---
_id: '14514'
abstract:
- lang: eng
text: 'The elastic Leidenfrost effect occurs when a vaporizable soft solid is lowered
onto a hot surface. Evaporative flow couples to elastic deformation, giving spontaneous
bouncing or steady-state floating. The effect embodies an unexplored interplay
between thermodynamics, elasticity, and lubrication: despite being observed, its
basic theoretical description remains a challenge. Here, we provide a theory of
elastic Leidenfrost floating. As weight increases, a rigid solid sits closer to
the hot surface. By contrast, we discover an elasticity-dominated regime where
the heavier the solid, the higher it floats. This geometry-governed behavior is
reminiscent of the dynamics of large liquid Leidenfrost drops. We show that this
elastic regime is characterized by Hertzian behavior of the solid’s underbelly
and derive how the float height scales with materials parameters. Introducing
a dimensionless elastic Leidenfrost number, we capture the crossover between rigid
and Hertzian behavior. Our results provide theoretical underpinning for recent
experiments, and point to the design of novel soft machines.'
acknowledgement: "We are grateful to Dominic Vella, Jens Eggers, John Kolinski, Joshua
Dijksman, and Daniel Bonn for insightful discussions. J. B. and A. S. acknowledge
the support of the Engineering and Physical Sciences Research Council (EPSRC) through
New Investigator Award No. EP/\r\nT000961/1. A. S. acknowledges the support of Royal
Society under Grant No. RGS/R2/202135. J. E. S. acknowledges EPSRC Grants No. EP/N016602/1,
EP/S022848/1, EP/S029966/1, and EP/P031684/1."
article_number: '168201'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jack
full_name: Binysh, Jack
last_name: Binysh
- first_name: Indrajit
full_name: Chakraborty, Indrajit
last_name: Chakraborty
- first_name: Mykyta V.
full_name: Chubynsky, Mykyta V.
last_name: Chubynsky
- first_name: Vicente L
full_name: Diaz Melian, Vicente L
id: b6798902-eea0-11ea-9cbc-a8e14286c631
last_name: Diaz Melian
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: James E.
full_name: Sprittles, James E.
last_name: Sprittles
- first_name: Anton
full_name: Souslov, Anton
last_name: Souslov
citation:
ama: Binysh J, Chakraborty I, Chubynsky MV, et al. Modeling Leidenfrost levitation
of soft elastic solids. Physical Review Letters. 2023;131(16). doi:10.1103/PhysRevLett.131.168201
apa: Binysh, J., Chakraborty, I., Chubynsky, M. V., Diaz Melian, V. L., Waitukaitis,
S. R., Sprittles, J. E., & Souslov, A. (2023). Modeling Leidenfrost levitation
of soft elastic solids. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/PhysRevLett.131.168201
chicago: Binysh, Jack, Indrajit Chakraborty, Mykyta V. Chubynsky, Vicente L Diaz
Melian, Scott R Waitukaitis, James E. Sprittles, and Anton Souslov. “Modeling
Leidenfrost Levitation of Soft Elastic Solids.” Physical Review Letters.
American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.131.168201.
ieee: J. Binysh et al., “Modeling Leidenfrost levitation of soft elastic
solids,” Physical Review Letters, vol. 131, no. 16. American Physical Society,
2023.
ista: Binysh J, Chakraborty I, Chubynsky MV, Diaz Melian VL, Waitukaitis SR, Sprittles
JE, Souslov A. 2023. Modeling Leidenfrost levitation of soft elastic solids. Physical
Review Letters. 131(16), 168201.
mla: Binysh, Jack, et al. “Modeling Leidenfrost Levitation of Soft Elastic Solids.”
Physical Review Letters, vol. 131, no. 16, 168201, American Physical Society,
2023, doi:10.1103/PhysRevLett.131.168201.
short: J. Binysh, I. Chakraborty, M.V. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis,
J.E. Sprittles, A. Souslov, Physical Review Letters 131 (2023).
date_created: 2023-11-12T23:00:55Z
date_published: 2023-10-20T00:00:00Z
date_updated: 2023-11-13T09:21:30Z
day: '20'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1103/PhysRevLett.131.168201
file:
- access_level: open_access
checksum: 1a419e25b762aadffbcc8eb2e609bd97
content_type: application/pdf
creator: dernst
date_created: 2023-11-13T09:12:58Z
date_updated: 2023-11-13T09:12:58Z
file_id: '14524'
file_name: 2023_PhysRevLetters_Binysh.pdf
file_size: 724098
relation: main_file
success: 1
file_date_updated: 2023-11-13T09:12:58Z
has_accepted_license: '1'
intvolume: ' 131'
issue: '16'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
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relation: research_data
status: public
scopus_import: '1'
status: public
title: Modeling Leidenfrost levitation of soft elastic solids
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: 131
year: '2023'
...
---
_id: '14523'
abstract:
- lang: eng
text: see Readme file
article_processing_charge: No
author:
- first_name: Jack
full_name: Binysh, Jack
last_name: Binysh
- first_name: Indrajit
full_name: Chakraborty, Indrajit
last_name: Chakraborty
- first_name: Mykyta
full_name: Chubynsky, Mykyta
last_name: Chubynsky
- first_name: Vicente L
full_name: Diaz Melian, Vicente L
id: b6798902-eea0-11ea-9cbc-a8e14286c631
last_name: Diaz Melian
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: James
full_name: Sprittles, James
last_name: Sprittles
- first_name: Anton
full_name: Souslov, Anton
last_name: Souslov
citation:
ama: 'Binysh J, Chakraborty I, Chubynsky M, et al. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
v1.0.1. 2023. doi:10.5281/ZENODO.8329143'
apa: 'Binysh, J., Chakraborty, I., Chubynsky, M., Diaz Melian, V. L., Waitukaitis,
S. R., Sprittles, J., & Souslov, A. (2023). SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
v1.0.1. Zenodo. https://doi.org/10.5281/ZENODO.8329143'
chicago: 'Binysh, Jack, Indrajit Chakraborty, Mykyta Chubynsky, Vicente L Diaz Melian,
Scott R Waitukaitis, James Sprittles, and Anton Souslov. “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
V1.0.1.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8329143.'
ieee: 'J. Binysh et al., “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
v1.0.1.” Zenodo, 2023.'
ista: 'Binysh J, Chakraborty I, Chubynsky M, Diaz Melian VL, Waitukaitis SR, Sprittles
J, Souslov A. 2023. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
v1.0.1, Zenodo, 10.5281/ZENODO.8329143.'
mla: 'Binysh, Jack, et al. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
V1.0.1. Zenodo, 2023, doi:10.5281/ZENODO.8329143.'
short: J. Binysh, I. Chakraborty, M. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis,
J. Sprittles, A. Souslov, (2023).
date_created: 2023-11-13T09:12:11Z
date_published: 2023-09-08T00:00:00Z
date_updated: 2023-11-13T09:21:31Z
day: '08'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.5281/ZENODO.8329143
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/ZENODO.8329143
month: '09'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14514'
relation: used_in_publication
status: public
status: public
title: 'SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1'
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14518'
abstract:
- lang: eng
text: We consider bidding games, a class of two-player zero-sum graph games. The
game proceeds as follows. Both players have bounded budgets. A token is placed
on a vertex of a graph, in each turn the players simultaneously submit bids, and
the higher bidder moves the token, where we break bidding ties in favor of Player
1. Player 1 wins the game iff the token visits a designated target vertex. We
consider, for the first time, poorman discrete-bidding in which the granularity
of the bids is restricted and the higher bid is paid to the bank. Previous work
either did not impose granularity restrictions or considered Richman bidding (bids
are paid to the opponent). While the latter mechanisms are technically more accessible,
the former is more appealing from a practical standpoint. Our study focuses on
threshold budgets, which is the necessary and sufficient initial budget required
for Player 1 to ensure winning against a given Player 2 budget. We first show
existence of thresholds. In DAGs, we show that threshold budgets can be approximated
with error bounds by thresholds under continuous-bidding and that they exhibit
a periodic behavior. We identify closed-form solutions in special cases. We implement
and experiment with an algorithm to find threshold budgets.
acknowledgement: This research was supported in part by ISF grant no. 1679/21, ERC
CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation
programme under the Marie SkłodowskaCurie Grant Agreement No. 665385.
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Tobias
full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
- first_name: Suman
full_name: Sadhukhan, Suman
last_name: Sadhukhan
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. Reachability poorman
discrete-bidding games. In: Frontiers in Artificial Intelligence and Applications.
Vol 372. IOS Press; 2023:141-148. doi:10.3233/FAIA230264'
apa: 'Avni, G., Meggendorfer, T., Sadhukhan, S., Tkadlec, J., & Zikelic, D.
(2023). Reachability poorman discrete-bidding games. In Frontiers in Artificial
Intelligence and Applications (Vol. 372, pp. 141–148). Krakow, Poland: IOS
Press. https://doi.org/10.3233/FAIA230264'
chicago: Avni, Guy, Tobias Meggendorfer, Suman Sadhukhan, Josef Tkadlec, and Dorde
Zikelic. “Reachability Poorman Discrete-Bidding Games.” In Frontiers in Artificial
Intelligence and Applications, 372:141–48. IOS Press, 2023. https://doi.org/10.3233/FAIA230264.
ieee: G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, and D. Zikelic, “Reachability
poorman discrete-bidding games,” in Frontiers in Artificial Intelligence and
Applications, Krakow, Poland, 2023, vol. 372, pp. 141–148.
ista: 'Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. 2023. Reachability
poorman discrete-bidding games. Frontiers in Artificial Intelligence and Applications.
ECAI: European Conference on Artificial Intelligence vol. 372, 141–148.'
mla: Avni, Guy, et al. “Reachability Poorman Discrete-Bidding Games.” Frontiers
in Artificial Intelligence and Applications, vol. 372, IOS Press, 2023, pp.
141–48, doi:10.3233/FAIA230264.
short: G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, D. Zikelic, in:, Frontiers
in Artificial Intelligence and Applications, IOS Press, 2023, pp. 141–148.
conference:
end_date: 2023-10-04
location: Krakow, Poland
name: 'ECAI: European Conference on Artificial Intelligence'
start_date: 2023-09-30
date_created: 2023-11-12T23:00:56Z
date_published: 2023-09-28T00:00:00Z
date_updated: 2023-11-13T10:18:45Z
day: '28'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
doi: 10.3233/FAIA230264
ec_funded: 1
external_id:
arxiv:
- '2307.15218'
file:
- access_level: open_access
checksum: 1390ca38480fa4cf286b0f1a42e8c12f
content_type: application/pdf
creator: dernst
date_created: 2023-11-13T10:16:10Z
date_updated: 2023-11-13T10:16:10Z
file_id: '14529'
file_name: 2023_FAIA_Avni.pdf
file_size: 501011
relation: main_file
success: 1
file_date_updated: 2023-11-13T10:16:10Z
has_accepted_license: '1'
intvolume: ' 372'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '09'
oa: 1
oa_version: Published Version
page: 141-148
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Frontiers in Artificial Intelligence and Applications
publication_identifier:
isbn:
- '9781643684369'
issn:
- 0922-6389
publication_status: published
publisher: IOS Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reachability poorman discrete-bidding games
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 372
year: '2023'
...
---
_id: '13096'
abstract:
- lang: eng
text: Eukaryotic cells can undergo different forms of programmed cell death, many
of which culminate in plasma membrane rupture as the defining terminal event1,2,3,4,5,6,7.
Plasma membrane rupture was long thought to be driven by osmotic pressure, but
it has recently been shown to be in many cases an active process, mediated by
the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the
mechanism by which it ruptures membranes. Super-resolution microscopy reveals
that NINJ1 clusters into structurally diverse assemblies in the membranes of dying
cells, in particular large, filamentous assemblies with branched morphology. A
cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like
array of transmembrane α-helices. Filament directionality and stability is defined
by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1
filament features a hydrophilic side and a hydrophobic side, and molecular dynamics
simulations show that it can stably cap membrane edges. The function of the resulting
supramolecular arrangement was validated by site-directed mutagenesis. Our data
thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1
insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic
filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore
an interactive component of the eukaryotic cell membrane that functions as an
in-built breaking point in response to activation of cell death.
acknowledged_ssus:
- _id: NMR
- _id: LifeSc
acknowledgement: "This work was supported by the Deutsche Forschungsgemeinschaft under
Germany’s Excellence Strategy EXC 2075–390740016 and the Stuttgart Center for Simulation
Science (SC SimTech) to K.P., by ERC-CoG 770988 (InflamCellDeath) and SNF Project
funding (310030B_198005, 310030B_192523) to P.B., by the Swiss Nanoscience Institute
and the Swiss National Science Foundation via the NCCR AntiResist (180541) to S.H.
and the NCCR Molecular Systems Engineering (51NF40-205608) to D.J.M., by the Helmholtz
Young Investigator Program of the Helmholtz Association to C.S., by the SNF Professorship
funding (PP00P3_198903) to C.P., EMBO postdoctoral fellowship ALTF 27-2022 to E.H.
and by the Scientific Service Units of IST Austria through resources provided by
the NMR and Life Science Facilities to P.S. Molecular dynamics simulations were
performed on the HoreKa supercomputer funded by the Ministry of Science, Research
and the Arts Baden-Württemberg and by the Federal Ministry of Education and Research.
The authors thank the BioEM Lab of the Biozentrum, University of Basel for support;
V. Mack, K. Shkarina and J. Fricke for technical support; D. Ricklin and S. Vogt
for peptide synthesis; P. Pelczar for support with animals; S.-J. Marrink and P.
Telles de Souza for supply with Martini3 parameters and scripts; and P. Radler und
M. Loose for help with QCM. Fig. 4g and Extended Data Fig. 1a were in part created
with BioRender.com.\r\nOpen access funding provided by University of Basel."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Morris
full_name: Degen, Morris
last_name: Degen
- first_name: José Carlos
full_name: Santos, José Carlos
last_name: Santos
- first_name: Kristyna
full_name: Pluhackova, Kristyna
last_name: Pluhackova
- first_name: Gonzalo
full_name: Cebrero, Gonzalo
last_name: Cebrero
- first_name: Saray
full_name: Ramos, Saray
last_name: Ramos
- first_name: Gytis
full_name: Jankevicius, Gytis
last_name: Jankevicius
- first_name: Ella
full_name: Hartenian, Ella
last_name: Hartenian
- first_name: Undina
full_name: Guillerm, Undina
id: bb74f472-ae54-11eb-9835-bc9c22fb1183
last_name: Guillerm
- first_name: Stefania A.
full_name: Mari, Stefania A.
last_name: Mari
- first_name: Bastian
full_name: Kohl, Bastian
last_name: Kohl
- first_name: Daniel J.
full_name: Müller, Daniel J.
last_name: Müller
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Timm
full_name: Maier, Timm
last_name: Maier
- first_name: Camilo
full_name: Perez, Camilo
last_name: Perez
- first_name: Christian
full_name: Sieben, Christian
last_name: Sieben
- first_name: Petr
full_name: Broz, Petr
last_name: Broz
- first_name: Sebastian
full_name: Hiller, Sebastian
last_name: Hiller
citation:
ama: Degen M, Santos JC, Pluhackova K, et al. Structural basis of NINJ1-mediated
plasma membrane rupture in cell death. Nature. 2023;618:1065-1071. doi:10.1038/s41586-023-05991-z
apa: Degen, M., Santos, J. C., Pluhackova, K., Cebrero, G., Ramos, S., Jankevicius,
G., … Hiller, S. (2023). Structural basis of NINJ1-mediated plasma membrane rupture
in cell death. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-05991-z
chicago: Degen, Morris, José Carlos Santos, Kristyna Pluhackova, Gonzalo Cebrero,
Saray Ramos, Gytis Jankevicius, Ella Hartenian, et al. “Structural Basis of NINJ1-Mediated
Plasma Membrane Rupture in Cell Death.” Nature. Springer Nature, 2023.
https://doi.org/10.1038/s41586-023-05991-z.
ieee: M. Degen et al., “Structural basis of NINJ1-mediated plasma membrane
rupture in cell death,” Nature, vol. 618. Springer Nature, pp. 1065–1071,
2023.
ista: Degen M, Santos JC, Pluhackova K, Cebrero G, Ramos S, Jankevicius G, Hartenian
E, Guillerm U, Mari SA, Kohl B, Müller DJ, Schanda P, Maier T, Perez C, Sieben
C, Broz P, Hiller S. 2023. Structural basis of NINJ1-mediated plasma membrane
rupture in cell death. Nature. 618, 1065–1071.
mla: Degen, Morris, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture
in Cell Death.” Nature, vol. 618, Springer Nature, 2023, pp. 1065–71, doi:10.1038/s41586-023-05991-z.
short: M. Degen, J.C. Santos, K. Pluhackova, G. Cebrero, S. Ramos, G. Jankevicius,
E. Hartenian, U. Guillerm, S.A. Mari, B. Kohl, D.J. Müller, P. Schanda, T. Maier,
C. Perez, C. Sieben, P. Broz, S. Hiller, Nature 618 (2023) 1065–1071.
date_created: 2023-05-28T22:01:04Z
date_published: 2023-06-29T00:00:00Z
date_updated: 2023-11-14T11:49:21Z
day: '29'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1038/s41586-023-05991-z
external_id:
isi:
- '000991386800011'
file:
- access_level: open_access
checksum: 0fab69252453bff1de7f0e2eceb76d34
content_type: application/pdf
creator: dernst
date_created: 2023-11-14T11:48:18Z
date_updated: 2023-11-14T11:48:18Z
file_id: '14533'
file_name: 2023_Nature_Degen.pdf
file_size: 12292188
relation: main_file
success: 1
file_date_updated: 2023-11-14T11:48:18Z
has_accepted_license: '1'
intvolume: ' 618'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1065-1071
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural basis of NINJ1-mediated plasma membrane rupture in cell death
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: 618
year: '2023'
...
---
_id: '13041'
abstract:
- lang: eng
text: A series of triarylamines was synthesised and screened for their suitability
as catholytes in redox flow batteries using cyclic voltammetry (CV). Tris(4-aminophenyl)amine
was found to be the strongest candidate. Solubility and initial electrochemical
performance were promising; however, polymerisation was observed during electrochemical
cycling leading to rapid capacity fade prescribed to a loss of accessible active
material and the limitation of ion transport processes within the cell. A mixed
electrolyte system of H3PO4 and HCl was found to inhibit polymerisation producing
oligomers that consumed less active material reducing rates of degradation in
the redox flow battery. Under these conditions Coulombic efficiency improved by
over 4 %, the maximum number of cycles more than quadrupled and an additional
theoretical capacity of 20 % was accessed. This paper is, to our knowledge, the
first example of triarylamines as catholytes in all-aqueous redox flow batteries
and emphasises the impact supporting electrolytes can have on electrochemical
performance.
acknowledgement: The authors (N.L.F and R.B.J) would like to acknowledge the funding
contributions of Shell and the EPRSC via I–Case studentships (grants no. EP/V519662/1
and EP/R511870/1 respectively). T.I would like to thank the ERC advanced Investigator
Grant for CPG (EC H2020 835073). Thank you to Zhen Wang from the University of Cambridge
for measuring GPC, the Yusuf Hamied Department of Chemistry's mass spectrometry
service for MS measurements and analysis and Dr Andrew Bond from the University
of Cambridge for XRD measurement and analysis.
article_number: e202300128
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Nadia L.
full_name: Farag, Nadia L.
last_name: Farag
- first_name: Rajesh B
full_name: Jethwa, Rajesh B
id: 4cc538d5-803f-11ed-ab7e-8139573aad8f
last_name: Jethwa
orcid: 0000-0002-0404-4356
- first_name: Alice E.
full_name: Beardmore, Alice E.
last_name: Beardmore
- first_name: Teresa
full_name: Insinna, Teresa
last_name: Insinna
- first_name: Christopher A.
full_name: O'Keefe, Christopher A.
last_name: O'Keefe
- first_name: Peter A.A.
full_name: Klusener, Peter A.A.
last_name: Klusener
- first_name: Clare P.
full_name: Grey, Clare P.
last_name: Grey
- first_name: Dominic S.
full_name: Wright, Dominic S.
last_name: Wright
citation:
ama: Farag NL, Jethwa RB, Beardmore AE, et al. Triarylamines as catholytes in aqueous
organic redox flow batteries. ChemSusChem. 2023;16(13). doi:10.1002/cssc.202300128
apa: Farag, N. L., Jethwa, R. B., Beardmore, A. E., Insinna, T., O’Keefe, C. A.,
Klusener, P. A. A., … Wright, D. S. (2023). Triarylamines as catholytes in aqueous
organic redox flow batteries. ChemSusChem. Wiley. https://doi.org/10.1002/cssc.202300128
chicago: Farag, Nadia L., Rajesh B Jethwa, Alice E. Beardmore, Teresa Insinna, Christopher
A. O’Keefe, Peter A.A. Klusener, Clare P. Grey, and Dominic S. Wright. “Triarylamines
as Catholytes in Aqueous Organic Redox Flow Batteries.” ChemSusChem. Wiley,
2023. https://doi.org/10.1002/cssc.202300128.
ieee: N. L. Farag et al., “Triarylamines as catholytes in aqueous organic
redox flow batteries,” ChemSusChem, vol. 16, no. 13. Wiley, 2023.
ista: Farag NL, Jethwa RB, Beardmore AE, Insinna T, O’Keefe CA, Klusener PAA, Grey
CP, Wright DS. 2023. Triarylamines as catholytes in aqueous organic redox flow
batteries. ChemSusChem. 16(13), e202300128.
mla: Farag, Nadia L., et al. “Triarylamines as Catholytes in Aqueous Organic Redox
Flow Batteries.” ChemSusChem, vol. 16, no. 13, e202300128, Wiley, 2023,
doi:10.1002/cssc.202300128.
short: N.L. Farag, R.B. Jethwa, A.E. Beardmore, T. Insinna, C.A. O’Keefe, P.A.A.
Klusener, C.P. Grey, D.S. Wright, ChemSusChem 16 (2023).
date_created: 2023-05-21T22:01:05Z
date_published: 2023-07-06T00:00:00Z
date_updated: 2023-11-14T11:28:23Z
day: '06'
ddc:
- '540'
department:
- _id: StFr
doi: 10.1002/cssc.202300128
external_id:
isi:
- '000985051300001'
pmid:
- '36970847'
file:
- access_level: open_access
checksum: efa0713289995af83a2147b3e8e1d6a6
content_type: application/pdf
creator: dernst
date_created: 2023-11-14T11:27:16Z
date_updated: 2023-11-14T11:27:16Z
file_id: '14532'
file_name: 2023_ChemSusChem_Farag.pdf
file_size: 1168683
relation: main_file
success: 1
file_date_updated: 2023-11-14T11:27:16Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '13'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: ChemSusChem
publication_identifier:
eissn:
- 1864-564X
issn:
- 1864-5631
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Triarylamines as catholytes in aqueous organic redox flow batteries
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: 16
year: '2023'
...
---
_id: '13118'
abstract:
- lang: eng
text: Under high pressures and temperatures, molecular systems with substantial
polarization charges, such as ammonia and water, are predicted to form superionic
phases and dense fluid states with dissociating molecules and high electrical
conductivity. This behaviour potentially plays a role in explaining the origin
of the multipolar magnetic fields of Uranus and Neptune, whose mantles are thought
to result from a mixture of H2O, NH3 and CH4 ices. Determining the stability domain,
melting curve and electrical conductivity of these superionic phases is therefore
crucial for modelling planetary interiors and dynamos. Here we report the melting
curve of superionic ammonia up to 300 GPa from laser-driven shock compression
of pre-compressed samples and atomistic calculations. We show that ammonia melts
at lower temperatures than water above 100 GPa and that fluid ammonia’s electrical
conductivity exceeds that of water at conditions predicted by hot, super-adiabatic
models for Uranus and Neptune, and enhances the conductivity in their fluid water-rich
dynamo layers.
acknowledgement: We acknowledge the crucial contribution of the LULI2000 laser and
support teams to the success of the experiments. We also thank S. Brygoo and P.
Loubeyre for useful discussions. This research was supported by the French National
Research Agency (ANR) through the projects POMPEI (grant no. ANR-16-CE31-0008) and
SUPER-ICES (grant ANR-15-CE30-008-01), and by the PLAS@PAR Federation. M.F. and
R.R. gratefully acknowledge support by the DFG within the Research Unit FOR 2440.
M.B. was supported by the European Union within the Marie Skłodowska-Curie actions
(xICE grant 894725) and the NOMIS foundation. The DFT-MD calculations were performed
at the North-German Supercomputing Alliance facilities.
article_processing_charge: No
article_type: original
author:
- first_name: J.-A.
full_name: Hernandez, J.-A.
last_name: Hernandez
- first_name: Mandy
full_name: Bethkenhagen, Mandy
id: 201939f4-803f-11ed-ab7e-d8da4bd1517f
last_name: Bethkenhagen
orcid: 0000-0002-1838-2129
- first_name: S.
full_name: Ninet, S.
last_name: Ninet
- first_name: M.
full_name: French, M.
last_name: French
- first_name: A.
full_name: Benuzzi-Mounaix, A.
last_name: Benuzzi-Mounaix
- first_name: F.
full_name: Datchi, F.
last_name: Datchi
- first_name: M.
full_name: Guarguaglini, M.
last_name: Guarguaglini
- first_name: F.
full_name: Lefevre, F.
last_name: Lefevre
- first_name: F.
full_name: Occelli, F.
last_name: Occelli
- first_name: R.
full_name: Redmer, R.
last_name: Redmer
- first_name: T.
full_name: Vinci, T.
last_name: Vinci
- first_name: A.
full_name: Ravasio, A.
last_name: Ravasio
citation:
ama: Hernandez J-A, Bethkenhagen M, Ninet S, et al. Melting curve of superionic
ammonia at planetary interior conditions. Nature Physics. 2023;19:1280-1285.
doi:10.1038/s41567-023-02074-8
apa: Hernandez, J.-A., Bethkenhagen, M., Ninet, S., French, M., Benuzzi-Mounaix,
A., Datchi, F., … Ravasio, A. (2023). Melting curve of superionic ammonia at planetary
interior conditions. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02074-8
chicago: Hernandez, J.-A., Mandy Bethkenhagen, S. Ninet, M. French, A. Benuzzi-Mounaix,
F. Datchi, M. Guarguaglini, et al. “Melting Curve of Superionic Ammonia at Planetary
Interior Conditions.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02074-8.
ieee: J.-A. Hernandez et al., “Melting curve of superionic ammonia at planetary
interior conditions,” Nature Physics, vol. 19. Springer Nature, pp. 1280–1285,
2023.
ista: Hernandez J-A, Bethkenhagen M, Ninet S, French M, Benuzzi-Mounaix A, Datchi
F, Guarguaglini M, Lefevre F, Occelli F, Redmer R, Vinci T, Ravasio A. 2023. Melting
curve of superionic ammonia at planetary interior conditions. Nature Physics.
19, 1280–1285.
mla: Hernandez, J. A., et al. “Melting Curve of Superionic Ammonia at Planetary
Interior Conditions.” Nature Physics, vol. 19, Springer Nature, 2023, pp.
1280–85, doi:10.1038/s41567-023-02074-8.
short: J.-A. Hernandez, M. Bethkenhagen, S. Ninet, M. French, A. Benuzzi-Mounaix,
F. Datchi, M. Guarguaglini, F. Lefevre, F. Occelli, R. Redmer, T. Vinci, A. Ravasio,
Nature Physics 19 (2023) 1280–1285.
date_created: 2023-06-04T22:01:02Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-11-14T12:58:31Z
day: '01'
department:
- _id: BiCh
doi: 10.1038/s41567-023-02074-8
external_id:
isi:
- '000996921200001'
intvolume: ' 19'
isi: 1
language:
- iso: eng
month: '09'
oa_version: None
page: 1280-1285
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: 10.1038/s41567-023-02130-3
scopus_import: '1'
status: public
title: Melting curve of superionic ammonia at planetary interior conditions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2023'
...
---
_id: '13119'
abstract:
- lang: eng
text: A density wave (DW) is a fundamental type of long-range order in quantum matter
tied to self-organization into a crystalline structure. The interplay of DW order
with superfluidity can lead to complex scenarios that pose a great challenge to
theoretical analysis. In the past decades, tunable quantum Fermi gases have served
as model systems for exploring the physics of strongly interacting fermions, including
most notably magnetic ordering1, pairing and superfluidity2, and the crossover
from a Bardeen–Cooper–Schrieffer superfluid to a Bose–Einstein condensate3. Here,
we realize a Fermi gas featuring both strong, tunable contact interactions and
photon-mediated, spatially structured long-range interactions in a transversely
driven high-finesse optical cavity. Above a critical long-range interaction strength,
DW order is stabilized in the system, which we identify via its superradiant light-scattering
properties. We quantitatively measure the variation of the onset of DW order as
the contact interaction is varied across the Bardeen–Cooper–Schrieffer superfluid
and Bose–Einstein condensate crossover, in qualitative agreement with a mean-field
theory. The atomic DW susceptibility varies over an order of magnitude upon tuning
the strength and the sign of the long-range interactions below the self-ordering
threshold, demonstrating independent and simultaneous control over the contact
and long-range interactions. Therefore, our experimental setup provides a fully
tunable and microscopically controllable platform for the experimental study of
the interplay of superfluidity and DW order.
acknowledgement: Open access funding provided by EPFL Lausanne.We acknowledge discussions
with T. Donner and T. Esslinger. We thank G. del Pace and T. Bühler for their assistance
in the final stages of the experiment. We acknowledge funding from the European
Research Council under the European Union Horizon 2020 Research and Innovation Programme
(Grant no. 714309) and the Swiss National Science Foundation (Grant no. 184654).
F.M. acknowledges financial support from the Austrian Science Fund (Stand-Alone
Project P 35891-N).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Victor
full_name: Helson, Victor
last_name: Helson
- first_name: Timo
full_name: Zwettler, Timo
last_name: Zwettler
- first_name: Farokh
full_name: Mivehvar, Farokh
last_name: Mivehvar
- first_name: Elvia
full_name: Colella, Elvia
last_name: Colella
- first_name: Kevin Etienne Robert
full_name: Roux, Kevin Etienne Robert
id: 53f93ea2-803f-11ed-ab7e-b283135794ef
last_name: Roux
- first_name: Hideki
full_name: Konishi, Hideki
last_name: Konishi
- first_name: Helmut
full_name: Ritsch, Helmut
last_name: Ritsch
- first_name: Jean Philippe
full_name: Brantut, Jean Philippe
last_name: Brantut
citation:
ama: Helson V, Zwettler T, Mivehvar F, et al. Density-wave ordering in a unitary
Fermi gas with photon-mediated interactions. Nature. 2023;618:716-720.
doi:10.1038/s41586-023-06018-3
apa: Helson, V., Zwettler, T., Mivehvar, F., Colella, E., Roux, K. E. R., Konishi,
H., … Brantut, J. P. (2023). Density-wave ordering in a unitary Fermi gas with
photon-mediated interactions. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06018-3
chicago: Helson, Victor, Timo Zwettler, Farokh Mivehvar, Elvia Colella, Kevin Etienne
Robert Roux, Hideki Konishi, Helmut Ritsch, and Jean Philippe Brantut. “Density-Wave
Ordering in a Unitary Fermi Gas with Photon-Mediated Interactions.” Nature.
Springer Nature, 2023. https://doi.org/10.1038/s41586-023-06018-3.
ieee: V. Helson et al., “Density-wave ordering in a unitary Fermi gas with
photon-mediated interactions,” Nature, vol. 618. Springer Nature, pp. 716–720,
2023.
ista: Helson V, Zwettler T, Mivehvar F, Colella E, Roux KER, Konishi H, Ritsch H,
Brantut JP. 2023. Density-wave ordering in a unitary Fermi gas with photon-mediated
interactions. Nature. 618, 716–720.
mla: Helson, Victor, et al. “Density-Wave Ordering in a Unitary Fermi Gas with Photon-Mediated
Interactions.” Nature, vol. 618, Springer Nature, 2023, pp. 716–20, doi:10.1038/s41586-023-06018-3.
short: V. Helson, T. Zwettler, F. Mivehvar, E. Colella, K.E.R. Roux, H. Konishi,
H. Ritsch, J.P. Brantut, Nature 618 (2023) 716–720.
date_created: 2023-06-04T22:01:03Z
date_published: 2023-06-22T00:00:00Z
date_updated: 2023-11-14T13:02:50Z
day: '22'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1038/s41586-023-06018-3
external_id:
isi:
- '001001139300008'
file:
- access_level: open_access
checksum: 4887a296e3b6f54e8c0b946cbfd24f49
content_type: application/pdf
creator: dernst
date_created: 2023-11-14T13:00:19Z
date_updated: 2023-11-14T13:00:19Z
file_id: '14534'
file_name: 2023_Nature_Helson.pdf
file_size: 8156497
relation: main_file
success: 1
file_date_updated: 2023-11-14T13:00:19Z
has_accepted_license: '1'
intvolume: ' 618'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 716-720
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Density-wave ordering in a unitary Fermi gas with photon-mediated interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 618
year: '2023'
...
---
_id: '12911'
abstract:
- lang: eng
text: 'This paper establishes new connections between many-body quantum systems,
One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport
(OT), by interpreting the problem of computing the ground-state energy of a finite-dimensional
composite quantum system at positive temperature as a non-commutative entropy
regularized Optimal Transport problem. We develop a new approach to fully characterize
the dual-primal solutions in such non-commutative setting. The mathematical formalism
is particularly relevant in quantum chemistry: numerical realizations of the many-electron
ground-state energy can be computed via a non-commutative version of Sinkhorn
algorithm. Our approach allows to prove convergence and robustness of this algorithm,
which, to our best knowledge, were unknown even in the two marginal case. Our
methods are based on a priori estimates in the dual problem, which we believe
to be of independent interest. Finally, the above results are extended in 1RDMFT
setting, where bosonic or fermionic symmetry conditions are enforced on the problem.'
acknowledgement: "This work started when A.G. was visiting the Erwin Schrödinger Institute
and then continued when D.F. and L.P visited the Theoretical Chemistry Department
of the Vrije Universiteit Amsterdam. The authors thank the hospitality of both places
and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature
suggestions in the early state of the project. The authors also thank J. Maas and
R. Seiringer for their feedback and useful comments to a first draft of the article.
Finally, we acknowledge the high quality review done by the anonymous referee of
our paper, who we would like to thank for the excellent work and constructive feedback.\r\nD.F
acknowledges support by the European Research Council (ERC) under the European Union's
Horizon 2020 research and innovation programme (grant agreements No 716117 and No
694227). A.G. acknowledges funding by the HORIZON EUROPE European Research Council
under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942] as well as partial support of
his research by the Canada Research Chairs Program (ID 2021-00234) and Natural Sciences
and Engineering Research Council of Canada, RGPIN-2022-05207. L.P. acknowledges
support by the Austrian Science Fund (FWF), grants No W1245 and No F65, and by the
Deutsche Forschungsgemeinschaft (DFG) - Project number 390685813."
article_number: '109963'
article_processing_charge: No
article_type: original
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
- first_name: Augusto
full_name: Gerolin, Augusto
last_name: Gerolin
- first_name: Lorenzo
full_name: Portinale, Lorenzo
id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
last_name: Portinale
citation:
ama: Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal
transport approach to quantum composite systems at positive temperature. Journal
of Functional Analysis. 2023;285(4). doi:10.1016/j.jfa.2023.109963
apa: Feliciangeli, D., Gerolin, A., & Portinale, L. (2023). A non-commutative
entropic optimal transport approach to quantum composite systems at positive temperature.
Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2023.109963
chicago: Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative
Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.”
Journal of Functional Analysis. Elsevier, 2023. https://doi.org/10.1016/j.jfa.2023.109963.
ieee: D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic
optimal transport approach to quantum composite systems at positive temperature,”
Journal of Functional Analysis, vol. 285, no. 4. Elsevier, 2023.
ista: Feliciangeli D, Gerolin A, Portinale L. 2023. A non-commutative entropic optimal
transport approach to quantum composite systems at positive temperature. Journal
of Functional Analysis. 285(4), 109963.
mla: Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach
to Quantum Composite Systems at Positive Temperature.” Journal of Functional
Analysis, vol. 285, no. 4, 109963, Elsevier, 2023, doi:10.1016/j.jfa.2023.109963.
short: D. Feliciangeli, A. Gerolin, L. Portinale, Journal of Functional Analysis
285 (2023).
date_created: 2023-05-07T22:01:02Z
date_published: 2023-08-15T00:00:00Z
date_updated: 2023-11-14T13:21:01Z
day: '15'
department:
- _id: RoSe
- _id: JaMa
doi: 10.1016/j.jfa.2023.109963
ec_funded: 1
external_id:
arxiv:
- '2106.11217'
isi:
- '000990804300001'
intvolume: ' 285'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2106.11217
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 260482E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: ' F06504'
name: Taming Complexity in Partial Di erential Systems
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '9792'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: A non-commutative entropic optimal transport approach to quantum composite
systems at positive temperature
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 285
year: '2023'
...
---
_id: '13177'
abstract:
- lang: eng
text: In this note we study the eigenvalue growth of infinite graphs with discrete
spectrum. We assume that the corresponding Dirichlet forms satisfy certain Sobolev-type
inequalities and that the total measure is finite. In this sense, the associated
operators on these graphs display similarities to elliptic operators on bounded
domains in the continuum. Specifically, we prove lower bounds on the eigenvalue
growth and show by examples that corresponding upper bounds cannot be established.
acknowledgement: The second author was supported by the priority program SPP2026 of
the German Research Foundation (DFG). The fourth author was supported by the German
Academic Scholarship Foundation (Studienstiftung des deutschen Volkes) and by the
German Research Foundation (DFG) via RTG 1523/2.
article_processing_charge: No
article_type: original
author:
- first_name: Bobo
full_name: Hua, Bobo
last_name: Hua
- first_name: Matthias
full_name: Keller, Matthias
last_name: Keller
- first_name: Michael
full_name: Schwarz, Michael
last_name: Schwarz
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
citation:
ama: Hua B, Keller M, Schwarz M, Wirth M. Sobolev-type inequalities and eigenvalue
growth on graphs with finite measure. Proceedings of the American Mathematical
Society. 2023;151(8):3401-3414. doi:10.1090/proc/14361
apa: Hua, B., Keller, M., Schwarz, M., & Wirth, M. (2023). Sobolev-type inequalities
and eigenvalue growth on graphs with finite measure. Proceedings of the American
Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/14361
chicago: Hua, Bobo, Matthias Keller, Michael Schwarz, and Melchior Wirth. “Sobolev-Type
Inequalities and Eigenvalue Growth on Graphs with Finite Measure.” Proceedings
of the American Mathematical Society. American Mathematical Society, 2023.
https://doi.org/10.1090/proc/14361.
ieee: B. Hua, M. Keller, M. Schwarz, and M. Wirth, “Sobolev-type inequalities and
eigenvalue growth on graphs with finite measure,” Proceedings of the American
Mathematical Society, vol. 151, no. 8. American Mathematical Society, pp.
3401–3414, 2023.
ista: Hua B, Keller M, Schwarz M, Wirth M. 2023. Sobolev-type inequalities and eigenvalue
growth on graphs with finite measure. Proceedings of the American Mathematical
Society. 151(8), 3401–3414.
mla: Hua, Bobo, et al. “Sobolev-Type Inequalities and Eigenvalue Growth on Graphs
with Finite Measure.” Proceedings of the American Mathematical Society,
vol. 151, no. 8, American Mathematical Society, 2023, pp. 3401–14, doi:10.1090/proc/14361.
short: B. Hua, M. Keller, M. Schwarz, M. Wirth, Proceedings of the American Mathematical
Society 151 (2023) 3401–3414.
date_created: 2023-07-02T22:00:43Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-11-14T13:07:09Z
day: '01'
department:
- _id: JaMa
doi: 10.1090/proc/14361
external_id:
arxiv:
- '1804.08353'
isi:
- '000988204400001'
intvolume: ' 151'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1804.08353'
month: '08'
oa: 1
oa_version: Preprint
page: 3401-3414
publication: Proceedings of the American Mathematical Society
publication_identifier:
eissn:
- 1088-6826
issn:
- 0002-9939
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sobolev-type inequalities and eigenvalue growth on graphs with finite measure
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 151
year: '2023'
...
---
_id: '14558'
abstract:
- lang: eng
text: "n the dynamic minimum set cover problem, the challenge is to minimize the
update time while guaranteeing a close-to-optimal min{O(log n), f} approximation
factor. (Throughout, n, m, f , and C are parameters denoting the maximum number
of elements, the number of sets, the frequency, and the cost range.) In the high-frequency
range, when f = Ω(log n) , this was achieved by a deterministic O(log n) -approximation
algorithm with O(f log n) amortized update time by Gupta et al. [Online and dynamic
algorithms for set cover, in Proceedings STOC 2017, ACM, pp. 537–550]. In this
paper we consider the low-frequency range, when f = O(log n) , and obtain deterministic
algorithms with a (1 + ∈)f -approximation ratio and the following guarantees on
the update time. (1) O ((f/∈)-log(Cn)) amortized update time: Prior to our work,
the best approximation ratio guaranteed by deterministic algorithms was O(f2)
of Bhattacharya, Henzinger, and Italiano [Design of dynamic algorithms via primal-dual
method, in Proceedings ICALP 2015, Springer, pp. 206–218]. In contrast, the only
result with O(f) -approximation was that of Abboud et al. [Dynamic set cover:
Improved algorithms and lower bounds, in Proceedings STOC 2019, ACM, pp. 114–125],
who designed a randomized (1+∈)f -approximation algorithm with amortized update
time. (2) O(f2/∈3 + (f/∈2).logC) amortized update time: This result improves the
above update time bound for most values of f\r\n in the low-frequency range, i.e.,
f=o(log n) . It is also the first result that is independent of m\r\n and n. It
subsumes the constant amortized update time of Bhattacharya and Kulkarni [Deterministically
maintaining a (2 + ∈) -approximate minimum vertex cover in O(1/∈2) amortized update
time, in Proceedings SODA 2019, SIAM, pp. 1872–1885] for unweighted dynamic vertex
cover (i.e., when f = 2 and C = 1). (3) O((f/∈3).log2(Cn)) worst-case update time:
No nontrivial worst-case update time was previously known for the dynamic set
cover problem. Our bound subsumes and improves by a logarithmic factor the O(log3n/poly
(∈)) \r\n worst-case update time for the unweighted dynamic vertex cover problem
(i.e., when f = 2\r\n and C =1) of Bhattacharya, Henzinger, and Nanongkai [Fully
dynamic approximate maximum matching and minimum vertex cover in O(log3)n worst
case update time, in Proceedings SODA 2017, SIAM, pp. 470–489]. We achieve our
results via the primal-dual approach, by maintaining a fractional packing solution
as a dual certificate. Prior work in dynamic algorithms that employs the primal-dual
approach uses a local update scheme that maintains relaxed complementary slackness
conditions for every set. For our first result we use instead a global update
scheme that does not always maintain complementary slackness conditions. For our
second result we combine the global and the local update schema. To achieve our
third result we use a hierarchy of background schedulers. It is an interesting
open question whether this background scheduler technique can also be used to
transform algorithms with amortized running time bounds into algorithms with worst-case
running time bounds."
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union's Horizon 2020 research and innovation programme
(grants 715672 and\r\n101019564 ``The Design of Modern Fully Dynamic Data Structures
(MoDynStruct)\"\") and from the Engineering and Physical Sciences Research Council,
UK (EPSRC) under grant EP/S03353X/1. The second author was also supported by the
Austrian Science Fund (FWF) project ``Fast Algorithms for a Reactive Network Layer
(ReactNet),\"\" P 33775-N, with additional funding from the netidee SCIENCE Stiftung,
2020--2024, project ``Static and Dynamic Hierarchical Graph Decompositions,\"\"I
5982-N, and project Z 422-N. The third author was also supported by the Swedish
Research Council (Reg. No. 2015-04659). The fourth author was also supported by
the Science and Technology Development Fund (FDCT), Macau SAR (file 0014/2022/AFJ,
0085/2022/A, 0143/2020/A3, and SKL-IOTSC-2021-2023)."
article_processing_charge: No
article_type: original
author:
- first_name: Sayan
full_name: Bhattacharya, Sayan
last_name: Bhattacharya
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
- first_name: Xiaowei
full_name: Wu, Xiaowei
last_name: Wu
citation:
ama: Bhattacharya S, Henzinger MH, Nanongkai D, Wu X. Deterministic near-optimal
approximation algorithms for dynamic set cover. SIAM Journal on Computing.
2023;52(5):1132-1192. doi:10.1137/21M1428649
apa: Bhattacharya, S., Henzinger, M. H., Nanongkai, D., & Wu, X. (2023). Deterministic
near-optimal approximation algorithms for dynamic set cover. SIAM Journal on
Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/21M1428649
chicago: Bhattacharya, Sayan, Monika H Henzinger, Danupon Nanongkai, and Xiaowei
Wu. “Deterministic Near-Optimal Approximation Algorithms for Dynamic Set Cover.”
SIAM Journal on Computing. Society for Industrial and Applied Mathematics,
2023. https://doi.org/10.1137/21M1428649.
ieee: S. Bhattacharya, M. H. Henzinger, D. Nanongkai, and X. Wu, “Deterministic
near-optimal approximation algorithms for dynamic set cover,” SIAM Journal
on Computing, vol. 52, no. 5. Society for Industrial and Applied Mathematics,
pp. 1132–1192, 2023.
ista: Bhattacharya S, Henzinger MH, Nanongkai D, Wu X. 2023. Deterministic near-optimal
approximation algorithms for dynamic set cover. SIAM Journal on Computing. 52(5),
1132–1192.
mla: Bhattacharya, Sayan, et al. “Deterministic Near-Optimal Approximation Algorithms
for Dynamic Set Cover.” SIAM Journal on Computing, vol. 52, no. 5, Society
for Industrial and Applied Mathematics, 2023, pp. 1132–92, doi:10.1137/21M1428649.
short: S. Bhattacharya, M.H. Henzinger, D. Nanongkai, X. Wu, SIAM Journal on Computing
52 (2023) 1132–1192.
date_created: 2023-11-19T23:00:56Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-11-20T08:21:07Z
day: '01'
department:
- _id: MoHe
doi: 10.1137/21M1428649
ec_funded: 1
intvolume: ' 52'
issue: '5'
language:
- iso: eng
month: '10'
oa_version: None
page: 1132-1192
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: 'P33775 '
name: Fast Algorithms for a Reactive Network Layer
- _id: 34def286-11ca-11ed-8bc3-da5948e1613c
grant_number: Z00422
name: Wittgenstein Award - Monika Henzinger
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
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'
scopus_import: '1'
status: public
title: Deterministic near-optimal approximation algorithms for dynamic set cover
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2023'
...
---
_id: '14559'
abstract:
- lang: eng
text: We consider the problem of learning control policies in discrete-time stochastic
systems which guarantee that the system stabilizes within some specified stabilization
region with probability 1. Our approach is based on the novel notion of stabilizing
ranking supermartingales (sRSMs) that we introduce in this work. Our sRSMs overcome
the limitation of methods proposed in previous works whose applicability is restricted
to systems in which the stabilizing region cannot be left once entered under any
control policy. We present a learning procedure that learns a control policy together
with an sRSM that formally certifies probability 1 stability, both learned as
neural networks. We show that this procedure can also be adapted to formally verifying
that, under a given Lipschitz continuous control policy, the stochastic system
stabilizes within some stabilizing region with probability 1. Our experimental
evaluation shows that our learning procedure can successfully learn provably stabilizing
policies in practice.
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093, ERC
CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Matin
full_name: Ansaripour, Matin
last_name: Ansaripour
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. Learning provably
stabilizing neural controllers for discrete-time stochastic systems. In: 21st
International Symposium on Automated Technology for Verification and Analysis.
Vol 14215. Springer Nature; 2023:357-379. doi:10.1007/978-3-031-45329-8_17'
apa: 'Ansaripour, M., Chatterjee, K., Henzinger, T. A., Lechner, M., & Zikelic,
D. (2023). Learning provably stabilizing neural controllers for discrete-time
stochastic systems. In 21st International Symposium on Automated Technology
for Verification and Analysis (Vol. 14215, pp. 357–379). Singapore, Singapore:
Springer Nature. https://doi.org/10.1007/978-3-031-45329-8_17'
chicago: Ansaripour, Matin, Krishnendu Chatterjee, Thomas A Henzinger, Mathias Lechner,
and Dorde Zikelic. “Learning Provably Stabilizing Neural Controllers for Discrete-Time
Stochastic Systems.” In 21st International Symposium on Automated Technology
for Verification and Analysis, 14215:357–79. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-45329-8_17.
ieee: M. Ansaripour, K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic,
“Learning provably stabilizing neural controllers for discrete-time stochastic
systems,” in 21st International Symposium on Automated Technology for Verification
and Analysis, Singapore, Singapore, 2023, vol. 14215, pp. 357–379.
ista: 'Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. Learning
provably stabilizing neural controllers for discrete-time stochastic systems.
21st International Symposium on Automated Technology for Verification and Analysis.
ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 14215, 357–379.'
mla: Ansaripour, Matin, et al. “Learning Provably Stabilizing Neural Controllers
for Discrete-Time Stochastic Systems.” 21st International Symposium on Automated
Technology for Verification and Analysis, vol. 14215, Springer Nature, 2023,
pp. 357–79, doi:10.1007/978-3-031-45329-8_17.
short: M. Ansaripour, K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:,
21st International Symposium on Automated Technology for Verification and Analysis,
Springer Nature, 2023, pp. 357–379.
conference:
end_date: 2023-10-27
location: Singapore, Singapore
name: 'ATVA: Automated Technology for Verification and Analysis'
start_date: 2023-10-24
date_created: 2023-11-19T23:00:56Z
date_published: 2023-10-22T00:00:00Z
date_updated: 2023-11-20T08:30:20Z
day: '22'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1007/978-3-031-45329-8_17
ec_funded: 1
intvolume: ' 14215'
language:
- iso: eng
month: '10'
oa_version: None
page: 357-379
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: 21st International Symposium on Automated Technology for Verification
and Analysis
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031453281'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Learning provably stabilizing neural controllers for discrete-time stochastic
systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14215
year: '2023'
...
---
_id: '14554'
abstract:
- lang: eng
text: 'The Regularised Inertial Dean–Kawasaki model (RIDK) – introduced by the authors
and J. Zimmer in earlier works – is a nonlinear stochastic PDE capturing fluctuations
around the meanfield limit for large-scale particle systems in both particle density
and momentum density. We focus on the following two aspects. Firstly, we set up
a Discontinuous Galerkin (DG) discretisation scheme for the RIDK model: we provide
suitable definitions of numerical fluxes at the interface of the mesh elements
which are consistent with the wave-type nature of the RIDK model and grant stability
of the simulations, and we quantify the rate of convergence in mean square to
the continuous RIDK model. Secondly, we introduce modifications of the RIDK model
in order to preserve positivity of the density (such a feature only holds in a
“high-probability sense” for the original RIDK model). By means of numerical simulations,
we show that the modifications lead to physically realistic and positive density
profiles. In one case, subject to additional regularity constraints, we also prove
positivity. Finally, we present an application of our methodology to a system
of diffusing and reacting particles. Our Python code is available in open-source
format.'
acknowledgement: "The authors thank the anonymous referees for their careful reading
of the manuscript and their\r\nvaluable suggestions. FC gratefully acknowledges
funding from the Austrian Science Fund (FWF) through the project F65, and from the
European Union’s Horizon 2020 research and innovation programme under the Marie
Sk lodowska-Curie grant agreement No. 754411 (the latter funding source covered
the first part of this project)."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Federico
full_name: Cornalba, Federico
id: 2CEB641C-A400-11E9-A717-D712E6697425
last_name: Cornalba
orcid: 0000-0002-6269-5149
- first_name: Tony
full_name: Shardlow, Tony
last_name: Shardlow
citation:
ama: 'Cornalba F, Shardlow T. The regularised inertial Dean’ Kawasaki equation:
Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM:
Mathematical Modelling and Numerical Analysis. 2023;57(5):3061-3090. doi:10.1051/m2an/2023077'
apa: 'Cornalba, F., & Shardlow, T. (2023). The regularised inertial Dean’ Kawasaki
equation: Discontinuous Galerkin approximation and modelling for low-density regime.
ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences. https://doi.org/10.1051/m2an/2023077'
chicago: 'Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’
Kawasaki Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density
Regime.” ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences,
2023. https://doi.org/10.1051/m2an/2023077.'
ieee: 'F. Cornalba and T. Shardlow, “The regularised inertial Dean’ Kawasaki equation:
Discontinuous Galerkin approximation and modelling for low-density regime,” ESAIM:
Mathematical Modelling and Numerical Analysis, vol. 57, no. 5. EDP Sciences,
pp. 3061–3090, 2023.'
ista: 'Cornalba F, Shardlow T. 2023. The regularised inertial Dean’ Kawasaki equation:
Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM:
Mathematical Modelling and Numerical Analysis. 57(5), 3061–3090.'
mla: 'Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’ Kawasaki
Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density Regime.”
ESAIM: Mathematical Modelling and Numerical Analysis, vol. 57, no. 5, EDP
Sciences, 2023, pp. 3061–90, doi:10.1051/m2an/2023077.'
short: 'F. Cornalba, T. Shardlow, ESAIM: Mathematical Modelling and Numerical Analysis
57 (2023) 3061–3090.'
date_created: 2023-11-19T23:00:55Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-11-20T08:38:47Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1051/m2an/2023077
ec_funded: 1
file:
- access_level: open_access
checksum: 3aef1475b1882c8dec112df9a5167c39
content_type: application/pdf
creator: dernst
date_created: 2023-11-20T08:34:57Z
date_updated: 2023-11-20T08:34:57Z
file_id: '14560'
file_name: 2023_ESAIM_Cornalba.pdf
file_size: 1508534
relation: main_file
success: 1
file_date_updated: 2023-11-20T08:34:57Z
has_accepted_license: '1'
intvolume: ' 57'
issue: '5'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 3061-3090
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 'ESAIM: Mathematical Modelling and Numerical Analysis'
publication_identifier:
eissn:
- 2804-7214
issn:
- 2822-7840
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/tonyshardlow/RIDK-FD
scopus_import: '1'
status: public
title: 'The regularised inertial Dean'' Kawasaki equation: Discontinuous Galerkin
approximation and modelling for low-density regime'
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: 57
year: '2023'
...
---
_id: '14556'
abstract:
- lang: eng
text: Inversions are structural mutations that reverse the sequence of a chromosome
segment and reduce the effective rate of recombination in the heterozygous state.
They play a major role in adaptation, as well as in other evolutionary processes
such as speciation. Although inversions have been studied since the 1920s, they
remain difficult to investigate because the reduced recombination conferred by
them strengthens the effects of drift and hitchhiking, which in turn can obscure
signatures of selection. Nonetheless, numerous inversions have been found to be
under selection. Given recent advances in population genetic theory and empirical
study, here we review how different mechanisms of selection affect the evolution
of inversions. A key difference between inversions and other mutations, such as
single nucleotide variants, is that the fitness of an inversion may be affected
by a larger number of frequently interacting processes. This considerably complicates
the analysis of the causes underlying the evolution of inversions. We discuss
the extent to which these mechanisms can be disentangled, and by which approach.
acknowledgement: 'We are grateful to two referees and Luke Holman for valuable comments
on a previous version of our manuscript. This paper was conceived at the ESEB Progress
Meeting ‘Disentangling neutral versus adaptive evolution in chromosomal inversions’,
organized by ELB, KJ and TF and held at Tjärnö Marine Laboratory (Sweden) between
28 February and 3 March 2022. We are indebted to ESEB for sponsoring our workshop
and to the following funding bodies for supporting our research: ERC AdG 101055327
to NHB; Swedish Research Council (VR) 2018-03695 and Leverhulme Trust RPG-2021-141
to RKB; Fundação para a Ciência e a Tecnologia (FCT) contract 2020.00275.CEECIND
and research project PTDC/BIA-1232 EVL/1614/2021 to RF; Fundação para a Ciência
e a Tecnologia (FCT) junior researcher contract CEECIND/02616/2018 to IF; Swiss
National Science Foundation (SNSF) Ambizione #PZ00P3_185952 to KJG; National Science
Foundation NSF-OCE 2043905 and NSF-DEB 1655701 to KEL; Swiss National Science Foundation
(SNSF) 310030_204681 to CLP; Swedish Research Council (VR) 2021-05243 to MR; Norwegian
Research Council grant 315287 to AMW; Swiss National Science Foundation (SNSF) 31003A-182262
and FZEB-0-214654 to TF. We also thank Luca Ferretti for the discussion and Eliane
Zinn (Flatt lab) for help with reference formatting.'
article_number: '14242'
article_processing_charge: No
article_type: review
author:
- first_name: Emma L.
full_name: Berdan, Emma L.
last_name: Berdan
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Inês
full_name: Fragata, Inês
last_name: Fragata
- first_name: Kimberly J.
full_name: Gilbert, Kimberly J.
last_name: Gilbert
- first_name: Paul
full_name: Jay, Paul
last_name: Jay
- first_name: Martin
full_name: Kapun, Martin
last_name: Kapun
- first_name: Katie E.
full_name: Lotterhos, Katie E.
last_name: Lotterhos
- first_name: Claire
full_name: Mérot, Claire
last_name: Mérot
- first_name: Esra
full_name: Durmaz Mitchell, Esra
last_name: Durmaz Mitchell
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
- first_name: Catherine L.
full_name: Peichel, Catherine L.
last_name: Peichel
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Stephen W.
full_name: Schaeffer, Stephen W.
last_name: Schaeffer
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Thomas
full_name: Flatt, Thomas
last_name: Flatt
citation:
ama: Berdan EL, Barton NH, Butlin R, et al. How chromosomal inversions reorient
the evolutionary process. Journal of Evolutionary Biology. 2023. doi:10.1111/jeb.14242
apa: Berdan, E. L., Barton, N. H., Butlin, R., Charlesworth, B., Faria, R., Fragata,
I., … Flatt, T. (2023). How chromosomal inversions reorient the evolutionary process.
Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14242
chicago: Berdan, Emma L., Nicholas H Barton, Roger Butlin, Brian Charlesworth, Rui
Faria, Inês Fragata, Kimberly J. Gilbert, et al. “How Chromosomal Inversions Reorient
the Evolutionary Process.” Journal of Evolutionary Biology. Wiley, 2023.
https://doi.org/10.1111/jeb.14242.
ieee: E. L. Berdan et al., “How chromosomal inversions reorient the evolutionary
process,” Journal of Evolutionary Biology. Wiley, 2023.
ista: Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert
KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel
CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. 2023. How
chromosomal inversions reorient the evolutionary process. Journal of Evolutionary
Biology., 14242.
mla: Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary
Process.” Journal of Evolutionary Biology, 14242, Wiley, 2023, doi:10.1111/jeb.14242.
short: E.L. Berdan, N.H. Barton, R. Butlin, B. Charlesworth, R. Faria, I. Fragata,
K.J. Gilbert, P. Jay, M. Kapun, K.E. Lotterhos, C. Mérot, E. Durmaz Mitchell,
M. Pascual, C.L. Peichel, M. Rafajlović, A.M. Westram, S.W. Schaeffer, K. Johannesson,
T. Flatt, Journal of Evolutionary Biology (2023).
date_created: 2023-11-19T23:00:55Z
date_published: 2023-11-08T00:00:00Z
date_updated: 2023-11-20T08:51:09Z
day: '08'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.14242
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jeb.14242
month: '11'
oa: 1
oa_version: Published Version
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: epub_ahead
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: How chromosomal inversions reorient the evolutionary process
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14555'
abstract:
- lang: eng
text: The intricate regulatory processes behind actin polymerization play a crucial
role in cellular biology, including essential mechanisms such as cell migration
or cell division. However, the self-organizing principles governing actin polymerization
are still poorly understood. In this perspective article, we compare the Belousov-Zhabotinsky
(BZ) reaction, a classic and well understood chemical oscillator known for its
self-organizing spatiotemporal dynamics, with the excitable dynamics of polymerizing
actin. While the BZ reaction originates from the domain of inorganic chemistry,
it shares remarkable similarities with actin polymerization, including the characteristic
propagating waves, which are influenced by geometry and external fields, and the
emergent collective behavior. Starting with a general description of emerging
patterns, we elaborate on single droplets or cell-level dynamics, the influence
of geometric confinements and conclude with collective interactions. Comparing
these two systems sheds light on the universal nature of self-organization principles
in both living and inanimate systems.
acknowledgement: The author(s) declare that no financial support was received for
the research, authorship, and/or publication of this article.
article_number: '1287420'
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: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Riedl M, Sixt MK. The excitable nature of polymerizing actin and the Belousov-Zhabotinsky
reaction. Frontiers in Cell and Developmental Biology. 2023;11. doi:10.3389/fcell.2023.1287420
apa: Riedl, M., & Sixt, M. K. (2023). The excitable nature of polymerizing actin
and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental
Biology. Frontiers. https://doi.org/10.3389/fcell.2023.1287420
chicago: Riedl, Michael, and Michael K Sixt. “The Excitable Nature of Polymerizing
Actin and the Belousov-Zhabotinsky Reaction.” Frontiers in Cell and Developmental
Biology. Frontiers, 2023. https://doi.org/10.3389/fcell.2023.1287420.
ieee: M. Riedl and M. K. Sixt, “The excitable nature of polymerizing actin and the
Belousov-Zhabotinsky reaction,” Frontiers in Cell and Developmental Biology,
vol. 11. Frontiers, 2023.
ista: Riedl M, Sixt MK. 2023. The excitable nature of polymerizing actin and the
Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. 11,
1287420.
mla: Riedl, Michael, and Michael K. Sixt. “The Excitable Nature of Polymerizing
Actin and the Belousov-Zhabotinsky Reaction.” Frontiers in Cell and Developmental
Biology, vol. 11, 1287420, Frontiers, 2023, doi:10.3389/fcell.2023.1287420.
short: M. Riedl, M.K. Sixt, Frontiers in Cell and Developmental Biology 11 (2023).
date_created: 2023-11-19T23:00:55Z
date_published: 2023-10-31T00:00:00Z
date_updated: 2023-11-20T08:44:17Z
day: '31'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.3389/fcell.2023.1287420
file:
- access_level: open_access
checksum: 61857fc3ebf019354932e7ee684658ce
content_type: application/pdf
creator: dernst
date_created: 2023-11-20T08:41:15Z
date_updated: 2023-11-20T08:41:15Z
file_id: '14561'
file_name: 2023_FrontiersCellDevBio_Riedl.pdf
file_size: 2047622
relation: main_file
success: 1
file_date_updated: 2023-11-20T08:41:15Z
has_accepted_license: '1'
intvolume: ' 11'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Frontiers in Cell and Developmental Biology
publication_identifier:
eissn:
- 2296-634X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction
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: 11
year: '2023'
...
---
_id: '14543'
abstract:
- lang: eng
text: The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed,
plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation
of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function
in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology.
Utilizing exome sequencing and extensive international data sharing efforts, we
identified 45 affected individuals from 28 unrelated families (consanguinity 93%)
with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in
ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9
and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical
proteomics in the model organisms and human cells, with the latter also being
subjected further to ACBD6 peroxisomal localization studies. The affected individuals
(23 males and 22 females), with ages ranging from 1 to 50 years old, typically
present with a complex and progressive disease involving moderate-to-severe global
developmental delay/intellectual disability (100%) with significant expressive
language impairment (98%), movement disorders (97%), facial dysmorphism (95%),
and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia
(76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%),
microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement
disorder was dystonia (94%), frequently leading to early-onset progressive postural
deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor
in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing
with advancing age (32%), and simple motor and vocal tics were among other frequent
movement disorders. Midline brain malformations including corpus callosum abnormalities
(70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and
small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava
(24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus
models effectively recapitulated many clinical phenotypes reported in patients
including movement disorders, progressive neuromotor impairment, seizures, microcephaly,
craniofacial dysmorphism, and midbrain defects accompanied by developmental delay
with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal
localisation and ACBD6-deficiency was not associated with altered peroxisomal
parameters in patient fibroblasts. Significant differences in YnMyr-labelling
were observed for 68 co- and 18 post-translationally N-myristoylated proteins
in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient
zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related
proteins implicated in neurological diseases. The present study provides evidence
that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental
syndrome accompanied by complex and progressive cognitive and movement disorders.
article_number: awad380
article_processing_charge: No
article_type: original
author:
- first_name: Rauan
full_name: Kaiyrzhanov, Rauan
last_name: Kaiyrzhanov
- first_name: Aboulfazl
full_name: Rad, Aboulfazl
last_name: Rad
- first_name: Sheng-Jia
full_name: Lin, Sheng-Jia
last_name: Lin
- first_name: Aida
full_name: Bertoli-Avella, Aida
last_name: Bertoli-Avella
- first_name: Wouter W
full_name: Kallemeijn, Wouter W
last_name: Kallemeijn
- first_name: Annie
full_name: Godwin, Annie
last_name: Godwin
- first_name: Maha S
full_name: Zaki, Maha S
last_name: Zaki
- first_name: Kevin
full_name: Huang, Kevin
id: 3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3
last_name: Huang
orcid: 0000-0002-2512-7812
- first_name: Tracy
full_name: Lau, Tracy
last_name: Lau
- first_name: Cassidy
full_name: Petree, Cassidy
last_name: Petree
- first_name: Stephanie
full_name: Efthymiou, Stephanie
last_name: Efthymiou
- first_name: Ehsan
full_name: Ghayoor Karimiani, Ehsan
last_name: Ghayoor Karimiani
- first_name: Maja
full_name: Hempel, Maja
last_name: Hempel
- first_name: Elizabeth A
full_name: Normand, Elizabeth A
last_name: Normand
- first_name: Sabine
full_name: Rudnik-Schöneborn, Sabine
last_name: Rudnik-Schöneborn
- first_name: Ulrich A
full_name: Schatz, Ulrich A
last_name: Schatz
- first_name: Marc P
full_name: Baggelaar, Marc P
last_name: Baggelaar
- first_name: Muhammad
full_name: Ilyas, Muhammad
last_name: Ilyas
- first_name: Tipu
full_name: Sultan, Tipu
last_name: Sultan
- first_name: Javeria Raza
full_name: Alvi, Javeria Raza
last_name: Alvi
- first_name: Manizha
full_name: Ganieva, Manizha
last_name: Ganieva
- first_name: Ben
full_name: Fowler, Ben
last_name: Fowler
- first_name: Ruxandra
full_name: Aanicai, Ruxandra
last_name: Aanicai
- first_name: Gulsen
full_name: Akay Tayfun, Gulsen
last_name: Akay Tayfun
- first_name: Abdulaziz
full_name: Al Saman, Abdulaziz
last_name: Al Saman
- first_name: Abdulrahman
full_name: Alswaid, Abdulrahman
last_name: Alswaid
- first_name: Nafise
full_name: Amiri, Nafise
last_name: Amiri
- first_name: Nilufar
full_name: Asilova, Nilufar
last_name: Asilova
- first_name: Vorasuk
full_name: Shotelersuk, Vorasuk
last_name: Shotelersuk
- first_name: Patra
full_name: Yeetong, Patra
last_name: Yeetong
- first_name: Matloob
full_name: Azam, Matloob
last_name: Azam
- first_name: Meisam
full_name: Babaei, Meisam
last_name: Babaei
- first_name: Gholamreza
full_name: Bahrami Monajemi, Gholamreza
last_name: Bahrami Monajemi
- first_name: Pouria
full_name: Mohammadi, Pouria
last_name: Mohammadi
- first_name: Saeed
full_name: Samie, Saeed
last_name: Samie
- first_name: Selina Husna
full_name: Banu, Selina Husna
last_name: Banu
- first_name: Jorge Pinto
full_name: Basto, Jorge Pinto
last_name: Basto
- first_name: Fanny
full_name: Kortüm, Fanny
last_name: Kortüm
- first_name: Mislen
full_name: Bauer, Mislen
last_name: Bauer
- first_name: Peter
full_name: Bauer, Peter
last_name: Bauer
- first_name: Christian
full_name: Beetz, Christian
last_name: Beetz
- first_name: Masoud
full_name: Garshasbi, Masoud
last_name: Garshasbi
- first_name: Awatif
full_name: Hameed Issa, Awatif
last_name: Hameed Issa
- first_name: Wafaa
full_name: Eyaid, Wafaa
last_name: Eyaid
- first_name: Hind
full_name: Ahmed, Hind
last_name: Ahmed
- first_name: Narges
full_name: Hashemi, Narges
last_name: Hashemi
- first_name: Kazem
full_name: Hassanpour, Kazem
last_name: Hassanpour
- first_name: Isabella
full_name: Herman, Isabella
last_name: Herman
- first_name: Sherozjon
full_name: Ibrohimov, Sherozjon
last_name: Ibrohimov
- first_name: Ban A
full_name: Abdul-Majeed, Ban A
last_name: Abdul-Majeed
- first_name: Maria
full_name: Imdad, Maria
last_name: Imdad
- first_name: Maksudjon
full_name: Isrofilov, Maksudjon
last_name: Isrofilov
- first_name: Qassem
full_name: Kaiyal, Qassem
last_name: Kaiyal
- first_name: Suliman
full_name: Khan, Suliman
last_name: Khan
- first_name: Brian
full_name: Kirmse, Brian
last_name: Kirmse
- first_name: Janet
full_name: Koster, Janet
last_name: Koster
- first_name: Charles Marques
full_name: Lourenço, Charles Marques
last_name: Lourenço
- first_name: Tadahiro
full_name: Mitani, Tadahiro
last_name: Mitani
- first_name: Oana
full_name: Moldovan, Oana
last_name: Moldovan
- first_name: David
full_name: Murphy, David
last_name: Murphy
- first_name: Maryam
full_name: Najafi, Maryam
last_name: Najafi
- first_name: Davut
full_name: Pehlivan, Davut
last_name: Pehlivan
- first_name: Maria Eugenia
full_name: Rocha, Maria Eugenia
last_name: Rocha
- first_name: Vincenzo
full_name: Salpietro, Vincenzo
last_name: Salpietro
- first_name: Miriam
full_name: Schmidts, Miriam
last_name: Schmidts
- first_name: Adel
full_name: Shalata, Adel
last_name: Shalata
- first_name: Mohammad
full_name: Mahroum, Mohammad
last_name: Mahroum
- first_name: Jawabreh Kassem
full_name: Talbeya, Jawabreh Kassem
last_name: Talbeya
- first_name: Robert W
full_name: Taylor, Robert W
last_name: Taylor
- first_name: Dayana
full_name: Vazquez, Dayana
last_name: Vazquez
- first_name: Annalisa
full_name: Vetro, Annalisa
last_name: Vetro
- first_name: Hans R
full_name: Waterham, Hans R
last_name: Waterham
- first_name: Mashaya
full_name: Zaman, Mashaya
last_name: Zaman
- first_name: Tina A
full_name: Schrader, Tina A
last_name: Schrader
- first_name: Wendy K
full_name: Chung, Wendy K
last_name: Chung
- first_name: Renzo
full_name: Guerrini, Renzo
last_name: Guerrini
- first_name: James R
full_name: Lupski, James R
last_name: Lupski
- first_name: Joseph
full_name: Gleeson, Joseph
last_name: Gleeson
- first_name: Mohnish
full_name: Suri, Mohnish
last_name: Suri
- first_name: Yalda
full_name: Jamshidi, Yalda
last_name: Jamshidi
- first_name: Kailash P
full_name: Bhatia, Kailash P
last_name: Bhatia
- first_name: Barbara
full_name: Vona, Barbara
last_name: Vona
- first_name: Michael
full_name: Schrader, Michael
last_name: Schrader
- first_name: Mariasavina
full_name: Severino, Mariasavina
last_name: Severino
- first_name: Matthew
full_name: Guille, Matthew
last_name: Guille
- first_name: Edward W
full_name: Tate, Edward W
last_name: Tate
- first_name: Gaurav K
full_name: Varshney, Gaurav K
last_name: Varshney
- first_name: Henry
full_name: Houlden, Henry
last_name: Houlden
- first_name: Reza
full_name: Maroofian, Reza
last_name: Maroofian
citation:
ama: Kaiyrzhanov R, Rad A, Lin S-J, et al. Bi-allelic ACBD6 variants lead to a neurodevelopmental
syndrome with progressive and complex movement disorders. Brain. 2023.
doi:10.1093/brain/awad380
apa: Kaiyrzhanov, R., Rad, A., Lin, S.-J., Bertoli-Avella, A., Kallemeijn, W. W.,
Godwin, A., … Maroofian, R. (2023). Bi-allelic ACBD6 variants lead to a neurodevelopmental
syndrome with progressive and complex movement disorders. Brain. Oxford
University Press. https://doi.org/10.1093/brain/awad380
chicago: Kaiyrzhanov, Rauan, Aboulfazl Rad, Sheng-Jia Lin, Aida Bertoli-Avella,
Wouter W Kallemeijn, Annie Godwin, Maha S Zaki, et al. “Bi-Allelic ACBD6 Variants
Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.”
Brain. Oxford University Press, 2023. https://doi.org/10.1093/brain/awad380.
ieee: R. Kaiyrzhanov et al., “Bi-allelic ACBD6 variants lead to a neurodevelopmental
syndrome with progressive and complex movement disorders,” Brain. Oxford
University Press, 2023.
ista: Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A,
Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M,
Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi
JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri
N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G,
Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C,
Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman
I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse
B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D,
Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW,
Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski
JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M,
Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. 2023. Bi-allelic ACBD6
variants lead to a neurodevelopmental syndrome with progressive and complex movement
disorders. Brain., awad380.
mla: Kaiyrzhanov, Rauan, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental
Syndrome with Progressive and Complex Movement Disorders.” Brain, awad380,
Oxford University Press, 2023, doi:10.1093/brain/awad380.
short: R. Kaiyrzhanov, A. Rad, S.-J. Lin, A. Bertoli-Avella, W.W. Kallemeijn, A.
Godwin, M.S. Zaki, K. Huang, T. Lau, C. Petree, S. Efthymiou, E. Ghayoor Karimiani,
M. Hempel, E.A. Normand, S. Rudnik-Schöneborn, U.A. Schatz, M.P. Baggelaar, M.
Ilyas, T. Sultan, J.R. Alvi, M. Ganieva, B. Fowler, R. Aanicai, G. Akay Tayfun,
A. Al Saman, A. Alswaid, N. Amiri, N. Asilova, V. Shotelersuk, P. Yeetong, M.
Azam, M. Babaei, G. Bahrami Monajemi, P. Mohammadi, S. Samie, S.H. Banu, J.P.
Basto, F. Kortüm, M. Bauer, P. Bauer, C. Beetz, M. Garshasbi, A. Hameed Issa,
W. Eyaid, H. Ahmed, N. Hashemi, K. Hassanpour, I. Herman, S. Ibrohimov, B.A. Abdul-Majeed,
M. Imdad, M. Isrofilov, Q. Kaiyal, S. Khan, B. Kirmse, J. Koster, C.M. Lourenço,
T. Mitani, O. Moldovan, D. Murphy, M. Najafi, D. Pehlivan, M.E. Rocha, V. Salpietro,
M. Schmidts, A. Shalata, M. Mahroum, J.K. Talbeya, R.W. Taylor, D. Vazquez, A.
Vetro, H.R. Waterham, M. Zaman, T.A. Schrader, W.K. Chung, R. Guerrini, J.R. Lupski,
J. Gleeson, M. Suri, Y. Jamshidi, K.P. Bhatia, B. Vona, M. Schrader, M. Severino,
M. Guille, E.W. Tate, G.K. Varshney, H. Houlden, R. Maroofian, Brain (2023).
date_created: 2023-11-16T12:36:51Z
date_published: 2023-11-10T00:00:00Z
date_updated: 2023-11-20T10:17:32Z
day: '10'
department:
- _id: GradSch
doi: 10.1093/brain/awad380
extern: '1'
keyword:
- Neurology (clinical)
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/brain/awad380
month: '11'
oa: 1
oa_version: Submitted Version
publication: Brain
publication_identifier:
eissn:
- 1460-2156
issn:
- 0006-8950
publication_status: epub_ahead
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive
and complex movement disorders
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14542'
abstract:
- lang: eng
text: "It is a remarkable property of BCS theory that the ratio of the energy gap
at zero temperature Ξ\r\n and the critical temperature Tc is (approximately) given
by a universal constant, independent of the microscopic details of the fermionic
interaction. This universality has rigorously been proven quite recently in three
spatial dimensions and three different limiting regimes: weak coupling, low density
and high density. The goal of this short note is to extend the universal behavior
to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit."
acknowledgement: We thank Robert Seiringer for comments on the paper. J. H. gratefully
acknowledges partial financial support by the ERC Advanced Grant “RMTBeyond”No.
101020331.This research was funded in part by the Austrian Science Fund (FWF) grantnumber
I6427.
article_number: '2360005 '
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Sven Joscha
full_name: Henheik, Sven Joscha
id: 31d731d7-d235-11ea-ad11-b50331c8d7fb
last_name: Henheik
orcid: 0000-0003-1106-327X
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
- first_name: Barbara
full_name: Roos, Barbara
id: 5DA90512-D80F-11E9-8994-2E2EE6697425
last_name: Roos
orcid: 0000-0002-9071-5880
citation:
ama: Henheik SJ, Lauritsen AB, Roos B. Universality in low-dimensional BCS theory.
Reviews in Mathematical Physics. 2023. doi:10.1142/s0129055x2360005x
apa: Henheik, S. J., Lauritsen, A. B., & Roos, B. (2023). Universality in low-dimensional
BCS theory. Reviews in Mathematical Physics. World Scientific Publishing.
https://doi.org/10.1142/s0129055x2360005x
chicago: Henheik, Sven Joscha, Asbjørn Bækgaard Lauritsen, and Barbara Roos. “Universality
in Low-Dimensional BCS Theory.” Reviews in Mathematical Physics. World
Scientific Publishing, 2023. https://doi.org/10.1142/s0129055x2360005x.
ieee: S. J. Henheik, A. B. Lauritsen, and B. Roos, “Universality in low-dimensional
BCS theory,” Reviews in Mathematical Physics. World Scientific Publishing,
2023.
ista: Henheik SJ, Lauritsen AB, Roos B. 2023. Universality in low-dimensional BCS
theory. Reviews in Mathematical Physics., 2360005.
mla: Henheik, Sven Joscha, et al. “Universality in Low-Dimensional BCS Theory.”
Reviews in Mathematical Physics, 2360005, World Scientific Publishing,
2023, doi:10.1142/s0129055x2360005x.
short: S.J. Henheik, A.B. Lauritsen, B. Roos, Reviews in Mathematical Physics (2023).
date_created: 2023-11-15T23:48:14Z
date_published: 2023-10-31T00:00:00Z
date_updated: 2023-11-20T10:04:38Z
day: '31'
department:
- _id: GradSch
- _id: LaEr
- _id: RoSe
doi: 10.1142/s0129055x2360005x
ec_funded: 1
external_id:
arxiv:
- '2301.05621'
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1142/S0129055X2360005X
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
- _id: bda63fe5-d553-11ed-ba76-a16e3d2f256b
grant_number: I06427
name: Mathematical Challenges in BCS Theory of Superconductivity
publication: Reviews in Mathematical Physics
publication_identifier:
eissn:
- 1793-6659
issn:
- 0129-055X
publication_status: epub_ahead
publisher: World Scientific Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Universality in low-dimensional BCS theory
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14553'
abstract:
- lang: eng
text: Quantum state tomography is an essential component of modern quantum technology.
In application to continuous-variable harmonic-oscillator systems, such as the
electromagnetic field, existing tomography methods typically reconstruct the state
in discrete bases, and are hence limited to states with relatively low amplitudes
and energies. Here, we overcome this limitation by utilizing a feed-forward neural
network to obtain the density matrix directly in the continuous position basis.
An important benefit of our approach is the ability to choose specific regions
in the phase space for detailed reconstruction. This results in a relatively slow
scaling of the amount of resources required for the reconstruction with the state
amplitude, and hence allows us to dramatically increase the range of amplitudes
accessible with our method.
article_number: '042430'
article_processing_charge: No
article_type: original
author:
- first_name: Ekaterina
full_name: Fedotova, Ekaterina
id: c1bea5e1-878e-11ee-9dff-d7404e4422ab
last_name: Fedotova
orcid: 0000-0001-7242-015X
- first_name: Nikolai
full_name: Kuznetsov, Nikolai
last_name: Kuznetsov
- first_name: Egor
full_name: Tiunov, Egor
last_name: Tiunov
- first_name: A. E.
full_name: Ulanov, A. E.
last_name: Ulanov
- first_name: A. I.
full_name: Lvovsky, A. I.
last_name: Lvovsky
citation:
ama: Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. Continuous-variable
quantum tomography of high-amplitude states. Physical Review A. 2023;108(4).
doi:10.1103/PhysRevA.108.042430
apa: Fedotova, E., Kuznetsov, N., Tiunov, E., Ulanov, A. E., & Lvovsky, A. I.
(2023). Continuous-variable quantum tomography of high-amplitude states. Physical
Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.108.042430
chicago: Fedotova, Ekaterina, Nikolai Kuznetsov, Egor Tiunov, A. E. Ulanov, and
A. I. Lvovsky. “Continuous-Variable Quantum Tomography of High-Amplitude States.”
Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.108.042430.
ieee: E. Fedotova, N. Kuznetsov, E. Tiunov, A. E. Ulanov, and A. I. Lvovsky, “Continuous-variable
quantum tomography of high-amplitude states,” Physical Review A, vol. 108,
no. 4. American Physical Society, 2023.
ista: Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. 2023. Continuous-variable
quantum tomography of high-amplitude states. Physical Review A. 108(4), 042430.
mla: Fedotova, Ekaterina, et al. “Continuous-Variable Quantum Tomography of High-Amplitude
States.” Physical Review A, vol. 108, no. 4, 042430, American Physical
Society, 2023, doi:10.1103/PhysRevA.108.042430.
short: E. Fedotova, N. Kuznetsov, E. Tiunov, A.E. Ulanov, A.I. Lvovsky, Physical
Review A 108 (2023).
date_created: 2023-11-19T23:00:54Z
date_published: 2023-10-30T00:00:00Z
date_updated: 2023-11-20T10:26:51Z
day: '30'
department:
- _id: JoFi
doi: 10.1103/PhysRevA.108.042430
external_id:
arxiv:
- '2212.07406'
intvolume: ' 108'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2212.07406
month: '10'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Continuous-variable quantum tomography of high-amplitude states
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '14557'
abstract:
- lang: eng
text: Motivated by a problem posed in [10], we investigate the closure operators
of the category SLatt of join semilattices and its subcategory SLattO of join
semilattices with bottom element. In particular, we show that there are only finitely
many closure operators of both categories, and provide a complete classification.
We use this result to deduce the known fact that epimorphisms of SLatt and SLattO
are surjective. We complement the paper with two different proofs of this result
using either generators or Isbell’s zigzag theorem.
acknowledgement: "The first and second named authors are members of GNSAGA – INdAM.\r\nThe
third named author was supported by the FWF Grant, Project number I4245–N35"
article_processing_charge: No
article_type: original
author:
- first_name: D.
full_name: Dikranjan, D.
last_name: Dikranjan
- first_name: A.
full_name: Giordano Bruno, A.
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: Dikranjan D, Giordano Bruno A, Zava N. Epimorphisms and closure operators of
categories of semilattices. Quaestiones Mathematicae. 2023;46(S1):191-221.
doi:10.2989/16073606.2023.2247731
apa: Dikranjan, D., Giordano Bruno, A., & Zava, N. (2023). Epimorphisms and
closure operators of categories of semilattices. Quaestiones Mathematicae.
Taylor & Francis. https://doi.org/10.2989/16073606.2023.2247731
chicago: Dikranjan, D., A. Giordano Bruno, and Nicolò Zava. “Epimorphisms and Closure
Operators of Categories of Semilattices.” Quaestiones Mathematicae. Taylor
& Francis, 2023. https://doi.org/10.2989/16073606.2023.2247731.
ieee: D. Dikranjan, A. Giordano Bruno, and N. Zava, “Epimorphisms and closure operators
of categories of semilattices,” Quaestiones Mathematicae, vol. 46, no.
S1. Taylor & Francis, pp. 191–221, 2023.
ista: Dikranjan D, Giordano Bruno A, Zava N. 2023. Epimorphisms and closure operators
of categories of semilattices. Quaestiones Mathematicae. 46(S1), 191–221.
mla: Dikranjan, D., et al. “Epimorphisms and Closure Operators of Categories of
Semilattices.” Quaestiones Mathematicae, vol. 46, no. S1, Taylor &
Francis, 2023, pp. 191–221, doi:10.2989/16073606.2023.2247731.
short: D. Dikranjan, A. Giordano Bruno, N. Zava, Quaestiones Mathematicae 46 (2023)
191–221.
date_created: 2023-11-19T23:00:55Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2023-11-20T09:24:48Z
day: '01'
department:
- _id: HeEd
doi: 10.2989/16073606.2023.2247731
intvolume: ' 46'
issue: S1
language:
- iso: eng
month: '11'
oa_version: None
page: 191-221
project:
- _id: 26AD5D90-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I04245
name: Algebraic Footprints of Geometric Features in Homology
publication: Quaestiones Mathematicae
publication_identifier:
eissn:
- 1727-933X
issn:
- 1607-3606
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Epimorphisms and closure operators of categories of semilattices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2023'
...
---
_id: '14552'
abstract:
- lang: eng
text: Interactions between plants and herbivores are central in most ecosystems,
but their strength is highly variable. The amount of variability within a system
is thought to influence most aspects of plant-herbivore biology, from ecological
stability to plant defense evolution. Our understanding of what influences variability,
however, is limited by sparse data. We collected standardized surveys of herbivory
for 503 plant species at 790 sites across 116° of latitude. With these data, we
show that within-population variability in herbivory increases with latitude,
decreases with plant size, and is phylogenetically structured. Differences in
the magnitude of variability are thus central to how plant-herbivore biology varies
across macroscale gradients. We argue that increased focus on interaction variability
will advance understanding of patterns of life on Earth.
acknowledgement: The authors acknowledge funding for central project coordination
from NSF Research Coordination Network grant DEB-2203582; the Ecology, Evolution,
and Behavior Program at Michigan State University; and AgBioResearch at Michigan
State University. Site-specific funding is listed in the supplementary materials.
article_processing_charge: No
article_type: original
author:
- first_name: M. L.
full_name: Robinson, M. L.
last_name: Robinson
- first_name: P. G.
full_name: Hahn, P. G.
last_name: Hahn
- first_name: B. D.
full_name: Inouye, B. D.
last_name: Inouye
- first_name: N.
full_name: Underwood, N.
last_name: Underwood
- first_name: S. R.
full_name: Whitehead, S. R.
last_name: Whitehead
- first_name: K. C.
full_name: Abbott, K. C.
last_name: Abbott
- first_name: E. M.
full_name: Bruna, E. M.
last_name: Bruna
- first_name: N. I.
full_name: Cacho, N. I.
last_name: Cacho
- first_name: L. A.
full_name: Dyer, L. A.
last_name: Dyer
- first_name: L.
full_name: Abdala-Roberts, L.
last_name: Abdala-Roberts
- first_name: W. J.
full_name: Allen, W. J.
last_name: Allen
- first_name: J. F.
full_name: Andrade, J. F.
last_name: Andrade
- first_name: D. F.
full_name: Angulo, D. F.
last_name: Angulo
- first_name: D.
full_name: Anjos, D.
last_name: Anjos
- first_name: D. N.
full_name: Anstett, D. N.
last_name: Anstett
- first_name: R.
full_name: Bagchi, R.
last_name: Bagchi
- first_name: S.
full_name: Bagchi, S.
last_name: Bagchi
- first_name: M.
full_name: Barbosa, M.
last_name: Barbosa
- first_name: S.
full_name: Barrett, S.
last_name: Barrett
- first_name: Carina
full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- first_name: E.
full_name: Ben-Simchon, E.
last_name: Ben-Simchon
- first_name: K. J.
full_name: Bloodworth, K. J.
last_name: Bloodworth
- first_name: J. L.
full_name: Bronstein, J. L.
last_name: Bronstein
- first_name: Y. M.
full_name: Buckley, Y. M.
last_name: Buckley
- first_name: K. T.
full_name: Burghardt, K. T.
last_name: Burghardt
- first_name: C.
full_name: Bustos-Segura, C.
last_name: Bustos-Segura
- first_name: E. S.
full_name: Calixto, E. S.
last_name: Calixto
- first_name: R. L.
full_name: Carvalho, R. L.
last_name: Carvalho
- first_name: B.
full_name: Castagneyrol, B.
last_name: Castagneyrol
- first_name: M. C.
full_name: Chiuffo, M. C.
last_name: Chiuffo
- first_name: D.
full_name: Cinoğlu, D.
last_name: Cinoğlu
- first_name: E.
full_name: Cinto Mejía, E.
last_name: Cinto Mejía
- first_name: M. C.
full_name: Cock, M. C.
last_name: Cock
- first_name: R.
full_name: Cogni, R.
last_name: Cogni
- first_name: O. L.
full_name: Cope, O. L.
last_name: Cope
- first_name: T.
full_name: Cornelissen, T.
last_name: Cornelissen
- first_name: D. R.
full_name: Cortez, D. R.
last_name: Cortez
- first_name: D. W.
full_name: Crowder, D. W.
last_name: Crowder
- first_name: C.
full_name: Dallstream, C.
last_name: Dallstream
- first_name: W.
full_name: Dáttilo, W.
last_name: Dáttilo
- first_name: J. K.
full_name: Davis, J. K.
last_name: Davis
- first_name: R. D.
full_name: Dimarco, R. D.
last_name: Dimarco
- first_name: H. E.
full_name: Dole, H. E.
last_name: Dole
- first_name: I. N.
full_name: Egbon, I. N.
last_name: Egbon
- first_name: M.
full_name: Eisenring, M.
last_name: Eisenring
- first_name: A.
full_name: Ejomah, A.
last_name: Ejomah
- first_name: B. D.
full_name: Elderd, B. D.
last_name: Elderd
- first_name: M. J.
full_name: Endara, M. J.
last_name: Endara
- first_name: M. D.
full_name: Eubanks, M. D.
last_name: Eubanks
- first_name: S. E.
full_name: Everingham, S. E.
last_name: Everingham
- first_name: K. N.
full_name: Farah, K. N.
last_name: Farah
- first_name: R. P.
full_name: Farias, R. P.
last_name: Farias
- first_name: A. P.
full_name: Fernandes, A. P.
last_name: Fernandes
- first_name: G. W.
full_name: Fernandes, G. W.
last_name: Fernandes
- first_name: M.
full_name: Ferrante, M.
last_name: Ferrante
- first_name: A.
full_name: Finn, A.
last_name: Finn
- first_name: G. A.
full_name: Florjancic, G. A.
last_name: Florjancic
- first_name: M. L.
full_name: Forister, M. L.
last_name: Forister
- first_name: Q. N.
full_name: Fox, Q. N.
last_name: Fox
- first_name: E.
full_name: Frago, E.
last_name: Frago
- first_name: F. M.
full_name: França, F. M.
last_name: França
- first_name: A. S.
full_name: Getman-Pickering, A. S.
last_name: Getman-Pickering
- first_name: Z.
full_name: Getman-Pickering, Z.
last_name: Getman-Pickering
- first_name: E.
full_name: Gianoli, E.
last_name: Gianoli
- first_name: B.
full_name: Gooden, B.
last_name: Gooden
- first_name: M. M.
full_name: Gossner, M. M.
last_name: Gossner
- first_name: K. A.
full_name: Greig, K. A.
last_name: Greig
- first_name: S.
full_name: Gripenberg, S.
last_name: Gripenberg
- first_name: R.
full_name: Groenteman, R.
last_name: Groenteman
- first_name: P.
full_name: Grof-Tisza, P.
last_name: Grof-Tisza
- first_name: N.
full_name: Haack, N.
last_name: Haack
- first_name: L.
full_name: Hahn, L.
last_name: Hahn
- first_name: S. M.
full_name: Haq, S. M.
last_name: Haq
- first_name: A. M.
full_name: Helms, A. M.
last_name: Helms
- first_name: J.
full_name: Hennecke, J.
last_name: Hennecke
- first_name: S. L.
full_name: Hermann, S. L.
last_name: Hermann
- first_name: L. M.
full_name: Holeski, L. M.
last_name: Holeski
- first_name: S.
full_name: Holm, S.
last_name: Holm
- first_name: M. C.
full_name: Hutchinson, M. C.
last_name: Hutchinson
- first_name: E. E.
full_name: Jackson, E. E.
last_name: Jackson
- first_name: S.
full_name: Kagiya, S.
last_name: Kagiya
- first_name: A.
full_name: Kalske, A.
last_name: Kalske
- first_name: M.
full_name: Kalwajtys, M.
last_name: Kalwajtys
- first_name: R.
full_name: Karban, R.
last_name: Karban
- first_name: R.
full_name: Kariyat, R.
last_name: Kariyat
- first_name: T.
full_name: Keasar, T.
last_name: Keasar
- first_name: M. F.
full_name: Kersch-Becker, M. F.
last_name: Kersch-Becker
- first_name: H. M.
full_name: Kharouba, H. M.
last_name: Kharouba
- first_name: T. N.
full_name: Kim, T. N.
last_name: Kim
- first_name: D. M.
full_name: Kimuyu, D. M.
last_name: Kimuyu
- first_name: J.
full_name: Kluse, J.
last_name: Kluse
- first_name: S. E.
full_name: Koerner, S. E.
last_name: Koerner
- first_name: K. J.
full_name: Komatsu, K. J.
last_name: Komatsu
- first_name: S.
full_name: Krishnan, S.
last_name: Krishnan
- first_name: M.
full_name: Laihonen, M.
last_name: Laihonen
- first_name: L.
full_name: Lamelas-López, L.
last_name: Lamelas-López
- first_name: M. C.
full_name: Lascaleia, M. C.
last_name: Lascaleia
- first_name: N.
full_name: Lecomte, N.
last_name: Lecomte
- first_name: C. R.
full_name: Lehn, C. R.
last_name: Lehn
- first_name: X.
full_name: Li, X.
last_name: Li
- first_name: R. L.
full_name: Lindroth, R. L.
last_name: Lindroth
- first_name: E. F.
full_name: Lopresti, E. F.
last_name: Lopresti
- first_name: M.
full_name: Losada, M.
last_name: Losada
- first_name: A. M.
full_name: Louthan, A. M.
last_name: Louthan
- first_name: V. J.
full_name: Luizzi, V. J.
last_name: Luizzi
- first_name: S. C.
full_name: Lynch, S. C.
last_name: Lynch
- first_name: J. S.
full_name: Lynn, J. S.
last_name: Lynn
- first_name: N. J.
full_name: Lyon, N. J.
last_name: Lyon
- first_name: L. F.
full_name: Maia, L. F.
last_name: Maia
- first_name: R. A.
full_name: Maia, R. A.
last_name: Maia
- first_name: T. L.
full_name: Mannall, T. L.
last_name: Mannall
- first_name: B. S.
full_name: Martin, B. S.
last_name: Martin
- first_name: T. J.
full_name: Massad, T. J.
last_name: Massad
- first_name: A. C.
full_name: Mccall, A. C.
last_name: Mccall
- first_name: K.
full_name: Mcgurrin, K.
last_name: Mcgurrin
- first_name: A. C.
full_name: Merwin, A. C.
last_name: Merwin
- first_name: Z.
full_name: Mijango-Ramos, Z.
last_name: Mijango-Ramos
- first_name: C. H.
full_name: Mills, C. H.
last_name: Mills
- first_name: A. T.
full_name: Moles, A. T.
last_name: Moles
- first_name: C. M.
full_name: Moore, C. M.
last_name: Moore
- first_name: X.
full_name: Moreira, X.
last_name: Moreira
- first_name: C. R.
full_name: Morrison, C. R.
last_name: Morrison
- first_name: M. C.
full_name: Moshobane, M. C.
last_name: Moshobane
- first_name: A.
full_name: Muola, A.
last_name: Muola
- first_name: R.
full_name: Nakadai, R.
last_name: Nakadai
- first_name: K.
full_name: Nakajima, K.
last_name: Nakajima
- first_name: S.
full_name: Novais, S.
last_name: Novais
- first_name: C. O.
full_name: Ogbebor, C. O.
last_name: Ogbebor
- first_name: H.
full_name: Ohsaki, H.
last_name: Ohsaki
- first_name: V. S.
full_name: Pan, V. S.
last_name: Pan
- first_name: N. A.
full_name: Pardikes, N. A.
last_name: Pardikes
- first_name: M.
full_name: Pareja, M.
last_name: Pareja
- first_name: N.
full_name: Parthasarathy, N.
last_name: Parthasarathy
- first_name: R. R.
full_name: Pawar, R. R.
last_name: Pawar
- first_name: Q.
full_name: Paynter, Q.
last_name: Paynter
- first_name: I. S.
full_name: Pearse, I. S.
last_name: Pearse
- first_name: R. M.
full_name: Penczykowski, R. M.
last_name: Penczykowski
- first_name: A. A.
full_name: Pepi, A. A.
last_name: Pepi
- first_name: C. C.
full_name: Pereira, C. C.
last_name: Pereira
- first_name: S. S.
full_name: Phartyal, S. S.
last_name: Phartyal
- first_name: F. I.
full_name: Piper, F. I.
last_name: Piper
- first_name: K.
full_name: Poveda, K.
last_name: Poveda
- first_name: E. G.
full_name: Pringle, E. G.
last_name: Pringle
- first_name: J.
full_name: Puy, J.
last_name: Puy
- first_name: T.
full_name: Quijano, T.
last_name: Quijano
- first_name: C.
full_name: Quintero, C.
last_name: Quintero
- first_name: S.
full_name: Rasmann, S.
last_name: Rasmann
- first_name: C.
full_name: Rosche, C.
last_name: Rosche
- first_name: L. Y.
full_name: Rosenheim, L. Y.
last_name: Rosenheim
- first_name: J. A.
full_name: Rosenheim, J. A.
last_name: Rosenheim
- first_name: J. B.
full_name: Runyon, J. B.
last_name: Runyon
- first_name: A.
full_name: Sadeh, A.
last_name: Sadeh
- first_name: Y.
full_name: Sakata, Y.
last_name: Sakata
- first_name: D. M.
full_name: Salcido, D. M.
last_name: Salcido
- first_name: C.
full_name: Salgado-Luarte, C.
last_name: Salgado-Luarte
- first_name: B. A.
full_name: Santos, B. A.
last_name: Santos
- first_name: Y.
full_name: Sapir, Y.
last_name: Sapir
- first_name: Y.
full_name: Sasal, Y.
last_name: Sasal
- first_name: Y.
full_name: Sato, Y.
last_name: Sato
- first_name: M.
full_name: Sawant, M.
last_name: Sawant
- first_name: H.
full_name: Schroeder, H.
last_name: Schroeder
- first_name: I.
full_name: Schumann, I.
last_name: Schumann
- first_name: M.
full_name: Segoli, M.
last_name: Segoli
- first_name: H.
full_name: Segre, H.
last_name: Segre
- first_name: O.
full_name: Shelef, O.
last_name: Shelef
- first_name: N.
full_name: Shinohara, N.
last_name: Shinohara
- first_name: R. P.
full_name: Singh, R. P.
last_name: Singh
- first_name: D. S.
full_name: Smith, D. S.
last_name: Smith
- first_name: M.
full_name: Sobral, M.
last_name: Sobral
- first_name: G. C.
full_name: Stotz, G. C.
last_name: Stotz
- first_name: A. J.M.
full_name: Tack, A. J.M.
last_name: Tack
- first_name: M.
full_name: Tayal, M.
last_name: Tayal
- first_name: J. F.
full_name: Tooker, J. F.
last_name: Tooker
- first_name: D.
full_name: Torrico-Bazoberry, D.
last_name: Torrico-Bazoberry
- first_name: K.
full_name: Tougeron, K.
last_name: Tougeron
- first_name: A. M.
full_name: Trowbridge, A. M.
last_name: Trowbridge
- first_name: S.
full_name: Utsumi, S.
last_name: Utsumi
- first_name: O.
full_name: Uyi, O.
last_name: Uyi
- first_name: J. L.
full_name: Vaca-Uribe, J. L.
last_name: Vaca-Uribe
- first_name: A.
full_name: Valtonen, A.
last_name: Valtonen
- first_name: L. J.A.
full_name: Van Dijk, L. J.A.
last_name: Van Dijk
- first_name: V.
full_name: Vandvik, V.
last_name: Vandvik
- first_name: J.
full_name: Villellas, J.
last_name: Villellas
- first_name: L. P.
full_name: Waller, L. P.
last_name: Waller
- first_name: M. G.
full_name: Weber, M. G.
last_name: Weber
- first_name: A.
full_name: Yamawo, A.
last_name: Yamawo
- first_name: S.
full_name: Yim, S.
last_name: Yim
- first_name: P. L.
full_name: Zarnetske, P. L.
last_name: Zarnetske
- first_name: L. N.
full_name: Zehr, L. N.
last_name: Zehr
- first_name: Z.
full_name: Zhong, Z.
last_name: Zhong
- first_name: W. C.
full_name: Wetzel, W. C.
last_name: Wetzel
citation:
ama: Robinson ML, Hahn PG, Inouye BD, et al. Plant size, latitude, and phylogeny
explain within-population variability in herbivory. Science. 2023;382(6671):679-683.
doi:10.1126/science.adh8830
apa: Robinson, M. L., Hahn, P. G., Inouye, B. D., Underwood, N., Whitehead, S. R.,
Abbott, K. C., … Wetzel, W. C. (2023). Plant size, latitude, and phylogeny explain
within-population variability in herbivory. Science. AAAS. https://doi.org/10.1126/science.adh8830
chicago: Robinson, M. L., P. G. Hahn, B. D. Inouye, N. Underwood, S. R. Whitehead,
K. C. Abbott, E. M. Bruna, et al. “Plant Size, Latitude, and Phylogeny Explain
within-Population Variability in Herbivory.” Science. AAAS, 2023. https://doi.org/10.1126/science.adh8830.
ieee: M. L. Robinson et al., “Plant size, latitude, and phylogeny explain
within-population variability in herbivory,” Science, vol. 382, no. 6671.
AAAS, pp. 679–683, 2023.
ista: Robinson ML et al. 2023. Plant size, latitude, and phylogeny explain within-population
variability in herbivory. Science. 382(6671), 679–683.
mla: Robinson, M. L., et al. “Plant Size, Latitude, and Phylogeny Explain within-Population
Variability in Herbivory.” Science, vol. 382, no. 6671, AAAS, 2023, pp.
679–83, doi:10.1126/science.adh8830.
short: M.L. Robinson, P.G. Hahn, B.D. Inouye, N. Underwood, S.R. Whitehead, K.C.
Abbott, E.M. Bruna, N.I. Cacho, L.A. Dyer, L. Abdala-Roberts, W.J. Allen, J.F.
Andrade, D.F. Angulo, D. Anjos, D.N. Anstett, R. Bagchi, S. Bagchi, M. Barbosa,
S. Barrett, C. Baskett, E. Ben-Simchon, K.J. Bloodworth, J.L. Bronstein, Y.M.
Buckley, K.T. Burghardt, C. Bustos-Segura, E.S. Calixto, R.L. Carvalho, B. Castagneyrol,
M.C. Chiuffo, D. Cinoğlu, E. Cinto Mejía, M.C. Cock, R. Cogni, O.L. Cope, T. Cornelissen,
D.R. Cortez, D.W. Crowder, C. Dallstream, W. Dáttilo, J.K. Davis, R.D. Dimarco,
H.E. Dole, I.N. Egbon, M. Eisenring, A. Ejomah, B.D. Elderd, M.J. Endara, M.D.
Eubanks, S.E. Everingham, K.N. Farah, R.P. Farias, A.P. Fernandes, G.W. Fernandes,
M. Ferrante, A. Finn, G.A. Florjancic, M.L. Forister, Q.N. Fox, E. Frago, F.M.
França, A.S. Getman-Pickering, Z. Getman-Pickering, E. Gianoli, B. Gooden, M.M.
Gossner, K.A. Greig, S. Gripenberg, R. Groenteman, P. Grof-Tisza, N. Haack, L.
Hahn, S.M. Haq, A.M. Helms, J. Hennecke, S.L. Hermann, L.M. Holeski, S. Holm,
M.C. Hutchinson, E.E. Jackson, S. Kagiya, A. Kalske, M. Kalwajtys, R. Karban,
R. Kariyat, T. Keasar, M.F. Kersch-Becker, H.M. Kharouba, T.N. Kim, D.M. Kimuyu,
J. Kluse, S.E. Koerner, K.J. Komatsu, S. Krishnan, M. Laihonen, L. Lamelas-López,
M.C. Lascaleia, N. Lecomte, C.R. Lehn, X. Li, R.L. Lindroth, E.F. Lopresti, M.
Losada, A.M. Louthan, V.J. Luizzi, S.C. Lynch, J.S. Lynn, N.J. Lyon, L.F. Maia,
R.A. Maia, T.L. Mannall, B.S. Martin, T.J. Massad, A.C. Mccall, K. Mcgurrin, A.C.
Merwin, Z. Mijango-Ramos, C.H. Mills, A.T. Moles, C.M. Moore, X. Moreira, C.R.
Morrison, M.C. Moshobane, A. Muola, R. Nakadai, K. Nakajima, S. Novais, C.O. Ogbebor,
H. Ohsaki, V.S. Pan, N.A. Pardikes, M. Pareja, N. Parthasarathy, R.R. Pawar, Q.
Paynter, I.S. Pearse, R.M. Penczykowski, A.A. Pepi, C.C. Pereira, S.S. Phartyal,
F.I. Piper, K. Poveda, E.G. Pringle, J. Puy, T. Quijano, C. Quintero, S. Rasmann,
C. Rosche, L.Y. Rosenheim, J.A. Rosenheim, J.B. Runyon, A. Sadeh, Y. Sakata, D.M.
Salcido, C. Salgado-Luarte, B.A. Santos, Y. Sapir, Y. Sasal, Y. Sato, M. Sawant,
H. Schroeder, I. Schumann, M. Segoli, H. Segre, O. Shelef, N. Shinohara, R.P.
Singh, D.S. Smith, M. Sobral, G.C. Stotz, A.J.M. Tack, M. Tayal, J.F. Tooker,
D. Torrico-Bazoberry, K. Tougeron, A.M. Trowbridge, S. Utsumi, O. Uyi, J.L. Vaca-Uribe,
A. Valtonen, L.J.A. Van Dijk, V. Vandvik, J. Villellas, L.P. Waller, M.G. Weber,
A. Yamawo, S. Yim, P.L. Zarnetske, L.N. Zehr, Z. Zhong, W.C. Wetzel, Science 382
(2023) 679–683.
date_created: 2023-11-19T23:00:54Z
date_published: 2023-11-09T00:00:00Z
date_updated: 2023-11-20T11:17:34Z
day: '09'
department:
- _id: NiBa
doi: 10.1126/science.adh8830
external_id:
pmid:
- '37943897'
intvolume: ' 382'
issue: '6671'
language:
- iso: eng
month: '11'
oa_version: None
page: 679-683
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: AAAS
quality_controlled: '1'
related_material:
record:
- id: '14579'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Plant size, latitude, and phylogeny explain within-population variability in
herbivory
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 382
year: '2023'
...
---
_id: '14551'
abstract:
- lang: eng
text: Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome
functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How
mCG is established and transmitted across generations despite imperfect enzyme
fidelity is unclear. Whether mCG variation in natural populations is governed
by genetic or epigenetic inheritance also remains mysterious. Here, we show that
MET1 de novo activity, which is enhanced by existing proximate methylation, seeds
and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted
by active demethylation and suppressed by histone variant H2A.Z, producing localized
mCG patterns. Based on these observations, we develop a stochastic mathematical
model that precisely recapitulates mCG inheritance dynamics and predicts intragenic
mCG patterns and their population-scale variation given only CG site spacing.
Our results demonstrate that intragenic mCG establishment, inheritance, and variance
constitute a unified epigenetic process, revealing that intragenic mCG undergoes
large, millennia-long epigenetic fluctuations and can therefore mediate evolution
on this timescale.
acknowledgement: We would like to thank Xiaoqi Feng, Ander Movilla Miangolarra, and
Suzanne de Bruijn for discussions. This work was supported by BBSRC Institute Strategic
Programme GEN (BB/P013511/1) to M.H. and D.Z. and by a European Research Council
grant MaintainMeth (725746) to D.Z.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Amy
full_name: Briffa, Amy
last_name: Briffa
- first_name: Elizabeth
full_name: Hollwey, Elizabeth
id: b8c4f54b-e484-11eb-8fdc-a54df64ef6dd
last_name: Hollwey
- first_name: Zaigham
full_name: Shahzad, Zaigham
last_name: Shahzad
- first_name: Jonathan D.
full_name: Moore, Jonathan D.
last_name: Moore
- first_name: David B.
full_name: Lyons, David B.
last_name: Lyons
- first_name: Martin
full_name: Howard, Martin
last_name: Howard
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Briffa A, Hollwey E, Shahzad Z, et al. Millennia-long epigenetic fluctuations
generate intragenic DNA methylation variance in Arabidopsis populations. Cell
Systems. 2023;14(11):953-967. doi:10.1016/j.cels.2023.10.007
apa: Briffa, A., Hollwey, E., Shahzad, Z., Moore, J. D., Lyons, D. B., Howard, M.,
& Zilberman, D. (2023). Millennia-long epigenetic fluctuations generate intragenic
DNA methylation variance in Arabidopsis populations. Cell Systems. Elsevier.
https://doi.org/10.1016/j.cels.2023.10.007
chicago: Briffa, Amy, Elizabeth Hollwey, Zaigham Shahzad, Jonathan D. Moore, David
B. Lyons, Martin Howard, and Daniel Zilberman. “Millennia-Long Epigenetic Fluctuations
Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” Cell
Systems. Elsevier, 2023. https://doi.org/10.1016/j.cels.2023.10.007.
ieee: A. Briffa et al., “Millennia-long epigenetic fluctuations generate
intragenic DNA methylation variance in Arabidopsis populations,” Cell Systems,
vol. 14, no. 11. Elsevier, pp. 953–967, 2023.
ista: Briffa A, Hollwey E, Shahzad Z, Moore JD, Lyons DB, Howard M, Zilberman D.
2023. Millennia-long epigenetic fluctuations generate intragenic DNA methylation
variance in Arabidopsis populations. Cell Systems. 14(11), 953–967.
mla: Briffa, Amy, et al. “Millennia-Long Epigenetic Fluctuations Generate Intragenic
DNA Methylation Variance in Arabidopsis Populations.” Cell Systems, vol.
14, no. 11, Elsevier, 2023, pp. 953–67, doi:10.1016/j.cels.2023.10.007.
short: A. Briffa, E. Hollwey, Z. Shahzad, J.D. Moore, D.B. Lyons, M. Howard, D.
Zilberman, Cell Systems 14 (2023) 953–967.
date_created: 2023-11-19T23:00:54Z
date_published: 2023-11-15T00:00:00Z
date_updated: 2023-11-20T11:24:34Z
day: '15'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1016/j.cels.2023.10.007
ec_funded: 1
external_id:
pmid:
- '37944515'
file:
- access_level: open_access
checksum: 101fdac59e6f1102d68ef91f2b5bd51a
content_type: application/pdf
creator: dernst
date_created: 2023-11-20T11:22:52Z
date_updated: 2023-11-20T11:22:52Z
file_id: '14580'
file_name: 2023_CellSystems_Briffa.pdf
file_size: 5587897
relation: main_file
success: 1
file_date_updated: 2023-11-20T11:22:52Z
has_accepted_license: '1'
intvolume: ' 14'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 953-967
pmid: 1
project:
- _id: 62935a00-2b32-11ec-9570-eff30fa39068
call_identifier: H2020
grant_number: '725746'
name: Quantitative analysis of DNA methylation maintenance with chromatin
publication: Cell Systems
publication_identifier:
eissn:
- 2405-4720
issn:
- 2405-4712
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Millennia-long epigenetic fluctuations generate intragenic DNA methylation
variance in Arabidopsis populations
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: '14579'
abstract:
- lang: eng
text: "This is associated with our paper \"Plant size, latitude, and phylogeny explain
within-population variability in herbivory\" published in Science.\r\n"
article_processing_charge: No
author:
- first_name: William
full_name: Wetzel, William
last_name: Wetzel
citation:
ama: 'Wetzel W. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. 2023. doi:10.5281/ZENODO.8133117'
apa: 'Wetzel, W. (2023). HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. Zenodo.
https://doi.org/10.5281/ZENODO.8133117'
chicago: 'Wetzel, William. “HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.”
Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133117.'
ieee: 'W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo,
2023.'
ista: 'Wetzel W. 2023. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0, Zenodo,
10.5281/ZENODO.8133117.'
mla: 'Wetzel, William. HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.
Zenodo, 2023, doi:10.5281/ZENODO.8133117.'
short: W. Wetzel, (2023).
date_created: 2023-11-20T11:07:45Z
date_published: 2023-07-11T00:00:00Z
date_updated: 2023-11-20T11:17:33Z
day: '11'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5281/ZENODO.8133117
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8133118
month: '07'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14552'
relation: used_in_publication
status: public
status: public
title: 'HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0'
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12334'
abstract:
- lang: eng
text: Regulation of the Arp2/3 complex is required for productive nucleation of
branched actin networks. An emerging aspect of regulation is the incorporation
of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit
isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity
and branch junction stability. We have combined reverse genetics and cellular
structural biology to describe how ArpC5 and ArpC5L differentially affect cell
migration. Both define the structural stability of ArpC1 in branch junctions and,
in turn, by determining protrusion characteristics, affect protein dynamics and
actin network ultrastructure. ArpC5 isoforms also affect the positioning of members
of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament
elongators, which mediate ArpC5 isoform–specific effects on the actin assembly
level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling
pathway enhancing cell migration.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
acknowledgement: "We would like to thank K. von Peinen and B. Denker (Helmholtz Centre
for Infection Research, Braunschweig, Germany) for experimental and technical assistance,
respectively.\r\nThis research was supported by the Scientific Service Units (SSUs)
of ISTA through resources provided by Scientific Computing (SciComp), the Life Science
Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy
Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund
(FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz
Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and
K.R."
article_number: add6495
article_processing_charge: No
article_type: original
author:
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Manjunath
full_name: Javoor, Manjunath
id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2
last_name: Javoor
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- first_name: Hermann
full_name: Döring, Hermann
last_name: Döring
- first_name: Florian
full_name: Hofer, Florian
id: b9d234ba-9e33-11ed-95b6-cd561df280e6
last_name: Hofer
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning. Science Advances.
2023;9(3). doi:10.1126/sciadv.add6495
apa: Fäßler, F., Javoor, M., Datler, J., Döring, H., Hofer, F., Dimchev, G. A.,
… Schur, F. K. (2023). ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion
through differential Ena/VASP positioning. Science Advances. American Association
for the Advancement of Science. https://doi.org/10.1126/sciadv.add6495
chicago: Fäßler, Florian, Manjunath Javoor, Julia Datler, Hermann Döring, Florian
Hofer, Georgi A Dimchev, Victor-Valentin Hodirnau, Jan Faix, Klemens Rottner,
and Florian KM Schur. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion
through Differential Ena/VASP Positioning.” Science Advances. American
Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.add6495.
ieee: F. Fäßler et al., “ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning,” Science Advances,
vol. 9, no. 3. American Association for the Advancement of Science, 2023.
ista: Fäßler F, Javoor M, Datler J, Döring H, Hofer F, Dimchev GA, Hodirnau V-V,
Faix J, Rottner K, Schur FK. 2023. ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning. Science Advances. 9(3),
add6495.
mla: Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion
through Differential Ena/VASP Positioning.” Science Advances, vol. 9, no.
3, add6495, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.add6495.
short: F. Fäßler, M. Javoor, J. Datler, H. Döring, F. Hofer, G.A. Dimchev, V.-V.
Hodirnau, J. Faix, K. Rottner, F.K. Schur, Science Advances 9 (2023).
date_created: 2023-01-23T07:26:42Z
date_published: 2023-01-20T00:00:00Z
date_updated: 2023-11-21T08:05:35Z
day: '20'
ddc:
- '570'
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- _id: EM-Fac
doi: 10.1126/sciadv.add6495
external_id:
isi:
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- iso: eng
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grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publication: Science Advances
publication_identifier:
issn:
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publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
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scopus_import: '1'
status: public
title: ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential
Ena/VASP positioning
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: '14562'
abstract:
- lang: eng
text: "Regulation of the Arp2/3 complex is required for productive nucleation of
branched actin networks. An emerging aspect of regulation is the incorporation
of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit
isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity
and branch junction stability. We have combined reverse genetics and cellular
structural biology to describe how ArpC5 and ArpC5L differentially affect cell
migration. Both define the structural stability of ArpC1 in branch junctions and,
in turn, by determining protrusion characteristics, affect protein dynamics and
actin network ultrastructure. ArpC5 isoforms also affect the positioning of members
of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament
elongators, which mediate ArpC5 isoform–specific effects on the actin assembly
level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling
pathway enhancing cell migration.\r\n"
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: ScienComp
- _id: EM-Fac
acknowledgement: "We would like to thank K. von Peinen and B. Denker (Helmholtz Centre
for Infection Research, Braunschweig, Germany) for experimental and technical assistance,
respectively.\r\nFunding: This research was supported by the Scientific Service
Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp),
the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the
Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the
Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group
GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft
(DFG) to J.F. and K.R."
article_processing_charge: No
author:
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3
complex-dependent protrusion through differential Ena/VASP positioning.” 2023.
doi:10.15479/AT:ISTA:14562
apa: Schur, F. K. (2023). Research data of the publication “ArpC5 isoforms regulate
Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14562
chicago: Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate
Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14562.
ieee: F. K. Schur, “Research data of the publication ‘ArpC5 isoforms regulate Arp2/3
complex-dependent protrusion through differential Ena/VASP positioning.’” Institute
of Science and Technology Austria, 2023.
ista: Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate
Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:14562.
mla: Schur, Florian KM. Research Data of the Publication “ArpC5 Isoforms Regulate
Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.”
Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14562.
short: F.K. Schur, (2023).
contributor:
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first_name: Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- contributor_type: researcher
first_name: Manjunath
id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2
last_name: Javoor
- contributor_type: researcher
first_name: Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- contributor_type: researcher
first_name: Hermann
last_name: Döring
- contributor_type: researcher
first_name: Florian
id: b9d234ba-9e33-11ed-95b6-cd561df280e6
last_name: Hofer
- contributor_type: researcher
first_name: Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- contributor_type: researcher
first_name: Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- contributor_type: researcher
first_name: Jan
last_name: Faix
- contributor_type: researcher
first_name: Klemens
last_name: Rottner
- contributor_type: researcher
first_name: Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
date_created: 2023-11-20T09:22:33Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2023-11-21T08:05:34Z
day: '21'
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grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publisher: Institute of Science and Technology Austria
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status: public
title: Research data of the publication "ArpC5 isoforms regulate Arp2/3 complex-dependent
protrusion through differential Ena/VASP positioning"
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
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year: '2023'
...
---
_id: '14502'
abstract:
- lang: eng
text: A precise quantitative description of the ultrastructural characteristics
underlying biological mechanisms is often key to their understanding. This is
particularly true for dynamic extra- and intracellular filamentous assemblies,
playing a role in cell motility, cell integrity, cytokinesis, tissue formation
and maintenance. For example, genetic manipulation or modulation of actin regulatory
proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural
architecture of actin filament-rich cell peripheral structures, such as lamellipodia
or filopodia. However, the observed ultrastructural effects often remain subtle
and require sufficiently large datasets for appropriate quantitative analysis.
The acquisition of such large datasets has been enabled by recent advances in
high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates
the development of complementary approaches to maximize the extraction of relevant
biological information. We have developed a computational toolbox for the semi-automatic
quantification of segmented and vectorized fila- mentous networks from pre-processed
cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple
experimental conditions. GUI-based components simplify the processing of data
and allow users to obtain a large number of ultrastructural parameters describing
filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing
cryo-ET data of untreated and chemically perturbed branched actin filament networks
and that of parallel actin filament arrays. In principle, the computational toolbox
presented here is applicable for data analysis comprising any type of filaments
in regular (i.e. parallel) or random arrangement. We show that it can ease the
identification of key differences between experimental groups and facilitate the
in-depth analysis of ultrastructural data in a time-efficient manner.
author:
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Behnam
full_name: Amiri, Behnam
last_name: Amiri
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Martin
full_name: Falcke, Martin
last_name: Falcke
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for
ultrastructural quantitative analysis of filament networks in cryo-ET data. 2023.
doi:10.15479/AT:ISTA:14502
apa: Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2023).
Computational toolbox for ultrastructural quantitative analysis of filament networks
in cryo-ET data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14502
chicago: Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian
KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of
Filament Networks in Cryo-ET Data.” Institute of Science and Technology Austria,
2023. https://doi.org/10.15479/AT:ISTA:14502.
ieee: G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational
toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET
data.” Institute of Science and Technology Austria, 2023.
ista: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2023. Computational toolbox
for ultrastructural quantitative analysis of filament networks in cryo-ET data,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:14502.
mla: Dimchev, Georgi A., et al. Computational Toolbox for Ultrastructural Quantitative
Analysis of Filament Networks in Cryo-ET Data. Institute of Science and Technology
Austria, 2023, doi:10.15479/AT:ISTA:14502.
short: G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, (2023).
date_created: 2023-11-08T19:40:54Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2023-11-21T08:36:02Z
day: '21'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.15479/AT:ISTA:14502
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creator: fschur
date_created: 2023-11-08T20:23:07Z
date_updated: 2023-11-08T20:23:07Z
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file_name: Computational_Toolbox_v1.2.zip
file_size: 347641117
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checksum: 14db2addbfca61a085ba301ed6f2900b
content_type: text/plain
creator: dernst
date_created: 2023-11-21T08:20:23Z
date_updated: 2023-11-21T08:20:23Z
file_id: '14586'
file_name: Readme.txt
file_size: 1522
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success: 1
file_date_updated: 2023-11-21T08:20:23Z
has_accepted_license: '1'
keyword:
- cryo-electron tomography
- actin cytoskeleton
- toolbox
license: https://choosealicense.com/licenses/agpl-3.0/
month: '11'
oa: 1
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10290'
relation: used_for_analysis_in
status: public
status: public
title: Computational toolbox for ultrastructural quantitative analysis of filament
networks in cryo-ET data
tmp:
legal_code_url: https://www.gnu.org/licenses/agpl-3.0.html
name: GNU Affero General Public License v3.0
short: 'GNU AGPLv3 '
type: software
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13342'
abstract:
- lang: eng
text: Motile cells moving in multicellular organisms encounter microenvironments
of locally heterogeneous mechanochemical composition. Individual compositional
parameters like chemotactic signals, adhesiveness, and pore sizes are well known
to be sensed by motile cells, providing individual guidance cues for cellular
pathfinding. However, motile cells encounter diverse mechanochemical signals at
the same time, raising the question of how cells respond to locally diverse and
potentially competing signals on their migration routes. Here, we reveal that
motile amoeboid cells require nuclear repositioning, termed nucleokinesis, for
adaptive pathfinding in heterogeneous mechanochemical microenvironments. Using
mammalian immune cells and the amoebaDictyostelium discoideum,
we discover that frequent, rapid and long-distance nucleokinesis is a basic component
of amoeboid pathfinding, enabling cells to reorientate quickly between locally
competing cues. Amoeboid nucleokinesis comprises a two-step cell polarity switch
and is driven by myosin II-forces, sliding the nucleus from a ‘losing’ to the
‘winning’ leading edge to re-adjust the nuclear to the cellular path. Impaired
nucleokinesis distorts fast path adaptions and causes cellular arrest in the microenvironment.
Our findings establish that nucleokinesis is required for amoeboid cell navigation.
Given that motile single-cell amoebae, many immune cells, and some cancer cells
utilize an amoeboid migration strategy, these results suggest that amoeboid nucleokinesis
underlies cellular navigation during unicellular biology, immunity, and disease.
acknowledgement: We thank Christoph Mayr and Bingzhi Wang for initial experiments
on amoeboid nucleokinesis, Ana-Maria Lennon-Duménil and Aline Yatim for bone marrow
from MyoIIA-Flox*CD11c-Cre mice, Michael Sixt and Aglaja Kopf for EMTB-mCherry,
EB3-mCherry, Lifeact-GFP, Lfc knockout, and Myh9-GFP expressing HoxB8 cells, Malte
Benjamin Braun, Mauricio Ruiz, and Madeleine T. Schmitt for critical reading of
the manuscript, and the Core Facility Bioimaging, the Core Facility Flow Cytometry,
and the Animal Core Facility of the Biomedical Center (BMC) for excellent support.
This study was supported by the Peter Hans Hofschneider Professorship of the foundation
“Stiftung Experimentelle Biomedizin” (to JR), the LMU Institutional Strategy LMU-Excellent
within the framework of the German Excellence Initiative (to JR), and the Deutsche
Forschungsgemeinschaft (DFG; German Research Foundation; SFB914 project A12, to
JR), and the CZI grant DAF2020-225401 (https://doi.org/10.37921/120055ratwvi) from
the Chan Zuckerberg Initiative DAF (to RH; an advised fund of Silicon Valley Community
Foundation (funder https://doi.org/10.13039/100014989)). Open Access funding enabled
and organized by Projekt DEAL.
article_number: e114557
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Janina
full_name: Kroll, Janina
last_name: Kroll
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Arthur
full_name: Kuznetcov, Arthur
last_name: Kuznetcov
- first_name: Kasia
full_name: Stefanowski, Kasia
last_name: Stefanowski
- first_name: Monika D.
full_name: Hermann, Monika D.
last_name: Hermann
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Lubuna B
full_name: Shafeek, Lubuna B
id: 3CD37A82-F248-11E8-B48F-1D18A9856A87
last_name: Shafeek
orcid: 0000-0001-7180-6050
- first_name: Annette
full_name: Müller-Taubenberger, Annette
last_name: Müller-Taubenberger
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
citation:
ama: Kroll J, Hauschild R, Kuznetcov A, et al. Adaptive pathfinding by nucleokinesis
during amoeboid migration. EMBO Journal. 2023. doi:10.15252/embj.2023114557
apa: Kroll, J., Hauschild, R., Kuznetcov, A., Stefanowski, K., Hermann, M. D., Merrin,
J., … Renkawitz, J. (2023). Adaptive pathfinding by nucleokinesis during amoeboid
migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2023114557
chicago: Kroll, Janina, Robert Hauschild, Arthur Kuznetcov, Kasia Stefanowski, Monika
D. Hermann, Jack Merrin, Lubuna B Shafeek, Annette Müller-Taubenberger, and Jörg
Renkawitz. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.”
EMBO Journal. Embo Press, 2023. https://doi.org/10.15252/embj.2023114557.
ieee: J. Kroll et al., “Adaptive pathfinding by nucleokinesis during amoeboid
migration,” EMBO Journal. Embo Press, 2023.
ista: Kroll J, Hauschild R, Kuznetcov A, Stefanowski K, Hermann MD, Merrin J, Shafeek
LB, Müller-Taubenberger A, Renkawitz J. 2023. Adaptive pathfinding by nucleokinesis
during amoeboid migration. EMBO Journal., e114557.
mla: Kroll, Janina, et al. “Adaptive Pathfinding by Nucleokinesis during Amoeboid
Migration.” EMBO Journal, e114557, Embo Press, 2023, doi:10.15252/embj.2023114557.
short: J. Kroll, R. Hauschild, A. Kuznetcov, K. Stefanowski, M.D. Hermann, J. Merrin,
L.B. Shafeek, A. Müller-Taubenberger, J. Renkawitz, EMBO Journal (2023).
date_created: 2023-08-01T08:59:06Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2023-11-27T08:47:45Z
day: '21'
ddc:
- '570'
department:
- _id: NanoFab
- _id: Bio
doi: 10.15252/embj.2023114557
external_id:
pmid:
- '37987147'
file:
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checksum: 6261d0041c7e8d284c39712c40079730
content_type: application/pdf
creator: dernst
date_created: 2023-11-27T08:45:56Z
date_updated: 2023-11-27T08:45:56Z
file_id: '14611'
file_name: 2023_EmboJournal_Kroll.pdf
file_size: 4862497
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file_date_updated: 2023-11-27T08:45:56Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: EMBO Journal
publication_identifier:
eissn:
- 1460-2075
issn:
- 0261-4189
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adaptive pathfinding by nucleokinesis during amoeboid migration
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14610'
abstract:
- lang: eng
text: AbstractEndomembrane damage represents a
form of stress that is detrimental for eukaryotic cells1,2.
To cope with this threat, cells possess mechanisms that repair the damage and
restore cellular homeostasis3–7. Endomembrane damage also
results in organelle instability and the mechanisms by which cells stabilize damaged
endomembranes to enable membrane repair remains unknown. Here, by combining in
vitro and in cellulo studies with computational modelling we uncover a biological
function for stress granules whereby these biomolecular condensates form rapidly
at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane.
Functionally, we demonstrate that stress granule formation and membrane stabilization
enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal
sorting complex required for transport)-dependent and independent mechanisms.
We also show that blocking stress granule formation in human macrophages creates
a permissive environment for Mycobacterium tuberculosis,
a human pathogen that exploits endomembrane damage to survive within the host.
acknowledgement: "We thank the Human Embryonic Stem Cell Unit, Advanced Light Microscopy
and High-throughput Screening facilities at the Crick for their support in various
aspects of the work. We thank the laboratory of P. Anderson for providing the G3BP-DKO
U2OS cells. The authors thank N. Chen for providing the purified glycinin protein;
Z. Zhao for providing the microfluidic chip wafers; and M. Amaral and F. Frey for
helpful discussions and valuable input regarding analysis methods. This work was
supported by the Francis Crick Institute (to M.G.G.), which receives its core funding
from Cancer Research UK (FC001092), the UK Medical Research Council (FC001092) and
the Wellcome Trust (FC001092). This project has received funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
programme (grant agreement no. 772022 to M.G.G.). C.B. has received funding from
the European Respiratory Society and the European Union’s H2020 research and innovation
programme under the Marie Sklodowska-Curie grant agreement no. 713406. A.M. acknowledges
support from Alexander von Humboldt Foundation and C.V.-C. acknowledges funding
by the Royal Society and the European Research Council under the European Union’s
Horizon 2020 Research and Innovation Programme (grant no. 802960 to A.S.). All simulations
were carried out on the high-performance computing cluster at the Institute of Science
and Technology Austria. For the purpose of Open Access, the author has applied a
CC BY public copyright licence to any Author Accepted Manuscript version arising
from this submission.\r\nOpen Access funding provided by The Francis Crick Institute."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Claudio
full_name: Bussi, Claudio
last_name: Bussi
- first_name: Agustín
full_name: Mangiarotti, Agustín
last_name: Mangiarotti
- first_name: Christian Eduardo
full_name: Vanhille-Campos, Christian Eduardo
id: 3adeca52-9313-11ed-b1ac-c170b2505714
last_name: Vanhille-Campos
- first_name: Beren
full_name: Aylan, Beren
last_name: Aylan
- first_name: Enrica
full_name: Pellegrino, Enrica
last_name: Pellegrino
- first_name: Natalia
full_name: Athanasiadi, Natalia
last_name: Athanasiadi
- first_name: Antony
full_name: Fearns, Antony
last_name: Fearns
- first_name: Angela
full_name: Rodgers, Angela
last_name: Rodgers
- first_name: Titus M.
full_name: Franzmann, Titus M.
last_name: Franzmann
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Rumiana
full_name: Dimova, Rumiana
last_name: Dimova
- first_name: Maximiliano G.
full_name: Gutierrez, Maximiliano G.
last_name: Gutierrez
citation:
ama: Bussi C, Mangiarotti A, Vanhille-Campos CE, et al. Stress granules plug and
stabilize damaged endolysosomal membranes. Nature. 2023. doi:10.1038/s41586-023-06726-w
apa: Bussi, C., Mangiarotti, A., Vanhille-Campos, C. E., Aylan, B., Pellegrino,
E., Athanasiadi, N., … Gutierrez, M. G. (2023). Stress granules plug and stabilize
damaged endolysosomal membranes. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06726-w
chicago: Bussi, Claudio, Agustín Mangiarotti, Christian Eduardo Vanhille-Campos,
Beren Aylan, Enrica Pellegrino, Natalia Athanasiadi, Antony Fearns, et al. “Stress
Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Nature. Springer
Nature, 2023. https://doi.org/10.1038/s41586-023-06726-w.
ieee: C. Bussi et al., “Stress granules plug and stabilize damaged endolysosomal
membranes,” Nature. Springer Nature, 2023.
ista: Bussi C, Mangiarotti A, Vanhille-Campos CE, Aylan B, Pellegrino E, Athanasiadi
N, Fearns A, Rodgers A, Franzmann TM, Šarić A, Dimova R, Gutierrez MG. 2023. Stress
granules plug and stabilize damaged endolysosomal membranes. Nature.
mla: Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal
Membranes.” Nature, Springer Nature, 2023, doi:10.1038/s41586-023-06726-w.
short: C. Bussi, A. Mangiarotti, C.E. Vanhille-Campos, B. Aylan, E. Pellegrino,
N. Athanasiadi, A. Fearns, A. Rodgers, T.M. Franzmann, A. Šarić, R. Dimova, M.G.
Gutierrez, Nature (2023).
date_created: 2023-11-27T07:56:37Z
date_published: 2023-11-15T00:00:00Z
date_updated: 2023-11-27T09:05:08Z
day: '15'
department:
- _id: AnSa
doi: 10.1038/s41586-023-06726-w
external_id:
pmid:
- '37968398'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41586-023-06726-w
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-023-06882-z
record:
- id: '14472'
relation: research_data
status: public
status: public
title: Stress granules plug and stabilize damaged endolysosomal membranes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14472'
abstract:
- lang: eng
text: "Data related to the following paper:\r\n\"Stress granules plug and stabilize
damaged endolysosomal membranes\" (https://doi.org/10.1038/s41586-023-06726-w)\r\n\r\nAbstract:
\r\nEndomembrane damage represents a form of stress that is detrimental for eukaryotic
cells. To cope with this threat, cells possess mechanisms that repair the damage
and restore cellular homeostasis. Endomembrane damage also results in organelle
instability and the mechanisms by which cells stabilize damaged endomembranes
to enable membrane repair remains unknown. In this work we use a minimal coarse-grained
molecular dynamics system to explore how lipid vesicles undergoing poration in
a protein-rich medium can be plugged and stabilised by condensate formation. The
solution of proteins in and out of the vesicle is described by beads dispersed
in implicit solvent. The membrane is described as a one-bead-thick fluid elastic
layer of mechanical properties that mimic biological membranes. We tune the interactions
between solution beads in the different compartments to capture the differences
between the cytoplasmic and endosomal protein solutions and explore how the system
responds to different degrees of membrane poration. We find that, in the right
interaction regime, condensates form rapidly at the damage site upon solution
mixing and act as a plug that prevents futher mixing and destabilisation of the
vesicle. Further, when the condensate can interact with the membrane (wetting
interactions) we find that it mediates pore sealing and membrane repair. This
research is part of the work published in \"Stress granules plug and stabilize
damaged endolysosomal membranes\", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w."
article_processing_charge: No
author:
- first_name: Christian Eduardo
full_name: Vanhille-Campos, Christian Eduardo
id: 3adeca52-9313-11ed-b1ac-c170b2505714
last_name: Vanhille-Campos
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Vanhille-Campos CE, Šarić A. Stress granules plug and stabilize damaged endolysosomal
membranes. 2023. doi:10.15479/AT:ISTA:14472
apa: Vanhille-Campos, C. E., & Šarić, A. (2023). Stress granules plug and stabilize
damaged endolysosomal membranes. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:14472
chicago: Vanhille-Campos, Christian Eduardo, and Anđela Šarić. “Stress Granules
Plug and Stabilize Damaged Endolysosomal Membranes.” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14472.
ieee: C. E. Vanhille-Campos and A. Šarić, “Stress granules plug and stabilize damaged
endolysosomal membranes.” Institute of Science and Technology Austria, 2023.
ista: Vanhille-Campos CE, Šarić A. 2023. Stress granules plug and stabilize damaged
endolysosomal membranes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14472.
mla: Vanhille-Campos, Christian Eduardo, and Anđela Šarić. Stress Granules Plug
and Stabilize Damaged Endolysosomal Membranes. Institute of Science and Technology
Austria, 2023, doi:10.15479/AT:ISTA:14472.
short: C.E. Vanhille-Campos, A. Šarić, (2023).
date_created: 2023-10-30T16:38:32Z
date_published: 2023-10-31T00:00:00Z
date_updated: 2023-11-27T09:05:07Z
day: '31'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.15479/AT:ISTA:14472
file:
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checksum: a18706e952e8660c51ede52a167270b7
content_type: application/zip
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date_created: 2023-10-30T16:31:08Z
date_updated: 2023-10-30T16:31:08Z
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date_created: 2023-10-31T08:57:50Z
date_updated: 2023-10-31T08:57:50Z
file_id: '14474'
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file_size: 1697
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license: https://creativecommons.org/publicdomain/zero/1.0/
month: '10'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
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relation: used_in_publication
status: public
status: public
title: Stress granules plug and stabilize damaged endolysosomal membranes
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12747'
abstract:
- lang: eng
text: Muscle degeneration is the most prevalent cause for frailty and dependency
in inherited diseases and ageing. Elucidation of pathophysiological mechanisms,
as well as effective treatments for muscle diseases, represents an important goal
in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine
cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency
in PCYT2 causes a severe disease with failure to thrive and progressive weakness.
pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the
participant phenotypes, with failure to thrive, progressive muscle weakness and
accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular
bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity
declines in ageing muscles of mice and humans, and adeno-associated virus-based
delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice,
offering a therapy for individuals with a rare disease and muscle ageing. Thus,
PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking
PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing.
acknowledgement: 'The authors thank the participants and their families for participating
in the study. We thank all members of our laboratories for helpful discussions.
We are grateful to Vienna BioCenter Core Facilities: Mouse Phenotyping Unit, Histopathology
Unit, Bioinformatics Unit, BioOptics Unit, Electron Microscopy Unit and Comparative
Medicine Unit. We are grateful to the Lipidomics Facility, and K. Klavins and T.
Hannich at the CeMM Research Center for Molecular Medicine of the Austrian Academy
of Sciences for assistance with lipidomics analysis. We also thank T. Huan and A.
Hui (UBC Vancouver) for mouse tissue and mitochondria lipidomics analysis. We thank
A. Klymchenko (Laboratoire de Bioimagerie et Pathologies Université de Strasbourg,
Strasbourg, France) for providing the NR12S probe. We are thankful to the Sen. Paul
D. Wellstone Muscular Dystrophy Cooperative Specialized Research Center Viral Vector
Core Facility for AAV6 production. We also thank K. P. Campbell and M. E. Anderson
(University of Iowa, Carver College of Medicine) for advice on muscle tissue handling.
We thank A. Al-Qassabi from the Sultan Qaboos University for the clinical assessment
of the participants. D.C. and J.M.P. are supported by the Austrian Federal Ministry
of Education, Science and Research, the Austrian Academy of Sciences, and the City
of Vienna, and grants from the Austrian Science Fund (FWF) Wittgenstein award (Z
271-B19), the T. von Zastrow Foundation, and a Canada 150 Research Chairs Program
(F18-01336). J.S.C. is supported by grants RO1AR44533 and P50AR065139 from the US
National Institutes of Health. C.K. is supported by a grant from the Agence Nationale
de la Recherche (ANR-18-CE14-0007-01). A.V.K. is supported by European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
no. 67544, and an Austrian Science Fund (FWF; no P-33799). A.W. is supported by
Austrian Research Promotion Agency (FFG) project no 867674. E.S. is supported by
a SciLifeLab fellowship and Karolinska Institutet Foundation Grants. Work in the
laboratory of G.S.-F. is supported by the Austrian Academy of Sciences, the European
Research Council (ERC AdG 695214 GameofGates) and the Innovative Medicines Initiative
2 Joint Undertaking (grant agreement no. 777372, ReSOLUTE). S.B., M.L. and R.Y.
acknowledge the support of the Spastic Paraplegia Foundation.'
article_processing_charge: No
article_type: original
author:
- first_name: Domagoj
full_name: Cikes, Domagoj
last_name: Cikes
- first_name: Kareem
full_name: Elsayad, Kareem
last_name: Elsayad
- first_name: Erdinc
full_name: Sezgin, Erdinc
last_name: Sezgin
- first_name: Erika
full_name: Koitai, Erika
last_name: Koitai
- first_name: Torma
full_name: Ferenc, Torma
last_name: Ferenc
- first_name: Michael
full_name: Orthofer, Michael
last_name: Orthofer
- first_name: Rebecca
full_name: Yarwood, Rebecca
last_name: Yarwood
- first_name: Leonhard X.
full_name: Heinz, Leonhard X.
last_name: Heinz
- first_name: Vitaly
full_name: Sedlyarov, Vitaly
last_name: Sedlyarov
- first_name: Nasser
full_name: Darwish-Miranda, Nasser
id: 39CD9926-F248-11E8-B48F-1D18A9856A87
last_name: Darwish-Miranda
orcid: 0000-0002-8821-8236
- first_name: Adrian
full_name: Taylor, Adrian
last_name: Taylor
- first_name: Sophie
full_name: Grapentine, Sophie
last_name: Grapentine
- first_name: Fathiya
full_name: al-Murshedi, Fathiya
last_name: al-Murshedi
- first_name: Anne
full_name: Abot, Anne
last_name: Abot
- first_name: Adelheid
full_name: Weidinger, Adelheid
last_name: Weidinger
- first_name: Candice
full_name: Kutchukian, Candice
last_name: Kutchukian
- first_name: Colline
full_name: Sanchez, Colline
last_name: Sanchez
- first_name: Shane J. F.
full_name: Cronin, Shane J. F.
last_name: Cronin
- first_name: Maria
full_name: Novatchkova, Maria
last_name: Novatchkova
- first_name: Anoop
full_name: Kavirayani, Anoop
last_name: Kavirayani
- first_name: Thomas
full_name: Schuetz, Thomas
last_name: Schuetz
- first_name: Bernhard
full_name: Haubner, Bernhard
last_name: Haubner
- first_name: Lisa
full_name: Haas, Lisa
last_name: Haas
- first_name: Astrid
full_name: Hagelkruys, Astrid
last_name: Hagelkruys
- first_name: Suzanne
full_name: Jackowski, Suzanne
last_name: Jackowski
- first_name: Andrey
full_name: Kozlov, Andrey
last_name: Kozlov
- first_name: Vincent
full_name: Jacquemond, Vincent
last_name: Jacquemond
- first_name: Claude
full_name: Knauf, Claude
last_name: Knauf
- first_name: Giulio
full_name: Superti-Furga, Giulio
last_name: Superti-Furga
- first_name: Eric
full_name: Rullman, Eric
last_name: Rullman
- first_name: Thomas
full_name: Gustafsson, Thomas
last_name: Gustafsson
- first_name: John
full_name: McDermot, John
last_name: McDermot
- first_name: Martin
full_name: Lowe, Martin
last_name: Lowe
- first_name: Zsolt
full_name: Radak, Zsolt
last_name: Radak
- first_name: Jeffrey S.
full_name: Chamberlain, Jeffrey S.
last_name: Chamberlain
- first_name: Marica
full_name: Bakovic, Marica
last_name: Bakovic
- first_name: Siddharth
full_name: Banka, Siddharth
last_name: Banka
- first_name: Josef M.
full_name: Penninger, Josef M.
last_name: Penninger
citation:
ama: Cikes D, Elsayad K, Sezgin E, et al. PCYT2-regulated lipid biosynthesis is
critical to muscle health and ageing. Nature Metabolism. 2023;5:495-515.
doi:10.1038/s42255-023-00766-2
apa: Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Ferenc, T., Orthofer, M., …
Penninger, J. M. (2023). PCYT2-regulated lipid biosynthesis is critical to muscle
health and ageing. Nature Metabolism. Springer Nature. https://doi.org/10.1038/s42255-023-00766-2
chicago: Cikes, Domagoj, Kareem Elsayad, Erdinc Sezgin, Erika Koitai, Torma Ferenc,
Michael Orthofer, Rebecca Yarwood, et al. “PCYT2-Regulated Lipid Biosynthesis
Is Critical to Muscle Health and Ageing.” Nature Metabolism. Springer Nature,
2023. https://doi.org/10.1038/s42255-023-00766-2.
ieee: D. Cikes et al., “PCYT2-regulated lipid biosynthesis is critical to
muscle health and ageing,” Nature Metabolism, vol. 5. Springer Nature,
pp. 495–515, 2023.
ista: Cikes D, Elsayad K, Sezgin E, Koitai E, Ferenc T, Orthofer M, Yarwood R, Heinz
LX, Sedlyarov V, Darwish-Miranda N, Taylor A, Grapentine S, al-Murshedi F, Abot
A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani
A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov A, Jacquemond
V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak
Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. 2023. PCYT2-regulated lipid
biosynthesis is critical to muscle health and ageing. Nature Metabolism. 5, 495–515.
mla: Cikes, Domagoj, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle
Health and Ageing.” Nature Metabolism, vol. 5, Springer Nature, 2023, pp.
495–515, doi:10.1038/s42255-023-00766-2.
short: D. Cikes, K. Elsayad, E. Sezgin, E. Koitai, T. Ferenc, M. Orthofer, R. Yarwood,
L.X. Heinz, V. Sedlyarov, N. Darwish-Miranda, A. Taylor, S. Grapentine, F. al-Murshedi,
A. Abot, A. Weidinger, C. Kutchukian, C. Sanchez, S.J.F. Cronin, M. Novatchkova,
A. Kavirayani, T. Schuetz, B. Haubner, L. Haas, A. Hagelkruys, S. Jackowski, A.
Kozlov, V. Jacquemond, C. Knauf, G. Superti-Furga, E. Rullman, T. Gustafsson,
J. McDermot, M. Lowe, Z. Radak, J.S. Chamberlain, M. Bakovic, S. Banka, J.M. Penninger,
Nature Metabolism 5 (2023) 495–515.
date_created: 2023-03-23T12:58:43Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2023-11-28T07:31:33Z
day: '20'
department:
- _id: Bio
doi: 10.1038/s42255-023-00766-2
external_id:
isi:
- '000992064000002'
pmid:
- '36941451'
intvolume: ' 5'
isi: 1
keyword:
- Cell Biology
- Physiology (medical)
- Endocrinology
- Diabetes and Metabolism
- Internal Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2022.03.02.482658
month: '03'
oa: 1
oa_version: Preprint
page: 495-515
pmid: 1
publication: Nature Metabolism
publication_identifier:
issn:
- 2522-5812
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s42255-023-00791-1
scopus_import: '1'
status: public
title: PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2023'
...
---
_id: '14605'
abstract:
- lang: eng
text: The phonon transport mechanisms and ultralow lattice thermal conductivities
(κL) in silver halide AgX (X=Cl,Br,I) compounds are not yet well understood. Herein,
we study the lattice dynamics and thermal property of AgX under the framework
of perturbation theory and the two-channel Wigner thermal transport model based
on accurate machine learning potentials. We find that an accurate extraction of
the third-order atomic force constants from largely displaced configurations is
significant for the calculation of the κL of AgX, and the coherence thermal transport
is also non-negligible. In AgI, however, the calculated κL still considerably
overestimates the experimental values even including four-phonon scatterings.
Molecular dynamics (MD) simulations using machine learning potential suggest an
important role of the higher-than-fourth-order lattice anharmonicity in the low-frequency
phonon linewidths of AgI at room temperature, which can be related to the simultaneous
restrictions of the three- and four-phonon phase spaces. The κL of AgI calculated
using MD phonon lifetimes including full-order lattice anharmonicity shows a better
agreement with experiments.
acknowledgement: This work is supported by the Research Grants Council of Hong Kong
(Grants No. 17318122 and No. 17306721). The authors are grateful for the research
computing facilities offered by ITS, HKU. Z.Z. acknowledges the European Union’s
Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant
Agreement No. 101034413.
article_number: '174302'
article_processing_charge: No
article_type: original
author:
- first_name: Niuchang
full_name: Ouyang, Niuchang
last_name: Ouyang
- first_name: Zezhu
full_name: Zeng, Zezhu
id: 54a2c730-803f-11ed-ab7e-95b29d2680e7
last_name: Zeng
- first_name: Chen
full_name: Wang, Chen
last_name: Wang
- first_name: Qi
full_name: Wang, Qi
last_name: Wang
- first_name: Yue
full_name: Chen, Yue
last_name: Chen
citation:
ama: Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. Role of high-order lattice anharmonicity
in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). Physical
Review B. 2023;108(17). doi:10.1103/PhysRevB.108.174302
apa: Ouyang, N., Zeng, Z., Wang, C., Wang, Q., & Chen, Y. (2023). Role of high-order
lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br,
I). Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.174302
chicago: Ouyang, Niuchang, Zezhu Zeng, Chen Wang, Qi Wang, and Yue Chen. “Role of
High-Order Lattice Anharmonicity in the Phonon Thermal Transport of Silver Halide
AgX (X=Cl,Br, I).” Physical Review B. American Physical Society, 2023.
https://doi.org/10.1103/PhysRevB.108.174302.
ieee: N. Ouyang, Z. Zeng, C. Wang, Q. Wang, and Y. Chen, “Role of high-order lattice
anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I),”
Physical Review B, vol. 108, no. 17. American Physical Society, 2023.
ista: Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. 2023. Role of high-order lattice
anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I).
Physical Review B. 108(17), 174302.
mla: Ouyang, Niuchang, et al. “Role of High-Order Lattice Anharmonicity in the Phonon
Thermal Transport of Silver Halide AgX (X=Cl,Br, I).” Physical Review B,
vol. 108, no. 17, 174302, American Physical Society, 2023, doi:10.1103/PhysRevB.108.174302.
short: N. Ouyang, Z. Zeng, C. Wang, Q. Wang, Y. Chen, Physical Review B 108 (2023).
date_created: 2023-11-26T23:00:54Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2023-11-28T07:48:55Z
day: '01'
department:
- _id: BiCh
doi: 10.1103/PhysRevB.108.174302
ec_funded: 1
intvolume: ' 108'
issue: '17'
language:
- iso: eng
month: '11'
oa_version: None
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
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: Role of high-order lattice anharmonicity in the phonon thermal transport of
silver halide AgX (X=Cl,Br, I)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '14609'
abstract:
- lang: eng
text: "Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems
without a trusted party. DKG is an essential building block to many decentralized
protocols such as randomness beacons, threshold signatures, Byzantine consensus,
and multiparty computation. While significant progress has been made recently,
existing asynchronous DKG constructions are inefficient when the reconstruction
threshold is larger than one-third of the total nodes. In this paper, we present
a simple and concretely efficient asynchronous DKG (ADKG) protocol among n = 3t
+ 1 nodes that can tolerate up to t malicious nodes and support any reconstruction
threshold ℓ ≥ t. Our protocol has an expected O(κn3) communication cost, where
κ is the security parameter, and only assumes the hardness of the Discrete Logarithm.
The\r\ncore ingredient of our ADKG protocol is an asynchronous protocol to secret
share a random polynomial of degree ℓ ≥ t, which has other applications, such
as asynchronous proactive secret sharing and asynchronous multiparty computation.
We implement our high-threshold ADKG protocol and evaluate it using a network
of up to 128 geographically distributed nodes. Our evaluation shows that our high-threshold
ADKG protocol reduces the running time by 90% and bandwidth usage by 80% over
the state-of-the-art."
acknowledgement: The authors would like to thank Amit Agarwal, Andrew Miller, and
Tom Yurek for the helpful discussions related to the paper. This work is funded
in part by a VMware early career faculty grant, a Chainlink Labs Ph.D. fellowship,
the National Science Foundation, and the Austrian Science Fund (FWF) F8512-N.
article_processing_charge: No
author:
- first_name: Sourav
full_name: Das, Sourav
last_name: Das
- first_name: Zhuolun
full_name: Xiang, Zhuolun
last_name: Xiang
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Ling
full_name: Ren, Ling
last_name: Ren
citation:
ama: 'Das S, Xiang Z, Kokoris Kogias E, Ren L. Practical asynchronous high-threshold
distributed key generation and distributed polynomial sampling. In: 32nd USENIX
Security Symposium. Vol 8. Usenix; 2023:5359-5376.'
apa: 'Das, S., Xiang, Z., Kokoris Kogias, E., & Ren, L. (2023). Practical asynchronous
high-threshold distributed key generation and distributed polynomial sampling.
In 32nd USENIX Security Symposium (Vol. 8, pp. 5359–5376). Anaheim, CA,
United States: Usenix.'
chicago: Das, Sourav, Zhuolun Xiang, Eleftherios Kokoris Kogias, and Ling Ren. “Practical
Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial
Sampling.” In 32nd USENIX Security Symposium, 8:5359–76. Usenix, 2023.
ieee: S. Das, Z. Xiang, E. Kokoris Kogias, and L. Ren, “Practical asynchronous high-threshold
distributed key generation and distributed polynomial sampling,” in 32nd USENIX
Security Symposium, Anaheim, CA, United States, 2023, vol. 8, pp. 5359–5376.
ista: Das S, Xiang Z, Kokoris Kogias E, Ren L. 2023. Practical asynchronous high-threshold
distributed key generation and distributed polynomial sampling. 32nd USENIX Security
Symposium. USENIX Security Symposium vol. 8, 5359–5376.
mla: Das, Sourav, et al. “Practical Asynchronous High-Threshold Distributed Key
Generation and Distributed Polynomial Sampling.” 32nd USENIX Security Symposium,
vol. 8, Usenix, 2023, pp. 5359–76.
short: S. Das, Z. Xiang, E. Kokoris Kogias, L. Ren, in:, 32nd USENIX Security Symposium,
Usenix, 2023, pp. 5359–5376.
conference:
end_date: 2023-08-11
location: Anaheim, CA, United States
name: USENIX Security Symposium
start_date: 2023-08-09
date_created: 2023-11-26T23:00:55Z
date_published: 2023-08-15T00:00:00Z
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grant_number: F8512
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publication_identifier:
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publisher: Usenix
quality_controlled: '1'
scopus_import: '1'
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title: Practical asynchronous high-threshold distributed key generation and distributed
polynomial sampling
type: conference
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volume: 8
year: '2023'
...
---
_id: '14603'
abstract:
- lang: eng
text: Computing the solubility of crystals in a solvent using atomistic simulations
is notoriously challenging due to the complexities and convergence issues associated
with free-energy methods, as well as the slow equilibration in direct-coexistence
simulations. This paper introduces a molecular-dynamics workflow that simplifies
and robustly computes the solubility of molecular or ionic crystals. This method
is considerably more straightforward than the state-of-the-art, as we have streamlined
and optimised each step of the process. Specifically, we calculate the chemical
potential of the crystal using the gas-phase molecule as a reference state, and
employ the S0 method to determine the concentration dependence of the chemical
potential of the solute. We use this workflow to predict the solubilities of sodium
chloride in water, urea polymorphs in water, and paracetamol polymorphs in both
water and ethanol. Our findings indicate that the predicted solubility is sensitive
to the chosen potential energy surface. Furthermore, we note that the harmonic
approximation often fails for both molecular crystals and gas molecules at or
above room temperature, and that the assumption of an ideal solution becomes less
valid for highly soluble substances.
acknowledgement: A.R. and B.C. acknowledge resources provided by the Cambridge Tier-2
system operated by the University of Cambridge Research Computing Service funded
by EPSRC Tier-2 capital Grant No. EP/P020259/1. P.Y.C. acknowledges support from
the Ernest Oppenheimer Fund and the Winton Programme for the Physics of Sustainability.
article_number: '184110'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Aleks
full_name: Reinhardt, Aleks
last_name: Reinhardt
- first_name: Pin Yu
full_name: Chew, Pin Yu
last_name: Chew
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Reinhardt A, Chew PY, Cheng B. A streamlined molecular-dynamics workflow for
computing solubilities of molecular and ionic crystals. Journal of Chemical
Physics. 2023;159(18). doi:10.1063/5.0173341
apa: Reinhardt, A., Chew, P. Y., & Cheng, B. (2023). A streamlined molecular-dynamics
workflow for computing solubilities of molecular and ionic crystals. Journal
of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0173341
chicago: Reinhardt, Aleks, Pin Yu Chew, and Bingqing Cheng. “A Streamlined Molecular-Dynamics
Workflow for Computing Solubilities of Molecular and Ionic Crystals.” Journal
of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0173341.
ieee: A. Reinhardt, P. Y. Chew, and B. Cheng, “A streamlined molecular-dynamics
workflow for computing solubilities of molecular and ionic crystals,” Journal
of Chemical Physics, vol. 159, no. 18. AIP Publishing, 2023.
ista: Reinhardt A, Chew PY, Cheng B. 2023. A streamlined molecular-dynamics workflow
for computing solubilities of molecular and ionic crystals. Journal of Chemical
Physics. 159(18), 184110.
mla: Reinhardt, Aleks, et al. “A Streamlined Molecular-Dynamics Workflow for Computing
Solubilities of Molecular and Ionic Crystals.” Journal of Chemical Physics,
vol. 159, no. 18, 184110, AIP Publishing, 2023, doi:10.1063/5.0173341.
short: A. Reinhardt, P.Y. Chew, B. Cheng, Journal of Chemical Physics 159 (2023).
date_created: 2023-11-26T23:00:54Z
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doi: 10.1063/5.0173341
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---
_id: '14604'
abstract:
- lang: eng
text: Sex chromosomes have evolved independently multiple times, but why some are
conserved for more than 100 million years whereas others turnover rapidly remains
an open question. Here, we examine the homology of sex chromosomes across nine
orders of insects, plus the outgroup springtails. We find that the X chromosome
is likely homologous across insects and springtails; the only exception is in
the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system.
These results suggest the ancestral insect X chromosome has persisted for more
than 450 million years—the oldest known sex chromosome to date. Further, we propose
that the shrinking of gene content the dipteran X chromosome has allowed for a
burst of sex-chromosome turnover that is absent from other speciose insect orders.
acknowledgement: All computational analyses were performed on the server at Institute
of Science and Technology Austria. We thank Marwan Elkrewi and Vincent Bett for
analytical advice, and Tanja Schwander and Vincent Merel for useful discussions.
We also thank Matthew Hahn for comments on an earlier version of the manuscript.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
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full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Toups MA, Vicoso B. The X chromosome of insects likely predates the origin
of class Insecta. Evolution. 2023;77(11):2504-2511. doi:10.1093/evolut/qpad169
apa: Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates
the origin of class Insecta. Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpad169
chicago: Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely
Predates the Origin of Class Insecta.” Evolution. Oxford University Press,
2023. https://doi.org/10.1093/evolut/qpad169.
ieee: M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the
origin of class Insecta,” Evolution, vol. 77, no. 11. Oxford University
Press, pp. 2504–2511, 2023.
ista: Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the
origin of class Insecta. Evolution. 77(11), 2504–2511.
mla: Toups, Melissa A., and Beatriz Vicoso. “The X Chromosome of Insects Likely
Predates the Origin of Class Insecta.” Evolution, vol. 77, no. 11, Oxford
University Press, 2023, pp. 2504–11, doi:10.1093/evolut/qpad169.
short: M.A. Toups, B. Vicoso, Evolution 77 (2023) 2504–2511.
date_created: 2023-11-26T23:00:54Z
date_published: 2023-11-02T00:00:00Z
date_updated: 2023-11-28T08:25:28Z
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title: The X chromosome of insects likely predates the origin of class Insecta
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user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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year: '2023'
...
---
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abstract:
- lang: eng
text: Sex chromosomes have evolved independently multiple times, but why some are
conserved for more than 100 million years whereas others turnover rapidly remains
an open question. Here, we examine the homology of sex chromosomes across nine
orders of insects, plus the outgroup springtails. We find that the X chromosome
is likely homologous across insects and springtails; the only exception is in
the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system.
These results suggest the ancestral insect X chromosome has persisted for more
than 450 million years – the oldest known sex chromosome to date. Further, we
propose that the shrinking of gene content of the Dipteran X chromosome has allowed
for a burst of sex-chromosome turnover that is absent from other speciose insect
orders.
article_processing_charge: No
author:
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Toups MA, Vicoso B. The X chromosome of insects likely predates the origin
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apa: Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates
the origin of Class Insecta. Dryad. https://doi.org/10.5061/DRYAD.HX3FFBGKT
chicago: Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely
Predates the Origin of Class Insecta.” Dryad, 2023. https://doi.org/10.5061/DRYAD.HX3FFBGKT.
ieee: M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the
origin of Class Insecta.” Dryad, 2023.
ista: Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the
origin of Class Insecta, Dryad, 10.5061/DRYAD.HX3FFBGKT.
mla: Toups, Melissa A., and Beatriz Vicoso. The X Chromosome of Insects Likely
Predates the Origin of Class Insecta. Dryad, 2023, doi:10.5061/DRYAD.HX3FFBGKT.
short: M.A. Toups, B. Vicoso, (2023).
date_created: 2023-11-28T08:01:53Z
date_published: 2023-09-15T00:00:00Z
date_updated: 2023-11-28T08:17:31Z
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abstract:
- lang: eng
text: Sex chromosomes have evolved independently multiple times, but why some are
conserved for more than 100 million years whereas others turnover rapidly remains
an open question. Here, we examine the homology of sex chromosomes across nine
orders of insects, plus the outgroup springtails. We find that the X chromosome
is likely homologous across insects and springtails; the only exception is in
the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system.
These results suggest the ancestral insect X chromosome has persisted for more
than 450 million years – the oldest known sex chromosome to date. Further, we
propose that the shrinking of gene content of the Dipteran X chromosome has allowed
for a burst of sex-chromosome turnover that is absent from other speciose insect
orders.
article_processing_charge: No
author:
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Toups MA, Vicoso B. The X chromosome of insects likely predates the origin
of Class Insecta. 2023. doi:10.5281/ZENODO.8138705
apa: Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates
the origin of Class Insecta. Zenodo. https://doi.org/10.5281/ZENODO.8138705
chicago: Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely
Predates the Origin of Class Insecta.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8138705.
ieee: M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the
origin of Class Insecta.” Zenodo, 2023.
ista: Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the
origin of Class Insecta, Zenodo, 10.5281/ZENODO.8138705.
mla: Toups, Melissa A., and Beatriz Vicoso. The X Chromosome of Insects Likely
Predates the Origin of Class Insecta. Zenodo, 2023, doi:10.5281/ZENODO.8138705.
short: M.A. Toups, B. Vicoso, (2023).
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date_updated: 2023-11-28T08:25:28Z
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title: The X chromosome of insects likely predates the origin of Class Insecta
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14619'
abstract:
- lang: eng
text: Data underlying the publication "A streamlined molecular-dynamics workflow
for computing solubilities of molecular and ionic crystals" (DOI https://doi.org/10.1063/5.0173341).
article_processing_charge: No
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: 'Cheng B. BingqingCheng/solubility: V1.0. 2023. doi:10.5281/ZENODO.8398094'
apa: 'Cheng, B. (2023). BingqingCheng/solubility: V1.0. Zenodo. https://doi.org/10.5281/ZENODO.8398094'
chicago: 'Cheng, Bingqing. “BingqingCheng/Solubility: V1.0.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8398094.'
ieee: 'B. Cheng, “BingqingCheng/solubility: V1.0.” Zenodo, 2023.'
ista: 'Cheng B. 2023. BingqingCheng/solubility: V1.0, Zenodo, 10.5281/ZENODO.8398094.'
mla: 'Cheng, Bingqing. BingqingCheng/Solubility: V1.0. Zenodo, 2023, doi:10.5281/ZENODO.8398094.'
short: B. Cheng, (2023).
date_created: 2023-11-28T08:32:18Z
date_published: 2023-10-02T00:00:00Z
date_updated: 2023-11-28T08:39:22Z
day: '02'
ddc:
- '530'
department:
- _id: BiCh
doi: 10.5281/ZENODO.8398094
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8398094
month: '10'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14603'
relation: used_in_publication
status: public
status: public
title: 'BingqingCheng/solubility: V1.0'
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14564'
abstract:
- lang: eng
text: Cumulus parameterization (CP) in state‐of‐the‐art global climate models is
based on the quasi‐equilibrium assumption (QEA), which views convection as the
action of an ensemble of cumulus clouds, in a state of equilibrium with respect
to a slowly varying atmospheric state. This view is not compatible with the organization
and dynamical interactions across multiple scales of cloud systems in the tropics
and progress in this research area was slow over decades despite the widely recognized
major shortcomings. Novel ideas on how to represent key physical processes of
moist convection‐large‐scale interaction to overcome the QEA have surged recently.
The stochastic multicloud model (SMCM) CP in particular mimics the dynamical interactions
of multiple cloud types that characterize organized tropical convection. Here,
the SMCM is used to modify the Zhang‐McFarlane (ZM) CP by changing the way in
which the bulk mass flux and bulk entrainment and detrainment rates are calculated.
This is done by introducing a stochastic ensemble of plumes characterized by randomly
varying detrainment level distributions based on the cloud area fraction of the
SMCM. The SMCM is here extended to include shallow cumulus clouds resulting in
a unified shallow‐deep CP. The new stochastic multicloud plume CP is validated
against the control ZM scheme in the context of the single column Community Climate
Model of the National Center for Atmospheric Research using data from both tropical
ocean and midlatitude land convection. Some key features of the SMCM CP such as
it capability to represent the tri‐modal nature of organized convection are emphasized.
acknowledgement: The research of B.K. is supported in part by a Discovery Grant from
the Natural Sciences and Engineering Research Council of Canada (RGPIN-04246-2020).
This research was conducted during the visits of P.M. Krishna to the Center for
Prototype Climate Models at NYU Abu Dhabi and University of Victoria from November
2018 to June 2019 and July 2019 and October 2019, respectively. The authors are
very grateful to the three anonymous reviewers who provided very thoughtful and
constructive comments during the review process that helped greatly improve and
shape the final version of the manuscript.
article_number: e2022MS003391
article_processing_charge: Yes
article_type: original
author:
- first_name: B.
full_name: Khouider, B.
last_name: Khouider
- first_name: BIDYUT B
full_name: GOSWAMI, BIDYUT B
id: 3a4ac09c-6d61-11ec-bf66-884cde66b64b
last_name: GOSWAMI
orcid: 0000-0001-8602-3083
- first_name: R.
full_name: Phani, R.
last_name: Phani
- first_name: A. J.
full_name: Majda, A. J.
last_name: Majda
citation:
ama: Khouider B, GOSWAMI BB, Phani R, Majda AJ. A shallow‐deep unified stochastic
mass flux cumulus parameterization in the single column community climate model.
Journal of Advances in Modeling Earth Systems. 2023;15(11). doi:10.1029/2022ms003391
apa: Khouider, B., GOSWAMI, B. B., Phani, R., & Majda, A. J. (2023). A shallow‐deep
unified stochastic mass flux cumulus parameterization in the single column community
climate model. Journal of Advances in Modeling Earth Systems. American
Geophysical Union. https://doi.org/10.1029/2022ms003391
chicago: Khouider, B., BIDYUT B GOSWAMI, R. Phani, and A. J. Majda. “A Shallow‐deep
Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community
Climate Model.” Journal of Advances in Modeling Earth Systems. American
Geophysical Union, 2023. https://doi.org/10.1029/2022ms003391.
ieee: B. Khouider, B. B. GOSWAMI, R. Phani, and A. J. Majda, “A shallow‐deep unified
stochastic mass flux cumulus parameterization in the single column community climate
model,” Journal of Advances in Modeling Earth Systems, vol. 15, no. 11.
American Geophysical Union, 2023.
ista: Khouider B, GOSWAMI BB, Phani R, Majda AJ. 2023. A shallow‐deep unified stochastic
mass flux cumulus parameterization in the single column community climate model.
Journal of Advances in Modeling Earth Systems. 15(11), e2022MS003391.
mla: Khouider, B., et al. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization
in the Single Column Community Climate Model.” Journal of Advances in Modeling
Earth Systems, vol. 15, no. 11, e2022MS003391, American Geophysical Union,
2023, doi:10.1029/2022ms003391.
short: B. Khouider, B.B. GOSWAMI, R. Phani, A.J. Majda, Journal of Advances in Modeling
Earth Systems 15 (2023).
date_created: 2023-11-20T09:18:21Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2023-11-28T12:04:42Z
day: '01'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1029/2022ms003391
file:
- access_level: open_access
checksum: e30329dd985559de0ddc7021ca7382b4
content_type: application/pdf
creator: dernst
date_created: 2023-11-20T11:29:16Z
date_updated: 2023-11-20T11:29:16Z
file_id: '14582'
file_name: 2023_JAMES_Khoulder.pdf
file_size: 6435697
relation: main_file
success: 1
file_date_updated: 2023-11-20T11:29:16Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '11'
keyword:
- General Earth and Planetary Sciences
- Environmental Chemistry
- Global and Planetary Change
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Journal of Advances in Modeling Earth Systems
publication_identifier:
eissn:
- 1942-2466
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: A shallow‐deep unified stochastic mass flux cumulus parameterization in the
single column community climate model
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2023'
...
