---
_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
license: https://creativecommons.org/licenses/by/4.0/
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'
...
---
_id: '14377'
abstract:
- lang: eng
text: Coherent flows of self-propelled particles are characterized by vortices and
jets that sustain chaotic flows, referred to as active turbulence. Here, we reveal
a crossover between defect-free active turbulence and active turbulence laden
with topological defects. Interestingly, we show that concurrent to the crossover
from defect-free to defect-laden active turbulence is the restoration of the previously
broken SO(2) symmetry signaled by the fast decay of the two-point correlations.
By stability analyses of the topological charge density field, we provide theoretical
insights on the criterion for the crossover to the defect-laden active turbulent
state. Despite the distinct symmetry features between these two active turbulence
regimes, the flow fluctuations exhibit universal statistical scaling behaviors
at large scales, while the spectrum of polarity fluctuations decays exponentially
at small length scales compared to the active energy injection length. These findings
reveal a dynamical crossover between distinct spatiotemporal organization patterns
in polar active matter.
article_number: '063101'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Benjamin H.
full_name: Andersen, Benjamin H.
last_name: Andersen
- first_name: Julian B
full_name: Renaud, Julian B
id: 7af6767d-14eb-11ed-b536-a32449ae867c
last_name: Renaud
- first_name: Jonas
full_name: Rønning, Jonas
last_name: Rønning
- first_name: Luiza
full_name: Angheluta, Luiza
last_name: Angheluta
- first_name: Amin
full_name: Doostmohammadi, Amin
last_name: Doostmohammadi
citation:
ama: Andersen BH, Renaud JB, Rønning J, Angheluta L, Doostmohammadi A. Symmetry-restoring
crossover from defect-free to defect-laden turbulence in polar active matter.
Physical Review Fluids. 2023;8(6). doi:10.1103/physrevfluids.8.063101
apa: Andersen, B. H., Renaud, J. B., Rønning, J., Angheluta, L., & Doostmohammadi,
A. (2023). Symmetry-restoring crossover from defect-free to defect-laden turbulence
in polar active matter. Physical Review Fluids. American Physical Society.
https://doi.org/10.1103/physrevfluids.8.063101
chicago: Andersen, Benjamin H., Julian B Renaud, Jonas Rønning, Luiza Angheluta,
and Amin Doostmohammadi. “Symmetry-Restoring Crossover from Defect-Free to Defect-Laden
Turbulence in Polar Active Matter.” Physical Review Fluids. American Physical
Society, 2023. https://doi.org/10.1103/physrevfluids.8.063101.
ieee: B. H. Andersen, J. B. Renaud, J. Rønning, L. Angheluta, and A. Doostmohammadi,
“Symmetry-restoring crossover from defect-free to defect-laden turbulence in polar
active matter,” Physical Review Fluids, vol. 8, no. 6. American Physical
Society, 2023.
ista: Andersen BH, Renaud JB, Rønning J, Angheluta L, Doostmohammadi A. 2023. Symmetry-restoring
crossover from defect-free to defect-laden turbulence in polar active matter.
Physical Review Fluids. 8(6), 063101.
mla: Andersen, Benjamin H., et al. “Symmetry-Restoring Crossover from Defect-Free
to Defect-Laden Turbulence in Polar Active Matter.” Physical Review Fluids,
vol. 8, no. 6, 063101, American Physical Society, 2023, doi:10.1103/physrevfluids.8.063101.
short: B.H. Andersen, J.B. Renaud, J. Rønning, L. Angheluta, A. Doostmohammadi,
Physical Review Fluids 8 (2023).
date_created: 2023-09-29T08:46:47Z
date_published: 2023-06-14T00:00:00Z
date_updated: 2023-10-03T07:25:39Z
day: '14'
doi: 10.1103/physrevfluids.8.063101
extern: '1'
external_id:
arxiv:
- '2209.10916'
intvolume: ' 8'
issue: '6'
keyword:
- Fluid Flow and Transfer Processes
- Modeling and Simulation
- Computational Mechanics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2209.10916
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review Fluids
publication_identifier:
issn:
- 2469-990X
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Symmetry-restoring crossover from defect-free to defect-laden turbulence in
polar active matter
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2023'
...
---
_id: '14378'
abstract:
- lang: eng
text: 'Branching morphogenesis is a ubiquitous process that gives rise to high exchange
surfaces in the vasculature and epithelial organs. Lymphatic capillaries form
branched networks, which play a key role in the circulation of tissue fluid and
immune cells. Although mouse models and correlative patient data indicate that
the lymphatic capillary density directly correlates with functional output, i.e.,
tissue fluid drainage and trafficking efficiency of dendritic cells, the mechanisms
ensuring efficient tissue coverage remain poorly understood. Here, we use the
mouse ear pinna lymphatic vessel network as a model system and combine lineage-tracing,
genetic perturbations, whole-organ reconstructions and theoretical modeling to
show that the dermal lymphatic capillaries tile space in an optimal, space-filling
manner. This coverage is achieved by two complementary mechanisms: initial tissue
invasion provides a non-optimal global scaffold via self-organized branching morphogenesis,
while VEGF-C dependent side-branching from existing capillaries rapidly optimizes
local coverage by directionally targeting low-density regions. With these two
ingredients, we show that a minimal biophysical model can reproduce quantitatively
whole-network reconstructions, across development and perturbations. Our results
show that lymphatic capillary networks can exploit local self-organizing mechanisms
to achieve tissue-scale optimization.'
acknowledgement: "We thank Dr. Kari Alitalo (University of Helsinki and Wihuri Research
Institute) for critical reading of the manuscript, providing Vegfc+/− and Clp24ΔEC
mouse strains and for hosting K.V.’s Academy of Finland postdoctoral researcher
period (2015–2018). We thank Dr. Sara Wickström (University of Helsinki and Wihuri
Research Institute) for providing Sox9:Egfp mouse\r\nstrain and the discussions.
