---
OA_place: repository
OA_type: green
_id: '18446'
abstract:
- lang: eng
text: How living systems achieve precision in form and function despite their intrinsic
stochasticity is a fundamental yet ongoing question in biology. We generated morphomaps
of preimplantation embryogenesis in mouse, rabbit, and monkey embryos, and these
morphomaps revealed that although blastomere divisions desynchronized passively,
8-cell embryos converged toward robust three-dimensional shapes. Using topological
analysis and genetic perturbations, we found that embryos progressively changed
their cellular connectivity to a preferred topology, which could be predicted
by a physical model in which actomyosin contractility and noise facilitate topological
transitions, lowering surface energy. This mechanism favored regular embryo packing
and promoted a higher number of inner cells in the 16-cell embryo. Synchronized
division reduced embryo packing and generated substantially more misallocated
cells and fewer inner-cell–mass cells. These findings suggest that stochasticity
in division timing contributes to robust patterning.
acknowledgement: "We are grateful to the members of the Hiiragi laboratory for discussions
and comments on the manuscript: R. Bloehs, S. Friese, S. Hozeifi, L. Pérez, and
W. Schwarzer for their technical support; V. Janssen for establishing the PAB protocol;
members of the Tsukiyama group for the animal care with monkeys, in particular H.
Tsuchiya and M. Nakaya; Unité Commune d’Expérimentation Animale (UCEA, Jouy-en-Josas,
France) for the animal care with rabbits; the EMBL electronic and mechanical workshops
and the EMBL animal facility for their support; We thank Luxendo for the close collaboration
in developing the light-sheet microscopy for mammalian embryos.\r\nFunding: This
work was funded by the following: EMBL Interdisciplinary Postdoc Program (EIPOD)
under Marie Sklodowska Curie Actions COFUND III RTD (to D.F.); JSPS Overseas Research
Fellowship (to T.I.); Field of excellence “Complexity of life in basic research
and innovation” of the University of Graz (to B.C.M.); European Research Council,
ERC Advanced Grant “SelforganisingEmbryo”, grant agreement 742732; ERC Advanced
Grant “COORDINATION” grant agreement 101055287 (to T.H.); Stichting LSH-TKI, grant
LSHM21020 (to T.H.) JSPS KAKENHI grants JP21H05038 and JP22H05166 (to T.H.)"
article_number: eadh1145
article_processing_charge: No
article_type: original
author:
- first_name: Dimitri
full_name: Fabrèges, Dimitri
last_name: Fabrèges
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Prachiti
full_name: Moghe, Prachiti
last_name: Moghe
- first_name: Alison
full_name: Kickuth, Alison
last_name: Kickuth
- first_name: Takafumi
full_name: Ichikawa, Takafumi
last_name: Ichikawa
- first_name: Chizuru
full_name: Iwatani, Chizuru
last_name: Iwatani
- first_name: Tomoyuki
full_name: Tsukiyama, Tomoyuki
last_name: Tsukiyama
- first_name: Nathalie
full_name: Daniel, Nathalie
last_name: Daniel
- first_name: Julie
full_name: Gering, Julie
last_name: Gering
- first_name: Anniek
full_name: Stokkermans, Anniek
last_name: Stokkermans
- first_name: Adrian
full_name: Wolny, Adrian
last_name: Wolny
- first_name: Anna
full_name: Kreshuk, Anna
last_name: Kreshuk
- first_name: Véronique
full_name: Duranthon, Véronique
last_name: Duranthon
- first_name: Virginie
full_name: Uhlman, Virginie
last_name: Uhlman
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Takashi
full_name: Hiiragi, Takashi
last_name: Hiiragi
citation:
ama: Fabrèges D, Corominas-Murtra B, Moghe P, et al. Temporal variability and cell
mechanics control robustness in mammalian embryogenesis. Science. 2024;386(6718).
doi:10.1126/science.adh1145
apa: Fabrèges, D., Corominas-Murtra, B., Moghe, P., Kickuth, A., Ichikawa, T., Iwatani,
C., … Hiiragi, T. (2024). Temporal variability and cell mechanics control robustness
in mammalian embryogenesis. Science. AAAS. https://doi.org/10.1126/science.adh1145
chicago: Fabrèges, Dimitri, Bernat Corominas-Murtra, Prachiti Moghe, Alison Kickuth,
Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, et al. “Temporal Variability
and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” Science.
AAAS, 2024. https://doi.org/10.1126/science.adh1145.
ieee: D. Fabrèges et al., “Temporal variability and cell mechanics control
robustness in mammalian embryogenesis,” Science, vol. 386, no. 6718. AAAS,
2024.
ista: Fabrèges D, Corominas-Murtra B, Moghe P, Kickuth A, Ichikawa T, Iwatani C,
Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon
V, Uhlman V, Hannezo EB, Hiiragi T. 2024. Temporal variability and cell mechanics
control robustness in mammalian embryogenesis. Science. 386(6718), eadh1145.
mla: Fabrèges, Dimitri, et al. “Temporal Variability and Cell Mechanics Control
Robustness in Mammalian Embryogenesis.” Science, vol. 386, no. 6718, eadh1145,
AAAS, 2024, doi:10.1126/science.adh1145.
short: D. Fabrèges, B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani,
T. Tsukiyama, N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon,
V. Uhlman, E.B. Hannezo, T. Hiiragi, Science 386 (2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: "All original code and data reported in this paper is publicly
available as of the date of publication on Zenodo (124).\r\n124\r\nD. Fabrèges,
B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani, T. Tsukiyama,
N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon, V. Uhlmann,
E. Hannezo, T. Hiiragi, Temporal variability and cell mechanics control robustness
in mammalian embryogenesis, version 1.0, Zenodo (2024); https://doi.org/10.5281/ZENODO.12819781."
date_created: 2024-10-20T22:02:06Z
date_published: 2024-10-11T00:00:00Z
date_updated: 2026-10-01T10:54:32Z
day: '11'
department:
- _id: EdHa
doi: 10.1126/science.adh1145
external_id:
isi:
- '001422132300018'
pmid:
- '39388574'
fulldoi: https://doi.org/10.1126/science.adh1145
intvolume: ' 386'
isi: 1
issue: '6718'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.inrae.fr/hal-04447081v1/file/2023.01.24.525420.full.pdf
month: '10'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: AAAS
quality_controlled: '1'
related_material:
record:
- id: '23023'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Temporal variability and cell mechanics control robustness in mammalian embryogenesis
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 386
year: '2024'
...
---
_id: '18071'
abstract:
- lang: eng
text: Recent advancements on DAG-based consensus protocols allow for blockchains
with improved metrics and properties, such as throughput and censorship-resistance.
Variants of the Bullshark [18] consensus protocol are adopted for practical use
by the Sui blockchain, for improved latency. However, the protocol is leader-based,
and is strongly affected by crashed leaders that can lead to various performance
issues, for example, decreased transaction throughput. In this paper, we propose
HammerHead, a DAG-based consensus protocol, that is inspired by Carousel [8] and
provides Leader-Utilization. Our proposal differs from Carousel, which is built
for a chained consensus protocol; in HammerHead chain quality is inherited by
the DAG. HammerHead needs to preserve safety and liveness, despite validators
committing leader vertices asynchronously. The key idea is to update leader schedules
dynamically, based on the validators' scores during the previous schedule. We
implement HammerHead and show a minor improvement in performance for cases without
faults. The major improvements in comparison to Bullshark appear in faulty settings.
Specifically, we show a drastic, 2x-latency improvement and up to 40% increased
throughput when crash faults occur (100 validators, 33 faults).
acknowledgement: This work is supported by Mysten Labs. We thank the Mysten Labs Engineering
teams for valuable feedback broadly, and specifically to Laura Makdah for helping
implementing the early reputation score system for validators and Dmitry Perelman
for managing the overall implementation effort.
article_processing_charge: No
arxiv: 1
author:
- first_name: Giorgos
full_name: Tsimos, Giorgos
last_name: Tsimos
- first_name: Anastasios
full_name: Kichidis, Anastasios
last_name: Kichidis
- first_name: Alberto
full_name: Sonnino, Alberto
last_name: Sonnino
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
orcid: 0000-0002-8827-3382
citation:
ama: 'Tsimos G, Kichidis A, Sonnino A, Kokoris Kogias E. HammerHead: Leader reputation
for dynamic scheduling. In: Proceedings - International Conference on Distributed
Computing Systems. IEEE; 2024:1377-1387. doi:10.1109/ICDCS60910.2024.00129'
apa: 'Tsimos, G., Kichidis, A., Sonnino, A., & Kokoris Kogias, E. (2024). HammerHead:
Leader reputation for dynamic scheduling. In Proceedings - International Conference
on Distributed Computing Systems (pp. 1377–1387). Jersey City, NJ, United
States: IEEE. https://doi.org/10.1109/ICDCS60910.2024.00129'
chicago: 'Tsimos, Giorgos, Anastasios Kichidis, Alberto Sonnino, and Eleftherios
Kokoris Kogias. “HammerHead: Leader Reputation for Dynamic Scheduling.” In Proceedings
- International Conference on Distributed Computing Systems, 1377–87. IEEE,
2024. https://doi.org/10.1109/ICDCS60910.2024.00129.'
ieee: 'G. Tsimos, A. Kichidis, A. Sonnino, and E. Kokoris Kogias, “HammerHead: Leader
reputation for dynamic scheduling,” in Proceedings - International Conference
on Distributed Computing Systems, Jersey City, NJ, United States, 2024, pp.
1377–1387.'
ista: 'Tsimos G, Kichidis A, Sonnino A, Kokoris Kogias E. 2024. HammerHead: Leader
reputation for dynamic scheduling. Proceedings - International Conference on Distributed
Computing Systems. ICDCS: International Conference on Distributed Computing Systems,
1377–1387.'
mla: 'Tsimos, Giorgos, et al. “HammerHead: Leader Reputation for Dynamic Scheduling.”
Proceedings - International Conference on Distributed Computing Systems,
IEEE, 2024, pp. 1377–87, doi:10.1109/ICDCS60910.2024.00129.'
short: G. Tsimos, A. Kichidis, A. Sonnino, E. Kokoris Kogias, in:, Proceedings -
International Conference on Distributed Computing Systems, IEEE, 2024, pp. 1377–1387.
conference:
end_date: 2024-07-26
location: Jersey City, NJ, United States
name: 'ICDCS: International Conference on Distributed Computing Systems'
start_date: 2024-07-23
das_tickbox: '0'
date_created: 2024-09-15T22:01:41Z
date_published: 2024-07-26T00:00:00Z
date_updated: 2026-10-01T11:04:17Z
day: '26'
department:
- _id: ElKo
doi: 10.1109/ICDCS60910.2024.00129
external_id:
arxiv:
- '2309.12713'
isi:
- '001304430200120'
fulldoi: https://doi.org/10.1109/ICDCS60910.2024.00129
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2309.12713
month: '07'
oa: 1
oa_version: Preprint
page: 1377-1387
publication: Proceedings - International Conference on Distributed Computing Systems
publication_identifier:
eissn:
- 2575-8411
isbn:
- '9798350386059'
issn:
- 1063-6927
publication_status: published
publisher: IEEE
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'HammerHead: Leader reputation for dynamic scheduling'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '17284'
abstract:
- lang: eng
text: Platelet homeostasis is essential for vascular integrity and immune defence1,2.
Although the process of platelet formation by fragmenting megakaryocytes (MKs;
thrombopoiesis) has been extensively studied, the cellular and molecular mechanisms
required to constantly replenish the pool of MKs by their progenitor cells (megakaryopoiesis)
remains unclear3,4. Here we use intravital imaging to track the cellular dynamics
of megakaryopoiesis over days. We identify plasmacytoid dendritic cells (pDCs)
as homeostatic sensors that monitor the bone marrow for apoptotic MKs and deliver
IFNα to the MK niche triggering local on-demand proliferation and maturation of
MK progenitors. This pDC-dependent feedback loop is crucial for MK and platelet
homeostasis at steady state and under stress. pDCs are best known for their ability
to function as vigilant detectors of viral infection5. We show that virus-induced
activation of pDCs interferes with their function as homeostatic sensors of megakaryopoiesis.
Consequently, activation of pDCs by SARS-CoV-2 leads to excessive megakaryopoiesis.
Together, we identify a pDC-dependent homeostatic circuit that involves innate
immune sensing and demand-adapted release of inflammatory mediators to maintain
homeostasis of the megakaryocytic lineage.
acknowledgement: 'We thank S. Helmer, N. Blount, E. Raatz and Z. Sisic for technical
assistance. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German
Research Foundation) SFB 1123 (S.M. project B06); SFB 914 (S.M. projects B02 and
Z01, H.I.-A. project Z01, S.S. project A06, K.S. project B02, C. Schulz project
A10, B.W. project A02, C. Scheiermann project B09); SFB 1054 (T.B. project B03);
FOR2033 (F.G., R.A.J.O., S.M.); Individual research grant project ID: 514478744
(F.G.); Heisenberg Programme project ID: 514477451 (F.G.); the DZHK (German Center
for Cardiovascular Research) (MHA 1.4VD (S.M.), Postdoc Start-up Grant, 81×3600213
(F.G.)); and LMUexcellence NFF (F.G.). W.F. received funding from China Scholarship
Council (CSC, no. 201306270012). P.B. is supported by the German Research Foundation
(DFG, project IDs 322900939, 432698239 and 445703531), European Research Council
(ERC Consolidator grant no. 101001791) and the Federal Ministry of Education and
Research (BMBF, STOP-FSGS-01GM2202C and NATON within the framework of the Network
of University Medicine, no. 01KX2121). S.v.S. is supported by the START-Program
of the Faculty of Medicine of the RWTH Aachen University (AZ 125/17). A.D. and S.E.
are supported by the German Research Foundation (SFB TRR 267); S.E. by the BMBF
in the framework of the Cluster4future program (CNATM—Cluster for Nucleic Acid Therapeutics
Munich). 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. 833440 to S.M.). F.G. received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
no. 747687. The project is funded by the European Union (ERC, MEKanics, 101078110).
Views and opinions expressed are those of the author(s) only and do not necessarily
reflect those of the European Union or the European Research Council Executive Agency.