---
_id: '12789'
abstract:
- lang: eng
text: Experiments have shown that charge distributions of granular materials are
non-Gaussian, with broad tails that indicate many particles with high charge.
This observation has consequences for the behavior of granular materials in many
settings, and may bear relevance to the underlying charge transfer mechanism.
However, there is the unaddressed possibility that broad tails arise due to experimental
uncertainties, as determining the shapes of tails is nontrivial. Here we show
that measurement uncertainties can indeed account for most of the tail broadening
previously observed. The clue that reveals this is that distributions are sensitive
to the electric field at which they are measured; ones measured at low (high)
fields have larger (smaller) tails. Accounting for sources of uncertainty, we
reproduce this broadening in silico. Finally, we use our results to back out the
true charge distribution without broadening, which we find is still non-Guassian,
though with substantially different behavior at the tails and indicating significantly
fewer highly charged particles. These results have implications in many natural
settings where electrostatic interactions, especially among highly charged particles,
strongly affect granular behavior.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: This research was supported by Grants QUIMAL 160001 and Fondecyt
1221597. This project has received funding from the European Research Council (ERC)
under the European Union's Horizon 2020 research and innovation programme (Grant
Agreement No. 949120). This research was supported by the Scientific Service Units
of The Institute of Science and Technology Austria (ISTA) through resources provided
by the Miba Machine Shop. We thank the machine shop technical assistance of Ricardo
Silva and Andrés Espinosa at Departamento de Física, Universidad de Chile.
article_number: '034901'
article_processing_charge: No
article_type: original
author:
- first_name: Nicolás
full_name: Mujica, Nicolás
last_name: Mujica
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: Mujica N, Waitukaitis SR. Accurate determination of the shapes of granular
charge distributions. Physical Review E. 2023;107(3). doi:10.1103/PhysRevE.107.034901
apa: Mujica, N., & Waitukaitis, S. R. (2023). Accurate determination of the
shapes of granular charge distributions. Physical Review E. American Physical
Society. https://doi.org/10.1103/PhysRevE.107.034901
chicago: Mujica, Nicolás, and Scott R Waitukaitis. “Accurate Determination of the
Shapes of Granular Charge Distributions.” Physical Review E. American Physical
Society, 2023. https://doi.org/10.1103/PhysRevE.107.034901.
ieee: N. Mujica and S. R. Waitukaitis, “Accurate determination of the shapes of
granular charge distributions,” Physical Review E, vol. 107, no. 3. American
Physical Society, 2023.
ista: Mujica N, Waitukaitis SR. 2023. Accurate determination of the shapes of granular
charge distributions. Physical Review E. 107(3), 034901.
mla: Mujica, Nicolás, and Scott R. Waitukaitis. “Accurate Determination of the Shapes
of Granular Charge Distributions.” Physical Review E, vol. 107, no. 3,
034901, American Physical Society, 2023, doi:10.1103/PhysRevE.107.034901.
short: N. Mujica, S.R. Waitukaitis, Physical Review E 107 (2023).
date_created: 2023-04-02T22:01:10Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-11-28T09:22:25Z
day: '01'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1103/PhysRevE.107.034901
ec_funded: 1
external_id:
isi:
- '000992142700001'
file:
- access_level: open_access
checksum: 48f5dfe4e5f1c46c3c86805cd8f84bea
content_type: application/pdf
creator: swaituka
date_created: 2023-11-27T09:51:48Z
date_updated: 2023-11-27T09:51:48Z
file_id: '14612'
file_name: PhysRevE.107.034901 (1).pdf
file_size: 1428631
relation: main_file
success: 1
file_date_updated: 2023-11-27T09:51:48Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa
call_identifier: H2020
grant_number: '949120'
name: 'Tribocharge: a multi-scale approach to an enduring problem in physics'
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Accurate determination of the shapes of granular charge distributions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 107
year: '2023'
...
---
_id: '13238'
abstract:
- lang: eng
text: "We consider a natural problem dealing with weighted packet selection across
a rechargeable link, which e.g., finds applications in cryptocurrency networks.
The capacity of a link (u, v) is determined by how much nodes u and v allocate
for this link. Specifically, the input is a finite ordered sequence of packets
that arrive in both directions along a link. Given (u, v) and a packet of weight
x going from u to v, node u can either accept or reject the packet. If u accepts
the packet, the capacity on link (u, v) decreases by x. Correspondingly, v’s capacity
on (u, v) increases by x. If a node rejects the packet, this will entail a cost
affinely linear in the weight of the packet. A link is “rechargeable” in the sense
that the total capacity of the link has to remain constant, but the allocation
of capacity at the ends of the link can depend arbitrarily on the nodes’ decisions.
The goal is to minimise the sum of the capacity injected into the link and the
cost of rejecting packets. We show that the problem is NP-hard, but can be approximated
efficiently with a ratio of (1+ε)⋅(1+3–√) for some arbitrary ε>0.\r\n."
acknowledgement: We thank Mahsa Bastankhah and Mohammad Ali Maddah-Ali for fruitful
discussions about different variants of the problem. This work is supported by the
European Research Council (ERC) Consolidator Project 864228 (AdjustNet), 2020-2025,
the ERC CoG 863818 (ForM-SMArt), and the German Research Foundation (DFG) grant
470029389 (FlexNets), 2021–2024.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
citation:
ama: 'Schmid S, Svoboda J, Yeo MX. Weighted packet selection for rechargeable links
in cryptocurrency networks: Complexity and approximation. In: SIROCCO 2023:
Structural Information and Communication Complexity . Vol 13892. Springer
Nature; 2023:576-594. doi:10.1007/978-3-031-32733-9_26'
apa: 'Schmid, S., Svoboda, J., & Yeo, M. X. (2023). Weighted packet selection
for rechargeable links in cryptocurrency networks: Complexity and approximation.
In SIROCCO 2023: Structural Information and Communication Complexity (Vol.
13892, pp. 576–594). Alcala de Henares, Spain: Springer Nature. https://doi.org/10.1007/978-3-031-32733-9_26'
chicago: 'Schmid, Stefan, Jakub Svoboda, and Michelle X Yeo. “Weighted Packet Selection
for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.”
In SIROCCO 2023: Structural Information and Communication Complexity ,
13892:576–94. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-32733-9_26.'
ieee: 'S. Schmid, J. Svoboda, and M. X. Yeo, “Weighted packet selection for rechargeable
links in cryptocurrency networks: Complexity and approximation,” in SIROCCO
2023: Structural Information and Communication Complexity , Alcala de Henares,
Spain, 2023, vol. 13892, pp. 576–594.'
ista: 'Schmid S, Svoboda J, Yeo MX. 2023. Weighted packet selection for rechargeable
links in cryptocurrency networks: Complexity and approximation. SIROCCO 2023:
Structural Information and Communication Complexity . SIROCCO: Structural Information
and Communication Complexity, LNCS, vol. 13892, 576–594.'
mla: 'Schmid, Stefan, et al. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency
Networks: Complexity and Approximation.” SIROCCO 2023: Structural Information
and Communication Complexity , vol. 13892, Springer Nature, 2023, pp. 576–94,
doi:10.1007/978-3-031-32733-9_26.'
short: 'S. Schmid, J. Svoboda, M.X. Yeo, in:, SIROCCO 2023: Structural Information
and Communication Complexity , Springer Nature, 2023, pp. 576–594.'
conference:
end_date: 2023-06-09
location: Alcala de Henares, Spain
name: 'SIROCCO: Structural Information and Communication Complexity'
start_date: 2023-06-06
date_created: 2023-07-16T22:01:12Z
date_published: 2023-05-25T00:00:00Z
date_updated: 2023-11-30T10:54:51Z
day: '25'
department:
- _id: KrPi
- _id: KrCh
doi: 10.1007/978-3-031-32733-9_26
ec_funded: 1
external_id:
arxiv:
- '2204.13459'
intvolume: ' 13892'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2204.13459
month: '05'
oa: 1
oa_version: Preprint
page: 576-594
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 'SIROCCO 2023: Structural Information and Communication Complexity '
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031327322'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '14506'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Weighted packet selection for rechargeable links in cryptocurrency networks:
Complexity and approximation'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13892
year: '2023'
...
---
_id: '14506'
abstract:
- lang: eng
text: "Payment channel networks are a promising approach to improve the scalability
bottleneck\r\nof cryptocurrencies. Two design principles behind payment channel
networks are\r\nefficiency and privacy. Payment channel networks improve efficiency
by allowing users\r\nto transact in a peer-to-peer fashion along multi-hop routes
in the network, avoiding\r\nthe lengthy process of consensus on the blockchain.
Transacting over payment channel\r\nnetworks also improves privacy as these transactions
are not broadcast to the blockchain.\r\nDespite the influx of recent protocols
built on top of payment channel networks and\r\ntheir analysis, a common shortcoming
of many of these protocols is that they typically\r\nfocus only on either improving
efficiency or privacy, but not both. Another limitation\r\non the efficiency front
is that the models used to model actions, costs and utilities of\r\nusers are
limited or come with unrealistic assumptions.\r\nThis thesis aims to address some
of the shortcomings of recent protocols and algorithms\r\non payment channel networks,
particularly in their privacy and efficiency aspects. We\r\nfirst present a payment
route discovery protocol based on hub labelling and private\r\ninformation retrieval
that hides the route query and is also efficient. We then present\r\na rebalancing
protocol that formulates the rebalancing problem as a linear program\r\nand solves
the linear program using multiparty computation so as to hide the channel\r\nbalances.
The rebalancing solution as output by our protocol is also globally optimal.\r\nWe
go on to develop more realistic models of the action space, costs, and utilities
of\r\nboth existing and new users that want to join the network. In each of these
settings,\r\nwe also develop algorithms to optimise the utility of these users
with good guarantees\r\non the approximation and competitive ratios."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
citation:
ama: Yeo MX. Advances in efficiency and privacy in payment channel network analysis.
2023. doi:10.15479/14506
apa: Yeo, M. X. (2023). Advances in efficiency and privacy in payment channel
network analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/14506
chicago: Yeo, Michelle X. “Advances in Efficiency and Privacy in Payment Channel
Network Analysis.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14506.
ieee: M. X. Yeo, “Advances in efficiency and privacy in payment channel network
analysis,” Institute of Science and Technology Austria, 2023.
ista: Yeo MX. 2023. Advances in efficiency and privacy in payment channel network
analysis. Institute of Science and Technology Austria.
mla: Yeo, Michelle X. Advances in Efficiency and Privacy in Payment Channel Network
Analysis. Institute of Science and Technology Austria, 2023, doi:10.15479/14506.
short: M.X. Yeo, Advances in Efficiency and Privacy in Payment Channel Network Analysis,
Institute of Science and Technology Austria, 2023.
date_created: 2023-11-10T08:10:43Z
date_published: 2023-11-10T00:00:00Z
date_updated: 2023-11-30T10:54:51Z
day: '10'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: KrPi
doi: 10.15479/14506
ec_funded: 1
file:
- access_level: closed
checksum: 521c72818d720a52b377207b2ee87b6a
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2023-11-23T10:29:55Z
date_updated: 2023-11-23T10:29:55Z
file_id: '14598'
file_name: thesis_yeo.zip
file_size: 3037720
relation: source_file
- access_level: open_access
checksum: 0ed5d16899687aecf13d843c9878c9f2
content_type: application/pdf
creator: cchlebak
date_created: 2023-11-23T10:30:08Z
date_updated: 2023-11-23T10:30:08Z
file_id: '14599'
file_name: thesis_yeo.pdf
file_size: 2717256
relation: main_file
success: 1
file_date_updated: 2023-11-23T10:30:08Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '162'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9969'
relation: part_of_dissertation
status: public
- id: '13238'
relation: part_of_dissertation
status: public
- id: '14490'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
title: Advances in efficiency and privacy in payment channel network analysis
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14490'
abstract:
- lang: eng
text: Payment channel networks (PCNs) are a promising solution to the scalability
problem of cryptocurrencies. Any two users connected by a payment channel in the
network can theoretically send an unbounded number of instant, costless transactions
between them. Users who are not directly connected can also transact with each
other in a multi-hop fashion. In this work, we study the incentive structure behind
the creation of payment channel networks, particularly from the point of view
of a single user that wants to join the network. We define a utility function
for a new user in terms of expected revenue, expected fees, and the cost of creating
channels, and then provide constant factor approximation algorithms that optimise
the utility function given a certain budget. Additionally, we take a step back
from a single user to the whole network and examine the parameter spaces under
which simple graph topologies form a Nash equilibrium.
acknowledgement: The work was partially supported by the Austrian Science Fund (FWF)
through the project CoRaF (grant 2020388). It was also partially supported by NCN
Grant 2019/35/B/ST6/04138 and ERC Grant 885666.
article_processing_charge: No
author:
- first_name: Zeta
full_name: Avarikioti, Zeta
last_name: Avarikioti
- first_name: Tomasz
full_name: Lizurej, Tomasz
last_name: Lizurej
- first_name: Tomasz
full_name: Michalak, Tomasz
last_name: Michalak
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
citation:
ama: 'Avarikioti Z, Lizurej T, Michalak T, Yeo MX. Lightning creation games. In:
43rd International Conference on Distributed Computing Systems. Vol 2023.
IEEE; 2023:603-613. doi:10.1109/ICDCS57875.2023.00037'
apa: 'Avarikioti, Z., Lizurej, T., Michalak, T., & Yeo, M. X. (2023). Lightning
creation games. In 43rd International Conference on Distributed Computing Systems
(Vol. 2023, pp. 603–613). Hong Kong, China: IEEE. https://doi.org/10.1109/ICDCS57875.2023.00037'
chicago: Avarikioti, Zeta, Tomasz Lizurej, Tomasz Michalak, and Michelle X Yeo.
“Lightning Creation Games.” In 43rd International Conference on Distributed
Computing Systems, 2023:603–13. IEEE, 2023. https://doi.org/10.1109/ICDCS57875.2023.00037.
ieee: Z. Avarikioti, T. Lizurej, T. Michalak, and M. X. Yeo, “Lightning creation
games,” in 43rd International Conference on Distributed Computing Systems,
Hong Kong, China, 2023, vol. 2023, pp. 603–613.
ista: 'Avarikioti Z, Lizurej T, Michalak T, Yeo MX. 2023. Lightning creation games.
43rd International Conference on Distributed Computing Systems. ICDCS: International
Conference on Distributed Computing Systems vol. 2023, 603–613.'
mla: Avarikioti, Zeta, et al. “Lightning Creation Games.” 43rd International
Conference on Distributed Computing Systems, vol. 2023, IEEE, 2023, pp. 603–13,
doi:10.1109/ICDCS57875.2023.00037.
short: Z. Avarikioti, T. Lizurej, T. Michalak, M.X. Yeo, in:, 43rd International
Conference on Distributed Computing Systems, IEEE, 2023, pp. 603–613.
conference:
end_date: 2023-07-21
location: Hong Kong, China
name: 'ICDCS: International Conference on Distributed Computing Systems'
start_date: 2023-07-18
date_created: 2023-11-05T23:00:54Z
date_published: 2023-10-11T00:00:00Z
date_updated: 2023-11-30T10:54:51Z
day: '11'
department:
- _id: KrPi
doi: 10.1109/ICDCS57875.2023.00037
external_id:
arxiv:
- '2306.16006'
intvolume: ' 2023'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2306.16006
month: '10'
oa: 1
oa_version: Preprint
page: 603-613
publication: 43rd International Conference on Distributed Computing Systems
publication_identifier:
eissn:
- 2575-8411
isbn:
- '9798350339864'
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '14506'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Lightning creation games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2023
year: '2023'
...
---
_id: '12726'
abstract:
- lang: eng
text: "Most motions of many-body systems at any scale in nature with sufficient
degrees\r\nof freedom tend to be chaotic; reaching from the orbital motion of
planets, the air\r\ncurrents in our atmosphere, down to the water flowing through
our pipelines or\r\nthe movement of a population of bacteria. To the observer
it is therefore intriguing\r\nwhen a moving collective exhibits order. Collective
motion of flocks of birds, schools\r\nof fish or swarms of self-propelled particles
or robots have been studied extensively\r\nover the past decades but the mechanisms
involved in the transition from chaos to\r\norder remain unclear. Here, the interactions,
that in most systems give rise to chaos,\r\nsustain order. In this thesis we investigate
mechanisms that preserve, destabilize\r\nor lead to the ordered state. We show
that endothelial cells migrating in circular\r\nconfinements transition to a collective
rotating state and concomitantly synchronize\r\nthe frequencies of nucleating
actin waves within individual cells. Consequently,\r\nthe frequency dependent
cell migration speed uniformizes across the population.\r\nComplementary to the
WAVE dependent nucleation of traveling actin waves, we\r\nshow that in leukocytes
the actin polymerization depending on WASp generates\r\npushing forces locally
at stationary patches. Next, in pipe flows, we study methods\r\nto disrupt the
self–sustaining cycle of turbulence and therefore relaminarize the\r\nflow. While
we find in pulsating flow conditions that turbulence emerges through a\r\nhelical
instability during the decelerating phase. Finally, we show quantitatively in\r\nbrain
slices of mice that wild-type control neurons can compensate the migratory\r\ndeficits
of a genetically modified neuronal sub–population in the developing cortex."
acknowledged_ssus:
- _id: M-Shop
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michael
full_name: Riedl, Michael
id: 3BE60946-F248-11E8-B48F-1D18A9856A87
last_name: Riedl
orcid: 0000-0003-4844-6311
citation:
ama: Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/at:ista:12726
apa: Riedl, M. (2023). Synchronization in collectively moving active matter.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12726
chicago: Riedl, Michael. “Synchronization in Collectively Moving Active Matter.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12726.
ieee: M. Riedl, “Synchronization in collectively moving active matter,” Institute
of Science and Technology Austria, 2023.
ista: Riedl M. 2023. Synchronization in collectively moving active matter. Institute
of Science and Technology Austria.
mla: Riedl, Michael. Synchronization in Collectively Moving Active Matter.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12726.
short: M. Riedl, Synchronization in Collectively Moving Active Matter, Institute
of Science and Technology Austria, 2023.
date_created: 2023-03-15T13:22:13Z
date_published: 2023-03-23T00:00:00Z
date_updated: 2023-11-30T10:55:13Z
day: '23'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BjHo
doi: 10.15479/at:ista:12726
file:
- access_level: closed
checksum: eba0e19fe57a8c15e7aeab55a845efb7
content_type: application/pdf
creator: cchlebak
date_created: 2023-03-23T12:49:23Z
date_updated: 2023-11-24T11:57:46Z
description: the main file is missing the bibliography. See new thesis record 14530
for updated files.
file_id: '12745'
file_name: Thesis_Riedl_2023.pdf
file_size: 63734746
relation: main_file
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checksum: 0eb7b650cc8ae843bcec7c8a6109ae03
content_type: application/octet-stream
creator: cchlebak
date_created: 2023-03-23T12:54:34Z
date_updated: 2023-09-24T22:30:03Z
embargo_to: open_access
file_id: '12746'
file_name: Thesis_Riedl_2023_source.rar
file_size: 339473651
relation: source_file
file_date_updated: 2023-11-24T11:57:46Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: '260'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10703'
relation: part_of_dissertation
status: public
- id: '10791'
relation: part_of_dissertation
status: public
- id: '7932'
relation: part_of_dissertation
status: public
- id: '461'
relation: part_of_dissertation
status: public
- id: '14530'
relation: new_edition
status: public
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: Synchronization in collectively moving active matter
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14530'
abstract:
- lang: eng
text: 'Most motions of many-body systems at any scale in nature with sufficient
degrees of freedom tend to be chaotic; reaching from the orbital motion of planets,
the air currents in our atmosphere, down to the water flowing through our pipelines
or the movement of a population of bacteria. To the observer it is therefore intriguing
when a moving collective exhibits order. Collective motion of flocks of birds,
schools of fish or swarms of self-propelled particles or robots have been studied
extensively over the past decades but the mechanisms involved in the transition
from chaos to order remain unclear. Here, the interactions, that in most systems
give rise to chaos, sustain order. In this thesis we investigate mechanisms that
preserve, destabilize or lead to the ordered state. We show that endothelial cells
migrating in circular confinements transition to a collective rotating state and
concomitantly synchronize the frequencies of nucleating actin waves within individual
cells. Consequently, the frequency dependent cell migration speed uniformizes
across the population. Complementary to the WAVE dependent nucleation of traveling
actin waves, we show that in leukocytes the actin polymerization depending on
WASp generates pushing forces locally at stationary patches. Next, in pipe flows,
we study methods to disrupt the self--sustaining cycle of turbulence and therefore
relaminarize the flow. While we find in pulsating flow conditions that turbulence
emerges through a helical instability during the decelerating phase. Finally,
we show quantitatively in brain slices of mice that wild-type control neurons
can compensate the migratory deficits of a genetically modified neuronal sub--population
in the developing cortex. '
acknowledged_ssus:
- _id: M-Shop
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michael
full_name: Riedl, Michael
id: 3BE60946-F248-11E8-B48F-1D18A9856A87
last_name: Riedl
orcid: 0000-0003-4844-6311
citation:
ama: Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/14530
apa: Riedl, M. (2023). Synchronization in collectively moving active matter.
Institute of Science and Technology Austria. https://doi.org/10.15479/14530
chicago: Riedl, Michael. “Synchronization in Collectively Moving Active Matter.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14530.
ieee: M. Riedl, “Synchronization in collectively moving active matter,” Institute
of Science and Technology Austria, 2023.
ista: Riedl M. 2023. Synchronization in collectively moving active matter. Institute
of Science and Technology Austria.
mla: Riedl, Michael. Synchronization in Collectively Moving Active Matter.
Institute of Science and Technology Austria, 2023, doi:10.15479/14530.
short: M. Riedl, Synchronization in Collectively Moving Active Matter, Institute
of Science and Technology Austria, 2023.
date_created: 2023-11-15T09:59:03Z
date_published: 2023-11-16T00:00:00Z
date_updated: 2023-11-30T10:55:13Z
day: '16'
ddc:
- '530'
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MiSi
doi: 10.15479/14530
file:
- access_level: open_access
checksum: 52e1d0ab6c1abe59c82dfe8c9ff5f83a
content_type: application/pdf
creator: mriedl
date_created: 2023-11-15T09:52:54Z
date_updated: 2023-11-15T09:52:54Z
file_id: '14536'
file_name: Thesis_Riedl_2023_corr.pdf
file_size: 36743942
relation: main_file
success: 1
file_date_updated: 2023-11-15T09:52:54Z
has_accepted_license: '1'
keyword:
- Synchronization
- Collective Movement
- Active Matter
- Cell Migration
- Active Colloids
language:
- iso: eng
month: '11'
oa: 1
oa_version: Updated Version
page: '260'
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10703'
relation: part_of_dissertation
status: public
- id: '10791'
relation: part_of_dissertation
status: public
- id: '7932'
relation: part_of_dissertation
status: public
- id: '461'
relation: part_of_dissertation
status: public
- id: '12726'
relation: old_edition
status: public
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: Synchronization in collectively moving active matter
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14547'
abstract:
- lang: eng
text: "Superconductor-semiconductor heterostructures currently capture a significant
amount of research interest and they serve as the physical platform in many proposals
towards topological quantum computation.\r\nDespite being under extensive investigations,
historically using transport techniques, the basic properties of the interface
between the superconductor and the semiconductor remain to be understood.\r\n\r\nIn
this thesis, two separate studies on the Al-InAs heterostructures are reported
with the first focusing on the physics of the material motivated by the emergence
of a new phase, the Bogoliubov-Fermi surface. \r\nThe second focuses on a technological
application, a gate-tunable Josephson parametric amplifier.\r\n\r\nIn the first
study, we investigate the hypothesized unconventional nature of the induced superconductivity
at the interface between the Al thin film and the InAs quantum well.\r\nWe embed
a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing
measurements of change in inductance.\r\nThe behaviour of the resonance in a range
of temperature and in-plane magnetic field has been studied and compared with
the theory of conventional s-wave superconductor and a two-component theory that
includes both contribution of the $s$-wave pairing in Al and the intraband $p
\\pm ip$ pairing in InAs.\r\nMeasuring the temperature dependence of resonant
frequency, no discrepancy is found between data and the conventional theory.\r\nWe
observe the breakdown of superconductivity due to an applied magnetic field which
contradicts the conventional theory.\r\nIn contrast, the data can be captured
quantitatively by fitting to a two-component model.\r\nWe find the evidence of
the intraband $p \\pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi
surfaces due to magnetic field with the characteristic value $B^* = 0.33~\\mathrm{T}$.\r\nFrom
the fits, the sheet resistance of Al, the carrier density and mobility in InAs
are determined.\r\nBy systematically studying the anisotropy of the circuit response,
we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B
> B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency
versus field angle.\r\nStrong resemblance between the field dependence of dissipation
and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface
that is burried in the dissipation data.\r\n\r\nIn the second study, we realize
a parametric amplifier with a Josephson field effect transistor as the active
element.\r\nThe device's modest construction consists of a gated SNS weak link
embedded at the center of a coplanar waveguide resonator.\r\nBy applying a gate
voltage, the resonant frequency is field-effect tunable over a range of 2 GHz.\r\nModelling
the JoFET minimally as a parallel RL circuit, the dissipation introduced by the
JoFET can be quantitatively related to the gate voltage.\r\nWe observed gate-tunable
Kerr nonlinearity qualitatively in line with expectation.\r\nThe JoFET amplifier
has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point
of -125.5 dBm when operated at a fixed resonant frequency.\r\nIn general, the
signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated
compared.\r\nThe noise of the measurement chain and insertion loss of relevant
circuit elements are calibrated to determine the expected and the real noise performance
of the JoFET amplifier.\r\nAs a quantification of the noise performance, the measured
total input-referred noise of the JoFET amplifier is in good agreement with the
estimated expectation which takes device loss into account.\r\nWe found that the
noise performance of the device reported in this document approaches one photon
of total input-referred added noise which is the quantum limit imposed in nondegenerate
parametric amplifier."
acknowledged_ssus:
- _id: NanoFab
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Duc T
full_name: Phan, Duc T
id: 29C8C0B4-F248-11E8-B48F-1D18A9856A87
last_name: Phan
citation:
ama: Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:10.15479/14547
apa: Phan, D. T. (2023). Resonant microwave spectroscopy of Al-InAs. Institute
of Science and Technology Austria. https://doi.org/10.15479/14547
chicago: Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of
Science and Technology Austria, 2023. https://doi.org/10.15479/14547.
ieee: D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science
and Technology Austria, 2023.
ista: Phan DT. 2023. Resonant microwave spectroscopy of Al-InAs. Institute of Science
and Technology Austria.
mla: Phan, Duc T. Resonant Microwave Spectroscopy of Al-InAs. Institute of
Science and Technology Austria, 2023, doi:10.15479/14547.
short: D.T. Phan, Resonant Microwave Spectroscopy of Al-InAs, Institute of Science
and Technology Austria, 2023.
date_created: 2023-11-17T13:45:26Z
date_published: 2023-11-16T00:00:00Z
date_updated: 2023-11-30T10:56:04Z
day: '16'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: AnHi
doi: 10.15479/14547
file:
- access_level: open_access
checksum: db0c37d213bc002125bd59690e9db246
content_type: application/pdf
creator: pduc
date_created: 2023-11-17T13:36:44Z
date_updated: 2023-11-22T09:46:06Z
file_id: '14548'
file_name: Phan_Thesis_pdfa.pdf
file_size: 34828019
relation: main_file
- access_level: closed
checksum: 8d3bd6afa279a0078ffd13e06bb6d56d
content_type: application/zip
creator: pduc
date_created: 2023-11-17T13:44:53Z
date_updated: 2023-11-17T13:47:54Z
file_id: '14549'
file_name: dissertation_src.zip
file_size: 279319709
relation: source_file
file_date_updated: 2023-11-22T09:46:06Z
has_accepted_license: '1'
keyword:
- superconductor-semiconductor
- superconductivity
- Al
- InAs
- p-wave
- superconductivity
- JPA
- microwave
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: '80'
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10851'
relation: part_of_dissertation
status: public
- id: '13264'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
title: Resonant microwave spectroscopy of Al-InAs
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '13264'
abstract:
- lang: eng
text: "We build a parametric amplifier with a Josephson field-effect transistor
(JoFET) as the active element. The resonant frequency of the device is field-effect
tunable over a range of 2 GHz. The JoFET amplifier has 20 dB of gain, 4 MHz of
instantaneous bandwidth, and a 1-dB compression point of -125.5 dBm when operated
at a fixed resonance frequency.\r\n\r\n"
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
acknowledgement: We thank Shyam Shankar for helpful feedback on the manuscript. We
gratefully acknowledge the support of the ISTA nanofabrication facility, the Miba
Machine Shop, and the eMachine Shop. The NYU team acknowledges support from Army
Research Office Grant No. W911NF2110303.
article_number: '064032'
article_processing_charge: No
article_type: original
author:
- first_name: Duc T
full_name: Phan, Duc T
id: 29C8C0B4-F248-11E8-B48F-1D18A9856A87
last_name: Phan
- first_name: Paul
full_name: Falthansl-Scheinecker, Paul
id: 85b43b21-15b2-11ec-abd3-e2c252cc2285
last_name: Falthansl-Scheinecker
- first_name: Umang
full_name: Mishra, Umang
id: 4328fa4c-f128-11eb-9611-c107b0fe4d51
last_name: Mishra
- first_name: W. M.
full_name: Strickland, W. M.
last_name: Strickland
- first_name: D.
full_name: Langone, D.
last_name: Langone
- first_name: J.
full_name: Shabani, J.
last_name: Shabani
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Phan DT, Falthansl-Scheinecker P, Mishra U, et al. Gate-tunable superconductor-semiconductor
parametric amplifier. Physical Review Applied. 2023;19(6). doi:10.1103/PhysRevApplied.19.064032
apa: Phan, D. T., Falthansl-Scheinecker, P., Mishra, U., Strickland, W. M., Langone,
D., Shabani, J., & Higginbotham, A. P. (2023). Gate-tunable superconductor-semiconductor
parametric amplifier. Physical Review Applied. American Physical Society.
https://doi.org/10.1103/PhysRevApplied.19.064032
chicago: Phan, Duc T, Paul Falthansl-Scheinecker, Umang Mishra, W. M. Strickland,
D. Langone, J. Shabani, and Andrew P Higginbotham. “Gate-Tunable Superconductor-Semiconductor
Parametric Amplifier.” Physical Review Applied. American Physical Society,
2023. https://doi.org/10.1103/PhysRevApplied.19.064032.
ieee: D. T. Phan et al., “Gate-tunable superconductor-semiconductor parametric
amplifier,” Physical Review Applied, vol. 19, no. 6. American Physical
Society, 2023.
ista: Phan DT, Falthansl-Scheinecker P, Mishra U, Strickland WM, Langone D, Shabani
J, Higginbotham AP. 2023. Gate-tunable superconductor-semiconductor parametric
amplifier. Physical Review Applied. 19(6), 064032.
mla: Phan, Duc T., et al. “Gate-Tunable Superconductor-Semiconductor Parametric
Amplifier.” Physical Review Applied, vol. 19, no. 6, 064032, American Physical
Society, 2023, doi:10.1103/PhysRevApplied.19.064032.
short: D.T. Phan, P. Falthansl-Scheinecker, U. Mishra, W.M. Strickland, D. Langone,
J. Shabani, A.P. Higginbotham, Physical Review Applied 19 (2023).
date_created: 2023-07-23T22:01:12Z
date_published: 2023-06-09T00:00:00Z
date_updated: 2023-11-30T10:56:03Z
day: '09'
department:
- _id: AnHi
- _id: OnHo
doi: 10.1103/PhysRevApplied.19.064032
external_id:
arxiv:
- '2206.05746'
isi:
- '001012022600004'
intvolume: ' 19'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2206.05746
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review Applied
publication_identifier:
eissn:
- 2331-7019
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '14547'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Gate-tunable superconductor-semiconductor parametric amplifier
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 19
year: '2023'
...
---
_id: '14591'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth
and development by controlling plasma membrane protein composition and cargo uptake.
CME relies on the precise recruitment of regulators for vesicle maturation and
release. Homologues of components of mammalian vesicle scission are strong candidates
to be part of the scissin machinery in plants, but the precise roles of these
proteins in this process is not fully understood. Here, we characterised the roles
of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein
2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin,
in the CME by combining high-resolution imaging of endocytic events in vivo and
characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive
similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3
triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants
suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis.
These observations imply that despite the presence of many well-conserved endocytic
components, plants have acquired a distinct mechanism for CME. One Sentence Summary
In contrast to predictions based on mammalian systems, plant Dynamin-related proteins
2 are recruited to the site of Clathrin-mediated endocytosis independently of
BAR-SH3 proteins.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
article_processing_charge: No
author:
- first_name: Nataliia
full_name: Gnyliukh, Nataliia
id: 390C1120-F248-11E8-B48F-1D18A9856A87
last_name: Gnyliukh
orcid: 0000-0002-2198-0509
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Marie-Kristin
full_name: Nagel, Marie-Kristin
last_name: Nagel
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: Annamaria
full_name: Hlavata, Annamaria
id: 36062FEC-F248-11E8-B48F-1D18A9856A87
last_name: Hlavata
- first_name: Erika
full_name: Isono, Erika
last_name: Isono
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins
2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. doi:10.1101/2023.10.09.561523
apa: Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono,
E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated
endocytosis in plants. bioRxiv. https://doi.org/10.1101/2023.10.09.561523
chicago: Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer,
Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related
Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv,
n.d. https://doi.org/10.1101/2023.10.09.561523.
ieee: N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in
clathrin-mediated endocytosis in plants,” bioRxiv. .
ista: Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M,
Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis
in plants. bioRxiv, 10.1101/2023.10.09.561523.
mla: Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in
Clathrin-Mediated Endocytosis in Plants.” BioRxiv, doi:10.1101/2023.10.09.561523.
short: N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono,
M. Loose, J. Friml, BioRxiv (n.d.).
date_created: 2023-11-22T10:17:49Z
date_published: 2023-10-10T00:00:00Z
date_updated: 2023-12-01T13:51:06Z
day: '10'
department:
- _id: JiFr
- _id: MaLo
- _id: CaBe
doi: 10.1101/2023.10.09.561523
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2023.10.09.561523v2
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: bioRxiv
publication_status: submitted
related_material:
record:
- id: '14510'
relation: dissertation_contains
status: public
status: public
title: Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis
in plants
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14639'
abstract:
- lang: eng
text: "Background: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate
dehydrogenase complex, have been associated with highly heterogeneous neurological
and neurodevelopmental disorders. However, the validity of this association remains
to be confirmed. A second OGDHL patient cohort was recruited to carefully assess
the gene-disease relationship.\r\nMethods: Using an unbiased genotype-first approach,
we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic
OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl,
ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during
development. Functional complementation with patient variant transcripts was conducted
to systematically assess protein functionality as a readout for pathogenicity.\r\nResults:
A cohort of 14 individuals from 12 unrelated families exhibited highly variable
clinical phenotypes, with the majority of them presenting at least one additional
variant, potentially accounting for a blended phenotype and complicating phenotypic
understanding. We also uncovered extreme clinical heterogeneity and high allele
frequencies, occasionally incompatible with a fully penetrant recessive disorder.
Human cDNA of previously described and new variants were tested in an ogdhl zebrafish
knockout model, adding functional evidence for variant reclassification. We disclosed
evidence of hypomorphic alleles as well as a loss-of-function variant without
deleterious effects in zebrafish variant testing also showing discordant familial
segregation, challenging the relationship of OGDHL as a conventional Mendelian
gene. Going further, we uncovered evidence for a complex compensatory relationship
among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental
disorders and exhibit complex transcriptional compensation patterns with partial
functional redundancy.\r\nConclusions: Based on the results of genetic, clinical,
and functional studies, we formed three hypotheses in which to frame observations:
biallelic OGDHL variants lead to a highly variable monogenic disorder, variants
in OGDHL are following a complex pattern of inheritance, or they may not be causative
at all. Our study further highlights the continuing challenges of assessing the
validity of reported disease-gene associations and effects of variants identified
in these genes. This is particularly more complicated in making genetic diagnoses
based on identification of variants in genes presenting a highly heterogenous
phenotype such as “OGDHL-related disorders”."
article_number: '102'
article_processing_charge: Yes
article_type: original
author:
- first_name: Sheng-Jia
full_name: Lin, Sheng-Jia
last_name: Lin
- first_name: Barbara
full_name: Vona, Barbara
last_name: Vona
- first_name: Tracy
full_name: Lau, Tracy
last_name: Lau
- first_name: Kevin
full_name: Huang, Kevin
id: 3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3
last_name: Huang
orcid: 0000-0002-2512-7812
- first_name: Maha S.
full_name: Zaki, Maha S.
last_name: Zaki
- first_name: Huda Shujaa
full_name: Aldeen, Huda Shujaa
last_name: Aldeen
- first_name: Ehsan Ghayoor
full_name: Karimiani, Ehsan Ghayoor
last_name: Karimiani
- first_name: Clarissa
full_name: Rocca, Clarissa
last_name: Rocca
- first_name: Mahmoud M.
full_name: Noureldeen, Mahmoud M.
last_name: Noureldeen
- first_name: Ahmed K.
full_name: Saad, Ahmed K.
last_name: Saad
- first_name: Cassidy
full_name: Petree, Cassidy
last_name: Petree
- first_name: Tobias
full_name: Bartolomaeus, Tobias
last_name: Bartolomaeus
- first_name: Rami
full_name: Abou Jamra, Rami
last_name: Abou Jamra
- first_name: Giovanni
full_name: Zifarelli, Giovanni
last_name: Zifarelli
- first_name: Aditi
full_name: Gotkhindikar, Aditi
last_name: Gotkhindikar
- first_name: Ingrid M.
full_name: Wentzensen, Ingrid M.
last_name: Wentzensen
- first_name: Mingjuan
full_name: Liao, Mingjuan
last_name: Liao
- first_name: Emalyn Elise
full_name: Cork, Emalyn Elise
last_name: Cork
- first_name: Pratishtha
full_name: Varshney, Pratishtha
last_name: Varshney
- first_name: Narges
full_name: Hashemi, Narges
last_name: Hashemi
- first_name: Mohammad Hasan
full_name: Mohammadi, Mohammad Hasan
last_name: Mohammadi
- first_name: Aboulfazl
full_name: Rad, Aboulfazl
last_name: Rad
- first_name: Juanita
full_name: Neira, Juanita
last_name: Neira
- first_name: Mehran Beiraghi
full_name: Toosi, Mehran Beiraghi
last_name: Toosi
- first_name: Cordula
full_name: Knopp, Cordula
last_name: Knopp
- first_name: Ingo
full_name: Kurth, Ingo
last_name: Kurth
- first_name: Thomas D.
full_name: Challman, Thomas D.
last_name: Challman
- first_name: Rebecca
full_name: Smith, Rebecca
last_name: Smith
- first_name: Asmahan
full_name: Abdalla, Asmahan
last_name: Abdalla
- first_name: Thomas
full_name: Haaf, Thomas
last_name: Haaf
- first_name: Mohnish
full_name: Suri, Mohnish
last_name: Suri
- first_name: Manali
full_name: Joshi, Manali
last_name: Joshi
- first_name: Wendy K.
full_name: Chung, Wendy K.
last_name: Chung
- first_name: Andres
full_name: Moreno-De-Luca, Andres
last_name: Moreno-De-Luca
- first_name: Henry
full_name: Houlden, Henry
last_name: Houlden
- first_name: Reza
full_name: Maroofian, Reza
last_name: Maroofian
- first_name: Gaurav K.
full_name: Varshney, Gaurav K.
last_name: Varshney
citation:
ama: Lin S-J, Vona B, Lau T, et al. Evaluating the association of biallelic OGDHL
variants with significant phenotypic heterogeneity. Genome Medicine. 2023;15.
doi:10.1186/s13073-023-01258-4
apa: Lin, S.-J., Vona, B., Lau, T., Huang, K., Zaki, M. S., Aldeen, H. S., … Varshney,
G. K. (2023). Evaluating the association of biallelic OGDHL variants with significant
phenotypic heterogeneity. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-023-01258-4
chicago: Lin, Sheng-Jia, Barbara Vona, Tracy Lau, Kevin Huang, Maha S. Zaki, Huda
Shujaa Aldeen, Ehsan Ghayoor Karimiani, et al. “Evaluating the Association of
Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” Genome
Medicine. Springer Nature, 2023. https://doi.org/10.1186/s13073-023-01258-4.
ieee: S.-J. Lin et al., “Evaluating the association of biallelic OGDHL variants
with significant phenotypic heterogeneity,” Genome Medicine, vol. 15. Springer
Nature, 2023.
ista: Lin S-J, Vona B, Lau T, Huang K, Zaki MS, Aldeen HS, Karimiani EG, Rocca C,
Noureldeen MM, Saad AK, Petree C, Bartolomaeus T, Abou Jamra R, Zifarelli G, Gotkhindikar
A, Wentzensen IM, Liao M, Cork EE, Varshney P, Hashemi N, Mohammadi MH, Rad A,
Neira J, Toosi MB, Knopp C, Kurth I, Challman TD, Smith R, Abdalla A, Haaf T,
Suri M, Joshi M, Chung WK, Moreno-De-Luca A, Houlden H, Maroofian R, Varshney
GK. 2023. Evaluating the association of biallelic OGDHL variants with significant
phenotypic heterogeneity. Genome Medicine. 15, 102.
mla: Lin, Sheng-Jia, et al. “Evaluating the Association of Biallelic OGDHL Variants
with Significant Phenotypic Heterogeneity.” Genome Medicine, vol. 15, 102,
Springer Nature, 2023, doi:10.1186/s13073-023-01258-4.
short: S.-J. Lin, B. Vona, T. Lau, K. Huang, M.S. Zaki, H.S. Aldeen, E.G. Karimiani,
C. Rocca, M.M. Noureldeen, A.K. Saad, C. Petree, T. Bartolomaeus, R. Abou Jamra,
G. Zifarelli, A. Gotkhindikar, I.M. Wentzensen, M. Liao, E.E. Cork, P. Varshney,
N. Hashemi, M.H. Mohammadi, A. Rad, J. Neira, M.B. Toosi, C. Knopp, I. Kurth,
T.D. Challman, R. Smith, A. Abdalla, T. Haaf, M. Suri, M. Joshi, W.K. Chung, A.
Moreno-De-Luca, H. Houlden, R. Maroofian, G.K. Varshney, Genome Medicine 15 (2023).
date_created: 2023-12-04T08:10:55Z
date_published: 2023-11-23T00:00:00Z
date_updated: 2023-12-04T08:17:22Z
day: '23'
ddc:
- '570'
doi: 10.1186/s13073-023-01258-4
extern: '1'
file:
- access_level: open_access
checksum: 279efd212005549aba817a487d56d363
content_type: application/pdf
creator: dernst
date_created: 2023-12-04T08:15:43Z
date_updated: 2023-12-04T08:15:43Z
file_id: '14640'
file_name: 2023_GenomeMed_Lin.pdf
file_size: 14791081
relation: main_file
success: 1
file_date_updated: 2023-12-04T08:15:43Z
has_accepted_license: '1'
intvolume: ' 15'
keyword:
- Genetics (clinical)
- Genetics
- Molecular Biology
- Molecular Medicine
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Genome Medicine
publication_identifier:
issn:
- 1756-994X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Evaluating the association of biallelic OGDHL variants with significant phenotypic
heterogeneity
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: '14628'
abstract:
- lang: eng
text: We introduce a compact, intuitive procedural graph representation for cellular
metamaterials, which are small-scale, tileable structures that can be architected
to exhibit many useful material properties. Because the structures’ “architectures”
vary widely—with elements such as beams, thin shells, and solid bulks—it is difficult
to explore them using existing representations. Generic approaches like voxel
grids are versatile, but it is cumbersome to represent and edit individual structures;
architecture-specific approaches address these issues, but are incompatible with
one another. By contrast, our procedural graph succinctly represents the construction
process for any structure using a simple skeleton annotated with spatially varying
thickness. To express the highly constrained triply periodic minimal surfaces
(TPMS) in this manner, we present the first fully automated version of the conjugate
surface construction method, which allows novices to create complex TPMS from
intuitive input. We demonstrate our representation’s expressiveness, accuracy,
and compactness by constructing a wide range of established structures and hundreds
of novel structures with diverse architectures and material properties. We also
conduct a user study to verify our representation’s ease-of-use and ability to
expand engineers’ capacity for exploration.
acknowledgement: "The authors thank Mina Konaković Luković and Michael Foshey for
their early contributions to this project, David Palmer and Paul Zhang for their
insightful discussions about minimal surfaces and the CSCM, Julian Panetta for providing
the Elastic Textures code, and Hannes Hergeth for his feedback and support. We also
thank our user study participants and anonymous reviewers.\r\nThis material is based
upon work supported by the National Science Foundation\r\n(NSF) Graduate Research
Fellowship under Grant No. 2141064; the MIT Morningside\r\nAcademy for Design Fellowship;
the Defense Advanced Research Projects Agency\r\n(DARPA) Grant No. FA8750-20-C-0075;
the ERC Consolidator Grant No. 101045083,\r\n“CoDiNA: Computational Discovery of
Numerical Algorithms for Animation and Simulation of Natural Phenomena”; and the
NewSat project, which is co-funded by the Operational Program for Competitiveness
and Internationalisation (COMPETE2020), Portugal 2020, the European Regional Development
Fund (ERDF), and the Portuguese Foundation for Science and Technology (FTC) under
the MIT Portugal program."
article_number: '168'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Liane
full_name: Makatura, Liane
last_name: Makatura
- first_name: Bohan
full_name: Wang, Bohan
last_name: Wang
- first_name: Yi-Lu
full_name: Chen, Yi-Lu
id: 0b467602-dbcd-11ea-9d1d-ed480aa46b70
last_name: Chen
- first_name: Bolei
full_name: Deng, Bolei
last_name: Deng
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
citation:
ama: 'Makatura L, Wang B, Chen Y-L, et al. Procedural metamaterials: A unified procedural
graph for metamaterial design. ACM Transactions on Graphics. 2023;42(5).
doi:10.1145/3605389'
apa: 'Makatura, L., Wang, B., Chen, Y.-L., Deng, B., Wojtan, C., Bickel, B., &
Matusik, W. (2023). Procedural metamaterials: A unified procedural graph for metamaterial
design. ACM Transactions on Graphics. Association for Computing Machinery.
https://doi.org/10.1145/3605389'
chicago: 'Makatura, Liane, Bohan Wang, Yi-Lu Chen, Bolei Deng, Chris Wojtan, Bernd
Bickel, and Wojciech Matusik. “Procedural Metamaterials: A Unified Procedural
Graph for Metamaterial Design.” ACM Transactions on Graphics. Association
for Computing Machinery, 2023. https://doi.org/10.1145/3605389.'
ieee: 'L. Makatura et al., “Procedural metamaterials: A unified procedural
graph for metamaterial design,” ACM Transactions on Graphics, vol. 42,
no. 5. Association for Computing Machinery, 2023.'
ista: 'Makatura L, Wang B, Chen Y-L, Deng B, Wojtan C, Bickel B, Matusik W. 2023.
Procedural metamaterials: A unified procedural graph for metamaterial design.
ACM Transactions on Graphics. 42(5), 168.'
mla: 'Makatura, Liane, et al. “Procedural Metamaterials: A Unified Procedural Graph
for Metamaterial Design.” ACM Transactions on Graphics, vol. 42, no. 5,
168, Association for Computing Machinery, 2023, doi:10.1145/3605389.'
short: L. Makatura, B. Wang, Y.-L. Chen, B. Deng, C. Wojtan, B. Bickel, W. Matusik,
ACM Transactions on Graphics 42 (2023).
date_created: 2023-11-29T15:02:03Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-12-04T08:09:05Z
day: '01'
ddc:
- '531'
- '006'
department:
- _id: GradSch
- _id: ChWo
- _id: BeBi
doi: 10.1145/3605389
file:
- access_level: open_access
checksum: 0192f597d7a2ceaf89baddfd6190d4c8
content_type: application/zip
creator: yichen
date_created: 2023-11-29T15:16:01Z
date_updated: 2023-11-29T15:16:01Z
file_id: '14630'
file_name: tog-22-0089-File004.zip
file_size: 95467870
relation: main_file
success: 1
- access_level: open_access
checksum: 7fb024963be81933494f38de191e4710
content_type: application/zip
creator: yichen
date_created: 2023-11-29T15:16:01Z
date_updated: 2023-11-29T15:16:01Z
file_id: '14631'
file_name: tog-22-0089-File005.zip
file_size: 103731880
relation: main_file
success: 1
- access_level: open_access
checksum: b7d6829ce396e21cac9fae0ec7130a6b
content_type: application/pdf
creator: dernst
date_created: 2023-12-04T08:04:14Z
date_updated: 2023-12-04T08:04:14Z
file_id: '14638'
file_name: 2023_ACMToG_Makatura.pdf
file_size: 57067476
relation: main_file
success: 1
file_date_updated: 2023-12-04T08:04:14Z
has_accepted_license: '1'
intvolume: ' 42'
issue: '5'
keyword:
- Computer Graphics and Computer-Aided Design
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088
grant_number: '101045083'
name: Computational Discovery of Numerical Algorithms for Animation and Simulation
of Natural Phenomena
publication: ACM Transactions on Graphics
publication_identifier:
issn:
- 0730-0301
- 1557-7368
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: 'Procedural metamaterials: A unified procedural graph for metamaterial design'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '14644'
abstract:
- lang: eng
text: Transcription by RNA polymerase II (Pol II) can be repressed by noncoding
RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs
repress transcription remains unclear. Here we present cryo-electron microscopy
structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA
and RNA bind to Pol II during transcription elongation. Further, we show how domains
of the general transcription factor TFIIF affect complex dynamics and control
repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian
gene expression.
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
- _id: PreCl
acknowledgement: "We thank B. Kaczmarek and other members of the Bernecky lab for
helpful discussions. We thank V.-V. Hodirnau for SerialEM data collection and support
with EPU data collection. We thank D. Slade for the wild type TFIIF expression\r\nplasmid.
We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. We thank
C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported
by Austrian Science Fund (FWF) grant P34185. This research was further supported
by the Scientific Service Units (SSU) of IST Austria through resources provided
by the Lab Support Facility (LSF), Electron Microscopy Facility (EMF), Scientific
Computing (SciComp), and the Preclinical Facility (PCF)."
article_processing_charge: No
author:
- first_name: Katarina
full_name: Tluckova, Katarina
id: 4AC7D980-F248-11E8-B48F-1D18A9856A87
last_name: Tluckova
- first_name: Anita P
full_name: Testa Salmazo, Anita P
id: 41F1F098-F248-11E8-B48F-1D18A9856A87
last_name: Testa Salmazo
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
citation:
ama: Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional
repression by noncoding RNA. doi:10.15479/AT:ISTA:14644
apa: Tluckova, K., Testa Salmazo, A. P., & Bernecky, C. (n.d.). Mechanism of
mammalian transcriptional repression by noncoding RNA. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:14644
chicago: Tluckova, Katarina, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism
of Mammalian Transcriptional Repression by Noncoding RNA.” Institute of Science
and Technology Austria, n.d. https://doi.org/10.15479/AT:ISTA:14644.
ieee: K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian
transcriptional repression by noncoding RNA.” Institute of Science and Technology
Austria.
ista: Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional
repression by noncoding RNA. 10.15479/AT:ISTA:14644.
mla: Tluckova, Katarina, et al. Mechanism of Mammalian Transcriptional Repression
by Noncoding RNA. Institute of Science and Technology Austria, doi:10.15479/AT:ISTA:14644.
short: K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.).
date_created: 2023-12-04T14:51:00Z
date_published: 2023-12-05T00:00:00Z
date_updated: 2023-12-05T10:37:28Z
day: '05'
ddc:
- '572'
department:
- _id: CaBe
doi: 10.15479/AT:ISTA:14644
file:
- access_level: open_access
checksum: c45608cb97ee36d7b50ba518db8e07b0
content_type: application/pdf
creator: dernst
date_created: 2023-12-05T10:37:02Z
date_updated: 2023-12-05T10:37:02Z
file_id: '14646'
file_name: 2023_Tluckova_etal_REx.pdf
file_size: 4892920
relation: main_file
success: 1
file_date_updated: 2023-12-05T10:37:02Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
project:
- _id: c08a6700-5a5b-11eb-8a69-82a722b2bc30
grant_number: P34185
name: Regulation of mammalian transcription by noncoding RNA
publication_status: submitted
publisher: Institute of Science and Technology Austria
status: public
title: Mechanism of mammalian transcriptional repression by noncoding RNA
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14658'
abstract:
- lang: eng
text: "We investigate spin-charge separation of a spin-\r\n1\r\n2\r\n Fermi system
confined in a triple well where multiple bands are occupied. We assume that our
finite fermionic system is close to fully spin polarized while being doped by
a hole and an impurity fermion with opposite spin. Our setup involves ferromagnetic
couplings among the particles in different bands, leading to the development of
strong spin-transport correlations in an intermediate interaction regime. Interactions
are then strong enough to lift the degeneracy among singlet and triplet spin configurations
in the well of the spin impurity but not strong enough to prohibit hole-induced
magnetic excitations to the singlet state. Despite the strong spin-hole correlations,
the system exhibits spin-charge deconfinement allowing for long-range entanglement
of the spatial and spin degrees of freedom."
acknowledgement: This work has been funded by the Cluster of Excellence “Advanced
Imaging of Matter” of the Deutsche Forschungsgemeinschaft (DFG)-EXC 2056-Project
ID No. 390715994. G.M.K. gratefully acknowledges funding from the European Union’s
Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 101034413.
article_number: '043039'
article_processing_charge: Yes
article_type: original
author:
- first_name: J. M.
full_name: Becker, J. M.
last_name: Becker
- first_name: Georgios
full_name: Koutentakis, Georgios
id: d7b23d3a-9e21-11ec-b482-f76739596b95
last_name: Koutentakis
- first_name: P.
full_name: Schmelcher, P.
last_name: Schmelcher
citation:
ama: Becker JM, Koutentakis G, Schmelcher P. Spin-charge correlations in finite
one-dimensional multiband Fermi systems. Physical Review Research. 2023;5(4).
doi:10.1103/PhysRevResearch.5.043039
apa: Becker, J. M., Koutentakis, G., & Schmelcher, P. (2023). Spin-charge correlations
in finite one-dimensional multiband Fermi systems. Physical Review Research.
American Physical Society. https://doi.org/10.1103/PhysRevResearch.5.043039
chicago: Becker, J. M., Georgios Koutentakis, and P. Schmelcher. “Spin-Charge Correlations
in Finite One-Dimensional Multiband Fermi Systems.” Physical Review Research.
American Physical Society, 2023. https://doi.org/10.1103/PhysRevResearch.5.043039.
ieee: J. M. Becker, G. Koutentakis, and P. Schmelcher, “Spin-charge correlations
in finite one-dimensional multiband Fermi systems,” Physical Review Research,
vol. 5, no. 4. American Physical Society, 2023.
ista: Becker JM, Koutentakis G, Schmelcher P. 2023. Spin-charge correlations in
finite one-dimensional multiband Fermi systems. Physical Review Research. 5(4),
043039.
mla: Becker, J. M., et al. “Spin-Charge Correlations in Finite One-Dimensional Multiband
Fermi Systems.” Physical Review Research, vol. 5, no. 4, 043039, American
Physical Society, 2023, doi:10.1103/PhysRevResearch.5.043039.
short: J.M. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 5 (2023).
date_created: 2023-12-10T23:00:58Z
date_published: 2023-10-12T00:00:00Z
date_updated: 2023-12-11T10:55:52Z
day: '12'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/PhysRevResearch.5.043039
ec_funded: 1
external_id:
arxiv:
- '2305.09529'
file:
- access_level: open_access
checksum: ee31c0d0de5d1b65591990ae6705a601
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T10:49:07Z
date_updated: 2023-12-11T10:49:07Z
file_id: '14672'
file_name: 2023_PhysReviewResearch_Becker.pdf
file_size: 2362158
relation: main_file
success: 1
file_date_updated: 2023-12-11T10:49:07Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '4'
language:
- iso: eng
month: '10'
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: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spin-charge correlations in finite one-dimensional multiband Fermi systems
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2023'
...
