---
_id: '10772'
abstract:
- lang: eng
text: We introduce tropical corals, balanced trees in a half-space, and show that
they correspond to holomorphic polygons capturing the product rule in Lagrangian
Floer theory for the elliptic curve. We then prove a correspondence theorem equating
counts of tropical corals to punctured log Gromov–Witten invariants of the Tate
curve. This implies that the homogeneous coordinate ring of the mirror to the
Tate curve is isomorphic to the degree-zero part of symplectic cohomology, confirming
a prediction of homological mirror symmetry.
acknowledgement: 'This paper is based on my PhD thesis, which would not be possible
without the support of my advisor Bernd Siebert. I also thank Dan Abramovich, Mohammed
Abouzaid, Mark Gross, Tom Coates and Dimitri Zvonkine for many useful conversations.
Finally, I thank the anonymous referees for their many insightful comments and valuable
suggestions which have resulted in major improvements to this article. This project
has received funding from the EuropeanResearch Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (Grant Agreement Number:
682603), and from Fondation Mathématique Jacques Hadamard. '
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Nuroemuer Huelya
full_name: Arguez, Nuroemuer Huelya
id: 3c26b22e-c843-11eb-aa56-d38ffa0bdd08
last_name: Arguez
citation:
ama: Arguez NH. Mirror symmetry for the Tate curve via tropical and log corals.
Journal of the London Mathematical Society. 2022;105(1):343-411. doi:10.1112/jlms.12515
apa: Arguez, N. H. (2022). Mirror symmetry for the Tate curve via tropical and log
corals. Journal of the London Mathematical Society. London Mathematical
Society. https://doi.org/10.1112/jlms.12515
chicago: Arguez, Nuroemuer Huelya. “Mirror Symmetry for the Tate Curve via Tropical
and Log Corals.” Journal of the London Mathematical Society. London Mathematical
Society, 2022. https://doi.org/10.1112/jlms.12515.
ieee: N. H. Arguez, “Mirror symmetry for the Tate curve via tropical and log corals,”
Journal of the London Mathematical Society, vol. 105, no. 1. London Mathematical
Society, pp. 343–411, 2022.
ista: Arguez NH. 2022. Mirror symmetry for the Tate curve via tropical and log corals.
Journal of the London Mathematical Society. 105(1), 343–411.
mla: Arguez, Nuroemuer Huelya. “Mirror Symmetry for the Tate Curve via Tropical
and Log Corals.” Journal of the London Mathematical Society, vol. 105,
no. 1, London Mathematical Society, 2022, pp. 343–411, doi:10.1112/jlms.12515.
short: N.H. Arguez, Journal of the London Mathematical Society 105 (2022) 343–411.
date_created: 2022-02-20T23:01:33Z
date_published: 2022-02-05T00:00:00Z
date_updated: 2023-08-02T14:29:50Z
day: '05'
ddc:
- '510'
department:
- _id: TaHa
doi: 10.1112/jlms.12515
external_id:
arxiv:
- '1712.10260'
isi:
- '000751600600001'
file:
- access_level: open_access
checksum: 8bd0fd9694be894a191857ddf27678f0
content_type: application/pdf
creator: dernst
date_created: 2022-02-21T11:22:58Z
date_updated: 2022-02-21T11:22:58Z
file_id: '10783'
file_name: 2022_JournLondonMathSociety_Arguez.pdf
file_size: 936873
relation: main_file
success: 1
file_date_updated: 2022-02-21T11:22:58Z
has_accepted_license: '1'
intvolume: ' 105'
isi: 1
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 343-411
publication: Journal of the London Mathematical Society
publication_identifier:
eissn:
- 1469-7750
issn:
- 0024-6107
publication_status: published
publisher: London Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mirror symmetry for the Tate curve via tropical and log corals
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 105
year: '2022'
...
---
_id: '10773'
abstract:
- lang: eng
text: The Voronoi tessellation in Rd is defined by locally minimizing the power
distance to given weighted points. Symmetrically, the Delaunay mosaic can be defined
by locally maximizing the negative power distance to other such points. We prove
that the average of the two piecewise quadratic functions is piecewise linear,
and that all three functions have the same critical points and values. Discretizing
the two piecewise quadratic functions, we get the alpha shapes as sublevel sets
of the discrete function on the Delaunay mosaic, and analogous shapes as superlevel
sets of the discrete function on the Voronoi tessellation. For the same non-critical
value, the corresponding shapes are disjoint, separated by a narrow channel that
contains no critical points but the entire level set of the piecewise linear function.
acknowledgement: Open access funding provided by the Institute of Science and Technology
(IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Sebastiano
full_name: Cultrera Di Montesano, Sebastiano
id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
last_name: Cultrera Di Montesano
orcid: 0000-0001-6249-0832
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Morteza
full_name: Saghafian, Morteza
last_name: Saghafian
citation:
ama: Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Continuous
and discrete radius functions on Voronoi tessellations and Delaunay mosaics. Discrete
and Computational Geometry. 2022;67:811-842. doi:10.1007/s00454-022-00371-2
apa: Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., & Saghafian, M.
(2022). Continuous and discrete radius functions on Voronoi tessellations and
Delaunay mosaics. Discrete and Computational Geometry. Springer Nature.
https://doi.org/10.1007/s00454-022-00371-2
chicago: Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner,
and Morteza Saghafian. “Continuous and Discrete Radius Functions on Voronoi Tessellations
and Delaunay Mosaics.” Discrete and Computational Geometry. Springer Nature,
2022. https://doi.org/10.1007/s00454-022-00371-2.
ieee: R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Continuous
and discrete radius functions on Voronoi tessellations and Delaunay mosaics,”
Discrete and Computational Geometry, vol. 67. Springer Nature, pp. 811–842,
2022.
ista: Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. 2022. Continuous
and discrete radius functions on Voronoi tessellations and Delaunay mosaics. Discrete
and Computational Geometry. 67, 811–842.
mla: Biswas, Ranita, et al. “Continuous and Discrete Radius Functions on Voronoi
Tessellations and Delaunay Mosaics.” Discrete and Computational Geometry,
vol. 67, Springer Nature, 2022, pp. 811–42, doi:10.1007/s00454-022-00371-2.
short: R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Discrete
and Computational Geometry 67 (2022) 811–842.
date_created: 2022-02-20T23:01:34Z
date_published: 2022-04-01T00:00:00Z
date_updated: 2023-08-02T14:31:25Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1007/s00454-022-00371-2
external_id:
isi:
- '000752175300002'
file:
- access_level: open_access
checksum: 9383d3b70561bacee905e335dc922680
content_type: application/pdf
creator: dernst
date_created: 2022-08-02T06:07:55Z
date_updated: 2022-08-02T06:07:55Z
file_id: '11718'
file_name: 2022_DiscreteCompGeometry_Biswas.pdf
file_size: 2518111
relation: main_file
success: 1
file_date_updated: 2022-08-02T06:07:55Z
has_accepted_license: '1'
intvolume: ' 67'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 811-842
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Continuous and discrete radius functions on Voronoi tessellations and Delaunay
mosaics
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 67
year: '2022'
...
---
_id: '10774'
abstract:
- lang: eng
text: We study the problem of specifying sequential information-flow properties
of systems. Information-flow properties are hyperproperties, as they compare different
traces of a system. Sequential information-flow properties can express changes,
over time, in the information-flow constraints. For example, information-flow
constraints during an initialization phase of a system may be different from information-flow
constraints that are required during the operation phase. We formalize several
variants of interpreting sequential information-flow constraints, which arise
from different assumptions about what can be observed of the system. For this
purpose, we introduce a first-order logic, called Hypertrace Logic, with both
trace and time quantifiers for specifying linear-time hyperproperties. We prove
that HyperLTL, which corresponds to a fragment of Hypertrace Logic with restricted
quantifier prefixes, cannot specify the majority of the studied variants of sequential
information flow, including all variants in which the transition between sequential
phases (such as initialization and operation) happens asynchronously. Our results
rely on new equivalences between sets of traces that cannot be distinguished by
certain classes of formulas from Hypertrace Logic. This presents a new approach
to proving inexpressiveness results for HyperLTL.
acknowledgement: This work was funded in part by the Wittgenstein Award Z211-N23 of
the Austrian Science Fund (FWF) and by the FWF project W1255-N23.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Ana Oliveira
full_name: Da Costa, Ana Oliveira
last_name: Da Costa
citation:
ama: 'Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. Flavors of sequential
information flow. In: Lecture Notes in Computer Science (Including Subseries
Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).
Vol 13182. Springer Nature; 2022:1-19. doi:10.1007/978-3-030-94583-1_1'
apa: 'Bartocci, E., Ferrere, T., Henzinger, T. A., Nickovic, D., & Da Costa,
A. O. (2022). Flavors of sequential information flow. In Lecture Notes in Computer
Science (including subseries Lecture Notes in Artificial Intelligence and Lecture
Notes in Bioinformatics) (Vol. 13182, pp. 1–19). Philadelphia, PA, United
States: Springer Nature. https://doi.org/10.1007/978-3-030-94583-1_1'
chicago: Bartocci, Ezio, Thomas Ferrere, Thomas A Henzinger, Dejan Nickovic, and
Ana Oliveira Da Costa. “Flavors of Sequential Information Flow.” In Lecture
Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence
and Lecture Notes in Bioinformatics), 13182:1–19. Springer Nature, 2022. https://doi.org/10.1007/978-3-030-94583-1_1.
ieee: E. Bartocci, T. Ferrere, T. A. Henzinger, D. Nickovic, and A. O. Da Costa,
“Flavors of sequential information flow,” in Lecture Notes in Computer Science
(including subseries Lecture Notes in Artificial Intelligence and Lecture Notes
in Bioinformatics), Philadelphia, PA, United States, 2022, vol. 13182, pp.
1–19.
ista: 'Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. 2022. Flavors
of sequential information flow. Lecture Notes in Computer Science (including subseries
Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).
VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 13182,
1–19.'
mla: Bartocci, Ezio, et al. “Flavors of Sequential Information Flow.” Lecture
Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence
and Lecture Notes in Bioinformatics), vol. 13182, Springer Nature, 2022, pp.
1–19, doi:10.1007/978-3-030-94583-1_1.
short: E. Bartocci, T. Ferrere, T.A. Henzinger, D. Nickovic, A.O. Da Costa, in:,
Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial
Intelligence and Lecture Notes in Bioinformatics), Springer Nature, 2022, pp.
1–19.
conference:
end_date: 2022-01-18
location: Philadelphia, PA, United States
name: 'VMCAI: Verifcation, Model Checking, and Abstract Interpretation'
start_date: 2022-01-16
date_created: 2022-02-20T23:01:34Z
date_published: 2022-01-14T00:00:00Z
date_updated: 2022-08-05T09:02:56Z
day: '14'
department:
- _id: ToHe
doi: 10.1007/978-3-030-94583-1_1
external_id:
arxiv:
- '2105.02013'
intvolume: ' 13182'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2105.02013'
month: '01'
oa: 1
oa_version: Preprint
page: 1-19
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Lecture Notes in Computer Science (including subseries Lecture Notes
in Artificial Intelligence and Lecture Notes in Bioinformatics)
publication_identifier:
eissn:
- '16113349'
isbn:
- '9783030945824'
issn:
- '03029743'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Flavors of sequential information flow
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13182
year: '2022'
...
---
_id: '10775'
abstract:
- lang: eng
text: List-decodability of Reed–Solomon codes has received a lot of attention, but
the best-possible dependence between the parameters is still not well-understood.
