---
_id: '14313'
abstract:
- lang: eng
text: To respond to auxin, the chief orchestrator of their multicellularity, plants
evolved multiple receptor systems and signal transduction cascades. Despite decades
of research, however, we are still lacking a satisfactory synthesis of various
auxin signaling mechanisms. The chief discrepancy and historical controversy of
the field is that of rapid and slow auxin effects on plant physiology and development.
How is it possible that ions begin to trickle across the plasma membrane as soon
as auxin enters the cell, even though the best-characterized transcriptional auxin
pathway can take effect only after tens of minutes? Recently, unexpected progress
has been made in understanding this and other unknowns of auxin signaling. We
provide a perspective on these exciting developments and concepts whose general
applicability might have ramifications beyond auxin signaling.
acknowledgement: The opening quote is not intended to reflect any political views
of the authors. The authors by no means endorse the rhetoric of Donald Rumsfeld
or the 2003 invasion of Iraq by the United States. Nevertheless, Rumsfeld's quote
led to both public and academic debates on the concept of known and unknown unknowns,
which can be applied to the recent unexpected developments in the auxin signaling
field. We thank Linlin Qi and Huihuang Chen for their suggestions on figure presentation
and inspiring discussions of TIR1/AFB signaling. Finally, we thank Aroosa Hussain
for discussion of Greek mythology.
article_number: '102443'
article_processing_charge: No
article_type: review
author:
- first_name: Lukas
full_name: Fiedler, Lukas
id: 7c417475-8972-11ed-ae7b-8b674ca26986
last_name: Fiedler
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Fiedler L, Friml J. Rapid auxin signaling: Unknowns old and new. Current
Opinion in Plant Biology. 2023;75(10). doi:10.1016/j.pbi.2023.102443'
apa: 'Fiedler, L., & Friml, J. (2023). Rapid auxin signaling: Unknowns old and
new. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2023.102443'
chicago: 'Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and
New.” Current Opinion in Plant Biology. Elsevier, 2023. https://doi.org/10.1016/j.pbi.2023.102443.'
ieee: 'L. Fiedler and J. Friml, “Rapid auxin signaling: Unknowns old and new,” Current
Opinion in Plant Biology, vol. 75, no. 10. Elsevier, 2023.'
ista: 'Fiedler L, Friml J. 2023. Rapid auxin signaling: Unknowns old and new. Current
Opinion in Plant Biology. 75(10), 102443.'
mla: 'Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.”
Current Opinion in Plant Biology, vol. 75, no. 10, 102443, Elsevier, 2023,
doi:10.1016/j.pbi.2023.102443.'
short: L. Fiedler, J. Friml, Current Opinion in Plant Biology 75 (2023).
corr_author: '1'
date_created: 2023-09-10T22:01:11Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2025-09-09T12:54:16Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.pbi.2023.102443
external_id:
isi:
- '001080095300001'
pmid:
- '37666097'
file:
- access_level: open_access
checksum: 1c476c3414d2dfb0c85db0cb6cfd8a28
content_type: application/pdf
creator: amally
date_created: 2023-11-02T17:03:20Z
date_updated: 2023-11-02T17:03:20Z
file_id: '14482'
file_name: Fiedler CurrOpinOlantBiol 2023_revised.pdf
file_size: 737872
relation: main_file
success: 1
file_date_updated: 2023-11-02T17:03:20Z
has_accepted_license: '1'
intvolume: ' 75'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Current Opinion in Plant Biology
publication_identifier:
issn:
- 1369-5266
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Rapid auxin signaling: Unknowns old and new'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 75
year: '2023'
...
---
_id: '14314'
abstract:
- lang: eng
text: The execution of cognitive functions requires coordinated circuit activity
across different brain areas that involves the associated firing of neuronal assemblies.
Here, we tested the circuit mechanism behind assembly interactions between the
hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording
neuronal populations during a rule-switching task. We identified functionally
coupled CA1-mPFC cells that synchronized their activity beyond that expected from
common spatial coding or oscillatory firing. When such cell pairs fired together,
the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent
theta firing phases, independent of the theta timing of their CA1 counterpart.
These functionally connected CA1-mPFC cells formed interconnected assemblies.
While firing together with their CA1 assembly partners, mPFC cells fired along
specific theta sequences. Our results suggest that upregulated theta oscillatory
firing of mPFC cells can signal transient interactions with specific CA1 assemblies,
thus enabling distributed computations.
acknowledgement: We thank A. Cumpelik, H. Chiossi, and L. Bollman for comments on
an earlier version of this manuscript. This work was funded by EU-FP7 MC-ITN IN-SENS
(grant 607616).
article_number: '113015'
article_processing_charge: Yes
article_type: original
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Karola
full_name: Käfer, Karola
id: 2DAA49AA-F248-11E8-B48F-1D18A9856A87
last_name: Käfer
- first_name: Federico
full_name: Stella, Federico
id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
last_name: Stella
orcid: 0000-0001-9439-3148
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Nardin M, Käfer K, Stella F, Csicsvari JL. Theta oscillations as a substrate
for medial prefrontal-hippocampal assembly interactions. Cell Reports.
2023;42(9). doi:10.1016/j.celrep.2023.113015
apa: Nardin, M., Käfer, K., Stella, F., & Csicsvari, J. L. (2023). Theta oscillations
as a substrate for medial prefrontal-hippocampal assembly interactions. Cell
Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.113015
chicago: Nardin, Michele, Karola Käfer, Federico Stella, and Jozsef L Csicsvari.
“Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly
Interactions.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.113015.
ieee: M. Nardin, K. Käfer, F. Stella, and J. L. Csicsvari, “Theta oscillations as
a substrate for medial prefrontal-hippocampal assembly interactions,” Cell
Reports, vol. 42, no. 9. Elsevier, 2023.
ista: Nardin M, Käfer K, Stella F, Csicsvari JL. 2023. Theta oscillations as a substrate
for medial prefrontal-hippocampal assembly interactions. Cell Reports. 42(9),
113015.
mla: Nardin, Michele, et al. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal
Assembly Interactions.” Cell Reports, vol. 42, no. 9, 113015, Elsevier,
2023, doi:10.1016/j.celrep.2023.113015.
short: M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023).
corr_author: '1'
date_created: 2023-09-10T22:01:11Z
date_published: 2023-09-26T00:00:00Z
date_updated: 2025-09-09T12:53:32Z
day: '26'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1016/j.celrep.2023.113015
ec_funded: 1
external_id:
isi:
- '001068779200001'
pmid:
- '37632747'
file:
- access_level: open_access
checksum: ca77a304fb813c292550b8604b0fb41d
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T07:12:46Z
date_updated: 2023-09-15T07:12:46Z
file_id: '14337'
file_name: 2023_CellPress_Nardin.pdf
file_size: 4879455
relation: main_file
success: 1
file_date_updated: 2023-09-15T07:12:46Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '9'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 257BBB4C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '607616'
name: inter-and intracellular signalling in schizophrenia
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Theta oscillations as a substrate for medial prefrontal-hippocampal assembly
interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 42
year: '2023'
...
---
_id: '14315'
abstract:
- lang: eng
text: During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly
demolish the nuclear pore complex. However, for poorly understood reasons, caspases
are also activated during cell differentiation. Here, we show that sublethal activation
of caspases during myogenesis results in the transient proteolysis of four peripheral
Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective,
and we identified in an unbiased manner several classes of cytoplasmic, plasma
membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC
trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic
reticulum stress. Our results suggest that caspases can reversibly modulate nuclear
transport activity, which allows them to function as agents of cell differentiation
and adaptation at sublethal levels.
acknowledgement: 'We thank the members of the Hetzer laboratory, Tony Hunter (Salk),
Lorenzo Puri (Sanford Burnham Prebys), and Jongmin Kim (Massachusetts General Hospital)
for the critical reading of the manuscript; Kenneth Diffenderfer and Aimee Pankonin
(Stem Cell Core at the Salk Institute) for help with neurogenesis; Carol Marchetto
and Fred Gage (Salk) for providing H9 embryonic stem cells; Lorenzo Puri, Alexandra
Sacco, and Luca Caputo (Sanford Burnham Prebys) for helpful discussions and sharing
mouse primary myoblasts. This work was supported by a Glenn Foundation for Medical
Research Postdoctoral Fellowship in Aging Research (UHC), the NOMIS foundation (MWH),
and the National Institutes of Health (R01 NS096786 to MWH and K01 AR080828 to UHC).
This work was also supported by the Mass Spectrometry Core of the Salk Institute
with funding from NIH-NCI CCSG: P30 014195 and the Helmsley Center for Genomic Medicine.
We thank Jolene Diedrich and Antonio Pinto for technical support.'
article_number: RP89066
article_processing_charge: Yes
article_type: original
author:
- first_name: Ukrae H.
full_name: Cho, Ukrae H.
last_name: Cho
- first_name: Martin W
full_name: Hetzer, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: Hetzer
orcid: 0000-0002-2111-992X
citation:
ama: Cho UH, Hetzer M. Caspase-mediated nuclear pore complex trimming in cell differentiation
and endoplasmic reticulum stress. eLife. 2023;12. doi:10.7554/eLife.89066
apa: Cho, U. H., & Hetzer, M. (2023). Caspase-mediated nuclear pore complex
trimming in cell differentiation and endoplasmic reticulum stress. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.89066
chicago: Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex
Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife.
eLife Sciences Publications, 2023. https://doi.org/10.7554/eLife.89066.
ieee: U. H. Cho and M. Hetzer, “Caspase-mediated nuclear pore complex trimming in
cell differentiation and endoplasmic reticulum stress,” eLife, vol. 12.
eLife Sciences Publications, 2023.
ista: Cho UH, Hetzer M. 2023. Caspase-mediated nuclear pore complex trimming in
cell differentiation and endoplasmic reticulum stress. eLife. 12, RP89066.
mla: Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming
in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife, vol.
