---
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'
...
---
_id: '15298'
abstract:
- lang: eng
text: Mountains are important suppliers of freshwater to downstream areas, affecting
large populations in particular in High Mountain Asia (HMA). Yet, the propagation
of water from HMA headwaters to downstream areas is not fully understood, as interactions
in the mountain water cycle between the cryo-, hydro- and biosphere remain elusive.
We review the definition of blue and green water fluxes as liquid water that contributes
to runoff at the outlet of the selected domain (blue) and water lost to the atmosphere
through vapor fluxes, that is evaporation from water, ground, and interception
plus transpiration (green) and propose to add the term white water to account
for the (often neglected) evaporation and sublimation from snow and ice. We provide
an assessment of models that can simulate the cryo-hydro-biosphere continuum and
the interactions between spheres in high mountain catchments, going beyond disciplinary
separations. Land surface models are uniquely able to account for such complexity,
since they solve the coupled fluxes of water, energy, and carbon between the land
surface and atmosphere. Due to the mechanistic nature of such models, specific
variables can be compared systematically to independent remote sensing observations
– providing vital insights into model accuracy and enabling the understanding
of the complex watersheds of HMA. We discuss recent developments in spaceborne
earth observation products that have the potential to support catchment modeling
in high mountain regions. We then present a pilot study application of the mechanistic
land surface model Tethys & Chloris to a glacierized watershed in the Nepalese
Himalayas and discuss the use of high-resolution earth observation data to constrain
the meteorological forcing uncertainty and validate model results. We use these
insights to highlight the remaining challenges and future opportunities that remote
sensing data presents for land surface modeling in HMA.
acknowledgement: 'This work was supported by the ESA and NRSCC Dragon 5 cooperation
project “Cryosphere-hydrosphere interactions of the Asian water towers: using remote
sensing to drive hyper-resolution ecohydrological modelling” [Grant no. 59199].
PB and FP acknowledge funding from the SNSF (High-elevation precipitation in High
Mountain Asia, HOPE)) [Grant no. 183633]. ESM, MK, SFu and FP acknowledge funding
from the ERC under the European Union’s Horizon 2020 research and innovation program
(Rapid mass losses of debris-covered glaciers in High Mountain Asia, RAVEN) [Grant
no. 772751]. LJ, CZ and MMe acknowledge the Second Tibetan Plateau Scientific Expedition
and Research Program (STEP) [grant no. 2019QZKK010308, no. 2019QZKK0206], the National
Natural Science Foundation of China projects (Grant no. 42171039, no. 91737205),
the Chinese Academy of Sciences President’s International Fellowship Initiative
[Grant no. 2020VTA0001], and the MOST High-Level Foreign Expert Program [Grant no.
G2022055010L].'
article_processing_charge: Yes
article_type: original
author:
- first_name: Pascal
full_name: Buri, Pascal
last_name: Buri
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
- first_name: Thomas
full_name: Shaw, Thomas
id: 3caa3f91-1f03-11ee-96ce-e0e553054d6e
last_name: Shaw
orcid: 0000-0001-7640-6152
- first_name: Catriona Louise
full_name: Fyffe, Catriona Louise
id: 001b0422-8d15-11ed-bc51-cab6c037a228
last_name: Fyffe
- first_name: Evan S.
full_name: Miles, Evan S.
last_name: Miles
- first_name: Michael
full_name: Mccarthy, Michael
id: 22a2674a-61ce-11ee-94b5-d18813baf16f
last_name: Mccarthy
- first_name: Marin
full_name: Kneib, Marin
last_name: Kneib
- first_name: Shaoting
full_name: Ren, Shaoting
last_name: Ren
- first_name: Achille
full_name: Jouberton, Achille
last_name: Jouberton
- first_name: Stefan
full_name: Fugger, Stefan
last_name: Fugger
- first_name: Li
full_name: Jia, Li
last_name: Jia
- first_name: Jing
full_name: Zhang, Jing
last_name: Zhang
- first_name: Cong
full_name: Shen, Cong
last_name: Shen
- first_name: Chaolei
full_name: Zheng, Chaolei
last_name: Zheng
- first_name: Massimo
full_name: Menenti, Massimo
last_name: Menenti
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
orcid: 0000-0002-5554-8087
citation:
ama: 'Buri P, Fatichi S, Shaw T, et al. Land surface modeling informed by earth
observation data: Toward understanding blue–green–white water fluxes in High Mountain
Asia. Geo-Spatial Information Science. 2024;27(3):703-727. doi:10.1080/10095020.2024.2330546'
apa: 'Buri, P., Fatichi, S., Shaw, T., Fyffe, C. L., Miles, E. S., McCarthy, M.,
… Pellicciotti, F. (2024). Land surface modeling informed by earth observation
data: Toward understanding blue–green–white water fluxes in High Mountain Asia.
Geo-Spatial Information Science. Taylor & Francis. https://doi.org/10.1080/10095020.2024.2330546'
chicago: 'Buri, Pascal, Simone Fatichi, Thomas Shaw, Catriona Louise Fyffe, Evan
S. Miles, Michael McCarthy, Marin Kneib, et al. “Land Surface Modeling Informed
by Earth Observation Data: Toward Understanding Blue–Green–White Water Fluxes
in High Mountain Asia.” Geo-Spatial Information Science. Taylor & Francis,
2024. https://doi.org/10.1080/10095020.2024.2330546.'
ieee: 'P. Buri et al., “Land surface modeling informed by earth observation
data: Toward understanding blue–green–white water fluxes in High Mountain Asia,”
Geo-Spatial Information Science, vol. 27, no. 3. Taylor & Francis,
pp. 703–727, 2024.'
ista: 'Buri P, Fatichi S, Shaw T, Fyffe CL, Miles ES, McCarthy M, Kneib M, Ren S,
Jouberton A, Fugger S, Jia L, Zhang J, Shen C, Zheng C, Menenti M, Pellicciotti
F. 2024. Land surface modeling informed by earth observation data: Toward understanding
blue–green–white water fluxes in High Mountain Asia. Geo-Spatial Information Science.
27(3), 703–727.'
mla: 'Buri, Pascal, et al. “Land Surface Modeling Informed by Earth Observation
Data: Toward Understanding Blue–Green–White Water Fluxes in High Mountain Asia.”
Geo-Spatial Information Science, vol. 27, no. 3, Taylor & Francis,
2024, pp. 703–27, doi:10.1080/10095020.2024.2330546.'
short: P. Buri, S. Fatichi, T. Shaw, C.L. Fyffe, E.S. Miles, M. McCarthy, M. Kneib,
S. Ren, A. Jouberton, S. Fugger, L. Jia, J. Zhang, C. Shen, C. Zheng, M. Menenti,
F. Pellicciotti, Geo-Spatial Information Science 27 (2024) 703–727.
das_tickbox: '0'
date_created: 2024-04-07T22:00:56Z
date_published: 2024-03-22T00:00:00Z
date_updated: 2026-10-02T09:12:24Z
day: '22'
ddc:
- '550'
department:
- _id: FrPe
doi: 10.1080/10095020.2024.2330546
external_id:
isi:
- '001189470100001'
file:
- access_level: open_access
checksum: afbfc4e9f1bf2a00711efc30ad667c40
content_type: application/pdf
creator: dernst
date_created: 2024-07-29T11:34:54Z
date_updated: 2024-07-29T11:34:54Z
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file_size: 15678450
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isi: 1
issue: '3'
language:
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month: '03'
oa: 1
oa_version: Published Version
page: 703-727
publication: Geo-Spatial Information Science
publication_identifier:
issn:
- 1009-5020
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: 'Land surface modeling informed by earth observation data: Toward understanding
blue–green–white water fluxes in 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: 27
year: '2024'
...
