---
_id: '14798'
abstract:
- lang: eng
text: 'A faithful reproduction of gloss is inherently difficult because of the limited
dynamic range, peak luminance, and 3D capabilities of display devices. This work
investigates how the display capabilities affect gloss appearance with respect
to a real-world reference object. To this end, we employ an accurate imaging pipeline
to achieve a perceptual gloss match between a virtual and real object presented
side-by-side on an augmented-reality high-dynamic-range (HDR) stereoscopic display,
which has not been previously attained to this extent. Based on this precise gloss
reproduction, we conduct a series of gloss matching experiments to study how gloss
perception degrades based on individual factors: object albedo, display luminance,
dynamic range, stereopsis, and tone mapping. We support the study with a detailed
analysis of individual factors, followed by an in-depth discussion on the observed
perceptual effects. Our experiments demonstrate that stereoscopic presentation
has a limited effect on the gloss matching task on our HDR display. However, both
reduced luminance and dynamic range of the display reduce the perceived gloss.
This means that the visual system cannot compensate for the changes in gloss appearance
across luminance (lack of gloss constancy), and the tone mapping operator should
be carefully selected when reproducing gloss on a low dynamic range (LDR) display.'
acknowledgement: "This work is supported by FWF Lise Meitner (Grant M 3319), Spanish
Agencia Estatal de Investigación (project PID2022-141539NBI00), European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement\r\nN◦ 725253–EyeCode), Swiss National Science Foundation (Grant
no. 200502), and academic gifts from Meta. We thank Dmitry Lubyako and Ali Özgür
Yöntem for building the turntable for our experiment."
article_number: '90'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Bin
full_name: Chen, Bin
last_name: Chen
- first_name: Akshay
full_name: Jindal, Akshay
last_name: Jindal
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
orcid: 0000-0002-5062-4474
- first_name: Chao
full_name: Wang, Chao
last_name: Wang
- 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
- first_name: Ana
full_name: Serrano, Ana
last_name: Serrano
- first_name: Rafał K.
full_name: Mantiuk, Rafał K.
last_name: Mantiuk
citation:
ama: 'Chen B, Jindal A, Piovarci M, et al. The effect of display capabilities on
the gloss consistency between real and virtual objects. In: Proceedings of
the SIGGRAPH Asia 2023 Conference. Association for Computing Machinery; 2023.
doi:10.1145/3610548.3618226'
apa: 'Chen, B., Jindal, A., Piovarci, M., Wang, C., Seidel, H. P., Didyk, P., …
Mantiuk, R. K. (2023). The effect of display capabilities on the gloss consistency
between real and virtual objects. In Proceedings of the SIGGRAPH Asia 2023
Conference. Sydney, Australia: Association for Computing Machinery. https://doi.org/10.1145/3610548.3618226'
chicago: Chen, Bin, Akshay Jindal, Michael Piovarci, Chao Wang, Hans Peter Seidel,
Piotr Didyk, Karol Myszkowski, Ana Serrano, and Rafał K. Mantiuk. “The Effect
of Display Capabilities on the Gloss Consistency between Real and Virtual Objects.”
In Proceedings of the SIGGRAPH Asia 2023 Conference. Association for Computing
Machinery, 2023. https://doi.org/10.1145/3610548.3618226.
ieee: B. Chen et al., “The effect of display capabilities on the gloss consistency
between real and virtual objects,” in Proceedings of the SIGGRAPH Asia 2023
Conference, Sydney, Australia, 2023.
ista: 'Chen B, Jindal A, Piovarci M, Wang C, Seidel HP, Didyk P, Myszkowski K, Serrano
A, Mantiuk RK. 2023. The effect of display capabilities on the gloss consistency
between real and virtual objects. Proceedings of the SIGGRAPH Asia 2023 Conference.
SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 90.'
mla: Chen, Bin, et al. “The Effect of Display Capabilities on the Gloss Consistency
between Real and Virtual Objects.” Proceedings of the SIGGRAPH Asia 2023 Conference,
90, Association for Computing Machinery, 2023, doi:10.1145/3610548.3618226.
short: B. Chen, A. Jindal, M. Piovarci, C. Wang, H.P. Seidel, P. Didyk, K. Myszkowski,
A. Serrano, R.K. Mantiuk, in:, Proceedings of the SIGGRAPH Asia 2023 Conference,
Association for Computing Machinery, 2023.
conference:
end_date: 2023-12-15
location: Sydney, Australia
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference'
start_date: 2023-12-12
date_created: 2024-01-14T23:00:57Z
date_published: 2023-12-10T00:00:00Z
date_updated: 2024-01-17T08:38:35Z
day: '10'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3610548.3618226
file:
- access_level: open_access
checksum: 8abe27432ed222b50d1af9b3388db1b0
content_type: application/pdf
creator: dernst
date_created: 2024-01-17T08:33:06Z
date_updated: 2024-01-17T08:33:06Z
file_id: '14823'
file_name: 2023_SA_Chen.pdf
file_size: 95967451
relation: main_file
success: 1
file_date_updated: 2024-01-17T08:33:06Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: eb901961-77a9-11ec-83b8-f5c883a62027
grant_number: M03319
name: Perception-Aware Appearance Fabrication
publication: Proceedings of the SIGGRAPH Asia 2023 Conference
publication_identifier:
isbn:
- '9798400703157'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: The effect of display capabilities on the gloss consistency between real and
virtual objects
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14815'
abstract:
- lang: eng
text: In the last few years, various communication compression techniques have emerged
as an indispensable tool helping to alleviate the communication bottleneck in
distributed learning. However, despite the fact biased compressors often show
superior performance in practice when compared to the much more studied and understood
unbiased compressors, very little is known about them. In this work we study three
classes of biased compression operators, two of which are new, and their performance
when applied to (stochastic) gradient descent and distributed (stochastic) gradient
descent. We show for the first time that biased compressors can lead to linear
convergence rates both in the single node and distributed settings. We prove that
distributed compressed SGD method, employed with error feedback mechanism, enjoys
the ergodic rate O(δLexp[−μKδL]+(C+δD)Kμ), where δ≥1 is a compression parameter
which grows when more compression is applied, L and μ are the smoothness and strong
convexity constants, C captures stochastic gradient noise (C=0 if full gradients
are computed on each node) and D captures the variance of the gradients at the
optimum (D=0 for over-parameterized models). Further, via a theoretical study
of several synthetic and empirical distributions of communicated gradients, we
shed light on why and by how much biased compressors outperform their unbiased
variants. Finally, we propose several new biased compressors with promising theoretical
guarantees and practical performance.
acknowledgement: 'The work in Sections 1-5 was conducted while A. Beznosikov was a
research intern in the Optimizationand Machine Learning Lab of Peter Richtárik at
KAUST; this visit was funded by the KAUST Baseline Research Funding Scheme. The
work of A. Beznosikov in Section 6 was conducted in Skoltech and was supported by
Ministry of Science and Higher Education grant No. 075-10-2021-068. '
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Aleksandr
full_name: Beznosikov, Aleksandr
last_name: Beznosikov
- first_name: Samuel
full_name: Horvath, Samuel
last_name: Horvath
- first_name: Peter
full_name: Richtarik, Peter
last_name: Richtarik
- first_name: Mher
full_name: Safaryan, Mher
id: dd546b39-0804-11ed-9c55-ef075c39778d
last_name: Safaryan
citation:
ama: Beznosikov A, Horvath S, Richtarik P, Safaryan M. On biased compression for
distributed learning. Journal of Machine Learning Research. 2023;24:1-50.
apa: Beznosikov, A., Horvath, S., Richtarik, P., & Safaryan, M. (2023). On biased
compression for distributed learning. Journal of Machine Learning Research.
Journal of Machine Learning Research.
chicago: Beznosikov, Aleksandr, Samuel Horvath, Peter Richtarik, and Mher Safaryan.
“On Biased Compression for Distributed Learning.” Journal of Machine Learning
Research. Journal of Machine Learning Research, 2023.
ieee: A. Beznosikov, S. Horvath, P. Richtarik, and M. Safaryan, “On biased compression
for distributed learning,” Journal of Machine Learning Research, vol. 24.
Journal of Machine Learning Research, pp. 1–50, 2023.
ista: Beznosikov A, Horvath S, Richtarik P, Safaryan M. 2023. On biased compression
for distributed learning. Journal of Machine Learning Research. 24, 1–50.
mla: Beznosikov, Aleksandr, et al. “On Biased Compression for Distributed Learning.”
Journal of Machine Learning Research, vol. 24, Journal of Machine Learning
Research, 2023, pp. 1–50.
short: A. Beznosikov, S. Horvath, P. Richtarik, M. Safaryan, Journal of Machine
Learning Research 24 (2023) 1–50.
date_created: 2024-01-16T12:13:36Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-01-17T09:14:13Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
external_id:
arxiv:
- '2002.12410'
isi:
- '001111578500001'
file:
- access_level: open_access
checksum: c50f2b9db53938b755e30a085f464059
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T12:13:27Z
date_updated: 2024-01-16T12:13:27Z
file_id: '14816'
file_name: 2023_JMLR_Beznosikov.pdf
file_size: 1510993
relation: main_file
success: 1
file_date_updated: 2024-01-16T12:13:27Z
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1-50
publication: Journal of Machine Learning Research
publication_identifier:
eissn:
- 1533-7928
publication_status: published
publisher: Journal of Machine Learning Research
quality_controlled: '1'
status: public
title: On biased compression for distributed learning
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2023'
...
---
_id: '14456'
abstract:
- lang: eng
text: In this paper, we present novel algorithms that efficiently compute a shortest
reconfiguration sequence between two given dominating sets in trees and interval
graphs under the TOKEN SLIDING model. In this problem, a graph is provided along
with its two dominating sets, which can be imagined as tokens placed on vertices.
The objective is to find a shortest sequence of dominating sets that transforms
one set into the other, with each set in the sequence resulting from sliding a
single token in the previous set. While identifying any sequence has been well
studied, our work presents the first polynomial algorithms for this optimization
variant in the context of dominating sets.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Jan Matyáš
full_name: Křišťan, Jan Matyáš
last_name: Křišťan
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
citation:
ama: 'Křišťan JM, Svoboda J. Shortest dominating set reconfiguration under token
sliding. In: 24th International Symposium on Fundamentals of Computation Theory.
Vol 14292. Springer Nature; 2023:333-347. doi:10.1007/978-3-031-43587-4_24'
apa: 'Křišťan, J. M., & Svoboda, J. (2023). Shortest dominating set reconfiguration
under token sliding. In 24th International Symposium on Fundamentals of Computation
Theory (Vol. 14292, pp. 333–347). Trier, Germany: Springer Nature. https://doi.org/10.1007/978-3-031-43587-4_24'
chicago: Křišťan, Jan Matyáš, and Jakub Svoboda. “Shortest Dominating Set Reconfiguration
under Token Sliding.” In 24th International Symposium on Fundamentals of Computation
Theory, 14292:333–47. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-43587-4_24.
ieee: J. M. Křišťan and J. Svoboda, “Shortest dominating set reconfiguration under
token sliding,” in 24th International Symposium on Fundamentals of Computation
Theory, Trier, Germany, 2023, vol. 14292, pp. 333–347.
ista: 'Křišťan JM, Svoboda J. 2023. Shortest dominating set reconfiguration under
token sliding. 24th International Symposium on Fundamentals of Computation Theory.
FCT: Fundamentals of Computation Theory, LNCS, vol. 14292, 333–347.'
mla: Křišťan, Jan Matyáš, and Jakub Svoboda. “Shortest Dominating Set Reconfiguration
under Token Sliding.” 24th International Symposium on Fundamentals of Computation
Theory, vol. 14292, Springer Nature, 2023, pp. 333–47, doi:10.1007/978-3-031-43587-4_24.
short: J.M. Křišťan, J. Svoboda, in:, 24th International Symposium on Fundamentals
of Computation Theory, Springer Nature, 2023, pp. 333–347.
conference:
end_date: 2023-09-21
location: Trier, Germany
name: 'FCT: Fundamentals of Computation Theory'
start_date: 2023-09-18
date_created: 2023-10-29T23:01:16Z
date_published: 2023-09-21T00:00:00Z
date_updated: 2024-01-22T08:10:49Z
day: '21'
department:
- _id: KrCh
doi: 10.1007/978-3-031-43587-4_24
external_id:
arxiv:
- '2307.10847'
intvolume: ' 14292'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2307.10847
month: '09'
oa: 1
oa_version: Preprint
page: 333-347
publication: 24th International Symposium on Fundamentals of Computation Theory
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031435867'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/978-3-031-43587-4_31
scopus_import: '1'
status: public
title: Shortest dominating set reconfiguration under token sliding
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14292
year: '2023'
...
---
_id: '14829'
abstract:
- lang: eng
text: 'This paper explores a modular design architecture aimed at helping blockchains
(and other SMR implementation) to scale to a very large number of processes. This
comes in contrast to existing monolithic architectures that interleave transaction
dissemination, ordering, and execution in a single functionality. To achieve this
we first split the monolith to multiple layers which can use existing distributed
computing primitives. The exact specifications of the data dissemination part
are formally defined by the Proof of Availability & Retrieval (PoA &R) abstraction.
Solutions to the PoA &R problem contain two related sub-protocols: one that “pushes”
information into the network and another that “pulls” this information. Regarding
the latter, there is a dearth of research literature which is rectified in this
paper. We present a family of pulling sub-protocols and rigorously analyze them.
Extensive simulations support the theoretical claims of efficiency and robustness
in case of a very large number of players. Finally, actual implementation and
deployment on a small number of machines (roughly the size of several industrial
systems) demonstrates the viability of the architecture’s paradigm.'
acknowledgement: 'This work is partially supported by Meta. Eleftherios Kokoris-Kogias
is partially supported by Austrian Science Fund (FWF) grant No: F8512-N. Shir Cohen
is supported by the Adams Fellowship Program of the Israel Academy of Sciences and
Humanities.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Shir
full_name: Cohen, Shir
last_name: Cohen
- first_name: Guy
full_name: Goren, Guy
last_name: Goren
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Alberto
full_name: Sonnino, Alberto
last_name: Sonnino
- first_name: Alexander
full_name: Spiegelman, Alexander
last_name: Spiegelman
citation:
ama: 'Cohen S, Goren G, Kokoris Kogias E, Sonnino A, Spiegelman A. Proof of availability
and retrieval in a modular blockchain architecture. In: 27th International
Conference on Financial Cryptography and Data Security. Vol 13951. Springer
Nature; 2023:36-53. doi:10.1007/978-3-031-47751-5_3'
apa: 'Cohen, S., Goren, G., Kokoris Kogias, E., Sonnino, A., & Spiegelman, A.
(2023). Proof of availability and retrieval in a modular blockchain architecture.
In 27th International Conference on Financial Cryptography and Data Security
(Vol. 13951, pp. 36–53). Bol, Brac, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-47751-5_3'
chicago: Cohen, Shir, Guy Goren, Eleftherios Kokoris Kogias, Alberto Sonnino, and
Alexander Spiegelman. “Proof of Availability and Retrieval in a Modular Blockchain
Architecture.” In 27th International Conference on Financial Cryptography and
Data Security, 13951:36–53. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-47751-5_3.
ieee: S. Cohen, G. Goren, E. Kokoris Kogias, A. Sonnino, and A. Spiegelman, “Proof
of availability and retrieval in a modular blockchain architecture,” in 27th
International Conference on Financial Cryptography and Data Security, Bol,
Brac, Croatia, 2023, vol. 13951, pp. 36–53.
ista: 'Cohen S, Goren G, Kokoris Kogias E, Sonnino A, Spiegelman A. 2023. Proof
of availability and retrieval in a modular blockchain architecture. 27th International
Conference on Financial Cryptography and Data Security. FC: Financial Cryptography
and Data Security, LNCS, vol. 13951, 36–53.'
mla: Cohen, Shir, et al. “Proof of Availability and Retrieval in a Modular Blockchain
Architecture.” 27th International Conference on Financial Cryptography and
Data Security, vol. 13951, Springer Nature, 2023, pp. 36–53, doi:10.1007/978-3-031-47751-5_3.
short: S. Cohen, G. Goren, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, in:, 27th
International Conference on Financial Cryptography and Data Security, Springer
Nature, 2023, pp. 36–53.
conference:
end_date: 2023-05-05
location: Bol, Brac, Croatia
name: 'FC: Financial Cryptography and Data Security'
start_date: 2023-05-01
date_created: 2024-01-18T07:41:12Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-01-22T13:58:07Z
day: '01'
department:
- _id: ElKo
doi: 10.1007/978-3-031-47751-5_3
intvolume: ' 13951'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://fc23.ifca.ai/preproceedings/150.pdf
month: '12'
oa: 1
oa_version: Submitted Version
page: 36-53
project:
- _id: 34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f
grant_number: F8512
name: Secure Network and Hardware for Efficient Blockchains
publication: 27th International Conference on Financial Cryptography and Data Security
publication_identifier:
eisbn:
- '9783031477515'
eissn:
- 1611-3349
isbn:
- '9783031477508'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Proof of availability and retrieval in a modular blockchain architecture
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13951
year: '2023'
...
---
_id: '14833'
abstract:
- lang: eng
text: Understanding the factors that have shaped the current distributions and diversity
of species is a central and longstanding aim of evolutionary biology. The recent
inclusion of genomic data into phylogeographic studies has dramatically improved
our understanding in organisms where evolutionary relationships have been challenging
to infer. We used whole-genome sequences to study the phylogeography of the intertidal
snail Littorina saxatilis, which has successfully colonized and diversified across
a broad range of coastal environments in the Northern Hemisphere amid repeated
cycles of glaciation. Building on past studies based on short DNA sequences, we
used genome-wide data to provide a clearer picture of the relationships among
samples spanning most of the species natural range. Our results confirm the trans-Atlantic
colonization of North America from Europe, and have allowed us to identify rough
locations of glacial refugia and to infer likely routes of colonization within
Europe. We also investigated the signals in different datasets to account for
the effects of genomic architecture and non-neutral evolution, which provides
new insights about diversification of four ecotypes of L. saxatilis (the crab,
wave, barnacle, and brackish ecotypes) at different spatial scales. Overall, we
provide a much clearer picture of the biogeography of L. saxatilis, providing
a foundation for more detailed phylogenomic and demographic studies.
acknowledgement: Isobel Eyres, Richard Turney, Graciela Sotelo, Jenny Larson, and
Stéphane Loisel helped with the collection and processing of samples. Petri Kemppainen
kindly provided samples from Trondheim Fjord. Mark Dunning helped with the development
of bioinformatic pipelines. The analysis of genomic data was conducted on the University
of Sheffield high-performance computing cluster, ShARC. Funding was provided by
the Natural Environment Research Council (NERC) and the European Research Council
(ERC). J.G. was funded by a Juntas Industriales y Navales (JIN) project (Ministerio
de Ciencia, Innovación y Universidades, code RTI2018-101274-J-I00).
article_number: kzad002
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Zuzanna B
full_name: Zagrodzka, Zuzanna B
last_name: Zagrodzka
- first_name: Juan
full_name: Galindo, Juan
last_name: Galindo
- first_name: Mauricio
full_name: Montaño-Rendón, Mauricio
last_name: Montaño-Rendón
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Natalia
full_name: Mikhailova, Natalia
last_name: Mikhailova
- first_name: April M H
full_name: Blakeslee, April M H
last_name: Blakeslee
- first_name: Einar
full_name: Arnason, Einar
last_name: Arnason
- first_name: Thomas
full_name: Broquet, Thomas
last_name: Broquet
- first_name: Hernán E
full_name: Morales, Hernán E
last_name: Morales
- first_name: John W
full_name: Grahame, John W
last_name: Grahame
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K
full_name: Butlin, Roger K
last_name: Butlin
citation:
ama: Stankowski S, Zagrodzka ZB, Galindo J, et al. Whole-genome phylogeography of
the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean
Society. 2023;2(1). doi:10.1093/evolinnean/kzad002
apa: Stankowski, S., Zagrodzka, Z. B., Galindo, J., Montaño-Rendón, M., Faria, R.,
Mikhailova, N., … Butlin, R. K. (2023). Whole-genome phylogeography of the intertidal
snail Littorina saxatilis. Evolutionary Journal of the Linnean Society.
Oxford University Press. https://doi.org/10.1093/evolinnean/kzad002
chicago: Stankowski, Sean, Zuzanna B Zagrodzka, Juan Galindo, Mauricio Montaño-Rendón,
Rui Faria, Natalia Mikhailova, April M H Blakeslee, et al. “Whole-Genome Phylogeography
of the Intertidal Snail Littorina Saxatilis.” Evolutionary Journal of the Linnean
Society. Oxford University Press, 2023. https://doi.org/10.1093/evolinnean/kzad002.
ieee: S. Stankowski et al., “Whole-genome phylogeography of the intertidal
snail Littorina saxatilis,” Evolutionary Journal of the Linnean Society,
vol. 2, no. 1. Oxford University Press, 2023.
ista: Stankowski S, Zagrodzka ZB, Galindo J, Montaño-Rendón M, Faria R, Mikhailova
N, Blakeslee AMH, Arnason E, Broquet T, Morales HE, Grahame JW, Westram AM, Johannesson
K, Butlin RK. 2023. Whole-genome phylogeography of the intertidal snail Littorina
saxatilis. Evolutionary Journal of the Linnean Society. 2(1), kzad002.
mla: Stankowski, Sean, et al. “Whole-Genome Phylogeography of the Intertidal Snail
Littorina Saxatilis.” Evolutionary Journal of the Linnean Society, vol.
2, no. 1, kzad002, Oxford University Press, 2023, doi:10.1093/evolinnean/kzad002.
short: S. Stankowski, Z.B. Zagrodzka, J. Galindo, M. Montaño-Rendón, R. Faria, N.
Mikhailova, A.M.H. Blakeslee, E. Arnason, T. Broquet, H.E. Morales, J.W. Grahame,
A.M. Westram, K. Johannesson, R.K. Butlin, Evolutionary Journal of the Linnean
Society 2 (2023).
date_created: 2024-01-18T07:54:10Z
date_published: 2023-08-17T00:00:00Z
date_updated: 2024-01-23T08:13:43Z
day: '17'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/evolinnean/kzad002
file:
- access_level: open_access
checksum: ba6f9102d3a9fe6631c4fa398c5e4313
content_type: application/pdf
creator: dernst
date_created: 2024-01-23T08:10:00Z
date_updated: 2024-01-23T08:10:00Z
file_id: '14875'
file_name: 2023_EvolJourLinneanSociety_Stankowski.pdf
file_size: 3408944
relation: main_file
success: 1
file_date_updated: 2024-01-23T08:10:00Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '08'
oa: 1
oa_version: Published Version
publication: Evolutionary Journal of the Linnean Society
publication_identifier:
eissn:
- 2752-938X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Whole-genome phylogeography of the intertidal snail Littorina saxatilis
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2023'
...
---
_id: '14831'
abstract:
- lang: eng
text: Catalysis, the acceleration of product formation by a substance that is left
unchanged, typically results from multiple elementary processes, including diffusion
of the reactants toward the catalyst, chemical steps, and release of the products.
While efforts to design catalysts are often focused on accelerating the chemical
reaction on the catalyst, catalysis is a global property of the catalytic cycle
that involves all processes. These are controlled by both intrinsic parameters
such as the composition and shape of the catalyst and extrinsic parameters such
as the concentration of the chemical species at play. We examine here the conditions
that catalysis imposes on the different steps of a reaction cycle and the respective
role of intrinsic and extrinsic parameters of the system on the emergence of catalysis
by using an approach based on first-passage times. We illustrate this approach
for various decompositions of a catalytic cycle into elementary steps, including
non-Markovian decompositions, which are useful when the presence and nature of
intermediate states are a priori unknown. Our examples cover different types of
reactions and clarify the constraints on elementary steps and the impact of species
concentrations on catalysis.
acknowledgement: We acknowledge funding from ANR-22-CE06-0037-02. This work has received
funding from the European Unions Horizon 2020 research and innovation program under
the Marie Sklodowska-Curie grant agreement No. 754387.
article_processing_charge: No
article_type: original
author:
- first_name: Yann
full_name: Sakref, Yann
last_name: Sakref
- first_name: Maitane
full_name: Muñoz Basagoiti, Maitane
id: 1a8a7950-82cd-11ed-bd4f-9624c913a607
last_name: Muñoz Basagoiti
orcid: 0000-0003-1483-1457
- first_name: Zorana
full_name: Zeravcic, Zorana
last_name: Zeravcic
- first_name: Olivier
full_name: Rivoire, Olivier
last_name: Rivoire
citation:
ama: Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. On kinetic constraints
that catalysis imposes on elementary processes. The Journal of Physical Chemistry
B. 2023;127(51):10950-10959. doi:10.1021/acs.jpcb.3c04627
apa: Sakref, Y., Muñoz Basagoiti, M., Zeravcic, Z., & Rivoire, O. (2023). On
kinetic constraints that catalysis imposes on elementary processes. The Journal
of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/acs.jpcb.3c04627
chicago: Sakref, Yann, Maitane Muñoz Basagoiti, Zorana Zeravcic, and Olivier Rivoire.
“On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” The
Journal of Physical Chemistry B. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpcb.3c04627.
ieee: Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, and O. Rivoire, “On kinetic constraints
that catalysis imposes on elementary processes,” The Journal of Physical Chemistry
B, vol. 127, no. 51. American Chemical Society, pp. 10950–10959, 2023.
ista: Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. 2023. On kinetic constraints
that catalysis imposes on elementary processes. The Journal of Physical Chemistry
B. 127(51), 10950–10959.
mla: Sakref, Yann, et al. “On Kinetic Constraints That Catalysis Imposes on Elementary
Processes.” The Journal of Physical Chemistry B, vol. 127, no. 51, American
Chemical Society, 2023, pp. 10950–59, doi:10.1021/acs.jpcb.3c04627.
short: Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, O. Rivoire, The Journal of Physical
Chemistry B 127 (2023) 10950–10959.
date_created: 2024-01-18T07:47:11Z
date_published: 2023-12-13T00:00:00Z
date_updated: 2024-01-23T07:58:27Z
day: '13'
department:
- _id: AnSa
doi: 10.1021/acs.jpcb.3c04627
external_id:
arxiv:
- '2312.15940'
isi:
- '001134068000001'
intvolume: ' 127'
isi: 1
issue: '51'
keyword:
- Materials Chemistry
- Surfaces
- Coatings and Films
- Physical and Theoretical Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2312.15940
month: '12'
oa: 1
oa_version: Preprint
page: 10950-10959
publication: The Journal of Physical Chemistry B
publication_identifier:
eissn:
- 1520-5207
issn:
- 1520-6106
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: On kinetic constraints that catalysis imposes on elementary processes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 127
year: '2023'
...
---
_id: '14844'
abstract:
- lang: eng
text: 'Many cell functions require a concerted effort from multiple membrane proteins,
for example, for signaling, cell division, and endocytosis. One contribution to
their successful self-organization stems from the membrane deformations that these
proteins induce. While the pairwise interaction potential of two membrane-deforming
spheres has recently been measured, membrane-deformation-induced interactions
have been predicted to be nonadditive, and hence their collective behavior cannot
be deduced from this measurement. We here employ a colloidal model system consisting
of adhesive spheres and giant unilamellar vesicles to test these predictions by
measuring the interaction potential of the simplest case of three membrane-deforming,
spherical particles. We quantify their interactions and arrangements and, for
the first time, experimentally confirm and quantify the nonadditive nature of
membrane-deformation-induced interactions. We furthermore conclude that there
exist two favorable configurations on the membrane: (1) a linear and (2) a triangular
arrangement of the three spheres. Using Monte Carlo simulations, we corroborate
the experimentally observed energy minima and identify a lowering of the membrane
deformation as the cause for the observed configurations. The high symmetry of
the preferred arrangements for three particles suggests that arrangements of many
membrane-deforming objects might follow simple rules.'
acknowledgement: We gratefully acknowledge useful discussions with Casper van der
Wel, help by Yogesh Shelke with PAA coverslip preparation, and support by Rachel
Doherty with particle functionalization. A.A. and D.J.K. would like to thank Timon
Idema and George Dadunashvili for initial attempts to simulate the experimental
system. D.J.K. would like to thank the physics department at Leiden University for
funding the PhD position of A.A. B.M. and A.Š. acknowledge funding by the European
Union’s Horizon 2020 research and innovation programme (ERC starting grant no. 802960).
article_processing_charge: No
article_type: original
author:
- first_name: Ali
full_name: Azadbakht, Ali
last_name: Azadbakht
- first_name: Billie
full_name: Meadowcroft, Billie
id: a4725fd6-932b-11ed-81e2-c098c7f37ae1
last_name: Meadowcroft
orcid: 0000-0003-3441-1337
- first_name: Juraj
full_name: Majek, Juraj
id: 3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1
last_name: Majek
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Daniela J.
full_name: Kraft, Daniela J.
last_name: Kraft
citation:
ama: Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions
between three membrane-wrapped colloidal spheres. Biophysical Journal.
doi:10.1016/j.bpj.2023.12.020
apa: Azadbakht, A., Meadowcroft, B., Majek, J., Šarić, A., & Kraft, D. J. (n.d.).
Nonadditivity in interactions between three membrane-wrapped colloidal spheres.
Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2023.12.020
chicago: Azadbakht, Ali, Billie Meadowcroft, Juraj Majek, Anđela Šarić, and Daniela
J. Kraft. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal
Spheres.” Biophysical Journal. Elsevier, n.d. https://doi.org/10.1016/j.bpj.2023.12.020.
ieee: A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, and D. J. Kraft, “Nonadditivity
in interactions between three membrane-wrapped colloidal spheres,” Biophysical
Journal. Elsevier.
ista: Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions
between three membrane-wrapped colloidal spheres. Biophysical Journal.
mla: Azadbakht, Ali, et al. “Nonadditivity in Interactions between Three Membrane-Wrapped
Colloidal Spheres.” Biophysical Journal, Elsevier, doi:10.1016/j.bpj.2023.12.020.
short: A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, D.J. Kraft, Biophysical
Journal (n.d.).
date_created: 2024-01-21T23:00:56Z
date_published: 2023-12-29T00:00:00Z
date_updated: 2024-01-23T09:26:35Z
day: '29'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1016/j.bpj.2023.12.020
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.bpj.2023.12.020
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Biophysical Journal
publication_identifier:
eissn:
- 1542-0086
issn:
- 0006-3495
publication_status: inpress
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nonadditivity in interactions between three membrane-wrapped colloidal spheres
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14861'
abstract:
- lang: eng
text: Cover Page
article_number: ' e202304138'
article_processing_charge: No
author:
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
- first_name: Mélanie
full_name: Berbon, Mélanie
last_name: Berbon
- first_name: Alicia
full_name: Vallet, Alicia
last_name: Vallet
- first_name: Axelle
full_name: Grelard, Axelle
last_name: Grelard
- first_name: Estelle
full_name: Morvan, Estelle
last_name: Morvan
- first_name: Benjamin
full_name: Bardiaux, Benjamin
last_name: Bardiaux
- first_name: Roman
full_name: Lichtenecker, Roman
last_name: Lichtenecker
- first_name: Matthias
full_name: Ernst, Matthias
last_name: Ernst
- first_name: Antoine
full_name: Loquet, Antoine
last_name: Loquet
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Becker LM, Berbon M, Vallet A, et al. Cover Picture: The Rigid Core and
Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy
of Aromatic Residues. Vol 62. Wiley; 2023. doi:10.1002/anie.202304138'
apa: 'Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux,
B., … Schanda, P. (2023). Cover Picture: The rigid core and flexible surface
of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic
residues. Angewandte Chemie International Edition (Vol. 62). Wiley.
https://doi.org/10.1002/anie.202304138'
chicago: 'Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle
Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet,
and Paul Schanda. Cover Picture: The Rigid Core and Flexible Surface of Amyloid
Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues.
Angewandte Chemie International Edition. Vol. 62. Wiley, 2023. https://doi.org/10.1002/anie.202304138.'
ieee: 'L. M. Becker et al., Cover Picture: The rigid core and flexible
surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of
aromatic residues, vol. 62, no. 19. Wiley, 2023.'
ista: 'Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker
R, Ernst M, Loquet A, Schanda P. 2023. Cover Picture: The rigid core and flexible
surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of
aromatic residues, Wiley,p.'
mla: 'Becker, Lea Marie, et al. “Cover Picture: The Rigid Core and Flexible Surface
of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic
Residues.” Angewandte Chemie International Edition, vol. 62, no. 19, e202304138,
Wiley, 2023, doi:10.1002/anie.202304138.'
short: 'L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R.
Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Cover Picture: The Rigid Core and
Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy
of Aromatic Residues, Wiley, 2023.'
date_created: 2024-01-22T11:54:34Z
date_published: 2023-05-02T00:00:00Z
date_updated: 2024-01-23T08:48:14Z
day: '02'
department:
- _id: PaSc
doi: 10.1002/anie.202304138
intvolume: ' 62'
issue: '19'
keyword:
- General Chemistry
- Catalysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/anie.202304138
month: '05'
oa: 1
oa_version: Published Version
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
related_material:
link:
- relation: translation
url: https://doi.org/10.1002/ange.202304138
record:
- id: '12675'
relation: other
status: public
status: public
title: 'Cover Picture: The rigid core and flexible surface of amyloid fibrils probed
by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues'
type: other_academic_publication
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 62
year: '2023'
...
---
_id: '14849'
abstract:
- lang: eng
text: We establish a precise three-term asymptotic expansion, with an optimal estimate
of the error term, for the rightmost eigenvalue of an n×n random matrix with independent
identically distributed complex entries as n tends to infinity. All terms in the
expansion are universal.
acknowledgement: "The second and the fourth author were supported by the ERC Advanced
Grant\r\n“RMTBeyond” No. 101020331. The third author was supported by Dr. Max Rössler,
the\r\nWalter Haefner Foundation and the ETH Zürich Foundation."
article_processing_charge: No
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
- first_name: Yuanyuan
full_name: Xu, Yuanyuan
last_name: Xu
citation:
ama: Cipolloni G, Erdös L, Schröder DJ, Xu Y. On the rightmost eigenvalue of non-Hermitian
random matrices. The Annals of Probability. 2023;51(6):2192-2242. doi:10.1214/23-aop1643
apa: Cipolloni, G., Erdös, L., Schröder, D. J., & Xu, Y. (2023). On the rightmost
eigenvalue of non-Hermitian random matrices. The Annals of Probability.
Institute of Mathematical Statistics. https://doi.org/10.1214/23-aop1643
chicago: Cipolloni, Giorgio, László Erdös, Dominik J Schröder, and Yuanyuan Xu.
“On the Rightmost Eigenvalue of Non-Hermitian Random Matrices.” The Annals
of Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/23-aop1643.
ieee: G. Cipolloni, L. Erdös, D. J. Schröder, and Y. Xu, “On the rightmost eigenvalue
of non-Hermitian random matrices,” The Annals of Probability, vol. 51,
no. 6. Institute of Mathematical Statistics, pp. 2192–2242, 2023.
ista: Cipolloni G, Erdös L, Schröder DJ, Xu Y. 2023. On the rightmost eigenvalue
of non-Hermitian random matrices. The Annals of Probability. 51(6), 2192–2242.
mla: Cipolloni, Giorgio, et al. “On the Rightmost Eigenvalue of Non-Hermitian Random
Matrices.” The Annals of Probability, vol. 51, no. 6, Institute of Mathematical
Statistics, 2023, pp. 2192–242, doi:10.1214/23-aop1643.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Y. Xu, The Annals of Probability 51
(2023) 2192–2242.
date_created: 2024-01-22T08:08:41Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2024-01-23T10:56:30Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/23-aop1643
ec_funded: 1
external_id:
arxiv:
- '2206.04448'
intvolume: ' 51'
issue: '6'
keyword:
- Statistics
- Probability and Uncertainty
- Statistics and Probability
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2206.04448
month: '11'
oa: 1
oa_version: Preprint
page: 2192-2242
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: The Annals of Probability
publication_identifier:
issn:
- 0091-1798
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
status: public
title: On the rightmost eigenvalue of non-Hermitian random matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2023'
...
---
_id: '14835'
abstract:
- lang: ger
text: Aromatische Seitenketten sind wichtige Indikatoren für die Plastizität von
Proteinen und bilden oft entscheidende Kontakte bei Protein‐Protein‐Wechselwirkungen.
Wir untersuchten aromatische Reste in den beiden strukturell homologen cross‐β
Amyloidfibrillen HET‐s und HELLF mit Hilfe eines spezifischen Ansatzes zur Isotopenmarkierung
und Festkörper NMR mit Drehung am magischen Winkel. Das dynamische Verhalten der
aromatischen Reste Phe und Tyr deutet darauf hin, dass der hydrophobe Amyloidkern
starr ist und keine Anzeichen von “atmenden Bewegungen” auf einer Zeitskala von
Hunderten von Millisekunden zeigt. Aromatische Reste, die exponiert an der Fibrillenoberfläche
sitzen, haben zwar eine starre Ringachse, weisen aber Ringflips auf verschiedenen
Zeitskalen von Nanosekunden bis Mikrosekunden auf. Unser Ansatz bietet einen direkten
Einblick in die Bewegungen des hydrophoben Kerns und ermöglicht eine bessere Bewertung
der Konformationsheterogenität, die aus einem NMR‐Strukturensemble einer solchen
Cross‐β‐Amyloidstruktur hervorgeht.
acknowledgement: Wir danken Albert A. Smith (Leipzig) für aufschlussreiche Diskussionen.
Diese Arbeit wurde mit Mitteln des Europäischen Forschungsrats (StG-2012-311318
an P.S.) unterstützt und nutzte die Plattformen des Grenoble Instruct-ERIC Center
(ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) im Rahmen der Grenoble Partnership for Structural
Biology (PSB) sowie die Einrichtungen und das Fachwissen der Biophysical and Structural
Chemistry Platform (BPCS) am IECB, CNRS UAR3033, INSERM US001 und der Universität
Bordeaux.
article_number: e202219314
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
- first_name: Mélanie
full_name: Berbon, Mélanie
last_name: Berbon
- first_name: Alicia
full_name: Vallet, Alicia
last_name: Vallet
- first_name: Axelle
full_name: Grelard, Axelle
last_name: Grelard
- first_name: Estelle
full_name: Morvan, Estelle
last_name: Morvan
- first_name: Benjamin
full_name: Bardiaux, Benjamin
last_name: Bardiaux
- first_name: Roman
full_name: Lichtenecker, Roman
last_name: Lichtenecker
- first_name: Matthias
full_name: Ernst, Matthias
last_name: Ernst
- first_name: Antoine
full_name: Loquet, Antoine
last_name: Loquet
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Becker LM, Berbon M, Vallet A, et al. Der starre Kern und die flexible Oberfläche
von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen
Resten. Angewandte Chemie. 2023;135(19). doi:10.1002/ange.202219314
apa: Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B.,
… Schanda, P. (2023). Der starre Kern und die flexible Oberfläche von Amyloidfibrillen
– Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. Angewandte
Chemie. Wiley. https://doi.org/10.1002/ange.202219314
chicago: Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle
Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet,
and Paul Schanda. “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen
– Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.” Angewandte
Chemie. Wiley, 2023. https://doi.org/10.1002/ange.202219314.
ieee: L. M. Becker et al., “Der starre Kern und die flexible Oberfläche von
Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten,”
Angewandte Chemie, vol. 135, no. 19. Wiley, 2023.
ista: Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker
R, Ernst M, Loquet A, Schanda P. 2023. Der starre Kern und die flexible Oberfläche
von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen
Resten. Angewandte Chemie. 135(19), e202219314.
mla: Becker, Lea Marie, et al. “Der starre Kern und die flexible Oberfläche von
Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.”
Angewandte Chemie, vol. 135, no. 19, e202219314, Wiley, 2023, doi:10.1002/ange.202219314.
short: L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R.
Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie 135 (2023).
date_created: 2024-01-18T10:01:01Z
date_published: 2023-05-02T00:00:00Z
date_updated: 2024-01-23T12:23:35Z
day: '02'
ddc:
- '540'
department:
- _id: PaSc
doi: 10.1002/ange.202219314
file:
- access_level: open_access
checksum: 98e68d370159f7be52a3d7c8a8ee1198
content_type: application/pdf
creator: dernst
date_created: 2024-01-23T08:57:01Z
date_updated: 2024-01-23T08:57:01Z
file_id: '14876'
file_name: 2023_AngewChem_Becker.pdf
file_size: 1004676
relation: main_file
success: 1
file_date_updated: 2024-01-23T08:57:01Z
has_accepted_license: '1'
intvolume: ' 135'
issue: '19'
keyword:
- General Medicine
language:
- iso: ger
month: '05'
oa: 1
oa_version: Published Version
publication: Angewandte Chemie
publication_identifier:
eissn:
- 1521-3757
issn:
- 0044-8249
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning
NMR Spektroskopie von aromatischen Resten
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 135
year: '2023'
...
---
_id: '14847'
abstract:
- lang: eng
text: Understanding the mechanisms of chaperones at the atomic level generally requires
producing chaperone–client complexes in vitro. This task comes with significant
challenges, because one needs to find conditions in which the client protein is
presented to the chaperone in a state that binds and at the same time avoid the
pitfalls of protein aggregation that are often inherent to such states. The strategy
differs significantly for different client proteins and chaperones, but there
are common underlying principles. Here, we discuss these principles and deduce
the strategies that can be successfully applied for different chaperone–client
complexes. We review successful biochemical strategies applied to making the client
protein “binding competent” and illustrate the different strategies with examples
of recent biophysical and biochemical studies.
alternative_title:
- New Developments in NMR
article_processing_charge: No
author:
- first_name: I.
full_name: Sučec, I.
last_name: Sučec
- 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, Schanda P. Preparing Chaperone–Client Protein Complexes for Biophysical
and Structural Studies. In: Hiller S, Liu M, He L, eds. Biophysics of Molecular
Chaperones. Vol 29. Royal Society of Chemistry; 2023:136-161. doi:10.1039/bk9781839165986-00136'
apa: Sučec, I., & Schanda, P. (2023). Preparing Chaperone–Client Protein Complexes
for Biophysical and Structural Studies. In S. Hiller, M. Liu, & L. He (Eds.),
Biophysics of Molecular Chaperones (Vol. 29, pp. 136–161). Royal Society
of Chemistry. https://doi.org/10.1039/bk9781839165986-00136
chicago: Sučec, I., and Paul Schanda. “Preparing Chaperone–Client Protein Complexes
for Biophysical and Structural Studies.” In Biophysics of Molecular Chaperones,
edited by Sebastian Hiller, Maili Liu, and Lichun He, 29:136–61. Royal Society
of Chemistry, 2023. https://doi.org/10.1039/bk9781839165986-00136.
ieee: I. Sučec and P. Schanda, “Preparing Chaperone–Client Protein Complexes for
Biophysical and Structural Studies,” in Biophysics of Molecular Chaperones,
vol. 29, S. Hiller, M. Liu, and L. He, Eds. Royal Society of Chemistry, 2023,
pp. 136–161.
ista: 'Sučec I, Schanda P. 2023.Preparing Chaperone–Client Protein Complexes for
Biophysical and Structural Studies. In: Biophysics of Molecular Chaperones. New
Developments in NMR, vol. 29, 136–161.'
mla: Sučec, I., and Paul Schanda. “Preparing Chaperone–Client Protein Complexes
for Biophysical and Structural Studies.” Biophysics of Molecular Chaperones,
edited by Sebastian Hiller et al., vol. 29, Royal Society of Chemistry, 2023,
pp. 136–61, doi:10.1039/bk9781839165986-00136.
short: I. Sučec, P. Schanda, in:, S. Hiller, M. Liu, L. He (Eds.), Biophysics of
Molecular Chaperones, Royal Society of Chemistry, 2023, pp. 136–161.
date_created: 2024-01-22T08:04:57Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2024-01-23T11:50:10Z
day: '01'
department:
- _id: PaSc
doi: 10.1039/bk9781839165986-00136
editor:
- first_name: Sebastian
full_name: Hiller, Sebastian
last_name: Hiller
- first_name: Maili
full_name: Liu, Maili
last_name: Liu
- first_name: Lichun
full_name: He, Lichun
last_name: He
intvolume: ' 29'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.26434/chemrxiv-2023-rpn28
month: '11'
oa: 1
oa_version: Preprint
page: 136-161
publication: Biophysics of Molecular Chaperones
publication_identifier:
eisbn:
- '9781839165993'
isbn:
- '9781839162824'
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: Preparing Chaperone–Client Protein Complexes for Biophysical and Structural
Studies
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2023'
...
---
_id: '14867'
abstract:
- lang: eng
text: Starting with the empty graph on $[n]$, at each round, a set of $K=K(n)$
edges is presented chosen uniformly at random from the ones that have not been
presented yet. We are then asked to choose at most one of the presented edges
and add it to the current graph. Our goal is to construct a Hamiltonian graph
with $(1+o(1))n$ edges within as few rounds as possible. We show that in this
process, one can build a Hamiltonian graph of size $(1+o(1))n$ in $(1+o(1))(1+(\log
n)/2K) n$ rounds w.h.p. The case $K=1$ implies that w.h.p. one can build a Hamiltonian
graph by choosing $(1+o(1))n$ edges in an online fashion as they appear along
the first $(0.5+o(1))n\log n$ rounds of the random graph process. This answers
a question of Frieze, Krivelevich and Michaeli. Observe that the number of rounds
is asymptotically optimal as the first $0.5n\log n$ edges do not span a Hamilton
cycle w.h.p. The case $K=\Theta(\log n)$ implies that the Hamiltonicity threshold
of the corresponding Achlioptas process is at most $(1+o(1))(1+(\log n)/2K) n$.
This matches the $(1-o(1))(1+(\log n)/2K) n$ lower bound due to Krivelevich, Lubetzky
and Sudakov and resolves the problem of determining the Hamiltonicity threshold
of the Achlioptas process with $K=\Theta(\log n)$. We also show that in the above
process one can construct a graph $G$ that spans a matching of size $\lfloor V(G)/2)
\rfloor$ and $(0.5+o(1))n$ edges within $(1+o(1))(0.5+(\log n)/2K) n$ rounds w.h.p.
Our proof relies on a robust Hamiltonicity property of the strong $4$-core of
the binomial random graph which we use as a black-box. This property allows it
to absorb paths covering vertices outside the strong $4$-core into a cycle.
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 101034413.\r\n"
article_processing_charge: No
author:
- first_name: Michael
full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
citation:
ama: 'Anastos M. Constructing Hamilton cycles and perfect matchings efficiently.
In: Proceedings of the 12th European Conference on Combinatorics, Graph Theory
and Applications. Masaryk University Press; 2023:36-41. doi:10.5817/cz.muni.eurocomb23-005'
apa: 'Anastos, M. (2023). Constructing Hamilton cycles and perfect matchings efficiently.
In Proceedings of the 12th European Conference on Combinatorics, Graph Theory
and Applications (pp. 36–41). Prague, Czech Republic: Masaryk University Press.
https://doi.org/10.5817/cz.muni.eurocomb23-005'
chicago: Anastos, Michael. “Constructing Hamilton Cycles and Perfect Matchings Efficiently.”
In Proceedings of the 12th European Conference on Combinatorics, Graph Theory
and Applications, 36–41. Masaryk University Press, 2023. https://doi.org/10.5817/cz.muni.eurocomb23-005.
ieee: M. Anastos, “Constructing Hamilton cycles and perfect matchings efficiently,”
in Proceedings of the 12th European Conference on Combinatorics, Graph Theory
and Applications, Prague, Czech Republic, 2023, pp. 36–41.
ista: 'Anastos M. 2023. Constructing Hamilton cycles and perfect matchings efficiently.
