---
_id: '14319'
abstract:
- lang: eng
text: "We study multigraphs whose edge-sets are the union of three perfect matchings,
M1, M2, and M3. Given such a graph G and any a1; a2; a3 2 N with a1 +a2 +a3 6
n - 2, we show there exists a matching M of G with jM \\ Mij = ai for each i 2
f1; 2; 3g. The bound n - 2 in the theorem is best possible in general. We conjecture
however that if G is bipartite, the same result holds with n - 2 replaced by n
- 1. We give a construction that shows such a result would be tight. We\r\nalso
make a conjecture generalising the Ryser-Brualdi-Stein conjecture with colour\r\nmultiplicities."
acknowledgement: Anastos has received funding from the European Union’s Horizon 2020
research and in-novation programme under the Marie Sk lodowska-Curie grant agreement
No 101034413.Fabian’s research is supported by the Deutsche Forschungsgemeinschaft
(DFG, GermanResearch Foundation) Graduiertenkolleg “Facets of Complexity” (GRK 2434).
article_number: P3.10
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
- first_name: David
full_name: Fabian, David
last_name: Fabian
- first_name: Alp
full_name: Müyesser, Alp
last_name: Müyesser
- first_name: Tibor
full_name: Szabó, Tibor
last_name: Szabó
citation:
ama: Anastos M, Fabian D, Müyesser A, Szabó T. Splitting matchings and the Ryser-Brualdi-Stein
conjecture for multisets. Electronic Journal of Combinatorics. 2023;30(3).
doi:10.37236/11714
apa: Anastos, M., Fabian, D., Müyesser, A., & Szabó, T. (2023). Splitting matchings
and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of
Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/11714
chicago: Anastos, Michael, David Fabian, Alp Müyesser, and Tibor Szabó. “Splitting
Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” Electronic
Journal of Combinatorics. Electronic Journal of Combinatorics, 2023. https://doi.org/10.37236/11714.
ieee: M. Anastos, D. Fabian, A. Müyesser, and T. Szabó, “Splitting matchings and
the Ryser-Brualdi-Stein conjecture for multisets,” Electronic Journal of Combinatorics,
vol. 30, no. 3. Electronic Journal of Combinatorics, 2023.
ista: Anastos M, Fabian D, Müyesser A, Szabó T. 2023. Splitting matchings and the
Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics.
30(3), P3.10.
mla: Anastos, Michael, et al. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture
for Multisets.” Electronic Journal of Combinatorics, vol. 30, no. 3, P3.10,
Electronic Journal of Combinatorics, 2023, doi:10.37236/11714.
short: M. Anastos, D. Fabian, A. Müyesser, T. Szabó, Electronic Journal of Combinatorics
30 (2023).
date_created: 2023-09-10T22:01:12Z
date_published: 2023-07-28T00:00:00Z
date_updated: 2025-09-09T12:54:51Z
day: '28'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.37236/11714
ec_funded: 1
external_id:
arxiv:
- '2212.03100'
isi:
- '001042382200001'
file:
- access_level: open_access
checksum: 52c46c8cb329f9aaee9ade01525f317b
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T08:02:09Z
date_updated: 2023-09-15T08:02:09Z
file_id: '14338'
file_name: 2023_elecJournCombinatorics_Anastos.pdf
file_size: 247917
relation: main_file
success: 1
file_date_updated: 2023-09-15T08:02:09Z
has_accepted_license: '1'
intvolume: ' 30'
isi: 1
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Electronic Journal of Combinatorics
publication_identifier:
eissn:
- 1077-8926
publication_status: published
publisher: Electronic Journal of Combinatorics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 30
year: '2023'
...
---
_id: '14320'
abstract:
- lang: eng
text: The development of two-dimensional materials has resulted in a diverse range
of novel, high-quality compounds with increasing complexity. A key requirement
for a comprehensive quantitative theory is the accurate determination of these
materials' band structure parameters. However, this task is challenging due to
the intricate band structures and the indirect nature of experimental probes.
In this work, we introduce a general framework to derive band structure parameters
from experimental data using deep neural networks. We applied our method to the
penetration field capacitance measurement of trilayer graphene, an effective probe
of its density of states. First, we demonstrate that a trained deep network gives
accurate predictions for the penetration field capacitance as a function of tight-binding
parameters. Next, we use the fast and accurate predictions from the trained network
to automatically determine tight-binding parameters directly from experimental
data, with extracted parameters being in a good agreement with values in the literature.
We conclude by discussing potential applications of our method to other materials
and experimental techniques beyond penetration field capacitance.
acknowledgement: A.F.Y. acknowledges primary support from the Department of Energy
under award DE-SC0020043, and additional support from the Gordon and Betty Moore
Foundation under award GBMF9471 for group operations.
article_number: '125411'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Paul M
full_name: Henderson, Paul M
id: 13C09E74-18D9-11E9-8878-32CFE5697425
last_name: Henderson
orcid: 0000-0002-5198-7445
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Alexander A.
full_name: Zibrov, Alexander A.
last_name: Zibrov
- first_name: Andrea F.
full_name: Young, Andrea F.
last_name: Young
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: 'Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. Deep learning extraction
of band structure parameters from density of states: A case study on trilayer
graphene. Physical Review B. 2023;108(12). doi:10.1103/physrevb.108.125411'
apa: 'Henderson, P. M., Ghazaryan, A., Zibrov, A. A., Young, A. F., & Serbyn,
M. (2023). Deep learning extraction of band structure parameters from density
of states: A case study on trilayer graphene. Physical Review B. American
Physical Society. https://doi.org/10.1103/physrevb.108.125411'
chicago: 'Henderson, Paul M, Areg Ghazaryan, Alexander A. Zibrov, Andrea F. Young,
and Maksym Serbyn. “Deep Learning Extraction of Band Structure Parameters from
Density of States: A Case Study on Trilayer Graphene.” Physical Review B.
American Physical Society, 2023. https://doi.org/10.1103/physrevb.108.125411.'
ieee: 'P. M. Henderson, A. Ghazaryan, A. A. Zibrov, A. F. Young, and M. Serbyn,
“Deep learning extraction of band structure parameters from density of states:
A case study on trilayer graphene,” Physical Review B, vol. 108, no. 12.
American Physical Society, 2023.'
ista: 'Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. 2023. Deep learning
extraction of band structure parameters from density of states: A case study on
trilayer graphene. Physical Review B. 108(12), 125411.'
mla: 'Henderson, Paul M., et al. “Deep Learning Extraction of Band Structure Parameters
from Density of States: A Case Study on Trilayer Graphene.” Physical Review
B, vol. 108, no. 12, 125411, American Physical Society, 2023, doi:10.1103/physrevb.108.125411.'
short: P.M. Henderson, A. Ghazaryan, A.A. Zibrov, A.F. Young, M. Serbyn, Physical
Review B 108 (2023).
date_created: 2023-09-12T07:12:12Z
date_published: 2023-09-15T00:00:00Z
date_updated: 2023-09-20T09:38:24Z
day: '15'
department:
- _id: MaSe
- _id: ChLa
- _id: MiLe
doi: 10.1103/physrevb.108.125411
external_id:
arxiv:
- '2210.06310'
intvolume: ' 108'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2210.06310
month: '09'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Deep learning extraction of band structure parameters from density of states:
A case study on trilayer graphene'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '14321'
abstract:
- lang: eng
text: We demonstrate the possibility of a coupling between the magnetization direction
of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate
the mechanism of the coupling, we analyze a minimal Stoner model that includes
Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet.
The proposed mechanism allows us to study magnetic anisotropy of the system with
an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can
change magnetocrystalline anisotropy of the substrate. Our research aims to motivate
further experimental studies of the current-free chirality induced spin selectivity
effect involving both enantiomers.
acknowledgement: "We thank Zhanybek Alpichshev, Mohammad Reza Safari, Binghai Yan,
and Yossi Paltiel for enlightening discussions.\r\nM.L. acknowledges support from
the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A. C. received
funding from the European Union’s Horizon Europe research and innovation program
under the Marie Skłodowska-Curie Grant Agreement No. 101062862 - NeqMolRot."
article_number: '104103'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Ragheed
full_name: Al Hyder, Ragheed
id: d1c405be-ae15-11ed-8510-ccf53278162e
last_name: Al Hyder
- first_name: Alberto
full_name: Cappellaro, Alberto
id: 9d13b3cb-30a2-11eb-80dc-f772505e8660
last_name: Cappellaro
orcid: 0000-0001-6110-2359
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. Achiral dipoles on a ferromagnet
can affect its magnetization direction. The Journal of Chemical Physics.
2023;159(10). doi:10.1063/5.0165806
apa: Al Hyder, R., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Achiral
dipoles on a ferromagnet can affect its magnetization direction. The Journal
of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0165806
chicago: Al Hyder, Ragheed, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev.
“Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” The
Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0165806.
ieee: R. Al Hyder, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Achiral dipoles
on a ferromagnet can affect its magnetization direction,” The Journal of Chemical
Physics, vol. 159, no. 10. AIP Publishing, 2023.
ista: Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. 2023. Achiral dipoles on
a ferromagnet can affect its magnetization direction. The Journal of Chemical
Physics. 159(10), 104103.
mla: Al Hyder, Ragheed, et al. “Achiral Dipoles on a Ferromagnet Can Affect Its
Magnetization Direction.” The Journal of Chemical Physics, vol. 159, no.
10, 104103, AIP Publishing, 2023, doi:10.1063/5.0165806.
short: R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical
Physics 159 (2023).
corr_author: '1'
date_created: 2023-09-13T09:25:09Z
date_published: 2023-09-11T00:00:00Z
date_updated: 2025-09-09T12:57:42Z
day: '11'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1063/5.0165806
ec_funded: 1
external_id:
arxiv:
- '2306.17592'
isi:
- '001133333600011'
pmid:
- '37694742'
file:
- access_level: open_access
checksum: 507ab65ab29e2c987c94cabad7c5370b
content_type: application/pdf
creator: acappell
date_created: 2023-09-13T09:34:20Z
date_updated: 2023-09-13T09:34:20Z
file_id: '14322'
file_name: 104103_1_5.0165806.pdf
file_size: 5749653
relation: main_file
success: 1
file_date_updated: 2023-09-13T09:34:20Z
has_accepted_license: '1'
intvolume: ' 159'
isi: 1
issue: '10'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: bd7b5202-d553-11ed-ba76-9b1c1b258338
grant_number: '101062862'
name: Non-Equilibrium Field Theory of Molecular Rotations
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Achiral dipoles on a ferromagnet can affect its magnetization direction
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 159
year: '2023'
...
---
_id: '14333'
abstract:
- lang: eng
text: "As causal ground truth is incredibly rare, causal discovery algorithms are\r\ncommonly
only evaluated on simulated data. This is concerning, given that\r\nsimulations
reflect common preconceptions about generating processes regarding\r\nnoise distributions,
model classes, and more. In this work, we propose a novel\r\nmethod for falsifying
the output of a causal discovery algorithm in the absence\r\nof ground truth.
Our key insight is that while statistical learning seeks\r\nstability across subsets
of data points, causal learning should seek stability\r\nacross subsets of variables.
Motivated by this insight, our method relies on a\r\nnotion of compatibility between
causal graphs learned on different subsets of\r\nvariables. We prove that detecting
incompatibilities can falsify wrongly\r\ninferred causal relations due to violation
of assumptions or errors from finite\r\nsample effects. Although passing such
compatibility tests is only a necessary\r\ncriterion for good performance, we
argue that it provides strong evidence for\r\nthe causal models whenever compatibility
entails strong implications for the\r\njoint distribution. We also demonstrate
experimentally that detection of\r\nincompatibilities can aid in causal model
selection."
article_number: '2307.09552'
article_processing_charge: No
arxiv: 1
author:
- first_name: Philipp M.
full_name: Faller, Philipp M.
last_name: Faller
- first_name: Leena Chennuru
full_name: Vankadara, Leena Chennuru
last_name: Vankadara
- first_name: Atalanti A.
full_name: Mastakouri, Atalanti A.
last_name: Mastakouri
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Dominik
full_name: Janzing, Dominik
last_name: Janzing
citation:
ama: 'Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility:
Evaluating causal discovery without ground truth. arXiv. doi:10.48550/arXiv.2307.09552'
apa: 'Faller, P. M., Vankadara, L. C., Mastakouri, A. A., Locatello, F., & Janzing,
D. (n.d.). Self-compatibility: Evaluating causal discovery without ground truth.
arXiv. https://doi.org/10.48550/arXiv.2307.09552'
chicago: 'Faller, Philipp M., Leena Chennuru Vankadara, Atalanti A. Mastakouri,
Francesco Locatello, and Dominik Janzing. “Self-Compatibility: Evaluating Causal
Discovery without Ground Truth.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2307.09552.'
ieee: 'P. M. Faller, L. C. Vankadara, A. A. Mastakouri, F. Locatello, and D. Janzing,
“Self-compatibility: Evaluating causal discovery without ground truth,” arXiv.
.'
ista: 'Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility:
Evaluating causal discovery without ground truth. arXiv, 2307.09552.'
mla: 'Faller, Philipp M., et al. “Self-Compatibility: Evaluating Causal Discovery
without Ground Truth.” ArXiv, 2307.09552, doi:10.48550/arXiv.2307.09552.'
short: P.M. Faller, L.C. Vankadara, A.A. Mastakouri, F. Locatello, D. Janzing, ArXiv
(n.d.).
date_created: 2023-09-13T12:44:59Z
date_published: 2023-07-18T00:00:00Z
date_updated: 2024-10-14T12:31:20Z
day: '18'
department:
- _id: FrLo
doi: 10.48550/arXiv.2307.09552
extern: '1'
external_id:
arxiv:
- '2307.09552'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2307.09552
month: '07'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: 'Self-compatibility: Evaluating causal discovery without ground truth'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14334'
abstract:
- lang: eng
text: Quantum kinetically constrained models have recently attracted significant
attention due to their anomalous dynamics and thermalization. In this work, we
introduce a hitherto unexplored family of kinetically constrained models featuring
conserved particle number and strong inversion-symmetry breaking due to facilitated
hopping. We demonstrate that these models provide a generic example of so-called
quantum Hilbert space fragmentation, that is manifested in disconnected sectors
in the Hilbert space that are not apparent in the computational basis. Quantum
Hilbert space fragmentation leads to an exponential in system size number of eigenstates
with exactly zero entanglement entropy across several bipartite cuts. These eigenstates
can be probed dynamically using quenches from simple initial product states. In
addition, we study the particle spreading under unitary dynamics launched from
the domain wall state, and find faster than diffusive dynamics at high particle
densities, that crosses over into logarithmically slow relaxation at smaller densities.
Using a classically simulable cellular automaton, we reproduce the logarithmic
dynamics observed in the quantum case. Our work suggests that particle conserving
constrained models with inversion symmetry breaking realize so far unexplored
dynamical behavior and invite their further theoretical and experimental studies.
acknowledgement: "We would like to thank Raimel A. Medina, Hansveer Singh, and Dmitry
Abanin for useful\r\ndiscussions.The authors acknowledge support by the European
Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation
program (Grant\r\nAgreement No. 850899). We acknowledge support by the Erwin Schrödinger
International\r\nInstitute for Mathematics and Physics (ESI)."
article_number: '093'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Pietro
full_name: Brighi, Pietro
id: 4115AF5C-F248-11E8-B48F-1D18A9856A87
last_name: Brighi
orcid: 0000-0002-7969-2729
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
orcid: 0000-0003-0038-7068
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Brighi P, Ljubotina M, Serbyn M. Hilbert space fragmentation and slow dynamics
in particle-conserving quantum East models. SciPost Physics. 2023;15(3).
doi:10.21468/scipostphys.15.3.093
apa: Brighi, P., Ljubotina, M., & Serbyn, M. (2023). Hilbert space fragmentation
and slow dynamics in particle-conserving quantum East models. SciPost Physics.
SciPost Foundation. https://doi.org/10.21468/scipostphys.15.3.093
chicago: Brighi, Pietro, Marko Ljubotina, and Maksym Serbyn. “Hilbert Space Fragmentation
and Slow Dynamics in Particle-Conserving Quantum East Models.” SciPost Physics.
SciPost Foundation, 2023. https://doi.org/10.21468/scipostphys.15.3.093.
ieee: P. Brighi, M. Ljubotina, and M. Serbyn, “Hilbert space fragmentation and slow
dynamics in particle-conserving quantum East models,” SciPost Physics,
vol. 15, no. 3. SciPost Foundation, 2023.
ista: Brighi P, Ljubotina M, Serbyn M. 2023. Hilbert space fragmentation and slow
dynamics in particle-conserving quantum East models. SciPost Physics. 15(3), 093.
mla: Brighi, Pietro, et al. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving
Quantum East Models.” SciPost Physics, vol. 15, no. 3, 093, SciPost Foundation,
2023, doi:10.21468/scipostphys.15.3.093.
short: P. Brighi, M. Ljubotina, M. Serbyn, SciPost Physics 15 (2023).
corr_author: '1'
date_created: 2023-09-14T13:08:23Z
date_published: 2023-09-13T00:00:00Z
date_updated: 2025-04-14T07:52:05Z
day: '13'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.21468/scipostphys.15.3.093
ec_funded: 1
external_id:
arxiv:
- '2210.15607'
file:
- access_level: open_access
checksum: 4cef6a8021f6b6c47ab2f2f2b1387ac2
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T10:46:10Z
date_updated: 2023-09-20T10:46:10Z
file_id: '14350'
file_name: 2023_SciPostPhysics_Brighi.pdf
file_size: 4866506
relation: main_file
success: 1
file_date_updated: 2023-09-20T10:46:10Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '3'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: SciPost Physics
publication_identifier:
issn:
- 2542-4653
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
related_material:
record:
- id: '12750'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Hilbert space fragmentation and slow dynamics in particle-conserving quantum
East models
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2023'
...