---
_id: '14885'
abstract:
- lang: eng
text: The near-surface boundary layer can mediate the response of mountain glaciers
to external climate, cooling the overlying air and promoting a density-driven
glacier wind. The fundamental processes are conceptually well understood, though
the magnitudes of cooling and presence of glacier winds are poorly quantified
in space and time, increasing the forcing uncertainty for melt models. We utilize
a new data set of on-glacier meteorological measurements on three neighboring
glaciers in the Swiss Alps to explore their distinct response to regional climate
under the extreme 2022 summer. We find that synoptic wind origins and local terrain
modifications, not only glacier size, play an important role in the ability of
a glacier to cool the near-surface air. Warm air intrusions from valley or synoptically-driven
winds onto the glacier can occur between ∼19% and 64% of the time and contribute
between 3% and 81% of the total sensible heat flux to the surface during warm
afternoon hours, depending on the fetch of the glacier flowline and its susceptibility
to boundary layer erosion. In the context of extreme summer warmth, indicative
of future conditions, the boundary layer cooling (up to 6.5°C cooler than its
surroundings) and resultant katabatic wind flow are highly heterogeneous between
the study glaciers, highlighting the complex and likely non-linear response of
glaciers to an uncertain future.
acknowledgement: This project has received funding from the European Union's Horizon
2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement
No. 101026058. The authors acknowledge the invaluable field assistance of Marta
Corrà, Achille Jouberton, Marin Kneib, Stefan Fugger, Celine Ducret and Alexander
Groos. The authors would also like to thank Luca Carturan for advice regarding AWS
setup and maintenance and Simone Fatichi for provision and support in the use of
the Tethys-Chloris model. Open access funding provided by ETH-Bereich Forschungsanstalten.
article_number: e2023JD040214
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Thomas
full_name: Shaw, Thomas
id: 3caa3f91-1f03-11ee-96ce-e0e553054d6e
last_name: Shaw
orcid: 0000-0001-7640-6152
- 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: Evan S.
full_name: Miles, Evan S.
last_name: Miles
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
orcid: 0000-0002-5554-8087
citation:
ama: 'Shaw T, Buri P, McCarthy M, Miles ES, Pellicciotti F. Local controls on near-surface
glacier cooling under warm atmospheric conditions. Journal of Geophysical Research:
Atmospheres. 2024;129(2). doi:10.1029/2023JD040214'
apa: 'Shaw, T., Buri, P., McCarthy, M., Miles, E. S., & Pellicciotti, F. (2024).
Local controls on near-surface glacier cooling under warm atmospheric conditions.
Journal of Geophysical Research: Atmospheres. Wiley. https://doi.org/10.1029/2023JD040214'
chicago: 'Shaw, Thomas, Pascal Buri, Michael McCarthy, Evan S. Miles, and Francesca
Pellicciotti. “Local Controls on Near-Surface Glacier Cooling under Warm Atmospheric
Conditions.” Journal of Geophysical Research: Atmospheres. Wiley, 2024.
https://doi.org/10.1029/2023JD040214.'
ieee: 'T. Shaw, P. Buri, M. McCarthy, E. S. Miles, and F. Pellicciotti, “Local controls
on near-surface glacier cooling under warm atmospheric conditions,” Journal
of Geophysical Research: Atmospheres, vol. 129, no. 2. Wiley, 2024.'
ista: 'Shaw T, Buri P, McCarthy M, Miles ES, Pellicciotti F. 2024. Local controls
on near-surface glacier cooling under warm atmospheric conditions. Journal of
Geophysical Research: Atmospheres. 129(2), e2023JD040214.'
mla: 'Shaw, Thomas, et al. “Local Controls on Near-Surface Glacier Cooling under
Warm Atmospheric Conditions.” Journal of Geophysical Research: Atmospheres,
vol. 129, no. 2, e2023JD040214, Wiley, 2024, doi:10.1029/2023JD040214.'
short: 'T. Shaw, P. Buri, M. McCarthy, E.S. Miles, F. Pellicciotti, Journal of Geophysical
Research: Atmospheres 129 (2024).'
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: 'The meteorological data used in this analysis (Shaw, Buri,
McCarthy, Miles, & Pelliciotti, 2023) are made publicly available at the following
repository: https://zenodo.org/record/8277285. The source code of the T&C model
is available at https://doi.org/10.24433/CO.0905087.v2. Reanalysis data are openly
available from the ECMWF (https://cds.climate.copernicus.eu/). MeteoSwiss data can
be acquired through direct request to the company.'
date_created: 2024-01-28T23:01:42Z
date_published: 2024-01-28T00:00:00Z
date_updated: 2026-10-02T08:59:02Z
day: '28'
ddc:
- '550'
department:
- _id: FrPe
doi: 10.1029/2023JD040214
external_id:
isi:
- '001146838000001'
file:
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checksum: cad5b93caadb40c14e5faedc34f7bba7
content_type: application/pdf
creator: dernst
date_created: 2024-02-06T08:38:27Z
date_updated: 2024-02-06T08:38:27Z
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relation: main_file
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file_date_updated: 2024-02-06T08:38:27Z
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intvolume: ' 129'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: 'Journal of Geophysical Research: Atmospheres'
publication_identifier:
eissn:
- 2169-8996
issn:
- 2169-897X
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '14919'
relation: research_data
status: public
- id: '23030'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Local controls on near-surface glacier cooling under warm atmospheric conditions
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: 129
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18628'
abstract:
- lang: eng
text: 'Arctic tidewater glaciers are retreating, serving as key indicators of global
warming. This study aims to assess how subglacial hydrology affects glacier front
retreat by comparing two glacier–fjord models of the Hansbreen glacier: one incorporating
a detailed subglacial hydrology model and another simplifying the subglacial discharge
to a single channel centered in the flow line. We first validate the subglacial
hydrology model by comparing its discharge channels with observations of plume
activity. Simulations conducted from April to December 2010 revealed that the
glacier front position aligns more closely with the observations in the coupled
model than in the simplified version. Furthermore, the mass loss due to calving
and submarine melting is greater in the coupled model, with the calving mass loss
reaching 6 Mt by the end of the simulation compared to 4 Mt in the simplified
model. These findings highlight the critical role of subglacial hydrology in predicting
glacier dynamics and emphasize the importance of detailed modeling in understanding
the responses of Arctic tidewater glaciers to climate change.'
acknowledgement: "E. De Andrés is supported by Margarita-Salas Grant No. UP2021-035
under the Next Generation-EU program. This research was also funded by grant PID2020-113051RB-C31
from MCIN/AEI/10.13039/501100011033/FEDER, UE.\r\nWe gratefully acknowledge Michal
Cieply and Dariusz Ignatiuk from the Faculty of Natural Sciences, University of
Silesia in Katowice, Poland, for their essential contributions to the Hansbreen
data collection. We also extend our sincere thanks to Waldemar Walczowski from the
Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland, for providing
Hansbuka data. Additionally, we would like to thank two anonymous reviewers for
their constructive feedback, which helped to enhance the quality and clarity of
this work."
article_number: '193'
article_processing_charge: Yes
article_type: original
author:
- first_name: Eva
full_name: De Andrés, Eva
last_name: De Andrés
- first_name: José M
full_name: Muñoz Hermosilla, José M
id: e1037a6d-646e-11ef-b402-e0ed9ab0901e
last_name: Muñoz Hermosilla
orcid: 0000-0002-1990-8508
- first_name: Kaian
full_name: Shahateet, Kaian
last_name: Shahateet
- first_name: Jaime
full_name: Otero, Jaime
last_name: Otero
citation:
ama: 'De Andrés E, Muñoz Hermosilla JM, Shahateet K, Otero J. The importance of
solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen,
Svalbard. Hydrology. 2024;11(11). doi:10.3390/hydrology11110193'
apa: 'De Andrés, E., Muñoz Hermosilla, J. M., Shahateet, K., & Otero, J. (2024).
