---
_id: '9345'
abstract:
- lang: eng
text: Modeling a crystal as a periodic point set, we present a fingerprint consisting
of density functionsthat facilitates the efficient search for new materials and
material properties. We prove invarianceunder isometries, continuity, and completeness
in the generic case, which are necessary featuresfor the reliable comparison of
crystals. The proof of continuity integrates methods from discretegeometry and
lattice theory, while the proof of generic completeness combines techniques fromgeometry
with analysis. The fingerprint has a fast algorithm based on Brillouin zones and
relatedinclusion-exclusion formulae. We have implemented the algorithm and describe
its application tocrystal structure prediction.
acknowledgement: The authors thank Janos Pach for insightful discussions on the topic
of thispaper, Morteza Saghafian for finding the one-dimensional counterexample mentioned
in Section 5,and Larry Andrews for generously sharing his crystallographic perspective.
alternative_title:
- LIPIcs
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Teresa
full_name: Heiss, Teresa
id: 4879BB4E-F248-11E8-B48F-1D18A9856A87
last_name: Heiss
orcid: 0000-0002-1780-2689
- first_name: Vitaliy
full_name: ' Kurlin , Vitaliy'
last_name: ' Kurlin '
- first_name: Philip
full_name: Smith, Philip
last_name: Smith
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: 'Edelsbrunner H, Heiss T, Kurlin V, Smith P, Wintraecken M. The density fingerprint
of a periodic point set. In: 37th International Symposium on Computational
Geometry (SoCG 2021). Vol 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2021:32:1-32:16. doi:10.4230/LIPIcs.SoCG.2021.32'
apa: 'Edelsbrunner, H., Heiss, T., Kurlin , V., Smith, P., & Wintraecken, M.
(2021). The density fingerprint of a periodic point set. In 37th International
Symposium on Computational Geometry (SoCG 2021) (Vol. 189, p. 32:1-32:16).
Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2021.32'
chicago: Edelsbrunner, Herbert, Teresa Heiss, Vitaliy Kurlin , Philip Smith, and
Mathijs Wintraecken. “The Density Fingerprint of a Periodic Point Set.” In 37th
International Symposium on Computational Geometry (SoCG 2021), 189:32:1-32:16.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.SoCG.2021.32.
ieee: H. Edelsbrunner, T. Heiss, V. Kurlin , P. Smith, and M. Wintraecken, “The
density fingerprint of a periodic point set,” in 37th International Symposium
on Computational Geometry (SoCG 2021), Virtual, 2021, vol. 189, p. 32:1-32:16.
ista: 'Edelsbrunner H, Heiss T, Kurlin V, Smith P, Wintraecken M. 2021. The density
fingerprint of a periodic point set. 37th International Symposium on Computational
Geometry (SoCG 2021). SoCG: Symposium on Computational Geometry, LIPIcs, vol.
189, 32:1-32:16.'
mla: Edelsbrunner, Herbert, et al. “The Density Fingerprint of a Periodic Point
Set.” 37th International Symposium on Computational Geometry (SoCG 2021),
vol. 189, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, p. 32:1-32:16,
doi:10.4230/LIPIcs.SoCG.2021.32.
short: H. Edelsbrunner, T. Heiss, V. Kurlin , P. Smith, M. Wintraecken, in:, 37th
International Symposium on Computational Geometry (SoCG 2021), Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2021, p. 32:1-32:16.
conference:
end_date: 2021-06-11
location: Virtual
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2021-06-07
date_created: 2021-04-22T08:09:58Z
date_published: 2021-06-02T00:00:00Z
date_updated: 2023-02-23T13:55:40Z
day: '02'
ddc:
- '004'
- '516'
department:
- _id: HeEd
doi: 10.4230/LIPIcs.SoCG.2021.32
ec_funded: 1
file:
- access_level: open_access
checksum: 1787baef1523d6d93753b90d0c109a6d
content_type: application/pdf
creator: mwintrae
date_created: 2021-04-22T08:08:14Z
date_updated: 2021-04-22T08:08:14Z
file_id: '9346'
file_name: df_socg_final_version.pdf
file_size: 3117435
relation: main_file
success: 1
file_date_updated: 2021-04-22T08:08:14Z
has_accepted_license: '1'
intvolume: ' 189'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 32:1-32:16
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316
grant_number: I4887
name: Discretization in Geometry and Dynamics
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 37th International Symposium on Computational Geometry (SoCG 2021)
publication_identifier:
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
status: public
title: The density fingerprint of a periodic point set
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 189
year: '2021'
...
---
_id: '9348'
abstract:
- lang: eng
text: We consider the stochastic quantization of a quartic double-well energy functional
in the semiclassical regime and derive optimal asymptotics for the exponentially
small splitting of the ground state energy. Our result provides an infinite-dimensional
version of some sharp tunneling estimates known in finite dimensions for semiclassical
Witten Laplacians in degree zero. From a stochastic point of view it proves that
the L2 spectral gap of the stochastic one-dimensional Allen-Cahn equation in finite
volume satisfies a Kramers-type formula in the limit of vanishing noise. We work
with finite-dimensional lattice approximations and establish semiclassical estimates
which are uniform in the dimension. Our key estimate shows that the constant separating
the two exponentially small eigenvalues from the rest of the spectrum can be taken
independently of the dimension.
acknowledgement: GDG gratefully acknowledges the financial support of HIM Bonn in
the framework of the 2019 Junior Trimester Programs “Kinetic Theory” and “Randomness,
PDEs and Nonlinear Fluctuations” and the hospitality at the University of Rome La
Sapienza during his frequent visits.
article_number: '109029'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Morris
full_name: Brooks, Morris
id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425
last_name: Brooks
orcid: 0000-0002-6249-0928
- first_name: Giacomo
full_name: Di Gesù, Giacomo
last_name: Di Gesù
citation:
ama: Brooks M, Di Gesù G. Sharp tunneling estimates for a double-well model in infinite
dimension. Journal of Functional Analysis. 2021;281(3). doi:10.1016/j.jfa.2021.109029
apa: Brooks, M., & Di Gesù, G. (2021). Sharp tunneling estimates for a double-well
model in infinite dimension. Journal of Functional Analysis. Elsevier.
https://doi.org/10.1016/j.jfa.2021.109029
chicago: Brooks, Morris, and Giacomo Di Gesù. “Sharp Tunneling Estimates for a Double-Well
Model in Infinite Dimension.” Journal of Functional Analysis. Elsevier,
2021. https://doi.org/10.1016/j.jfa.2021.109029.
ieee: M. Brooks and G. Di Gesù, “Sharp tunneling estimates for a double-well model
in infinite dimension,” Journal of Functional Analysis, vol. 281, no. 3.
Elsevier, 2021.
ista: Brooks M, Di Gesù G. 2021. Sharp tunneling estimates for a double-well model
in infinite dimension. Journal of Functional Analysis. 281(3), 109029.
mla: Brooks, Morris, and Giacomo Di Gesù. “Sharp Tunneling Estimates for a Double-Well
Model in Infinite Dimension.” Journal of Functional Analysis, vol. 281,
no. 3, 109029, Elsevier, 2021, doi:10.1016/j.jfa.2021.109029.
short: M. Brooks, G. Di Gesù, Journal of Functional Analysis 281 (2021).
date_created: 2021-04-25T22:01:29Z
date_published: 2021-04-07T00:00:00Z
date_updated: 2023-08-08T13:15:11Z
day: '07'
department:
- _id: RoSe
doi: 10.1016/j.jfa.2021.109029
external_id:
arxiv:
- '1911.03187'
isi:
- '000644702800005'
intvolume: ' 281'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1911.03187
month: '04'
oa: 1
oa_version: Preprint
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sharp tunneling estimates for a double-well model in infinite dimension
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 281
year: '2021'
...