12, RP89066, eLife Sciences Publications, 2023, doi:10.7554/eLife.89066.
short: U.H. Cho, M. Hetzer, ELife 12 (2023).
corr_author: '1'
date_created: 2023-09-10T22:01:11Z
date_published: 2023-09-04T00:00:00Z
date_updated: 2024-10-09T21:06:57Z
day: '04'
ddc:
- '570'
department:
- _id: MaHe
doi: 10.7554/eLife.89066
external_id:
pmid:
- '37665327'
file:
- access_level: open_access
checksum: db24bf3d595507387b48d3799c33e289
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T06:59:10Z
date_updated: 2023-09-15T06:59:10Z
file_id: '14336'
file_name: 2023_eLife_Cho.pdf
file_size: 3703097
relation: main_file
success: 1
file_date_updated: 2023-09-15T06:59:10Z
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Caspase-mediated nuclear pore complex trimming in cell differentiation and
endoplasmic reticulum stress
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: 12
year: '2023'
...
---
_id: '14316'
abstract:
- lang: eng
text: Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport.
In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted
to generate distinct transport vesicles at the trans-Golgi network (TGN), and
the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories
for these adaptors. Recently, we showed that vesicle transport from the TGN is
crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p
are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However,
these observations were incompatible with previous studies showing that these
adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall
mechanism responsible for regulation of Vps21p activity remains ambiguous. Here,
we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated
Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired
transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to
the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA
adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and
Ypt32p were found to have partially overlapping functions for recruitment of AP-1
and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors
for Vps21p activation in the TGN–endosome trafficking pathway.
article_number: jcs261448
article_processing_charge: No
article_type: original
author:
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Kaito
full_name: Aoshima, Kaito
last_name: Aoshima
- first_name: Hiroki
full_name: Shimamura, Hiroki
last_name: Shimamura
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Junko Y.
full_name: Toshima, Junko Y.
last_name: Toshima
- first_name: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. Distinct
role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome
trafficking pathway. Journal of Cell Science. 2023;136(17). doi:10.1242/jcs.261448
apa: Nagano, M., Aoshima, K., Shimamura, H., Siekhaus, D. E., Toshima, J. Y., &
Toshima, J. (2023). Distinct role of TGN-resident clathrin adaptors for Vps21p
activation in the TGN-endosome trafficking pathway. Journal of Cell Science.
The Company of Biologists. https://doi.org/10.1242/jcs.261448
chicago: Nagano, Makoto, Kaito Aoshima, Hiroki Shimamura, Daria E Siekhaus, Junko
Y. Toshima, and Jiro Toshima. “Distinct Role of TGN-Resident Clathrin Adaptors
for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of
Cell Science. The Company of Biologists, 2023. https://doi.org/10.1242/jcs.261448.
ieee: M. Nagano, K. Aoshima, H. Shimamura, D. E. Siekhaus, J. Y. Toshima, and J.
Toshima, “Distinct role of TGN-resident clathrin adaptors for Vps21p activation
in the TGN-endosome trafficking pathway,” Journal of Cell Science, vol.
136, no. 17. The Company of Biologists, 2023.
ista: Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. 2023.
Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome
trafficking pathway. Journal of Cell Science. 136(17), jcs261448.
mla: Nagano, Makoto, et al. “Distinct Role of TGN-Resident Clathrin Adaptors for
Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of Cell
Science, vol. 136, no. 17, jcs261448, The Company of Biologists, 2023, doi:10.1242/jcs.261448.
short: M. Nagano, K. Aoshima, H. Shimamura, D.E. Siekhaus, J.Y. Toshima, J. Toshima,
Journal of Cell Science 136 (2023).
date_created: 2023-09-10T22:01:12Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2025-09-09T12:56:46Z
day: '01'
department:
- _id: DaSi
doi: 10.1242/jcs.261448
external_id:
isi:
- '001112832300005'
pmid:
- '37539494'
intvolume: ' 136'
isi: 1
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.03.27.534325
month: '09'
oa: 1
oa_version: Preprint
pmid: 1
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the
TGN-endosome trafficking pathway
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 136
year: '2023'
...
---
_id: '14317'
abstract:
- lang: eng
text: "Markov decision processes can be viewed as transformers of probability distributions.
While this view is useful from a practical standpoint to reason about trajectories
of distributions, basic reachability and safety problems are known to be computationally
intractable (i.e., Skolem-hard) to solve in such models. Further, we show that
even for simple examples of MDPs, strategies for safety objectives over distributions
can require infinite memory and randomization.\r\nIn light of this, we present
a novel overapproximation approach to synthesize strategies in an MDP, such that
a safety objective over the distributions is met. More precisely, we develop a
new framework for template-based synthesis of certificates as affine distributional
and inductive invariants for safety objectives in MDPs. We provide two algorithms
within this framework. One can only synthesize memoryless strategies, but has
relative completeness guarantees, while the other can synthesize general strategies.
The runtime complexity of both algorithms is in PSPACE. We implement these algorithms
and show that they can solve several non-trivial examples."
acknowledgement: This work was supported in part by the ERC CoG 863818 (FoRM-SMArt)
and the European Union’s Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 665385 as well as DST/CEFIPRA/INRIA project
EQuaVE and SERB Matrices grant MTR/2018/00074.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: S.
full_name: Akshay, S.
last_name: Akshay
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Tobias
full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. MDPs as distribution transformers:
Affine invariant synthesis for safety objectives. In: International Conference
on Computer Aided Verification. Vol 13966. Springer Nature; 2023:86-112. doi:10.1007/978-3-031-37709-9_5'
apa: 'Akshay, S., Chatterjee, K., Meggendorfer, T., & Zikelic, D. (2023). MDPs
as distribution transformers: Affine invariant synthesis for safety objectives.
In International Conference on Computer Aided Verification (Vol. 13966,
pp. 86–112). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_5'
chicago: 'Akshay, S., Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic.
“MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.”
In International Conference on Computer Aided Verification, 13966:86–112.
Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_5.'
ieee: 'S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “MDPs as distribution
transformers: Affine invariant synthesis for safety objectives,” in International
Conference on Computer Aided Verification, Paris, France, 2023, vol. 13966,
pp. 86–112.'
ista: 'Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2023. MDPs as distribution
transformers: Affine invariant synthesis for safety objectives. International
Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS,
vol. 13966, 86–112.'
mla: 'Akshay, S., et al. “MDPs as Distribution Transformers: Affine Invariant Synthesis
for Safety Objectives.” International Conference on Computer Aided Verification,
vol. 13966, Springer Nature, 2023, pp. 86–112, doi:10.1007/978-3-031-37709-9_5.'
short: S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, International
Conference on Computer Aided Verification, Springer Nature, 2023, pp. 86–112.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-10T22:01:12Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2025-09-09T12:56:00Z
day: '17'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-031-37709-9_5
ec_funded: 1
external_id:
isi:
- '001310805600005'
file:
- access_level: open_access
checksum: f143c8eedf609f20f2aad2eeb496d53f
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T08:46:43Z
date_updated: 2023-09-20T08:46:43Z
file_id: '14349'
file_name: 2023_LNCS_Akshay.pdf
file_size: 531745
relation: main_file
success: 1
file_date_updated: 2023-09-20T08:46:43Z
has_accepted_license: '1'
intvolume: ' 13966'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 86-112
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: International Conference on Computer Aided Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377082'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'MDPs as distribution transformers: Affine invariant synthesis for safety objectives'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13966
year: '2023'
...
---
_id: '14318'
abstract:
- lang: eng
text: "Probabilistic recurrence relations (PRRs) are a standard formalism for describing
the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider
the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime
T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims
at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem,
the classical and most well-known approach is the cookbook method by Karp (JACM
1994), while other approaches are mostly limited to deriving tail bounds of specific
PRRs via involved custom analysis.\r\nIn this work, we propose a novel approach
for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing
time and random passed sizes observe discrete or (piecewise) uniform distribution
and whose recursive call is either a single procedure call or a divide-and-conquer.
We first establish a theoretical approach via Markov’s inequality, and then instantiate
the theoretical approach with a template-based algorithmic approach via a refined
treatment of exponentiation. Experimental evaluation shows that our algorithmic
approach is capable of deriving tail bounds that are (i) asymptotically tighter
than Karp’s method, (ii) match the best-known manually-derived asymptotic tail
bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor)
than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover,
our algorithmic approach handles all examples (including realistic PRRs such as
QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing
that our approach is efficient in practice."
acknowledgement: We thank Prof. Bican Xia for valuable information on the exponential
theory of reals. The work is partially supported by the National Natural Science
Foundation of China (NSFC) with Grant No. 62172271, ERC CoG 863818 (ForM-SMArt),
the Hong Kong Research Grants Council ECS Project Number 26208122, the HKUST-Kaisa
Joint Research Institute Project Grant HKJRI3A-055 and the HKUST Startup Grant R9272.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Yican
full_name: Sun, Yican
last_name: Sun
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: 'Sun Y, Fu H, Chatterjee K, Goharshady AK. Automated tail bound analysis for probabilistic
recurrence relations. In: Computer Aided Verification. Vol 13966. Springer
Nature; 2023:16-39. doi:10.1007/978-3-031-37709-9_2'
apa: 'Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2023). Automated
tail bound analysis for probabilistic recurrence relations. In Computer Aided
Verification (Vol. 13966, pp. 16–39). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_2'
chicago: Sun, Yican, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady.
“Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” In Computer
Aided Verification, 13966:16–39. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_2.
ieee: Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Automated tail bound
analysis for probabilistic recurrence relations,” in Computer Aided Verification,
Paris, France, 2023, vol. 13966, pp. 16–39.
ista: 'Sun Y, Fu H, Chatterjee K, Goharshady AK. 2023. Automated tail bound analysis
for probabilistic recurrence relations. Computer Aided Verification. CAV: Computer
Aided Verification, LNCS, vol. 13966, 16–39.'
mla: Sun, Yican, et al. “Automated Tail Bound Analysis for Probabilistic Recurrence
Relations.” Computer Aided Verification, vol. 13966, Springer Nature, 2023,
pp. 16–39, doi:10.1007/978-3-031-37709-9_2.
short: Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification,
Springer Nature, 2023, pp. 16–39.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-10T22:01:12Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2025-09-09T12:55:28Z
day: '17'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-031-37709-9_2
ec_funded: 1
external_id:
isi:
- '001310805600002'
file:
- access_level: open_access
checksum: 42917e086f8c7699f3bccf84f74fe000
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T08:24:47Z
date_updated: 2023-09-20T08:24:47Z
file_id: '14348'
file_name: 2023_LNCS_Sun.pdf
file_size: 624647
relation: main_file
success: 1
file_date_updated: 2023-09-20T08:24:47Z
has_accepted_license: '1'
intvolume: ' 13966'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 16-39
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Computer Aided Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377082'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/boyvolcano/PRR
scopus_import: '1'
status: public
title: Automated tail bound analysis for probabilistic recurrence relations
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13966
year: '2023'
...
---
_id: '14319'
abstract:
- lang: eng
text: "We study multigraphs whose edge-sets are the union of three perfect matchings,
M1, M2, and M3. Given such a graph G and any a1; a2; a3 2 N with a1 +a2 +a3 6
n - 2, we show there exists a matching M of G with jM \\ Mij = ai for each i 2
f1; 2; 3g. The bound n - 2 in the theorem is best possible in general. We conjecture
however that if G is bipartite, the same result holds with n - 2 replaced by n
- 1. We give a construction that shows such a result would be tight. We\r\nalso
make a conjecture generalising the Ryser-Brualdi-Stein conjecture with colour\r\nmultiplicities."
acknowledgement: Anastos has received funding from the European Union’s Horizon 2020
research and in-novation programme under the Marie Sk lodowska-Curie grant agreement
No 101034413.Fabian’s research is supported by the Deutsche Forschungsgemeinschaft
(DFG, GermanResearch Foundation) Graduiertenkolleg “Facets of Complexity” (GRK 2434).
article_number: P3.10
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
- first_name: David
full_name: Fabian, David
last_name: Fabian
- first_name: Alp
full_name: Müyesser, Alp
last_name: Müyesser
- first_name: Tibor
full_name: Szabó, Tibor
last_name: Szabó
citation:
ama: Anastos M, Fabian D, Müyesser A, Szabó T. Splitting matchings and the Ryser-Brualdi-Stein
conjecture for multisets. Electronic Journal of Combinatorics. 2023;30(3).
doi:10.37236/11714
apa: Anastos, M., Fabian, D., Müyesser, A., & Szabó, T. (2023). Splitting matchings
and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of
Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/11714
chicago: Anastos, Michael, David Fabian, Alp Müyesser, and Tibor Szabó. “Splitting
Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” Electronic
Journal of Combinatorics. Electronic Journal of Combinatorics, 2023. https://doi.org/10.37236/11714.
ieee: M. Anastos, D. Fabian, A. Müyesser, and T. Szabó, “Splitting matchings and
the Ryser-Brualdi-Stein conjecture for multisets,” Electronic Journal of Combinatorics,
vol. 30, no. 3. Electronic Journal of Combinatorics, 2023.
ista: Anastos M, Fabian D, Müyesser A, Szabó T. 2023. Splitting matchings and the
Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics.
30(3), P3.10.
mla: Anastos, Michael, et al. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture
for Multisets.” Electronic Journal of Combinatorics, vol. 30, no. 3, P3.10,
Electronic Journal of Combinatorics, 2023, doi:10.37236/11714.
short: M. Anastos, D. Fabian, A. Müyesser, T. Szabó, Electronic Journal of Combinatorics
30 (2023).
date_created: 2023-09-10T22:01:12Z
date_published: 2023-07-28T00:00:00Z
date_updated: 2025-09-09T12:54:51Z
day: '28'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.37236/11714
ec_funded: 1
external_id:
arxiv:
- '2212.03100'
isi:
- '001042382200001'
file:
- access_level: open_access
checksum: 52c46c8cb329f9aaee9ade01525f317b
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T08:02:09Z
date_updated: 2023-09-15T08:02:09Z
file_id: '14338'
file_name: 2023_elecJournCombinatorics_Anastos.pdf
file_size: 247917
relation: main_file
success: 1
file_date_updated: 2023-09-15T08:02:09Z
has_accepted_license: '1'
intvolume: ' 30'
isi: 1
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Electronic Journal of Combinatorics
publication_identifier:
eissn:
- 1077-8926
publication_status: published
publisher: Electronic Journal of Combinatorics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 30
year: '2023'
...
---
_id: '14320'
abstract:
- lang: eng
text: The development of two-dimensional materials has resulted in a diverse range
of novel, high-quality compounds with increasing complexity. A key requirement
for a comprehensive quantitative theory is the accurate determination of these
materials' band structure parameters. However, this task is challenging due to
the intricate band structures and the indirect nature of experimental probes.
In this work, we introduce a general framework to derive band structure parameters
from experimental data using deep neural networks. We applied our method to the
penetration field capacitance measurement of trilayer graphene, an effective probe
of its density of states. First, we demonstrate that a trained deep network gives
accurate predictions for the penetration field capacitance as a function of tight-binding
parameters. Next, we use the fast and accurate predictions from the trained network
to automatically determine tight-binding parameters directly from experimental
data, with extracted parameters being in a good agreement with values in the literature.
We conclude by discussing potential applications of our method to other materials
and experimental techniques beyond penetration field capacitance.
acknowledgement: A.F.Y. acknowledges primary support from the Department of Energy
under award DE-SC0020043, and additional support from the Gordon and Betty Moore
Foundation under award GBMF9471 for group operations.
article_number: '125411'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Paul M
full_name: Henderson, Paul M
id: 13C09E74-18D9-11E9-8878-32CFE5697425
last_name: Henderson
orcid: 0000-0002-5198-7445
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Alexander A.
full_name: Zibrov, Alexander A.
last_name: Zibrov
- first_name: Andrea F.
full_name: Young, Andrea F.
last_name: Young
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: 'Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. Deep learning extraction
of band structure parameters from density of states: A case study on trilayer
graphene. Physical Review B. 2023;108(12). doi:10.1103/physrevb.108.125411'
apa: 'Henderson, P. M., Ghazaryan, A., Zibrov, A. A., Young, A. F., & Serbyn,
M. (2023). Deep learning extraction of band structure parameters from density
of states: A case study on trilayer graphene. Physical Review B. American
Physical Society. https://doi.org/10.1103/physrevb.108.125411'
chicago: 'Henderson, Paul M, Areg Ghazaryan, Alexander A. Zibrov, Andrea F. Young,
and Maksym Serbyn. “Deep Learning Extraction of Band Structure Parameters from
Density of States: A Case Study on Trilayer Graphene.” Physical Review B.
American Physical Society, 2023. https://doi.org/10.1103/physrevb.108.125411.'
ieee: 'P. M. Henderson, A. Ghazaryan, A. A. Zibrov, A. F. Young, and M. Serbyn,
“Deep learning extraction of band structure parameters from density of states:
A case study on trilayer graphene,” Physical Review B, vol. 108, no. 12.
American Physical Society, 2023.'
ista: 'Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. 2023. Deep learning
extraction of band structure parameters from density of states: A case study on
trilayer graphene. Physical Review B. 108(12), 125411.'
mla: 'Henderson, Paul M., et al. “Deep Learning Extraction of Band Structure Parameters
from Density of States: A Case Study on Trilayer Graphene.” Physical Review
B, vol. 108, no. 12, 125411, American Physical Society, 2023, doi:10.1103/physrevb.108.125411.'
short: P.M. Henderson, A. Ghazaryan, A.A. Zibrov, A.F. Young, M. Serbyn, Physical
Review B 108 (2023).
date_created: 2023-09-12T07:12:12Z
date_published: 2023-09-15T00:00:00Z
date_updated: 2023-09-20T09:38:24Z
day: '15'
department:
- _id: MaSe
- _id: ChLa
- _id: MiLe
doi: 10.1103/physrevb.108.125411
external_id:
arxiv:
- '2210.06310'
intvolume: ' 108'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2210.06310
month: '09'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Deep learning extraction of band structure parameters from density of states:
A case study on trilayer graphene'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '14321'
abstract:
- lang: eng
text: We demonstrate the possibility of a coupling between the magnetization direction
of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate
the mechanism of the coupling, we analyze a minimal Stoner model that includes
Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet.
The proposed mechanism allows us to study magnetic anisotropy of the system with
an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can
change magnetocrystalline anisotropy of the substrate. Our research aims to motivate
further experimental studies of the current-free chirality induced spin selectivity
effect involving both enantiomers.
acknowledgement: "We thank Zhanybek Alpichshev, Mohammad Reza Safari, Binghai Yan,
and Yossi Paltiel for enlightening discussions.\r\nM.L. acknowledges support from
the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A. C. received
funding from the European Union’s Horizon Europe research and innovation program
under the Marie Skłodowska-Curie Grant Agreement No. 101062862 - NeqMolRot."
article_number: '104103'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Ragheed
full_name: Al Hyder, Ragheed
id: d1c405be-ae15-11ed-8510-ccf53278162e
last_name: Al Hyder
- first_name: Alberto
full_name: Cappellaro, Alberto
id: 9d13b3cb-30a2-11eb-80dc-f772505e8660
last_name: Cappellaro
orcid: 0000-0001-6110-2359
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. Achiral dipoles on a ferromagnet
can affect its magnetization direction. The Journal of Chemical Physics.
2023;159(10). doi:10.1063/5.0165806
apa: Al Hyder, R., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Achiral
dipoles on a ferromagnet can affect its magnetization direction. The Journal
of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0165806
chicago: Al Hyder, Ragheed, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev.
“Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” The
Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0165806.
ieee: R. Al Hyder, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Achiral dipoles
on a ferromagnet can affect its magnetization direction,” The Journal of Chemical
Physics, vol. 159, no. 10. AIP Publishing, 2023.
ista: Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. 2023. Achiral dipoles on
a ferromagnet can affect its magnetization direction. The Journal of Chemical
Physics. 159(10), 104103.
mla: Al Hyder, Ragheed, et al. “Achiral Dipoles on a Ferromagnet Can Affect Its
Magnetization Direction.” The Journal of Chemical Physics, vol. 159, no.
10, 104103, AIP Publishing, 2023, doi:10.1063/5.0165806.
short: R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical
Physics 159 (2023).
corr_author: '1'
date_created: 2023-09-13T09:25:09Z
date_published: 2023-09-11T00:00:00Z
date_updated: 2025-09-09T12:57:42Z
day: '11'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1063/5.0165806
ec_funded: 1
external_id:
arxiv:
- '2306.17592'
isi:
- '001133333600011'
pmid:
- '37694742'
file:
- access_level: open_access
checksum: 507ab65ab29e2c987c94cabad7c5370b
content_type: application/pdf
creator: acappell
date_created: 2023-09-13T09:34:20Z
date_updated: 2023-09-13T09:34:20Z
file_id: '14322'
file_name: 104103_1_5.0165806.pdf
file_size: 5749653
relation: main_file
success: 1
file_date_updated: 2023-09-13T09:34:20Z
has_accepted_license: '1'
intvolume: ' 159'
isi: 1
issue: '10'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: bd7b5202-d553-11ed-ba76-9b1c1b258338
grant_number: '101062862'
name: Non-Equilibrium Field Theory of Molecular Rotations
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Achiral dipoles on a ferromagnet can affect its magnetization direction
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 159
year: '2023'
...
---
_id: '14333'
abstract:
- lang: eng
text: "As causal ground truth is incredibly rare, causal discovery algorithms are\r\ncommonly
only evaluated on simulated data. This is concerning, given that\r\nsimulations
reflect common preconceptions about generating processes regarding\r\nnoise distributions,
model classes, and more. In this work, we propose a novel\r\nmethod for falsifying
the output of a causal discovery algorithm in the absence\r\nof ground truth.
Our key insight is that while statistical learning seeks\r\nstability across subsets
of data points, causal learning should seek stability\r\nacross subsets of variables.
Motivated by this insight, our method relies on a\r\nnotion of compatibility between
causal graphs learned on different subsets of\r\nvariables. We prove that detecting
incompatibilities can falsify wrongly\r\ninferred causal relations due to violation
of assumptions or errors from finite\r\nsample effects. Although passing such
compatibility tests is only a necessary\r\ncriterion for good performance, we
argue that it provides strong evidence for\r\nthe causal models whenever compatibility
entails strong implications for the\r\njoint distribution. We also demonstrate
experimentally that detection of\r\nincompatibilities can aid in causal model
selection."
article_number: '2307.09552'
article_processing_charge: No
arxiv: 1
author:
- first_name: Philipp M.
full_name: Faller, Philipp M.
last_name: Faller
- first_name: Leena Chennuru
full_name: Vankadara, Leena Chennuru
last_name: Vankadara
- first_name: Atalanti A.
full_name: Mastakouri, Atalanti A.
last_name: Mastakouri
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Dominik
full_name: Janzing, Dominik
last_name: Janzing
citation:
ama: 'Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility:
Evaluating causal discovery without ground truth. arXiv. doi:10.48550/arXiv.2307.09552'
apa: 'Faller, P. M., Vankadara, L. C., Mastakouri, A. A., Locatello, F., & Janzing,
D. (n.d.). Self-compatibility: Evaluating causal discovery without ground truth.
arXiv. https://doi.org/10.48550/arXiv.2307.09552'
chicago: 'Faller, Philipp M., Leena Chennuru Vankadara, Atalanti A. Mastakouri,
Francesco Locatello, and Dominik Janzing. “Self-Compatibility: Evaluating Causal
Discovery without Ground Truth.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2307.09552.'
ieee: 'P. M. Faller, L. C. Vankadara, A. A. Mastakouri, F. Locatello, and D. Janzing,
“Self-compatibility: Evaluating causal discovery without ground truth,” arXiv.
.'
ista: 'Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility:
Evaluating causal discovery without ground truth. arXiv, 2307.09552.'
mla: 'Faller, Philipp M., et al. “Self-Compatibility: Evaluating Causal Discovery
without Ground Truth.” ArXiv, 2307.09552, doi:10.48550/arXiv.2307.09552.'
short: P.M. Faller, L.C. Vankadara, A.A. Mastakouri, F. Locatello, D. Janzing, ArXiv
(n.d.).
date_created: 2023-09-13T12:44:59Z
date_published: 2023-07-18T00:00:00Z
date_updated: 2024-10-14T12:31:20Z
day: '18'
department:
- _id: FrLo
doi: 10.48550/arXiv.2307.09552
extern: '1'
external_id:
arxiv:
- '2307.09552'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2307.09552
month: '07'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: 'Self-compatibility: Evaluating causal discovery without ground truth'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14334'
abstract:
- lang: eng
text: Quantum kinetically constrained models have recently attracted significant
attention due to their anomalous dynamics and thermalization. In this work, we
introduce a hitherto unexplored family of kinetically constrained models featuring
conserved particle number and strong inversion-symmetry breaking due to facilitated
hopping. We demonstrate that these models provide a generic example of so-called
quantum Hilbert space fragmentation, that is manifested in disconnected sectors
in the Hilbert space that are not apparent in the computational basis. Quantum
Hilbert space fragmentation leads to an exponential in system size number of eigenstates
with exactly zero entanglement entropy across several bipartite cuts. These eigenstates
can be probed dynamically using quenches from simple initial product states. In
addition, we study the particle spreading under unitary dynamics launched from
the domain wall state, and find faster than diffusive dynamics at high particle
densities, that crosses over into logarithmically slow relaxation at smaller densities.
Using a classically simulable cellular automaton, we reproduce the logarithmic
dynamics observed in the quantum case. Our work suggests that particle conserving
constrained models with inversion symmetry breaking realize so far unexplored
dynamical behavior and invite their further theoretical and experimental studies.
acknowledgement: "We would like to thank Raimel A. Medina, Hansveer Singh, and Dmitry
Abanin for useful\r\ndiscussions.The authors acknowledge support by the European
Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation
program (Grant\r\nAgreement No. 850899). We acknowledge support by the Erwin Schrödinger
International\r\nInstitute for Mathematics and Physics (ESI)."
article_number: '093'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Pietro
full_name: Brighi, Pietro
id: 4115AF5C-F248-11E8-B48F-1D18A9856A87
last_name: Brighi
orcid: 0000-0002-7969-2729
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
orcid: 0000-0003-0038-7068
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Brighi P, Ljubotina M, Serbyn M. Hilbert space fragmentation and slow dynamics
in particle-conserving quantum East models. SciPost Physics. 2023;15(3).
doi:10.21468/scipostphys.15.3.093
apa: Brighi, P., Ljubotina, M., & Serbyn, M. (2023). Hilbert space fragmentation
and slow dynamics in particle-conserving quantum East models. SciPost Physics.
SciPost Foundation. https://doi.org/10.21468/scipostphys.15.3.093
chicago: Brighi, Pietro, Marko Ljubotina, and Maksym Serbyn. “Hilbert Space Fragmentation
and Slow Dynamics in Particle-Conserving Quantum East Models.” SciPost Physics.
SciPost Foundation, 2023. https://doi.org/10.21468/scipostphys.15.3.093.
ieee: P. Brighi, M. Ljubotina, and M. Serbyn, “Hilbert space fragmentation and slow
dynamics in particle-conserving quantum East models,” SciPost Physics,
vol. 15, no. 3. SciPost Foundation, 2023.
ista: Brighi P, Ljubotina M, Serbyn M. 2023. Hilbert space fragmentation and slow
dynamics in particle-conserving quantum East models. SciPost Physics. 15(3), 093.
mla: Brighi, Pietro, et al. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving
Quantum East Models.” SciPost Physics, vol. 15, no. 3, 093, SciPost Foundation,
2023, doi:10.21468/scipostphys.15.3.093.
short: P. Brighi, M. Ljubotina, M. Serbyn, SciPost Physics 15 (2023).
corr_author: '1'
date_created: 2023-09-14T13:08:23Z
date_published: 2023-09-13T00:00:00Z
date_updated: 2025-04-14T07:52:05Z
day: '13'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.21468/scipostphys.15.3.093
ec_funded: 1
external_id:
arxiv:
- '2210.15607'
file:
- access_level: open_access
checksum: 4cef6a8021f6b6c47ab2f2f2b1387ac2
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T10:46:10Z
date_updated: 2023-09-20T10:46:10Z
file_id: '14350'
file_name: 2023_SciPostPhysics_Brighi.pdf
file_size: 4866506
relation: main_file
success: 1
file_date_updated: 2023-09-20T10:46:10Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '3'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: SciPost Physics
publication_identifier:
issn:
- 2542-4653
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
related_material:
record:
- id: '12750'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Hilbert space fragmentation and slow dynamics in particle-conserving quantum
East models
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: 15
year: '2023'
...