We thank Maija Atuegwu and Tapio Tainola for technical assistance. This work received
funding from the Academy of Finland (K.V., 315710), Sigrid Juselius Foundation (K.V.),
University of Helsinki (K.V.), Wihuri Research Institute (K.V.), the ERC under the
European Union’s Horizon 2020 research and innovation program (grant agreement\r\nNo.
851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411
(to M.C.U.). Part of the work was carried out with the support of HiLIFE Laboratory
Animal Centre Core Facility, University of Helsinki, Finland. Imaging was performed
at the Biomedicum Imaging Unit, Helsinki University, Helsinki, Finland, with the
support of Biocenter Finland. The AAVpreparations were produced at the Helsinki
Virus (HelVi) Core."
article_number: '5878'
article_processing_charge: Yes
article_type: original
author:
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Emmi
full_name: Tiilikainen, Emmi
last_name: Tiilikainen
- first_name: Inam
full_name: Liaqat, Inam
last_name: Liaqat
- first_name: Emma
full_name: Jakobsson, Emma
last_name: Jakobsson
- first_name: Harri
full_name: Nurmi, Harri
last_name: Nurmi
- first_name: Kari
full_name: Vaahtomeri, Kari
id: 368EE576-F248-11E8-B48F-1D18A9856A87
last_name: Vaahtomeri
orcid: 0000-0001-7829-3518
citation:
ama: Ucar MC, Hannezo EB, Tiilikainen E, et al. Self-organized and directed branching
results in optimal coverage in developing dermal lymphatic networks. Nature
Communications. 2023;14. doi:10.1038/s41467-023-41456-7
apa: Ucar, M. C., Hannezo, E. B., Tiilikainen, E., Liaqat, I., Jakobsson, E., Nurmi,
H., & Vaahtomeri, K. (2023). Self-organized and directed branching results
in optimal coverage in developing dermal lymphatic networks. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-023-41456-7
chicago: Ucar, Mehmet C, Edouard B Hannezo, Emmi Tiilikainen, Inam Liaqat, Emma
Jakobsson, Harri Nurmi, and Kari Vaahtomeri. “Self-Organized and Directed Branching
Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” Nature
Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41456-7.
ieee: M. C. Ucar et al., “Self-organized and directed branching results in
optimal coverage in developing dermal lymphatic networks,” Nature Communications,
vol. 14. Springer Nature, 2023.
ista: Ucar MC, Hannezo EB, Tiilikainen E, Liaqat I, Jakobsson E, Nurmi H, Vaahtomeri
K. 2023. Self-organized and directed branching results in optimal coverage in
developing dermal lymphatic networks. Nature Communications. 14, 5878.
mla: Ucar, Mehmet C., et al. “Self-Organized and Directed Branching Results in Optimal
Coverage in Developing Dermal Lymphatic Networks.” Nature Communications,
vol. 14, 5878, Springer Nature, 2023, doi:10.1038/s41467-023-41456-7.
short: M.C. Ucar, E.B. Hannezo, E. Tiilikainen, I. Liaqat, E. Jakobsson, H. Nurmi,
K. Vaahtomeri, Nature Communications 14 (2023).
corr_author: '1'
date_created: 2023-10-01T22:01:13Z
date_published: 2023-09-21T00:00:00Z
date_updated: 2025-04-14T07:43:56Z
day: '21'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1038/s41467-023-41456-7
ec_funded: 1
external_id:
isi:
- '001075884500007'
pmid:
- '37735168'
file:
- access_level: open_access
checksum: 4fe5423403f2531753bcd9e0fea48e05
content_type: application/pdf
creator: dernst
date_created: 2023-10-03T07:46:36Z
date_updated: 2023-10-03T07:46:36Z
file_id: '14384'
file_name: 2023_NatureComm_Ucar.pdf
file_size: 8143264
relation: main_file
success: 1
file_date_updated: 2023-10-03T07:46:36Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-organized and directed branching results in optimal coverage in developing
dermal lymphatic networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '14401'
abstract:
- lang: eng
text: "Background: \r\nPro-apoptotic BAX is a central mediator of retinal ganglion
cell (RGC) death after optic nerve damage. BAX activation occurs in two stages
including translocation of latent BAX to the mitochondrial outer membrane (MOM)
and then permeabilization of the MOM to facilitate the release of apoptotic signaling
molecules. As a critical component of RGC death, BAX is an attractive target for
neuroprotective therapies and an understanding of the kinetics of BAX activation
and the mechanisms controlling the two stages of this process in RGCs is potentially
valuable in informing the development of a neuroprotective strategy.\r\nMethods:\r\nThe
kinetics of BAX translocation were assessed by both static and live-cell imaging
of a GFP-BAX fusion protein introduced into RGCs using AAV2-mediated gene transfer
in mice. Activation of BAX was achieved using an acute optic nerve crush (ONC)
protocol. Live-cell imaging of GFP-BAX was achieved using explants of mouse retina
harvested 7 days after ONC. Kinetics of translocation in RGCs were compared to
GFP-BAX translocation in 661W tissue culture cells. Permeabilization of GFP-BAX
was assessed by staining with the 6A7 monoclonal antibody, which recognizes a
conformational change in this protein after MOM insertion. Assessment of individual
kinases associated with both stages of activation was made using small molecule
inhibitors injected into the vitreous either independently or in concert with
ONC surgery. The contribution of the Dual Leucine Zipper-JUN-N-Terminal Kinase
cascade was evaluated using mice with a double conditional knock-out of both Mkk4
and Mkk7.\r\nResults:\r\nONC induces the translocation of GFP-BAX in RGCs at a
slower rate and with less intracellular synchronicity than 661W cells, but exhibits
less variability among mitochondrial foci within a single cell. GFP-BAX was also
found to translocate in all compartments of an RGC including the dendritic arbor
and axon. Approximately 6% of translocating RGCs exhibited retrotranslocation
of BAX immediately following translocation. Unlike tissue culture cells, which
exhibit simultaneous translocation and permeabilization, RGCs exhibited a significant
delay between these two stages, similar to detached cells undergoing anoikis.
