---
_id: '17170'
abstract:
- lang: eng
text: "In this article we extend and strengthen the seminal work by Niyogi, Smale,
and Weinberger on the learning of the homotopy type from a sample of an underlying
space. In their work, Niyogi, Smale, and Weinberger studied samples of C² manifolds
with positive reach embedded in ℝ^d. We extend their results in the following
ways: - As the ambient space we consider both ℝ^d and Riemannian manifolds with
lower bounded sectional curvature. - In both types of ambient spaces, we study
sets of positive reach - a significantly more general setting than C² manifolds
- as well as general manifolds of positive reach. - The sample P of a set (or
a manifold) \U0001D4AE of positive reach may be noisy. We work with two one-sided
Hausdorff distances - ε and δ - between P and \U0001D4AE. We provide tight bounds
in terms of ε and δ, that guarantee that there exists a parameter r such that
the union of balls of radius r centred at the sample P deformation-retracts to
\U0001D4AE. We exhibit their tightness by an explicit construction. We carefully
distinguish the roles of δ and ε. This is not only essential to achieve tight
bounds, but also sensible in practical situations, since it allows one to adapt
the bound according to sample density and the amount of noise present in the sample
separately."
acknowledgement: "This research has been supported by the European Research Council
(ERC), grant No. 788183, by the Wittgenstein Prize, Austrian Science Fund (FWF),
grant No. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian
Science Fund (FWF), grant No. I 02979-N35.\r\nWintraecken, Mathijs: Supported by
the European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curie grant agreement No. 754411, the Austrian science fund (FWF) grant
No. M-3073, and the welcome package from IDEX of the Université Côte d'Azur."
alternative_title:
- LIPIcs
article_processing_charge: No
arxiv: 1
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: Hana
full_name: Kourimska, Hana
id: D9B8E14C-3C26-11EA-98F5-1F833DDC885E
last_name: Kourimska
orcid: 0000-0001-7841-0091
- first_name: Christopher D
full_name: Fillmore, Christopher D
id: 35638A5C-AAC7-11E9-B0BF-5503E6697425
last_name: Fillmore
- first_name: Ishika
full_name: Ghosh, Ishika
id: ee449b28-344d-11ef-a6d5-9ca430e9e9ff
last_name: Ghosh
- first_name: André
full_name: Lieutier, André
last_name: Lieutier
- first_name: Elizabeth R
full_name: Stephenson, Elizabeth R
id: 2D04F932-F248-11E8-B48F-1D18A9856A87
last_name: Stephenson
orcid: 0000-0002-6862-208X
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: 'Attali D, Kourimska H, Fillmore CD, et al. Tight bounds for the learning of
homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and
of Riemannian manifolds. In: 40th International Symposium on Computational
Geometry. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024:11:1-11:19.
doi:10.4230/LIPIcs.SoCG.2024.11'
apa: 'Attali, D., Kourimska, H., Fillmore, C. D., Ghosh, I., Lieutier, A., Stephenson,
E. R., & Wintraecken, M. (2024). Tight bounds for the learning of homotopy
à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian
manifolds. In 40th International Symposium on Computational Geometry (Vol.
293, p. 11:1-11:19). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.SoCG.2024.11'
chicago: Attali, Dominique, Hana Kourimska, Christopher D Fillmore, Ishika Ghosh,
André Lieutier, Elizabeth R Stephenson, and Mathijs Wintraecken. “Tight Bounds
for the Learning of Homotopy à La Niyogi, Smale, and Weinberger for Subsets of
Euclidean Spaces and of Riemannian Manifolds.” In 40th International Symposium
on Computational Geometry, 293:11:1-11:19. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2024. https://doi.org/10.4230/LIPIcs.SoCG.2024.11.
ieee: D. Attali et al., “Tight bounds for the learning of homotopy à la Niyogi,
Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds,”
in 40th International Symposium on Computational Geometry, Athens, Greece,
2024, vol. 293, p. 11:1-11:19.
ista: 'Attali D, Kourimska H, Fillmore CD, Ghosh I, Lieutier A, Stephenson ER, Wintraecken
M. 2024. Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger
for subsets of euclidean spaces and of Riemannian manifolds. 40th International
Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry,
LIPIcs, vol. 293, 11:1-11:19.'
mla: Attali, Dominique, et al. “Tight Bounds for the Learning of Homotopy à La Niyogi,
Smale, and Weinberger for Subsets of Euclidean Spaces and of Riemannian Manifolds.”
40th International Symposium on Computational Geometry, vol. 293, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 11:1-11:19, doi:10.4230/LIPIcs.SoCG.2024.11.
short: D. Attali, H. Kourimska, C.D. Fillmore, I. Ghosh, A. Lieutier, E.R. Stephenson,
M. Wintraecken, in:, 40th International Symposium on Computational Geometry, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 11:1-11:19.
conference:
end_date: 2024-06-14
location: Athens, Greece
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2024-06-11
date_created: 2024-06-25T11:45:58Z
date_published: 2024-06-06T00:00:00Z
date_updated: 2025-04-15T07:16:57Z
day: '06'
ddc:
- '516'
department:
- _id: GradSch
- _id: HeEd
doi: 10.4230/LIPIcs.SoCG.2024.11
ec_funded: 1
external_id:
arxiv:
- '2206.10485'
file:
- access_level: open_access
checksum: 6a2ddc8b51aa58f197a8b294750f1f8d
content_type: application/pdf
creator: cfillmor
date_created: 2024-06-25T11:47:26Z
date_updated: 2024-06-25T11:47:26Z
file_id: '17171'
file_name: LIPIcs.SoCG.2024.11.pdf
file_size: 20886142
relation: main_file
success: 1
file_date_updated: 2024-06-25T11:47:26Z
has_accepted_license: '1'
intvolume: ' 293'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 11:1-11:19
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: Mathematics, Computer Science
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
- _id: fc390959-9c52-11eb-aca3-afa58bd282b2
grant_number: M03073
name: Learning and triangulating manifolds via collapses
publication: 40th International Symposium on Computational Geometry
publication_identifier:
eissn:
- 1868-8969
isbn:
- '9783959773164'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger
for subsets of euclidean spaces and of Riemannian manifolds
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 293
year: '2024'
...
---
APC_amount: 804 EUR
OA_place: publisher
OA_type: gold
_id: '17187'
abstract:
- lang: eng
text: "The generation of diverse cell types during development is fundamental to
brain\r\nfunctions. We outline a protocol to quantitatively assess the clonal
output of individual neural progenitors using mosaic analysis with double markers
(MADM) in\r\nmice. We first describe steps to acquire and reconstruct adult MADM
clones in\r\nthe superior colliculus. Then we detail analysis pipelines to determine
clonal\r\ncomposition and architecture. This protocol enables the buildup of quantitative\r\nframeworks
of lineage progression with precise spatial resolution in the brain.\r\nFor complete
details on the use and execution of this protocol, please refer to\r\nCheung et
al.1"
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: We thank A. Heger for mouse breeding support. This work was supported
by the Scientific Service Units of IST Austria through resources provided by the
Imaging & Optics and Preclinical facilities. G.C. received funding from the European
Commission (IST plus postdoctoral fellowship); S.H. was funded by ISTA institutional
funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro
Stem Modulation).
article_number: '103157'
article_processing_charge: Yes
article_type: original
author:
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Cheung GT, Streicher C, Hippenmeyer S. Protocol for quantitative reconstruction
of cell lineage using mosaic analysis with double markers in mice. STAR Protocols.
2024;5(3). doi:10.1016/j.xpro.2024.103157
apa: Cheung, G. T., Streicher, C., & Hippenmeyer, S. (2024). Protocol for quantitative
reconstruction of cell lineage using mosaic analysis with double markers in mice.
STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103157
chicago: Cheung, Giselle T, Carmen Streicher, and Simon Hippenmeyer. “Protocol for
Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double
Markers in Mice.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103157.
ieee: G. T. Cheung, C. Streicher, and S. Hippenmeyer, “Protocol for quantitative
reconstruction of cell lineage using mosaic analysis with double markers in mice,”
STAR Protocols, vol. 5, no. 3. Elsevier, 2024.
ista: Cheung GT, Streicher C, Hippenmeyer S. 2024. Protocol for quantitative reconstruction
of cell lineage using mosaic analysis with double markers in mice. STAR Protocols.
5(3), 103157.
mla: Cheung, Giselle T., et al. “Protocol for Quantitative Reconstruction of Cell
Lineage Using Mosaic Analysis with Double Markers in Mice.” STAR Protocols,
vol. 5, no. 3, 103157, Elsevier, 2024, doi:10.1016/j.xpro.2024.103157.
short: G.T. Cheung, C. Streicher, S. Hippenmeyer, STAR Protocols 5 (2024).
corr_author: '1'
date_created: 2024-06-30T22:01:04Z
date_published: 2024-09-20T00:00:00Z
date_updated: 2025-12-30T10:54:11Z
day: '20'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.xpro.2024.103157
ec_funded: 1
external_id:
pmid:
- '38935508'
file:
- access_level: open_access
checksum: d8a8cdba82a394e731aa699ace1ae433
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T12:12:40Z
date_updated: 2025-01-09T12:12:40Z
file_id: '18809'
file_name: 2024_STARProtoc_Cheung.pdf
file_size: 5186071
relation: main_file
success: 1
file_date_updated: 2025-01-09T12:12:40Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F7805
name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
Mechanisms of Neural Stem Cell Lineage Progression
publication: STAR Protocols
publication_identifier:
eissn:
- 2666-1667
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protocol for quantitative reconstruction of cell lineage using mosaic analysis
with double markers in mice
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17188'
abstract:
- lang: eng
text: "In a delegation problem, a principal P with commitment power tries to pick
one out of \U0001D45B options.\r\nEach option is drawn independently from a known
distribution. Instead of inspecting the options\r\nherself, P delegates the information
acquisition to a rational and self-interested agent A. After\r\ninspection, A
proposes one of the options, and P can accept or reject.\r\nDelegation is a classic
setting in economic information design with many prominent applications,\r\nbut
the computational problems are only poorly understood. In this paper, we study
a natural\r\nonline variant of delegation, in which the agent searches through
the options in an online fashion.\r\nFor each option, he has to irrevocably decide
if he wants to propose the current option or discard\r\nit, before seeing information
on the next option(s). How can we design algorithms for P that\r\napproximate
the utility of her best option in hindsight?\r\nWe show that in general P can
obtain a Θ(1∕\U0001D45B)-approximation and extend this result to ratios\r\nof
Θ(\U0001D458∕\U0001D45B) in case (1) A has a lookahead of \U0001D458 rounds, or
(2) A can propose up to \U0001D458 different\r\noptions. We provide fine-grained
bounds independent of \U0001D45B based on three parameters. If the ratio\r\nof
maximum and minimum utility for A is bounded by a factor \U0001D6FC, we obtain
an Ω(loglog \U0001D6FC∕ log \U0001D6FC)-\r\napproximation algorithm, and we show
that this is best possible. Additionally, if P cannot\r\ndistinguish options with
the same value for herself, we show that ratios polynomial in 1∕\U0001D6FC cannot\r\nbe
avoided. If there are at most \U0001D6FD different utility values for A, we show
a Θ(1∕\U0001D6FD)-approximation.\r\nIf the utilities of P and A for each option
are related by a factor \U0001D6FE, we obtain an Ω(1∕ log \U0001D6FE)-\r\napproximation,
where \U0001D442(log log \U0001D6FE∕ log \U0001D6FE) is best possible."
acknowledgement: Hahn gratefully acknowledges the support of GIF grant I-1419-118.4/2017.