---
_id: '9349'
abstract:
- lang: eng
text: 'The way in which interactions between mechanics and biochemistry lead to
the emergence of complex cell and tissue organization is an old question that
has recently attracted renewed interest from biologists, physicists, mathematicians
and computer scientists. Rapid advances in optical physics, microscopy and computational
image analysis have greatly enhanced our ability to observe and quantify spatiotemporal
patterns of signalling, force generation, deformation, and flow in living cells
and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation
are allowing us to perturb the underlying machinery that generates these patterns
in increasingly sophisticated ways. Rapid advances in theory and computing have
made it possible to construct predictive models that describe how cell and tissue
organization and dynamics emerge from the local coupling of biochemistry and mechanics.
Together, these advances have opened up a wealth of new opportunities to explore
how mechanochemical patterning shapes organismal development. In this roadmap,
we present a series of forward-looking case studies on mechanochemical patterning
in development, written by scientists working at the interface between the physical
and biological sciences, and covering a wide range of spatial and temporal scales,
organisms, and modes of development. Together, these contributions highlight the
many ways in which the dynamic coupling of mechanics and biochemistry shapes biological
dynamics: from mechanoenzymes that sense force to tune their activity and motor
output, to collectives of cells in tissues that flow and redistribute biochemical
signals during development.'
acknowledgement: The AK group is supported by IST Austria and by the ERC under European
Union Horizon 2020 research and innovation programme Grant 680037. Apologies to
those whose work could not be mentioned due to limited space. We thank all my lab
members, both past and present, for stimulating discussion. This work was funded
by a Singapore Ministry of Education Tier 3 Grant, MOE2016-T3-1-005. We thank Francis
Corson for continuous discussion and collaboration contributing to these views and
for figure 4(A). PC is sponsored by the Institut Pasteur and the European Union's
Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie
Grant Agreement No. 665807. Research in JG's laboratory is funded by the European
Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC
Grant Agreement No. 337635, Institut Pasteur, CNRS, Cercle FSER, Fondation pour
la Recherche Medicale, the Vallee Foundation and the ANR-19-CE-13-0024 Grant. We
thank Erez Braun and Alex Mogilner for comments on the manuscript and Niv Ierushalmi
for help with figure 5. This project has received funding from the European Union's
Horizon 2020 research and innovation programme under Grant Agreement No. ERC-2018-COG
Grant 819174-HydraMechanics awarded to KK. EH thanks all lab members, as well as
Pierre Recho, Tsuyoshi Hirashima, Diana Pinheiro and Carl-Philip Heisenberg, for
fruitful discussions on these topics—and apologize for not being able to cite many
very relevant publications due to the strict 10-reference limit. EH acknowledges
the support of Austrian Science Fund (FWF) (P 31639) and the European Research Council
under the European Union's Horizon 2020 Research and Innovation Programme Grant
Agreements (851288). The authors acknowledge the inspiring scientists whose work
could not be cited in this perspective due to space constraints; the members of
the Gartner Lab for helpful discussions; the Barbara and Gerson Bakar Foundation,
the Chan Zuckerberg Biohub Investigators Programme, the National Institute of Health,
and the Centre for Cellular Construction, an NSF Science and Technology Centre.
The Minc laboratory is currently funded by the CNRS and the European Research Council
(CoG Forcaster No. 647073). Research in the lab of J-LM is supported by the Institut
Curie, the Centre National de la Recherche Scientifique (CNRS), the Institut National
de la Santé Et de la Recherche Médicale (INSERM), and is funded by grants from the
ATIP-Avenir programme, the Fondation Schlumberger pour l'Éducation et la Recherche
via the Fondation pour la Recherche Médicale, the European Research Council Starting
Grant ERC-2017-StG 757557, the European Molecular Biology Organization Young Investigator
programme (EMBO YIP), the INSERM transversal programme Human Development Cell Atlas
(HuDeCA), Paris Sciences Lettres (PSL) 'nouvelle équipe' and QLife (17-CONV-0005)
grants and Labex DEEP (ANR-11-LABX-0044) which are part of the IDEX PSL (ANR-10-IDEX-0001-02).
We acknowledge useful discussions with Massimo Vergassola, Sebastian Streichan and
my lab members. Work in my laboratory on Drosophila embryogenesis is partly supported
by NIH-R01GM122936. The authors acknowledge the support by a grant from the European
Research Council (Grant No. 682161). Lenne group is funded by a grant from the 'Investissements
d'Avenir' French Government programme managed by the French National Research Agency
(ANR-16-CONV-0001) and by the Excellence Initiative of Aix-Marseille University—A*MIDEX,
and ANR projects MechaResp (ANR-17-CE13-0032) and AdGastrulo (ANR-19-CE13-0022).
article_number: '041501'
article_processing_charge: No
article_type: original
author:
- first_name: Pierre François
full_name: Lenne, Pierre François
last_name: Lenne
- first_name: Edwin
full_name: Munro, Edwin
last_name: Munro
- first_name: Idse
full_name: Heemskerk, Idse
last_name: Heemskerk
- first_name: Aryeh
full_name: Warmflash, Aryeh
last_name: Warmflash
- first_name: Laura
full_name: Bocanegra, Laura
id: 4896F754-F248-11E8-B48F-1D18A9856A87
last_name: Bocanegra
- first_name: Kasumi
full_name: Kishi, Kasumi
id: 3065DFC4-F248-11E8-B48F-1D18A9856A87
last_name: Kishi
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Yuchen
full_name: Long, Yuchen
last_name: Long
- first_name: Antoine
full_name: Fruleux, Antoine
last_name: Fruleux
- first_name: Arezki
full_name: Boudaoud, Arezki
last_name: Boudaoud
- first_name: Timothy E.
full_name: Saunders, Timothy E.
last_name: Saunders
- first_name: Paolo
full_name: Caldarelli, Paolo
last_name: Caldarelli
- first_name: Arthur
full_name: Michaut, Arthur
last_name: Michaut
- first_name: Jerome
full_name: Gros, Jerome
last_name: Gros
- first_name: Yonit
full_name: Maroudas-Sacks, Yonit
last_name: Maroudas-Sacks
- first_name: Kinneret
full_name: Keren, Kinneret
last_name: Keren
- 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: Zev J.
full_name: Gartner, Zev J.
last_name: Gartner
- first_name: Benjamin
full_name: Stormo, Benjamin
last_name: Stormo
- first_name: Amy
full_name: Gladfelter, Amy
last_name: Gladfelter
- first_name: Alan
full_name: Rodrigues, Alan
last_name: Rodrigues
- first_name: Amy
full_name: Shyer, Amy
last_name: Shyer
- first_name: Nicolas
full_name: Minc, Nicolas
last_name: Minc
- first_name: Jean Léon
full_name: Maître, Jean Léon
last_name: Maître
- first_name: Stefano
full_name: Di Talia, Stefano
last_name: Di Talia
- first_name: Bassma
full_name: Khamaisi, Bassma
last_name: Khamaisi
- first_name: David
full_name: Sprinzak, David
last_name: Sprinzak
- first_name: Sham
full_name: Tlili, Sham
last_name: Tlili
citation:
ama: Lenne PF, Munro E, Heemskerk I, et al. Roadmap for the multiscale coupling
of biochemical and mechanical signals during development. Physical biology.
2021;18(4). doi:10.1088/1478-3975/abd0db
apa: Lenne, P. F., Munro, E., Heemskerk, I., Warmflash, A., Bocanegra, L., Kishi,
K., … Tlili, S. (2021). Roadmap for the multiscale coupling of biochemical and
mechanical signals during development. Physical Biology. IOP Publishing.
https://doi.org/10.1088/1478-3975/abd0db
chicago: Lenne, Pierre François, Edwin Munro, Idse Heemskerk, Aryeh Warmflash, Laura
Bocanegra, Kasumi Kishi, Anna Kicheva, et al. “Roadmap for the Multiscale Coupling
of Biochemical and Mechanical Signals during Development.” Physical Biology.
