip
of an atom in the link. A temperature gradient accelerates the impurity in one
direction more than in the other, leading to an overall spin current similar to
the spin Seebeck effect.
acknowledgement: The authors acknowledge support from the European QuantERA ERA-NET
Cofund in Quantum Technologies (Project QTFLAG Grant Agreement No. 731473) (R.E.B),
CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) Brazil (A.F.),
the European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curie Grant Agreement No. 754411 (A.G.V.), the Independent Research Fund
Denmark, the Carlsberg Foundation, and Aarhus University Research Foundation under
the Jens Christian Skou fellowship program (N.T.Z).
article_number: '252'
article_processing_charge: No
article_type: original
author:
- first_name: Rafael E.
full_name: Barfknecht, Rafael E.
last_name: Barfknecht
- first_name: Angela
full_name: Foerster, Angela
last_name: Foerster
- first_name: Nikolaj T.
full_name: Zinner, Nikolaj T.
last_name: Zinner
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Barfknecht RE, Foerster A, Zinner NT, Volosniev A. Generation of spin currents
by a temperature gradient in a two-terminal device. Communications Physics.
2021;4(1). doi:10.1038/s42005-021-00753-7
apa: Barfknecht, R. E., Foerster, A., Zinner, N. T., & Volosniev, A. (2021).
Generation of spin currents by a temperature gradient in a two-terminal device.
Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-021-00753-7
chicago: Barfknecht, Rafael E., Angela Foerster, Nikolaj T. Zinner, and Artem Volosniev.
“Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.”
Communications Physics. Springer Nature, 2021. https://doi.org/10.1038/s42005-021-00753-7.
ieee: R. E. Barfknecht, A. Foerster, N. T. Zinner, and A. Volosniev, “Generation
of spin currents by a temperature gradient in a two-terminal device,” Communications
Physics, vol. 4, no. 1. Springer Nature, 2021.
ista: Barfknecht RE, Foerster A, Zinner NT, Volosniev A. 2021. Generation of spin
currents by a temperature gradient in a two-terminal device. Communications Physics.
4(1), 252.
mla: Barfknecht, Rafael E., et al. “Generation of Spin Currents by a Temperature
Gradient in a Two-Terminal Device.” Communications Physics, vol. 4, no.
1, 252, Springer Nature, 2021, doi:10.1038/s42005-021-00753-7.
short: R.E. Barfknecht, A. Foerster, N.T. Zinner, A. Volosniev, Communications Physics
4 (2021).
date_created: 2021-12-05T23:01:39Z
date_published: 2021-11-26T00:00:00Z
date_updated: 2023-08-14T13:04:34Z
day: '26'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1038/s42005-021-00753-7
ec_funded: 1
external_id:
arxiv:
- '2101.02020'
isi:
- 10.1038/s42005-021-00753-7
file:
- access_level: open_access
checksum: 9097319952cb9a3d96e7fd3aa9813a03
content_type: application/pdf
creator: alisjak
date_created: 2021-12-06T14:53:41Z
date_updated: 2021-12-06T14:53:41Z
file_id: '10420'
file_name: 2021_NatComm_Barfknecht.pdf
file_size: 1068984
relation: main_file
success: 1
file_date_updated: 2021-12-06T14:53:41Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Communications Physics
publication_identifier:
eissn:
- '23993650'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Generation of spin currents by a temperature gradient in a two-terminal device
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: 4
year: '2021'
...
---
_id: '10404'
abstract:
- lang: eng
text: While convolutional neural networks (CNNs) have found wide adoption as state-of-the-art
models for image-related tasks, their predictions are often highly sensitive to
small input perturbations, which the human vision is robust against. This paper
presents Perturber, a web-based application that allows users to instantaneously
explore how CNN activations and predictions evolve when a 3D input scene is interactively
perturbed. Perturber offers a large variety of scene modifications, such as camera
controls, lighting and shading effects, background modifications, object morphing,
as well as adversarial attacks, to facilitate the discovery of potential vulnerabilities.
Fine-tuned model versions can be directly compared for qualitative evaluation
of their robustness. Case studies with machine learning experts have shown that
Perturber helps users to quickly generate hypotheses about model vulnerabilities
and to qualitatively compare model behavior. Using quantitative analyses, we could
replicate users’ insights with other CNN architectures and input images, yielding
new insights about the vulnerability of adversarially trained models.
acknowledgement: "We thank Robert Geirhos and Roland Zimmermann for their participation
in the case study and valuable feedback, Chris Olah and Nick Cammarata for valuable
discussions in the early phase of the project, as well as the Distill Slack workspace
as a platform for discussions. M.L. is supported in part by the Austrian Science
Fund (FWF) under grant Z211-N23 (Wittgenstein Award). J.B. is supported by the German
Federal Ministry of Education and Research\r\n(BMBF) through the Competence Center
for Machine Learning (TUE.AI, FKZ 01IS18039A) and the International Max Planck Research
School for Intelligent Systems (IMPRS-IS). R.H. is partially supported by Boeing
and Horizon-2020 ECSEL (grant 783163, iDev40).\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Stefan
full_name: Sietzen, Stefan
last_name: Sietzen
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Judy
full_name: Borowski, Judy
last_name: Borowski
- first_name: Ramin
full_name: Hasani, Ramin
last_name: Hasani
- first_name: Manuela
full_name: Waldner, Manuela
last_name: Waldner
citation:
ama: Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. Interactive analysis
of CNN robustness. Computer Graphics Forum. 2021;40(7):253-264. doi:10.1111/cgf.14418
apa: Sietzen, S., Lechner, M., Borowski, J., Hasani, R., & Waldner, M. (2021).
Interactive analysis of CNN robustness. Computer Graphics Forum. Wiley.
https://doi.org/10.1111/cgf.14418
chicago: Sietzen, Stefan, Mathias Lechner, Judy Borowski, Ramin Hasani, and Manuela
Waldner. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum.
Wiley, 2021. https://doi.org/10.1111/cgf.14418.
ieee: S. Sietzen, M. Lechner, J. Borowski, R. Hasani, and M. Waldner, “Interactive
analysis of CNN robustness,” Computer Graphics Forum, vol. 40, no. 7. Wiley,
pp. 253–264, 2021.
ista: Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. 2021. Interactive analysis
of CNN robustness. Computer Graphics Forum. 40(7), 253–264.
mla: Sietzen, Stefan, et al. “Interactive Analysis of CNN Robustness.” Computer
Graphics Forum, vol. 40, no. 7, Wiley, 2021, pp. 253–64, doi:10.1111/cgf.14418.
short: S. Sietzen, M. Lechner, J. Borowski, R. Hasani, M. Waldner, Computer Graphics
Forum 40 (2021) 253–264.
date_created: 2021-12-05T23:01:40Z
date_published: 2021-11-27T00:00:00Z
date_updated: 2023-08-14T13:11:42Z
day: '27'
department:
- _id: ToHe
doi: 10.1111/cgf.14418
external_id:
arxiv:
- '2110.07667'
isi:
- '000722952000024'
intvolume: ' 40'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2110.07667
month: '11'
oa: 1
oa_version: Preprint
page: 253-264
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Computer Graphics Forum
publication_identifier:
eissn:
- 1467-8659
issn:
- 0167-7055
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interactive analysis of CNN robustness
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2021'
...