In this work, we focus on the case where the list-decoding radius is of the form
r = 1-ε for ε tending to zero. Our main result states that there exist Reed–Solomon
codes with rate Ω(ε) which are (1 - ε, O(1/ε))-list-decodable, meaning that any
Hamming ball of radius 1-ε contains at most O(1/ε) codewords. This trade-off between
rate and list-decoding radius is best-possible for any code with list size less
than exponential in the block length. By achieving this trade-off between rate
and list-decoding radius we improve a recent result of Guo, Li, Shangguan, Tamo,
and Wootters, and resolve the main motivating question of their work. Moreover,
while their result requires the field to be exponentially large in the block length,
we only need the field size to be polynomially large (and in fact, almost-linear
suffices). We deduce our main result from a more general theorem, in which we
prove good list-decodability properties of random puncturings of any given code
with very large distance.
acknowledgement: Research supported by NSF Award DMS-1953990.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Asaf
full_name: Ferber, Asaf
last_name: Ferber
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Lisa
full_name: Sauermann, Lisa
last_name: Sauermann
citation:
ama: Ferber A, Kwan MA, Sauermann L. List-decodability with large radius for Reed-Solomon
codes. IEEE Transactions on Information Theory. 2022;68(6):3823-3828. doi:10.1109/TIT.2022.3148779
apa: Ferber, A., Kwan, M. A., & Sauermann, L. (2022). List-decodability with
large radius for Reed-Solomon codes. IEEE Transactions on Information Theory.
IEEE. https://doi.org/10.1109/TIT.2022.3148779
chicago: Ferber, Asaf, Matthew Alan Kwan, and Lisa Sauermann. “List-Decodability
with Large Radius for Reed-Solomon Codes.” IEEE Transactions on Information
Theory. IEEE, 2022. https://doi.org/10.1109/TIT.2022.3148779.
ieee: A. Ferber, M. A. Kwan, and L. Sauermann, “List-decodability with large radius
for Reed-Solomon codes,” IEEE Transactions on Information Theory, vol.
68, no. 6. IEEE, pp. 3823–3828, 2022.
ista: Ferber A, Kwan MA, Sauermann L. 2022. List-decodability with large radius
for Reed-Solomon codes. IEEE Transactions on Information Theory. 68(6), 3823–3828.
mla: Ferber, Asaf, et al. “List-Decodability with Large Radius for Reed-Solomon
Codes.” IEEE Transactions on Information Theory, vol. 68, no. 6, IEEE,
2022, pp. 3823–28, doi:10.1109/TIT.2022.3148779.
short: A. Ferber, M.A. Kwan, L. Sauermann, IEEE Transactions on Information Theory
68 (2022) 3823–3828.
date_created: 2022-02-20T23:01:34Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2023-08-03T06:57:01Z
day: '01'
department:
- _id: MaKw
doi: 10.1109/TIT.2022.3148779
external_id:
arxiv:
- '2012.10584'
isi:
- '000799622500022'
intvolume: ' 68'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2012.10584
month: '06'
oa: 1
oa_version: Preprint
page: 3823-3828
publication: IEEE Transactions on Information Theory
publication_identifier:
eissn:
- 1557-9654
issn:
- 0018-9448
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '11145'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: List-decodability with large radius for Reed-Solomon codes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 68
year: '2022'
...
---
_id: '10776'
abstract:
- lang: eng
text: 'Let K be a convex body in Rn (i.e., a compact convex set with nonempty interior).
Given a point p in the interior of K, a hyperplane h passing through p is called
barycentric if p is the barycenter of K∩h. In 1961, Grünbaum raised the question
whether, for every K, there exists an interior point p through which there are
at least n+1 distinct barycentric hyperplanes. Two years later, this was seemingly
resolved affirmatively by showing that this is the case if p=p0 is the point of
maximal depth in K. However, while working on a related question, we noticed that
one of the auxiliary claims in the proof is incorrect. Here, we provide a counterexample;
this re-opens Grünbaum’s question. It follows from known results that for n≥2,
there are always at least three distinct barycentric cuts through the point p0∈K
of maximal depth. Using tools related to Morse theory we are able to improve this
bound: four distinct barycentric cuts through p0 are guaranteed if n≥3.'
acknowledgement: The work by Zuzana Patáková has been partially supported by Charles
University Research Center Program No. UNCE/SCI/022, and part of it was done during
her research stay at IST Austria. The work by Martin Tancer is supported by the
GAČR Grant 19-04113Y and by the Charles University Projects PRIMUS/17/SCI/3 and
UNCE/SCI/004.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Zuzana
full_name: Patakova, Zuzana
id: 48B57058-F248-11E8-B48F-1D18A9856A87
last_name: Patakova
orcid: 0000-0002-3975-1683
- first_name: Martin
full_name: Tancer, Martin
last_name: Tancer
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Patakova Z, Tancer M, Wagner U. Barycentric cuts through a convex body. Discrete
and Computational Geometry. 2022;68:1133-1154. doi:10.1007/s00454-021-00364-7
apa: Patakova, Z., Tancer, M., & Wagner, U. (2022). Barycentric cuts through
a convex body. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-021-00364-7
chicago: Patakova, Zuzana, Martin Tancer, and Uli Wagner. “Barycentric Cuts through
a Convex Body.” Discrete and Computational Geometry. Springer Nature, 2022.
https://doi.org/10.1007/s00454-021-00364-7.
ieee: Z. Patakova, M. Tancer, and U. Wagner, “Barycentric cuts through a convex
body,” Discrete and Computational Geometry, vol. 68. Springer Nature, pp.
1133–1154, 2022.
ista: Patakova Z, Tancer M, Wagner U. 2022. Barycentric cuts through a convex body.
Discrete and Computational Geometry. 68, 1133–1154.
mla: Patakova, Zuzana, et al. “Barycentric Cuts through a Convex Body.” Discrete
and Computational Geometry, vol. 68, Springer Nature, 2022, pp. 1133–54, doi:10.1007/s00454-021-00364-7.
short: Z. Patakova, M. Tancer, U. Wagner, Discrete and Computational Geometry 68
(2022) 1133–1154.
date_created: 2022-02-20T23:01:35Z
date_published: 2022-12-01T00:00:00Z
date_updated: 2023-08-02T14:38:58Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s00454-021-00364-7
external_id:
arxiv:
- '2003.13536'
isi:
- '000750681500001'
intvolume: ' 68'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2003.13536
month: '12'
oa: 1
oa_version: Preprint
page: 1133-1154
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Barycentric cuts through a convex body
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 68
year: '2022'
...
---
_id: '10787'
abstract:
- lang: eng
text: "A species distributed across diverse environments may adapt to local conditions.
We ask how quickly such a species changes its range in response to changed conditions.
Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in
metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210))
used the infinite island model to find the stationary distribution of allele frequencies
and deme sizes. We extend this to find how a metapopulation responds to changes
in carrying capacity, selection strength, or migration rate when deme sizes are
fixed. We further develop a ‘fixed-state’ approximation. Under this approximation,
polymorphism is only possible for a narrow range of habitat proportions when selection
is weak compared to drift, but for a much wider range otherwise. When rates of
selection or migration relative to drift change in a single deme of the metapopulation,
the population takes a time of order m−1 to reach the new equilibrium. However,
even with many loci, there can be substantial fluctuations in net adaptation,
because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation,
variation may gradually be lost by chance, even if it would persist in an infinite
metapopulation. When conditions change across the whole metapopulation, there
can be rapid change, which is predicted well by the fixed-state approximation.
This work helps towards an understanding of how metapopulations extend their range
across diverse environments.\r\nThis article is part of the theme issue ‘Species’
ranges in the face of changing environments (Part II)’."
acknowledgement: This research was partly funded by the Austrian Science Fund (FWF)
[FWF P-32896B].
article_processing_charge: No
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Oluwafunmilola O
full_name: Olusanya, Oluwafunmilola O
id: 41AD96DC-F248-11E8-B48F-1D18A9856A87
last_name: Olusanya
orcid: 0000-0003-1971-8314
citation:
ama: 'Barton NH, Olusanya OO. The response of a metapopulation to a changing environment.
Philosophical Transactions of the Royal Society B: Biological Sciences.
2022;377(1848). doi:10.1098/rstb.2021.0009'
apa: 'Barton, N. H., & Olusanya, O. O. (2022). The response of a metapopulation
to a changing environment. Philosophical Transactions of the Royal Society
B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2021.0009'
chicago: 'Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a
Metapopulation to a Changing Environment.” Philosophical Transactions of the
Royal Society B: Biological Sciences. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0009.'
ieee: 'N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing
environment,” Philosophical Transactions of the Royal Society B: Biological
Sciences, vol. 377, no. 1848. The Royal Society, 2022.'
ista: 'Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing
environment. Philosophical Transactions of the Royal Society B: Biological Sciences.
377(1848).'
mla: 'Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation
to a Changing Environment.” Philosophical Transactions of the Royal Society
B: Biological Sciences, vol. 377, no. 1848, The Royal Society, 2022, doi:10.1098/rstb.2021.0009.'
short: 'N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society
B: Biological Sciences 377 (2022).'
date_created: 2022-02-21T16:08:10Z
date_published: 2022-04-11T00:00:00Z
date_updated: 2025-05-26T09:05:09Z
day: '11'
ddc:
- '570'
department:
- _id: GradSch
- _id: NiBa
doi: 10.1098/rstb.2021.0009
external_id:
isi:
- '000758140300001'
pmid:
- '35184588'
file:
- access_level: open_access
checksum: 3b0243738f01bf3c07e0d7e8dc64f71d
content_type: application/pdf
creator: dernst
date_created: 2022-08-02T06:14:32Z
date_updated: 2022-08-02T06:14:32Z
file_id: '11719'
file_name: 2022_PhilosophicalTransactionsRSB_Barton.pdf
file_size: 1349672
relation: main_file
success: 1
file_date_updated: 2022-08-02T06:14:32Z
has_accepted_license: '1'
intvolume: ' 377'
isi: 1
issue: '1848'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8
grant_number: P32896
name: Causes and consequences of population fragmentation
publication: 'Philosophical Transactions of the Royal Society B: Biological Sciences'
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
related_material:
record:
- id: '14711'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The response of a metapopulation to a changing environment
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 377
year: '2022'
...
---
_id: '10788'
abstract:
- lang: eng
text: "We determine an asymptotic formula for the number of integral points of\r\nbounded
height on a certain toric variety, which is incompatible with part of a\r\npreprint
by Chambert-Loir and Tschinkel. We provide an alternative\r\ninterpretation of
the asymptotic formula we get. To do so, we construct an\r\nanalogue of Peyre's
constant $\\alpha$ and describe its relation to a new\r\nobstruction to the Zariski
density of integral points in certain regions of\r\nvarieties."
acknowledgement: "Part of this work was conducted as a guest at the Institut de Mathématiques
de Jussieu–Paris Rive Gauche invited by Antoine Chambert-Loir and funded by DAAD.\r\nDuring
this time, I had interesting and fruitful discussions on the interpretation of the
result for\r\nthe toric variety discussed in Section 3 with Antoine Chambert-Loir.