Hoefer gratefully acknowledges the support of GIF grant I-1419-118.4/2017, DFG Research
Unit ADYN (project number 411362735), and DFG grant Ho 3831/9-1 (project number
514505843).
article_number: '104171'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Pirmin
full_name: Braun, Pirmin
last_name: Braun
- first_name: Niklas
full_name: Hahn, Niklas
id: 0a01c7b2-b823-11ed-9928-cc3f874f9ffd
last_name: Hahn
- first_name: Martin
full_name: Hoefer, Martin
last_name: Hoefer
- first_name: Conrad
full_name: Schecker, Conrad
last_name: Schecker
citation:
ama: Braun P, Hahn N, Hoefer M, Schecker C. Delegated online search. Artificial
Intelligence. 2024;334. doi:10.1016/j.artint.2024.104171
apa: Braun, P., Hahn, N., Hoefer, M., & Schecker, C. (2024). Delegated online
search. Artificial Intelligence. Elsevier. https://doi.org/10.1016/j.artint.2024.104171
chicago: Braun, Pirmin, Niklas Hahn, Martin Hoefer, and Conrad Schecker. “Delegated
Online Search.” Artificial Intelligence. Elsevier, 2024. https://doi.org/10.1016/j.artint.2024.104171.
ieee: P. Braun, N. Hahn, M. Hoefer, and C. Schecker, “Delegated online search,”
Artificial Intelligence, vol. 334. Elsevier, 2024.
ista: Braun P, Hahn N, Hoefer M, Schecker C. 2024. Delegated online search. Artificial
Intelligence. 334, 104171.
mla: Braun, Pirmin, et al. “Delegated Online Search.” Artificial Intelligence,
vol. 334, 104171, Elsevier, 2024, doi:10.1016/j.artint.2024.104171.
short: P. Braun, N. Hahn, M. Hoefer, C. Schecker, Artificial Intelligence 334 (2024).
corr_author: '1'
date_created: 2024-06-30T22:01:05Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2025-09-08T08:00:42Z
day: '01'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.1016/j.artint.2024.104171
external_id:
arxiv:
- '2203.01084'
isi:
- '001260448100001'
file:
- access_level: open_access
checksum: f02a56bc7ea88f41fcc68968e4ceddf3
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T10:45:24Z
date_updated: 2025-01-09T10:45:24Z
file_id: '18806'
file_name: 2024_ArtificialIntelligence_Braun.pdf
file_size: 772226
relation: main_file
success: 1
file_date_updated: 2025-01-09T10:45:24Z
has_accepted_license: '1'
intvolume: ' 334'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Artificial Intelligence
publication_identifier:
issn:
- 0004-3702
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Delegated online search
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: 334
year: '2024'
...
---
OA_type: closed access
_id: '17189'
abstract:
- lang: eng
text: Supergranules, which are solar flow features with a lateral scale of 30,000–40,000 km
and a lifetime of ~24 h, form a prominent component of the Sun’s convective spectrum.
However, their internal flows, which can be probed only by helioseismology, are
not well understood. We analyse dopplergrams recorded by the Solar Dynamics Observatory
satellite to identify and characterize ~23,000 supergranules. We find that the
vertical flows peak at a depth of ~10,000 km, and remain invariant over the full
range of lateral supergranular scales, contrary to numerical predictions. We also
infer that, within the local seismic resolution (≳5,000 km), downflows are ~40%
weaker than upflows, indicating an apparent mass-flux imbalance. This may imply
that the descending flows also comprise plumes, which maintain the mass balance
but are simply too small to be detected by seismic waves. These results challenge
the widely used mixing-length description of solar convection.
acknowledgement: "We thank F. J. Simons for the codes for computing Slepian functions,\r\nM.
Rempel and R. Cameron for their insights into solar convection, J.\r\nW. Lord for
the numerical simulations and J. Naranjo for his help with\r\nthe NYUAD NetDRMS
system. This research was carried out with the\r\nHigh Performance Computing resources
at NYUAD. The datasets were\r\nprepared in the data centre at the Center for Space
Science of NYUAD.\r\nThis research is based upon work supported by Tamkeen under
the\r\nNYUAD Research Institute (Grant Nos G1502 and CASS to C.S.H,\r\nS.H. and
K.R.S.). S.H. acknowledges funding from the Department\r\nof Atomic Energy, India.
K.R.S. and S.H. acknowledge support from\r\nthe Ofice of Sponsored Research of King
Abdullah University of\r\nScience and Technology (Award No. OSR-CRG2020-4342). S.B.D.\r\nacknowledges
funding from the Elisabeth H. and F. A. Dahlen Award\r\n2022 by the Department of
Geosciences, Princeton University. S.B.D.\r\nalso acknowledges funding from the
European Union’s Horizon 2020\r\nresearch and innovation programme under a Marie
Skłodowska-Curie\r\ngrant (Grant Agreement No. 101034413). Some data products were\r\nprocessed
and downloaded from the German Data Center for SDO,\r\nwhich is funded by the German
Aerospace Center (DLR Grant No.\r\n500L1701)."
article_processing_charge: No
article_type: original
author:
- first_name: Chris S.
full_name: Hanson, Chris S.
last_name: Hanson
- first_name: Srijan B
full_name: Das, Srijan B
id: 9ce7c423-dacf-11ed-8942-e09c6cb27149
last_name: Das
orcid: 0000-0003-0896-7972
- first_name: Prasad
full_name: Mani, Prasad
last_name: Mani
- first_name: Shravan
full_name: Hanasoge, Shravan
last_name: Hanasoge
- first_name: Katepalli R.
full_name: Sreenivasan, Katepalli R.
last_name: Sreenivasan
citation:
ama: Hanson CS, Das SB, Mani P, Hanasoge S, Sreenivasan KR. Supergranular-scale
solar convection not explained by mixing-length theory. Nature Astronomy.
2024;8:1088-1101. doi:10.1038/s41550-024-02304-w
apa: Hanson, C. S., Das, S. B., Mani, P., Hanasoge, S., & Sreenivasan, K. R.
(2024). Supergranular-scale solar convection not explained by mixing-length theory.
Nature Astronomy. Springer Nature. https://doi.org/10.1038/s41550-024-02304-w
chicago: Hanson, Chris S., Srijan B Das, Prasad Mani, Shravan Hanasoge, and Katepalli
R. Sreenivasan. “Supergranular-Scale Solar Convection Not Explained by Mixing-Length
Theory.” Nature Astronomy. Springer Nature, 2024. https://doi.org/10.1038/s41550-024-02304-w.
ieee: C. S. Hanson, S. B. Das, P. Mani, S. Hanasoge, and K. R. Sreenivasan, “Supergranular-scale
solar convection not explained by mixing-length theory,” Nature Astronomy,
vol. 8. Springer Nature, pp. 1088–1101, 2024.
ista: Hanson CS, Das SB, Mani P, Hanasoge S, Sreenivasan KR. 2024. Supergranular-scale
solar convection not explained by mixing-length theory. Nature Astronomy. 8, 1088–1101.
mla: Hanson, Chris S., et al. “Supergranular-Scale Solar Convection Not Explained
by Mixing-Length Theory.” Nature Astronomy, vol. 8, Springer Nature, 2024,
pp. 1088–101, doi:10.1038/s41550-024-02304-w.
short: C.S. Hanson, S.B. Das, P. Mani, S. Hanasoge, K.R. Sreenivasan, Nature Astronomy
8 (2024) 1088–1101.
date_created: 2024-06-30T22:01:05Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2025-09-08T08:04:56Z
day: '01'
department:
- _id: LiBu
doi: 10.1038/s41550-024-02304-w
ec_funded: 1
external_id:
isi:
- '001254181700001'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '09'
oa_version: None
page: 1088-1101
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Nature Astronomy
publication_identifier:
eissn:
- 2397-3366
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Supergranular-scale solar convection not explained by mixing-length theory
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
year: '2024'
...
---
_id: '17190'
abstract:
- lang: eng
text: "For a locally finite set, \U0001D434⊆ℝ\U0001D451\r\n, the \U0001D458\r\nth
Brillouin zone of \U0001D44E∈\U0001D434\r\n is the region of points \U0001D465∈ℝ\U0001D451\r\n
for which ‖\U0001D465−\U0001D44E‖\r\n is the \U0001D458\r\nth smallest among the
Euclidean distances between \U0001D465\r\n and the points in \U0001D434\r\n. If
\U0001D434\r\n is a lattice, the \U0001D458\r\nth Brillouin zones of the points
in \U0001D434\r\n are translates of each other, and together they tile space.
Depending on the value of \U0001D458\r\n, they express medium- or long-range order
in the set. We study fundamental geometric and combinatorial properties of Brillouin
zones, focusing on the integer lattice and its perturbations. Our results include
the stability of a Brillouin zone under perturbations, a linear upper bound on
the number of chambers in a zone for lattices in ℝ2\r\n, and the convergence of
the maximum volume of a chamber to zero for the integer lattice."
acknowledgement: The second author is partially supported by the Alexander von Humboldt
Foundation. The sixth author is supported by the European Union's Horizon 2020 research
and innovation programme under Marie Sklodowska-Curie grant agreement 754411, and
by Austrian Science Fund(FWF) grant M-3073. All other authors are supported by European
Research Council (ERC) grant 788183, by the Wittgenstein Prize, by Austrian Science
Fund (FWF) grant Z 342-N31, and by the DFG Collaborative Research Center TRR 109,
Austrian Science Fund (FWF) grant I 02979-N35.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Alexey
full_name: Garber, Alexey
last_name: Garber
- first_name: Mohadese
full_name: Ghafaris, Mohadese
last_name: Ghafaris
- first_name: Teresa
full_name: Heiss, Teresa
id: 4879BB4E-F248-11E8-B48F-1D18A9856A87
last_name: Heiss
orcid: 0000-0002-1780-2689
- first_name: Morteza
full_name: Saghafiant, Morteza
last_name: Saghafiant
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: Edelsbrunner H, Garber A, Ghafaris M, Heiss T, Saghafiant M, Wintraecken M.
Brillouin zones of integer lattices and their perturbations. SIAM Journal on
Discrete Mathematics. 2024;38(2):1784-1807. doi:10.1137/22M1489071
apa: Edelsbrunner, H., Garber, A., Ghafaris, M., Heiss, T., Saghafiant, M., &
Wintraecken, M. (2024). Brillouin zones of integer lattices and their perturbations.
SIAM Journal on Discrete Mathematics. Society for Industrial and Applied
Mathematics. https://doi.org/10.1137/22M1489071
chicago: Edelsbrunner, Herbert, Alexey Garber, Mohadese Ghafaris, Teresa Heiss,
Morteza Saghafiant, and Mathijs Wintraecken. “Brillouin Zones of Integer Lattices
and Their Perturbations.” SIAM Journal on Discrete Mathematics. Society
for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/22M1489071.
ieee: H. Edelsbrunner, A. Garber, M. Ghafaris, T. Heiss, M. Saghafiant, and M. Wintraecken,
“Brillouin zones of integer lattices and their perturbations,” SIAM Journal
on Discrete Mathematics, vol. 38, no. 2. Society for Industrial and Applied
Mathematics, pp. 1784–1807, 2024.
ista: Edelsbrunner H, Garber A, Ghafaris M, Heiss T, Saghafiant M, Wintraecken M.