The importance of solving Subglaciar hydrology in modeling glacier retreat: A
case study of Hansbreen, Svalbard. Hydrology. MDPI. https://doi.org/10.3390/hydrology11110193'
chicago: 'De Andrés, Eva, José M Muñoz Hermosilla, Kaian Shahateet, and Jaime Otero.
“The Importance of Solving Subglaciar Hydrology in Modeling Glacier Retreat: A
Case Study of Hansbreen, Svalbard.” Hydrology. MDPI, 2024. https://doi.org/10.3390/hydrology11110193.'
ieee: 'E. De Andrés, J. M. Muñoz Hermosilla, K. Shahateet, and J. Otero, “The importance
of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen,
Svalbard,” Hydrology, vol. 11, no. 11. MDPI, 2024.'
ista: 'De Andrés E, Muñoz Hermosilla JM, Shahateet K, Otero J. 2024. The importance
of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen,
Svalbard. Hydrology. 11(11), 193.'
mla: 'De Andrés, Eva, et al. “The Importance of Solving Subglaciar Hydrology in
Modeling Glacier Retreat: A Case Study of Hansbreen, Svalbard.” Hydrology,
vol. 11, no. 11, 193, MDPI, 2024, doi:10.3390/hydrology11110193.'
short: E. De Andrés, J.M. Muñoz Hermosilla, K. Shahateet, J. Otero, Hydrology 11
(2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The data that support the results of this study and form
the basis for all the figures presented in this paper are openly available from
Zenodo at https://doi.org/10.5281/zenodo.8005258 (accessed on 6 November 2024).
date_created: 2024-12-08T23:01:55Z
date_published: 2024-11-12T00:00:00Z
date_updated: 2026-10-02T09:16:55Z
day: '12'
ddc:
- '550'
department:
- _id: FrPe
doi: 10.3390/hydrology11110193
file:
- access_level: open_access
checksum: 0665c5bfca97782bf0b041f23dd7e8d7
content_type: application/pdf
creator: dernst
date_created: 2024-12-09T09:43:33Z
date_updated: 2024-12-09T09:43:33Z
file_id: '18635'
file_name: 2024_Hydrology_deAndres.pdf
file_size: 5709093
relation: main_file
success: 1
file_date_updated: 2024-12-09T09:43:33Z
fulldoi: https://doi.org/10.3390/hydrology11110193
has_accepted_license: '1'
intvolume: ' 11'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Hydrology
publication_identifier:
eissn:
- 2306-5338
publication_status: published
publisher: MDPI
quality_controlled: '1'
related_material:
record:
- id: '18634'
relation: used_in_publication
status: public
- id: '23031'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'The importance of solving Subglaciar hydrology in modeling glacier retreat:
A case study of Hansbreen, Svalbard'
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: 11
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15362'
abstract:
- lang: eng
text: Constitutional heterozygous pathogenic variants in the exonuclease domain
of POLE and POLD1, which affect the proofreading activity of the corresponding
polymerases, cause a cancer predisposition syndrome characterized by increased
risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and
other tumor types. The generally accepted explanation for the connection between
the disruption of the proofreading activity of polymerases epsilon and delta and
cancer development is through an increase in the somatic mutation rate. Here we
studied an extended family with multiple members heterozygous for the pathogenic
POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and
cancer phenotypes. Through the analysis of mutational patterns of patient-derived
fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons,
we concluded that heterozygous POLD1 L474P just subtly increases the somatic and
germline mutation burden. In contrast, tumors developed in individuals with a
heterozygous mutation in the exonuclease domain of POLD1, including L474P, have
an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d.
We solved this contradiction through the observation that tumorigenesis involves
somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease
deficiency of polymerase delta has a recessive effect on mutation rate.
acknowledgement: 'This study was funded by the Spanish Ministry of Science and Innovation
(Agencia Estatal de Investigación), co-funded by FEDER funds a way to build Europe
[PID2020-112595RB-I00 (LV)], Instituto de Salud Carlos III [CIBERONC CB16/12/00234
(LV); ISCIII-AES-2017 PI17/01082 (JLS), PMP22/00064], Government of Catalonia [AGAUR
2021SGR01112, CERCA Program for institutional support (LV)], Scientific Foundation
Asociación Española Contra el Cáncer [AECC Investigador (MT)], Austrian Science
Fund FWF [Grant Agreement # I5127-B (FK)], German Research Foundation DFG [Grant
Agreement # 429960716 (FK)], and ERC Consolidator [Grant Agreement # 771209 ChrFL
(FK)].'
article_processing_charge: No
article_type: original
author:
- first_name: Maria A.
full_name: Andrianova, Maria A.
last_name: Andrianova
- first_name: Vladimir B.
full_name: Seplyarskiy, Vladimir B.
last_name: Seplyarskiy
- first_name: Mariona
full_name: Terradas, Mariona
last_name: Terradas
- first_name: Ana Beatriz
full_name: Sánchez-Heras, Ana Beatriz
last_name: Sánchez-Heras
- first_name: Pilar
full_name: Mur, Pilar
last_name: Mur
- first_name: José Luis
full_name: Soto, José Luis
last_name: Soto
- first_name: Gemma
full_name: Aiza, Gemma
last_name: Aiza
- first_name: Emma
full_name: Borràs, Emma
last_name: Borràs
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey S.
full_name: Kondrashov, Alexey S.
last_name: Kondrashov
- first_name: Georgii A.
full_name: Bazykin, Georgii A.
last_name: Bazykin
- first_name: Laura
full_name: Valle, Laura
last_name: Valle
citation:
ama: Andrianova MA, Seplyarskiy VB, Terradas M, et al. Discovery of recessive effect
of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated
normal and cancer cells. European Journal of Human Genetics. 2024;32:837-845.
doi:10.1038/s41431-024-01598-8
apa: Andrianova, M. A., Seplyarskiy, V. B., Terradas, M., Sánchez-Heras, A. B.,
Mur, P., Soto, J. L., … Valle, L. (2024). Discovery of recessive effect of human
polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated
normal and cancer cells. European Journal of Human Genetics. Springer Nature.
https://doi.org/10.1038/s41431-024-01598-8
chicago: Andrianova, Maria A., Vladimir B. Seplyarskiy, Mariona Terradas, Ana Beatriz
Sánchez-Heras, Pilar Mur, José Luis Soto, Gemma Aiza, et al. “Discovery of Recessive
Effect of Human Polymerase δ Proofreading Deficiency through Mutational Analysis
of POLD1-Mutated Normal and Cancer Cells.” European Journal of Human Genetics.