Translocation, with minimal permeabilization could be induced in a subset of RGCs
using an inhibitor of Focal Adhesion Kinase (PF573228). Permeabilization after
ONC, in a majority of RGCs, could be inhibited with a broad spectrum kinase inhibitor
(sunitinib) or a selective inhibitor for p38/MAPK14 (SB203580). Intervention of
DLK-JNK axis signaling abrogated GFP-BAX translocation after ONC.\r\nConclusions:\r\nA
comparison between BAX activation kinetics in tissue culture cells and in cells
of a complex tissue environment shows distinct differences indicating that caution
should be used when translating findings from one condition to the other. RGCs
exhibit both a delay between translocation and permeabilization and the ability
for translocated BAX to be retrotranslocated, suggesting several stages at which
intervention of the activation process could be exploited in the design of a therapeutic
strategy."
acknowledgement: "The authors would like to thank Mr. Joel Dietz for management of
the mouse colony and helpful advice for conducting quantitative PCR studies and
Mr. Santoshi Kinoshita at the Translational Research Initiative in Pathology laboratory
at the University of Wisconsin-Madison for cutting sections analyzed in this study.\r\nThis
work was supported by National Eye Institute grants R01 EY030123 (RWN), R01 EY018606
(RTL), P30 EY016665 (Department of Ophthalmology and Visual Sciences, University
of Wisconsin-Madison), T32 EY027721 (RJD) and F31 EY030739 (OJM). Additional funding
was provided by the BrightFocus Foundation (RWN) and unrestricted grants from Research
to Prevent Blindness, Inc to the Department of Ophthalmology and Visual Sciences
(University of Wisconsin-Madison) and to the Department of Ophthalmology (University
of Rochester)."
article_number: '67'
article_processing_charge: Yes
article_type: original
author:
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Ryan J.
full_name: Donahue, Ryan J.
last_name: Donahue
- first_name: Cassandra L.
full_name: Schlamp, Cassandra L.
last_name: Schlamp
- first_name: Olivia J.
full_name: Marola, Olivia J.
last_name: Marola
- first_name: Richard T.
full_name: Libby, Richard T.
last_name: Libby
- first_name: Robert W.
full_name: Nickells, Robert W.
last_name: Nickells
citation:
ama: Maes ME, Donahue RJ, Schlamp CL, Marola OJ, Libby RT, Nickells RW. BAX activation
in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct
steps. Molecular Neurodegeneration. 2023;18. doi:10.1186/s13024-023-00659-8
apa: Maes, M. E., Donahue, R. J., Schlamp, C. L., Marola, O. J., Libby, R. T., &
Nickells, R. W. (2023). BAX activation in mouse retinal ganglion cells occurs
in two temporally and mechanistically distinct steps. Molecular Neurodegeneration.
Springer Nature. https://doi.org/10.1186/s13024-023-00659-8
chicago: Maes, Margaret E, Ryan J. Donahue, Cassandra L. Schlamp, Olivia J. Marola,
Richard T. Libby, and Robert W. Nickells. “BAX Activation in Mouse Retinal Ganglion
Cells Occurs in Two Temporally and Mechanistically Distinct Steps.” Molecular
Neurodegeneration. Springer Nature, 2023. https://doi.org/10.1186/s13024-023-00659-8.
ieee: M. E. Maes, R. J. Donahue, C. L. Schlamp, O. J. Marola, R. T. Libby, and R.
W. Nickells, “BAX activation in mouse retinal ganglion cells occurs in two temporally
and mechanistically distinct steps,” Molecular Neurodegeneration, vol.
18. Springer Nature, 2023.
ista: Maes ME, Donahue RJ, Schlamp CL, Marola OJ, Libby RT, Nickells RW. 2023. BAX
activation in mouse retinal ganglion cells occurs in two temporally and mechanistically
distinct steps. Molecular Neurodegeneration. 18, 67.
mla: Maes, Margaret E., et al. “BAX Activation in Mouse Retinal Ganglion Cells Occurs
in Two Temporally and Mechanistically Distinct Steps.” Molecular Neurodegeneration,
vol. 18, 67, Springer Nature, 2023, doi:10.1186/s13024-023-00659-8.
short: M.E. Maes, R.J. Donahue, C.L. Schlamp, O.J. Marola, R.T. Libby, R.W. Nickells,
Molecular Neurodegeneration 18 (2023).
date_created: 2023-10-08T22:01:15Z
date_published: 2023-09-26T00:00:00Z
date_updated: 2025-04-23T13:09:05Z
day: '26'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1186/s13024-023-00659-8
external_id:
isi:
- '001071403800001'
pmid:
- '37752598'
file:
- access_level: open_access
checksum: 3aa218ddea4a082d8fd5e196ae55ca06
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T14:33:31Z
date_updated: 2024-01-30T14:33:31Z
file_id: '14917'
file_name: 2023_MolecularNeurodegeneration_Maes.pdf
file_size: 11568350
relation: main_file
success: 1
file_date_updated: 2024-01-30T14:33:31Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Neurodegeneration
publication_identifier:
eissn:
- 1750-1326
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: BAX activation in mouse retinal ganglion cells occurs in two temporally and
mechanistically distinct steps
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2023'
...