---
_id: '14339'
abstract:
- lang: eng
text: Lateral roots are typically maintained at non-vertical angles with respect
to gravity. These gravitropic setpoint angles are intriguing because their maintenance
requires that roots are able to effect growth response both with and against the
gravity vector, a phenomenon previously attributed to gravitropism acting against
an antigravitropic offset mechanism. Here we show how the components mediating
gravitropism in the vertical primary root—PINs and phosphatases acting upon them—are
reconfigured in their regulation such that lateral root growth at a range of angles
can be maintained. We show that the ability of Arabidopsis lateral roots to bend
both downward and upward requires the generation of auxin asymmetries and is driven
by angle-dependent variation in downward gravitropic auxin flux acting against
angle-independent upward, antigravitropic flux. Further, we demonstrate a symmetry
in auxin distribution in lateral roots at gravitropic setpoint angle that can
be traced back to a net, balanced polarization of PIN3 and PIN7 auxin transporters
in the columella. These auxin fluxes are shifted by altering PIN protein phosphoregulation
in the columella, either by introducing PIN3 phosphovariant versions or via manipulation
of levels of the phosphatase subunit PP2A/RCN1. Finally, we show that auxin, in
addition to driving lateral root directional growth, acts within the lateral root
columella to induce more vertical growth by increasing RCN1 levels, causing a
downward shift in PIN3 localization, thereby diminishing the magnitude of the
upward, antigravitropic auxin flux.
acknowledgement: We thank D. Weijers, C. Schwechheimer and R. Offringa for generous
sharing of published and unpublished materials and P. Masson for advice on the use
of the ARL2 promoter. We are grateful to M. Del Bianco and O. Leyser for critical
reading of the manuscript. This work was supported by the BBSRC (grants BB/N010124/1
and BB/R000859/1 to S.K.), the Gatsby Charitable Foundation and the Leverhulme Trust
(RPG-2018-137 to S.K.).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: S
full_name: Roychoudhry, S
last_name: Roychoudhry
- first_name: K
full_name: Sageman-Furnas, K
last_name: Sageman-Furnas
- first_name: C
full_name: Wolverton, C
last_name: Wolverton
- first_name: Peter
full_name: Grones, Peter
id: 399876EC-F248-11E8-B48F-1D18A9856A87
last_name: Grones
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Gergely
full_name: Molnar, Gergely
id: 34F1AF46-F248-11E8-B48F-1D18A9856A87
last_name: Molnar
- first_name: M
full_name: De Angelis, M
last_name: De Angelis
- first_name: HL
full_name: Goodman, HL
last_name: Goodman
- first_name: N
full_name: Capstaff, N
last_name: Capstaff
- first_name: Lloyd
full_name: JPB, Lloyd
last_name: JPB
- first_name: J
full_name: Mullen, J
last_name: Mullen
- first_name: R
full_name: Hangarter, R
last_name: Hangarter
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: S
full_name: Kepinski, S
last_name: Kepinski
citation:
ama: Roychoudhry S, Sageman-Furnas K, Wolverton C, et al. Antigravitropic PIN polarization
maintains non-vertical growth in lateral roots. Nature Plants. 2023;9:1500-1513.
doi:10.1038/s41477-023-01478-x
apa: Roychoudhry, S., Sageman-Furnas, K., Wolverton, C., Grones, P., Tan, S., Molnar,
G., … Kepinski, S. (2023). Antigravitropic PIN polarization maintains non-vertical
growth in lateral roots. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-023-01478-x
chicago: Roychoudhry, S, K Sageman-Furnas, C Wolverton, Peter Grones, Shutang Tan,
Gergely Molnar, M De Angelis, et al. “Antigravitropic PIN Polarization Maintains
Non-Vertical Growth in Lateral Roots.” Nature Plants. Springer Nature,
2023. https://doi.org/10.1038/s41477-023-01478-x.
ieee: S. Roychoudhry et al., “Antigravitropic PIN polarization maintains
non-vertical growth in lateral roots,” Nature Plants, vol. 9. Springer
Nature, pp. 1500–1513, 2023.
ista: Roychoudhry S, Sageman-Furnas K, Wolverton C, Grones P, Tan S, Molnar G, De
Angelis M, Goodman H, Capstaff N, JPB L, Mullen J, Hangarter R, Friml J, Kepinski
S. 2023. Antigravitropic PIN polarization maintains non-vertical growth in lateral
roots. Nature Plants. 9, 1500–1513.
mla: Roychoudhry, S., et al. “Antigravitropic PIN Polarization Maintains Non-Vertical
Growth in Lateral Roots.” Nature Plants, vol. 9, Springer Nature, 2023,
pp. 1500–13, doi:10.1038/s41477-023-01478-x.
short: S. Roychoudhry, K. Sageman-Furnas, C. Wolverton, P. Grones, S. Tan, G. Molnar,
M. De Angelis, H. Goodman, N. Capstaff, L. JPB, J. Mullen, R. Hangarter, J. Friml,
S. Kepinski, Nature Plants 9 (2023) 1500–1513.
date_created: 2023-09-15T09:56:01Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2024-10-21T06:01:33Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41477-023-01478-x
external_id:
isi:
- '001069238800014'
pmid:
- '37666965'
file:
- access_level: open_access
checksum: 3d6d5d5abb937c14a5f6f0afba3b8624
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T10:51:31Z
date_updated: 2023-09-20T10:51:31Z
file_id: '14351'
file_name: 2023_NaturePlants_Roychoudhry.pdf
file_size: 9647103
relation: main_file
success: 1
file_date_updated: 2023-09-20T10:51:31Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1500-1513
pmid: 1
publication: Nature Plants
publication_identifier:
issn:
- 2055-0278
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Antigravitropic PIN polarization maintains non-vertical growth in lateral roots
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2023'
...
---
_id: '14341'
abstract:
- lang: eng
text: Flows through pipes and channels are, in practice, almost always turbulent,
and the multiscale eddying motion is responsible for a major part of the encountered
friction losses and pumping costs1. Conversely, for pulsatile flows, in particular
for aortic blood flow, turbulence levels remain low despite relatively large peak
velocities. For aortic blood flow, high turbulence levels are intolerable as they
would damage the shear-sensitive endothelial cell layer2,3,4,5. Here we show that
turbulence in ordinary pipe flow is diminished if the flow is driven in a pulsatile
mode that incorporates all the key features of the cardiac waveform. At Reynolds
numbers comparable to those of aortic blood flow, turbulence is largely inhibited,
whereas at much higher speeds, the turbulent drag is reduced by more than 25%.
This specific operation mode is more efficient when compared with steady driving,
which is the present situation for virtually all fluid transport processes ranging
from heating circuits to water, gas and oil pipelines.
acknowledged_ssus:
- _id: M-Shop
- _id: ScienComp
acknowledgement: We acknowledge the assistance of the Miba machine shop and the team
of the ISTA-HPC cluster. We thank M. Quadrio for the discussions. The work was supported
by the Simons Foundation (grant no. 662960) and by the Austrian Science Fund (grant
no. I4188-N30), within Deutsche Forschungsgemeinschaft research unit FOR 2688.
article_processing_charge: No
article_type: original
author:
- first_name: Davide
full_name: Scarselli, Davide
id: 40315C30-F248-11E8-B48F-1D18A9856A87
last_name: Scarselli
orcid: 0000-0001-5227-4271
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Scarselli D, Lopez Alonso JM, Varshney A, Hof B. Turbulence suppression by
cardiac-cycle-inspired driving of pipe flow. Nature. 2023;621(7977):71-74.
doi:10.1038/s41586-023-06399-5
apa: Scarselli, D., Lopez Alonso, J. M., Varshney, A., & Hof, B. (2023). Turbulence
suppression by cardiac-cycle-inspired driving of pipe flow. Nature. Springer
Nature. https://doi.org/10.1038/s41586-023-06399-5
chicago: Scarselli, Davide, Jose M Lopez Alonso, Atul Varshney, and Björn Hof. “Turbulence
Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” Nature. Springer
Nature, 2023. https://doi.org/10.1038/s41586-023-06399-5.
ieee: D. Scarselli, J. M. Lopez Alonso, A. Varshney, and B. Hof, “Turbulence suppression
by cardiac-cycle-inspired driving of pipe flow,” Nature, vol. 621, no.