2024. Brillouin zones of integer lattices and their perturbations. SIAM Journal
on Discrete Mathematics. 38(2), 1784–1807.
mla: Edelsbrunner, Herbert, et al. “Brillouin Zones of Integer Lattices and Their
Perturbations.” SIAM Journal on Discrete Mathematics, vol. 38, no. 2, Society
for Industrial and Applied Mathematics, 2024, pp. 1784–807, doi:10.1137/22M1489071.
short: H. Edelsbrunner, A. Garber, M. Ghafaris, T. Heiss, M. Saghafiant, M. Wintraecken,
SIAM Journal on Discrete Mathematics 38 (2024) 1784–1807.
corr_author: '1'
date_created: 2024-06-30T22:01:05Z
date_published: 2024-06-07T00:00:00Z
date_updated: 2025-09-08T08:06:04Z
day: '07'
department:
- _id: HeEd
doi: 10.1137/22M1489071
ec_funded: 1
external_id:
arxiv:
- '2204.01077'
isi:
- '001292728600001'
intvolume: ' 38'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2204.01077
month: '06'
oa: 1
oa_version: Preprint
page: 1784-1807
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: fc390959-9c52-11eb-aca3-afa58bd282b2
grant_number: M03073
name: Learning and triangulating manifolds via collapses
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: Mathematics, Computer Science
publication: SIAM Journal on Discrete Mathematics
publication_identifier:
issn:
- 0895-4801
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Brillouin zones of integer lattices and their perturbations
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 38
year: '2024'
...
---
_id: '17191'
abstract:
- lang: eng
text: Dendritic cells migrate to and from lymph nodes in response to chemokine gradients.Data
now show that steady-state migration of these cells can be triggered by a mechanosensitive
pathway.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Sergio
full_name: Lembo, Sergio
id: d993a7b2-292f-11ed-aaac-fb045a912e31
last_name: Lembo
orcid: 0000-0002-2253-8771
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Lembo S, Sixt MK. Nuclear squeezing wakes up dendritic cells. Nature Immunology.
2024;25:1131–1132. doi:10.1038/s41590-024-01881-2
apa: Lembo, S., & Sixt, M. K. (2024). Nuclear squeezing wakes up dendritic cells.
Nature Immunology. Springer Nature. https://doi.org/10.1038/s41590-024-01881-2
chicago: Lembo, Sergio, and Michael K Sixt. “Nuclear Squeezing Wakes up Dendritic
Cells.” Nature Immunology. Springer Nature, 2024. https://doi.org/10.1038/s41590-024-01881-2.
ieee: S. Lembo and M. K. Sixt, “Nuclear squeezing wakes up dendritic cells,” Nature
Immunology, vol. 25. Springer Nature, pp. 1131–1132, 2024.
ista: Lembo S, Sixt MK. 2024. Nuclear squeezing wakes up dendritic cells. Nature
Immunology. 25, 1131–1132.
mla: Lembo, Sergio, and Michael K. Sixt. “Nuclear Squeezing Wakes up Dendritic Cells.”
Nature Immunology, vol. 25, Springer Nature, 2024, pp. 1131–1132, doi:10.1038/s41590-024-01881-2.
short: S. Lembo, M.K. Sixt, Nature Immunology 25 (2024) 1131–1132.
corr_author: '1'
date_created: 2024-06-30T22:01:05Z
date_published: 2024-06-21T00:00:00Z
date_updated: 2025-09-08T08:06:56Z
day: '21'
department:
- _id: MiSi
doi: 10.1038/s41590-024-01881-2
external_id:
isi:
- '001251509300001'
pmid:
- '38907047'
intvolume: ' 25'
isi: 1
language:
- iso: eng
month: '06'
oa_version: None
page: '1131–1132 '
pmid: 1
publication: Nature Immunology
publication_identifier:
eissn:
- 1529-2916
issn:
- 1529-2908
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nuclear squeezing wakes up dendritic cells
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 25
year: '2024'
...
---
_id: '17196'
abstract:
- lang: eng
text: This .zip File contains the data for the figures presented in the main text
and supplementary material of "A gate tunable transmon qubit in planar Ge" by
O.Sagi et al. The measurements were done using Qcodes. The description of the
files and the instructions on opening the data can be found in the Readme. An
additional Jupyter Notebook is attached that walks through the data analysis.
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
acknowledgement: 'This research was supported by the Scientific Service Units of ISTA
through resources provided by the MIBA Machine Shop and the Nanofabrication facility. '
article_processing_charge: No
author:
- first_name: Oliver
full_name: Sagi, Oliver
id: 71616374-A8E9-11E9-A7CA-09ECE5697425
last_name: Sagi
citation:
ama: Sagi O. A gate-tunable transmon in planar Ge. 2024. doi:10.15479/AT:ISTA:17196
apa: Sagi, O. (2024). A gate-tunable transmon in planar Ge. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:17196
chicago: Sagi, Oliver. “A Gate-Tunable Transmon in Planar Ge.” Institute of Science
and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:17196.
ieee: O. Sagi, “A gate-tunable transmon in planar Ge.” Institute of Science and
Technology Austria, 2024.
ista: Sagi O. 2024. A gate-tunable transmon in planar Ge, Institute of Science and
Technology Austria, 10.15479/AT:ISTA:17196.
mla: Sagi, Oliver. A Gate-Tunable Transmon in Planar Ge. Institute of Science
and Technology Austria, 2024, doi:10.15479/AT:ISTA:17196.
short: O. Sagi, (2024).
contributor:
- contributor_type: project_member
first_name: Alessandro
id: 1F2B21A2-F6E7-11E9-9B82-F7DBE5697425
last_name: Crippa
orcid: 0000-0002-2968-611X
- contributor_type: project_member
first_name: Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
- contributor_type: project_member
first_name: Marian
id: 396A1950-F248-11E8-B48F-1D18A9856A87
last_name: Janik
- contributor_type: project_member
first_name: Levon
id: 7aa1f788-b527-11ee-aa9e-e6111a79e0c7
last_name: Baghumyan
- contributor_type: project_member
first_name: Giorgio
id: 298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352
last_name: Fabris
- contributor_type: project_member
first_name: Lucky
id: 84b9700b-15b2-11ec-abd3-831089e67615
last_name: Kapoor
- contributor_type: project_member
first_name: Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- contributor_type: project_member
first_name: Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- contributor_type: project_member
first_name: Stefano
last_name: Calcaterra
- contributor_type: project_member
first_name: Daniel
last_name: Chrastina
- contributor_type: project_member
first_name: Giovanni
last_name: Isella
- contributor_type: supervisor
first_name: Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
corr_author: '1'
date_created: 2024-07-04T10:14:34Z
date_published: 2024-07-04T00:00:00Z
date_updated: 2026-04-16T12:20:39Z
day: '04'
ddc:
- '530'
department:
- _id: GradSch
- _id: GeKa
- _id: JoFi
doi: 10.15479/AT:ISTA:17196
file:
- access_level: open_access
checksum: a9f640a0b72a92171353f3ea14406f0b
content_type: application/octet-stream
creator: osagi
date_created: 2024-07-04T10:01:51Z
date_updated: 2024-07-04T10:01:51Z
file_id: '17197'
file_name: GeGatemon_DataAnalysis.ipynb
file_size: 1960182
relation: main_file
success: 1
- access_level: open_access
checksum: f0feec931233e8e845ade56165c1588f
content_type: application/vnd.openxmlformats-officedocument.presentationml.presentation
creator: osagi
date_created: 2024-07-04T10:01:50Z
date_updated: 2024-07-04T10:01:50Z
file_id: '17198'
file_name: OlSa_Readme.pptx
file_size: 34194
relation: main_file
success: 1
- access_level: open_access
checksum: 92bb11e3a508d736d01ff0738a1172c7
content_type: application/x-zip-compressed
creator: osagi
date_created: 2024-07-04T10:11:16Z
date_updated: 2024-07-04T10:11:16Z
file_id: '17199'
file_name: Al_Transmon.zip
file_size: 72939292
relation: main_file
success: 1
- access_level: open_access
checksum: 871e96fe0ecc97581196e883045cd516
content_type: application/x-zip-compressed
creator: osagi
date_created: 2024-07-04T10:11:40Z
date_updated: 2024-07-04T10:11:40Z
file_id: '17200'
file_name: Gatemon_RT_5nm_1.zip
file_size: 465618029
relation: main_file
success: 1
- access_level: open_access
checksum: a3e141af90f0104b7269c8a72370848a
content_type: application/x-zip-compressed
creator: osagi
date_created: 2024-07-04T10:11:35Z
date_updated: 2024-07-04T10:11:35Z
file_id: '17201'
file_name: Gatemon_RT_5nm_2.zip
file_size: 281503513
relation: main_file
success: 1
file_date_updated: 2024-07-04T10:11:40Z
has_accepted_license: '1'
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1
grant_number: I05060
name: High impedance circuit quantum electrodynamics with hole spins
- _id: 262116AA-B435-11E9-9278-68D0E5697425
name: Hybrid Semiconductor - Superconductor Quantum Devices
- _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a
grant_number: P36507
name: Merging spin and superconducting qubits in planar Ge
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '17202'
relation: used_in_publication
status: public
status: public
title: A gate-tunable transmon in planar Ge
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: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2024'
...
---
APC_amount: 6828 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18444'
abstract:
- lang: eng
text: Animals rely on compensatory actions to maintain stability and navigate their
environment efficiently. These actions depend on global visual motion cues known
as optic-flow. While the optomotor response has been the traditional focus for
studying optic-flow compensation in insects, its simplicity has been insufficient
to determine the role of the intricate optic-flow processing network involved
in visual course control. Here, we reveal a series of course control behaviours
in Drosophila and link them to specific neural circuits. We show that bilateral
electrical coupling of optic-flow-sensitive neurons in the fly’s lobula plate
are required for a proper course control. This electrical interaction works alongside
chemical synapses within the HS-H2 network to control the dynamics and direction
of turning behaviours. Our findings reveal how insects use bilateral motion cues
for navigation, assigning a new functional significance to the HS-H2 network and
suggesting a previously unknown role for gap junctions in non-linear operations.
acknowledged_ssus:
- _id: Bio
- _id: M-Shop
- _id: LifeSc
acknowledgement: We thank Georg Ammer and Alexander Borst for sharing anti-ShakB serum
antibodies. We thank Nélia Varela and Eugenia Chiappe for the w1118;+;10XUAS-IVS-eGFPKir2.1/TM6B
fly line, Augustin Hrvoje for the shakB[2] line, as well as Jesse Isaacman-Beck
and Thomas R Clandinin for the gift of y1,w*;20XUAS-IVS-PhiC31;+ fly line. We also
thank Armel Nicolas and Tomas Masson for the proteomic analysis, Ece Sönmez for
help with fly crosses and dissections for protein analysis, and Lisa Hofer for assistance
with the reconstruction experiments. We would also like to thank Laura Burnett for
drawing scientific illustrations used in the figures. We are particularly grateful
to members of the Siekhaus, the Kondrashov, and the Chiappe group for providing
material support and technical advice. We are grateful to Daria Siekhaus, Eugenia
Chiappe, Alexander Borst, Ben deBivort, and all the members of the Joesch laboratory
for valuable discussions and comments on the manuscript. Stocks from the Bloomington
Drosophila Stock Center (NIH P40OD018537) and the Vienna Drosophila Resource Center
were used in this study. The Scientific Service Units of ISTA supported the project
through resources provided by the Imaging and Optics Facility, MIBA Machine Shop,
and the Lab Support Facility, as well as Vienna Drosophila Research Centre. This
work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)
as part of the SPP 2205 – 429960716 (M.J.).
article_number: '8830'
article_processing_charge: Yes
article_type: original
author:
- first_name: Victoria
full_name: Pokusaeva, Victoria
id: 3184041C-F248-11E8-B48F-1D18A9856A87
last_name: Pokusaeva
orcid: 0000-0001-7660-444X
- first_name: Roshan K
full_name: Satapathy, Roshan K
id: 46046B7A-F248-11E8-B48F-1D18A9856A87
last_name: Satapathy
orcid: 0009-0006-2974-5075
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
orcid: 0000-0003-2012-9947
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
citation:
ama: Pokusaeva V, Satapathy RK, Symonova O, Jösch MA. Bilateral interactions of
optic-flow sensitive neurons coordinate course control in flies. Nature Communications.