Neither the European Union nor the granting authority can be held responsible for
them.'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
- first_name: Hellen
full_name: Ishikawa-Ankerhold, Hellen
last_name: Ishikawa-Ankerhold
- first_name: Susanne
full_name: Stutte, Susanne
last_name: Stutte
- first_name: Wenwen
full_name: Fu, Wenwen
last_name: Fu
- first_name: Jutta
full_name: Weitz, Jutta
last_name: Weitz
- first_name: Anne
full_name: Dueck, Anne
last_name: Dueck
- first_name: Bhavishya
full_name: Nelakuditi, Bhavishya
last_name: Nelakuditi
- first_name: Valeria
full_name: Fumagalli, Valeria
last_name: Fumagalli
- first_name: Dominic
full_name: Van Den Heuvel, Dominic
last_name: Van Den Heuvel
- first_name: Larissa
full_name: Belz, Larissa
last_name: Belz
- first_name: Gulnoza
full_name: Sobirova, Gulnoza
last_name: Sobirova
- first_name: Zhe
full_name: Zhang, Zhe
last_name: Zhang
- first_name: Anna
full_name: Titova, Anna
last_name: Titova
- first_name: Alejandro Martinez
full_name: Navarro, Alejandro Martinez
last_name: Navarro
- first_name: Kami
full_name: Pekayvaz, Kami
last_name: Pekayvaz
- first_name: Michael
full_name: Lorenz, Michael
last_name: Lorenz
- first_name: Louisa
full_name: Von Baumgarten, Louisa
last_name: Von Baumgarten
- first_name: Jan
full_name: Kranich, Jan
last_name: Kranich
- first_name: Tobias
full_name: Straub, Tobias
last_name: Straub
- first_name: Bastian
full_name: Popper, Bastian
last_name: Popper
- first_name: Vanessa
full_name: Zheden, Vanessa
id: 39C5A68A-F248-11E8-B48F-1D18A9856A87
last_name: Zheden
orcid: 0000-0002-9438-4783
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Chenglong
full_name: Guo, Chenglong
last_name: Guo
- first_name: Guido
full_name: Piontek, Guido
last_name: Piontek
- first_name: Saskia
full_name: Von Stillfried, Saskia
last_name: Von Stillfried
- first_name: Peter
full_name: Boor, Peter
last_name: Boor
- first_name: Marco
full_name: Colonna, Marco
last_name: Colonna
- first_name: Sebastian
full_name: Clauß, Sebastian
last_name: Clauß
- first_name: Christian
full_name: Schulz, Christian
last_name: Schulz
- first_name: Thomas
full_name: Brocker, Thomas
last_name: Brocker
- first_name: Barbara
full_name: Walzog, Barbara
last_name: Walzog
- first_name: Christoph
full_name: Scheiermann, Christoph
last_name: Scheiermann
- first_name: William C.
full_name: Aird, William C.
last_name: Aird
- first_name: Claus
full_name: Nerlov, Claus
last_name: Nerlov
- first_name: Konstantin
full_name: Stark, Konstantin
last_name: Stark
- first_name: Tobias
full_name: Petzold, Tobias
last_name: Petzold
- first_name: Stefan
full_name: Engelhardt, Stefan
last_name: Engelhardt
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Martina
full_name: Rudelius, Martina
last_name: Rudelius
- first_name: Robert A.J.
full_name: Oostendorp, Robert A.J.
last_name: Oostendorp
- first_name: Matteo
full_name: Iannacone, Matteo
last_name: Iannacone
- first_name: Matthias
full_name: Heinig, Matthias
last_name: Heinig
- first_name: Steffen
full_name: Massberg, Steffen
last_name: Massberg
citation:
ama: Gärtner FR, Ishikawa-Ankerhold H, Stutte S, et al. Plasmacytoid dendritic cells
control homeostasis of megakaryopoiesis. Nature. 2024;631:645-653. doi:10.1038/s41586-024-07671-y
apa: Gärtner, F. R., Ishikawa-Ankerhold, H., Stutte, S., Fu, W., Weitz, J., Dueck,
A., … Massberg, S. (2024). Plasmacytoid dendritic cells control homeostasis of
megakaryopoiesis. Nature. Springer Nature. https://doi.org/10.1038/s41586-024-07671-y
chicago: Gärtner, Florian R, Hellen Ishikawa-Ankerhold, Susanne Stutte, Wenwen Fu,
Jutta Weitz, Anne Dueck, Bhavishya Nelakuditi, et al. “Plasmacytoid Dendritic
Cells Control Homeostasis of Megakaryopoiesis.” Nature. Springer Nature,
2024. https://doi.org/10.1038/s41586-024-07671-y.
ieee: F. R. Gärtner et al., “Plasmacytoid dendritic cells control homeostasis
of megakaryopoiesis,” Nature, vol. 631. Springer Nature, pp. 645–653, 2024.
ista: Gärtner FR, Ishikawa-Ankerhold H, Stutte S, Fu W, Weitz J, Dueck A, Nelakuditi
B, Fumagalli V, Van Den Heuvel D, Belz L, Sobirova G, Zhang Z, Titova A, Navarro
AM, Pekayvaz K, Lorenz M, Von Baumgarten L, Kranich J, Straub T, Popper B, Zheden
V, Kaufmann W, Guo C, Piontek G, Von Stillfried S, Boor P, Colonna M, Clauß S,
Schulz C, Brocker T, Walzog B, Scheiermann C, Aird WC, Nerlov C, Stark K, Petzold
T, Engelhardt S, Sixt MK, Hauschild R, Rudelius M, Oostendorp RAJ, Iannacone M,
Heinig M, Massberg S. 2024. Plasmacytoid dendritic cells control homeostasis of
megakaryopoiesis. Nature. 631, 645–653.
mla: Gärtner, Florian R., et al. “Plasmacytoid Dendritic Cells Control Homeostasis
of Megakaryopoiesis.” Nature, vol. 631, Springer Nature, 2024, pp. 645–53,
doi:10.1038/s41586-024-07671-y.
short: F.R. Gärtner, H. Ishikawa-Ankerhold, S. Stutte, W. Fu, J. Weitz, A. Dueck,
B. Nelakuditi, V. Fumagalli, D. Van Den Heuvel, L. Belz, G. Sobirova, Z. Zhang,
A. Titova, A.M. Navarro, K. Pekayvaz, M. Lorenz, L. Von Baumgarten, J. Kranich,
T. Straub, B. Popper, V. Zheden, W. Kaufmann, C. Guo, G. Piontek, S. Von Stillfried,
P. Boor, M. Colonna, S. Clauß, C. Schulz, T. Brocker, B. Walzog, C. Scheiermann,
W.C. Aird, C. Nerlov, K. Stark, T. Petzold, S. Engelhardt, M.K. Sixt, R. Hauschild,
M. Rudelius, R.A.J. Oostendorp, M. Iannacone, M. Heinig, S. Massberg, Nature 631
(2024) 645–653.
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: Imaging and flow cytometry raw data are available on request.
scRNA-seq data are accessible at the GEO (GSE261996). Bulk RNA-seq data are accessible
at the GEO (GSE185488). Source data are provided with this paper.
date_created: 2024-07-21T22:01:02Z
date_published: 2024-07-18T00:00:00Z
date_updated: 2026-10-01T11:17:11Z
day: '18'
ddc:
- '570'
department:
- _id: EM-Fac
- _id: MiSi
- _id: Bio
doi: 10.1038/s41586-024-07671-y
ec_funded: 1
external_id:
isi:
- '001281636500020'
pmid:
- '38987596'
file:
- access_level: open_access
checksum: aa004afc72d2489f0fb0fcbc9919fbbd
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T06:16:11Z
date_updated: 2024-07-22T06:16:11Z
file_id: '17286'
file_name: 2024_Nature_Gaertner.pdf
file_size: 15704819
relation: main_file
success: 1
file_date_updated: 2024-07-22T06:16:11Z
fulldoi: https://doi.org/10.1038/s41586-024-07671-y
has_accepted_license: '1'
intvolume: ' 631'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 645-653
pmid: 1
project:
- _id: 260AA4E2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '747687'
name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/heiniglab/gaertner_megakaryocytes
researchdata_availability: upon request
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 631
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18920'
abstract:
- lang: eng
text: The globally distributed marine alga Emiliania huxleyi has cooling effect
on the Earth’s climate. The population density of E. huxleyi is restricted by
Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite
the impact of E. huxleyi viruses on the climate, there is limited information
about their structure and replication. Here, we show that the dsDNA genome inside
the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane.
EhV-201 virions infect E. huxleyi by using fivefold vertices to bind to and fuse
the virus’ inner membrane with the cell plasma membrane. Progeny virions assemble
in the cytoplasm at the surface of endoplasmic reticulum–derived membrane segments.
Genome packaging initiates synchronously with the capsid assembly and completes
through an aperture in the forming capsid. The genome-filled capsids acquire an
outer membrane by budding into intracellular vesicles. EhV-201 infection induces
a loss of surface protective layers from E. huxleyi cells, which enables the continuous
release of virions by exocytosis.
acknowledgement: We acknowledge (i) the Cryo-Electron Microscopy and Tomography Core
Facility and Proteomics Core Facility of the Central European Institute of Technology
(CEITEC), Masaryk University, supported by the Ministry of Education, Youth, and
Sports of the Czech Republic (grant LM2018127); (ii) the Cellular Imaging Core Facility
supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR);
and (iii) Plant Sciences Core Facility for support with obtaining scientific data
presented here. We acknowledge support from the project National Institute of Virology
and Bacteriology (Program EXCELES, ID project no. LX22NPO5103), funded by the European
Union - Next Generation EU. This work received funding from the Czech Science Foundation
grant GX 19-259882X to P.P., from European Regional Development Fund-Project “MSCAfellow2@MUNI”
(no. CZ.02.2.69/0.0/0.0/18_070/0009846) to C.R.B., and from Brno PhD talent scholarship
funded by Brno city municipality to M.H.
article_number: 'eadk1954 '
article_processing_charge: Yes
article_type: original
author:
- first_name: Miroslav
full_name: Homola, Miroslav
last_name: Homola
- first_name: Renate Carina
full_name: Büttner, Renate Carina
id: 3b7984c9-17ff-11ed-b6fe-f943c4a5b626
last_name: Büttner
- first_name: Tibor
full_name: Füzik, Tibor
last_name: Füzik
- first_name: Pavel
full_name: Křepelka, Pavel
last_name: Křepelka
- first_name: Radka
full_name: Holbová, Radka
last_name: Holbová
- first_name: Jiří
full_name: Nováček, Jiří
last_name: Nováček
- first_name: Marten L.
full_name: Chaillet, Marten L.
last_name: Chaillet
- first_name: Jakub
full_name: Žák, Jakub
last_name: Žák
- first_name: Danyil
full_name: Grybchuk, Danyil
last_name: Grybchuk
- first_name: Friedrich
full_name: Förster, Friedrich
last_name: Förster
- first_name: William H.
full_name: Wilson, William H.
last_name: Wilson
- first_name: Declan C.
full_name: Schroeder, Declan C.
last_name: Schroeder
- first_name: Pavel
full_name: Plevka, Pavel
last_name: Plevka
citation:
ama: Homola M, Büttner RC, Füzik T, et al. Structure and replication cycle of a
virus infecting climate-modulating alga Emiliania huxleyi. Science Advances.
2024;10(15). doi:10.1126/sciadv.adk1954
apa: Homola, M., Büttner, R. C., Füzik, T., Křepelka, P., Holbová, R., Nováček,
J., … Plevka, P. (2024). Structure and replication cycle of a virus infecting
climate-modulating alga Emiliania huxleyi. Science Advances. American Association
for the Advancement of Science. https://doi.org/10.1126/sciadv.adk1954
chicago: Homola, Miroslav, Renate Carina Büttner, Tibor Füzik, Pavel Křepelka, Radka
Holbová, Jiří Nováček, Marten L. Chaillet, et al. “Structure and Replication Cycle
of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” Science Advances.
American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adk1954.
ieee: M. Homola et al., “Structure and replication cycle of a virus infecting
climate-modulating alga Emiliania huxleyi,” Science Advances, vol. 10,
no. 15. American Association for the Advancement of Science, 2024.
ista: Homola M, Büttner RC, Füzik T, Křepelka P, Holbová R, Nováček J, Chaillet
ML, Žák J, Grybchuk D, Förster F, Wilson WH, Schroeder DC, Plevka P. 2024. Structure
and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi.
Science Advances. 10(15), eadk1954.
mla: Homola, Miroslav, et al. “Structure and Replication Cycle of a Virus Infecting
Climate-Modulating Alga Emiliania Huxleyi.” Science Advances, vol. 10,
no. 15, eadk1954, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adk1954.
short: M. Homola, R.C. Büttner, T. Füzik, P. Křepelka, R. Holbová, J. Nováček, M.L.
Chaillet, J. Žák, D. Grybchuk, F. Förster, W.H. Wilson, D.C. Schroeder, P. Plevka,
Science Advances 10 (2024).
das_tickbox: '1'
dataavailabilitystatement: 'Cryo-EM maps and structure coordinates were deposited
to the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB), respectively,
with the following accession numbers: (i) EhV-201 virion vertex reconstructed using
a single-particle approach and a mask with the diameter of 50 nm (EMD-17650); (ii)
EhV-201 virion vertex reconstructed using sub-tomogram averaging and a mask with
the diameter of 50 nm (EMD-17649); (iii) EhV-201 virion vertex reconstructed using
sub-tomogram averaging and a mask with the diameter of 50 nm and a mask covering
only the capsid layer (EMD-19036) and the fitted structure of AlphaFold2 predicted
EhV-201 major capsid protein and penton protein (PDB 8RBT); (iv) EhV-201 virion
vertex reconstructed by sub-tomogram averaging and a mask with the diameter of 120
nm (EMD-17651); and (v) composite map of the EhV201 virion (EMD-19035) and corresponding
structure of icosahedral asymmetric unit (PDB 8RBS). All custom scripts used during
tomographic reconstruction have been made available at https://github.com/fuzikt/tomostarpy.