Proceedings of the 12th European Conference on Combinatorics, Graph Theory and
Applications. EUROCOMB: European Conference on Combinatorics, Graph Theory and
Applications, 36–41.'
mla: Anastos, Michael. “Constructing Hamilton Cycles and Perfect Matchings Efficiently.”
Proceedings of the 12th European Conference on Combinatorics, Graph Theory
and Applications, Masaryk University Press, 2023, pp. 36–41, doi:10.5817/cz.muni.eurocomb23-005.
short: M. Anastos, in:, Proceedings of the 12th European Conference on Combinatorics,
Graph Theory and Applications, Masaryk University Press, 2023, pp. 36–41.
conference:
end_date: 2023-09-01
location: Prague, Czech Republic
name: 'EUROCOMB: European Conference on Combinatorics, Graph Theory and Applications'
start_date: 2023-08-28
date_created: 2024-01-22T12:20:15Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2024-01-24T09:38:44Z
day: '01'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.5817/cz.muni.eurocomb23-005
ec_funded: 1
external_id:
arxiv:
- '2209.09860'
file:
- access_level: open_access
checksum: fb1d9a1e7389d90ec0e5e76934373cf8
content_type: application/pdf
creator: dernst
date_created: 2024-01-24T09:34:43Z
date_updated: 2024-01-24T09:34:43Z
file_id: '14881'
file_name: 2023_Eurocomb_Anastos.pdf
file_size: 464230
relation: main_file
success: 1
file_date_updated: 2024-01-24T09:34:43Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 36-41
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Proceedings of the 12th European Conference on Combinatorics, Graph Theory
and Applications
publication_identifier:
eissn:
- 2788-3116
publication_status: published
publisher: Masaryk University Press
quality_controlled: '1'
status: public
title: Constructing Hamilton cycles and perfect matchings efficiently
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14864'
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Starting Grant (No. 949120).
article_number: '6166'
article_processing_charge: No
author:
- first_name: Andrea
full_name: Stöllner, Andrea
id: 4bdcf7f6-eb97-11eb-a6c2-9981bbdc3bed
last_name: Stöllner
orcid: 0000-0002-0464-8440
- first_name: Isaac C
full_name: Lenton, Isaac C
id: a550210f-223c-11ec-8182-e2d45e817efb
last_name: Lenton
orcid: 0000-0002-5010-6984
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: 'Stöllner A, Lenton IC, Muller CJ, Waitukaitis SR. Measuring spontaneous charging
of single aerosol particles. In: EGU General Assembly 2023. European Geosciences
Union; 2023. doi:10.5194/egusphere-egu23-6166'
apa: 'Stöllner, A., Lenton, I. C., Muller, C. J., & Waitukaitis, S. R. (2023).
Measuring spontaneous charging of single aerosol particles. In EGU General
Assembly 2023. Vienna, Austria & Virtual: European Geosciences Union.
https://doi.org/10.5194/egusphere-egu23-6166'
chicago: Stöllner, Andrea, Isaac C Lenton, Caroline J Muller, and Scott R Waitukaitis.
“Measuring Spontaneous Charging of Single Aerosol Particles.” In EGU General
Assembly 2023. European Geosciences Union, 2023. https://doi.org/10.5194/egusphere-egu23-6166.
ieee: A. Stöllner, I. C. Lenton, C. J. Muller, and S. R. Waitukaitis, “Measuring
spontaneous charging of single aerosol particles,” in EGU General Assembly
2023, Vienna, Austria & Virtual, 2023.
ista: Stöllner A, Lenton IC, Muller CJ, Waitukaitis SR. 2023. Measuring spontaneous
charging of single aerosol particles. EGU General Assembly 2023. EGU General Assembly,
6166.
mla: Stöllner, Andrea, et al. “Measuring Spontaneous Charging of Single Aerosol
Particles.” EGU General Assembly 2023, 6166, European Geosciences Union,
2023, doi:10.5194/egusphere-egu23-6166.
short: A. Stöllner, I.C. Lenton, C.J. Muller, S.R. Waitukaitis, in:, EGU General
Assembly 2023, European Geosciences Union, 2023.
conference:
end_date: 2023-04-28
location: Vienna, Austria & Virtual
name: EGU General Assembly
start_date: 2023-04-23
date_created: 2024-01-22T12:09:07Z
date_published: 2023-04-23T00:00:00Z
date_updated: 2024-01-24T11:21:42Z
day: '23'
ddc:
- '530'
department:
- _id: CaMu
- _id: ScWa
doi: 10.5194/egusphere-egu23-6166
ec_funded: 1
file:
- access_level: open_access
checksum: 8d6ddbb359e584b156f991f00196d86b
content_type: application/pdf
creator: dernst
date_created: 2024-01-23T13:00:26Z
date_updated: 2024-01-23T13:00:26Z
file_id: '14880'
file_name: 2023_EGU_Stoellner.pdf
file_size: 419736
relation: main_file
success: 1
file_date_updated: 2024-01-23T13:00:26Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa
call_identifier: H2020
grant_number: '949120'
name: 'Tribocharge: a multi-scale approach to an enduring problem in physics'
publication: EGU General Assembly 2023
publication_status: published
publisher: European Geosciences Union
status: public
title: Measuring spontaneous charging of single aerosol particles
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_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14862'
article_number: ckad160.597
article_processing_charge: No
author:
- first_name: Simon
full_name: Rella, Simon
id: B4765ACA-AA38-11E9-AC9A-0930E6697425
last_name: Rella
- first_name: Y
full_name: Kulikova, Y
last_name: Kulikova
- first_name: Aygul
full_name: Minnegalieva, Aygul
id: 87DF77F0-1D9A-11EA-B6AE-CE443DDC885E
last_name: Minnegalieva
- 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 Y, Minnegalieva A, Kondrashov F. Complex vaccination strategies
prevent the emergence of vaccine resistance. In: European Journal of Public
Health. Vol 33. Oxford University Press; 2023. doi:10.1093/eurpub/ckad160.597'
apa: Rella, S., Kulikova, Y., Minnegalieva, A., & Kondrashov, F. (2023). Complex
vaccination strategies prevent the emergence of vaccine resistance. In European
Journal of Public Health (Vol. 33). Oxford University Press. https://doi.org/10.1093/eurpub/ckad160.597
chicago: Rella, Simon, Y Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov. “Complex
Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” In European
Journal of Public Health, Vol. 33. Oxford University Press, 2023. https://doi.org/10.1093/eurpub/ckad160.597.
ieee: S. Rella, Y. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination
strategies prevent the emergence of vaccine resistance,” in European Journal
of Public Health, 2023, vol. 33, no. Supplement_2.
ista: Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. 2023. Complex vaccination
strategies prevent the emergence of vaccine resistance. European Journal of Public
Health. vol. 33, ckad160.597.
mla: Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence
of Vaccine Resistance.” European Journal of Public Health, vol. 33, no.
Supplement_2, ckad160.597, Oxford University Press, 2023, doi:10.1093/eurpub/ckad160.597.
short: S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal
of Public Health, Oxford University Press, 2023.
date_created: 2024-01-22T12:02:28Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-01-24T11:16:09Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1093/eurpub/ckad160.597
file:
- access_level: open_access
checksum: 98706755bb4cc5d553818ade7660a7d2
content_type: application/pdf
creator: dernst
date_created: 2024-01-24T11:12:33Z
date_updated: 2024-01-24T11:12:33Z
file_id: '14882'
file_name: 2023_EurJourPublicHealth_Rella.pdf
file_size: 71057
relation: main_file
success: 1
file_date_updated: 2024-01-24T11:12:33Z
has_accepted_license: '1'
intvolume: ' 33'
issue: Supplement_2
keyword:
- Public Health
- Environmental and Occupational Health
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: European Journal of Public Health
publication_identifier:
eissn:
- 1464-360X
issn:
- 1101-1262
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Complex vaccination strategies prevent the emergence of vaccine resistance
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: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2023'
...
---
_id: '14863'
article_number: EGU23-6157
article_processing_charge: No
author:
- first_name: Andrea
full_name: Polesello, Andrea
id: 74c777f4-32da-11ee-b498-874db0835561
last_name: Polesello
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Claudia
full_name: Pasquero, Claudia
last_name: Pasquero
- first_name: Agostino N.
full_name: Meroni, Agostino N.
last_name: Meroni
citation:
ama: 'Polesello A, Muller CJ, Pasquero C, Meroni AN. Intensification mechanisms
of tropical cyclones. In: EGU General Assembly 2023. European Geosciences
Union; 2023. doi:10.5194/egusphere-egu23-6157'
apa: 'Polesello, A., Muller, C. J., Pasquero, C., & Meroni, A. N. (2023). Intensification
mechanisms of tropical cyclones. In EGU General Assembly 2023. Vienna,
Austria & Virtual: European Geosciences Union. https://doi.org/10.5194/egusphere-egu23-6157'
chicago: Polesello, Andrea, Caroline J Muller, Claudia Pasquero, and Agostino N.
Meroni. “Intensification Mechanisms of Tropical Cyclones.” In EGU General Assembly
2023. European Geosciences Union, 2023. https://doi.org/10.5194/egusphere-egu23-6157.
ieee: A. Polesello, C. J. Muller, C. Pasquero, and A. N. Meroni, “Intensification
mechanisms of tropical cyclones,” in EGU General Assembly 2023, Vienna,
Austria & Virtual, 2023.
ista: Polesello A, Muller CJ, Pasquero C, Meroni AN. 2023. Intensification mechanisms
of tropical cyclones. EGU General Assembly 2023. EGU General Assembly, EGU23-6157.
mla: Polesello, Andrea, et al. “Intensification Mechanisms of Tropical Cyclones.”
EGU General Assembly 2023, EGU23-6157, European Geosciences Union, 2023,
doi:10.5194/egusphere-egu23-6157.
short: A. Polesello, C.J. Muller, C. Pasquero, A.N. Meroni, in:, EGU General Assembly
2023, European Geosciences Union, 2023.
conference:
end_date: 2023-04-28
location: Vienna, Austria & Virtual
name: EGU General Assembly
start_date: 2023-04-23
date_created: 2024-01-22T12:08:12Z
date_published: 2023-04-13T00:00:00Z
date_updated: 2024-01-24T11:25:07Z
day: '13'
ddc:
- '550'
department:
- _id: CaMu
- _id: GradSch
doi: 10.5194/egusphere-egu23-6157
file:
- access_level: open_access
checksum: 8cb88c1bc80ccee328478a62064d98f7
content_type: application/pdf
creator: dernst
date_created: 2024-01-24T11:19:54Z
date_updated: 2024-01-24T11:19:54Z
file_id: '14883'
file_name: 2023_EGU_Polesello.pdf
file_size: 296769
relation: main_file
success: 1
file_date_updated: 2024-01-24T11:19:54Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: EGU General Assembly 2023
publication_status: published
publisher: European Geosciences Union
status: public
title: Intensification mechanisms of tropical cyclones
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_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14732'
abstract:
- lang: eng
text: 'Fragmented landscapes pose a significant threat to the persistence of species
as they are highly susceptible to heightened risk of extinction due to the combined
effects of genetic and demographic factors such as genetic drift and demographic
stochasticity. This paper explores the intricate interplay between genetic load
and extinction risk within metapopulations with a focus on understanding the impact
of eco-evolutionary feedback mechanisms. We distinguish between two models of
selection: soft selection, characterised by subpopulations maintaining carrying
capacity despite load, and hard selection, where load can significantly affect
population size. Within the soft selection framework, we investigate the impact
of gene flow on genetic load at a single locus, while also considering the effect
of selection strength and dominance coefficient. We subsequently build on this
to examine how gene flow influences both population size and load under hard selection
as well as identify critical thresholds for metapopulation persistence. Our analysis
employs the diffusion, semi-deterministic and effective migration approximations.
Our findings reveal that under soft selection, even modest levels of migration
can significantly alleviate the burden of load. In sharp contrast, with hard selection,
a much higher degree of gene flow is required to mitigate load and prevent the
collapse of the metapopulation. Overall, this study sheds light into the crucial
role migration plays in shaping the dynamics of genetic load and extinction risk
in fragmented landscapes, offering valuable insights for conservation strategies
and the preservation of diversity in a changing world.'
article_processing_charge: No
author:
- first_name: Oluwafunmilola O
full_name: Olusanya, Oluwafunmilola O
id: 41AD96DC-F248-11E8-B48F-1D18A9856A87
last_name: Olusanya
orcid: 0000-0003-1971-8314
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
citation:
ama: Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback
and extinction in a metapopulation. bioRxiv. doi:10.1101/2023.12.02.569702
apa: Olusanya, O. O., Khudiakova, K., & Sachdeva, H. (n.d.). Genetic load, eco-evolutionary
feedback and extinction in a metapopulation. bioRxiv. https://doi.org/10.1101/2023.12.02.569702
chicago: Olusanya, Oluwafunmilola O, Kseniia Khudiakova, and Himani Sachdeva. “Genetic
Load, Eco-Evolutionary Feedback and Extinction in a Metapopulation.” BioRxiv,
n.d. https://doi.org/10.1101/2023.12.02.569702.
ieee: O. O. Olusanya, K. Khudiakova, and H. Sachdeva, “Genetic load, eco-evolutionary
feedback and extinction in a metapopulation,” bioRxiv. .
ista: Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback
and extinction in a metapopulation. bioRxiv, 10.1101/2023.12.02.569702.
mla: Olusanya, Oluwafunmilola O., et al. “Genetic Load, Eco-Evolutionary Feedback
and Extinction in a Metapopulation.” BioRxiv, doi:10.1101/2023.12.02.569702.
short: O.O. Olusanya, K. Khudiakova, H. Sachdeva, BioRxiv (n.d.).
date_created: 2024-01-04T09:35:54Z
date_published: 2023-12-04T00:00:00Z
date_updated: 2024-01-26T12:00:53Z
day: '04'
department:
- _id: NiBa
- _id: JaMa
doi: 10.1101/2023.12.02.569702
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2023.12.02.569702v1
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8
grant_number: P32896
name: Causes and consequences of population fragmentation
- _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8
grant_number: '26293'
name: The impact of deleterious mutations on small populations
- _id: 34c872fe-11ca-11ed-8bc3-8534b82131e6
grant_number: '26380'
name: Polygenic Adaptation in a Metapopulation
publication: bioRxiv
publication_status: submitted
related_material:
record:
- id: '14711'
relation: dissertation_contains
status: public
status: public
title: Genetic load, eco-evolutionary feedback and extinction in a metapopulation
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: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '13049'
abstract:
- lang: eng
text: "We propose a computational design approach for covering a surface with individually
addressable RGB LEDs, effectively forming a low-resolution surface screen. To
achieve a low-cost and scalable approach, we propose creating designs from flat
PCB panels bent in-place along the surface of a 3D printed core. Working with
standard rigid PCBs enables the use of\r\nestablished PCB manufacturing services,
allowing the fabrication of designs with several hundred LEDs. \r\nOur approach
optimizes the PCB geometry for folding, and then jointly optimizes the LED packing,
circuit and routing, solving a challenging layout problem under strict manufacturing
requirements. Unlike paper, PCBs cannot bend beyond a certain point without breaking.
Therefore, we introduce parametric cut patterns acting as hinges, designed to
allow bending while remaining compact. To tackle the joint optimization of placement,
circuit and routing, we propose a specialized algorithm that splits the global
problem into one sub-problem per triangle, which is then individually solved.\r\nOur
technique generates PCB blueprints in a completely automated way. After being
fabricated by a PCB manufacturing service, the boards are bent and glued by the
user onto the 3D printed support. We demonstrate our technique on a range of physical
models and virtual examples, creating intricate surface light patterns from hundreds
of LEDs."
acknowledged_ssus:
- _id: M-Shop
acknowledgement: We thank the reviewers for the valuable feedback. We also thank the
Miba Machine Shop at ISTA, PCBWay, and PragoBoard for helping us with fabrication
and assembly. This project was supported by the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation program (Grant Agreement
No. 715767 – MATERIALIZABLE).
article_number: '142'
article_processing_charge: No
article_type: original
author:
- first_name: Marco
full_name: Freire, Marco
last_name: Freire
- first_name: Manas
full_name: Bhargava, Manas
id: FF8FA64C-AA6A-11E9-99AD-50D4E5697425
last_name: Bhargava
orcid: 0009-0007-6138-6890
- first_name: Camille
full_name: Schreck, Camille
id: 2B14B676-F248-11E8-B48F-1D18A9856A87
last_name: Schreck
- first_name: Pierre-Alexandre
full_name: Hugron, Pierre-Alexandre
last_name: Hugron
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Sylvain
full_name: Lefebvre, Sylvain
last_name: Lefebvre
citation:
ama: 'Freire M, Bhargava M, Schreck C, Hugron P-A, Bickel B, Lefebvre S. PCBend:
Light up your 3D shapes with foldable circuit boards. Transactions on Graphics.
2023;42(4). doi:10.1145/3592411'
apa: 'Freire, M., Bhargava, M., Schreck, C., Hugron, P.-A., Bickel, B., & Lefebvre,
S. (2023). PCBend: Light up your 3D shapes with foldable circuit boards. Transactions
on Graphics. Los Angeles, CA, United States: Association for Computing Machinery.
https://doi.org/10.1145/3592411'
chicago: 'Freire, Marco, Manas Bhargava, Camille Schreck, Pierre-Alexandre Hugron,
Bernd Bickel, and Sylvain Lefebvre. “PCBend: Light up Your 3D Shapes with Foldable
Circuit Boards.” Transactions on Graphics. Association for Computing Machinery,
2023. https://doi.org/10.1145/3592411.'
ieee: 'M. Freire, M. Bhargava, C. Schreck, P.-A. Hugron, B. Bickel, and S. Lefebvre,
“PCBend: Light up your 3D shapes with foldable circuit boards,” Transactions
on Graphics, vol. 42, no. 4. Association for Computing Machinery, 2023.'
ista: 'Freire M, Bhargava M, Schreck C, Hugron P-A, Bickel B, Lefebvre S. 2023.
PCBend: Light up your 3D shapes with foldable circuit boards. Transactions on
Graphics. 42(4), 142.'
mla: 'Freire, Marco, et al. “PCBend: Light up Your 3D Shapes with Foldable Circuit
Boards.” Transactions on Graphics, vol. 42, no. 4, 142, Association for
Computing Machinery, 2023, doi:10.1145/3592411.'
short: M. Freire, M. Bhargava, C. Schreck, P.-A. Hugron, B. Bickel, S. Lefebvre,
Transactions on Graphics 42 (2023).
conference:
end_date: 2023-08-10
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference'
start_date: 2023-08-06
date_created: 2023-05-22T08:37:04Z
date_published: 2023-07-26T00:00:00Z
date_updated: 2024-01-29T10:30:49Z
day: '26'
ddc:
- '006'
department:
- _id: GradSch
- _id: BeBi
doi: 10.1145/3592411
ec_funded: 1
external_id:
isi:
- '001044671300108'
file:
- access_level: open_access
checksum: a0b0ba3b36f43a94388e8824613d812a
content_type: application/pdf
creator: dernst
date_created: 2023-06-19T11:02:23Z
date_updated: 2023-06-19T11:02:23Z
file_id: '13156'
file_name: 2023_ACMToG_Freire.pdf
file_size: 78940724
relation: main_file
success: 1
- access_level: open_access
checksum: b9206bbb67af82df49b7e7cdbde3410c
content_type: application/pdf
creator: dernst
date_created: 2023-06-20T12:20:51Z
date_updated: 2023-06-20T12:20:51Z
file_id: '13157'
file_name: 2023_ACMToG_SuppMaterial_Freire.pdf
file_size: 34345905
relation: main_file
success: 1
file_date_updated: 2023-06-20T12:20:51Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '4'
keyword:
- PCB design and layout
- Mesh geometry models
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: 'PCBend: Light up your 3D shapes with foldable circuit boards'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '13212'
abstract:
- lang: eng
text: Auxin is the major plant hormone regulating growth and development (Friml,
2022). Forward genetic approaches in the model plant Arabidopsis thaliana have
identified major components of auxin signalling and established the canonical
mechanism mediating transcriptional and thus developmental reprogramming. In this
textbook view, TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFBs)
are auxin receptors, which act as F-box subunits determining the substrate specificity
of the Skp1-Cullin1-F box protein (SCF) type E3 ubiquitin ligase complex. Auxin
acts as a “molecular glue” increasing the affinity between TIR1/AFBs and the Aux/IAA
repressors. Subsequently, Aux/IAAs are ubiquitinated and degraded, thus releasing
auxin transcription factors from their repression making them free to mediate
transcription of auxin response genes (Yu et al., 2022). Nonetheless, accumulating
evidence suggests existence of rapid, non-transcriptional responses downstream
of TIR1/AFBs such as auxin-induced cytosolic calcium (Ca2+) transients, plasma
membrane depolarization and apoplast alkalinisation, all converging on the process
of root growth inhibition and root gravitropism (Li et al., 2022). Particularly,
these rapid responses are mostly contributed by predominantly cytosolic AFB1,
while the long-term growth responses are mediated by mainly nuclear TIR1 and AFB2-AFB5
(Li et al., 2021; Prigge et al., 2020; Serre et al., 2021). How AFB1 conducts
auxin-triggered rapid responses and how it is different from TIR1 and AFB2-AFB5
remains elusive. Here, we compare the roles of TIR1 and AFB1 in transcriptional
and rapid responses by modulating their subcellular localization in Arabidopsis
and by testing their ability to mediate transcriptional responses when part of
the minimal auxin circuit reconstituted in yeast.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: We thank all the authors for sharing the published materials. This
research was supported by the Lab Support Facility and the Imaging and Optics Facility
of ISTA. We thank Lukáš Fiedler (ISTA) for critical reading of the manuscript. This
project was funded by the European Research Council Advanced Grant (ETAP-742985).
article_processing_charge: Yes (via OA deal)
article_type: letter_note
author:
- first_name: Huihuang
full_name: Chen, Huihuang
id: 83c96512-15b2-11ec-abd3-b7eede36184f
last_name: Chen
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Minxia
full_name: Zou, Minxia
id: 5c243f41-03f3-11ec-841c-96faf48a7ef9
last_name: Zou
- first_name: Linlin
full_name: Qi, Linlin
id: 44B04502-A9ED-11E9-B6FC-583AE6697425
last_name: Qi
orcid: 0000-0001-5187-8401
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Chen H, Li L, Zou M, Qi L, Friml J. Distinct functions of TIR1 and AFB1 receptors
in auxin signalling. Molecular Plant. 2023;16(7):1117-1119. doi:10.1016/j.molp.2023.06.007
apa: Chen, H., Li, L., Zou, M., Qi, L., & Friml, J. (2023). Distinct functions
of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. Elsevier
. https://doi.org/10.1016/j.molp.2023.06.007
chicago: Chen, Huihuang, Lanxin Li, Minxia Zou, Linlin Qi, and Jiří Friml. “Distinct
Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” Molecular Plant.
Elsevier , 2023. https://doi.org/10.1016/j.molp.2023.06.007.
ieee: H. Chen, L. Li, M. Zou, L. Qi, and J. Friml, “Distinct functions of TIR1 and
AFB1 receptors in auxin signalling.,” Molecular Plant, vol. 16, no. 7.
Elsevier , pp. 1117–1119, 2023.
ista: Chen H, Li L, Zou M, Qi L, Friml J. 2023. Distinct functions of TIR1 and AFB1
receptors in auxin signalling. Molecular Plant. 16(7), 1117–1119.
mla: Chen, Huihuang, et al. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin
Signalling.” Molecular Plant, vol. 16, no. 7, Elsevier , 2023, pp. 1117–19,
doi:10.1016/j.molp.2023.06.007.
short: H. Chen, L. Li, M. Zou, L. Qi, J. Friml, Molecular Plant 16 (2023) 1117–1119.
date_created: 2023-07-12T07:32:46Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2024-01-29T10:38:57Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.molp.2023.06.007
ec_funded: 1
external_id:
isi:
- '001044410900001'
pmid:
- '37393433'
file:
- access_level: open_access
checksum: 6012b7e4a2f680ee6c1f84001e2b945f
content_type: application/pdf
creator: dernst
date_created: 2024-01-29T10:37:05Z
date_updated: 2024-01-29T10:37:05Z
file_id: '14894'
file_name: 2023_MolecularPlant_Chen.pdf
file_size: 1000871
relation: main_file
success: 1
file_date_updated: 2024-01-29T10:37:05Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1117-1119
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Molecular Plant
publication_identifier:
eissn:
- 1674-2052
issn:
- 1752-9867
publication_status: published
publisher: 'Elsevier '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct functions of TIR1 and AFB1 receptors in auxin signalling.
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2023'
...
---
_id: '12984'
abstract:
- lang: eng
text: Tattoos are a highly popular medium, with both artistic and medical applications.
Although the mechanical process of tattoo application has evolved historically,
the results are reliant on the artisanal skill of the artist. This can be especially
challenging for some skin tones, or in cases where artists lack experience. We
provide the first systematic overview of tattooing as a computational fabrication
technique. We built an automated tattooing rig and a recipe for the creation of
silicone sheets mimicking realistic skin tones, which allowed us to create an
accurate model predicting tattoo appearance. This enables several exciting applications
including tattoo previewing, color retargeting, novel ink spectra optimization,
color-accurate prosthetics, and more.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: We thank Todor Asenov and the Miba Machine Shop for their help in
assembling the tattoo machine and manufacturing the substrates. We thank Geysler
Rodrigues for the insightful discussions on tattooing practices from a professional
artist's perspective. We thank Maria Fernanda Portugal for sharing a doctor's perspective
on medical applications of tattoos. This work is graciously supported by the FWF
Lise Meitner (Grant M 3319).
article_number: '67'
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
orcid: 0000-0002-5062-4474
- first_name: Alexandre
full_name: Chapiro, Alexandre
last_name: Chapiro
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: 'Piovarci M, Chapiro A, Bickel B. Skin-Screen: A computational fabrication
framework for color tattoos. Transactions on Graphics. 2023;42(4). doi:10.1145/3592432'
apa: 'Piovarci, M., Chapiro, A., & Bickel, B. (2023). Skin-Screen: A computational
fabrication framework for color tattoos. Transactions on Graphics. Los
Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3592432'
chicago: 'Piovarci, Michael, Alexandre Chapiro, and Bernd Bickel. “Skin-Screen:
A Computational Fabrication Framework for Color Tattoos.” Transactions on Graphics.
Association for Computing Machinery, 2023. https://doi.org/10.1145/3592432.'
ieee: 'M. Piovarci, A. Chapiro, and B. Bickel, “Skin-Screen: A computational fabrication
framework for color tattoos,” Transactions on Graphics, vol. 42, no. 4.
Association for Computing Machinery, 2023.'
ista: 'Piovarci M, Chapiro A, Bickel B. 2023. Skin-Screen: A computational fabrication
framework for color tattoos. Transactions on Graphics. 42(4), 67.'
mla: 'Piovarci, Michael, et al. “Skin-Screen: A Computational Fabrication Framework
for Color Tattoos.” Transactions on Graphics, vol. 42, no. 4, 67, Association
for Computing Machinery, 2023, doi:10.1145/3592432.'
short: M. Piovarci, A. Chapiro, B. Bickel, Transactions on Graphics 42 (2023).
conference:
end_date: 2023-08-10
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference'
start_date: 2023-08-06
date_created: 2023-05-16T09:39:14Z
date_published: 2023-07-26T00:00:00Z
date_updated: 2024-01-29T10:27:23Z
day: '26'
ddc:
- '004'
department:
- _id: BeBi
doi: 10.1145/3592432
external_id:
isi:
- '001044671300033'
file:
- access_level: open_access
checksum: 5f0a6867689e025a661bd0b4fd90b821
content_type: application/pdf
creator: mpiovarc
date_created: 2023-05-16T09:38:25Z
date_updated: 2023-05-16T09:38:25Z
file_id: '12985'
file_name: Piovarci2023.pdf
file_size: 30817343
relation: main_file
success: 1
file_date_updated: 2023-05-16T09:38:25Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '4'
keyword:
- appearance
- modeling
- reproduction
- tattoo
- skin color
- gamut mapping
- ink-optimization
- prosthetic
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: eb901961-77a9-11ec-83b8-f5c883a62027
grant_number: M03319
name: Perception-Aware Appearance Fabrication
publication: Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: 'Skin-Screen: A computational fabrication framework for color tattoos'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '14892'
abstract:
- lang: eng
text: 'Code and data necessary to reproduce the simulations and data analyses reported
in our manuscript: Tomé, D.F., Zhang, Y., Aida, T., Mosto, O., Lu, Y., Chen, M.,
Sadeh, S., Roy, D. S., Clopath, C. Dynamic and selective engrams emerge with memory
consolidation. 2023.'
article_processing_charge: No
author:
- first_name: Douglas
full_name: Feitosa Tomé, Douglas
id: 0eed2d40-3d48-11ec-8d38-f789cc2e40b2
last_name: Feitosa Tomé
citation:
ama: 'Feitosa Tomé D. douglastome/dynamic-engrams: Dynamic and selective engrams
emerge with memory consolidation. 2023. doi:10.5281/ZENODO.10251087'
apa: 'Feitosa Tomé, D. (2023). douglastome/dynamic-engrams: Dynamic and selective
engrams emerge with memory consolidation. Zenodo. https://doi.org/10.5281/ZENODO.10251087'
chicago: 'Feitosa Tomé, Douglas. “Douglastome/Dynamic-Engrams: Dynamic and Selective
Engrams Emerge with Memory Consolidation.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.10251087.'
ieee: 'D. Feitosa Tomé, “douglastome/dynamic-engrams: Dynamic and selective engrams
emerge with memory consolidation.” Zenodo, 2023.'
ista: 'Feitosa Tomé D. 2023. douglastome/dynamic-engrams: Dynamic and selective
engrams emerge with memory consolidation, Zenodo, 10.5281/ZENODO.10251087.'
mla: 'Feitosa Tomé, Douglas. Douglastome/Dynamic-Engrams: Dynamic and Selective
Engrams Emerge with Memory Consolidation. Zenodo, 2023, doi:10.5281/ZENODO.10251087.'
short: D. Feitosa Tomé, (2023).
date_created: 2024-01-29T09:06:43Z
date_published: 2023-12-02T00:00:00Z
date_updated: 2024-01-29T09:22:01Z
day: '02'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.5281/ZENODO.10251087
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.10251087
month: '12'
oa: 1
oa_version: None
publisher: Zenodo
related_material:
record:
- id: '14887'
relation: used_in_publication
status: public
status: public
title: 'douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory
consolidation'
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: '2023'
...
---
_id: '14032'
abstract:
- lang: eng
text: Arrays of Josephson junctions are governed by a competition between superconductivity
and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature
resistance when interactions exceed a critical level. Here we report a study of
the transport and microwave response of Josephson arrays with interactions exceeding
this level. Contrary to expectations, we observe that the array resistance drops
dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and
then saturates at low temperature. Applying a magnetic field, we eventually observe
a transition to a highly resistive regime. These observations can be understood
within a theoretical picture that accounts for the effect of thermal fluctuations
on the insulating phase. On the basis of the agreement between experiment and
theory, we suggest that apparent superconductivity in our Josephson arrays arises
from melting the zero-temperature insulator.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: We thank D. Haviland, J. Pekola, C. Ciuti, A. Bubis and A. Shnirman
for helpful feedback on the paper. This research was supported by the Scientific
Service Units of IST Austria through resources provided by the MIBA Machine Shop
and the Nanofabrication Facility. Work supported by the Austrian FWF grant P33692-N
(S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (J.S.) and
a NOMIS foundation research grant (J.M.F. and A.P.H.).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Soham
full_name: Mukhopadhyay, Soham
id: FDE60288-A89D-11E9-947F-1AF6E5697425
last_name: Mukhopadhyay
- first_name: Jorden L
full_name: Senior, Jorden L
id: 5479D234-2D30-11EA-89CC-40953DDC885E
last_name: Senior
orcid: 0000-0002-0672-9295
- first_name: Jaime
full_name: Saez Mollejo, Jaime
id: e0390f72-f6e0-11ea-865d-862393336714
last_name: Saez Mollejo
- first_name: Denise
full_name: Puglia, Denise
id: 4D495994-AE37-11E9-AC72-31CAE5697425
last_name: Puglia
orcid: 0000-0003-1144-2763
- 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
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Mukhopadhyay S, Senior JL, Saez Mollejo J, et al. Superconductivity from a
melted insulator in Josephson junction arrays. Nature Physics. 2023;19:1630-1635.
doi:10.1038/s41567-023-02161-w
apa: Mukhopadhyay, S., Senior, J. L., Saez Mollejo, J., Puglia, D., Zemlicka, M.,
Fink, J. M., & Higginbotham, A. P. (2023). Superconductivity from a melted
insulator in Josephson junction arrays. Nature Physics. Springer Nature.
https://doi.org/10.1038/s41567-023-02161-w
chicago: Mukhopadhyay, Soham, Jorden L Senior, Jaime Saez Mollejo, Denise Puglia,
Martin Zemlicka, Johannes M Fink, and Andrew P Higginbotham. “Superconductivity
from a Melted Insulator in Josephson Junction Arrays.” Nature Physics.
Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02161-w.
ieee: S. Mukhopadhyay et al., “Superconductivity from a melted insulator
in Josephson junction arrays,” Nature Physics, vol. 19. Springer Nature,
pp. 1630–1635, 2023.
ista: Mukhopadhyay S, Senior JL, Saez Mollejo J, Puglia D, Zemlicka M, Fink JM,
Higginbotham AP. 2023. Superconductivity from a melted insulator in Josephson
junction arrays. Nature Physics. 19, 1630–1635.
mla: Mukhopadhyay, Soham, et al. “Superconductivity from a Melted Insulator in Josephson
Junction Arrays.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1630–35,
doi:10.1038/s41567-023-02161-w.
short: S. Mukhopadhyay, J.L. Senior, J. Saez Mollejo, D. Puglia, M. Zemlicka, J.M.
Fink, A.P. Higginbotham, Nature Physics 19 (2023) 1630–1635.
date_created: 2023-08-11T07:41:17Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2024-01-29T11:27:49Z
day: '01'
ddc:
- '530'
department:
- _id: GradSch
- _id: AnHi
- _id: JoFi
doi: 10.1038/s41567-023-02161-w
ec_funded: 1
external_id:
isi:
- '001054563800006'
file:
- access_level: open_access
checksum: 1fc86d71bfbf836e221c1e925343adc5
content_type: application/pdf
creator: dernst
date_created: 2024-01-29T11:25:38Z
date_updated: 2024-01-29T11:25:38Z
file_id: '14899'
file_name: 2023_NaturePhysics_Mukhopadhyay.pdf
file_size: 1977706
relation: main_file
success: 1
file_date_updated: 2024-01-29T11:25:38Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1630-1635
project:
- _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931
grant_number: P33692
name: Cavity electromechanics across a quantum phase transition
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2
name: Protected states of quantum matter
- _id: bd5b4ec5-d553-11ed-ba76-a6eedb083344
name: Protected states of quantum matter
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Superconductivity from a melted insulator in Josephson junction arrays
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2023'
...
---
_id: '13266'
abstract:
- lang: eng
text: The 3′,5′-cyclic adenosine monophosphate (cAMP) is a versatile second messenger
in many mammalian signaling pathways. However, its role in plants remains not
well-recognized. Recent discovery of adenylate cyclase (AC) activity for transport
inhibitor response 1/auxin-signaling F-box proteins (TIR1/AFB) auxin receptors
and the demonstration of its importance for canonical auxin signaling put plant
cAMP research back into spotlight. This insight briefly summarizes the well-established
cAMP signaling pathways in mammalian cells and describes the turbulent and controversial
history of plant cAMP research highlighting the major progress and the unresolved
points. We also briefly review the current paradigm of auxin signaling to provide
a background for the discussion on the AC activity of TIR1/AFB auxin receptors
and its potential role in transcriptional auxin signaling as well as impact of
these discoveries on plant cAMP research in general.
acknowledgement: 'We gratefully acknowledge our brave colleagues, whose excellent
efforts kept the plant cAMP research going in the last two decades. The authors
were financially supported by the Austrian Science Fund (FWF): I 6123 and P 37051-B.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Linlin
full_name: Qi, Linlin
id: 44B04502-A9ED-11E9-B6FC-583AE6697425
last_name: Qi
orcid: 0000-0001-5187-8401
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Qi L, Friml J. Tale of cAMP as a second messenger in auxin signaling and beyond.
New Phytologist. 2023;240(2):489-495. doi:10.1111/nph.19123
apa: Qi, L., & Friml, J. (2023). Tale of cAMP as a second messenger in auxin
signaling and beyond. New Phytologist. Wiley. https://doi.org/10.1111/nph.19123
chicago: Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin
Signaling and Beyond.” New Phytologist. Wiley, 2023. https://doi.org/10.1111/nph.19123.
ieee: L. Qi and J. Friml, “Tale of cAMP as a second messenger in auxin signaling
and beyond,” New Phytologist, vol. 240, no. 2. Wiley, pp. 489–495, 2023.
ista: Qi L, Friml J. 2023. Tale of cAMP as a second messenger in auxin signaling
and beyond. New Phytologist. 240(2), 489–495.
mla: Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling
and Beyond.” New Phytologist, vol. 240, no. 2, Wiley, 2023, pp. 489–95,
doi:10.1111/nph.19123.
short: L. Qi, J. Friml, New Phytologist 240 (2023) 489–495.
date_created: 2023-07-23T22:01:13Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-01-29T11:21:55Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/nph.19123
external_id:
isi:
- '001026321500001'
pmid:
- '37434303'
file:
- access_level: open_access
checksum: 6d9bbd45b8e7bb3ceee2586d447bacb2
content_type: application/pdf
creator: dernst
date_created: 2024-01-29T11:21:43Z
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file_name: 2023_NewPhytologist_Qi.pdf
file_size: 974464
relation: main_file
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file_date_updated: 2024-01-29T11:21:43Z
has_accepted_license: '1'
intvolume: ' 240'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 489-495
pmid: 1
project:
- _id: bd76d395-d553-11ed-ba76-f678c14f9033
grant_number: I06123
name: Peptide receptor complexes for auxin canalization and regeneration in Arabidopsis
- _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6
grant_number: P37051
name: Guanylate cyclase activity of TIR1/AFBs auxin receptors
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: Tale of cAMP as a second messenger in auxin signaling and beyond
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 240
year: '2023'
...
---
_id: '13136'
abstract:
- lang: eng
text: Despite its fundamental importance for development, the question of how organs
achieve their correct size and shape is poorly understood. This complex process
requires coordination between the generation of cell mass and the morphogenetic
mechanisms that sculpt tissues. These processes are regulated by morphogen signalling
pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical
and mechanical signalling are quantitatively interpreted to determine the behaviours
of individual cells and how they contribute to growth and morphogenesis at the
tissue scale. In this review, we discuss the development of the vertebrate neural
tube and somites as an example of the state of knowledge, as well as the challenges
in understanding the mechanisms of tissue size control in vertebrate organogenesis.
We highlight how the recent advances in stem cell differentiation and organoid
approaches can be harnessed to provide new insights into this question.
acknowledgement: 'We thank J. Briscoe for comments on the manuscript. Work in the
AK lab is supported by ISTA, the European Research Council under Horizon Europe:
grant 101044579, and Austrian Science Fund (FWF): F78 (Stem Cell Modulation). SR
is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship
SC19-011.'
article_number: '100459'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Thomas
full_name: Minchington, Thomas
id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f
last_name: Minchington
- first_name: Stefanie
full_name: Rus, Stefanie
id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87
last_name: Rus
orcid: 0000-0001-8703-1093
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: Minchington T, Rus S, Kicheva A. Control of tissue dimensions in the developing
neural tube and somites. Current Opinion in Systems Biology. 2023;35. doi:10.1016/j.coisb.2023.100459
apa: Minchington, T., Rus, S., & Kicheva, A. (2023). Control of tissue dimensions
in the developing neural tube and somites. Current Opinion in Systems Biology.
Elsevier. https://doi.org/10.1016/j.coisb.2023.100459
chicago: Minchington, Thomas, Stefanie Rus, and Anna Kicheva. “Control of Tissue
Dimensions in the Developing Neural Tube and Somites.” Current Opinion in Systems
Biology. Elsevier, 2023. https://doi.org/10.1016/j.coisb.2023.100459.
ieee: T. Minchington, S. Rus, and A. Kicheva, “Control of tissue dimensions in the
developing neural tube and somites,” Current Opinion in Systems Biology,
vol. 35. Elsevier, 2023.
ista: Minchington T, Rus S, Kicheva A. 2023. Control of tissue dimensions in the
developing neural tube and somites. Current Opinion in Systems Biology. 35, 100459.
mla: Minchington, Thomas, et al. “Control of Tissue Dimensions in the Developing
Neural Tube and Somites.” Current Opinion in Systems Biology, vol. 35,
100459, Elsevier, 2023, doi:10.1016/j.coisb.2023.100459.
short: T. Minchington, S. Rus, A. Kicheva, Current Opinion in Systems Biology 35
(2023).
date_created: 2023-06-18T22:00:46Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2024-01-29T11:07:47Z
day: '01'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1016/j.coisb.2023.100459
file:
- access_level: open_access
checksum: 8a75c4e29fd9b62e3c50663c2265b173
content_type: application/pdf
creator: dernst
date_created: 2024-01-29T11:06:45Z
date_updated: 2024-01-29T11:06:45Z
file_id: '14896'
file_name: 2023_CurrOpSystBioloy_Minchington.pdf
file_size: 598842
relation: main_file
success: 1
file_date_updated: 2024-01-29T11:06:45Z
has_accepted_license: '1'
intvolume: ' 35'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa
grant_number: '101044579'
name: Mechanisms of tissue size regulation in spinal cord development
- _id: 059DF620-7A3F-11EA-A408-12923DDC885E
grant_number: F07802
name: Morphogen control of growth and pattern in the spinal cord
- _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A
grant_number: SC19-011
name: The regulatory logic of pattern formation in the vertebrate dorsal neural
tube
publication: Current Opinion in Systems Biology
publication_identifier:
eissn:
- 2452-3100
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Control of tissue dimensions in the developing neural tube and somites
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2023'
...
---
_id: '13135'
abstract:
- lang: eng
text: In this paper we consider a class of stochastic reaction-diffusion equations.
We provide local well-posedness, regularity, blow-up criteria and positivity of
solutions. The key novelties of this work are related to the use transport noise,
critical spaces and the proof of higher order regularity of solutions – even in
case of non-smooth initial data. Crucial tools are Lp(Lp)-theory, maximal regularity
estimates and sharp blow-up criteria. We view the results of this paper as a general
toolbox for establishing global well-posedness for a large class of reaction-diffusion
systems of practical interest, of which many are completely open. In our follow-up
work [8], the results of this paper are applied in the specific cases of the Lotka-Volterra
equations and the Brusselator model.
acknowledgement: The first author has received funding from the European Research
Council (ERC) under the European Union's Horizon 2020 research and innovation programme
(grant agreement No. 948819) Image 1. The second author is supported by the VICI
subsidy VI.C.212.027 of the Netherlands Organisation for Scientific Research (NWO).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Antonio
full_name: Agresti, Antonio
id: 673cd0cc-9b9a-11eb-b144-88f30e1fbb72
last_name: Agresti
orcid: 0000-0002-9573-2962
- first_name: Mark
full_name: Veraar, Mark
last_name: Veraar
citation:
ama: 'Agresti A, Veraar M. Reaction-diffusion equations with transport noise and
critical superlinear diffusion: Local well-posedness and positivity. Journal
of Differential Equations. 2023;368(9):247-300. doi:10.1016/j.jde.2023.05.038'
apa: 'Agresti, A., & Veraar, M. (2023). Reaction-diffusion equations with transport
noise and critical superlinear diffusion: Local well-posedness and positivity.
Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2023.05.038'
chicago: 'Agresti, Antonio, and Mark Veraar. “Reaction-Diffusion Equations with
Transport Noise and Critical Superlinear Diffusion: Local Well-Posedness and Positivity.”
Journal of Differential Equations. Elsevier, 2023. https://doi.org/10.1016/j.jde.2023.05.038.'
ieee: 'A. Agresti and M. Veraar, “Reaction-diffusion equations with transport noise
and critical superlinear diffusion: Local well-posedness and positivity,” Journal
of Differential Equations, vol. 368, no. 9. Elsevier, pp. 247–300, 2023.'
ista: 'Agresti A, Veraar M. 2023. Reaction-diffusion equations with transport noise
and critical superlinear diffusion: Local well-posedness and positivity. Journal
of Differential Equations. 368(9), 247–300.'
mla: 'Agresti, Antonio, and Mark Veraar. “Reaction-Diffusion Equations with Transport
Noise and Critical Superlinear Diffusion: Local Well-Posedness and Positivity.”
Journal of Differential Equations, vol. 368, no. 9, Elsevier, 2023, pp.
247–300, doi:10.1016/j.jde.2023.05.038.'
short: A. Agresti, M. Veraar, Journal of Differential Equations 368 (2023) 247–300.
date_created: 2023-06-18T22:00:45Z
date_published: 2023-09-25T00:00:00Z
date_updated: 2024-01-29T11:04:41Z
day: '25'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1016/j.jde.2023.05.038
ec_funded: 1
external_id:
isi:
- '001019018700001'
file:
- access_level: open_access
checksum: 246b703b091dfe047bfc79abf0891a63
content_type: application/pdf
creator: dernst
date_created: 2024-01-29T11:03:09Z
date_updated: 2024-01-29T11:03:09Z
file_id: '14895'
file_name: 2023_JourDifferentialEquations_Agresti.pdf
file_size: 834638
relation: main_file
success: 1
file_date_updated: 2024-01-29T11:03:09Z
has_accepted_license: '1'
intvolume: ' 368'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 247-300
project:
- _id: 0aa76401-070f-11eb-9043-b5bb049fa26d
call_identifier: H2020
grant_number: '948819'
name: Bridging Scales in Random Materials
publication: Journal of Differential Equations
publication_identifier:
eissn:
- 1090-2732
issn:
- 0022-0396
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Reaction-diffusion equations with transport noise and critical superlinear
diffusion: Local well-posedness and positivity'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 368
year: '2023'
...
---
_id: '13270'
abstract:
- lang: eng
text: "Consider a geodesic triangle on a surface of constant curvature and subdivide
it recursively into four triangles by joining the midpoints of its edges. We show
the existence of a uniform δ>0\r\n such that, at any step of the subdivision,
all the triangle angles lie in the interval (δ,π−δ)\r\n. Additionally, we exhibit
stabilising behaviours for both angles and lengths as this subdivision progresses."
acknowledgement: Open access funding provided by the Institute of Science and Technology
(IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Florestan R
full_name: Brunck, Florestan R
id: 6ab6e556-f394-11eb-9cf6-9dfb78f00d8d
last_name: Brunck
citation:
ama: Brunck FR. Iterated medial triangle subdivision in surfaces of constant curvature.