---
_id: '14402'
abstract:
- lang: eng
text: Alpha oscillations are a distinctive feature of the awake resting state of
the human brain. However, their functional role in resting-state neuronal dynamics
remains poorly understood. Here we show that, during resting wakefulness, alpha
oscillations drive an alternation of attenuation and amplification bouts in neural
activity. Our analysis indicates that inhibition is activated in pulses that last
for a single alpha cycle and gradually suppress neural activity, while excitation
is successively enhanced over a few alpha cycles to amplify neural activity. Furthermore,
we show that long-term alpha amplitude fluctuations—the “waxing and waning” phenomenon—are
an attenuation-amplification mechanism described by a power-law decay of the activity
rate in the “waning” phase. Importantly, we do not observe such dynamics during
non-rapid eye movement (NREM) sleep with marginal alpha oscillations. The results
suggest that alpha oscillations modulate neural activity not only through pulses
of inhibition (pulsed inhibition hypothesis) but also by timely enhancement of
excitation (or disinhibition).
acknowledgement: This research was funded in whole or in part by the Austrian Science
Fund (FWF) (grant PT1013M03318 to F.L.). For the purpose of open access, the author
has applied a CC BY public copyright license to any Author Accepted Manuscript version
arising from this submission. The study was supported by the European Union Horizon
2020 Research and Innovation Program under the Marie Sklodowska-Curie action (grant
agreement 754411 to F.L.) and in part by the NextGenerationEU through the grant
TAlent in ReSearch@University of Padua – STARS@UNIPD (to F.L.) (project BRAINCIP
[brain criticality and information processing]). L.d.A. acknowledges support from
the Italian MIUR project PRIN2017WZFTZP and partial support from NEXTGENERATIONEU
(NGEU) funded by the Ministry of University and Research (MUR), National Recovery
and Resilience Plan (NRRP), and project MNESYS (PE0000006)—a multiscale integrated
approach to the study of the nervous system in health and disease (DN. 1553 11.10.2022).
O.S. acknowledges support from the Israel Science Foundation, grant 504/17. The
work was supported in part by DIRP ZIAMH02797 (to D.P.).
article_number: '113162'
article_processing_charge: Yes
article_type: original
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Hans J.
full_name: Herrmann, Hans J.
last_name: Herrmann
- first_name: Liborio
full_name: Parrino, Liborio
last_name: Parrino
- first_name: Dietmar
full_name: Plenz, Dietmar
last_name: Plenz
- first_name: Silvia
full_name: Scarpetta, Silvia
last_name: Scarpetta
- first_name: Anna Elisabetta
full_name: Vaudano, Anna Elisabetta
last_name: Vaudano
- first_name: Lucilla
full_name: De Arcangelis, Lucilla
last_name: De Arcangelis
- first_name: Oren
full_name: Shriki, Oren
last_name: Shriki
citation:
ama: 'Lombardi F, Herrmann HJ, Parrino L, et al. Beyond pulsed inhibition: Alpha
oscillations modulate attenuation and amplification of neural activity in the
awake resting state. Cell Reports. 2023;42(10). doi:10.1016/j.celrep.2023.113162'
apa: 'Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano,
A. E., … Shriki, O. (2023). Beyond pulsed inhibition: Alpha oscillations modulate
attenuation and amplification of neural activity in the awake resting state. Cell
Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.113162'
chicago: 'Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz,
Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla De Arcangelis, and Oren Shriki.
“Beyond Pulsed Inhibition: Alpha Oscillations Modulate Attenuation and Amplification
of Neural Activity in the Awake Resting State.” Cell Reports. Elsevier,
2023. https://doi.org/10.1016/j.celrep.2023.113162.'
ieee: 'F. Lombardi et al., “Beyond pulsed inhibition: Alpha oscillations
modulate attenuation and amplification of neural activity in the awake resting
state,” Cell Reports, vol. 42, no. 10. Elsevier, 2023.'
ista: 'Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, De
Arcangelis L, Shriki O. 2023. Beyond pulsed inhibition: Alpha oscillations modulate
attenuation and amplification of neural activity in the awake resting state. Cell
Reports. 42(10), 113162.'
mla: 'Lombardi, Fabrizio, et al. “Beyond Pulsed Inhibition: Alpha Oscillations Modulate
Attenuation and Amplification of Neural Activity in the Awake Resting State.”