Additional files have been made available at https://doi.org/10.5061/dryad.p5hqbzkw0:
(i) cryo-ET tilt series of lamellas of control and EhV-201 infected E. huxleyi cells;
(ii) segmentations of cryo-tomograms of infected and control cells; (iii) block
face imaging data series of high-pressure frozen and resin-embedded E. huxleyi infected
by EhV-201; (iv) scripts used during tomographic reconstruction; (v) fluorescence
microscopy images of E. huxleyi infected by EhV-201; and (vi) mass spectrometry
report of EhV-201 virion protein composition. Cryo-ET tilt series used for EhV-201
virion structure determination were deposited to EMPIAR and linked to the file EMD-17649.
All other data needed to evaluate the conclusions in the paper are present in the
paper and/or the Supplementary Materials.'
date_created: 2025-01-27T14:32:34Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2026-10-01T11:15:30Z
day: '01'
ddc:
- '570'
department:
- _id: EM-Fac
doi: 10.1126/sciadv.adk1954
external_id:
pmid:
- '38598627'
file:
- access_level: open_access
checksum: 291dd7ceccbe6bfd8e0a9157584f88e9
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T14:40:08Z
date_updated: 2025-01-27T14:40:08Z
file_id: '18921'
file_name: 2024_ScienceAdv_Homola.pdf
file_size: 40623405
relation: main_file
success: 1
file_date_updated: 2025-01-27T14:40:08Z
fulldoi: https://doi.org/10.1126/sciadv.adk1954
has_accepted_license: '1'
intvolume: ' 10'
issue: '15'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: ' https://github.com/fuzikt/tomostarpy.'
record:
- id: '23025'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Structure and replication cycle of a virus infecting climate-modulating alga
Emiliania huxleyi
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 10
year: '2024'
...
---
_id: '18052'
abstract:
- lang: eng
text: Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL)
is an electron microscope (EM) sample preparation technique which allows for high-resolution
visualization of membrane proteins with high sensitivity. However, image acquisition
of specific replica profiles such as synapses in a large field of EM view needs
a valid experience and a long time for manual searching. Here, we describe how
to utilize deep learning for automatizing image acquisition of specific profiles
of interest in replica samples. This protocol facilitates the labor-intensive
collection of EM images, in particular for rare profiles. We provide instructions
for using SerialEM image acquisition software in conjunction with object detection
by our newly developed deep learning software DarEM, to automatically acquire
tilt series of all synapses in a selected region. We then show how to perform
a mostly automated analysis of gold particle labeling in the acquired images by
utilizing Darea software.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: This research was supported by the European Research Council Advanced
Grant 694539 to RS and by the Scientific Service Units of IST Austria through resources
provided by the Electron Microscopy Facility.
alternative_title:
- Neuromethods
article_processing_charge: No
author:
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: 'Kleindienst D, Costanzo T, Shigemoto R. Automated Imaging and Analysis of
Synapses in Freeze-Fracture Replica Samples with Deep Learning. In: Lübke JHR,
Rollenhagen A, eds. New Aspects in Analyzing the Synaptic Organization of the
Brain. 1st ed. New York: Springer Nature; 2024:123-137. doi:10.1007/978-1-0716-4019-7_8'
apa: 'Kleindienst, D., Costanzo, T., & Shigemoto, R. (2024). Automated Imaging
and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning.
In J. H. R. Lübke & A. Rollenhagen (Eds.), New Aspects in Analyzing the
Synaptic Organization of the Brain (1st ed., pp. 123–137). New York: Springer
Nature. https://doi.org/10.1007/978-1-0716-4019-7_8'
chicago: 'Kleindienst, David, Tommaso Costanzo, and Ryuichi Shigemoto. “Automated
Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep
Learning.” In New Aspects in Analyzing the Synaptic Organization of the Brain,
edited by Joachim H.R. Lübke and Astrid Rollenhagen, 1st ed., 123–37. New York:
Springer Nature, 2024. https://doi.org/10.1007/978-1-0716-4019-7_8.'
ieee: 'D. Kleindienst, T. Costanzo, and R. Shigemoto, “Automated Imaging and Analysis
of Synapses in Freeze-Fracture Replica Samples with Deep Learning,” in New
Aspects in Analyzing the Synaptic Organization of the Brain, 1st ed., J. H.
R. Lübke and A. Rollenhagen, Eds. New York: Springer Nature, 2024, pp. 123–137.'
ista: 'Kleindienst D, Costanzo T, Shigemoto R. 2024.Automated Imaging and Analysis
of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In: New Aspects
in Analyzing the Synaptic Organization of the Brain. Neuromethods, , 123–137.'
mla: Kleindienst, David, et al. “Automated Imaging and Analysis of Synapses in Freeze-Fracture
Replica Samples with Deep Learning.” New Aspects in Analyzing the Synaptic
Organization of the Brain, edited by Joachim H.R. Lübke and Astrid Rollenhagen,
1st ed., Springer Nature, 2024, pp. 123–37, doi:10.1007/978-1-0716-4019-7_8.
short: D. Kleindienst, T. Costanzo, R. Shigemoto, in:, J.H.R. Lübke, A. Rollenhagen
(Eds.), New Aspects in Analyzing the Synaptic Organization of the Brain, 1st ed.,
Springer Nature, New York, 2024, pp. 123–137.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-09-10T12:32:38Z
date_published: 2024-08-27T00:00:00Z
date_updated: 2026-10-01T11:17:28Z
day: '27'
department:
- _id: EM-Fac
- _id: RySh
doi: 10.1007/978-1-0716-4019-7_8
ec_funded: 1
edition: '1'
editor:
- first_name: 'Joachim H.R. '
full_name: 'Lübke, Joachim H.R. '
last_name: Lübke
- first_name: Astrid
full_name: Rollenhagen, Astrid
last_name: Rollenhagen
fulldoi: https://doi.org/10.1007/978-1-0716-4019-7_8
language:
- iso: eng
month: '08'
oa_version: None
page: 123-137
place: New York
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
publication: New Aspects in Analyzing the Synaptic Organization of the Brain
publication_identifier:
eisbn:
- '9781071640197'
eissn:
- 1940-6045
isbn:
- '9781071640180'
issn:
- 0893-2336
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples
with Deep Learning
type: book_chapter
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '14842'
abstract:
- lang: eng
text: Eva Benkova received a PhD in Biophysics at the Institute of Biophysics of
the Czech Academy of Sciences in 1998. After working as a postdoc at the Max Planck
Institute in Cologne and the Center for Plant Molecular Biology (ZMBP) in Tübingen,
she became a group leader at the Plant Systems Biology Department of the Vlaams
Instituut voor Biotechnologie (VIB) in Gent. In 2012, she transitioned to an Assistant
Professor position at the Institute of Science and Technology Austria (ISTA) where
she was later promoted to Professor. Since 2021, she has served as the Dean of
the ISTA Graduate School. As a plant developmental biologist, she focuses on unraveling
the molecular mechanisms and principles that underlie hormonal interactions in
plants. In her current work, she explores the intricate connections between hormones
and regulatory pathways that mediate the perception of environmental stimuli,
including abiotic stress and nitrate availability.
article_processing_charge: No
author:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Benková E. Eva Benkova. Vol 34. Elsevier; 2024:R3-R5. doi:10.1016/j.cub.2023.11.039
apa: Benková, E. (2024). Eva Benkova. Current Biology (Vol. 34, pp.
R3–R5). Elsevier. https://doi.org/10.1016/j.cub.2023.11.039
chicago: Benková, Eva. Eva Benkova. Current Biology. Vol. 34. Elsevier,
2024. https://doi.org/10.1016/j.cub.2023.11.039.
ieee: E. Benková, Eva Benkova, vol. 34, no. 1. Elsevier, 2024, pp. R3–R5.
ista: Benková E. 2024. Eva Benkova, Elsevier,p.
mla: Benková, Eva. “Eva Benkova.” Current Biology, vol. 34, no. 1, Elsevier,
2024, pp. R3–5, doi:10.1016/j.cub.2023.11.039.
short: E. Benková, Eva Benkova, Elsevier, 2024.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-01-21T23:00:56Z
date_published: 2024-01-08T00:00:00Z
date_updated: 2026-10-01T11:17:58Z
day: '08'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.1016/j.cub.2023.11.039
external_id:
pmid:
- '38194926'
fulldoi: https://doi.org/10.1016/j.cub.2023.11.039
intvolume: ' 34'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2023.11.039
month: '01'
oa: 1
oa_version: Published Version
page: R3-R5
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
publication_status: published
publisher: Elsevier
quality_controlled: '1'
researchdata_availability: not applicable
status: public
supplementarymaterial: no
title: Eva Benkova
type: other_academic_publication
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 34
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '23025'
abstract:
- lang: eng
text: The globally distributed marine alga Emiliania huxleyi produces reflective
calcite disks (coccoliths) that increase the albedo of ocean water and thus reduce
the heat absorption in the ocean, which cools the Earth’s climate. The population
density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E.
huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate,
there is limited information about their structure and replication. Here we show
that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane,
capsid, and outer membrane decorated with numerous transmembrane proteins. The
virions are prone to deformation, and parts of their capsids deviate from the
icosahedral arrangement. EhV-201 virions infect E. huxleyi by using their fivefold
vertex to bind to a host cell and fuse the virus’s inner membrane with the plasma
membrane. Whereas the replication of EhV-201 probably occurs in the nucleus, virions
assemble in the cytoplasm at the surface of endoplasmic reticulum-derived membrane
segments. Genome packaging initiates synchronously with the capsid assembly and
completes through an aperture in the forming capsid. Upon the completion of genome
packaging, the capsids change conformation, which enables them to acquire an outer
membrane by budding into intracellular vesicles. EhV-201 infection induces a loss
of surface protective layers from E. huxleyi cells, which allows the continuous
release of virions by exocytosis. Our results provide insight into how EhVs bypass
the surface protective layers of E. huxleyi and exploit the organelles of an infected
cell for progeny assembly.
article_processing_charge: No
author:
- first_name: Miroslav
full_name: Homola, Miroslav
last_name: Homola
- first_name: Carina
full_name: Büttner, Carina
last_name: Büttner
- first_name: Tibor
full_name: Füzik, Tibor
last_name: Füzik
- first_name: Pavel
full_name: Krepelka, Pavel
last_name: Krepelka
- first_name: Radka
full_name: Holbová, Radka
last_name: Holbová
- first_name: Marten
full_name: Chaillet, Marten
last_name: Chaillet
- first_name: Jiří
full_name: Nováček, Jiří
last_name: Nováček
- first_name: Friedrich
full_name: Förster, Friedrich
last_name: Förster
- first_name: William
full_name: Wilson, William
last_name: Wilson
- first_name: Declan
full_name: Schroeder, Declan
last_name: Schroeder
- first_name: Pavel
full_name: Plevka, Pavel
last_name: Plevka
citation:
ama: 'Homola M, Büttner C, Füzik T, et al. Data: Structure and replication cycle
of a virus infecting climate-modulating alga Emiliania huxleyi. 2024. doi:10.5061/dryad.p5hqbzkw0'
apa: 'Homola, M., Büttner, C., Füzik, T., Krepelka, P., Holbová, R., Chaillet, M.,
… Plevka, P. (2024). Data: Structure and replication cycle of a virus infecting
climate-modulating alga Emiliania huxleyi. Dryad. https://doi.org/10.5061/dryad.p5hqbzkw0'
chicago: 'Homola, Miroslav, Carina Büttner, Tibor Füzik, Pavel Krepelka, Radka Holbová,
Marten Chaillet, Jiří Nováček, et al. “Data: Structure and Replication Cycle of
a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” Dryad, 2024. https://doi.org/10.5061/dryad.p5hqbzkw0.'
ieee: 'M. Homola et al., “Data: Structure and replication cycle of a virus
infecting climate-modulating alga Emiliania huxleyi.” Dryad, 2024.'
ista: 'Homola M, Büttner C, Füzik T, Krepelka P, Holbová R, Chaillet M, Nováček
J, Förster F, Wilson W, Schroeder D, Plevka P. 2024. Data: Structure and replication
cycle of a virus infecting climate-modulating alga Emiliania huxleyi, Dryad, 10.5061/dryad.p5hqbzkw0.'
mla: 'Homola, Miroslav, et al. Data: Structure and Replication Cycle of a Virus
Infecting Climate-Modulating Alga Emiliania Huxleyi. Dryad, 2024, doi:10.5061/dryad.p5hqbzkw0.'
short: M. Homola, C. Büttner, T. Füzik, P. Krepelka, R. Holbová, M. Chaillet, J.
Nováček, F. Förster, W. Wilson, D. Schroeder, P. Plevka, (2024).
date_created: 2026-10-01T11:13:02Z
date_published: 2024-02-07T00:00:00Z
date_updated: 2026-10-01T11:15:29Z
day: '07'
ddc:
- '570'
department:
- _id: EM-Fac
doi: 10.5061/dryad.p5hqbzkw0
fulldoi: https://doi.org/10.5061/dryad.p5hqbzkw0
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.p5hqbzkw0
month: '02'
oa: 1
oa_version: None
publisher: Dryad
related_material:
record:
- id: '18920'
relation: used_in_publication
status: public
status: public
title: 'Data: Structure and replication cycle of a virus infecting climate-modulating
alga Emiliania huxleyi'
type: research_data_reference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '15146'
abstract:
- lang: eng
text: The extracellular matrix (ECM) serves as a scaffold for cells and plays an
essential role in regulating numerous cellular processes, including cell migration
and proliferation. Due to limitations in specimen preparation for conventional
room-temperature electron microscopy, we lack structural knowledge on how ECM
components are secreted, remodeled, and interact with surrounding cells. We have
developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion
beam milling, the lift-out extraction procedure, and cryo-electron tomography.
Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting
in a versatile tool closely mimicking ECM environments. This allows us to visualize
ECM for the first time in its hydrated, native context. Our data reveal an intricate
network of extracellular fibers, their positioning relative to matrix-secreting
cells, and previously unresolved structural entities. Our workflow and results
add to the structural atlas of the ECM, providing novel insights into its secretion
and assembly.
acknowledged_ssus:
- _id: LifeSc
- _id: ScienComp
- _id: EM-Fac
- _id: M-Shop
acknowledgement: "Open Access funding provided by IST Austria. We thank Armel Nicolas
and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante,
and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and
Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the
Miba Machine shop for their support. We also thank Wanda Kukulski (University of
Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group
for helpful discussions. Matt Swulius and Jessica Heebner provided great support
in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure
illustration.\r\n\r\nThis research was supported by the Scientific Service Units
of ISTA through resources provided by Scientific Computing, the Lab Support Facility,
and the Electron Microscopy Facility. We acknowledge funding support from the following
sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation
of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds
(to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the
European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt),
and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been
made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg
from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community
Foundation (to F.K.M. Schur)."
article_number: e202309125
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Bettina
full_name: Zens, Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
orcid: 0000-0002-9561-1239
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Jesse
full_name: Hansen, Jesse
id: 1063c618-6f9b-11ec-9123-f912fccded63
last_name: Hansen
orcid: 0000-0001-7967-2085
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
orcid: 0000-0003-3904-947X
- first_name: Vanessa
full_name: Zheden, Vanessa
id: 39C5A68A-F248-11E8-B48F-1D18A9856A87
last_name: Zheden
orcid: 0000-0002-9438-4783
- first_name: Jonna H
full_name: Alanko, Jonna H
id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87
last_name: Alanko
orcid: 0000-0002-7698-3061
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal
the ultrastructural landscape of extracellular matrix. Journal of Cell Biology.
2024;223(6). doi:10.1083/jcb.202309125
apa: Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V.,
… Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural
landscape of extracellular matrix. Journal of Cell Biology. Rockefeller
University Press. https://doi.org/10.1083/jcb.202309125
chicago: Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler,
Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and
Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural
Landscape of Extracellular Matrix.” Journal of Cell Biology. Rockefeller
University Press, 2024. https://doi.org/10.1083/jcb.202309125.
ieee: B. Zens et al., “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural
landscape of extracellular matrix,” Journal of Cell Biology, vol. 223,
no. 6. Rockefeller University Press, 2024.
ista: Zens B, Fäßler F, Hansen J, Hauschild R, Datler J, Hodirnau V-V, Zheden V,
Alanko JH, Sixt MK, Schur FK. 2024. Lift-out cryo-FIBSEM and cryo-ET reveal the
ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 223(6),
e202309125.
mla: Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural
Landscape of Extracellular Matrix.” Journal of Cell Biology, vol. 223,
no. 6, e202309125, Rockefeller University Press, 2024, doi:10.1083/jcb.202309125.
short: B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V.
Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: 'Representative tomograms containing the data shown in
Fig. 3, and Figs. S5 and S9 have been deposited in the Electron Microscopy Data
Bank under accession codes: EMD-18490, EMD-18491, EMD-18492, EMD-18493, and EMD-18494.
All tilt series, including frames, raw tilt series, and reconstructed IsoNet-filtered
tomograms, were deposited in the Electron Microscopy Public Image Archive database
under the accession code EMPIAR-11897.'
date_created: 2024-03-21T06:45:51Z
date_published: 2024-03-20T00:00:00Z
date_updated: 2026-10-01T11:24:27Z
day: '20'
ddc:
- '570'
department:
- _id: FlSc
- _id: MiSi
- _id: Bio
- _id: EM-Fac
doi: 10.1083/jcb.202309125
ec_funded: 1
external_id:
isi:
- '001264190100001'
pmid:
- '38506714'
file:
- access_level: open_access
checksum: 90d1984a93660735e506c2a304bc3f73
content_type: application/pdf
creator: dernst
date_created: 2024-03-25T12:52:04Z
date_updated: 2024-03-25T12:52:04Z
file_id: '15188'
file_name: 2024_JCB_Zens.pdf
file_size: 11907016
relation: main_file
success: 1
file_date_updated: 2024-03-25T12:52:04Z
fulldoi: https://doi.org/10.1083/jcb.202309125
has_accepted_license: '1'
intvolume: ' 223'
isi: 1
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
- _id: 7bd318a1-9f16-11ee-852c-cc9217763180
grant_number: E435
name: In Situ Actin Structures via Hybrid Cryo-electron Microscopy
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular Navigation Along Spatial Gradients
- _id: 059B463C-7A3F-11EA-A408-12923DDC885E
name: "NÃ\x96-Fonds Preis für die Jungforscherin des Jahres am IST Austria"
- _id: 2615199A-B435-11E9-9278-68D0E5697425
grant_number: '21317'
name: Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis
- _id: 62909c6f-2b32-11ec-9570-e1476aab5308
grant_number: CZI01
name: CryoMinflux-guided in-situ visual proteomics and structure determination
publication: Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
issn:
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular
matrix
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 223
year: '2024'
...
---
_id: '17463'
abstract:
- lang: eng
text: Allosteric modulation of protein function, wherein the binding of an effector
to a protein triggers conformational changes at distant functional sites, plays
a central part in the control of metabolism and cell signalling1,2,3. There has
been considerable interest in designing allosteric systems, both to gain insight
into the mechanisms underlying such ‘action at a distance’ modulation and to create
synthetic proteins whose functions can be regulated by effectors4,5,6,7. However,
emulating the subtle conformational changes distributed across many residues,
characteristic of natural allosteric proteins, is a significant challenge8,9.
Here, inspired by the classic Monod–Wyman–Changeux model of cooperativity10, we
investigate the de novo design of allostery through rigid-body coupling of peptide-switchable
hinge modules11 to protein interfaces12 that direct the formation of alternative
oligomeric states. We find that this approach can be used to generate a wide variety
of allosterically switchable systems, including cyclic rings that incorporate
or eject subunits in response to peptide binding and dihedral cages that undergo
effector-induced disassembly. Size-exclusion chromatography, mass photometry13
and electron microscopy reveal that these designed allosteric protein assemblies
closely resemble the design models in both the presence and absence of peptide
effectors and can have ligand-binding cooperativity comparable to classic natural
systems such as haemoglobin14. Our results indicate that allostery can arise from
global coupling of the energetics of protein substructures without optimized side-chain–side-chain
allosteric communication pathways and provide a roadmap for generating allosterically
triggerable delivery systems, protein nanomachines and cellular feedback control
circuitry.
acknowledgement: We thank D. D. Sahtoe, R. D. Kiber, Y. Hsia, N. Bethel and A. Favor
for helpful discussions and K. VanWormer and L. Goldschmidt for technical support.
We also thank X. Li and M. Lamb for mass spectrometry support. This work was supported
by the Washington Research Foundation Postdoctoral Fellowship (grant no. GR027504,
A. Pillai), a National Science Foundation Graduate Research Fellowship (grant no.
DGE-2140004, A.I.), a Human Frontier Science Program Long Term Fellowship (grant
no. LT000880/2019, F.P.), the Audacious Project at the Institute for Protein Design
(A.B., A. Pillai, A. Philomin, A.I. and D.B.), a National Energy Research Scientific
Computing Centre award (grant no. BER-ERCAP0022018), the Howard Hughes Medical Institute
(D.B.), the Open Philanthropy Project Improving Protein Design Fund (P.J.Y.L., C.D.
and D.B.) a gift from Microsoft (D.B.) and a grant from DARPA supporting the Harnessing
Enzymatic Activity for Lifesaving Remedies programme (grant no. HR001120S0052, contract
no. HR0011-21-2-0012, D.B.).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Arvind
full_name: Pillai, Arvind
last_name: Pillai
- first_name: Abbas
full_name: Idris, Abbas
last_name: Idris
- first_name: Annika
full_name: Philomin, Annika
last_name: Philomin
- first_name: Connor
full_name: Weidle, Connor
last_name: Weidle
- first_name: Rebecca
full_name: Skotheim, Rebecca
last_name: Skotheim
- first_name: Philip J.Y.
full_name: Leung, Philip J.Y.
last_name: Leung
- first_name: Adam
full_name: Broerman, Adam
last_name: Broerman
- first_name: Cullen
full_name: Demakis, Cullen
last_name: Demakis
- first_name: Andrew J.
full_name: Borst, Andrew J.
last_name: Borst
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
orcid: 0000-0002-0806-8101
- first_name: David
full_name: Baker, David
last_name: Baker
citation:
ama: Pillai A, Idris A, Philomin A, et al. De novo design of allosterically switchable
protein assemblies. Nature. 2024;632:911–920. doi:10.1038/s41586-024-07813-2
apa: Pillai, A., Idris, A., Philomin, A., Weidle, C., Skotheim, R., Leung, P. J.
Y., … Baker, D. (2024). De novo design of allosterically switchable protein assemblies.
Nature. Springer Nature. https://doi.org/10.1038/s41586-024-07813-2
chicago: Pillai, Arvind, Abbas Idris, Annika Philomin, Connor Weidle, Rebecca Skotheim,
Philip J.Y. Leung, Adam Broerman, et al. “De Novo Design of Allosterically Switchable
Protein Assemblies.” Nature. Springer Nature, 2024. https://doi.org/10.1038/s41586-024-07813-2.
ieee: A. Pillai et al., “De novo design of allosterically switchable protein
assemblies,” Nature, vol. 632. Springer Nature, pp. 911–920, 2024.
ista: Pillai A, Idris A, Philomin A, Weidle C, Skotheim R, Leung PJY, Broerman A,
Demakis C, Borst AJ, Praetorius FM, Baker D. 2024. De novo design of allosterically
switchable protein assemblies. Nature. 632, 911–920.
mla: Pillai, Arvind, et al. “De Novo Design of Allosterically Switchable Protein
Assemblies.” Nature, vol. 632, Springer Nature, 2024, pp. 911–920, doi:10.1038/s41586-024-07813-2.
short: A. Pillai, A. Idris, A. Philomin, C. Weidle, R. Skotheim, P.J.Y. Leung, A.
Broerman, C. Demakis, A.J. Borst, F.M. Praetorius, D. Baker, Nature 632 (2024)
911–920.
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: All data are available either in the main text or as Supplementary
Information. PDB models and sequences for designs shown in main text figures are
available in the attached Supplementary Information, along with source data for
plots in main text figures. Structures determined by cryo-EM were deposited in the
PDB as 8UP1, 8URE and 8UTM, and maps were deposited in the EMDB under accession
numbers EMD-42442, EMD-42491 and EMD-42542.
date_created: 2024-08-25T22:01:08Z
date_published: 2024-08-22T00:00:00Z
date_updated: 2026-10-01T11:19:54Z
day: '22'
ddc:
- '570'
department:
- _id: FlPr
doi: 10.1038/s41586-024-07813-2
external_id:
isi:
- '001300534300019'
pmid:
- '39143214'
file:
- access_level: open_access
checksum: 39127601621a360ec0edc538627eb211
content_type: application/pdf
creator: dernst
date_created: 2024-09-09T12:01:14Z
date_updated: 2024-09-09T12:01:14Z
file_id: '18005'
file_name: 2024_Nature_Pillai.pdf
file_size: 16572040
relation: main_file
success: 1
file_date_updated: 2024-09-09T12:01:14Z
fulldoi: https://doi.org/10.1038/s41586-024-07813-2
has_accepted_license: '1'
intvolume: ' 632'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '08'
oa: 1
oa_version: Published Version
page: '911–920 '
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: yes (supplementary data)
scopus_import: '1'
status: public
supplementarymaterial: yes
title: De novo design of allosterically switchable protein assemblies
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 632
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18934'
abstract:
- lang: eng
text: The assembly of biomolecular condensate in eukaryotic cells and the accumulation
of amyloid deposits in neurons are processes involving the nucleation and growth
(NAG) of new protein phases. To therapeutically target protein phase separation,
drug candidates are tested in in vitro assays that monitor the increase in the
mass or size of the new phase. Limited mechanistic insight is, however, provided
if empirical or untestable kinetic models are fitted to these progress curves.
Here we present the web server NAGPKin that quantifies NAG rates using mass-based
or size-based progress curves as the input data. A report is generated containing
the fitted NAG parameters and elucidating the phase separation mechanisms at play.
The NAG parameters can be used to predict particle size distributions of, for
example, protein droplets formed by liquid-liquid phase separation (LLPS) or amyloid
fibrils formed by protein aggregation. Because minimal intervention is required
from the user, NAGPKin is a good platform for standardized reporting of LLPS and
protein self-assembly data. NAGPKin is useful for drug discovery as well as for
fundamental studies on protein phase separation. NAGPKin is freely available (no
login required) at https://nagpkin.i3s.up.pt .
acknowledgement: We thank Professor José Paulo Leal, Department of Computer Science
− Faculdade de Ciências da Universidade do Porto, for his invaluable help during
the Implementation of NAGPKin. This work is part of a project that has received
funding from the European Union’s Horizon 2020 research and innovation programme
under grant agreement no. 952334 (PhasAGE). This research was funded by the Portuguese
Foundation for Science and Technology (FCT) in the framework of project PTDC/QUI-COL/2444/2021.
article_number: mr1
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Zsuzsa
full_name: Sárkány, Zsuzsa
last_name: Sárkány
- first_name: Francisco
full_name: Figueiredo, Francisco
id: 8125cbe2-9661-11ed-a754-afe96018f37d
last_name: Figueiredo
- first_name: Sandra
full_name: Macedo-Ribeiro, Sandra
last_name: Macedo-Ribeiro
- first_name: Pedro M.
full_name: Martins, Pedro M.
last_name: Martins
citation:
ama: 'Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. NAGPKin: Nucleation-and-growth
parameters from the kinetics of protein phase separation. Molecular Biology
of the Cell. 2024;35(3). doi:10.1091/mbc.e23-07-0289'
apa: 'Sárkány, Z., Figueiredo, F., Macedo-Ribeiro, S., & Martins, P. M. (2024).
NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation.
Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.e23-07-0289'
chicago: 'Sárkány, Zsuzsa, Francisco Figueiredo, Sandra Macedo-Ribeiro, and Pedro
M. Martins. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein
Phase Separation.” Molecular Biology of the Cell. American Society for
Cell Biology, 2024. https://doi.org/10.1091/mbc.e23-07-0289.'
ieee: 'Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, and P. M. Martins, “NAGPKin:
Nucleation-and-growth parameters from the kinetics of protein phase separation,”
Molecular Biology of the Cell, vol. 35, no. 3. American Society for Cell
Biology, 2024.'
ista: 'Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. 2024. NAGPKin: Nucleation-and-growth
parameters from the kinetics of protein phase separation. Molecular Biology of
the Cell. 35(3), mr1.'
mla: 'Sárkány, Zsuzsa, et al. “NAGPKin: Nucleation-and-Growth Parameters from the
Kinetics of Protein Phase Separation.” Molecular Biology of the Cell, vol.