IOP Publishing, 2021. https://doi.org/10.1088/1478-3975/abd0db.
ieee: P. F. Lenne et al., “Roadmap for the multiscale coupling of biochemical
and mechanical signals during development,” Physical biology, vol. 18,
no. 4. IOP Publishing, 2021.
ista: Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra L, Kishi K, Kicheva
A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J,
Maroudas-Sacks Y, Keren K, Hannezo EB, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues
A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. 2021.
Roadmap for the multiscale coupling of biochemical and mechanical signals during
development. Physical biology. 18(4), 041501.
mla: Lenne, Pierre François, et al. “Roadmap for the Multiscale Coupling of Biochemical
and Mechanical Signals during Development.” Physical Biology, vol. 18,
no. 4, 041501, IOP Publishing, 2021, doi:10.1088/1478-3975/abd0db.
short: P.F. Lenne, E. Munro, I. Heemskerk, A. Warmflash, L. Bocanegra, K. Kishi,
A. Kicheva, Y. Long, A. Fruleux, A. Boudaoud, T.E. Saunders, P. Caldarelli, A.
Michaut, J. Gros, Y. Maroudas-Sacks, K. Keren, E.B. Hannezo, Z.J. Gartner, B.
Stormo, A. Gladfelter, A. Rodrigues, A. Shyer, N. Minc, J.L. Maître, S. Di Talia,
B. Khamaisi, D. Sprinzak, S. Tlili, Physical Biology 18 (2021).
date_created: 2021-04-25T22:01:29Z
date_published: 2021-04-14T00:00:00Z
date_updated: 2023-08-08T13:15:46Z
day: '14'
ddc:
- '570'
department:
- _id: AnKi
- _id: EdHa
doi: 10.1088/1478-3975/abd0db
ec_funded: 1
external_id:
isi:
- '000640396400001'
pmid:
- '33276350'
file:
- access_level: open_access
checksum: 4f52082549d3561c4c15d4d8d84ca5d8
content_type: application/pdf
creator: cziletti
date_created: 2021-04-27T08:38:35Z
date_updated: 2021-04-27T08:38:35Z
file_id: '9355'
file_name: 2021_PhysBio_Lenne.pdf
file_size: 6296324
relation: main_file
success: 1
file_date_updated: 2021-04-27T08:38:35Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
- _id: 268294B6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31639
name: Active mechano-chemical description of the cell cytoskeleton
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Physical biology
publication_identifier:
eissn:
- 1478-3975
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
related_material:
record:
- id: '13081'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Roadmap for the multiscale coupling of biochemical and mechanical signals during
development
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: 18
year: '2021'
...
---
_id: '9350'
abstract:
- lang: eng
text: Intercellular adhesion is the key to multicellularity, and its malfunction
plays an important role in various developmental and disease-related processes.
Although it has been intensively studied by both biologists and physicists, a
commonly accepted definition of cell-cell adhesion is still being debated. Cell-cell
adhesion has been described at the molecular scale as a function of adhesion receptors
controlling binding affinity, at the cellular scale as resistance to detachment
forces or modulation of surface tension, and at the tissue scale as a regulator
of cellular rearrangements and morphogenesis. In this review, we aim to summarize
and discuss recent advances in the molecular, cellular, and theoretical description
of cell-cell adhesion, ranging from biomimetic models to the complexity of cells
and tissues in an organismal context. In particular, we will focus on cadherin-mediated
cell-cell adhesion and the role of adhesion signaling and mechanosensation therein,
two processes central for understanding the biological and physical basis of cell-cell
adhesion.
acknowledgement: T.S. acknowledges funding by the research program “The Active Matter
Physics of Collective Metastasis,” which is financed by the Dutch Research Council
(NWO).
article_processing_charge: No
article_type: original
author:
- first_name: Feyza N
full_name: Arslan, Feyza N
id: 49DA7910-F248-11E8-B48F-1D18A9856A87
last_name: Arslan
orcid: 0000-0001-5809-9566
- first_name: Julia
full_name: Eckert, Julia
last_name: Eckert
- first_name: Thomas
full_name: Schmidt, Thomas
last_name: Schmidt
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: 'Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. Holding it together: when
cadherin meets cadherin. Biophysical Journal. 2021;120:4182-4192. doi:10.1016/j.bpj.2021.03.025'
apa: 'Arslan, F. N., Eckert, J., Schmidt, T., & Heisenberg, C.-P. J. (2021).
Holding it together: when cadherin meets cadherin. Biophysical Journal.
Biophysical Society. https://doi.org/10.1016/j.bpj.2021.03.025'
chicago: 'Arslan, Feyza N, Julia Eckert, Thomas Schmidt, and Carl-Philipp J Heisenberg.
“Holding It Together: When Cadherin Meets Cadherin.” Biophysical Journal.
Biophysical Society, 2021. https://doi.org/10.1016/j.bpj.2021.03.025.'
ieee: 'F. N. Arslan, J. Eckert, T. Schmidt, and C.-P. J. Heisenberg, “Holding it
together: when cadherin meets cadherin,” Biophysical Journal, vol. 120.
Biophysical Society, pp. 4182–4192, 2021.'
ista: 'Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. 2021. Holding it together:
when cadherin meets cadherin. Biophysical Journal. 120, 4182–4192.'
mla: 'Arslan, Feyza N., et al. “Holding It Together: When Cadherin Meets Cadherin.”
Biophysical Journal, vol. 120, Biophysical Society, 2021, pp. 4182–92,
doi:10.1016/j.bpj.2021.03.025.'
short: F.N. Arslan, J. Eckert, T. Schmidt, C.-P.J. Heisenberg, Biophysical Journal
120 (2021) 4182–4192.
date_created: 2021-04-25T22:01:30Z
date_published: 2021-10-05T00:00:00Z
date_updated: 2023-08-08T13:14:10Z
day: '05'
department:
- _id: CaHe
doi: 10.1016/j.bpj.2021.03.025
external_id:
isi:
- '000704646900006'
pmid:
- '33794149'
intvolume: ' 120'
isi: 1
language:
- iso: eng
main_file_link:
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url: https://scholarlypublications.universiteitleiden.nl/access/item%3A3251048/view
month: '10'
oa: 1
oa_version: Published Version
page: 4182-4192
pmid: 1
publication: Biophysical Journal
publication_identifier:
eissn:
- 1542-0086
issn:
- 0006-3495
publication_status: published
publisher: Biophysical Society
quality_controlled: '1'
related_material:
record:
- id: '12368'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Holding it together: when cadherin meets cadherin'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 120
year: '2021'
...
---
_id: '9351'
abstract:
- lang: eng
text: 'We consider the many-body quantum evolution of a factorized initial data,
in the mean-field regime. We show that fluctuations around the limiting Hartree
dynamics satisfy large deviation estimates that are consistent with central limit
theorems that have been established in the last years. '
acknowledgement: The authors gratefully acknowledge Gérard Ben Arous for suggesting
this kind of result. K.L.K. was partially supported by NSF CAREER Award DMS-125479
and a Simons Sabbatical Fellowship. S.R. acknowledges funding from the European
Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 754411. B. S. gratefully acknowledges partial support from the
NCCR SwissMAP, from the Swiss National Science Foundation through the Grant “Dynamical
and energetic properties of Bose–Einstein condensates” and from the European Research
Council through the ERC-AdG CLaQS. Funding Open access funding provided by Institute
of Science and Technology (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Kay
full_name: Kirkpatrick, Kay
last_name: Kirkpatrick
- first_name: Simone Anna Elvira
full_name: Rademacher, Simone Anna Elvira
id: 856966FE-A408-11E9-977E-802DE6697425
last_name: Rademacher
orcid: 0000-0001-5059-4466
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
citation:
ama: Kirkpatrick K, Rademacher SAE, Schlein B. A large deviation principle in many-body
quantum dynamics. Annales Henri Poincare. 2021;22:2595-2618. doi:10.1007/s00023-021-01044-1
apa: Kirkpatrick, K., Rademacher, S. A. E., & Schlein, B. (2021). A large deviation
principle in many-body quantum dynamics. Annales Henri Poincare. Springer
Nature. https://doi.org/10.1007/s00023-021-01044-1
chicago: Kirkpatrick, Kay, Simone Anna Elvira Rademacher, and Benjamin Schlein.