Discrete and Computational Geometry. 2023;70(3):1059-1089. doi:10.1007/s00454-023-00500-5
apa: Brunck, F. R. (2023). Iterated medial triangle subdivision in surfaces of constant
curvature. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-023-00500-5
chicago: Brunck, Florestan R. “Iterated Medial Triangle Subdivision in Surfaces
of Constant Curvature.” Discrete and Computational Geometry. Springer Nature,
2023. https://doi.org/10.1007/s00454-023-00500-5.
ieee: F. R. Brunck, “Iterated medial triangle subdivision in surfaces of constant
curvature,” Discrete and Computational Geometry, vol. 70, no. 3. Springer
Nature, pp. 1059–1089, 2023.
ista: Brunck FR. 2023. Iterated medial triangle subdivision in surfaces of constant
curvature. Discrete and Computational Geometry. 70(3), 1059–1089.
mla: Brunck, Florestan R. “Iterated Medial Triangle Subdivision in Surfaces of Constant
Curvature.” Discrete and Computational Geometry, vol. 70, no. 3, Springer
Nature, 2023, pp. 1059–89, doi:10.1007/s00454-023-00500-5.
short: F.R. Brunck, Discrete and Computational Geometry 70 (2023) 1059–1089.
date_created: 2023-07-23T22:01:14Z
date_published: 2023-07-05T00:00:00Z
date_updated: 2024-01-29T11:16:16Z
day: '05'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.1007/s00454-023-00500-5
external_id:
arxiv:
- '2107.04112'
isi:
- '001023742800003'
file:
- access_level: open_access
checksum: 865e68daafdd4edcfc280172ec50f5ea
content_type: application/pdf
creator: dernst
date_created: 2024-01-29T11:15:22Z
date_updated: 2024-01-29T11:15:22Z
file_id: '14897'
file_name: 2023_DiscreteComputGeometry_Brunck.pdf
file_size: 1466020
relation: main_file
success: 1
file_date_updated: 2024-01-29T11:15:22Z
has_accepted_license: '1'
intvolume: ' 70'
isi: 1
issue: '3'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1059-1089
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Iterated medial triangle subdivision in surfaces of constant curvature
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 70
year: '2023'
...
---
_id: '13269'
abstract:
- lang: eng
text: This paper is a collection of results on combinatorial properties of codes
for the Z-channel . A Z-channel with error fraction τ takes as input a length-
n binary codeword and injects in an adversarial manner up to n τ asymmetric errors,
i.e., errors that only zero out bits but do not flip 0’s to 1’s. It is known that
the largest ( L - 1)-list-decodable code for the Z-channel with error fraction
τ has exponential size (in n ) if τ is less than a critical value that we call
the ( L - 1)- list-decoding Plotkin point and has constant size if τ is larger
than the threshold. The ( L -1)-list-decoding Plotkin point is known to be L -1/L-1
– L -L/ L-1 , which equals 1/4 for unique-decoding with L -1 = 1. In this paper,
we derive various results for the size of the largest codes above and below the
list-decoding Plotkin point. In particular, we show that the largest ( L -1)-list-decodable
code ε-above the Plotkin point, for any given sufficiently small positive constant
ε > 0, has size Θ L (ε -3/2 ) for any L - 1 ≥ 1. We also devise upper and lower
bounds on the exponential size of codes below the list-decoding Plotkin point.
acknowledgement: "Nikita Polyanskii’s research was conducted in part during October
2020 - December 2021 with the Technical University of Munich and the Skolkovo Institute
of Science and Technology. His work was supported by the German Research Foundation
(Deutsche Forschungsgemeinschaft, DFG) under Grant No. WA3907/1-1 and the Russian
Foundation for Basic Research (RFBR)\r\nunder Grant No. 20-01-00559.\r\nYihan Zhang
is supported by funding from the European Union’s Horizon 2020 research and innovation
programme under grant agreement No 682203-ERC-[Inf-Speed-Tradeoff]."
article_processing_charge: No
article_type: original
author:
- first_name: Nikita
full_name: Polyanskii, Nikita
last_name: Polyanskii
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
orcid: 0000-0002-6465-6258
citation:
ama: Polyanskii N, Zhang Y. Codes for the Z-channel. IEEE Transactions on Information
Theory. 2023;69(10):6340-6357. doi:10.1109/TIT.2023.3292219
apa: Polyanskii, N., & Zhang, Y. (2023). Codes for the Z-channel. IEEE Transactions
on Information Theory. Institute of Electrical and Electronics Engineers.
https://doi.org/10.1109/TIT.2023.3292219
chicago: Polyanskii, Nikita, and Yihan Zhang. “Codes for the Z-Channel.” IEEE
Transactions on Information Theory. Institute of Electrical and Electronics
Engineers, 2023. https://doi.org/10.1109/TIT.2023.3292219.
ieee: N. Polyanskii and Y. Zhang, “Codes for the Z-channel,” IEEE Transactions
on Information Theory, vol. 69, no. 10. Institute of Electrical and Electronics
Engineers, pp. 6340–6357, 2023.
ista: Polyanskii N, Zhang Y. 2023. Codes for the Z-channel. IEEE Transactions on
Information Theory. 69(10), 6340–6357.
mla: Polyanskii, Nikita, and Yihan Zhang. “Codes for the Z-Channel.” IEEE Transactions
on Information Theory, vol. 69, no. 10, Institute of Electrical and Electronics
Engineers, 2023, pp. 6340–57, doi:10.1109/TIT.2023.3292219.
short: N. Polyanskii, Y. Zhang, IEEE Transactions on Information Theory 69 (2023)
6340–6357.
date_created: 2023-07-23T22:01:14Z
date_published: 2023-07-04T00:00:00Z
date_updated: 2024-01-29T11:10:54Z
day: '04'
department:
- _id: MaMo
doi: 10.1109/TIT.2023.3292219
external_id:
arxiv:
- '2105.01427'
isi:
- '001069680100011'
intvolume: ' 69'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2105.01427
month: '07'
oa: 1
oa_version: Preprint
page: 6340-6357
publication: IEEE Transactions on Information Theory
publication_identifier:
eissn:
- 1557-9654
issn:
- 0018-9448
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Codes for the Z-channel
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 69
year: '2023'
...
---
_id: '13128'
abstract:
- lang: eng
text: "Given A⊆GL2(Fq), we prove that there exist disjoint subsets B,C⊆A such
that A=B⊔C and their additive and multiplicative energies satisfying max{E+(B),E×(C)}≪|A|3/M(|A|),
where\r\nM(|A|)=min{q4/3/|A|1/3(log|A|)2/3,|A|4/5/q13/5(log|A|)27/10}.\r\n We
also study some related questions on moderate expanders over matrix rings, namely,
for A,B,C⊆GL2(Fq), we have |AB+C|, |(A+B)C|≫q4, whenever |A||B||C|≫q10+1/2.
These improve earlier results due to Karabulut, Koh, Pham, Shen, and Vinh ([2019],
Expanding phenomena over matrix rings, ForumMath., 31, 951–970).\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Ali
full_name: Mohammadi, Ali
last_name: Mohammadi
- first_name: Thang
full_name: Pham, Thang
last_name: Pham
- first_name: Yiting
full_name: Wang, Yiting
id: 1917d194-076e-11ed-97cd-837255f88785
last_name: Wang
orcid: 0000-0002-2856-767X
citation:
ama: Mohammadi A, Pham T, Wang Y. An energy decomposition theorem for matrices and
related questions. Canadian Mathematical Bulletin. 2023;66(4):1280-1295.
doi:10.4153/S000843952300036X
apa: Mohammadi, A., Pham, T., & Wang, Y. (2023). An energy decomposition theorem
for matrices and related questions. Canadian Mathematical Bulletin. Cambridge
University Press. https://doi.org/10.4153/S000843952300036X
chicago: Mohammadi, Ali, Thang Pham, and Yiting Wang. “An Energy Decomposition Theorem
for Matrices and Related Questions.” Canadian Mathematical Bulletin. Cambridge
University Press, 2023. https://doi.org/10.4153/S000843952300036X.
ieee: A. Mohammadi, T. Pham, and Y. Wang, “An energy decomposition theorem for matrices
and related questions,” Canadian Mathematical Bulletin, vol. 66, no. 4.
Cambridge University Press, pp. 1280–1295, 2023.
ista: Mohammadi A, Pham T, Wang Y. 2023. An energy decomposition theorem for matrices
and related questions. Canadian Mathematical Bulletin. 66(4), 1280–1295.
mla: Mohammadi, Ali, et al. “An Energy Decomposition Theorem for Matrices and Related
Questions.” Canadian Mathematical Bulletin, vol. 66, no. 4, Cambridge University
Press, 2023, pp. 1280–95, doi:10.4153/S000843952300036X.
short: A. Mohammadi, T. Pham, Y. Wang, Canadian Mathematical Bulletin 66 (2023)
1280–1295.
date_created: 2023-06-11T22:00:40Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-01-29T11:00:46Z
day: '01'
department:
- _id: GradSch
doi: 10.4153/S000843952300036X
external_id:
arxiv:
- '2106.07328'
isi:
- '001011963000001'
intvolume: ' 66'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2106.07328
month: '12'
oa: 1
oa_version: Preprint
page: 1280-1295
publication: Canadian Mathematical Bulletin
publication_identifier:
eissn:
- 1496-4287
issn:
- 0008-4395
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: An energy decomposition theorem for matrices and related questions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 66
year: '2023'
...
---
_id: '13209'
abstract:
- lang: eng
text: The phytohormone auxin plays central roles in many growth and developmental
processes in plants. Development of chemical tools targeting the auxin pathway
is useful for both plant biology and agriculture. Here we reveal that naproxen,
a synthetic compound with anti-inflammatory activity in humans, acts as an auxin
transport inhibitor targeting PIN-FORMED (PIN) transporters in plants. Physiological
experiments indicate that exogenous naproxen treatment affects pleiotropic auxin-regulated
developmental processes. Additional cellular and biochemical evidence indicates
that naproxen suppresses auxin transport, specifically PIN-mediated auxin efflux.
Moreover, biochemical and structural analyses confirm that naproxen binds directly
to PIN1 protein via the same binding cavity as the indole-3-acetic acid substrate.
Thus, by combining cellular, biochemical, and structural approaches, this study
clearly establishes that naproxen is a PIN inhibitor and elucidates the underlying
mechanisms. Further use of this compound may advance our understanding of the
molecular mechanisms of PIN-mediated auxin transport and expand our toolkit in
auxin biology and agriculture.
acknowledgement: "This work was supported by the Strategic Priority Research Program
of the Chinese Academy of Sciences (XDB37020103 to Linfeng Sun); research funds
from the Center for Advanced Interdisciplinary Science\r\nand Biomedicine of IHM,
Division of Life Sciences and Medicine, University of Science and Technology of
China (QYPY20220012 to S.T.); start-up funding from the University of Science and
Technology of China and the\r\nChinese Academy of Sciences (GG9100007007, KY9100000026,KY9100000051,
and KJ2070000079 to S.T.); the National Natural Science Foundation of China (31900885
to X.L. and 31870732 to Linfeng Sun); the Natural Science Foundation of Anhui Province
(2008085MC90 to X.L. and 2008085J15 to Linfeng Sun); the Fundamental Research Funds
for the Central Universities (WK9100000021 to S.T. and WK9100000031 to Linfeng Sun);
and the USTC Research Funds of the Double First-Class Initiative (YD9100002016 to
S.T. and YD9100002004 to Linfeng Sun). Linfeng Sun is supported by an Outstanding
Young Scholar Award from the Qiu Shi Science and Technologies Foundation and a Young
Scholar Award from the Cyrus Tang Foundation.We thank Dr. Yang Zhao for sharing
published materials (Center for Excellence in Molecular Plant Sciences, Chinese
Academy of Sciences) and the Cryo-EM Center of the University of Science and Technology
of China for the EM facility support. We are grateful to Y. Gao and all other staff
members for their technical support on cryo-EM data collection. "
article_number: '100632'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jing
full_name: Xia, Jing
last_name: Xia
- first_name: Mengjuan
full_name: Kong, Mengjuan
last_name: Kong
- first_name: Zhisen
full_name: Yang, Zhisen
last_name: Yang
- first_name: Lianghanxiao
full_name: Sun, Lianghanxiao
last_name: Sun
- first_name: Yakun
full_name: Peng, Yakun
last_name: Peng
- first_name: Yanbo
full_name: Mao, Yanbo
last_name: Mao
- first_name: Hong
full_name: Wei, Hong
last_name: Wei
- first_name: Wei
full_name: Ying, Wei
last_name: Ying
- first_name: Yongxiao
full_name: Gao, Yongxiao
last_name: Gao
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jianping
full_name: Weng, Jianping
last_name: Weng
- first_name: Xin
full_name: Liu, Xin
last_name: Liu
- first_name: Linfeng
full_name: Sun, Linfeng
last_name: Sun
- first_name: Shutang
full_name: Tan, Shutang
last_name: Tan
citation:
ama: Xia J, Kong M, Yang Z, et al. Chemical inhibition of Arabidopsis PIN-FORMED
auxin transporters by the anti-inflammatory drug naproxen. Plant Communications.
2023;4(6). doi:10.1016/j.xplc.2023.100632
apa: Xia, J., Kong, M., Yang, Z., Sun, L., Peng, Y., Mao, Y., … Tan, S. (2023).
Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory
drug naproxen. Plant Communications. Elsevier . https://doi.org/10.1016/j.xplc.2023.100632
chicago: Xia, Jing, Mengjuan Kong, Zhisen Yang, Lianghanxiao Sun, Yakun Peng, Yanbo
Mao, Hong Wei, et al. “Chemical Inhibition of Arabidopsis PIN-FORMED Auxin Transporters
by the Anti-Inflammatory Drug Naproxen.” Plant Communications. Elsevier
, 2023. https://doi.org/10.1016/j.xplc.2023.100632.
ieee: J. Xia et al., “Chemical inhibition of Arabidopsis PIN-FORMED auxin
transporters by the anti-inflammatory drug naproxen,” Plant Communications,
vol. 4, no. 6. Elsevier , 2023.
ista: Xia J, Kong M, Yang Z, Sun L, Peng Y, Mao Y, Wei H, Ying W, Gao Y, Friml J,
Weng J, Liu X, Sun L, Tan S. 2023. Chemical inhibition of Arabidopsis PIN-FORMED
auxin transporters by the anti-inflammatory drug naproxen. Plant Communications.
4(6), 100632.
mla: Xia, Jing, et al. “Chemical Inhibition of Arabidopsis PIN-FORMED Auxin Transporters
by the Anti-Inflammatory Drug Naproxen.” Plant Communications, vol. 4,
no. 6, 100632, Elsevier , 2023, doi:10.1016/j.xplc.2023.100632.
short: J. Xia, M. Kong, Z. Yang, L. Sun, Y. Peng, Y. Mao, H. Wei, W. Ying, Y. Gao,
J. Friml, J. Weng, X. Liu, L. Sun, S. Tan, Plant Communications 4 (2023).
date_created: 2023-07-12T07:32:00Z
date_published: 2023-11-13T00:00:00Z
date_updated: 2024-01-30T10:55:34Z
day: '13'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.xplc.2023.100632
external_id:
isi:
- '001113003000001'
pmid:
- '37254481'
file:
- access_level: open_access
checksum: f8ef92af6096834f91ce38587fb1db9f
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T10:54:40Z
date_updated: 2024-01-30T10:54:40Z
file_id: '14900'
file_name: 2023_PlantCommunications_Xia.pdf
file_size: 1434862
relation: main_file
success: 1
file_date_updated: 2024-01-30T10:54:40Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Plant Communications
publication_identifier:
eissn:
- 2590-3462
publication_status: published
publisher: 'Elsevier '
quality_controlled: '1'
status: public
title: Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory
drug naproxen
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2023'
...
---
_id: '13971'
abstract:
- lang: eng
text: When in equilibrium, thermal forces agitate molecules, which then diffuse,
collide and bind to form materials. However, the space of accessible structures
in which micron-scale particles can be organized by thermal forces is limited,
owing to the slow dynamics and metastable states. Active agents in a passive fluid
generate forces and flows, forming a bath with active fluctuations. Two unanswered
questions are whether those active agents can drive the assembly of passive components
into unconventional states and which material properties they will exhibit. Here
we show that passive, sticky beads immersed in a bath of swimming Escherichia
coli bacteria aggregate into unconventional clusters and gels that are controlled
by the activity of the bath. We observe a slow but persistent rotation of the
aggregates that originates in the chirality of the E. coli flagella and directs
aggregation into structures that are not accessible thermally. We elucidate the
aggregation mechanism with a numerical model of spinning, sticky beads and reproduce
quantitatively the experimental results. We show that internal activity controls
the phase diagram and the structure of the aggregates. Overall, our results highlight
the promising role of active baths in designing the structural and mechanical
properties of materials with unconventional phases.
acknowledgement: D.G. and J.P. thank E. Krasnopeeva, C. Guet, G. Guessous and T. Hwa
for providing the E. coli strains. This material is based upon work supported by
the US Department of Energy under award DE-SC0019769. I.P. acknowledges funding
by the European Union’s Horizon 2020 research and innovation programme under Marie
Skłodowska-Curie Grant Agreement No. 101034413. A.Š. acknowledges funding from the
European Research Council under the European Union’s Horizon 2020 research and innovation
programme (Grant No. 802960). M.C.U. acknowledges funding from the European Union’s
Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant
Agreement No. 754411.
article_processing_charge: Yes
article_type: original
author:
- first_name: Daniel
full_name: Grober, Daniel
id: abdfc56f-34fb-11ee-bd33-fd766fce5a99
last_name: Grober
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- 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: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- 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: Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. Unconventional
colloidal aggregation in chiral bacterial baths. Nature Physics. 2023;19:1680-1688.
doi:10.1038/s41567-023-02136-x
apa: Grober, D., Palaia, I., Ucar, M. C., Hannezo, E. B., Šarić, A., & Palacci,
J. A. (2023). Unconventional colloidal aggregation in chiral bacterial baths.
Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02136-x
chicago: Grober, Daniel, Ivan Palaia, Mehmet C Ucar, Edouard B Hannezo, Anđela Šarić,
and Jérémie A Palacci. “Unconventional Colloidal Aggregation in Chiral Bacterial
Baths.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02136-x.
ieee: D. Grober, I. Palaia, M. C. Ucar, E. B. Hannezo, A. Šarić, and J. A. Palacci,
“Unconventional colloidal aggregation in chiral bacterial baths,” Nature Physics,
vol. 19. Springer Nature, pp. 1680–1688, 2023.
ista: Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. 2023. Unconventional
colloidal aggregation in chiral bacterial baths. Nature Physics. 19, 1680–1688.
mla: Grober, Daniel, et al. “Unconventional Colloidal Aggregation in Chiral Bacterial
Baths.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1680–88, doi:10.1038/s41567-023-02136-x.
short: D. Grober, I. Palaia, M.C. Ucar, E.B. Hannezo, A. Šarić, J.A. Palacci, Nature
Physics 19 (2023) 1680–1688.
date_created: 2023-08-06T22:01:11Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2024-01-30T12:26:55Z
day: '01'
ddc:
- '530'
department:
- _id: EdHa
- _id: AnSa
- _id: JePa
doi: 10.1038/s41567-023-02136-x
ec_funded: 1
external_id:
isi:
- '001037346400005'
file:
- access_level: open_access
checksum: 7e282c2ebc0ac82125a04f6b4742d4c1
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:26:08Z
date_updated: 2024-01-30T12:26:08Z
file_id: '14906'
file_name: 2023_NaturePhysics_Grober.pdf
file_size: 6365607
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:26:08Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1680-1688
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unconventional colloidal aggregation in chiral bacterial baths
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2023'
...
---
_id: '10551'
abstract:
- lang: eng
text: 'The Dean–Kawasaki equation—a strongly singular SPDE—is a basic equation of
fluctuating hydrodynamics; it has been proposed in the physics literature to describe
the fluctuations of the density of N independent diffusing particles in the regime
of large particle numbers N≫1. The singular nature of the Dean–Kawasaki equation
presents a substantial challenge for both its analysis and its rigorous mathematical
justification. Besides being non-renormalisable by the theory of regularity structures
by Hairer et al., it has recently been shown to not even admit nontrivial martingale
solutions. In the present work, we give a rigorous and fully quantitative justification
of the Dean–Kawasaki equation by considering the natural regularisation provided
by standard numerical discretisations: We show that structure-preserving discretisations
of the Dean–Kawasaki equation may approximate the density fluctuations of N non-interacting
diffusing particles to arbitrary order in N−1 (in suitable weak metrics). In
other words, the Dean–Kawasaki equation may be interpreted as a “recipe” for accurate
and efficient numerical simulations of the density fluctuations of independent
diffusing particles.'
acknowledgement: "We thank the anonymous referee for his/her careful reading of the
manuscript and valuable suggestions. FC gratefully acknowledges funding from the
Austrian Science Fund (FWF) through the project F65, and from the European Union’s
Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 754411.\r\nOpen access funding provided by Austrian Science
Fund (FWF)."
article_number: '76'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Federico
full_name: Cornalba, Federico
id: 2CEB641C-A400-11E9-A717-D712E6697425
last_name: Cornalba
orcid: 0000-0002-6269-5149
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: Cornalba F, Fischer JL. The Dean-Kawasaki equation and the structure of density
fluctuations in systems of diffusing particles. Archive for Rational Mechanics
and Analysis. 2023;247(5). doi:10.1007/s00205-023-01903-7
apa: Cornalba, F., & Fischer, J. L. (2023). The Dean-Kawasaki equation and the
structure of density fluctuations in systems of diffusing particles. Archive
for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-023-01903-7
chicago: Cornalba, Federico, and Julian L Fischer. “The Dean-Kawasaki Equation and
the Structure of Density Fluctuations in Systems of Diffusing Particles.” Archive
for Rational Mechanics and Analysis. Springer Nature, 2023. https://doi.org/10.1007/s00205-023-01903-7.
ieee: F. Cornalba and J. L. Fischer, “The Dean-Kawasaki equation and the structure
of density fluctuations in systems of diffusing particles,” Archive for Rational
Mechanics and Analysis, vol. 247, no. 5. Springer Nature, 2023.
ista: Cornalba F, Fischer JL. 2023. The Dean-Kawasaki equation and the structure
of density fluctuations in systems of diffusing particles. Archive for Rational
Mechanics and Analysis. 247(5), 76.
mla: Cornalba, Federico, and Julian L. Fischer. “The Dean-Kawasaki Equation and
the Structure of Density Fluctuations in Systems of Diffusing Particles.” Archive
for Rational Mechanics and Analysis, vol. 247, no. 5, 76, Springer Nature,
2023, doi:10.1007/s00205-023-01903-7.
short: F. Cornalba, J.L. Fischer, Archive for Rational Mechanics and Analysis 247
(2023).
date_created: 2021-12-16T12:16:03Z
date_published: 2023-08-04T00:00:00Z
date_updated: 2024-01-30T12:10:10Z
day: '04'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s00205-023-01903-7
ec_funded: 1
external_id:
arxiv:
- '2109.06500'
isi:
- '001043086800001'
file:
- access_level: open_access
checksum: 4529eeff170b6745a461d397ee611b5a
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:09:34Z
date_updated: 2024-01-30T12:09:34Z
file_id: '14904'
file_name: 2023_ArchiveRationalMech_Cornalba.pdf
file_size: 1851185
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:09:34Z
has_accepted_license: '1'
intvolume: ' 247'
isi: 1
issue: '5'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _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: Archive for Rational Mechanics and Analysis
publication_identifier:
eissn:
- 1432-0673
issn:
- 0003-9527
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Dean-Kawasaki equation and the structure of density fluctuations in systems
of diffusing particles
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 247
year: '2023'
...
---
_id: '13234'
abstract:
- lang: eng
text: Neural-network classifiers achieve high accuracy when predicting the class
of an input that they were trained to identify. Maintaining this accuracy in dynamic
environments, where inputs frequently fall outside the fixed set of initially
known classes, remains a challenge. We consider the problem of monitoring the
classification decisions of neural networks in the presence of novel classes.
For this purpose, we generalize our recently proposed abstraction-based monitor
from binary output to real-valued quantitative output. This quantitative output
enables new applications, two of which we investigate in the paper. As our first
application, we introduce an algorithmic framework for active monitoring of a
neural network, which allows us to learn new classes dynamically and yet maintain
high monitoring performance. As our second application, we present an offline
procedure to retrain the neural network to improve the monitor’s detection performance
without deteriorating the network’s classification accuracy. Our experimental
evaluation demonstrates both the benefits of our active monitoring framework in
dynamic scenarios and the effectiveness of the retraining procedure.
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093, by
DIREC - Digital Research Centre Denmark, and by the Villum Investigator Grant S4OS.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Konstantin
full_name: Kueffner, Konstantin
id: 8121a2d0-dc85-11ea-9058-af578f3b4515
last_name: Kueffner
orcid: 0000-0001-8974-2542
- first_name: Anna
full_name: Lukina, Anna
id: CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425
last_name: Lukina
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Kueffner K, Lukina A, Schilling C, Henzinger TA. Into the unknown: Active
monitoring of neural networks (extended version). International Journal on
Software Tools for Technology Transfer. 2023;25:575-592. doi:10.1007/s10009-023-00711-4'
apa: 'Kueffner, K., Lukina, A., Schilling, C., & Henzinger, T. A. (2023). Into
the unknown: Active monitoring of neural networks (extended version). International
Journal on Software Tools for Technology Transfer. Springer Nature. https://doi.org/10.1007/s10009-023-00711-4'
chicago: 'Kueffner, Konstantin, Anna Lukina, Christian Schilling, and Thomas A Henzinger.
“Into the Unknown: Active Monitoring of Neural Networks (Extended Version).” International
Journal on Software Tools for Technology Transfer. Springer Nature, 2023.
https://doi.org/10.1007/s10009-023-00711-4.'
ieee: 'K. Kueffner, A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown:
Active monitoring of neural networks (extended version),” International Journal
on Software Tools for Technology Transfer, vol. 25. Springer Nature, pp. 575–592,
2023.'
ista: 'Kueffner K, Lukina A, Schilling C, Henzinger TA. 2023. Into the unknown:
Active monitoring of neural networks (extended version). International Journal
on Software Tools for Technology Transfer. 25, 575–592.'
mla: 'Kueffner, Konstantin, et al. “Into the Unknown: Active Monitoring of Neural
Networks (Extended Version).” International Journal on Software Tools for Technology
Transfer, vol. 25, Springer Nature, 2023, pp. 575–92, doi:10.1007/s10009-023-00711-4.'
short: K. Kueffner, A. Lukina, C. Schilling, T.A. Henzinger, International Journal
on Software Tools for Technology Transfer 25 (2023) 575–592.
date_created: 2023-07-16T22:01:11Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2024-01-30T12:06:57Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/s10009-023-00711-4
ec_funded: 1
external_id:
arxiv:
- '2009.06429'
isi:
- '001020160000001'
file:
- access_level: open_access
checksum: 3c4b347f39412a76872f9a6f30101f94
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:06:07Z
date_updated: 2024-01-30T12:06:07Z
file_id: '14903'
file_name: 2023_JourSoftwareTools_Kueffner.pdf
file_size: 13387667
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:06:07Z
has_accepted_license: '1'
intvolume: ' 25'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 575-592
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: International Journal on Software Tools for Technology Transfer
publication_identifier:
eissn:
- 1433-2787
issn:
- 1433-2779
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '10206'
relation: shorter_version
status: public
scopus_import: '1'
status: public
title: 'Into the unknown: Active monitoring of neural networks (extended version)'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2023'
...
---
_id: '14036'
abstract:
- lang: eng
text: Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) is establishing
itself as a powerful method for the characterization of protein dynamics at the
atomic scale. We discuss here how R1ρ MAS relaxation dispersion NMR can explore
microsecond-to-millisecond motions. Progress in instrumentation, isotope labeling,
and pulse sequence design has paved the way for quantitative analyses of even
rare structural fluctuations. In addition to isotropic chemical-shift fluctuations
exploited in solution-state NMR relaxation dispersion experiments, MAS NMR has
a wider arsenal of observables, allowing to see motions even if the exchanging
states do not differ in their chemical shifts. We demonstrate the potential of
the technique for probing motions in challenging large enzymes, membrane proteins,
and protein assemblies.
acknowledgement: We thank Petra Rovó for critical reading of this manuscript. We acknowledge
the Austrian Science Foundation FWF (project AlloSpace, number I5812–B) and funding
by the Institute of Science and Technology Austria.
article_number: '102660'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Federico
full_name: Napoli, Federico
id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b
last_name: Napoli
orcid: 0000-0002-9043-136X
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Napoli F, Becker LM, Schanda P. Protein dynamics detected by magic-angle spinning
relaxation dispersion NMR. Current Opinion in Structural Biology. 2023;82(10).
doi:10.1016/j.sbi.2023.102660
apa: Napoli, F., Becker, L. M., & Schanda, P. (2023). Protein dynamics detected
by magic-angle spinning relaxation dispersion NMR. Current Opinion in Structural
Biology. Elsevier. https://doi.org/10.1016/j.sbi.2023.102660
chicago: Napoli, Federico, Lea Marie Becker, and Paul Schanda. “Protein Dynamics
Detected by Magic-Angle Spinning Relaxation Dispersion NMR.” Current Opinion
in Structural Biology. Elsevier, 2023. https://doi.org/10.1016/j.sbi.2023.102660.
ieee: F. Napoli, L. M. Becker, and P. Schanda, “Protein dynamics detected by magic-angle
spinning relaxation dispersion NMR,” Current Opinion in Structural Biology,
vol. 82, no. 10. Elsevier, 2023.
ista: Napoli F, Becker LM, Schanda P. 2023. Protein dynamics detected by magic-angle
spinning relaxation dispersion NMR. Current Opinion in Structural Biology. 82(10),
102660.
mla: Napoli, Federico, et al. “Protein Dynamics Detected by Magic-Angle Spinning
Relaxation Dispersion NMR.” Current Opinion in Structural Biology, vol.
82, no. 10, 102660, Elsevier, 2023, doi:10.1016/j.sbi.2023.102660.
short: F. Napoli, L.M. Becker, P. Schanda, Current Opinion in Structural Biology
82 (2023).
date_created: 2023-08-13T22:01:11Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-01-30T12:37:36Z
day: '01'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1016/j.sbi.2023.102660
external_id:
isi:
- '001053616200001'
pmid:
- '37536064'
file:
- access_level: open_access
checksum: c850f7ac8a4234319755b672c1df69ae
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:36:39Z
date_updated: 2024-01-30T12:36:39Z
file_id: '14907'
file_name: 2023_CurrentOpinionStrucBio_Napoli.pdf
file_size: 1231998
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:36:39Z
intvolume: ' 82'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
grant_number: I05812
name: AlloSpace. The emergence and mechanisms of allostery
publication: Current Opinion in Structural Biology
publication_identifier:
eissn:
- 1879-033X
issn:
- 0959-440X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protein dynamics detected by magic-angle spinning relaxation dispersion NMR
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 82
year: '2023'
...
---
_id: '14043'
abstract:
- lang: eng
text: 'Over the last two decades, a significant line of work in theoretical algorithms
has made progress in solving linear systems of the form Lx=b, where L is the Laplacian
matrix of a weighted graph with weights w(i,j)>0 on the edges. The solution x
of the linear system can be interpreted as the potentials of an electrical flow
in which the resistance on edge (i, j) is 1/w(i, j). Kelner et al. (in: Proceedings
of the 45th Annual ACM Symposium on the Theory of Computing, pp 911–920, 2013.
https://doi.org/10.1145/2488608.2488724) give a combinatorial, near-linear time
algorithm that maintains the Kirchoff Current Law, and gradually enforces the
Kirchoff Potential Law by updating flows around cycles (cycle toggling). In this
paper, we consider a dual version of the algorithm that maintains the Kirchoff
Potential Law, and gradually enforces the Kirchoff Current Law by cut toggling:
each iteration updates all potentials on one side of a fundamental cut of a spanning
tree by the same amount. We prove that this dual algorithm also runs in a near-linear
number of iterations. We show, however, that if we abstract cut toggling as a
natural data structure problem, this problem can be reduced to the online vector–matrix-vector
problem, which has been conjectured to be difficult for dynamic algorithms (Henzinger
et al., in: Proceedings of the 47th Annual ACM Symposium on the Theory of Computing,
pp 21–30, 2015. https://doi.org/10.1145/2746539.2746609). The conjecture implies
that the data structure does not have an O(n1−ϵ) time algorithm for any ϵ>0, and
thus a straightforward implementation of the cut-toggling algorithm requires essentially
linear time per iteration. To circumvent the lower bound, we batch update steps,
and perform them simultaneously instead of sequentially. An appropriate choice
of batching leads to an O˜(m1.5) time cut-toggling algorithm for solving Laplacian
systems. Furthermore, we show that if we sparsify the graph and call our algorithm
recursively on the Laplacian system implied by batching and sparsifying, we can
reduce the running time to O(m1+ϵ) for any ϵ>0. Thus, the dual cut-toggling algorithm
can achieve (almost) the same running time as its primal cycle-toggling counterpart.'
acknowledgement: Monika Henzinger was supported by funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures
(MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms
for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from
the netidee SCIENCE Stiftung, 2020–2024. Billy Jin was Supported in part by NSERC
fellowship PGSD3-532673-2019 and NSF grant CCF-2007009. Richard Peng was supported
in part by an NSERC Discovery Grant and NSF grant CCF-1846218. David P. Williamson
was supported in part by NSF grant CCF-2007009.
article_processing_charge: No
article_type: original
author:
- 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: Billy
full_name: Jin, Billy
last_name: Jin
- first_name: Richard
full_name: Peng, Richard
last_name: Peng
- first_name: David P.
full_name: Williamson, David P.
last_name: Williamson
citation:
ama: Henzinger MH, Jin B, Peng R, Williamson DP. A combinatorial cut-toggling algorithm
for solving Laplacian linear systems. Algorithmica. 2023;85:2680-3716.
doi:10.1007/s00453-023-01154-8
apa: Henzinger, M. H., Jin, B., Peng, R., & Williamson, D. P. (2023). A combinatorial
cut-toggling algorithm for solving Laplacian linear systems. Algorithmica.
Springer Nature. https://doi.org/10.1007/s00453-023-01154-8
chicago: Henzinger, Monika H, Billy Jin, Richard Peng, and David P. Williamson.
“A Combinatorial Cut-Toggling Algorithm for Solving Laplacian Linear Systems.”
Algorithmica. Springer Nature, 2023. https://doi.org/10.1007/s00453-023-01154-8.
ieee: M. H. Henzinger, B. Jin, R. Peng, and D. P. Williamson, “A combinatorial cut-toggling
algorithm for solving Laplacian linear systems,” Algorithmica, vol. 85.
Springer Nature, pp. 2680–3716, 2023.
ista: Henzinger MH, Jin B, Peng R, Williamson DP. 2023. A combinatorial cut-toggling
algorithm for solving Laplacian linear systems. Algorithmica. 85, 2680–3716.
mla: Henzinger, Monika H., et al. “A Combinatorial Cut-Toggling Algorithm for Solving
Laplacian Linear Systems.” Algorithmica, vol. 85, Springer Nature, 2023,
pp. 2680–3716, doi:10.1007/s00453-023-01154-8.
short: M.H. Henzinger, B. Jin, R. Peng, D.P. Williamson, Algorithmica 85 (2023)
2680–3716.
date_created: 2023-08-13T22:01:13Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-01-30T12:33:10Z
day: '01'
department:
- _id: MoHe
doi: 10.1007/s00453-023-01154-8
ec_funded: 1
external_id:
arxiv:
- '2010.16316'
isi:
- '001041254900002'
intvolume: ' 85'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2010.16316
month: '12'
oa: 1
oa_version: Preprint
page: 2680-3716
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: 'P33775 '
name: Fast Algorithms for a Reactive Network Layer
publication: Algorithmica
publication_identifier:
eissn:
- 1432-0541
issn:
- 0178-4617
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A combinatorial cut-toggling algorithm for solving Laplacian linear systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 85
year: '2023'
...
---
_id: '14087'
abstract:
- lang: eng
text: Polar active matter of self-propelled particles sustain spontaneous flows
through the full-integer topological defects. We study theoretically the incompressible
flow profiles around ±1 defects induced by polar and dipolar active forces. We
show that dipolar forces induce vortical flows around the +1 defect, while the
flow around the −1 defect has an 8-fold rotational symmetry. The vortical flow
changes its chirality near the +1 defect core in the absence of the friction with
a substrate. We show analytically that the flow induced by polar active forces
is vortical near the +1 defect and is 4-fold symmetric near the −1 defect, while
it becomes uniform in the far-field. For a pair of oppositely charged defects,
this polar flow contributes to a mutual interaction force that depends only on
the orientation of the defect pair relative to the background polarization, and
that enhances defect pair annihilation. This is in contradiction with the effect
of dipolar active forces which decay inversely proportional with the defect separation
distance. As such, our analyses reveals a long-ranged mechanism for the pairwise
interaction between topological defects in polar active matter.
acknowledgement: J. Rø and L. A. acknowledge support from the Research Council of
Norway through the Center of Excellence funding scheme, Project No. 262644 (PoreLab).
A. D. acknowledges funding from the Novo Nordisk Foundation (grant No. NNF18SA0035142
and NERD grant No. NNF21OC0068687), Villum Fonden Grant no. 29476, and the European
Union via the ERC-Starting Grant PhysCoMeT. Views and opinions expressed are however
those of the authors only and do not necessarily reflect those of the European Union
or the European Research Council. Neither the European Union nor the granting authority
can be held responsible for them.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jonas
full_name: Rønning, Jonas
last_name: Rønning
- first_name: Julian B
full_name: Renaud, Julian B
id: 7af6767d-14eb-11ed-b536-a32449ae867c
last_name: Renaud
- first_name: Amin
full_name: Doostmohammadi, Amin
last_name: Doostmohammadi
- first_name: Luiza
full_name: Angheluta, Luiza
last_name: Angheluta
citation:
ama: Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. Spontaneous flows and
dynamics of full-integer topological defects in polar active matter. Soft Matter.
2023;39:7513-7527. doi:10.1039/d3sm00316g
apa: Rønning, J., Renaud, J. B., Doostmohammadi, A., & Angheluta, L. (2023).
Spontaneous flows and dynamics of full-integer topological defects in polar active
matter. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d3sm00316g
chicago: Rønning, Jonas, Julian B Renaud, Amin Doostmohammadi, and Luiza Angheluta.
“Spontaneous Flows and Dynamics of Full-Integer Topological Defects in Polar Active
Matter.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3sm00316g.
ieee: J. Rønning, J. B. Renaud, A. Doostmohammadi, and L. Angheluta, “Spontaneous
flows and dynamics of full-integer topological defects in polar active matter,”
Soft Matter, vol. 39. Royal Society of Chemistry, pp. 7513–7527, 2023.
ista: Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. 2023. Spontaneous flows
and dynamics of full-integer topological defects in polar active matter. Soft
Matter. 39, 7513–7527.
mla: Rønning, Jonas, et al. “Spontaneous Flows and Dynamics of Full-Integer Topological
Defects in Polar Active Matter.” Soft Matter, vol. 39, Royal Society of
Chemistry, 2023, pp. 7513–27, doi:10.1039/d3sm00316g.
short: J. Rønning, J.B. Renaud, A. Doostmohammadi, L. Angheluta, Soft Matter 39
(2023) 7513–7527.
date_created: 2023-08-20T22:01:15Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2024-01-30T12:49:24Z
day: '01'
ddc:
- '540'
department:
- _id: GradSch
doi: 10.1039/d3sm00316g
external_id:
arxiv:
- '2303.07063'
isi:
- '001035766100001'
file:
- access_level: open_access
checksum: b936747170d0b708172b518078c4081a
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:48:24Z
date_updated: 2024-01-30T12:48:24Z
file_id: '14908'
file_name: 2023_SoftMatter_Ronning.pdf
file_size: 7660662
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:48:24Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 7513-7527
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spontaneous flows and dynamics of full-integer topological defects in polar
active matter
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2023'
...
---
_id: '13319'
abstract:
- lang: eng
text: We prove that the generator of the L2 implementation of a KMS-symmetric quantum
Markov semigroup can be expressed as the square of a derivation with values in
a Hilbert bimodule, extending earlier results by Cipriani and Sauvageot for tracially
symmetric semigroups and the second-named author for GNS-symmetric semigroups.
This result hinges on the introduction of a new completely positive map on the
algebra of bounded operators on the GNS Hilbert space. This transformation maps
symmetric Markov operators to symmetric Markov operators and is essential to obtain
the required inner product on the Hilbert bimodule.
acknowledgement: The authors are grateful to Martijn Caspers for helpful comments
on a preliminary version of this manuscript. M. V. was supported by the NWO Vidi
grant VI.Vidi.192.018 ‘Non-commutative harmonic analysis and rigidity of operator
algebras’. M. W. was funded by the Austrian Science Fund (FWF) under the Esprit
Programme [ESP 156]. For the purpose of Open Access, the authors have applied a
CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising
from this submission. Open access funding provided by Austrian Science Fund (FWF).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Matthijs
full_name: Vernooij, Matthijs
last_name: Vernooij
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
citation:
ama: Vernooij M, Wirth M. Derivations and KMS-symmetric quantum Markov semigroups.
Communications in Mathematical Physics. 2023;403:381-416. doi:10.1007/s00220-023-04795-6
apa: Vernooij, M., & Wirth, M. (2023). Derivations and KMS-symmetric quantum
Markov semigroups. Communications in Mathematical Physics. Springer Nature.
https://doi.org/10.1007/s00220-023-04795-6
chicago: Vernooij, Matthijs, and Melchior Wirth. “Derivations and KMS-Symmetric
Quantum Markov Semigroups.” Communications in Mathematical Physics. Springer
Nature, 2023. https://doi.org/10.1007/s00220-023-04795-6.
ieee: M. Vernooij and M. Wirth, “Derivations and KMS-symmetric quantum Markov semigroups,”
Communications in Mathematical Physics, vol. 403. Springer Nature, pp.
381–416, 2023.
ista: Vernooij M, Wirth M. 2023. Derivations and KMS-symmetric quantum Markov semigroups.
Communications in Mathematical Physics. 403, 381–416.
mla: Vernooij, Matthijs, and Melchior Wirth. “Derivations and KMS-Symmetric Quantum
Markov Semigroups.” Communications in Mathematical Physics, vol. 403, Springer
Nature, 2023, pp. 381–416, doi:10.1007/s00220-023-04795-6.
short: M. Vernooij, M. Wirth, Communications in Mathematical Physics 403 (2023)
381–416.
date_created: 2023-07-30T22:01:03Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-01-30T12:16:32Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s00220-023-04795-6
external_id:
arxiv:
- '2303.15949'
isi:
- '001033655400002'
file:
- access_level: open_access
checksum: cca204e81891270216a0c84eb8bcd398
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:15:11Z
date_updated: 2024-01-30T12:15:11Z
file_id: '14905'
file_name: 2023_CommMathPhysics_Vernooij.pdf
file_size: 481209
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:15:11Z
has_accepted_license: '1'
intvolume: ' 403'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 381-416
project:
- _id: 34c6ea2d-11ca-11ed-8bc3-c04f3c502833
grant_number: ESP156_N
name: Gradient flow techniques for quantum Markov semigroups
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: Derivations and KMS-symmetric 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 403
year: '2023'
...
---
_id: '14402'
abstract:
- lang: eng
text: Alpha oscillations are a distinctive feature of the awake resting state of
the human brain. However, their functional role in resting-state neuronal dynamics
remains poorly understood. Here we show that, during resting wakefulness, alpha
oscillations drive an alternation of attenuation and amplification bouts in neural
activity. Our analysis indicates that inhibition is activated in pulses that last
for a single alpha cycle and gradually suppress neural activity, while excitation
is successively enhanced over a few alpha cycles to amplify neural activity. Furthermore,
we show that long-term alpha amplitude fluctuations—the “waxing and waning” phenomenon—are
an attenuation-amplification mechanism described by a power-law decay of the activity
rate in the “waning” phase. Importantly, we do not observe such dynamics during
non-rapid eye movement (NREM) sleep with marginal alpha oscillations. The results
suggest that alpha oscillations modulate neural activity not only through pulses
of inhibition (pulsed inhibition hypothesis) but also by timely enhancement of
excitation (or disinhibition).
acknowledgement: This research was funded in whole or in part by the Austrian Science
Fund (FWF) (grant PT1013M03318 to F.L.). For the purpose of open access, the author
has applied a CC BY public copyright license to any Author Accepted Manuscript version
arising from this submission. The study was supported by the European Union Horizon
2020 Research and Innovation Program under the Marie Sklodowska-Curie action (grant
agreement 754411 to F.L.) and in part by the NextGenerationEU through the grant
TAlent in ReSearch@University of Padua – STARS@UNIPD (to F.L.) (project BRAINCIP
[brain criticality and information processing]). L.d.A. acknowledges support from
the Italian MIUR project PRIN2017WZFTZP and partial support from NEXTGENERATIONEU
(NGEU) funded by the Ministry of University and Research (MUR), National Recovery
and Resilience Plan (NRRP), and project MNESYS (PE0000006)—a multiscale integrated
approach to the study of the nervous system in health and disease (DN. 1553 11.10.2022).
O.S. acknowledges support from the Israel Science Foundation, grant 504/17. The
work was supported in part by DIRP ZIAMH02797 (to D.P.).
article_number: '113162'
article_processing_charge: Yes
article_type: original
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Hans J.
full_name: Herrmann, Hans J.
last_name: Herrmann
- first_name: Liborio
full_name: Parrino, Liborio
last_name: Parrino
- first_name: Dietmar
full_name: Plenz, Dietmar
last_name: Plenz
- first_name: Silvia
full_name: Scarpetta, Silvia
last_name: Scarpetta
- first_name: Anna Elisabetta
full_name: Vaudano, Anna Elisabetta
last_name: Vaudano
- first_name: Lucilla
full_name: De Arcangelis, Lucilla
last_name: De Arcangelis
- first_name: Oren
full_name: Shriki, Oren
last_name: Shriki
citation:
ama: 'Lombardi F, Herrmann HJ, Parrino L, et al. Beyond pulsed inhibition: Alpha
oscillations modulate attenuation and amplification of neural activity in the
awake resting state. Cell Reports. 2023;42(10). doi:10.1016/j.celrep.2023.113162'
apa: 'Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano,
A. E., … Shriki, O. (2023). Beyond pulsed inhibition: Alpha oscillations modulate
attenuation and amplification of neural activity in the awake resting state. Cell
Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.113162'
chicago: 'Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz,
Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla De Arcangelis, and Oren Shriki.
“Beyond Pulsed Inhibition: Alpha Oscillations Modulate Attenuation and Amplification
of Neural Activity in the Awake Resting State.” Cell Reports. Elsevier,
2023. https://doi.org/10.1016/j.celrep.2023.113162.'
ieee: 'F. Lombardi et al., “Beyond pulsed inhibition: Alpha oscillations
modulate attenuation and amplification of neural activity in the awake resting
state,” Cell Reports, vol. 42, no. 10. Elsevier, 2023.'
ista: 'Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, De
Arcangelis L, Shriki O. 2023. Beyond pulsed inhibition: Alpha oscillations modulate
attenuation and amplification of neural activity in the awake resting state. Cell
Reports. 42(10), 113162.'
mla: 'Lombardi, Fabrizio, et al. “Beyond Pulsed Inhibition: Alpha Oscillations Modulate
Attenuation and Amplification of Neural Activity in the Awake Resting State.”
Cell Reports, vol. 42, no. 10, 113162, Elsevier, 2023, doi:10.1016/j.celrep.2023.113162.'
short: F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano,
L. De Arcangelis, O. Shriki, Cell Reports 42 (2023).
date_created: 2023-10-08T22:01:15Z
date_published: 2023-10-31T00:00:00Z
date_updated: 2024-01-30T14:07:40Z
day: '31'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1016/j.celrep.2023.113162
ec_funded: 1
external_id:
isi:
- '001086695500001'
pmid:
- '37777965'
file:
- access_level: open_access
checksum: 9c71eb2a03aa160415f01ad95f49ceb5
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T14:07:08Z
date_updated: 2024-01-30T14:07:08Z
file_id: '14914'
file_name: 2023_CellReports_Lombardi.pdf
file_size: 5599007
relation: main_file
success: 1
file_date_updated: 2024-01-30T14:07:08Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: eb943429-77a9-11ec-83b8-9f471cdf5c67
grant_number: M03318
name: Functional Advantages of Critical Brain Dynamics
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification
of neural activity in the awake resting state'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '14258'
abstract:
- lang: eng
text: There is currently little evidence that the genetic basis of human phenotype
varies significantly across the lifespan. However, time-to-event phenotypes are
understudied and can be thought of as reflecting an underlying hazard, which is
unlikely to be constant through life when values take a broad range. Here, we
find that 74% of 245 genome-wide significant genetic associations with age at
natural menopause (ANM) in the UK Biobank show a form of age-specific effect.