---
_id: '14339'
abstract:
- lang: eng
text: Lateral roots are typically maintained at non-vertical angles with respect
to gravity. These gravitropic setpoint angles are intriguing because their maintenance
requires that roots are able to effect growth response both with and against the
gravity vector, a phenomenon previously attributed to gravitropism acting against
an antigravitropic offset mechanism. Here we show how the components mediating
gravitropism in the vertical primary root—PINs and phosphatases acting upon them—are
reconfigured in their regulation such that lateral root growth at a range of angles
can be maintained. We show that the ability of Arabidopsis lateral roots to bend
both downward and upward requires the generation of auxin asymmetries and is driven
by angle-dependent variation in downward gravitropic auxin flux acting against
angle-independent upward, antigravitropic flux. Further, we demonstrate a symmetry
in auxin distribution in lateral roots at gravitropic setpoint angle that can
be traced back to a net, balanced polarization of PIN3 and PIN7 auxin transporters
in the columella. These auxin fluxes are shifted by altering PIN protein phosphoregulation
in the columella, either by introducing PIN3 phosphovariant versions or via manipulation
of levels of the phosphatase subunit PP2A/RCN1. Finally, we show that auxin, in
addition to driving lateral root directional growth, acts within the lateral root
columella to induce more vertical growth by increasing RCN1 levels, causing a
downward shift in PIN3 localization, thereby diminishing the magnitude of the
upward, antigravitropic auxin flux.
acknowledgement: We thank D. Weijers, C. Schwechheimer and R. Offringa for generous
sharing of published and unpublished materials and P. Masson for advice on the use
of the ARL2 promoter. We are grateful to M. Del Bianco and O. Leyser for critical
reading of the manuscript. This work was supported by the BBSRC (grants BB/N010124/1
and BB/R000859/1 to S.K.), the Gatsby Charitable Foundation and the Leverhulme Trust
(RPG-2018-137 to S.K.).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: S
full_name: Roychoudhry, S
last_name: Roychoudhry
- first_name: K
full_name: Sageman-Furnas, K
last_name: Sageman-Furnas
- first_name: C
full_name: Wolverton, C
last_name: Wolverton
- first_name: Peter
full_name: Grones, Peter
id: 399876EC-F248-11E8-B48F-1D18A9856A87
last_name: Grones
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Gergely
full_name: Molnar, Gergely
id: 34F1AF46-F248-11E8-B48F-1D18A9856A87
last_name: Molnar
- first_name: M
full_name: De Angelis, M
last_name: De Angelis
- first_name: HL
full_name: Goodman, HL
last_name: Goodman
- first_name: N
full_name: Capstaff, N
last_name: Capstaff
- first_name: Lloyd
full_name: JPB, Lloyd
last_name: JPB
- first_name: J
full_name: Mullen, J
last_name: Mullen
- first_name: R
full_name: Hangarter, R
last_name: Hangarter
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: S
full_name: Kepinski, S
last_name: Kepinski
citation:
ama: Roychoudhry S, Sageman-Furnas K, Wolverton C, et al. Antigravitropic PIN polarization
maintains non-vertical growth in lateral roots. Nature Plants. 2023;9:1500-1513.
doi:10.1038/s41477-023-01478-x
apa: Roychoudhry, S., Sageman-Furnas, K., Wolverton, C., Grones, P., Tan, S., Molnar,
G., … Kepinski, S. (2023). Antigravitropic PIN polarization maintains non-vertical
growth in lateral roots. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-023-01478-x
chicago: Roychoudhry, S, K Sageman-Furnas, C Wolverton, Peter Grones, Shutang Tan,
Gergely Molnar, M De Angelis, et al. “Antigravitropic PIN Polarization Maintains
Non-Vertical Growth in Lateral Roots.” Nature Plants. Springer Nature,
2023. https://doi.org/10.1038/s41477-023-01478-x.
ieee: S. Roychoudhry et al., “Antigravitropic PIN polarization maintains
non-vertical growth in lateral roots,” Nature Plants, vol. 9. Springer
Nature, pp. 1500–1513, 2023.
ista: Roychoudhry S, Sageman-Furnas K, Wolverton C, Grones P, Tan S, Molnar G, De
Angelis M, Goodman H, Capstaff N, JPB L, Mullen J, Hangarter R, Friml J, Kepinski
S. 2023. Antigravitropic PIN polarization maintains non-vertical growth in lateral
roots. Nature Plants. 9, 1500–1513.
mla: Roychoudhry, S., et al. “Antigravitropic PIN Polarization Maintains Non-Vertical
Growth in Lateral Roots.” Nature Plants, vol. 9, Springer Nature, 2023,
pp. 1500–13, doi:10.1038/s41477-023-01478-x.
short: S. Roychoudhry, K. Sageman-Furnas, C. Wolverton, P. Grones, S. Tan, G. Molnar,
M. De Angelis, H. Goodman, N. Capstaff, L. JPB, J. Mullen, R. Hangarter, J. Friml,
S. Kepinski, Nature Plants 9 (2023) 1500–1513.
date_created: 2023-09-15T09:56:01Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2024-10-21T06:01:33Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41477-023-01478-x
external_id:
isi:
- '001069238800014'
pmid:
- '37666965'
file:
- access_level: open_access
checksum: 3d6d5d5abb937c14a5f6f0afba3b8624
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T10:51:31Z
date_updated: 2023-09-20T10:51:31Z
file_id: '14351'
file_name: 2023_NaturePlants_Roychoudhry.pdf
file_size: 9647103
relation: main_file
success: 1
file_date_updated: 2023-09-20T10:51:31Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1500-1513
pmid: 1
publication: Nature Plants
publication_identifier:
issn:
- 2055-0278
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Antigravitropic PIN polarization maintains non-vertical growth in lateral roots
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2023'
...
---
_id: '14341'
abstract:
- lang: eng
text: Flows through pipes and channels are, in practice, almost always turbulent,
and the multiscale eddying motion is responsible for a major part of the encountered
friction losses and pumping costs1. Conversely, for pulsatile flows, in particular
for aortic blood flow, turbulence levels remain low despite relatively large peak
velocities. For aortic blood flow, high turbulence levels are intolerable as they
would damage the shear-sensitive endothelial cell layer2,3,4,5. Here we show that
turbulence in ordinary pipe flow is diminished if the flow is driven in a pulsatile
mode that incorporates all the key features of the cardiac waveform. At Reynolds
numbers comparable to those of aortic blood flow, turbulence is largely inhibited,
whereas at much higher speeds, the turbulent drag is reduced by more than 25%.
This specific operation mode is more efficient when compared with steady driving,
which is the present situation for virtually all fluid transport processes ranging
from heating circuits to water, gas and oil pipelines.
acknowledged_ssus:
- _id: M-Shop
- _id: ScienComp
acknowledgement: We acknowledge the assistance of the Miba machine shop and the team
of the ISTA-HPC cluster. We thank M. Quadrio for the discussions. The work was supported
by the Simons Foundation (grant no. 662960) and by the Austrian Science Fund (grant
no. I4188-N30), within Deutsche Forschungsgemeinschaft research unit FOR 2688.
article_processing_charge: No
article_type: original
author:
- first_name: Davide
full_name: Scarselli, Davide
id: 40315C30-F248-11E8-B48F-1D18A9856A87
last_name: Scarselli
orcid: 0000-0001-5227-4271
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Scarselli D, Lopez Alonso JM, Varshney A, Hof B. Turbulence suppression by
cardiac-cycle-inspired driving of pipe flow. Nature. 2023;621(7977):71-74.
doi:10.1038/s41586-023-06399-5
apa: Scarselli, D., Lopez Alonso, J. M., Varshney, A., & Hof, B. (2023). Turbulence
suppression by cardiac-cycle-inspired driving of pipe flow. Nature. Springer
Nature. https://doi.org/10.1038/s41586-023-06399-5
chicago: Scarselli, Davide, Jose M Lopez Alonso, Atul Varshney, and Björn Hof. “Turbulence
Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” Nature. Springer
Nature, 2023. https://doi.org/10.1038/s41586-023-06399-5.
ieee: D. Scarselli, J. M. Lopez Alonso, A. Varshney, and B. Hof, “Turbulence suppression
by cardiac-cycle-inspired driving of pipe flow,” Nature, vol. 621, no.
7977. Springer Nature, pp. 71–74, 2023.
ista: Scarselli D, Lopez Alonso JM, Varshney A, Hof B. 2023. Turbulence suppression
by cardiac-cycle-inspired driving of pipe flow. Nature. 621(7977), 71–74.
mla: Scarselli, Davide, et al. “Turbulence Suppression by Cardiac-Cycle-Inspired
Driving of Pipe Flow.” Nature, vol. 621, no. 7977, Springer Nature, 2023,
pp. 71–74, doi:10.1038/s41586-023-06399-5.
short: D. Scarselli, J.M. Lopez Alonso, A. Varshney, B. Hof, Nature 621 (2023) 71–74.
corr_author: '1'
date_created: 2023-09-17T22:01:09Z
date_published: 2023-09-07T00:00:00Z
date_updated: 2025-09-09T12:59:04Z
day: '07'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1038/s41586-023-06399-5
external_id:
isi:
- '001168947700009'
pmid:
- '37673988'
file:
- access_level: open_access
checksum: 9c9f172ba0a9a301d76fff4229812464
content_type: application/pdf
creator: dernst
date_created: 2024-06-04T09:24:34Z
date_updated: 2024-06-04T09:24:34Z
file_id: '17118'
file_name: 2023_submittedversion.pdf
file_size: 3247252
relation: main_file
success: 1
file_date_updated: 2024-06-04T09:24:34Z
has_accepted_license: '1'
intvolume: ' 621'
isi: 1
issue: '7977'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 71-74
pmid: 1
project:
- _id: 238598C6-32DE-11EA-91FC-C7463DDC885E
grant_number: '662960'
name: Revisiting the Turbulence Problem Using Statistical Mechanics
- _id: 238B8092-32DE-11EA-91FC-C7463DDC885E
call_identifier: FWF
grant_number: I04188
name: Instabilities in pulsating pipe flow in complex fluids
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://www.ista.ac.at/en/news/pumping-like-the-heart/
scopus_import: '1'
status: public
title: Turbulence suppression by cardiac-cycle-inspired driving of pipe flow
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 621
year: '2023'
...