7977. Springer Nature, pp. 71–74, 2023.
ista: Scarselli D, Lopez Alonso JM, Varshney A, Hof B. 2023. Turbulence suppression
by cardiac-cycle-inspired driving of pipe flow. Nature. 621(7977), 71–74.
mla: Scarselli, Davide, et al. “Turbulence Suppression by Cardiac-Cycle-Inspired
Driving of Pipe Flow.” Nature, vol. 621, no. 7977, Springer Nature, 2023,
pp. 71–74, doi:10.1038/s41586-023-06399-5.
short: D. Scarselli, J.M. Lopez Alonso, A. Varshney, B. Hof, Nature 621 (2023) 71–74.
corr_author: '1'
date_created: 2023-09-17T22:01:09Z
date_published: 2023-09-07T00:00:00Z
date_updated: 2025-09-09T12:59:04Z
day: '07'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1038/s41586-023-06399-5
external_id:
isi:
- '001168947700009'
pmid:
- '37673988'
file:
- access_level: open_access
checksum: 9c9f172ba0a9a301d76fff4229812464
content_type: application/pdf
creator: dernst
date_created: 2024-06-04T09:24:34Z
date_updated: 2024-06-04T09:24:34Z
file_id: '17118'
file_name: 2023_submittedversion.pdf
file_size: 3247252
relation: main_file
success: 1
file_date_updated: 2024-06-04T09:24:34Z
has_accepted_license: '1'
intvolume: ' 621'
isi: 1
issue: '7977'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 71-74
pmid: 1
project:
- _id: 238598C6-32DE-11EA-91FC-C7463DDC885E
grant_number: '662960'
name: Revisiting the Turbulence Problem Using Statistical Mechanics
- _id: 238B8092-32DE-11EA-91FC-C7463DDC885E
call_identifier: FWF
grant_number: I04188
name: Instabilities in pulsating pipe flow in complex fluids
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://www.ista.ac.at/en/news/pumping-like-the-heart/
scopus_import: '1'
status: public
title: Turbulence suppression by cardiac-cycle-inspired driving of pipe flow
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 621
year: '2023'
...
---
_id: '14342'
abstract:
- lang: eng
text: We propose a simple method to measure nonlinear Kerr refractive index in mid-infrared
frequency range that avoids using sophisticated infrared detectors. Our approach
is based on using a near-infrared probe beam which interacts with a mid-IR beam
via wavelength-non-degenerate cross-phase modulation (XPM). By carefully measuring
XPM-induced spectral modifications in the probe beam and comparing the experimental
data with simulation results, we extract the value for the non-degenerate Kerr
index. Finally, in order to obtain the value of degenerate mid-IR Kerr index,
we use the well-established two-band formalism of Sheik-Bahae et al., which is
shown to become particularly simple in the limit of low frequencies. The proposed
technique is complementary to the conventional techniques, such as z-scan, and
has the advantage of not requiring any mid-infrared detectors.
acknowledgement: The work was supported by IST Austria. The authors would like to
gratefully acknowledge the help and assistance of Professor John M. Dudley.
article_number: '091104'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Dusan
full_name: Lorenc, Dusan
id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87
last_name: Lorenc
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
citation:
ama: Lorenc D, Alpichshev Z. Mid-infrared Kerr index evaluation via cross-phase
modulation with a near-infrared probe beam. Applied Physics Letters. 2023;123(9).
doi:10.1063/5.0161713
apa: Lorenc, D., & Alpichshev, Z. (2023). Mid-infrared Kerr index evaluation
via cross-phase modulation with a near-infrared probe beam. Applied Physics
Letters. AIP Publishing. https://doi.org/10.1063/5.0161713
chicago: Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation
via Cross-Phase Modulation with a near-Infrared Probe Beam.” Applied Physics
Letters. AIP Publishing, 2023. https://doi.org/10.1063/5.0161713.
ieee: D. Lorenc and Z. Alpichshev, “Mid-infrared Kerr index evaluation via cross-phase
modulation with a near-infrared probe beam,” Applied Physics Letters, vol.
123, no. 9. AIP Publishing, 2023.
ista: Lorenc D, Alpichshev Z. 2023. Mid-infrared Kerr index evaluation via cross-phase
modulation with a near-infrared probe beam. Applied Physics Letters. 123(9), 091104.
mla: Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation
via Cross-Phase Modulation with a near-Infrared Probe Beam.” Applied Physics
Letters, vol. 123, no. 9, 091104, AIP Publishing, 2023, doi:10.1063/5.0161713.
short: D. Lorenc, Z. Alpichshev, Applied Physics Letters 123 (2023).
corr_author: '1'
date_created: 2023-09-17T22:01:09Z
date_published: 2023-08-28T00:00:00Z
date_updated: 2025-09-09T12:58:23Z
day: '28'
ddc:
- '530'
department:
- _id: ZhAl
doi: 10.1063/5.0161713
external_id:
arxiv:
- '2306.09043'
isi:
- '001145465400004'
file:
- access_level: open_access
checksum: 89a1b604d58b209fec66c6b6f919ac98
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T11:36:16Z
date_updated: 2023-09-20T11:36:16Z
file_id: '14353'
file_name: 2023_ApplPhysLetter_Lorenc.pdf
file_size: 1486715
relation: main_file
success: 1
file_date_updated: 2023-09-20T11:36:16Z
has_accepted_license: '1'
intvolume: ' 123'
isi: 1
issue: '9'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Applied Physics Letters
publication_identifier:
issn:
- 0003-6951
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared
probe beam
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 123
year: '2023'
...
---
_id: '14344'
abstract:
- lang: eng
text: We study the Hamilton cycle problem with input a random graph G ~ G(n,p) in
two different settings. In the first one, G is given to us in the form of randomly
ordered adjacency lists while in the second one, we are given the adjacency matrix
of G. In each of the two settings we derive a deterministic algorithm that w.h.p.
either finds a Hamilton cycle or returns a certificate that such a cycle does
not exist for p = p(n) ≥ 0. The running times of our algorithms are O(n) and respectively,
each being best possible in its own setting.
article_processing_charge: No
arxiv: 1
author:
- first_name: Michael
full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
citation:
ama: 'Anastos M. Fast algorithms for solving the Hamilton cycle problem with high
probability. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms.
Vol 2023. Society for Industrial and Applied Mathematics; 2023:2286-2323. doi:10.1137/1.9781611977554.ch88'
apa: 'Anastos, M. (2023). Fast algorithms for solving the Hamilton cycle problem
with high probability. In Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms (Vol. 2023, pp. 2286–2323). Florence, Italy: Society for Industrial
and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch88'
chicago: Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem
with High Probability.” In Proceedings of the Annual ACM-SIAM Symposium on
Discrete Algorithms, 2023:2286–2323. Society for Industrial and Applied Mathematics,
2023. https://doi.org/10.1137/1.9781611977554.ch88.
ieee: M. Anastos, “Fast algorithms for solving the Hamilton cycle problem with high
probability,” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms,
Florence, Italy, 2023, vol. 2023, pp. 2286–2323.
ista: 'Anastos M. 2023. Fast algorithms for solving the Hamilton cycle problem with
high probability. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms.
SODA: Symposium on Discrete Algorithms vol. 2023, 2286–2323.'
mla: Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with
High Probability.” Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms, vol. 2023, Society for Industrial and Applied Mathematics, 2023,
pp. 2286–323, doi:10.1137/1.9781611977554.ch88.
short: M. Anastos, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 2286–2323.
conference:
end_date: 2023-01-25
location: Florence, Italy
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2023-01-22
corr_author: '1'
date_created: 2023-09-17T22:01:10Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2024-10-09T21:07:01Z
day: '01'
department:
- _id: MaKw
doi: 10.1137/1.9781611977554.ch88
external_id:
arxiv:
- '2111.14759'
intvolume: ' 2023'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2111.14759
month: '01'
oa: 1
oa_version: Preprint
page: 2286-2323
publication: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
isbn:
- '9781611977554'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast algorithms for solving the Hamilton cycle problem with high probability
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2023
year: '2023'
...
---
_id: '14361'
abstract:
- lang: eng
text: Whether one considers swarming insects, flocking birds, or bacterial colonies,
collective motion arises from the coordination of individuals and entails the
adjustment of their respective velocities. In particular, in close confinements,
such as those encountered by dense cell populations during development or regeneration,
collective migration can only arise coordinately. Yet, how individuals unify their
velocities is often not understood. Focusing on a finite number of cells in circular
confinements, we identify waves of polymerizing actin that function as a pacemaker
governing the speed of individual cells. We show that the onset of collective
motion coincides with the synchronization of the wave nucleation frequencies across
the population. Employing a simpler and more readily accessible mechanical model
system of active spheres, we identify the synchronization of the individuals’
internal oscillators as one of the essential requirements to reach the corresponding
collective state. The mechanical ‘toy’ experiment illustrates that the global
synchronous state is achieved by nearest neighbor coupling. We suggest by analogy
that local coupling and the synchronization of actin waves are essential for the
emergent, self-organized motion of cell collectives.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: M-Shop
acknowledgement: We thank K. O’Keeffe, E. Hannezo, P. Devreotes, C. Dessalles, and
E. Martens for discussion and/or critical reading of the manuscript; the Bioimaging
Facility of ISTA for excellent support, as well as the Life Science Facility and
the Miba Machine Shop of ISTA. This work was supported by the European Research
Council (ERC StG 281556 and CoG 724373) to M.S.
article_number: '5633'
article_processing_charge: Yes
article_type: original
author:
- first_name: Michael
full_name: Riedl, Michael
id: 3BE60946-F248-11E8-B48F-1D18A9856A87
last_name: Riedl
orcid: 0000-0003-4844-6311
- first_name: Isabelle D
full_name: Mayer, Isabelle D
id: 61763940-15b2-11ec-abd3-cfaddfbc66b4
last_name: Mayer
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. Synchronization in collectively
moving inanimate and living active matter. Nature Communications. 2023;14.
doi:10.1038/s41467-023-41432-1
apa: Riedl, M., Mayer, I. D., Merrin, J., Sixt, M. K., & Hof, B. (2023). Synchronization
in collectively moving inanimate and living active matter. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-023-41432-1
chicago: Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn
Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.”
Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41432-1.
ieee: M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization
in collectively moving inanimate and living active matter,” Nature Communications,
vol. 14. Springer Nature, 2023.
ista: Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. 2023. Synchronization in collectively
moving inanimate and living active matter. Nature Communications. 14, 5633.
mla: Riedl, Michael, et al. “Synchronization in Collectively Moving Inanimate and
Living Active Matter.” Nature Communications, vol. 14, 5633, Springer Nature,
2023, doi:10.1038/s41467-023-41432-1.
short: M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications
14 (2023).
corr_author: '1'
date_created: 2023-09-24T22:01:10Z
date_published: 2023-09-13T00:00:00Z
date_updated: 2025-04-14T13:10:03Z
day: '13'
ddc:
- '530'
- '570'
department:
- _id: MiSi
- _id: NanoFab
- _id: BjHo
doi: 10.1038/s41467-023-41432-1
ec_funded: 1
external_id:
isi:
- '001087583700030'
pmid:
- '37704595'
file:
- access_level: open_access
checksum: 82d2d4ad736cc8493db8ce45cd313f7b
content_type: application/pdf
creator: dernst
date_created: 2023-09-25T08:32:37Z
date_updated: 2023-09-25T08:32:37Z
file_id: '14366'
file_name: 2023_NatureComm_Riedl.pdf
file_size: 2317272
relation: main_file
success: 1
file_date_updated: 2023-09-25T08:32:37Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular Navigation Along Spatial Gradients
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synchronization in collectively moving inanimate and living active matter
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '14362'
abstract:
- lang: eng
text: "Motivated by recent applications to entropy theory in dynamical systems,
we generalise notions introduced by Matthews and define weakly weighted and componentwise
weakly weighted (generalised) quasi-metrics. We then systematise and extend to
full generality the correspondences between these objects and other structures
arising in theoretical computer science and dynamics. In particular, we study
the correspondences with weak partial metrics and, if the underlying space is
a semilattice, with invariant (generalised) quasi-metrics satisfying the descending
path condition, and with strictly monotone semi(-co-)valuations.\r\nWe conclude
discussing, for endomorphisms of generalised quasi-metric semilattices, a generalisation
of both the known intrinsic semilattice entropy and the semigroup entropy."
article_number: '114129'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ilaria
full_name: Castellano, Ilaria
last_name: Castellano
- first_name: Anna
full_name: Giordano Bruno, Anna
last_name: Giordano Bruno
- first_name: Nicolò
full_name: Zava, Nicolò
id: c8b3499c-7a77-11eb-b046-aa368cbbf2ad
last_name: Zava
orcid: 0000-0001-8686-1888
citation:
ama: Castellano I, Giordano Bruno A, Zava N. Weakly weighted generalised quasi-metric
spaces and semilattices. Theoretical Computer Science. 2023;977. doi:10.1016/j.tcs.2023.114129
apa: Castellano, I., Giordano Bruno, A., & Zava, N. (2023). Weakly weighted
generalised quasi-metric spaces and semilattices. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2023.114129
chicago: Castellano, Ilaria, Anna Giordano Bruno, and Nicolò Zava. “Weakly Weighted
Generalised Quasi-Metric Spaces and Semilattices.” Theoretical Computer Science.
Elsevier, 2023. https://doi.org/10.1016/j.tcs.2023.114129.
ieee: I. Castellano, A. Giordano Bruno, and N. Zava, “Weakly weighted generalised
quasi-metric spaces and semilattices,” Theoretical Computer Science, vol.
977. Elsevier, 2023.
ista: Castellano I, Giordano Bruno A, Zava N. 2023. Weakly weighted generalised
quasi-metric spaces and semilattices. Theoretical Computer Science. 977, 114129.
mla: Castellano, Ilaria, et al. “Weakly Weighted Generalised Quasi-Metric Spaces
and Semilattices.” Theoretical Computer Science, vol. 977, 114129, Elsevier,
2023, doi:10.1016/j.tcs.2023.114129.
short: I. Castellano, A. Giordano Bruno, N. Zava, Theoretical Computer Science 977
(2023).
corr_author: '1'
date_created: 2023-09-24T22:01:11Z
date_published: 2023-10-25T00:00:00Z
date_updated: 2024-10-09T21:07:00Z
day: '25'
department:
- _id: HeEd
doi: 10.1016/j.tcs.2023.114129
external_id:
arxiv:
- '2212.08424'
isi:
- '001076934000001'
intvolume: ' 977'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.48550/arXiv.2212.08424 '
month: '10'
oa: 1
oa_version: Preprint
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Weakly weighted generalised quasi-metric spaces and semilattices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 977
year: '2023'
...
---
_id: '14363'
abstract:
- lang: eng
text: Mitochondrial networks remodel their connectivity, content, and subcellular
localization to support optimized energy production in conditions of increased
environmental or cellular stress. Microglia rely on mitochondria to respond to
these stressors, however our knowledge about mitochondrial networks and their
adaptations in microglia in vivo is limited. Here, we generate a mouse model that
selectively labels mitochondria in microglia. We identify that mitochondrial networks
are more fragmented with increased content and perinuclear localization in vitro
vs. in vivo. Mitochondrial networks adapt similarly in microglia closest to the
injury site after optic nerve crush. Preventing microglial UCP2 increase after
injury by selective knockout induces cellular stress. This results in mitochondrial
hyperfusion in male microglia, a phenotype absent in females due to circulating
estrogens. Our results establish the foundation for mitochondrial network analysis
of microglia in vivo, emphasizing the importance of mitochondrial-based sex effects
of microglia in other pathologies.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
acknowledgement: We thank the Scientific Service Units (SSU) of ISTA through resources
provided by the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF),
and the Pre-Clinical Facility (PCF) team, specifically Sonja Haslinger and Michael
Schunn for excellent mouse colony management and support. This research was supported
by the FWF Sonderforschungsbereich F83 (to E.E.P). We thank Bálint Nagy, Ryan John
A. Cubero, Marco Benevento and all members of the Siegert group for constant feedback
on the project and article.
article_number: '107780'
article_processing_charge: Yes
article_type: original
author:
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Gloria
full_name: Colombo, Gloria
id: 3483CF6C-F248-11E8-B48F-1D18A9856A87
last_name: Colombo
orcid: 0000-0001-9434-8902
- first_name: Florianne E
full_name: Schoot Uiterkamp, Florianne E
id: 3526230C-F248-11E8-B48F-1D18A9856A87
last_name: Schoot Uiterkamp
- first_name: Felix
full_name: Sternberg, Felix
last_name: Sternberg
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Elena E.
full_name: Pohl, Elena E.
last_name: Pohl
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Maes ME, Colombo G, Schoot Uiterkamp FE, et al. Mitochondrial network adaptations
of microglia reveal sex-specific stress response after injury and UCP2 knockout.
iScience. 2023;26(10). doi:10.1016/j.isci.2023.107780
apa: Maes, M. E., Colombo, G., Schoot Uiterkamp, F. E., Sternberg, F., Venturino,
A., Pohl, E. E., & Siegert, S. (2023). Mitochondrial network adaptations of
microglia reveal sex-specific stress response after injury and UCP2 knockout.
IScience. Elsevier. https://doi.org/10.1016/j.isci.2023.107780
chicago: Maes, Margaret E, Gloria Colombo, Florianne E Schoot Uiterkamp, Felix Sternberg,
Alessandro Venturino, Elena E. Pohl, and Sandra Siegert. “Mitochondrial Network
Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and
UCP2 Knockout.” IScience. Elsevier, 2023. https://doi.org/10.1016/j.isci.2023.107780.
ieee: M. E. Maes et al., “Mitochondrial network adaptations of microglia
reveal sex-specific stress response after injury and UCP2 knockout,” iScience,
vol. 26, no. 10. Elsevier, 2023.
ista: Maes ME, Colombo G, Schoot Uiterkamp FE, Sternberg F, Venturino A, Pohl EE,
Siegert S. 2023. Mitochondrial network adaptations of microglia reveal sex-specific
stress response after injury and UCP2 knockout. iScience. 26(10), 107780.
mla: Maes, Margaret E., et al. “Mitochondrial Network Adaptations of Microglia Reveal
Sex-Specific Stress Response after Injury and UCP2 Knockout.” IScience,
vol. 26, no. 10, 107780, Elsevier, 2023, doi:10.1016/j.isci.2023.107780.
short: M.E. Maes, G. Colombo, F.E. Schoot Uiterkamp, F. Sternberg, A. Venturino,
E.E. Pohl, S. Siegert, IScience 26 (2023).
corr_author: '1'
date_created: 2023-09-24T22:01:11Z
date_published: 2023-10-20T00:00:00Z
date_updated: 2024-10-09T21:07:01Z
day: '20'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1016/j.isci.2023.107780
external_id:
isi:
- '001080403500001'
pmid:
- '37731609'
file:
- access_level: open_access
checksum: be1a560efdd96d20712311f4fc54aac2
content_type: application/pdf
creator: dernst
date_created: 2023-11-07T08:53:21Z
date_updated: 2023-11-07T08:53:21Z
file_id: '14497'
file_name: 2023_iScience_Maes.pdf
file_size: 8197935
relation: main_file
success: 1
file_date_updated: 2023-11-07T08:53:21Z
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: iScience
publication_identifier:
eissn:
- 2589-0042
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mitochondrial network adaptations of microglia reveal sex-specific stress response
after injury and UCP2 knockout
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2023'
...