Nineteen of these replicated discoveries are identified only by our modeling framework,
which determines the time dependency of DNA-variant age-at-onset associations
without a significant multiple-testing burden. Across the range of early to late
menopause, we find evidence for significantly different underlying biological
pathways, changes in the signs of genetic correlations of ANM to health indicators
and outcomes, and differences in inferred causal relationships. We find that DNA
damage response processes only act to shape ovarian reserve and depletion for
women of early ANM. Genetically mediated delays in ANM were associated with increased
relative risk of breast cancer and leiomyoma at all ages and with high cholesterol
and heart failure for late-ANM women. These findings suggest that a better understanding
of the age dependency of genetic risk factor relationships among health indicators
and outcomes is achievable through appropriate statistical modeling of large-scale
biobank data.
acknowledgement: This project was funded by an SNSF Eccellenza grant to M.R.R. (PCEGP3-181181)
and by core funding from the Institute of Science and Technology Austria. K.L. and
R.M. were supported by the Estonian Research Council grant 1911. Estonian Biobank
computations were performed in the High-Performance Computing Center, University
of Tartu. We thank Triin Laisk for her valuable insights and comments that helped
greatly. We would like to acknowledge the participants and investigators of UK Biobank
and Estonian Biobank studies. This project uses UK Biobank data under project number
35520.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Sven E.
full_name: Ojavee, Sven E.
last_name: Ojavee
- first_name: Liza
full_name: Darrous, Liza
last_name: Darrous
- first_name: Marion
full_name: Patxot, Marion
last_name: Patxot
- first_name: Kristi
full_name: Läll, Kristi
last_name: Läll
- first_name: Krista
full_name: Fischer, Krista
last_name: Fischer
- first_name: Reedik
full_name: Mägi, Reedik
last_name: Mägi
- first_name: Zoltan
full_name: Kutalik, Zoltan
last_name: Kutalik
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: Ojavee SE, Darrous L, Patxot M, et al. Genetic insights into the age-specific
biological mechanisms governing human ovarian aging. American Journal of Human
Genetics. 2023;110(9):1549-1563. doi:10.1016/j.ajhg.2023.07.006
apa: Ojavee, S. E., Darrous, L., Patxot, M., Läll, K., Fischer, K., Mägi, R., …
Robinson, M. R. (2023). Genetic insights into the age-specific biological mechanisms
governing human ovarian aging. American Journal of Human Genetics. Elsevier.
https://doi.org/10.1016/j.ajhg.2023.07.006
chicago: Ojavee, Sven E., Liza Darrous, Marion Patxot, Kristi Läll, Krista Fischer,
Reedik Mägi, Zoltan Kutalik, and Matthew Richard Robinson. “Genetic Insights into
the Age-Specific Biological Mechanisms Governing Human Ovarian Aging.” American
Journal of Human Genetics. Elsevier, 2023. https://doi.org/10.1016/j.ajhg.2023.07.006.
ieee: S. E. Ojavee et al., “Genetic insights into the age-specific biological
mechanisms governing human ovarian aging,” American Journal of Human Genetics,
vol. 110, no. 9. Elsevier, pp. 1549–1563, 2023.
ista: Ojavee SE, Darrous L, Patxot M, Läll K, Fischer K, Mägi R, Kutalik Z, Robinson
MR. 2023. Genetic insights into the age-specific biological mechanisms governing
human ovarian aging. American Journal of Human Genetics. 110(9), 1549–1563.
mla: Ojavee, Sven E., et al. “Genetic Insights into the Age-Specific Biological
Mechanisms Governing Human Ovarian Aging.” American Journal of Human Genetics,
vol. 110, no. 9, Elsevier, 2023, pp. 1549–63, doi:10.1016/j.ajhg.2023.07.006.
short: S.E. Ojavee, L. Darrous, M. Patxot, K. Läll, K. Fischer, R. Mägi, Z. Kutalik,
M.R. Robinson, American Journal of Human Genetics 110 (2023) 1549–1563.
date_created: 2023-09-03T22:01:15Z
date_published: 2023-09-07T00:00:00Z
date_updated: 2024-01-30T13:21:05Z
day: '07'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1016/j.ajhg.2023.07.006
external_id:
pmid:
- '37543033'
file:
- access_level: open_access
checksum: 4108b031dc726ae6b4a5ae7e021ba188
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T13:20:35Z
date_updated: 2024-01-30T13:20:35Z
file_id: '14912'
file_name: 2023_AJHG_Ojavee.pdf
file_size: 2551276
relation: main_file
success: 1
file_date_updated: 2024-01-30T13:20:35Z
has_accepted_license: '1'
intvolume: ' 110'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1549-1563
pmid: 1
publication: American Journal of Human Genetics
publication_identifier:
eissn:
- 1537-6605
issn:
- 0002-9297
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic insights into the age-specific biological mechanisms governing human
ovarian aging
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2023'
...
---
_id: '14244'
abstract:
- lang: eng
text: "In this paper, we determine the motivic class — in particular, the weight
polynomial and conjecturally the Poincaré polynomial — of the open de Rham space,
defined and studied by Boalch, of certain moduli spaces of irregular meromorphic
connections on the trivial rank \r\n bundle on P1. The computation is by motivic
Fourier transform. We show that the result satisfies the purity conjecture, that
is, it agrees with the pure part of the conjectured mixed Hodge polynomial of
the corresponding wild character variety. We also identify the open de Rham spaces
with quiver varieties with multiplicities of Yamakawa and Geiss–Leclerc–Schröer.
We finish with constructing natural complete hyperkähler metrics on them, which
in the four-dimensional cases are expected to be of type ALF."
acknowledgement: We would like to thank Gergely Bérczy, Roger Bielawski, Philip Boalch,
Sergey Cherkis, Andrew Dancer, Brent Doran, Eloïse Hamilton, Frances Kirwan, Bernard
Leclerc, Emmanuel Letellier, Alessia Mandini, Maxence Mayrand, András Némethi, Szilárd
Szabó, and Daisuke Yamakawa for discussions related to the paper. We especially
thank the referee for an extensive list of very careful comments. At various stages
of this project, the authors were supported by the Advanced Grant “Arithmetic and
physics of Higgs moduli spaces” no. 320593 of the European Research Council, by
grant no. 153627 and NCCR SwissMAP, both funded by the Swiss National Science Foundation
as well as by EPF Lausanne and IST Austria. In the final stages of this project,
MLW was supported by SFB/TR 45 “Periods, moduli and arithmetic of algebraic varieties,”
subproject M08-10 “Moduli of vector bundles on higher-dimensional varieties.” DW
was also supported by the Fondation Sciences Mathématiques de Paris, as well as
public grants overseen by the Agence national de la recherche (ANR) of France as
part of the Investissements d'avenir program, under reference numbers ANR-10-LABX-0098
and ANR-15-CE40-0008 (Défigéo).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Tamás
full_name: Hausel, Tamás
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Michael Lennox
full_name: Wong, Michael Lennox
last_name: Wong
- first_name: Dimitri
full_name: Wyss, Dimitri
last_name: Wyss
citation:
ama: Hausel T, Wong ML, Wyss D. Arithmetic and metric aspects of open de Rham spaces.
Proceedings of the London Mathematical Society. 2023;127(4):958-1027. doi:10.1112/plms.12555
apa: Hausel, T., Wong, M. L., & Wyss, D. (2023). Arithmetic and metric aspects
of open de Rham spaces. Proceedings of the London Mathematical Society.
Wiley. https://doi.org/10.1112/plms.12555
chicago: Hausel, Tamás, Michael Lennox Wong, and Dimitri Wyss. “Arithmetic and Metric
Aspects of Open de Rham Spaces.” Proceedings of the London Mathematical Society.
Wiley, 2023. https://doi.org/10.1112/plms.12555.
ieee: T. Hausel, M. L. Wong, and D. Wyss, “Arithmetic and metric aspects of open
de Rham spaces,” Proceedings of the London Mathematical Society, vol. 127,
no. 4. Wiley, pp. 958–1027, 2023.
ista: Hausel T, Wong ML, Wyss D. 2023. Arithmetic and metric aspects of open de
Rham spaces. Proceedings of the London Mathematical Society. 127(4), 958–1027.
mla: Hausel, Tamás, et al. “Arithmetic and Metric Aspects of Open de Rham Spaces.”
Proceedings of the London Mathematical Society, vol. 127, no. 4, Wiley,
2023, pp. 958–1027, doi:10.1112/plms.12555.
short: T. Hausel, M.L. Wong, D. Wyss, Proceedings of the London Mathematical Society
127 (2023) 958–1027.
date_created: 2023-08-27T22:01:18Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-01-30T12:56:10Z
day: '01'
ddc:
- '510'
department:
- _id: TaHa
doi: 10.1112/plms.12555
ec_funded: 1
external_id:
arxiv:
- '1807.04057'
isi:
- '001049312700001'
file:
- access_level: open_access
checksum: 2af4d2d6a8ae42f7d3fba0188e79ae82
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:56:00Z
date_updated: 2024-01-30T12:56:00Z
file_id: '14910'
file_name: 2023_ProcLondonMathSoc_Hausel.pdf
file_size: 651335
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:56:00Z
has_accepted_license: '1'
intvolume: ' 127'
isi: 1
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 958-1027
project:
- _id: 25E549F4-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '320593'
name: Arithmetic and physics of Higgs moduli spaces
- _id: 25E6C798-B435-11E9-9278-68D0E5697425
grant_number: '153627'
name: Arithmetic quantization of character and quiver varities
publication: Proceedings of the London Mathematical Society
publication_identifier:
eissn:
- 1460-244X
issn:
- 0024-6115
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arithmetic and metric aspects of open de Rham spaces
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 127
year: '2023'
...
---
_id: '14080'
abstract:
- lang: eng
text: Extracellular signal-regulated kinase (ERK) has been recognized as a critical
regulator in various physiological and pathological processes. Extensive research
has elucidated the signaling mechanisms governing ERK activation via biochemical
regulations with upstream molecules, particularly receptor tyrosine kinases (RTKs).
However, recent advances have highlighted the role of mechanical forces in activating
the RTK–ERK signaling pathways, thereby opening new avenues of research into mechanochemical
interplay in multicellular tissues. Here, we review the force-induced ERK activation
in cells and propose possible mechanosensing mechanisms underlying the mechanoresponsive
ERK activation. We conclude that mechanical forces are not merely passive factors
shaping cells and tissues but also active regulators of cellular signaling pathways
controlling collective cell behaviors.
acknowledgement: TH was supported by JSPS KAKENHI Grant (no. 21H05290) and the Ministry
of Education under the Research Centres of Excellence programme through the Mechanobiology
Institute at National University of Singapore and by Department of Physiology at
National University of Singapore. NH was supported by JSPS KAKENHI Grant (no. 20K22653).
KA was supported by JSPS KAKENHI Grants (no. 19H05798 and no. 22H02625). MM was
supported by JSPS KAKENHI Grants (no. 19H00993 and no. 20H05898) and JST Moonshot
R&D Grant JPMJPS2022. We appreciate Virgile Viasnoff and the lab members for their
valuable comments on the manuscript. We apologize to authors whose work could not
be highlighted due to space limitations.
article_number: '102217'
article_processing_charge: Yes (in subscription journal)
article_type: review
author:
- first_name: Tsuyoshi
full_name: Hirashima, Tsuyoshi
last_name: Hirashima
- first_name: Naoya
full_name: Hino, Naoya
id: 5299a9ce-7679-11eb-a7bc-d1e62b936307
last_name: Hino
- first_name: Kazuhiro
full_name: Aoki, Kazuhiro
last_name: Aoki
- first_name: Michiyuki
full_name: Matsuda, Michiyuki
last_name: Matsuda
citation:
ama: Hirashima T, Hino N, Aoki K, Matsuda M. Stretching the limits of extracellular
signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation.
Current Opinion in Cell Biology. 2023;84(10). doi:10.1016/j.ceb.2023.102217
apa: Hirashima, T., Hino, N., Aoki, K., & Matsuda, M. (2023). Stretching the
limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing
to ERK activation. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2023.102217
chicago: Hirashima, Tsuyoshi, Naoya Hino, Kazuhiro Aoki, and Michiyuki Matsuda.
“Stretching the Limits of Extracellular Signal-Related Kinase (ERK) Signaling
— Cell Mechanosensing to ERK Activation.” Current Opinion in Cell Biology.
Elsevier, 2023. https://doi.org/10.1016/j.ceb.2023.102217.
ieee: T. Hirashima, N. Hino, K. Aoki, and M. Matsuda, “Stretching the limits of
extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK
activation,” Current Opinion in Cell Biology, vol. 84, no. 10. Elsevier,
2023.
ista: Hirashima T, Hino N, Aoki K, Matsuda M. 2023. Stretching the limits of extracellular
signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation.
Current Opinion in Cell Biology. 84(10), 102217.
mla: Hirashima, Tsuyoshi, et al. “Stretching the Limits of Extracellular Signal-Related
Kinase (ERK) Signaling — Cell Mechanosensing to ERK Activation.” Current Opinion
in Cell Biology, vol. 84, no. 10, 102217, Elsevier, 2023, doi:10.1016/j.ceb.2023.102217.
short: T. Hirashima, N. Hino, K. Aoki, M. Matsuda, Current Opinion in Cell Biology
84 (2023).
date_created: 2023-08-20T22:01:12Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-01-30T12:52:42Z
day: '01'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1016/j.ceb.2023.102217
external_id:
isi:
- '001054692200001'
pmid:
- '37574635'
file:
- access_level: open_access
checksum: 25923f8ae71344e8974530dd23c71bdc
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:52:12Z
date_updated: 2024-01-30T12:52:12Z
file_id: '14909'
file_name: 2023_CurrentOpinionCellBio_Hirashima.pdf
file_size: 1173762
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:52:12Z
has_accepted_license: '1'
intvolume: ' 84'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Current Opinion in Cell Biology
publication_identifier:
eissn:
- 1879-0410
issn:
- 0955-0674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stretching the limits of extracellular signal-related kinase (ERK) signaling
— Cell mechanosensing to ERK activation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 84
year: '2023'
...
---
_id: '13165'
abstract:
- lang: eng
text: "A graph G=(V, E) is called fully regular if for every independent set I c
V, the number of vertices in V\\I that are not connected to any element of I
depends only on the size of I. A linear ordering of the vertices of G is called
successive if for every i, the first i vertices induce a connected subgraph of
G. We give an explicit formula for the number of successive vertex orderings of
a fully regular graph.\r\nAs an application of our results, we give alternative
proofs of two theorems of Stanley and Gao & Peng, determining the number of linear
edge orderings of complete graphs and complete bipartite graphs, respectively,
with the property that the first i edges induce a connected subgraph.\r\nAs another
application, we give a simple product formula for the number of linear orderings
of the hyperedges of a complete 3-partite 3-uniform hypergraph such that, for
every i, the first i hyperedges induce a connected subgraph. We found similar
formulas for complete (non-partite) 3-uniform hypergraphs and in another closely
related case, but we managed to verify them only when the number of vertices is
small."
article_number: '105776'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Lixing
full_name: Fang, Lixing
last_name: Fang
- first_name: Hao
full_name: Huang, Hao
last_name: Huang
- first_name: János
full_name: Pach, János
id: E62E3130-B088-11EA-B919-BF823C25FEA4
last_name: Pach
- first_name: Gábor
full_name: Tardos, Gábor
last_name: Tardos
- first_name: Junchi
full_name: Zuo, Junchi
last_name: Zuo
citation:
ama: Fang L, Huang H, Pach J, Tardos G, Zuo J. Successive vertex orderings of fully
regular graphs. Journal of Combinatorial Theory Series A. 2023;199(10).
doi:10.1016/j.jcta.2023.105776
apa: Fang, L., Huang, H., Pach, J., Tardos, G., & Zuo, J. (2023). Successive
vertex orderings of fully regular graphs. Journal of Combinatorial Theory.
Series A. Elsevier. https://doi.org/10.1016/j.jcta.2023.105776
chicago: Fang, Lixing, Hao Huang, János Pach, Gábor Tardos, and Junchi Zuo. “Successive
Vertex Orderings of Fully Regular Graphs.” Journal of Combinatorial Theory.
Series A. Elsevier, 2023. https://doi.org/10.1016/j.jcta.2023.105776.
ieee: L. Fang, H. Huang, J. Pach, G. Tardos, and J. Zuo, “Successive vertex orderings
of fully regular graphs,” Journal of Combinatorial Theory. Series A, vol.
199, no. 10. Elsevier, 2023.
ista: Fang L, Huang H, Pach J, Tardos G, Zuo J. 2023. Successive vertex orderings
of fully regular graphs. Journal of Combinatorial Theory. Series A. 199(10), 105776.
mla: Fang, Lixing, et al. “Successive Vertex Orderings of Fully Regular Graphs.”
Journal of Combinatorial Theory. Series A, vol. 199, no. 10, 105776, Elsevier,
2023, doi:10.1016/j.jcta.2023.105776.
short: L. Fang, H. Huang, J. Pach, G. Tardos, J. Zuo, Journal of Combinatorial Theory.
Series A 199 (2023).
date_created: 2023-06-25T22:00:45Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-01-30T12:03:51Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1016/j.jcta.2023.105776
external_id:
arxiv:
- '2206.13592'
file:
- access_level: open_access
checksum: 9eebc213b4182a66063a99083ff5bd04
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:03:10Z
date_updated: 2024-01-30T12:03:10Z
file_id: '14902'
file_name: 2023_JourCombinatiorialTheory_Fang.pdf
file_size: 352555
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:03:10Z
has_accepted_license: '1'
intvolume: ' 199'
issue: '10'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '10'
oa: 1
oa_version: Published Version
publication: Journal of Combinatorial Theory. Series A
publication_identifier:
eissn:
- 1096-0899
issn:
- 0097-3165
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Successive vertex orderings of fully regular graphs
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 199
year: '2023'
...
---
_id: '14409'
abstract:
- lang: eng
text: We present a photon- and metal-free approach for the radical fluorination
of aliphatic oxalate-activated alcohols. The method relies on the spontaneous
generation of the N-(chloromethyl)triethylenediamine radical dication, a potent
single electron oxidant, from Selectfluor and 4-(dimethylamino)pyridine. The protocol
is easily scalable and provides the desired fluorinated products within only a
few minutes reaction time.
acknowledgement: We gratefully acknowledge the Max-Planck Society and the Institute
of Science and Technology Austria (ISTA) for generous financial support. We also
thank the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under
Germany's Excellence Strategy – EXC 2008 – 390540038 – UniSysCat for funding. B.P.
thanks the Boehringer Ingelheim Foundation for funding through the Plus 3 Perspectives
Programme.
article_number: e202300769
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Haralds
full_name: Baunis, Haralds
id: 2eea55ec-e8ec-11ed-86cb-d9c76787acfe
last_name: Baunis
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
citation:
ama: Baunis H, Pieber B. Formal radical deoxyfluorination of oxalate-activated alcohols
triggered by the selectfluor-DMAP charge-transfer complex. European Journal
of Organic Chemistry. 2023;26(42). doi:10.1002/ejoc.202300769
apa: Baunis, H., & Pieber, B. (2023). Formal radical deoxyfluorination of oxalate-activated
alcohols triggered by the selectfluor-DMAP charge-transfer complex. European
Journal of Organic Chemistry. Wiley. https://doi.org/10.1002/ejoc.202300769
chicago: Baunis, Haralds, and Bartholomäus Pieber. “Formal Radical Deoxyfluorination
of Oxalate-Activated Alcohols Triggered by the Selectfluor-DMAP Charge-Transfer
Complex.” European Journal of Organic Chemistry. Wiley, 2023. https://doi.org/10.1002/ejoc.202300769.
ieee: H. Baunis and B. Pieber, “Formal radical deoxyfluorination of oxalate-activated
alcohols triggered by the selectfluor-DMAP charge-transfer complex,” European
Journal of Organic Chemistry, vol. 26, no. 42. Wiley, 2023.
ista: Baunis H, Pieber B. 2023. Formal radical deoxyfluorination of oxalate-activated
alcohols triggered by the selectfluor-DMAP charge-transfer complex. European Journal
of Organic Chemistry. 26(42), e202300769.
mla: Baunis, Haralds, and Bartholomäus Pieber. “Formal Radical Deoxyfluorination
of Oxalate-Activated Alcohols Triggered by the Selectfluor-DMAP Charge-Transfer
Complex.” European Journal of Organic Chemistry, vol. 26, no. 42, e202300769,
Wiley, 2023, doi:10.1002/ejoc.202300769.
short: H. Baunis, B. Pieber, European Journal of Organic Chemistry 26 (2023).
date_created: 2023-10-08T22:01:18Z
date_published: 2023-11-07T00:00:00Z
date_updated: 2024-01-30T14:05:14Z
day: '07'
ddc:
- '540'
department:
- _id: BaPi
doi: 10.1002/ejoc.202300769
external_id:
isi:
- '001072666500001'
file:
- access_level: open_access
checksum: e8ad7865acd94672e476f273ccf3d542
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T14:04:44Z
date_updated: 2024-01-30T14:04:44Z
file_id: '14913'
file_name: 2023_EurJOrgChem_Baunis.pdf
file_size: 3277622
relation: main_file
success: 1
file_date_updated: 2024-01-30T14:04:44Z
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
issue: '42'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: European Journal of Organic Chemistry
publication_identifier:
eissn:
- 1099-0690
issn:
- 1434-193X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Formal radical deoxyfluorination of oxalate-activated alcohols triggered by
the selectfluor-DMAP charge-transfer complex
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2023'
...
---
_id: '14254'
abstract:
- lang: eng
text: In [10] Nam proved a Lieb–Thirring Inequality for the kinetic energy of a
fermionic quantum system, with almost optimal (semi-classical) constant and a
gradient correction term. We present a stronger version of this inequality, with
a much simplified proof. As a corollary we obtain a simple proof of the original
Lieb–Thirring inequality.
acknowledgement: J.P.S. thanks the Institute of Science and Technology Austria for
the hospitality and support during a visit where this work was done. J.P.S. was
also partially supported by the VILLUM Centre of Excellence for the Mathematics
of Quantum Theory (QMATH) (grant No. 10059).
article_number: '110129'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jan Philip
full_name: Solovej, Jan Philip
last_name: Solovej
citation:
ama: Seiringer R, Solovej JP. A simple approach to Lieb-Thirring type inequalities.
Journal of Functional Analysis. 2023;285(10). doi:10.1016/j.jfa.2023.110129
apa: Seiringer, R., & Solovej, J. P. (2023). A simple approach to Lieb-Thirring
type inequalities. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2023.110129
chicago: Seiringer, Robert, and Jan Philip Solovej. “A Simple Approach to Lieb-Thirring
Type Inequalities.” Journal of Functional Analysis. Elsevier, 2023. https://doi.org/10.1016/j.jfa.2023.110129.
ieee: R. Seiringer and J. P. Solovej, “A simple approach to Lieb-Thirring type inequalities,”
Journal of Functional Analysis, vol. 285, no. 10. Elsevier, 2023.
ista: Seiringer R, Solovej JP. 2023. A simple approach to Lieb-Thirring type inequalities.
Journal of Functional Analysis. 285(10), 110129.
mla: Seiringer, Robert, and Jan Philip Solovej. “A Simple Approach to Lieb-Thirring
Type Inequalities.” Journal of Functional Analysis, vol. 285, no. 10, 110129,
Elsevier, 2023, doi:10.1016/j.jfa.2023.110129.
short: R. Seiringer, J.P. Solovej, Journal of Functional Analysis 285 (2023).
date_created: 2023-09-03T22:01:14Z
date_published: 2023-11-15T00:00:00Z
date_updated: 2024-01-30T14:17:23Z
day: '15'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1016/j.jfa.2023.110129
external_id:
arxiv:
- '2303.04504'
isi:
- '001071552300001'
file:
- access_level: open_access
checksum: 28e424ad91be6219e9d321054ce3a412
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T14:15:16Z
date_updated: 2024-01-30T14:15:16Z
file_id: '14915'
file_name: 2023_JourFunctionalAnalysis_Seiringer.pdf
file_size: 232934
relation: main_file
success: 1
file_date_updated: 2024-01-30T14:15:16Z
has_accepted_license: '1'
intvolume: ' 285'
isi: 1
issue: '10'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
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: A simple approach to Lieb-Thirring type inequalities
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 285
year: '2023'
...
---
_id: '14362'
abstract:
- lang: eng
text: "Motivated by recent applications to entropy theory in dynamical systems,
we generalise notions introduced by Matthews and define weakly weighted and componentwise
weakly weighted (generalised) quasi-metrics. We then systematise and extend to
full generality the correspondences between these objects and other structures
arising in theoretical computer science and dynamics. In particular, we study
the correspondences with weak partial metrics and, if the underlying space is
a semilattice, with invariant (generalised) quasi-metrics satisfying the descending
path condition, and with strictly monotone semi(-co-)valuations.\r\nWe conclude
discussing, for endomorphisms of generalised quasi-metric semilattices, a generalisation
of both the known intrinsic semilattice entropy and the semigroup entropy."
article_number: '114129'
article_processing_charge: No
article_type: original
author:
- first_name: Ilaria
full_name: Castellano, Ilaria
last_name: Castellano
- first_name: Anna
full_name: Giordano Bruno, Anna
last_name: Giordano Bruno
- first_name: Nicolò
full_name: Zava, Nicolò
id: c8b3499c-7a77-11eb-b046-aa368cbbf2ad
last_name: Zava
orcid: 0000-0001-8686-1888
citation:
ama: Castellano I, Giordano Bruno A, Zava N. Weakly weighted generalised quasi-metric
spaces and semilattices. Theoretical Computer Science. 2023;977. doi:10.1016/j.tcs.2023.114129
apa: Castellano, I., Giordano Bruno, A., & Zava, N. (2023). Weakly weighted
generalised quasi-metric spaces and semilattices. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2023.114129
chicago: Castellano, Ilaria, Anna Giordano Bruno, and Nicolò Zava. “Weakly Weighted
Generalised Quasi-Metric Spaces and Semilattices.” Theoretical Computer Science.
Elsevier, 2023. https://doi.org/10.1016/j.tcs.2023.114129.
ieee: I. Castellano, A. Giordano Bruno, and N. Zava, “Weakly weighted generalised
quasi-metric spaces and semilattices,” Theoretical Computer Science, vol.
977. Elsevier, 2023.
ista: Castellano I, Giordano Bruno A, Zava N. 2023. Weakly weighted generalised
quasi-metric spaces and semilattices. Theoretical Computer Science. 977, 114129.
mla: Castellano, Ilaria, et al. “Weakly Weighted Generalised Quasi-Metric Spaces
and Semilattices.” Theoretical Computer Science, vol. 977, 114129, Elsevier,
2023, doi:10.1016/j.tcs.2023.114129.
short: I. Castellano, A. Giordano Bruno, N. Zava, Theoretical Computer Science 977
(2023).
date_created: 2023-09-24T22:01:11Z
date_published: 2023-10-25T00:00:00Z
date_updated: 2024-01-30T13:22:04Z
day: '25'
department:
- _id: HeEd
doi: 10.1016/j.tcs.2023.114129
external_id:
arxiv:
- '2212.08424'
isi:
- '001076934000001'
intvolume: ' 977'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.48550/arXiv.2212.08424 '
month: '10'
oa: 1
oa_version: Preprint
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Weakly weighted generalised quasi-metric spaces and semilattices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 977
year: '2023'
...
---
_id: '14401'
abstract:
- lang: eng
text: "Background: \r\nPro-apoptotic BAX is a central mediator of retinal ganglion
cell (RGC) death after optic nerve damage. BAX activation occurs in two stages
including translocation of latent BAX to the mitochondrial outer membrane (MOM)
and then permeabilization of the MOM to facilitate the release of apoptotic signaling
molecules. As a critical component of RGC death, BAX is an attractive target for
neuroprotective therapies and an understanding of the kinetics of BAX activation
and the mechanisms controlling the two stages of this process in RGCs is potentially
valuable in informing the development of a neuroprotective strategy.\r\nMethods:\r\nThe
kinetics of BAX translocation were assessed by both static and live-cell imaging
of a GFP-BAX fusion protein introduced into RGCs using AAV2-mediated gene transfer
in mice. Activation of BAX was achieved using an acute optic nerve crush (ONC)
protocol. Live-cell imaging of GFP-BAX was achieved using explants of mouse retina
harvested 7 days after ONC. Kinetics of translocation in RGCs were compared to
GFP-BAX translocation in 661W tissue culture cells. Permeabilization of GFP-BAX
was assessed by staining with the 6A7 monoclonal antibody, which recognizes a
conformational change in this protein after MOM insertion. Assessment of individual
kinases associated with both stages of activation was made using small molecule
inhibitors injected into the vitreous either independently or in concert with
ONC surgery. The contribution of the Dual Leucine Zipper-JUN-N-Terminal Kinase
cascade was evaluated using mice with a double conditional knock-out of both Mkk4
and Mkk7.\r\nResults:\r\nONC induces the translocation of GFP-BAX in RGCs at a
slower rate and with less intracellular synchronicity than 661W cells, but exhibits
less variability among mitochondrial foci within a single cell. GFP-BAX was also
found to translocate in all compartments of an RGC including the dendritic arbor
and axon. Approximately 6% of translocating RGCs exhibited retrotranslocation
of BAX immediately following translocation. Unlike tissue culture cells, which
exhibit simultaneous translocation and permeabilization, RGCs exhibited a significant
delay between these two stages, similar to detached cells undergoing anoikis.
Translocation, with minimal permeabilization could be induced in a subset of RGCs
using an inhibitor of Focal Adhesion Kinase (PF573228). Permeabilization after
ONC, in a majority of RGCs, could be inhibited with a broad spectrum kinase inhibitor
(sunitinib) or a selective inhibitor for p38/MAPK14 (SB203580). Intervention of
DLK-JNK axis signaling abrogated GFP-BAX translocation after ONC.\r\nConclusions:\r\nA
comparison between BAX activation kinetics in tissue culture cells and in cells
of a complex tissue environment shows distinct differences indicating that caution
should be used when translating findings from one condition to the other. RGCs
exhibit both a delay between translocation and permeabilization and the ability
for translocated BAX to be retrotranslocated, suggesting several stages at which
intervention of the activation process could be exploited in the design of a therapeutic
strategy."
acknowledgement: "The authors would like to thank Mr. Joel Dietz for management of
the mouse colony and helpful advice for conducting quantitative PCR studies and
Mr. Santoshi Kinoshita at the Translational Research Initiative in Pathology laboratory
at the University of Wisconsin-Madison for cutting sections analyzed in this study.\r\nThis
work was supported by National Eye Institute grants R01 EY030123 (RWN), R01 EY018606
(RTL), P30 EY016665 (Department of Ophthalmology and Visual Sciences, University
of Wisconsin-Madison), T32 EY027721 (RJD) and F31 EY030739 (OJM). Additional funding
was provided by the BrightFocus Foundation (RWN) and unrestricted grants from Research
to Prevent Blindness, Inc to the Department of Ophthalmology and Visual Sciences
(University of Wisconsin-Madison) and to the Department of Ophthalmology (University
of Rochester)."
article_number: '67'
article_processing_charge: Yes
article_type: original
author:
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Ryan J.
full_name: Donahue, Ryan J.
last_name: Donahue
- first_name: Cassandra L.
full_name: Schlamp, Cassandra L.
last_name: Schlamp
- first_name: Olivia J.
full_name: Marola, Olivia J.
last_name: Marola
- first_name: Richard T.
full_name: Libby, Richard T.
last_name: Libby
- first_name: Robert W.
full_name: Nickells, Robert W.
last_name: Nickells
citation:
ama: Maes ME, Donahue RJ, Schlamp CL, Marola OJ, Libby RT, Nickells RW. BAX activation
in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct
steps. Molecular Neurodegeneration. 2023;18. doi:10.1186/s13024-023-00659-8
apa: Maes, M. E., Donahue, R. J., Schlamp, C. L., Marola, O. J., Libby, R. T., &
Nickells, R. W. (2023). BAX activation in mouse retinal ganglion cells occurs
in two temporally and mechanistically distinct steps. Molecular Neurodegeneration.
Springer Nature. https://doi.org/10.1186/s13024-023-00659-8
chicago: Maes, Margaret E, Ryan J. Donahue, Cassandra L. Schlamp, Olivia J. Marola,
Richard T. Libby, and Robert W. Nickells. “BAX Activation in Mouse Retinal Ganglion
Cells Occurs in Two Temporally and Mechanistically Distinct Steps.” Molecular
Neurodegeneration. Springer Nature, 2023. https://doi.org/10.1186/s13024-023-00659-8.
ieee: M. E. Maes, R. J. Donahue, C. L. Schlamp, O. J. Marola, R. T. Libby, and R.
W. Nickells, “BAX activation in mouse retinal ganglion cells occurs in two temporally
and mechanistically distinct steps,” Molecular Neurodegeneration, vol.
18. Springer Nature, 2023.
ista: Maes ME, Donahue RJ, Schlamp CL, Marola OJ, Libby RT, Nickells RW. 2023. BAX
activation in mouse retinal ganglion cells occurs in two temporally and mechanistically
distinct steps. Molecular Neurodegeneration. 18, 67.
mla: Maes, Margaret E., et al. “BAX Activation in Mouse Retinal Ganglion Cells Occurs
in Two Temporally and Mechanistically Distinct Steps.” Molecular Neurodegeneration,
vol. 18, 67, Springer Nature, 2023, doi:10.1186/s13024-023-00659-8.
short: M.E. Maes, R.J. Donahue, C.L. Schlamp, O.J. Marola, R.T. Libby, R.W. Nickells,
Molecular Neurodegeneration 18 (2023).
date_created: 2023-10-08T22:01:15Z
date_published: 2023-09-26T00:00:00Z
date_updated: 2024-01-30T14:34:21Z
day: '26'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1186/s13024-023-00659-8
external_id:
isi:
- '001071403800001'
pmid:
- '37292963'
file:
- access_level: open_access
checksum: 3aa218ddea4a082d8fd5e196ae55ca06
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T14:33:31Z
date_updated: 2024-01-30T14:33:31Z
file_id: '14917'
file_name: 2023_MolecularNeurodegeneration_Maes.pdf
file_size: 11568350
relation: main_file
success: 1
file_date_updated: 2024-01-30T14:33:31Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Neurodegeneration
publication_identifier:
eissn:
- 1750-1326
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: BAX activation in mouse retinal ganglion cells occurs in two temporally and
mechanistically distinct steps
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2023'
...
---
_id: '14489'
abstract:
- lang: eng
text: Microwave-optics entanglement is a vital component for building hybrid quantum
networks. Here, a new mechanism for preparing stationary entanglement between
microwave and optical cavity fields in a cavity optomagnomechanical system is
proposed. It consists of a magnon mode in a ferrimagnetic crystal that couples
directly to a microwave cavity mode via the magnetic dipole interaction and indirectly
to an optical cavity through the deformation displacement of the crystal. The
mechanical displacement is induced by the magnetostrictive force and coupled to
the optical cavity via radiation pressure. Both the opto- and magnomechanical
couplings are dispersive. Magnon–phonon entanglement is created via magnomechanical
parametric down-conversion, which is further distributed to optical and microwave
photons via simultaneous optomechanical beamsplitter interaction and electromagnonic
state-swap interaction, yielding stationary microwave-optics entanglement. The
microwave-optics entanglement is robust against thermal noise, which will find
broad potential applications in quantum networks and quantum information processing
with hybrid quantum systems.
acknowledgement: This work was supported by the National Key Research and Development
Program of China (Grant no. 2022YFA1405200), the National Natural Science Foundation
of China (Nos. 92265202), and the European Research Council (ERC CoG Q-ECHOS, 101001005).
article_number: '2200866'
article_processing_charge: No
article_type: original
author:
- first_name: Zhi Yuan
full_name: Fan, Zhi Yuan
last_name: Fan
- first_name: Liu
full_name: Qiu, Liu
id: 45e99c0d-1eb1-11eb-9b96-ed8ab2983cac
last_name: Qiu
orcid: 0000-0003-4345-4267
- first_name: Simon
full_name: Gröblacher, Simon
last_name: Gröblacher
- first_name: Jie
full_name: Li, Jie
last_name: Li
citation:
ama: Fan ZY, Qiu L, Gröblacher S, Li J. Microwave-optics entanglement via cavity
optomagnomechanics. Laser and Photonics Reviews. 2023;17(12). doi:10.1002/lpor.202200866
apa: Fan, Z. Y., Qiu, L., Gröblacher, S., & Li, J. (2023). Microwave-optics
entanglement via cavity optomagnomechanics. Laser and Photonics Reviews.
Wiley. https://doi.org/10.1002/lpor.202200866
chicago: Fan, Zhi Yuan, Liu Qiu, Simon Gröblacher, and Jie Li. “Microwave-Optics
Entanglement via Cavity Optomagnomechanics.” Laser and Photonics Reviews.
Wiley, 2023. https://doi.org/10.1002/lpor.202200866.
ieee: Z. Y. Fan, L. Qiu, S. Gröblacher, and J. Li, “Microwave-optics entanglement
via cavity optomagnomechanics,” Laser and Photonics Reviews, vol. 17, no.
12. Wiley, 2023.
ista: Fan ZY, Qiu L, Gröblacher S, Li J. 2023. Microwave-optics entanglement via
cavity optomagnomechanics. Laser and Photonics Reviews. 17(12), 2200866.
mla: Fan, Zhi Yuan, et al. “Microwave-Optics Entanglement via Cavity Optomagnomechanics.”
Laser and Photonics Reviews, vol. 17, no. 12, 2200866, Wiley, 2023, doi:10.1002/lpor.202200866.
short: Z.Y. Fan, L. Qiu, S. Gröblacher, J. Li, Laser and Photonics Reviews 17 (2023).
date_created: 2023-11-05T23:00:54Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-01-30T14:36:42Z
day: '01'
department:
- _id: JoFi
doi: 10.1002/lpor.202200866
external_id:
arxiv:
- '2208.10703'
intvolume: ' 17'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2208.10703
month: '12'
oa: 1
oa_version: Preprint
publication: Laser and Photonics Reviews
publication_identifier:
eissn:
- 1863-8899
issn:
- 1863-8880
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Microwave-optics entanglement via cavity optomagnomechanics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2023'
...
---
_id: '13097'
abstract:
- lang: eng
text: 'Vertebrate movement is orchestrated by spinal inter- and motor neurons that,
together with sensory and cognitive input, produce dynamic motor behaviors. These
behaviors vary from the simple undulatory swimming of fish and larval aquatic
species to the highly coordinated running, reaching and grasping of mice, humans
and other mammals. This variation raises the fundamental question of how spinal
circuits have changed in register with motor behavior. In simple, undulatory fish,
exemplified by the lamprey, two broad classes of interneurons shape motor neuron
output: ipsilateral-projecting excitatory neurons, and commissural-projecting
inhibitory neurons. An additional class of ipsilateral inhibitory neurons is required
to generate escape swim behavior in larval zebrafish and tadpoles. In limbed vertebrates,
a more complex spinal neuron composition is observed. In this review, we provide
evidence that movement elaboration correlates with an increase and specialization
of these three basic interneuron types into molecularly, anatomically, and functionally
distinct subpopulations. We summarize recent work linking neuron types to movement-pattern
generation across fish, amphibians, reptiles, birds and mammals.'
acknowledgement: 'This work was supported by the ERC Starting grant, ERC-2021-STG
#101041551.'
article_number: '1146449'
article_processing_charge: Yes
article_type: original
author:
- first_name: Alexia C
full_name: Wilson, Alexia C
id: 5230e794-15b2-11ec-abd3-e2d5335ebd1d
last_name: Wilson
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
citation:
ama: 'Wilson AC, Sweeney LB. Spinal cords: Symphonies of interneurons across species.
Frontiers in Neural Circuits. 2023;17. doi:10.3389/fncir.2023.1146449'
apa: 'Wilson, A. C., & Sweeney, L. B. (2023). Spinal cords: Symphonies of interneurons
across species. Frontiers in Neural Circuits. Frontiers. https://doi.org/10.3389/fncir.2023.1146449'
chicago: 'Wilson, Alexia C, and Lora B. Sweeney. “Spinal Cords: Symphonies of Interneurons
across Species.” Frontiers in Neural Circuits. Frontiers, 2023. https://doi.org/10.3389/fncir.2023.1146449.'
ieee: 'A. C. Wilson and L. B. Sweeney, “Spinal cords: Symphonies of interneurons
across species,” Frontiers in Neural Circuits, vol. 17. Frontiers, 2023.'
ista: 'Wilson AC, Sweeney LB. 2023. Spinal cords: Symphonies of interneurons across
species. Frontiers in Neural Circuits. 17, 1146449.'
mla: 'Wilson, Alexia C., and Lora B. Sweeney. “Spinal Cords: Symphonies of Interneurons
across Species.” Frontiers in Neural Circuits, vol. 17, 1146449, Frontiers,
2023, doi:10.3389/fncir.2023.1146449.'
short: A.C. Wilson, L.B. Sweeney, Frontiers in Neural Circuits 17 (2023).
date_created: 2023-05-28T22:01:04Z
date_published: 2023-04-26T00:00:00Z
date_updated: 2024-01-31T10:15:53Z
day: '26'
ddc:
- '570'
department:
- _id: LoSw
doi: 10.3389/fncir.2023.1146449
external_id:
isi:
- '000984606200001'
pmid:
- '37180760'
file:
- access_level: open_access
checksum: 7efd06de284a28e91e97127611a9c3fd
content_type: application/pdf
creator: dernst
date_created: 2024-01-03T13:33:21Z
date_updated: 2024-01-03T13:33:21Z
file_id: '14729'
file_name: 2023_FrontiersNeuralCircuits_Wilson.pdf
file_size: 6667157
relation: main_file
success: 1
file_date_updated: 2024-01-03T13:33:21Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae
grant_number: '101041551'
name: Development and Evolution of Tetrapod Motor Circuits
publication: Frontiers in Neural Circuits
publication_identifier:
issn:
- 1662-5110
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Spinal cords: Symphonies of interneurons across species'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2023'
...
---
_id: '14865'
article_number: EGU23-4968
article_processing_charge: No
author:
- first_name: Yi-Ling
full_name: Hwong, Yi-Ling
id: 1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22
last_name: Hwong
orcid: 0000-0001-9281-3479
- first_name: Maxime
full_name: Colin, Maxime
last_name: Colin
- first_name: Philipp
full_name: Aglas, Philipp
id: 02eace56-97fc-11ee-b81a-f0939ca85a77
last_name: Aglas
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Steven
full_name: Sherwood, Steven
last_name: Sherwood
citation:
ama: 'Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood S. Evaluating memory properties
in convection schemes using idealised tests. In: EGU General Assembly 2023.
European Geosciences Union; 2023. doi:10.5194/egusphere-egu23-4968'
apa: 'Hwong, Y.-L., Colin, M., Aglas, P., Muller, C. J., & Sherwood, S. (2023).
Evaluating memory properties in convection schemes using idealised tests. In EGU
General Assembly 2023. Vienna, Austria & Virtual: European Geosciences
Union. https://doi.org/10.5194/egusphere-egu23-4968'
chicago: Hwong, Yi-Ling, Maxime Colin, Philipp Aglas, Caroline J Muller, and Steven
Sherwood. “Evaluating Memory Properties in Convection Schemes Using Idealised
Tests.” In EGU General Assembly 2023. European Geosciences Union, 2023.
https://doi.org/10.5194/egusphere-egu23-4968.
ieee: Y.-L. Hwong, M. Colin, P. Aglas, C. J. Muller, and S. Sherwood, “Evaluating
memory properties in convection schemes using idealised tests,” in EGU General
Assembly 2023, Vienna, Austria & Virtual, 2023.
ista: Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood S. 2023. Evaluating memory
properties in convection schemes using idealised tests. EGU General Assembly 2023.
EGU General Assembly, EGU23-4968.
mla: Hwong, Yi-Ling, et al. “Evaluating Memory Properties in Convection Schemes
Using Idealised Tests.” EGU General Assembly 2023, EGU23-4968, European
Geosciences Union, 2023, doi:10.5194/egusphere-egu23-4968.
short: Y.-L. Hwong, M. Colin, P. Aglas, C.J. Muller, S. Sherwood, in:, EGU General
Assembly 2023, European Geosciences Union, 2023.
conference:
end_date: 2023-04-28
location: Vienna, Austria & Virtual
name: EGU General Assembly
start_date: 2023-04-23
date_created: 2024-01-22T12:10:32Z
date_published: 2023-04-23T00:00:00Z
date_updated: 2024-02-05T08:49:49Z
day: '23'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.5194/egusphere-egu23-4968
file:
- access_level: open_access
checksum: 628a27caff437855ab320be46b9e8dcc
content_type: application/pdf
creator: dernst
date_created: 2024-02-05T08:48:41Z
date_updated: 2024-02-05T08:48:41Z
file_id: '14936'
file_name: 2023_EGU_Hwong.pdf
file_size: 317541
relation: main_file
success: 1
file_date_updated: 2024-02-05T08:48:41Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: EGU General Assembly 2023
publication_status: published
publisher: European Geosciences Union
status: public
title: Evaluating memory properties in convection schemes using idealised tests
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_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14866'
article_number: EGU23-15870
article_processing_charge: No
author:
- first_name: Sophie
full_name: Abramian, Sophie
last_name: Abramian
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Camille
full_name: Risi, Camille
last_name: Risi
citation:
ama: 'Abramian S, Muller CJ, Risi C. Extreme precipitation in tropical squall lines.
In: EGU General Assembly 2023. European Geosciences Union; 2023. doi:10.5194/egusphere-egu23-15870'
apa: 'Abramian, S., Muller, C. J., & Risi, C. (2023). Extreme precipitation
in tropical squall lines. In EGU General Assembly 2023. Vienna, Austria
& Virtual: European Geosciences Union. https://doi.org/10.5194/egusphere-egu23-15870'
chicago: Abramian, Sophie, Caroline J Muller, and Camille Risi. “Extreme Precipitation
in Tropical Squall Lines.” In EGU General Assembly 2023. European Geosciences
Union, 2023. https://doi.org/10.5194/egusphere-egu23-15870.
ieee: S. Abramian, C. J. Muller, and C. Risi, “Extreme precipitation in tropical
squall lines,” in EGU General Assembly 2023, Vienna, Austria & Virtual,
2023.
ista: Abramian S, Muller CJ, Risi C. 2023. Extreme precipitation in tropical squall
lines. EGU General Assembly 2023. EGU General Assembly, EGU23-15870.
mla: Abramian, Sophie, et al. “Extreme Precipitation in Tropical Squall Lines.”