35, no. 3, mr1, American Society for Cell Biology, 2024, doi:10.1091/mbc.e23-07-0289.'
short: Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, P.M. Martins, Molecular Biology
of the Cell 35 (2024).
das_tickbox: '0'
date_created: 2025-01-29T07:58:40Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2026-10-01T11:22:53Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1091/mbc.e23-07-0289
external_id:
pmid:
- '38117593'
file:
- access_level: open_access
checksum: d7deb6390f294da69321cfbe352ed611
content_type: application/pdf
creator: dernst
date_created: 2025-01-29T08:12:11Z
date_updated: 2025-01-29T08:12:11Z
file_id: '18935'
file_name: 2024_MolecularBioCell_Sarkany.pdf
file_size: 1699180
relation: main_file
success: 1
file_date_updated: 2025-01-29T08:12:11Z
fulldoi: https://doi.org/10.1091/mbc.e23-07-0289
has_accepted_license: '1'
intvolume: ' 35'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Biology of the Cell
publication_identifier:
eissn:
- 1939-4586
issn:
- 1059-1524
publication_status: published
publisher: American Society for Cell Biology
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase
separation'
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 35
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18757'
abstract:
- lang: eng
text: 'Segmentation is a critical data processing step in many applications of cryo-electron
tomography. Downstream analyses, such as subtomogram averaging, are often based
on segmentation results, and are thus critically dependent on the availability
of open-source software for accurate as well as high-throughput tomogram segmentation.
There is a need for more user-friendly, flexible, and comprehensive segmentation
software that offers an insightful overview of all steps involved in preparing
automated segmentations. Here, we present Ais: a dedicated tomogram segmentation
package that is geared towards both high performance and accessibility, available
on GitHub. In this report, we demonstrate two common processing steps that can
be greatly accelerated with Ais: particle picking for subtomogram averaging, and
generating many-feature segmentations of cellular architecture based on in situ
tomography data. Featuring comprehensive annotation, segmentation, and rendering
functionality, as well as an open repository for trained models at aiscryoet.org,
we hope that Ais will help accelerate research and dissemination of data involving
cryoET.'
acknowledgement: 'We thank A Koster and M Barcena for helpful discussions and kindly
sharing the coronaviral replication organelle datasets. We are also grateful to
van den Hoek et al., 2022 and Wu et al., 2023, for uploading the data that we used
for Figure 5 onto EMPIAR and EMDB, as well as to the authors of various other datasets
uploaded to these databases that are not discussed in this manuscript but that were
useful for testing the software. We also thank the reviewers, whose comments were
very helpful in improving the manuscript and the software. Finally, we are grateful
the early Ais users who provided us with feedback on the software and reported issues.
This research was supported by the following grants to THS: European Research Council
H202 Grant 759517; European Union’s Horizon Europe Program IMAGINE grant 101094250,
and the Netherlands Organization for Scientific Research Grant VI.Vidi.193.014.'
article_number: '98552'
article_processing_charge: Yes
article_type: original
author:
- first_name: Mart G.F.
full_name: Last, Mart G.F.
last_name: Last
- first_name: Leoni
full_name: Abendstein, Leoni
id: 14f1f051-cd9d-11ef-9c94-8b942a882560
last_name: Abendstein
orcid: 0000-0001-7634-5353
- first_name: Lenard M.
full_name: Voortman, Lenard M.
last_name: Voortman
- first_name: Thomas H.
full_name: Sharp, Thomas H.
last_name: Sharp
citation:
ama: Last MGF, Abendstein L, Voortman LM, Sharp TH. Streamlining segmentation of
cryo-electron tomography datasets with Ais. eLife. 2024;13. doi:10.7554/eLife.98552
apa: Last, M. G. F., Abendstein, L., Voortman, L. M., & Sharp, T. H. (2024).
Streamlining segmentation of cryo-electron tomography datasets with Ais. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.98552
chicago: Last, Mart G.F., Leoni Abendstein, Lenard M. Voortman, and Thomas H. Sharp.
“Streamlining Segmentation of Cryo-Electron Tomography Datasets with Ais.” ELife.
eLife Sciences Publications, 2024. https://doi.org/10.7554/eLife.98552.
ieee: M. G. F. Last, L. Abendstein, L. M. Voortman, and T. H. Sharp, “Streamlining
segmentation of cryo-electron tomography datasets with Ais,” eLife, vol.
13. eLife Sciences Publications, 2024.
ista: Last MGF, Abendstein L, Voortman LM, Sharp TH. 2024. Streamlining segmentation
of cryo-electron tomography datasets with Ais. eLife. 13, 98552.
mla: Last, Mart G. F., et al. “Streamlining Segmentation of Cryo-Electron Tomography
Datasets with Ais.” ELife, vol. 13, 98552, eLife Sciences Publications,
2024, doi:10.7554/eLife.98552.
short: M.G.F. Last, L. Abendstein, L.M. Voortman, T.H. Sharp, ELife 13 (2024).
das_tickbox: '1'
dataavailabilitystatement: Source code is available via GitHub, (copy archived at
Last, 2024), software available on the python package index as 'Ais-cryoET'. Trained
neural networks have been uploaded to aiscryoet.org.
date_created: 2025-01-05T23:01:57Z
date_published: 2024-12-20T00:00:00Z
date_updated: 2026-10-01T11:22:32Z
day: '20'
ddc:
- '570'
department:
- _id: FlPr
doi: 10.7554/eLife.98552
external_id:
pmid:
- '39704648'
file:
- access_level: open_access
checksum: a4f0f906e4d5c1078208b317e78699d1
content_type: application/pdf
creator: dernst
date_created: 2025-01-08T08:51:45Z
date_updated: 2025-01-08T08:51:45Z
file_id: '18774'
file_name: 2024_eLife_Last.pdf
file_size: 7445664
relation: main_file
success: 1
file_date_updated: 2025-01-08T08:51:45Z
fulldoi: https://doi.org/10.7554/eLife.98552
has_accepted_license: '1'
intvolume: ' 13'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Streamlining segmentation of cryo-electron tomography datasets with Ais
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '18445'
abstract:
- lang: eng
text: Acquisition of specialized cellular features is controlled by the ordered
expression of transcription factors (TFs) along differentiation trajectories.
Here, we find a member of the Onecut TF family, ONECUT3, expressed in postmitotic
neurons that leave their Ascl1+/Onecut1/2+ proliferative domain in the vertebrate
hypothalamus to instruct neuronal differentiation. We combined single-cell RNA-seq
and gain-of-function experiments for gene network reconstruction to show that
ONECUT3 affects the polarization and morphogenesis of both hypothalamic GABA-derived
dopamine and thyrotropin-releasing hormone (TRH)+ glutamate neurons through neuron
navigator-2 (NAV2). In vivo, siRNA-mediated knockdown of ONECUT3 in neonatal mice
reduced NAV2 mRNA, as well as neurite complexity in Onecut3-containing neurons,
while genetic deletion of Onecut3/ceh-48 in C. elegans impaired neurocircuit wiring,
and sensory discrimination-based behaviors. Thus, ONECUT3, conserved across neuronal
subtypes and many species, underpins the polarization and morphological plasticity
of phenotypically distinct neurons that descend from a common pool of Ascl1+ progenitors
in the hypothalamus.
acknowledgement: "The authors thank Z. Máté, G. Szabó, and F. Erdélyi for the custom
generation of transgenic mouse lines, C. Fekete for Trh transgenic tissues (all
from the Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest,
Hungary), A. Goudmaeker for IVF recovery of a frozen mouse line (SSS animal facility,
Université catholique de Louvain), and Y. Yanagawa (Department of Genetic and Behavioral
Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Japan) for
providing GAD67gfp/+ mice. We also thank S. Cloer, D. Preininger, and A. Weissenbacher
(Tiergarten Schönbrunn, Vienna, Austria) for providing naked mole rats, Seba’s fruit
bats, and Indian flying foxes, as well as F. Aujard (CNRS, UMR 7179 ‘Adaptive mechanisms
and evolution’, France) for Microcebus tissues. I. Milenkovic and G.G. Kovács (Clinical
Institute of Neurology, Medical University of Vienna, Vienna, Austria) are acknowledged
for providing post-mortem human brain samples. We are indebted to S. Rehman (Medical
University of Vienna), M. Kalusa (University of Leipzig, Leipzig, Germany), and
W. Reimann (Paul Flechsig Institute for Brain Research, Leipzig, Germany) for their
technical assistance. C. elegans strains were provided by the National Bioresource
Project for the nematode, Japan, and the CGC, with the latter being funded by the
NIH Office of Research Infrastructure Programs (P40 OD010440). This work was supported
by the Austrian Science Fund (FWF, P 34121-B; to E.K.), the Swedish Research Council
(2023-03058, T.Ha; 2020-01688, T.Hö.), the Swedish Brain Foundation (Hjärnfonden,
FO2022-0300, to T.Ha.), the Novo Nordisk Foundation (NNF23OC0084476, to T.Ha.),
the European Research Council (FOODFORLIFE, ERC-2020-AdG-101021016; to T.Ha.), the
Université Catholique de Louvain (‘Fonds spéciaux de recherche’-FSR, to F.C.), and
Fonds de la Recherche Scientifique F.R.S.-FNRS (‘Project de recherche (PDR)’ #T.0039.21,
to F.C.). S.J.E. is supported by the Simons Foundation #543069. I.L. is supported
by a post-doctoral fellowship from the Human Frontiers Science Program (LT000335/2020-L).
E.R. holds a PhD grant from the FRIA (F.R.S.-FNRS, Belgium). F.C. is a Research
Director of the F.R.S.-FNRS (Belgium).\r\nOpen access funding provided by Karolinska
Institute."
article_number: '8631'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Maja
full_name: Zupančič, Maja
last_name: Zupančič
- first_name: Erik
full_name: Keimpema, Erik
last_name: Keimpema
- first_name: Evgenii O.
full_name: Tretiakov, Evgenii O.
last_name: Tretiakov
- first_name: Stephanie J.
full_name: Eder, Stephanie J.
last_name: Eder
- first_name: Itamar
full_name: Lev, Itamar
last_name: Lev
- first_name: Lukas
full_name: Englmaier, Lukas
last_name: Englmaier
- first_name: Pradeep
full_name: Bhandari, Pradeep
id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87
last_name: Bhandari
orcid: 0000-0003-0863-4481
- first_name: Simone A.
full_name: Fietz, Simone A.
last_name: Fietz
- first_name: Wolfgang
full_name: Härtig, Wolfgang
last_name: Härtig
- first_name: Estelle
full_name: Renaux, Estelle
last_name: Renaux
- first_name: Andreas
full_name: Villunger, Andreas
last_name: Villunger
- first_name: Tomas
full_name: Hökfelt, Tomas
last_name: Hökfelt
- first_name: Manuel
full_name: Zimmer, Manuel
last_name: Zimmer
- first_name: Frédéric
full_name: Clotman, Frédéric
last_name: Clotman
- first_name: Tibor
full_name: Harkany, Tibor
last_name: Harkany
citation:
ama: Zupančič M, Keimpema E, Tretiakov EO, et al. Concerted transcriptional regulation
of the morphogenesis of hypothalamic neurons by ONECUT3. Nature Communications.
2024;15. doi:10.1038/s41467-024-52762-z
apa: Zupančič, M., Keimpema, E., Tretiakov, E. O., Eder, S. J., Lev, I., Englmaier,
L., … Harkany, T. (2024). Concerted transcriptional regulation of the morphogenesis
of hypothalamic neurons by ONECUT3. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-024-52762-z
chicago: Zupančič, Maja, Erik Keimpema, Evgenii O. Tretiakov, Stephanie J. Eder,
Itamar Lev, Lukas Englmaier, Pradeep Bhandari, et al. “Concerted Transcriptional
Regulation of the Morphogenesis of Hypothalamic Neurons by ONECUT3.” Nature
Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-52762-z.
ieee: M. Zupančič et al., “Concerted transcriptional regulation of the morphogenesis
of hypothalamic neurons by ONECUT3,” Nature Communications, vol. 15. Springer
Nature, 2024.
ista: Zupančič M, Keimpema E, Tretiakov EO, Eder SJ, Lev I, Englmaier L, Bhandari
P, Fietz SA, Härtig W, Renaux E, Villunger A, Hökfelt T, Zimmer M, Clotman F,
Harkany T. 2024. Concerted transcriptional regulation of the morphogenesis of
hypothalamic neurons by ONECUT3. Nature Communications. 15, 8631.
mla: Zupančič, Maja, et al. “Concerted Transcriptional Regulation of the Morphogenesis
of Hypothalamic Neurons by ONECUT3.” Nature Communications, vol. 15, 8631,
Springer Nature, 2024, doi:10.1038/s41467-024-52762-z.
short: M. Zupančič, E. Keimpema, E.O. Tretiakov, S.J. Eder, I. Lev, L. Englmaier,
P. Bhandari, S.A. Fietz, W. Härtig, E. Renaux, A. Villunger, T. Hökfelt, M. Zimmer,
F. Clotman, T. Harkany, Nature Communications 15 (2024).
das_tickbox: '1'
dataavailabilitystatement: The snRNA-seq data generated in this study have been deposited
in the NCBI Gene Expression Omnibus database under accession code GSE132730 and
as ‘Supplementary Data 1 - Neuro2a-onecut3-overexpression’. All other primary data
were made publically available at https://github.com/Harkany-Lab/Zupancic_2023 and
deposited to Figshare.com with https://doi.org/10.6084/m9.figshare.22680433. Source
data are provided with this paper.
date_created: 2024-10-20T22:02:05Z
date_published: 2024-10-05T00:00:00Z
date_updated: 2026-10-01T12:17:25Z
day: '05'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1038/s41467-024-52762-z
external_id:
isi:
- '001409493300014'
pmid:
- '39366958'
file:
- access_level: open_access
checksum: 03d6dd1b84efa24e9e9ede748d08764d
content_type: application/pdf
creator: dernst
date_created: 2024-10-21T12:15:38Z
date_updated: 2024-10-21T12:15:38Z
file_id: '18460'
file_name: 2024_NatureComm_Zupancic.pdf
file_size: 7215329
relation: main_file
success: 1
file_date_updated: 2024-10-21T12:15:38Z
fulldoi: https://doi.org/10.1038/s41467-024-52762-z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '22961'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons
by ONECUT3
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15
year: '2024'
...