Cell Reports, vol. 42, no. 10, 113162, Elsevier, 2023, doi:10.1016/j.celrep.2023.113162.'
short: F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano,
L. De Arcangelis, O. Shriki, Cell Reports 42 (2023).
corr_author: '1'
date_created: 2023-10-08T22:01:15Z
date_published: 2023-10-31T00:00:00Z
date_updated: 2025-04-15T06:55:02Z
day: '31'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1016/j.celrep.2023.113162
ec_funded: 1
external_id:
isi:
- '001086695500001'
pmid:
- '37777965'
file:
- access_level: open_access
checksum: 9c71eb2a03aa160415f01ad95f49ceb5
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T14:07:08Z
date_updated: 2024-01-30T14:07:08Z
file_id: '14914'
file_name: 2023_CellReports_Lombardi.pdf
file_size: 5599007
relation: main_file
success: 1
file_date_updated: 2024-01-30T14:07:08Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: eb943429-77a9-11ec-83b8-9f471cdf5c67
grant_number: M03318
name: Functional Advantages of Critical Brain Dynamics
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '10821'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification
of neural activity in the awake resting state'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '14405'
abstract:
- lang: eng
text: We introduce hypernode automata as a new specification formalism for hyperproperties
of concurrent systems. They are finite automata with nodes labeled with hypernode
logic formulas and transitions labeled with actions. A hypernode logic formula
specifies relations between sequences of variable values in different system executions.
Unlike HyperLTL, hypernode logic takes an asynchronous view on execution traces
by constraining the values and the order of value changes of each variable without
correlating the timing of the changes. Different execution traces are synchronized
solely through the transitions of hypernode automata. Hypernode automata naturally
combine asynchronicity at the node level with synchronicity at the transition
level. We show that the model-checking problem for hypernode automata is decidable
over action-labeled Kripke structures, whose actions induce transitions of the
specification automata. For this reason, hypernode automaton is a suitable formalism
for specifying and verifying asynchronous hyperproperties, such as declassifying
observational determinism in multi-threaded programs.
acknowledgement: "This work was supported in part by the Austrian Science Fund (FWF)
SFB project\r\nSpyCoDe F8502, by the FWF projects ZK-35 and W1255-N23, and by the
ERC Advanced Grant\r\nVAMOS 101020093."
alternative_title:
- LIPIcs
article_number: '21'
article_processing_charge: Yes
arxiv: 1
author:
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Ana
full_name: Oliveira da Costa, Ana
id: f347ec37-6676-11ee-b395-a888cb7b4fb4
last_name: Oliveira da Costa
orcid: 0000-0002-8741-5799
citation:
ama: 'Bartocci E, Henzinger TA, Nickovic D, Oliveira da Costa A. Hypernode automata.
In: 34th International Conference on Concurrency Theory. Vol 279. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.CONCUR.2023.21'
apa: 'Bartocci, E., Henzinger, T. A., Nickovic, D., & Oliveira da Costa, A.
(2023). Hypernode automata. In 34th International Conference on Concurrency
Theory (Vol. 279). Antwerp, Belgium: Schloss Dagstuhl - Leibniz-Zentrum für
Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2023.21'
chicago: Bartocci, Ezio, Thomas A Henzinger, Dejan Nickovic, and Ana Oliveira da
Costa. “Hypernode Automata.” In 34th International Conference on Concurrency
Theory, Vol. 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.
https://doi.org/10.4230/LIPIcs.CONCUR.2023.21.
ieee: E. Bartocci, T. A. Henzinger, D. Nickovic, and A. Oliveira da Costa, “Hypernode
automata,” in 34th International Conference on Concurrency Theory, Antwerp,
Belgium, 2023, vol. 279.
ista: 'Bartocci E, Henzinger TA, Nickovic D, Oliveira da Costa A. 2023. Hypernode
automata. 34th International Conference on Concurrency Theory. CONCUR: Conference
on Concurrency Theory, LIPIcs, vol. 279, 21.'
mla: Bartocci, Ezio, et al. “Hypernode Automata.” 34th International Conference
on Concurrency Theory, vol. 279, 21, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2023, doi:10.4230/LIPIcs.CONCUR.2023.21.
short: E. Bartocci, T.A. Henzinger, D. Nickovic, A. Oliveira da Costa, in:, 34th
International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023.
conference:
end_date: 2023-09-22
location: Antwerp, Belgium
name: 'CONCUR: Conference on Concurrency Theory'
start_date: 2023-09-19
corr_author: '1'
date_created: 2023-10-08T22:01:16Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2026-01-05T12:27:40Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.CONCUR.2023.21
ec_funded: 1
external_id:
arxiv:
- '2305.02836'
file:
- access_level: open_access
checksum: 215765e40454d806174ac0a223e8d6fa
content_type: application/pdf
creator: dernst
date_created: 2023-10-09T07:42:45Z
date_updated: 2023-10-09T07:42:45Z
file_id: '14413'
file_name: 2023_LIPcs_Bartocci.pdf
file_size: 795790
relation: main_file
success: 1
file_date_updated: 2023-10-09T07:42:45Z
has_accepted_license: '1'
intvolume: ' 279'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 34th International Conference on Concurrency Theory
publication_identifier:
isbn:
- '9783959772990'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '20866'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Hypernode automata
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 279
year: '2023'
...