I wish to thank him for these\r\nopportunities and for his useful remarks on earlier
versions of this article. This work was partly\r\nfunded by FWF grant P 32428-N35."
article_number: '2202.10909'
article_processing_charge: No
arxiv: 1
author:
- first_name: Florian Alexander
full_name: Wilsch, Florian Alexander
id: 560601DA-8D36-11E9-A136-7AC1E5697425
last_name: Wilsch
orcid: 0000-0001-7302-8256
citation:
ama: Wilsch FA. Integral points of bounded height on a certain toric variety. arXiv.
doi:10.48550/arXiv.2202.10909
apa: Wilsch, F. A. (n.d.). Integral points of bounded height on a certain toric
variety. arXiv. https://doi.org/10.48550/arXiv.2202.10909
chicago: Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Certain
Toric Variety.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2202.10909.
ieee: F. A. Wilsch, “Integral points of bounded height on a certain toric variety,”
arXiv. .
ista: Wilsch FA. Integral points of bounded height on a certain toric variety. arXiv,
2202.10909.
mla: Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Certain
Toric Variety.” ArXiv, 2202.10909, doi:10.48550/arXiv.2202.10909.
short: F.A. Wilsch, ArXiv (n.d.).
date_created: 2022-02-23T09:04:43Z
date_published: 2022-02-22T00:00:00Z
date_updated: 2023-05-03T07:46:35Z
day: '22'
department:
- _id: TiBr
doi: 10.48550/arXiv.2202.10909
external_id:
arxiv:
- '2202.10909'
keyword:
- Integral point
- toric variety
- Manin's conjecture
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2202.10909
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 26AEDAB2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P32428
name: New frontiers of the Manin conjecture
publication: arXiv
publication_status: submitted
status: public
title: Integral points of bounded height on a certain toric variety
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '10791'
abstract:
- lang: eng
text: The mammalian neocortex is composed of diverse neuronal and glial cell classes
that broadly arrange in six distinct laminae. Cortical layers emerge during development
and defects in the developmental programs that orchestrate cortical lamination
are associated with neurodevelopmental diseases. The developmental principle of
cortical layer formation depends on concerted radial projection neuron migration,
from their birthplace to their final target position. Radial migration occurs
in defined sequential steps, regulated by a large array of signaling pathways.
However, based on genetic loss-of-function experiments, most studies have thus
far focused on the role of cell-autonomous gene function. Yet, cortical neuron
migration in situ is a complex process and migrating neurons traverse along diverse
cellular compartments and environments. The role of tissue-wide properties and
genetic state in radial neuron migration is however not clear. Here we utilized
mosaic analysis with double markers (MADM) technology to either sparsely or globally
delete gene function, followed by quantitative single-cell phenotyping. The MADM-based
gene ablation paradigms in combination with computational modeling demonstrated
that global tissue-wide effects predominate cell-autonomous gene function albeit
in a gene-specific manner. Our results thus suggest that the genetic landscape
in a tissue critically affects the overall migration phenotype of individual cortical
projection neurons. In a broader context, our findings imply that global tissue-wide
effects represent an essential component of the underlying etiology associated
with focal malformations of cortical development in particular, and neurological
diseases in general.
acknowledged_ssus:
- _id: LifeSc
- _id: PreCl
- _id: Bio
acknowledgement: "A.H.H. was a recipient of a DOC Fellowship (24812) of the Austrian
Academy of Sciences. This work also received support from IST Austria institutional
funds; the People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme (FP7/2007–2013) under REA grant agreement No 618444 to S.H.\r\nAPC
funding was obtained by IST Austria institutional funds.\r\nWe thank A. Sommer and
C. Czepe (VBCF GmbH, NGS Unit), L. Andersen, J. Sonntag and J. Renno for technical
support and/or initial experiments; M. Sixt, J. Nimpf and all members of the Hippenmeyer
lab for discussion. This research was supported by the Scientific Service Units
of IST Austria through resources provided by the Imaging and Optics Facility, Lab
Support Facility and Preclinical Facility."
article_number: kvac009
article_processing_charge: No
article_type: original
author:
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Michael
full_name: Riedl, Michael
id: 3BE60946-F248-11E8-B48F-1D18A9856A87
last_name: Riedl
orcid: 0000-0003-4844-6311
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Anna-Magdalena
full_name: Heger, Anna-Magdalena
id: 4B76FFD2-F248-11E8-B48F-1D18A9856A87
last_name: Heger
- first_name: Susanne
full_name: Laukoter, Susanne
id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87
last_name: Laukoter
orcid: 0000-0002-7903-3010
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Li Huei
full_name: Tsai, Li Huei
last_name: Tsai
- first_name: Thomas
full_name: Rülicke, Thomas
last_name: Rülicke
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Hansen AH, Pauler F, Riedl M, et al. Tissue-wide effects override cell-intrinsic
gene function in radial neuron migration. Oxford Open Neuroscience. 2022;1(1).
doi:10.1093/oons/kvac009
apa: Hansen, A. H., Pauler, F., Riedl, M., Streicher, C., Heger, A.-M., Laukoter,
S., … Hippenmeyer, S. (2022). Tissue-wide effects override cell-intrinsic gene
function in radial neuron migration. Oxford Open Neuroscience. Oxford Academic.
https://doi.org/10.1093/oons/kvac009
chicago: Hansen, Andi H, Florian Pauler, Michael Riedl, Carmen Streicher, Anna-Magdalena
Heger, Susanne Laukoter, Christoph M Sommer, et al. “Tissue-Wide Effects Override
Cell-Intrinsic Gene Function in Radial Neuron Migration.” Oxford Open Neuroscience.
Oxford Academic, 2022. https://doi.org/10.1093/oons/kvac009.
ieee: A. H. Hansen et al., “Tissue-wide effects override cell-intrinsic gene
function in radial neuron migration,” Oxford Open Neuroscience, vol. 1,
no. 1. Oxford Academic, 2022.
ista: Hansen AH, Pauler F, Riedl M, Streicher C, Heger A-M, Laukoter S, Sommer CM,
Nicolas A, Hof B, Tsai LH, Rülicke T, Hippenmeyer S. 2022. Tissue-wide effects
override cell-intrinsic gene function in radial neuron migration. Oxford Open
Neuroscience. 1(1), kvac009.
mla: Hansen, Andi H., et al. “Tissue-Wide Effects Override Cell-Intrinsic Gene Function
in Radial Neuron Migration.” Oxford Open Neuroscience, vol. 1, no. 1, kvac009,
Oxford Academic, 2022, doi:10.1093/oons/kvac009.
short: A.H. Hansen, F. Pauler, M. Riedl, C. Streicher, A.-M. Heger, S. Laukoter,
C.M. Sommer, A. Nicolas, B. Hof, L.H. Tsai, T. Rülicke, S. Hippenmeyer, Oxford
Open Neuroscience 1 (2022).
date_created: 2022-02-25T07:52:11Z
date_published: 2022-07-07T00:00:00Z
date_updated: 2023-11-30T10:55:12Z
day: '07'
ddc:
- '570'
department:
- _id: SiHi
- _id: BjHo
- _id: LifeSc
- _id: EM-Fac
doi: 10.1093/oons/kvac009
ec_funded: 1
file:
- access_level: open_access
checksum: 822e76e056c07099d1fb27d1ece5941b
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T08:00:30Z
date_updated: 2023-08-16T08:00:30Z
file_id: '14061'
file_name: 2023_OxfordOpenNeuroscience_Hansen.pdf
file_size: 4846551
relation: main_file
success: 1
file_date_updated: 2023-08-16T08:00:30Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
grant_number: '24812'
name: Molecular Mechanisms of Radial Neuronal Migration
publication: Oxford Open Neuroscience
publication_identifier:
eissn:
- 2753-149X
publication_status: published
publisher: Oxford Academic
quality_controlled: '1'
related_material:
record:
- id: '12726'
relation: dissertation_contains
status: public
- id: '14530'
relation: dissertation_contains
status: public
status: public
title: Tissue-wide effects override cell-intrinsic gene function in radial neuron
migration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2022'
...
---
_id: '10792'
abstract:
- lang: eng
text: "Background\r\nProper cerebral cortical development depends on the tightly
orchestrated migration of newly born neurons from the inner ventricular and subventricular
zones to the outer cortical plate. Any disturbance in this process during prenatal
stages may lead to neuronal migration disorders (NMDs), which can vary in extent
from focal to global. Furthermore, NMDs show a substantial comorbidity with other
neurodevelopmental disorders, notably autism spectrum disorders (ASDs). Our previous
work demonstrated focal neuronal migration defects in mice carrying loss-of-function
alleles of the recognized autism risk gene WDFY3. However, the cellular origins
of these defects in Wdfy3 mutant mice remain elusive and uncovering it will provide
critical insight into WDFY3-dependent disease pathology .\r\nMethods\r\nHere,
in an effort to untangle the origins of NMDs in Wdfy3lacZ mice, we employed mosaic
analysis with double markers (MADM). MADM technology enabled us to genetically
distinctly track and phenotypically analyze mutant and wild type cells concomitantly
in vivo using immunofluorescent techniques.\r\nResults\r\nWe revealed a cell autonomous
requirement of WDFY3 for accurate laminar positioning of cortical projection neurons
and elimination of mispositioned cells during early postnatal life. In addition,
we identified significant deviations in dendritic arborization, as well as synaptic
density and morphology between wild type, heterozygous, and homozygous Wdfy3 mutant
neurons in Wdfy3-MADM reporter mice at postnatal stages. Limitations While Wdfy3
mutant mice have provided valuable insight into prenatal aspects of ASD pathology
that remain inaccessible to investigation in humans, like most animal models,
they do not a perfectly replicate all aspects of human ASD biology. The lack of
human data makes it indeterminate whether morphological deviations described here
apply to ASD patients.\r\nConclusions\r\n\uFEFFOur genetic approach revealed several
cell autonomous requirements of Wdfy3 in neuronal development that could underly
the pathogenic mechanisms of WDFY3-related ASD conditions. The results are also
consistent with findings in other ASD animal models and patients and suggest an
important role for Wdfy3 in regulating neuronal function and interconnectivity
in postnatal life."
article_processing_charge: No
author:
- first_name: Zachary
full_name: Schaaf, Zachary
last_name: Schaaf
- first_name: Lyvin
full_name: Tat, Lyvin
last_name: Tat
- first_name: Noemi
full_name: Cannizzaro, Noemi
last_name: Cannizzaro
- first_name: Ralph
full_name: Green, Ralph
last_name: Green
- first_name: Thomas
full_name: Rülicke, Thomas
last_name: Rülicke
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: K
full_name: Zarbalis, K
last_name: Zarbalis
citation:
ama: Schaaf Z, Tat L, Cannizzaro N, et al. WDFY3 cell autonomously controls neuronal
migration. doi:10.21203/rs.3.rs-1316167/v1
apa: Schaaf, Z., Tat, L., Cannizzaro, N., Green, R., Rülicke, T., Hippenmeyer, S.,
& Zarbalis, K. (n.d.). WDFY3 cell autonomously controls neuronal migration.
Research Square. https://doi.org/10.21203/rs.3.rs-1316167/v1
chicago: Schaaf, Zachary, Lyvin Tat, Noemi Cannizzaro, Ralph Green, Thomas Rülicke,
Simon Hippenmeyer, and K Zarbalis. “WDFY3 Cell Autonomously Controls Neuronal
Migration.” Research Square, n.d. https://doi.org/10.21203/rs.3.rs-1316167/v1.
ieee: Z. Schaaf et al., “WDFY3 cell autonomously controls neuronal migration.”