---
_id: '14364'
abstract:
- lang: eng
text: We introduce extension-based proofs, a class of impossibility proofs that
includes valency arguments. They are modelled as an interaction between a prover
and a protocol. Using proofs based on combinatorial topology, it has been shown
that it is impossible to deterministically solve -set agreement among processes
or approximate agreement on a cycle of length 4 among processes in a wait-free
manner in asynchronous models where processes communicate using objects that can
be constructed from shared registers. However, it was unknown whether proofs based
on simpler techniques were possible. We show that these impossibility results
cannot be obtained by extension-based proofs in the iterated snapshot model and,
hence, extension-based proofs are limited in power.
acknowledgement: "We would like to thank Valerie King, Toniann Pitassi, and Michael
Saks for helpful discussions and Shi Hao Liu for his useful feedback.\r\nThis research
was supported by the Natural Science and Engineering Research Council of Canada
under grants RGPIN-2015-05080 and RGPIN-2020-04178, a postgraduate scholarship,
and a postdoctoral fellowship; a University of Toronto postdoctoral fellowship;
the National Science Foundation under grants CCF-1217921, CCF-1301926, CCF-1637385,
CCF-1650596, and IIS-1447786; the U.S. Department of Energy under grant ER26116/DE-SC0008923;
the European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation programme grant agreement 805223 ScaleML; and the Oracle and Intel
corporations. Some of the work on this paper was done while Faith Ellen was visiting
IST Austria."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: Faith
full_name: Ellen, Faith
last_name: Ellen
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Leqi
full_name: Zhu, Leqi
id: a2117c59-cee4-11ed-b9d0-874ecf0f8ac5
last_name: Zhu
citation:
ama: Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based proofs
fail. SIAM Journal on Computing. 2023;52(4):913-944. doi:10.1137/20M1375851
apa: Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2023).
Why extension-based proofs fail. SIAM Journal on Computing. Society for
Industrial and Applied Mathematics. https://doi.org/10.1137/20M1375851
chicago: Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi
Zhu. “Why Extension-Based Proofs Fail.” SIAM Journal on Computing. Society
for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/20M1375851.
ieee: D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based
proofs fail,” SIAM Journal on Computing, vol. 52, no. 4. Society for Industrial
and Applied Mathematics, pp. 913–944, 2023.
ista: Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2023. Why extension-based
proofs fail. SIAM Journal on Computing. 52(4), 913–944.
mla: Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” SIAM Journal
on Computing, vol. 52, no. 4, Society for Industrial and Applied Mathematics,
2023, pp. 913–44, doi:10.1137/20M1375851.
short: D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, SIAM Journal
on Computing 52 (2023) 913–944.
date_created: 2023-09-24T22:01:11Z
date_published: 2023-07-25T00:00:00Z
date_updated: 2025-05-14T11:26:06Z
day: '25'
department:
- _id: DaAl
doi: 10.1137/20M1375851
ec_funded: 1
external_id:
arxiv:
- '1811.01421'
isi:
- '001082972300004'
intvolume: ' 52'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1811.01421
month: '07'
oa: 1
oa_version: Preprint
page: 913-944
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: SIAM Journal on Computing
publication_identifier:
eissn:
- 1095-7111
issn:
- 0097-5397
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
related_material:
record:
- id: '6676'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Why extension-based proofs fail
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2023'
...
---
_id: '14368'
abstract:
- lang: eng
text: "Purpose: \r\nBiallelic variants in TARS2, encoding the mitochondrial threonyl-tRNA-synthetase,
have been reported in a small group of individuals displaying a neurodevelopmental
phenotype but with limited neuroradiological data and insufficient evidence for
causality of the variants.\r\nMethods:\r\nExome or genome sequencing was carried
out in 15 families. Clinical and neuroradiological evaluation was performed for
all affected individuals, including review of 10 previously reported individuals.
The pathogenicity of TARS2 variants was evaluated using in vitro assays and a
zebrafish model.\r\nResults:\r\nWe report 18 new individuals harboring biallelic
TARS2 variants. Phenotypically, these individuals show developmental delay/intellectual
disability, regression, cerebellar and cerebral atrophy, basal ganglia signal
alterations, hypotonia, cerebellar signs, and increased blood lactate. In vitro
studies showed that variants within the TARS2301-381 region had decreased binding
to Rag GTPases, likely impairing mTORC1 activity. The zebrafish model recapitulated
key features of the human phenotype and unraveled dysregulation of downstream
targets of mTORC1 signaling. Functional testing of the variants confirmed the
pathogenicity in a zebrafish model.\r\nConclusion:\r\nWe define the clinico-radiological
spectrum of TARS2-related mitochondrial disease, unveil the likely involvement
of the mTORC1 signaling pathway as a distinct molecular mechanism, and establish
a TARS2 zebrafish model as an important tool to study variant pathogenicity."
article_number: '100938'
article_processing_charge: No
article_type: original
author:
- first_name: Andrea
full_name: Accogli, Andrea
last_name: Accogli
- first_name: Sheng-Jia
full_name: Lin, Sheng-Jia
last_name: Lin
- first_name: Mariasavina
full_name: Severino, Mariasavina
last_name: Severino
- first_name: Sung-Hoon
full_name: Kim, Sung-Hoon
last_name: Kim
- first_name: Kevin
full_name: Huang, Kevin
id: 3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3
last_name: Huang
orcid: 0000-0002-2512-7812
- first_name: Clarissa
full_name: Rocca, Clarissa
last_name: Rocca
- first_name: Megan
full_name: Landsverk, Megan
last_name: Landsverk
- first_name: Maha S.
full_name: Zaki, Maha S.
last_name: Zaki
- first_name: Almundher
full_name: Al-Maawali, Almundher
last_name: Al-Maawali
- first_name: Varunvenkat M.
full_name: Srinivasan, Varunvenkat M.
last_name: Srinivasan
- first_name: Khalid
full_name: Al-Thihli, Khalid
last_name: Al-Thihli
- first_name: G. Bradly
full_name: Schaefer, G. Bradly
last_name: Schaefer
- first_name: Monica
full_name: Davis, Monica
last_name: Davis
- first_name: Davide
full_name: Tonduti, Davide
last_name: Tonduti
- first_name: Chiara
full_name: Doneda, Chiara
last_name: Doneda
- first_name: Lara M.
full_name: Marten, Lara M.
last_name: Marten
- first_name: Chris
full_name: Mühlhausen, Chris
last_name: Mühlhausen
- first_name: Maria
full_name: Gomez, Maria
last_name: Gomez
- first_name: Eleonora
full_name: Lamantea, Eleonora
last_name: Lamantea
- first_name: Rafael
full_name: Mena, Rafael
last_name: Mena
- first_name: Mathilde
full_name: Nizon, Mathilde
last_name: Nizon
- first_name: Vincent
full_name: Procaccio, Vincent
last_name: Procaccio
- first_name: Amber
full_name: Begtrup, Amber
last_name: Begtrup
- first_name: Aida
full_name: Telegrafi, Aida
last_name: Telegrafi
- first_name: Hong
full_name: Cui, Hong
last_name: Cui
- first_name: Heidi L.
full_name: Schulz, Heidi L.
last_name: Schulz
- first_name: Julia
full_name: Mohr, Julia
last_name: Mohr
- first_name: Saskia
full_name: Biskup, Saskia
last_name: Biskup
- first_name: Mariana Amina
full_name: Loos, Mariana Amina
last_name: Loos
- first_name: Hilda Verónica
full_name: Aráoz, Hilda Verónica
last_name: Aráoz
- first_name: Vincenzo
full_name: Salpietro, Vincenzo
last_name: Salpietro
- first_name: Laura Davis
full_name: Keppen, Laura Davis
last_name: Keppen
- first_name: Manali
full_name: Chitre, Manali
last_name: Chitre
- first_name: Cassidy
full_name: Petree, Cassidy
last_name: Petree
- first_name: Lucy
full_name: Raymond, Lucy
last_name: Raymond
- first_name: Julie
full_name: Vogt, Julie
last_name: Vogt
- first_name: Lindsey B.
full_name: Sawyer, Lindsey B.
last_name: Sawyer
- first_name: Alice A.
full_name: Basinger, Alice A.
last_name: Basinger
- first_name: Signe Vandal
full_name: Pedersen, Signe Vandal
last_name: Pedersen
- first_name: Toni S.