2024;15. doi:10.1038/s41467-024-53173-w
apa: Pokusaeva, V., Satapathy, R. K., Symonova, O., & Jösch, M. A. (2024). Bilateral
interactions of optic-flow sensitive neurons coordinate course control in flies.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-53173-w
chicago: Pokusaeva, Victoria, Roshan K Satapathy, Olga Symonova, and Maximilian
A Jösch. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course
Control in Flies.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-53173-w.
ieee: V. Pokusaeva, R. K. Satapathy, O. Symonova, and M. A. Jösch, “Bilateral interactions
of optic-flow sensitive neurons coordinate course control in flies,” Nature
Communications, vol. 15. Springer Nature, 2024.
ista: Pokusaeva V, Satapathy RK, Symonova O, Jösch MA. 2024. Bilateral interactions
of optic-flow sensitive neurons coordinate course control in flies. Nature Communications.
15, 8830.
mla: Pokusaeva, Victoria, et al. “Bilateral Interactions of Optic-Flow Sensitive
Neurons Coordinate Course Control in Flies.” Nature Communications, vol.
15, 8830, Springer Nature, 2024, doi:10.1038/s41467-024-53173-w.
short: V. Pokusaeva, R.K. Satapathy, O. Symonova, M.A. Jösch, Nature Communications
15 (2024).
corr_author: '1'
date_created: 2024-10-20T22:02:05Z
date_published: 2024-10-12T00:00:00Z
date_updated: 2026-06-10T07:58:34Z
day: '12'
ddc:
- '570'
department:
- _id: MaJö
doi: 10.1038/s41467-024-53173-w
external_id:
isi:
- '001336422500001'
pmid:
- '39396050'
file:
- access_level: open_access
checksum: 2af4d6e7364329107aa94d072d594ce0
content_type: application/pdf
creator: dernst
date_created: 2024-10-21T12:11:10Z
date_updated: 2024-10-21T12:11:10Z
file_id: '18459'
file_name: 2024_NatureComm_Pokusaeva.pdf
file_size: 8276667
relation: main_file
success: 1
file_date_updated: 2024-10-21T12:11:10Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B767A34-BA93-11EA-9121-9846C619BF3A
grant_number: '429960716'
name: Evolution of Sensorimotor Transformation Across Diptera
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '18568'
relation: dissertation_contains
status: public
- id: '17488'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Bilateral interactions of optic-flow sensitive neurons coordinate course control
in flies
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'
...
---
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).
date_created: 2024-10-20T22:02:05Z
date_published: 2024-10-05T00:00:00Z
date_updated: 2025-09-08T14:25:06Z
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
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'
scopus_import: '1'
status: public
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'
...
---
OA_place: repository
OA_type: green
_id: '18446'
abstract:
- lang: eng
text: How living systems achieve precision in form and function despite their intrinsic
stochasticity is a fundamental yet ongoing question in biology. We generated morphomaps
of preimplantation embryogenesis in mouse, rabbit, and monkey embryos, and these
morphomaps revealed that although blastomere divisions desynchronized passively,
8-cell embryos converged toward robust three-dimensional shapes. Using topological
analysis and genetic perturbations, we found that embryos progressively changed
their cellular connectivity to a preferred topology, which could be predicted
by a physical model in which actomyosin contractility and noise facilitate topological
transitions, lowering surface energy. This mechanism favored regular embryo packing
and promoted a higher number of inner cells in the 16-cell embryo. Synchronized
division reduced embryo packing and generated substantially more misallocated
cells and fewer inner-cell–mass cells. These findings suggest that stochasticity
in division timing contributes to robust patterning.
acknowledgement: "We are grateful to the members of the Hiiragi laboratory for discussions
and comments on the manuscript: R. Bloehs, S. Friese, S. Hozeifi, L. Pérez, and
W. Schwarzer for their technical support; V. Janssen for establishing the PAB protocol;
members of the Tsukiyama group for the animal care with monkeys, in particular H.
Tsuchiya and M. Nakaya; Unité Commune d’Expérimentation Animale (UCEA, Jouy-en-Josas,
France) for the animal care with rabbits; the EMBL electronic and mechanical workshops
and the EMBL animal facility for their support; We thank Luxendo for the close collaboration
in developing the light-sheet microscopy for mammalian embryos.\r\nFunding: This
work was funded by the following: EMBL Interdisciplinary Postdoc Program (EIPOD)
under Marie Sklodowska Curie Actions COFUND III RTD (to D.F.); JSPS Overseas Research
Fellowship (to T.I.); Field of excellence “Complexity of life in basic research
and innovation” of the University of Graz (to B.C.M.); European Research Council,
ERC Advanced Grant “SelforganisingEmbryo”, grant agreement 742732; ERC Advanced
Grant “COORDINATION” grant agreement 101055287 (to T.H.); Stichting LSH-TKI, grant
LSHM21020 (to T.H.) JSPS KAKENHI grants JP21H05038 and JP22H05166 (to T.H.)"
article_number: eadh1145
article_processing_charge: No
article_type: original
author:
- first_name: Dimitri
full_name: Fabrèges, Dimitri
last_name: Fabrèges
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Prachiti
full_name: Moghe, Prachiti
last_name: Moghe
- first_name: Alison
full_name: Kickuth, Alison
last_name: Kickuth
- first_name: Takafumi
full_name: Ichikawa, Takafumi
last_name: Ichikawa
- first_name: Chizuru
full_name: Iwatani, Chizuru
last_name: Iwatani
- first_name: Tomoyuki
full_name: Tsukiyama, Tomoyuki
last_name: Tsukiyama
- first_name: Nathalie
full_name: Daniel, Nathalie
last_name: Daniel
- first_name: Julie
full_name: Gering, Julie
last_name: Gering
- first_name: Anniek
full_name: Stokkermans, Anniek
last_name: Stokkermans
- first_name: Adrian
full_name: Wolny, Adrian
last_name: Wolny
- first_name: Anna
full_name: Kreshuk, Anna
last_name: Kreshuk
- first_name: Véronique
full_name: Duranthon, Véronique
last_name: Duranthon
- first_name: Virginie
full_name: Uhlman, Virginie
last_name: Uhlman
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Takashi
full_name: Hiiragi, Takashi
last_name: Hiiragi
citation:
ama: Fabrèges D, Corominas-Murtra B, Moghe P, et al. Temporal variability and cell
mechanics control robustness in mammalian embryogenesis. Science. 2024;386(6718).
doi:10.1126/science.adh1145
apa: Fabrèges, D., Corominas-Murtra, B., Moghe, P., Kickuth, A., Ichikawa, T., Iwatani,
C., … Hiiragi, T. (2024). Temporal variability and cell mechanics control robustness
in mammalian embryogenesis. Science. AAAS. https://doi.org/10.1126/science.adh1145
chicago: Fabrèges, Dimitri, Bernat Corominas-Murtra, Prachiti Moghe, Alison Kickuth,
Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, et al. “Temporal Variability
and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” Science.
AAAS, 2024. https://doi.org/10.1126/science.adh1145.
ieee: D. Fabrèges et al., “Temporal variability and cell mechanics control
robustness in mammalian embryogenesis,” Science, vol. 386, no. 6718. AAAS,
2024.
ista: Fabrèges D, Corominas-Murtra B, Moghe P, Kickuth A, Ichikawa T, Iwatani C,
Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon
V, Uhlman V, Hannezo EB, Hiiragi T. 2024. Temporal variability and cell mechanics
control robustness in mammalian embryogenesis. Science. 386(6718), eadh1145.
mla: Fabrèges, Dimitri, et al. “Temporal Variability and Cell Mechanics Control
Robustness in Mammalian Embryogenesis.” Science, vol. 386, no. 6718, eadh1145,
AAAS, 2024, doi:10.1126/science.adh1145.
short: D. Fabrèges, B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani,
T. Tsukiyama, N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon,
V. Uhlman, E.B. Hannezo, T. Hiiragi, Science 386 (2024).
corr_author: '1'
date_created: 2024-10-20T22:02:06Z
date_published: 2024-10-11T00:00:00Z
date_updated: 2025-09-08T14:22:13Z
day: '11'
department:
- _id: EdHa
doi: 10.1126/science.adh1145
external_id:
isi:
- '001422132300018'
pmid:
- '39388574'
intvolume: ' 386'
isi: 1
issue: '6718'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.inrae.fr/hal-04447081v1/file/2023.01.24.525420.full.pdf
month: '10'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Temporal variability and cell mechanics control robustness in mammalian embryogenesis
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 386
year: '2024'
...
---
OA_type: closed access
_id: '18450'
abstract:
- lang: eng
text: In this work we present the engineering of a portable platform for sensing
SERS signals in droplets microfluidics. This system comprised not only the read-out
platform but also a design for the microfluidic devices optimized to enhanced
the obtained SERS signals.
acknowledgement: The authors acknowledge the financial support of the project HfPT
– Health from Portugal, with the reference n.° C644937233-00000047, co-funded by
Component C5 – Capitalisation and Business Innovation under the Portuguese Resilience
and Recovery Plan, through the NextGenerationEU Fund.
article_processing_charge: No
author:
- first_name: Sergio
full_name: Quintero, Sergio
last_name: Quintero
- first_name: Maria
full_name: Relvas, Maria
last_name: Relvas
- first_name: Marta
full_name: Aranda, Marta
last_name: Aranda
- first_name: Fernando
full_name: Nodal, Fernando
id: 8ad43d5a-1ffe-11ee-8b67-8176f59de781
last_name: Nodal
orcid: 0009-0006-4119-4376
- first_name: Lorena
full_name: Dieguez, Lorena
last_name: Dieguez
- first_name: Sara
full_name: Abalde-Cela, Sara
last_name: Abalde-Cela
citation:
ama: 'Quintero S, Relvas M, Aranda M, Nodal F, Dieguez L, Abalde-Cela S. Portable
Raman platform for SERS droplets microfludics. In: 2024 International Conference
on Optical MEMS and Nanophotonics. Institute of Electrical and Electronics
Engineers; 2024. doi:10.1109/OMN61224.2024.10685279'
apa: 'Quintero, S., Relvas, M., Aranda, M., Nodal, F., Dieguez, L., & Abalde-Cela,
S. (2024). Portable Raman platform for SERS droplets microfludics. In 2024
International Conference on Optical MEMS and Nanophotonics. San Sebastian,
Spain: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/OMN61224.2024.10685279'
chicago: Quintero, Sergio, Maria Relvas, Marta Aranda, Fernando Nodal, Lorena Dieguez,
and Sara Abalde-Cela. “Portable Raman Platform for SERS Droplets Microfludics.”