Springer Nature, 2024. https://doi.org/10.1038/s41431-024-01598-8.
ieee: M. A. Andrianova et al., “Discovery of recessive effect of human polymerase
δ proofreading deficiency through mutational analysis of POLD1-mutated normal
and cancer cells,” European Journal of Human Genetics, vol. 32. Springer
Nature, pp. 837–845, 2024.
ista: Andrianova MA, Seplyarskiy VB, Terradas M, Sánchez-Heras AB, Mur P, Soto JL,
Aiza G, Borràs E, Kondrashov F, Kondrashov AS, Bazykin GA, Valle L. 2024. Discovery
of recessive effect of human polymerase δ proofreading deficiency through mutational
analysis of POLD1-mutated normal and cancer cells. European Journal of Human Genetics.
32, 837–845.
mla: Andrianova, Maria A., et al. “Discovery of Recessive Effect of Human Polymerase
δ Proofreading Deficiency through Mutational Analysis of POLD1-Mutated Normal
and Cancer Cells.” European Journal of Human Genetics, vol. 32, Springer
Nature, 2024, pp. 837–45, doi:10.1038/s41431-024-01598-8.
short: M.A. Andrianova, V.B. Seplyarskiy, M. Terradas, A.B. Sánchez-Heras, P. Mur,
J.L. Soto, G. Aiza, E. Borràs, F. Kondrashov, A.S. Kondrashov, G.A. Bazykin, L.
Valle, European Journal of Human Genetics 32 (2024) 837–845.
das_tickbox: '1'
dataavailabilitystatement: DNA sequencing data are deposited in the European Genome-Phenome
Archive (EGA) with accession code EGAS00001006434. Called de novo and somatic mutations
are available online (https://figshare.com/account/home#/projects/156404).
date_created: 2024-05-05T22:01:04Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-10-02T09:48:07Z
day: '01'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41431-024-01598-8
ec_funded: 1
external_id:
isi:
- '001207703200001'
pmid:
- '38658779'
file:
- access_level: open_access
checksum: e45fc987f4e9ebafdd0ec4f0e9027de4
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T09:21:25Z
date_updated: 2025-01-09T09:21:25Z
file_id: '18799'
file_name: 2024_EJHG_Andrianova.pdf
file_size: 3060724
relation: main_file
success: 1
file_date_updated: 2025-01-09T09:21:25Z
fulldoi: https://doi.org/10.1038/s41431-024-01598-8
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 837-845
pmid: 1
project:
- _id: 9B767A34-BA93-11EA-9121-9846C619BF3A
grant_number: '429960716'
name: Evolution of Sensorimotor Transformation Across Diptera
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: 34e076d6-11ca-11ed-8bc3-aec76c41a181
grant_number: I05127
name: Evolutionary analysis of gene regulation
publication: European Journal of Human Genetics
publication_identifier:
eissn:
- 1476-5438
issn:
- 1018-4813
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Discovery of recessive effect of human polymerase δ proofreading deficiency
through mutational analysis of POLD1-mutated normal and cancer cells
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: 32
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '15179'
abstract:
- lang: eng
text: The fungal bioluminescence pathway can be reconstituted in other organisms
allowing luminescence imaging without exogenously supplied substrate. The pathway
starts from hispidin biosynthesis—a step catalyzed by a large fungal polyketide
synthase that requires a posttranslational modification for activity. Here, we
report identification of alternative compact hispidin synthases encoded by a phylogenetically
diverse group of plants. A hybrid bioluminescence pathway that combines plant
and fungal genes is more compact, not dependent on availability of machinery for
posttranslational modifications, and confers autonomous bioluminescence in yeast,
mammalian, and plant hosts. The compact size of plant hispidin synthases enables
additional modes of delivery of autoluminescence, such as delivery with viral
vectors.
acknowledgement: "We thank Milaboratory (milaboratory.com) for the access to computing
and storage infrastructure. We thank J. Petrasek for providing the BY-2 cell culture
line. We thank Konstantin Lukyanov laboratory and Sergey Deyev laboratory for assistance
with experiments.\r\nThis study was partially funded by Light Bio and Planta. The
Synthetic biology Group is funded by the MRC London Institute of Medical Sciences
(UKRI MC-A658-5QEA0). Cloning and luminescent assays performed in BY-2 were partially
supported by RSF, project number 22-14-00400, https://rscf.ru/project/22-14-00400/.
Plant transformations were funded by RFBR and MOST, project number 21-54-52004.
Plant imaging experiments were funded by RSF, project number 22-74-00124, https://rscf.ru/project/22-74-00124/.
Viral delivery experiments were funded by the grant PID2019-108203RB-I00 Plan Nacional
I + D from the Ministerio de Ciencia e Innovación (Spain) through the Agencia Estatal
de Investigación (cofinanced by the European Regional Development Fund)."
article_number: adk1992
article_processing_charge: Yes
article_type: original
author:
- first_name: Kseniia A.
full_name: Palkina, Kseniia A.
last_name: Palkina
- first_name: Tatiana A.
full_name: Karataeva, Tatiana A.
last_name: Karataeva
- first_name: Maxim M.
full_name: Perfilov, Maxim M.
last_name: Perfilov
- first_name: Liliia I.
full_name: Fakhranurova, Liliia I.
last_name: Fakhranurova
- first_name: Nadezhda M.
full_name: Markina, Nadezhda M.
last_name: Markina
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Elena
full_name: Garcia-Perez, Elena
last_name: Garcia-Perez
- first_name: Marta
full_name: Vazquez-Vilar, Marta
last_name: Vazquez-Vilar
- first_name: Marta
full_name: Rodriguez-Rodriguez, Marta
last_name: Rodriguez-Rodriguez
- first_name: Victor
full_name: Vazquez-Vilriales, Victor
last_name: Vazquez-Vilriales
- first_name: Ekaterina S.
full_name: Shakhova, Ekaterina S.
last_name: Shakhova
- first_name: Tatiana
full_name: Mitiouchkina, Tatiana
last_name: Mitiouchkina
- first_name: Olga A.
full_name: Belozerova, Olga A.
last_name: Belozerova
- first_name: Sergey I.
full_name: Kovalchuk, Sergey I.
last_name: Kovalchuk
- first_name: Anna
full_name: Alekberova, Anna
last_name: Alekberova
- first_name: Alena K.
full_name: Malyshevskaia, Alena K.
last_name: Malyshevskaia
- first_name: Evgenia N.
full_name: Bugaeva, Evgenia N.
last_name: Bugaeva
- first_name: Elena B.
full_name: Guglya, Elena B.
last_name: Guglya
- first_name: Anastasia
full_name: Balakireva, Anastasia
last_name: Balakireva
- first_name: Nikita
full_name: Sytov, Nikita
last_name: Sytov
- first_name: Anastasia
full_name: Bezlikhotnova, Anastasia
last_name: Bezlikhotnova
- first_name: Daria I.
full_name: Boldyreva, Daria I.
last_name: Boldyreva
- first_name: Vladislav V.
full_name: Babenko, Vladislav V.
last_name: Babenko
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Vladimir V.
full_name: Choob, Vladimir V.
last_name: Choob
- first_name: Diego
full_name: Orzaez, Diego
last_name: Orzaez
- first_name: Ilia V.
full_name: Yampolsky, Ilia V.
last_name: Yampolsky
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Karen S.
full_name: Sarkisyan, Karen S.
last_name: Sarkisyan
citation:
ama: Palkina KA, Karataeva TA, Perfilov MM, et al. A hybrid pathway for self-sustained
luminescence. Science Advances. 2024;10(10). doi:10.1126/sciadv.adk1992
apa: Palkina, K. A., Karataeva, T. A., Perfilov, M. M., Fakhranurova, L. I., Markina,
N. M., Gonzalez Somermeyer, L., … Sarkisyan, K. S. (2024). A hybrid pathway for
self-sustained luminescence. Science Advances. American Association for
the Advancement of Science. https://doi.org/10.1126/sciadv.adk1992
chicago: Palkina, Kseniia A., Tatiana A. Karataeva, Maxim M. Perfilov, Liliia I.