Research Square.
ista: Schaaf Z, Tat L, Cannizzaro N, Green R, Rülicke T, Hippenmeyer S, Zarbalis
K. WDFY3 cell autonomously controls neuronal migration. 10.21203/rs.3.rs-1316167/v1.
mla: Schaaf, Zachary, et al. WDFY3 Cell Autonomously Controls Neuronal Migration.
Research Square, doi:10.21203/rs.3.rs-1316167/v1.
short: Z. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K.
Zarbalis, (n.d.).
date_created: 2022-02-25T07:53:26Z
date_published: 2022-02-16T00:00:00Z
date_updated: 2023-10-17T13:06:52Z
day: '16'
department:
- _id: SiHi
doi: 10.21203/rs.3.rs-1316167/v1
external_id:
pmid:
- PPR454733
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.21203/rs.3.rs-1316167/v1
month: '02'
oa: 1
oa_version: Preprint
page: '30'
pmid: 1
publication_identifier:
eissn:
- 2693-5015
publication_status: submitted
publisher: Research Square
status: public
title: WDFY3 cell autonomously controls neuronal migration
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '10797'
abstract:
- lang: eng
text: We consider symmetric partial exclusion and inclusion processes in a general
graph in contact with reservoirs, where we allow both for edge disorder and well-chosen
site disorder. We extend the classical dualities to this context and then we derive
new orthogonal polynomial dualities. From the classical dualities, we derive the
uniqueness of the non-equilibrium steady state and obtain correlation inequalities.
Starting from the orthogonal polynomial dualities, we show universal properties
of n-point correlation functions in the non-equilibrium steady state for systems
with at most two different reservoir parameters, such as a chain with reservoirs
at left and right ends.
- lang: fre
text: Nous considérons des processus d’exclusion partielle, et des processus d’inclusion
sur un graphe général en contact avec des réservoirs. Nous autorisons la présence
de inhomogenéités sur les arrêts ainsi que sur les sommets du graph. Nous généralisons
les “dualités classiques” dans ce contexte et nous démontrons des nouvelles dualités
orthogonales. À partir des dualités classiques, nous démontrons l’unicité de l’état
stationnaire non-équilibre, ainsi que des inégalités de corrélation. À partir
des dualités orthogonales nous démontrons des propriétés universelles des fonctions
de corrélation à n points dans l’état stationnaire non-équilibre pour des systèmes
avec deux paramètres de réservoirs inégaux, comme par exemple une chaîne avec
des réservoirs à droite et à gauche.
acknowledgement: The authors would like to thank Gioia Carinci and Cristian Giardinà
for useful discussions. F.R. and S.F. thank Jean-René Chazottes for a stay at CPHT
(Institut Polytechnique de Paris), in the realm of Chaire d’Alembert (Paris-Saclay
University), where part of this work was performed. S.F. acknowledges Simona Villa
for her support in creating the picture. S.F. acknowledges financial support from
NWO via the grant TOP1.17.019. F.S. acknowledges financial support from the European
Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie
grant agreement No. 754411.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Simone
full_name: Floreani, Simone
last_name: Floreani
- first_name: Frank
full_name: Redig, Frank
last_name: Redig
- first_name: Federico
full_name: Sau, Federico
id: E1836206-9F16-11E9-8814-AEFDE5697425
last_name: Sau
citation:
ama: Floreani S, Redig F, Sau F. Orthogonal polynomial duality of boundary driven
particle systems and non-equilibrium correlations. Annales de l’institut Henri
Poincare (B) Probability and Statistics. 2022;58(1):220-247. doi:10.1214/21-AIHP1163
apa: Floreani, S., Redig, F., & Sau, F. (2022). Orthogonal polynomial duality
of boundary driven particle systems and non-equilibrium correlations. Annales
de l’institut Henri Poincare (B) Probability and Statistics. Institute of
Mathematical Statistics. https://doi.org/10.1214/21-AIHP1163
chicago: Floreani, Simone, Frank Redig, and Federico Sau. “Orthogonal Polynomial
Duality of Boundary Driven Particle Systems and Non-Equilibrium Correlations.”
Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute
of Mathematical Statistics, 2022. https://doi.org/10.1214/21-AIHP1163.
ieee: S. Floreani, F. Redig, and F. Sau, “Orthogonal polynomial duality of boundary
driven particle systems and non-equilibrium correlations,” Annales de l’institut
Henri Poincare (B) Probability and Statistics, vol. 58, no. 1. Institute of
Mathematical Statistics, pp. 220–247, 2022.
ista: Floreani S, Redig F, Sau F. 2022. Orthogonal polynomial duality of boundary
driven particle systems and non-equilibrium correlations. Annales de l’institut
Henri Poincare (B) Probability and Statistics. 58(1), 220–247.
mla: Floreani, Simone, et al. “Orthogonal Polynomial Duality of Boundary Driven
Particle Systems and Non-Equilibrium Correlations.” Annales de l’institut Henri
Poincare (B) Probability and Statistics, vol. 58, no. 1, Institute of Mathematical
Statistics, 2022, pp. 220–47, doi:10.1214/21-AIHP1163.
short: S. Floreani, F. Redig, F. Sau, Annales de l’institut Henri Poincare (B) Probability
and Statistics 58 (2022) 220–247.
date_created: 2022-02-27T23:01:50Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2023-10-17T12:49:43Z
day: '01'
department:
- _id: JaMa
doi: 10.1214/21-AIHP1163
ec_funded: 1
external_id:
arxiv:
- '2007.08272'
isi:
- '000752489300010'
intvolume: ' 58'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2007.08272
month: '02'
oa: 1
oa_version: Preprint
page: 220-247
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Annales de l'institut Henri Poincare (B) Probability and Statistics
publication_identifier:
issn:
- 0246-0203
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium
correlations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2022'
...
---
_id: '10799'
abstract:
- lang: eng
text: "Because of the increasing popularity of machine learning methods, it is becoming
important to understand the impact of learned components on automated decision-making
systems and to guarantee that their consequences are beneficial to society. In
other words, it is necessary to ensure that machine learning is sufficiently trustworthy
to be used in real-world applications. This thesis studies two properties of machine
learning models that are highly desirable for the\r\nsake of reliability: robustness
and fairness. In the first part of the thesis we study the robustness of learning
algorithms to training data corruption. Previous work has shown that machine learning
models are vulnerable to a range\r\nof training set issues, varying from label
noise through systematic biases to worst-case data manipulations. This is an especially
relevant problem from a present perspective, since modern machine learning methods
are particularly data hungry and therefore practitioners often have to rely on
data collected from various external sources, e.g. from the Internet, from app
users or via crowdsourcing. Naturally, such sources vary greatly in the quality
and reliability of the\r\ndata they provide. With these considerations in mind,
we study the problem of designing machine learning algorithms that are robust
to corruptions in data coming from multiple sources. We show that, in contrast
to the case of a single dataset with outliers, successful learning within this
model is possible both theoretically and practically, even under worst-case data
corruptions. The second part of this thesis deals with fairness-aware machine
learning. There are multiple areas where machine learning models have shown promising
results, but where careful considerations are required, in order to avoid discrimanative
decisions taken by such learned components. Ensuring fairness can be particularly
challenging, because real-world training datasets are expected to contain various
forms of historical bias that may affect the learning process. In this thesis
we show that data corruption can indeed render the problem of achieving fairness
impossible, by tightly characterizing the theoretical limits of fair learning
under worst-case data manipulations. However, assuming access to clean data, we
also show how fairness-aware learning can be made practical in contexts beyond
binary classification, in particular in the challenging learning to rank setting."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nikola H
full_name: Konstantinov, Nikola H
id: 4B9D76E4-F248-11E8-B48F-1D18A9856A87
last_name: Konstantinov
citation:
ama: Konstantinov NH. Robustness and fairness in machine learning. 2022. doi:10.15479/at:ista:10799
apa: Konstantinov, N. H. (2022). Robustness and fairness in machine learning.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10799
chicago: Konstantinov, Nikola H. “Robustness and Fairness in Machine Learning.”
Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10799.
ieee: N. H. Konstantinov, “Robustness and fairness in machine learning,” Institute
of Science and Technology Austria, 2022.
ista: Konstantinov NH. 2022. Robustness and fairness in machine learning. Institute
of Science and Technology Austria.
mla: Konstantinov, Nikola H. Robustness and Fairness in Machine Learning.
Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10799.
short: N.H. Konstantinov, Robustness and Fairness in Machine Learning, Institute
of Science and Technology Austria, 2022.
date_created: 2022-02-28T13:03:49Z
date_published: 2022-03-08T00:00:00Z
date_updated: 2023-10-17T12:31:54Z
day: '08'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: ChLa
doi: 10.15479/at:ista:10799
ec_funded: 1
file:
- access_level: open_access
checksum: 626bc523ae8822d20e635d0e2d95182e
content_type: application/pdf
creator: nkonstan
date_created: 2022-03-06T11:42:54Z
date_updated: 2022-03-06T11:42:54Z
file_id: '10823'
file_name: thesis.pdf
file_size: 4204905
relation: main_file
success: 1
- access_level: closed
checksum: e2ca2b88350ac8ea1515b948885cbcb1
content_type: application/x-zip-compressed
creator: nkonstan
date_created: 2022-03-06T11:42:57Z
date_updated: 2022-03-10T12:11:48Z
file_id: '10824'
file_name: thesis.zip
file_size: 22841103
relation: source_file
file_date_updated: 2022-03-10T12:11:48Z
has_accepted_license: '1'
keyword:
- robustness
- fairness
- machine learning
- PAC learning
- adversarial learning
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '176'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-015-2
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8724'
relation: part_of_dissertation
status: public
- id: '10803'
relation: part_of_dissertation
status: public
- id: '10802'
relation: part_of_dissertation
status: public
- id: '6590'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
title: Robustness and fairness in machine learning
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2022'
...
---
_id: '10802'
abstract:
- lang: eng
text: "Addressing fairness concerns about machine learning models is a crucial step
towards their long-term adoption in real-world automated systems. While many approaches
have been developed for training fair models from data, little is known about
the robustness of these methods to data corruption. In this work we consider fairness-aware
learning under worst-case data manipulations. We show that an adversary can in
some situations force any learner to return an overly biased classifier, regardless
of the sample size and with or without degrading\r\naccuracy, and that the strength
of the excess bias increases for learning problems with underrepresented protected
groups in the data. We also prove that our hardness results are tight up to constant
factors. To this end, we study two natural learning algorithms that optimize for
both accuracy and fairness and show that these algorithms enjoy guarantees that
are order-optimal in terms of the corruption ratio and the protected groups frequencies
in the large data\r\nlimit."
acknowledgement: The authors thank Eugenia Iofinova and Bernd Prach for providing
feedback on early versions of this paper. This publication was made possible by
an ETH AI Center postdoctoral fellowship to Nikola Konstantinov.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nikola H
full_name: Konstantinov, Nikola H
id: 4B9D76E4-F248-11E8-B48F-1D18A9856A87
last_name: Konstantinov
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0002-4561-241X
citation:
ama: Konstantinov NH, Lampert C. Fairness-aware PAC learning from corrupted data.