---
_id: '14650'
abstract:
- lang: eng
text: We study the out-of-equilibrium quantum dynamics of dipolar polarons, i.e.,
impurities immersed in a dipolar Bose-Einstein condensate, after a quench of the
impurity-boson interaction. We show that the dipolar nature of the condensate
and of the impurity results in anisotropic relaxation dynamics, in particular,
anisotropic dressing of the polaron. More relevantly for cold-atom setups, quench
dynamics is strongly affected by the interplay between dipolar anisotropy and
trap geometry. Our findings pave the way for simulating impurities in anisotropic
media utilizing experiments with dipolar mixtures.
acknowledgement: "We thank Lauriane Chomaz for useful discussions and comments on
the manuscript. We also\r\nthank Ragheed Al Hyder for comments on the manuscript.\r\nG.B.
acknowledges support from the Austrian Science Fund (FWF),\r\nunder Project No.
M2641-N27. This work is supported by the Deutsche Forschungsgemeinschaft (DFG, German
Research Foundation) under Germany’s Excellence Strategy EXC2181/1-\r\n390900948
(the Heidelberg STRUCTURES Excellence Cluster). A. G. V. acknowledges support from
the European Union’s Horizon 2020 research and innovation programme under the\r\nMarie
Skłodowska-Curie Grant Agreement No. 754411. L.A.P.A acknowledges by the PNRR\r\nMUR
project PE0000023 - NQSTI and the Deutsche Forschungsgemeinschaft (DFG, German\r\nResearch
Foundation) under Germany’s Excellence Strategy - EXC - 2123 Quantum Frontiers390837967
and FOR2247."
article_number: '232'
article_processing_charge: No
article_type: original
author:
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Luis
full_name: Santos, Luis
last_name: Santos
- first_name: Luisllu A.
full_name: Peña Ardila, Luisllu A.
last_name: Peña Ardila
citation:
ama: Volosniev A, Bighin G, Santos L, Peña Ardila LA. Non-equilibrium dynamics of
dipolar polarons. SciPost Physics. 2023;15(6). doi:10.21468/scipostphys.15.6.232
apa: Volosniev, A., Bighin, G., Santos, L., & Peña Ardila, L. A. (2023). Non-equilibrium
dynamics of dipolar polarons. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.15.6.232
chicago: Volosniev, Artem, Giacomo Bighin, Luis Santos, and Luisllu A. Peña Ardila.
“Non-Equilibrium Dynamics of Dipolar Polarons.” SciPost Physics. SciPost
Foundation, 2023. https://doi.org/10.21468/scipostphys.15.6.232.
ieee: A. Volosniev, G. Bighin, L. Santos, and L. A. Peña Ardila, “Non-equilibrium
dynamics of dipolar polarons,” SciPost Physics, vol. 15, no. 6. SciPost
Foundation, 2023.
ista: Volosniev A, Bighin G, Santos L, Peña Ardila LA. 2023. Non-equilibrium dynamics
of dipolar polarons. SciPost Physics. 15(6), 232.
mla: Volosniev, Artem, et al. “Non-Equilibrium Dynamics of Dipolar Polarons.” SciPost
Physics, vol. 15, no. 6, 232, SciPost Foundation, 2023, doi:10.21468/scipostphys.15.6.232.
short: A. Volosniev, G. Bighin, L. Santos, L.A. Peña Ardila, SciPost Physics 15
(2023).
date_created: 2023-12-10T13:03:07Z
date_published: 2023-12-07T00:00:00Z
date_updated: 2023-12-11T07:44:08Z
day: '07'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.21468/scipostphys.15.6.232
ec_funded: 1
external_id:
arxiv:
- '2305.17969'
file:
- access_level: open_access
checksum: e664372a1fe9d628a9bb1d135ebab7d8
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T07:42:04Z
date_updated: 2023-12-11T07:42:04Z
file_id: '14669'
file_name: 2023_SciPostPhysics_Volosniev.pdf
file_size: 3543541
relation: main_file
success: 1
file_date_updated: 2023-12-11T07:42:04Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '6'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 26986C82-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02641
name: A path-integral approach to composite impurities
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: SciPost Physics
publication_identifier:
issn:
- 2542-4653
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
status: public
title: Non-equilibrium dynamics of dipolar polarons
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: '14653'
abstract:
- lang: eng
text: 'Mass spectrometry imaging (MSI) is a powerful analytical technique for the
two-dimensional (2D) localization of chemicals on surfaces. Conventional MSI experiments
require to predefine the surface of interest based on photographic or microscopic
images. Typically, these boundaries can no longer be changed or adjusted once
the experiment has been started. In terms of a more interactive approach we recently
developed a pen-like ionization interface which is directly connected to the mass
spectrometer. The device allows the user to ionize chemicals by desorption electrospray
ionization (DESI) and to freely move the interface over a surface of interest.
A mini camera, which is mounted on the tip of the pen, magnifies the desorption
area and enables a simple positioning of the pen. The combination of optical data
from the camera module and chemical data obtained by mass analysis facilitates
a novel type of imaging experiment: interactive mass spectrometry imaging (IMSI).
For this application, we present a novel approach for a robust, optical flow-based
motion detection. While the live video stream from the camera is used to track
the pen''s motion across the surface a post-acquisition algorithm correlates the
coordinates of the pen trajectory with respective mass spectra obtained from a
simultaneous mass spectrometric data acquisition. This algorithm is no longer
dependent on a single, manually applied optical marker on the sample surface,
which has to be visible on all video frames throughout the analysis. The advanced
DESI-IMSI method was successfully tested on inkjet-printed letters as well as
mouse brain tissue samples. Validation of the results was done by comparing DESI-IMSI
with standard DESI-MSI data.'
acknowledgement: We would like to thank Marco Sealey Cardona, PhD for help with the
mouse brain samples and acknowledge the financial support by 1669 Förderkreis of
the University of Innsbruck, Austria Wirtschaftsservice (AWS), D. Swarovski KG and
Tyrolean Science Fund (TWF).
article_number: '117168'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Florian
full_name: Kluibenschedl, Florian
id: 7499e70e-eb2c-11ec-b98b-f925648bc9d9
last_name: Kluibenschedl
- first_name: Anna
full_name: Ploner, Anna
last_name: Ploner
- first_name: Christina
full_name: Meisenbichler, Christina
last_name: Meisenbichler
- first_name: Robert
full_name: Konrat, Robert
last_name: Konrat
- first_name: Thomas
full_name: Müller, Thomas
last_name: Müller
citation:
ama: Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. Advanced motion
tracking for interactive mass spectrometry imaging (IMSI). International Journal
of Mass Spectrometry. 2023;495. doi:10.1016/j.ijms.2023.117168
apa: Kluibenschedl, F., Ploner, A., Meisenbichler, C., Konrat, R., & Müller,
T. (2023). Advanced motion tracking for interactive mass spectrometry imaging
(IMSI). International Journal of Mass Spectrometry. Elsevier. https://doi.org/10.1016/j.ijms.2023.117168
chicago: Kluibenschedl, Florian, Anna Ploner, Christina Meisenbichler, Robert Konrat,
and Thomas Müller. “Advanced Motion Tracking for Interactive Mass Spectrometry
Imaging (IMSI).” International Journal of Mass Spectrometry. Elsevier,
2023. https://doi.org/10.1016/j.ijms.2023.117168.
ieee: F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, and T. Müller, “Advanced
motion tracking for interactive mass spectrometry imaging (IMSI),” International
Journal of Mass Spectrometry, vol. 495. Elsevier, 2023.
ista: Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. 2023. Advanced
motion tracking for interactive mass spectrometry imaging (IMSI). International
Journal of Mass Spectrometry. 495, 117168.
mla: Kluibenschedl, Florian, et al. “Advanced Motion Tracking for Interactive Mass
Spectrometry Imaging (IMSI).” International Journal of Mass Spectrometry,
vol. 495, 117168, Elsevier, 2023, doi:10.1016/j.ijms.2023.117168.
short: F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, T. Müller, International
Journal of Mass Spectrometry 495 (2023).
date_created: 2023-12-10T23:00:57Z
date_published: 2023-11-23T00:00:00Z
date_updated: 2023-12-11T08:16:35Z
day: '23'
department:
- _id: GradSch
doi: 10.1016/j.ijms.2023.117168
intvolume: ' 495'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.ijms.2023.117168
month: '11'
oa: 1
oa_version: Published Version
publication: International Journal of Mass Spectrometry
publication_identifier:
issn:
- 1387-3806
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Advanced motion tracking for interactive mass spectrometry imaging (IMSI)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 495
year: '2023'
...
---
_id: '14647'
abstract:
- lang: eng
text: In the developing vertebrate central nervous system, neurons and glia typically
arise sequentially from common progenitors. Here, we report that the transcription
factor Forkhead Box G1 (Foxg1) regulates gliogenesis in the mouse neocortex via
distinct cell-autonomous roles in progenitors and in postmitotic neurons that
regulate different aspects of the gliogenic FGF signalling pathway. We demonstrate
that loss of Foxg1 in cortical progenitors at neurogenic stages causes premature
astrogliogenesis. We identify a novel FOXG1 target, the pro-gliogenic FGF pathway
component Fgfr3, which is suppressed by FOXG1 cell-autonomously to maintain neurogenesis.
Furthermore, FOXG1 can also suppress premature astrogliogenesis triggered by the
augmentation of FGF signalling. We identify a second novel function of FOXG1 in
regulating the expression of gliogenic ligand FGF18 in new born neocortical upper-layer
neurons. Loss of FOXG1 in postmitotic neurons increases Fgf18 expression and enhances
gliogenesis in the progenitors. These results fit well with the model that new
born neurons secrete cues that trigger progenitors to produce the next wave of
cell types, astrocytes. If FGF signalling is attenuated in Foxg1 null progenitors,
they progress to oligodendrocyte production. Therefore, loss of FOXG1 transitions
the progenitor to a gliogenic state, producing either astrocytes or oligodendrocytes
depending on FGF signalling levels. Our results uncover how FOXG1 integrates extrinsic
signalling via the FGF pathway to regulate the sequential generation of neurons,
astrocytes, and oligodendrocytes in the cerebral cortex.
acknowledgement: "We thank Dr. Shital Suryavanshi and the animal house staff of the
Tata Institute of\r\nFundamental Research (TIFR) for their excellent support; Gord
Fishell and Goichi Miyoshi for\r\nthe Foxg1 floxed mouse line; Hiroshi Kawasaki
for the plasmids pCAG-FGF8 and pCAGsFGFR3c. We thank Prof. S.K. Lee for the Foxg1lox/lox
genotyping primers and protocol. We thank Dr. Deepak Modi and Dr. Vainav Patel for
allowing us to use the NIRRCH FACS Facility and the staff of the NIRRCH and TIFR
FACS facilities for their assistance.\r\nWe thank Denis Jabaudon for his critical
comments on the manuscript and members of the\r\nJabaudon lab for helpful discussions.
This work was funded by the Department of Atomic\r\nEnergy (DAE), Govt. of India
(Project Identification no. RTI4003, DAE OM no.\r\n1303/2/2019/R&D-II/DAE/2079)."
article_processing_charge: No
author:
- first_name: Mahima
full_name: Bose, Mahima
last_name: Bose
- first_name: Varun
full_name: Suresh, Varun
last_name: Suresh
- first_name: Urvi
full_name: Mishra, Urvi
last_name: Mishra
- first_name: Ishita
full_name: Talwar, Ishita
last_name: Talwar
- first_name: Anuradha
full_name: Yadav, Anuradha
last_name: Yadav
- first_name: Shiona
full_name: Biswas, Shiona
last_name: Biswas
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Shubha
full_name: Tole, Shubha
last_name: Tole
citation:
ama: Bose M, Suresh V, Mishra U, et al. Dual role of FOXG1 in regulating gliogenesis
in the developing neocortex via the FGF signalling pathway. bioRxiv. doi:10.1101/2023.11.30.569337
apa: Bose, M., Suresh, V., Mishra, U., Talwar, I., Yadav, A., Biswas, S., … Tole,
S. (n.d.). Dual role of FOXG1 in regulating gliogenesis in the developing neocortex
via the FGF signalling pathway. bioRxiv. Cold Spring Harbor Laboratory.
https://doi.org/10.1101/2023.11.30.569337
chicago: Bose, Mahima, Varun Suresh, Urvi Mishra, Ishita Talwar, Anuradha Yadav,
Shiona Biswas, Simon Hippenmeyer, and Shubha Tole. “Dual Role of FOXG1 in Regulating
Gliogenesis in the Developing Neocortex via the FGF Signalling Pathway.” BioRxiv.
Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2023.11.30.569337.
ieee: M. Bose et al., “Dual role of FOXG1 in regulating gliogenesis in the
developing neocortex via the FGF signalling pathway,” bioRxiv. Cold Spring
Harbor Laboratory.
ista: Bose M, Suresh V, Mishra U, Talwar I, Yadav A, Biswas S, Hippenmeyer S, Tole
S. Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via
the FGF signalling pathway. bioRxiv, 10.1101/2023.11.30.569337.
mla: Bose, Mahima, et al. “Dual Role of FOXG1 in Regulating Gliogenesis in the Developing
Neocortex via the FGF Signalling Pathway.” BioRxiv, Cold Spring Harbor
Laboratory, doi:10.1101/2023.11.30.569337.
short: M. Bose, V. Suresh, U. Mishra, I. Talwar, A. Yadav, S. Biswas, S. Hippenmeyer,
S. Tole, BioRxiv (n.d.).
date_created: 2023-12-06T13:07:01Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2023-12-11T07:37:17Z
day: '01'
department:
- _id: SiHi
doi: 10.1101/2023.11.30.569337
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.11.30.569337
month: '12'
oa: 1
oa_version: Preprint
publication: bioRxiv
publication_status: submitted
publisher: Cold Spring Harbor Laboratory
status: public
title: Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via
the FGF signalling pathway
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14655'
abstract:
- lang: eng
text: The kinetics of the assembly of semiflexible filaments through end-to-end
annealing is key to the structure of the cytoskeleton, but is not understood.
We analyze this problem through scaling theory and simulations, and uncover a
regime where filaments’ ends find each other through bending fluctuations without
the need for the whole filament to diffuse. This results in a very substantial
speedup of assembly in physiological regimes, and could help with understanding
the dynamics of actin and intermediate filaments in biological processes such
as wound healing and cell division.
acknowledgement: The authors thank C´ecile Leduc and Duc-Quang Tran for invaluable
help with understanding the experimental behavior of intermediate filaments, and
Raphael Voituriez, Nicolas Levernier, and Alexander Grosberg for fruitful discussion
on the theoretical model. V. S. also thanks Davide Michieletto, Maria Panoukidou,
and Lorenzo Rovigatti for very helpful suggestions on the simulation model. M. L.
was supported by Marie Curie Integration Grant No. PCIG12-GA-2012-334053, “Investissements
d’Avenir” LabEx PALM (ANR-10-LABX- 0039-PALM), ANR Grants No. ANR-15-CE13-0004-03,
No. ANR-21-CE11-0004-02 and No. ANR-22-CE30-0024, as well as ERC Starting Grant
No. 677532. M.L.’s group belongs to the CNRS consortium AQV. Part of this work was
performed using HPC resources from GENCI–IDRIS (Grants No. 2020-A0090712066 and
No. 2021-A0110712066).
article_number: '228401'
article_processing_charge: No
article_type: original
author:
- first_name: Valerio
full_name: Sorichetti, Valerio
id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b
last_name: Sorichetti
orcid: 0000-0002-9645-6576
- first_name: Martin
full_name: Lenz, Martin
last_name: Lenz
citation:
ama: Sorichetti V, Lenz M. Transverse fluctuations control the assembly of semiflexible
filaments. Physical Review Letters. 2023;131(22). doi:10.1103/PhysRevLett.131.228401
apa: Sorichetti, V., & Lenz, M. (2023). Transverse fluctuations control the
assembly of semiflexible filaments. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/PhysRevLett.131.228401
chicago: Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control
the Assembly of Semiflexible Filaments.” Physical Review Letters. American
Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.131.228401.
ieee: V. Sorichetti and M. Lenz, “Transverse fluctuations control the assembly of
semiflexible filaments,” Physical Review Letters, vol. 131, no. 22. American
Physical Society, 2023.
ista: Sorichetti V, Lenz M. 2023. Transverse fluctuations control the assembly of
semiflexible filaments. Physical Review Letters. 131(22), 228401.
mla: Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the
Assembly of Semiflexible Filaments.” Physical Review Letters, vol. 131,
no. 22, 228401, American Physical Society, 2023, doi:10.1103/PhysRevLett.131.228401.
short: V. Sorichetti, M. Lenz, Physical Review Letters 131 (2023).
date_created: 2023-12-10T23:00:57Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2023-12-11T07:59:25Z
day: '01'
department:
- _id: AnSa
doi: 10.1103/PhysRevLett.131.228401
external_id:
arxiv:
- '2303.03088'
intvolume: ' 131'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2303.03088
month: '12'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transverse fluctuations control the assembly of semiflexible filaments
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2023'
...
---
_id: '14660'
abstract:
- lang: eng
text: "The classical Steinitz theorem states that if the origin belongs to the interior
of the convex hull of a set \U0001D446⊂ℝ\U0001D451, then there are at most 2\U0001D451
points of \U0001D446 whose convex hull contains the origin in the interior. Bárány,
Katchalski,and Pach proved the following quantitative version of Steinitz’s theorem.
Let \U0001D444 be a convex polytope in ℝ\U0001D451 containing the standard Euclidean
unit ball \U0001D401\U0001D451. Then there exist at most 2\U0001D451 vertices
of \U0001D444 whose convex hull \U0001D444′ satisfies \U0001D45F\U0001D401\U0001D451⊂\U0001D444′
with \U0001D45F⩾\U0001D451−2\U0001D451. They conjectured that \U0001D45F⩾\U0001D450\U0001D451−1∕2
holds with a universal constant \U0001D450>0. We prove \U0001D45F⩾15\U0001D4512,
the first polynomial lower bound on \U0001D45F. Furthermore, we show that \U0001D45F
is not greater than 2/√\U0001D451."
acknowledgement: M.N. was supported by the János Bolyai Scholarship of the Hungarian
Academy of Sciences aswell as the National Research, Development and Innovation
Fund (NRDI) grants K119670 andK131529, and the ÚNKP-22-5 New National Excellence
Program of the Ministry for Innovationand Technology from the source of the NRDI
as well as the ELTE TKP 2021-NKTA-62 fundingscheme
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Grigory
full_name: Ivanov, Grigory
id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E
last_name: Ivanov
- first_name: Márton
full_name: Naszódi, Márton
last_name: Naszódi
citation:
ama: 'Ivanov G, Naszódi M. Quantitative Steinitz theorem: A polynomial bound. Bulletin
of the London Mathematical Society. 2023. doi:10.1112/blms.12965'
apa: 'Ivanov, G., & Naszódi, M. (2023). Quantitative Steinitz theorem: A polynomial
bound. Bulletin of the London Mathematical Society. London Mathematical
Society. https://doi.org/10.1112/blms.12965'
chicago: 'Ivanov, Grigory, and Márton Naszódi. “Quantitative Steinitz Theorem: A
Polynomial Bound.” Bulletin of the London Mathematical Society. London
Mathematical Society, 2023. https://doi.org/10.1112/blms.12965.'
ieee: 'G. Ivanov and M. Naszódi, “Quantitative Steinitz theorem: A polynomial bound,”
Bulletin of the London Mathematical Society. London Mathematical Society,
2023.'
ista: 'Ivanov G, Naszódi M. 2023. Quantitative Steinitz theorem: A polynomial bound.
Bulletin of the London Mathematical Society.'
mla: 'Ivanov, Grigory, and Márton Naszódi. “Quantitative Steinitz Theorem: A Polynomial
Bound.” Bulletin of the London Mathematical Society, London Mathematical
Society, 2023, doi:10.1112/blms.12965.'
short: G. Ivanov, M. Naszódi, Bulletin of the London Mathematical Society (2023).
date_created: 2023-12-10T23:00:58Z
date_published: 2023-12-04T00:00:00Z
date_updated: 2023-12-11T10:03:54Z
day: '04'
department:
- _id: UlWa
doi: 10.1112/blms.12965
external_id:
arxiv:
- '2212.04308'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.1112/blms.12965'
month: '12'
oa: 1
oa_version: Published Version
publication: Bulletin of the London Mathematical Society
publication_identifier:
eissn:
- 1469-2120
issn:
- 0024-6093
publication_status: epub_ahead
publisher: London Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Quantitative Steinitz theorem: A polynomial bound'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14666'
abstract:
- lang: eng
text: So-called spontaneous activity is a central hallmark of most nervous systems.
Such non-causal firing is contrary to the tenet of spikes as a means of communication,
and its purpose remains unclear. We propose that self-initiated firing can serve
as a release valve to protect neurons from the toxic conditions arising in mitochondria
from lower-than-baseline energy consumption. To demonstrate the viability of our
hypothesis, we built a set of models that incorporate recent experimental results
indicating homeostatic control of metabolic products—Adenosine triphosphate (ATP),
adenosine diphosphate (ADP), and reactive oxygen species (ROS)—by changes in firing.
We explore the relationship of metabolic cost of spiking with its effect on the
temporal patterning of spikes and reproduce experimentally observed changes in
intrinsic firing in the fruitfly dorsal fan-shaped body neuron in a model with
ROS-modulated potassium channels. We also show that metabolic spiking homeostasis
can produce indefinitely sustained avalanche dynamics in cortical circuits. Our
theory can account for key features of neuronal activity observed in many studies
ranging from ion channel function all the way to resting state dynamics. We finish
with a set of experimental predictions that would confirm an integrated, crucial
role for metabolically regulated spiking and firmly link metabolic homeostasis
and neuronal function.
acknowledgement: We thank Prof. C. Nazaret and Prof. J.-P. Mazat for sharing the code
of their mitochondrial model. We also thank G. Miesenböck, E. Marder, L. Abbott,
A. Kempf, P. Hasenhuetl, W. Podlaski, F. Zenke, E. Agnes, P. Bozelos, J. Watson,
B. Confavreux, and G. Christodoulou, and the rest of the Vogels Lab for their feedback.
This work was funded by Wellcome Trust and Royal Society Sir Henry Dale Research
Fellowship (WT100000), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z),
and a UK Research and Innovation, Biotechnology and Biological Sciences Research
Council grant (UKRI-BBSRC BB/N019512/1).
article_number: e2306525120
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Chaitanya
full_name: Chintaluri, Chaitanya
id: E4EDB536-3485-11EA-98D2-20AF3DDC885E
last_name: Chintaluri
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Chintaluri C, Vogels TP. Metabolically regulated spiking could serve neuronal
energy homeostasis and protect from reactive oxygen species. Proceedings of
the National Academy of Sciences of the United States of America. 2023;120(48).
doi:10.1073/pnas.2306525120
apa: Chintaluri, C., & Vogels, T. P. (2023). Metabolically regulated spiking
could serve neuronal energy homeostasis and protect from reactive oxygen species.
Proceedings of the National Academy of Sciences of the United States of America.
National Academy of Sciences. https://doi.org/10.1073/pnas.2306525120
chicago: Chintaluri, Chaitanya, and Tim P Vogels. “Metabolically Regulated Spiking
Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.”
Proceedings of the National Academy of Sciences of the United States of America.
National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2306525120.
ieee: C. Chintaluri and T. P. Vogels, “Metabolically regulated spiking could serve
neuronal energy homeostasis and protect from reactive oxygen species,” Proceedings
of the National Academy of Sciences of the United States of America, vol.
120, no. 48. National Academy of Sciences, 2023.
ista: Chintaluri C, Vogels TP. 2023. Metabolically regulated spiking could serve
neuronal energy homeostasis and protect from reactive oxygen species. Proceedings
of the National Academy of Sciences of the United States of America. 120(48),
e2306525120.
mla: Chintaluri, Chaitanya, and Tim P. Vogels. “Metabolically Regulated Spiking
Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 120, no. 48, e2306525120, National Academy of Sciences, 2023, doi:10.1073/pnas.2306525120.
short: C. Chintaluri, T.P. Vogels, Proceedings of the National Academy of Sciences
of the United States of America 120 (2023).
date_created: 2023-12-10T23:01:00Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2023-12-11T12:47:41Z
day: '21'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1073/pnas.2306525120
external_id:
pmid:
- '37988463'
file:
- access_level: open_access
checksum: bf4ec38602a70dae4338077a5a4d497f
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T12:45:12Z
date_updated: 2023-12-11T12:45:12Z
file_id: '14678'
file_name: 2023_PNAS_Chintaluri.pdf
file_size: 16891602
relation: main_file
success: 1
file_date_updated: 2023-12-11T12:45:12Z
has_accepted_license: '1'
intvolume: ' 120'
issue: '48'
language:
- iso: eng
month: '11'
oa: 1
oa_version: None
pmid: 1
project:
- _id: c084a126-5a5b-11eb-8a69-d75314a70a87
grant_number: 214316/Z/18/Z
name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent
neuronal networks.
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/ccluri/metabolic_spiking
scopus_import: '1'
status: public
title: Metabolically regulated spiking could serve neuronal energy homeostasis and
protect from reactive oxygen species
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 120
year: '2023'
...
---
_id: '14656'
abstract:
- lang: eng
text: Although much is known about how single neurons in the hippocampus represent
an animal's position, how circuit interactions contribute to spatial coding is
less well understood. Using a novel statistical estimator and theoretical modeling,
both developed in the framework of maximum entropy models, we reveal highly structured
CA1 cell-cell interactions in male rats during open field exploration. The statistics
of these interactions depend on whether the animal is in a familiar or novel environment.
In both conditions the circuit interactions optimize the encoding of spatial information,
but for regimes that differ in the informativeness of their spatial inputs. This
structure facilitates linear decodability, making the information easy to read
out by downstream circuits. Overall, our findings suggest that the efficient coding
hypothesis is not only applicable to individual neuron properties in the sensory
periphery, but also to neural interactions in the central brain.
acknowledgement: M.N. was supported by the European Union Horizon 2020 Grant 665385.
J.C. was supported by the European Research Council Consolidator Grant 281511. G.T.
was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported
by an Institute of Science and Technology fellow award and by the National Science
Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and
Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella,
Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi,
Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
citation:
ama: Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1
interactions optimizes spatial coding across experience. The Journal of Neuroscience.
2023;43(48):8140-8156. doi:10.1523/JNEUROSCI.0194-23.2023
apa: Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (2023). The structure
of hippocampal CA1 interactions optimizes spatial coding across experience. The
Journal of Neuroscience. Society of Neuroscience. https://doi.org/10.1523/JNEUROSCI.0194-23.2023
chicago: Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin.
“The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across
Experience.” The Journal of Neuroscience. Society of Neuroscience, 2023.
https://doi.org/10.1523/JNEUROSCI.0194-23.2023.
ieee: M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal
CA1 interactions optimizes spatial coding across experience,” The Journal of
Neuroscience, vol. 43, no. 48. Society of Neuroscience, pp. 8140–8156, 2023.
ista: Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal
CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience.
43(48), 8140–8156.
mla: Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes
Spatial Coding across Experience.” The Journal of Neuroscience, vol. 43,
no. 48, Society of Neuroscience, 2023, pp. 8140–56, doi:10.1523/JNEUROSCI.0194-23.2023.
short: M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience
43 (2023) 8140–8156.
date_created: 2023-12-10T23:00:58Z
date_published: 2023-11-29T00:00:00Z
date_updated: 2023-12-11T11:37:20Z
day: '29'
ddc:
- '570'
department:
- _id: JoCs
- _id: GaTk
doi: 10.1523/JNEUROSCI.0194-23.2023
ec_funded: 1
external_id:
pmid:
- '37758476'
file:
- access_level: closed
checksum: e2503c8f84be1050e28f64320f1d5bd2
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T11:30:37Z
date_updated: 2023-12-11T11:30:37Z
embargo: 2024-06-01
embargo_to: open_access
file_id: '14674'
file_name: 2023_JourNeuroscience_Nardin.pdf
file_size: 2280632
relation: main_file
file_date_updated: 2023-12-11T11:30:37Z
has_accepted_license: '1'
intvolume: ' 43'
issue: '48'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1523/JNEUROSCI.0194-23.2023
month: '11'
oa: 1
oa_version: Published Version
page: 8140-8156
pmid: 1
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: The Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
publication_status: published
publisher: Society of Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: The structure of hippocampal CA1 interactions optimizes spatial coding across
experience
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: 43
year: '2023'
...
---
_id: '14657'
abstract:
- lang: eng
text: 'Natural selection is usually studied between mutants that differ in reproductive
rate, but are subject to the same population structure. Here we explore how natural
selection acts on mutants that have the same reproductive rate, but different
population structures. In our framework, population structure is given by a graph
that specifies where offspring can disperse. The invading mutant disperses offspring
on a different graph than the resident wild-type. We find that more densely connected
dispersal graphs tend to increase the invader’s fixation probability, but the
exact relationship between structure and fixation probability is subtle. We present
three main results. First, we prove that if both invader and resident are on complete
dispersal graphs, then removing a single edge in the invader’s dispersal graph
reduces its fixation probability. Second, we show that for certain island models
higher invader’s connectivity increases its fixation probability, but the magnitude
of the effect depends on the exact layout of the connections. Third, we show that
for lattices the effect of different connectivity is comparable to that of different
fitness: for large population size, the invader’s fixation probability is either
constant or exponentially small, depending on whether it is more or less connected
than the resident.'
acknowledgement: K.C. acknowledges support from the ERC CoG 863818(ForM-SMArt). J.T.
is supported by Center for Foundations ofModern Computer Science (Charles Univ.
project UNCE/SCI/004).
article_number: '20230355'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Kamran
full_name: Kaveh, Kamran
last_name: Kaveh
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin A.
full_name: Nowak, Martin A.
last_name: Nowak
citation:
ama: Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. Evolutionary dynamics of mutants
that modify population structure. Journal of the Royal Society, Interface.
2023;20(208). doi:10.1098/rsif.2023.0355
apa: Tkadlec, J., Kaveh, K., Chatterjee, K., & Nowak, M. A. (2023). Evolutionary
dynamics of mutants that modify population structure. Journal of the Royal
Society, Interface. The Royal Society. https://doi.org/10.1098/rsif.2023.0355
chicago: Tkadlec, Josef, Kamran Kaveh, Krishnendu Chatterjee, and Martin A. Nowak.
“Evolutionary Dynamics of Mutants That Modify Population Structure.” Journal
of the Royal Society, Interface. The Royal Society, 2023. https://doi.org/10.1098/rsif.2023.0355.
ieee: J. Tkadlec, K. Kaveh, K. Chatterjee, and M. A. Nowak, “Evolutionary dynamics
of mutants that modify population structure,” Journal of the Royal Society,
Interface, vol. 20, no. 208. The Royal Society, 2023.
ista: Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. 2023. Evolutionary dynamics of
mutants that modify population structure. Journal of the Royal Society, Interface.
20(208), 20230355.
mla: Tkadlec, Josef, et al. “Evolutionary Dynamics of Mutants That Modify Population
Structure.” Journal of the Royal Society, Interface, vol. 20, no. 208,
20230355, The Royal Society, 2023, doi:10.1098/rsif.2023.0355.
short: J. Tkadlec, K. Kaveh, K. Chatterjee, M.A. Nowak, Journal of the Royal Society,
Interface 20 (2023).
date_created: 2023-12-10T23:00:58Z
date_published: 2023-11-29T00:00:00Z
date_updated: 2023-12-11T11:17:53Z
day: '29'
ddc:
- '000'
- '570'
department:
- _id: KrCh
doi: 10.1098/rsif.2023.0355
ec_funded: 1
external_id:
pmid:
- '38016637'
file:
- access_level: open_access
checksum: 2eefab13127c7786dbd33303c482a004
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T11:10:32Z
date_updated: 2023-12-11T11:10:32Z
file_id: '14673'
file_name: 2023_RoyalInterface_Tkadlec.pdf
file_size: 1720243
relation: main_file
success: 1
file_date_updated: 2023-12-11T11:10:32Z
has_accepted_license: '1'
intvolume: ' 20'
issue: '208'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Journal of the Royal Society, Interface
publication_identifier:
eissn:
- 1742-5662
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionary dynamics of mutants that modify population structure
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: 20
year: '2023'
...
---
_id: '14664'
abstract:
- lang: eng
text: The architecture of self-assembled host molecules can profoundly affect the
properties of the encapsulated guests. For example, a rigid cage with small windows
can efficiently protect its contents from the environment; in contrast, tube-shaped,
flexible hosts with large openings and an easily accessible cavity are ideally
suited for catalysis. Here, we report a “Janus” nature of a Pd6L4 coordination
host previously reported to exist exclusively as a tube isomer (T). We show that
upon encapsulating various tetrahedrally shaped guests, T can reconfigure into
a cage-shaped host (C) in quantitative yield. Extracting the guest affords empty
C, which is metastable and spontaneously relaxes to T, and the T⇄C interconversion
can be repeated for multiple cycles. Reversible toggling between two vastly different
isomers paves the way toward controlling functional properties of coordination
hosts “on demand”.
acknowledgement: We acknowledge funding from the European Union’s Horizon 2020 Research
and Innovation Program under the European Research Council (grant agreement 820008).We
also thank the Deutsche Forschungsgemeinschaft (DFG) for support through priority
program SPP1807(CL489/3-2) and RESOLV Cluster of Excellence EXC2033 (project number
390677874). A.B.G. acknowledges funding from the Zuckerman STEM Leadership Program.
DFT calculations were carried out using resources provided by the Wrocław Center
for Networking and Supercomputing, grant 329.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Kuntrapakam
full_name: Hema, Kuntrapakam
last_name: Hema
- first_name: Angela B.
full_name: Grommet, Angela B.
last_name: Grommet
- first_name: Michał J.
full_name: Białek, Michał J.
last_name: Białek
- first_name: Jinhua
full_name: Wang, Jinhua
last_name: Wang
- first_name: Laura
full_name: Schneider, Laura
last_name: Schneider
- first_name: Christoph
full_name: Drechsler, Christoph
last_name: Drechsler
- first_name: Oksana
full_name: Yanshyna, Oksana
last_name: Yanshyna
- first_name: Yael
full_name: Diskin-Posner, Yael
last_name: Diskin-Posner
- first_name: Guido H.
full_name: Clever, Guido H.
last_name: Clever
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Hema K, Grommet AB, Białek MJ, et al. Guest encapsulation alters the thermodynamic
landscape of a coordination host. Journal of the American Chemical Society.
2023;145(45):24755-24764. doi:10.1021/jacs.3c08666
apa: Hema, K., Grommet, A. B., Białek, M. J., Wang, J., Schneider, L., Drechsler,
C., … Klajn, R. (2023). Guest encapsulation alters the thermodynamic landscape
of a coordination host. Journal of the American Chemical Society. American
Chemical Society. https://doi.org/10.1021/jacs.3c08666
chicago: Hema, Kuntrapakam, Angela B. Grommet, Michał J. Białek, Jinhua Wang, Laura
Schneider, Christoph Drechsler, Oksana Yanshyna, Yael Diskin-Posner, Guido H.
Clever, and Rafal Klajn. “Guest Encapsulation Alters the Thermodynamic Landscape
of a Coordination Host.” Journal of the American Chemical Society. American
Chemical Society, 2023. https://doi.org/10.1021/jacs.3c08666.
ieee: K. Hema et al., “Guest encapsulation alters the thermodynamic landscape
of a coordination host,” Journal of the American Chemical Society, vol.
145, no. 45. American Chemical Society, pp. 24755–24764, 2023.
ista: Hema K, Grommet AB, Białek MJ, Wang J, Schneider L, Drechsler C, Yanshyna
O, Diskin-Posner Y, Clever GH, Klajn R. 2023. Guest encapsulation alters the thermodynamic
landscape of a coordination host. Journal of the American Chemical Society. 145(45),
24755–24764.
mla: Hema, Kuntrapakam, et al. “Guest Encapsulation Alters the Thermodynamic Landscape
of a Coordination Host.” Journal of the American Chemical Society, vol.
145, no. 45, American Chemical Society, 2023, pp. 24755–64, doi:10.1021/jacs.3c08666.
short: K. Hema, A.B. Grommet, M.J. Białek, J. Wang, L. Schneider, C. Drechsler,
O. Yanshyna, Y. Diskin-Posner, G.H. Clever, R. Klajn, Journal of the American
Chemical Society 145 (2023) 24755–24764.
date_created: 2023-12-10T23:00:59Z
date_published: 2023-11-02T00:00:00Z
date_updated: 2023-12-11T11:47:07Z
day: '02'
ddc:
- '540'
department:
- _id: RaKl
doi: 10.1021/jacs.3c08666
external_id:
pmid:
- '37917939'
file:
- access_level: open_access
checksum: a1f37df6b83f88f51ba64468ce0c1589
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T11:44:54Z
date_updated: 2023-12-11T11:44:54Z
file_id: '14675'
file_name: 2023_JACS_Hema.pdf
file_size: 4304472
relation: main_file
success: 1
file_date_updated: 2023-12-11T11:44:54Z
has_accepted_license: '1'
intvolume: ' 145'
issue: '45'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 24755-24764
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Guest encapsulation alters the thermodynamic landscape of a coordination host
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: 145
year: '2023'
...
---
_id: '14663'
abstract:
- lang: eng
text: As a bottleneck in the direct synthesis of hydrogen peroxide, the development
of an efficient palladium-based catalyst has garnered great attention. However,
elusive active centers and reaction mechanism issues inhibit further optimization
of its performance. In this work, advanced microkinetic modeling with the adsorbate–adsorbate
interaction and nanoparticle size effect based on first-principles calculations
is developed. A full mechanism uncovering the significance of adsorbate–adsorbate
interaction is determined on Pd nanoparticles. We demonstrate unambiguously that
Pd(100) with main coverage species of O2 and H is beneficial to H2O2 production,
being consistent with experimental operando observation, while H2O forms on Pd(111)
covered by O species and Pd(211) covered by O and OH species. Kinetic analyses
further enable quantitative estimation of the influence of temperature, pressure,
and particle size. Large-size Pd nanoparticles are found to achieve a high H2O2
reaction rate when the operating conditions are moderate temperature and higher
oxygen partial pressure. We reveal that specific facets of the Pd nanoparticles
are crucial factors for their selectivity and activity. Consistent with the experiment,
the production of H2O2 is discovered to be more favorable on Pd nanoparticles
containing Pd(100) facets. The ratio of H2/O2 induces substantial variations in
the coverage of intermediates of O2 and H on Pd(100), resulting in a change in
product selectivity.
acknowledgement: The authors acknowledge the financial support from the National Natural
Science Foundation of China (22008211, 92045303, U21A20298), the National Key Research
and Development Project of China (2021YFA1500900, 2022YFE0113800), and Zhejiang
Innovation Team (2017R5203).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jinyan
full_name: Zhao, Jinyan
last_name: Zhao
- first_name: Zihao
full_name: Yao, Zihao
last_name: Yao
- first_name: Rhys
full_name: Bunting, Rhys
id: 91deeae8-1207-11ec-b130-c194ad5b50c6
last_name: Bunting
orcid: 0000-0001-6928-074X
- first_name: P.
full_name: Hu, P.
last_name: Hu
- first_name: Jianguo
full_name: Wang, Jianguo
last_name: Wang
citation:
ama: Zhao J, Yao Z, Bunting R, Hu P, Wang J. Microkinetic modeling with size-dependent
and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd
nanoparticles. ACS Catalysis. 2023;13(22):15054-15073. doi:10.1021/acscatal.3c03893
apa: Zhao, J., Yao, Z., Bunting, R., Hu, P., & Wang, J. (2023). Microkinetic
modeling with size-dependent and adsorbate-adsorbate interactions for the direct
synthesis of H₂O₂ over Pd nanoparticles. ACS Catalysis. American Chemical
Society. https://doi.org/10.1021/acscatal.3c03893
chicago: Zhao, Jinyan, Zihao Yao, Rhys Bunting, P. Hu, and Jianguo Wang. “Microkinetic
Modeling with Size-Dependent and Adsorbate-Adsorbate Interactions for the Direct
Synthesis of H₂O₂ over Pd Nanoparticles.” ACS Catalysis. American Chemical
Society, 2023. https://doi.org/10.1021/acscatal.3c03893.
ieee: J. Zhao, Z. Yao, R. Bunting, P. Hu, and J. Wang, “Microkinetic modeling with
size-dependent and adsorbate-adsorbate interactions for the direct synthesis of
H₂O₂ over Pd nanoparticles,” ACS Catalysis, vol. 13, no. 22. American Chemical
Society, pp. 15054–15073, 2023.
ista: Zhao J, Yao Z, Bunting R, Hu P, Wang J. 2023. Microkinetic modeling with size-dependent
and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd
nanoparticles. ACS Catalysis. 13(22), 15054–15073.
mla: Zhao, Jinyan, et al. “Microkinetic Modeling with Size-Dependent and Adsorbate-Adsorbate
Interactions for the Direct Synthesis of H₂O₂ over Pd Nanoparticles.” ACS Catalysis,
vol. 13, no. 22, American Chemical Society, 2023, pp. 15054–73, doi:10.1021/acscatal.3c03893.
short: J. Zhao, Z. Yao, R. Bunting, P. Hu, J. Wang, ACS Catalysis 13 (2023) 15054–15073.
date_created: 2023-12-10T23:00:59Z
date_published: 2023-11-06T00:00:00Z
date_updated: 2023-12-11T11:55:35Z
day: '06'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1021/acscatal.3c03893
file:
- access_level: open_access
checksum: a97c771077af71ddfb2249e34530895c
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T11:55:09Z
date_updated: 2023-12-11T11:55:09Z
file_id: '14676'
file_name: 2023_ACSCatalysis_.pdf
file_size: 14813812
relation: main_file
success: 1
file_date_updated: 2023-12-11T11:55:09Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '22'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 15054-15073
publication: ACS Catalysis
publication_identifier:
eissn:
- 2155-5435
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions
for the direct synthesis of H₂O₂ over Pd nanoparticles
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: 13
year: '2023'
...
---
_id: '14667'
abstract:
- lang: eng
text: 'For large dimensional non-Hermitian random matrices X with real or complex
independent, identically distributed, centered entries, we consider the fluctuations
of f (X) as a matrix where f is an analytic function around the spectrum of X.
We prove that for a generic bounded square matrix A, the quantity Tr f (X)A exhibits
Gaussian fluctuations as the matrix size grows to infinity, which consists of
two independent modes corresponding to the tracial and traceless parts of A. We
find a new formula for the variance of the traceless part that involves the Frobenius
norm of A and the L2-norm of f on the boundary of the limiting spectrum. '
- lang: fre
text: On étudie les fluctuations de f (X), où X est une matrice aléatoire non-hermitienne
de grande taille à coefficients i.i.d. (réels ou complexes), et f une fonction
analytique sur un domaine qui contient le spectre de X. On prouve que, pour une
matrice carrée générique et bornée A, les fluctuations de la quantité tr f (X)A
sont asymptotiquement gaussiennes et comportent deux modes indépendants, correspondant
aux composantes traciale et de trace nulle de A. Une nouvelle formule est établie
pour la variance de la composante de trace nulle, qui fait intervenir la norme
de Frobenius de A et la norme L2 de f sur la frontière du spectre limite.
acknowledgement: "The first author was partially supported by ERC Advanced Grant “RMTBeyond”
No. 101020331. The second author was supported by ERC Advanced Grant “RMTBeyond”
No. 101020331.\r\nThe authors are grateful to the anonymous referees and associated
editor for carefully reading this paper and providing helpful comments that improved
the quality of the article. Also the authors would like to thank Peter Forrester
for pointing out the reference [12] that was absent in the previous version of the
manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Hong Chang
full_name: Ji, Hong Chang
id: dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d
last_name: Ji
citation:
ama: Erdös L, Ji HC. Functional CLT for non-Hermitian random matrices. Annales
de l’institut Henri Poincare (B) Probability and Statistics. 2023;59(4):2083-2105.
doi:10.1214/22-AIHP1304
apa: Erdös, L., & Ji, H. C. (2023). Functional CLT for non-Hermitian random
matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics.
Institute of Mathematical Statistics. https://doi.org/10.1214/22-AIHP1304
chicago: Erdös, László, and Hong Chang Ji. “Functional CLT for Non-Hermitian Random
Matrices.” Annales de l’institut Henri Poincare (B) Probability and Statistics.
Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/22-AIHP1304.
ieee: L. Erdös and H. C. Ji, “Functional CLT for non-Hermitian random matrices,”
Annales de l’institut Henri Poincare (B) Probability and Statistics, vol.
59, no. 4. Institute of Mathematical Statistics, pp. 2083–2105, 2023.
ista: Erdös L, Ji HC. 2023. Functional CLT for non-Hermitian random matrices. Annales
de l’institut Henri Poincare (B) Probability and Statistics. 59(4), 2083–2105.
mla: Erdös, László, and Hong Chang Ji. “Functional CLT for Non-Hermitian Random
Matrices.” Annales de l’institut Henri Poincare (B) Probability and Statistics,
vol. 59, no. 4, Institute of Mathematical Statistics, 2023, pp. 2083–105, doi:10.1214/22-AIHP1304.
short: L. Erdös, H.C. Ji, Annales de l’institut Henri Poincare (B) Probability and
Statistics 59 (2023) 2083–2105.
date_created: 2023-12-10T23:01:00Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2023-12-11T12:36:56Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/22-AIHP1304
ec_funded: 1
external_id:
arxiv:
- '2112.11382'
intvolume: ' 59'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2112.11382
month: '11'
oa: 1
oa_version: Preprint
page: 2083-2105
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Annales de l'institut Henri Poincare (B) Probability and Statistics
publication_identifier:
issn:
- 0246-0203
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Functional CLT for non-Hermitian random matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 59
year: '2023'
...
---
_id: '14662'
abstract:
- lang: eng
text: "We consider a class of polaron models, including the Fröhlich model, at zero
total\r\nmomentum, and show that at sufficiently weak coupling there are no excited
eigenvalues below\r\nthe essential spectrum."
article_processing_charge: Yes
article_type: original
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Seiringer R. Absence of excited eigenvalues for Fröhlich type polaron models
at weak coupling. Journal of Spectral Theory. 2023;13(3):1045-1055. doi:10.4171/JST/469
apa: Seiringer, R. (2023). Absence of excited eigenvalues for Fröhlich type polaron
models at weak coupling. Journal of Spectral Theory. EMS Press. https://doi.org/10.4171/JST/469
chicago: Seiringer, Robert. “Absence of Excited Eigenvalues for Fröhlich Type Polaron
Models at Weak Coupling.” Journal of Spectral Theory. EMS Press, 2023.
https://doi.org/10.4171/JST/469.
ieee: R. Seiringer, “Absence of excited eigenvalues for Fröhlich type polaron models
at weak coupling,” Journal of Spectral Theory, vol. 13, no. 3. EMS Press,
pp. 1045–1055, 2023.
ista: Seiringer R. 2023. Absence of excited eigenvalues for Fröhlich type polaron
models at weak coupling. Journal of Spectral Theory. 13(3), 1045–1055.
mla: Seiringer, Robert. “Absence of Excited Eigenvalues for Fröhlich Type Polaron
Models at Weak Coupling.” Journal of Spectral Theory, vol. 13, no. 3, EMS
Press, 2023, pp. 1045–55, doi:10.4171/JST/469.
short: R. Seiringer, Journal of Spectral Theory 13 (2023) 1045–1055.
date_created: 2023-12-10T23:00:59Z
date_published: 2023-11-25T00:00:00Z
date_updated: 2023-12-11T12:12:14Z
day: '25'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.4171/JST/469
external_id:
arxiv:
- '2210.17123'
file:
- access_level: open_access
checksum: 9ce96ca87d56ea9a70d2eb9a32839f8d
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T12:03:12Z
date_updated: 2023-12-11T12:03:12Z
file_id: '14677'
file_name: 2023_JST_Seiringer.pdf
file_size: 201513
relation: main_file
success: 1
file_date_updated: 2023-12-11T12:03:12Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '3'
language:
- iso: eng
month: '11'
oa: 1
oa_version: None
page: 1045-1055
publication: Journal of Spectral Theory
publication_identifier:
eissn:
- 1664-0403
issn:
- 1664-039X
publication_status: published
publisher: EMS Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling
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: 13
year: '2023'
...
---
_id: '14652'
abstract:
- lang: eng
text: In order to demonstrate the stability of newly proposed iridium-based Ir2Cr(In,Sn)
and IrRhCr(In,Sn) heusler alloys, we present ab-initio analysis of these alloys
by examining various properties to prove their stability. The stability of these
alloys can be inferred from different cohesive and formation energies as well
as positive phonon frequencies. Their electronic structure results indicate that
they are semi-metals in nature. The magnetic moments are computed using the Slater-Pauling
formula and exhibit a high value, with the Cr atom contributing the most in all
alloys. Mulliken’s charge analysis results show that our alloys contain a range
of linkages, mainly ionic and covalent ones. The ductility and mechanical stability
of these alloys are confirmed by elastic constants viz. Poisson’s ratio, Pugh’s
ratio, and many different types of elastic moduli.
article_number: '415539'
article_processing_charge: No
article_type: original
author:
- first_name: Shyam Lal
full_name: Gupta, Shyam Lal
last_name: Gupta
- first_name: Saurabh
full_name: Singh, Saurabh
id: 12d625da-9cb3-11ed-9667-af09d37d3f0a
last_name: Singh
orcid: 0000-0003-2209-5269
- first_name: Sumit
full_name: Kumar, Sumit
last_name: Kumar
- first_name: Unknown
full_name: Anupam, Unknown
last_name: Anupam
- first_name: Samjeet Singh
full_name: Thakur, Samjeet Singh
last_name: Thakur
- first_name: Ashish
full_name: Kumar, Ashish
last_name: Kumar
- first_name: Sanjay
full_name: Panwar, Sanjay
last_name: Panwar
- first_name: D.
full_name: Diwaker, D.
last_name: Diwaker
citation:
ama: 'Gupta SL, Singh S, Kumar S, et al. Ab-initio stability of Iridium based newly
proposed full and quaternary heusler alloys. Physica B: Condensed Matter.
2023;674. doi:10.1016/j.physb.2023.415539'
apa: 'Gupta, S. L., Singh, S., Kumar, S., Anupam, U., Thakur, S. S., Kumar, A.,
… Diwaker, D. (2023). Ab-initio stability of Iridium based newly proposed full
and quaternary heusler alloys. Physica B: Condensed Matter. Elsevier. https://doi.org/10.1016/j.physb.2023.415539'
chicago: 'Gupta, Shyam Lal, Saurabh Singh, Sumit Kumar, Unknown Anupam, Samjeet
Singh Thakur, Ashish Kumar, Sanjay Panwar, and D. Diwaker. “Ab-Initio Stability
of Iridium Based Newly Proposed Full and Quaternary Heusler Alloys.” Physica
B: Condensed Matter. Elsevier, 2023. https://doi.org/10.1016/j.physb.2023.415539.'
ieee: 'S. L. Gupta et al., “Ab-initio stability of Iridium based newly proposed
full and quaternary heusler alloys,” Physica B: Condensed Matter, vol.
674. Elsevier, 2023.'
ista: 'Gupta SL, Singh S, Kumar S, Anupam U, Thakur SS, Kumar A, Panwar S, Diwaker
D. 2023. Ab-initio stability of Iridium based newly proposed full and quaternary
heusler alloys. Physica B: Condensed Matter. 674, 415539.'
mla: 'Gupta, Shyam Lal, et al. “Ab-Initio Stability of Iridium Based Newly Proposed
Full and Quaternary Heusler Alloys.” Physica B: Condensed Matter, vol.
674, 415539, Elsevier, 2023, doi:10.1016/j.physb.2023.415539.'
short: 'S.L. Gupta, S. Singh, S. Kumar, U. Anupam, S.S. Thakur, A. Kumar, S. Panwar,
D. Diwaker, Physica B: Condensed Matter 674 (2023).'
date_created: 2023-12-10T23:00:56Z
date_published: 2023-11-28T00:00:00Z
date_updated: 2023-12-12T08:22:23Z
day: '28'
department:
- _id: MaIb
doi: 10.1016/j.physb.2023.415539
intvolume: ' 674'
language:
- iso: eng
month: '11'
oa_version: None
publication: 'Physica B: Condensed Matter'
publication_identifier:
issn:
- 0921-4526
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ab-initio stability of Iridium based newly proposed full and quaternary heusler
alloys
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 674
year: '2023'
...
---
_id: '12487'
abstract:
- lang: eng
text: Sleep plays a key role in preserving brain function, keeping the brain network
in a state that ensures optimal computational capabilities. Empirical evidence
indicates that such a state is consistent with criticality, where scale-free neuronal
avalanches emerge. However, the relationship between sleep, emergent avalanches,
and criticality remains poorly understood. Here we fully characterize the critical
behavior of avalanches during sleep, and study their relationship with the sleep
macro- and micro-architecture, in particular the cyclic alternating pattern (CAP).
We show that avalanche size and duration distributions exhibit robust power laws
with exponents approximately equal to −3/2 e −2, respectively. Importantly, we
find that sizes scale as a power law of the durations, and that all critical exponents
for neuronal avalanches obey robust scaling relations, which are consistent with
the mean-field directed percolation universality class. Our analysis demonstrates
that avalanche dynamics depends on the position within the NREM-REM cycles, with
the avalanche density increasing in the descending phases and decreasing in the
ascending phases of sleep cycles. Moreover, we show that, within NREM sleep, avalanche
occurrence correlates with CAP activation phases, particularly A1, which are the
expression of slow wave sleep propensity and have been proposed to be beneficial
for cognitive processes. The results suggest that neuronal avalanches, and thus
tuning to criticality, actively contribute to sleep development and play a role
in preserving network function. Such findings, alongside characterization of the
universality class for avalanches, open new avenues to the investigation of functional
role of criticality during sleep with potential clinical application.Significance
statementWe fully characterize the critical behavior of neuronal
avalanches during sleep, and show that avalanches follow precise scaling laws
that are consistent with the mean-field directed percolation universality class.
The analysis provides first evidence of a functional relationship between avalanche
occurrence, slow-wave sleep dynamics, sleep stage transitions and occurrence of
CAP phase A during NREM sleep. Because CAP is considered one of the major guardians
of NREM sleep that allows the brain to dynamically react to external perturbation
and contributes to the cognitive consolidation processes occurring in sleep, our
observations suggest that neuronal avalanches at criticality are associated with
flexible response to external inputs and to cognitive processes, a key assumption
of the critical brain hypothesis.
acknowledgement: FL acknowledges support from the European Union’s Horizon 2020 research
and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411,
and from the Austrian Science Fund (FWF) under the Lise Meitner fellowship No. PT1013M03318.
IA acknowledges financial support from the MIUR PRIN 2017WZFTZP.
article_processing_charge: Yes
article_type: original
author:
- first_name: Silvia
full_name: Scarpetta, Silvia
last_name: Scarpetta
- first_name: Niccolò
full_name: Morrisi, Niccolò
last_name: Morrisi
- first_name: Carlotta
full_name: Mutti, Carlotta
last_name: Mutti
- first_name: Nicoletta
full_name: Azzi, Nicoletta
last_name: Azzi
- first_name: Irene
full_name: Trippi, Irene
last_name: Trippi
- first_name: Rosario
full_name: Ciliento, Rosario
last_name: Ciliento
- first_name: Ilenia
full_name: Apicella, Ilenia
last_name: Apicella
- first_name: Giovanni
full_name: Messuti, Giovanni
last_name: Messuti
- first_name: Marianna
full_name: Angiolelli, Marianna
last_name: Angiolelli
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Liborio
full_name: Parrino, Liborio
last_name: Parrino
- first_name: Anna Elisabetta
full_name: Vaudano, Anna Elisabetta
last_name: Vaudano
citation:
ama: Scarpetta S, Morrisi N, Mutti C, et al. Criticality of neuronal avalanches
in human sleep and their relationship with sleep macro- and micro-architecture.
iScience. 2023;26(10):107840. doi:10.1016/j.isci.2023.107840
apa: Scarpetta, S., Morrisi, N., Mutti, C., Azzi, N., Trippi, I., Ciliento, R.,
… Vaudano, A. E. (2023). Criticality of neuronal avalanches in human sleep and
their relationship with sleep macro- and micro-architecture. IScience.