Fakhranurova, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, Elena Garcia-Perez,
et al. “A Hybrid Pathway for Self-Sustained Luminescence.” Science Advances.
American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adk1992.
ieee: K. A. Palkina et al., “A hybrid pathway for self-sustained luminescence,”
Science Advances, vol. 10, no. 10. American Association for the Advancement
of Science, 2024.
ista: Palkina KA, Karataeva TA, Perfilov MM, Fakhranurova LI, Markina NM, Gonzalez
Somermeyer L, Garcia-Perez E, Vazquez-Vilar M, Rodriguez-Rodriguez M, Vazquez-Vilriales
V, Shakhova ES, Mitiouchkina T, Belozerova OA, Kovalchuk SI, Alekberova A, Malyshevskaia
AK, Bugaeva EN, Guglya EB, Balakireva A, Sytov N, Bezlikhotnova A, Boldyreva DI,
Babenko VV, Kondrashov F, Choob VV, Orzaez D, Yampolsky IV, Mishin AS, Sarkisyan
KS. 2024. A hybrid pathway for self-sustained luminescence. Science Advances.
10(10), adk1992.
mla: Palkina, Kseniia A., et al. “A Hybrid Pathway for Self-Sustained Luminescence.”
Science Advances, vol. 10, no. 10, adk1992, American Association for the
Advancement of Science, 2024, doi:10.1126/sciadv.adk1992.
short: K.A. Palkina, T.A. Karataeva, M.M. Perfilov, L.I. Fakhranurova, N.M. Markina,
L. Gonzalez Somermeyer, E. Garcia-Perez, M. Vazquez-Vilar, M. Rodriguez-Rodriguez,
V. Vazquez-Vilriales, E.S. Shakhova, T. Mitiouchkina, O.A. Belozerova, S.I. Kovalchuk,
A. Alekberova, A.K. Malyshevskaia, E.N. Bugaeva, E.B. Guglya, A. Balakireva, N.
Sytov, A. Bezlikhotnova, D.I. Boldyreva, V.V. Babenko, F. Kondrashov, V.V. Choob,
D. Orzaez, I.V. Yampolsky, A.S. Mishin, K.S. Sarkisyan, Science Advances 10 (2024).
das_tickbox: '1'
dataavailabilitystatement: All data needed to evaluate the conclusions in the paper
are present in the paper and/or the Supplementary Materials. The plasmids used in
this study will be made available for noncommercial use through Addgene under the
terms of UBMTA (www.addgene.org/agreement/1). The data are available at https://doi.org/10.6084/m9.figshare.24772872.
date_created: 2024-03-25T08:54:33Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2026-10-02T09:22:29Z
day: '01'
ddc:
- '580'
department:
- _id: FyKo
doi: 10.1126/sciadv.adk1992
external_id:
isi:
- '001187580500013'
pmid:
- '38457503'
file:
- access_level: open_access
checksum: a19c43b260ea0bbaf895a29712e3153c
content_type: application/pdf
creator: dernst
date_created: 2024-03-25T09:42:10Z
date_updated: 2024-03-25T09:42:10Z
file_id: '15185'
file_name: 2024_ScienceAdv_Palkina.pdf
file_size: 1499302
relation: main_file
success: 1
file_date_updated: 2024-03-25T09:42:10Z
fulldoi: https://doi.org/10.1126/sciadv.adk1992
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '10'
language:
- iso: eng
month: '03'
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:
record:
- id: '23032'
relation: research_data
status: public
researchdata_availability: yes (supplementary data)
scopus_import: '1'
status: public
supplementarymaterial: yes
title: A hybrid pathway for self-sustained luminescence
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'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18779'
abstract:
- lang: eng
text: Unsupervised segmentation in biological and non-biological images is only
partially resolved. Segmentation either requires arbitrary thresholds or large
teaching datasets. Here, we propose a spatial autocorrelation method based on
Local Moran’s I coefficient to differentiate signal,
background, and noise in any type of image. The method, originally described for
geoinformatics, does not require a predefined intensity threshold or teaching
algorithm for image segmentation and allows quantitative comparison of samples
obtained in different conditions. It utilizes relative intensity as well as spatial
information of neighboring elements to select spatially contiguous groups of pixels.
We demonstrate that Moran’s method outperforms threshold-based method in both
artificially generated as well as in natural images especially when background
noise is substantial. This superior performance can be attributed to the exclusion
of false positive pixels resulting from isolated, high intensity pixels in high
noise conditions. To test the method’s power in real situation, we used high power
confocal images of the somatosensory thalamus immunostained for Kv4.2 and Kv4.3
(A-type) voltage-gated potassium channels in mice. Moran’s method identified high-intensity
Kv4.2 and Kv4.3 ion channel clusters in the thalamic neuropil. Spatial distribution
of these clusters displayed strong correlation with large sensory axon terminals
of subcortical origin. The unique association of the special presynaptic terminals
and a postsynaptic voltage-gated ion channel cluster was confirmed with electron
microscopy. These data demonstrate that Moran’s method is a rapid, simple image
segmentation method optimal for variable and high noise conditions.
acknowledgement: "This research was supported by the Wellcome Trust (ZN, LA). In addition,
LA was supported by an ERC Advanced Grant (FRONTHAL, 742595) and the European Union
project RRF-2.3.1-\r\n21-2022-00004 within the framework of the Artificial Intelligence
National Laboratory and Lendület_2023_90. ZN is the recipient of a Hungarian Academy
of Sciences Momentum Grant (Lendület, LP2012-29) and an ERC Advanced Grant (293681).
We thank the Light Microscopy Center at Institute of Experimental Medicine for kindly
providing microscopy support. Authors would like to express their deepest gratitude
to Prof Luc Anselin (Center for Spatial Data Science, University of Chicago) and
Dr Szabolcs Káli (Instiute of Experimental Medicine, Budapest) for the valuable
discussion about analysis of spatial association, and to Krisztina Faddi for the
excellent technical assistance. "
article_number: '89361'
article_processing_charge: Yes
article_type: original
author:
- first_name: Csaba
full_name: Dávid, Csaba
last_name: Dávid
- first_name: Kristóf
full_name: Giber, Kristóf
last_name: Giber
- first_name: Margit Katalin
full_name: Szigeti, Margit Katalin
id: 44F4BDC0-F248-11E8-B48F-1D18A9856A87
last_name: Szigeti
orcid: 0000-0001-9500-8758
- first_name: Mihály
full_name: Köllő, Mihály
last_name: Köllő
- first_name: Zoltan
full_name: Nusser, Zoltan
last_name: Nusser
- first_name: Laszlo
full_name: Acsady, Laszlo
last_name: Acsady
citation:
ama: Dávid C, Giber K, Szigeti MK, Köllő M, Nusser Z, Acsady L. A novel image segmentation
method based on spatial autocorrelation identifies A-type potassium channel clusters
in the thalamus. eLife. 2024;12. doi:10.7554/elife.89361
apa: Dávid, C., Giber, K., Szigeti, M. K., Köllő, M., Nusser, Z., & Acsady,
L. (2024). A novel image segmentation method based on spatial autocorrelation
identifies A-type potassium channel clusters in the thalamus. ELife. eLife
Sciences Publications. https://doi.org/10.7554/elife.89361
chicago: Dávid, Csaba, Kristóf Giber, Margit Katalin Szigeti, Mihály Köllő, Zoltan
Nusser, and Laszlo Acsady. “A Novel Image Segmentation Method Based on Spatial
Autocorrelation Identifies A-Type Potassium Channel Clusters in the Thalamus.”
ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.89361.
ieee: C. Dávid, K. Giber, M. K. Szigeti, M. Köllő, Z. Nusser, and L. Acsady, “A
novel image segmentation method based on spatial autocorrelation identifies A-type
potassium channel clusters in the thalamus,” eLife, vol. 12. eLife Sciences
Publications, 2024.
ista: Dávid C, Giber K, Szigeti MK, Köllő M, Nusser Z, Acsady L. 2024. A novel image
segmentation method based on spatial autocorrelation identifies A-type potassium
channel clusters in the thalamus. eLife. 12, 89361.
mla: Dávid, Csaba, et al. “A Novel Image Segmentation Method Based on Spatial Autocorrelation
Identifies A-Type Potassium Channel Clusters in the Thalamus.” ELife, vol.
12, 89361, eLife Sciences Publications, 2024, doi:10.7554/elife.89361.
short: C. Dávid, K. Giber, M.K. Szigeti, M. Köllő, Z. Nusser, L. Acsady, ELife 12
(2024).
das_tickbox: '1'
dataavailabilitystatement: 'The code for the analysis is available online as a user-friendly
MATLAB script at: https://github.com/dcsabaCD225/Moran_Matlab/blob/main/moran_local.m
(copy archived at Csaba, 2024). All source data relevant to figures and charts are
included in source data files.'
date_created: 2025-01-08T13:25:45Z
date_published: 2024-12-10T00:00:00Z
date_updated: 2026-10-02T09:53:20Z
day: '10'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.7554/elife.89361
file:
- access_level: open_access
checksum: 1d64265f62a3bf14550b4f5c684f1782
content_type: application/pdf
creator: dernst
date_created: 2025-01-08T13:33:05Z
date_updated: 2025-01-08T13:33:05Z
file_id: '18780'
file_name: 2024_eLife_David.pdf
file_size: 9992462
relation: main_file
success: 1
file_date_updated: 2025-01-08T13:33:05Z
fulldoi: https://doi.org/10.7554/elife.89361
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: A novel image segmentation method based on spatial autocorrelation identifies
A-type potassium channel clusters in the thalamus
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: 12
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17331'
abstract:
- lang: eng
text: Amyloidosis are a group of diseases in which soluble proteins aggregate and
deposit in fibrillar conformation extracellularly in tissues. The effectiveness
of therapeutic strategies depends on the specific protein involved, being crucial
to accurately determine its nature. Moreover, following the diagnosis, the search
for the mutation within relatives allows the clinical advice. Here we report the
precise diagnosis and explored the possible reasons of the structural pathogenicity
for a renal amyloidosis related to a fibrinogen Aα-chain variant. Whole-exome
sequencing and GATK calling pipeline were leveraged to characterize the protein
variant present in a patient with kidney failure. Bioinformatics strategies were
applied to suggest potential explanations of the variants aggregation. Our pipeline
allowed the identification of a single-point variant of fibrinogen Aα-chain, which
opened the possibility of curative transplantation. In silico structural analysis
suggested that the pathogenicity of the variant may be attributed to a heightened
susceptibility to yield a peptide prone to deposit as an oligomer with a β-sheet
structure. Exploiting the comprehensive coverage of whole-genome sequencing, we
managed to fill a vacant stage in the diagnosis of hereditary amyloidosis and
to stimulate the advancement in biomedicine.
acknowledgement: The authors acknowledge Rosana del Cid for her help with English
corrections, Mario Ramos for the figure editions, and Gabriela Finarelli for technical
assistance. S.A. Rosú, N.A. Ramella, and M.A. Tricerri acknowledge support from
Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) (Grant PIP
11220200102381), Agencia Nacional de Promoción Científica y Tecnológica (PICT 2019-03592),
Universidad Nacional de La Plata (UNLP) (Grants M234 and PPID M014), and Fundación
Florencio Fiorini. The authors warmly thank M.P. for her willingness to conduct
these studies.
article_processing_charge: No
article_type: original
author:
- first_name: Elizabeth R
full_name: Cattaneo, Elizabeth R
last_name: Cattaneo
- first_name: Romina A
full_name: Gisonno, Romina A
id: a9e08d76-6a98-11ec-8f7b-c777fe5ca519
last_name: Gisonno
- first_name: Martín C
full_name: Abba, Martín C
last_name: Abba
- first_name: Marianela
full_name: Santana, Marianela
last_name: Santana
- first_name: Silvana A
full_name: Rosú, Silvana A
last_name: Rosú
- first_name: Elsa
full_name: Nucifora, Elsa
last_name: Nucifora
- first_name: María A
full_name: Aguirre, María A
last_name: Aguirre
- first_name: María C
full_name: Giordani, María C
last_name: Giordani
- first_name: M. Alejandra
full_name: Tricerri, M. Alejandra
last_name: Tricerri
- first_name: Nahuel A
full_name: Ramella, Nahuel A
last_name: Ramella
citation:
ama: 'Cattaneo ER, Gisonno RA, Abba MC, et al. Hereditary amyloidosis: Insights
into a fibrinogen A variant protein. Proteins: Structure, Function and Bioinformatics.
2024;92(12):1366-1374. doi:10.1002/prot.26732'
apa: 'Cattaneo, E. R., Gisonno, R. A., Abba, M. C., Santana, M., Rosú, S. A., Nucifora,
E., … Ramella, N. A. (2024). Hereditary amyloidosis: Insights into a fibrinogen
A variant protein. Proteins: Structure, Function and Bioinformatics. Wiley.
https://doi.org/10.1002/prot.26732'
chicago: 'Cattaneo, Elizabeth R, Romina A Gisonno, Martín C Abba, Marianela Santana,
Silvana A Rosú, Elsa Nucifora, María A Aguirre, María C Giordani, M. Alejandra
Tricerri, and Nahuel A Ramella. “Hereditary Amyloidosis: Insights into a Fibrinogen
A Variant Protein.” Proteins: Structure, Function and Bioinformatics. Wiley,
2024. https://doi.org/10.1002/prot.26732.'
ieee: 'E. R. Cattaneo et al., “Hereditary amyloidosis: Insights into a fibrinogen
A variant protein,” Proteins: Structure, Function and Bioinformatics, vol.
92, no. 12. Wiley, pp. 1366–1374, 2024.'
ista: 'Cattaneo ER, Gisonno RA, Abba MC, Santana M, Rosú SA, Nucifora E, Aguirre
MA, Giordani MC, Tricerri MA, Ramella NA. 2024. Hereditary amyloidosis: Insights
into a fibrinogen A variant protein. Proteins: Structure, Function and Bioinformatics.