---
_id: '14342'
abstract:
- lang: eng
text: We propose a simple method to measure nonlinear Kerr refractive index in mid-infrared
frequency range that avoids using sophisticated infrared detectors. Our approach
is based on using a near-infrared probe beam which interacts with a mid-IR beam
via wavelength-non-degenerate cross-phase modulation (XPM). By carefully measuring
XPM-induced spectral modifications in the probe beam and comparing the experimental
data with simulation results, we extract the value for the non-degenerate Kerr
index. Finally, in order to obtain the value of degenerate mid-IR Kerr index,
we use the well-established two-band formalism of Sheik-Bahae et al., which is
shown to become particularly simple in the limit of low frequencies. The proposed
technique is complementary to the conventional techniques, such as z-scan, and
has the advantage of not requiring any mid-infrared detectors.
acknowledgement: The work was supported by IST Austria. The authors would like to
gratefully acknowledge the help and assistance of Professor John M. Dudley.
article_number: '091104'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Dusan
full_name: Lorenc, Dusan
id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87
last_name: Lorenc
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
citation:
ama: Lorenc D, Alpichshev Z. Mid-infrared Kerr index evaluation via cross-phase
modulation with a near-infrared probe beam. Applied Physics Letters. 2023;123(9).
doi:10.1063/5.0161713
apa: Lorenc, D., & Alpichshev, Z. (2023). Mid-infrared Kerr index evaluation
via cross-phase modulation with a near-infrared probe beam. Applied Physics
Letters. AIP Publishing. https://doi.org/10.1063/5.0161713
chicago: Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation
via Cross-Phase Modulation with a near-Infrared Probe Beam.” Applied Physics
Letters. AIP Publishing, 2023. https://doi.org/10.1063/5.0161713.
ieee: D. Lorenc and Z. Alpichshev, “Mid-infrared Kerr index evaluation via cross-phase
modulation with a near-infrared probe beam,” Applied Physics Letters, vol.
123, no. 9. AIP Publishing, 2023.
ista: Lorenc D, Alpichshev Z. 2023. Mid-infrared Kerr index evaluation via cross-phase
modulation with a near-infrared probe beam. Applied Physics Letters. 123(9), 091104.
mla: Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation
via Cross-Phase Modulation with a near-Infrared Probe Beam.” Applied Physics
Letters, vol. 123, no. 9, 091104, AIP Publishing, 2023, doi:10.1063/5.0161713.
short: D. Lorenc, Z. Alpichshev, Applied Physics Letters 123 (2023).
corr_author: '1'
date_created: 2023-09-17T22:01:09Z
date_published: 2023-08-28T00:00:00Z
date_updated: 2025-09-09T12:58:23Z
day: '28'
ddc:
- '530'
department:
- _id: ZhAl
doi: 10.1063/5.0161713
external_id:
arxiv:
- '2306.09043'
isi:
- '001145465400004'
file:
- access_level: open_access
checksum: 89a1b604d58b209fec66c6b6f919ac98
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T11:36:16Z
date_updated: 2023-09-20T11:36:16Z
file_id: '14353'
file_name: 2023_ApplPhysLetter_Lorenc.pdf
file_size: 1486715
relation: main_file
success: 1
file_date_updated: 2023-09-20T11:36:16Z
has_accepted_license: '1'
intvolume: ' 123'
isi: 1
issue: '9'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Applied Physics Letters
publication_identifier:
issn:
- 0003-6951
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared
probe beam
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 123
year: '2023'
...
---
_id: '14344'
abstract:
- lang: eng
text: We study the Hamilton cycle problem with input a random graph G ~ G(n,p) in
two different settings. In the first one, G is given to us in the form of randomly
ordered adjacency lists while in the second one, we are given the adjacency matrix
of G. In each of the two settings we derive a deterministic algorithm that w.h.p.
either finds a Hamilton cycle or returns a certificate that such a cycle does
not exist for p = p(n) ≥ 0. The running times of our algorithms are O(n) and respectively,
each being best possible in its own setting.
article_processing_charge: No
arxiv: 1
author:
- first_name: Michael
full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
citation:
ama: 'Anastos M. Fast algorithms for solving the Hamilton cycle problem with high
probability. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms.
Vol 2023. Society for Industrial and Applied Mathematics; 2023:2286-2323. doi:10.1137/1.9781611977554.ch88'
apa: 'Anastos, M. (2023). Fast algorithms for solving the Hamilton cycle problem
with high probability. In Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms (Vol. 2023, pp. 2286–2323). Florence, Italy: Society for Industrial
and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch88'
chicago: Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem
with High Probability.” In Proceedings of the Annual ACM-SIAM Symposium on
Discrete Algorithms, 2023:2286–2323. Society for Industrial and Applied Mathematics,
2023. https://doi.org/10.1137/1.9781611977554.ch88.
ieee: M. Anastos, “Fast algorithms for solving the Hamilton cycle problem with high
probability,” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms,
Florence, Italy, 2023, vol. 2023, pp. 2286–2323.
ista: 'Anastos M. 2023. Fast algorithms for solving the Hamilton cycle problem with
high probability. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms.
SODA: Symposium on Discrete Algorithms vol. 2023, 2286–2323.'
mla: Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with
High Probability.” Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms, vol. 2023, Society for Industrial and Applied Mathematics, 2023,
pp. 2286–323, doi:10.1137/1.9781611977554.ch88.
short: M. Anastos, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 2286–2323.
conference:
end_date: 2023-01-25
location: Florence, Italy
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2023-01-22
corr_author: '1'
date_created: 2023-09-17T22:01:10Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2024-10-09T21:07:01Z
day: '01'
department:
- _id: MaKw
doi: 10.1137/1.9781611977554.ch88
external_id:
arxiv:
- '2111.14759'
intvolume: ' 2023'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2111.14759
month: '01'
oa: 1
oa_version: Preprint
page: 2286-2323
publication: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
isbn:
- '9781611977554'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast algorithms for solving the Hamilton cycle problem with high probability
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2023
year: '2023'
...
---
_id: '14361'
abstract:
- lang: eng
text: Whether one considers swarming insects, flocking birds, or bacterial colonies,
collective motion arises from the coordination of individuals and entails the
adjustment of their respective velocities. In particular, in close confinements,
such as those encountered by dense cell populations during development or regeneration,
collective migration can only arise coordinately. Yet, how individuals unify their
velocities is often not understood. Focusing on a finite number of cells in circular
confinements, we identify waves of polymerizing actin that function as a pacemaker
governing the speed of individual cells. We show that the onset of collective
motion coincides with the synchronization of the wave nucleation frequencies across
the population. Employing a simpler and more readily accessible mechanical model
system of active spheres, we identify the synchronization of the individuals’
internal oscillators as one of the essential requirements to reach the corresponding
collective state. The mechanical ‘toy’ experiment illustrates that the global
synchronous state is achieved by nearest neighbor coupling. We suggest by analogy
that local coupling and the synchronization of actin waves are essential for the
emergent, self-organized motion of cell collectives.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: M-Shop
acknowledgement: We thank K. O’Keeffe, E. Hannezo, P. Devreotes, C. Dessalles, and
E. Martens for discussion and/or critical reading of the manuscript; the Bioimaging
Facility of ISTA for excellent support, as well as the Life Science Facility and
the Miba Machine Shop of ISTA. This work was supported by the European Research
Council (ERC StG 281556 and CoG 724373) to M.S.
article_number: '5633'
article_processing_charge: Yes
article_type: original
author:
- first_name: Michael
full_name: Riedl, Michael
id: 3BE60946-F248-11E8-B48F-1D18A9856A87
last_name: Riedl
orcid: 0000-0003-4844-6311
- first_name: Isabelle D
full_name: Mayer, Isabelle D
id: 61763940-15b2-11ec-abd3-cfaddfbc66b4
last_name: Mayer
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. Synchronization in collectively
moving inanimate and living active matter. Nature Communications. 2023;14.
doi:10.1038/s41467-023-41432-1
apa: Riedl, M., Mayer, I. D., Merrin, J., Sixt, M. K., & Hof, B. (2023). Synchronization
in collectively moving inanimate and living active matter. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-023-41432-1
chicago: Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn
Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.”
Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41432-1.
ieee: M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization
in collectively moving inanimate and living active matter,” Nature Communications,
vol. 14. Springer Nature, 2023.
ista: Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. 2023. Synchronization in collectively
moving inanimate and living active matter. Nature Communications. 14, 5633.
mla: Riedl, Michael, et al. “Synchronization in Collectively Moving Inanimate and
Living Active Matter.” Nature Communications, vol. 14, 5633, Springer Nature,
2023, doi:10.1038/s41467-023-41432-1.
short: M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications
14 (2023).
corr_author: '1'
date_created: 2023-09-24T22:01:10Z
date_published: 2023-09-13T00:00:00Z
date_updated: 2025-04-14T13:10:03Z
day: '13'
ddc:
- '530'
- '570'
department:
- _id: MiSi
- _id: NanoFab
- _id: BjHo
doi: 10.1038/s41467-023-41432-1
ec_funded: 1
external_id:
isi:
- '001087583700030'
pmid:
- '37704595'
file:
- access_level: open_access
checksum: 82d2d4ad736cc8493db8ce45cd313f7b
content_type: application/pdf
creator: dernst
date_created: 2023-09-25T08:32:37Z
date_updated: 2023-09-25T08:32:37Z
file_id: '14366'
file_name: 2023_NatureComm_Riedl.pdf
file_size: 2317272
relation: main_file
success: 1
file_date_updated: 2023-09-25T08:32:37Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular Navigation Along Spatial Gradients
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synchronization in collectively moving inanimate and living 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: 14
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
arxiv: 1
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).