EGU General Assembly 2023, EGU23-15870, European Geosciences Union, 2023,
doi:10.5194/egusphere-egu23-15870.
short: S. Abramian, C.J. Muller, C. Risi, in:, EGU General Assembly 2023, European
Geosciences Union, 2023.
conference:
end_date: 2023-04-28
location: Vienna, Austria & Virtual
name: EGU General Assembly
start_date: 2023-04-23
date_created: 2024-01-22T12:10:52Z
date_published: 2023-04-23T00:00:00Z
date_updated: 2024-02-05T08:13:12Z
day: '23'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.5194/egusphere-egu23-15870
file:
- access_level: open_access
checksum: 8cd5bb8bf3d48ceefb395b6875819147
content_type: application/pdf
creator: dernst
date_created: 2024-02-05T08:10:43Z
date_updated: 2024-02-05T08:10:43Z
file_id: '14935'
file_name: 2023_EGU_Abramian.pdf
file_size: 294690
relation: main_file
success: 1
file_date_updated: 2024-02-05T08:10:43Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: EGU General Assembly 2023
publication_status: published
publisher: European Geosciences Union
status: public
title: Extreme precipitation in tropical squall lines
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_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14920'
abstract:
- lang: eng
text: "We consider fixpoint algorithms for two-player games on graphs with $\\omega$-regular
winning conditions, where the environment is constrained by a strong transition
fairness assumption. Strong transition fairness is a widely occurring special
case of strong fairness, which requires that any execution is strongly fair with
respect to a specified set of live edges: whenever the\r\nsource vertex of a live
edge is visited infinitely often along a play, the edge itself is traversed infinitely
often along the play as well. We show that, surprisingly, strong transition fairness
retains the algorithmic characteristics of the fixpoint algorithms for $\\omega$-regular
games -- the new algorithms have the same alternation depth as the classical algorithms
but invoke a new type of predecessor operator. For Rabin games with $k$ pairs,
the complexity of the new algorithm is $O(n^{k+2}k!)$ symbolic steps, which is
independent of the number of live edges in the strong transition fairness assumption.
Further, we show that GR(1) specifications with strong transition fairness assumptions
can be solved with a 3-nested fixpoint algorithm, same as the usual algorithm.
In contrast, strong fairness necessarily requires increasing the alternation depth
depending on the number of fairness assumptions. We get symbolic algorithms for
(generalized) Rabin, parity and GR(1) objectives under strong transition fairness
assumptions as well as a direct symbolic algorithm for qualitative winning in
stochastic\r\n$\\omega$-regular games that runs in $O(n^{k+2}k!)$ symbolic steps,
improving the state of the art. Finally, we have implemented a BDD-based synthesis
engine based on our algorithm. We show on a set of synthetic and real benchmarks
that our algorithm is scalable, parallelizable, and outperforms previous algorithms
by orders of magnitude."
acknowledgement: A previous version of this paper has appeared in TACAS 2022. Authors
ordered alphabetically. T. Banerjee was interning with MPI-SWS when this research
was conducted. R. Majumdar and A.-K. Schmuck are partially supported by DFG project
389792660 TRR 248–CPEC. A.-K. Schmuck is additionally funded through DFG project
(SCHM 3541/1-1). K. Mallik is supported by the ERC project ERC-2020-AdG 101020093.
article_number: '4'
article_processing_charge: Yes
article_type: original
author:
- first_name: Tamajit
full_name: Banerjee, Tamajit
last_name: Banerjee
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
- first_name: Anne-Kathrin
full_name: Schmuck, Anne-Kathrin
last_name: Schmuck
- first_name: Sadegh
full_name: Soudjani, Sadegh
last_name: Soudjani
citation:
ama: Banerjee T, Majumdar R, Mallik K, Schmuck A-K, Soudjani S. Fast symbolic algorithms
for mega-regular games under strong transition fairness. TheoretiCS. 2023;2.
doi:10.46298/theoretics.23.4
apa: Banerjee, T., Majumdar, R., Mallik, K., Schmuck, A.-K., & Soudjani, S.
(2023). Fast symbolic algorithms for mega-regular games under strong transition
fairness. TheoretiCS. EPI Sciences. https://doi.org/10.46298/theoretics.23.4
chicago: Banerjee, Tamajit, Rupak Majumdar, Kaushik Mallik, Anne-Kathrin Schmuck,
and Sadegh Soudjani. “Fast Symbolic Algorithms for Mega-Regular Games under Strong
Transition Fairness.” TheoretiCS. EPI Sciences, 2023. https://doi.org/10.46298/theoretics.23.4.
ieee: T. Banerjee, R. Majumdar, K. Mallik, A.-K. Schmuck, and S. Soudjani, “Fast
symbolic algorithms for mega-regular games under strong transition fairness,”
TheoretiCS, vol. 2. EPI Sciences, 2023.
ista: Banerjee T, Majumdar R, Mallik K, Schmuck A-K, Soudjani S. 2023. Fast symbolic
algorithms for mega-regular games under strong transition fairness. TheoretiCS.
2, 4.
mla: Banerjee, Tamajit, et al. “Fast Symbolic Algorithms for Mega-Regular Games
under Strong Transition Fairness.” TheoretiCS, vol. 2, 4, EPI Sciences,
2023, doi:10.46298/theoretics.23.4.
short: T. Banerjee, R. Majumdar, K. Mallik, A.-K. Schmuck, S. Soudjani, TheoretiCS
2 (2023).
date_created: 2024-01-31T13:40:49Z
date_published: 2023-02-24T00:00:00Z
date_updated: 2024-02-05T10:21:51Z
day: '24'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.46298/theoretics.23.4
ec_funded: 1
external_id:
arxiv:
- '2202.07480'
file:
- access_level: open_access
checksum: 2972d531122a6f15727b396110fb3f5c
content_type: application/pdf
creator: dernst
date_created: 2024-02-05T10:19:35Z
date_updated: 2024-02-05T10:19:35Z
file_id: '14940'
file_name: 2023_TheoretiCS_Banerjee.pdf
file_size: 917076
relation: main_file
success: 1
file_date_updated: 2024-02-05T10:19:35Z
has_accepted_license: '1'
intvolume: ' 2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: TheoretiCS
publication_identifier:
issn:
- 2751-4838
publication_status: published
publisher: EPI Sciences
quality_controlled: '1'
status: public
title: Fast symbolic algorithms for mega-regular games under strong transition fairness
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2023'
...
---
_id: '12859'
abstract:
- lang: eng
text: 'Machine learning models are vulnerable to adversarial perturbations, and
a thought-provoking paper by Bubeck and Sellke has analyzed this phenomenon through
the lens of over-parameterization: interpolating smoothly the data requires significantly
more parameters than simply memorizing it. However, this "universal" law provides
only a necessary condition for robustness, and it is unable to discriminate between
models. In this paper, we address these gaps by focusing on empirical risk minimization
in two prototypical settings, namely, random features and the neural tangent kernel
(NTK). We prove that, for random features, the model is not robust for any degree
of over-parameterization, even when the necessary condition coming from the universal
law of robustness is satisfied. In contrast, for even activations, the NTK model
meets the universal lower bound, and it is robust as soon as the necessary condition
on over-parameterization is fulfilled. This also addresses a conjecture in prior
work by Bubeck, Li and Nagaraj. Our analysis decouples the effect of the kernel
of the model from an "interaction matrix", which describes the interaction with
the test data and captures the effect of the activation. Our theoretical results
are corroborated by numerical evidence on both synthetic and standard datasets
(MNIST, CIFAR-10).'
acknowledgement: "Simone Bombari and Marco Mondelli were partially supported by the
2019 Lopez-Loreta prize, and\r\nthe authors would like to thank Hamed Hassani for
helpful discussions.\r\n"
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Simone
full_name: Bombari, Simone
id: ca726dda-de17-11ea-bc14-f9da834f63aa
last_name: Bombari
- first_name: Shayan
full_name: Kiyani, Shayan
id: f5a2b424-e339-11ed-8435-ff3b4fe70cf8
last_name: Kiyani
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: 'Bombari S, Kiyani S, Mondelli M. Beyond the universal law of robustness: Sharper
laws for random features and neural tangent kernels. In: Proceedings of the
40th International Conference on Machine Learning. Vol 202. ML Research Press;
2023:2738-2776.'
apa: 'Bombari, S., Kiyani, S., & Mondelli, M. (2023). Beyond the universal law
of robustness: Sharper laws for random features and neural tangent kernels. In
Proceedings of the 40th International Conference on Machine Learning (Vol.
202, pp. 2738–2776). Honolulu, HI, United States: ML Research Press.'
chicago: 'Bombari, Simone, Shayan Kiyani, and Marco Mondelli. “Beyond the Universal
Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.”
In Proceedings of the 40th International Conference on Machine Learning,
202:2738–76. ML Research Press, 2023.'
ieee: 'S. Bombari, S. Kiyani, and M. Mondelli, “Beyond the universal law of robustness:
Sharper laws for random features and neural tangent kernels,” in Proceedings
of the 40th International Conference on Machine Learning, Honolulu, HI, United
States, 2023, vol. 202, pp. 2738–2776.'
ista: 'Bombari S, Kiyani S, Mondelli M. 2023. Beyond the universal law of robustness:
Sharper laws for random features and neural tangent kernels. Proceedings of the
40th International Conference on Machine Learning. ICML: International Conference
on Machine Learning, PMLR, vol. 202, 2738–2776.'
mla: 'Bombari, Simone, et al. “Beyond the Universal Law of Robustness: Sharper Laws
for Random Features and Neural Tangent Kernels.” Proceedings of the 40th International
Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 2738–76.'
short: S. Bombari, S. Kiyani, M. Mondelli, in:, Proceedings of the 40th International
Conference on Machine Learning, ML Research Press, 2023, pp. 2738–2776.
conference:
end_date: 2023-07-29
location: Honolulu, HI, United States
name: 'ICML: International Conference on Machine Learning'
start_date: 2023-07-23
date_created: 2023-04-23T16:11:03Z
date_published: 2023-10-27T00:00:00Z
date_updated: 2024-02-06T07:42:00Z
day: '27'
department:
- _id: GradSch
- _id: MaMo
external_id:
arxiv:
- '2302.01629'
intvolume: ' 202'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2302.01629
month: '10'
oa: 1
oa_version: Preprint
page: 2738-2776
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: Proceedings of the 40th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/simone-bombari/beyond-universal-robustness
status: public
title: 'Beyond the universal law of robustness: Sharper laws for random features and
neural tangent kernels'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2023'
...
---
_id: '14921'
abstract:
- lang: eng
text: Neural collapse (NC) refers to the surprising structure of the last layer
of deep neural networks in the terminal phase of gradient descent training. Recently,
an increasing amount of experimental evidence has pointed to the propagation of
NC to earlier layers of neural networks. However, while the NC in the last layer
is well studied theoretically, much less is known about its multi-layered counterpart
- deep neural collapse (DNC). In particular, existing work focuses either on linear
layers or only on the last two layers at the price of an extra assumption. Our
paper fills this gap by generalizing the established analytical framework for
NC - the unconstrained features model - to multiple non-linear layers. Our key
technical contribution is to show that, in a deep unconstrained features model,
the unique global optimum for binary classification exhibits all the properties
typical of DNC. This explains the existing experimental evidence of DNC. We also
empirically show that (i) by optimizing deep unconstrained features models via
gradient descent, the resulting solution agrees well with our theory, and (ii)
trained networks recover the unconstrained features suitable for the occurrence
of DNC, thus supporting the validity of this modeling principle.
acknowledgement: M. M. is partially supported by the 2019 Lopez-Loreta Prize. The
authors would like to thank Eugenia Iofinova, Bernd Prach and Simone Bombari for
valuable feedback on the manuscript.
alternative_title:
- NeurIPS
article_processing_charge: No
author:
- first_name: Peter
full_name: Súkeník, Peter
id: d64d6a8d-eb8e-11eb-b029-96fd216dec3c
last_name: Súkeník
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Súkeník P, Mondelli M, Lampert C. Deep neural collapse is provably optimal
for the deep unconstrained features model. In: 37th Annual Conference on Neural
Information Processing Systems.'
apa: Súkeník, P., Mondelli, M., & Lampert, C. (n.d.). Deep neural collapse is
provably optimal for the deep unconstrained features model. In 37th Annual
Conference on Neural Information Processing Systems. New Orleans, LA, United
States.
chicago: Súkeník, Peter, Marco Mondelli, and Christoph Lampert. “Deep Neural Collapse
Is Provably Optimal for the Deep Unconstrained Features Model.” In 37th Annual
Conference on Neural Information Processing Systems, n.d.
ieee: P. Súkeník, M. Mondelli, and C. Lampert, “Deep neural collapse is provably
optimal for the deep unconstrained features model,” in 37th Annual Conference
on Neural Information Processing Systems, New Orleans, LA, United States.
ista: 'Súkeník P, Mondelli M, Lampert C. Deep neural collapse is provably optimal
for the deep unconstrained features model. 37th Annual Conference on Neural Information
Processing Systems. NeurIPS: Neural Information Processing Systems, NeurIPS, .'
mla: Súkeník, Peter, et al. “Deep Neural Collapse Is Provably Optimal for the Deep
Unconstrained Features Model.” 37th Annual Conference on Neural Information
Processing Systems.
short: P. Súkeník, M. Mondelli, C. Lampert, in:, 37th Annual Conference on Neural
Information Processing Systems, n.d.
conference:
end_date: 2023-12-16
location: New Orleans, LA, United States
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2023-12-10
date_created: 2024-02-02T11:17:41Z
date_published: 2023-12-15T00:00:00Z
date_updated: 2024-02-06T07:53:26Z
day: '15'
department:
- _id: MaMo
- _id: ChLa
external_id:
arxiv:
- '2305.13165'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2305.13165'
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: 37th Annual Conference on Neural Information Processing Systems
publication_status: inpress
quality_controlled: '1'
status: public
title: Deep neural collapse is provably optimal for the deep unconstrained features
model
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14924'
abstract:
- lang: eng
text: "The stochastic heavy ball method (SHB), also known as stochastic gradient
descent (SGD) with Polyak's momentum, is widely used in training neural networks.
However, despite the remarkable success of such algorithm in practice, its theoretical
characterization remains limited. In this paper, we focus on neural networks with
two and three layers and provide a rigorous understanding of the properties of
the solutions found by SHB: \\emph{(i)} stability after dropping out part of the
neurons, \\emph{(ii)} connectivity along a low-loss path, and \\emph{(iii)} convergence
to the global optimum.\r\nTo achieve this goal, we take a mean-field view and
relate the SHB dynamics to a certain partial differential equation in the limit
of large network widths. This mean-field perspective has inspired a recent line
of work focusing on SGD while, in contrast, our paper considers an algorithm with
momentum. More specifically, after proving existence and uniqueness of the limit
differential equations, we show convergence to the global optimum and give a quantitative
bound between the mean-field limit and the SHB dynamics of a finite-width network.
Armed with this last bound, we are able to establish the dropout-stability and
connectivity of SHB solutions."
acknowledgement: D. Wu and M. Mondelli are partially supported by the 2019 Lopez-Loreta
Prize. V. Kungurtsev was supported by the OP VVV project CZ.02.1.01/0.0/0.0/16_019/0000765
"Research Center for Informatics".
alternative_title:
- TMLR
article_processing_charge: No
author:
- first_name: Diyuan
full_name: Wu, Diyuan
id: 1a5914c2-896a-11ed-bdf8-fb80621a0635
last_name: Wu
- first_name: Vyacheslav
full_name: Kungurtsev, Vyacheslav
last_name: Kungurtsev
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: 'Wu D, Kungurtsev V, Mondelli M. Mean-field analysis for heavy ball methods:
Dropout-stability, connectivity, and global convergence. In: Transactions on
Machine Learning Research. ML Research Press; 2023.'
apa: 'Wu, D., Kungurtsev, V., & Mondelli, M. (2023). Mean-field analysis for
heavy ball methods: Dropout-stability, connectivity, and global convergence. In
Transactions on Machine Learning Research. ML Research Press.'
chicago: 'Wu, Diyuan, Vyacheslav Kungurtsev, and Marco Mondelli. “Mean-Field Analysis
for Heavy Ball Methods: Dropout-Stability, Connectivity, and Global Convergence.”
In Transactions on Machine Learning Research. ML Research Press, 2023.'
ieee: 'D. Wu, V. Kungurtsev, and M. Mondelli, “Mean-field analysis for heavy ball
methods: Dropout-stability, connectivity, and global convergence,” in Transactions
on Machine Learning Research, 2023.'
ista: 'Wu D, Kungurtsev V, Mondelli M. 2023. Mean-field analysis for heavy ball
methods: Dropout-stability, connectivity, and global convergence. Transactions
on Machine Learning Research. , TMLR, .'
mla: 'Wu, Diyuan, et al. “Mean-Field Analysis for Heavy Ball Methods: Dropout-Stability,
Connectivity, and Global Convergence.” Transactions on Machine Learning Research,
ML Research Press, 2023.'
short: D. Wu, V. Kungurtsev, M. Mondelli, in:, Transactions on Machine Learning
Research, ML Research Press, 2023.
date_created: 2024-02-02T11:21:56Z
date_published: 2023-02-28T00:00:00Z
date_updated: 2024-02-06T08:53:15Z
day: '28'
department:
- _id: MaMo
external_id:
arxiv:
- '2210.06819'
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2210.06819
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: Transactions on Machine Learning Research
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
status: public
title: 'Mean-field analysis for heavy ball methods: Dropout-stability, connectivity,
and global convergence'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14919'
abstract:
- lang: eng
text: "GLACIER METEOROLOGICAL DATA SWISS ALPS -2022\r\n"
article_processing_charge: No
author:
- first_name: Thomas
full_name: Shaw, Thomas
id: 3caa3f91-1f03-11ee-96ce-e0e553054d6e
last_name: Shaw
orcid: 0000-0001-7640-6152
- first_name: Pascal
full_name: Buri, Pascal
id: 317987aa-9421-11ee-ac5a-b941b041abba
last_name: Buri
- first_name: Michael
full_name: McCarthy, Michael
last_name: McCarthy
- first_name: Evan
full_name: Miles, Evan
last_name: Miles
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
orcid: 0000-0002-5554-8087
citation:
ama: Shaw T, Buri P, McCarthy M, Miles E, Pellicciotti F. Air temperature and near-surface
meteorology datasets on three Swiss glaciers - Extreme 2022 Summer. 2023. doi:10.5281/ZENODO.8277285
apa: Shaw, T., Buri, P., McCarthy, M., Miles, E., & Pellicciotti, F. (2023).
Air temperature and near-surface meteorology datasets on three Swiss glaciers
- Extreme 2022 Summer. Zenodo. https://doi.org/10.5281/ZENODO.8277285
chicago: Shaw, Thomas, Pascal Buri, Michael McCarthy, Evan Miles, and Francesca
Pellicciotti. “Air Temperature and Near-Surface Meteorology Datasets on Three
Swiss Glaciers - Extreme 2022 Summer.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8277285.
ieee: T. Shaw, P. Buri, M. McCarthy, E. Miles, and F. Pellicciotti, “Air temperature
and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer.”
Zenodo, 2023.
ista: Shaw T, Buri P, McCarthy M, Miles E, Pellicciotti F. 2023. Air temperature
and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer,
Zenodo, 10.5281/ZENODO.8277285.
mla: Shaw, Thomas, et al. Air Temperature and Near-Surface Meteorology Datasets
on Three Swiss Glaciers - Extreme 2022 Summer. Zenodo, 2023, doi:10.5281/ZENODO.8277285.
short: T. Shaw, P. Buri, M. McCarthy, E. Miles, F. Pellicciotti, (2023).
date_created: 2024-01-31T12:08:26Z
date_published: 2023-08-23T00:00:00Z
date_updated: 2024-02-06T08:44:01Z
day: '23'
ddc:
- '550'
department:
- _id: FrPe
doi: 10.5281/ZENODO.8277285
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/ZENODO.8277285
month: '08'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14885'
relation: used_in_publication
status: public
status: public
title: Air temperature and near-surface meteorology datasets on three Swiss glaciers
- Extreme 2022 Summer
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13107'
abstract:
- lang: eng
text: "Within the human body, the brain exhibits the highest rate of energy consumption
amongst all organs, with the majority of generated ATP being utilized to sustain
neuronal activity. Therefore, the metabolism of the mature cerebral cortex is
geared towards preserving metabolic homeostasis whilst generating significant
amounts of energy. This requires a precise interplay between diverse metabolic
pathways, spanning from a tissue-wide scale to the level of individual neurons.
Disturbances to this delicate metabolic equilibrium, such as those resulting from
maternal malnutrition\r\nor mutations affecting metabolic enzymes, often result
in neuropathological variants of neurodevelopment. For instance, mutations in
SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs),
have been associated with autism and microcephaly. However, despite recent progress
in the field, the extent of metabolic restructuring that occurs within the developing
brain and the corresponding alterations in nutrient demands during various critical
periods remain largely unknown. To investigate this, we performed metabolomic
profiling of the murine cerebral cortex to characterize the metabolic state of
the forebrain at different developmental stages. We found that the developing
cortex undergoes substantial metabolic reprogramming, with specific sets of metabolites
displaying stage-specific changes. According to our observations, we determined
a distinct temporal period in postnatal development during which the cortex displays
heightened reliance on LNAAs. Hence, using a conditional knock-out mouse model,
we deleted Slc7a5 in neural cells, allowing us to monitor the impact of a perturbed
neuronal metabolic state across multiple developmental stages of corticogenesis.
We found that manipulating the levels of essential LNAAs in cortical neurons in
vivo affects one particular perinatal developmental period critical for cortical
network refinement. Abnormally low intracellular LNAA levels result in cell-autonomous
alterations in neuronal lipid metabolism, excitability, and survival during this
particular time window. Although most of the effects of Slc7a5 deletion on neuronal
physiology are transient, derailment of these processes during this brief but
crucial window leads to long-term circuit dysfunction in mice. In conclusion,
out data indicate that the cerebral cortex undergoes significant metabolic reorganization
during development. This process involves the intricate integration of multiple
metabolic pathways to ensure optimal neuronal function throughout different developmental
stages. Our findings offer a paradigm for understanding how neurons synchronize
the expression of nutrient-related genes with their activity to allow proper brain
maturation. Further, our results demonstrate that disruptions in these precisely
calibrated metabolic processes during critical periods of brain development may
result in neuropathological outcomes in mice and in humans."
acknowledged_ssus:
- _id: PreCl
- _id: Bio
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lisa
full_name: Knaus, Lisa
id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87
last_name: Knaus
citation:
ama: 'Knaus L. The metabolism of the developing brain : How large neutral amino
acids modulate perinatal neuronal excitability and survival. 2023. doi:10.15479/at:ista:13107'
apa: 'Knaus, L. (2023). The metabolism of the developing brain : How large neutral
amino acids modulate perinatal neuronal excitability and survival. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:13107'
chicago: 'Knaus, Lisa. “The Metabolism of the Developing Brain : How Large Neutral
Amino Acids Modulate Perinatal Neuronal Excitability and Survival.” Institute
of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13107.'
ieee: 'L. Knaus, “The metabolism of the developing brain : How large neutral amino
acids modulate perinatal neuronal excitability and survival,” Institute of Science
and Technology Austria, 2023.'
ista: 'Knaus L. 2023. The metabolism of the developing brain : How large neutral
amino acids modulate perinatal neuronal excitability and survival. Institute of
Science and Technology Austria.'
mla: 'Knaus, Lisa. The Metabolism of the Developing Brain : How Large Neutral
Amino Acids Modulate Perinatal Neuronal Excitability and Survival. Institute
of Science and Technology Austria, 2023, doi:10.15479/at:ista:13107.'
short: 'L. Knaus, The Metabolism of the Developing Brain : How Large Neutral Amino
Acids Modulate Perinatal Neuronal Excitability and Survival, Institute of Science
and Technology Austria, 2023.'
date_created: 2023-06-01T09:05:24Z
date_published: 2023-05-31T00:00:00Z
date_updated: 2024-02-07T08:03:33Z
day: '31'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: GaNo
doi: 10.15479/at:ista:13107
ec_funded: 1
file:
- access_level: closed
checksum: 4b69a4ac0bbf4163d59c0b58dcb4f2c3
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: lknaus
date_created: 2023-06-01T13:48:41Z
date_updated: 2023-06-01T13:48:41Z
file_id: '13112'
file_name: Thesis_Lisa Knaus_approved_final.docx
file_size: 12991551
relation: source_file
- access_level: open_access
checksum: 6903d152aa01181d87a696085af31c83
content_type: application/pdf
creator: lknaus
date_created: 2023-06-02T09:47:29Z
date_updated: 2023-06-07T08:41:49Z
file_id: '13114'
file_name: Thesis_Lisa Knaus_approved_final_pdfa2b.pdf
file_size: 9309015
relation: main_file
file_date_updated: 2023-06-07T08:41:49Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '147'
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_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12802'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
title: 'The metabolism of the developing brain : How large neutral amino acids modulate
perinatal neuronal excitability and survival'
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '12802'
abstract:
- lang: eng
text: Little is known about the critical metabolic changes that neural cells have
to undergo during development and how temporary shifts in this program can influence
brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5,
a transporter of metabolically essential large neutral amino acids (LNAAs), lead
to autism, we employed metabolomic profiling to study the metabolic states of
the cerebral cortex across different developmental stages. We found that the forebrain
undergoes significant metabolic remodeling throughout development, with certain
groups of metabolites showing stage-specific changes, but what are the consequences
of perturbing this metabolic program? By manipulating Slc7a5 expression in neural
cells, we found that the metabolism of LNAAs and lipids are interconnected in
the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state,
leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific
alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction.
acknowledged_ssus:
- _id: PreCl
- _id: EM-Fac
- _id: Bio
- _id: LifeSc
acknowledgement: We thank A. Freeman and V. Voronin for technical assistance, S. Deixler,
A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal
colony. We thank L. Andersen and J. Sonntag, who were involved in generating the
MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance
with the proteomic analysis, as well as the ISTA electron microscopy and Imaging
and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed
by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge
the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular
metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was
performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated
using Biorender.com. This work was supported by the Austrian Science Fund (FWF,
DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program
(ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lisa
full_name: Knaus, Lisa
id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87
last_name: Knaus
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Daniel
full_name: Malzl, Daniel
last_name: Malzl
- first_name: Maria
full_name: Gerykova Bujalkova, Maria
last_name: Gerykova Bujalkova
- first_name: Mateja
full_name: Smogavec, Mateja
last_name: Smogavec
- first_name: Lena A.
full_name: Schwarz, Lena A.
last_name: Schwarz
- first_name: Sarah
full_name: Gorkiewicz, Sarah
id: f141a35d-15a9-11ec-9fb2-fef6becc7b6f
last_name: Gorkiewicz
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Christian
full_name: Knittl-Frank, Christian
last_name: Knittl-Frank
- first_name: Marianna
full_name: Tassinari, Marianna
id: 7af593f1-d44a-11ed-bf94-a3646a6bb35e
last_name: Tassinari
- first_name: Nuno
full_name: Maulide, Nuno
last_name: Maulide
- first_name: Thomas
full_name: Rülicke, Thomas
last_name: Rülicke
- first_name: Jörg
full_name: Menche, Jörg
last_name: Menche
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal
neuronal excitability and survival. Cell. 2023;186(9):1950-1967.e25. doi:10.1016/j.cell.2023.02.037
apa: Knaus, L., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz,
L. A., … Novarino, G. (2023). Large neutral amino acid levels tune perinatal neuronal
excitability and survival. Cell. Elsevier. https://doi.org/10.1016/j.cell.2023.02.037
chicago: Knaus, Lisa, Bernadette Basilico, Daniel Malzl, Maria Gerykova Bujalkova,
Mateja Smogavec, Lena A. Schwarz, Sarah Gorkiewicz, et al. “Large Neutral Amino
Acid Levels Tune Perinatal Neuronal Excitability and Survival.” Cell. Elsevier,
2023. https://doi.org/10.1016/j.cell.2023.02.037.
ieee: L. Knaus et al., “Large neutral amino acid levels tune perinatal neuronal
excitability and survival,” Cell, vol. 186, no. 9. Elsevier, p. 1950–1967.e25,
2023.
ista: Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA,
Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke
T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels
tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25.
mla: Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal
Excitability and Survival.” Cell, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25,
doi:10.1016/j.cell.2023.02.037.
short: L. Knaus, B. Basilico, D. Malzl, M. Gerykova Bujalkova, M. Smogavec, L.A.
Schwarz, S. Gorkiewicz, N. Amberg, F. Pauler, C. Knittl-Frank, M. Tassinari, N.
Maulide, T. Rülicke, J. Menche, S. Hippenmeyer, G. Novarino, Cell 186 (2023) 1950–1967.e25.
date_created: 2023-04-05T08:15:40Z
date_published: 2023-04-27T00:00:00Z
date_updated: 2024-02-07T08:03:32Z
day: '27'
ddc:
- '570'
department:
- _id: SiHi
- _id: GaNo
doi: 10.1016/j.cell.2023.02.037
ec_funded: 1
external_id:
isi:
- '000991468700001'
file:
- access_level: open_access
checksum: 47e94fbe19e86505b429cb7a5b503ce6
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T09:26:21Z
date_updated: 2023-05-02T09:26:21Z
file_id: '12889'
file_name: 2023_Cell_Knaus.pdf
file_size: 15712841
relation: main_file
success: 1
file_date_updated: 2023-05-02T09:26:21Z
has_accepted_license: '1'
intvolume: ' 186'
isi: 1
issue: '9'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1950-1967.e25
project:
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 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
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/feed-them-or-lose-them/
record:
- id: '13107'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Large neutral amino acid levels tune perinatal neuronal excitability and survival
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: 186
year: '2023'
...
---
_id: '13312'
abstract:
- lang: eng
text: "Superconductor/semiconductor hybrid devices have attracted increasing\r\ninterest
in the past years. Superconducting electronics aims to complement\r\nsemiconductor
technology, while hybrid architectures are at the forefront of\r\nnew ideas such
as topological superconductivity and protected qubits. In this\r\nwork, we engineer
the induced superconductivity in two-dimensional germanium\r\nhole gas by varying
the distance between the quantum well and the aluminum. We\r\ndemonstrate a hard
superconducting gap and realize an electrically and flux\r\ntunable superconducting
diode using a superconducting quantum interference\r\ndevice (SQUID). This allows
to tune the current phase relation (CPR), to a\r\nregime where single Cooper pair
tunneling is suppressed, creating a $ \\sin\r\n\\left( 2 \\varphi \\right)$ CPR.
Shapiro experiments complement this\r\ninterpretation and the microwave drive
allows to create a diode with $ \\approx\r\n100 \\%$ efficiency. The reported
results open up the path towards monolithic\r\nintegration of spin qubit devices,
microwave resonators and (protected)\r\nsuperconducting qubits on a silicon technology
compatible platform."
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: "The authors acknowledge Alexander Brinkmann, Alessandro Crippa,
Andrew Higginbotham, Andrea Iorio, Giordano\r\nScappucci and Christian Schonenberger
for helpful discussions. We thank Marcel Verheijen for the support in the\r\nTEM
analysis. This research and related results were made\r\npossible with the support
of the NOMIS Foundation. It was\r\nsupported by the Scientific Service Units of
ISTA through resources provided by the MIBA Machine Shop and the\r\nnanofabrication
facility, the European Union’s Horizon 2020\r\nresearch and innovation programme
under Grant Agreement\r\nNo 862046, the HORIZON-RIA 101069515 project and the\r\nFWF
Projects #P-32235, #P-36507 and #F-8606. R.S.S.\r\nacknowledges Spanish CM “Talento
Program” Project No.\r\n2022-T1/IND-24070."
article_number: '2306.07109'
article_processing_charge: No
author:
- first_name: Marco
full_name: Valentini, Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
- first_name: Oliver
full_name: Sagi, Oliver
id: 71616374-A8E9-11E9-A7CA-09ECE5697425
last_name: Sagi
- first_name: Levon
full_name: Baghumyan, Levon
last_name: Baghumyan
- first_name: Thijs de
full_name: Gijsel, Thijs de
last_name: Gijsel
- first_name: Jason
full_name: Jung, Jason
id: 4C9ACE7A-F248-11E8-B48F-1D18A9856A87
last_name: Jung
- first_name: Stefano
full_name: Calcaterra, Stefano
last_name: Calcaterra
- first_name: Andrea
full_name: Ballabio, Andrea
last_name: Ballabio
- first_name: Juan Aguilera
full_name: Servin, Juan Aguilera
last_name: Servin
- first_name: Kushagra
full_name: Aggarwal, Kushagra
id: b22ab905-3539-11eb-84c3-fc159dcd79cb
last_name: Aggarwal
orcid: 0000-0001-9985-9293
- first_name: Marian
full_name: Janik, Marian
id: 396A1950-F248-11E8-B48F-1D18A9856A87
last_name: Janik
- first_name: Thomas
full_name: Adletzberger, Thomas
id: 38756BB2-F248-11E8-B48F-1D18A9856A87
last_name: Adletzberger
- first_name: Rubén Seoane
full_name: Souto, Rubén Seoane
last_name: Souto
- first_name: Martin
full_name: Leijnse, Martin
last_name: Leijnse
- first_name: Jeroen
full_name: Danon, Jeroen
last_name: Danon
- first_name: Constantin
full_name: Schrade, Constantin
last_name: Schrade
- first_name: Erik
full_name: Bakkers, Erik
last_name: Bakkers
- first_name: Daniel
full_name: Chrastina, Daniel
last_name: Chrastina
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Valentini M, Sagi O, Baghumyan L, et al. Radio frequency driven superconducting
diode and parity conserving Cooper pair transport in a two-dimensional germanium
hole gas. arXiv. doi:10.48550/arXiv.2306.07109
apa: Valentini, M., Sagi, O., Baghumyan, L., Gijsel, T. de, Jung, J., Calcaterra,
S., … Katsaros, G. (n.d.). Radio frequency driven superconducting diode and parity
conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv.
https://doi.org/10.48550/arXiv.2306.07109
chicago: Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason
Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Radio Frequency Driven Superconducting
Diode and Parity Conserving Cooper Pair Transport in a Two-Dimensional Germanium
Hole Gas.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2306.07109.
ieee: M. Valentini et al., “Radio frequency driven superconducting diode
and parity conserving Cooper pair transport in a two-dimensional germanium hole
gas,” arXiv. .
ista: Valentini M, Sagi O, Baghumyan L, Gijsel T de, Jung J, Calcaterra S, Ballabio
A, Servin JA, Aggarwal K, Janik M, Adletzberger T, Souto RS, Leijnse M, Danon
J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. Radio frequency driven
superconducting diode and parity conserving Cooper pair transport in a two-dimensional
germanium hole gas. arXiv, 2306.07109.
mla: Valentini, Marco, et al. “Radio Frequency Driven Superconducting Diode and
Parity Conserving Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.”
ArXiv, 2306.07109, doi:10.48550/arXiv.2306.07109.
short: M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra,
A. Ballabio, J.A. Servin, K. Aggarwal, M. Janik, T. Adletzberger, R.S. Souto,
M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella, G. Katsaros,
ArXiv (n.d.).
date_created: 2023-07-26T11:17:20Z
date_published: 2023-06-13T00:00:00Z
date_updated: 2024-02-07T07:52:32Z
day: '13'
ddc:
- '530'
department:
- _id: GeKa
- _id: M-Shop
doi: 10.48550/arXiv.2306.07109
ec_funded: 1
external_id:
arxiv:
- '2306.07109'
keyword:
- Mesoscale and Nanoscale Physics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2306.07109
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 237E5020-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862046'
name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS
- _id: 237B3DA4-32DE-11EA-91FC-C7463DDC885E
call_identifier: FWF
grant_number: P32235
name: Towards scalable hut wire quantum devices
- _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a
grant_number: P36507
name: Merging spin and superconducting qubits in planar Ge
- _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e
grant_number: F8606
name: Conventional and unconventional topological superconductors
- _id: bd5b4ec5-d553-11ed-ba76-a6eedb083344
name: Protected states of quantum matter
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '13286'
relation: dissertation_contains
status: public
status: public
title: Radio frequency driven superconducting diode and parity conserving Cooper
pair transport in a two-dimensional germanium hole gas
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14949'
abstract:
- lang: eng
text: Many approaches have been proposed to use diffusion models to augment training
datasets for downstream tasks, such as classification. However, diffusion models
are themselves trained on large datasets, often with noisy annotations, and it
remains an open question to which extent these models contribute to downstream
classification performance. In particular, it remains unclear if they generalize
enough to improve over directly using the additional data of their pre-training
process for augmentation. We systematically evaluate a range of existing methods
to generate images from diffusion models and study new extensions to assess their
benefit for data augmentation. Personalizing diffusion models towards the target
data outperforms simpler prompting strategies. However, using the pre-training
data of the diffusion model alone, via a simple nearest-neighbor retrieval procedure,
leads to even stronger downstream performance. Our study explores the potential
of diffusion models in generating new training data, and surprisingly finds that
these sophisticated models are not yet able to beat a simple and strong image
retrieval baseline on simple downstream vision tasks.
acknowledgement: The authors would like to thank Varad Gunjal and Vishaal Udandarao.
MFB thanks the International Max Planck Research School for Intelligent Systems
(IMPRS-IS).
alternative_title:
- TMLR
article_processing_charge: No
article_type: original
author:
- first_name: Max
full_name: Burg, Max
last_name: Burg
- first_name: Florian
full_name: Wenzel, Florian
last_name: Wenzel
- first_name: Dominik
full_name: Zietlow, Dominik
last_name: Zietlow
- first_name: Max
full_name: Horn, Max
last_name: Horn
- first_name: Osama
full_name: Makansi, Osama
last_name: Makansi
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Chris
full_name: Russell, Chris
last_name: Russell
citation:
ama: Burg M, Wenzel F, Zietlow D, et al. Image retrieval outperforms diffusion models
on data augmentation. Journal of Machine Learning Research. 2023.
apa: Burg, M., Wenzel, F., Zietlow, D., Horn, M., Makansi, O., Locatello, F., &
Russell, C. (2023). Image retrieval outperforms diffusion models on data augmentation.
Journal of Machine Learning Research. ML Research Press.
chicago: Burg, Max, Florian Wenzel, Dominik Zietlow, Max Horn, Osama Makansi, Francesco
Locatello, and Chris Russell. “Image Retrieval Outperforms Diffusion Models on
Data Augmentation.” Journal of Machine Learning Research. ML Research Press,
2023.
ieee: M. Burg et al., “Image retrieval outperforms diffusion models on data
augmentation,” Journal of Machine Learning Research. ML Research Press,
2023.
ista: Burg M, Wenzel F, Zietlow D, Horn M, Makansi O, Locatello F, Russell C. 2023.
Image retrieval outperforms diffusion models on data augmentation. Journal of
Machine Learning Research.
mla: Burg, Max, et al. “Image Retrieval Outperforms Diffusion Models on Data Augmentation.”
Journal of Machine Learning Research, ML Research Press, 2023.
short: M. Burg, F. Wenzel, D. Zietlow, M. Horn, O. Makansi, F. Locatello, C. Russell,
Journal of Machine Learning Research (2023).
date_created: 2024-02-07T14:57:39Z
date_published: 2023-12-10T00:00:00Z
date_updated: 2024-02-12T08:30:21Z
day: '10'
ddc:
- '000'
department:
- _id: FrLo
file:
- access_level: open_access
checksum: af87ddea7908923426365347b9c87ba7
content_type: application/pdf
creator: ptazenko
date_created: 2024-02-07T14:57:32Z
date_updated: 2024-02-07T14:57:32Z
file_id: '14950'
file_name: Burg_et_al_2023_Image_retrieval_outperforms.pdf
file_size: 27325153
relation: main_file
file_date_updated: 2024-02-07T14:57:32Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://openreview.net/forum?id=xflYdGZMpv
month: '12'
oa: 1
oa_version: Published Version
publication: Journal of Machine Learning Research
publication_identifier:
eissn:
- 2835-8856
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
status: public
title: Image retrieval outperforms diffusion models on data augmentation
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: '2023'
...
---
_id: '14946'
abstract:
- lang: eng
text: "We present a unified framework for studying the identifiability of\r\nrepresentations
learned from simultaneously observed views, such as different\r\ndata modalities.
We allow a partially observed setting in which each view\r\nconstitutes a nonlinear
mixture of a subset of underlying latent variables,\r\nwhich can be causally related.
We prove that the information shared across all\r\nsubsets of any number of views
can be learned up to a smooth bijection using\r\ncontrastive learning and a single
encoder per view. We also provide graphical\r\ncriteria indicating which latent
variables can be identified through a simple\r\nset of rules, which we refer to
as identifiability algebra. Our general\r\nframework and theoretical results unify
and extend several previous works on\r\nmulti-view nonlinear ICA, disentanglement,
and causal representation learning.\r\nWe experimentally validate our claims on
numerical, image, and multi-modal data\r\nsets. Further, we demonstrate that the
performance of prior methods is\r\nrecovered in different special cases of our
setup. Overall, we find that access\r\nto multiple partial views enables us to
identify a more fine-grained\r\nrepresentation, under the generally milder assumption
of partial observability."
acknowledgement: "This work was initiated at the Second Bellairs Workshop on Causality
held at the Bellairs Research Institute, January 6–13, 2022; we thank all workshop
participants for providing a stimulating research environment. Further, we thank
Cian Eastwood, Luigi Gresele, Stefano Soatto, Marco Bagatella, and A. René Geist
for helpful discussion. GM is a member of the Machine Learning Cluster of Excellence,
EXC number 2064/1 – Project number 390727645. JvK and GM acknowledge support from
the German Federal Ministry of Education and Research (BMBF) through the Tübingen
AI Center (FKZ: 01IS18039B). The research of DX and SM was supported by the Air
Force Office of Scientific Research under award number FA8655-22-1-7155. Any opinions,
findings, and conclusions or recommendations expressed in\r\nthis material are those
of the author(s) and do not necessarily reflect the views of the United States Air
Force. We also thank SURF for the support in using the Dutch National Supercomputer
Snellius. DY was supported by an Amazon fellowship and the International Max Planck
Research School for Intelligent Systems (IMPRS-IS). Work done outside of Amazon.
SL was supported by an IVADO excellence PhD scholarship and by Samsung Electronics
Co., Ldt."
article_number: '2311.04056'
article_processing_charge: No
author:
- first_name: Dingling
full_name: Yao, Dingling
id: d3e02e50-48a8-11ee-8f62-c108061797fa
last_name: Yao
- first_name: Danru
full_name: Xu, Danru
last_name: Xu
- first_name: Sébastien
full_name: Lachapelle, Sébastien
last_name: Lachapelle
- first_name: Sara
full_name: Magliacane, Sara
last_name: Magliacane
- first_name: Perouz
full_name: Taslakian, Perouz
last_name: Taslakian
- first_name: Georg
full_name: Martius, Georg
last_name: Martius
- first_name: Julius von
full_name: Kügelgen, Julius von
last_name: Kügelgen
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
citation:
ama: Yao D, Xu D, Lachapelle S, et al. Multi-view causal representation learning
with partial observability. arXiv. doi:10.48550/arXiv.2311.04056
apa: Yao, D., Xu, D., Lachapelle, S., Magliacane, S., Taslakian, P., Martius, G.,
… Locatello, F. (n.d.). Multi-view causal representation learning with partial
observability. arXiv. https://doi.org/10.48550/arXiv.2311.04056
chicago: Yao, Dingling, Danru Xu, Sébastien Lachapelle, Sara Magliacane, Perouz
Taslakian, Georg Martius, Julius von Kügelgen, and Francesco Locatello. “Multi-View
Causal Representation Learning with Partial Observability.” ArXiv, n.d.
https://doi.org/10.48550/arXiv.2311.04056.
ieee: D. Yao et al., “Multi-view causal representation learning with partial
observability,” arXiv. .
ista: Yao D, Xu D, Lachapelle S, Magliacane S, Taslakian P, Martius G, Kügelgen
J von, Locatello F. Multi-view causal representation learning with partial observability.
arXiv, 2311.04056.
mla: Yao, Dingling, et al. “Multi-View Causal Representation Learning with Partial
Observability.” ArXiv, 2311.04056, doi:10.48550/arXiv.2311.04056.
short: D. Yao, D. Xu, S. Lachapelle, S. Magliacane, P. Taslakian, G. Martius, J.
von Kügelgen, F. Locatello, ArXiv (n.d.).
date_created: 2024-02-07T14:28:34Z
date_published: 2023-11-07T00:00:00Z
date_updated: 2024-02-12T08:07:33Z
day: '07'
department:
- _id: FrLo
doi: 10.48550/arXiv.2311.04056
external_id:
arxiv:
- '2311.04056'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2311.04056
month: '11'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Multi-view causal representation learning with partial observability
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14952'
abstract:
- lang: eng
text: "While different neural models often exhibit latent spaces that are alike
when exposed to semantically related data, this intrinsic similarity is not always
immediately discernible. Towards a better understanding of this phenomenon, our
work shows how representations learned from these neural modules can be translated
between different pre-trained networks via simpler transformations than previously
thought. An advantage of this approach is the ability to\r\nestimate these transformations
using standard, well-understood algebraic procedures that have closed-form solutions.
Our method directly estimates a transformation between two given latent spaces,
thereby enabling effective stitching of encoders and decoders without additional
training. We extensively validate the adaptability of this translation procedure
in different\r\nexperimental settings: across various trainings, domains, architectures
(e.g., ResNet, CNN, ViT), and in multiple downstream tasks (classification, reconstruction).
Notably, we show how it is possible to zero-shot stitch text encoders and vision
decoders, or vice-versa, yielding surprisingly good classification performance
in this multimodal setting."
acknowledgement: "This work is supported by the ERC grant no.802554 (SPECGEO), PRIN
2020 project no.2020TA3K9N (LEGO.AI), and PNRR MUR project PE0000013-FAIR. Francesco\r\nLocatello
did not contribute to this work at Amazon."
article_number: '2311.00664'
article_processing_charge: No
author:
- first_name: Valentino
full_name: Maiorca, Valentino
last_name: Maiorca
- first_name: Luca
full_name: Moschella, Luca
last_name: Moschella
- first_name: Antonio
full_name: Norelli, Antonio
last_name: Norelli
- first_name: Marco
full_name: Fumero, Marco
last_name: Fumero
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Emanuele
full_name: Rodolà, Emanuele
last_name: Rodolà
citation:
ama: Maiorca V, Moschella L, Norelli A, Fumero M, Locatello F, Rodolà E. Latent
space translation via semantic alignment. arXiv. doi:10.48550/arXiv.2311.00664
apa: Maiorca, V., Moschella, L., Norelli, A., Fumero, M., Locatello, F., & Rodolà,
E. (n.d.). Latent space translation via semantic alignment. arXiv. https://doi.org/10.48550/arXiv.2311.00664
chicago: Maiorca, Valentino, Luca Moschella, Antonio Norelli, Marco Fumero, Francesco
Locatello, and Emanuele Rodolà. “Latent Space Translation via Semantic Alignment.”
ArXiv, n.d. https://doi.org/10.48550/arXiv.2311.00664.
ieee: V. Maiorca, L. Moschella, A. Norelli, M. Fumero, F. Locatello, and E. Rodolà,
“Latent space translation via semantic alignment,” arXiv. .
ista: Maiorca V, Moschella L, Norelli A, Fumero M, Locatello F, Rodolà E. Latent
space translation via semantic alignment. arXiv, 2311.00664.
mla: Maiorca, Valentino, et al. “Latent Space Translation via Semantic Alignment.”