“A Large Deviation Principle in Many-Body Quantum Dynamics.” Annales Henri
Poincare. Springer Nature, 2021. https://doi.org/10.1007/s00023-021-01044-1.
ieee: K. Kirkpatrick, S. A. E. Rademacher, and B. Schlein, “A large deviation principle
in many-body quantum dynamics,” Annales Henri Poincare, vol. 22. Springer
Nature, pp. 2595–2618, 2021.
ista: Kirkpatrick K, Rademacher SAE, Schlein B. 2021. A large deviation principle
in many-body quantum dynamics. Annales Henri Poincare. 22, 2595–2618.
mla: Kirkpatrick, Kay, et al. “A Large Deviation Principle in Many-Body Quantum
Dynamics.” Annales Henri Poincare, vol. 22, Springer Nature, 2021, pp.
2595–618, doi:10.1007/s00023-021-01044-1.
short: K. Kirkpatrick, S.A.E. Rademacher, B. Schlein, Annales Henri Poincare 22
(2021) 2595–2618.
date_created: 2021-04-25T22:01:30Z
date_published: 2021-04-08T00:00:00Z
date_updated: 2023-08-08T13:14:40Z
day: '08'
ddc:
- '530'
department:
- _id: RoSe
doi: 10.1007/s00023-021-01044-1
ec_funded: 1
external_id:
arxiv:
- '2010.13754'
isi:
- '000638022600001'
file:
- access_level: open_access
checksum: 1a0fb963f2f415ba470881a794f20eb6
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-15T11:15:40Z
date_updated: 2021-10-15T11:15:40Z
file_id: '10143'
file_name: 2021_Annales_Kirkpatrick.pdf
file_size: 522669
relation: main_file
success: 1
file_date_updated: 2021-10-15T11:15:40Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 2595-2618
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Annales Henri Poincare
publication_identifier:
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A large deviation principle in many-body quantum dynamics
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: 22
year: '2021'
...
---
_id: '9352'
abstract:
- lang: eng
text: This paper provides an a priori error analysis of a localized orthogonal decomposition
method for the numerical stochastic homogenization of a model random diffusion
problem. If the uniformly elliptic and bounded random coefficient field of the
model problem is stationary and satisfies a quantitative decorrelation assumption
in the form of the spectral gap inequality, then the expected $L^2$ error of the
method can be estimated, up to logarithmic factors, by $H+(\varepsilon/H)^{d/2}$,
$\varepsilon$ being the small correlation length of the random coefficient and
$H$ the width of the coarse finite element mesh that determines the spatial resolution.
The proof bridges recent results of numerical homogenization and quantitative
stochastic homogenization.
acknowledgement: 'This work was initiated while the authors enjoyed the kind hospitality
of the Hausdorff Institute for Mathematics in Bonn during the trimester program
Multiscale Problems: Algorithms, Numerical Analysis, and Computation. D. Peterseim
would like to acknowledge the kind hospitality of the Erwin Schrödinger International
Institute for Mathematics and Physics (ESI), where parts of this research were
developed under the frame of the thematic program Numerical Analysis of Complex
PDE Models in the Sciences.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Dietmar
full_name: Gallistl, Dietmar
last_name: Gallistl
- first_name: Dietmar
full_name: Peterseim, Dietmar
last_name: Peterseim
citation:
ama: Fischer JL, Gallistl D, Peterseim D. A priori error analysis of a numerical
stochastic homogenization method. SIAM Journal on Numerical Analysis. 2021;59(2):660-674.
doi:10.1137/19M1308992
apa: Fischer, J. L., Gallistl, D., & Peterseim, D. (2021). A priori error analysis
of a numerical stochastic homogenization method. SIAM Journal on Numerical
Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19M1308992
chicago: Fischer, Julian L, Dietmar Gallistl, and Dietmar Peterseim. “A Priori Error
Analysis of a Numerical Stochastic Homogenization Method.” SIAM Journal on
Numerical Analysis. Society for Industrial and Applied Mathematics, 2021.
https://doi.org/10.1137/19M1308992.
ieee: J. L. Fischer, D. Gallistl, and D. Peterseim, “A priori error analysis of
a numerical stochastic homogenization method,” SIAM Journal on Numerical Analysis,
vol. 59, no. 2. Society for Industrial and Applied Mathematics, pp. 660–674, 2021.
ista: Fischer JL, Gallistl D, Peterseim D. 2021. A priori error analysis of a numerical
stochastic homogenization method. SIAM Journal on Numerical Analysis. 59(2), 660–674.
mla: Fischer, Julian L., et al. “A Priori Error Analysis of a Numerical Stochastic
Homogenization Method.” SIAM Journal on Numerical Analysis, vol. 59, no.
2, Society for Industrial and Applied Mathematics, 2021, pp. 660–74, doi:10.1137/19M1308992.
short: J.L. Fischer, D. Gallistl, D. Peterseim, SIAM Journal on Numerical Analysis
59 (2021) 660–674.
date_created: 2021-04-25T22:01:31Z
date_published: 2021-03-09T00:00:00Z
date_updated: 2023-08-08T13:13:37Z
day: '09'
department:
- _id: JuFi
doi: 10.1137/19M1308992
external_id:
arxiv:
- '1912.11646'
isi:
- '000646030400003'
intvolume: ' 59'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1912.11646
month: '03'
oa: 1
oa_version: Preprint
page: 660-674
publication: SIAM Journal on Numerical Analysis
publication_identifier:
issn:
- 0036-1429
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: A priori error analysis of a numerical stochastic homogenization method
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 59
year: '2021'
...
---
_id: '9356'
abstract:
- lang: eng
text: 'In runtime verification, a monitor watches a trace of a system and, if possible,
decides after observing each finite prefix whether or not the unknown infinite
trace satisfies a given specification. We generalize the theory of runtime verification
to monitors that attempt to estimate numerical values of quantitative trace properties
(instead of attempting to conclude boolean values of trace specifications), such
as maximal or average response time along a trace. Quantitative monitors are approximate:
with every finite prefix, they can improve their estimate of the infinite trace''s
unknown property value. Consequently, quantitative monitors can be compared with
regard to a precision-cost trade-off: better approximations of the property value
require more monitor resources, such as states (in the case of finite-state monitors)
or registers, and additional resources yield better approximations. We introduce
a formal framework for quantitative and approximate monitoring, show how it conservatively
generalizes the classical boolean setting for monitoring, and give several precision-cost
trade-offs for monitors. For example, we prove that there are quantitative properties
for which every additional register improves monitoring precision.'
acknowledgement: We thank the anonymous reviewers for their helpful comments. This
research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23
(Wittgenstein Award).
article_number: '9470547'
article_processing_charge: No
arxiv: 1
author:
- 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: Naci E
full_name: Sarac, Naci E
id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425
last_name: Sarac
citation:
ama: 'Henzinger TA, Sarac NE. Quantitative and approximate monitoring. In: Proceedings
of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute
of Electrical and Electronics Engineers; 2021. doi:10.1109/LICS52264.2021.9470547'
apa: 'Henzinger, T. A., & Sarac, N. E. (2021). Quantitative and approximate
monitoring. In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in
Computer Science. Online: Institute of Electrical and Electronics Engineers.
https://doi.org/10.1109/LICS52264.2021.9470547'
chicago: Henzinger, Thomas A, and Naci E Sarac. “Quantitative and Approximate Monitoring.”