In 2024 International Conference on Optical MEMS and Nanophotonics. Institute
of Electrical and Electronics Engineers, 2024. https://doi.org/10.1109/OMN61224.2024.10685279.
ieee: S. Quintero, M. Relvas, M. Aranda, F. Nodal, L. Dieguez, and S. Abalde-Cela,
“Portable Raman platform for SERS droplets microfludics,” in 2024 International
Conference on Optical MEMS and Nanophotonics, San Sebastian, Spain, 2024.
ista: 'Quintero S, Relvas M, Aranda M, Nodal F, Dieguez L, Abalde-Cela S. 2024.
Portable Raman platform for SERS droplets microfludics. 2024 International Conference
on Optical MEMS and Nanophotonics. OMN: Conference on Optical MEMS and Nanophotonics.'
mla: Quintero, Sergio, et al. “Portable Raman Platform for SERS Droplets Microfludics.”
2024 International Conference on Optical MEMS and Nanophotonics, Institute
of Electrical and Electronics Engineers, 2024, doi:10.1109/OMN61224.2024.10685279.
short: S. Quintero, M. Relvas, M. Aranda, F. Nodal, L. Dieguez, S. Abalde-Cela,
in:, 2024 International Conference on Optical MEMS and Nanophotonics, Institute
of Electrical and Electronics Engineers, 2024.
conference:
end_date: 2024-08-01
location: San Sebastian, Spain
name: 'OMN: Conference on Optical MEMS and Nanophotonics'
start_date: 2024-07-28
date_created: 2024-10-20T22:02:07Z
date_published: 2024-09-27T00:00:00Z
date_updated: 2025-09-08T14:19:49Z
day: '27'
department:
- _id: GradSch
doi: 10.1109/OMN61224.2024.10685279
external_id:
isi:
- '001327768000060'
isi: 1
language:
- iso: eng
month: '09'
oa_version: None
publication: 2024 International Conference on Optical MEMS and Nanophotonics
publication_identifier:
eissn:
- 2160-5041
isbn:
- '9798350384925'
issn:
- 2160-5033
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Portable Raman platform for SERS droplets microfludics
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18451'
abstract:
- lang: eng
text: Inorganic nanoparticles can be assembled into superlattices with unique optical
and magnetic properties arising from collective behavior. Protein cages can be
utilized to guide this assembly by encapsulating nanoparticles and promoting their
assembly into ordered structures. However, creating ordered multi-component structures
with different protein cage types and sizes remains a challenge. Here, the co-crystallization
of two different protein cages (cowpea chlorotic mottle virus and ferritin) characterized
by opposing surface charges and unequal diameter is shown. Precise tuning of the
electrostatic attraction between the cages enabled the preparation of binary crystals
with dimensions up to several tens of micrometers. Additionally, binary metal
nanoparticle superlattices are achieved by loading gold and iron oxide nanoparticles
inside the cavities of the protein cages. The resulting structure adopts an AB2FCC
configuration that also impacts the dipolar coupling between the particles and
hence the optical properties of the crystals, providing key insight for the future
preparation of plasmonic and magnetic nanoparticle metamaterials.
acknowledgement: This work has received funding from the European Research Council
(ERC) under the European Union's Horizon 2020 research and innovation programme
(Grant Agreement No. 101002258). The authors acknowledge the provision of facilities
and technical support by Aalto University Bioeconomy Facilities and OtaNanoNanomicroscopy
Center (Aalto-NMC). This work was carried out under the Academy of Finland's Centers
of Excellence Programme, Life Inspired Hybrid Materials (LIBER) Center of Excellence
(2022–2029), project number 346110 and 346112.
article_number: '2408416'
article_processing_charge: Yes
article_type: original
author:
- first_name: Yu
full_name: Zhou, Yu
last_name: Zhou
- first_name: Ahmed
full_name: Shaukat, Ahmed
last_name: Shaukat
- first_name: Jani
full_name: Seitsonen, Jani
last_name: Seitsonen
- first_name: Carlo
full_name: Rigoni, Carlo
id: c5df3b62-5f9e-11ef-ba3c-b97f5b5b5ef0
last_name: Rigoni
- first_name: Jaakko V.I.
full_name: Timonen, Jaakko V.I.
last_name: Timonen
- first_name: Mauri A.
full_name: Kostiainen, Mauri A.
last_name: Kostiainen
citation:
ama: Zhou Y, Shaukat A, Seitsonen J, Rigoni C, Timonen JVI, Kostiainen MA. Protein
cage directed assembly of binary nanoparticle superlattices. Advanced Science.
2024;11(45). doi:10.1002/advs.202408416
apa: Zhou, Y., Shaukat, A., Seitsonen, J., Rigoni, C., Timonen, J. V. I., &
Kostiainen, M. A. (2024). Protein cage directed assembly of binary nanoparticle
superlattices. Advanced Science. Wiley. https://doi.org/10.1002/advs.202408416
chicago: Zhou, Yu, Ahmed Shaukat, Jani Seitsonen, Carlo Rigoni, Jaakko V.I. Timonen,
and Mauri A. Kostiainen. “Protein Cage Directed Assembly of Binary Nanoparticle
Superlattices.” Advanced Science. Wiley, 2024. https://doi.org/10.1002/advs.202408416.
ieee: Y. Zhou, A. Shaukat, J. Seitsonen, C. Rigoni, J. V. I. Timonen, and M. A.
Kostiainen, “Protein cage directed assembly of binary nanoparticle superlattices,”
Advanced Science, vol. 11, no. 45. Wiley, 2024.
ista: Zhou Y, Shaukat A, Seitsonen J, Rigoni C, Timonen JVI, Kostiainen MA. 2024.
Protein cage directed assembly of binary nanoparticle superlattices. Advanced
Science. 11(45), 2408416.
mla: Zhou, Yu, et al. “Protein Cage Directed Assembly of Binary Nanoparticle Superlattices.”
Advanced Science, vol. 11, no. 45, 2408416, Wiley, 2024, doi:10.1002/advs.202408416.
short: Y. Zhou, A. Shaukat, J. Seitsonen, C. Rigoni, J.V.I. Timonen, M.A. Kostiainen,
Advanced Science 11 (2024).
date_created: 2024-10-20T22:02:07Z
date_published: 2024-12-04T00:00:00Z
date_updated: 2025-09-08T14:20:31Z
day: '04'
ddc:
- '540'
department:
- _id: RaKl
doi: 10.1002/advs.202408416
external_id:
isi:
- '001330745600001'
pmid:
- '39401426'
file:
- access_level: open_access
checksum: 00451eeb2c9eecf1ff41ad243c793a51
content_type: application/pdf
creator: dernst
date_created: 2025-01-13T09:16:25Z
date_updated: 2025-01-13T09:16:25Z
file_id: '18834'
file_name: 2024_AdvancedScience_Zhou.pdf
file_size: 7040083
relation: main_file
success: 1
file_date_updated: 2025-01-13T09:16:25Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '45'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Advanced Science
publication_identifier:
eissn:
- 2198-3844
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protein cage directed assembly of binary nanoparticle superlattices
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: '18452'
abstract:
- lang: eng
text: 'Diffusion models have recently emerged as powerful tools for the generation
of new molecular and material structures. The key insight is that the noise in
these models is related to the response of the atoms to displacement, and the
denoising step is thus analogous to the geometry relaxation of atomistic systems
starting from a random structure. Building on this, we present a generative method
called Response Matching (RM), which leverages the fact that each stable material
or molecule exists at the minimum of its potential energy surface. Any perturbation
induces a response in energy and stress, driving the structure back to equilibrium.
Matching this response is closely related to score matching in diffusion models.
Another important aspect of state-of-the-art diffusion models is the incorporation
of physical symmetries such as translation, rotation, and periodicity. RM employs
a machine learning interatomic potential and random structure search as the denoising
model, inherently respecting these symmetries and exploiting the locality of atomic
interactions. RM handles both molecules and bulk materials under the same framework.
Its efficiency and generalization are demonstrated on three systems: a small organic
molecular data set, stable crystals from the Materials Project, and one-shot learning
on a single diamond configuration.'
acknowledgement: B.C. thanks Chris Pickard for enlightening discussions.
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Cheng B. Response matching for generating materials and molecules. Journal
of Chemical Theory and Computation. 2024;20(20):9259-9266. doi:10.1021/acs.jctc.4c00998
apa: Cheng, B. (2024). Response matching for generating materials and molecules.
Journal of Chemical Theory and Computation. American Chemical Society.
https://doi.org/10.1021/acs.jctc.4c00998
chicago: Cheng, Bingqing. “Response Matching for Generating Materials and Molecules.”
Journal of Chemical Theory and Computation. American Chemical Society,
2024. https://doi.org/10.1021/acs.jctc.4c00998.
ieee: B. Cheng, “Response matching for generating materials and molecules,” Journal
of Chemical Theory and Computation, vol. 20, no. 20. American Chemical Society,
pp. 9259–9266, 2024.
ista: Cheng B. 2024. Response matching for generating materials and molecules. Journal
of Chemical Theory and Computation. 20(20), 9259–9266.
mla: Cheng, Bingqing. “Response Matching for Generating Materials and Molecules.”
Journal of Chemical Theory and Computation, vol. 20, no. 20, American Chemical
Society, 2024, pp. 9259–66, doi:10.1021/acs.jctc.4c00998.
short: B. Cheng, Journal of Chemical Theory and Computation 20 (2024) 9259–9266.
corr_author: '1'
date_created: 2024-10-20T22:02:07Z
date_published: 2024-10-22T00:00:00Z
date_updated: 2025-09-08T14:21:30Z
day: '22'
ddc:
- '540'
department:
- _id: BiCh
doi: 10.1021/acs.jctc.4c00998
external_id:
arxiv:
- '2405.09057'
isi:
- '001330001500001'
pmid:
- '39365029'
file:
- access_level: open_access
checksum: aca0011bba4846140809b5af583daa9a
content_type: application/pdf
creator: dernst
date_created: 2025-01-13T09:11:09Z
date_updated: 2025-01-13T09:11:09Z
file_id: '18832'
file_name: 2024_JCTC_Cheng.pdf
file_size: 4758251
relation: main_file
success: 1
file_date_updated: 2025-01-13T09:11:09Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '20'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 9259-9266
pmid: 1
publication: Journal of Chemical Theory and Computation
publication_identifier:
eissn:
- 1549-9626
issn:
- 1549-9618
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/BingqingCheng/cace
scopus_import: '1'
status: public
title: Response matching for generating materials and molecules
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: 20
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18465'
abstract:
- lang: eng
text: The phytohormone auxin is polarly transported in plants by PIN-FORMED (PIN)
transporters and controls virtually all growth and developmental processes. Canonical
PINs possess a long, largely disordered cytosolic loop. Auxin transport by canonical
PINs is activated by loop phosphorylation by certain kinases. The structure of
the PIN transmembrane domains was recently determined, their transport properties
remained poorly characterized, and the role of the loop in the transport process
was unclear. Here, we determined the quantitative kinetic parameters of auxin
transport mediated by Arabidopsis PINs to mathematically model auxin distribution
in roots and to test these predictions in vivo. Using chimeras between transmembrane
and loop domains of different PINs, we demonstrate a strong correlation between
transport parameters and physiological output, indicating that the loop domain
is not only required to activate PIN-mediated auxin transport, but it has an additional
role in the transport process by a currently unknown mechanism.
acknowledgement: This work was funded by DFG3468/6-1, DFG3468/6-3, and SFB924 to U.Z.H.