ArXiv, 2311.00664, doi:10.48550/arXiv.2311.00664.
short: V. Maiorca, L. Moschella, A. Norelli, M. Fumero, F. Locatello, E. Rodolà,
ArXiv (n.d.).
date_created: 2024-02-07T15:08:55Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2024-02-12T09:40:23Z
day: '01'
department:
- _id: FrLo
doi: 10.48550/arXiv.2311.00664
external_id:
arxiv:
- '2311.00664'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2311.00664
month: '11'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Latent space translation via semantic alignment
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14948'
abstract:
- lang: eng
text: "The extraction of modular object-centric representations for downstream tasks\r\nis
an emerging area of research. Learning grounded representations of objects\r\nthat
are guaranteed to be stable and invariant promises robust performance\r\nacross
different tasks and environments. Slot Attention (SA) learns\r\nobject-centric
representations by assigning objects to \\textit{slots}, but\r\npresupposes a
\\textit{single} distribution from which all slots are randomly\r\ninitialised.
This results in an inability to learn \\textit{specialized} slots\r\nwhich bind
to specific object types and remain invariant to identity-preserving\r\nchanges
in object appearance. To address this, we present\r\n\\emph{\\textsc{Co}nditional
\\textsc{S}lot \\textsc{A}ttention} (\\textsc{CoSA})\r\nusing a novel concept
of \\emph{Grounded Slot Dictionary} (GSD) inspired by\r\nvector quantization.
Our proposed GSD comprises (i) canonical object-level\r\nproperty vectors and
(ii) parametric Gaussian distributions, which define a\r\nprior over the slots.
We demonstrate the benefits of our method in multiple\r\ndownstream tasks such
as scene generation, composition, and task adaptation,\r\nwhilst remaining competitive
with SA in popular object discovery benchmarks."
acknowledgement: "This work was supported by supported by UKRI (grant agreement no.
EP/S023356/1), in the UKRI\r\nCentre for Doctoral Training in Safe and Trusted AI
via A. Kori."
article_number: '2307.09437'
article_processing_charge: No
author:
- first_name: Avinash
full_name: Kori, Avinash
last_name: Kori
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Fabio De Sousa
full_name: Ribeiro, Fabio De Sousa
last_name: Ribeiro
- first_name: Francesca
full_name: Toni, Francesca
last_name: Toni
- first_name: Ben
full_name: Glocker, Ben
last_name: Glocker
citation:
ama: Kori A, Locatello F, Ribeiro FDS, Toni F, Glocker B. Grounded object centric
learning. arXiv. doi:10.48550/arXiv.2307.09437
apa: Kori, A., Locatello, F., Ribeiro, F. D. S., Toni, F., & Glocker, B. (n.d.).
Grounded object centric learning. arXiv. https://doi.org/10.48550/arXiv.2307.09437
chicago: Kori, Avinash, Francesco Locatello, Fabio De Sousa Ribeiro, Francesca Toni,
and Ben Glocker. “Grounded Object Centric Learning.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2307.09437.
ieee: A. Kori, F. Locatello, F. D. S. Ribeiro, F. Toni, and B. Glocker, “Grounded
object centric learning,” arXiv. .
ista: Kori A, Locatello F, Ribeiro FDS, Toni F, Glocker B. Grounded object centric
learning. arXiv, 2307.09437.
mla: Kori, Avinash, et al. “Grounded Object Centric Learning.” ArXiv, 2307.09437,
doi:10.48550/arXiv.2307.09437.
short: A. Kori, F. Locatello, F.D.S. Ribeiro, F. Toni, B. Glocker, ArXiv (n.d.).
date_created: 2024-02-07T14:47:04Z
date_published: 2023-07-18T00:00:00Z
date_updated: 2024-02-12T08:13:12Z
day: '18'
department:
- _id: FrLo
doi: 10.48550/arXiv.2307.09437
external_id:
arxiv:
- '2307.09437'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2307.09437
month: '07'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Grounded object centric learning
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14953'
abstract:
- lang: eng
text: This paper provides statistical sample complexity bounds for score-matching
and its applications in causal discovery. We demonstrate that accurate estimation
of the score function is achievable by training a standard deep ReLU neural network
using stochastic gradient descent. We establish bounds on the error rate of recovering
causal relationships using the score-matching-based causal discovery method of
Rolland et al. [2022], assuming a sufficiently good estimation of the score function.
Finally, we analyze the upper bound of score-matching estimation within the score-based
generative modeling, which has been applied for causal discovery but is also of
independent interest within the domain of generative models.
acknowledgement: 'We are thankful to the reviewers for providing constructive feedback
and Kun Zhang and Dominik Janzing for helpful discussion on the special case of
deterministic children. This work was supported by Hasler Foundation Program: Hasler
Responsible AI (project number 21043). This work was supported by the Swiss National
Science Foundation (SNSF) under grant number 200021_205011. Francesco Locatello
did not contribute to this work at Amazon. '
article_number: '2310.18123'
article_processing_charge: No
author:
- first_name: Zhenyu
full_name: Zhu, Zhenyu
last_name: Zhu
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Volkan
full_name: Cevher, Volkan
last_name: Cevher
citation:
ama: 'Zhu Z, Locatello F, Cevher V. Sample complexity bounds for score-matching:
Causal discovery and generative modeling. arXiv. doi:10.48550/arXiv.2310.18123'
apa: 'Zhu, Z., Locatello, F., & Cevher, V. (n.d.). Sample complexity bounds
for score-matching: Causal discovery and generative modeling. arXiv. https://doi.org/10.48550/arXiv.2310.18123'
chicago: 'Zhu, Zhenyu, Francesco Locatello, and Volkan Cevher. “Sample Complexity
Bounds for Score-Matching: Causal Discovery and Generative Modeling.” ArXiv,
n.d. https://doi.org/10.48550/arXiv.2310.18123.'
ieee: 'Z. Zhu, F. Locatello, and V. Cevher, “Sample complexity bounds for score-matching:
Causal discovery and generative modeling,” arXiv. .'
ista: 'Zhu Z, Locatello F, Cevher V. Sample complexity bounds for score-matching:
Causal discovery and generative modeling. arXiv, 2310.18123.'
mla: 'Zhu, Zhenyu, et al. “Sample Complexity Bounds for Score-Matching: Causal Discovery
and Generative Modeling.” ArXiv, 2310.18123, doi:10.48550/arXiv.2310.18123.'
short: Z. Zhu, F. Locatello, V. Cevher, ArXiv (n.d.).
date_created: 2024-02-07T15:11:11Z
date_published: 2023-10-27T00:00:00Z
date_updated: 2024-02-12T09:45:58Z
day: '27'
department:
- _id: FrLo
doi: 10.48550/arXiv.2310.18123
external_id:
arxiv:
- '2310.18123'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2310.18123
month: '10'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: 'Sample complexity bounds for score-matching: Causal discovery and generative
modeling'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14954'
abstract:
- lang: eng
text: "When domain knowledge is limited and experimentation is restricted by ethical,
financial, or time constraints, practitioners turn to observational causal discovery
methods to recover the causal structure, exploiting the statistical properties
of their data. Because causal discovery without further assumptions is an ill-posed
problem, each algorithm comes with its own set of\r\nusually untestable assumptions,
some of which are hard to meet in real datasets. Motivated by these considerations,
this paper extensively benchmarks the empirical performance of recent causal discovery
methods on observational i.i.d. data generated under different background conditions,
allowing for violations of the critical assumptions required by each selected
approach. Our experimental findings show that score matching-based methods demonstrate\r\nsurprising
performance in the false positive and false negative rate of the inferred graph
in these challenging scenarios, and we provide theoretical insights into their
performance. This work is also the first effort to benchmark the stability of
causal discovery algorithms with respect to the values of their hyperparameters.
Finally, we hope this paper will set a new standard for the evaluation of causal
discovery methods and can serve as an accessible entry point for practitioners
interested in the field, highlighting the empirical implications of different
algorithm choices."
acknowledgement: "We thank Kun Zhang and Carl-Johann Simon-Gabriel for the insightful
discussions. This work\r\nhas been supported by AFOSR, grant n. FA8655-20-1-7035.
FM is supported by Programma\r\nOperativo Nazionale ricerca e innovazione 2014-2020.
FM partially contributed to this work during an internship at Amazon Web Services
with FL. FL partially contributed while at AWS."
article_number: '2310.13387'
article_processing_charge: No
author:
- first_name: Francesco
full_name: Montagna, Francesco
last_name: Montagna
- first_name: Atalanti A.
full_name: Mastakouri, Atalanti A.
last_name: Mastakouri
- first_name: Elias
full_name: Eulig, Elias
last_name: Eulig
- first_name: Nicoletta
full_name: Noceti, Nicoletta
last_name: Noceti
- first_name: Lorenzo
full_name: Rosasco, Lorenzo
last_name: Rosasco
- first_name: Dominik
full_name: Janzing, Dominik
last_name: Janzing
- first_name: Bryon
full_name: Aragam, Bryon
last_name: Aragam
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
citation:
ama: Montagna F, Mastakouri AA, Eulig E, et al. Assumption violations in causal
discovery and the robustness of score matching. arXiv. doi:10.48550/arXiv.2310.13387
apa: Montagna, F., Mastakouri, A. A., Eulig, E., Noceti, N., Rosasco, L., Janzing,
D., … Locatello, F. (n.d.). Assumption violations in causal discovery and the
robustness of score matching. arXiv. https://doi.org/10.48550/arXiv.2310.13387
chicago: Montagna, Francesco, Atalanti A. Mastakouri, Elias Eulig, Nicoletta Noceti,
Lorenzo Rosasco, Dominik Janzing, Bryon Aragam, and Francesco Locatello. “Assumption
Violations in Causal Discovery and the Robustness of Score Matching.” ArXiv,
n.d. https://doi.org/10.48550/arXiv.2310.13387.
ieee: F. Montagna et al., “Assumption violations in causal discovery and
the robustness of score matching,” arXiv. .
ista: Montagna F, Mastakouri AA, Eulig E, Noceti N, Rosasco L, Janzing D, Aragam
B, Locatello F. Assumption violations in causal discovery and the robustness of
score matching. arXiv, 2310.13387.
mla: Montagna, Francesco, et al. “Assumption Violations in Causal Discovery and
the Robustness of Score Matching.” ArXiv, 2310.13387, doi:10.48550/arXiv.2310.13387.
short: F. Montagna, A.A. Mastakouri, E. Eulig, N. Noceti, L. Rosasco, D. Janzing,
B. Aragam, F. Locatello, ArXiv (n.d.).
date_created: 2024-02-07T15:11:56Z
date_published: 2023-10-20T00:00:00Z
date_updated: 2024-02-12T09:51:15Z
day: '20'
department:
- _id: FrLo
doi: 10.48550/arXiv.2310.13387
external_id:
arxiv:
- '2310.13387'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2310.13387
month: '10'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Assumption violations in causal discovery and the robustness of score matching
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14210'
abstract:
- lang: eng
text: Recovering the latent factors of variation of high dimensional data has so
far focused on simple synthetic settings. Mostly building on unsupervised and
weakly-supervised objectives, prior work missed out on the positive implications
for representation learning on real world data. In this work, we propose to leverage
knowledge extracted from a diversified set of supervised tasks to learn a common
disentangled representation. Assuming each supervised task only depends on an
unknown subset of the factors of variation, we disentangle the feature space of
a supervised multi-task model, with features activating sparsely across different
tasks and information being shared as appropriate. Importantly, we never directly
observe the factors of variations but establish that access to multiple tasks
is sufficient for identifiability under sufficiency and minimality assumptions.
We validate our approach on six real world distribution shift benchmarks, and
different data modalities (images, text), demonstrating how disentangled representations
can be transferred to real settings.
article_number: '2304.07939'
article_processing_charge: No
author:
- first_name: Marco
full_name: Fumero, Marco
last_name: Fumero
- first_name: Florian
full_name: Wenzel, Florian
last_name: Wenzel
- first_name: Luca
full_name: Zancato, Luca
last_name: Zancato
- first_name: Alessandro
full_name: Achille, Alessandro
last_name: Achille
- first_name: Emanuele
full_name: Rodolà, Emanuele
last_name: Rodolà
- first_name: Stefano
full_name: Soatto, Stefano
last_name: Soatto
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
citation:
ama: Fumero M, Wenzel F, Zancato L, et al. Leveraging sparse and shared feature
activations for disentangled representation learning. arXiv. doi:10.48550/arXiv.2304.07939
apa: Fumero, M., Wenzel, F., Zancato, L., Achille, A., Rodolà, E., Soatto, S., …
Locatello, F. (n.d.). Leveraging sparse and shared feature activations for disentangled
representation learning. arXiv. https://doi.org/10.48550/arXiv.2304.07939
chicago: Fumero, Marco, Florian Wenzel, Luca Zancato, Alessandro Achille, Emanuele
Rodolà, Stefano Soatto, Bernhard Schölkopf, and Francesco Locatello. “Leveraging
Sparse and Shared Feature Activations for Disentangled Representation Learning.”
ArXiv, n.d. https://doi.org/10.48550/arXiv.2304.07939.
ieee: M. Fumero et al., “Leveraging sparse and shared feature activations
for disentangled representation learning,” arXiv. .
ista: Fumero M, Wenzel F, Zancato L, Achille A, Rodolà E, Soatto S, Schölkopf B,
Locatello F. Leveraging sparse and shared feature activations for disentangled
representation learning. arXiv, 2304.07939.
mla: Fumero, Marco, et al. “Leveraging Sparse and Shared Feature Activations for
Disentangled Representation Learning.” ArXiv, 2304.07939, doi:10.48550/arXiv.2304.07939.
short: M. Fumero, F. Wenzel, L. Zancato, A. Achille, E. Rodolà, S. Soatto, B. Schölkopf,
F. Locatello, ArXiv (n.d.).
date_created: 2023-08-22T14:19:03Z
date_published: 2023-04-17T00:00:00Z
date_updated: 2024-02-12T09:55:48Z
day: '17'
department:
- _id: FrLo
doi: 10.48550/arXiv.2304.07939
external_id:
arxiv:
- '2304.07939'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2304.07939
month: '04'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Leveraging sparse and shared feature activations for disentangled representation
learning
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14207'
abstract:
- lang: eng
text: The binding problem in human cognition, concerning how the brain represents
and connects objects within a fixed network of neural connections, remains a subject
of intense debate. Most machine learning efforts addressing this issue in an unsupervised
setting have focused on slot-based methods, which may be limiting due to their
discrete nature and difficulty to express uncertainty. Recently, the Complex AutoEncoder
was proposed as an alternative that learns continuous and distributed object-centric
representations. However, it is only applicable to simple toy data. In this paper,
we present Rotating Features, a generalization of complex-valued features to higher
dimensions, and a new evaluation procedure for extracting objects from distributed
representations. Additionally, we show the applicability of our approach to pre-trained
features. Together, these advancements enable us to scale distributed object-centric
representations from simple toy to real-world data. We believe this work advances
a new paradigm for addressing the binding problem in machine learning and has
the potential to inspire further innovation in the field.
article_number: '2306.00600'
article_processing_charge: No
author:
- first_name: Sindy
full_name: Löwe, Sindy
last_name: Löwe
- first_name: Phillip
full_name: Lippe, Phillip
last_name: Lippe
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Max
full_name: Welling, Max
last_name: Welling
citation:
ama: Löwe S, Lippe P, Locatello F, Welling M. Rotating features for object discovery.
arXiv. doi:10.48550/arXiv.2306.00600
apa: Löwe, S., Lippe, P., Locatello, F., & Welling, M. (n.d.). Rotating features
for object discovery. arXiv. https://doi.org/10.48550/arXiv.2306.00600
chicago: Löwe, Sindy, Phillip Lippe, Francesco Locatello, and Max Welling. “Rotating
Features for Object Discovery.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2306.00600.
ieee: S. Löwe, P. Lippe, F. Locatello, and M. Welling, “Rotating features for object
discovery,” arXiv. .
ista: Löwe S, Lippe P, Locatello F, Welling M. Rotating features for object discovery.
arXiv, 2306.00600.
mla: Löwe, Sindy, et al. “Rotating Features for Object Discovery.” ArXiv,
2306.00600, doi:10.48550/arXiv.2306.00600.
short: S. Löwe, P. Lippe, F. Locatello, M. Welling, ArXiv (n.d.).
date_created: 2023-08-22T14:18:00Z
date_published: 2023-06-01T00:00:00Z
date_updated: 2024-02-12T09:53:44Z
day: '01'
department:
- _id: FrLo
doi: 10.48550/arXiv.2306.00600
external_id:
arxiv:
- '2306.00600'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2306.00600
month: '06'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Rotating features for object discovery
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14961'
abstract:
- lang: eng
text: "The use of simulated data in the field of causal discovery is ubiquitous
due to the scarcity of annotated real data. Recently, Reisach et al., 2021 highlighted
the emergence of patterns in simulated linear data, which displays increasing
marginal variance in the casual direction. As an ablation in their experiments,
Montagna et al., 2023 found that similar patterns may emerge in\r\nnonlinear models
for the variance of the score vector $\\nabla \\log p_{\\mathbf{X}}$, and introduced
the ScoreSort algorithm. In this work, we formally define and characterize this
score-sortability pattern of nonlinear additive noise models. We find that it
defines a class of identifiable (bivariate) causal models overlapping with nonlinear
additive noise models. We\r\ntheoretically demonstrate the advantages of ScoreSort
in terms of statistical efficiency compared to prior state-of-the-art score matching-based
methods and empirically show the score-sortability of the most common synthetic
benchmarks in the literature. Our findings remark (1) the lack of diversity in
the data as an important limitation in the evaluation of nonlinear causal discovery
approaches, (2) the importance of thoroughly testing different settings within
a problem class, and (3) the importance of analyzing statistical properties in\r\ncausal
discovery, where research is often limited to defining identifiability conditions
of the model. "
article_number: '2310.14246'
article_processing_charge: No
author:
- first_name: Francesco
full_name: Montagna, Francesco
last_name: Montagna
- first_name: Nicoletta
full_name: Noceti, Nicoletta
last_name: Noceti
- first_name: Lorenzo
full_name: Rosasco, Lorenzo
last_name: Rosasco
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
citation:
ama: Montagna F, Noceti N, Rosasco L, Locatello F. Shortcuts for causal discovery
of nonlinear models by score matching. arXiv. doi:10.48550/arXiv.2310.14246
apa: Montagna, F., Noceti, N., Rosasco, L., & Locatello, F. (n.d.). Shortcuts
for causal discovery of nonlinear models by score matching. arXiv. https://doi.org/10.48550/arXiv.2310.14246
chicago: Montagna, Francesco, Nicoletta Noceti, Lorenzo Rosasco, and Francesco Locatello.
“Shortcuts for Causal Discovery of Nonlinear Models by Score Matching.” ArXiv,
n.d. https://doi.org/10.48550/arXiv.2310.14246.
ieee: F. Montagna, N. Noceti, L. Rosasco, and F. Locatello, “Shortcuts for causal
discovery of nonlinear models by score matching,” arXiv. .
ista: Montagna F, Noceti N, Rosasco L, Locatello F. Shortcuts for causal discovery
of nonlinear models by score matching. arXiv, 2310.14246.
mla: Montagna, Francesco, et al. “Shortcuts for Causal Discovery of Nonlinear Models
by Score Matching.” ArXiv, 2310.14246, doi:10.48550/arXiv.2310.14246.
short: F. Montagna, N. Noceti, L. Rosasco, F. Locatello, ArXiv (n.d.).
date_created: 2024-02-08T15:31:46Z
date_published: 2023-10-22T00:00:00Z
date_updated: 2024-02-12T10:03:33Z
day: '22'
department:
- _id: FrLo
doi: 10.48550/arXiv.2310.14246
external_id:
arxiv:
- '2310.14246'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2310.14246
month: '10'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Shortcuts for causal discovery of nonlinear models by score matching
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14958'
abstract:
- lang: eng
text: Causal representation learning (CRL) aims at identifying high-level causal
variables from low-level data, e.g. images. Current methods usually assume that
all causal variables are captured in the high-dimensional observations. In this
work, we focus on learning causal representations from data under partial observability,
i.e., when some of the causal variables are not observed in the measurements,
and the set of masked variables changes across the different samples. We introduce
some initial theoretical results for identifying causal variables under partial
observability by exploiting a sparsity regularizer, focusing in particular on
the linear and piecewise linear mixing function case. We provide a theorem that
allows us to identify the causal variables up to permutation and element-wise
linear transformations in the linear case and a lemma that allows us to identify
causal variables up to linear transformation in the piecewise case. Finally, we
provide a conjecture that would allow us to identify the causal variables up to
permutation and element-wise linear transformations also in the piecewise linear
case. We test the theorem and conjecture on simulated data, showing the effectiveness
of our method.
acknowledgement: "This work was initiated at the Second Bellairs Workshop on Causality
held at the Bellairs Research Institute, January 6–13, 2022; we thank all workshop
participants for providing a stimulating research environment. The research of DX
and SM was supported by the Air Force Office of Scientific Research under award
number FA8655-22-1-7155. Any opinions, findings, and conclusions or recommendations
expressed in this material are those of the author(s) and do not necessarily reflect
the views of the United States Air Force. We also thank SURF for the support in
using the Dutch National Supercomputer Snellius. DY was supported by an Amazon fellowship
and the International Max Planck Research School for Intelligent Systems (IMPRS-IS).
Work done outside of Amazon. SL was supported by an IVADO excellence PhD scholarship
and by Samsung Electronics Co., Ldt. JvK acknowledges support from the German Federal
Ministry of Education and Research (BMBF)\r\nthrough the Tübingen AI Center (FKZ:
01IS18039B).\r\n"
article_number: '54'
article_processing_charge: No
author:
- first_name: Danru
full_name: Xu, Danru
last_name: Xu
- first_name: Dingling
full_name: Yao, Dingling
id: d3e02e50-48a8-11ee-8f62-c108061797fa
last_name: Yao
- first_name: Sebastien
full_name: Lachapelle, Sebastien
last_name: Lachapelle
- first_name: Perouz
full_name: Taslakian, Perouz
last_name: Taslakian
- first_name: Julius
full_name: von Kügelgen, Julius
last_name: von Kügelgen
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Sara
full_name: Magliacane, Sara
last_name: Magliacane
citation:
ama: 'Xu D, Yao D, Lachapelle S, et al. A sparsity principle for partially observable
causal representation learning. In: Causal Representation Learning Workshop
at NeurIPS 2023. OpenReview; 2023.'
apa: 'Xu, D., Yao, D., Lachapelle, S., Taslakian, P., von Kügelgen, J., Locatello,
F., & Magliacane, S. (2023). A sparsity principle for partially observable
causal representation learning. In Causal Representation Learning Workshop
at NeurIPS 2023. New Orleans, LA, United States: OpenReview.'
chicago: Xu, Danru, Dingling Yao, Sebastien Lachapelle, Perouz Taslakian, Julius
von Kügelgen, Francesco Locatello, and Sara Magliacane. “A Sparsity Principle
for Partially Observable Causal Representation Learning.” In Causal Representation
Learning Workshop at NeurIPS 2023. OpenReview, 2023.
ieee: D. Xu et al., “A sparsity principle for partially observable causal
representation learning,” in Causal Representation Learning Workshop at NeurIPS
2023, New Orleans, LA, United States, 2023.
ista: 'Xu D, Yao D, Lachapelle S, Taslakian P, von Kügelgen J, Locatello F, Magliacane
S. 2023. A sparsity principle for partially observable causal representation learning.
Causal Representation Learning Workshop at NeurIPS 2023. CRL: Causal Representation
Learning Workshop at NeurIPS, 54.'
mla: Xu, Danru, et al. “A Sparsity Principle for Partially Observable Causal Representation
Learning.” Causal Representation Learning Workshop at NeurIPS 2023, 54,
OpenReview, 2023.
short: D. Xu, D. Yao, S. Lachapelle, P. Taslakian, J. von Kügelgen, F. Locatello,
S. Magliacane, in:, Causal Representation Learning Workshop at NeurIPS 2023, OpenReview,
2023.
conference:
end_date: 2023-12-15
location: New Orleans, LA, United States
name: 'CRL: Causal Representation Learning Workshop at NeurIPS'
start_date: 2023-12-15
date_created: 2024-02-07T15:17:51Z
date_published: 2023-12-05T00:00:00Z
date_updated: 2024-02-13T08:59:27Z
day: '05'
ddc:
- '000'
department:
- _id: FrLo
file:
- access_level: open_access
checksum: 484efc27bda75ed6666044989695d9b6
content_type: application/pdf
creator: dernst
date_created: 2024-02-13T08:50:53Z
date_updated: 2024-02-13T08:50:53Z
file_id: '14982'
file_name: 2023_CRL_Xu.pdf
file_size: 552357
relation: main_file
success: 1
file_date_updated: 2024-02-13T08:50:53Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://openreview.net/forum?id=Whr6uobelR
month: '12'
oa: 1
oa_version: Published Version
publication: Causal Representation Learning Workshop at NeurIPS 2023
publication_status: published
publisher: OpenReview
quality_controlled: '1'
status: public
title: A sparsity principle for partially observable causal representation learning
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14923'
abstract:
- lang: eng
text: We study the performance of a Bayesian statistician who estimates a rank-one
signal corrupted by non-symmetric rotationally invariant noise with a generic
distribution of singular values. As the signal-to-noise ratio and the noise structure
are unknown, a Gaussian setup is incorrectly assumed. We derive the exact analytic
expression for the error of the mismatched Bayes estimator and also provide the
analysis of an approximate message passing (AMP) algorithm. The first result exploits
the asymptotic behavior of spherical integrals for rectangular matrices and of
low-rank matrix perturbations; the second one relies on the design and analysis
of an auxiliary AMP. The numerical experiments show that there is a performance
gap between the AMP and Bayes estimators, which is due to the incorrect estimation
of the signal norm.
article_processing_charge: No
author:
- first_name: Teng
full_name: Fu, Teng
last_name: Fu
- first_name: YuHao
full_name: Liu, YuHao
last_name: Liu
- first_name: Jean
full_name: Barbier, Jean
last_name: Barbier
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: ShanSuo
full_name: Liang, ShanSuo
last_name: Liang
- first_name: TianQi
full_name: Hou, TianQi
last_name: Hou
citation:
ama: 'Fu T, Liu Y, Barbier J, Mondelli M, Liang S, Hou T. Mismatched estimation
of non-symmetric rank-one matrices corrupted by structured noise. In: Proceedings
of 2023 IEEE International Symposium on Information Theory. IEEE. doi:10.1109/isit54713.2023.10206671'
apa: 'Fu, T., Liu, Y., Barbier, J., Mondelli, M., Liang, S., & Hou, T. (n.d.).
Mismatched estimation of non-symmetric rank-one matrices corrupted by structured
noise. In Proceedings of 2023 IEEE International Symposium on Information Theory.
Taipei, Taiwan: IEEE. https://doi.org/10.1109/isit54713.2023.10206671'
chicago: Fu, Teng, YuHao Liu, Jean Barbier, Marco Mondelli, ShanSuo Liang, and TianQi
Hou. “Mismatched Estimation of Non-Symmetric Rank-One Matrices Corrupted by Structured
Noise.” In Proceedings of 2023 IEEE International Symposium on Information
Theory. IEEE, n.d. https://doi.org/10.1109/isit54713.2023.10206671.
ieee: T. Fu, Y. Liu, J. Barbier, M. Mondelli, S. Liang, and T. Hou, “Mismatched
estimation of non-symmetric rank-one matrices corrupted by structured noise,”
in Proceedings of 2023 IEEE International Symposium on Information Theory,
Taipei, Taiwan.
ista: 'Fu T, Liu Y, Barbier J, Mondelli M, Liang S, Hou T. Mismatched estimation
of non-symmetric rank-one matrices corrupted by structured noise. Proceedings
of 2023 IEEE International Symposium on Information Theory. ISIT: IEEE International
Symposium on Information Theory.'
mla: Fu, Teng, et al. “Mismatched Estimation of Non-Symmetric Rank-One Matrices
Corrupted by Structured Noise.” Proceedings of 2023 IEEE International Symposium
on Information Theory, IEEE, doi:10.1109/isit54713.2023.10206671.
short: T. Fu, Y. Liu, J. Barbier, M. Mondelli, S. Liang, T. Hou, in:, Proceedings
of 2023 IEEE International Symposium on Information Theory, IEEE, n.d.
conference:
end_date: 2023-06-30
location: Taipei, Taiwan
name: 'ISIT: IEEE International Symposium on Information Theory'
start_date: 2023-06-25
date_created: 2024-02-02T11:20:39Z
date_published: 2023-06-30T00:00:00Z
date_updated: 2024-02-14T14:34:03Z
day: '30'
department:
- _id: MaMo
doi: 10.1109/isit54713.2023.10206671
external_id:
arxiv:
- '2302.03306'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2302.03306
month: '06'
oa: 1
oa_version: Preprint
publication: Proceedings of 2023 IEEE International Symposium on Information Theory
publication_status: inpress
publisher: IEEE
quality_controlled: '1'
status: public
title: Mismatched estimation of non-symmetric rank-one matrices corrupted by structured
noise
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14466'
abstract:
- lang: eng
text: The first long-lived turbulent structures observable in planar shear flows
take the form of localized stripes, inclined with respect to the mean flow direction.
The dynamics of these stripes is central to transition, and recent studies proposed
an analogy to directed percolation where the stripes’ proliferation is ultimately
responsible for the turbulence becoming sustained. In the present study we focus
on the internal stripe dynamics as well as on the eventual stripe expansion, and
we compare the underlying mechanisms in pressure- and shear-driven planar flows,
respectively, plane-Poiseuille and plane-Couette flow. Despite the similarities
of the overall laminar–turbulence patterns, the stripe proliferation processes
in the two cases are fundamentally different. Starting from the growth and sustenance
of individual stripes, we find that in plane-Couette flow new streaks are created
stochastically throughout the stripe whereas in plane-Poiseuille flow streak creation
is deterministic and occurs locally at the downstream tip. Because of the up/downstream
symmetry, Couette stripes, in contrast to Poiseuille stripes, have two weak and
two strong laminar turbulent interfaces. These differences in symmetry as well
as in internal growth give rise to two fundamentally different stripe splitting
mechanisms. In plane-Poiseuille flow splitting is connected to the elongational
growth of the original stripe, and it results from a break-off/shedding of the
stripe's tail. In plane-Couette flow splitting follows from a broadening of the
original stripe and a division along the stripe into two slimmer stripes.
acknowledgement: E.M. acknowledges funding from the ISTplus fellowship programme.
G.Y. and B.H. acknowledge a grant from the Simons Foundation (662960, BH).
article_number: A21
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Elena
full_name: Marensi, Elena
id: 0BE7553A-1004-11EA-B805-18983DDC885E
last_name: Marensi
orcid: 0000-0001-7173-4923
- first_name: Gökhan
full_name: Yalniz, Gökhan
id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425
last_name: Yalniz
orcid: 0000-0002-8490-9312
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Marensi E, Yalniz G, Hof B. Dynamics and proliferation of turbulent stripes
in plane-Poiseuille and plane-Couette flows. Journal of Fluid Mechanics.
2023;974. doi:10.1017/jfm.2023.780
apa: Marensi, E., Yalniz, G., & Hof, B. (2023). Dynamics and proliferation of
turbulent stripes in plane-Poiseuille and plane-Couette flows. Journal of Fluid
Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2023.780
chicago: Marensi, Elena, Gökhan Yalniz, and Björn Hof. “Dynamics and Proliferation
of Turbulent Stripes in Plane-Poiseuille and Plane-Couette Flows.” Journal
of Fluid Mechanics. Cambridge University Press, 2023. https://doi.org/10.1017/jfm.2023.780.
ieee: E. Marensi, G. Yalniz, and B. Hof, “Dynamics and proliferation of turbulent
stripes in plane-Poiseuille and plane-Couette flows,” Journal of Fluid Mechanics,
vol. 974. Cambridge University Press, 2023.
ista: Marensi E, Yalniz G, Hof B. 2023. Dynamics and proliferation of turbulent
stripes in plane-Poiseuille and plane-Couette flows. Journal of Fluid Mechanics.
974, A21.
mla: Marensi, Elena, et al. “Dynamics and Proliferation of Turbulent Stripes in
Plane-Poiseuille and Plane-Couette Flows.” Journal of Fluid Mechanics,
vol. 974, A21, Cambridge University Press, 2023, doi:10.1017/jfm.2023.780.
short: E. Marensi, G. Yalniz, B. Hof, Journal of Fluid Mechanics 974 (2023).
date_created: 2023-10-30T09:32:28Z
date_published: 2023-11-10T00:00:00Z
date_updated: 2024-02-15T09:06:23Z
day: '10'
ddc:
- '530'
department:
- _id: GradSch
- _id: BjHo
doi: 10.1017/jfm.2023.780
external_id:
arxiv:
- '2212.12406'
isi:
- '001088363700001'
file:
- access_level: open_access
checksum: 17c64c1fb0d5f73252364bf98b0b9e1a
content_type: application/pdf
creator: dernst
date_created: 2024-02-15T09:05:21Z
date_updated: 2024-02-15T09:05:21Z
file_id: '14996'
file_name: 2023_JourFluidMechanics_Marensi.pdf
file_size: 2804641
relation: main_file
success: 1
file_date_updated: 2024-02-15T09:05:21Z
has_accepted_license: '1'
intvolume: ' 974'
isi: 1
keyword:
- turbulence
- transition to turbulence
- patterns
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 238598C6-32DE-11EA-91FC-C7463DDC885E
grant_number: '662960'
name: 'Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental
Studies on Transitional and Turbulent Flows'
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- 1469-7645
issn:
- 0022-1120
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
status: public
title: Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette
flows
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 974
year: '2023'
...
---
_id: '14687'
abstract:
- lang: eng
text: The short history of research on Li-O2 batteries has seen a remarkable number
of mechanistic U-turns over the years. From the initial use of carbonate electrolytes,
that were then found to be entirely unsuitable, to the belief that (su)peroxide
was solely responsible for degradation, before the more reactive singlet oxygen
was found to form, to the hypothesis that capacity depends on a competing surface/solution
mechanism before a practically exclusive solution mechanism was identified. Herein,
we argue for an ever-fresh look at the reported data without bias towards supposedly
established explanations. We explain how the latest findings on rate and capacity
limits, as well as the origin of side reactions, are connected via the disproportionation
(DISP) step in the (dis)charge mechanism. Therefrom, directions emerge for the
design of electrolytes and mediators on how to suppress side reactions and to
enable high rate and high reversible capacity.
article_number: e202316476
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Rajesh B
full_name: Jethwa, Rajesh B
id: 4cc538d5-803f-11ed-ab7e-8139573aad8f
last_name: Jethwa
orcid: 0000-0002-0404-4356
- first_name: Soumyadip
full_name: Mondal, Soumyadip
id: d25d21ef-dc8d-11ea-abe3-ec4576307f48
last_name: Mondal
- first_name: Bhargavi
full_name: Pant, Bhargavi
id: 50c64d4d-eb97-11eb-a6c2-d33e5e14f112
last_name: Pant
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Jethwa RB, Mondal S, Pant B, Freunberger SA. To DISP or not? The far‐reaching
reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International
Edition. 2023. doi:10.1002/anie.202316476
apa: Jethwa, R. B., Mondal, S., Pant, B., & Freunberger, S. A. (2023). To DISP
or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries.
Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202316476
chicago: Jethwa, Rajesh B, Soumyadip Mondal, Bhargavi Pant, and Stefan Alexander
Freunberger. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning
Lithium‐air Batteries.” Angewandte Chemie International Edition. Wiley,
2023. https://doi.org/10.1002/anie.202316476.
ieee: R. B. Jethwa, S. Mondal, B. Pant, and S. A. Freunberger, “To DISP or not?
The far‐reaching reaction mechanisms underpinning Lithium‐air batteries,” Angewandte
Chemie International Edition. Wiley, 2023.
ista: Jethwa RB, Mondal S, Pant B, Freunberger SA. 2023. To DISP or not? The far‐reaching
reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International
Edition., e202316476.
mla: Jethwa, Rajesh B., et al. “To DISP or Not? The Far‐reaching Reaction Mechanisms
Underpinning Lithium‐air Batteries.” Angewandte Chemie International Edition,
e202316476, Wiley, 2023, doi:10.1002/anie.202316476.
short: R.B. Jethwa, S. Mondal, B. Pant, S.A. Freunberger, Angewandte Chemie International
Edition (2023).
date_created: 2023-12-15T16:10:13Z
date_published: 2023-12-14T00:00:00Z
date_updated: 2024-02-15T14:43:05Z
day: '14'
department:
- _id: StFr
- _id: GradSch
doi: 10.1002/anie.202316476
keyword:
- General Chemistry
- Catalysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.1002/anie.202316476'
month: '12'
oa: 1
oa_version: Published Version
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: epub_ahead
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air
batteries
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14985'
abstract:
- lang: eng
text: Lead sulfide (PbS) presents large potential in thermoelectric application
due to its earth-abundant S element. However, its inferior average ZT (ZTave)
value makes PbS less competitive with its analogs PbTe and PbSe. To promote its
thermoelectric performance, this study implements strategies of continuous Se
alloying and Cu interstitial doping to synergistically tune thermal and electrical
transport properties in n-type PbS. First, the lattice parameter of 5.93 Å in
PbS is linearly expanded to 6.03 Å in PbS0.5Se0.5 with increasing Se alloying
content. This expanded lattice in Se-alloyed PbS not only intensifies phonon scattering
but also facilitates the formation of Cu interstitials. Based on the PbS0.6Se0.4
content with the minimal lattice thermal conductivity, Cu interstitials are introduced
to improve the electron density, thus boosting the peak power factor, from 3.88 μW cm−1 K−2
in PbS0.6Se0.4 to 20.58 μW cm−1 K−2 in PbS0.6Se0.4−1%Cu. Meanwhile, the lattice
thermal conductivity in PbS0.6Se0.4−x%Cu (x = 0–2) is further suppressed due to
the strong strain field caused by Cu interstitials. Finally, with the lowered
thermal conductivity and high electrical transport properties, a peak ZT ~1.1
and ZTave ~0.82 can be achieved in PbS0.6Se0.4 − 1%Cu at 300–773K, which outperforms
previously reported n-type PbS.
acknowledgement: 'The authors would like to acknowledge the strong supportof microstructure
observation from Center for HighPressure Science and Technology Advanced Research(HPSTAR).
We acknowledge the financial support fromthe National Natural Science Foundation of China:52172236,
the Fundamental Research Funds for theCentral Universities: xtr042021007, Top Young
TalentsProgramme of Xi''an Jiaotong University and NationalScience Fund for Distinguished
Young Scholars: 51925101.'
article_processing_charge: Yes
article_type: original
author:
- first_name: Zhengtao
full_name: Liu, Zhengtao
last_name: Liu
- first_name: Tao
full_name: Hong, Tao
last_name: Hong
- first_name: Liqing
full_name: Xu, Liqing
last_name: Xu
- first_name: Sining
full_name: Wang, Sining
last_name: Wang
- first_name: Xiang
full_name: Gao, Xiang
last_name: Gao
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Xiangdong
full_name: Ding, Xiangdong
last_name: Ding
- first_name: Yu
full_name: Xiao, Yu
last_name: Xiao
- first_name: Li‐Dong
full_name: Zhao, Li‐Dong
last_name: Zhao
citation:
ama: Liu Z, Hong T, Xu L, et al. Lattice expansion enables interstitial doping to
achieve a high average ZT in n‐type PbS. Interdisciplinary Materials. 2023;2(1):161-170.
doi:10.1002/idm2.12056
apa: Liu, Z., Hong, T., Xu, L., Wang, S., Gao, X., Chang, C., … Zhao, L. (2023).
Lattice expansion enables interstitial doping to achieve a high average ZT in
n‐type PbS. Interdisciplinary Materials. Wiley. https://doi.org/10.1002/idm2.12056
chicago: Liu, Zhengtao, Tao Hong, Liqing Xu, Sining Wang, Xiang Gao, Cheng Chang,
Xiangdong Ding, Yu Xiao, and Li‐Dong Zhao. “Lattice Expansion Enables Interstitial
Doping to Achieve a High Average ZT in N‐type PbS.” Interdisciplinary Materials.
Wiley, 2023. https://doi.org/10.1002/idm2.12056.
ieee: Z. Liu et al., “Lattice expansion enables interstitial doping to achieve
a high average ZT in n‐type PbS,” Interdisciplinary Materials, vol. 2,
no. 1. Wiley, pp. 161–170, 2023.
ista: Liu Z, Hong T, Xu L, Wang S, Gao X, Chang C, Ding X, Xiao Y, Zhao L. 2023.
Lattice expansion enables interstitial doping to achieve a high average ZT in
n‐type PbS. Interdisciplinary Materials. 2(1), 161–170.
mla: Liu, Zhengtao, et al. “Lattice Expansion Enables Interstitial Doping to Achieve
a High Average ZT in N‐type PbS.” Interdisciplinary Materials, vol. 2,
no. 1, Wiley, 2023, pp. 161–70, doi:10.1002/idm2.12056.
short: Z. Liu, T. Hong, L. Xu, S. Wang, X. Gao, C. Chang, X. Ding, Y. Xiao, L. Zhao,
Interdisciplinary Materials 2 (2023) 161–170.
date_created: 2024-02-14T12:12:17Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2024-02-19T10:01:26Z
day: '01'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1002/idm2.12056
file:
- access_level: open_access
checksum: 7b5e8210ef1434feb173022c6dbbee0c
content_type: application/pdf
creator: dernst
date_created: 2024-02-19T09:58:32Z
date_updated: 2024-02-19T09:58:32Z
file_id: '15015'
file_name: 2023_InterdiscMaterials_Liu.pdf
file_size: 4675941
relation: main_file
success: 1
file_date_updated: 2024-02-19T09:58:32Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 161-170
publication: Interdisciplinary Materials
publication_identifier:
eissn:
- 2767-441X
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Lattice expansion enables interstitial doping to achieve a high average ZT
in n‐type PbS
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2023'
...
---
_id: '14989'
abstract:
- lang: eng
text: "Encryption alone is not enough for secure end-to end encrypted messaging:
a server must also honestly serve public keys to users. Key transparency has been
presented as an efficient\r\nsolution for detecting (and hence deterring) a server
that attempts to dishonestly serve keys. Key transparency involves two major components:
(1) a username to public key mapping, stored and cryptographically committed to
by the server, and, (2) an outof-band consistency protocol for serving short commitments
to users. In the setting of real-world deployments and supporting production scale,
new challenges must be considered for both of these components. We enumerate these
challenges and provide solutions to address them. In particular, we design and
implement a memory-optimized and privacy-preserving verifiable data structure
for committing to the username to public key store.\r\nTo make this implementation
viable for production, we also integrate support for persistent and distributed
storage. We also propose a future-facing solution, termed “compaction”, as\r\na
mechanism for mitigating practical issues that arise from dealing with infinitely
growing server data structures. Finally, we implement a consensusless solution
that achieves the minimum requirements for a service that consistently distributes
commitments for a transparency application, providing a much more efficient protocol
for distributing small and consistent\r\ncommitments to users. This culminates
in our production-grade implementation of a key transparency system (Parakeet)
which we have open-sourced, along with a demonstration of feasibility through
our benchmarks."
acknowledgement: This work is supported by the Novi team at Meta and funded in part
by IC3 industry partners and NSF grant 1943499.
article_processing_charge: No
author:
- first_name: Harjasleen
full_name: Malvai, Harjasleen
last_name: Malvai
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Alberto
full_name: Sonnino, Alberto
last_name: Sonnino
- first_name: Esha
full_name: Ghosh, Esha
last_name: Ghosh
- first_name: Ercan
full_name: Oztürk, Ercan
last_name: Oztürk
- first_name: Kevin
full_name: Lewi, Kevin
last_name: Lewi
- first_name: Sean
full_name: Lawlor, Sean
last_name: Lawlor
citation:
ama: 'Malvai H, Kokoris Kogias E, Sonnino A, et al. Parakeet: Practical key transparency
for end-to-end eEncrypted messaging. In: Proceedings of the 2023 Network and
Distributed System Security Symposium. Internet Society; 2023. doi:10.14722/ndss.2023.24545'
apa: 'Malvai, H., Kokoris Kogias, E., Sonnino, A., Ghosh, E., Oztürk, E., Lewi,
K., & Lawlor, S. (2023). Parakeet: Practical key transparency for end-to-end
eEncrypted messaging. In Proceedings of the 2023 Network and Distributed System
Security Symposium. San Diego, CA, United States: Internet Society. https://doi.org/10.14722/ndss.2023.24545'
chicago: 'Malvai, Harjasleen, Eleftherios Kokoris Kogias, Alberto Sonnino, Esha
Ghosh, Ercan Oztürk, Kevin Lewi, and Sean Lawlor. “Parakeet: Practical Key Transparency
for End-to-End EEncrypted Messaging.” In Proceedings of the 2023 Network and
Distributed System Security Symposium. Internet Society, 2023. https://doi.org/10.14722/ndss.2023.24545.'
ieee: 'H. Malvai et al., “Parakeet: Practical key transparency for end-to-end
eEncrypted messaging,” in Proceedings of the 2023 Network and Distributed System
Security Symposium, San Diego, CA, United States, 2023.'
ista: 'Malvai H, Kokoris Kogias E, Sonnino A, Ghosh E, Oztürk E, Lewi K, Lawlor
S. 2023. Parakeet: Practical key transparency for end-to-end eEncrypted messaging.
Proceedings of the 2023 Network and Distributed System Security Symposium. NDSS:
Network and Distributed Systems Security.'
mla: 'Malvai, Harjasleen, et al. “Parakeet: Practical Key Transparency for End-to-End
EEncrypted Messaging.” Proceedings of the 2023 Network and Distributed System
Security Symposium, Internet Society, 2023, doi:10.14722/ndss.2023.24545.'
short: H. Malvai, E. Kokoris Kogias, A. Sonnino, E. Ghosh, E. Oztürk, K. Lewi, S.
Lawlor, in:, Proceedings of the 2023 Network and Distributed System Security Symposium,
Internet Society, 2023.
conference:
end_date: 2023-03-03
location: San Diego, CA, United States
name: 'NDSS: Network and Distributed Systems Security'
start_date: 2023-02-27
date_created: 2024-02-14T14:20:40Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2024-02-19T12:11:15Z
day: '01'
department:
- _id: ElKo
doi: 10.14722/ndss.2023.24545
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2023/081
month: '03'
oa: 1
oa_version: Published Version
publication: Proceedings of the 2023 Network and Distributed System Security Symposium
publication_identifier:
isbn:
- '1891562835'
publication_status: published
publisher: Internet Society
quality_controlled: '1'
status: public
title: 'Parakeet: Practical key transparency for end-to-end eEncrypted messaging'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14411'
abstract:
- lang: eng
text: "Partially specified Boolean networks (PSBNs) represent a promising framework
for the qualitative modelling of biological systems in which the logic of interactions
is not completely known. Phenotype control aims to stabilise the network in states
exhibiting specific traits.\r\nIn this paper, we define the phenotype control
problem in the context of asynchronous PSBNs and propose a novel semi-symbolic
algorithm for solving this problem with permanent variable perturbations."
acknowledgement: This work was supported by the Czech Foundation grant No. GA22-10845S,
Grant Agency of Masaryk University grant No. MUNI/G/1771/2020, and the European
Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 101034413.
alternative_title:
- LNBI
article_processing_charge: No
author:
- first_name: Nikola
full_name: Beneš, Nikola
last_name: Beneš
- first_name: Luboš
full_name: Brim, Luboš
last_name: Brim
- first_name: Samuel
full_name: Pastva, Samuel
id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b
last_name: Pastva
orcid: 0000-0003-1993-0331
- first_name: David
full_name: Šafránek, David
last_name: Šafránek
- first_name: Eva
full_name: Šmijáková, Eva
last_name: Šmijáková
citation:
ama: 'Beneš N, Brim L, Pastva S, Šafránek D, Šmijáková E. Phenotype control of partially
specified boolean networks. In: 21st International Conference on Computational
Methods in Systems Biology. Vol 14137. Springer Nature; 2023:18-35. doi:10.1007/978-3-031-42697-1_2'
apa: 'Beneš, N., Brim, L., Pastva, S., Šafránek, D., & Šmijáková, E. (2023).