Elsevier. https://doi.org/10.1016/j.isci.2023.107840
chicago: Scarpetta, Silvia, Niccolò Morrisi, Carlotta Mutti, Nicoletta Azzi, Irene
Trippi, Rosario Ciliento, Ilenia Apicella, et al. “Criticality of Neuronal Avalanches
in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.”
IScience. Elsevier, 2023. https://doi.org/10.1016/j.isci.2023.107840.
ieee: S. Scarpetta et al., “Criticality of neuronal avalanches in human sleep
and their relationship with sleep macro- and micro-architecture,” iScience,
vol. 26, no. 10. Elsevier, p. 107840, 2023.
ista: Scarpetta S, Morrisi N, Mutti C, Azzi N, Trippi I, Ciliento R, Apicella I,
Messuti G, Angiolelli M, Lombardi F, Parrino L, Vaudano AE. 2023. Criticality
of neuronal avalanches in human sleep and their relationship with sleep macro-
and micro-architecture. iScience. 26(10), 107840.
mla: Scarpetta, Silvia, et al. “Criticality of Neuronal Avalanches in Human Sleep
and Their Relationship with Sleep Macro- and Micro-Architecture.” IScience,
vol. 26, no. 10, Elsevier, 2023, p. 107840, doi:10.1016/j.isci.2023.107840.
short: S. Scarpetta, N. Morrisi, C. Mutti, N. Azzi, I. Trippi, R. Ciliento, I. Apicella,
G. Messuti, M. Angiolelli, F. Lombardi, L. Parrino, A.E. Vaudano, IScience 26
(2023) 107840.
date_created: 2023-02-02T10:50:17Z
date_published: 2023-10-20T00:00:00Z
date_updated: 2023-12-13T11:11:24Z
day: '20'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1016/j.isci.2023.107840
ec_funded: 1
external_id:
isi:
- '001082331200001'
pmid:
- '37766992'
file:
- access_level: open_access
checksum: f499836af172ecc9865de4bb41fa99d1
content_type: application/pdf
creator: dernst
date_created: 2023-10-09T07:23:46Z
date_updated: 2023-10-09T07:23:46Z
file_id: '14412'
file_name: 2023_iScience_Scarpetta.pdf
file_size: 4872708
relation: main_file
success: 1
file_date_updated: 2023-10-09T07:23:46Z
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '107840'
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: eb943429-77a9-11ec-83b8-9f471cdf5c67
grant_number: M03318
name: Functional Advantages of Critical Brain Dynamics
publication: iScience
publication_identifier:
eissn:
- 2589-0042
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Criticality of neuronal avalanches in human sleep and their relationship with
sleep macro- and micro-architecture
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: '12696'
abstract:
- lang: eng
text: "Background: Fighting disease while fighting rivals exposes males to constraints
and tradeoffs during male-male competition. We here tested how both the stage
and intensity of infection with the fungal pathogen Metarhizium robertsii interfered
with fighting success in Cardiocondyla obscurior ant males. Males of this species
have evolved long lifespans during which they can gain many matings with the young
queens of the colony, if successful in male-male competition. Since male fights
occur inside the colony, the outcome of male-male competition can further be biased
by interference of the colony’s worker force.\r\nResults: We found that severe,
but not yet mild, infection strongly impaired male fighting success. In late-stage
infection, this could be attributed to worker aggression directed towards the
infected rather than the healthy male and an already very high male morbidity
even in the absence of fighting. Shortly after pathogen exposure, however, male
mortality was particularly increased during combat. Since these males mounted
a strong immune response, their reduced fighting success suggests a trade-off
between immune investment and competitive ability already early in the infection.
Even if the males themselves showed no difference in the number of attacks they
raised against their healthy rivals across infection stages and levels, severely
infected males were thus losing in male-male competition from an early stage of
infection on.\r\nConclusions: Males of the ant C. obscurior have evolved high
immune investment, triggering an effective immune response very fast after fungal
exposure. This allows them to cope with mild pathogen exposures without cost to
their success in male-male competition, and hence to gain multiple mating opportunities
with the emerging virgin queens of the colony. Under severe infection, however,
they are weak fighters and rarely survive a combat already at early infection
when raising an immune response, as well as at progressed infection, when they
are morbid and preferentially targeted by worker aggression. Workers thereby remove
males that pose a future disease threat by biasing male-male competition. Our
study thus revealed a novel social immunity mechanism how social insect workers
protect the colony against disease risk."
acknowledged_ssus:
- _id: LifeSc
acknowledgement: "We are thankful to Mike Bidochka for the fungal strain, Lukas Schrader
for sharing the C. obscurior genome data for primer development, the Lab Support
Facility of ISTA for general laboratory support and help with the permit approval
procedures, and the Finca El Quinto for letting us collect ants on their property.
We thank the Social Immunity Team at ISTA for help with ant collection and experimental
help, in particular Elina Hanhimäki and Marta Gorecka for behavioural observation,
and Elisabeth Naderlinger for spore load PCRs. We further thank the Social Immunity
Team and Jürgen Heinze for continued discussion and comments on the manuscript.\r\nOpen
access funding provided by Institute of Science and Technology Austria (ISTA). This
project received funding from the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (grant agreement No 771402
to SC). "
article_number: '37'
article_processing_charge: Yes
article_type: original
author:
- first_name: Sina
full_name: Metzler, Sina
id: 48204546-F248-11E8-B48F-1D18A9856A87
last_name: Metzler
orcid: 0000-0002-9547-2494
- first_name: Jessica
full_name: Kirchner, Jessica
id: 21516227-15aa-11ec-9fb2-c6e8ffc155d3
last_name: Kirchner
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Metzler S, Kirchner J, Grasse AV, Cremer S. Trade-offs between immunity and
competitive ability in fighting ant males. BMC Ecology and Evolution. 2023;23.
doi:10.1186/s12862-023-02137-7
apa: Metzler, S., Kirchner, J., Grasse, A. V., & Cremer, S. (2023). Trade-offs
between immunity and competitive ability in fighting ant males. BMC Ecology
and Evolution. Springer Nature. https://doi.org/10.1186/s12862-023-02137-7
chicago: Metzler, Sina, Jessica Kirchner, Anna V Grasse, and Sylvia Cremer. “Trade-Offs
between Immunity and Competitive Ability in Fighting Ant Males.” BMC Ecology
and Evolution. Springer Nature, 2023. https://doi.org/10.1186/s12862-023-02137-7.
ieee: S. Metzler, J. Kirchner, A. V. Grasse, and S. Cremer, “Trade-offs between
immunity and competitive ability in fighting ant males,” BMC Ecology and Evolution,
vol. 23. Springer Nature, 2023.
ista: Metzler S, Kirchner J, Grasse AV, Cremer S. 2023. Trade-offs between immunity
and competitive ability in fighting ant males. BMC Ecology and Evolution. 23,
37.
mla: Metzler, Sina, et al. “Trade-Offs between Immunity and Competitive Ability
in Fighting Ant Males.” BMC Ecology and Evolution, vol. 23, 37, Springer
Nature, 2023, doi:10.1186/s12862-023-02137-7.
short: S. Metzler, J. Kirchner, A.V. Grasse, S. Cremer, BMC Ecology and Evolution
23 (2023).
date_created: 2023-02-28T07:38:17Z
date_published: 2023-08-07T00:00:00Z
date_updated: 2023-12-13T11:13:14Z
day: '07'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1186/s12862-023-02137-7
ec_funded: 1
external_id:
isi:
- '001042643600002'
pmid:
- '37550612'
file:
- access_level: open_access
checksum: 95966dc7d242d2c85bdd4fe14233dbd8
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T07:51:47Z
date_updated: 2023-08-14T07:51:47Z
file_id: '14048'
file_name: 2023_BMCEcology_Metzler.pdf
file_size: 2004276
relation: main_file
success: 1
file_date_updated: 2023-08-14T07:51:47Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
publication: BMC Ecology and Evolution
publication_identifier:
issn:
- 2730-7182
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '12693'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Trade-offs between immunity and competitive ability in fighting ant males
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: 23
year: '2023'
...
---
_id: '14659'
abstract:
- lang: eng
text: Understanding the response of Himalayan glaciers to global warming is vital
because of their role as a water source for the Asian subcontinent. However, great
uncertainties still exist on the climate drivers of past and present glacier changes
across scales. Here, we analyse continuous hourly climate station data from a
glacierized elevation (Pyramid station, Mount Everest) since 1994 together with
other ground observations and climate reanalysis. We show that a decrease in maximum
air temperature and precipitation occurred during the last three decades at Pyramid
in response to global warming. Reanalysis data suggest a broader occurrence of
this effect in the glacierized areas of the Himalaya. We hypothesize that the
counterintuitive cooling is caused by enhanced sensible heat exchange and the
associated increase in glacier katabatic wind, which draws cool air downward from
higher elevations. The stronger katabatic winds have also lowered the elevation
of local wind convergence, thereby diminishing precipitation in glacial areas
and negatively affecting glacier mass balance. This local cooling may have partially
preserved glaciers from melting and could help protect the periglacial environment.
acknowledgement: This work was carried out within the framework of the EV-K2-CNR and
Nepal Academy of Science and Technology. K.Y. was supported by the Second Tibetan
Plateau Scientific Expedition and Research Program (grant no. 2019QZKK0206). N.C.
was supported by the project NODES, which has received funding from the MUR–M4C2
1.5 of PNRR funded by the European Union - NextGeneration EU (Grant agreement no.
ECS00000036). T.E.S. has received funding from the European Union’s Horizon 2020
research and innovation programme under the Marie Sklodowska-Curie grant no. 101026058.
F.P. has received funding from the European Research Council under the European
Union’s Horizon 2020 research and innovation programme grant no. 772751, RAVEN,
‘Rapid mass losses of debris-covered glaciers in High Mountain Asia’ and has been
supported by the SNSF grant ‘High-elevation precipitation in High Mountain Asia’
(grant no. 183633). A.A. was supported by the European Union’s Horizon 2020 research
and innovation program under grant agreement no. 101004156 (CONFESS project) and
by the European Union’s Horizon Europe research and innovation program under grant
agreement no. 101081193 (OptimESM project). We thank H. Wehrli for valuable comments
and suggestions and J. Giannitrapani for the graphic support. We thank A. Da Polenza
and K. Bista of EV-K2-CNR for believing that studying the high elevations is relevant
for the whole globe.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Franco
full_name: Salerno, Franco
last_name: Salerno
- first_name: Nicolas
full_name: Guyennon, Nicolas
last_name: Guyennon
- first_name: Kun
full_name: Yang, Kun
last_name: Yang
- first_name: Thomas
full_name: Shaw, Thomas
id: 3caa3f91-1f03-11ee-96ce-e0e553054d6e
last_name: Shaw
orcid: 0000-0001-7640-6152
- first_name: Changgui
full_name: Lin, Changgui
last_name: Lin
- first_name: Nicola
full_name: Colombo, Nicola
last_name: Colombo
- first_name: Emanuele
full_name: Romano, Emanuele
last_name: Romano
- first_name: Stephan
full_name: Gruber, Stephan
last_name: Gruber
- first_name: Tobias
full_name: Bolch, Tobias
last_name: Bolch
- first_name: Andrea
full_name: Alessandri, Andrea
last_name: Alessandri
- first_name: Paolo
full_name: Cristofanelli, Paolo
last_name: Cristofanelli
- first_name: Davide
full_name: Putero, Davide
last_name: Putero
- first_name: Guglielmina
full_name: Diolaiuti, Guglielmina
last_name: Diolaiuti
- first_name: Gianni
full_name: Tartari, Gianni
last_name: Tartari
- first_name: Gianpietro
full_name: Verza, Gianpietro
last_name: Verza
- first_name: Sudeep
full_name: Thakuri, Sudeep
last_name: Thakuri
- first_name: Gianpaolo
full_name: Balsamo, Gianpaolo
last_name: Balsamo
- first_name: Evan S.
full_name: Miles, Evan S.
last_name: Miles
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
orcid: 0000-0002-5554-8087
citation:
ama: Salerno F, Guyennon N, Yang K, et al. Local cooling and drying induced by Himalayan
glaciers under global warming. Nature Geoscience. 2023;16:1120-1127. doi:10.1038/s41561-023-01331-y
apa: Salerno, F., Guyennon, N., Yang, K., Shaw, T., Lin, C., Colombo, N., … Pellicciotti,
F. (2023). Local cooling and drying induced by Himalayan glaciers under global
warming. Nature Geoscience. Springer Nature. https://doi.org/10.1038/s41561-023-01331-y
chicago: Salerno, Franco, Nicolas Guyennon, Kun Yang, Thomas Shaw, Changgui Lin,
Nicola Colombo, Emanuele Romano, et al. “Local Cooling and Drying Induced by Himalayan
Glaciers under Global Warming.” Nature Geoscience. Springer Nature, 2023.
https://doi.org/10.1038/s41561-023-01331-y.
ieee: F. Salerno et al., “Local cooling and drying induced by Himalayan glaciers
under global warming,” Nature Geoscience, vol. 16. Springer Nature, pp.
1120–1127, 2023.
ista: Salerno F, Guyennon N, Yang K, Shaw T, Lin C, Colombo N, Romano E, Gruber
S, Bolch T, Alessandri A, Cristofanelli P, Putero D, Diolaiuti G, Tartari G, Verza
G, Thakuri S, Balsamo G, Miles ES, Pellicciotti F. 2023. Local cooling and drying
induced by Himalayan glaciers under global warming. Nature Geoscience. 16, 1120–1127.
mla: Salerno, Franco, et al. “Local Cooling and Drying Induced by Himalayan Glaciers
under Global Warming.” Nature Geoscience, vol. 16, Springer Nature, 2023,
pp. 1120–27, doi:10.1038/s41561-023-01331-y.
short: F. Salerno, N. Guyennon, K. Yang, T. Shaw, C. Lin, N. Colombo, E. Romano,
S. Gruber, T. Bolch, A. Alessandri, P. Cristofanelli, D. Putero, G. Diolaiuti,
G. Tartari, G. Verza, S. Thakuri, G. Balsamo, E.S. Miles, F. Pellicciotti, Nature
Geoscience 16 (2023) 1120–1127.
date_created: 2023-12-10T23:00:58Z
date_published: 2023-12-04T00:00:00Z
date_updated: 2023-12-13T11:01:10Z
day: '04'
ddc:
- '550'
department:
- _id: FrPe
doi: 10.1038/s41561-023-01331-y
file:
- access_level: open_access
checksum: d5ae0d17069eebc6f454c8608cf83e21
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T10:11:19Z
date_updated: 2023-12-11T10:11:19Z
file_id: '14671'
file_name: 2023_NatureGeoscience_Salerno.pdf
file_size: 6072603
relation: main_file
success: 1
file_date_updated: 2023-12-11T10:11:19Z
has_accepted_license: '1'
intvolume: ' 16'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 1120-1127
publication: Nature Geoscience
publication_identifier:
eissn:
- 1752-0908
issn:
- 1752-0894
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/wind-of-climate-change/
scopus_import: '1'
status: public
title: Local cooling and drying induced by Himalayan glaciers under global warming
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: 16
year: '2023'
...
---
_id: '12786'
abstract:
- lang: eng
text: AMPA glutamate receptors (AMPARs) mediate excitatory neurotransmission throughout
the brain. Their signalling is uniquely diversified by brain region-specific auxiliary
subunits, providing an opportunity for the development of selective therapeutics.
AMPARs associated with TARP γ8 are enriched in the hippocampus, and are targets
of emerging anti-epileptic drugs. To understand their therapeutic activity, we
determined cryo-EM structures of the GluA1/2-γ8 receptor associated with three
potent, chemically diverse ligands. We find that despite sharing a lipid-exposed
and water-accessible binding pocket, drug action is differentially affected by
binding-site mutants. Together with patch-clamp recordings and MD simulations
we also demonstrate that ligand-triggered reorganisation of the AMPAR-TARP interface
contributes to modulation. Unexpectedly, one ligand (JNJ-61432059) acts bifunctionally,
negatively affecting GluA1 but exerting positive modulatory action on GluA2-containing
AMPARs, in a TARP stoichiometry-dependent manner. These results further illuminate
the action of TARPs, demonstrate the sensitive balance between positive and negative
modulatory action, and provide a mechanistic platform for development of both
positive and negative selective AMPAR modulators.
acknowledgement: We thank James Krieger for generating the ‘proDy’ interaction maps
in Fig. 5B and S7C, and Jan-Niklas Dohrke for critically reading the manuscript.
We thank members of the Greger lab for insightful comments during this study. We
acknowledge Trevor Rutherford for confirming ligand integrity by NMR. We are also
grateful to LMB scientific computing and the EM facility for their support. This
research was funded in part by the Wellcome Trust (223194/Z/21/Z) to I.H.G. For
the purpose of Open Access, the MRC Laboratory of Molecular Biology has applied
a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version
arising from this submission. Further funding came from the Medical Research Council
(MRU105174197) to I.H.G, and NIH grant (R56/R01MH123474) to T.N.
article_number: '1659'
article_processing_charge: No
article_type: original
author:
- first_name: Danyang
full_name: Zhang, Danyang
last_name: Zhang
- first_name: Remigijus
full_name: Lape, Remigijus
last_name: Lape
- first_name: Saher A.
full_name: Shaikh, Saher A.
last_name: Shaikh
- first_name: Bianka K.
full_name: Kohegyi, Bianka K.
last_name: Kohegyi
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Ondrej
full_name: Cais, Ondrej
last_name: Cais
- first_name: Terunaga
full_name: Nakagawa, Terunaga
last_name: Nakagawa
- first_name: Ingo H.
full_name: Greger, Ingo H.
last_name: Greger
citation:
ama: Zhang D, Lape R, Shaikh SA, et al. Modulatory mechanisms of TARP γ8-selective
AMPA receptor therapeutics. Nature Communications. 2023;14. doi:10.1038/s41467-023-37259-5
apa: Zhang, D., Lape, R., Shaikh, S. A., Kohegyi, B. K., Watson, J., Cais, O., …
Greger, I. H. (2023). Modulatory mechanisms of TARP γ8-selective AMPA receptor
therapeutics. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37259-5
chicago: Zhang, Danyang, Remigijus Lape, Saher A. Shaikh, Bianka K. Kohegyi, Jake
Watson, Ondrej Cais, Terunaga Nakagawa, and Ingo H. Greger. “Modulatory Mechanisms
of TARP Γ8-Selective AMPA Receptor Therapeutics.” Nature Communications.
Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37259-5.
ieee: D. Zhang et al., “Modulatory mechanisms of TARP γ8-selective AMPA receptor
therapeutics,” Nature Communications, vol. 14. Springer Nature, 2023.
ista: Zhang D, Lape R, Shaikh SA, Kohegyi BK, Watson J, Cais O, Nakagawa T, Greger
IH. 2023. Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics.
Nature Communications. 14, 1659.
mla: Zhang, Danyang, et al. “Modulatory Mechanisms of TARP Γ8-Selective AMPA Receptor
Therapeutics.” Nature Communications, vol. 14, 1659, Springer Nature, 2023,
doi:10.1038/s41467-023-37259-5.
short: D. Zhang, R. Lape, S.A. Shaikh, B.K. Kohegyi, J. Watson, O. Cais, T. Nakagawa,
I.H. Greger, Nature Communications 14 (2023).
date_created: 2023-04-02T22:01:09Z
date_published: 2023-03-25T00:00:00Z
date_updated: 2023-12-13T11:15:58Z
day: '25'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/s41467-023-37259-5
external_id:
isi:
- '001066658700003'
file:
- access_level: open_access
checksum: 0a97b31191432dae5853bbb5ccb7698d
content_type: application/pdf
creator: dernst
date_created: 2023-04-03T06:38:56Z
date_updated: 2023-04-03T06:38:56Z
file_id: '12797'
file_name: 2023_NatureComm_Zhang.pdf
file_size: 2613996
relation: main_file
success: 1
file_date_updated: 2023-04-03T06:38:56Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics
tmp:
image: /images/cc_by.png
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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: '12693'
abstract:
- lang: eng
text: See Readme File for further information.
article_processing_charge: No
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Cremer S. Source data for Metzler et al, 2023: Trade-offs between immunity
and competitive ability in fighting ant males . 2023. doi:10.15479/AT:ISTA:12693'
apa: 'Cremer, S. (2023). Source data for Metzler et al, 2023: Trade-offs between
immunity and competitive ability in fighting ant males . Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:12693'
chicago: 'Cremer, Sylvia. “Source Data for Metzler et Al, 2023: Trade-Offs between
Immunity and Competitive Ability in Fighting Ant Males .” Institute of Science
and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12693.'
ieee: 'S. Cremer, “Source data for Metzler et al, 2023: Trade-offs between immunity
and competitive ability in fighting ant males .” Institute of Science and Technology
Austria, 2023.'
ista: 'Cremer S. 2023. Source data for Metzler et al, 2023: Trade-offs between immunity
and competitive ability in fighting ant males , Institute of Science and Technology
Austria, 10.15479/AT:ISTA:12693.'
mla: 'Cremer, Sylvia. Source Data for Metzler et Al, 2023: Trade-Offs between
Immunity and Competitive Ability in Fighting Ant Males . Institute of Science
and Technology Austria, 2023, doi:10.15479/AT:ISTA:12693.'
short: S. Cremer, (2023).
contributor:
- contributor_type: data_collector
first_name: Sina
id: 48204546-F248-11E8-B48F-1D18A9856A87
last_name: Metzler
- contributor_type: data_collector
first_name: Jessica
id: 21516227-15aa-11ec-9fb2-c6e8ffc155d3
last_name: Kirchner
- contributor_type: data_collector
first_name: Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
date_created: 2023-02-28T06:38:37Z
date_published: 2023-02-28T00:00:00Z
date_updated: 2023-12-13T11:13:13Z
day: '28'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.15479/AT:ISTA:12693
file:
- access_level: open_access
checksum: c1565d655ca05601acfd84e0d12b8563
content_type: application/pdf
creator: scremer
date_created: 2023-02-28T06:34:08Z
date_updated: 2023-02-28T06:34:08Z
file_id: '12694'
file_name: Metzler_ReadMe.pdf
file_size: 77070
relation: main_file
success: 1
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checksum: 75c4c4948563d6261cb7548f80d909f1
content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
creator: scremer
date_created: 2023-02-28T06:34:12Z
date_updated: 2023-02-28T06:34:12Z
file_id: '12695'
file_name: Metzler_RepositoryData.xlsx
file_size: 88001
relation: main_file
success: 1
file_date_updated: 2023-02-28T06:34:12Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12696'
relation: used_in_publication
status: public
status: public
title: 'Source data for Metzler et al, 2023: Trade-offs between immunity and competitive
ability in fighting ant males '
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13168'
abstract:
- lang: eng
text: Urban-living individuals are exposed to many environmental factors that may
combine and interact to influence mental health. While individual factors of an
urban environment have been investigated in isolation, no attempt has been made
to model how complex, real-life exposure to living in the city relates to brain
and mental health, and how this is moderated by genetic factors. Using the data
of 156,075 participants from the UK Biobank, we carried out sparse canonical correlation
analyses to investigate the relationships between urban environments and psychiatric
symptoms. We found an environmental profile of social deprivation, air pollution,
street network and urban land-use density that was positively correlated with
an affective symptom group (r = 0.22, Pperm < 0.001), mediated by brain volume
differences consistent with reward processing, and moderated by genes enriched
for stress response, including CRHR1, explaining 2.01% of the variance in brain
volume differences. Protective factors such as greenness and generous destination
accessibility were negatively correlated with an anxiety symptom group (r = 0.10,
Pperm < 0.001), mediated by brain regions necessary for emotion regulation and
moderated by EXD3, explaining 1.65% of the variance. The third urban environmental
profile was correlated with an emotional instability symptom group (r = 0.03,
Pperm < 0.001). Our findings suggest that different environmental profiles of
urban living may influence specific psychiatric symptom groups through distinct
neurobiological pathways.
acknowledgement: This work received support from the European Union-funded Horizon
Europe project ‘environMENTAL’ (no. 101057429 to G.S., A.M. and M.M.N.) and cofunding
by UK Research and Innovation under the UK Government’s Horizon Europe funding guarantee
(nos. 10041392 and 10038599) for study design and data analysis; the Horizon 2020-funded
European Research Council Advanced Grant ‘STRATIFY’ (no. 695313 to G.S. for study
design and data analysis); the Human Brain Project (HBP SGA3, no. 945539 to G.S.
for study design and data analysis); the National Institutes of Health (grant no.
R01DA049238 to G.S. for study design and data analysis); the German Research Foundation
(COPE; grant no. 675346 to G.S. for study design and data analysis); the National
Natural Science Foundation of China (grant no. 82001797 to J.X., grant no. 82030053
to C.Y., grant no. 82202093 to J.T. and grant no. 82150710554 to G.S. for study
design, data analysis and preparation of the manuscript); National Key Research
and Development Program of China (grant no. 2018YFC1314301 to C.Y. for study design
and data analysis); Tianjin Applied Basic Research Diversified Investment Foundation
(grant no. 21JCYBJC01360 to J.X. for study design and data analysis); Tianjin Health
Technology Project (grant no. TJWJ2021QN002 to J.X. for preparation of the manuscript);
Science & Technology Development Fund of the Tianjin Education Commission for Higher
Education (grant no. 2019KJ195 to J.X. for preparation of the manuscript); the Tianjin
Medical University ‘Clinical Talent Training 123 Climbing Plan’ to J.X. for the
preparation of the manuscript; Tianjin Key Medical Discipline (Specialty) Construction
Project (grant no. TJYXZDXK-001A to C.Y. for preparation of the manuscript); the
National Key R&D Program of China (grant no. 2022YFE0209400 to L.Y. for study design
and data analysis); the Tsinghua University Initiative Scientific Research Program
(grant no. 2021Z11GHX002 to L.Y. for study design and data analysis); the National
Key Scientific and Technological Infrastructure Project ‘Earth System Science Numerical
Simulator Facility’ (EarthLab to L.Y. for study design and data analysis); the Chinese
National High-end Foreign Expert Recruitment Plan to G.S.; and the Alexander von
Humboldt Foundation to G.S. for study design and data analysis.
article_processing_charge: No
article_type: original
author:
- first_name: Jiayuan
full_name: Xu, Jiayuan
last_name: Xu
- first_name: Nana
full_name: Liu, Nana
last_name: Liu
- first_name: Elli
full_name: Polemiti, Elli
last_name: Polemiti
- first_name: Liliana
full_name: Garcia-Mondragon, Liliana
last_name: Garcia-Mondragon
- first_name: Jie
full_name: Tang, Jie
last_name: Tang
- first_name: Xiaoxuan
full_name: Liu, Xiaoxuan
last_name: Liu
- first_name: Tristram
full_name: Lett, Tristram
last_name: Lett
- first_name: Le
full_name: Yu, Le
last_name: Yu
- first_name: Markus M.
full_name: Nöthen, Markus M.
last_name: Nöthen
- first_name: Jianfeng
full_name: Feng, Jianfeng
last_name: Feng
- first_name: Chunshui
full_name: Yu, Chunshui
last_name: Yu
- first_name: Andre
full_name: Marquand, Andre
last_name: Marquand
- first_name: Gunter
full_name: Schumann, Gunter
last_name: Schumann
- first_name: Henrik
full_name: Walter, Henrik
last_name: Walter
- first_name: Andreas
full_name: Heinz, Andreas
last_name: Heinz
- first_name: Markus
full_name: Ralser, Markus
last_name: Ralser
- first_name: Sven
full_name: Twardziok, Sven
last_name: Twardziok
- first_name: Nilakshi
full_name: Vaidya, Nilakshi
last_name: Vaidya
- first_name: Emin
full_name: Serin, Emin
last_name: Serin
- first_name: Marcel
full_name: Jentsch, Marcel
last_name: Jentsch
- first_name: Esther
full_name: Hitchen, Esther
last_name: Hitchen
- first_name: Roland
full_name: Eils, Roland
last_name: Eils
- first_name: Ulrike Helene
full_name: Taron, Ulrike Helene
last_name: Taron
- first_name: Tatjana
full_name: Schütz, Tatjana
last_name: Schütz
- first_name: Kerstin
full_name: Schepanski, Kerstin
last_name: Schepanski
- first_name: Jamie
full_name: Banks, Jamie
last_name: Banks
- first_name: Tobias
full_name: Banaschewski, Tobias
last_name: Banaschewski
- first_name: Karina
full_name: Jansone, Karina
last_name: Jansone
- first_name: Nina
full_name: Christmann, Nina
last_name: Christmann
- first_name: Andreas
full_name: Meyer-Lindenberg, Andreas
last_name: Meyer-Lindenberg
- first_name: Heike
full_name: Tost, Heike
last_name: Tost
- first_name: Nathalie
full_name: Holz, Nathalie
last_name: Holz
- first_name: Emanuel
full_name: Schwarz, Emanuel
last_name: Schwarz
- first_name: Argyris
full_name: Stringaris, Argyris
last_name: Stringaris
- first_name: Maja
full_name: Neidhart, Maja
last_name: Neidhart
- first_name: Frauke
full_name: Nees, Frauke
last_name: Nees
- first_name: Sebastian
full_name: Siehl, Sebastian
last_name: Siehl
- first_name: Ole
full_name: A. Andreassen, Ole
last_name: A. Andreassen
- first_name: Lars
full_name: T. Westlye, Lars
last_name: T. Westlye
- first_name: Dennis
full_name: Van Der Meer, Dennis
last_name: Van Der Meer
- first_name: Sara
full_name: Fernandez, Sara
last_name: Fernandez
- first_name: Rikka
full_name: Kjelkenes, Rikka
last_name: Kjelkenes
- first_name: Helga
full_name: Ask, Helga
last_name: Ask
- first_name: Michael
full_name: Rapp, Michael
last_name: Rapp
- first_name: Mira
full_name: Tschorn, Mira
last_name: Tschorn
- first_name: Sarah Jane
full_name: Böttger, Sarah Jane
last_name: Böttger
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Lena
full_name: Marr, Lena
id: 4406F586-F248-11E8-B48F-1D18A9856A87
last_name: Marr
- first_name: Mel
full_name: Slater, Mel
last_name: Slater
- first_name: Guillem Feixas
full_name: Viapiana, Guillem Feixas
last_name: Viapiana
- first_name: Francisco Eiroa
full_name: Orosa, Francisco Eiroa
last_name: Orosa
- first_name: Jaime
full_name: Gallego, Jaime
last_name: Gallego
- first_name: Alvaro
full_name: Pastor, Alvaro
last_name: Pastor
- first_name: Andreas
full_name: Forstner, Andreas
last_name: Forstner
- first_name: Per
full_name: Hoffmann, Per
last_name: Hoffmann
- first_name: Markus
full_name: M. Nöthen, Markus
last_name: M. Nöthen
- first_name: Andreas
full_name: J. Forstner, Andreas
last_name: J. Forstner
- first_name: Isabelle
full_name: Claus, Isabelle
last_name: Claus
- first_name: Abbi
full_name: Miller, Abbi
last_name: Miller
- first_name: Stefanie
full_name: Heilmann-Heimbach, Stefanie
last_name: Heilmann-Heimbach
- first_name: Peter
full_name: Sommer, Peter
last_name: Sommer
- first_name: Mona
full_name: Boye, Mona
last_name: Boye
- first_name: Johannes
full_name: Wilbertz, Johannes
last_name: Wilbertz
- first_name: Karen
full_name: Schmitt, Karen
last_name: Schmitt
- first_name: Viktor
full_name: Jirsa, Viktor
last_name: Jirsa
- first_name: Spase
full_name: Petkoski, Spase
last_name: Petkoski
- first_name: Séverine
full_name: Pitel, Séverine
last_name: Pitel
- first_name: Lisa
full_name: Otten, Lisa
last_name: Otten
- first_name: Anastasios Polykarpos
full_name: Athanasiadis, Anastasios Polykarpos
last_name: Athanasiadis
- first_name: Charlie
full_name: Pearmund, Charlie
last_name: Pearmund
- first_name: Bernhard
full_name: Spanlang, Bernhard
last_name: Spanlang
- first_name: Elena
full_name: Alvarez, Elena
last_name: Alvarez
- first_name: Mavi
full_name: Sanchez, Mavi
last_name: Sanchez
- first_name: Arantxa
full_name: Giner, Arantxa
last_name: Giner
- first_name: Sören
full_name: Hese, Sören
last_name: Hese
- first_name: Paul
full_name: Renner, Paul
last_name: Renner
- first_name: Tianye
full_name: Jia, Tianye
last_name: Jia
- first_name: Yanting
full_name: Gong, Yanting
last_name: Gong
- first_name: Yunman
full_name: Xia, Yunman
last_name: Xia
- first_name: Xiao
full_name: Chang, Xiao
last_name: Chang
- first_name: Vince
full_name: Calhoun, Vince
last_name: Calhoun
- first_name: Jingyu
full_name: Liu, Jingyu
last_name: Liu
- first_name: Paul
full_name: Thompson, Paul
last_name: Thompson
- first_name: Nicholas
full_name: Clinton, Nicholas
last_name: Clinton
- first_name: Sylvane
full_name: Desrivieres, Sylvane
last_name: Desrivieres
- first_name: Allan
full_name: H. Young, Allan
last_name: H. Young
- first_name: Bernd
full_name: Stahl, Bernd
last_name: Stahl
- first_name: George
full_name: Ogoh, George
last_name: Ogoh
citation:
ama: Xu J, Liu N, Polemiti E, et al. Effects of urban living environments on mental
health in adults. Nature Medicine. 2023;29:1456-1467. doi:10.1038/s41591-023-02365-w
apa: Xu, J., Liu, N., Polemiti, E., Garcia-Mondragon, L., Tang, J., Liu, X., … Ogoh,
G. (2023). Effects of urban living environments on mental health in adults. Nature
Medicine. Springer Nature. https://doi.org/10.1038/s41591-023-02365-w
chicago: Xu, Jiayuan, Nana Liu, Elli Polemiti, Liliana Garcia-Mondragon, Jie Tang,
Xiaoxuan Liu, Tristram Lett, et al. “Effects of Urban Living Environments on Mental
Health in Adults.” Nature Medicine. Springer Nature, 2023. https://doi.org/10.1038/s41591-023-02365-w.
ieee: J. Xu et al., “Effects of urban living environments on mental health
in adults,” Nature Medicine, vol. 29. Springer Nature, pp. 1456–1467, 2023.
ista: Xu J, Liu N, Polemiti E, Garcia-Mondragon L, Tang J, Liu X, Lett T, Yu L,
Nöthen MM, Feng J, Yu C, Marquand A, Schumann G, Walter H, Heinz A, Ralser M,
Twardziok S, Vaidya N, Serin E, Jentsch M, Hitchen E, Eils R, Taron UH, Schütz
T, Schepanski K, Banks J, Banaschewski T, Jansone K, Christmann N, Meyer-Lindenberg
A, Tost H, Holz N, Schwarz E, Stringaris A, Neidhart M, Nees F, Siehl S, A. Andreassen
O, T. Westlye L, Van Der Meer D, Fernandez S, Kjelkenes R, Ask H, Rapp M, Tschorn
M, Böttger SJ, Novarino G, Marr L, Slater M, Viapiana GF, Orosa FE, Gallego J,
Pastor A, Forstner A, Hoffmann P, M. Nöthen M, J. Forstner A, Claus I, Miller
A, Heilmann-Heimbach S, Sommer P, Boye M, Wilbertz J, Schmitt K, Jirsa V, Petkoski
S, Pitel S, Otten L, Athanasiadis AP, Pearmund C, Spanlang B, Alvarez E, Sanchez
M, Giner A, Hese S, Renner P, Jia T, Gong Y, Xia Y, Chang X, Calhoun V, Liu J,
Thompson P, Clinton N, Desrivieres S, H. Young A, Stahl B, Ogoh G. 2023. Effects
of urban living environments on mental health in adults. Nature Medicine. 29,
1456–1467.
mla: Xu, Jiayuan, et al. “Effects of Urban Living Environments on Mental Health
in Adults.” Nature Medicine, vol. 29, Springer Nature, 2023, pp. 1456–67,
doi:10.1038/s41591-023-02365-w.
short: J. Xu, N. Liu, E. Polemiti, L. Garcia-Mondragon, J. Tang, X. Liu, T. Lett,
L. Yu, M.M. Nöthen, J. Feng, C. Yu, A. Marquand, G. Schumann, H. Walter, A. Heinz,
M. Ralser, S. Twardziok, N. Vaidya, E. Serin, M. Jentsch, E. Hitchen, R. Eils,
U.H. Taron, T. Schütz, K. Schepanski, J. Banks, T. Banaschewski, K. Jansone, N.
Christmann, A. Meyer-Lindenberg, H. Tost, N. Holz, E. Schwarz, A. Stringaris,
M. Neidhart, F. Nees, S. Siehl, O. A. Andreassen, L. T. Westlye, D. Van Der Meer,
S. Fernandez, R. Kjelkenes, H. Ask, M. Rapp, M. Tschorn, S.J. Böttger, G. Novarino,
L. Marr, M. Slater, G.F. Viapiana, F.E. Orosa, J. Gallego, A. Pastor, A. Forstner,
P. Hoffmann, M. M. Nöthen, A. J. Forstner, I. Claus, A. Miller, S. Heilmann-Heimbach,
P. Sommer, M. Boye, J. Wilbertz, K. Schmitt, V. Jirsa, S. Petkoski, S. Pitel,
L. Otten, A.P. Athanasiadis, C. Pearmund, B. Spanlang, E. Alvarez, M. Sanchez,
A. Giner, S. Hese, P. Renner, T. Jia, Y. Gong, Y. Xia, X. Chang, V. Calhoun, J.
Liu, P. Thompson, N. Clinton, S. Desrivieres, A. H. Young, B. Stahl, G. Ogoh,
Nature Medicine 29 (2023) 1456–1467.
date_created: 2023-06-25T22:00:46Z
date_published: 2023-06-15T00:00:00Z
date_updated: 2023-12-13T11:25:55Z
day: '15'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1038/s41591-023-02365-w
external_id:
isi:
- '001013172700001'
file:
- access_level: open_access
checksum: bcd3225b2731c3442fa98987fd3bd46d
content_type: application/pdf
creator: dernst
date_created: 2023-06-26T10:15:44Z
date_updated: 2023-06-26T10:15:44Z
file_id: '13171'
file_name: 2023_NatureMedicine_Xu.pdf
file_size: 7365360
relation: main_file
success: 1
file_date_updated: 2023-06-26T10:15:44Z
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1456-1467
publication: Nature Medicine
publication_identifier:
eissn:
- 1546-170X
issn:
- 1078-8956
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effects of urban living environments on mental health in adults
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: 29
year: '2023'
...
---
_id: '12976'
abstract:
- lang: eng
text: "3D printing based on continuous deposition of materials, such as filament-based
3D printing, has seen widespread adoption thanks to its versatility in working
with a wide range of materials. An important shortcoming of this type of technology
is its limited multi-material capabilities. While there are simple hardware designs
that enable multi-material printing in principle, the required software is heavily
underdeveloped. A typical hardware design fuses together individual materials
fed into a single chamber from multiple inlets before they are deposited. This
design, however, introduces a time delay between the intended material mixture
and its actual deposition. In this work, inspired by diverse path planning research
in robotics, we show that this mechanical challenge can be addressed via improved
printer control. We propose to formulate the search for optimal multi-material
printing policies in a reinforcement\r\nlearning setup. We put forward a simple
numerical deposition model that takes into account the non-linear material mixing
and delayed material deposition. To validate our system we focus on color fabrication,
a problem known for its strict requirements for varying material mixtures at a
high spatial frequency. We demonstrate that our learned control policy outperforms
state-of-the-art hand-crafted algorithms."
acknowledgement: This work is graciously supported by FWF Lise Meitner (Grant M 3319).
Kang Liao sincerely thank Emiliano Luci, Chunyu Lin, and Yao Zhao for their huge
support.
article_processing_charge: No
author:
- first_name: Kang
full_name: Liao, Kang
last_name: Liao
- first_name: Thibault
full_name: Tricard, Thibault
last_name: Tricard
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
orcid: 0000-0002-5062-4474
- first_name: Hans-Peter
full_name: Seidel, Hans-Peter
last_name: Seidel
- first_name: Vahid
full_name: Babaei, Vahid
last_name: Babaei
citation:
ama: 'Liao K, Tricard T, Piovarci M, Seidel H-P, Babaei V. Learning deposition policies
for fused multi-material 3D printing. In: 2023 IEEE International Conference
on Robotics and Automation. Vol 2023. IEEE; 2023:12345-12352. doi:10.1109/ICRA48891.2023.10160465'
apa: 'Liao, K., Tricard, T., Piovarci, M., Seidel, H.-P., & Babaei, V. (2023).
Learning deposition policies for fused multi-material 3D printing. In 2023
IEEE International Conference on Robotics and Automation (Vol. 2023, pp. 12345–12352).
London, United Kingdom: IEEE. https://doi.org/10.1109/ICRA48891.2023.10160465'
chicago: Liao, Kang, Thibault Tricard, Michael Piovarci, Hans-Peter Seidel, and
Vahid Babaei. “Learning Deposition Policies for Fused Multi-Material 3D Printing.”
In 2023 IEEE International Conference on Robotics and Automation, 2023:12345–52.
IEEE, 2023. https://doi.org/10.1109/ICRA48891.2023.10160465.
ieee: K. Liao, T. Tricard, M. Piovarci, H.-P. Seidel, and V. Babaei, “Learning deposition
policies for fused multi-material 3D printing,” in 2023 IEEE International
Conference on Robotics and Automation, London, United Kingdom, 2023, vol.
2023, pp. 12345–12352.
ista: 'Liao K, Tricard T, Piovarci M, Seidel H-P, Babaei V. 2023. Learning deposition
policies for fused multi-material 3D printing. 2023 IEEE International Conference
on Robotics and Automation. ICRA: International Conference on Robotics and Automation
vol. 2023, 12345–12352.'
mla: Liao, Kang, et al. “Learning Deposition Policies for Fused Multi-Material 3D
Printing.” 2023 IEEE International Conference on Robotics and Automation,
vol. 2023, IEEE, 2023, pp. 12345–52, doi:10.1109/ICRA48891.2023.10160465.
short: K. Liao, T. Tricard, M. Piovarci, H.-P. Seidel, V. Babaei, in:, 2023 IEEE
International Conference on Robotics and Automation, IEEE, 2023, pp. 12345–12352.
conference:
end_date: 2023-06-02
location: London, United Kingdom
name: 'ICRA: International Conference on Robotics and Automation'
start_date: 2023-05-29
date_created: 2023-05-16T09:14:09Z
date_published: 2023-07-04T00:00:00Z
date_updated: 2023-12-13T11:20:00Z
day: '04'
ddc:
- '004'
department:
- _id: BeBi
doi: 10.1109/ICRA48891.2023.10160465
external_id:
isi:
- '001048371104068'
file:
- access_level: open_access
checksum: daeaa67124777d88487f933ea3f77164
content_type: application/pdf
creator: mpiovarc
date_created: 2023-05-16T09:12:05Z
date_updated: 2023-05-16T09:12:05Z
file_id: '12977'
file_name: Liao2023.pdf
file_size: 5367986
relation: main_file
success: 1
file_date_updated: 2023-05-16T09:12:05Z
has_accepted_license: '1'
intvolume: ' 2023'
isi: 1
keyword:
- reinforcement learning
- deposition
- control
- color
- multi-filament
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 12345-12352
project:
- _id: eb901961-77a9-11ec-83b8-f5c883a62027
grant_number: M03319
name: Perception-Aware Appearance Fabrication
publication: 2023 IEEE International Conference on Robotics and Automation
publication_identifier:
eisbn:
- '9798350323658'
issn:
- 1050-4729
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Learning deposition policies for fused multi-material 3D printing
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2023
year: '2023'
...
---
_id: '13164'
abstract:
- lang: eng
text: Molecular compatibility between gametes is a prerequisite for successful fertilization.
As long as a sperm and egg can recognize and bind each other via their surface
proteins, gamete fusion may occur even between members of separate species, resulting
in hybrids that can impact speciation. The egg membrane protein Bouncer confers
species specificity to gamete interactions between medaka and zebrafish, preventing
their cross-fertilization. Here, we leverage this specificity to uncover distinct
amino acid residues and N-glycosylation patterns that differentially influence
the function of medaka and zebrafish Bouncer and contribute to cross-species incompatibility.
Curiously, in contrast to the specificity observed for medaka and zebrafish Bouncer,
seahorse and fugu Bouncer are compatible with both zebrafish and medaka sperm,
in line with the pervasive purifying selection that dominates Bouncer’s evolution.
The Bouncer-sperm interaction is therefore the product of seemingly opposing evolutionary
forces that, for some species, restrict fertilization to closely related fish,
and for others, allow broad gamete compatibility that enables hybridization.
acknowledgement: We thank Manfred Schartl for sharing RNA-seq data from medaka ovaries
and testes prior to publication; Maria Novatchkova for help with RNA-seq analysis;
Katharina Lust for advice on medaka techniques; Milan Malinsky for input on Lake
Malawi cichlid Bouncer sequences; Felicia Spitzer, Mirjam Binner, and Anna Bandura
for help with genotyping; Friedrich Puhl, Kerstin Rattner, Julia Koenig, and Dijana
Sunjic for taking care of zebrafish and medaka; and the Pauli lab for helpful discussions
about the project and feedback on the manuscript. K.R.B.G. was supported by a DOC
Fellowship from the Austrian Academy of Sciences. Work in the Pauli lab was supported
by the FWF START program (Y 1031-B28 to A.P.), the ERC CoG 101044495/GaMe, the HFSP
Career Development Award (CDA00066/2015 to A.P.), a HFSP Young Investigator Award
(RGY0079/2020 to A.P.) and the FWF SFB RNA-Deco (project number F80). The IMP receives
institutional funding from Boehringer Ingelheim and the Austrian Research Promotion
Agency (Headquarter grant FFG-852936). Work by J.S. and Y.M. in this project was
supported by the Israel Science Foundation grant 636/21 to Y.M. Work by L.J. was
supported by the Swedish Research Council grant 2020-04936 and the Knut and Alice
Wallenberg Foundation grant 2018.0042. For the purpose of Open Access, the author
has applied a CC BY public copyright license to any Author Accepted Manuscript (AAM)
version arising from this submission.
article_number: '3506'
article_processing_charge: No
article_type: original
author:
- first_name: Krista R.B.
full_name: Gert, Krista R.B.
last_name: Gert
- first_name: Karin
full_name: Panser, Karin
last_name: Panser
- first_name: Joachim
full_name: Surm, Joachim
last_name: Surm
- first_name: Benjamin S.
full_name: Steinmetz, Benjamin S.
last_name: Steinmetz
- first_name: Alexander
full_name: Schleiffer, Alexander
last_name: Schleiffer
- first_name: Luca
full_name: Jovine, Luca
last_name: Jovine
- first_name: Yehu
full_name: Moran, Yehu
last_name: Moran
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Andrea
full_name: Pauli, Andrea
last_name: Pauli
citation:
ama: Gert KRB, Panser K, Surm J, et al. Divergent molecular signatures in fish Bouncer
proteins define cross-fertilization boundaries. Nature Communications.
2023;14. doi:10.1038/s41467-023-39317-4
apa: Gert, K. R. B., Panser, K., Surm, J., Steinmetz, B. S., Schleiffer, A., Jovine,
L., … Pauli, A. (2023). Divergent molecular signatures in fish Bouncer proteins
define cross-fertilization boundaries. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-023-39317-4
chicago: Gert, Krista R.B., Karin Panser, Joachim Surm, Benjamin S. Steinmetz, Alexander
Schleiffer, Luca Jovine, Yehu Moran, Fyodor Kondrashov, and Andrea Pauli. “Divergent
Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.”
Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-39317-4.
ieee: K. R. B. Gert et al., “Divergent molecular signatures in fish Bouncer
proteins define cross-fertilization boundaries,” Nature Communications,
vol. 14. Springer Nature, 2023.
ista: Gert KRB, Panser K, Surm J, Steinmetz BS, Schleiffer A, Jovine L, Moran Y,
Kondrashov F, Pauli A. 2023. Divergent molecular signatures in fish Bouncer proteins
define cross-fertilization boundaries. Nature Communications. 14, 3506.
mla: Gert, Krista R. B., et al. “Divergent Molecular Signatures in Fish Bouncer
Proteins Define Cross-Fertilization Boundaries.” Nature Communications,
vol. 14, 3506, Springer Nature, 2023, doi:10.1038/s41467-023-39317-4.
short: K.R.B. Gert, K. Panser, J. Surm, B.S. Steinmetz, A. Schleiffer, L. Jovine,
Y. Moran, F. Kondrashov, A. Pauli, Nature Communications 14 (2023).
date_created: 2023-06-25T22:00:45Z
date_published: 2023-06-14T00:00:00Z
date_updated: 2023-12-13T11:26:34Z
day: '14'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41467-023-39317-4
external_id:
isi:
- '001048208600023'
file:
- access_level: open_access
checksum: d6165f41c7f1c2c04b04256ec9f003fb
content_type: application/pdf
creator: dernst
date_created: 2023-06-26T10:26:04Z
date_updated: 2023-06-26T10:26:04Z
file_id: '13172'
file_name: 2023_NatureComm_Gert.pdf
file_size: 1555006
relation: main_file
success: 1
file_date_updated: 2023-06-26T10:26:04Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divergent molecular signatures in fish Bouncer proteins define cross-fertilization
boundaries
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: '12313'
abstract:
- lang: eng
text: Let P be a nontorsion point on an elliptic curve defined over a number field
K and consider the sequence {Bn}n∈N of the denominators of x(nP). We prove that
every term of the sequence of the Bn has a primitive divisor for n greater than
an effectively computable constant that we will explicitly compute. This constant
will depend only on the model defining the curve.
acknowledgement: "This paper is part of the author’s PhD thesis at Università of Pisa.
Moreover, this\r\nproject has received funding from the European Union’s Horizon
2020 research\r\nand innovation programme under the Marie Skłodowska-Curie Grant
Agreement\r\nNo. 101034413. I thank the referee for many helpful comments."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Matteo
full_name: Verzobio, Matteo
id: 7aa8f170-131e-11ed-88e1-a9efd01027cb
last_name: Verzobio
orcid: 0000-0002-0854-0306
citation:
ama: Verzobio M. Some effectivity results for primitive divisors of elliptic divisibility
sequences. Pacific Journal of Mathematics. 2023;325(2):331-351. doi:10.2140/pjm.2023.325.331
apa: Verzobio, M. (2023). Some effectivity results for primitive divisors of elliptic
divisibility sequences. Pacific Journal of Mathematics. Mathematical Sciences
Publishers. https://doi.org/10.2140/pjm.2023.325.331
chicago: Verzobio, Matteo. “Some Effectivity Results for Primitive Divisors of Elliptic
Divisibility Sequences.” Pacific Journal of Mathematics. Mathematical
Sciences Publishers, 2023. https://doi.org/10.2140/pjm.2023.325.331.
ieee: M. Verzobio, “Some effectivity results for primitive divisors of elliptic
divisibility sequences,” Pacific Journal of Mathematics, vol. 325, no.
2. Mathematical Sciences Publishers, pp. 331–351, 2023.
ista: Verzobio M. 2023. Some effectivity results for primitive divisors of elliptic
divisibility sequences. Pacific Journal of Mathematics. 325(2), 331–351.
mla: Verzobio, Matteo. “Some Effectivity Results for Primitive Divisors of Elliptic
Divisibility Sequences.” Pacific Journal of Mathematics, vol. 325, no.
2, Mathematical Sciences Publishers, 2023, pp. 331–51, doi:10.2140/pjm.2023.325.331.
short: M. Verzobio, Pacific Journal of Mathematics 325 (2023) 331–351.
date_created: 2023-01-16T11:46:19Z
date_published: 2023-11-03T00:00:00Z
date_updated: 2023-12-13T11:18:14Z
day: '03'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.2140/pjm.2023.325.331
ec_funded: 1
external_id:
arxiv:
- '2001.02987'
isi:
- '001104766900001'
file:
- access_level: open_access
checksum: b6218d16a72742d8bb38d6fc3c9bb8c6
content_type: application/pdf
creator: dernst
date_created: 2023-11-13T09:50:41Z
date_updated: 2023-11-13T09:50:41Z
file_id: '14525'
file_name: 2023_PacificJourMaths_Verzobio.pdf
file_size: 389897
relation: main_file
success: 1
file_date_updated: 2023-11-13T09:50:41Z
has_accepted_license: '1'
intvolume: ' 325'
isi: 1
issue: '2'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 331-351
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Pacific Journal of Mathematics
publication_identifier:
eissn:
- 0030-8730
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Some effectivity results for primitive divisors of elliptic divisibility sequences
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: 325
year: '2023'
...
---
_id: '13145'
abstract:
- lang: eng
text: We prove a characterization of the Dirichlet–Ferguson measure over an arbitrary
finite diffuse measure space. We provide an interpretation of this characterization
in analogy with the Mecke identity for Poisson point processes.
acknowledgement: Research supported by the Sfb 1060 The Mathematics of Emergent Effects
(University of Bonn). L.D.S. gratefully acknowledges funding of his current position
by the Austrian Science Fund (FWF) through project ESPRIT 208.
article_processing_charge: No
article_type: original
author:
- first_name: Lorenzo
full_name: Dello Schiavo, Lorenzo
id: ECEBF480-9E4F-11EA-B557-B0823DDC885E
last_name: Dello Schiavo
orcid: 0000-0002-9881-6870
- first_name: Eugene
full_name: Lytvynov, Eugene
last_name: Lytvynov
citation:
ama: Dello Schiavo L, Lytvynov E. A Mecke-type characterization of the Dirichlet–Ferguson
measure. Electronic Communications in Probability. 2023;28:1-12. doi:10.1214/23-ECP528
apa: Dello Schiavo, L., & Lytvynov, E. (2023). A Mecke-type characterization
of the Dirichlet–Ferguson measure. Electronic Communications in Probability.
Institute of Mathematical Statistics. https://doi.org/10.1214/23-ECP528
chicago: Dello Schiavo, Lorenzo, and Eugene Lytvynov. “A Mecke-Type Characterization
of the Dirichlet–Ferguson Measure.” Electronic Communications in Probability.
Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/23-ECP528.
ieee: L. Dello Schiavo and E. Lytvynov, “A Mecke-type characterization of the Dirichlet–Ferguson
measure,” Electronic Communications in Probability, vol. 28. Institute
of Mathematical Statistics, pp. 1–12, 2023.
ista: Dello Schiavo L, Lytvynov E. 2023. A Mecke-type characterization of the Dirichlet–Ferguson
measure. Electronic Communications in Probability. 28, 1–12.
mla: Dello Schiavo, Lorenzo, and Eugene Lytvynov. “A Mecke-Type Characterization
of the Dirichlet–Ferguson Measure.” Electronic Communications in Probability,
vol. 28, Institute of Mathematical Statistics, 2023, pp. 1–12, doi:10.1214/23-ECP528.
short: L. Dello Schiavo, E. Lytvynov, Electronic Communications in Probability 28
(2023) 1–12.
date_created: 2023-06-18T22:00:48Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2023-12-13T11:24:57Z
day: '05'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1214/23-ECP528
external_id:
isi:
- '001042025400001'
file:
- access_level: open_access
checksum: 4a543fe4b3f9e747cc52167c17bfb524
content_type: application/pdf
creator: dernst
date_created: 2023-06-19T09:37:40Z
date_updated: 2023-06-19T09:37:40Z
file_id: '13152'
file_name: 2023_ElectronCommProbability_Schiavo.pdf
file_size: 271434
relation: main_file
success: 1
file_date_updated: 2023-06-19T09:37:40Z
has_accepted_license: '1'
intvolume: ' 28'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1-12
project:
- _id: 34dbf174-11ca-11ed-8bc3-afe9d43d4b9c
grant_number: E208
name: Configuration Spaces over Non-Smooth Spaces
publication: Electronic Communications in Probability
publication_identifier:
eissn:
- 1083-589X
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: A Mecke-type characterization of the Dirichlet–Ferguson measure
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: 28
year: '2023'
...
---
_id: '12838'
abstract:
- lang: eng
text: We study the problem of high-dimensional multiple packing in Euclidean space.