We thank Angela Alkofer and Helene Prunkl for excellent technical assistance and
Xenopus maintenance. Christian Luschnig is acknowledged for sharing unpublished
results and valuable discussions.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: DP
full_name: Janacek, DP
last_name: Janacek
- first_name: M
full_name: Kolb, M
last_name: Kolb
- first_name: L
full_name: Schulz, L
last_name: Schulz
- first_name: J
full_name: Mergner, J
last_name: Mergner
- first_name: B
full_name: Kuster, B
last_name: Kuster
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: K
full_name: Ten Tusscher, K
last_name: Ten Tusscher
- first_name: C
full_name: Schwechheimer, C
last_name: Schwechheimer
- first_name: UZ
full_name: Hammes, UZ
last_name: Hammes
citation:
ama: Janacek D, Kolb M, Schulz L, et al. Transport properties of canonical PIN-FORMED
proteins from Arabidopsis and the role of the loop domain in auxin transport.
Developmental Cell. 2024;59(14):S1534-5807(24)00569-0. doi:10.1016/j.devcel.2024.09.020
apa: Janacek, D., Kolb, M., Schulz, L., Mergner, J., Kuster, B., Glanc, M., … Hammes,
U. (2024). Transport properties of canonical PIN-FORMED proteins from Arabidopsis
and the role of the loop domain in auxin transport. Developmental Cell.
Elsevier. https://doi.org/10.1016/j.devcel.2024.09.020
chicago: Janacek, DP, M Kolb, L Schulz, J Mergner, B Kuster, Matous Glanc, Jiří
Friml, K Ten Tusscher, C Schwechheimer, and UZ Hammes. “Transport Properties of
Canonical PIN-FORMED Proteins from Arabidopsis and the Role of the Loop Domain
in Auxin Transport.” Developmental Cell. Elsevier, 2024. https://doi.org/10.1016/j.devcel.2024.09.020.
ieee: D. Janacek et al., “Transport properties of canonical PIN-FORMED proteins
from Arabidopsis and the role of the loop domain in auxin transport,” Developmental
Cell, vol. 59, no. 14. Elsevier, pp. S1534-5807(24)00569–0, 2024.
ista: Janacek D, Kolb M, Schulz L, Mergner J, Kuster B, Glanc M, Friml J, Ten Tusscher
K, Schwechheimer C, Hammes U. 2024. Transport properties of canonical PIN-FORMED
proteins from Arabidopsis and the role of the loop domain in auxin transport.
Developmental Cell. 59(14), S1534-5807(24)00569–0.
mla: Janacek, DP, et al. “Transport Properties of Canonical PIN-FORMED Proteins
from Arabidopsis and the Role of the Loop Domain in Auxin Transport.” Developmental
Cell, vol. 59, no. 14, Elsevier, 2024, pp. S1534-5807(24)00569-0, doi:10.1016/j.devcel.2024.09.020.
short: D. Janacek, M. Kolb, L. Schulz, J. Mergner, B. Kuster, M. Glanc, J. Friml,
K. Ten Tusscher, C. Schwechheimer, U. Hammes, Developmental Cell 59 (2024) S1534-5807(24)00569–0.
date_created: 2024-10-23T08:41:27Z
date_published: 2024-12-16T00:00:00Z
date_updated: 2025-09-08T14:33:17Z
day: '16'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1016/j.devcel.2024.09.020
external_id:
isi:
- '001390774300001'
pmid:
- '39413780'
file:
- access_level: open_access
checksum: 34423ee9fb4e30334f3572eddf1da2ae
content_type: application/pdf
creator: dernst
date_created: 2025-01-13T09:20:15Z
date_updated: 2025-01-13T09:20:15Z
file_id: '18835'
file_name: 2024_DevelopmentalCell_Janacek.pdf
file_size: 3675955
relation: main_file
success: 1
file_date_updated: 2025-01-13T09:20:15Z
has_accepted_license: '1'
intvolume: ' 59'
isi: 1
issue: '14'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: S1534-5807(24)00569-0
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transport properties of canonical PIN-FORMED proteins from Arabidopsis and
the role of the loop domain in auxin transport
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 59
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18479'
abstract:
- lang: eng
text: The dominance of beneficial mutations is a key evolutionary parameter affecting
the rate and genetic basis of adaptation, yet it is notoriously difficult to estimate.
A leading method to infer it is to compare the relative rates of adaptive substitution
for X-linked and autosomal genes, which—according to a classic model by Charlesworth
et al. (1987)—is a simple function of the dominance of new beneficial mutations.
Recent evidence that rates of adaptive substitution are faster for X-linked genes
implies, accordingly, that beneficial mutations are usually recessive. However,
this conclusion is incompatible with leading theories of dominance, which predict
that beneficial mutations tend to be dominant or overdominant with respect to
fitness. To address this incompatibility, we use Fisher’s geometric model to predict
the distribution of fitness effects of new mutations and the relative rates of
positively selected substitution on the X and autosomes. Previous predictions
of faster-X theory emerge as a special case of our model in which the phenotypic
effects of mutations are small relative to the distance to the phenotypic optimum.
But as mutational effects become large relative to the optimum, we observe an
elevated tempo of positively selected substitutions on the X relative to the autosomes
across a broader range of dominance conditions, including those predicted by theories
of dominance. Our results imply that, contrary to previous models, dominant and
overdominant beneficial mutations can plausibly generate patterns of faster-X
adaptation. We discuss resulting implications for genomic studies of adaptation
and inferences of dominance.
acknowledgement: This work was supported by funds from the Australian Research Council
and The School of Biological Sciences at Monash University. F.R. was funded by a
H2020 Marie Skłodowska-Curie COFUND Action (No. 101034413). We thank three anonymous
reviewers for suggestions that substantially improved the paper and breadth of the
analysis.
article_number: e2406335121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Yasmine
full_name: Mcdonough, Yasmine
last_name: Mcdonough
- first_name: Filip
full_name: Ruzicka, Filip
id: 347955dd-57b0-11ee-9095-c28bdd368f4b
last_name: Ruzicka
- first_name: Tim
full_name: Connallon, Tim
last_name: Connallon
citation:
ama: Mcdonough Y, Ruzicka F, Connallon T. Reconciling theories of dominance with
the relative rates of adaptive substitution on sex chromosomes and autosomes.
Proceedings of the National Academy of Sciences of the United States of America.
2024;121(44). doi:10.1073/pnas.2406335121
apa: Mcdonough, Y., Ruzicka, F., & Connallon, T. (2024). Reconciling theories
of dominance with the relative rates of adaptive substitution on sex chromosomes
and autosomes. Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2406335121
chicago: Mcdonough, Yasmine, Filip Ruzicka, and Tim Connallon. “Reconciling Theories
of Dominance with the Relative Rates of Adaptive Substitution on Sex Chromosomes
and Autosomes.” Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2406335121.
ieee: Y. Mcdonough, F. Ruzicka, and T. Connallon, “Reconciling theories of dominance
with the relative rates of adaptive substitution on sex chromosomes and autosomes,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 121, no. 44. National Academy of Sciences, 2024.
ista: Mcdonough Y, Ruzicka F, Connallon T. 2024. Reconciling theories of dominance
with the relative rates of adaptive substitution on sex chromosomes and autosomes.
Proceedings of the National Academy of Sciences of the United States of America.
121(44), e2406335121.
mla: Mcdonough, Yasmine, et al. “Reconciling Theories of Dominance with the Relative
Rates of Adaptive Substitution on Sex Chromosomes and Autosomes.” Proceedings
of the National Academy of Sciences of the United States of America, vol.
121, no. 44, e2406335121, National Academy of Sciences, 2024, doi:10.1073/pnas.2406335121.
short: Y. Mcdonough, F. Ruzicka, T. Connallon, Proceedings of the National Academy
of Sciences of the United States of America 121 (2024).
date_created: 2024-10-27T23:01:44Z
date_published: 2024-10-29T00:00:00Z
date_updated: 2025-09-08T14:31:58Z
day: '29'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1073/pnas.2406335121
ec_funded: 1
external_id:
isi:
- '001359216400017'
pmid:
- '39436652'
file:
- access_level: open_access
checksum: 73db3c87b35753e0f4324417f164a35e
content_type: application/pdf
creator: dernst
date_created: 2024-11-04T10:29:43Z
date_updated: 2024-11-04T10:29:43Z
file_id: '18501'
file_name: 2024_PNAS_McDonough.pdf
file_size: 1299095
relation: main_file
success: 1
file_date_updated: 2024-11-04T10:29:43Z
has_accepted_license: '1'
intvolume: ' 121'
isi: 1
issue: '44'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reconciling theories of dominance with the relative rates of adaptive substitution
on sex chromosomes and autosomes
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: 121
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18480'
abstract:
- lang: eng
text: Caloric restriction (CR) can extend the organism life- and health-span by
improving glucose homeostasis. How CR affects the structure-function of pancreatic
beta cells remains unknown. We used single nucleus transcriptomics to show that
CR increases the expression of genes for beta cell identity, protein processing,
and organelle homeostasis. Gene regulatory network analysis reveal that CR activates
transcription factors important for beta cell identity and homeostasis, while
imaging metabolomics demonstrates that beta cells upon CR are more energetically
competent. In fact, high-resolution microscopy show that CR reduces beta cell
mitophagy to increase mitochondria mass and the potential for ATP generation.
However, CR beta cells have impaired adaptive proliferation in response to high
fat diet feeding. Finally, we show that long-term CR delays the onset of beta
cell aging hallmarks and promotes cell longevity by reducing beta cell turnover.