Journal of Machine Learning Research. 2022;23:1-60.
apa: Konstantinov, N. H., & Lampert, C. (2022). Fairness-aware PAC learning
from corrupted data. Journal of Machine Learning Research. ML Research
Press.
chicago: Konstantinov, Nikola H, and Christoph Lampert. “Fairness-Aware PAC Learning
from Corrupted Data.” Journal of Machine Learning Research. ML Research
Press, 2022.
ieee: N. H. Konstantinov and C. Lampert, “Fairness-aware PAC learning from corrupted
data,” Journal of Machine Learning Research, vol. 23. ML Research Press,
pp. 1–60, 2022.
ista: Konstantinov NH, Lampert C. 2022. Fairness-aware PAC learning from corrupted
data. Journal of Machine Learning Research. 23, 1–60.
mla: Konstantinov, Nikola H., and Christoph Lampert. “Fairness-Aware PAC Learning
from Corrupted Data.” Journal of Machine Learning Research, vol. 23, ML
Research Press, 2022, pp. 1–60.
short: N.H. Konstantinov, C. Lampert, Journal of Machine Learning Research 23 (2022)
1–60.
date_created: 2022-02-28T14:05:42Z
date_published: 2022-05-01T00:00:00Z
date_updated: 2023-09-26T10:44:37Z
day: '01'
ddc:
- '004'
department:
- _id: ChLa
external_id:
arxiv:
- '2102.06004'
file:
- access_level: open_access
checksum: 9cac897b54a0ddf3a553a2c33e88cfda
content_type: application/pdf
creator: kschuh
date_created: 2022-07-12T15:08:28Z
date_updated: 2022-07-12T15:08:28Z
file_id: '11570'
file_name: 2022_JournalMachineLearningResearch_Konstantinov.pdf
file_size: 551862
relation: main_file
success: 1
file_date_updated: 2022-07-12T15:08:28Z
has_accepted_license: '1'
intvolume: ' 23'
keyword:
- Fairness
- robustness
- data poisoning
- trustworthy machine learning
- PAC learning
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1-60
publication: Journal of Machine Learning Research
publication_identifier:
eissn:
- 1533-7928
issn:
- 1532-4435
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
record:
- id: '10799'
relation: dissertation_contains
status: public
- id: '13241'
relation: shorter_version
status: public
scopus_import: '1'
status: public
title: Fairness-aware PAC learning from corrupted data
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2022'
...
---
_id: '10812'
abstract:
- lang: eng
text: Several promising strategies based on combining or cycling different antibiotics
have been proposed to increase efficacy and counteract resistance evolution, but
we still lack a deep understanding of the physiological responses and genetic
mechanisms that underlie antibiotic interactions and the clinical applicability
of these strategies. In antibiotic-exposed bacteria, the combined effects of physiological
stress responses and emerging resistance mutations (occurring at different time
scales) generate complex and often unpredictable dynamics. In this Review, we
present our current understanding of bacterial cell physiology and genetics of
responses to antibiotics. We emphasize recently discovered mechanisms of synergistic
and antagonistic drug interactions, hysteresis in temporal interactions between
antibiotics that arise from microbial physiology and interactions between antibiotics
and resistance mutations that can cause collateral sensitivity or cross-resistance.
We discuss possible connections between the different phenomena and indicate relevant
research directions. A better and more unified understanding of drug and genetic
interactions is likely to advance antibiotic therapy.
acknowledgement: The authors thank B. Kavčič and H. Schulenburg for constructive feedback
on the manuscript.
article_processing_charge: No
article_type: review
author:
- first_name: Roderich
full_name: Römhild, Roderich
id: 68E56E44-62B0-11EA-B963-444F3DDC885E
last_name: Römhild
orcid: 0000-0001-9480-5261
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Dan I.
full_name: Andersson, Dan I.
last_name: Andersson
citation:
ama: Römhild R, Bollenbach MT, Andersson DI. The physiology and genetics of bacterial
responses to antibiotic combinations. Nature Reviews Microbiology. 2022;20:478-490.
doi:10.1038/s41579-022-00700-5
apa: Römhild, R., Bollenbach, M. T., & Andersson, D. I. (2022). The physiology
and genetics of bacterial responses to antibiotic combinations. Nature Reviews
Microbiology. Springer Nature. https://doi.org/10.1038/s41579-022-00700-5
chicago: Römhild, Roderich, Mark Tobias Bollenbach, and Dan I. Andersson. “The Physiology
and Genetics of Bacterial Responses to Antibiotic Combinations.” Nature Reviews
Microbiology. Springer Nature, 2022. https://doi.org/10.1038/s41579-022-00700-5.
ieee: R. Römhild, M. T. Bollenbach, and D. I. Andersson, “The physiology and genetics
of bacterial responses to antibiotic combinations,” Nature Reviews Microbiology,
vol. 20. Springer Nature, pp. 478–490, 2022.
ista: Römhild R, Bollenbach MT, Andersson DI. 2022. The physiology and genetics
of bacterial responses to antibiotic combinations. Nature Reviews Microbiology.
20, 478–490.
mla: Römhild, Roderich, et al. “The Physiology and Genetics of Bacterial Responses
to Antibiotic Combinations.” Nature Reviews Microbiology, vol. 20, Springer
Nature, 2022, pp. 478–90, doi:10.1038/s41579-022-00700-5.
short: R. Römhild, M.T. Bollenbach, D.I. Andersson, Nature Reviews Microbiology
20 (2022) 478–490.
date_created: 2022-03-04T04:33:49Z
date_published: 2022-08-01T00:00:00Z
date_updated: 2023-08-02T14:41:44Z
day: '01'
department:
- _id: CaGu
doi: 10.1038/s41579-022-00700-5
external_id:
isi:
- '000763891900001'
pmid:
- '35241807'
intvolume: ' 20'
isi: 1
keyword:
- General Immunology and Microbiology
- Microbiology
- Infectious Diseases
language:
- iso: eng
month: '08'
oa_version: None
page: 478-490
pmid: 1
publication: Nature Reviews Microbiology
publication_identifier:
eissn:
- 1740-1534
issn:
- 1740-1526
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The physiology and genetics of bacterial responses to antibiotic combinations
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 20
year: '2022'
...
---
_id: '10813'
abstract:
- lang: eng
text: Redox mediators could catalyse otherwise slow and energy-inefficient cycling
of Li–S and Li–O2 batteries by shuttling electrons or holes between the electrode
and the solid insulating storage materials. For mediators to work efficiently
they need to oxidize the solid with fast kinetics but with the lowest possible
overpotential. However, the dependence of kinetics and overpotential is unclear,
which hinders informed improvement. Here, we find that when the redox potentials
of mediators are tuned via, for example, Li+ concentration in the electrolyte,
they exhibit distinct threshold potentials, where the kinetics accelerate several-fold
within a range as small as 10 mV. This phenomenon is independent of types of mediator
and electrolyte. The acceleration originates from the overpotentials required
to activate fast Li+/e− extraction and the following chemical step at specific
abundant surface facets. Efficient redox catalysis at insulating solids therefore
requires careful consideration of the surface conditions of the storage materials
and electrolyte-dependent redox potentials, which may be tuned by salt concentrations
or solvents.
acknowledgement: This work was financially supported by the National Natural Science
Foundation of China (grant nos. 51773092, 21975124, 11874254, 51802187 and U2030206).
It was further supported by Fujian science & technology innovation laboratory for
energy devices of China (21C-LAB), Key Research Project of Zhejiang Laboratory (grant
no. 2021PE0AC02) and the Cultivation Program for the Excellent Doctoral Dissertation
of Nanjing Tech University. S.A.F. is indebted to IST Austria for support.
article_processing_charge: No
article_type: original
author:
- first_name: Deqing
full_name: Cao, Deqing
last_name: Cao
- first_name: Xiaoxiao
full_name: Shen, Xiaoxiao
last_name: Shen
- first_name: Aiping
full_name: Wang, Aiping
last_name: Wang
- first_name: Fengjiao
full_name: Yu, Fengjiao
last_name: Yu
- first_name: Yuping
full_name: Wu, Yuping
last_name: Wu
- first_name: Siqi
full_name: Shi, Siqi
last_name: Shi
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Yuhui
full_name: Chen, Yuhui
last_name: Chen
citation:
ama: Cao D, Shen X, Wang A, et al. Threshold potentials for fast kinetics during
mediated redox catalysis of insulators in Li–O2 and Li–S batteries. Nature
Catalysis. 2022;5:193-201. doi:10.1038/s41929-022-00752-z
apa: Cao, D., Shen, X., Wang, A., Yu, F., Wu, Y., Shi, S., … Chen, Y. (2022). Threshold
potentials for fast kinetics during mediated redox catalysis of insulators in
Li–O2 and Li–S batteries. Nature Catalysis. Springer Nature. https://doi.org/10.1038/s41929-022-00752-z
chicago: Cao, Deqing, Xiaoxiao Shen, Aiping Wang, Fengjiao Yu, Yuping Wu, Siqi Shi,
Stefan Alexander Freunberger, and Yuhui Chen. “Threshold Potentials for Fast Kinetics
during Mediated Redox Catalysis of Insulators in Li–O2 and Li–S Batteries.” Nature
Catalysis. Springer Nature, 2022. https://doi.org/10.1038/s41929-022-00752-z.
ieee: D. Cao et al., “Threshold potentials for fast kinetics during mediated
redox catalysis of insulators in Li–O2 and Li–S batteries,” Nature Catalysis,
vol. 5. Springer Nature, pp. 193–201, 2022.
ista: Cao D, Shen X, Wang A, Yu F, Wu Y, Shi S, Freunberger SA, Chen Y. 2022. Threshold
potentials for fast kinetics during mediated redox catalysis of insulators in
Li–O2 and Li–S batteries. Nature Catalysis. 5, 193–201.
mla: Cao, Deqing, et al. “Threshold Potentials for Fast Kinetics during Mediated
Redox Catalysis of Insulators in Li–O2 and Li–S Batteries.” Nature Catalysis,
vol. 5, Springer Nature, 2022, pp. 193–201, doi:10.1038/s41929-022-00752-z.
short: D. Cao, X. Shen, A. Wang, F. Yu, Y. Wu, S. Shi, S.A. Freunberger, Y. Chen,
Nature Catalysis 5 (2022) 193–201.
date_created: 2022-03-04T07:50:10Z
date_published: 2022-03-03T00:00:00Z
date_updated: 2023-10-17T13:06:28Z
day: '03'
department:
- _id: StFr
doi: 10.1038/s41929-022-00752-z
external_id:
isi:
- '000763879400001'
intvolume: ' 5'
isi: 1
keyword:
- Process Chemistry and Technology
- Biochemistry
- Bioengineering
- Catalysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.21203/rs.3.rs-750965/v1
month: '03'
oa: 1
oa_version: Preprint
page: 193-201
publication: Nature Catalysis
publication_identifier:
issn:
- 2520-1158
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '9978'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Threshold potentials for fast kinetics during mediated redox catalysis of insulators
in Li–O2 and Li–S batteries
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2022'
...