---
_id: '14213'
abstract:
- lang: eng
text: We introduce a method to segment the visual field into independently moving
regions, trained with no ground truth or supervision. It consists of an adversarial
conditional encoder-decoder architecture based on Slot Attention, modified to
use the image as context to decode optical flow without attempting to reconstruct
the image itself. In the resulting multi-modal representation, one modality (flow)
feeds the encoder to produce separate latent codes (slots), whereas the other
modality (image) conditions the decoder to generate the first (flow) from the
slots. This design frees the representation from having to encode complex nuisance
variability in the image due to, for instance, illumination and reflectance properties
of the scene. Since customary autoencoding based on minimizing the reconstruction
error does not preclude the entire flow from being encoded into a single slot,
we modify the loss to an adversarial criterion based on Contextual Information
Separation. The resulting min-max optimization fosters the separation of objects
and their assignment to different attention slots, leading to Divided Attention,
or DivA. DivA outperforms recent unsupervised multi-object motion segmentation
methods while tripling run-time speed up to 104FPS and reducing the performance
gap from supervised methods to 12% or less. DivA can handle different numbers
of objects and different image sizes at training and test time, is invariant to
permutation of object labels, and does not require explicit regularization.
article_processing_charge: No
arxiv: 1
author:
- first_name: Dong
full_name: Lao, Dong
last_name: Lao
- first_name: Zhengyang
full_name: Hu, Zhengyang
last_name: Hu
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Yanchao
full_name: Yang, Yanchao
last_name: Yang
- first_name: Stefano
full_name: Soatto, Stefano
last_name: Soatto
citation:
ama: 'Lao D, Hu Z, Locatello F, Yang Y, Soatto S. Divided attention: Unsupervised
multi-object discovery with contextually separated slots. In: 1st Conference
on Parsimony and Learning. ; 2024.'
apa: 'Lao, D., Hu, Z., Locatello, F., Yang, Y., & Soatto, S. (2024). Divided
attention: Unsupervised multi-object discovery with contextually separated slots.
In 1st Conference on Parsimony and Learning. Hong Kong, China.'
chicago: 'Lao, Dong, Zhengyang Hu, Francesco Locatello, Yanchao Yang, and Stefano
Soatto. “Divided Attention: Unsupervised Multi-Object Discovery with Contextually
Separated Slots.” In 1st Conference on Parsimony and Learning, 2024.'
ieee: 'D. Lao, Z. Hu, F. Locatello, Y. Yang, and S. Soatto, “Divided attention:
Unsupervised multi-object discovery with contextually separated slots,” in 1st
Conference on Parsimony and Learning, Hong Kong, China, 2024.'
ista: 'Lao D, Hu Z, Locatello F, Yang Y, Soatto S. 2024. Divided attention: Unsupervised
multi-object discovery with contextually separated slots. 1st Conference on Parsimony
and Learning. CPAL: Conference on Parsimony and Learning.'
mla: 'Lao, Dong, et al. “Divided Attention: Unsupervised Multi-Object Discovery
with Contextually Separated Slots.” 1st Conference on Parsimony and Learning,
2024.'
short: D. Lao, Z. Hu, F. Locatello, Y. Yang, S. Soatto, in:, 1st Conference on Parsimony
and Learning, 2024.
conference:
end_date: 2024-01-03
location: Hong Kong, China
name: 'CPAL: Conference on Parsimony and Learning'
start_date: 2024-01-03
das_tickbox: '0'
date_created: 2023-08-22T14:19:59Z
date_published: 2024-01-03T00:00:00Z
date_updated: 2026-10-01T11:25:45Z
day: '03'
ddc:
- '000'
department:
- _id: FrLo
external_id:
arxiv:
- '2304.01430'
file:
- access_level: open_access
checksum: 8fad894c34f1b3d5a14fb8ffb12f7277
content_type: application/pdf
creator: dernst
date_created: 2024-02-12T08:40:36Z
date_updated: 2024-02-12T08:40:36Z
file_id: '14978'
file_name: 2024_CPAL_Lao.pdf
file_size: 8038511
relation: main_file
success: 1
file_date_updated: 2024-02-12T08:40:36Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: 1st Conference on Parsimony and Learning
publication_status: published
quality_controlled: '1'
researchdata_availability: no
status: public
supplementarymaterial: no
title: 'Divided attention: Unsupervised multi-object discovery with contextually separated
slots'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: publisher
OA_type: diamond
_id: '18114'
abstract:
- lang: eng
text: This paper presents Mechanistic Neural Networks, a neural network design for
machine learning applications in the sciences. It incorporates a new Mechanistic
Block in standard architectures to explicitly learn governing differential equations
as representations, revealing the underlying dynamics of data and enhancing interpretability
and efficiency in data modeling. Central to our approach is a novel Relaxed Linear
Programming Solver (NeuRLP) inspired by a technique that reduces solving linear
ODEs to solving linear programs. This integrates well with neural networks and
surpasses the limitations of traditional ODE solvers enabling scalable GPU parallel
processing. Overall, Mechanistic Neural Networks demonstrate their versatility
for scientific machine learning applications, adeptly managing tasks from equation
discovery to dynamic systems modeling. We prove their comprehensive capabilities
in analyzing and interpreting complex scientific data across various applications,
showing significant performance against specialized state-of-the-art methods.
Source code is available at https://github.com/alpz/mech-nn.
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Adeel A
full_name: Pervez, Adeel A
id: fca6d90c-d47f-11ee-bc87-93ff51604981
last_name: Pervez
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Efstratios
full_name: Gavves, Efstratios
last_name: Gavves
citation:
ama: 'Pervez AA, Locatello F, Gavves E. Mechanistic neural networks for scientific
machine learning. In: Proceedings of the 41st International Conference on Machine
Learning. Vol 235. ML Research Press; 2024:40484-40501.'
apa: 'Pervez, A. A., Locatello, F., & Gavves, E. (2024). Mechanistic neural
networks for scientific machine learning. In Proceedings of the 41st International
Conference on Machine Learning (Vol. 235, pp. 40484–40501). Vienna, Austria:
ML Research Press.'
chicago: Pervez, Adeel A, Francesco Locatello, and Efstratios Gavves. “Mechanistic
Neural Networks for Scientific Machine Learning.” In Proceedings of the 41st
International Conference on Machine Learning, 235:40484–501. ML Research Press,
2024.
ieee: A. A. Pervez, F. Locatello, and E. Gavves, “Mechanistic neural networks for
scientific machine learning,” in Proceedings of the 41st International Conference
on Machine Learning, Vienna, Austria, 2024, vol. 235, pp. 40484–40501.
ista: 'Pervez AA, Locatello F, Gavves E. 2024. Mechanistic neural networks for scientific
machine learning. Proceedings of the 41st International Conference on Machine
Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235,
40484–40501.'
mla: Pervez, Adeel A., et al. “Mechanistic Neural Networks for Scientific Machine
Learning.” Proceedings of the 41st International Conference on Machine Learning,
vol. 235, ML Research Press, 2024, pp. 40484–501.
short: A.A. Pervez, F. Locatello, E. Gavves, in:, Proceedings of the 41st International
Conference on Machine Learning, ML Research Press, 2024, pp. 40484–40501.
conference:
end_date: 2024-07-27
location: Vienna, Austria
name: 'ICML: International Conference on Machine Learning'
start_date: 2024-07-21
das_tickbox: '0'
date_created: 2024-09-22T22:01:43Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2026-10-01T11:26:09Z
day: '01'
ddc:
- '000'
department:
- _id: FrLo
external_id:
arxiv:
- '2402.13077'
intvolume: ' 235'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2402.13077
month: '09'
oa: 1
oa_version: Published Version
page: 40484-40501
publication: Proceedings of the 41st International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/alpz/mech-nn
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Mechanistic neural networks for scientific machine learning
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 235
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18964'
abstract:
- lang: eng
text: Object-centric learning (OCL) extracts the representation of objects with
slots, offering an exceptional blend of flexibility and interpretability for abstracting
low-level perceptual features. A widely adopted method within OCL is slot attention,
which utilizes attention mechanisms to iteratively refine slot representations.
However, a major draw-back of most object-centric models, including slot attention,
is their reliance on predefining the number of slots. This not only necessitates
prior knowledge of the dataset but also overlooks the inherent variability in
the number of objects present in each instance. To overcome this fundamental limitation,
we present a novel complexity-aware object auto-encoder framework. Within this
framework, we introduce an adaptive slot attention (AdaSlot) mecha-nism that dynamically
determines the optimal number of slots based on the content of the data. This
is achieved by proposing a discrete slot sampling module that is responsible for
selecting an appropriate number of slots from a candidate list. Furthermore, we
introduce a masked slot decoder that suppresses unselected slots during the decoding
process. Our framework, tested extensively on object discovery tasks with various
datasets, shows performance matching or exceeding top fixed-slot models. Moreover,
our analysis substantiates that our method exhibits the capability to dynamically
adapt the slot number according to each instance's complexity, offering the potential
for further exploration in slot attention research. Project will be available
at https://kfan21.github.io/AdaSlot/
acknowledgement: Yanwei Fu is the corresponding authour. Yanwei Fu is with School
of Data Science, Fudan University, Shanghai Key Lab of Intelligent Information Processing,
Fudan University, and Fudan ISTBI-ZJNU Algorithm Centre for Brain-inspired Intelligence,
Zhejiang Normal University, Jinhua, China.
article_processing_charge: No
arxiv: 1
author:
- first_name: Ke
full_name: Fan, Ke
last_name: Fan
- first_name: Zechen
full_name: Bai, Zechen
last_name: Bai
- first_name: Tianjun
full_name: Xiao, Tianjun
last_name: Xiao
- first_name: Tong
full_name: He, Tong
last_name: He
- first_name: Max
full_name: Horn, Max
last_name: Horn
- first_name: Yanwei
full_name: Fu, Yanwei
last_name: Fu
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Zheng
full_name: Zhang, Zheng
last_name: Zhang
citation:
ama: 'Fan K, Bai Z, Xiao T, et al. Adaptive slot attention: Object discovery with
dynamic slot number. In: 2024 IEEE/CVF Conference on Computer Vision and Pattern
Recognition. IEEE; 2024. doi:10.1109/cvpr52733.2024.02176'
apa: 'Fan, K., Bai, Z., Xiao, T., He, T., Horn, M., Fu, Y., … Zhang, Z. (2024).
Adaptive slot attention: Object discovery with dynamic slot number. In 2024
IEEE/CVF Conference on Computer Vision and Pattern Recognition. Seattle, WA,
United States: IEEE. https://doi.org/10.1109/cvpr52733.2024.02176'
chicago: 'Fan, Ke, Zechen Bai, Tianjun Xiao, Tong He, Max Horn, Yanwei Fu, Francesco
Locatello, and Zheng Zhang. “Adaptive Slot Attention: Object Discovery with Dynamic
Slot Number.” In 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition.
IEEE, 2024. https://doi.org/10.1109/cvpr52733.2024.02176.'
ieee: 'K. Fan et al., “Adaptive slot attention: Object discovery with dynamic
slot number,” in 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition,
Seattle, WA, United States, 2024.'
ista: 'Fan K, Bai Z, Xiao T, He T, Horn M, Fu Y, Locatello F, Zhang Z. 2024. Adaptive
slot attention: Object discovery with dynamic slot number. 2024 IEEE/CVF Conference
on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision
and Pattern Recognition.'
mla: 'Fan, Ke, et al. “Adaptive Slot Attention: Object Discovery with Dynamic Slot
Number.” 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition,
IEEE, 2024, doi:10.1109/cvpr52733.2024.02176.'
short: K. Fan, Z. Bai, T. Xiao, T. He, M. Horn, Y. Fu, F. Locatello, Z. Zhang, in:,
2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2024.
conference:
end_date: 2024-06-22
location: Seattle, WA, United States
name: 'CVPR: Conference on Computer Vision and Pattern Recognition'
start_date: 2024-06-16
das_tickbox: '0'
date_created: 2025-01-29T14:27:39Z
date_published: 2024-06-15T00:00:00Z
date_updated: 2026-10-02T08:47:53Z
day: '15'
department:
- _id: FrLo
doi: 10.1109/cvpr52733.2024.02176
external_id:
arxiv:
- '2406.09196'
isi:
- '001342515506043'
fulldoi: https://doi.org/10.1109/cvpr52733.2024.02176
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2406.09196
month: '06'
oa: 1
oa_version: Preprint
publication: 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition
publication_identifier:
eisbn:
- '9798350353006'
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://kfan21.github.io/AdaSlot/
researchdata_availability: yes
status: public
supplementarymaterial: no
title: 'Adaptive slot attention: Object discovery with dynamic slot number'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18956'
abstract:
- lang: eng
text: 'Group Activity Recognition (GAR) aims to detect the activity performed by
multiple actors in a scene. Prior works model the spatio-temporal features based
on the RGB, optical flow or keypoint data types. On the contrary, our hypothesis
is that by only using the RGB data without temporality, the performance can be
maintained with a negligible loss in accuracy. To that end, we propose a novel
GAR technique for volleyball videos, DECOMPL, which consists of two complementary
branches. In the visual branch, it extracts the features using attention pooling.