In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science.
Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/LICS52264.2021.9470547.
ieee: T. A. Henzinger and N. E. Sarac, “Quantitative and approximate monitoring,”
in Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science,
Online, 2021.
ista: 'Henzinger TA, Sarac NE. 2021. Quantitative and approximate monitoring. Proceedings
of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium
on Logic in Computer Science, 9470547.'
mla: Henzinger, Thomas A., and Naci E. Sarac. “Quantitative and Approximate Monitoring.”
Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science,
9470547, Institute of Electrical and Electronics Engineers, 2021, doi:10.1109/LICS52264.2021.9470547.
short: T.A. Henzinger, N.E. Sarac, in:, Proceedings of the 36th Annual ACM/IEEE
Symposium on Logic in Computer Science, Institute of Electrical and Electronics
Engineers, 2021.
conference:
end_date: 2021-07-02
location: Online
name: 'LICS: Symposium on Logic in Computer Science'
start_date: 2021-06-29
date_created: 2021-04-30T17:30:47Z
date_published: 2021-06-29T00:00:00Z
date_updated: 2023-08-08T13:52:56Z
day: '29'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.1109/LICS52264.2021.9470547
external_id:
arxiv:
- '2105.08353'
isi:
- '000947350400021'
file:
- access_level: open_access
checksum: 6e4cba3f72775f479c5b1b75d1a4a0c4
content_type: application/pdf
creator: esarac
date_created: 2021-06-16T08:23:54Z
date_updated: 2021-06-16T08:23:54Z
file_id: '9557'
file_name: qam.pdf
file_size: 641990
relation: main_file
success: 1
file_date_updated: 2021-06-16T08:23:54Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer
Science
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantitative and approximate monitoring
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9359'
abstract:
- lang: eng
text: "We prove that the factorization homologies of a scheme with coefficients
in truncated polynomial algebras compute the cohomologies of its generalized configuration
spaces. Using Koszul duality between commutative algebras and Lie algebras, we
obtain new expressions for the cohomologies of the latter. As a consequence, we
obtain a uniform and conceptual approach for treating homological stability, homological
densities, and arithmetic densities of generalized configuration spaces. Our results
categorify, generalize, and in fact provide a conceptual understanding of the
coincidences appearing in the work of Farb--Wolfson--Wood. Our computation of
the stable homological densities also yields rational homotopy types, answering
a question posed by Vakil--Wood. Our approach hinges on the study of homological
stability of cohomological Chevalley complexes, which is of independent interest.\r\n"
acknowledgement: "This paper owes an obvious intellectual debt to the illuminating
treatments of factorization homology by J.\r\nFrancis, D. Gaitsgory, and J. Lurie
in [GL,G1, FG]. The author would like to thank B. Farb and J. Wolfson for\r\nbringing
the question of explaining coincidences in homological densities to his attention.
Moreover, the author\r\nthanks J. Wolfson for many helpful conversations on the
subject, O. Randal-Williams for many comments which\r\ngreatly help improve the
exposition, and G. C. Drummond-Cole for many useful conversations on L∞-algebras.\r\nFinally,
the author is grateful to the anonymous referee for carefully reading the manuscript
and for providing\r\nnumerous comments which greatly helped improve the clarity
and precision of the exposition.\r\nThis work is supported by the Advanced Grant
“Arithmetic and Physics of Higgs moduli spaces” No. 320593 of\r\nthe European Research
Council and the Lise Meitner fellowship “Algebro-Geometric Applications of Factorization\r\nHomology,”
Austrian Science Fund (FWF): M 2751."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Quoc P
full_name: Ho, Quoc P
id: 3DD82E3C-F248-11E8-B48F-1D18A9856A87
last_name: Ho
citation:
ama: Ho QP. Homological stability and densities of generalized configuration spaces.
Geometry & Topology. 2021;25(2):813-912. doi:10.2140/gt.2021.25.813
apa: Ho, Q. P. (2021). Homological stability and densities of generalized configuration
spaces. Geometry & Topology. Mathematical Sciences Publishers. https://doi.org/10.2140/gt.2021.25.813
chicago: Ho, Quoc P. “Homological Stability and Densities of Generalized Configuration
Spaces.” Geometry & Topology. Mathematical Sciences Publishers, 2021.
https://doi.org/10.2140/gt.2021.25.813.
ieee: Q. P. Ho, “Homological stability and densities of generalized configuration
spaces,” Geometry & Topology, vol. 25, no. 2. Mathematical Sciences
Publishers, pp. 813–912, 2021.
ista: Ho QP. 2021. Homological stability and densities of generalized configuration
spaces. Geometry & Topology. 25(2), 813–912.
mla: Ho, Quoc P. “Homological Stability and Densities of Generalized Configuration
Spaces.” Geometry & Topology, vol. 25, no. 2, Mathematical Sciences
Publishers, 2021, pp. 813–912, doi:10.2140/gt.2021.25.813.
short: Q.P. Ho, Geometry & Topology 25 (2021) 813–912.
date_created: 2021-05-02T06:59:33Z
date_published: 2021-04-27T00:00:00Z
date_updated: 2023-08-08T13:28:59Z
day: '27'
ddc:
- '514'
- '516'
- '512'
department:
- _id: TaHa
doi: 10.2140/gt.2021.25.813
ec_funded: 1
external_id:
arxiv:
- '1802.07948'
isi:
- '000682738600005'
file:
- access_level: open_access
checksum: 643a8d2d6f06f0888dcd7503f55d0920
content_type: application/pdf
creator: qho
date_created: 2021-05-03T06:54:06Z
date_updated: 2021-05-03T06:54:06Z
file_id: '9366'
file_name: densities.pdf
file_size: 479268
relation: main_file
success: 1
file_date_updated: 2021-05-03T06:54:06Z
has_accepted_license: '1'
intvolume: ' 25'
isi: 1
issue: '2'
keyword:
- Generalized configuration spaces
- homological stability
- homological densities
- chiral algebras
- chiral homology
- factorization algebras
- Koszul duality
- Ran space
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 813-912
project:
- _id: 25E549F4-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '320593'
name: Arithmetic and physics of Higgs moduli spaces
- _id: 26B96266-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02751
name: Algebro-Geometric Applications of Factorization Homology
publication: Geometry & Topology
publication_identifier:
issn:
- 1364-0380
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
status: public
title: Homological stability and densities of generalized configuration spaces
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 25
year: '2021'
...