---
_id: '10818'
abstract:
- lang: eng
text: Microglia cells are active players in regulating synaptic development and
plasticity in the brain. However, how they influence the normal functioning of
synapses is largely unknown. In this study, we characterized the effects of pharmacological
microglia depletion, achieved by administration of PLX5622, on hippocampal CA3-CA1
synapses of adult wild type mice. Following microglial depletion, we observed
a reduction of spontaneous and evoked glutamatergic activity associated with a
decrease of dendritic spine density. We also observed the appearance of immature
synaptic features and higher levels of plasticity. Microglia depleted mice showed
a deficit in the acquisition of the Novel Object Recognition task. These events
were accompanied by hippocampal astrogliosis, although in the absence ofneuroinflammatory
condition. PLX-induced synaptic changes were absent in Cx3cr1−/− mice, highlighting
the role of CX3CL1/CX3CR1 axis in microglia control of synaptic functioning. Remarkably,
microglia repopulation after PLX5622 withdrawal was associated with the recovery
of hippocampal synapses and learning functions. Altogether, these data demonstrate
that microglia contribute to normal synaptic functioning in the adult brain and
that their removal induces reversible changes in organization and activity of
glutamatergic synapses.
acknowledgement: The work was supported by a grant from MIUR (PRIN 2017HPTFFC_003)
to Davide Ragozzino and in part by funds to Silvia Di Angelantonio (CrestOptics-IIT
JointLab for Advanced Microscopy) and Daniele Caprioli (Istituto Pasteur-Fondazione
Cenci Bolognetti). Bernadette Basilico, and Laura Ferrucci were supported by the
PhD program in Clinical-Experimental Neuroscience and Psychiatry, Sapienza University,
Rome; Caterina Sanchini was supported by the PhD program in Life Science, Sapienza
University, Rome and by the Italian Institute of Technology, Rome. The authors thank
Alessandro Felici, Claudia Valeri, Arsenio Armagno, and Senthilkumar Deivasigamani
for help with animal husbandry and transgenic colonies management. They also wish
to thank Piotr Bregestovski and Michal Schwartz for helpful discussions and criticism.
PLX5622 was provided under Materials Transfer Agreement by Plexxikon Inc. (Berkeley,
CA). Open Access Funding provided by Universita degli Studi di Roma La Sapienza
within the CRUI-CARE Agreement.
article_processing_charge: No
article_type: original
author:
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Laura
full_name: Ferrucci, Laura
last_name: Ferrucci
- first_name: Patrizia
full_name: Ratano, Patrizia
last_name: Ratano
- first_name: Maria T.
full_name: Golia, Maria T.
last_name: Golia
- first_name: Alfonso
full_name: Grimaldi, Alfonso
last_name: Grimaldi
- first_name: Maria
full_name: Rosito, Maria
last_name: Rosito
- first_name: Valentina
full_name: Ferretti, Valentina
last_name: Ferretti
- first_name: Ingrid
full_name: Reverte, Ingrid
last_name: Reverte
- first_name: Caterina
full_name: Sanchini, Caterina
last_name: Sanchini
- first_name: Maria C.
full_name: Marrone, Maria C.
last_name: Marrone
- first_name: Maria
full_name: Giubettini, Maria
last_name: Giubettini
- first_name: Valeria
full_name: De Turris, Valeria
last_name: De Turris
- first_name: Debora
full_name: Salerno, Debora
last_name: Salerno
- first_name: Stefano
full_name: Garofalo, Stefano
last_name: Garofalo
- first_name: Marie‐Kim
full_name: St‐Pierre, Marie‐Kim
last_name: St‐Pierre
- first_name: Micael
full_name: Carrier, Micael
last_name: Carrier
- first_name: Massimiliano
full_name: Renzi, Massimiliano
last_name: Renzi
- first_name: Francesca
full_name: Pagani, Francesca
last_name: Pagani
- first_name: Brijesh
full_name: Modi, Brijesh
last_name: Modi
- first_name: Marcello
full_name: Raspa, Marcello
last_name: Raspa
- first_name: Ferdinando
full_name: Scavizzi, Ferdinando
last_name: Scavizzi
- first_name: Cornelius T.
full_name: Gross, Cornelius T.
last_name: Gross
- first_name: Silvia
full_name: Marinelli, Silvia
last_name: Marinelli
- first_name: Marie‐Ève
full_name: Tremblay, Marie‐Ève
last_name: Tremblay
- first_name: Daniele
full_name: Caprioli, Daniele
last_name: Caprioli
- first_name: Laura
full_name: Maggi, Laura
last_name: Maggi
- first_name: Cristina
full_name: Limatola, Cristina
last_name: Limatola
- first_name: Silvia
full_name: Di Angelantonio, Silvia
last_name: Di Angelantonio
- first_name: Davide
full_name: Ragozzino, Davide
last_name: Ragozzino
citation:
ama: Basilico B, Ferrucci L, Ratano P, et al. Microglia control glutamatergic synapses
in the adult mouse hippocampus. Glia. 2022;70(1):173-195. doi:10.1002/glia.24101
apa: Basilico, B., Ferrucci, L., Ratano, P., Golia, M. T., Grimaldi, A., Rosito,
M., … Ragozzino, D. (2022). Microglia control glutamatergic synapses in the adult
mouse hippocampus. Glia. Wiley. https://doi.org/10.1002/glia.24101
chicago: Basilico, Bernadette, Laura Ferrucci, Patrizia Ratano, Maria T. Golia,
Alfonso Grimaldi, Maria Rosito, Valentina Ferretti, et al. “Microglia Control
Glutamatergic Synapses in the Adult Mouse Hippocampus.” Glia. Wiley, 2022.
https://doi.org/10.1002/glia.24101.
ieee: B. Basilico et al., “Microglia control glutamatergic synapses in the
adult mouse hippocampus,” Glia, vol. 70, no. 1. Wiley, pp. 173–195, 2022.
ista: Basilico B, Ferrucci L, Ratano P, Golia MT, Grimaldi A, Rosito M, Ferretti
V, Reverte I, Sanchini C, Marrone MC, Giubettini M, De Turris V, Salerno D, Garofalo
S, St‐Pierre M, Carrier M, Renzi M, Pagani F, Modi B, Raspa M, Scavizzi F, Gross
CT, Marinelli S, Tremblay M, Caprioli D, Maggi L, Limatola C, Di Angelantonio
S, Ragozzino D. 2022. Microglia control glutamatergic synapses in the adult mouse
hippocampus. Glia. 70(1), 173–195.
mla: Basilico, Bernadette, et al. “Microglia Control Glutamatergic Synapses in the
Adult Mouse Hippocampus.” Glia, vol. 70, no. 1, Wiley, 2022, pp. 173–95,
doi:10.1002/glia.24101.
short: B. Basilico, L. Ferrucci, P. Ratano, M.T. Golia, A. Grimaldi, M. Rosito,
V. Ferretti, I. Reverte, C. Sanchini, M.C. Marrone, M. Giubettini, V. De Turris,
D. Salerno, S. Garofalo, M. St‐Pierre, M. Carrier, M. Renzi, F. Pagani, B. Modi,
M. Raspa, F. Scavizzi, C.T. Gross, S. Marinelli, M. Tremblay, D. Caprioli, L.
Maggi, C. Limatola, S. Di Angelantonio, D. Ragozzino, Glia 70 (2022) 173–195.
date_created: 2022-03-04T08:53:37Z
date_published: 2022-01-01T00:00:00Z
date_updated: 2023-09-05T16:01:23Z
day: '01'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1002/glia.24101
external_id:
isi:
- '000708025800001'
pmid:
- '34661306'
file:
- access_level: open_access
checksum: f10a897290e66c0a062e04ba91db6c17
content_type: application/pdf
creator: dernst
date_created: 2022-03-04T08:55:27Z
date_updated: 2022-03-04T08:55:27Z
file_id: '10819'
file_name: 2021_Glia_Basilico.pdf
file_size: 5340294
relation: main_file
success: 1
file_date_updated: 2022-03-04T08:55:27Z
has_accepted_license: '1'
intvolume: ' 70'
isi: 1
issue: '1'
keyword:
- Cellular and Molecular Neuroscience
- Neurology
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 173-195
pmid: 1
publication: Glia
publication_identifier:
eissn:
- 1098-1136
issn:
- 0894-1491
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Microglia control glutamatergic synapses in the adult mouse hippocampus
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 70
year: '2022'
...
---
_id: '10820'
abstract:
- lang: eng
text: Streaky structures in the boundary layers are often generated by surface roughness
elements and/or free-stream turbulence, and are known to have significant effects
on boundary-layer instability. In this paper, we investigate the impact of two
forms of streaks on the instability of supersonic boundary layers. The first concerns
the streaks generated by an array of spanwise periodic and streamwise elongated
surface roughness elements, and our interest is how these streaks influence the
lower-branch viscous first modes, whose characteristic wavelength and frequency
are on the classical triple-deck scales. By adapting the triple-deck theory in
the incompressible regime to the supersonic one, we first derived a simplified
system which allows for efficient calculation of the streaks. The asymptotic analysis
simplifies a bi-global eigenvalue problem to a one-dimensional problem in the
spanwise direction, showing that the instability is controlled at leading order
solely by the spanwise-dependent wall shear. In the fundamental configuration,
the streaks stabilize first modes at low frequencies but destabilize the high-frequency
ones. In the subharmonic configuration, the streaks generally destabilize the
first mode across the entire frequency band. Importantly, the spanwise even modes
are of radiating nature, i.e. they emit acoustic waves spontaneously to the far
field. Streaks of the second form are generated by low-frequency vortical disturbances
representing free-stream turbulence. They alter the flow in the entire layer and
their effects on instability are investigated by solving the inviscid bi-global
eigenvalue problem. Different from the incompressible case, a multitude of compressible
instability modes exists, of which the dominant mode is an inviscid instability
associated with the spanwise shear. In addition, there exists a separate branch
of instability modes that have smaller growth rates but are spontaneously radiating.
acknowledgement: The work is supported by the National Key Research and Development
Program of China (No. 2016YFA0401200), the National Natural Science Foundation of
China (Grant Nos. 91952202 and 11402167).
article_processing_charge: No
author:
- first_name: Jianxin
full_name: Liu, Jianxin
last_name: Liu
- first_name: Elena
full_name: Marensi, Elena
id: 0BE7553A-1004-11EA-B805-18983DDC885E
last_name: Marensi
- first_name: Xuesong
full_name: Wu, Xuesong
last_name: Wu
citation:
ama: 'Liu J, Marensi E, Wu X. Effects of streaky structures on the instability of
supersonic boundary layers. In: Sherwin S, Schmid P, Wu X, eds. IUTAM Laminar-Turbulent
Transition. Vol 38. 1st ed. IUTAM Bookseries. Cham: Springer Nature; 2022:587-598.
doi:10.1007/978-3-030-67902-6_51'
apa: 'Liu, J., Marensi, E., & Wu, X. (2022). Effects of streaky structures on
the instability of supersonic boundary layers. In S. Sherwin, P. Schmid, &
X. Wu (Eds.), IUTAM Laminar-Turbulent Transition (1st ed., Vol. 38, pp.
587–598). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-67902-6_51'
chicago: 'Liu, Jianxin, Elena Marensi, and Xuesong Wu. “Effects of Streaky Structures
on the Instability of Supersonic Boundary Layers.” In IUTAM Laminar-Turbulent
Transition, edited by Spencer Sherwin, Peter Schmid, and Xuesong Wu, 1st ed.,
38:587–98. IUTAM Bookseries. Cham: Springer Nature, 2022. https://doi.org/10.1007/978-3-030-67902-6_51.'
ieee: 'J. Liu, E. Marensi, and X. Wu, “Effects of streaky structures on the instability
of supersonic boundary layers,” in IUTAM Laminar-Turbulent Transition,
1st ed., vol. 38, S. Sherwin, P. Schmid, and X. Wu, Eds. Cham: Springer Nature,
2022, pp. 587–598.'
ista: 'Liu J, Marensi E, Wu X. 2022.Effects of streaky structures on the instability
of supersonic boundary layers. In: IUTAM Laminar-Turbulent Transition. vol. 38,
587–598.'