Phenotype control of partially specified boolean networks. In 21st International
Conference on Computational Methods in Systems Biology (Vol. 14137, pp. 18–35).
Luxembourg City, Luxembourg: Springer Nature. https://doi.org/10.1007/978-3-031-42697-1_2'
chicago: Beneš, Nikola, Luboš Brim, Samuel Pastva, David Šafránek, and Eva Šmijáková.
“Phenotype Control of Partially Specified Boolean Networks.” In 21st International
Conference on Computational Methods in Systems Biology, 14137:18–35. Springer
Nature, 2023. https://doi.org/10.1007/978-3-031-42697-1_2.
ieee: N. Beneš, L. Brim, S. Pastva, D. Šafránek, and E. Šmijáková, “Phenotype control
of partially specified boolean networks,” in 21st International Conference
on Computational Methods in Systems Biology, Luxembourg City, Luxembourg,
2023, vol. 14137, pp. 18–35.
ista: 'Beneš N, Brim L, Pastva S, Šafránek D, Šmijáková E. 2023. Phenotype control
of partially specified boolean networks. 21st International Conference on Computational
Methods in Systems Biology. CMSB: Computational Methods in Systems Biology, LNBI,
vol. 14137, 18–35.'
mla: Beneš, Nikola, et al. “Phenotype Control of Partially Specified Boolean Networks.”
21st International Conference on Computational Methods in Systems Biology,
vol. 14137, Springer Nature, 2023, pp. 18–35, doi:10.1007/978-3-031-42697-1_2.
short: N. Beneš, L. Brim, S. Pastva, D. Šafránek, E. Šmijáková, in:, 21st International
Conference on Computational Methods in Systems Biology, Springer Nature, 2023,
pp. 18–35.
conference:
end_date: 2023-09-15
location: Luxembourg City, Luxembourg
name: 'CMSB: Computational Methods in Systems Biology'
start_date: 2023-09-13
date_created: 2023-10-08T22:01:18Z
date_published: 2023-09-09T00:00:00Z
date_updated: 2024-02-20T09:02:04Z
day: '09'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-031-42697-1_2
ec_funded: 1
file:
- access_level: open_access
checksum: 6f71bdaedb770b52380222fd9f4d7937
content_type: application/pdf
creator: spastva
date_created: 2024-02-16T08:26:32Z
date_updated: 2024-02-16T08:26:32Z
file_id: '14997'
file_name: cmsb2023.pdf
file_size: 691582
relation: main_file
success: 1
file_date_updated: 2024-02-16T08:26:32Z
has_accepted_license: '1'
intvolume: ' 14137'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 18-35
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: 21st International Conference on Computational Methods in Systems Biology
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031426964'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phenotype control of partially specified boolean networks
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14137
year: '2023'
...
---
_id: '14992'
abstract:
- lang: eng
text: In this chapter we first review the Levy–Lieb functional, which gives the
lowest kinetic and interaction energy that can be reached with all possible quantum
states having a given density. We discuss two possible convex generalizations
of this functional, corresponding to using mixed canonical and grand-canonical
states, respectively. We present some recent works about the local density approximation,
in which the functionals get replaced by purely local functionals constructed
using the uniform electron gas energy per unit volume. We then review the known
upper and lower bounds on the Levy–Lieb functionals. We start with the kinetic
energy alone, then turn to the classical interaction alone, before we are able
to put everything together. A later section is devoted to the Hohenberg–Kohn theorem
and the role of many-body unique continuation in its proof.
alternative_title:
- Mathematics and Molecular Modeling
article_processing_charge: No
author:
- first_name: Mathieu
full_name: Lewin, Mathieu
last_name: Lewin
- first_name: Elliott H.
full_name: Lieb, Elliott H.
last_name: Lieb
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Lewin M, Lieb EH, Seiringer R. Universal Functionals in Density Functional
Theory. In: Cances E, Friesecke G, eds. Density Functional Theory. 1st
ed. MAMOMO. Springer; 2023:115-182. doi:10.1007/978-3-031-22340-2_3'
apa: Lewin, M., Lieb, E. H., & Seiringer, R. (2023). Universal Functionals in
Density Functional Theory. In E. Cances & G. Friesecke (Eds.), Density
Functional Theory (1st ed., pp. 115–182). Springer. https://doi.org/10.1007/978-3-031-22340-2_3
chicago: Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “Universal Functionals
in Density Functional Theory.” In Density Functional Theory, edited by
Eric Cances and Gero Friesecke, 1st ed., 115–82. MAMOMO. Springer, 2023. https://doi.org/10.1007/978-3-031-22340-2_3.
ieee: M. Lewin, E. H. Lieb, and R. Seiringer, “Universal Functionals in Density
Functional Theory,” in Density Functional Theory, 1st ed., E. Cances and
G. Friesecke, Eds. Springer, 2023, pp. 115–182.
ista: 'Lewin M, Lieb EH, Seiringer R. 2023.Universal Functionals in Density Functional
Theory. In: Density Functional Theory. Mathematics and Molecular Modeling, , 115–182.'
mla: Lewin, Mathieu, et al. “Universal Functionals in Density Functional Theory.”
Density Functional Theory, edited by Eric Cances and Gero Friesecke, 1st
ed., Springer, 2023, pp. 115–82, doi:10.1007/978-3-031-22340-2_3.
short: M. Lewin, E.H. Lieb, R. Seiringer, in:, E. Cances, G. Friesecke (Eds.), Density
Functional Theory, 1st ed., Springer, 2023, pp. 115–182.
date_created: 2024-02-14T14:44:33Z
date_published: 2023-07-19T00:00:00Z
date_updated: 2024-02-20T08:33:06Z
day: '19'
department:
- _id: RoSe
doi: 10.1007/978-3-031-22340-2_3
edition: '1'
editor:
- first_name: Eric
full_name: Cances, Eric
last_name: Cances
- first_name: Gero
full_name: Friesecke, Gero
last_name: Friesecke
external_id:
arxiv:
- '1912.10424'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1912.10424
month: '07'
oa: 1
oa_version: Preprint
page: 115-182
publication: Density Functional Theory
publication_identifier:
eisbn:
- '9783031223402'
isbn:
- '9783031223396'
issn:
- 3005-0286
publication_status: published
publisher: Springer
quality_controlled: '1'
series_title: MAMOMO
status: public
title: Universal Functionals in Density Functional Theory
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12675'
abstract:
- lang: eng
text: Aromatic side chains are important reporters of the plasticity of proteins,
and often form important contacts in protein--protein interactions. By studying
a pair of structurally homologous cross-β amyloid fibrils, HET-s and HELLF, with
a specific isotope-labeling approach and magic-angle-spinning (MAS) NMR, we have
characterized the dynamic behavior of Phe and Tyr aromatic rings to show that
the hydrophobic amyloid core is rigid, without any sign of "breathing motions"
over hundreds of milliseconds at least. Aromatic residues exposed at the fibril
surface have a rigid ring axis but undergo ring flips, on a variety of time scales
from ns to µs. Our approach provides direct insight into hydrophobic-core motions,
enabling a better evaluation of the conformational heterogeneity generated from
a NMR structural ensemble of such amyloid cross-β architecture.
acknowledgement: We thank AlbertA. Smith (Leipzig)for insightful discussions. This
work was supported by funding from the European Research Council (StG-2012-311318
to P.S.) and used the platforms of the Grenoble Instruct-ERIC center (ISBG;UMS 3518
CNRS-CEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology(PSB) and
facilities and expertiseof the Biophysical and Structural Chemistry platform (BPCS)
at IECB,CNRSUAR3033,INSERMUS001 and Bordeaux University.
article_number: e202219314
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
- first_name: Mélanie
full_name: Berbon, Mélanie
last_name: Berbon
- first_name: Alicia
full_name: Vallet, Alicia
last_name: Vallet
- first_name: Axelle
full_name: Grelard, Axelle
last_name: Grelard
- first_name: Estelle
full_name: Morvan, Estelle
last_name: Morvan
- first_name: Benjamin
full_name: Bardiaux, Benjamin
last_name: Bardiaux
- first_name: Roman
full_name: Lichtenecker, Roman
last_name: Lichtenecker
- first_name: Matthias
full_name: Ernst, Matthias
last_name: Ernst
- first_name: Antoine
full_name: Loquet, Antoine
last_name: Loquet
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Becker LM, Berbon M, Vallet A, et al. The rigid core and flexible surface of
amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte
Chemie International Edition. 2023;62(19). doi:10.1002/anie.202219314
apa: Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B.,
… Schanda, P. (2023). The rigid core and flexible surface of amyloid fibrils probed
by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International
Edition. Wiley. https://doi.org/10.1002/anie.202219314
chicago: Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle
Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet,
and Paul Schanda. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed
by Magic‐Angle Spinning NMR of Aromatic Residues.” Angewandte Chemie International
Edition. Wiley, 2023. https://doi.org/10.1002/anie.202219314.
ieee: L. M. Becker et al., “The rigid core and flexible surface of amyloid
fibrils probed by Magic‐Angle Spinning NMR of aromatic residues,” Angewandte
Chemie International Edition, vol. 62, no. 19. Wiley, 2023.
ista: Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker
R, Ernst M, Loquet A, Schanda P. 2023. The rigid core and flexible surface of
amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte
Chemie International Edition. 62(19), e202219314.
mla: Becker, Lea Marie, et al. “The Rigid Core and Flexible Surface of Amyloid Fibrils
Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” Angewandte Chemie
International Edition, vol. 62, no. 19, e202219314, Wiley, 2023, doi:10.1002/anie.202219314.
short: L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R.
Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie International
Edition 62 (2023).
date_created: 2023-02-24T10:45:01Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2024-02-21T12:14:06Z
day: '01'
ddc:
- '540'
department:
- _id: GradSch
- _id: PaSc
doi: 10.1002/anie.202219314
external_id:
isi:
- '000956919900001'
pmid:
- '36738230'
file:
- access_level: open_access
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- Catalysis
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month: '05'
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record:
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relation: research_data
status: public
status: public
title: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle
Spinning NMR of aromatic residues
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)
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year: '2023'
...
---
_id: '12497'
abstract:
- lang: eng
text: Aromatic side chains are important reporters of the plasticity of proteins,
and often form important contacts in protein–protein interactions. We studied
aromatic residues in the two structurally homologous cross-β amyloid fibrils HET-s,
and HELLF by employing a specific isotope-labeling approach and magic-angle-spinning
NMR. The dynamic behavior of the aromatic residues Phe and Tyr indicates that
the hydrophobic amyloid core is rigid, without any sign of "breathing motions"
over hundreds of milliseconds at least. Aromatic residues exposed at the fibril
surface have a rigid ring axis but undergo ring flips on a variety of time scales
from nanoseconds to microseconds. Our approach provides direct insight into hydrophobic-core
motions, enabling a better evaluation of the conformational heterogeneity generated
from an NMR structural ensemble of such amyloid cross-β architecture.
article_processing_charge: No
author:
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Becker LM, Schanda P. Research data to: The rigid core and flexible surface
of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic
residues. 2023. doi:10.15479/AT:ISTA:12497'
apa: 'Becker, L. M., & Schanda, P. (2023). Research data to: The rigid core
and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy
of aromatic residues. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12497'
chicago: 'Becker, Lea Marie, and Paul Schanda. “Research Data to: The Rigid Core
and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy
of Aromatic Residues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12497.'
ieee: 'L. M. Becker and P. Schanda, “Research data to: The rigid core and flexible
surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of
aromatic residues.” Institute of Science and Technology Austria, 2023.'
ista: 'Becker LM, Schanda P. 2023. Research data to: The rigid core and flexible
surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of
aromatic residues, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12497.'
mla: 'Becker, Lea Marie, and Paul Schanda. Research Data to: The Rigid Core and
Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy
of Aromatic Residues. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12497.'
short: L.M. Becker, P. Schanda, (2023).
contributor:
- contributor_type: researcher
first_name: Mélanie
last_name: Berbon
- contributor_type: researcher
first_name: Alicia
last_name: Vallet
- contributor_type: researcher
first_name: Axelle
last_name: Grelard
- contributor_type: researcher
first_name: Estelle
last_name: Morvan
- contributor_type: researcher
first_name: Benjamin
last_name: Bardiaux
- contributor_type: researcher
first_name: Roman
last_name: Lichtenecker
- contributor_type: researcher
first_name: Matthias
last_name: Ernst
- contributor_type: researcher
first_name: Antoine
last_name: Loquet
- contributor_type: contact_person
first_name: Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- contributor_type: researcher
first_name: Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
date_created: 2023-02-03T08:08:02Z
date_published: 2023-03-23T00:00:00Z
date_updated: 2024-02-21T12:14:06Z
day: '23'
ddc:
- '572'
department:
- _id: GradSch
- _id: PaSc
doi: 10.15479/AT:ISTA:12497
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keyword:
- aromatic side chains
- isotopic labeling
- protein dynamics
- ring flips
- spin relaxation
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oa_version: Published Version
publisher: Institute of Science and Technology Austria
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status: public
title: 'Research data to: The rigid core and flexible surface of amyloid fibrils probed
by magic-angle-spinning NMR spectroscopy of aromatic residues'
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: research_data
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...
---
_id: '13126'
abstract:
- lang: eng
text: Mapping the complex and dense arrangement of cells and their connectivity
in brain tissue demands nanoscale spatial resolution imaging. Super-resolution
optical microscopy excels at visualizing specific molecules and individual cells
but fails to provide tissue context. Here, we developed Comprehensive Analysis
of Tissues across Scales (CATS), a technology to densely map brain tissue architecture
from millimeter regional to nanometer synaptic scales in diverse chemically fixed
brain preparations, including rodent and human. CATS uses fixation-compatible
extracellular labeling and optical imaging, including stimulated emission depletion
or expansion microscopy, to comprehensively delineate cellular structures. It
enables three-dimensional reconstruction of single synapses and mapping of synaptic
connectivity by identification and analysis of putative synaptic cleft regions.
Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed
and quantified the synaptic input and output structure of identified neurons.
We furthermore demonstrate applicability to clinically derived human tissue samples,
including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing
the cellular architecture of brain tissue in health and disease.
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
- _id: PreCl
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: "We thank Jakob Vorlaufer, Nathalie Agudelo-Dueñas, Wiebke Jahr,
Andreas Wartak for microscope maintenance and troubleshooting, Caroline Kreuzinger,
Anna Freeman, and Irene Erber for technical assistance and Matthias Tomschik for
support with obtaining human samples. We gratefully acknowledge Eder Miguel for
setting up webKnossos and Marek Šuplata for computational support and hardware control.
We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and
Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading
of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University
of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing,
imaging and optics, preclinical, and lab support facilities, and by the Library
and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources:
\r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF)
grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein
award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and
DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022
(JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European
Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon
2020 research and innovation programme, European Research Council (ERC) grant 692692
– GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under
the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual
Fellowship 101026635 under the EU Horizon 2020 program (JFW)"
article_processing_charge: No
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Danzl JG. Research data for the publication “Imaging brain tissue architecture
across millimeter to nanometer scales.” 2023. doi:10.15479/AT:ISTA:13126
apa: Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue
architecture across millimeter to nanometer scales.” Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:13126
chicago: Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue
Architecture across Millimeter to Nanometer Scales.’” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13126.
ieee: J. G. Danzl, “Research data for the publication ‘Imaging brain tissue architecture
across millimeter to nanometer scales.’” Institute of Science and Technology Austria,
2023.
ista: Danzl JG. 2023. Research data for the publication ‘Imaging brain tissue architecture
across millimeter to nanometer scales’, Institute of Science and Technology Austria,
10.15479/AT:ISTA:13126.
mla: Danzl, Johann G. Research Data for the Publication “Imaging Brain Tissue
Architecture across Millimeter to Nanometer Scales.” Institute of Science
and Technology Austria, 2023, doi:10.15479/AT:ISTA:13126.
short: J.G. Danzl, (2023).
contributor:
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last_name: Michalska
- first_name: Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
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id: ee3cb6ca-ec98-11ea-ae11-ff703e2254ed
last_name: Stefanickova
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id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Alban
id: 9ac8f577-2357-11eb-997a-e566c5550886
last_name: Cenameri
- first_name: Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
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id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
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last_name: Roessler
- first_name: Thomas
last_name: Czech
- first_name: Romana
last_name: Höftberger
- first_name: Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
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id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
date_created: 2023-06-07T07:15:12Z
date_published: 2023-08-04T00:00:00Z
date_updated: 2024-02-21T12:18:19Z
day: '04'
ddc:
- '610'
department:
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- _id: SaSi
- _id: GaNo
- _id: PeJo
- _id: Bio
- _id: RySh
doi: 10.15479/AT:ISTA:13126
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related_material:
link:
- description: 'Original data for Fig. 5d, Fig. 5d (N2V) and Fig. 5f-i, provided
via an external link due to the large size (>10GB) of the datasets. '
relation: research_data
url: https://pub.ista.ac.at/group_danzl/data/CATS/
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status: public
title: Research data for the publication "Imaging brain tissue architecture across
millimeter to nanometer scales"
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13116'
abstract:
- lang: eng
text: 'The emergence of large-scale order in self-organized systems relies on local
interactions between individual components. During bacterial cell division, FtsZ
-- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into
treadmilling filaments that further organize into a cytoskeletal ring. In vitro,
FtsZ filaments can form dynamic chiral assemblies. However, how the active and
passive properties of individual filaments relate to these large-scale self-organized
structures remains poorly understood. Here, we connect single filament properties
with the mesoscopic scale by combining minimal active matter simulations and biochemical
reconstitution experiments. We show that density and flexibility of active chiral
filaments define their global order. At intermediate densities, curved, flexible
filaments organize into chiral rings and polar bands. An effectively nematic organization
dominates for high densities and for straight, mutant filaments with increased
rigidity. Our predicted phase diagram captures these features quantitatively,
demonstrating how the flexibility, density and chirality of active filaments affect
their collective behaviour. Our findings shed light on the fundamental properties
of active chiral matter and explain how treadmilling FtsZ filaments organize during
bacterial cell division. '
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: 'This work was supported by the European Research Council through
grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607
to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM
collaborative research program. Z.D. has received funding from Doctoral Programme
of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan
Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria),
Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments
on the manuscript. We are also thankful for the support by the Scientific Service
Units (SSU) of IST Austria through resources provided by the Imaging and Optics
Facility (IOF) and the Lab Support Facility (LSF). '
article_processing_charge: No
author:
- first_name: Zuzana
full_name: Dunajova, Zuzana
id: 4B39F286-F248-11E8-B48F-1D18A9856A87
last_name: Dunajova
- first_name: Batirtze
full_name: Prats Mateu, Batirtze
id: 299FE892-F248-11E8-B48F-1D18A9856A87
last_name: Prats Mateu
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
- first_name: Keesiang
full_name: Lim, Keesiang
last_name: Lim
- first_name: Dörte
full_name: Brandis, Dörte
last_name: Brandis
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Richard W.
full_name: Wong, Richard W.
last_name: Wong
- first_name: Jens
full_name: Elgeti, Jens
last_name: Elgeti
- 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: Martin
full_name: Loose, Martin
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last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible
active filaments. 2023. doi:10.15479/AT:ISTA:13116
apa: Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P.,
… Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13116
chicago: Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte
Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of
Flexible Active Filaments.” Institute of Science and Technology Austria, 2023.
https://doi.org/10.15479/AT:ISTA:13116.
ieee: Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments.”
Institute of Science and Technology Austria, 2023.
ista: Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG,
Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible
active filaments, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13116.
mla: Dunajova, Zuzana, et al. Chiral and Nematic Phases of Flexible Active Filaments.
Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13116.
short: Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G.
Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, (2023).
date_created: 2023-06-02T12:30:40Z
date_published: 2023-07-26T00:00:00Z
date_updated: 2024-02-21T12:19:09Z
day: '26'
ddc:
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department:
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- _id: EdHa
- _id: JoDa
doi: 10.15479/AT:ISTA:13116
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project:
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call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
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grant_number: P34607
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grant_number: '26360'
name: Motile active matter models of migrating cells and chiral filaments
publisher: Institute of Science and Technology Austria
related_material:
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relation: used_in_publication
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status: public
title: Chiral and nematic phases of flexible active filaments
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14613'
abstract:
- lang: eng
text: 'Many insects carry an ancient X chromosome - the Drosophila Muller element
F - that likely predates their origin. Interestingly, the X has undergone turnover
in multiple fly species (Diptera) after being conserved for more than 450 MY.
The long evolutionary distance between Diptera and other sequenced insect clades
makes it difficult to infer what could have contributed to this sudden increase
in rate of turnover. Here, we produce the first genome and transcriptome of a
long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly
Panorpa cognata X-chromosome gene content, expression, and structure, to that
of several dipteran species as well as more distantly-related insect orders (Orthoptera
and Blattodea). We find high conservation of gene content between the mecopteran
X and the dipteran Muller F element, as well as several shared biological features,
such as the presence of dosage compensation and a low amount of genetic diversity,
consistent with a low recombination rate. However, the two homologous X chromosomes
differ strikingly in their size and number of genes they carry. Our results therefore
support a common ancestry of the mecopteran and ancestral dipteran X chromosomes,
and suggest that Muller element F shrank in size and gene content after the split
of Diptera and Mecoptera, which may have contributed to its turnover in dipteran
insects.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank the Vicoso lab for their assistance with specimen collection,
and Tim Connallon for valuable comments and suggestions on earlier versions of the
manuscript. Computational resources and support were provided by the Scientific
Computing unit at the ISTA. This research was supported by grants from the Austrian
Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10)."
article_number: msad245
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Clementine
full_name: Lasne, Clementine
id: 02225f57-50d2-11eb-9ed8-8c92b9a34237
last_name: Lasne
orcid: 0000-0002-1197-8616
- 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: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Lorena Alexandra
full_name: Layana Franco, Lorena Alexandra
id: 02814589-eb8f-11eb-b029-a70074f3f18f
last_name: Layana Franco
orcid: 0000-0002-1253-6297
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly
(Panorpa cognata) genome highlights conserved and derived features of the peculiar
dipteran X chromosome. Molecular Biology and Evolution. 2023;40(12). doi:10.1093/molbev/msad245
apa: Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., &
Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved
and derived features of the peculiar dipteran X chromosome. Molecular Biology
and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msad245
chicago: Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra
Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata)
Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.”
Molecular Biology and Evolution. Oxford University Press, 2023. https://doi.org/10.1093/molbev/msad245.
ieee: C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B.
Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived
features of the peculiar dipteran X chromosome,” Molecular Biology and Evolution,
vol. 40, no. 12. Oxford University Press, 2023.
ista: Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023.
The scorpionfly (Panorpa cognata) genome highlights conserved and derived features
of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12),
msad245.
mla: Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights
Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Molecular
Biology and Evolution, vol. 40, no. 12, msad245, Oxford University Press,
2023, doi:10.1093/molbev/msad245.
short: C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso,
Molecular Biology and Evolution 40 (2023).
date_created: 2023-11-27T16:14:37Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-02-21T12:18:35Z
day: '01'
ddc:
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department:
- _id: BeVi
doi: 10.1093/molbev/msad245
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creator: dernst
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success: 1
file_date_updated: 2024-01-02T11:39:38Z
has_accepted_license: '1'
intvolume: ' 40'
issue: '12'
keyword:
- Genetics
- Molecular Biology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
- _id: ebb230e0-77a9-11ec-83b8-87a37e0241d3
grant_number: ESP39 49461
name: Mechanisms and Evolution of Reproductive Plasticity
publication: Molecular Biology and Evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- description: News on ISTA webpage
relation: press_release
url: https://ista.ac.at/en/news/on-the-hunt/
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scopus_import: '1'
status: public
title: The scorpionfly (Panorpa cognata) genome highlights conserved and derived features
of the peculiar dipteran X chromosome
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2023'
...
---
_id: '13314'
abstract:
- lang: eng
text: The emergence of large-scale order in self-organized systems relies on local
interactions between individual components. During bacterial cell division, FtsZ—a
prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling
filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments
can form dynamic chiral assemblies. However, how the active and passive properties
of individual filaments relate to these large-scale self-organized structures
remains poorly understood. Here we connect single-filament properties with the
mesoscopic scale by combining minimal active matter simulations and biochemical
reconstitution experiments. We show that the density and flexibility of active
chiral filaments define their global order. At intermediate densities, curved,
flexible filaments organize into chiral rings and polar bands. An effectively
nematic organization dominates for high densities and for straight, mutant filaments
with increased rigidity. Our predicted phase diagram quantitatively captures these
features, demonstrating how the flexibility, density and chirality of the active
filaments affect their collective behaviour. Our findings shed light on the fundamental
properties of active chiral matter and explain how treadmilling FtsZ filaments
organize during bacterial cell division.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: 'This work was supported by the European Research Council through
grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607
to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM
collaborative research program. Z.D. has received funding from Doctoral Programme
of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan
Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria),
Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments
on the manuscript. We are also thankful for the support by the Scientific Service
Units (SSU) of IST Austria through resources provided by the Imaging and Optics
Facility (IOF) and the Lab Support Facility (LSF).'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Zuzana
full_name: Dunajova, Zuzana
id: 4B39F286-F248-11E8-B48F-1D18A9856A87
last_name: Dunajova
- first_name: Batirtze
full_name: Prats Mateu, Batirtze
id: 299FE892-F248-11E8-B48F-1D18A9856A87
last_name: Prats Mateu
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
- first_name: Keesiang
full_name: Lim, Keesiang
last_name: Lim
- first_name: Dörte
full_name: Brandis, Dörte
id: 21d64d35-f128-11eb-9611-b8bcca7a12fd
last_name: Brandis
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Richard W.
full_name: Wong, Richard W.
last_name: Wong
- first_name: Jens
full_name: Elgeti, Jens
last_name: Elgeti
- 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: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible
active filaments. Nature Physics. 2023;19:1916-1926. doi:10.1038/s41567-023-02218-w
apa: Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P.,
… Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Nature
Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02218-w
chicago: Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte
Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of
Flexible Active Filaments.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02218-w.
ieee: Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments,”
Nature Physics, vol. 19. Springer Nature, pp. 1916–1926, 2023.
ista: Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG,
Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible
active filaments. Nature Physics. 19, 1916–1926.
mla: Dunajova, Zuzana, et al. “Chiral and Nematic Phases of Flexible Active Filaments.”
Nature Physics, vol. 19, Springer Nature, 2023, pp. 1916–26, doi:10.1038/s41567-023-02218-w.
short: Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G.
Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, Nature Physics 19 (2023)
1916–1926.
date_created: 2023-07-27T14:44:45Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-02-21T12:19:08Z
day: '01'
ddc:
- '530'
department:
- _id: JoDa
- _id: EdHa
- _id: MaLo
- _id: GradSch
doi: 10.1038/s41567-023-02218-w
ec_funded: 1
external_id:
pmid:
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month: '12'
oa: 1
oa_version: Published Version
page: 1916-1926
pmid: 1
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: "Understanding bacterial cell division by in vitro\r\nreconstitution"
- _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d
grant_number: '26360'
name: Motile active matter models of migrating cells and chiral filaments
publication: Nature Physics
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- 1745-2481
issn:
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title: Chiral and nematic phases of flexible active filaments
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2023'
...
---
_id: '14257'
abstract:
- lang: eng
text: Mapping the complex and dense arrangement of cells and their connectivity
in brain tissue demands nanoscale spatial resolution imaging. Super-resolution
optical microscopy excels at visualizing specific molecules and individual cells
but fails to provide tissue context. Here we developed Comprehensive Analysis
of Tissues across Scales (CATS), a technology to densely map brain tissue architecture
from millimeter regional to nanometer synaptic scales in diverse chemically fixed
brain preparations, including rodent and human. CATS uses fixation-compatible
extracellular labeling and optical imaging, including stimulated emission depletion
or expansion microscopy, to comprehensively delineate cellular structures. It
enables three-dimensional reconstruction of single synapses and mapping of synaptic
connectivity by identification and analysis of putative synaptic cleft regions.
Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed
and quantified the synaptic input and output structure of identified neurons.
We furthermore demonstrate applicability to clinically derived human tissue samples,
including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing
the cellular architecture of brain tissue in health and disease.
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
- _id: PreCl
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: 'We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak
for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I.
Erber for technical assistance; and M. Tomschik for support with obtaining human
samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata
for computational support and hardware control. We are grateful to R. Shigemoto
and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University)
for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly
provided by S. Grant (University of Edinburgh). We acknowledge expert support by
Institute of Science and Technology Austria’s scientific computing, imaging and
optics, preclinical and lab support facilities and by the Miba machine shop and
library. We gratefully acknowledge funding by the following sources: Austrian Science
Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232
(J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award
(P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27
(R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.);
European Union’s Horizon 2020 research and innovation programme, European Research
Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020
research and innovation programme, European Research Council (ERC) grant 692692
– GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under
the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions
Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Julia M
full_name: Michalska, Julia M
id: 443DB6DE-F248-11E8-B48F-1D18A9856A87
last_name: Michalska
orcid: 0000-0003-3862-1235
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
- first_name: Hana
full_name: Korinkova, Hana
id: ee3cb6ca-ec98-11ea-ae11-ff703e2254ed
last_name: Korinkova
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Alban
full_name: Cenameri, Alban
id: 9ac8f577-2357-11eb-997a-e566c5550886
last_name: Cenameri
- 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: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Karl
full_name: Roessler, Karl
last_name: Roessler
- first_name: Thomas
full_name: Czech, Thomas
last_name: Czech
- first_name: Romana
full_name: Höftberger, Romana
last_name: Höftberger
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture
across millimeter to nanometer scales. Nature Biotechnology. 2023. doi:10.1038/s41587-023-01911-8
apa: Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri,
A., … Danzl, J. G. (2023). Imaging brain tissue architecture across millimeter
to nanometer scales. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-023-01911-8
chicago: Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake
Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture
across Millimeter to Nanometer Scales.” Nature Biotechnology. Springer
Nature, 2023. https://doi.org/10.1038/s41587-023-01911-8.
ieee: J. M. Michalska et al., “Imaging brain tissue architecture across millimeter
to nanometer scales,” Nature Biotechnology. Springer Nature, 2023.
ista: Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer
CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino
G, Jonas PM, Danzl JG. 2023. Imaging brain tissue architecture across millimeter
to nanometer scales. Nature Biotechnology.
mla: Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter
to Nanometer Scales.” Nature Biotechnology, Springer Nature, 2023, doi:10.1038/s41587-023-01911-8.
short: J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri,
C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S.
Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology (2023).
date_created: 2023-09-03T22:01:15Z
date_published: 2023-08-31T00:00:00Z
date_updated: 2024-02-21T12:18:18Z
day: '31'
department:
- _id: SaSi
- _id: GaNo
- _id: PeJo
- _id: JoDa
- _id: Bio
- _id: RySh
doi: 10.1038/s41587-023-01911-8
ec_funded: 1
external_id:
isi:
- '001065254200001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41587-023-01911-8
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: 23889792-32DE-11EA-91FC-C7463DDC885E
name: High content imaging to decode human immune cell interactions in health and
allergic disease
- _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: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
call_identifier: H2020
grant_number: '101026635'
name: Synaptic computations of the hippocampal CA3 circuitry
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/danzllab/CATS
record:
- id: '13126'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Imaging brain tissue architecture across millimeter to nanometer scales
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14614'
abstract:
- lang: eng
text: 'Many insects carry an ancient X chromosome—the Drosophila Muller element
F—that likely predates their origin. Interestingly, the X has undergone turnover
in multiple fly species (Diptera) after being conserved for more than 450 My.
The long evolutionary distance between Diptera and other sequenced insect clades
makes it difficult to infer what could have contributed to this sudden increase
in rate of turnover. Here, we produce the first genome and transcriptome of scorpionflies
(genus Panorpa), an insect belonging to a long overlooked sister-order to Diptera:
Mecoptera. Combining our genome assembly with genomic short-read data, we obtain
genome coverage and identify X-linked super-scaffolds. We further perform a gene
homology analysis between the Panorpa X and a closely related Diptera species,
and we assess the conservation of the Panorpa X-linked gene content with that
of more distantly related insect species. We explored the structure of the Panorpa
X by determining its repeat content, GC content, and nucleotide diversity. Finally,
we used RNAseq data to detect the presence of dosage compensation in somatic tissues,
as well as to explore gene expression tissue-specificity, and sex-bias in gene
expression. We find high conservation of gene content between the mecopteran X
and the dipteran Muller F element, as well as several shared biological features,
such as the presence of dosage compensation and a low amount of genetic diversity,
consistent with a low recombination rate. However, the 2 homologous X chromosomes
differ strikingly in their size and number of genes they carry. Our results therefore
support a common ancestry of the mecopteran and ancestral dipteran X chromosomes,
and suggest that Muller element F shrank in size and gene content after the split
of Diptera and Mecoptera, which may have contributed to its turnover in dipteran
insects.'
article_processing_charge: No
author:
- first_name: Clementine
full_name: Lasne, Clementine
id: 02225f57-50d2-11eb-9ed8-8c92b9a34237
last_name: Lasne
orcid: 0000-0002-1197-8616
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
citation:
ama: Lasne C, Elkrewi MN. The scorpionfly (Panorpa cognata) genome highlights conserved
and derived features of the peculiar dipteran X chromosome. 2023. doi:10.15479/AT:ISTA:14614
apa: Lasne, C., & Elkrewi, M. N. (2023). The scorpionfly (Panorpa cognata) genome
highlights conserved and derived features of the peculiar dipteran X chromosome.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14614
chicago: Lasne, Clementine, and Marwan N Elkrewi. “The Scorpionfly (Panorpa Cognata)
Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14614.
ieee: C. Lasne and M. N. Elkrewi, “The scorpionfly (Panorpa cognata) genome highlights
conserved and derived features of the peculiar dipteran X chromosome.” Institute
of Science and Technology Austria, 2023.
ista: Lasne C, Elkrewi MN. 2023. The scorpionfly (Panorpa cognata) genome highlights
conserved and derived features of the peculiar dipteran X chromosome, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:14614.
mla: Lasne, Clementine, and Marwan N. Elkrewi. The Scorpionfly (Panorpa Cognata)
Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.
Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14614.
short: C. Lasne, M.N. Elkrewi, (2023).
contributor:
- contributor_type: researcher
first_name: Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
date_created: 2023-11-27T16:39:19Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-02-21T12:18:35Z
day: '01'
ddc:
- '576'
department:
- _id: BeVi
doi: 10.15479/AT:ISTA:14614
file:
- access_level: open_access
checksum: cd0f13322b5156819ecaebd2bc8e7d12
content_type: application/zip
creator: clasne
date_created: 2023-11-28T13:15:26Z
date_updated: 2023-11-28T13:15:26Z
file_id: '14625'
file_name: panorpaX.zip
file_size: 404968272
relation: main_file
success: 1
- access_level: open_access
checksum: 9ff600416577687a737cb3c96dfcb26c
content_type: text/plain
creator: clasne
date_created: 2023-11-30T14:16:59Z
date_updated: 2023-11-30T14:16:59Z
file_id: '14634'
file_name: panorpa_readme.txt
file_size: 2625
relation: main_file
success: 1
file_date_updated: 2023-11-30T14:16:59Z
has_accepted_license: '1'
keyword:
- Panorpa
- scorpionfly
- genome
- transcriptome
month: '12'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14613'
relation: used_in_publication
status: public
status: public
title: The scorpionfly (Panorpa cognata) genome highlights conserved and derived features
of the peculiar dipteran X chromosome
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13286'
abstract:
- lang: eng
text: Semiconductor-superconductor hybrid systems are the harbour of many intriguing
mesoscopic phenomena. This material combination leads to spatial variations of
the superconducting properties, which gives rise to Andreev bound states (ABSs).
Some of these states might exhibit remarkable properties that render them highly
desirable for topological quantum computing. The most prominent and hunted of
such states are Majorana zero modes (MZMs), quasiparticles equals to their own
quasiparticles that they follow non-abelian statistics. In this thesis, we first
introduce the general framework of such hybrid systems and, then, we unveil a
series of mesoscopic phenomena that we discovered. Firstly, we show tunneling
spectroscopy experiments on full-shell nanowires (NWs) showing that unwanted quantum-dot
states coupled to superconductors (Yu-Shiba-Rusinov states) can mimic MZMs signatures.
Then, we introduce a novel protocol which allowed the integration of tunneling
spectroscopy with Coulomb spectroscopy within the same device. Employing this
approach on both full-shell NWs and partial-shell NWs, we demonstrated that longitudinally
confined states reveal charge transport phenomenology similar to the one expected
for MZMs. These findings shed light on the intricate interplay between superconductivity
and quantum confinement, which brought us to explore another material platform,
i.e. a two-dimensional Germanium hole gas. After developing a robust way to induce
superconductivity in such system, we showed how to engineer the proximity effect
and we revealed a superconducting hard gap. Finally, we created a superconducting
radio frequency driven ideal diode and a generator of non-sinusoidal current-phase
relations. Our results open the path for the exploration of protected superconducting
qubits and more complex hybrid devices in planar Germanium, like Kitaev chains
and hybrid qubit devices.
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Marco
full_name: Valentini, Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
citation:
ama: 'Valentini M. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices :
From full-shell nanowires to two-dimensional hole gas in germanium. 2023. doi:10.15479/at:ista:13286'
apa: 'Valentini, M. (2023). Mesoscopic phenomena in hybrid semiconductor-superconductor
nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13286'
chicago: 'Valentini, Marco. “Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor
Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13286.'
ieee: 'M. Valentini, “Mesoscopic phenomena in hybrid semiconductor-superconductor
nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium,”
Institute of Science and Technology Austria, 2023.'
ista: 'Valentini M. 2023. Mesoscopic phenomena in hybrid semiconductor-superconductor
nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium.
Institute of Science and Technology Austria.'
mla: 'Valentini, Marco. Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor
Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13286.'
short: 'M. Valentini, Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor
Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium,
Institute of Science and Technology Austria, 2023.'
date_created: 2023-07-24T14:10:45Z
date_published: 2023-07-21T00:00:00Z
date_updated: 2024-02-21T12:35:34Z
day: '21'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: GeKa
doi: 10.15479/at:ista:13286
ec_funded: 1
file:
- access_level: closed
checksum: 666ee31c7eade89679806287c062fa14
content_type: application/x-zip-compressed
creator: mvalenti
date_created: 2023-08-11T09:27:39Z
date_updated: 2023-08-11T10:01:34Z
file_id: '14033'
file_name: PhD_thesis_Valentini_final.zip
file_size: 56121429
relation: source_file
- access_level: open_access
checksum: 0992f2ebef152dee8e70055350ebbb55
content_type: application/pdf
creator: mvalenti
date_created: 2023-08-11T14:39:17Z
date_updated: 2023-08-11T14:39:17Z
file_id: '14035'
file_name: PhD_thesis_Valentini_final_validated.pdf
file_size: 38199711
relation: main_file
file_date_updated: 2023-08-11T14:39:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '184'
project:
- _id: 262116AA-B435-11E9-9278-68D0E5697425
name: Hybrid Semiconductor - Superconductor Quantum Devices
- _id: 237E5020-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862046'
name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS
- _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e
grant_number: F8606
name: Conventional and unconventional topological superconductors
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '13312'
relation: part_of_dissertation
status: public
- id: '12118'
relation: part_of_dissertation
status: public
- id: '8910'
relation: part_of_dissertation
status: public
- id: '12522'
relation: research_data
status: public
status: public
supervisor:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
title: 'Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices :
From full-shell nanowires to two-dimensional hole gas in germanium'
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '15027'
abstract:
- lang: eng
text: 'This data repository underpins the paper, published in PNAS (doi pending)
and bioarxiv (doi: https://doi.org/10.1101/2023.07.05.547777).'
article_processing_charge: No
author:
- first_name: Samo
full_name: Curk, Samo
id: 031eff0d-d481-11ee-8508-cd12a7a86e5b
last_name: Curk
orcid: 0000-0001-6160-9766
citation:
ama: Curk S. aggregation_data. 2023.
apa: Curk, S. (2023). aggregation_data. Figshare.
chicago: Curk, Samo. “Aggregation_data.” Figshare, 2023.
ieee: S. Curk, “aggregation_data.” Figshare, 2023.
ista: Curk S. 2023. aggregation_data, Figshare.
mla: Curk, Samo. Aggregation_data. Figshare, 2023.
short: S. Curk, (2023).
date_created: 2024-02-26T08:37:57Z
date_published: 2023-12-13T00:00:00Z
date_updated: 2024-02-26T08:45:55Z
day: '13'
ddc:
- '570'
department:
- _id: AnSa
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://figshare.com/s/85798bba4ebc68d822ed
month: '12'
oa: 1
oa_version: Published Version
publisher: Figshare
related_material:
record:
- id: '15001'
relation: used_in_publication
status: public
status: public
title: aggregation_data
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: '2023'
...
---
_id: '14758'
abstract:
- lang: eng
text: 'We present a flexible and efficient toolchain to symbolically solve (standard)
Rabin games, fair-adversarial Rabin games, and 2 1/2 license type-player Rabin
games. To our best knowledge, our tools are the first ones to be able to solve
these problems. Furthermore, using these flexible game solvers as a back-end,
we implemented a tool for computing correct-by-construction controllers for stochastic
dynamical systems under LTL specifications. Our implementations use the recent
theoretical result that all of these games can be solved using the same symbolic
fixpoint algorithm but utilizing different, domain specific calculations of the
involved predecessor operators. The main feature of our toolchain is the utilization
of two programming abstractions: one to separate the symbolic fixpoint computations
from the predecessor calculations, and another one to allow the integration of
different BDD libraries as back-ends. In particular, we employ a multi-threaded
execution of the fixpoint algorithm by using the multi-threaded BDD library Sylvan,
which leads to enormous computational savings.'
acknowledgement: 'Authors ordered alphabetically. R. Majumdar and A.-K. Schmuck are
partially supported by DFG project 389792660 TRR 248-CPEC. A.-K. Schmuck is additionally
funded through DFG project (SCHM 3541/1-1). K. Mallik is supported by the ERC project
ERC-2020-AdG 101020093. M. Rychlicki is supported by the EPSRC project EP/V00252X/1.
S. Soudjani is supported by the following projects: EPSRC EP/V043676/1, EIC 101070802,
and ERC 101089047.'
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
- first_name: Mateusz
full_name: Rychlicki, Mateusz
last_name: Rychlicki
- first_name: Anne-Kathrin
full_name: Schmuck, Anne-Kathrin
last_name: Schmuck
- first_name: Sadegh
full_name: Soudjani, Sadegh
last_name: Soudjani
citation:
ama: 'Majumdar R, Mallik K, Rychlicki M, Schmuck A-K, Soudjani S. A flexible toolchain
for symbolic rabin games under fair and stochastic uncertainties. In: 35th
International Conference on Computer Aided Verification. Vol 13966. Springer
Nature; 2023:3-15. doi:10.1007/978-3-031-37709-9_1'
apa: 'Majumdar, R., Mallik, K., Rychlicki, M., Schmuck, A.-K., & Soudjani, S.
(2023). A flexible toolchain for symbolic rabin games under fair and stochastic
uncertainties. In 35th International Conference on Computer Aided Verification
(Vol. 13966, pp. 3–15). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_1'
chicago: Majumdar, Rupak, Kaushik Mallik, Mateusz Rychlicki, Anne-Kathrin Schmuck,
and Sadegh Soudjani. “A Flexible Toolchain for Symbolic Rabin Games under Fair
and Stochastic Uncertainties.” In 35th International Conference on Computer
Aided Verification, 13966:3–15. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_1.
ieee: R. Majumdar, K. Mallik, M. Rychlicki, A.-K. Schmuck, and S. Soudjani, “A flexible
toolchain for symbolic rabin games under fair and stochastic uncertainties,” in
35th International Conference on Computer Aided Verification, Paris, France,
2023, vol. 13966, pp. 3–15.
ista: 'Majumdar R, Mallik K, Rychlicki M, Schmuck A-K, Soudjani S. 2023. A flexible
toolchain for symbolic rabin games under fair and stochastic uncertainties. 35th
International Conference on Computer Aided Verification. CAV: Computer Aided Verification,
LNCS, vol. 13966, 3–15.'
mla: Majumdar, Rupak, et al. “A Flexible Toolchain for Symbolic Rabin Games under
Fair and Stochastic Uncertainties.” 35th International Conference on Computer
Aided Verification, vol. 13966, Springer Nature, 2023, pp. 3–15, doi:10.1007/978-3-031-37709-9_1.
short: R. Majumdar, K. Mallik, M. Rychlicki, A.-K. Schmuck, S. Soudjani, in:, 35th
International Conference on Computer Aided Verification, Springer Nature, 2023,
pp. 3–15.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2024-01-08T13:18:00Z
date_published: 2023-07-16T00:00:00Z
date_updated: 2024-02-27T07:39:51Z
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month: '07'
oa: 1
oa_version: Published Version
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call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 35th International Conference on Computer Aided Verification
publication_identifier:
eisbn:
- '9783031377099'
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- 1611-3349
isbn:
- '9783031377082'
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title: A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties
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abstract:
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text: Two assumptions commonly applied in convection schemes—the diagnostic and
quasi-equilibrium assumptions—imply that convective activity (e.g., convective
precipitation) is controlled only by the large-scale (macrostate) environment
at the time. In contrast, numerical experiments indicate a “memory” or dependence
of convection also on its own previous activity whereby subgrid-scale (microstate)
structures boost but are also boosted by convection. In this study we investigated
this memory by comparing single-column model behavior in two idealized tests previously
executed by a cloud-resolving model (CRM). Conventional convection schemes that
employ the diagnostic assumption fail to reproduce the CRM behavior. The memory-capable
org and Laboratoire de Météorologie Dynamique Zoom cold pool schemes partially
capture the behavior, but fail to fully exhibit the strong reinforcing feedbacks
implied by the CRM. Analysis of this failure suggests that it is because the CRM
supports a linear (or superlinear) dependence of the subgrid structure growth
rate on the precipitation rate, while the org scheme assumes a sublinear dependence.
Among varying versions of the org scheme, the growth rate of the org variable
representing subgrid structure is strongly associated with memory strength. These
results demonstrate the importance of parameterizing convective memory, and the
ability of idealized tests to reveal shortcomings of convection schemes and constrain
model structural assumptions.
acknowledgement: YLH is supported by funding from the European Union's Horizon 2020
research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
No. 101034413. CJM gratefully acknowledges funding from the European Research Council
under the European Union's Horizon 2020 research and innovation program (Project
CLUSTER, Grant Agreement No. 805041). YLH and SCS were supported by the Australian
Research Council (FL150100035). The authors thank Brian Mapes, David Fuchs and Siwon
Song for stimulating and helpful discussions. MC warmly thanks the LMD team in Paris
for their assistance with the LMDZ model. We thank the two anonymous reviewers for
their constructive comments that greatly improved this manuscript.
article_number: e2023MS003726
article_processing_charge: Yes
article_type: original
author:
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full_name: Hwong, Yi-Ling
id: 1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22
last_name: Hwong
orcid: 0000-0001-9281-3479
- first_name: M.
full_name: Colin, M.
last_name: Colin
- first_name: Philipp
full_name: Aglas, Philipp
id: 02eace56-97fc-11ee-b81a-f0939ca85a77
last_name: Aglas
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: S. C.
full_name: Sherwood, S. C.
last_name: Sherwood
citation:
ama: Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. Assessing memory in convection
schemes using idealized tests. Journal of Advances in Modeling Earth Systems.