---
_id: '9362'
abstract:
- lang: eng
text: A central goal in systems neuroscience is to understand the functions performed
by neural circuits. Previous top-down models addressed this question by comparing
the behaviour of an ideal model circuit, optimised to perform a given function,
with neural recordings. However, this requires guessing in advance what function
is being performed, which may not be possible for many neural systems. To address
this, we propose an inverse reinforcement learning (RL) framework for inferring
the function performed by a neural network from data. We assume that the responses
of each neuron in a network are optimised so as to drive the network towards ‘rewarded’
states, that are desirable for performing a given function. We then show how one
can use inverse RL to infer the reward function optimised by the network from
observing its responses. This inferred reward function can be used to predict
how the neural network should adapt its dynamics to perform the same function
when the external environment or network structure changes. This could lead to
theoretical predictions about how neural network dynamics adapt to deal with cell
death and/or varying sensory stimulus statistics.
acknowledgement: The authors would like to thank Ulisse Ferrari for useful discussions
and feedback.
article_number: e0248940
article_processing_charge: No
article_type: original
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
citation:
ama: Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent
neural network. PLoS ONE. 2021;16(4). doi:10.1371/journal.pone.0248940
apa: Chalk, M. J., Tkačik, G., & Marre, O. (2021). Inferring the function performed
by a recurrent neural network. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0248940
chicago: Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function
Performed by a Recurrent Neural Network.” PLoS ONE. Public Library of Science,
2021. https://doi.org/10.1371/journal.pone.0248940.
ieee: M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by
a recurrent neural network,” PLoS ONE, vol. 16, no. 4. Public Library of
Science, 2021.
ista: Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent
neural network. PLoS ONE. 16(4), e0248940.
mla: Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent
Neural Network.” PLoS ONE, vol. 16, no. 4, e0248940, Public Library of
Science, 2021, doi:10.1371/journal.pone.0248940.
short: M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).
date_created: 2021-05-02T22:01:28Z
date_published: 2021-04-15T00:00:00Z
date_updated: 2023-10-18T08:17:42Z
day: '15'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0248940
external_id:
isi:
- '000641474900072'
pmid:
- '33857170'
file:
- access_level: open_access
checksum: c52da133850307d2031f552d998f00e8
content_type: application/pdf
creator: kschuh
date_created: 2021-05-04T13:22:19Z
date_updated: 2021-05-04T13:22:19Z
file_id: '9371'
file_name: 2021_pone_Chalk.pdf
file_size: 2768282
relation: main_file
success: 1
file_date_updated: 2021-05-04T13:22:19Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS ONE
publication_identifier:
eissn:
- '19326203'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inferring the function performed by a recurrent neural network
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: 16
year: '2021'
...
---
_id: '9363'
abstract:
- lang: eng
text: Optogenetics has been harnessed to shed new mechanistic light on current and
future therapeutic strategies. This has been to date achieved by the regulation
of ion flow and electrical signals in neuronal cells and neural circuits that
are known to be affected by disease. In contrast, the optogenetic delivery of
trophic biochemical signals, which support cell survival and are implicated in
degenerative disorders, has never been demonstrated in an animal model of disease.
Here, we reengineered the human and Drosophila melanogaster REarranged during
Transfection (hRET and dRET) receptors to be activated by light, creating one-component
optogenetic tools termed Opto-hRET and Opto-dRET. Upon blue light stimulation,
these receptors robustly induced the MAPK/ERK proliferative signaling pathway
in cultured cells. In PINK1B9 flies that exhibit loss of PTEN-induced putative
kinase 1 (PINK1), a kinase associated with familial Parkinson’s disease (PD),
light activation of Opto-dRET suppressed mitochondrial defects, tissue degeneration
and behavioral deficits. In human cells with PINK1 loss-of-function, mitochondrial
fragmentation was rescued using Opto-dRET via the PI3K/NF-кB pathway. Our results
demonstrate that a light-activated receptor can ameliorate disease hallmarks in
a genetic model of PD. The optogenetic delivery of trophic signals is cell type-specific
and reversible and thus has the potential to inspire novel strategies towards
a spatio-temporal regulation of tissue repair.
acknowledgement: We thank R. Cagan, A. Whitworth and J. Nagpal for fly lines and advice,
S. Herlitze for provision of a tissue culture illuminator, and Verian Bader for
help with statistical analysis.
article_processing_charge: No
author:
- first_name: Álvaro
full_name: Inglés Prieto, Álvaro
id: 2A9DB292-F248-11E8-B48F-1D18A9856A87
last_name: Inglés Prieto
orcid: 0000-0002-5409-8571
- first_name: Nikolas
full_name: Furthmann, Nikolas
last_name: Furthmann
- first_name: Samuel H.
full_name: Crossman, Samuel H.
last_name: Crossman
- first_name: Alexandra Madelaine
full_name: Tichy, Alexandra Madelaine
last_name: Tichy
- first_name: Nina
full_name: Hoyer, Nina
last_name: Hoyer
- first_name: Meike
full_name: Petersen, Meike
last_name: Petersen
- first_name: Vanessa
full_name: Zheden, Vanessa
id: 39C5A68A-F248-11E8-B48F-1D18A9856A87
last_name: Zheden
- first_name: Julia
full_name: Bicher, Julia
id: 3CCBB46E-F248-11E8-B48F-1D18A9856A87
last_name: Bicher
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Peter
full_name: Soba, Peter
last_name: Soba
- first_name: Konstanze F.
full_name: Winklhofer, Konstanze F.
last_name: Winklhofer
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Inglés Prieto Á, Furthmann N, Crossman SH, et al. Optogenetic delivery of trophic
signals in a genetic model of Parkinson’s disease. PLoS genetics. 2021;17(4):e1009479.
doi:10.1371/journal.pgen.1009479
apa: Inglés Prieto, Á., Furthmann, N., Crossman, S. H., Tichy, A. M., Hoyer, N.,
Petersen, M., … Janovjak, H. L. (2021). Optogenetic delivery of trophic signals
in a genetic model of Parkinson’s disease. PLoS Genetics. Public Library
of Science. https://doi.org/10.1371/journal.pgen.1009479
chicago: Inglés Prieto, Álvaro, Nikolas Furthmann, Samuel H. Crossman, Alexandra
Madelaine Tichy, Nina Hoyer, Meike Petersen, Vanessa Zheden, et al. “Optogenetic
Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” PLoS
Genetics. Public Library of Science, 2021. https://doi.org/10.1371/journal.pgen.1009479.
ieee: Á. Inglés Prieto et al., “Optogenetic delivery of trophic signals in
a genetic model of Parkinson’s disease,” PLoS genetics, vol. 17, no. 4.
Public Library of Science, p. e1009479, 2021.
ista: Inglés Prieto Á, Furthmann N, Crossman SH, Tichy AM, Hoyer N, Petersen M,
Zheden V, Bicher J, Gschaider-Reichhart E, György A, Siekhaus DE, Soba P, Winklhofer
KF, Janovjak HL. 2021. Optogenetic delivery of trophic signals in a genetic model
of Parkinson’s disease. PLoS genetics. 17(4), e1009479.
mla: Inglés Prieto, Álvaro, et al. “Optogenetic Delivery of Trophic Signals in a
Genetic Model of Parkinson’s Disease.” PLoS Genetics, vol. 17, no. 4, Public
Library of Science, 2021, p. e1009479, doi:10.1371/journal.pgen.1009479.
short: Á. Inglés Prieto, N. Furthmann, S.H. Crossman, A.M. Tichy, N. Hoyer, M. Petersen,
V. Zheden, J. Bicher, E. Gschaider-Reichhart, A. György, D.E. Siekhaus, P. Soba,
K.F. Winklhofer, H.L. Janovjak, PLoS Genetics 17 (2021) e1009479.
date_created: 2021-05-02T22:01:29Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2023-08-08T13:17:47Z
day: '01'
ddc:
- '570'
department:
- _id: EM-Fac
- _id: LoSw
- _id: DaSi
doi: 10.1371/journal.pgen.1009479
external_id:
isi:
- '000640606700001'
file:
- access_level: open_access
checksum: 82a74668f863e8dfb22fdd4f845c92ce
content_type: application/pdf
creator: kschuh
date_created: 2021-05-04T09:05:27Z
date_updated: 2021-05-04T09:05:27Z
file_id: '9369'
file_name: 2021_PLOS_Ingles-Prieto.pdf
file_size: 3072764
relation: main_file
success: 1
file_date_updated: 2021-05-04T09:05:27Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: e1009479
publication: PLoS genetics
publication_identifier:
eissn:
- '15537404'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease
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: 17
year: '2021'
...