corr_author: '1'
date_created: 2023-09-24T22:01:11Z
date_published: 2023-10-25T00:00:00Z
date_updated: 2024-10-09T21:07:00Z
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: '14363'
abstract:
- lang: eng
text: Mitochondrial networks remodel their connectivity, content, and subcellular
localization to support optimized energy production in conditions of increased
environmental or cellular stress. Microglia rely on mitochondria to respond to
these stressors, however our knowledge about mitochondrial networks and their
adaptations in microglia in vivo is limited. Here, we generate a mouse model that
selectively labels mitochondria in microglia. We identify that mitochondrial networks
are more fragmented with increased content and perinuclear localization in vitro
vs. in vivo. Mitochondrial networks adapt similarly in microglia closest to the
injury site after optic nerve crush. Preventing microglial UCP2 increase after
injury by selective knockout induces cellular stress. This results in mitochondrial
hyperfusion in male microglia, a phenotype absent in females due to circulating
estrogens. Our results establish the foundation for mitochondrial network analysis
of microglia in vivo, emphasizing the importance of mitochondrial-based sex effects
of microglia in other pathologies.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
acknowledgement: We thank the Scientific Service Units (SSU) of ISTA through resources
provided by the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF),
and the Pre-Clinical Facility (PCF) team, specifically Sonja Haslinger and Michael
Schunn for excellent mouse colony management and support. This research was supported
by the FWF Sonderforschungsbereich F83 (to E.E.P). We thank Bálint Nagy, Ryan John
A. Cubero, Marco Benevento and all members of the Siegert group for constant feedback
on the project and article.
article_number: '107780'
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: Gloria
full_name: Colombo, Gloria
id: 3483CF6C-F248-11E8-B48F-1D18A9856A87
last_name: Colombo
orcid: 0000-0001-9434-8902
- first_name: Florianne E
full_name: Schoot Uiterkamp, Florianne E
id: 3526230C-F248-11E8-B48F-1D18A9856A87
last_name: Schoot Uiterkamp
- first_name: Felix
full_name: Sternberg, Felix
last_name: Sternberg
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Elena E.
full_name: Pohl, Elena E.
last_name: Pohl
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Maes ME, Colombo G, Schoot Uiterkamp FE, et al. Mitochondrial network adaptations
of microglia reveal sex-specific stress response after injury and UCP2 knockout.
iScience. 2023;26(10). doi:10.1016/j.isci.2023.107780
apa: Maes, M. E., Colombo, G., Schoot Uiterkamp, F. E., Sternberg, F., Venturino,
A., Pohl, E. E., & Siegert, S. (2023). Mitochondrial network adaptations of
microglia reveal sex-specific stress response after injury and UCP2 knockout.
IScience. Elsevier. https://doi.org/10.1016/j.isci.2023.107780
chicago: Maes, Margaret E, Gloria Colombo, Florianne E Schoot Uiterkamp, Felix Sternberg,
Alessandro Venturino, Elena E. Pohl, and Sandra Siegert. “Mitochondrial Network
Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and
UCP2 Knockout.” IScience. Elsevier, 2023. https://doi.org/10.1016/j.isci.2023.107780.
ieee: M. E. Maes et al., “Mitochondrial network adaptations of microglia
reveal sex-specific stress response after injury and UCP2 knockout,” iScience,
vol. 26, no. 10. Elsevier, 2023.
ista: Maes ME, Colombo G, Schoot Uiterkamp FE, Sternberg F, Venturino A, Pohl EE,
Siegert S. 2023. Mitochondrial network adaptations of microglia reveal sex-specific
stress response after injury and UCP2 knockout. iScience. 26(10), 107780.
mla: Maes, Margaret E., et al. “Mitochondrial Network Adaptations of Microglia Reveal
Sex-Specific Stress Response after Injury and UCP2 Knockout.” IScience,
vol. 26, no. 10, 107780, Elsevier, 2023, doi:10.1016/j.isci.2023.107780.
short: M.E. Maes, G. Colombo, F.E. Schoot Uiterkamp, F. Sternberg, A. Venturino,
E.E. Pohl, S. Siegert, IScience 26 (2023).
corr_author: '1'
date_created: 2023-09-24T22:01:11Z
date_published: 2023-10-20T00:00:00Z
date_updated: 2024-10-09T21:07:01Z
day: '20'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1016/j.isci.2023.107780
external_id:
isi:
- '001080403500001'
pmid:
- '37731609'
file:
- access_level: open_access
checksum: be1a560efdd96d20712311f4fc54aac2
content_type: application/pdf
creator: dernst
date_created: 2023-11-07T08:53:21Z
date_updated: 2023-11-07T08:53:21Z
file_id: '14497'
file_name: 2023_iScience_Maes.pdf
file_size: 8197935
relation: main_file
success: 1
file_date_updated: 2023-11-07T08:53:21Z
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: iScience
publication_identifier:
eissn:
- 2589-0042
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mitochondrial network adaptations of microglia reveal sex-specific stress response
after injury and UCP2 knockout
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: 26
year: '2023'
...
---
_id: '14364'
abstract:
- lang: eng
text: We introduce extension-based proofs, a class of impossibility proofs that
includes valency arguments. They are modelled as an interaction between a prover
and a protocol. Using proofs based on combinatorial topology, it has been shown
that it is impossible to deterministically solve -set agreement among processes
or approximate agreement on a cycle of length 4 among processes in a wait-free
manner in asynchronous models where processes communicate using objects that can
be constructed from shared registers. However, it was unknown whether proofs based
on simpler techniques were possible. We show that these impossibility results
cannot be obtained by extension-based proofs in the iterated snapshot model and,
hence, extension-based proofs are limited in power.
acknowledgement: "We would like to thank Valerie King, Toniann Pitassi, and Michael
Saks for helpful discussions and Shi Hao Liu for his useful feedback.\r\nThis research
was supported by the Natural Science and Engineering Research Council of Canada
under grants RGPIN-2015-05080 and RGPIN-2020-04178, a postgraduate scholarship,
and a postdoctoral fellowship; a University of Toronto postdoctoral fellowship;
the National Science Foundation under grants CCF-1217921, CCF-1301926, CCF-1637385,
CCF-1650596, and IIS-1447786; the U.S. Department of Energy under grant ER26116/DE-SC0008923;
the European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation programme grant agreement 805223 ScaleML; and the Oracle and Intel
corporations. Some of the work on this paper was done while Faith Ellen was visiting
IST Austria."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: Faith
full_name: Ellen, Faith
last_name: Ellen
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Leqi
full_name: Zhu, Leqi
id: a2117c59-cee4-11ed-b9d0-874ecf0f8ac5
last_name: Zhu
citation:
ama: Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based proofs
fail. SIAM Journal on Computing. 2023;52(4):913-944. doi:10.1137/20M1375851
apa: Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2023).
Why extension-based proofs fail. SIAM Journal on Computing. Society for
Industrial and Applied Mathematics. https://doi.org/10.1137/20M1375851
chicago: Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi
Zhu. “Why Extension-Based Proofs Fail.” SIAM Journal on Computing. Society
for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/20M1375851.
ieee: D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based
proofs fail,” SIAM Journal on Computing, vol. 52, no. 4. Society for Industrial
and Applied Mathematics, pp. 913–944, 2023.
ista: Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2023. Why extension-based
proofs fail. SIAM Journal on Computing. 52(4), 913–944.
mla: Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” SIAM Journal
on Computing, vol. 52, no. 4, Society for Industrial and Applied Mathematics,
2023, pp. 913–44, doi:10.1137/20M1375851.
short: D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, SIAM Journal
on Computing 52 (2023) 913–944.
date_created: 2023-09-24T22:01:11Z
date_published: 2023-07-25T00:00:00Z
date_updated: 2025-05-14T11:26:06Z
day: '25'
department:
- _id: DaAl
doi: 10.1137/20M1375851
ec_funded: 1
external_id:
arxiv:
- '1811.01421'
isi:
- '001082972300004'
intvolume: ' 52'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1811.01421
month: '07'
oa: 1
oa_version: Preprint
page: 913-944
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: SIAM Journal on Computing
publication_identifier:
eissn:
- 1095-7111
issn:
- 0097-5397
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
related_material:
record:
- id: '6676'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Why extension-based proofs fail
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2023'
...
---
_id: '14368'
abstract:
- lang: eng
text: "Purpose: \r\nBiallelic variants in TARS2, encoding the mitochondrial threonyl-tRNA-synthetase,
have been reported in a small group of individuals displaying a neurodevelopmental
phenotype but with limited neuroradiological data and insufficient evidence for
causality of the variants.\r\nMethods:\r\nExome or genome sequencing was carried
out in 15 families. Clinical and neuroradiological evaluation was performed for
all affected individuals, including review of 10 previously reported individuals.