---
_id: '14406'
abstract:
- lang: eng
text: "Recently, a concept of generalized multifractality, which characterizes fluctuations
and correlations of critical eigenstates, was introduced and explored for all
10 symmetry classes of disordered systems. Here, by using the nonlinear sigma-model
(\r\nNL\r\nσ\r\nM\r\n) field theory, we extend the theory of generalized multifractality
to boundaries of systems at criticality. Our numerical simulations on two-dimensional
systems of symmetry classes A, C, and AII fully confirm the analytical predictions
of pure-scaling observables and Weyl symmetry relations between critical exponents
of surface generalized multifractality. This demonstrates the validity of the
\r\nNL\r\nσ\r\nM\r\n for the description of Anderson-localization critical phenomena,
not only in the bulk but also on the boundary. The critical exponents strongly
violate generalized parabolicity, in analogy with earlier results for the bulk,
corroborating the conclusion that the considered Anderson-localization critical
points are not described by conformal field theories. We further derive relations
between generalized surface multifractal spectra and linear combinations of Lyapunov
exponents of a strip in quasi-one-dimensional geometry, which hold under the assumption
of invariance with respect to a logarithmic conformal map. Our numerics demonstrate
that these relations hold with an excellent accuracy. Taken together, our results
indicate an intriguing situation: the conformal invariance is broken but holds
partially at critical points of Anderson localization."
acknowledgement: "We thank Ilya Gruzberg for many illuminating discussions. S.S.B.,
J.F.K., and A.D.M. acknowledge support by the Deutsche Forschungsgemeinschaft (DFG)
via the Grant\r\nNo. MI 658/14-1. I.S.B. acknowledges support from Russian Science
Foundation (Grant No. 22-42-04416)."
article_number: '104205'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Serafim
full_name: Babkin, Serafim
id: 41e64307-6672-11ee-b9ad-cc7a0075a479
last_name: Babkin
orcid: 0009-0003-7382-8036
- first_name: Jonas F.
full_name: Karcher, Jonas F.
last_name: Karcher
- first_name: Igor S.
full_name: Burmistrov, Igor S.
last_name: Burmistrov
- first_name: Alexander D.
full_name: Mirlin, Alexander D.
last_name: Mirlin
citation:
ama: Babkin S, Karcher JF, Burmistrov IS, Mirlin AD. Generalized surface multifractality
in two-dimensional disordered systems. Physical Review B. 2023;108(10).
doi:10.1103/PhysRevB.108.104205
apa: Babkin, S., Karcher, J. F., Burmistrov, I. S., & Mirlin, A. D. (2023).
Generalized surface multifractality in two-dimensional disordered systems. Physical
Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.104205
chicago: Babkin, Serafim, Jonas F. Karcher, Igor S. Burmistrov, and Alexander D.
Mirlin. “Generalized Surface Multifractality in Two-Dimensional Disordered Systems.”
Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.104205.
ieee: S. Babkin, J. F. Karcher, I. S. Burmistrov, and A. D. Mirlin, “Generalized
surface multifractality in two-dimensional disordered systems,” Physical Review
B, vol. 108, no. 10. American Physical Society, 2023.
ista: Babkin S, Karcher JF, Burmistrov IS, Mirlin AD. 2023. Generalized surface
multifractality in two-dimensional disordered systems. Physical Review B. 108(10),
104205.
mla: Babkin, Serafim, et al. “Generalized Surface Multifractality in Two-Dimensional
Disordered Systems.” Physical Review B, vol. 108, no. 10, 104205, American
Physical Society, 2023, doi:10.1103/PhysRevB.108.104205.
short: S. Babkin, J.F. Karcher, I.S. Burmistrov, A.D. Mirlin, Physical Review B
108 (2023).
date_created: 2023-10-08T22:01:17Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2025-09-09T13:03:44Z
day: '01'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.108.104205
external_id:
arxiv:
- '2306.09455'
isi:
- '001186160100001'
intvolume: ' 108'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2306.09455
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: Generalized surface multifractality in two-dimensional disordered systems
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 108
year: '2023'
...
---
_id: '14409'
abstract:
- lang: eng
text: We present a photon- and metal-free approach for the radical fluorination
of aliphatic oxalate-activated alcohols. The method relies on the spontaneous
generation of the N-(chloromethyl)triethylenediamine radical dication, a potent
single electron oxidant, from Selectfluor and 4-(dimethylamino)pyridine. The protocol
is easily scalable and provides the desired fluorinated products within only a
few minutes reaction time.
acknowledgement: We gratefully acknowledge the Max-Planck Society and the Institute
of Science and Technology Austria (ISTA) for generous financial support. We also
thank the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under
Germany's Excellence Strategy – EXC 2008 – 390540038 – UniSysCat for funding. B.P.
thanks the Boehringer Ingelheim Foundation for funding through the Plus 3 Perspectives
Programme.
article_number: e202300769
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Haralds
full_name: Baunis, Haralds
id: 2eea55ec-e8ec-11ed-86cb-d9c76787acfe
last_name: Baunis
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
citation:
ama: Baunis H, Pieber B. Formal radical deoxyfluorination of oxalate-activated alcohols
triggered by the selectfluor-DMAP charge-transfer complex. European Journal
of Organic Chemistry. 2023;26(42). doi:10.1002/ejoc.202300769
apa: Baunis, H., & Pieber, B. (2023). Formal radical deoxyfluorination of oxalate-activated
alcohols triggered by the selectfluor-DMAP charge-transfer complex. European
Journal of Organic Chemistry. Wiley. https://doi.org/10.1002/ejoc.202300769
chicago: Baunis, Haralds, and Bartholomäus Pieber. “Formal Radical Deoxyfluorination
of Oxalate-Activated Alcohols Triggered by the Selectfluor-DMAP Charge-Transfer
Complex.” European Journal of Organic Chemistry. Wiley, 2023. https://doi.org/10.1002/ejoc.202300769.