---
_id: '9365'
abstract:
- lang: eng
text: In this paper, we propose a new iterative method with alternated inertial
step for solving split common null point problem in real Hilbert spaces. We obtain
weak convergence of the proposed iterative algorithm. Furthermore, we introduce
the notion of bounded linear regularity property for the split common null point
problem and obtain the linear convergence property for the new algorithm under
some mild assumptions. Finally, we provide some numerical examples to demonstrate
the performance and efficiency of the proposed method.
acknowledgement: The second author has received funding from the European Research
Council (ERC) under the European Union's Seventh Framework Program (FP7-2007-2013)
(Grant agreement No. 616160).
article_processing_charge: No
article_type: original
author:
- first_name: Ferdinard U.
full_name: Ogbuisi, Ferdinard U.
last_name: Ogbuisi
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
- first_name: Jen Chih
full_name: Yao, Jen Chih
last_name: Yao
citation:
ama: Ogbuisi FU, Shehu Y, Yao JC. Convergence analysis of new inertial method for
the split common null point problem. Optimization. 2021. doi:10.1080/02331934.2021.1914035
apa: Ogbuisi, F. U., Shehu, Y., & Yao, J. C. (2021). Convergence analysis of
new inertial method for the split common null point problem. Optimization.
Taylor and Francis. https://doi.org/10.1080/02331934.2021.1914035
chicago: Ogbuisi, Ferdinard U., Yekini Shehu, and Jen Chih Yao. “Convergence Analysis
of New Inertial Method for the Split Common Null Point Problem.” Optimization.
Taylor and Francis, 2021. https://doi.org/10.1080/02331934.2021.1914035.
ieee: F. U. Ogbuisi, Y. Shehu, and J. C. Yao, “Convergence analysis of new inertial
method for the split common null point problem,” Optimization. Taylor and
Francis, 2021.
ista: Ogbuisi FU, Shehu Y, Yao JC. 2021. Convergence analysis of new inertial method
for the split common null point problem. Optimization.
mla: Ogbuisi, Ferdinard U., et al. “Convergence Analysis of New Inertial Method
for the Split Common Null Point Problem.” Optimization, Taylor and Francis,
2021, doi:10.1080/02331934.2021.1914035.
short: F.U. Ogbuisi, Y. Shehu, J.C. Yao, Optimization (2021).
date_created: 2021-05-02T22:01:29Z
date_published: 2021-04-14T00:00:00Z
date_updated: 2023-10-10T09:48:41Z
day: '14'
department:
- _id: VlKo
doi: 10.1080/02331934.2021.1914035
ec_funded: 1
external_id:
isi:
- '000640109300001'
isi: 1
language:
- iso: eng
month: '04'
oa_version: None
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Optimization
publication_identifier:
eissn:
- 1029-4945
issn:
- 0233-1934
publication_status: published
publisher: Taylor and Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Convergence analysis of new inertial method for the split common null point
problem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9368'
abstract:
- lang: eng
text: The quality control system for messenger RNA (mRNA) is fundamental for cellular
activities in eukaryotes. To elucidate the molecular mechanism of 3'-Phosphoinositide-Dependent
Protein Kinase1 (PDK1), a master regulator that is essential throughout eukaryotic
growth and development, we employed a forward genetic approach to screen for suppressors
of the loss-of-function T-DNA insertion double mutant pdk1.1 pdk1.2 in Arabidopsis
thaliana. Notably, the severe growth attenuation of pdk1.1 pdk1.2 was rescued
by sop21 (suppressor of pdk1.1 pdk1.2), which harbours a loss-of-function mutation
in PELOTA1 (PEL1). PEL1 is a homologue of mammalian PELOTA and yeast (Saccharomyces
cerevisiae) DOM34p, which each form a heterodimeric complex with the GTPase HBS1
(HSP70 SUBFAMILY B SUPPRESSOR1, also called SUPERKILLER PROTEIN7, SKI7), a protein
that is responsible for ribosomal rescue and thereby assures the quality and fidelity
of mRNA molecules during translation. Genetic analysis further revealed that a
dysfunctional PEL1-HBS1 complex failed to degrade the T-DNA-disrupted PDK1 transcripts,
which were truncated but functional, and thus rescued the growth and developmental
defects of pdk1.1 pdk1.2. Our studies demonstrated the functionality of a homologous
PELOTA-HBS1 complex and identified its essential regulatory role in plants, providing
insights into the mechanism of mRNA quality control.
acknowledgement: 'We gratefully acknowledge the Arabidopsis Biological Resource Centre
(ABRC) for providing T-DNA insertional mutants, and Prof. Remko Offringa for sharing
published seeds. We thank Yuchuan Liu (Shanghai OE Biotech Co., Ltd) for help with
proteomics data analysis, Xixi Zhang (IST Austria) for providing the pDONR-P4P1r-mCherry
plasmid, and Yao Xiao (Technical University of Munich), Alexander Johnson (IST Austria)
and Hana Semeradova (IST Austria) for helpful discussions. The study was supported
by National Natural Science Foundation of China (NSFC, 31721001, 91954206, to H.-W.
X.), “Ten-Thousand Talent Program” (to H.-W. X.) and Collaborative Innovation Center
of Crop Stress Biology, Henan Province, and Austrian Science Fund (FWF): I 3630-B25
(to J. F.). S.T. was funded by a European Molecular Biology Organization (EMBO)
long-term postdoctoral fellowship (ALTF 723-2015).'
article_processing_charge: No
article_type: original
author:
- first_name: W
full_name: Kong, W
last_name: Kong
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Q
full_name: Zhao, Q
last_name: Zhao
- first_name: DL
full_name: Lin, DL
last_name: Lin
- first_name: ZH
full_name: Xu, ZH
last_name: Xu
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: HW
full_name: Xue, HW
last_name: Xue
citation:
ama: Kong W, Tan S, Zhao Q, et al. mRNA surveillance complex PELOTA-HBS1 eegulates
phosphoinositide-sependent protein kinase1 and plant growth. Plant Physiology.
2021;186(4):2003-2020. doi:10.1093/plphys/kiab199
apa: Kong, W., Tan, S., Zhao, Q., Lin, D., Xu, Z., Friml, J., & Xue, H. (2021).
mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein
kinase1 and plant growth. Plant Physiology. American Society of Plant Biologists.
https://doi.org/10.1093/plphys/kiab199
chicago: Kong, W, Shutang Tan, Q Zhao, DL Lin, ZH Xu, Jiří Friml, and HW Xue. “MRNA
Surveillance Complex PELOTA-HBS1 Eegulates Phosphoinositide-Sependent Protein
Kinase1 and Plant Growth.” Plant Physiology. American Society of Plant
Biologists, 2021. https://doi.org/10.1093/plphys/kiab199.
ieee: W. Kong et al., “mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent
protein kinase1 and plant growth,” Plant Physiology, vol. 186, no. 4. American
Society of Plant Biologists, pp. 2003–2020, 2021.
ista: Kong W, Tan S, Zhao Q, Lin D, Xu Z, Friml J, Xue H. 2021. mRNA surveillance
complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant
growth. Plant Physiology. 186(4), 2003–2020.
mla: Kong, W., et al. “MRNA Surveillance Complex PELOTA-HBS1 Eegulates Phosphoinositide-Sependent
Protein Kinase1 and Plant Growth.” Plant Physiology, vol. 186, no. 4, American
Society of Plant Biologists, 2021, pp. 2003–20, doi:10.1093/plphys/kiab199.
short: W. Kong, S. Tan, Q. Zhao, D. Lin, Z. Xu, J. Friml, H. Xue, Plant Physiology
186 (2021) 2003–2020.
date_created: 2021-05-03T13:28:20Z
date_published: 2021-04-30T00:00:00Z
date_updated: 2023-09-05T12:20:27Z
day: '30'
department:
- _id: JiFr
doi: 10.1093/plphys/kiab199
external_id:
isi:
- '000703922000025'
pmid:
- '33930167'
intvolume: ' 186'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/plphys/kiab199
month: '04'
oa: 1
oa_version: Published Version
page: 2003-2020
pmid: 1
project:
- _id: 256FEF10-B435-11E9-9278-68D0E5697425
grant_number: 723-2015
name: Long Term Fellowship
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
issn:
- 0032-0889
publication_status: published
publisher: American Society of Plant Biologists
quality_controlled: '1'
status: public
title: mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent
protein kinase1 and plant growth
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 186
year: '2021'
...