In the coordinate branch, it considers the configuration of the players and extracts
the spatial information from the box coordinates. Moreover, we analyzed the Volleyball
dataset that the recent literature is mostly based on, and systematically reannotated
it to emphasize the group concept. Experimental results demonstrated the effectiveness
of the proposed model DECOMPL, which delivered the best/second best GAR performance
with the reannotations/original annotations among the comparable state-of-the-art
methods. Code and new annotations are available at GitHub: https://github.com/berkerdemirel/decompl'
article_processing_charge: No
arxiv: 1
author:
- first_name: Berker
full_name: Demirel, Berker
id: 8b4bc47f-3200-11ee-973b-8f0e7be21a9f
last_name: Demirel
- first_name: Huseyin
full_name: Ozkan, Huseyin
last_name: Ozkan
citation:
ama: 'Demirel B, Ozkan H. Decompl: Decompositional learning with attention pooling
for group activity recognition from a single volleyball image. In: 2024 IEEE
International Conference on Image Processing. IEEE; 2024:977-983. doi:10.1109/icip51287.2024.10647499'
apa: 'Demirel, B., & Ozkan, H. (2024). Decompl: Decompositional learning with
attention pooling for group activity recognition from a single volleyball image.
In 2024 IEEE International Conference on Image Processing (pp. 977–983).
Abu Dhabi, United Arab Emirates: IEEE. https://doi.org/10.1109/icip51287.2024.10647499'
chicago: 'Demirel, Berker, and Huseyin Ozkan. “Decompl: Decompositional Learning
with Attention Pooling for Group Activity Recognition from a Single Volleyball
Image.” In 2024 IEEE International Conference on Image Processing, 977–83.
IEEE, 2024. https://doi.org/10.1109/icip51287.2024.10647499.'
ieee: 'B. Demirel and H. Ozkan, “Decompl: Decompositional learning with attention
pooling for group activity recognition from a single volleyball image,” in 2024
IEEE International Conference on Image Processing, Abu Dhabi, United Arab
Emirates, 2024, pp. 977–983.'
ista: 'Demirel B, Ozkan H. 2024. Decompl: Decompositional learning with attention
pooling for group activity recognition from a single volleyball image. 2024 IEEE
International Conference on Image Processing. ICIP: International Conference on
Image Processing, 977–983.'
mla: 'Demirel, Berker, and Huseyin Ozkan. “Decompl: Decompositional Learning with
Attention Pooling for Group Activity Recognition from a Single Volleyball Image.”
2024 IEEE International Conference on Image Processing, IEEE, 2024, pp.
977–83, doi:10.1109/icip51287.2024.10647499.'
short: B. Demirel, H. Ozkan, in:, 2024 IEEE International Conference on Image Processing,
IEEE, 2024, pp. 977–983.
conference:
end_date: 2024-10-30
location: Abu Dhabi, United Arab Emirates
name: 'ICIP: International Conference on Image Processing'
start_date: 2024-10-27
corr_author: '1'
das_tickbox: '0'
date_created: 2025-01-29T12:22:24Z
date_published: 2024-11-01T00:00:00Z
date_updated: 2026-10-02T08:47:17Z
day: '01'
department:
- _id: FrLo
doi: 10.1109/icip51287.2024.10647499
external_id:
arxiv:
- '2303.06439'
isi:
- '001442947000143'
fulldoi: https://doi.org/10.1109/icip51287.2024.10647499
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2303.06439
month: '11'
oa: 1
oa_version: Preprint
page: 977-983
publication: 2024 IEEE International Conference on Image Processing
publication_identifier:
eisbn:
- '9798350349399'
eissn:
- 2381-8549
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/berkerdemirel/decompl
researchdata_availability: yes
status: public
supplementarymaterial: no
title: 'Decompl: Decompositional learning with attention pooling for group activity
recognition from a single volleyball image'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '14946'
abstract:
- lang: eng
text: We present a unified framework for studying the identifiability of representations
learned from simultaneously observed views, such as different data modalities.
We allow a partially observed setting in which each view constitutes a nonlinear
mixture of a subset of underlying latent variables, which can be causally related.
We prove that the information shared across all subsets of any number of views
can be learned up to a smooth bijection using contrastive learning and a single
encoder per view. We also provide graphical criteria indicating which latent variables
can be identified through a simple set of rules, which we refer to as identifiability
algebra. Our general framework and theoretical results unify and extend several
previous work on multi-view nonlinear ICA, disentanglement, and causal representation
learning. We experimentally validate our claims on numerical, image, and multi-modal
data sets. Further, we demonstrate that the performance of prior methods is recovered
in different special cases of our setup. Overall, we find that access to multiple
partial views offers unique opportunities for identifiable representation learning,
enabling the discovery of latent structures from purely observational data.
acknowledgement: 'This work was initiated at the Second Bellairs Workshop on Causality
held at the Bellairs Research Institute, January 6–13, 2022; we thank all workshop
participants for providing a stimulating research environment. Further, we thank
Cian Eastwood, Luigi Gresele, Stefano Soatto, Marco Bagatella and A. René Geist
for helpful discussion. GM is a member of the Machine Learning Cluster of Excellence,
EXC number 2064/1 – Project number 390727645. JvK and GM acknowledge support from
the German Federal Ministry of Education and Research (BMBF) through the Tübingen
AI Center (FKZ: 01IS18039B). The research of DX and SM was supported by the Air
Force Office of Scientific Research under award number FA8655-22-1-7155. Any opinions,
findings, and conclusions or recommendations expressed in this material are those
of the author(s) and do not necessarily reflect the views of the United States Air
Force. We also thank SURF for the support in using the Dutch National Supercomputer
Snellius. SL was supported by an IVADO excellence PhD scholarship and by Samsung
Electronics Co., Ldt. DY was supported by an Amazon fellowship, the International
Max Planck Research School for Intelligent Systems (IMPRS-IS) and the ISTA graduate
school. Work done outside of Amazon.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Dingling
full_name: Yao, Dingling
id: d3e02e50-48a8-11ee-8f62-c108061797fa
last_name: Yao
- first_name: Danru
full_name: Xu, Danru
last_name: Xu
- first_name: Sébastien
full_name: Lachapelle, Sébastien
last_name: Lachapelle
- first_name: Sara
full_name: Magliacane, Sara
last_name: Magliacane
- first_name: Perouz
full_name: Taslakian, Perouz
last_name: Taslakian
- first_name: Georg
full_name: Martius, Georg
last_name: Martius
- first_name: Julius von
full_name: Kügelgen, Julius von
last_name: Kügelgen
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
citation:
ama: 'Yao D, Xu D, Lachapelle S, et al. Multi-view causal representation learning
with partial observability. In: 12th International Conference on Learning Representations.
Curran Associates; 2024.'
apa: 'Yao, D., Xu, D., Lachapelle, S., Magliacane, S., Taslakian, P., Martius, G.,
… Locatello, F. (2024). Multi-view causal representation learning with partial
observability. In 12th International Conference on Learning Representations.
Vienna, Austria: Curran Associates.'
chicago: Yao, Dingling, Danru Xu, Sébastien Lachapelle, Sara Magliacane, Perouz
Taslakian, Georg Martius, Julius von Kügelgen, and Francesco Locatello. “Multi-View
Causal Representation Learning with Partial Observability.” In 12th International
Conference on Learning Representations. Curran Associates, 2024.
ieee: D. Yao et al., “Multi-view causal representation learning with partial
observability,” in 12th International Conference on Learning Representations,
Vienna, Austria, 2024.
ista: 'Yao D, Xu D, Lachapelle S, Magliacane S, Taslakian P, Martius G, Kügelgen
J von, Locatello F. 2024. Multi-view causal representation learning with partial
observability. 12th International Conference on Learning Representations. ICLR:
International Conference on Learning Representations.'
mla: Yao, Dingling, et al. “Multi-View Causal Representation Learning with Partial
Observability.” 12th International Conference on Learning Representations,
Curran Associates, 2024.
short: D. Yao, D. Xu, S. Lachapelle, S. Magliacane, P. Taslakian, G. Martius, J.
von Kügelgen, F. Locatello, in:, 12th International Conference on Learning Representations,
Curran Associates, 2024.
conference:
end_date: 2024-05-07
location: Vienna, Austria
name: 'ICLR: International Conference on Learning Representations'
start_date: 2024-05-07
corr_author: '1'
das_tickbox: '0'
date_created: 2024-02-07T14:28:34Z
date_published: 2024-11-07T00:00:00Z
date_updated: 2026-10-02T08:48:50Z
day: '07'
ddc:
- '000'
department:
- _id: FrLo
external_id:
arxiv:
- '2311.04056'
file:
- access_level: open_access
checksum: 8ed3c34706eeec622c7e8968dc0f747a
content_type: application/pdf
creator: dernst
date_created: 2025-02-04T12:34:23Z
date_updated: 2025-02-04T12:34:23Z
file_id: '18995'
file_name: 2024_ICLR_Yao.pdf
file_size: 1713606
relation: main_file
success: 1
file_date_updated: 2025-02-04T12:34:23Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: 12th International Conference on Learning Representations
publication_status: published
publisher: Curran Associates
quality_controlled: '1'
researchdata_availability: no
status: public
supplementarymaterial: no
title: Multi-view causal representation learning with partial observability
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17302'
abstract:
- lang: eng
text: The mountain cryosphere and groundwater play pivotal roles in shaping the
hydrological cycle, yet their connectivity remains incompletely understood. Current
knowledge on meltwater recharge and consequent groundwater discharge processes
is better developed for snow–groundwater connectivity than for glacier–groundwater
connectivity. Estimates of meltwater recharge vary considerably, which is probably
a function of not only inherent catchment characteristics but also of the different
spatio-temporal scales involved and the uncertainties in the methods used. This
hinders a comprehensive understanding of the mountain water cycle. As glaciers
retreat, permafrost thaws and snowpack diminishes, the relative importance of
mountain groundwater is expected to increase. However, shifting and declining
recharge from the cryosphere may decrease absolute groundwater amounts and fluxes
with as-yet unknown effects on catchment-scale hydrological processes. We therefore
stress the need to better quantify mountain cryosphere–groundwater connectivity
to predict climate change impacts on mountain water supply and to support sustainable
water resource management of downstream socio-ecological systems.
acknowledgement: 'We acknowledge the Mountain Research Initiative (MRI) for sponsoring
the workshop ‘Cryosphere-groundwater Interactions: A Missing Link in Mountain Water
Research’ via their funding from the Swiss Academy of Sciences (SCNAT) under project
no. FNW0004 004-2019-00. M.v.T. was supported by a Walter Benjamin fellowship from
the German Research Foundation (DFG) under project no. 510684314. C.A.-W. was supported
by the Banting Postdoctoral Fellowships programme, administered by the government
of Canada. G.C. acknowledges the support of the DFG research unit (FOR2793/2) investigating
the ‘Sensitivity of High Alpine Geosystems to Climate Change since 1850’ (SEHAG)
under grant CH981/3-2. F.D. acknowledges funding from the Dirección de Fomento de
la Investigación at PUCP. I.d.G. acknowledges funding from the European Research
Council (ERC) under grant agreement GROW-101041110. V.Y. was supported by Nazarbayev
University under CRP research grant no. 021220CRP2122. We thank D. Masovic of VAW,
ETH Zurich, for drawing Fig. 1.'
article_processing_charge: No
article_type: original
author:
- first_name: Marit
full_name: van Tiel, Marit
last_name: van Tiel
- first_name: Caroline
full_name: Aubry-Wake, Caroline
last_name: Aubry-Wake
- first_name: Lauren
full_name: Somers, Lauren
last_name: Somers
- first_name: Christoff
full_name: Andermann, Christoff
last_name: Andermann
- first_name: Francesco
full_name: Avanzi, Francesco
last_name: Avanzi
- first_name: Michel
full_name: Baraer, Michel
last_name: Baraer
- first_name: Gabriele
full_name: Chiogna, Gabriele
last_name: Chiogna
- first_name: Clémence
full_name: Daigre, Clémence
last_name: Daigre
- first_name: Soumik
full_name: Das, Soumik
last_name: Das
- first_name: Fabian
full_name: Drenkhan, Fabian
last_name: Drenkhan
- first_name: Daniel
full_name: Farinotti, Daniel
last_name: Farinotti
- first_name: Catriona Louise
full_name: Fyffe, Catriona Louise
id: 001b0422-8d15-11ed-bc51-cab6c037a228
last_name: Fyffe
- first_name: Inge
full_name: de Graaf, Inge
last_name: de Graaf
- first_name: Sarah
full_name: Hanus, Sarah
last_name: Hanus
- first_name: Walter
full_name: Immerzeel, Walter
last_name: Immerzeel
- first_name: Franziska
full_name: Koch, Franziska
last_name: Koch
- first_name: Jeffrey M.
full_name: McKenzie, Jeffrey M.
last_name: McKenzie
- first_name: Tom
full_name: Müller, Tom
last_name: Müller
- first_name: Andrea L.
full_name: Popp, Andrea L.
last_name: Popp
- first_name: Zarina
full_name: Saidaliyeva, Zarina
last_name: Saidaliyeva
- first_name: Bettina
full_name: Schaefli, Bettina
last_name: Schaefli
- first_name: Oliver S.
full_name: Schilling, Oliver S.
last_name: Schilling
- first_name: Kapiolani
full_name: Teagai, Kapiolani
last_name: Teagai
- first_name: James M.
full_name: Thornton, James M.
last_name: Thornton
- first_name: Vadim
full_name: Yapiyev, Vadim
last_name: Yapiyev
citation:
ama: van Tiel M, Aubry-Wake C, Somers L, et al. Cryosphere–groundwater connectivity
is a missing link in the mountain water cycle. Nature Water. 2024;2:624-637.
doi:10.1038/s44221-024-00277-8
apa: van Tiel, M., Aubry-Wake, C., Somers, L., Andermann, C., Avanzi, F., Baraer,
M., … Yapiyev, V. (2024). Cryosphere–groundwater connectivity is a missing link
in the mountain water cycle. Nature Water. Springer Nature. https://doi.org/10.1038/s44221-024-00277-8
chicago: Tiel, Marit van, Caroline Aubry-Wake, Lauren Somers, Christoff Andermann,
Francesco Avanzi, Michel Baraer, Gabriele Chiogna, et al. “Cryosphere–Groundwater
Connectivity Is a Missing Link in the Mountain Water Cycle.” Nature Water.