Therefore, CR could be a feasible approach to preserve compromised beta cell structure-function
during aging and diabetes.
acknowledgement: We are thankful to Michelle Reyzer from the Vanderbilt Mass Spectrometry
Research Center for assistance with MALDI-MS imaging and analysis, to the outstanding
team at the Vanderbilt Mouse Metabolic Phenotyping Center for all the assistance
with in vivo glucose homeostasis tests (DK135073, 1S10RR028101-01). We also thank
the University of Michigan Animal Phenotyping Core for conducting the bomb calorimetry
experiments (1U2CDK110768, DK020575, and DK089503). This research was supported
by recruitment funds from the Vanderbilt’s Department of Molecular Physiology and
Biophysics and NIH grants 1R03DK127484, 5U24DK097771, and 1R01DK138141 to RAeD,
by a grant from the Canadian Institutes of Health Research (CIHR; 487188) to PEM,
by and NIH DK132669 to D.D. PEM holds the Canada Research Chair in Islet Biology.
article_number: '9063'
article_processing_charge: Yes
article_type: original
author:
- first_name: Cristiane
full_name: Dos Santos, Cristiane
last_name: Dos Santos
- first_name: Amanda
full_name: Cambraia, Amanda
last_name: Cambraia
- first_name: Shristi
full_name: Shrestha, Shristi
last_name: Shrestha
- first_name: Melanie
full_name: Cutler, Melanie
last_name: Cutler
- first_name: Matthew
full_name: Cottam, Matthew
last_name: Cottam
- first_name: Guy
full_name: Perkins, Guy
last_name: Perkins
- first_name: Varda
full_name: Lev-Ram, Varda
last_name: Lev-Ram
- first_name: Birbickram
full_name: Roy, Birbickram
last_name: Roy
- first_name: Christopher
full_name: Acree, Christopher
last_name: Acree
- first_name: Keun Young
full_name: Kim, Keun Young
last_name: Kim
- first_name: Thomas
full_name: Deerinck, Thomas
last_name: Deerinck
- first_name: Danielle
full_name: Dean, Danielle
last_name: Dean
- first_name: Jean Philippe
full_name: Cartailler, Jean Philippe
last_name: Cartailler
- first_name: Patrick E.
full_name: Macdonald, Patrick E.
last_name: Macdonald
- first_name: Martin W
full_name: Hetzer, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: Hetzer
orcid: 0000-0002-2111-992X
- first_name: Mark
full_name: Ellisman, Mark
last_name: Ellisman
- first_name: Rafael
full_name: Arrojo E Drigo, Rafael
last_name: Arrojo E Drigo
citation:
ama: Dos Santos C, Cambraia A, Shrestha S, et al. Calorie restriction increases
insulin sensitivity to promote beta cell homeostasis and longevity in mice. Nature
Communications. 2024;15. doi:10.1038/s41467-024-53127-2
apa: Dos Santos, C., Cambraia, A., Shrestha, S., Cutler, M., Cottam, M., Perkins,
G., … Arrojo E Drigo, R. (2024). Calorie restriction increases insulin sensitivity
to promote beta cell homeostasis and longevity in mice. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-024-53127-2
chicago: Dos Santos, Cristiane, Amanda Cambraia, Shristi Shrestha, Melanie Cutler,
Matthew Cottam, Guy Perkins, Varda Lev-Ram, et al. “Calorie Restriction Increases
Insulin Sensitivity to Promote Beta Cell Homeostasis and Longevity in Mice.” Nature
Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-53127-2.
ieee: C. Dos Santos et al., “Calorie restriction increases insulin sensitivity
to promote beta cell homeostasis and longevity in mice,” Nature Communications,
vol. 15. Springer Nature, 2024.
ista: Dos Santos C, Cambraia A, Shrestha S, Cutler M, Cottam M, Perkins G, Lev-Ram
V, Roy B, Acree C, Kim KY, Deerinck T, Dean D, Cartailler JP, Macdonald PE, Hetzer
M, Ellisman M, Arrojo E Drigo R. 2024. Calorie restriction increases insulin sensitivity
to promote beta cell homeostasis and longevity in mice. Nature Communications.
15, 9063.
mla: Dos Santos, Cristiane, et al. “Calorie Restriction Increases Insulin Sensitivity
to Promote Beta Cell Homeostasis and Longevity in Mice.” Nature Communications,
vol. 15, 9063, Springer Nature, 2024, doi:10.1038/s41467-024-53127-2.
short: C. Dos Santos, A. Cambraia, S. Shrestha, M. Cutler, M. Cottam, G. Perkins,
V. Lev-Ram, B. Roy, C. Acree, K.Y. Kim, T. Deerinck, D. Dean, J.P. Cartailler,
P.E. Macdonald, M. Hetzer, M. Ellisman, R. Arrojo E Drigo, Nature Communications
15 (2024).
date_created: 2024-10-27T23:01:44Z
date_published: 2024-10-21T00:00:00Z
date_updated: 2025-09-08T14:32:38Z
day: '21'
ddc:
- '570'
department:
- _id: MaHe
doi: 10.1038/s41467-024-53127-2
external_id:
isi:
- '001426270600023'
pmid:
- '39433757'
file:
- access_level: open_access
checksum: b936b1c047f41cd427f00e3dc79327d3
content_type: application/pdf
creator: dernst
date_created: 2024-11-04T10:37:56Z
date_updated: 2024-11-04T10:37:56Z
file_id: '18502'
file_name: 2024_NatureComm_dosSantos.pdf
file_size: 7358742
relation: main_file
success: 1
file_date_updated: 2024-11-04T10:37:56Z
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'
scopus_import: '1'
status: public
title: Calorie restriction increases insulin sensitivity to promote beta cell homeostasis
and longevity in mice
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'
...
---
APC_amount: 3197,23 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18481'
abstract:
- lang: eng
text: A tight regulation of morphogen production is key for morphogen gradient formation
and thereby for reproducible and organised organ development. Although many genetic
interactions involved in the establishment of morphogen production domains are
known, the biophysical mechanisms of morphogen source formation are poorly understood.
Here we addressed this by focusing on the morphogen Sonic hedgehog (Shh) in the
vertebrate neural tube. Shh is produced by the adjacently located notochord and
by the floor plate of the neural tube. Using a data-constrained computational
screen, we identified different possible mechanisms by which floor plate formation
can occur, only one of which is consistent with experimental data. In this mechanism,
the floor plate is established rapidly in response to Shh from the notochord and
the dynamics of regulatory interactions within the neural tube. In this process,
uniform activators and Shh-dependent repressors are key for establishing the floor
plate size. Subsequently, the floor plate becomes insensitive to Shh and increases
in size due to tissue growth, leading to scaling of the floor plate with neural
tube size. In turn, this results in scaling of the Shh amplitude with tissue growth.
Thus, this mechanism ensures a separation of time scales in floor plate formation,
so that the floor plate domain becomes growth-dependent after an initial rapid
establishment phase. Our study raises the possibility that the time scale separation
between specification and growth might be a common strategy for scaling the morphogen
gradient amplitude in growing organs. The model that we developed provides a new
opportunity for quantitative studies of morphogen source formation in growing
tissues.
acknowledgement: "We thank Martina Greunz-Schindler for technical support, and Thomas
Minchington and James Briscoe for comments on the manuscript.\r\nRDJGH, MM and MZ
were supported by a grant from the Priority Research Area DigiWorld\r\nunder the
Strategic Programme Excellence Initiative at Jagiellonian University. The research\r\nwas
supported by the Polish National Agency for Academic Exchange, PN/PPO/2018/1/00011/U/00001
which paid the salary of MM and MZ up to Feb 2023. The research received support
from National Science Center, Poland, 2021/42/E/NZ2/00188 which paid salary of MZ.
Work in the AK labis supported by ISTA to KK and AK, the European\r\nResearch Council
under Horizon Europe: grant 101044579 to AK, and Austrian Science Fund\r\n(FWF):
Grant DOI 10.55776/F78 to AK. The salaries of AK and KK were paid by ISTA. The funders
had no role in study design, data collection and analysis, decision to publish,
or preparation of the manuscript."
article_number: e1012508
article_processing_charge: No
article_type: original
author:
- first_name: Richard D.J.G.
full_name: Ho, Richard D.J.G.
last_name: Ho
- first_name: Kasumi
full_name: Kishi, Kasumi
id: 3065DFC4-F248-11E8-B48F-1D18A9856A87
last_name: Kishi
orcid: 0000-0001-6060-4795
- first_name: Maciej
full_name: Majka, Maciej
last_name: Majka
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
citation:
ama: Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. Dynamics of morphogen source
formation in a growing tissue. PLoS Computational Biology. 2024;20. doi:10.1371/journal.pcbi.1012508
apa: Ho, R. D. J. G., Kishi, K., Majka, M., Kicheva, A., & Zagórski, M. P. (2024).
Dynamics of morphogen source formation in a growing tissue. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1012508
chicago: Ho, Richard D.J.G., Kasumi Kishi, Maciej Majka, Anna Kicheva, and Marcin
P Zagórski. “Dynamics of Morphogen Source Formation in a Growing Tissue.” PLoS
Computational Biology. Public Library of Science, 2024. https://doi.org/10.1371/journal.pcbi.1012508.
ieee: R. D. J. G. Ho, K. Kishi, M. Majka, A. Kicheva, and M. P. Zagórski, “Dynamics
of morphogen source formation in a growing tissue,” PLoS Computational Biology,
vol. 20. Public Library of Science, 2024.
ista: Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. 2024. Dynamics of morphogen
source formation in a growing tissue. PLoS Computational Biology. 20, e1012508.
mla: Ho, Richard D. J. G., et al. “Dynamics of Morphogen Source Formation in a Growing
Tissue.” PLoS Computational Biology, vol. 20, e1012508, Public Library
of Science, 2024, doi:10.1371/journal.pcbi.1012508.
short: R.D.J.G. Ho, K. Kishi, M. Majka, A. Kicheva, M.P. Zagórski, PLoS Computational
Biology 20 (2024).
corr_author: '1'
date_created: 2024-10-27T23:01:45Z
date_published: 2024-10-14T00:00:00Z
date_updated: 2026-04-07T12:31:58Z
day: '14'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1371/journal.pcbi.1012508
external_id:
isi:
- '001331700300003'
pmid:
- '39401260'
file:
- access_level: open_access
checksum: 42fa714459943cb3961b40fab8fd82c8
content_type: application/pdf
creator: dernst
date_created: 2024-10-29T11:59:09Z
date_updated: 2024-10-29T11:59:09Z
file_id: '18487'
file_name: 2024_PloSComBio_Ho.pdf
file_size: 3732443
relation: main_file
success: 1
file_date_updated: 2024-10-29T11:59:09Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa
grant_number: '101044579'
name: Mechanisms of tissue size regulation in spinal cord development
- _id: 059DF620-7A3F-11EA-A408-12923DDC885E
grant_number: F7802
name: Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen
control of growth and pattern in the spinal cord
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
issn:
- 1553-734X
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '20393'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Dynamics of morphogen source formation in a growing tissue
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: 20
year: '2024'
...