92(12), 1366–1374.'
mla: 'Cattaneo, Elizabeth R., et al. “Hereditary Amyloidosis: Insights into a Fibrinogen
A Variant Protein.” Proteins: Structure, Function and Bioinformatics, vol.
92, no. 12, Wiley, 2024, pp. 1366–74, doi:10.1002/prot.26732.'
short: 'E.R. Cattaneo, R.A. Gisonno, M.C. Abba, M. Santana, S.A. Rosú, E. Nucifora,
M.A. Aguirre, M.C. Giordani, M.A. Tricerri, N.A. Ramella, Proteins: Structure,
Function and Bioinformatics 92 (2024) 1366–1374.'
das_tickbox: '1'
dataavailabilitystatement: The data that support the findings of this study are available
on request from the corresponding author. The data are not publicly available due
to privacy or ethical restrictions.
date_created: 2024-07-28T22:01:10Z
date_published: 2024-12-01T00:00:00Z
date_updated: 2026-10-02T09:56:43Z
day: '01'
department:
- _id: GaNo
doi: 10.1002/prot.26732
external_id:
isi:
- '001272128100001'
pmid:
- '39031927'
fulldoi: https://doi.org/10.1002/prot.26732
intvolume: ' 92'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.22541/au.171804763.37967262/v1
month: '12'
oa: 1
oa_version: Preprint
page: 1366-1374
pmid: 1
publication: 'Proteins: Structure, Function and Bioinformatics'
publication_identifier:
eissn:
- 1097-0134
issn:
- 0887-3585
publication_status: published
publisher: Wiley
quality_controlled: '1'
researchdata_availability: upon request
scopus_import: '1'
status: public
supplementarymaterial: yes
title: 'Hereditary amyloidosis: Insights into a fibrinogen A variant protein'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 92
year: '2024'
...
---
_id: '17091'
abstract:
- lang: eng
text: DNA sequences are connected to genes and functions in the developing and adult
brain
article_processing_charge: No
article_type: letter_note
author:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
citation:
ama: Novarino G, Bock C. Mapping the brain’s gene-regulatory maze. Science.
2024;384(6698):860-861. doi:10.1126/science.adp4663
apa: Novarino, G., & Bock, C. (2024). Mapping the brain’s gene-regulatory maze.
Science. AAAS. https://doi.org/10.1126/science.adp4663
chicago: Novarino, Gaia, and Christoph Bock. “Mapping the Brain’s Gene-Regulatory
Maze.” Science. AAAS, 2024. https://doi.org/10.1126/science.adp4663.
ieee: G. Novarino and C. Bock, “Mapping the brain’s gene-regulatory maze,” Science,
vol. 384, no. 6698. AAAS, pp. 860–861, 2024.
ista: Novarino G, Bock C. 2024. Mapping the brain’s gene-regulatory maze. Science.
384(6698), 860–861.
mla: Novarino, Gaia, and Christoph Bock. “Mapping the Brain’s Gene-Regulatory Maze.”
Science, vol. 384, no. 6698, AAAS, 2024, pp. 860–61, doi:10.1126/science.adp4663.
short: G. Novarino, C. Bock, Science 384 (2024) 860–861.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-06-02T22:00:57Z
date_published: 2024-05-24T00:00:00Z
date_updated: 2026-10-02T09:50:30Z
day: '24'
department:
- _id: GaNo
doi: 10.1126/science.adp4663
external_id:
isi:
- '001230076500007'
pmid:
- '38781359'
fulldoi: https://doi.org/10.1126/science.adp4663
intvolume: ' 384'
isi: 1
issue: '6698'
language:
- iso: eng
month: '05'
oa_version: None
page: 860-861
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: AAAS
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Mapping the brain’s gene-regulatory maze
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 384
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18307'
abstract:
- lang: eng
text: Vaccination is the most effective tool to control infectious diseases. However,
the evolution of vaccine resistance, exemplified by vaccine resistance in SARS-CoV-2,
remains a concern. Here, we model complex vaccination strategies against a pathogen
with multiple epitopes—molecules targeted by the vaccine. We found that a vaccine
targeting one epitope was ineffective in preventing vaccine escape. Vaccine resistance
in highly infectious pathogens was prevented by the full-epitope vaccine, that
is, one targeting all available epitopes, but only when the rate of pathogen evolution
was low. Strikingly, a bet-hedging strategy of random administration of vaccines
targeting different epitopes was the most effective in preventing vaccine resistance
in pathogens with the low rate of infection and high rate of evolution. Thus,
complex vaccination strategies, when biologically feasible, may be preferable
to the currently used single-vaccine approaches for long-term control of disease
outbreaks, especially when applied to livestock with near 100% vaccination rates.
acknowledgement: We thank Raimundo Julian Saona Urmeneta, Maike Morrison, Sergey Kryazhimskiy,
Hiroki Ishikawa, Simone Pigolotti, and Shingo Miyauchi for fruitful discussions.
We also thank the participants of the FRISBI seminar at ISTA for useful comments.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Simon
full_name: Rella, Simon
id: B4765ACA-AA38-11E9-AC9A-0930E6697425
last_name: Rella
- first_name: Yuliya A.
full_name: Kulikova, Yuliya A.
last_name: Kulikova
- first_name: Aygul
full_name: Minnegalieva, Aygul
id: 87DF77F0-1D9A-11EA-B6AE-CE443DDC885E
last_name: Minnegalieva
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: 'Rella S, Kulikova YA, Minnegalieva A, Kondrashov F. Complex vaccination strategies
prevent the emergence of vaccine resistance. Evolution: International journal
of organic evolution. 2024;78(10):1722-1738. doi:10.1093/evolut/qpae106'
apa: 'Rella, S., Kulikova, Y. A., Minnegalieva, A., & Kondrashov, F. (2024).
Complex vaccination strategies prevent the emergence of vaccine resistance. Evolution:
International Journal of Organic Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpae106'
chicago: 'Rella, Simon, Yuliya A. Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov.
“Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.”
Evolution: International Journal of Organic Evolution. Oxford University
Press, 2024. https://doi.org/10.1093/evolut/qpae106.'
ieee: 'S. Rella, Y. A. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination
strategies prevent the emergence of vaccine resistance,” Evolution: International
journal of organic evolution, vol. 78, no. 10. Oxford University Press, pp.
1722–1738, 2024.'
ista: 'Rella S, Kulikova YA, Minnegalieva A, Kondrashov F. 2024. Complex vaccination
strategies prevent the emergence of vaccine resistance. Evolution: International
journal of organic evolution. 78(10), 1722–1738.'
mla: 'Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence
of Vaccine Resistance.” Evolution: International Journal of Organic Evolution,
vol. 78, no. 10, Oxford University Press, 2024, pp. 1722–38, doi:10.1093/evolut/qpae106.'
short: 'S. Rella, Y.A. Kulikova, A. Minnegalieva, F. Kondrashov, Evolution: International
Journal of Organic Evolution 78 (2024) 1722–1738.'