full_name: Pearson, Toni S.
last_name: Pearson
- first_name: Dorothy K.
full_name: Grange, Dorothy K.
last_name: Grange
- first_name: Lokesh
full_name: Lingappa, Lokesh
last_name: Lingappa
- first_name: Paige
full_name: McDunnah, Paige
last_name: McDunnah
- first_name: Rita
full_name: Horvath, Rita
last_name: Horvath
- first_name: Benjamin
full_name: Cognè, Benjamin
last_name: Cognè
- first_name: Bertrand
full_name: Isidor, Bertrand
last_name: Isidor
- first_name: Andreas
full_name: Hahn, Andreas
last_name: Hahn
- first_name: Karen W.
full_name: Gripp, Karen W.
last_name: Gripp
- first_name: Seyed Mehdi
full_name: Jafarnejad, Seyed Mehdi
last_name: Jafarnejad
- first_name: Elsebet
full_name: Østergaard, Elsebet
last_name: Østergaard
- first_name: Carlos E.
full_name: Prada, Carlos E.
last_name: Prada
- first_name: Daniele
full_name: Ghezzi, Daniele
last_name: Ghezzi
- first_name: Vykuntaraju K.
full_name: Gowda, Vykuntaraju K.
last_name: Gowda
- first_name: Robert W.
full_name: Taylor, Robert W.
last_name: Taylor
- first_name: Nahum
full_name: Sonenberg, Nahum
last_name: Sonenberg
- first_name: Henry
full_name: Houlden, Henry
last_name: Houlden
- first_name: Marie
full_name: Sissler, Marie
last_name: Sissler
- first_name: Gaurav K.
full_name: Varshney, Gaurav K.
last_name: Varshney
- first_name: Reza
full_name: Maroofian, Reza
last_name: Maroofian
citation:
ama: Accogli A, Lin S-J, Severino M, et al. Clinical, neuroradiological, and molecular
characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder.
Genetics in Medicine. 2023;25(11). doi:10.1016/j.gim.2023.100938
apa: Accogli, A., Lin, S.-J., Severino, M., Kim, S.-H., Huang, K., Rocca, C., …
Maroofian, R. (2023). Clinical, neuroradiological, and molecular characterization
of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. Genetics
in Medicine. Elsevier. https://doi.org/10.1016/j.gim.2023.100938
chicago: Accogli, Andrea, Sheng-Jia Lin, Mariasavina Severino, Sung-Hoon Kim, Kevin
Huang, Clarissa Rocca, Megan Landsverk, et al. “Clinical, Neuroradiological, and
Molecular Characterization of Mitochondrial Threonyl-TRNA-Synthetase (TARS2)-Related
Disorder.” Genetics in Medicine. Elsevier, 2023. https://doi.org/10.1016/j.gim.2023.100938.
ieee: A. Accogli et al., “Clinical, neuroradiological, and molecular characterization
of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder,” Genetics
in Medicine, vol. 25, no. 11. Elsevier, 2023.
ista: Accogli A, Lin S-J, Severino M, Kim S-H, Huang K, Rocca C, Landsverk M, Zaki
MS, Al-Maawali A, Srinivasan VM, Al-Thihli K, Schaefer GB, Davis M, Tonduti D,
Doneda C, Marten LM, Mühlhausen C, Gomez M, Lamantea E, Mena R, Nizon M, Procaccio
V, Begtrup A, Telegrafi A, Cui H, Schulz HL, Mohr J, Biskup S, Loos MA, Aráoz
HV, Salpietro V, Keppen LD, Chitre M, Petree C, Raymond L, Vogt J, Sawyer LB,
Basinger AA, Pedersen SV, Pearson TS, Grange DK, Lingappa L, McDunnah P, Horvath
R, Cognè B, Isidor B, Hahn A, Gripp KW, Jafarnejad SM, Østergaard E, Prada CE,
Ghezzi D, Gowda VK, Taylor RW, Sonenberg N, Houlden H, Sissler M, Varshney GK,
Maroofian R. 2023. Clinical, neuroradiological, and molecular characterization
of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. Genetics in
Medicine. 25(11), 100938.
mla: Accogli, Andrea, et al. “Clinical, Neuroradiological, and Molecular Characterization
of Mitochondrial Threonyl-TRNA-Synthetase (TARS2)-Related Disorder.” Genetics
in Medicine, vol. 25, no. 11, 100938, Elsevier, 2023, doi:10.1016/j.gim.2023.100938.
short: A. Accogli, S.-J. Lin, M. Severino, S.-H. Kim, K. Huang, C. Rocca, M. Landsverk,
M.S. Zaki, A. Al-Maawali, V.M. Srinivasan, K. Al-Thihli, G.B. Schaefer, M. Davis,
D. Tonduti, C. Doneda, L.M. Marten, C. Mühlhausen, M. Gomez, E. Lamantea, R. Mena,
M. Nizon, V. Procaccio, A. Begtrup, A. Telegrafi, H. Cui, H.L. Schulz, J. Mohr,
S. Biskup, M.A. Loos, H.V. Aráoz, V. Salpietro, L.D. Keppen, M. Chitre, C. Petree,
L. Raymond, J. Vogt, L.B. Sawyer, A.A. Basinger, S.V. Pedersen, T.S. Pearson,
D.K. Grange, L. Lingappa, P. McDunnah, R. Horvath, B. Cognè, B. Isidor, A. Hahn,
K.W. Gripp, S.M. Jafarnejad, E. Østergaard, C.E. Prada, D. Ghezzi, V.K. Gowda,
R.W. Taylor, N. Sonenberg, H. Houlden, M. Sissler, G.K. Varshney, R. Maroofian,
Genetics in Medicine 25 (2023).
date_created: 2023-09-25T08:44:29Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2023-09-25T08:50:10Z
day: '01'
ddc:
- '570'
doi: 10.1016/j.gim.2023.100938
extern: '1'
file:
- access_level: open_access
checksum: 440f0cd8a2ffcbe03c015c1746728387
content_type: application/pdf
creator: dernst
date_created: 2023-09-25T08:48:54Z
date_updated: 2023-09-25T08:48:54Z
file_id: '14369'
file_name: 2023_GeneticsMedicine_Accogli.pdf
file_size: 4105513
relation: main_file
success: 1
file_date_updated: 2023-09-25T08:48:54Z
has_accepted_license: '1'
intvolume: ' 25'
issue: '11'
keyword:
- Genetics (clinical)
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Genetics in Medicine
publication_identifier:
issn:
- 1098-3600
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Clinical, neuroradiological, and molecular characterization of mitochondrial
threonyl-tRNA-synthetase (TARS2)-related disorder
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2023'
...
---
OA_place: publisher
_id: '14374'
abstract:
- lang: eng
text: "Superconductivity has many important applications ranging from levitating
trains over qubits to MRI scanners. The phenomenon is successfully modeled by
Bardeen-Cooper-Schrieffer (BCS) theory. From a mathematical perspective, BCS theory
has been studied extensively for systems without boundary. However, little is
known in the presence of boundaries. With the help of numerical methods physicists
observed that the critical temperature may increase in the presence of a boundary.
The goal of this thesis is to understand the influence of boundaries on the critical
temperature in BCS theory and to give a first rigorous justification of these
observations. On the way, we also study two-body Schrödinger operators on domains
with boundaries and prove additional results for superconductors without boundary.\r\n\r\nBCS
theory is based on a non-linear functional, where the minimizer indicates whether
the system is superconducting or in the normal, non-superconducting state. By
considering the Hessian of the BCS functional at the normal state, one can analyze
whether the normal state is possibly a minimum of the BCS functional and estimate
the critical temperature. The Hessian turns out to be a linear operator resembling
a Schrödinger operator for two interacting particles, but with more complicated
kinetic energy. As a first step, we study the two-body Schrödinger operator in
the presence of boundaries.\r\nFor Neumann boundary conditions, we prove that
the addition of a boundary can create new eigenvalues, which correspond to the
two particles forming a bound state close to the boundary.\r\n\r\nSecond, we need
to understand superconductivity in the translation invariant setting. While in
three dimensions this has been extensively studied, there is no mathematical literature
for the one and two dimensional cases. In dimensions one and two, we compute the
weak coupling asymptotics of the critical temperature and the energy gap in the
translation invariant setting. We also prove that their ratio is independent of
the microscopic details of the model in the weak coupling limit; this property
is referred to as universality.\r\n\r\nIn the third part, we study the critical
temperature of superconductors in the presence of boundaries. We start by considering
the one-dimensional case of a half-line with contact interaction. Then, we generalize
the results to generic interactions and half-spaces in one, two and three dimensions.