mla: Liu, Jianxin, et al. “Effects of Streaky Structures on the Instability of Supersonic
Boundary Layers.” IUTAM Laminar-Turbulent Transition, edited by Spencer
Sherwin et al., 1st ed., vol. 38, Springer Nature, 2022, pp. 587–98, doi:10.1007/978-3-030-67902-6_51.
short: J. Liu, E. Marensi, X. Wu, in:, S. Sherwin, P. Schmid, X. Wu (Eds.), IUTAM
Laminar-Turbulent Transition, 1st ed., Springer Nature, Cham, 2022, pp. 587–598.
conference:
end_date: 2019-09-06
location: London, United Kingdom
name: IUTAM Symposium
start_date: 2019-09-02
date_created: 2022-03-04T09:14:34Z
date_published: 2022-01-01T00:00:00Z
date_updated: 2023-08-03T12:54:59Z
day: '01'
department:
- _id: BjHo
doi: 10.1007/978-3-030-67902-6_51
edition: '1'
editor:
- first_name: Spencer
full_name: Sherwin, Spencer
last_name: Sherwin
- first_name: Peter
full_name: Schmid, Peter
last_name: Schmid
- first_name: Xuesong
full_name: Wu, Xuesong
last_name: Wu
external_id:
isi:
- '000709087600051'
intvolume: ' 38'
isi: 1
language:
- iso: eng
month: '01'
oa_version: None
page: 587-598
place: Cham
publication: IUTAM Laminar-Turbulent Transition
publication_identifier:
eisbn:
- '9783030679026'
eissn:
- 1875-3493
isbn:
- '9783030679019'
issn:
- 1875-3507
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: IUTAM Bookseries
status: public
title: Effects of streaky structures on the instability of supersonic boundary layers
type: book_chapter
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 38
year: '2022'
...
---
_id: '10821'
abstract:
- lang: eng
text: 'Rhythmical cortical activity has long been recognized as a pillar in the
architecture of brain functions. Yet, the dynamic organization of its underlying
neuronal population activity remains elusive. Here we uncover a unique organizational
principle regulating collective neural dynamics associated with the alpha rhythm
in the awake resting-state. We demonstrate that cascades of neural activity obey
attenuation-amplification dynamics (AAD), with a transition from the attenuation
regime—within alpha cycles—to the amplification regime—across a few alpha cycles—that
correlates with the characteristic frequency of the alpha rhythm. We find that
this short-term AAD is part of a large-scale, size-dependent temporal structure
of neural cascades that obeys the Omori law: Following large cascades, smaller
cascades occur at a rate that decays as a power-law of the time elapsed from such
events—a long-term AAD regulating brain activity over the timescale of seconds.
We show that such an organization corresponds to the "waxing and waning" of the
alpha rhythm. Importantly, we observe that short- and long-term AAD are unique
to the awake resting-state, being absent during NREM sleep. These results provide
a quantitative, dynamical description of the so-far-qualitative notion of the
"waxing and waning" phenomenon, and suggest the AAD as a key principle governing
resting-state dynamics across timescales.'
acknowledgement: FL acknowledges support from the European Union’s Horizon 2020 research
and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411.
LdA acknowledges the Italian MIUR project PRIN2017WZFTZP for financial support and
the project E-PASSION of the program VALERE 2019 funded by the University of Campania,
Italy “L. Vanvitelli”. OS acknowledges support from the Israel Science Foundation,
Grant No. 504/17. Supported in part by DIRP ZIAMH02797 to DP.
article_processing_charge: No
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Hans J.
full_name: Herrmann, Hans J.
last_name: Herrmann
- first_name: Liborio
full_name: Parrino, Liborio
last_name: Parrino
- first_name: Dietmar
full_name: Plenz, Dietmar
last_name: Plenz
- first_name: Silvia
full_name: Scarpetta, Silvia
last_name: Scarpetta
- first_name: Anna Elisabetta
full_name: Vaudano, Anna Elisabetta
last_name: Vaudano
- first_name: Lucilla
full_name: de Arcangelis, Lucilla
last_name: de Arcangelis
- first_name: Oren
full_name: Shriki, Oren
last_name: Shriki
citation:
ama: Lombardi F, Herrmann HJ, Parrino L, et al. Alpha rhythm induces attenuation-amplification
dynamics in neural activity cascades. bioRxiv. 2022. doi:10.1101/2022.03.03.482657
apa: Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano,
A. E., … Shriki, O. (2022). Alpha rhythm induces attenuation-amplification dynamics
in neural activity cascades. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2022.03.03.482657
chicago: Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz, Silvia
Scarpetta, Anna Elisabetta Vaudano, Lucilla de Arcangelis, and Oren Shriki. “Alpha
Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.”
BioRxiv. Cold Spring Harbor Laboratory, 2022. https://doi.org/10.1101/2022.03.03.482657.
ieee: F. Lombardi et al., “Alpha rhythm induces attenuation-amplification
dynamics in neural activity cascades,” bioRxiv. Cold Spring Harbor Laboratory,
2022.
ista: Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, de Arcangelis
L, Shriki O. 2022. Alpha rhythm induces attenuation-amplification dynamics in
neural activity cascades. bioRxiv, 10.1101/2022.03.03.482657.
mla: Lombardi, Fabrizio, et al. “Alpha Rhythm Induces Attenuation-Amplification
Dynamics in Neural Activity Cascades.” BioRxiv, Cold Spring Harbor Laboratory,
2022, doi:10.1101/2022.03.03.482657.
short: F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano,
L. de Arcangelis, O. Shriki, BioRxiv (2022).
date_created: 2022-03-04T22:20:59Z
date_published: 2022-03-04T00:00:00Z
date_updated: 2022-03-07T07:28:34Z
day: '04'
department:
- _id: GaTk
doi: 10.1101/2022.03.03.482657
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2022.03.03.482657
month: '03'
oa: 1
oa_version: Preprint
page: '25'
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
status: public
title: Alpha rhythm induces attenuation-amplification dynamics in neural activity
cascades
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '10825'
abstract:
- lang: eng
text: In development, lineage segregation is coordinated in time and space. An important
example is the mammalian inner cell mass, in which the primitive endoderm (PrE,
founder of the yolk sac) physically segregates from the epiblast (EPI, founder
of the fetus). While the molecular requirements have been well studied, the physical
mechanisms determining spatial segregation between EPI and PrE remain elusive.
Here, we investigate the mechanical basis of EPI and PrE sorting. We find that
rather than the differences in static cell surface mechanical parameters as in
classical sorting models, it is the differences in surface fluctuations that robustly
ensure physical lineage sorting. These differential surface fluctuations systematically
correlate with differential cellular fluidity, which we propose together constitute
a non-equilibrium sorting mechanism for EPI and PrE lineages. By combining experiments
and modeling, we identify cell surface dynamics as a key factor orchestrating
the correct spatial segregation of the founder embryonic lineages.
acknowledgement: We are grateful to H. Niwa for Dox regulatable PB vector; G. Charras
for EzrinT567D cDNA; K. Jones for tdTomato ESCs, R26-Confetti ESCs, and laboratory
assistance; M. Kinoshita for pPB-CAG-H2B-BFP plasmid; P. Humphreys and D. Clements
for imaging support; G. Chu, P. Attlesey, and staff for animal husbandry; S. Pallett
for laboratory assistance; C. Mulas for critical feedback on the project; T. Boroviak
for single-cell RNA-seq; the EMBL Genomics Core Facility for sequencing; and M.
Merkel for developing and sharing the original version of the 3D Voronoi code. This
work was financially supported by BBSRC ( BB/Moo4023/1 and BB/T007044/1 to K.J.C.
and J.N., Alert16 grant BB/R000042 to E.K.P.), Leverhulme Trust ( RPG-2014-080 to
K.J.C. and J.N.), European Research Council ( 772798 -CellFateTech to K.J.C., 311637
-MorphoCorDiv and 820188 -NanoMechShape to E.K.P., Starting Grant 851288 to E.H.,
and 772426 -MeChemGui to K.F.), the Isaac Newton Trust (to E.K.P.), Medical Research
Council UK (MRC program award MC_UU_00012/5 to E.K.P.), the European Union’s Horizon
2020 research and innovation program under the Marie Sklodowska-Curie grant agreement
no. 641639 ( ITN Biopol , H.D.B. and E.K.P.), the Alexander von Humboldt Foundation
(Alexander von Humboldt Professorship to K.F.), EMBO ALTF 522-2021 (to P.S.), Centre
for Trophoblast Research (Next Generation fellowship to S.A.), and JSPS Overseas
Research Fellowships (to A.Y.). The Wellcome-MRC Cambridge Stem Cell Institute receives
core funding from Wellcome Trust ( 203151/Z/16/Z ) and MRC ( MC_PC_17230 ). For
the purpose of open access, the author has applied a CC BY public copyright licence
to any Author Accepted Manuscript version arising from this submission.
article_processing_charge: No
article_type: original
author:
- first_name: Ayaka
full_name: Yanagida, Ayaka
last_name: Yanagida
- first_name: Elena
full_name: Corujo-Simon, Elena
last_name: Corujo-Simon
- first_name: Christopher K.
full_name: Revell, Christopher K.
last_name: Revell
- first_name: Preeti
full_name: Sahu, Preeti
id: 55BA52EE-A185-11EA-88FD-18AD3DDC885E
last_name: Sahu
- first_name: Giuliano G.
full_name: Stirparo, Giuliano G.
last_name: Stirparo
- first_name: Irene M.
full_name: Aspalter, Irene M.
last_name: Aspalter
- first_name: Alex K.
full_name: Winkel, Alex K.
last_name: Winkel
- first_name: Ruby
full_name: Peters, Ruby
last_name: Peters
- first_name: Henry
full_name: De Belly, Henry
last_name: De Belly
- first_name: Davide A.D.
full_name: Cassani, Davide A.D.
last_name: Cassani
- first_name: Sarra
full_name: Achouri, Sarra
last_name: Achouri
- first_name: Raphael
full_name: Blumenfeld, Raphael
last_name: Blumenfeld
- first_name: Kristian
full_name: Franze, Kristian
last_name: Franze
- 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: Ewa K.
full_name: Paluch, Ewa K.
last_name: Paluch
- first_name: Jennifer
full_name: Nichols, Jennifer
last_name: Nichols
- first_name: Kevin J.
full_name: Chalut, Kevin J.
last_name: Chalut
citation:
ama: Yanagida A, Corujo-Simon E, Revell CK, et al. Cell surface fluctuations regulate
early embryonic lineage sorting. Cell. 2022;185(5):777-793.e20. doi:10.1016/j.cell.2022.01.022
apa: Yanagida, A., Corujo-Simon, E., Revell, C. K., Sahu, P., Stirparo, G. G., Aspalter,
I. M., … Chalut, K. J. (2022). Cell surface fluctuations regulate early embryonic
lineage sorting. Cell. Cell Press. https://doi.org/10.1016/j.cell.2022.01.022
chicago: Yanagida, Ayaka, Elena Corujo-Simon, Christopher K. Revell, Preeti Sahu,
Giuliano G. Stirparo, Irene M. Aspalter, Alex K. Winkel, et al. “Cell Surface
Fluctuations Regulate Early Embryonic Lineage Sorting.” Cell. Cell Press,
2022. https://doi.org/10.1016/j.cell.2022.01.022.
ieee: A. Yanagida et al., “Cell surface fluctuations regulate early embryonic
lineage sorting,” Cell, vol. 185, no. 5. Cell Press, p. 777–793.e20, 2022.