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: Results and figures derive from the model, described in
detail in the main text. The code is available at github.com/Simon-Re/complex-vaccination.
date_created: 2024-10-13T22:01:50Z
date_published: 2024-10-01T00:00:00Z
date_updated: 2026-10-02T10:12:20Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1093/evolut/qpae106
external_id:
isi:
- '001286581900001'
pmid:
- '38990788'
file:
- access_level: open_access
checksum: 5c6e8475bb88b07d424a5130d5e91e74
content_type: application/pdf
creator: dernst
date_created: 2024-10-21T09:34:50Z
date_updated: 2024-10-21T09:34:50Z
file_id: '18453'
file_name: 2024_Evolution_Rella.pdf
file_size: 29360811
relation: main_file
success: 1
file_date_updated: 2024-10-21T09:34:50Z
fulldoi: https://doi.org/10.1093/evolut/qpae106
has_accepted_license: '1'
intvolume: ' 78'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1722-1738
pmid: 1
publication: 'Evolution: International journal of organic evolution'
publication_identifier:
eissn:
- 1558-5646
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/Simon-Re/complex-vaccination
record:
- id: '14862'
relation: research_data
status: public
- id: '20811'
relation: dissertation_contains
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Complex vaccination strategies prevent the emergence of vaccine resistance
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: 78
year: '2024'
...
---
APC_amount: 6468 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '14793'
abstract:
- lang: eng
text: Superconductor/semiconductor hybrid devices have attracted increasing interest
in the past years. Superconducting electronics aims to complement semiconductor
technology, while hybrid architectures are at the forefront of new ideas such
as topological superconductivity and protected qubits. In this work, we engineer
the induced superconductivity in two-dimensional germanium hole gas by varying
the distance between the quantum well and the aluminum. We demonstrate a hard
superconducting gap and realize an electrically and flux tunable superconducting
diode using a superconducting quantum interference device (SQUID). This allows
to tune the current phase relation (CPR), to a regime where single Cooper pair
tunneling is suppressed, creating a sin(2y) CPR. Shapiro experiments complement
this interpretation and the microwave drive allows to create a diode with ≈ 100%
efficiency. The reported results open up the path towards integration of spin
qubit devices, microwave resonators and (protected) superconducting qubits on the
same silicon technology compatible platform.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: "We acknowledge Alexander Brinkmann, Alessandro Crippa, Francesco
Giazotto, Andrew Higginbotham, Andrea Iorio, Giordano Scappucci, Christian Schonenberger,
and Lukas Splitthoff for helpful discussions. We thank Marcel Verheijen for the
support in the TEM analysis. This research and related results were made possible
with the support of the NOMIS\r\nFoundation. It was supported by the Scientific
Service Units of ISTA through resources provided by the MIBA Machine Shop and the
nanofabrication facility, the European Union’s Horizon 2020 research andinnovation
programme under Grant Agreement No 862046, the HORIZONRIA\r\n101069515 project,
the European Innovation Council Pathfinder grant no. 101115315 (QuKiT), and the
FWF Projects #P-32235, #P-36507 and #F-8606. For the purpose of open access, the
authors have applied a CC BY public copyright licence to any Author Accepted Manuscript
version arising from this submission. R.S.S. acknowledges Spanish CM “Talento Program\"\r\nProject
No. 2022-T1/IND-24070. J.J. acknowledges European Research Council TOCINA 834290."
article_number: '169'
article_processing_charge: Yes
article_type: original
author:
- first_name: Marco
full_name: Valentini, Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
- first_name: Oliver
full_name: Sagi, Oliver
id: 71616374-A8E9-11E9-A7CA-09ECE5697425
last_name: Sagi
- first_name: Levon
full_name: Baghumyan, Levon
id: 7aa1f788-b527-11ee-aa9e-e6111a79e0c7
last_name: Baghumyan
- first_name: Thijs
full_name: de Gijsel, Thijs
id: a0ece13c-b527-11ee-929d-bad130106eee
last_name: de Gijsel
- first_name: Jason
full_name: Jung, Jason
id: 4C9ACE7A-F248-11E8-B48F-1D18A9856A87
last_name: Jung
- first_name: Stefano
full_name: Calcaterra, Stefano
last_name: Calcaterra
- first_name: Andrea
full_name: Ballabio, Andrea
last_name: Ballabio
- first_name: Juan L
full_name: Aguilera Servin, Juan L
id: 2A67C376-F248-11E8-B48F-1D18A9856A87
last_name: Aguilera Servin
orcid: 0000-0002-2862-8372
- first_name: Kushagra
full_name: Aggarwal, Kushagra
id: b22ab905-3539-11eb-84c3-fc159dcd79cb
last_name: Aggarwal
orcid: 0000-0001-9985-9293
- first_name: Marian
full_name: Janik, Marian
id: 396A1950-F248-11E8-B48F-1D18A9856A87
last_name: Janik
orcid: 0009-0003-9037-8831
- first_name: Thomas
full_name: Adletzberger, Thomas
id: 38756BB2-F248-11E8-B48F-1D18A9856A87
last_name: Adletzberger
- first_name: Rubén
full_name: Seoane Souto, Rubén
last_name: Seoane Souto
- first_name: Martin
full_name: Leijnse, Martin
last_name: Leijnse
- first_name: Jeroen
full_name: Danon, Jeroen
last_name: Danon
- first_name: Constantin
full_name: Schrade, Constantin
last_name: Schrade
- first_name: Erik
full_name: Bakkers, Erik
last_name: Bakkers
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full_name: Chrastina, Daniel
last_name: Chrastina
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Valentini M, Sagi O, Baghumyan L, et al. Parity-conserving Cooper-pair transport
and ideal superconducting diode in planar germanium. Nature Communications.
2024;15. doi:10.1038/s41467-023-44114-0
apa: Valentini, M., Sagi, O., Baghumyan, L., de Gijsel, T., Jung, J., Calcaterra,
S., … Katsaros, G. (2024). Parity-conserving Cooper-pair transport and ideal superconducting
diode in planar germanium. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-44114-0
chicago: Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason
Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Parity-Conserving Cooper-Pair
Transport and Ideal Superconducting Diode in Planar Germanium.” Nature Communications.
Springer Nature, 2024. https://doi.org/10.1038/s41467-023-44114-0.
ieee: M. Valentini et al., “Parity-conserving Cooper-pair transport and ideal
superconducting diode in planar germanium,” Nature Communications, vol.
15. Springer Nature, 2024.
ista: Valentini M, Sagi O, Baghumyan L, de Gijsel T, Jung J, Calcaterra S, Ballabio
A, Aguilera Servin JL, Aggarwal K, Janik M, Adletzberger T, Seoane Souto R, Leijnse
M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. 2024. Parity-conserving
Cooper-pair transport and ideal superconducting diode in planar germanium. Nature
Communications. 15, 169.
mla: Valentini, Marco, et al. “Parity-Conserving Cooper-Pair Transport and Ideal
Superconducting Diode in Planar Germanium.” Nature Communications, vol.
15, 169, Springer Nature, 2024, doi:10.1038/s41467-023-44114-0.
short: M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra,
A. Ballabio, J.L. Aguilera Servin, K. Aggarwal, M. Janik, T. Adletzberger, R.
Seoane Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella,
G. Katsaros, Nature Communications 15 (2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: All experimental data included in this work are available
at https://zenodo.org/records/10119346.
date_created: 2024-01-14T23:00:56Z
date_published: 2024-01-02T00:00:00Z
date_updated: 2026-10-02T10:23:53Z
day: '02'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1038/s41467-023-44114-0
ec_funded: 1
external_id:
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title: Parity-conserving Cooper-pair transport and ideal superconducting diode in
planar germanium
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...