Multiple packing is a natural generalization of sphere packing and is defined
as follows. Let N > 0 and L ∈ Z ≽2 . A multiple packing is a set C of points in
R n such that any point in R n lies in the intersection of at most L – 1 balls
of radius √ nN around points in C . Given a well-known connection with coding
theory, multiple packings can be viewed as the Euclidean analog of list-decodable
codes, which are well-studied for finite fields. In this paper, we derive the
best known lower bounds on the optimal density of list-decodable infinite constellations
for constant L under a stronger notion called average-radius multiple packing.
To this end, we apply tools from high-dimensional geometry and large deviation
theory.
acknowledgement: "YZ thanks Jiajin Li for making the observation given by Equation
(23). He also would like to thank Nir Ailon and Ely Porat for several helpful conversations
throughout this project, and Alexander Barg for insightful comments on the manuscript.\r\nYZ
has received funding from the European Union’s Horizon 2020 research and innovation
programme under grant agreement No 682203-ERC-[Inf-Speed-Tradeoff]. The work of
SV was supported by a seed grant from IIT Hyderabad and the start-up research grant
from the Science and Engineering Research Board, India (SRG/2020/000910)."
article_processing_charge: No
article_type: original
author:
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
orcid: 0000-0002-6465-6258
- first_name: Shashank
full_name: Vatedka, Shashank
last_name: Vatedka
citation:
ama: 'Zhang Y, Vatedka S. Multiple packing: Lower bounds via infinite constellations.
IEEE Transactions on Information Theory. 2023;69(7):4513-4527. doi:10.1109/TIT.2023.3260950'
apa: 'Zhang, Y., & Vatedka, S. (2023). Multiple packing: Lower bounds via infinite
constellations. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2023.3260950'
chicago: 'Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via
Infinite Constellations.” IEEE Transactions on Information Theory. IEEE,
2023. https://doi.org/10.1109/TIT.2023.3260950.'
ieee: 'Y. Zhang and S. Vatedka, “Multiple packing: Lower bounds via infinite constellations,”
IEEE Transactions on Information Theory, vol. 69, no. 7. IEEE, pp. 4513–4527,
2023.'
ista: 'Zhang Y, Vatedka S. 2023. Multiple packing: Lower bounds via infinite constellations.
IEEE Transactions on Information Theory. 69(7), 4513–4527.'
mla: 'Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Infinite
Constellations.” IEEE Transactions on Information Theory, vol. 69, no.
7, IEEE, 2023, pp. 4513–27, doi:10.1109/TIT.2023.3260950.'
short: Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 69 (2023) 4513–4527.
date_created: 2023-04-16T22:01:09Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-12-13T11:16:46Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/TIT.2023.3260950
external_id:
arxiv:
- '2211.04407'
isi:
- '001017307000023'
intvolume: ' 69'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2211.04407
month: '07'
oa: 1
oa_version: Preprint
page: 4513-4527
publication: IEEE Transactions on Information Theory
publication_identifier:
eissn:
- 1557-9654
issn:
- 0018-9448
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Multiple packing: Lower bounds via infinite constellations'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 69
year: '2023'
...
---
_id: '13228'
abstract:
- lang: eng
text: A machine-learned system that is fair in static decision-making tasks may
have biased societal impacts in the long-run. This may happen when the system
interacts with humans and feedback patterns emerge, reinforcing old biases in
the system and creating new biases. While existing works try to identify and mitigate
long-run biases through smart system design, we introduce techniques for monitoring
fairness in real time. Our goal is to build and deploy a monitor that will continuously
observe a long sequence of events generated by the system in the wild, and will
output, with each event, a verdict on how fair the system is at the current point
in time. The advantages of monitoring are two-fold. Firstly, fairness is evaluated
at run-time, which is important because unfair behaviors may not be eliminated
a priori, at design-time, due to partial knowledge about the system and the environment,
as well as uncertainties and dynamic changes in the system and the environment,
such as the unpredictability of human behavior. Secondly, monitors are by design
oblivious to how the monitored system is constructed, which makes them suitable
to be used as trusted third-party fairness watchdogs. They function as computationally
lightweight statistical estimators, and their correctness proofs rely on the rigorous
analysis of the stochastic process that models the assumptions about the underlying
dynamics of the system. We show, both in theory and experiments, how monitors
can warn us (1) if a bank’s credit policy over time has created an unfair distribution
of credit scores among the population, and (2) if a resource allocator’s allocation
policy over time has made unfair allocations. Our experiments demonstrate that
the monitors introduce very low overhead. We believe that runtime monitoring is
an important and mathematically rigorous new addition to the fairness toolbox.
acknowledgement: 'The authors would like to thank the anonymous reviewers for their
valuable comments and helpful suggestions. This work is supported by the European
Research Council under Grant No.: ERC-2020-AdG 101020093.'
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Mahyar
full_name: Karimi, Mahyar
last_name: Karimi
- first_name: Konstantin
full_name: Kueffner, Konstantin
id: 8121a2d0-dc85-11ea-9058-af578f3b4515
last_name: Kueffner
orcid: 0000-0001-8974-2542
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
citation:
ama: 'Henzinger TA, Karimi M, Kueffner K, Mallik K. Runtime monitoring of dynamic
fairness properties. In: FAccT ’23: Proceedings of the 2023 ACM Conference
on Fairness, Accountability, and Transparency. Association for Computing Machinery;
2023:604-614. doi:10.1145/3593013.3594028'
apa: 'Henzinger, T. A., Karimi, M., Kueffner, K., & Mallik, K. (2023). Runtime
monitoring of dynamic fairness properties. In FAccT ’23: Proceedings of the
2023 ACM Conference on Fairness, Accountability, and Transparency (pp. 604–614).
Chicago, IL, United States: Association for Computing Machinery. https://doi.org/10.1145/3593013.3594028'
chicago: 'Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik.
“Runtime Monitoring of Dynamic Fairness Properties.” In FAccT ’23: Proceedings
of the 2023 ACM Conference on Fairness, Accountability, and Transparency,
604–14. Association for Computing Machinery, 2023. https://doi.org/10.1145/3593013.3594028.'
ieee: 'T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Runtime monitoring
of dynamic fairness properties,” in FAccT ’23: Proceedings of the 2023 ACM
Conference on Fairness, Accountability, and Transparency, Chicago, IL, United
States, 2023, pp. 604–614.'
ista: 'Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Runtime monitoring of
dynamic fairness properties. FAccT ’23: Proceedings of the 2023 ACM Conference
on Fairness, Accountability, and Transparency. FAccT: Conference on Fairness,
Accountability and Transparency, 604–614.'
mla: 'Henzinger, Thomas A., et al. “Runtime Monitoring of Dynamic Fairness Properties.”
FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability,
and Transparency, Association for Computing Machinery, 2023, pp. 604–14, doi:10.1145/3593013.3594028.'
short: 'T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, FAccT ’23: Proceedings
of the 2023 ACM Conference on Fairness, Accountability, and Transparency, Association
for Computing Machinery, 2023, pp. 604–614.'
conference:
end_date: 2023-06-15
location: Chicago, IL, United States
name: 'FAccT: Conference on Fairness, Accountability and Transparency'
start_date: 2023-06-12
date_created: 2023-07-16T22:01:09Z
date_published: 2023-06-12T00:00:00Z
date_updated: 2023-12-13T11:30:31Z
day: '12'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/3593013.3594028
ec_funded: 1
external_id:
arxiv:
- '2305.04699'
isi:
- '001062819300057'
file:
- access_level: open_access
checksum: 96c759db9cdf94b81e37871a66a6ff48
content_type: application/pdf
creator: dernst
date_created: 2023-07-18T07:43:10Z
date_updated: 2023-07-18T07:43:10Z
file_id: '13245'
file_name: 2023_ACM_HenzingerT.pdf
file_size: 4100596
relation: main_file
success: 1
file_date_updated: 2023-07-18T07:43:10Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 604-614
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 'FAccT ''23: Proceedings of the 2023 ACM Conference on Fairness, Accountability,
and Transparency'
publication_identifier:
isbn:
- '9781450372527'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Runtime monitoring of dynamic fairness properties
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13225'
abstract:
- lang: eng
text: Recently the leading order of the correlation energy of a Fermi gas in a coupled
mean-field and semiclassical scaling regime has been derived, under the assumption
of an interaction potential with a small norm and with compact support in Fourier
space. We generalize this result to large interaction potentials, requiring only
|⋅|V^∈ℓ1(Z3). Our proof is based on approximate, collective bosonization in three
dimensions. Significant improvements compared to recent work include stronger
bounds on non-bosonizable terms and more efficient control on the bosonization
of the kinetic energy.
acknowledgement: "RS was supported by the European Research Council under the European
Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227).
MP acknowledges financial support from the European Research Council under the European
Union’s Horizon 2020 research and innovation programme (ERC StG MaMBoQ, Grant Agreement
No. 802901). BS acknowledges financial support from the NCCR SwissMAP, from the
Swiss National Science Foundation through the Grant “Dynamical and energetic properties
of Bose-Einstein condensates” and from the European Research Council through the
ERC AdG CLaQS (Grant Agreement No. 834782). NB and MP were supported by Gruppo Nazionale
per la Fisica Matematica (GNFM) of Italy. NB was supported by the European Research
Council’s Starting Grant FERMIMATH (Grant Agreement No. 101040991).\r\nOpen access
funding provided by Università degli Studi di Milano within the CRUI-CARE Agreement."
article_number: '65'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Niels P
full_name: Benedikter, Niels P
id: 3DE6C32A-F248-11E8-B48F-1D18A9856A87
last_name: Benedikter
orcid: 0000-0002-1071-6091
- first_name: Marcello
full_name: Porta, Marcello
last_name: Porta
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Benedikter NP, Porta M, Schlein B, Seiringer R. Correlation energy of a weakly
interacting Fermi gas with large interaction potential. Archive for Rational
Mechanics and Analysis. 2023;247(4). doi:10.1007/s00205-023-01893-6
apa: Benedikter, N. P., Porta, M., Schlein, B., & Seiringer, R. (2023). Correlation
energy of a weakly interacting Fermi gas with large interaction potential. Archive
for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-023-01893-6
chicago: Benedikter, Niels P, Marcello Porta, Benjamin Schlein, and Robert Seiringer.
“Correlation Energy of a Weakly Interacting Fermi Gas with Large Interaction Potential.”
Archive for Rational Mechanics and Analysis. Springer Nature, 2023. https://doi.org/10.1007/s00205-023-01893-6.
ieee: N. P. Benedikter, M. Porta, B. Schlein, and R. Seiringer, “Correlation energy
of a weakly interacting Fermi gas with large interaction potential,” Archive
for Rational Mechanics and Analysis, vol. 247, no. 4. Springer Nature, 2023.
ista: Benedikter NP, Porta M, Schlein B, Seiringer R. 2023. Correlation energy of
a weakly interacting Fermi gas with large interaction potential. Archive for Rational
Mechanics and Analysis. 247(4), 65.
mla: Benedikter, Niels P., et al. “Correlation Energy of a Weakly Interacting Fermi
Gas with Large Interaction Potential.” Archive for Rational Mechanics and Analysis,
vol. 247, no. 4, 65, Springer Nature, 2023, doi:10.1007/s00205-023-01893-6.
short: N.P. Benedikter, M. Porta, B. Schlein, R. Seiringer, Archive for Rational
Mechanics and Analysis 247 (2023).
date_created: 2023-07-16T22:01:08Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-12-13T11:31:14Z
day: '01'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s00205-023-01893-6
ec_funded: 1
external_id:
arxiv:
- '2106.13185'
isi:
- '001024369000001'
file:
- access_level: open_access
checksum: 2b45828d854a253b14bf7aa196ec55e9
content_type: application/pdf
creator: dernst
date_created: 2023-11-14T13:12:12Z
date_updated: 2023-11-14T13:12:12Z
file_id: '14535'
file_name: 2023_ArchiveRationalMechAnalysis_Benedikter.pdf
file_size: 851626
relation: main_file
success: 1
file_date_updated: 2023-11-14T13:12:12Z
has_accepted_license: '1'
intvolume: ' 247'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Archive for Rational Mechanics and Analysis
publication_identifier:
eissn:
- 1432-0673
issn:
- 0003-9527
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Correlation energy of a weakly interacting Fermi gas with large interaction
potential
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 247
year: '2023'
...
---
_id: '13226'
abstract:
- lang: eng
text: We consider the ground state and the low-energy excited states of a system
of N identical bosons with interactions in the mean-field scaling regime. For
the ground state, we derive a weak Edgeworth expansion for the fluctuations of
bounded one-body operators, which yields corrections to a central limit theorem
to any order in 1/N−−√. For suitable excited states, we show that the limiting
distribution is a polynomial times a normal distribution, and that higher-order
corrections are given by an Edgeworth-type expansion.
acknowledgement: "It is a pleasure to thank Martin Kolb, Simone Rademacher, Robert
Seiringer and Stefan Teufel for helpful discussions. Moreover, we thank the referee
for many constructive comments. L.B. gratefully acknowledges funding from the German
Research Foundation within the Munich Center of Quantum Science and Technology (EXC
2111) and from the European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie Grant Agreement No. 754411. We thank the Mathematical
Research Institute Oberwolfach, where part of this work was done, for their hospitality.\r\nOpen
Access funding enabled and organized by Projekt DEAL."
article_number: '77'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lea
full_name: Bossmann, Lea
id: A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425
last_name: Bossmann
orcid: 0000-0002-6854-1343
- first_name: Sören P
full_name: Petrat, Sören P
id: 40AC02DC-F248-11E8-B48F-1D18A9856A87
last_name: Petrat
orcid: 0000-0002-9166-5889
citation:
ama: Bossmann L, Petrat SP. Weak Edgeworth expansion for the mean-field Bose gas.
Letters in Mathematical Physics. 2023;113(4). doi:10.1007/s11005-023-01698-4
apa: Bossmann, L., & Petrat, S. P. (2023). Weak Edgeworth expansion for the
mean-field Bose gas. Letters in Mathematical Physics. Springer Nature.
https://doi.org/10.1007/s11005-023-01698-4
chicago: Bossmann, Lea, and Sören P Petrat. “Weak Edgeworth Expansion for the Mean-Field
Bose Gas.” Letters in Mathematical Physics. Springer Nature, 2023. https://doi.org/10.1007/s11005-023-01698-4.
ieee: L. Bossmann and S. P. Petrat, “Weak Edgeworth expansion for the mean-field
Bose gas,” Letters in Mathematical Physics, vol. 113, no. 4. Springer Nature,
2023.
ista: Bossmann L, Petrat SP. 2023. Weak Edgeworth expansion for the mean-field Bose
gas. Letters in Mathematical Physics. 113(4), 77.
mla: Bossmann, Lea, and Sören P. Petrat. “Weak Edgeworth Expansion for the Mean-Field
Bose Gas.” Letters in Mathematical Physics, vol. 113, no. 4, 77, Springer
Nature, 2023, doi:10.1007/s11005-023-01698-4.
short: L. Bossmann, S.P. Petrat, Letters in Mathematical Physics 113 (2023).
date_created: 2023-07-16T22:01:08Z
date_published: 2023-07-03T00:00:00Z
date_updated: 2023-12-13T11:31:50Z
day: '03'
department:
- _id: RoSe
doi: 10.1007/s11005-023-01698-4
ec_funded: 1
external_id:
arxiv:
- '2208.00199'
isi:
- '001022878900002'
intvolume: ' 113'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Letters in Mathematical Physics
publication_identifier:
eissn:
- 1573-0530
issn:
- 0377-9017
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Weak Edgeworth expansion for the mean-field Bose gas
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2023'
...
---
_id: '13227'
abstract:
- lang: eng
text: Currently available quantum processors are dominated by noise, which severely
limits their applicability and motivates the search for new physical qubit encodings.
In this work, we introduce the inductively shunted transmon, a weakly flux-tunable
superconducting qubit that offers charge offset protection for all levels and
a 20-fold reduction in flux dispersion compared to the state-of-the-art resulting
in a constant coherence over a full flux quantum. The parabolic confinement provided
by the inductive shunt as well as the linearity of the geometric superinductor
facilitates a high-power readout that resolves quantum jumps with a fidelity and
QND-ness of >90% and without the need for a Josephson parametric amplifier. Moreover,
the device reveals quantum tunneling physics between the two prepared fluxon ground
states with a measured average decay time of up to 3.5 h. In the future, fast
time-domain control of the transition matrix elements could offer a new path forward
to also achieve full qubit control in the decay-protected fluxon basis.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: The authors thank J. Koch for discussions and support with the scQubits
python package, I. Rozhansky and A. Poddubny for important insights into photon-assisted
tunneling, S. Barzanjeh and G. Arnold for theory, E. Redchenko, S. Pepic, the MIBA
workshop and the IST nanofabrication facility for technical contributions, as well
as L. Drmic, P. Zielinski and R. Sett for software development. We acknowledge the
prompt support of Quantum Machines to implement active state preparation with their
OPX+. This work was supported by a NOMIS foundation research grant (J.F.), the Austrian
Science Fund (FWF) through BeyondC F7105 (J.F.) and IST Austria.
article_number: '3968'
article_processing_charge: No
article_type: original
author:
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Lucky
full_name: Kapoor, Lucky
id: 84b9700b-15b2-11ec-abd3-831089e67615
last_name: Kapoor
- first_name: Andrea
full_name: Trioni, Andrea
id: 42F71B44-F248-11E8-B48F-1D18A9856A87
last_name: Trioni
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. Inductively
shunted transmons exhibit noise insensitive plasmon states and a fluxon decay
exceeding 3 hours. Nature Communications. 2023;14. doi:10.1038/s41467-023-39656-2
apa: Hassani, F., Peruzzo, M., Kapoor, L., Trioni, A., Zemlicka, M., & Fink,
J. M. (2023). Inductively shunted transmons exhibit noise insensitive plasmon
states and a fluxon decay exceeding 3 hours. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-023-39656-2
chicago: Hassani, Farid, Matilda Peruzzo, Lucky Kapoor, Andrea Trioni, Martin Zemlicka,
and Johannes M Fink. “Inductively Shunted Transmons Exhibit Noise Insensitive
Plasmon States and a Fluxon Decay Exceeding 3 Hours.” Nature Communications.
Springer Nature, 2023. https://doi.org/10.1038/s41467-023-39656-2.
ieee: F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, and J. M. Fink,
“Inductively shunted transmons exhibit noise insensitive plasmon states and a
fluxon decay exceeding 3 hours,” Nature Communications, vol. 14. Springer
Nature, 2023.
ista: Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. 2023. Inductively
shunted transmons exhibit noise insensitive plasmon states and a fluxon decay
exceeding 3 hours. Nature Communications. 14, 3968.
mla: Hassani, Farid, et al. “Inductively Shunted Transmons Exhibit Noise Insensitive
Plasmon States and a Fluxon Decay Exceeding 3 Hours.” Nature Communications,
vol. 14, 3968, Springer Nature, 2023, doi:10.1038/s41467-023-39656-2.
short: F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, J.M. Fink, Nature
Communications 14 (2023).
date_created: 2023-07-16T22:01:08Z
date_published: 2023-07-05T00:00:00Z
date_updated: 2023-12-13T11:32:25Z
day: '05'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1038/s41467-023-39656-2
external_id:
isi:
- '001024729900009'
pmid:
- '37407570'
file:
- access_level: open_access
checksum: a85773b5fe23516f60f7d5d31b55c200
content_type: application/pdf
creator: dernst
date_created: 2023-07-18T08:43:07Z
date_updated: 2023-07-18T08:43:07Z
file_id: '13248'
file_name: 2023_NatureComm_Hassani.pdf
file_size: 2899592
relation: main_file
success: 1
file_date_updated: 2023-07-18T08:43:07Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26927A52-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: F07105
name: Integrating superconducting quantum circuits
- _id: 2622978C-B435-11E9-9278-68D0E5697425
name: Hybrid Semiconductor - Superconductor Quantum Devices
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inductively shunted transmons exhibit noise insensitive plasmon states and
a fluxon decay exceeding 3 hours
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: '13321'
abstract:
- lang: eng
text: We consider the problem of reconstructing the signal and the hidden variables
from observations coming from a multi-layer network with rotationally invariant
weight matrices. The multi-layer structure models inference from deep generative
priors, and the rotational invariance imposed on the weights generalizes the i.i.d.
Gaussian assumption by allowing for a complex correlation structure, which is
typical in applications. In this work, we present a new class of approximate message
passing (AMP) algorithms and give a state evolution recursion which precisely
characterizes their performance in the large system limit. In contrast with the
existing multi-layer VAMP (ML-VAMP) approach, our proposed AMP – dubbed multilayer
rotationally invariant generalized AMP (ML-RI-GAMP) – provides a natural generalization
beyond Gaussian designs, in the sense that it recovers the existing Gaussian AMP
as a special case. Furthermore, ML-RI-GAMP exhibits a significantly lower complexity
than ML-VAMP, as the computationally intensive singular value decomposition is
replaced by an estimation of the moments of the design matrices. Finally, our
numerical results show that this complexity gain comes at little to no cost in
the performance of the algorithm.
acknowledgement: Marco Mondelli was partially supported by the 2019 Lopez-Loreta prize.
article_processing_charge: No
author:
- first_name: Yizhou
full_name: Xu, Yizhou
last_name: Xu
- first_name: Tian Qi
full_name: Hou, Tian Qi
last_name: Hou
- first_name: Shan Suo
full_name: Liang, Shan Suo
last_name: Liang
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: 'Xu Y, Hou TQ, Liang SS, Mondelli M. Approximate message passing for multi-layer
estimation in rotationally invariant models. In: 2023 IEEE Information Theory
Workshop. Institute of Electrical and Electronics Engineers; 2023:294-298.
doi:10.1109/ITW55543.2023.10160238'
apa: 'Xu, Y., Hou, T. Q., Liang, S. S., & Mondelli, M. (2023). Approximate message
passing for multi-layer estimation in rotationally invariant models. In 2023
IEEE Information Theory Workshop (pp. 294–298). Saint-Malo, France: Institute
of Electrical and Electronics Engineers. https://doi.org/10.1109/ITW55543.2023.10160238'
chicago: Xu, Yizhou, Tian Qi Hou, Shan Suo Liang, and Marco Mondelli. “Approximate
Message Passing for Multi-Layer Estimation in Rotationally Invariant Models.”
In 2023 IEEE Information Theory Workshop, 294–98. Institute of Electrical
and Electronics Engineers, 2023. https://doi.org/10.1109/ITW55543.2023.10160238.
ieee: Y. Xu, T. Q. Hou, S. S. Liang, and M. Mondelli, “Approximate message passing
for multi-layer estimation in rotationally invariant models,” in 2023 IEEE
Information Theory Workshop, Saint-Malo, France, 2023, pp. 294–298.
ista: 'Xu Y, Hou TQ, Liang SS, Mondelli M. 2023. Approximate message passing for
multi-layer estimation in rotationally invariant models. 2023 IEEE Information
Theory Workshop. ITW: Information Theory Workshop, 294–298.'
mla: Xu, Yizhou, et al. “Approximate Message Passing for Multi-Layer Estimation
in Rotationally Invariant Models.” 2023 IEEE Information Theory Workshop,
Institute of Electrical and Electronics Engineers, 2023, pp. 294–98, doi:10.1109/ITW55543.2023.10160238.
short: Y. Xu, T.Q. Hou, S.S. Liang, M. Mondelli, in:, 2023 IEEE Information Theory
Workshop, Institute of Electrical and Electronics Engineers, 2023, pp. 294–298.
conference:
end_date: 2023-04-28
location: Saint-Malo, France
name: 'ITW: Information Theory Workshop'
start_date: 2023-04-23
date_created: 2023-07-30T22:01:04Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2023-12-13T11:35:46Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/ITW55543.2023.10160238
external_id:
arxiv:
- '2212.01572'
isi:
- '001031733100053'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2212.01572
month: '05'
oa: 1
oa_version: Preprint
page: 294-298
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: 2023 IEEE Information Theory Workshop
publication_identifier:
eissn:
- 2475-4218
isbn:
- '9798350301496'
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Approximate message passing for multi-layer estimation in rotationally invariant
models
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13265'
abstract:
- lang: eng
text: In this study, we propose a computational framework for optimizing the continuity
of the toolpath in fabricating surface models on an extrusion-based 3D printer.
Toolpath continuity is a critical issue that influences both the quality and the
efficiency of extrusion-based fabrication. Transfer moves lead to rough and bumpy
surfaces, where this phenomenon worsens for materials with large viscosity, like
clay. The effects of continuity on the surface models are even more severe in
terms of the quality of the surface and the stability of the model. We introduce
a criterion called the one–path patch (OPP) to represent a patch on the surface
of the shell that can be traversed along one path by considering the constraints
on fabrication. We study the properties of the OPPs and their merging operations
to propose a bottom-up OPP merging procedure to decompose the given shell surface
into a minimal number of OPPs, and to generate the “as-continuous-as-possible”
(ACAP) toolpath. Furthermore, we augment the path planning algorithm with a curved-layer
printing scheme that reduces staircase defects and improves the continuity of
the toolpath by connecting multiple segments. We evaluated the ACAP algorithm
on ceramic and thermoplastic materials, and the results showed that it improves
the fabrication of surface models in terms of both efficiency and surface quality.
acknowledgement: 'This work was supported in part by grants from the NSFC (61972232),
Science and Technology Program of Shenzhen, China (CJGJZD20200617102202007). '
article_number: '26'
article_processing_charge: No
article_type: original
author:
- first_name: Fanchao
full_name: Zhong, Fanchao
last_name: Zhong
- first_name: Yonglai
full_name: Xu, Yonglai
last_name: Xu
- first_name: Haisen
full_name: Zhao, Haisen
id: fb7f793a-80d1-11eb-8869-d56e5b2a8ff4
last_name: Zhao
orcid: 0000-0002-6389-1045
- first_name: Lin
full_name: Lu, Lin
last_name: Lu
citation:
ama: Zhong F, Xu Y, Zhao H, Lu L. As-Continuous-As-Possible extrusion-based fabrication
of surface models. ACM Transactions on Graphics. 2023;42(3). doi:10.1145/3575859
apa: Zhong, F., Xu, Y., Zhao, H., & Lu, L. (2023). As-Continuous-As-Possible
extrusion-based fabrication of surface models. ACM Transactions on Graphics.
Association for Computing Machinery. https://doi.org/10.1145/3575859
chicago: Zhong, Fanchao, Yonglai Xu, Haisen Zhao, and Lin Lu. “As-Continuous-As-Possible
Extrusion-Based Fabrication of Surface Models.” ACM Transactions on Graphics.
Association for Computing Machinery, 2023. https://doi.org/10.1145/3575859.
ieee: F. Zhong, Y. Xu, H. Zhao, and L. Lu, “As-Continuous-As-Possible extrusion-based
fabrication of surface models,” ACM Transactions on Graphics, vol. 42,
no. 3. Association for Computing Machinery, 2023.
ista: Zhong F, Xu Y, Zhao H, Lu L. 2023. As-Continuous-As-Possible extrusion-based
fabrication of surface models. ACM Transactions on Graphics. 42(3), 26.
mla: Zhong, Fanchao, et al. “As-Continuous-As-Possible Extrusion-Based Fabrication
of Surface Models.” ACM Transactions on Graphics, vol. 42, no. 3, 26, Association
for Computing Machinery, 2023, doi:10.1145/3575859.
short: F. Zhong, Y. Xu, H. Zhao, L. Lu, ACM Transactions on Graphics 42 (2023).
date_created: 2023-07-23T22:01:13Z
date_published: 2023-03-17T00:00:00Z
date_updated: 2023-12-13T11:34:59Z
day: '17'
department:
- _id: BeBi
doi: 10.1145/3575859
external_id:
arxiv:
- '2201.02374'
isi:
- '001018739600002'
intvolume: ' 42'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2201.02374
month: '03'
oa: 1
oa_version: Preprint
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: As-Continuous-As-Possible extrusion-based fabrication of surface models
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '13318'
abstract:
- lang: eng
text: Bohnenblust–Hille inequalities for Boolean cubes have been proven with dimension-free
constants that grow subexponentially in the degree (Defant et al. in Math Ann
374(1):653–680, 2019). Such inequalities have found great applications in learning
low-degree Boolean functions (Eskenazis and Ivanisvili in Proceedings of the 54th
annual ACM SIGACT symposium on theory of computing, pp 203–207, 2022). Motivated
by learning quantum observables, a qubit analogue of Bohnenblust–Hille inequality
for Boolean cubes was recently conjectured in Rouzé et al. (Quantum Talagrand,
KKL and Friedgut’s theorems and the learnability of quantum Boolean functions,
2022. arXiv preprint arXiv:2209.07279). The conjecture was resolved in Huang et
al. (Learning to predict arbitrary quantum processes, 2022. arXiv preprint arXiv:2210.14894).
In this paper, we give a new proof of these Bohnenblust–Hille inequalities for
qubit system with constants that are dimension-free and of exponential growth
in the degree. As a consequence, we obtain a junta theorem for low-degree polynomials.
Using similar ideas, we also study learning problems of low degree quantum observables
and Bohr’s radius phenomenon on quantum Boolean cubes.
acknowledgement: The research of A.V. is supported by NSF DMS-1900286, DMS-2154402
and by Hausdorff Center for Mathematics. H.Z. is supported by the Lise Meitner fellowship,
Austrian Science Fund (FWF) M3337. This work is partially supported by NSF DMS-1929284
while both authors were in residence at the Institute for Computational and Experimental
Research in Mathematics in Providence, RI, during the Harmonic Analysis and Convexity
program.
article_processing_charge: No
article_type: original
author:
- first_name: Alexander
full_name: Volberg, Alexander
last_name: Volberg
- first_name: Haonan
full_name: Zhang, Haonan
id: D8F41E38-9E66-11E9-A9E2-65C2E5697425
last_name: Zhang
citation:
ama: Volberg A, Zhang H. Noncommutative Bohnenblust–Hille inequalities. Mathematische
Annalen. 2023. doi:10.1007/s00208-023-02680-0
apa: Volberg, A., & Zhang, H. (2023). Noncommutative Bohnenblust–Hille inequalities.
Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-023-02680-0
chicago: Volberg, Alexander, and Haonan Zhang. “Noncommutative Bohnenblust–Hille
Inequalities.” Mathematische Annalen. Springer Nature, 2023. https://doi.org/10.1007/s00208-023-02680-0.
ieee: A. Volberg and H. Zhang, “Noncommutative Bohnenblust–Hille inequalities,”
Mathematische Annalen. Springer Nature, 2023.
ista: Volberg A, Zhang H. 2023. Noncommutative Bohnenblust–Hille inequalities. Mathematische
Annalen.
mla: Volberg, Alexander, and Haonan Zhang. “Noncommutative Bohnenblust–Hille Inequalities.”
Mathematische Annalen, Springer Nature, 2023, doi:10.1007/s00208-023-02680-0.
short: A. Volberg, H. Zhang, Mathematische Annalen (2023).
date_created: 2023-07-30T22:01:03Z
date_published: 2023-07-24T00:00:00Z
date_updated: 2023-12-13T11:36:20Z
day: '24'
department:
- _id: JaMa
doi: 10.1007/s00208-023-02680-0
external_id:
arxiv:
- '2210.14468'
isi:
- '001035665500001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s00208-023-02680-0
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: eb958bca-77a9-11ec-83b8-c565cb50d8d6
grant_number: M03337
name: Curvature-dimension in noncommutative analysis
publication: Mathematische Annalen
publication_identifier:
eissn:
- 1432-1807
issn:
- 0025-5831
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Noncommutative Bohnenblust–Hille inequalities
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13271'
abstract:
- lang: eng
text: "In this paper, we prove the convexity of trace functionals (A,B,C)↦Tr|BpACq|s,\r\nfor
parameters (p, q, s) that are best possible, where B and C are any n-by-n positive-definite
matrices, and A is any n-by-n matrix. We also obtain the monotonicity versions
of trace functionals of this type. As applications, we extend some results in
Carlen et al. (Linear Algebra Appl 490:174–185, 2016), Hiai and Petz (Publ Res
Inst Math Sci 48(3):525-542, 2012) and resolve a conjecture in Al-Rashed and Zegarliński
(Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) in the matrix
setting. Other conjectures in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum
Probab Relat Top 17(4):1450029, 2014) will also be discussed. We also show that
some related trace functionals are not concave in general. Such concavity results
were expected to hold in different problems."
acknowledgement: I am grateful to Boguslaw Zegarliński for asking me the questions
in [3] and for helpful communication. I also want to thank Paata Ivanisvili for
drawing [25] to my attention and for useful correspondence. Many thanks to the anonymous
referee for the valuable comments and for pointing out some errors in an earlier
version of the paper. This work is partially supported by the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
No. 754411 and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337.
article_processing_charge: No
article_type: original
author:
- first_name: Haonan
full_name: Zhang, Haonan
id: D8F41E38-9E66-11E9-A9E2-65C2E5697425
last_name: Zhang
citation:
ama: Zhang H. Some convexity and monotonicity results of trace functionals. Annales
Henri Poincare. 2023. doi:10.1007/s00023-023-01345-7
apa: Zhang, H. (2023). Some convexity and monotonicity results of trace functionals.
Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-023-01345-7
chicago: Zhang, Haonan. “Some Convexity and Monotonicity Results of Trace Functionals.”
Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-023-01345-7.
ieee: H. Zhang, “Some convexity and monotonicity results of trace functionals,”
Annales Henri Poincare. Springer Nature, 2023.
ista: Zhang H. 2023. Some convexity and monotonicity results of trace functionals.
Annales Henri Poincare.
mla: Zhang, Haonan. “Some Convexity and Monotonicity Results of Trace Functionals.”
Annales Henri Poincare, Springer Nature, 2023, doi:10.1007/s00023-023-01345-7.
short: H. Zhang, Annales Henri Poincare (2023).
date_created: 2023-07-23T22:01:15Z
date_published: 2023-07-08T00:00:00Z
date_updated: 2023-12-13T11:33:46Z
day: '08'
department:
- _id: JaMa
doi: 10.1007/s00023-023-01345-7
ec_funded: 1
external_id:
arxiv:
- '2108.05785'
isi:
- '001025709100001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2108.05785
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: eb958bca-77a9-11ec-83b8-c565cb50d8d6
grant_number: M03337
name: Curvature-dimension in noncommutative analysis
publication: Annales Henri Poincare
publication_identifier:
issn:
- 1424-0637
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Some convexity and monotonicity results of trace functionals
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13258'
abstract:
- lang: eng
text: Many human interactions feature the characteristics of social dilemmas where
individual actions have consequences for the group and the environment. The feedback
between behavior and environment can be studied with the framework of stochastic
games. In stochastic games, the state of the environment can change, depending
on the choices made by group members. Past work suggests that such feedback can
reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic
games even if it is infeasible in each separate repeated game. In stochastic games,
participants have an interest in conditioning their strategies on the state of
the environment. Yet in many applications, precise information about the state
could be scarce. Here, we study how the availability of information (or lack thereof)
shapes evolution of cooperation. Already for simple examples of two state games
we find surprising effects. In some cases, cooperation is only possible if there
is precise information about the state of the environment. In other cases, cooperation
is most abundant when there is no information about the state of the environment.
We systematically analyze all stochastic games of a given complexity class, to
determine when receiving information about the environment is better, neutral,
or worse for evolution of cooperation.
acknowledgement: 'This work was supported by the European Research Council CoG 863818
(ForM-SMArt) (to K.C.), the European Research Council Starting Grant 850529: E-DIRECT
(to C.H.), the European Union’s Horizon 2020 research and innovation program under
the Marie Sklodowska-Curie Grant Agreement #754411 and the French Agence Nationale
de la Recherche (under the Investissement d’Avenir programme, ANR-17-EURE-0010)
(to M.K.).'
article_number: '4153'
article_processing_charge: Yes
article_type: original
author:
- first_name: Maria
full_name: Kleshnina, Maria
id: 4E21749C-F248-11E8-B48F-1D18A9856A87
last_name: Kleshnina
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Stepan
full_name: Simsa, Stepan
id: 409d615c-2f95-11ee-b934-90a352102c1e
last_name: Simsa
orcid: 0000-0001-6687-1210
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin A.
full_name: Nowak, Martin A.
last_name: Nowak
citation:
ama: Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. The effect of environmental
information on evolution of cooperation in stochastic games. Nature Communications.
2023;14. doi:10.1038/s41467-023-39625-9
apa: Kleshnina, M., Hilbe, C., Simsa, S., Chatterjee, K., & Nowak, M. A. (2023).
The effect of environmental information on evolution of cooperation in stochastic
games. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-39625-9
chicago: Kleshnina, Maria, Christian Hilbe, Stepan Simsa, Krishnendu Chatterjee,
and Martin A. Nowak. “The Effect of Environmental Information on Evolution of
Cooperation in Stochastic Games.” Nature Communications. Springer Nature,
2023. https://doi.org/10.1038/s41467-023-39625-9.
ieee: M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, and M. A. Nowak, “The effect
of environmental information on evolution of cooperation in stochastic games,”
Nature Communications, vol. 14. Springer Nature, 2023.
ista: Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. 2023. The effect of
environmental information on evolution of cooperation in stochastic games. Nature
Communications. 14, 4153.
mla: Kleshnina, Maria, et al. “The Effect of Environmental Information on Evolution
of Cooperation in Stochastic Games.” Nature Communications, vol. 14, 4153,
Springer Nature, 2023, doi:10.1038/s41467-023-39625-9.
short: M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, M.A. Nowak, Nature Communications
14 (2023).
date_created: 2023-07-23T22:01:11Z
date_published: 2023-07-12T00:00:00Z
date_updated: 2023-12-13T11:42:38Z
day: '12'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/s41467-023-39625-9
ec_funded: 1
external_id:
isi:
- '001029450400031'
pmid:
- '37438341'
file:
- access_level: open_access
checksum: 5aceefdfe76686267b93ae4fe81899f1
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T11:32:36Z
date_updated: 2023-07-31T11:32:36Z
file_id: '13337'
file_name: 2023_NatureComm_Kleshnina.pdf
file_size: 1601682
relation: main_file
success: 1
file_date_updated: 2023-07-31T11:32:36Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13336'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The effect of environmental information on evolution of cooperation in stochastic
games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '13263'
abstract:
- lang: eng
text: "Motivation: Boolean networks are simple but efficient mathematical formalism
for modelling complex biological systems. However, having only two levels of activation
is sometimes not enough to fully capture the dynamics of real-world biological
systems. Hence, the need for multi-valued networks (MVNs), a generalization of
Boolean networks. Despite the importance of MVNs for modelling biological systems,
only limited progress has been made on developing theories, analysis methods,
and tools that can support them. In particular, the recent use of trap spaces
in Boolean networks made a great impact on the field of systems biology, but there
has been no similar concept defined and studied for MVNs to date.\r\n\r\nResults:
In this work, we generalize the concept of trap spaces in Boolean networks to
that in MVNs. We then develop the theory and the analysis methods for trap spaces
in MVNs. In particular, we implement all proposed methods in a Python package
called trapmvn. Not only showing the applicability of our approach via a realistic
case study, we also evaluate the time efficiency of the method on a large collection
of real-world models. The experimental results confirm the time efficiency, which
we believe enables more accurate analysis on larger and more complex multi-valued
models."
acknowledgement: This work was supported by L’Institut Carnot STAR, Marseille, France,
and by the European Union’s Horizon 2020 research and innovation programme under
the Marie Skłodowska-Curie Grant Agreement No. [101034413].
article_processing_charge: Yes
article_type: original
author:
- first_name: Van Giang
full_name: Trinh, Van Giang
last_name: Trinh
- first_name: Belaid
full_name: Benhamou, Belaid
last_name: Benhamou
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Samuel
full_name: Pastva, Samuel
id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b
last_name: Pastva
orcid: 0000-0003-1993-0331
citation:
ama: 'Trinh VG, Benhamou B, Henzinger TA, Pastva S. Trap spaces of multi-valued
networks: Definition, computation, and applications. Bioinformatics. 2023;39(Supplement_1):i513-i522.
doi:10.1093/bioinformatics/btad262'
apa: 'Trinh, V. G., Benhamou, B., Henzinger, T. A., & Pastva, S. (2023). Trap
spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics.
Oxford Academic. https://doi.org/10.1093/bioinformatics/btad262'
chicago: 'Trinh, Van Giang, Belaid Benhamou, Thomas A Henzinger, and Samuel Pastva.
“Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.”
Bioinformatics. Oxford Academic, 2023. https://doi.org/10.1093/bioinformatics/btad262.'
ieee: 'V. G. Trinh, B. Benhamou, T. A. Henzinger, and S. Pastva, “Trap spaces of
multi-valued networks: Definition, computation, and applications,” Bioinformatics,
vol. 39, no. Supplement_1. Oxford Academic, pp. i513–i522, 2023.'
ista: 'Trinh VG, Benhamou B, Henzinger TA, Pastva S. 2023. Trap spaces of multi-valued
networks: Definition, computation, and applications. Bioinformatics. 39(Supplement_1),
i513–i522.'
mla: 'Trinh, Van Giang, et al. “Trap Spaces of Multi-Valued Networks: Definition,
Computation, and Applications.” Bioinformatics, vol. 39, no. Supplement_1,
Oxford Academic, 2023, pp. i513–22, doi:10.1093/bioinformatics/btad262.'
short: V.G. Trinh, B. Benhamou, T.A. Henzinger, S. Pastva, Bioinformatics 39 (2023)
i513–i522.
date_created: 2023-07-23T22:01:12Z
date_published: 2023-06-30T00:00:00Z
date_updated: 2023-12-13T11:41:52Z
day: '30'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1093/bioinformatics/btad262
ec_funded: 1
external_id:
isi:
- '001027457000060'
pmid:
- '37387165'
file:
- access_level: open_access
checksum: ba3abe1171df1958413b7c7f957f5486
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T11:09:05Z
date_updated: 2023-07-31T11:09:05Z
file_id: '13335'
file_name: 2023_Bioinformatics_Trinh.pdf
file_size: 641736
relation: main_file
success: 1
file_date_updated: 2023-07-31T11:09:05Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: Supplement_1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: i513-i522
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Bioinformatics
publication_identifier:
eissn:
- 1367-4811
issn:
- 1367-4803
publication_status: published
publisher: Oxford Academic
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/giang-trinh/trap-mvn
scopus_import: '1'
status: public
title: 'Trap spaces of multi-valued networks: Definition, computation, and applications'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2023'
...
---
_id: '13316'
abstract:
- lang: eng
text: Although budding yeast has been extensively used as a model organism for studying
organelle functions and intracellular vesicle trafficking, whether it possesses
an independent endocytic early/sorting compartment that sorts endocytic cargos
to the endo-lysosomal pathway or the recycling pathway has long been unclear.
The structure and properties of the endocytic early/sorting compartment differ
significantly between organisms; in plant cells, the trans-Golgi network (TGN)
serves this role, whereas in mammalian cells a separate intracellular structure
performs this function. The yeast syntaxin homolog Tlg2p, widely localizing to
the TGN and endosomal compartments, is presumed to act as a Q-SNARE for endocytic
vesicles, but which compartment is the direct target for endocytic vesicles remained
unanswered. Here we demonstrate by high-speed and high-resolution 4D imaging of
fluorescently labeled endocytic cargos that the Tlg2p-residing compartment within
the TGN functions as the early/sorting compartment. After arriving here, endocytic
cargos are recycled to the plasma membrane or transported to the yeast Rab5-residing
endosomal compartment through the pathway requiring the clathrin adaptors GGAs.
Interestingly, Gga2p predominantly localizes at the Tlg2p-residing compartment,
and the deletion of GGAs has little effect on another TGN region where Sec7p is
present but suppresses dynamics of the Tlg2-residing early/sorting compartment,
indicating that the Tlg2p- and Sec7p-residing regions are discrete entities in
the mutant. Thus, the Tlg2p-residing region seems to serve as an early/sorting
compartment and function independently of the Sec7p-residing region within the
TGN.
acknowledgement: 'This work was supported by JSPS KAKENHI grant #18K062291, and the
Takeda Science Foundation to JYT., as well as JSPS KAKENHI grant #19K065710, the
Takeda Science Foundation, and Life Science Foundation of Japan to JT.'
article_number: e84850
article_processing_charge: Yes
article_type: original
author:
- first_name: Junko Y.
full_name: Toshima, Junko Y.
last_name: Toshima
- first_name: Ayana
full_name: Tsukahara, Ayana
last_name: Tsukahara
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Takuro
full_name: Tojima, Takuro
last_name: Tojima
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Akihiko
full_name: Nakano, Akihiko
last_name: Nakano
- first_name: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Toshima JY, Tsukahara A, Nagano M, et al. The yeast endocytic early/sorting
compartment exists as an independent sub-compartment within the trans-Golgi network.
eLife. 2023;12. doi:10.7554/eLife.84850
apa: Toshima, J. Y., Tsukahara, A., Nagano, M., Tojima, T., Siekhaus, D. E., Nakano,
A., & Toshima, J. (2023). The yeast endocytic early/sorting compartment exists
as an independent sub-compartment within the trans-Golgi network. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.84850
chicago: Toshima, Junko Y., Ayana Tsukahara, Makoto Nagano, Takuro Tojima, Daria
E Siekhaus, Akihiko Nakano, and Jiro Toshima. “The Yeast Endocytic Early/Sorting
Compartment Exists as an Independent Sub-Compartment within the Trans-Golgi Network.”
ELife. eLife Sciences Publications, 2023. https://doi.org/10.7554/eLife.84850.
ieee: J. Y. Toshima et al., “The yeast endocytic early/sorting compartment
exists as an independent sub-compartment within the trans-Golgi network,” eLife,
vol. 12. eLife Sciences Publications, 2023.
ista: Toshima JY, Tsukahara A, Nagano M, Tojima T, Siekhaus DE, Nakano A, Toshima
J. 2023. The yeast endocytic early/sorting compartment exists as an independent
sub-compartment within the trans-Golgi network. eLife. 12, e84850.
mla: Toshima, Junko Y., et al. “The Yeast Endocytic Early/Sorting Compartment Exists
as an Independent Sub-Compartment within the Trans-Golgi Network.” ELife,
vol. 12, e84850, eLife Sciences Publications, 2023, doi:10.7554/eLife.84850.
short: J.Y. Toshima, A. Tsukahara, M. Nagano, T. Tojima, D.E. Siekhaus, A. Nakano,
J. Toshima, ELife 12 (2023).
date_created: 2023-07-30T22:01:02Z
date_published: 2023-07-21T00:00:00Z
date_updated: 2023-12-13T11:37:36Z
day: '21'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.7554/eLife.84850
external_id:
isi:
- '001035372800001'
pmid:
- '37477116'
file:
- access_level: open_access
checksum: 2af111a00cf5e3a956f7f0fd13199b15
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T07:43:00Z
date_updated: 2023-07-31T07:43:00Z
file_id: '13324'
file_name: 2023_eLife_Toshima.pdf
file_size: 11980913
relation: main_file
success: 1
file_date_updated: 2023-07-31T07:43:00Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: The yeast endocytic early/sorting compartment exists as an independent sub-compartment
within the trans-Golgi network
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2023'
...
---
_id: '13317'
abstract:
- lang: eng
text: We prove the Eigenstate Thermalisation Hypothesis (ETH) for local observables
in a typical translation invariant system of quantum spins with L-body interactions,
where L is the number of spins. This mathematically verifies the observation first
made by Santos and Rigol (Phys Rev E 82(3):031130, 2010, https://doi.org/10.1103/PhysRevE.82.031130)
that the ETH may hold for systems with additional translational symmetries for
a naturally restricted class of observables. We also present numerical support
for the same phenomenon for Hamiltonians with local interaction.
acknowledgement: "LE, JH, and VR were supported by ERC Advanced Grant “RMTBeyond”
No. 101020331. SS was supported by KAKENHI Grant Number JP22J14935 from the Japan
Society for the Promotion of Science (JSPS) and Forefront Physics and Mathematics
Program to Drive Transformation (FoPM), a World-leading Innovative Graduate Study
(WINGS) Program, the University of Tokyo.\r\nOpen access funding provided by The
University of Tokyo."
article_number: '128'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Shoki
full_name: Sugimoto, Shoki
last_name: Sugimoto
- first_name: Sven Joscha
full_name: Henheik, Sven Joscha
id: 31d731d7-d235-11ea-ad11-b50331c8d7fb
last_name: Henheik
orcid: 0000-0003-1106-327X
- first_name: Volodymyr
full_name: Riabov, Volodymyr
id: 1949f904-edfb-11eb-afb5-e2dfddabb93b
last_name: Riabov
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
citation:
ama: Sugimoto S, Henheik SJ, Riabov V, Erdös L. Eigenstate thermalisation hypothesis
for translation invariant spin systems. Journal of Statistical Physics.
2023;190(7). doi:10.1007/s10955-023-03132-4
apa: Sugimoto, S., Henheik, S. J., Riabov, V., & Erdös, L. (2023). Eigenstate
thermalisation hypothesis for translation invariant spin systems. Journal of
Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-023-03132-4
chicago: Sugimoto, Shoki, Sven Joscha Henheik, Volodymyr Riabov, and László Erdös.
“Eigenstate Thermalisation Hypothesis for Translation Invariant Spin Systems.”
Journal of Statistical Physics. Springer Nature, 2023. https://doi.org/10.1007/s10955-023-03132-4.
ieee: S. Sugimoto, S. J. Henheik, V. Riabov, and L. Erdös, “Eigenstate thermalisation
hypothesis for translation invariant spin systems,” Journal of Statistical
Physics, vol. 190, no. 7. Springer Nature, 2023.
ista: Sugimoto S, Henheik SJ, Riabov V, Erdös L. 2023. Eigenstate thermalisation
hypothesis for translation invariant spin systems. Journal of Statistical Physics.
190(7), 128.
mla: Sugimoto, Shoki, et al. “Eigenstate Thermalisation Hypothesis for Translation
Invariant Spin Systems.” Journal of Statistical Physics, vol. 190, no.
7, 128, Springer Nature, 2023, doi:10.1007/s10955-023-03132-4.
short: S. Sugimoto, S.J. Henheik, V. Riabov, L. Erdös, Journal of Statistical Physics
190 (2023).
date_created: 2023-07-30T22:01:02Z
date_published: 2023-07-21T00:00:00Z
date_updated: 2023-12-13T11:38:44Z
day: '21'
ddc:
- '510'
- '530'
department:
- _id: LaEr
doi: 10.1007/s10955-023-03132-4
ec_funded: 1
external_id:
arxiv:
- '2304.04213'
isi:
- '001035677200002'
file:
- access_level: open_access
checksum: c2ef6b2aecfee1ad6d03fab620507c2c
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T07:49:31Z
date_updated: 2023-07-31T07:49:31Z
file_id: '13325'
file_name: 2023_JourStatPhysics_Sugimoto.pdf
file_size: 612755
relation: main_file
success: 1
file_date_updated: 2023-07-31T07:49:31Z
has_accepted_license: '1'
intvolume: ' 190'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Journal of Statistical Physics
publication_identifier:
eissn:
- 1572-9613
issn:
- 0022-4715
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Eigenstate thermalisation hypothesis for translation invariant spin systems
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 190
year: '2023'
...
---
_id: '13278'
abstract:
- lang: eng
text: We present a numerical analysis of spin-1/2 fermions in a one-dimensional
harmonic potential in the presence of a magnetic point-like impurity at the center
of the trap. The model represents a few-body analogue of a magnetic impurity in
the vicinity of an s-wave superconductor. Already for a few particles we find
a ground-state level crossing between sectors with different fermion parities.
We interpret this crossing as a few-body precursor of a quantum phase transition,
which occurs when the impurity "breaks" a Cooper pair. This picture is further
corroborated by analyzing density-density correlations in momentum space. Finally,
we discuss how the system may be realized with existing cold-atoms platforms.
article_number: '006'
article_processing_charge: No
article_type: original
author:
- first_name: Lukas
full_name: Rammelmüller, Lukas
last_name: Rammelmüller
- first_name: David
full_name: Huber, David
last_name: Huber
- first_name: Matija
full_name: Čufar, Matija
last_name: Čufar
- first_name: Joachim
full_name: Brand, Joachim
last_name: Brand
- first_name: Hans-Werner
full_name: Hammer, Hans-Werner
last_name: Hammer
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Rammelmüller L, Huber D, Čufar M, Brand J, Hammer H-W, Volosniev A. Magnetic
impurity in a one-dimensional few-fermion system. SciPost Physics. 2023;14(1).
doi:10.21468/scipostphys.14.1.006
apa: Rammelmüller, L., Huber, D., Čufar, M., Brand, J., Hammer, H.-W., & Volosniev,
A. (2023). Magnetic impurity in a one-dimensional few-fermion system. SciPost
Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.14.1.006
chicago: Rammelmüller, Lukas, David Huber, Matija Čufar, Joachim Brand, Hans-Werner
Hammer, and Artem Volosniev. “Magnetic Impurity in a One-Dimensional Few-Fermion
System.” SciPost Physics. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphys.14.1.006.
ieee: L. Rammelmüller, D. Huber, M. Čufar, J. Brand, H.-W. Hammer, and A. Volosniev,
“Magnetic impurity in a one-dimensional few-fermion system,” SciPost Physics,
vol. 14, no. 1. SciPost Foundation, 2023.
ista: Rammelmüller L, Huber D, Čufar M, Brand J, Hammer H-W, Volosniev A. 2023.
Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. 14(1),
006.
mla: Rammelmüller, Lukas, et al. “Magnetic Impurity in a One-Dimensional Few-Fermion
System.” SciPost Physics, vol. 14, no. 1, 006, SciPost Foundation, 2023,
doi:10.21468/scipostphys.14.1.006.
short: L. Rammelmüller, D. Huber, M. Čufar, J. Brand, H.-W. Hammer, A. Volosniev,
SciPost Physics 14 (2023).
date_created: 2023-07-24T10:48:23Z
date_published: 2023-01-24T00:00:00Z
date_updated: 2023-12-13T11:39:32Z
day: '24'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.21468/scipostphys.14.1.006
external_id:
arxiv:
- '2204.01606'
isi:
- '001000325800008'
file:
- access_level: open_access
checksum: ffdb70b9ae7aa45ea4ea6096ecbd6431
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T08:44:38Z
date_updated: 2023-07-31T08:44:38Z
file_id: '13328'
file_name: 2023_SciPostPhysics_Rammelmueller.pdf
file_size: 1163444
relation: main_file
success: 1
file_date_updated: 2023-07-31T08:44:38Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '1'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: SciPost Physics
publication_identifier:
issn:
- 2542-4653
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Magnetic impurity in a one-dimensional few-fermion system
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: '13274'
abstract:
- lang: eng
text: Viscous flows through pipes and channels are steady and ordered until, with
increasing velocity, the laminar motion catastrophically breaks down and gives
way to turbulence. How this apparently discontinuous change from low- to high-dimensional
motion can be rationalized within the framework of the Navier-Stokes equations
is not well understood. Exploiting geometrical properties of transitional channel
flow we trace turbulence to far lower Reynolds numbers (Re) than previously possible
and identify the complete path that reversibly links fully turbulent motion to
an invariant solution. This precursor of turbulence destabilizes rapidly with
Re, and the accompanying explosive increase in attractor dimension effectively
marks the transition between deterministic and de facto stochastic dynamics.
acknowledgement: We thank Baofang Song as well as the developers of Channelflow for
sharing their numerical codes, and Mukund Vasudevan and Holger Kantz for fruitful
discussions. This work was supported by a grant from the Simons Foundation (662960,
B. H.).
article_number: '034002'
article_processing_charge: No
article_type: original
author:
- first_name: Chaitanya S
full_name: Paranjape, Chaitanya S
id: 3D85B7C4-F248-11E8-B48F-1D18A9856A87
last_name: Paranjape
- first_name: Gökhan
full_name: Yalniz, Gökhan
id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425
last_name: Yalniz
orcid: 0000-0002-8490-9312
- first_name: Yohann
full_name: Duguet, Yohann
last_name: Duguet
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. Direct path from turbulence
to time-periodic solutions. Physical Review Letters. 2023;131(3). doi:10.1103/physrevlett.131.034002
apa: Paranjape, C. S., Yalniz, G., Duguet, Y., Budanur, N. B., & Hof, B. (2023).