Finally, we compare the critical temperature of a quarter space in two dimensions
to the critical temperatures of a half-space and of the full space."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Barbara
full_name: Roos, Barbara
id: 5DA90512-D80F-11E9-8994-2E2EE6697425
last_name: Roos
orcid: 0000-0002-9071-5880
citation:
ama: Roos B. Boundary superconductivity in BCS theory. 2023. doi:10.15479/at:ista:14374
apa: Roos, B. (2023). Boundary superconductivity in BCS theory. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:14374
chicago: Roos, Barbara. “Boundary Superconductivity in BCS Theory.” Institute of
Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14374.
ieee: B. Roos, “Boundary superconductivity in BCS theory,” Institute of Science
and Technology Austria, 2023.
ista: Roos B. 2023. Boundary superconductivity in BCS theory. Institute of Science
and Technology Austria.
mla: Roos, Barbara. Boundary Superconductivity in BCS Theory. Institute of
Science and Technology Austria, 2023, doi:10.15479/at:ista:14374.
short: B. Roos, Boundary Superconductivity in BCS Theory, Institute of Science and
Technology Austria, 2023.
corr_author: '1'
date_created: 2023-09-28T14:23:04Z
date_published: 2023-09-30T00:00:00Z
date_updated: 2026-04-07T13:27:39Z
day: '30'
ddc:
- '515'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RoSe
doi: 10.15479/at:ista:14374
ec_funded: 1
file:
- access_level: open_access
checksum: ef039ffc3de2cb8dee5b14110938e9b6
content_type: application/pdf
creator: broos
date_created: 2023-10-06T11:35:56Z
date_updated: 2023-10-06T11:35:56Z
file_id: '14398'
file_name: phd-thesis-draft_pdfa_acrobat.pdf
file_size: 2365702
relation: main_file
- access_level: closed
checksum: 81dcac33daeefaf0111db52f41bb1fd0
content_type: application/x-zip-compressed
creator: broos
date_created: 2023-10-06T11:38:01Z
date_updated: 2023-10-06T11:38:01Z
file_id: '14399'
file_name: Version5.zip
file_size: 4691734
relation: source_file
file_date_updated: 2023-10-06T11:38:01Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '09'
oa: 1
oa_version: Published Version
page: '206'
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: bda63fe5-d553-11ed-ba76-a16e3d2f256b
grant_number: I06427
name: Mathematical Challenges in BCS Theory of Superconductivity
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10850'
relation: part_of_dissertation
status: public
- id: '13207'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
title: Boundary superconductivity in BCS theory
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
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: '14379'
abstract:
- lang: eng
text: We report on a simple surfactant/template free chemical route for the synthesis
of semi-polycrystalline polyaniline-graphite (SPani-graphite) composite and its
application as an electroactive material in electrochemical charge storage. The
synthesized material exhibits well-defined poly-crystallographic lattices in high
resolution transmission electron micrographs and sharp peaks in x-ray diffraction
spectra suggesting crystalline nature of the material. The specific capacitance
computed from the galvanostatic charge-discharge (GCD) data obtained from 3-electrode
cell configuration using 1 M aq. Na2SO4 as an electrolyte was 111.4 F g−1 at a
current density of 0.1 A g−1 which rises to 269 F g−1 at an elevated current density
of 1.0 A g−1. A similar pattern of increase in the specific capacitance values
with an increase in the current density was observed in the results obtained from
2-electrode symmetric device configuration using polymer gel electrolyte (xanthan
gum in 1 M aq. Na2SO4). The specific capacitance computed from the GCD data obtained
from the device configuration was 20 F g−1 at the current density of 1.0 A g−1.
The device delivers an energy density of 1.7 Wh kg−1 and a power density of 2.48
kWh kg−1 at an applied current density of 0.5 A g−1 suggesting an excellent rate
capability and power management. In addition, the device exhibits ⁓92 % specific
capacitance retention up to 8000 continuous GCD cycles and ⁓80 % coulombic efficiency
up to 10,000 continuous GCD cycles indicating excellent cycling stability. The
unique feature of increasing specific capacitance with respect to applied current
density is attributed to the presence of semi-polycrystalline phases in the SPani-graphite
matrix. The material behaves as a surface redox supercapacitor and its unique
mechanism of charge storage is discussed in detail in the article.
acknowledgement: This work was supported by 2023 Yeungnam University Research Grant.
article_number: '117463'
article_processing_charge: No
article_type: original
author:
- first_name: Neelima
full_name: Mahato, Neelima
last_name: Mahato
- first_name: Saurabh
full_name: Singh, Saurabh
id: 12d625da-9cb3-11ed-9667-af09d37d3f0a
last_name: Singh
orcid: 0000-0003-2209-5269
- first_name: Mohammad
full_name: Faisal, Mohammad
last_name: Faisal
- first_name: T. V.M.
full_name: Sreekanth, T. V.M.
last_name: Sreekanth
- first_name: Sutripto
full_name: Majumder, Sutripto
last_name: Majumder
- first_name: Kisoo
full_name: Yoo, Kisoo
last_name: Yoo
- first_name: Jonghoon
full_name: Kim, Jonghoon
last_name: Kim
citation:
ama: Mahato N, Singh S, Faisal M, et al. Polycrystalline phases grown in-situ engendering
unique mechanism of charge storage in polyaniline-graphite composite. Synthetic
Metals. 2023;299. doi:10.1016/j.synthmet.2023.117463
apa: Mahato, N., Singh, S., Faisal, M., Sreekanth, T. V. M., Majumder, S., Yoo,
K., & Kim, J. (2023). Polycrystalline phases grown in-situ engendering unique
mechanism of charge storage in polyaniline-graphite composite. Synthetic Metals.
Elsevier. https://doi.org/10.1016/j.synthmet.2023.117463
chicago: Mahato, Neelima, Saurabh Singh, Mohammad Faisal, T. V.M. Sreekanth, Sutripto
Majumder, Kisoo Yoo, and Jonghoon Kim. “Polycrystalline Phases Grown In-Situ Engendering
Unique Mechanism of Charge Storage in Polyaniline-Graphite Composite.” Synthetic
Metals. Elsevier, 2023. https://doi.org/10.1016/j.synthmet.2023.117463.
ieee: N. Mahato et al., “Polycrystalline phases grown in-situ engendering
unique mechanism of charge storage in polyaniline-graphite composite,” Synthetic
Metals, vol. 299. Elsevier, 2023.
ista: Mahato N, Singh S, Faisal M, Sreekanth TVM, Majumder S, Yoo K, Kim J. 2023.
Polycrystalline phases grown in-situ engendering unique mechanism of charge storage
in polyaniline-graphite composite. Synthetic Metals. 299, 117463.
mla: Mahato, Neelima, et al. “Polycrystalline Phases Grown In-Situ Engendering Unique
Mechanism of Charge Storage in Polyaniline-Graphite Composite.” Synthetic Metals,
vol. 299, 117463, Elsevier, 2023, doi:10.1016/j.synthmet.2023.117463.
short: N. Mahato, S. Singh, M. Faisal, T.V.M. Sreekanth, S. Majumder, K. Yoo, J.
Kim, Synthetic Metals 299 (2023).
date_created: 2023-10-01T22:01:13Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2024-01-30T13:55:50Z
day: '01'
department:
- _id: MaIb
doi: 10.1016/j.synthmet.2023.117463
external_id:
isi:
- '001083568900001'
intvolume: ' 299'
isi: 1
language:
- iso: eng
month: '11'
oa_version: None
publication: Synthetic Metals
publication_identifier:
issn:
- 0379-6779
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Polycrystalline phases grown in-situ engendering unique mechanism of charge
storage in polyaniline-graphite composite
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 299
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: '14404'
abstract:
- lang: eng
text: A light-triggered fabrication method extends the functionality of printable
nanomaterials
acknowledgement: The authors thank the Werner-Siemens-Stiftung and the Institute of
Science and Technology Austria for financial support.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Daniel
full_name: Balazs, Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: Balazs D, Ibáñez M. Widening the use of 3D printing. Science. 2023;381(6665):1413-1414.
doi:10.1126/science.adk3070
apa: Balazs, D., & Ibáñez, M. (2023). Widening the use of 3D printing. Science.
AAAS. https://doi.org/10.1126/science.adk3070
chicago: Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” Science.
AAAS, 2023. https://doi.org/10.1126/science.adk3070.
ieee: D. Balazs and M. Ibáñez, “Widening the use of 3D printing,” Science,
vol. 381, no. 6665. AAAS, pp. 1413–1414, 2023.
ista: Balazs D, Ibáñez M. 2023. Widening the use of 3D printing. Science. 381(6665),
1413–1414.
mla: Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” Science,
vol. 381, no. 6665, AAAS, 2023, pp. 1413–14, doi:10.1126/science.adk3070.
short: D. Balazs, M. Ibáñez, Science 381 (2023) 1413–1414.
corr_author: '1'
date_created: 2023-10-08T22:01:16Z
date_published: 2023-09-29T00:00:00Z
date_updated: 2025-09-09T13:04:47Z
day: '29'
department:
- _id: MaIb
- _id: LifeSc
doi: 10.1126/science.adk3070
external_id:
isi:
- '001100656800023'
pmid:
- '37769110'
intvolume: ' 381'
isi: 1
issue: '6665'
language:
- iso: eng
month: '09'
oa_version: None
page: 1413-1414
pmid: 1
project:
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Widening the use of 3D printing
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 381
year: '2023'
...