---
_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:
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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'
department:
- _id: FlSc
- _id: EM-Fac
doi: 10.1126/sciadv.add6495
external_id:
isi:
- '000964550100015'
file:
- access_level: open_access
checksum: ce81a6d0b84170e5e8c62f6acfa15d9e
content_type: application/pdf
creator: dernst
date_created: 2023-01-23T07:45:54Z
date_updated: 2023-01-23T07:45:54Z
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file_size: 1756234
relation: main_file
success: 1
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has_accepted_license: '1'
intvolume: ' 9'
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keyword:
- Multidisciplinary
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
record:
- id: '14562'
relation: research_data
status: public
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:
- contributor_type: researcher
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'
ddc:
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month: '11'
oa: 1
oa_version: Published Version
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:
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relation: used_in_publication
status: public
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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...
---
_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
file:
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checksum: a8b9adeb53a4109dea4d5e39fa1acccf
content_type: application/zip
creator: fschur
date_created: 2023-11-08T20:23:07Z
date_updated: 2023-11-08T20:23:07Z
file_id: '14503'
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
relation: main_file
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:
- access_level: open_access
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
relation: main_file
success: 1
file_date_updated: 2023-11-27T08:45:56Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
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
creator: ipalaia
date_created: 2023-10-30T16:31:08Z
date_updated: 2023-10-30T16:31:08Z
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file_size: 62821432
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success: 1
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checksum: 389eab31c6509dbc05795017fb618758
content_type: text/plain
creator: dernst
date_created: 2023-10-31T08:57:50Z
date_updated: 2023-10-31T08:57:50Z
file_id: '14474'
file_name: README.txt
file_size: 1697
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file_date_updated: 2023-10-31T08:57:50Z
has_accepted_license: '1'
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
date_updated: 2023-11-28T09:17:38Z
day: '15'
ddc:
- '000'
department:
- _id: ElKo
file:
- access_level: open_access
checksum: 1a730765930138e23c6efd2575872641
content_type: application/pdf
creator: dernst
date_created: 2023-11-28T09:14:34Z
date_updated: 2023-11-28T09:14:34Z
file_id: '14621'
file_name: 2023_USENIX_Das.pdf
file_size: 704331
relation: main_file
success: 1
file_date_updated: 2023-11-28T09:14:34Z
has_accepted_license: '1'
intvolume: ' 8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2022/1389
month: '08'
oa: 1
oa_version: Published Version
page: 5359-5376
project:
- _id: 34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f
grant_number: F8512
name: Secure Network and Hardware for Efficient Blockchains
publication: 32nd USENIX Security Symposium
publication_identifier:
isbn:
- '9781713879497'
publication_status: published
publisher: Usenix
quality_controlled: '1'
scopus_import: '1'
status: public
title: Practical asynchronous high-threshold distributed key generation and distributed
polynomial sampling
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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
date_published: 2023-11-14T00:00:00Z
date_updated: 2023-11-28T08:39:23Z
day: '14'
ddc:
- '530'
- '540'
department:
- _id: BiCh
doi: 10.1063/5.0173341
external_id:
arxiv:
- '2308.10886'
file:
- access_level: open_access
checksum: f668ee0d07096eef81159d05bc27aabc
content_type: application/pdf
creator: dernst
date_created: 2023-11-28T08:39:06Z
date_updated: 2023-11-28T08:39:06Z
file_id: '14620'
file_name: 2023_JourChemicalPhysics_Reinhardt.pdf
file_size: 6276059
relation: main_file
success: 1
file_date_updated: 2023-11-28T08:39:06Z
has_accepted_license: '1'
intvolume: ' 159'
issue: '18'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
record:
- id: '14619'
relation: research_data
status: public
scopus_import: '1'
status: public
title: A streamlined molecular-dynamics workflow for computing solubilities of molecular
and ionic crystals
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: 159
year: '2023'
...
---
_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:
- 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. 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
day: '02'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/evolut/qpad169
external_id:
pmid:
- '37738212'
file:
- access_level: open_access
checksum: b66dc10edae92d38918d534e64dda77c
content_type: application/pdf
creator: dernst
date_created: 2023-11-28T08:12:15Z
date_updated: 2023-11-28T08:12:15Z
file_id: '14618'
file_name: 2023_Evolution_Toups.pdf
file_size: 1399102
relation: main_file
success: 1
file_date_updated: 2023-11-28T08:12:15Z
has_accepted_license: '1'
intvolume: ' 77'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 2504-2511
pmid: 1
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://git.ista.ac.at/bvicoso/veryoldx
record:
- id: '14616'
relation: research_data
status: public
- id: '14617'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The X chromosome of insects likely predates the origin of class Insecta
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: 77
year: '2023'
...
---
_id: '14616'
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:10.5061/DRYAD.HX3FFBGKT
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
day: '15'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.5061/DRYAD.HX3FFBGKT
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.hx3ffbgkt
month: '09'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '14604'
relation: used_in_publication
status: public
status: public
title: The X chromosome of insects likely predates the origin of Class Insecta
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14617'
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).
date_created: 2023-11-28T08:04:03Z
date_published: 2023-09-15T00:00:00Z
date_updated: 2023-11-28T08:25:28Z
day: '15'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.5281/ZENODO.8138705
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8138705
month: '09'
oa: 1
oa_version: Published Version
other_data_license: MIT License
publisher: Zenodo
related_material:
record:
- id: '14604'
relation: used_in_publication
status: public
status: public
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:
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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
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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'
...