---
OA_type: closed access
_id: '18482'
abstract:
- lang: eng
text: "This paper is dedicated to an optimization problem. Let A, B ⊂ Rn be compact
convex sets. Consider the minimal number t0 > 0 such that t0B covers A after a
shift to a vector x0 ∈ \r\nRn. The goal is to find t0 and x0. In the special case
of B being a unit ball centered at zero, x0 and t0 are known as the Chebyshev
center and the Chebyshev radius of A. This paper focuses on the case in which
A and B are defined with their black-box support functions. An algorithm for solving
such problems efficiently is suggested. The algorithm has a superlinear convergence
rate, and it can solve hundred-dimensional test problems in a reasonable time,
but some additional conditions on A and B are required to guarantee the presence
of convergence. Additionally, the behavior of the algorithm for a simple special
case is investigated, which leads to a number of theoretical results. Perturbations
of this special case are also studied."
acknowledgement: The author is grateful to Maxim Balashov for setting the problem,
providing useful literature, important discussions and text review. Also, I thank
Dmitry Tsarev and Kseniia Petukhova for meaningful talks and support.
article_processing_charge: No
article_type: original
author:
- first_name: Pavel
full_name: Arkhipov, Pavel
id: b25f2ab2-1fed-11ee-8599-fe02d211784f
last_name: Arkhipov
citation:
ama: Arkhipov P. An algorithm for finding the generalized Chebyshev center of sets
defined via their support functions. Automation and Remote Control. 2024;85(6):522-532.
doi:10.1134/S0005117924060031
apa: Arkhipov, P. (2024). An algorithm for finding the generalized Chebyshev center
of sets defined via their support functions. Automation and Remote Control.
Springer Nature. https://doi.org/10.1134/S0005117924060031
chicago: Arkhipov, Pavel. “An Algorithm for Finding the Generalized Chebyshev Center
of Sets Defined via Their Support Functions.” Automation and Remote Control.
Springer Nature, 2024. https://doi.org/10.1134/S0005117924060031.
ieee: P. Arkhipov, “An algorithm for finding the generalized Chebyshev center of
sets defined via their support functions,” Automation and Remote Control,
vol. 85, no. 6. Springer Nature, pp. 522–532, 2024.
ista: Arkhipov P. 2024. An algorithm for finding the generalized Chebyshev center
of sets defined via their support functions. Automation and Remote Control. 85(6),
522–532.
mla: Arkhipov, Pavel. “An Algorithm for Finding the Generalized Chebyshev Center
of Sets Defined via Their Support Functions.” Automation and Remote Control,
vol. 85, no. 6, Springer Nature, 2024, pp. 522–32, doi:10.1134/S0005117924060031.
short: P. Arkhipov, Automation and Remote Control 85 (2024) 522–532.
corr_author: '1'
date_created: 2024-10-27T23:01:45Z
date_published: 2024-06-01T00:00:00Z
date_updated: 2025-09-08T14:27:08Z
day: '01'
department:
- _id: GradSch
doi: 10.1134/S0005117924060031
external_id:
isi:
- '001338721700007'
intvolume: ' 85'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 522-532
publication: Automation and Remote Control
publication_identifier:
eissn:
- 1608-3032
issn:
- 0005-1179
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: An algorithm for finding the generalized Chebyshev center of sets defined via
their support functions
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 85
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18483'
abstract:
- lang: eng
text: In this paper we prove a perturbative version of a remarkable Bialy–Mironov
(Ann. Math. 196(1):389–413, 2022) result. They prove non perturbative Birkhoff
conjecture for centrally-symmetric convex domains, namely, a centrally-symmetric
convex domain with integrable billiard is ellipse. We combine techniques from
Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) with a local result by Kaloshin–Sorrentino
(Ann. Math. 188(1):315–380, 2018) and show that a domain close enough to a centrally
symmetric one with integrable billiard is ellipse. To combine these results we
derive a slight extension of Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) by
proving that a notion of rational integrability is equivalent to the C0-integrability
condition used in their paper.
acknowledgement: We are grateful to the anonymous referee for their careful reading
and valuable remarks and comments which helped to improve significantly the paper.
Open access funding provided by Institute of Science and Technology (IST Austria).
V.K. and C.E.K. gratefully acknowledge support from the European Research Council
(ERC) through the Advanced Grant “SPERIG” (#885 707).
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Edmond
full_name: Koudjinan, Edmond
id: 52DF3E68-AEFA-11EA-95A4-124A3DDC885E
last_name: Koudjinan
orcid: 0000-0003-2640-4049
- first_name: Ke
full_name: Zhang, Ke
last_name: Zhang
citation:
ama: Kaloshin V, Koudjinan E, Zhang K. Birkhoff conjecture for nearly centrally
symmetric domains. Geometric and Functional Analysis. 2024;34:1973-2007.
doi:10.1007/s00039-024-00695-6
apa: Kaloshin, V., Koudjinan, E., & Zhang, K. (2024). Birkhoff conjecture for
nearly centrally symmetric domains. Geometric and Functional Analysis.
Springer Nature. https://doi.org/10.1007/s00039-024-00695-6
chicago: Kaloshin, Vadim, Edmond Koudjinan, and Ke Zhang. “Birkhoff Conjecture for
Nearly Centrally Symmetric Domains.” Geometric and Functional Analysis.
Springer Nature, 2024. https://doi.org/10.1007/s00039-024-00695-6.
ieee: V. Kaloshin, E. Koudjinan, and K. Zhang, “Birkhoff conjecture for nearly centrally
symmetric domains,” Geometric and Functional Analysis, vol. 34. Springer
Nature, pp. 1973–2007, 2024.
ista: Kaloshin V, Koudjinan E, Zhang K. 2024. Birkhoff conjecture for nearly centrally
symmetric domains. Geometric and Functional Analysis. 34, 1973–2007.
mla: Kaloshin, Vadim, et al. “Birkhoff Conjecture for Nearly Centrally Symmetric
Domains.” Geometric and Functional Analysis, vol. 34, Springer Nature,
2024, pp. 1973–2007, doi:10.1007/s00039-024-00695-6.
short: V. Kaloshin, E. Koudjinan, K. Zhang, Geometric and Functional Analysis 34
(2024) 1973–2007.
corr_author: '1'
date_created: 2024-10-27T23:01:45Z
date_published: 2024-12-01T00:00:00Z
date_updated: 2025-09-08T14:27:45Z
day: '01'
ddc:
- '510'
department:
- _id: VaKa
doi: 10.1007/s00039-024-00695-6
ec_funded: 1
external_id:
arxiv:
- '2306.12301'
isi:
- '001329804200001'
file:
- access_level: open_access
checksum: e7fcd9f78beb40408c7d858ac0625e27
content_type: application/pdf
creator: dernst
date_created: 2025-01-13T09:14:24Z
date_updated: 2025-01-13T09:14:24Z
file_id: '18833'
file_name: 2024_GeometricFunctionalAnalysis_Kaloshin.pdf
file_size: 2260980
relation: main_file
success: 1
file_date_updated: 2025-01-13T09:14:24Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 1973-2007
project:
- _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '885707'
name: Spectral rigidity and integrability for billiards and geodesic flows
publication: Geometric and Functional Analysis
publication_identifier:
eissn:
- 1420-8970
issn:
- 1016-443X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Birkhoff conjecture for nearly centrally symmetric domains
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: 34
year: '2024'
...
---
APC_amount: 3711,01 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18488'
abstract:
- lang: eng
text: The advancement of quantum simulators motivates the development of a theoretical
framework to assist with efficient state preparation in quantum many-body systems.
Generally, preparing a target entangled state via unitary evolution with time-dependent
couplings is a challenging task and very little is known about the existence of
solutions and their properties. In this work we develop a constructive approach
for preparing matrix product states (MPS) via continuous unitary evolution. We
provide an explicit construction of the operator that exactly implements the evolution
of a given MPS along a specified direction in its tangent space. This operator
can be written as a sum of local terms of finite range, yet it is in general non-Hermitian.
Relying on the explicit construction of the non-Hermitian generator of the dynamics,
we demonstrate the existence of a Hermitian sequence of operators that implements
the desired MPS evolution with an error that decreases exponentially with the
operator range. The construction is benchmarked on an explicit periodic trajectory
in a translationally invariant MPS manifold. We demonstrate that the Floquet unitary
generating the dynamics over one period of the trajectory features an approximate
MPS-like eigenstate embedded among a sea of thermalizing eigenstates. These results
show that our construction is not only useful for state preparation and control
of many-body systems, but also provides a generic route towards Floquet scars—periodically
driven models with quasilocal generators of dynamics that have exact MPS eigenstates
in their spectrum.
acknowledgement: We thank L. Piroli, S. Garratt, and A. Molnár for insightful discussions.
This research was funded in part by the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (Grant Agreements
No. 850899 and No. 863476), the Austrian Science Fund (FWF) (Grant DOIs 10.55776/COE1,
10.55776/P36305, and 10.55776/F71), and the European Union (NextGenerationEU). This
work was performed in part at the Aspen Center for Physics, which is supported by
National Science Foundation Grant PHY-2210452. This research was supported in part
by NSF Grant PHY-2309135 to the Kavli Institute for Theoretical Physics (KITP).
article_number: '040311'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
orcid: 0000-0003-0038-7068
- first_name: Elena
full_name: Petrova, Elena
id: 0ac84990-897b-11ed-a09c-f5abb56a4ede
last_name: Petrova
- first_name: Norbert
full_name: Schuch, Norbert
last_name: Schuch
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Ljubotina M, Petrova E, Schuch N, Serbyn M. Tangent space generators of matrix
product states and exact floquet quantum scars. PRX Quantum. 2024;5(4).
doi:10.1103/prxquantum.5.040311
apa: Ljubotina, M., Petrova, E., Schuch, N., & Serbyn, M. (2024). Tangent space
generators of matrix product states and exact floquet quantum scars. PRX Quantum.
American Physical Society. https://doi.org/10.1103/prxquantum.5.040311
chicago: Ljubotina, Marko, Elena Petrova, Norbert Schuch, and Maksym Serbyn. “Tangent
Space Generators of Matrix Product States and Exact Floquet Quantum Scars.” PRX
Quantum. American Physical Society, 2024. https://doi.org/10.1103/prxquantum.5.040311.
ieee: M. Ljubotina, E. Petrova, N. Schuch, and M. Serbyn, “Tangent space generators
of matrix product states and exact floquet quantum scars,” PRX Quantum,
vol. 5, no. 4. American Physical Society, 2024.
ista: Ljubotina M, Petrova E, Schuch N, Serbyn M. 2024. Tangent space generators
of matrix product states and exact floquet quantum scars. PRX Quantum. 5(4), 040311.
mla: Ljubotina, Marko, et al. “Tangent Space Generators of Matrix Product States
and Exact Floquet Quantum Scars.” PRX Quantum, vol. 5, no. 4, 040311, American
Physical Society, 2024, doi:10.1103/prxquantum.5.040311.
short: M. Ljubotina, E. Petrova, N. Schuch, M. Serbyn, PRX Quantum 5 (2024).
corr_author: '1'
date_created: 2024-10-29T16:04:05Z
date_published: 2024-10-23T00:00:00Z
date_updated: 2025-09-08T14:26:29Z
day: '23'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/prxquantum.5.040311
ec_funded: 1
external_id:
arxiv:
- '2403.12325'
isi:
- '001346198800001'
file:
- access_level: open_access
checksum: 2e057ba021744d0a74602517935326b3
content_type: application/pdf
creator: dernst
date_created: 2024-10-30T08:59:09Z
date_updated: 2024-10-30T08:59:09Z
file_id: '18489'
file_name: 2024_PRXQuantum_Ljubotina.pdf
file_size: 1151431
relation: main_file
success: 1
file_date_updated: 2024-10-30T08:59:09Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: PRX Quantum
publication_identifier:
eissn:
- 2691-3399
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tangent space generators of matrix product states and exact floquet quantum
scars
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: 5
year: '2024'
...