ieee: H. Baunis and B. Pieber, “Formal radical deoxyfluorination of oxalate-activated
alcohols triggered by the selectfluor-DMAP charge-transfer complex,” European
Journal of Organic Chemistry, vol. 26, no. 42. Wiley, 2023.
ista: Baunis H, Pieber B. 2023. Formal radical deoxyfluorination of oxalate-activated
alcohols triggered by the selectfluor-DMAP charge-transfer complex. European Journal
of Organic Chemistry. 26(42), e202300769.
mla: Baunis, Haralds, and Bartholomäus Pieber. “Formal Radical Deoxyfluorination
of Oxalate-Activated Alcohols Triggered by the Selectfluor-DMAP Charge-Transfer
Complex.” European Journal of Organic Chemistry, vol. 26, no. 42, e202300769,
Wiley, 2023, doi:10.1002/ejoc.202300769.
short: H. Baunis, B. Pieber, European Journal of Organic Chemistry 26 (2023).
corr_author: '1'
date_created: 2023-10-08T22:01:18Z
date_published: 2023-11-07T00:00:00Z
date_updated: 2024-10-09T21:07:03Z
day: '07'
ddc:
- '540'
department:
- _id: BaPi
doi: 10.1002/ejoc.202300769
external_id:
isi:
- '001072666500001'
file:
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checksum: e8ad7865acd94672e476f273ccf3d542
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T14:04:44Z
date_updated: 2024-01-30T14:04:44Z
file_id: '14913'
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file_size: 3277622
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success: 1
file_date_updated: 2024-01-30T14:04:44Z
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
issue: '42'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '11'
oa: 1
oa_version: Published Version
publication: European Journal of Organic Chemistry
publication_identifier:
eissn:
- 1099-0690
issn:
- 1434-193X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Formal radical deoxyfluorination of oxalate-activated alcohols triggered by
the selectfluor-DMAP charge-transfer complex
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2023'
...
---
_id: '14411'
abstract:
- lang: eng
text: "Partially specified Boolean networks (PSBNs) represent a promising framework
for the qualitative modelling of biological systems in which the logic of interactions
is not completely known. Phenotype control aims to stabilise the network in states
exhibiting specific traits.\r\nIn this paper, we define the phenotype control
problem in the context of asynchronous PSBNs and propose a novel semi-symbolic
algorithm for solving this problem with permanent variable perturbations."
acknowledgement: This work was supported by the Czech Foundation grant No. GA22-10845S,
Grant Agency of Masaryk University grant No. MUNI/G/1771/2020, and the European
Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 101034413.
alternative_title:
- LNBI
article_processing_charge: No
author:
- first_name: Nikola
full_name: Beneš, Nikola
last_name: Beneš
- first_name: Luboš
full_name: Brim, Luboš
last_name: Brim
- first_name: Samuel
full_name: Pastva, Samuel
id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b
last_name: Pastva
orcid: 0000-0003-1993-0331
- first_name: David
full_name: Šafránek, David
last_name: Šafránek
- first_name: Eva
full_name: Šmijáková, Eva
last_name: Šmijáková
citation:
ama: 'Beneš N, Brim L, Pastva S, Šafránek D, Šmijáková E. Phenotype control of partially
specified boolean networks. In: 21st International Conference on Computational
Methods in Systems Biology. Vol 14137. Springer Nature; 2023:18-35. doi:10.1007/978-3-031-42697-1_2'
apa: 'Beneš, N., Brim, L., Pastva, S., Šafránek, D., & Šmijáková, E. (2023).
Phenotype control of partially specified boolean networks. In 21st International
Conference on Computational Methods in Systems Biology (Vol. 14137, pp. 18–35).
Luxembourg City, Luxembourg: Springer Nature. https://doi.org/10.1007/978-3-031-42697-1_2'
chicago: Beneš, Nikola, Luboš Brim, Samuel Pastva, David Šafránek, and Eva Šmijáková.
“Phenotype Control of Partially Specified Boolean Networks.” In 21st International
Conference on Computational Methods in Systems Biology, 14137:18–35. Springer
Nature, 2023. https://doi.org/10.1007/978-3-031-42697-1_2.
ieee: N. Beneš, L. Brim, S. Pastva, D. Šafránek, and E. Šmijáková, “Phenotype control
of partially specified boolean networks,” in 21st International Conference
on Computational Methods in Systems Biology, Luxembourg City, Luxembourg,
2023, vol. 14137, pp. 18–35.
ista: 'Beneš N, Brim L, Pastva S, Šafránek D, Šmijáková E. 2023. Phenotype control
of partially specified boolean networks. 21st International Conference on Computational
Methods in Systems Biology. CMSB: Computational Methods in Systems Biology, LNBI,
vol. 14137, 18–35.'
mla: Beneš, Nikola, et al. “Phenotype Control of Partially Specified Boolean Networks.”
21st International Conference on Computational Methods in Systems Biology,
vol. 14137, Springer Nature, 2023, pp. 18–35, doi:10.1007/978-3-031-42697-1_2.
short: N. Beneš, L. Brim, S. Pastva, D. Šafránek, E. Šmijáková, in:, 21st International
Conference on Computational Methods in Systems Biology, Springer Nature, 2023,
pp. 18–35.
conference:
end_date: 2023-09-15
location: Luxembourg City, Luxembourg
name: 'CMSB: Computational Methods in Systems Biology'
start_date: 2023-09-13
date_created: 2023-10-08T22:01:18Z
date_published: 2023-09-09T00:00:00Z
date_updated: 2025-09-09T14:25:46Z
day: '09'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-031-42697-1_2
ec_funded: 1
external_id:
isi:
- '001156280600002'
file:
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checksum: 6f71bdaedb770b52380222fd9f4d7937
content_type: application/pdf
creator: spastva
date_created: 2024-02-16T08:26:32Z
date_updated: 2024-02-16T08:26:32Z
file_id: '14997'
file_name: cmsb2023.pdf
file_size: 691582
relation: main_file
success: 1
file_date_updated: 2024-02-16T08:26:32Z
has_accepted_license: '1'
intvolume: ' 14137'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 18-35
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: 21st International Conference on Computational Methods in Systems Biology
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031426964'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phenotype control of partially specified boolean networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 14137
year: '2023'
...