Springer Nature, 2024. https://doi.org/10.1038/s44221-024-00277-8.
ieee: M. van Tiel et al., “Cryosphere–groundwater connectivity is a missing
link in the mountain water cycle,” Nature Water, vol. 2. Springer Nature,
pp. 624–637, 2024.
ista: van Tiel M, Aubry-Wake C, Somers L, Andermann C, Avanzi F, Baraer M, Chiogna
G, Daigre C, Das S, Drenkhan F, Farinotti D, Fyffe CL, de Graaf I, Hanus S, Immerzeel
W, Koch F, McKenzie JM, Müller T, Popp AL, Saidaliyeva Z, Schaefli B, Schilling
OS, Teagai K, Thornton JM, Yapiyev V. 2024. Cryosphere–groundwater connectivity
is a missing link in the mountain water cycle. Nature Water. 2, 624–637.
mla: van Tiel, Marit, et al. “Cryosphere–Groundwater Connectivity Is a Missing Link
in the Mountain Water Cycle.” Nature Water, vol. 2, Springer Nature, 2024,
pp. 624–37, doi:10.1038/s44221-024-00277-8.
short: M. van Tiel, C. Aubry-Wake, L. Somers, C. Andermann, F. Avanzi, M. Baraer,
G. Chiogna, C. Daigre, S. Das, F. Drenkhan, D. Farinotti, C.L. Fyffe, I. de Graaf,
S. Hanus, W. Immerzeel, F. Koch, J.M. McKenzie, T. Müller, A.L. Popp, Z. Saidaliyeva,
B. Schaefli, O.S. Schilling, K. Teagai, J.M. Thornton, V. Yapiyev, Nature Water
2 (2024) 624–637.
das_tickbox: '0'
date_created: 2024-07-22T09:46:52Z
date_published: 2024-07-19T00:00:00Z
date_updated: 2026-10-02T08:51:26Z
day: '19'
department:
- _id: FrPe
doi: 10.1038/s44221-024-00277-8
external_id:
isi:
- '001390137500016'
fulldoi: https://doi.org/10.1038/s44221-024-00277-8
intvolume: ' 2'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://insu.hal.science/insu-04674297
month: '07'
oa: 1
oa_version: Submitted Version
page: 624-637
publication: Nature Water
publication_identifier:
issn:
- 2731-6084
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Cryosphere–groundwater connectivity is a missing link in the mountain water
cycle
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 2
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18971'
abstract:
- lang: eng
text: 'Models prone to spurious correlations in training data often produce brittle
predictions and introduce unintended biases. Addressing this challenge typically
involves methods relying on prior knowledge and group annotation to remove spurious
correlations, which may not be readily available in many applications. In this
paper, we establish a novel connection between unsupervised object-centric learning
and mitigation of spurious correlations. Instead of directly inferring subgroups
with varying correlations with labels, our approach focuses on discovering concepts:
discrete ideas that are shared across input samples. Leveraging existing object-centric
representation learning, we introduce CoBalT: a concept balancing technique that
effectively mitigates spurious correlations without requiring human labeling of
subgroups. Evaluation across the benchmark datasets for sub-population shifts
demonstrate superior or competitive performance compared state-of-the-art baselines,
without the need for group annotation. Code is available at https://github.com/rarefin/CoBalT'
acknowledgement: "We acknowledge the support of the Canada CIFAR AI Chair Program
and IVADO. We thank Mila and Compute Canada for providing computational resources.\r\n"
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Rifat
full_name: Arefin, Rifat
last_name: Arefin
- first_name: Yan
full_name: Zhang, Yan
last_name: Zhang
- first_name: Aristide
full_name: Baratin, Aristide
last_name: Baratin
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Irina
full_name: Rish, Irina
last_name: Rish
- first_name: Dianbo
full_name: Liu, Dianbo
last_name: Liu
- first_name: Kenji
full_name: Kawaguchi, Kenji
last_name: Kawaguchi
citation:
ama: 'Arefin R, Zhang Y, Baratin A, et al. Unsupervised concept discovery mitigates
spurious correlations. In: Proceedings of the 41st International Conference
on Machine Learning. Vol 235. ML Research Press; 2024:1672-1688.'
apa: 'Arefin, R., Zhang, Y., Baratin, A., Locatello, F., Rish, I., Liu, D., &
Kawaguchi, K. (2024). Unsupervised concept discovery mitigates spurious correlations.
In Proceedings of the 41st International Conference on Machine Learning
(Vol. 235, pp. 1672–1688). Vienna, Austria: ML Research Press.'
chicago: Arefin, Rifat, Yan Zhang, Aristide Baratin, Francesco Locatello, Irina
Rish, Dianbo Liu, and Kenji Kawaguchi. “Unsupervised Concept Discovery Mitigates
Spurious Correlations.” In Proceedings of the 41st International Conference
on Machine Learning, 235:1672–88. ML Research Press, 2024.
ieee: R. Arefin et al., “Unsupervised concept discovery mitigates spurious
correlations,” in Proceedings of the 41st International Conference on Machine
Learning, Vienna, Austria, 2024, vol. 235, pp. 1672–1688.
ista: 'Arefin R, Zhang Y, Baratin A, Locatello F, Rish I, Liu D, Kawaguchi K. 2024.
Unsupervised concept discovery mitigates spurious correlations. Proceedings of
the 41st International Conference on Machine Learning. ICML: International Conference
on Machine Learning, PMLR, vol. 235, 1672–1688.'
mla: Arefin, Rifat, et al. “Unsupervised Concept Discovery Mitigates Spurious Correlations.”
Proceedings of the 41st International Conference on Machine Learning, vol.
235, ML Research Press, 2024, pp. 1672–88.
short: R. Arefin, Y. Zhang, A. Baratin, F. Locatello, I. Rish, D. Liu, K. Kawaguchi,
in:, Proceedings of the 41st International Conference on Machine Learning, ML
Research Press, 2024, pp. 1672–1688.
conference:
end_date: 2024-07-27
location: Vienna, Austria
name: 'ICML: International Conference on Machine Learning'
start_date: 2024-07-21
das_tickbox: '0'
date_created: 2025-01-30T07:21:57Z
date_published: 2024-07-30T00:00:00Z
date_updated: 2026-10-02T08:48:23Z
day: '30'
department:
- _id: FrLo
external_id:
arxiv:
- '2402.13368'
intvolume: ' 235'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2402.13368
month: '07'
oa: 1
oa_version: Preprint
page: 1672-1688
publication: Proceedings of the 41st International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/rarefin/CoBalT
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Unsupervised concept discovery mitigates spurious correlations
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 235
year: '2024'
...
---
_id: '14938'
abstract:
- lang: eng
text: High elevation headwater catchments are complex hydrological systems that
seasonally buffer water and release it in the form of snow and ice melt, modulating
downstream runoff regimes and water availability. In High Mountain Asia (HMA),
where a wide range of climates from semi-arid to monsoonal exist, the importance
of the cryospheric contributions to the water budget varies with the amount and
seasonal distribution of precipitation. Losses due to evapotranspiration and sublimation
are to date largely unquantified components of the water budget in such catchments,
although they can be comparable in magnitude to glacier melt contributions to
streamflow. 
Here, we simulate the hydrology of three high elevation headwater
catchments in distinct climates in HMA over 10 years using an ecohydrological
model geared towards high-mountain areas including snow and glaciers, forced with
reanalysis data. 
Our results show that evapotranspiration and sublimation
together are most important at the semi-arid site, Kyzylsu, on the northernmost
slopes of the Pamir mountain range. Here, the evaporative loss amounts to 28%
of the water throughput, which we define as the total water added to, or removed
from the water balance within a year. In comparison, evaporative losses are 19%
at the Central Himalayan site Langtang and 13% at the wettest site, 24K, on the
Southeastern Tibetan Plateau. At the three sites, respectively, sublimation removes
15%, 13% and 6% of snowfall, while evapotranspiration removes the equivalent of
76%, 28% and 19% of rainfall. In absolute terms, and across a comparable elevation
range, the highest ET flux is 413 mm yr-1 at 24K, while the highest sublimation
flux is 91 mm yr-1 at Kyzylsu. During warm and dry years, glacier melt was found
to only partially compensate for the annual supply deficit.
acknowledgement: "We would like to thank the team at the Center for the Research of
Glaciers, Tajik National Academy of Sciences, Abduhamid Kayumov, Khusrav Kabutov,
Ardamehr Halimov, among others, for their invaluable support over multiple field
seasons in Kyzylsu. We thank Wei Yang, Zhao Xhuanxi and Zhen Cheng from the Institute
of Tibetan Plateau Research, Chinese Academy of Sciences, for facilitating and supporting
fieldwork and for sharing crucial data from the Parlung 24K catchment. We thank
Reeju Shrestha and Himalayan Research Expeditions for their great support in Langtang.
We extend our thanks to Jakob Steiner and the team at ICIMOD for their relentless
efforts in data acquisition and curation in Langtang. Additionally, we are indebted
to Masashi Niwano from the Meteorological Research Institute, Japan Meteorological
Agency, for providing NHM atmospheric simulation outputs, which proved very valuable
in the downscaling process.\r\nThis project has received funding from the European
Research Council (ERC) under the European Union's Horizon 2020 research and innovation
program Grant Agreements No. 772751 (RAVEN, Rapid mass losses of debris-covered
glaciers in High Mountain Asia). Further funding was provided by JSPS-SNSF (Japan
Society for the Promotion of Science and Swiss National Science Foundation) Bilateral
Programmes project (HOPE, High-elevation precipitation in High Mountain Asia; Grant
183633). Fieldwork support for Tajikistan was received from the Swiss Polar Institute
Flagship Programme PAMIR, SPI-FLAG-2021-001. The project also received funding from
the ESA and NRSCC Dragon 5 cooperation project 'Cryosphere-hydrosphere interactions
of the Asian water towers: using remote sensing to drive hyper-resolution ecohydrological
modeling' (grant no. 59199). The National Natural Science Foundation of China (41961134035)
financially supported the data collection at 24K."
article_number: '044057'
article_processing_charge: Yes
article_type: original
author:
- first_name: Stefan
full_name: Fugger, Stefan
id: 86698d64-c4c6-11ee-af02-cdf1e6a7d31f
last_name: Fugger
- first_name: Thomas
full_name: Shaw, Thomas
id: 3caa3f91-1f03-11ee-96ce-e0e553054d6e
last_name: Shaw
orcid: 0000-0001-7640-6152
- first_name: Achille
full_name: Jouberton, Achille
last_name: Jouberton
- first_name: Evan
full_name: Miles, Evan
last_name: Miles
- first_name: Pascal
full_name: Buri, Pascal
id: 317987aa-9421-11ee-ac5a-b941b041abba
last_name: Buri
- first_name: Michael
full_name: McCarthy, Michael
id: 22a2674a-61ce-11ee-94b5-d18813baf16f
last_name: McCarthy
- first_name: Catriona Louise
full_name: Fyffe, Catriona Louise
id: 001b0422-8d15-11ed-bc51-cab6c037a228
last_name: Fyffe
- first_name: Simone
full_name: Fatichi, Simone
last_name: Fatichi
- first_name: Marin
full_name: Kneib, Marin
last_name: Kneib
- first_name: Peter
full_name: Molnar, Peter
last_name: Molnar
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
orcid: 0000-0002-5554-8087
citation:
ama: Fugger S, Shaw T, Jouberton A, et al. Hydrological regimes and evaporative
flux partitioning at the climatic ends of High Mountain Asia. Environmental
Research Letters. 2024;19. doi:10.1088/1748-9326/ad25a0
apa: Fugger, S., Shaw, T., Jouberton, A., Miles, E., Buri, P., McCarthy, M., … Pellicciotti,
F. (2024). Hydrological regimes and evaporative flux partitioning at the climatic
ends of High Mountain Asia. Environmental Research Letters. IOP Publishing.
https://doi.org/10.1088/1748-9326/ad25a0
chicago: Fugger, Stefan, Thomas Shaw, Achille Jouberton, Evan Miles, Pascal Buri,
Michael McCarthy, Catriona Louise Fyffe, et al. “Hydrological Regimes and Evaporative
Flux Partitioning at the Climatic Ends of High Mountain Asia.” Environmental
Research Letters. IOP Publishing, 2024. https://doi.org/10.1088/1748-9326/ad25a0.
ieee: S. Fugger et al., “Hydrological regimes and evaporative flux partitioning
at the climatic ends of High Mountain Asia,” Environmental Research Letters,
vol. 19. IOP Publishing, 2024.
ista: Fugger S, Shaw T, Jouberton A, Miles E, Buri P, McCarthy M, Fyffe CL, Fatichi
S, Kneib M, Molnar P, Pellicciotti F. 2024. Hydrological regimes and evaporative
flux partitioning at the climatic ends of High Mountain Asia. Environmental Research
Letters. 19, 044057.
mla: Fugger, Stefan, et al. “Hydrological Regimes and Evaporative Flux Partitioning
at the Climatic Ends of High Mountain Asia.” Environmental Research Letters,
vol. 19, 044057, IOP Publishing, 2024, doi:10.1088/1748-9326/ad25a0.
short: S. Fugger, T. Shaw, A. Jouberton, E. Miles, P. Buri, M. McCarthy, C.L. Fyffe,
S. Fatichi, M. Kneib, P. Molnar, F. Pellicciotti, Environmental Research Letters
19 (2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: 'The data that support the findings of this study are openly
available at the following URL/DOI: 10.5281/zenodo.10407300.'
date_created: 2024-02-05T09:01:11Z
date_published: 2024-04-09T00:00:00Z
date_updated: 2026-10-02T09:04:55Z
day: '09'
ddc:
- '550'
department:
- _id: FrPe
doi: 10.1088/1748-9326/ad25a0
external_id:
isi:
- '001198892300001'
file:
- access_level: open_access
checksum: 27999359b51c30fec6d81e48cdf0ee0d
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T09:14:44Z
date_updated: 2024-07-22T09:14:44Z
file_id: '17295'
file_name: 2024_EnvironmResearch_Fugger.pdf
file_size: 4433401
relation: main_file
success: 1
file_date_updated: 2024-07-22T09:14:44Z
fulldoi: https://doi.org/10.1088/1748-9326/ad25a0
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
keyword:
- Public Health
- Environmental and Occupational Health
- General Environmental Science
- Renewable Energy
- Sustainability and the Environment
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Environmental Research Letters
publication_identifier:
issn:
- 1748-9326
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: no
title: Hydrological regimes and evaporative flux partitioning at the climatic ends
of High Mountain Asia
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 19
year: '2024'
...