The pathogenicity of TARS2 variants was evaluated using in vitro assays and a
zebrafish model.\r\nResults:\r\nWe report 18 new individuals harboring biallelic
TARS2 variants. Phenotypically, these individuals show developmental delay/intellectual
disability, regression, cerebellar and cerebral atrophy, basal ganglia signal
alterations, hypotonia, cerebellar signs, and increased blood lactate. In vitro
studies showed that variants within the TARS2301-381 region had decreased binding
to Rag GTPases, likely impairing mTORC1 activity. The zebrafish model recapitulated
key features of the human phenotype and unraveled dysregulation of downstream
targets of mTORC1 signaling. Functional testing of the variants confirmed the
pathogenicity in a zebrafish model.\r\nConclusion:\r\nWe define the clinico-radiological
spectrum of TARS2-related mitochondrial disease, unveil the likely involvement
of the mTORC1 signaling pathway as a distinct molecular mechanism, and establish
a TARS2 zebrafish model as an important tool to study variant pathogenicity."
article_number: '100938'
article_processing_charge: No
article_type: original
author:
- first_name: Andrea
full_name: Accogli, Andrea
last_name: Accogli
- first_name: Sheng-Jia
full_name: Lin, Sheng-Jia
last_name: Lin
- first_name: Mariasavina
full_name: Severino, Mariasavina
last_name: Severino
- first_name: Sung-Hoon
full_name: Kim, Sung-Hoon
last_name: Kim
- first_name: Kevin
full_name: Huang, Kevin
id: 3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3
last_name: Huang
orcid: 0000-0002-2512-7812
- first_name: Clarissa
full_name: Rocca, Clarissa
last_name: Rocca
- first_name: Megan
full_name: Landsverk, Megan
last_name: Landsverk
- first_name: Maha S.
full_name: Zaki, Maha S.
last_name: Zaki
- first_name: Almundher
full_name: Al-Maawali, Almundher
last_name: Al-Maawali
- first_name: Varunvenkat M.
full_name: Srinivasan, Varunvenkat M.
last_name: Srinivasan
- first_name: Khalid
full_name: Al-Thihli, Khalid
last_name: Al-Thihli
- first_name: G. Bradly
full_name: Schaefer, G. Bradly
last_name: Schaefer
- first_name: Monica
full_name: Davis, Monica
last_name: Davis
- first_name: Davide
full_name: Tonduti, Davide
last_name: Tonduti
- first_name: Chiara
full_name: Doneda, Chiara
last_name: Doneda
- first_name: Lara M.
full_name: Marten, Lara M.
last_name: Marten
- first_name: Chris
full_name: Mühlhausen, Chris
last_name: Mühlhausen
- first_name: Maria
full_name: Gomez, Maria
last_name: Gomez
- first_name: Eleonora
full_name: Lamantea, Eleonora
last_name: Lamantea
- first_name: Rafael
full_name: Mena, Rafael
last_name: Mena
- first_name: Mathilde
full_name: Nizon, Mathilde
last_name: Nizon
- first_name: Vincent
full_name: Procaccio, Vincent
last_name: Procaccio
- first_name: Amber
full_name: Begtrup, Amber
last_name: Begtrup
- first_name: Aida
full_name: Telegrafi, Aida
last_name: Telegrafi
- first_name: Hong
full_name: Cui, Hong
last_name: Cui
- first_name: Heidi L.
full_name: Schulz, Heidi L.
last_name: Schulz
- first_name: Julia
full_name: Mohr, Julia
last_name: Mohr
- first_name: Saskia
full_name: Biskup, Saskia
last_name: Biskup
- first_name: Mariana Amina
full_name: Loos, Mariana Amina
last_name: Loos
- first_name: Hilda Verónica
full_name: Aráoz, Hilda Verónica
last_name: Aráoz
- first_name: Vincenzo
full_name: Salpietro, Vincenzo
last_name: Salpietro
- first_name: Laura Davis
full_name: Keppen, Laura Davis
last_name: Keppen
- first_name: Manali
full_name: Chitre, Manali
last_name: Chitre
- first_name: Cassidy
full_name: Petree, Cassidy
last_name: Petree
- first_name: Lucy
full_name: Raymond, Lucy
last_name: Raymond
- first_name: Julie
full_name: Vogt, Julie
last_name: Vogt
- first_name: Lindsey B.
full_name: Sawyer, Lindsey B.
last_name: Sawyer
- first_name: Alice A.
full_name: Basinger, Alice A.
last_name: Basinger
- first_name: Signe Vandal
full_name: Pedersen, Signe Vandal
last_name: Pedersen
- first_name: Toni S.
full_name: Pearson, Toni S.
last_name: Pearson
- first_name: Dorothy K.
full_name: Grange, Dorothy K.
last_name: Grange
- first_name: Lokesh
full_name: Lingappa, Lokesh
last_name: Lingappa
- first_name: Paige
full_name: McDunnah, Paige
last_name: McDunnah
- first_name: Rita
full_name: Horvath, Rita
last_name: Horvath
- first_name: Benjamin
full_name: Cognè, Benjamin
last_name: Cognè
- first_name: Bertrand
full_name: Isidor, Bertrand
last_name: Isidor
- first_name: Andreas
full_name: Hahn, Andreas
last_name: Hahn
- first_name: Karen W.
full_name: Gripp, Karen W.
last_name: Gripp
- first_name: Seyed Mehdi
full_name: Jafarnejad, Seyed Mehdi
last_name: Jafarnejad
- first_name: Elsebet
full_name: Østergaard, Elsebet
last_name: Østergaard
- first_name: Carlos E.
full_name: Prada, Carlos E.
last_name: Prada
- first_name: Daniele
full_name: Ghezzi, Daniele
last_name: Ghezzi
- first_name: Vykuntaraju K.
full_name: Gowda, Vykuntaraju K.
last_name: Gowda
- first_name: Robert W.
full_name: Taylor, Robert W.
last_name: Taylor
- first_name: Nahum
full_name: Sonenberg, Nahum
last_name: Sonenberg
- first_name: Henry
full_name: Houlden, Henry
last_name: Houlden
- first_name: Marie
full_name: Sissler, Marie
last_name: Sissler
- first_name: Gaurav K.
full_name: Varshney, Gaurav K.
last_name: Varshney
- first_name: Reza
full_name: Maroofian, Reza
last_name: Maroofian
citation:
ama: Accogli A, Lin S-J, Severino M, et al. Clinical, neuroradiological, and molecular
characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder.
Genetics in Medicine. 2023;25(11). doi:10.1016/j.gim.2023.100938
apa: Accogli, A., Lin, S.-J., Severino, M., Kim, S.-H., Huang, K., Rocca, C., …
Maroofian, R. (2023). Clinical, neuroradiological, and molecular characterization
of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. Genetics
in Medicine. Elsevier. https://doi.org/10.1016/j.gim.2023.100938
chicago: Accogli, Andrea, Sheng-Jia Lin, Mariasavina Severino, Sung-Hoon Kim, Kevin
Huang, Clarissa Rocca, Megan Landsverk, et al. “Clinical, Neuroradiological, and
Molecular Characterization of Mitochondrial Threonyl-TRNA-Synthetase (TARS2)-Related
Disorder.” Genetics in Medicine. Elsevier, 2023. https://doi.org/10.1016/j.gim.2023.100938.
ieee: A. Accogli et al., “Clinical, neuroradiological, and molecular characterization
of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder,” Genetics
in Medicine, vol. 25, no. 11. Elsevier, 2023.
ista: Accogli A, Lin S-J, Severino M, Kim S-H, Huang K, Rocca C, Landsverk M, Zaki
MS, Al-Maawali A, Srinivasan VM, Al-Thihli K, Schaefer GB, Davis M, Tonduti D,
Doneda C, Marten LM, Mühlhausen C, Gomez M, Lamantea E, Mena R, Nizon M, Procaccio
V, Begtrup A, Telegrafi A, Cui H, Schulz HL, Mohr J, Biskup S, Loos MA, Aráoz
HV, Salpietro V, Keppen LD, Chitre M, Petree C, Raymond L, Vogt J, Sawyer LB,
Basinger AA, Pedersen SV, Pearson TS, Grange DK, Lingappa L, McDunnah P, Horvath
R, Cognè B, Isidor B, Hahn A, Gripp KW, Jafarnejad SM, Østergaard E, Prada CE,
Ghezzi D, Gowda VK, Taylor RW, Sonenberg N, Houlden H, Sissler M, Varshney GK,
Maroofian R. 2023. Clinical, neuroradiological, and molecular characterization
of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. Genetics in
Medicine. 25(11), 100938.
mla: Accogli, Andrea, et al. “Clinical, Neuroradiological, and Molecular Characterization
of Mitochondrial Threonyl-TRNA-Synthetase (TARS2)-Related Disorder.” Genetics
in Medicine, vol. 25, no. 11, 100938, Elsevier, 2023, doi:10.1016/j.gim.2023.100938.
short: A. Accogli, S.-J. Lin, M. Severino, S.-H. Kim, K. Huang, C. Rocca, M. Landsverk,
M.S. Zaki, A. Al-Maawali, V.M. Srinivasan, K. Al-Thihli, G.B. Schaefer, M. Davis,
D. Tonduti, C. Doneda, L.M. Marten, C. Mühlhausen, M. Gomez, E. Lamantea, R. Mena,
M. Nizon, V. Procaccio, A. Begtrup, A. Telegrafi, H. Cui, H.L. Schulz, J. Mohr,
S. Biskup, M.A. Loos, H.V. Aráoz, V. Salpietro, L.D. Keppen, M. Chitre, C. Petree,
L. Raymond, J. Vogt, L.B. Sawyer, A.A. Basinger, S.V. Pedersen, T.S. Pearson,
D.K. Grange, L. Lingappa, P. McDunnah, R. Horvath, B. Cognè, B. Isidor, A. Hahn,
K.W. Gripp, S.M. Jafarnejad, E. Østergaard, C.E. Prada, D. Ghezzi, V.K. Gowda,
R.W. Taylor, N. Sonenberg, H. Houlden, M. Sissler, G.K. Varshney, R. Maroofian,
Genetics in Medicine 25 (2023).
date_created: 2023-09-25T08:44:29Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2023-09-25T08:50:10Z
day: '01'
ddc:
- '570'
doi: 10.1016/j.gim.2023.100938
extern: '1'
file:
- access_level: open_access
checksum: 440f0cd8a2ffcbe03c015c1746728387
content_type: application/pdf
creator: dernst
date_created: 2023-09-25T08:48:54Z
date_updated: 2023-09-25T08:48:54Z
file_id: '14369'
file_name: 2023_GeneticsMedicine_Accogli.pdf
file_size: 4105513
relation: main_file
success: 1
file_date_updated: 2023-09-25T08:48:54Z
has_accepted_license: '1'
intvolume: ' 25'
issue: '11'
keyword:
- Genetics (clinical)
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Genetics in Medicine
publication_identifier:
issn:
- 1098-3600
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Clinical, neuroradiological, and molecular characterization of mitochondrial
threonyl-tRNA-synthetase (TARS2)-related disorder
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'
...