---
_id: '14417'
abstract:
- lang: eng
text: Entropic risk (ERisk) is an established risk measure in finance, quantifying
risk by an exponential re-weighting of rewards. We study ERisk for the first time
in the context of turn-based stochastic games with the total reward objective.
This gives rise to an objective function that demands the control of systems in
a risk-averse manner. We show that the resulting games are determined and, in
particular, admit optimal memoryless deterministic strategies. This contrasts
risk measures that previously have been considered in the special case of Markov
decision processes and that require randomization and/or memory. We provide several
results on the decidability and the computational complexity of the threshold
problem, i.e. whether the optimal value of ERisk exceeds a given threshold. In
the most general case, the problem is decidable subject to Shanuel’s conjecture.
If all inputs are rational, the resulting threshold problem can be solved using
algebraic numbers, leading to decidability via a polynomial-time reduction to
the existential theory of the reals. Further restrictions on the encoding of the
input allow the solution of the threshold problem in NP∩coNP. Finally, an approximation
algorithm for the optimal value of ERisk is provided.
acknowledgement: "This work was partly funded by the ERC CoG 863818 (ForM-SMArt),
the DFG Grant\r\n389792660 as part of TRR 248 (Foundations of Perspicuous Software
Systems), the Cluster of\r\nExcellence EXC 2050/1 (CeTI, project ID 390696704, as
part of Germany’s Excellence Strategy), and the DFG projects BA-1679/11-1 and BA-1679/12-1."
alternative_title:
- LIPIcs
article_number: '15'
article_processing_charge: Yes
arxiv: 1
author:
- first_name: Christel
full_name: Baier, Christel
last_name: Baier
- 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: Jakob
full_name: Piribauer, Jakob
last_name: Piribauer
citation:
ama: 'Baier C, Chatterjee K, Meggendorfer T, Piribauer J. Entropic risk for turn-based
stochastic games. In: 48th International Symposium on Mathematical Foundations
of Computer Science. Vol 272. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2023. doi:10.4230/LIPIcs.MFCS.2023.15'
apa: 'Baier, C., Chatterjee, K., Meggendorfer, T., & Piribauer, J. (2023). Entropic
risk for turn-based stochastic games. In 48th International Symposium on Mathematical
Foundations of Computer Science (Vol. 272). Bordeaux, France: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2023.15'
chicago: Baier, Christel, Krishnendu Chatterjee, Tobias Meggendorfer, and Jakob
Piribauer. “Entropic Risk for Turn-Based Stochastic Games.” In 48th International
Symposium on Mathematical Foundations of Computer Science, Vol. 272. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.MFCS.2023.15.
ieee: C. Baier, K. Chatterjee, T. Meggendorfer, and J. Piribauer, “Entropic risk
for turn-based stochastic games,” in 48th International Symposium on Mathematical
Foundations of Computer Science, Bordeaux, France, 2023, vol. 272.
ista: 'Baier C, Chatterjee K, Meggendorfer T, Piribauer J. 2023. Entropic risk for
turn-based stochastic games. 48th International Symposium on Mathematical Foundations
of Computer Science. MFCS: Mathematical Foundations of Computer Science, LIPIcs,
vol. 272, 15.'
mla: Baier, Christel, et al. “Entropic Risk for Turn-Based Stochastic Games.” 48th
International Symposium on Mathematical Foundations of Computer Science, vol.
272, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.MFCS.2023.15.
short: C. Baier, K. Chatterjee, T. Meggendorfer, J. Piribauer, in:, 48th International
Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl -
Leibniz-Zentrum für Informatik, 2023.
conference:
end_date: 2023-09-01
location: Bordeaux, France
name: 'MFCS: Mathematical Foundations of Computer Science'
start_date: 2023-08-28
corr_author: '1'
date_created: 2023-10-09T09:21:05Z
date_published: 2023-08-21T00:00:00Z
date_updated: 2025-09-08T09:10:05Z
day: '21'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.MFCS.2023.15
ec_funded: 1
external_id:
arxiv:
- '2307.06611'
file:
- access_level: open_access
checksum: 402281b17ed669bbf149d0fdf68ac201
content_type: application/pdf
creator: dernst
date_created: 2023-10-09T09:19:11Z
date_updated: 2023-10-09T09:19:11Z
file_id: '14418'
file_name: 2023_LIPIcsMFCS_Baier.pdf
file_size: 826843
relation: main_file
success: 1
file_date_updated: 2023-10-09T09:19:11Z
has_accepted_license: '1'
intvolume: ' 272'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 48th International Symposium on Mathematical Foundations of Computer
Science
publication_identifier:
eissn:
- 1868-8969
isbn:
- '9783959772921'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
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relation: later_version
status: public
scopus_import: '1'
status: public
title: Entropic risk for turn-based stochastic games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 272
year: '2023'
...