ista: Yanagida A, Corujo-Simon E, Revell CK, Sahu P, Stirparo GG, Aspalter IM, Winkel
AK, Peters R, De Belly H, Cassani DAD, Achouri S, Blumenfeld R, Franze K, Hannezo
EB, Paluch EK, Nichols J, Chalut KJ. 2022. Cell surface fluctuations regulate
early embryonic lineage sorting. Cell. 185(5), 777–793.e20.
mla: Yanagida, Ayaka, et al. “Cell Surface Fluctuations Regulate Early Embryonic
Lineage Sorting.” Cell, vol. 185, no. 5, Cell Press, 2022, p. 777–793.e20,
doi:10.1016/j.cell.2022.01.022.
short: A. Yanagida, E. Corujo-Simon, C.K. Revell, P. Sahu, G.G. Stirparo, I.M. Aspalter,
A.K. Winkel, R. Peters, H. De Belly, D.A.D. Cassani, S. Achouri, R. Blumenfeld,
K. Franze, E.B. Hannezo, E.K. Paluch, J. Nichols, K.J. Chalut, Cell 185 (2022)
777–793.e20.
date_created: 2022-03-06T23:01:52Z
date_published: 2022-02-22T00:00:00Z
date_updated: 2023-08-02T14:43:50Z
day: '22'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1016/j.cell.2022.01.022
ec_funded: 1
external_id:
isi:
- '000796293700007'
pmid:
- '35196500'
file:
- access_level: open_access
checksum: ae305060e8031297771b89dae9e36a29
content_type: application/pdf
creator: dernst
date_created: 2022-03-07T07:55:23Z
date_updated: 2022-03-07T07:55:23Z
file_id: '10831'
file_name: 2022_Cell_Yanagida.pdf
file_size: 8478995
relation: main_file
success: 1
file_date_updated: 2022-03-07T07:55:23Z
has_accepted_license: '1'
intvolume: ' 185'
isi: 1
issue: '5'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 777-793.e20
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Cell
publication_identifier:
eissn:
- '10974172'
issn:
- '00928674'
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell surface fluctuations regulate early embryonic lineage sorting
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 185
year: '2022'
...
---
_id: '10826'
abstract:
- lang: eng
text: Animals that lose one sensory modality often show augmented responses to other
sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly
understood. We probe such mechanisms by performing a forward genetic screen for
mutants with enhanced O2 perception in Caenorhabditis elegans. Multiple mutants
exhibiting increased O2 responsiveness concomitantly show defects in other sensory
responses. One mutant, qui-1, defective in a conserved NACHT/WD40 protein, abolishes
pheromone-evoked Ca2+ responses in the ADL pheromone-sensing neurons. At the same
time, ADL responsiveness to pre-synaptic input from O2-sensing neurons is heightened
in qui-1, and other sensory defective mutants, resulting in enhanced neurosecretion
although not increased Ca2+ responses. Expressing qui-1 selectively in ADL rescues
both the qui-1 ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling
ADL neurons in qui-1 mutants highlights extensive changes in gene expression,
notably of many neuropeptide receptors. We show that elevated ADL expression of
the conserved neuropeptide receptor NPR-22 is necessary for enhanced ADL neurosecretion
in qui-1 mutants, and is sufficient to confer increased ADL neurosecretion in
control animals. Sensory loss can thus confer cross-modal plasticity by changing
the peptidergic connectome.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: ScienComp
acknowledgement: "We would like to thank Gemma Chandratillake and Merav Cohen for
identifying mutants and José David Moñino Sánchez for his help on neurosecretion
assays. We are grateful to Kaveh Ashrafi (UCSF), Piali Sengupta (Brandeis), and
the Caenorhabditis Genetic Center (funded by National Institutes of Health Infrastructure
Program P40 OD010440) for strains and reagents ... and Rebecca Butcher (Univ. Florida)
for C9 pheromone. We thank Tim Stevens, Paula Freire-Pritchett, Alastair Crisp,
GurpreetGhattaoraya, and Fabian Amman for help with bioinformatic analysis, Ekaterina
Lashmanova for help with injections, Iris Hardege for strains, and Isabel Beets
(KU Leuven) and members of the de Bono Lab for comments on the manuscript. We thank
the CRUK Cambridge Research Institute Genomics Core for next generation sequencing
and the Flow Cytometry Facility at LMB for FACS. This research was supported by
the Scientific Service Units (SSU) of IST Austria through resources provided by
the Bioimaging Facility (BIF), the Life Science Facility (LSF) and Scientific Computing
(SciCo-p– Bioinformatics).\r\nThis work was supported by the Medical Research Council
UK (Studentship to GV), an\r\nAdvanced ERC grant (269,058 ACMO to MdB), and a Wellcome
Investigator Award (209504/Z/17/Z to MdB)."
article_number: e68040
article_processing_charge: No
article_type: original
author:
- first_name: Giulio
full_name: Valperga, Giulio
id: 67F289DE-0D8F-11EA-9BDD-54AE3DDC885E
last_name: Valperga
- first_name: Mario
full_name: De Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: De Bono
orcid: 0000-0001-8347-0443
citation:
ama: Valperga G, de Bono M. Impairing one sensory modality enhances another by reconfiguring
peptidergic signalling in Caenorhabditis elegans. eLife. 2022;11. doi:10.7554/eLife.68040
apa: Valperga, G., & de Bono, M. (2022). Impairing one sensory modality enhances
another by reconfiguring peptidergic signalling in Caenorhabditis elegans. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.68040
chicago: Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances
Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” ELife.
eLife Sciences Publications, 2022. https://doi.org/10.7554/eLife.68040.
ieee: G. Valperga and M. de Bono, “Impairing one sensory modality enhances another
by reconfiguring peptidergic signalling in Caenorhabditis elegans,” eLife,
vol. 11. eLife Sciences Publications, 2022.
ista: Valperga G, de Bono M. 2022. Impairing one sensory modality enhances another
by reconfiguring peptidergic signalling in Caenorhabditis elegans. eLife. 11,
e68040.
mla: Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances
Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” ELife,
vol. 11, e68040, eLife Sciences Publications, 2022, doi:10.7554/eLife.68040.
short: G. Valperga, M. de Bono, ELife 11 (2022).
date_created: 2022-03-06T23:01:52Z
date_published: 2022-02-24T00:00:00Z
date_updated: 2023-08-02T14:42:55Z
day: '24'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.7554/eLife.68040
external_id:
isi:
- '000763432300001'
pmid:
- '35201977'
file:
- access_level: open_access
checksum: cc1b9bf866d0f61f965556e0dd03d3ac
content_type: application/pdf
creator: dernst
date_created: 2022-03-07T07:39:25Z
date_updated: 2022-03-07T07:39:25Z
file_id: '10830'
file_name: 2022_eLife_Valperga.pdf
file_size: 4095591
relation: main_file
success: 1
file_date_updated: 2022-03-07T07:39:25Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 23870BE8-32DE-11EA-91FC-C7463DDC885E
grant_number: 209504/A/17/Z
name: Molecular mechanisms of neural circuit function
publication: eLife
publication_identifier:
eissn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Impairing one sensory modality enhances another by reconfiguring peptidergic
signalling in Caenorhabditis elegans
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2022'
...
---
_id: '10827'
abstract:
- lang: eng
text: Titanium dioxide has been extensively studied in the rutile or anatase phase,
while its high-pressure phases are less well-understood, despite that many are
thought to have interesting optical, mechanical, and electrochemical properties.
First-principles methods, such as density functional theory (DFT), are often used
to compute the enthalpies of TiO2 phases at 0 K, but they are expensive and, thus,
impractical for long time scale and large system-size simulations at finite temperatures.
On the other hand, cheap empirical potentials fail to capture the relative stabilities
of various polymorphs. To model the thermodynamic behaviors of ambient and high-pressure
phases of TiO2, we design an empirical model as a baseline and then train a machine
learning potential based on the difference between the DFT data and the empirical
model. This so-called Δ-learning potential contains long-range electrostatic interactions
and predicts the 0 K enthalpies of stable TiO2 phases that are in good agreement
with DFT. We construct a pressure–temperature phase diagram of TiO2 in the range
0 < P < 70 GPa and 100 < T < 1500 K. We then simulate dynamic phase transition
processes by compressing anatase at different temperatures. At 300 K, we predominantly
observe an anatase-to-baddeleyite transformation at about 20 GPa via a martensitic
two-step mechanism with a highly ordered and collective atomic motion. At 2000
K, anatase can transform into cotunnite around 45–55 GPa in a thermally activated
and probabilistic manner, accompanied by diffusive movement of oxygen atoms. The
pressures computed for these transitions show good agreement with experiments.
Our results shed light on how to synthesize and stabilize high-pressure TiO2 phases,
and our method is generally applicable to other functional materials with multiple
polymorphs.
acknowledgement: J.G.L. and B.C. acknowledge the resources provided by the Cambridge
Tier-2 system operated by the University of Cambridge Research Computing Service
funded by the EPSRC Tier-2 capital (Grant No. EP/P020259/1).
article_number: '074106'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jacob G.
full_name: Lee, Jacob G.
last_name: Lee
- first_name: Chris J.
full_name: Pickard, Chris J.
last_name: Pickard
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Lee JG, Pickard CJ, Cheng B. High-pressure phase behaviors of titanium dioxide
revealed by a Δ-learning potential. The Journal of chemical physics. 2022;156(7).
doi:10.1063/5.0079844
apa: Lee, J. G., Pickard, C. J., & Cheng, B. (2022). High-pressure phase behaviors
of titanium dioxide revealed by a Δ-learning potential. The Journal of Chemical
Physics. AIP Publishing. https://doi.org/10.1063/5.0079844
chicago: Lee, Jacob G., Chris J. Pickard, and Bingqing Cheng. “High-Pressure Phase
Behaviors of Titanium Dioxide Revealed by a Δ-Learning Potential.” The Journal
of Chemical Physics. AIP Publishing, 2022. https://doi.org/10.1063/5.0079844.
ieee: J. G. Lee, C. J. Pickard, and B. Cheng, “High-pressure phase behaviors of
titanium dioxide revealed by a Δ-learning potential,” The Journal of chemical
physics, vol. 156, no. 7. AIP Publishing, 2022.
ista: Lee JG, Pickard CJ, Cheng B. 2022. High-pressure phase behaviors of titanium
dioxide revealed by a Δ-learning potential. The Journal of chemical physics. 156(7),
074106.
mla: Lee, Jacob G., et al. “High-Pressure Phase Behaviors of Titanium Dioxide Revealed
by a Δ-Learning Potential.” The Journal of Chemical Physics, vol. 156,
no. 7, 074106, AIP Publishing, 2022, doi:10.1063/5.0079844.
short: J.G. Lee, C.J. Pickard, B. Cheng, The Journal of Chemical Physics 156 (2022).
date_created: 2022-03-06T23:01:53Z
date_published: 2022-02-16T00:00:00Z
date_updated: 2023-08-02T14:45:46Z
day: '16'
department:
- _id: BiCh
doi: 10.1063/5.0079844
external_id:
arxiv:
- '2111.12968'
isi:
- '000796704500014'
intvolume: ' 156'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2111.12968
month: '02'
oa: 1
oa_version: Preprint
publication: The Journal of chemical physics
publication_identifier:
eissn:
- '10897690'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning
potential
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 156
year: '2022'
...