2023;15(12). doi:10.1029/2023MS003726
apa: Hwong, Y.-L., Colin, M., Aglas, P., Muller, C. J., & Sherwood, S. C. (2023).
Assessing memory in convection schemes using idealized tests. Journal of Advances
in Modeling Earth Systems. Wiley. https://doi.org/10.1029/2023MS003726
chicago: Hwong, Yi-Ling, M. Colin, Philipp Aglas, Caroline J Muller, and S. C. Sherwood.
“Assessing Memory in Convection Schemes Using Idealized Tests.” Journal of
Advances in Modeling Earth Systems. Wiley, 2023. https://doi.org/10.1029/2023MS003726.
ieee: Y.-L. Hwong, M. Colin, P. Aglas, C. J. Muller, and S. C. Sherwood, “Assessing
memory in convection schemes using idealized tests,” Journal of Advances in
Modeling Earth Systems, vol. 15, no. 12. Wiley, 2023.
ista: Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. 2023. Assessing memory
in convection schemes using idealized tests. Journal of Advances in Modeling Earth
Systems. 15(12), e2023MS003726.
mla: Hwong, Yi-Ling, et al. “Assessing Memory in Convection Schemes Using Idealized
Tests.” Journal of Advances in Modeling Earth Systems, vol. 15, no. 12,
e2023MS003726, Wiley, 2023, doi:10.1029/2023MS003726.
short: Y.-L. Hwong, M. Colin, P. Aglas, C.J. Muller, S.C. Sherwood, Journal of Advances
in Modeling Earth Systems 15 (2023).
date_created: 2023-12-10T23:00:57Z
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date_updated: 2024-02-27T07:26:30Z
day: '01'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1029/2023MS003726
ec_funded: 1
file:
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checksum: 4d060b293da3d203de8769e398edf711
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creator: dernst
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date_updated: 2023-12-11T08:08:44Z
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oa: 1
oa_version: Published Version
project:
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call_identifier: H2020
grant_number: '805041'
name: organization of CLoUdS, and implications of Tropical cyclones and for the
Energetics of the tropics, in current and waRming climate
publication: Journal of Advances in Modeling Earth Systems
publication_identifier:
eissn:
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publication_status: published
publisher: Wiley
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---
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abstract:
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text: A classical problem for Markov chains is determining their stationary (or
steady-state) distribution. This problem has an equally classical solution based
on eigenvectors and linear equation systems. However, this approach does not scale
to large instances, and iterative solutions are desirable. It turns out that a
naive approach, as used by current model checkers, may yield completely wrong
results. We present a new approach, which utilizes recent advances in partial
exploration and mean payoff computation to obtain a correct, converging approximation.
alternative_title:
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article_processing_charge: No
author:
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full_name: Meggendorfer, Tobias
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last_name: Meggendorfer
orcid: 0000-0002-1712-2165
citation:
ama: 'Meggendorfer T. Correct approximation of stationary distributions. In: TACAS
2023: Tools and Algorithms for the Construction and Analysis of Systems. Vol
13993. Springer Nature; 2023:489-507. doi:10.1007/978-3-031-30823-9_25'
apa: 'Meggendorfer, T. (2023). Correct approximation of stationary distributions.
In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems
(Vol. 13993, pp. 489–507). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30823-9_25'
chicago: 'Meggendorfer, Tobias. “Correct Approximation of Stationary Distributions.”
In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems,
13993:489–507. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30823-9_25.'
ieee: 'T. Meggendorfer, “Correct approximation of stationary distributions,” in
TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems,
Paris, France, 2023, vol. 13993, pp. 489–507.'
ista: 'Meggendorfer T. 2023. Correct approximation of stationary distributions.
TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems.
TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS,
vol. 13993, 489–507.'
mla: 'Meggendorfer, Tobias. “Correct Approximation of Stationary Distributions.”
TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems,
vol. 13993, Springer Nature, 2023, pp. 489–507, doi:10.1007/978-3-031-30823-9_25.'
short: 'T. Meggendorfer, in:, TACAS 2023: Tools and Algorithms for the Construction
and Analysis of Systems, Springer Nature, 2023, pp. 489–507.'
conference:
end_date: 2023-04-27
location: Paris, France
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department:
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doi: 10.1007/978-3-031-30823-9_25
external_id:
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title: Correct approximation of stationary distributions
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type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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...
---
_id: '14991'
abstract:
- lang: eng
text: This repository contains the data, scripts, WRF codes and files required to
reproduce the results of the manuscript "Assessing Memory in Convection Schemes
Using Idealized Tests" submitted to the Journal of Advances in Modeling Earth
Systems (JAMES).
article_processing_charge: No
author:
- first_name: Yi-Ling
full_name: Hwong, Yi-Ling
id: 1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22
last_name: Hwong
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last_name: Colin
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last_name: Aglas
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Steven C.
full_name: Sherwood, Steven C.
last_name: Sherwood
citation:
ama: Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. Data-assessing memory
in convection schemes using idealized tests. 2023. doi:10.5281/ZENODO.7757041
apa: Hwong, Y.-L., Colin, M., Aglas, P., Muller, C. J., & Sherwood, S. C. (2023).
Data-assessing memory in convection schemes using idealized tests. Zenodo. https://doi.org/10.5281/ZENODO.7757041
chicago: Hwong, Yi-Ling, Maxime Colin, Philipp Aglas, Caroline J Muller, and Steven
C. Sherwood. “Data-Assessing Memory in Convection Schemes Using Idealized Tests.”
Zenodo, 2023. https://doi.org/10.5281/ZENODO.7757041.
ieee: Y.-L. Hwong, M. Colin, P. Aglas, C. J. Muller, and S. C. Sherwood, “Data-assessing
memory in convection schemes using idealized tests.” Zenodo, 2023.
ista: Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. 2023. Data-assessing
memory in convection schemes using idealized tests, Zenodo, 10.5281/ZENODO.7757041.
mla: Hwong, Yi-Ling, et al. Data-Assessing Memory in Convection Schemes Using
Idealized Tests. Zenodo, 2023, doi:10.5281/ZENODO.7757041.
short: Y.-L. Hwong, M. Colin, P. Aglas, C.J. Muller, S.C. Sherwood, (2023).
date_created: 2024-02-14T14:37:57Z
date_published: 2023-06-23T00:00:00Z
date_updated: 2024-02-27T07:26:31Z
day: '23'
ddc:
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call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publisher: Zenodo
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title: Data-assessing memory in convection schemes using idealized tests
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type: research_data_reference
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...
---
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abstract:
- lang: eng
text: The software artefact to evaluate the approximation of stationary distributions
implementation.
article_processing_charge: No
author:
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full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
citation:
ama: 'Meggendorfer T. Artefact for: Correct Approximation of Stationary Distributions.
2023. doi:10.5281/ZENODO.7548214'
apa: 'Meggendorfer, T. (2023). Artefact for: Correct Approximation of Stationary
Distributions. Zenodo. https://doi.org/10.5281/ZENODO.7548214'
chicago: 'Meggendorfer, Tobias. “Artefact for: Correct Approximation of Stationary
Distributions.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7548214.'
ieee: 'T. Meggendorfer, “Artefact for: Correct Approximation of Stationary Distributions.”
Zenodo, 2023.'
ista: 'Meggendorfer T. 2023. Artefact for: Correct Approximation of Stationary Distributions,
Zenodo, 10.5281/ZENODO.7548214.'
mla: 'Meggendorfer, Tobias. Artefact for: Correct Approximation of Stationary
Distributions. Zenodo, 2023, doi:10.5281/ZENODO.7548214.'
short: T. Meggendorfer, (2023).
date_created: 2024-02-14T14:27:06Z
date_published: 2023-01-18T00:00:00Z
date_updated: 2024-02-27T07:19:32Z
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ddc:
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main_file_link:
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url: https://doi.org/10.5281/zenodo.7548214
month: '01'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
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title: 'Artefact for: Correct Approximation of Stationary Distributions'
tmp:
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type: research_data_reference
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...
---
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abstract:
- lang: eng
text: "This paper presents Lincheck, a new practical and user-friendly framework
for testing concurrent algorithms on the Java Virtual Machine (JVM). Lincheck
provides a simple and declarative way to write concurrent tests: instead of describing
how to perform the test, users specify what to test by declaring all the operations
to examine; the framework automatically handles the rest. As a result, tests written
with Lincheck are concise and easy to understand. The framework automatically
generates a set of concurrent scenarios, examines them using stress-testing or
bounded model checking, and verifies that the results of each invocation are correct.
Notably, if an error is detected via model checking, Lincheck provides an easy-to-follow
trace to reproduce it, significantly simplifying the bug investigation.\r\n\r\nTo
the best of our knowledge, Lincheck is the first production-ready tool on the
JVM that offers such a simple way of writing concurrent tests, without requiring
special skills or expertise. We successfully integrated Lincheck in the development
process of several large projects, such as Kotlin Coroutines, and identified new
bugs in popular concurrency libraries, such as a race in Java’s standard ConcurrentLinkedDeque
and a liveliness bug in Java’s AbstractQueuedSynchronizer framework, which is
used in most of the synchronization primitives. We believe that Lincheck can significantly
improve the quality and productivity of concurrent algorithms research and development
and become the state-of-the-art tool for checking their correctness."
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- first_name: Alexander
full_name: Fedorov, Alexander
id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6
last_name: Fedorov
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full_name: Sokolova, Maria
last_name: Sokolova
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full_name: Tsitelov, Dmitry
last_name: Tsitelov
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full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical
framework for testing concurrent data structures on JVM. In: 35th International
Conference on Computer Aided Verification . Vol 13964. Springer Nature; 2023:156-169.
doi:10.1007/978-3-031-37706-8_8'
apa: 'Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., & Alistarh, D.-A.
(2023). Lincheck: A practical framework for testing concurrent data structures
on JVM. In 35th International Conference on Computer Aided Verification
(Vol. 13964, pp. 156–169). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_8'
chicago: 'Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and
Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data
Structures on JVM.” In 35th International Conference on Computer Aided Verification
, 13964:156–69. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_8.'
ieee: 'N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck:
A practical framework for testing concurrent data structures on JVM,” in 35th
International Conference on Computer Aided Verification , Paris, France, 2023,
vol. 13964, pp. 156–169.'
ista: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck:
A practical framework for testing concurrent data structures on JVM. 35th International
Conference on Computer Aided Verification . CAV: Computer Aided Verification,
LNCS, vol. 13964, 156–169.'
mla: 'Koval, Nikita, et al. “Lincheck: A Practical Framework for Testing Concurrent
Data Structures on JVM.” 35th International Conference on Computer Aided Verification
, vol. 13964, Springer Nature, 2023, pp. 156–69, doi:10.1007/978-3-031-37706-8_8.'
short: N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, in:, 35th
International Conference on Computer Aided Verification , Springer Nature, 2023,
pp. 156–169.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-03T22:01:16Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2024-02-27T07:46:52Z
day: '17'
ddc:
- '000'
department:
- _id: DaAl
- _id: GradSch
doi: 10.1007/978-3-031-37706-8_8
file:
- access_level: open_access
checksum: c346016393123a0a2338ad4d976f61bc
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T08:16:25Z
date_updated: 2023-09-06T08:16:25Z
file_id: '14275'
file_name: 2023_LNCS_Koval.pdf
file_size: 421408
relation: main_file
success: 1
file_date_updated: 2023-09-06T08:16:25Z
has_accepted_license: '1'
intvolume: ' 13964'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 156-169
publication: '35th International Conference on Computer Aided Verification '
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377051'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '14995'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'Lincheck: A practical framework for testing concurrent data structures on JVM'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13964
year: '2023'
...
---
_id: '14995'
abstract:
- lang: eng
text: "Lincheck is a new practical and user-friendly framework for testing concurrent
data structures on the Java Virtual Machine (JVM). It provides a simple and declarative
way to write concurrent tests. Instead of describing how to perform the test,
users specify what to test by declaring all the operations to examine; the framework
automatically handles the rest. As a result, tests written with Lincheck are concise
and easy to understand. \r\nThe artifact presents a collection of Lincheck tests
that discover new bugs in popular libraries and implementations from the concurrency
literature -- they are listed in Table 1, Section 3. To evaluate the performance
of Lincheck analysis, the collection of tests also includes those which check
correct data structures and, thus, always succeed. Similarly to Table 2, Section
3, the experiments demonstrate the reasonable time to perform a test. Finally,
Lincheck provides user-friendly output with an easy-to-follow trace to reproduce
a detected error, significantly simplifying further investigation."
article_processing_charge: No
author:
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- first_name: Alexander
full_name: Fedorov, Alexander
id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6
last_name: Fedorov
- first_name: Maria
full_name: Sokolova, Maria
last_name: Sokolova
- first_name: Dmitry
full_name: Tsitelov, Dmitry
last_name: Tsitelov
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical
framework for testing concurrent data structures on JVM. 2023. doi:10.5281/ZENODO.7877757'
apa: 'Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., & Alistarh, D.-A.
(2023). Lincheck: A practical framework for testing concurrent data structures
on JVM. Zenodo. https://doi.org/10.5281/ZENODO.7877757'
chicago: 'Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and
Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data
Structures on JVM.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7877757.'
ieee: 'N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck:
A practical framework for testing concurrent data structures on JVM.” Zenodo,
2023.'
ista: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck:
A practical framework for testing concurrent data structures on JVM, Zenodo, 10.5281/ZENODO.7877757.'
mla: 'Koval, Nikita, et al. Lincheck: A Practical Framework for Testing Concurrent
Data Structures on JVM. Zenodo, 2023, doi:10.5281/ZENODO.7877757.'
short: N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, (2023).
date_created: 2024-02-14T15:14:13Z
date_published: 2023-04-28T00:00:00Z
date_updated: 2024-02-27T07:46:52Z
day: '28'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.5281/ZENODO.7877757
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.7877757
month: '04'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14260'
relation: used_in_publication
status: public
status: public
title: 'Lincheck: A practical framework for testing concurrent data structures on
JVM'
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14994'
abstract:
- lang: eng
text: This resource contains the artifacts for reproducing the experimental results
presented in the paper titled "A Flexible Toolchain for Symbolic Rabin Games under
Fair and Stochastic Uncertainties" that has been submitted in CAV 2023.
article_processing_charge: No
author:
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
- first_name: Mateusz
full_name: Rychlicki, Mateusz
last_name: Rychlicki
- first_name: Anne-Kathrin
full_name: Schmuck, Anne-Kathrin
last_name: Schmuck
- first_name: Sadegh
full_name: Soudjani, Sadegh
last_name: Soudjani
citation:
ama: Majumdar R, Mallik K, Rychlicki M, Schmuck A-K, Soudjani S. A flexible toolchain
for symbolic rabin games under fair and stochastic uncertainties. 2023. doi:10.5281/ZENODO.7877790
apa: Majumdar, R., Mallik, K., Rychlicki, M., Schmuck, A.-K., & Soudjani, S.
(2023). A flexible toolchain for symbolic rabin games under fair and stochastic
uncertainties. Zenodo. https://doi.org/10.5281/ZENODO.7877790
chicago: Majumdar, Rupak, Kaushik Mallik, Mateusz Rychlicki, Anne-Kathrin Schmuck,
and Sadegh Soudjani. “A Flexible Toolchain for Symbolic Rabin Games under Fair
and Stochastic Uncertainties.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7877790.
ieee: R. Majumdar, K. Mallik, M. Rychlicki, A.-K. Schmuck, and S. Soudjani, “A flexible
toolchain for symbolic rabin games under fair and stochastic uncertainties.” Zenodo,
2023.
ista: Majumdar R, Mallik K, Rychlicki M, Schmuck A-K, Soudjani S. 2023. A flexible
toolchain for symbolic rabin games under fair and stochastic uncertainties, Zenodo,
10.5281/ZENODO.7877790.
mla: Majumdar, Rupak, et al. A Flexible Toolchain for Symbolic Rabin Games under
Fair and Stochastic Uncertainties. Zenodo, 2023, doi:10.5281/ZENODO.7877790.
short: R. Majumdar, K. Mallik, M. Rychlicki, A.-K. Schmuck, S. Soudjani, (2023).
date_created: 2024-02-14T15:13:00Z
date_published: 2023-04-28T00:00:00Z
date_updated: 2024-02-27T07:39:51Z
day: '28'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.5281/ZENODO.7877790
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.7877790
month: '04'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14758'
relation: used_in_publication
status: public
status: public
title: A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties
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: '2023'
...
---
_id: '15023'
abstract:
- lang: eng
text: Reinforcement learning has shown promising results in learning neural network
policies for complicated control tasks. However, the lack of formal guarantees
about the behavior of such policies remains an impediment to their deployment.
We propose a novel method for learning a composition of neural network policies
in stochastic environments, along with a formal certificate which guarantees that
a specification over the policy's behavior is satisfied with the desired probability.
Unlike prior work on verifiable RL, our approach leverages the compositional nature
of logical specifications provided in SpectRL, to learn over graphs of probabilistic
reach-avoid specifications. The formal guarantees are provided by learning neural
network policies together with reach-avoid supermartingales (RASM) for the graph’s
sub-tasks and then composing them into a global policy. We also derive a tighter
lower bound compared to previous work on the probability of reach-avoidance implied
by a RASM, which is required to find a compositional policy with an acceptable
probabilistic threshold for complex tasks with multiple edge policies. We implement
a prototype of our approach and evaluate it on a Stochastic Nine Rooms environment.
acknowledgement: "This work was supported in part by the ERC-2020-AdG 101020093 (VAMOS)
and the ERC-2020-\r\nCoG 863818 (FoRM-SMArt)."
article_processing_charge: No
author:
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Abhinav
full_name: Verma, Abhinav
id: a235593c-d7fa-11eb-a0c5-b22ca3c66ee6
last_name: Verma
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: 'Zikelic D, Lechner M, Verma A, Chatterjee K, Henzinger TA. Compositional policy
learning in stochastic control systems with formal guarantees. In: 37th Conference
on Neural Information Processing Systems. ; 2023.'
apa: Zikelic, D., Lechner, M., Verma, A., Chatterjee, K., & Henzinger, T. A.
(2023). Compositional policy learning in stochastic control systems with formal
guarantees. In 37th Conference on Neural Information Processing Systems.
New Orleans, LO, United States.
chicago: Zikelic, Dorde, Mathias Lechner, Abhinav Verma, Krishnendu Chatterjee,
and Thomas A Henzinger. “Compositional Policy Learning in Stochastic Control Systems
with Formal Guarantees.” In 37th Conference on Neural Information Processing
Systems, 2023.
ieee: D. Zikelic, M. Lechner, A. Verma, K. Chatterjee, and T. A. Henzinger, “Compositional
policy learning in stochastic control systems with formal guarantees,” in 37th
Conference on Neural Information Processing Systems, New Orleans, LO, United
States, 2023.
ista: 'Zikelic D, Lechner M, Verma A, Chatterjee K, Henzinger TA. 2023. Compositional
policy learning in stochastic control systems with formal guarantees. 37th Conference
on Neural Information Processing Systems. NeurIPS: Neural Information Processing
Systems.'
mla: Zikelic, Dorde, et al. “Compositional Policy Learning in Stochastic Control
Systems with Formal Guarantees.” 37th Conference on Neural Information Processing
Systems, 2023.
short: D. Zikelic, M. Lechner, A. Verma, K. Chatterjee, T.A. Henzinger, in:, 37th
Conference on Neural Information Processing Systems, 2023.
conference:
end_date: 2023-12-16
location: New Orleans, LO, United States
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2023-12-10
date_created: 2024-02-25T09:23:24Z
date_published: 2023-12-15T00:00:00Z
date_updated: 2024-02-28T12:20:11Z
day: '15'
department:
- _id: ToHe
- _id: KrCh
ec_funded: 1
external_id:
arxiv:
- '2312.01456'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2312.01456
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 37th Conference on Neural Information Processing Systems
publication_status: epub_ahead
quality_controlled: '1'
status: public
title: Compositional policy learning in stochastic control systems with formal guarantees
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14993'
abstract:
- lang: eng
text: "Traditional top-down approaches for global health have historically failed
to achieve social progress (Hoffman et al., 2015; Hoffman & Røttingen, 2015).
Recently, however, a more holistic, multi-level approach termed One Health (OH)
(Osterhaus et al., 2020) is being adopted. Several sets of challenges have been
identified for the implementation of OH (dos S. Ribeiro et al., 2019), including
policy and funding, education and training, and multi-actor, multi-domain, and
multi-level collaborations. These exist despite the increasing accessibility to\r\nknowledge
and digital collaborative research tools through the internet. To address some
of these challenges, we propose a general framework for grassroots community-based
means of participatory research. Additionally, we present a specific roadmap to
create a Machine Learning for Global Health community in Africa. The proposed
framework aims to enable any small group of individuals with scarce resources
to build and sustain an online community within approximately two years. We provide
a discussion on the potential impact of the proposed framework for global health
research collaborations."
acknowledgement: "Houcemeddine Turki’s contributions to this final output have been
funded through the Adapting\r\nWikidata to support clinical practice using Data
Science, Semantic Web and Machine Learning\r\nproject, which is part of the Wikimedia
Research Fund maintained by the Wikimedia Foundation in San Francisco, California,
United States of America."
article_processing_charge: No
author:
- first_name: Christopher
full_name: Currin, Christopher
id: e8321fc5-3091-11eb-8a53-83f309a11ac9
last_name: Currin
orcid: 0000-0002-4809-5059
- first_name: Mercy Nyamewaa
full_name: Asiedu , Mercy Nyamewaa
last_name: 'Asiedu '
- first_name: Chris
full_name: Fourie, Chris
last_name: Fourie
- first_name: Benjamin
full_name: Rosman, Benjamin
last_name: Rosman
- first_name: Houcemeddine
full_name: Turki, Houcemeddine
last_name: Turki
- first_name: Atnafu
full_name: Lambebo Tonja, Atnafu
last_name: Lambebo Tonja
- first_name: Jade
full_name: Abbott, Jade
last_name: Abbott
- first_name: Marvellous
full_name: Ajala, Marvellous
last_name: Ajala
- first_name: Sadiq Adewale
full_name: Adedayo, Sadiq Adewale
last_name: Adedayo
- first_name: Chris Chinenye
full_name: Emezue, Chris Chinenye
last_name: Emezue
- first_name: Daphne
full_name: Machangara, Daphne
last_name: Machangara
citation:
ama: 'Currin C, Asiedu MN, Fourie C, et al. A framework for grassroots research
collaboration in machine learning and global health. In: 1st Workshop on Machine
Learning & Global Health. OpenReview; 2023.'
apa: 'Currin, C., Asiedu , M. N., Fourie, C., Rosman, B., Turki, H., Lambebo Tonja,
A., … Machangara, D. (2023). A framework for grassroots research collaboration
in machine learning and global health. In 1st Workshop on Machine Learning
& Global Health. Kigali, Rwanda: OpenReview.'
chicago: Currin, Christopher, Mercy Nyamewaa Asiedu , Chris Fourie, Benjamin Rosman,
Houcemeddine Turki, Atnafu Lambebo Tonja, Jade Abbott, et al. “A Framework for
Grassroots Research Collaboration in Machine Learning and Global Health.” In 1st
Workshop on Machine Learning & Global Health. OpenReview, 2023.
ieee: C. Currin et al., “A framework for grassroots research collaboration
in machine learning and global health,” in 1st Workshop on Machine Learning
& Global Health, Kigali, Rwanda, 2023.
ista: 'Currin C, Asiedu MN, Fourie C, Rosman B, Turki H, Lambebo Tonja A, Abbott
J, Ajala M, Adedayo SA, Emezue CC, Machangara D. 2023. A framework for grassroots
research collaboration in machine learning and global health. 1st Workshop on
Machine Learning & Global Health. ICLR: International Conference on Learning
Representations.'
mla: Currin, Christopher, et al. “A Framework for Grassroots Research Collaboration
in Machine Learning and Global Health.” 1st Workshop on Machine Learning &
Global Health, OpenReview, 2023.
short: C. Currin, M.N. Asiedu , C. Fourie, B. Rosman, H. Turki, A. Lambebo Tonja,
J. Abbott, M. Ajala, S.A. Adedayo, C.C. Emezue, D. Machangara, in:, 1st Workshop
on Machine Learning & Global Health, OpenReview, 2023.
conference:
end_date: 2023-05-05
location: Kigali, Rwanda
name: 'ICLR: International Conference on Learning Representations'
start_date: 2023-05-05
date_created: 2024-02-14T15:11:48Z
date_published: 2023-03-02T00:00:00Z
date_updated: 2024-02-28T12:12:00Z
day: '02'
department:
- _id: TiVo
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://openreview.net/forum?id=jHY_G91R880
month: '03'
oa: 1
oa_version: Published Version
publication: 1st Workshop on Machine Learning & Global Health
publication_status: published
publisher: OpenReview
quality_controlled: '1'
status: public
title: A framework for grassroots research collaboration in machine learning and global
health
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12979'
abstract:
- lang: eng
text: 'Color and gloss are fundamental aspects of surface appearance. State-of-the-art
fabrication techniques can manipulate both properties of the printed 3D objects.
However, in the context of appearance reproduction, perceptual aspects of color
and gloss are usually handled separately, even though previous perceptual studies
suggest their interaction. Our work is motivated by previous studies demonstrating
a perceived color shift due to a change in the object''s gloss, i.e., two samples
with the same color but different surface gloss appear as they have different
colors. In this paper, we conduct new experiments which support this observation
and provide insights into the magnitude and direction of the perceived color change.
We use the observations as guidance to design a new method that estimates and
corrects the color shift enabling the fabrication of objects with the same perceived
color but different surface gloss. We formulate the problem as an optimization
procedure solved using differentiable rendering. We evaluate the effectiveness
of our method in perceptual experiments with 3D objects fabricated using a multi-material
3D printer and demonstrate potential applications. '
acknowledgement: We thank Matthew S Zurawski for the 3D model of the car speed shape.
This research has been supported by the Swiss National Science Foundation (SNSF,
Grant 200502) and the FWF Lise Meitner (Grant M 3319).
article_number: '21'
article_processing_charge: No
author:
- first_name: Jorge
full_name: Condor, Jorge
last_name: Condor
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
orcid: 0000-0002-5062-4474
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Piotr
full_name: Didyk, Piotr
last_name: Didyk
citation:
ama: 'Condor J, Piovarci M, Bickel B, Didyk P. Gloss-aware color correction for
3D printing. In: SIGGRAPH ’23 Conference Proceedings. Association for Computing
Machinery; 2023. doi:10.1145/3588432.3591546'
apa: 'Condor, J., Piovarci, M., Bickel, B., & Didyk, P. (2023). Gloss-aware
color correction for 3D printing. In SIGGRAPH ’23 Conference Proceedings.
Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3588432.3591546'
chicago: Condor, Jorge, Michael Piovarci, Bernd Bickel, and Piotr Didyk. “Gloss-Aware
Color Correction for 3D Printing.” In SIGGRAPH ’23 Conference Proceedings.
Association for Computing Machinery, 2023. https://doi.org/10.1145/3588432.3591546.
ieee: J. Condor, M. Piovarci, B. Bickel, and P. Didyk, “Gloss-aware color correction
for 3D printing,” in SIGGRAPH ’23 Conference Proceedings, Los Angeles,
CA, United States, 2023.
ista: 'Condor J, Piovarci M, Bickel B, Didyk P. 2023. Gloss-aware color correction
for 3D printing. SIGGRAPH ’23 Conference Proceedings. SIGGRAPH: Computer Graphics
and Interactive Techniques Conference, 21.'
mla: Condor, Jorge, et al. “Gloss-Aware Color Correction for 3D Printing.” SIGGRAPH
’23 Conference Proceedings, 21, Association for Computing Machinery, 2023,
doi:10.1145/3588432.3591546.
short: J. Condor, M. Piovarci, B. Bickel, P. Didyk, in:, SIGGRAPH ’23 Conference
Proceedings, Association for Computing Machinery, 2023.
conference:
end_date: 2023-08-10
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference'
start_date: 2023-08-06
date_created: 2023-05-16T09:34:13Z
date_published: 2023-07-23T00:00:00Z
date_updated: 2024-02-28T12:52:04Z
day: '23'
ddc:
- '004'
department:
- _id: BeBi
doi: 10.1145/3588432.3591546
external_id:
isi:
- '001117690500021'
file:
- access_level: open_access
checksum: 84a437739af5d46507928939b20c0c28
content_type: application/pdf
creator: mpiovarc
date_created: 2023-05-16T09:32:50Z
date_updated: 2023-05-16T09:32:50Z
file_id: '12983'
file_name: Condor2023_supplemental.pdf
file_size: 42323971
relation: main_file
success: 1
- access_level: open_access
checksum: 0f5c8b242e8e7c153c04888c4d0c6f37
content_type: application/pdf
creator: dernst
date_created: 2024-01-29T10:14:10Z
date_updated: 2024-01-29T10:14:10Z
file_id: '14893'
file_name: 2023_Siggraph_Condor.pdf
file_size: 26079404
relation: main_file
success: 1
file_date_updated: 2024-01-29T10:14:10Z
has_accepted_license: '1'
isi: 1
keyword:
- color
- gloss
- perception
- color compensation
- color management
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: eb901961-77a9-11ec-83b8-f5c883a62027
grant_number: M03319
name: Perception-Aware Appearance Fabrication
publication: SIGGRAPH ’23 Conference Proceedings
publication_identifier:
isbn:
- '9798400701597'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: Gloss-aware color correction for 3D printing
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14076'
abstract:
- lang: eng
text: Hyperproperties are properties that relate multiple execution traces. Previous
work on monitoring hyperproperties focused on synchronous hyperproperties, usually
specified in HyperLTL. When monitoring synchronous hyperproperties, all traces
are assumed to proceed at the same speed. We introduce (multi-trace) prefix transducers
and show how to use them for monitoring synchronous as well as, for the first
time, asynchronous hyperproperties. Prefix transducers map multiple input traces
into one or more output traces by incrementally matching prefixes of the input
traces against expressions similar to regular expressions. The prefixes of different
traces which are consumed by a single matching step of the monitor may have different
lengths. The deterministic and executable nature of prefix transducers makes them
more suitable as an intermediate formalism for runtime verification than logical
specifications, which tend to be highly non-deterministic, especially in the case
of asynchronous hyperproperties. We report on a set of experiments about monitoring
asynchronous version of observational determinism.
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093. The
authors would like to thank Ana Oliveira da Costa for commenting on a draft of the
paper.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Marek
full_name: Chalupa, Marek
id: 87e34708-d6c6-11ec-9f5b-9391e7be2463
last_name: Chalupa
- 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: 'Chalupa M, Henzinger TA. Monitoring hyperproperties with prefix transducers.
In: 23nd International Conference on Runtime Verification. Vol 14245. Springer
Nature; 2023:168-190. doi:10.1007/978-3-031-44267-4_9'
apa: 'Chalupa, M., & Henzinger, T. A. (2023). Monitoring hyperproperties with
prefix transducers. In 23nd International Conference on Runtime Verification
(Vol. 14245, pp. 168–190). Thessaloniki, Greek: Springer Nature. https://doi.org/10.1007/978-3-031-44267-4_9'
chicago: Chalupa, Marek, and Thomas A Henzinger. “Monitoring Hyperproperties with
Prefix Transducers.” In 23nd International Conference on Runtime Verification,
14245:168–90. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-44267-4_9.
ieee: M. Chalupa and T. A. Henzinger, “Monitoring hyperproperties with prefix transducers,”
in 23nd International Conference on Runtime Verification, Thessaloniki,
Greek, 2023, vol. 14245, pp. 168–190.
ista: 'Chalupa M, Henzinger TA. 2023. Monitoring hyperproperties with prefix transducers.
23nd International Conference on Runtime Verification. RV: Conference on Runtime
Verification, LNCS, vol. 14245, 168–190.'
mla: Chalupa, Marek, and Thomas A. Henzinger. “Monitoring Hyperproperties with Prefix
Transducers.” 23nd International Conference on Runtime Verification, vol.
14245, Springer Nature, 2023, pp. 168–90, doi:10.1007/978-3-031-44267-4_9.
short: M. Chalupa, T.A. Henzinger, in:, 23nd International Conference on Runtime
Verification, Springer Nature, 2023, pp. 168–190.
conference:
end_date: 2023-10-07
location: Thessaloniki, Greek
name: 'RV: Conference on Runtime Verification'
start_date: 2023-10-04
date_created: 2023-08-16T20:46:08Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-02-28T12:33:08Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-031-44267-4_9
ec_funded: 1
file:
- access_level: open_access
checksum: ee33bd6f1a26f4dae7a8192584869fd8
content_type: application/pdf
creator: dernst
date_created: 2023-10-16T07:15:11Z
date_updated: 2023-10-16T07:15:11Z
file_id: '14430'
file_name: 2023_LNCS_RV_Chalupa.pdf
file_size: 867256
relation: main_file
success: 1
file_date_updated: 2023-10-16T07:15:11Z
has_accepted_license: '1'
intvolume: ' 14245'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 168-190
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 23nd International Conference on Runtime Verification
publication_identifier:
eisbn:
- 978-3-031-44267-4
isbn:
- 978-3-031-44266-7
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '15035'
relation: research_data
status: public
status: public
title: Monitoring hyperproperties with prefix transducers
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14245
year: '2023'
...
---
_id: '14743'
abstract:
- lang: eng
text: Leader-based consensus algorithms are fast and efficient under normal conditions,
but lack robustness to adverse conditions due to their reliance on timeouts for
liveness. We present QuePaxa, the first protocol offering state-of-the-art normal-case
efficiency without depending on timeouts. QuePaxa uses a novel randomized asynchronous
consensus core to tolerate adverse conditions such as denial-of-service (DoS)
attacks, while a one-round-trip fast path preserves the normal-case efficiency
of Multi-Paxos or Raft. By allowing simultaneous proposers without destructive
interference, and using short hedging delays instead of conservative timeouts
to limit redundant effort, QuePaxa permits rapid recovery after leader failure
without risking costly view changes due to false timeouts. By treating leader
choice and hedging delay as a multi-armed-bandit optimization, QuePaxa achieves
responsiveness to prevalent conditions, and can choose the best leader even if
the current one has not failed. Experiments with a prototype confirm that QuePaxa
achieves normal-case LAN and WAN performance of 584k and 250k cmd/sec in throughput,
respectively, comparable to Multi-Paxos. Under conditions such as DoS attacks,
misconfigurations, or slow leaders that severely impact existing protocols, we
find that QuePaxa remains live with median latency under 380ms in WAN experiments.
acknowledgement: The authors would like to thank Marcos K. Aguilera, Pierluca Borsò,
Aleksey Charapko, Rachid Guerraoui, Jovan Komatovic, Derek Leung, Louis-Henri Merino,
Shailesh Mishra, Haochen Pan, Rodrigo Rodrigues, Lewis Tseng, and Haoqian Zhang
for their helpful feedback on early drafts of this paper.
article_processing_charge: No
author:
- first_name: Pasindu
full_name: Tennage, Pasindu
last_name: Tennage
- first_name: Cristina
full_name: Basescu, Cristina
last_name: Basescu
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Ewa
full_name: Syta, Ewa
last_name: Syta
- first_name: Philipp
full_name: Jovanovic, Philipp
last_name: Jovanovic
- first_name: Vero
full_name: Estrada-Galinanes, Vero
last_name: Estrada-Galinanes
- first_name: Bryan
full_name: Ford, Bryan
last_name: Ford
citation:
ama: 'Tennage P, Basescu C, Kokoris Kogias E, et al. QuePaxa: Escaping the tyranny
of timeouts in consensus. In: Proceedings of the 29th Symposium on Operating
Systems Principles. Association for Computing Machinery; 2023:281-297. doi:10.1145/3600006.3613150'
apa: 'Tennage, P., Basescu, C., Kokoris Kogias, E., Syta, E., Jovanovic, P., Estrada-Galinanes,
V., & Ford, B. (2023). QuePaxa: Escaping the tyranny of timeouts in consensus.
In Proceedings of the 29th Symposium on Operating Systems Principles (pp.
281–297). Koblenz, Germany: Association for Computing Machinery. https://doi.org/10.1145/3600006.3613150'
chicago: 'Tennage, Pasindu, Cristina Basescu, Eleftherios Kokoris Kogias, Ewa Syta,
Philipp Jovanovic, Vero Estrada-Galinanes, and Bryan Ford. “QuePaxa: Escaping
the Tyranny of Timeouts in Consensus.” In Proceedings of the 29th Symposium
on Operating Systems Principles, 281–97. Association for Computing Machinery,
2023. https://doi.org/10.1145/3600006.3613150.'
ieee: 'P. Tennage et al., “QuePaxa: Escaping the tyranny of timeouts in consensus,”
in Proceedings of the 29th Symposium on Operating Systems Principles, Koblenz,
Germany, 2023, pp. 281–297.'
ista: 'Tennage P, Basescu C, Kokoris Kogias E, Syta E, Jovanovic P, Estrada-Galinanes
V, Ford B. 2023. QuePaxa: Escaping the tyranny of timeouts in consensus. Proceedings
of the 29th Symposium on Operating Systems Principles. SOSP: Symposium on Operating
Systems Principles, 281–297.'
mla: 'Tennage, Pasindu, et al. “QuePaxa: Escaping the Tyranny of Timeouts in Consensus.”
Proceedings of the 29th Symposium on Operating Systems Principles, Association
for Computing Machinery, 2023, pp. 281–97, doi:10.1145/3600006.3613150.'
short: P. Tennage, C. Basescu, E. Kokoris Kogias, E. Syta, P. Jovanovic, V. Estrada-Galinanes,
B. Ford, in:, Proceedings of the 29th Symposium on Operating Systems Principles,
Association for Computing Machinery, 2023, pp. 281–297.
conference:
end_date: 2023-10-26
location: Koblenz, Germany
name: 'SOSP: Symposium on Operating Systems Principles'
start_date: 2023-10-23
date_created: 2024-01-08T12:54:35Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-02-28T12:51:24Z
day: '01'
department:
- _id: ElKo
doi: 10.1145/3600006.3613150
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/3600006.3613150
month: '10'
oa: 1
oa_version: Published Version
page: 281-297
publication: Proceedings of the 29th Symposium on Operating Systems Principles
publication_identifier:
isbn:
- '9798400702297'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'QuePaxa: Escaping the tyranny of timeouts in consensus'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '15035'
abstract:
- lang: eng
text: "This artifact aims to reproduce experiments from the paper Monitoring Hyperproperties
With Prefix Transducers accepted at RV'23, and give further pointers to implementation
of prefix transducers.\r\nIt has two parts: a pre-compiled docker image and sources
that one can use to compile (locally or in docker) the software and run the experiments."
article_processing_charge: No
author:
- first_name: Marek
full_name: Chalupa, Marek
id: 87e34708-d6c6-11ec-9f5b-9391e7be2463
last_name: Chalupa
- 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: Chalupa M, Henzinger TA. Monitoring hyperproperties with prefix transducers.
2023. doi:10.5281/ZENODO.8191723
apa: Chalupa, M., & Henzinger, T. A. (2023). Monitoring hyperproperties with
prefix transducers. Zenodo. https://doi.org/10.5281/ZENODO.8191723
chicago: Chalupa, Marek, and Thomas A Henzinger. “Monitoring Hyperproperties with
Prefix Transducers.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8191723.
ieee: M. Chalupa and T. A. Henzinger, “Monitoring hyperproperties with prefix transducers.”
Zenodo, 2023.
ista: Chalupa M, Henzinger TA. 2023. Monitoring hyperproperties with prefix transducers,
Zenodo, 10.5281/ZENODO.8191723.
mla: Chalupa, Marek, and Thomas A. Henzinger. Monitoring Hyperproperties with
Prefix Transducers. Zenodo, 2023, doi:10.5281/ZENODO.8191723.
short: M. Chalupa, T.A. Henzinger, (2023).
date_created: 2024-02-28T07:34:34Z
date_published: 2023-07-28T00:00:00Z
date_updated: 2024-02-28T12:33:09Z
day: '28'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.5281/ZENODO.8191723
ec_funded: 1
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8191722
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publisher: Zenodo
related_material:
record:
- id: '14076'
relation: used_in_publication
status: public
status: public
title: Monitoring hyperproperties with prefix transducers
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: '2023'
...
---
_id: '15039'
abstract:
- lang: eng
text: 'A crucial property for achieving secure, trustworthy and interpretable deep
learning systems is their robustness: small changes to a system''s inputs should
not result in large changes to its outputs. Mathematically, this means one strives
for networks with a small Lipschitz constant. Several recent works have focused
on how to construct such Lipschitz networks, typically by imposing constraints
on the weight matrices. In this work, we study an orthogonal aspect, namely the
role of the activation function. We show that commonly used activation functions,
such as MaxMin, as well as all piece-wise linear ones with two segments unnecessarily
restrict the class of representable functions, even in the simplest one-dimensional
setting. We furthermore introduce the new N-activation function that is provably
more expressive than currently popular activation functions. We provide code at
this https URL.'
article_number: '2311.06103'
article_processing_charge: No
author:
- first_name: Bernd
full_name: Prach, Bernd
id: 2D561D42-C427-11E9-89B4-9C1AE6697425
last_name: Prach
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Prach B, Lampert C. 1-Lipschitz neural networks are more expressive with N-activations.
arXiv. doi:10.48550/ARXIV.2311.06103
apa: Prach, B., & Lampert, C. (n.d.). 1-Lipschitz neural networks are more expressive
with N-activations. arXiv. https://doi.org/10.48550/ARXIV.2311.06103
chicago: Prach, Bernd, and Christoph Lampert. “1-Lipschitz Neural Networks Are More
Expressive with N-Activations.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2311.06103.
ieee: B. Prach and C. Lampert, “1-Lipschitz neural networks are more expressive
with N-activations,” arXiv. .
ista: Prach B, Lampert C. 1-Lipschitz neural networks are more expressive with N-activations.
arXiv, 2311.06103.
mla: Prach, Bernd, and Christoph Lampert. “1-Lipschitz Neural Networks Are More
Expressive with N-Activations.” ArXiv, 2311.06103, doi:10.48550/ARXIV.2311.06103.
short: B. Prach, C. Lampert, ArXiv (n.d.).
date_created: 2024-02-28T17:59:32Z
date_published: 2023-11-10T00:00:00Z
date_updated: 2024-03-04T07:02:39Z
day: '10'
department:
- _id: GradSch
- _id: ChLa
doi: 10.48550/ARXIV.2311.06103
external_id:
arxiv:
- '2311.06103'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2311.06103
month: '11'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: 1-Lipschitz neural networks are more expressive with N-activations
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14812'
abstract:
- lang: eng
text: This repository contains the code and VCF files needed to conduct the analyses
in our MS. Each folder contains a readMe document explaining the nature of each
file and dataset and the results and analyses that they relate to. The same anlaysis
code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode
article_processing_charge: No
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
citation:
ama: 'Stankowski S. Data and code for: The genetic architecture of a recent transition
to live-bearing in marine snails. 2023. doi:10.5281/ZENODO.8318995'
apa: 'Stankowski, S. (2023). Data and code for: The genetic architecture of a recent
transition to live-bearing in marine snails. Zenodo. https://doi.org/10.5281/ZENODO.8318995'
chicago: 'Stankowski, Sean. “Data and Code for: The Genetic Architecture of a Recent
Transition to Live-Bearing in Marine Snails.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8318995.'
ieee: 'S. Stankowski, “Data and code for: The genetic architecture of a recent transition
to live-bearing in marine snails.” Zenodo, 2023.'
ista: 'Stankowski S. 2023. Data and code for: The genetic architecture of a recent
transition to live-bearing in marine snails, Zenodo, 10.5281/ZENODO.8318995.'
mla: 'Stankowski, Sean. Data and Code for: The Genetic Architecture of a Recent
Transition to Live-Bearing in Marine Snails. Zenodo, 2023, doi:10.5281/ZENODO.8318995.'
short: S. Stankowski, (2023).
contributor:
- first_name: Zusanna
last_name: Zagrodzka
- first_name: Martin
last_name: Garlovsky
- first_name: Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Diego Fernando
id: ae681a14-dc74-11ea-a0a7-c6ef18161701
last_name: Garcia Castillo
- first_name: Hila
id: d6ab5470-2fb3-11ed-8633-986a9b84edac
last_name: Lifchitz
- first_name: Alan
last_name: Le Moan
- first_name: Erica
last_name: Leder
- first_name: James
last_name: Reeve
- first_name: Kerstin
last_name: Johannesson
- first_name: Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger
last_name: Butlin
date_created: 2024-01-16T10:23:01Z
date_published: 2023-09-05T00:00:00Z
date_updated: 2024-03-05T09:35:25Z
day: '05'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5281/ZENODO.8318995
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8318995
month: '09'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14796'
relation: used_in_publication
status: public
status: public
title: 'Data and code for: The genetic architecture of a recent transition to live-bearing
in marine snails'
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: '2023'
...
---
_id: '13214'
abstract:
- lang: eng
text: Nitrogen is an important macronutrient required for plant growth and development,
thus directly impacting agricultural productivity. In recent years, numerous studies
have shown that nitrogen-driven growth depends on pathways that control nitrate/nitrogen
homeostasis and hormonal networks that act both locally and systemically to coordinate
growth and development of plant organs. In this review, we will focus on recent
advances in understanding the role of the plant hormones auxin and cytokinin and
their crosstalk in nitrate-regulated growth and discuss the significance of novel
findings and possible missing links.
acknowledgement: 'This work was supported by the Austrian Academy of Sciences ÖAW:
Doc fellowship (26130) to Stefan Riegler.'
article_number: '1613'
article_processing_charge: Yes
article_type: review
author:
- first_name: R
full_name: Abualia, R
last_name: Abualia
- first_name: Stefan
full_name: Riegler, Stefan
id: FF6018E0-D806-11E9-8E43-0B14E6697425
last_name: Riegler
orcid: 0000-0003-3413-1343
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Abualia R, Riegler S, Benková E. Nitrate, auxin and cytokinin - a trio to tango.
Cells. 2023;12(12). doi:10.3390/cells12121613
apa: Abualia, R., Riegler, S., & Benková, E. (2023). Nitrate, auxin and cytokinin
- a trio to tango. Cells. MDPI. https://doi.org/10.3390/cells12121613
chicago: Abualia, R, Stefan Riegler, and Eva Benková. “Nitrate, Auxin and Cytokinin
- a Trio to Tango.” Cells. MDPI, 2023. https://doi.org/10.3390/cells12121613.
ieee: R. Abualia, S. Riegler, and E. Benková, “Nitrate, auxin and cytokinin - a
trio to tango,” Cells, vol. 12, no. 12. MDPI, 2023.
ista: Abualia R, Riegler S, Benková E. 2023. Nitrate, auxin and cytokinin - a trio
to tango. Cells. 12(12), 1613.
mla: Abualia, R., et al. “Nitrate, Auxin and Cytokinin - a Trio to Tango.” Cells,
vol. 12, no. 12, 1613, MDPI, 2023, doi:10.3390/cells12121613.
short: R. Abualia, S. Riegler, E. Benková, Cells 12 (2023).
date_created: 2023-07-12T07:41:25Z
date_published: 2023-06-13T00:00:00Z
date_updated: 2024-03-06T14:00:33Z
day: '13'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.3390/cells12121613
external_id:
isi:
- '001017033600001'
pmid:
- '37371083'
file:
- access_level: open_access
checksum: 6dc9df5f4f59fc27c509c275060354a5
content_type: application/pdf
creator: alisjak
date_created: 2023-07-12T10:01:54Z
date_updated: 2023-07-12T10:01:54Z
file_id: '13218'
file_name: 2023_cells_Abualia.pdf
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title: Nitrate, auxin and cytokinin - a trio to tango
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