Direct path from turbulence to time-periodic solutions. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/physrevlett.131.034002
chicago: Paranjape, Chaitanya S, Gökhan Yalniz, Yohann Duguet, Nazmi B Budanur,
and Björn Hof. “Direct Path from Turbulence to Time-Periodic Solutions.” Physical
Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.131.034002.
ieee: C. S. Paranjape, G. Yalniz, Y. Duguet, N. B. Budanur, and B. Hof, “Direct
path from turbulence to time-periodic solutions,” Physical Review Letters,
vol. 131, no. 3. American Physical Society, 2023.
ista: Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. 2023. Direct path from
turbulence to time-periodic solutions. Physical Review Letters. 131(3), 034002.
mla: Paranjape, Chaitanya S., et al. “Direct Path from Turbulence to Time-Periodic
Solutions.” Physical Review Letters, vol. 131, no. 3, 034002, American
Physical Society, 2023, doi:10.1103/physrevlett.131.034002.
short: C.S. Paranjape, G. Yalniz, Y. Duguet, N.B. Budanur, B. Hof, Physical Review
Letters 131 (2023).
date_created: 2023-07-24T09:43:59Z
date_published: 2023-07-21T00:00:00Z
date_updated: 2023-12-13T11:40:19Z
day: '21'
department:
- _id: GradSch
- _id: BjHo
doi: 10.1103/physrevlett.131.034002
external_id:
arxiv:
- '2306.05098'
isi:
- '001052929900004'
intvolume: ' 131'
isi: 1
issue: '3'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2306.05098
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 238598C6-32DE-11EA-91FC-C7463DDC885E
grant_number: '662960'
name: 'Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental
Studies on Transitional and Turbulent Flows'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Direct path from turbulence to time-periodic solutions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2023'
...
---
_id: '13261'
abstract:
- lang: eng
text: Chromosomes in the eukaryotic nucleus are highly compacted. However, for many
functional processes, including transcription initiation, the pairwise motion
of distal chromosomal elements such as enhancers and promoters is essential and
necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously
measure the positions of pairs of enhancers and promoters and their transcriptional
output while systematically varying the genomic separation between these two DNA
loci. Our analysis reveals the coexistence of a compact globular organization
and fast subdiffusive dynamics. These combined features cause an anomalous scaling
of polymer relaxation times with genomic separation leading to long-ranged correlations.
Thus, encounter times of DNA loci are much less dependent on genomic distance
than predicted by existing polymer models, with potential consequences for eukaryotic
gene expression.
acknowledgement: This work was supported in part by the U.S. National Science Foundation,
the Center for the Physics of Biological Function (grant PHY-1734030), and the National
Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B.
was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship
(ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship.
article_processing_charge: No
article_type: original
author:
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Hongtao
full_name: Chen, Hongtao
last_name: Chen
- first_name: Lev
full_name: Barinov, Lev
last_name: Barinov
- first_name: Benjamin
full_name: Zoller, Benjamin
last_name: Zoller
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
citation:
ama: Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional
dynamics of pairs of distal DNA loci on a compacted chromosome. Science.
2023;380(6652):1357-1362. doi:10.1126/science.adf5568
apa: Brückner, D., Chen, H., Barinov, L., Zoller, B., & Gregor, T. (2023). Stochastic
motion and transcriptional dynamics of pairs of distal DNA loci on a compacted
chromosome. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.adf5568
chicago: Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas
Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA
Loci on a Compacted Chromosome.” Science. American Association for the
Advancement of Science, 2023. https://doi.org/10.1126/science.adf5568.
ieee: D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion
and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,”
Science, vol. 380, no. 6652. American Association for the Advancement of
Science, pp. 1357–1362, 2023.
ista: Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion
and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome.
Science. 380(6652), 1357–1362.
mla: Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of
Pairs of Distal DNA Loci on a Compacted Chromosome.” Science, vol. 380,
no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62,
doi:10.1126/science.adf5568.
short: D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023)
1357–1362.
date_created: 2023-07-23T22:01:12Z
date_published: 2023-06-29T00:00:00Z
date_updated: 2023-12-13T11:41:07Z
day: '29'
department:
- _id: EdHa
doi: 10.1126/science.adf5568
external_id:
isi:
- '001106405600028'
intvolume: ' 380'
isi: 1
issue: '6652'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1126/science.adf5568
month: '06'
oa: 1
oa_version: Preprint
page: 1357-1362
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stochastic motion and transcriptional dynamics of pairs of distal DNA loci
on a compacted chromosome
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 380
year: '2023'
...
---
_id: '13336'
article_processing_charge: No
author:
- first_name: Maria
full_name: Kleshnina, Maria
id: 4E21749C-F248-11E8-B48F-1D18A9856A87
last_name: Kleshnina
citation:
ama: 'Kleshnina M. kleshnina/stochgames_info: The effect of environmental information
on evolution of cooperation in stochastic games. 2023. doi:10.5281/ZENODO.8059564'
apa: 'Kleshnina, M. (2023). kleshnina/stochgames_info: The effect of environmental
information on evolution of cooperation in stochastic games. Zenodo. https://doi.org/10.5281/ZENODO.8059564'
chicago: 'Kleshnina, Maria. “Kleshnina/Stochgames_info: The Effect of Environmental
Information on Evolution of Cooperation in Stochastic Games.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8059564.'
ieee: 'M. Kleshnina, “kleshnina/stochgames_info: The effect of environmental information
on evolution of cooperation in stochastic games.” Zenodo, 2023.'
ista: 'Kleshnina M. 2023. kleshnina/stochgames_info: The effect of environmental
information on evolution of cooperation in stochastic games, Zenodo, 10.5281/ZENODO.8059564.'
mla: 'Kleshnina, Maria. Kleshnina/Stochgames_info: The Effect of Environmental
Information on Evolution of Cooperation in Stochastic Games. Zenodo, 2023,
doi:10.5281/ZENODO.8059564.'
short: M. Kleshnina, (2023).
date_created: 2023-07-31T11:30:46Z
date_published: 2023-06-20T00:00:00Z
date_updated: 2023-12-13T11:42:37Z
day: '20'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.5281/ZENODO.8059564
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8059564
month: '06'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '13258'
relation: used_in_publication
status: public
status: public
title: 'kleshnina/stochgames_info: The effect of environmental information on evolution
of cooperation in stochastic games'
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13443'
abstract:
- lang: eng
text: 'The ages of solar-like stars have been at the center of many studies such
as exoplanet characterization or Galactic-archeology. While ages are usually computed
from stellar evolution models, relations linking ages to other stellar properties,
such as rotation and magnetic activity, have been investigated. With the large
catalog of 55,232 rotation periods, Prot, and photometric magnetic activity index,
Sph from Kepler data, we have the opportunity to look for such magneto-gyro-chronology
relations. Stellar ages are obtained with two stellar evolution codes that include
treatment of angular momentum evolution, hence using Prot as input in addition
to classical atmospheric parameters. We explore two different ways of predicting
stellar ages on three subsamples with spectroscopic observations: solar analogs,
late-F and G dwarfs, and K dwarfs. We first perform a Bayesian analysis to derive
relations between Sph and ages between 1 and 5 Gyr, and other stellar properties.
For late-F and G dwarfs, and K dwarfs, the multivariate regression favors the
model with Prot and Sph with median differences of 0.1% and 0.2%, respectively.
We also apply Machine Learning techniques with a Random Forest algorithm to predict
ages up to 14 Gyr with the same set of input parameters. For late-F, G and K dwarfs
together, predicted ages are on average within 5.3% of the model ages and improve
to 3.1% when including Prot. These are very promising results for a quick age
estimation for solar-like stars with photometric observations, especially with
current and future space missions.'
acknowledgement: 'This paper includes data collected by the Kepler mission and obtained
from the MAST data archive at the Space Telescope Science Institute (STScI). Funding
for the Kepler mission is provided by the NASA Science Mission Directorate. STScI
is operated by the Association of Universities for Research in Astronomy, Inc.,
under NASA contract NAS 5–26555. We acknowledge that this research was supported
in part by the National Science Foundation under grant No. NSF PHY-1748958. S.M.
acknowledges support from the Spanish Ministry of Science and Innovation (MICINN)
with the Ramón y Cajal fellowship No. RYC-2015-17697, the grant No. PID2019-107061GB-C66,
and through AEI under the Severo Ochoa Centres of Excellence Programme 2020–2023
(CEX2019-000920-S). S.M. and D.G.R. acknowledge support from the Spanish Ministry
of Science and Innovation (MICINN) with the grant No. PID2019-107187GB-I00. Z.R.C.
acknowledges support from National Aeronautics and Space Administration via the
TESS Guest Investigator Program (grant No. 80NSSC18K18584). The work presented here
was partially supported by the NASA grant NNX17AF27G. A.R.G.S. acknowledges the
support by FCT through national funds and by FEDER through COMPETE2020 by the following
grants: UIDB/04434/2020 and UIDP/04434/2020. A.R.G.S. is supported by FCT through
the work contract No. 2020.02480.CEECIND/CP1631/CT0001. R.A.G., L.A., and S.N.B.
acknowledge the support from PLATO and GOLF CNES grants. S.N.B. acknowledges support
from PLATO ASI-INAF agreement No. 2015-019-R.1-2018.'
article_number: '131'
article_processing_charge: Yes
article_type: original
author:
- first_name: Savita
full_name: Mathur, Savita
last_name: Mathur
- first_name: Zachary R.
full_name: Claytor, Zachary R.
last_name: Claytor
- first_name: Ângela R. G.
full_name: Santos, Ângela R. G.
last_name: Santos
- first_name: Rafael A.
full_name: García, Rafael A.
last_name: García
- first_name: Louis
full_name: Amard, Louis
last_name: Amard
- first_name: Lisa Annabelle
full_name: Bugnet, Lisa Annabelle
id: d9edb345-f866-11ec-9b37-d119b5234501
last_name: Bugnet
orcid: 0000-0003-0142-4000
- first_name: Enrico
full_name: Corsaro, Enrico
last_name: Corsaro
- first_name: Alfio
full_name: Bonanno, Alfio
last_name: Bonanno
- first_name: Sylvain N.
full_name: Breton, Sylvain N.
last_name: Breton
- first_name: Diego
full_name: Godoy-Rivera, Diego
last_name: Godoy-Rivera
- first_name: Marc H.
full_name: Pinsonneault, Marc H.
last_name: Pinsonneault
- first_name: Jennifer
full_name: van Saders, Jennifer
last_name: van Saders
citation:
ama: Mathur S, Claytor ZR, Santos ÂRG, et al. Magnetic activity evolution of solar-like
stars. I. Sph–age relation derived from Kepler observations. The Astrophysical
Journal. 2023;952(2). doi:10.3847/1538-4357/acd118
apa: Mathur, S., Claytor, Z. R., Santos, Â. R. G., García, R. A., Amard, L., Bugnet,
L. A., … van Saders, J. (2023). Magnetic activity evolution of solar-like stars.
I. Sph–age relation derived from Kepler observations. The Astrophysical Journal.
American Astronomical Society. https://doi.org/10.3847/1538-4357/acd118
chicago: Mathur, Savita, Zachary R. Claytor, Ângela R. G. Santos, Rafael A. García,
Louis Amard, Lisa Annabelle Bugnet, Enrico Corsaro, et al. “Magnetic Activity
Evolution of Solar-like Stars. I. Sph–Age Relation Derived from Kepler Observations.”
The Astrophysical Journal. American Astronomical Society, 2023. https://doi.org/10.3847/1538-4357/acd118.
ieee: S. Mathur et al., “Magnetic activity evolution of solar-like stars.
I. Sph–age relation derived from Kepler observations,” The Astrophysical Journal,
vol. 952, no. 2. American Astronomical Society, 2023.
ista: Mathur S, Claytor ZR, Santos ÂRG, García RA, Amard L, Bugnet LA, Corsaro E,
Bonanno A, Breton SN, Godoy-Rivera D, Pinsonneault MH, van Saders J. 2023. Magnetic
activity evolution of solar-like stars. I. Sph–age relation derived from Kepler
observations. The Astrophysical Journal. 952(2), 131.
mla: Mathur, Savita, et al. “Magnetic Activity Evolution of Solar-like Stars. I.
Sph–Age Relation Derived from Kepler Observations.” The Astrophysical Journal,
vol. 952, no. 2, 131, American Astronomical Society, 2023, doi:10.3847/1538-4357/acd118.
short: S. Mathur, Z.R. Claytor, Â.R.G. Santos, R.A. García, L. Amard, L.A. Bugnet,
E. Corsaro, A. Bonanno, S.N. Breton, D. Godoy-Rivera, M.H. Pinsonneault, J. van
Saders, The Astrophysical Journal 952 (2023).
date_created: 2023-08-01T14:19:16Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-12-13T12:00:15Z
day: '01'
ddc:
- '520'
department:
- _id: LiBu
doi: 10.3847/1538-4357/acd118
external_id:
isi:
- '001034185700001'
file:
- access_level: open_access
checksum: f12452834d7ed6748dbf5ace18af4723
content_type: application/pdf
creator: dernst
date_created: 2023-08-02T07:42:26Z
date_updated: 2023-08-02T07:42:26Z
file_id: '13448'
file_name: 2023_AstrophysicalJour_Mathur.pdf
file_size: 4192386
relation: main_file
success: 1
file_date_updated: 2023-08-02T07:42:26Z
has_accepted_license: '1'
intvolume: ' 952'
isi: 1
issue: '2'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: The Astrophysical Journal
publication_identifier:
eissn:
- 1538-4357
issn:
- 0004-637X
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
status: public
title: Magnetic activity evolution of solar-like stars. I. Sph–age relation derived
from Kepler observations
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: 952
year: '2023'
...
---
_id: '13259'
abstract:
- lang: eng
text: Plants can regenerate their bodies via de novo establishment of shoot apical
meristems (SAMs) from pluripotent callus. Only a small fraction of callus cells
is eventually specified into SAMs but the molecular mechanisms underlying fate
specification remain obscure. The expression of WUSCHEL (WUS) is an early hallmark
of SAM fate acquisition. Here, we show that a WUS paralog, WUSCHEL-RELATED HOMEOBOX
13 (WOX13), negatively regulates SAM formation from callus in Arabidopsis thaliana.
WOX13 promotes non-meristematic cell fate via transcriptional repression of WUS
and other SAM regulators and activation of cell wall modifiers. Our Quartz-Seq2–based
single cell transcriptome revealed that WOX13 plays key roles in determining cellular
identity of callus cell population. We propose that reciprocal inhibition between
WUS and WOX13 mediates critical cell fate determination in pluripotent cell population,
which has a major impact on regeneration efficiency.
acknowledgement: Wethank Y.Iwayama, K.Ohtawa, K.Fukumoto,andN. Mataga (RIKENRRD) for
technical assistance in Quartz-Seq2analyses; M. Mouri(RIKENCSRS)for technical support
with plasmid construction and transactivation assay; Y. Ikeda (NAIST) for technical
support with tissue culture; and A. Furuta for technical support in bulk RNA-seq
analysis. We also thank the Single-cell Omics Laboratory for technical consultation
in scRNA-seq analyses, the members of the Laboratory for Bioinformatics Research
at the RIKEN Center for Biosystems Dynamics Research, and A. Matsushima and T. Ichikawa
for IT infrastructure management. This work was supported by JSPS KAKENHI(17K15146,19H05670,20K06712,20H04894,20H05431,and
22H04713 to M.I. and 20H03284 and 20H05911 to K.S.), by the JST FOREST Program (JPMJFR214H
to M.I.), by The Naito Foundation to M.I.; by Takeda Science Foundation to M.I,and
by the Shiseido Female Researcher Science Grant to M.I. This work was partially
supported by RIKENE pigenome Control Program, Medical Research Center Initiative
for High Depth Omics, and JST CREST(JPMJCR16G3and JPMJCR1926)to I.N.
article_processing_charge: Yes
article_type: original
author:
- first_name: Nao
full_name: Ogura, Nao
last_name: Ogura
- first_name: Yohei
full_name: Sasagawa, Yohei
last_name: Sasagawa
- first_name: Tasuku
full_name: Ito, Tasuku
id: d5a17a4a-e534-11eb-93ec-91fa2aa9bd57
last_name: Ito
orcid: 0000-0002-2482-9089
- first_name: Toshiaki
full_name: Tameshige, Toshiaki
last_name: Tameshige
- first_name: Satomi
full_name: Kawai, Satomi
last_name: Kawai
- first_name: Masaki
full_name: Sano, Masaki
last_name: Sano
- first_name: Yuki
full_name: Doll, Yuki
last_name: Doll
- first_name: Akira
full_name: Iwase, Akira
last_name: Iwase
- first_name: Ayako
full_name: Kawamura, Ayako
last_name: Kawamura
- first_name: Takamasa
full_name: Suzuki, Takamasa
last_name: Suzuki
- first_name: Itoshi
full_name: Nikaido, Itoshi
last_name: Nikaido
- first_name: Keiko
full_name: Sugimoto, Keiko
last_name: Sugimoto
- first_name: Momoko
full_name: Ikeuchi, Momoko
last_name: Ikeuchi
citation:
ama: Ogura N, Sasagawa Y, Ito T, et al. WUSCHEL-RELATED HOMEOBOX 13 suppresses de
novo shoot regeneration via cell fate control of pluripotent callus. Science
Advances. 2023;9(27):eadg6983. doi:10.1126/sciadv.adg6983
apa: Ogura, N., Sasagawa, Y., Ito, T., Tameshige, T., Kawai, S., Sano, M., … Ikeuchi,
M. (2023). WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via
cell fate control of pluripotent callus. Science Advances. American Association
for the Advancement of Science. https://doi.org/10.1126/sciadv.adg6983
chicago: Ogura, Nao, Yohei Sasagawa, Tasuku Ito, Toshiaki Tameshige, Satomi Kawai,
Masaki Sano, Yuki Doll, et al. “WUSCHEL-RELATED HOMEOBOX 13 Suppresses de Novo
Shoot Regeneration via Cell Fate Control of Pluripotent Callus.” Science Advances.
American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.adg6983.
ieee: N. Ogura et al., “WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot
regeneration via cell fate control of pluripotent callus,” Science Advances,
vol. 9, no. 27. American Association for the Advancement of Science, p. eadg6983,
2023.
ista: Ogura N, Sasagawa Y, Ito T, Tameshige T, Kawai S, Sano M, Doll Y, Iwase A,
Kawamura A, Suzuki T, Nikaido I, Sugimoto K, Ikeuchi M. 2023. WUSCHEL-RELATED
HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent
callus. Science Advances. 9(27), eadg6983.
mla: Ogura, Nao, et al. “WUSCHEL-RELATED HOMEOBOX 13 Suppresses de Novo Shoot Regeneration
via Cell Fate Control of Pluripotent Callus.” Science Advances, vol. 9,
no. 27, American Association for the Advancement of Science, 2023, p. eadg6983,
doi:10.1126/sciadv.adg6983.
short: N. Ogura, Y. Sasagawa, T. Ito, T. Tameshige, S. Kawai, M. Sano, Y. Doll,
A. Iwase, A. Kawamura, T. Suzuki, I. Nikaido, K. Sugimoto, M. Ikeuchi, Science
Advances 9 (2023) eadg6983.
date_created: 2023-07-23T22:01:11Z
date_published: 2023-07-07T00:00:00Z
date_updated: 2023-12-13T11:59:29Z
day: '07'
ddc:
- '580'
doi: 10.1126/sciadv.adg6983
external_id:
isi:
- '001030983100012'
pmid:
- '37418524'
file:
- access_level: open_access
checksum: f59217e1083767777318b5d0cc5e141d
content_type: application/pdf
creator: dernst
date_created: 2023-08-01T06:40:35Z
date_updated: 2023-08-01T06:40:35Z
file_id: '13338'
file_name: 2023_ScienceAdvance_Ogura.pdf
file_size: 1759993
relation: main_file
success: 1
file_date_updated: 2023-08-01T06:40:35Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '27'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: eadg6983
pmid: 1
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell
fate control of pluripotent callus
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: '13976'
abstract:
- lang: eng
text: Conflicts and natural disasters affect entire populations of the countries
involved and, in addition to the thousands of lives destroyed, have a substantial
negative impact on the scientific advances these countries provide. The unprovoked
invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria,
and the ongoing conflicts in the Middle East are just a few examples. Millions
of people have been killed or displaced, their futures uncertain. These events
have resulted in extensive infrastructure collapse, with loss of electricity,
transportation, and access to services. Schools, universities, and research centers
have been destroyed along with decades’ worth of data, samples, and findings.
Scholars in disaster areas face short- and long-term problems in terms of what
they can accomplish now for obtaining grants and for employment in the long run.
In our interconnected world, conflicts and disasters are no longer a local problem
but have wide-ranging impacts on the entire world, both now and in the future.
Here, we focus on the current and ongoing impact of war on the scientific community
within Ukraine and from this draw lessons that can be applied to all affected
countries where scientists at risk are facing hardship. We present and classify
examples of effective and feasible mechanisms used to support researchers in countries
facing hardship and discuss how these can be implemented with help from the international
scientific community and what more is desperately needed. Reaching out, providing
accessible training opportunities, and developing collaborations should increase
inclusion and connectivity, support scientific advancements within affected communities,
and expedite postwar and disaster recovery.
acknowledgement: "Our article is dedicated to all freedom-loving people around the
world and to the people of Ukraine who fight for our freedom. Special thanks to
Anita Bandrowski, Oleksandra V. Ivashchenko, and Sanita Reinsone for the helpful
review, valuable criticism, and useful suggestions while preparing this manuscript,
and to Tetiana Yes'kova for helping with Ukrainian translation.\r\nAll authors volunteered
their time. No funding supported work on this article."
article_processing_charge: Yes
article_type: original
author:
- first_name: Walter
full_name: Wolfsberger, Walter
last_name: Wolfsberger
- first_name: Karishma
full_name: Chhugani, Karishma
last_name: Chhugani
- first_name: Khrystyna
full_name: Shchubelka, Khrystyna
last_name: Shchubelka
- first_name: Alina
full_name: Frolova, Alina
last_name: Frolova
- first_name: Yuriy
full_name: Salyha, Yuriy
last_name: Salyha
- first_name: Oksana
full_name: Zlenko, Oksana
last_name: Zlenko
- first_name: Mykhailo
full_name: Arych, Mykhailo
last_name: Arych
- first_name: Dmytro
full_name: Dziuba, Dmytro
last_name: Dziuba
- first_name: Andrii
full_name: Parkhomenko, Andrii
last_name: Parkhomenko
- first_name: Volodymyr
full_name: Smolanka, Volodymyr
last_name: Smolanka
- first_name: Zeynep H.
full_name: Gümüş, Zeynep H.
last_name: Gümüş
- first_name: Efe
full_name: Sezgin, Efe
last_name: Sezgin
- first_name: Alondra
full_name: Diaz-Lameiro, Alondra
last_name: Diaz-Lameiro
- first_name: Viktor R.
full_name: Toth, Viktor R.
last_name: Toth
- first_name: Megi
full_name: Maci, Megi
last_name: Maci
- first_name: Eric
full_name: Bortz, Eric
last_name: Bortz
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Patricia M.
full_name: Morton, Patricia M.
last_name: Morton
- first_name: Paweł P.
full_name: Łabaj, Paweł P.
last_name: Łabaj
- first_name: Veronika
full_name: Romero, Veronika
last_name: Romero
- first_name: Jakub
full_name: Hlávka, Jakub
last_name: Hlávka
- first_name: Serghei
full_name: Mangul, Serghei
last_name: Mangul
- first_name: Taras K.
full_name: Oleksyk, Taras K.
last_name: Oleksyk
citation:
ama: 'Wolfsberger W, Chhugani K, Shchubelka K, et al. Scientists without borders:
Lessons from Ukraine. GigaScience. 2023;12. doi:10.1093/gigascience/giad045'
apa: 'Wolfsberger, W., Chhugani, K., Shchubelka, K., Frolova, A., Salyha, Y., Zlenko,
O., … Oleksyk, T. K. (2023). Scientists without borders: Lessons from Ukraine.
GigaScience. Oxford Academic. https://doi.org/10.1093/gigascience/giad045'
chicago: 'Wolfsberger, Walter, Karishma Chhugani, Khrystyna Shchubelka, Alina Frolova,
Yuriy Salyha, Oksana Zlenko, Mykhailo Arych, et al. “Scientists without Borders:
Lessons from Ukraine.” GigaScience. Oxford Academic, 2023. https://doi.org/10.1093/gigascience/giad045.'
ieee: 'W. Wolfsberger et al., “Scientists without borders: Lessons from Ukraine,”
GigaScience, vol. 12. Oxford Academic, 2023.'
ista: 'Wolfsberger W, Chhugani K, Shchubelka K, Frolova A, Salyha Y, Zlenko O, Arych
M, Dziuba D, Parkhomenko A, Smolanka V, Gümüş ZH, Sezgin E, Diaz-Lameiro A, Toth
VR, Maci M, Bortz E, Kondrashov F, Morton PM, Łabaj PP, Romero V, Hlávka J, Mangul
S, Oleksyk TK. 2023. Scientists without borders: Lessons from Ukraine. GigaScience.
12.'
mla: 'Wolfsberger, Walter, et al. “Scientists without Borders: Lessons from Ukraine.”
GigaScience, vol. 12, Oxford Academic, 2023, doi:10.1093/gigascience/giad045.'
short: W. Wolfsberger, K. Chhugani, K. Shchubelka, A. Frolova, Y. Salyha, O. Zlenko,
M. Arych, D. Dziuba, A. Parkhomenko, V. Smolanka, Z.H. Gümüş, E. Sezgin, A. Diaz-Lameiro,
V.R. Toth, M. Maci, E. Bortz, F. Kondrashov, P.M. Morton, P.P. Łabaj, V. Romero,
J. Hlávka, S. Mangul, T.K. Oleksyk, GigaScience 12 (2023).
date_created: 2023-08-06T22:01:13Z
date_published: 2023-07-27T00:00:00Z
date_updated: 2023-12-13T12:01:46Z
day: '27'
department:
- _id: FyKo
doi: 10.1093/gigascience/giad045
external_id:
isi:
- '001081086100001'
pmid:
- '37496156'
intvolume: ' 12'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/gigascience/giad045
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: GigaScience
publication_identifier:
eissn:
- 2047-217X
publication_status: epub_ahead
publisher: Oxford Academic
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Scientists without borders: Lessons from Ukraine'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2023'
...
---
_id: '13973'
abstract:
- lang: eng
text: We construct families of log K3 surfaces and study the arithmetic of their
members. We use this to produce explicit surfaces with an order 5 Brauer–Manin
obstruction to the integral Hasse principle.
acknowledgement: "This paper was completed as part of a project which received funding
from the\r\nEuropean Union’s Horizon 2020 research and innovation programme under
the Marie\r\nSkłodowska-Curie grant agreement No. 754411."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Julian
full_name: Lyczak, Julian
id: 3572849A-F248-11E8-B48F-1D18A9856A87
last_name: Lyczak
citation:
ama: Lyczak J. Order 5 Brauer–Manin obstructions to the integral Hasse principle
on log K3 surfaces. Annales de l’Institut Fourier. 2023;73(2):447-478.
doi:10.5802/aif.3529
apa: Lyczak, J. (2023). Order 5 Brauer–Manin obstructions to the integral Hasse
principle on log K3 surfaces. Annales de l’Institut Fourier. Association
des Annales de l’Institut Fourier. https://doi.org/10.5802/aif.3529
chicago: Lyczak, Julian. “Order 5 Brauer–Manin Obstructions to the Integral Hasse
Principle on Log K3 Surfaces.” Annales de l’Institut Fourier. Association
des Annales de l’Institut Fourier, 2023. https://doi.org/10.5802/aif.3529.
ieee: J. Lyczak, “Order 5 Brauer–Manin obstructions to the integral Hasse principle
on log K3 surfaces,” Annales de l’Institut Fourier, vol. 73, no. 2. Association
des Annales de l’Institut Fourier, pp. 447–478, 2023.
ista: Lyczak J. 2023. Order 5 Brauer–Manin obstructions to the integral Hasse principle
on log K3 surfaces. Annales de l’Institut Fourier. 73(2), 447–478.
mla: Lyczak, Julian. “Order 5 Brauer–Manin Obstructions to the Integral Hasse Principle
on Log K3 Surfaces.” Annales de l’Institut Fourier, vol. 73, no. 2, Association
des Annales de l’Institut Fourier, 2023, pp. 447–78, doi:10.5802/aif.3529.
short: J. Lyczak, Annales de l’Institut Fourier 73 (2023) 447–478.
date_created: 2023-08-06T22:01:12Z
date_published: 2023-05-12T00:00:00Z
date_updated: 2023-12-13T12:03:04Z
day: '12'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.5802/aif.3529
ec_funded: 1
external_id:
arxiv:
- '2005.14013'
isi:
- '001000279500001'
file:
- access_level: open_access
checksum: daf53fc614c894422e4c0fb3d2a2ae3e
content_type: application/pdf
creator: dernst
date_created: 2023-08-07T07:19:42Z
date_updated: 2023-08-07T07:19:42Z
file_id: '13977'
file_name: 2023_AnnalesFourier_Lyczak.pdf
file_size: 1529821
relation: main_file
success: 1
file_date_updated: 2023-08-07T07:19:42Z
has_accepted_license: '1'
intvolume: ' 73'
isi: 1
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: 447-478
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Annales de l'Institut Fourier
publication_identifier:
issn:
- 0373-0956
publication_status: published
publisher: Association des Annales de l'Institut Fourier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3
surfaces
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 73
year: '2023'
...
---
_id: '13974'
abstract:
- lang: eng
text: The Tverberg theorem is one of the cornerstones of discrete geometry. It states
that, given a set X of at least (d+1)(r−1)+1 points in Rd, one can find a partition
X=X1∪⋯∪Xr of X, such that the convex hulls of the Xi, i=1,…,r, all share a common
point. In this paper, we prove a trengthening of this theorem that guarantees
a partition which, in addition to the above, has the property that the boundaries
of full-dimensional convex hulls have pairwise nonempty intersections. Possible
generalizations and algorithmic aspects are also discussed. As a concrete application,
we show that any n points in the plane in general position span ⌊n/3⌋ vertex-disjoint
triangles that are pairwise crossing, meaning that their boundaries have pairwise
nonempty intersections; this number is clearly best possible. A previous result
of Álvarez-Rebollar et al. guarantees ⌊n/6⌋pairwise crossing triangles. Our result
generalizes to a result about simplices in Rd, d≥2.
acknowledgement: "Part of the research leading to this paper was done during the 16th
Gremo Workshop on Open Problems (GWOP), Waltensburg, Switzerland, June 12–16, 2018.
We thank Patrick Schnider for suggesting the problem, and Stefan Felsner, Malte
Milatz, and Emo Welzl for fruitful discussions during the workshop. We also thank
Stefan Felsner and Manfred Scheucher for finding, communicating the example from
Sect. 3.3, and the kind permission to include their visualization of the point set.
We thank Dömötör Pálvölgyi, the SoCG reviewers, and DCG reviewers for various helpful
comments.\r\nR. Fulek gratefully acknowledges support from Austrian Science Fund
(FWF), Project M2281-N35. A. Kupavskii was supported by the Advanced Postdoc.Mobility
Grant no. P300P2_177839 of the Swiss National Science Foundation. Research by P.
Valtr was supported by the Grant no. 18-19158 S of the Czech Science Foundation
(GAČR)."
article_processing_charge: No
article_type: original
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Bernd
full_name: Gärtner, Bernd
last_name: Gärtner
- first_name: Andrey
full_name: Kupavskii, Andrey
last_name: Kupavskii
- first_name: Pavel
full_name: Valtr, Pavel
last_name: Valtr
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. The crossing Tverberg theorem.
Discrete and Computational Geometry. 2023. doi:10.1007/s00454-023-00532-x
apa: Fulek, R., Gärtner, B., Kupavskii, A., Valtr, P., & Wagner, U. (2023).
The crossing Tverberg theorem. Discrete and Computational Geometry. Springer
Nature. https://doi.org/10.1007/s00454-023-00532-x
chicago: Fulek, Radoslav, Bernd Gärtner, Andrey Kupavskii, Pavel Valtr, and Uli
Wagner. “The Crossing Tverberg Theorem.” Discrete and Computational Geometry.
Springer Nature, 2023. https://doi.org/10.1007/s00454-023-00532-x.
ieee: R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, and U. Wagner, “The crossing
Tverberg theorem,” Discrete and Computational Geometry. Springer Nature,
2023.
ista: Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. 2023. The crossing Tverberg
theorem. Discrete and Computational Geometry.
mla: Fulek, Radoslav, et al. “The Crossing Tverberg Theorem.” Discrete and Computational
Geometry, Springer Nature, 2023, doi:10.1007/s00454-023-00532-x.
short: R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, U. Wagner, Discrete and Computational
Geometry (2023).
date_created: 2023-08-06T22:01:12Z
date_published: 2023-07-27T00:00:00Z
date_updated: 2023-12-13T12:03:35Z
day: '27'
department:
- _id: UlWa
doi: 10.1007/s00454-023-00532-x
external_id:
arxiv:
- '1812.04911'
isi:
- '001038546500001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1812.04911
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '6647'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: The crossing Tverberg theorem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13975'
abstract:
- lang: eng
text: "We consider the spectrum of random Laplacian matrices of the form Ln=An−Dn
where An\r\n is a real symmetric random matrix and Dn is a diagonal matrix whose
entries are equal to the corresponding row sums of An. If An is a Wigner matrix
with entries in the domain of attraction of a Gaussian distribution, the empirical
spectral measure of Ln is known to converge to the free convolution of a semicircle
distribution and a standard real Gaussian distribution. We consider real symmetric
random matrices An with independent entries (up to symmetry) whose row sums converge
to a purely non-Gaussian infinitely divisible distribution, which fall into the
class of Lévy–Khintchine random matrices first introduced by Jung [Trans Am Math
Soc, 370, (2018)]. Our main result shows that the empirical spectral measure of
Ln converges almost surely to a deterministic limit. A key step in the proof
is to use the purely non-Gaussian nature of the row sums to build a random operator
to which Ln converges in an appropriate sense. This operator leads to a recursive
distributional equation uniquely describing the Stieltjes transform of the limiting
empirical spectral measure."
acknowledgement: "The first author thanks Yizhe Zhu for pointing out reference [30].
We thank David Renfrew for comments on an earlier draft. We thank the anonymous
referee for a careful reading and helpful comments.\r\nOpen access funding provided
by Institute of Science and Technology (IST Austria)."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Andrew J
full_name: Campbell, Andrew J
id: 582b06a9-1f1c-11ee-b076-82ffce00dde4
last_name: Campbell
- first_name: Sean
full_name: O’Rourke, Sean
last_name: O’Rourke
citation:
ama: Campbell AJ, O’Rourke S. Spectrum of Lévy–Khintchine random laplacian matrices.
Journal of Theoretical Probability. 2023. doi:10.1007/s10959-023-01275-4
apa: Campbell, A. J., & O’Rourke, S. (2023). Spectrum of Lévy–Khintchine random
laplacian matrices. Journal of Theoretical Probability. Springer Nature.
https://doi.org/10.1007/s10959-023-01275-4
chicago: Campbell, Andrew J, and Sean O’Rourke. “Spectrum of Lévy–Khintchine Random
Laplacian Matrices.” Journal of Theoretical Probability. Springer Nature,
2023. https://doi.org/10.1007/s10959-023-01275-4.
ieee: A. J. Campbell and S. O’Rourke, “Spectrum of Lévy–Khintchine random laplacian
matrices,” Journal of Theoretical Probability. Springer Nature, 2023.
ista: Campbell AJ, O’Rourke S. 2023. Spectrum of Lévy–Khintchine random laplacian
matrices. Journal of Theoretical Probability.
mla: Campbell, Andrew J., and Sean O’Rourke. “Spectrum of Lévy–Khintchine Random
Laplacian Matrices.” Journal of Theoretical Probability, Springer Nature,
2023, doi:10.1007/s10959-023-01275-4.
short: A.J. Campbell, S. O’Rourke, Journal of Theoretical Probability (2023).
date_created: 2023-08-06T22:01:13Z
date_published: 2023-07-26T00:00:00Z
date_updated: 2023-12-13T12:00:50Z
day: '26'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s10959-023-01275-4
external_id:
arxiv:
- '2210.07927'
isi:
- '001038341000001'
has_accepted_license: '1'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s10959-023-01275-4
month: '07'
oa: 1
oa_version: Published Version
publication: Journal of Theoretical Probability
publication_identifier:
eissn:
- 1572-9230
issn:
- 0894-9840
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spectrum of Lévy–Khintchine random laplacian matrices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13257'
abstract:
- lang: eng
text: The magnetotropic susceptibility is the thermodynamic coefficient associated
with the rotational anisotropy of the free energy in an external magnetic field
and is closely related to the magnetic susceptibility. It emerges naturally in
frequency-shift measurements of oscillating mechanical cantilevers, which are
becoming an increasingly important tool in the quantitative study of the thermodynamics
of modern condensed-matter systems. Here we discuss the basic properties of the
magnetotropic susceptibility as they relate to the experimental aspects of frequency-shift
measurements, as well as to the interpretation of those experiments in terms of
the intrinsic properties of the system under study.
acknowledgement: "We thank Aharon Kapitulnik, Philip Moll, and Andreas Rydh for illuminating
discussions. The work at the Los Alamos National Laboratory is supported by National
Science Foundation Cooperative Agreements No. DMR-1157490 and No. DMR-1644779, the
state of Florida, and the U.S. Department of Energy. A.S. acknowledges support from
the DOE/BES Science of 100T grant. B.J.R. acknowledges funding from the National
Science Foundation under Grant No.\r\nDMR-1752784."
article_number: '035111'
article_processing_charge: No
article_type: original
author:
- first_name: A.
full_name: Shekhter, A.
last_name: Shekhter
- first_name: R. D.
full_name: Mcdonald, R. D.
last_name: Mcdonald
- first_name: B. J.
full_name: Ramshaw, B. J.
last_name: Ramshaw
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
citation:
ama: Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. Magnetotropic susceptibility.
Physical Review B. 2023;108(3). doi:10.1103/PhysRevB.108.035111
apa: Shekhter, A., Mcdonald, R. D., Ramshaw, B. J., & Modic, K. A. (2023). Magnetotropic
susceptibility. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.035111
chicago: Shekhter, A., R. D. Mcdonald, B. J. Ramshaw, and Kimberly A Modic. “Magnetotropic
Susceptibility.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.035111.
ieee: A. Shekhter, R. D. Mcdonald, B. J. Ramshaw, and K. A. Modic, “Magnetotropic
susceptibility,” Physical Review B, vol. 108, no. 3. American Physical
Society, 2023.
ista: Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. 2023. Magnetotropic susceptibility.
Physical Review B. 108(3), 035111.
mla: Shekhter, A., et al. “Magnetotropic Susceptibility.” Physical Review B,
vol. 108, no. 3, 035111, American Physical Society, 2023, doi:10.1103/PhysRevB.108.035111.
short: A. Shekhter, R.D. Mcdonald, B.J. Ramshaw, K.A. Modic, Physical Review B 108
(2023).
date_created: 2023-07-23T22:01:10Z
date_published: 2023-07-15T00:00:00Z
date_updated: 2023-12-13T11:58:57Z
day: '15'
department:
- _id: KiMo
doi: 10.1103/PhysRevB.108.035111
external_id:
arxiv:
- '2208.10038'
isi:
- '001062708600002'
intvolume: ' 108'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2208.10038
month: '07'
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: Magnetotropic susceptibility
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '13972'
abstract:
- lang: eng
text: This Special Collection is dedicated to the field of photocatalytic synthesis
and contains a diverse selection of original research contributions. It includes
studies on catalyst development, mechanistic investigations, method development
and the use of enabling technologies, illustrating the many facets of state-of-the-art
research in photocatalytic synthesis. Further, emerging topics are surveyed and
discussed in three reviews and a concept article.
article_number: e202300683
article_processing_charge: No
article_type: letter_note
author:
- first_name: Line
full_name: Næsborg, Line
last_name: Næsborg
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
- first_name: Oliver S.
full_name: Wenger, Oliver S.
last_name: Wenger
citation:
ama: 'Næsborg L, Pieber B, Wenger OS. Special Collection: Photocatalytic synthesis.
ChemCatChem. 2023. doi:10.1002/cctc.202300683'
apa: 'Næsborg, L., Pieber, B., & Wenger, O. S. (2023). Special Collection: Photocatalytic
synthesis. ChemCatChem. Wiley. https://doi.org/10.1002/cctc.202300683'
chicago: 'Næsborg, Line, Bartholomäus Pieber, and Oliver S. Wenger. “Special Collection:
Photocatalytic Synthesis.” ChemCatChem. Wiley, 2023. https://doi.org/10.1002/cctc.202300683.'
ieee: 'L. Næsborg, B. Pieber, and O. S. Wenger, “Special Collection: Photocatalytic
synthesis,” ChemCatChem. Wiley, 2023.'
ista: 'Næsborg L, Pieber B, Wenger OS. 2023. Special Collection: Photocatalytic
synthesis. ChemCatChem., e202300683.'
mla: 'Næsborg, Line, et al. “Special Collection: Photocatalytic Synthesis.” ChemCatChem,
e202300683, Wiley, 2023, doi:10.1002/cctc.202300683.'
short: L. Næsborg, B. Pieber, O.S. Wenger, ChemCatChem (2023).
date_created: 2023-08-06T22:01:12Z
date_published: 2023-07-27T00:00:00Z
date_updated: 2023-12-13T12:02:26Z
day: '27'
department:
- _id: BaPi
doi: 10.1002/cctc.202300683
external_id:
isi:
- '001037859900001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/cctc.202300683
month: '07'
oa: 1
oa_version: Published Version
publication: ChemCatChem
publication_identifier:
eissn:
- 1867-3899
issn:
- 1867-3880
publication_status: epub_ahead
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Special Collection: Photocatalytic synthesis'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13968'
abstract:
- lang: eng
text: The use of multimodal readout mechanisms next to label-free real-time monitoring
of biomolecular interactions can provide valuable insight into surface-based reaction
mechanisms. To this end, the combination of an electrolyte-gated field-effect
transistor (EG-FET) with a fiber optic-coupled surface plasmon resonance (FO-SPR)
probe serving as gate electrode has been investigated to deconvolute surface mass
and charge density variations associated to surface reactions. However, applying
an electrochemical potential on such gold-coated FO-SPR gate electrodes can induce
gradual morphological changes of the thin gold film, leading to an irreversible
blue-shift of the SPR wavelength and a substantial signal drift. We show that
mild annealing leads to optical and electronic signal stabilization (20-fold lower
signal drift than as-sputtered fiber optic gates) and improved overall analytical
performance characteristics. The thermal treatment prevents morphological changes
of the thin gold-film occurring during operation, hence providing reliable and
stable data immediately upon gate voltage application. Thus, the readout output
of both transducing principles, the optical FO-SPR and electronic EG-FET, stays
constant throughout the whole sensing time-window and the long-term effect of
thermal treatment is also improved, providing stable signals even after 1 year
of storage. Annealing should therefore be considered a necessary modification
for applying fiber optic gate electrodes in real-time multimodal investigations
of surface reactions at the solid-liquid interface.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "This project has received funding from the European Union’s Horizon
2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement
No. 813863–BORGES. We further thank the office of the Federal Government of Lower
Austria, K3-Group–Culture, Science and Education, for their financial support as
part of the project “Responsive Wound Dressing”. We gratefully acknowledge the financial
support from the Austrian Research Promotion Agency (FFG; 888067).\r\nWe thank the
Electron Microscopy Facility at IST Austria for their support with sputter coating
the FO tips and Bernhard Pichler from AIT for software development to facilitate
data evaluation."
article_number: '1202132'
article_processing_charge: Yes
article_type: original
author:
- first_name: Roger
full_name: Hasler, Roger
last_name: Hasler
- first_name: Marie Helene
full_name: Steger-Polt, Marie Helene
last_name: Steger-Polt
- first_name: Ciril
full_name: Reiner-Rozman, Ciril
last_name: Reiner-Rozman
- first_name: Stefan
full_name: Fossati, Stefan
last_name: Fossati
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Patrik
full_name: Aspermair, Patrik
last_name: Aspermair
- first_name: Christoph
full_name: Kleber, Christoph
last_name: Kleber
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Jakub
full_name: Dostalek, Jakub
last_name: Dostalek
- first_name: Wolfgang
full_name: Knoll, Wolfgang
last_name: Knoll
citation:
ama: 'Hasler R, Steger-Polt MH, Reiner-Rozman C, et al. Optical and electronic signal
stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time
dual-mode biosensing. Frontiers in Physics. 2023;11. doi:10.3389/fphy.2023.1202132'
apa: 'Hasler, R., Steger-Polt, M. H., Reiner-Rozman, C., Fossati, S., Lee, S., Aspermair,
P., … Knoll, W. (2023). Optical and electronic signal stabilization of plasmonic
fiber optic gate electrodes: Towards improved real-time dual-mode biosensing.
Frontiers in Physics. Frontiers. https://doi.org/10.3389/fphy.2023.1202132'
chicago: 'Hasler, Roger, Marie Helene Steger-Polt, Ciril Reiner-Rozman, Stefan Fossati,
Seungho Lee, Patrik Aspermair, Christoph Kleber, Maria Ibáñez, Jakub Dostalek,
and Wolfgang Knoll. “Optical and Electronic Signal Stabilization of Plasmonic
Fiber Optic Gate Electrodes: Towards Improved Real-Time Dual-Mode Biosensing.”
Frontiers in Physics. Frontiers, 2023. https://doi.org/10.3389/fphy.2023.1202132.'
ieee: 'R. Hasler et al., “Optical and electronic signal stabilization of
plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing,”
Frontiers in Physics, vol. 11. Frontiers, 2023.'
ista: 'Hasler R, Steger-Polt MH, Reiner-Rozman C, Fossati S, Lee S, Aspermair P,
Kleber C, Ibáñez M, Dostalek J, Knoll W. 2023. Optical and electronic signal stabilization
of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode
biosensing. Frontiers in Physics. 11, 1202132.'
mla: 'Hasler, Roger, et al. “Optical and Electronic Signal Stabilization of Plasmonic
Fiber Optic Gate Electrodes: Towards Improved Real-Time Dual-Mode Biosensing.”
Frontiers in Physics, vol. 11, 1202132, Frontiers, 2023, doi:10.3389/fphy.2023.1202132.'
short: R. Hasler, M.H. Steger-Polt, C. Reiner-Rozman, S. Fossati, S. Lee, P. Aspermair,
C. Kleber, M. Ibáñez, J. Dostalek, W. Knoll, Frontiers in Physics 11 (2023).
date_created: 2023-08-06T22:01:11Z
date_published: 2023-07-14T00:00:00Z
date_updated: 2023-12-13T12:04:10Z
day: '14'
ddc:
- '530'
department:
- _id: MaIb
doi: 10.3389/fphy.2023.1202132
external_id:
isi:
- '001038636400001'
file:
- access_level: open_access
checksum: fb36dda665e57bab006a000bf0faacd5
content_type: application/pdf
creator: dernst
date_created: 2023-08-07T07:48:11Z
date_updated: 2023-08-07T07:48:11Z
file_id: '13978'
file_name: 2023_FrontiersPhysics_Hasler.pdf
file_size: 2421758
relation: main_file
success: 1
file_date_updated: 2023-08-07T07:48:11Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Frontiers in Physics
publication_identifier:
eissn:
- 2296-424X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Optical and electronic signal stabilization of plasmonic fiber optic gate
electrodes: Towards improved real-time dual-mode biosensing'
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: 11
year: '2023'
...
---
_id: '14042'
abstract:
- lang: eng
text: Long-time and large-data existence of weak solutions for initial- and boundary-value
problems concerning three-dimensional flows of incompressible fluids is nowadays
available not only for Navier–Stokes fluids but also for various fluid models
where the relation between the Cauchy stress tensor and the symmetric part of
the velocity gradient is nonlinear. The majority of such studies however concerns
models where such a dependence is explicit (the stress is a function of the velocity
gradient), which makes the class of studied models unduly restrictive. The same
concerns boundary conditions, or more precisely the slipping mechanisms on the
boundary, where the no-slip is still the most preferred condition considered in
the literature. Our main objective is to develop a robust mathematical theory
for unsteady internal flows of implicitly constituted incompressible fluids with
implicit relations between the tangential projections of the velocity and the
normal traction on the boundary. The theory covers numerous rheological models
used in chemistry, biorheology, polymer and food industry as well as in geomechanics.
It also includes, as special cases, nonlinear slip as well as stick–slip boundary
conditions. Unlike earlier studies, the conditions characterizing admissible classes
of constitutive equations are expressed by means of tools of elementary calculus.
In addition, a fully constructive proof (approximation scheme) is incorporated.
Finally, we focus on the question of uniqueness of such weak solutions.
acknowledgement: "M. Bulíček and J. Málek acknowledge the support of the project No.
20-11027X financed by the Czech Science foundation (GAČR). M. Bulíček and J. Málek
are members of the Nečas Center for Mathematical Modelling.\r\nOpen access publishing
supported by the National Technical Library in Prague."
article_number: '72'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Miroslav
full_name: Bulíček, Miroslav
last_name: Bulíček
- first_name: Josef
full_name: Málek, Josef
last_name: Málek
- first_name: Erika
full_name: Maringová, Erika
id: dbabca31-66eb-11eb-963a-fb9c22c880b4
last_name: Maringová
citation:
ama: Bulíček M, Málek J, Maringová E. On unsteady internal flows of incompressible
fluids characterized by implicit constitutive equations in the bulk and on the
boundary. Journal of Mathematical Fluid Mechanics. 2023;25(3). doi:10.1007/s00021-023-00803-w
apa: Bulíček, M., Málek, J., & Maringová, E. (2023). On unsteady internal flows
of incompressible fluids characterized by implicit constitutive equations in the
bulk and on the boundary. Journal of Mathematical Fluid Mechanics. Springer
Nature. https://doi.org/10.1007/s00021-023-00803-w
chicago: Bulíček, Miroslav, Josef Málek, and Erika Maringová. “On Unsteady Internal
Flows of Incompressible Fluids Characterized by Implicit Constitutive Equations
in the Bulk and on the Boundary.” Journal of Mathematical Fluid Mechanics.
Springer Nature, 2023. https://doi.org/10.1007/s00021-023-00803-w.
ieee: M. Bulíček, J. Málek, and E. Maringová, “On unsteady internal flows of incompressible
fluids characterized by implicit constitutive equations in the bulk and on the
boundary,” Journal of Mathematical Fluid Mechanics, vol. 25, no. 3. Springer
Nature, 2023.
ista: Bulíček M, Málek J, Maringová E. 2023. On unsteady internal flows of incompressible
fluids characterized by implicit constitutive equations in the bulk and on the
boundary. Journal of Mathematical Fluid Mechanics. 25(3), 72.
mla: Bulíček, Miroslav, et al. “On Unsteady Internal Flows of Incompressible Fluids
Characterized by Implicit Constitutive Equations in the Bulk and on the Boundary.”
Journal of Mathematical Fluid Mechanics, vol. 25, no. 3, 72, Springer Nature,
2023, doi:10.1007/s00021-023-00803-w.
short: M. Bulíček, J. Málek, E. Maringová, Journal of Mathematical Fluid Mechanics
25 (2023).
date_created: 2023-08-13T22:01:13Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-12-13T12:08:08Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s00021-023-00803-w
external_id:
arxiv:
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isi:
- '001040354900001'
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- iso: eng
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oa_version: Published Version
publication: Journal of Mathematical Fluid Mechanics
publication_identifier:
eissn:
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issn:
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publication_status: published
publisher: Springer Nature
quality_controlled: '1'
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title: On unsteady internal flows of incompressible fluids characterized by implicit
constitutive equations in the bulk and on the boundary
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)
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type: journal_article
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volume: 25
year: '2023'
...
---
_id: '14041'
abstract:
- lang: eng
text: Tissue morphogenesis and patterning during development involve the segregation
of cell types. Segregation is driven by differential tissue surface tensions generated
by cell types through controlling cell-cell contact formation by regulating adhesion
and actomyosin contractility-based cellular cortical tensions. We use vertebrate
tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional
heterotypic segregation and developed a quantitative analysis of their dynamics
based on 3D time-lapse microscopy. We show that general inhibition of actomyosin
contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific
inhibition of non-muscle myosin2 activity by overexpression of myosin assembly
inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction
during aggregation and inverted geometry observed during segregation. The same
is observed when we express a constitutively active Rho kinase isoform to ubiquitously
keep actomyosin contractility high at cell-cell and cell-medium interfaces and
thus overriding the interface-specific regulation of cortical tensions. Tissue
surface tension regulation can become an effective tool in tissue engineering.
acknowledgement: "We thank Marton Gulyas (ELTE Eötvös University) for development
of videomicroscopy experiment manager and image analysis software. Authors are grateful
to Gabor Forgacs (University of Missouri) for critical reading of earlier versions
of this manuscript as well as to Zsuzsa Akos and Andras Czirok (ELTE Eötvös University)
for fruitful discussions. This work was supported by EU FP7, ERC COLLMOT Project
No 227878 to TV, the National Research Development and Innovation Fund of Hungary,
K119359 and also Project No 2018-1.2.1-NKP-2018-00005 to LN. This project has received
funding from the European Union’s Horizon 2020 research and innovation programme
under the Marie Sklodowska-Curie grant agreement No 955576. MV was supported by
the Ja´nos Bolyai Fellowship of the Hungarian Academy of Sciences.\r\nOpen access
funding provided by Eötvös Loránd University."
article_number: '817'
article_processing_charge: Yes
article_type: original
author:
- first_name: Elod
full_name: Méhes, Elod
last_name: Méhes
- first_name: Enys
full_name: Mones, Enys
last_name: Mones
- first_name: Máté
full_name: Varga, Máté
last_name: Varga
- first_name: Áron
full_name: Zsigmond, Áron
last_name: Zsigmond
- first_name: Beáta
full_name: Biri-Kovács, Beáta
last_name: Biri-Kovács
- first_name: László
full_name: Nyitray, László
last_name: Nyitray
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Tamás
full_name: Vicsek, Tamás
last_name: Vicsek
citation:
ama: Méhes E, Mones E, Varga M, et al. 3D cell segregation geometry and dynamics
are governed by tissue surface tension regulation. Communications Biology.
2023;6. doi:10.1038/s42003-023-05181-7
apa: Méhes, E., Mones, E., Varga, M., Zsigmond, Á., Biri-Kovács, B., Nyitray, L.,
… Vicsek, T. (2023). 3D cell segregation geometry and dynamics are governed by
tissue surface tension regulation. Communications Biology. Springer Nature.
https://doi.org/10.1038/s42003-023-05181-7
chicago: Méhes, Elod, Enys Mones, Máté Varga, Áron Zsigmond, Beáta Biri-Kovács,
László Nyitray, Vanessa Barone, Gabriel Krens, Carl-Philipp J Heisenberg, and
Tamás Vicsek. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue
Surface Tension Regulation.” Communications Biology. Springer Nature, 2023.
https://doi.org/10.1038/s42003-023-05181-7.
ieee: E. Méhes et al., “3D cell segregation geometry and dynamics are governed
by tissue surface tension regulation,” Communications Biology, vol. 6.
Springer Nature, 2023.
ista: Méhes E, Mones E, Varga M, Zsigmond Á, Biri-Kovács B, Nyitray L, Barone V,
Krens G, Heisenberg C-PJ, Vicsek T. 2023. 3D cell segregation geometry and dynamics
are governed by tissue surface tension regulation. Communications Biology. 6,
817.
mla: Méhes, Elod, et al. “3D Cell Segregation Geometry and Dynamics Are Governed
by Tissue Surface Tension Regulation.” Communications Biology, vol. 6,
817, Springer Nature, 2023, doi:10.1038/s42003-023-05181-7.
short: E. Méhes, E. Mones, M. Varga, Á. Zsigmond, B. Biri-Kovács, L. Nyitray, V.
Barone, G. Krens, C.-P.J. Heisenberg, T. Vicsek, Communications Biology 6 (2023).
date_created: 2023-08-13T22:01:13Z
date_published: 2023-08-04T00:00:00Z
date_updated: 2023-12-13T12:07:33Z
day: '04'
ddc:
- '570'
department:
- _id: CaHe
- _id: Bio
doi: 10.1038/s42003-023-05181-7
external_id:
isi:
- '001042544100001'
pmid:
- '37542157'
file:
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checksum: 1f9324f736bdbb76426b07736651c4cd
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T07:17:36Z
date_updated: 2023-08-14T07:17:36Z
file_id: '14045'
file_name: 2023_CommBiology_Mehes.pdf
file_size: 10181997
relation: main_file
success: 1
file_date_updated: 2023-08-14T07:17:36Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Communications Biology
publication_identifier:
eissn:
- 2399-3642
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 3D cell segregation geometry and dynamics are governed by tissue surface tension
regulation
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: 6
year: '2023'
...