---
_id: '9374'
abstract:
- lang: eng
text: If there are no constraints on the process of speciation, then the number
of species might be expected to match the number of available niches and this
number might be indefinitely large. One possible constraint is the opportunity
for allopatric divergence. In 1981, Felsenstein used a simple and elegant model
to ask if there might also be genetic constraints. He showed that progress towards
speciation could be described by the build‐up of linkage disequilibrium among
divergently selected loci and between these loci and those contributing to other
forms of reproductive isolation. Therefore, speciation is opposed by recombination,
because it tends to break down linkage disequilibria. Felsenstein then introduced
a crucial distinction between “two‐allele” models, which are subject to this effect,
and “one‐allele” models, which are free from the recombination constraint. These
fundamentally important insights have been the foundation for both empirical and
theoretical studies of speciation ever since.
acknowledgement: RKB was funded by the Natural Environment Research Council (NE/P012272/1
& NE/P001610/1), the European Research Council (693030 BARRIERS), and the Swedish
Research Council (VR) (2018‐03695). MRS was funded by the National Science Foundation
(Grant No. DEB1939290).
article_processing_charge: No
article_type: original
author:
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
- first_name: Maria R.
full_name: Servedio, Maria R.
last_name: Servedio
- first_name: Carole M.
full_name: Smadja, Carole M.
last_name: Smadja
- first_name: Claudia
full_name: Bank, Claudia
last_name: Bank
- 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: Samuel M.
full_name: Flaxman, Samuel M.
last_name: Flaxman
- first_name: Tatiana
full_name: Giraud, Tatiana
last_name: Giraud
- first_name: Robin
full_name: Hopkins, Robin
last_name: Hopkins
- first_name: Erica L.
full_name: Larson, Erica L.
last_name: Larson
- first_name: Martine E.
full_name: Maan, Martine E.
last_name: Maan
- first_name: Joana
full_name: Meier, Joana
last_name: Meier
- first_name: Richard
full_name: Merrill, Richard
last_name: Merrill
- first_name: Mohamed A. F.
full_name: Noor, Mohamed A. F.
last_name: Noor
- first_name: Daniel
full_name: Ortiz‐Barrientos, Daniel
last_name: Ortiz‐Barrientos
- first_name: Anna
full_name: Qvarnström, Anna
last_name: Qvarnström
citation:
ama: Butlin RK, Servedio MR, Smadja CM, et al. Homage to Felsenstein 1981, or why
are there so few/many species? Evolution. 2021;75(5):978-988. doi:10.1111/evo.14235
apa: Butlin, R. K., Servedio, M. R., Smadja, C. M., Bank, C., Barton, N. H., Flaxman,
S. M., … Qvarnström, A. (2021). Homage to Felsenstein 1981, or why are there so
few/many species? Evolution. Wiley. https://doi.org/10.1111/evo.14235
chicago: Butlin, Roger K., Maria R. Servedio, Carole M. Smadja, Claudia Bank, Nicholas
H Barton, Samuel M. Flaxman, Tatiana Giraud, et al. “Homage to Felsenstein 1981,
or Why Are There so Few/Many Species?” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14235.
ieee: R. K. Butlin et al., “Homage to Felsenstein 1981, or why are there
so few/many species?,” Evolution, vol. 75, no. 5. Wiley, pp. 978–988, 2021.
ista: Butlin RK, Servedio MR, Smadja CM, Bank C, Barton NH, Flaxman SM, Giraud T,
Hopkins R, Larson EL, Maan ME, Meier J, Merrill R, Noor MAF, Ortiz‐Barrientos
D, Qvarnström A. 2021. Homage to Felsenstein 1981, or why are there so few/many
species? Evolution. 75(5), 978–988.
mla: Butlin, Roger K., et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many
Species?” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 978–88, doi:10.1111/evo.14235.
short: R.K. Butlin, M.R. Servedio, C.M. Smadja, C. Bank, N.H. Barton, S.M. Flaxman,
T. Giraud, R. Hopkins, E.L. Larson, M.E. Maan, J. Meier, R. Merrill, M.A.F. Noor,
D. Ortiz‐Barrientos, A. Qvarnström, Evolution 75 (2021) 978–988.
date_created: 2021-05-06T04:34:47Z
date_published: 2021-04-19T00:00:00Z
date_updated: 2023-09-05T15:44:33Z
day: '19'
department:
- _id: NiBa
doi: 10.1111/evo.14235
external_id:
isi:
- '000647224000001'
intvolume: ' 75'
isi: 1
issue: '5'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
- General Agricultural and Biological Sciences
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://onlinelibrary.wiley.com/doi/10.1111/evo.14235
month: '04'
oa: 1
oa_version: Published Version
page: 978-988
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Homage to Felsenstein 1981, or why are there so few/many species?
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: 75
year: '2021'
...
---
_id: '9375'
abstract:
- lang: eng
text: Genetic variation segregates as linked sets of variants, or haplotypes. Haplotypes
and linkage are central to genetics and underpin virtually all genetic and selection
analysis. And yet, genomic data often lack haplotype information, due to constraints
in sequencing technologies. Here we present “haplotagging”, a simple, low-cost
linked-read sequencing technique that allows sequencing of hundreds of individuals
while retaining linkage information. We apply haplotagging to construct megabase-size
haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene),
which form overlapping hybrid zones across an elevational gradient in Ecuador.
Haplotagging identifies loci controlling distinctive high- and lowland wing color
patterns. Divergent haplotypes are found at the same major loci in both species,
while chromosome rearrangements show no parallelism. Remarkably, in both species
the geographic clines for the major wing pattern loci are displaced by 18 km,
leading to the rise of a novel hybrid morph in the centre of the hybrid zone.
We propose that shared warning signalling (Müllerian mimicry) may couple the cline
shifts seen in both species, and facilitate the parallel co-emergence of a novel
hybrid morph in both co-mimetic species. Our results show the power of efficient
haplotyping methods when combined with large-scale sequencing data from natural
populations.
acknowledgement: 'We thank Felicity Jones for input into experimental design, helpful
discussion and improving the manuscript. We thank the Rolian, Jiggins, Chan and
Jones Labs members for support, insightful scientific discussion and improving the
manuscript. We thank the Rolian lab members, the Animal Resource Centre staff at
the University of Calgary, and Caroline Schmid and Ann-Katrin Geysel at the Friedrich
Miescher Laboratory for animal husbandry. We thank Christa Lanz, Rebecca Schwab
and Ilja Bezrukov for assistance with high-throughput sequencing and associated
data processing; Andre Noll and the MPI Tübingen IT team for computational support.
We thank Ben Haller and Richard Durbin for helpful discussions. We thank David M.
Kingsley for thoughtful input that has greatly improved our manuscript. J.I.M. is
supported by a Research Fellowship from St. John’s College, Cambridge. A.D. was
supported by a European Research Council Consolidator Grant (No. 617279 “EvolRecombAdapt”,
P/I Felicity Jones). C.R. is supported by Discovery Grant #4181932 from the Natural
Sciences and Engineering Research Council of Canada and by the Faculty of Veterinary
Medicine at the University of Calgary. C.D.J. is supported by a BBSRC grant BB/R007500
and a European Research Council Advanced Grant (No. 339873 “SpeciationGenetics”).
M.K. and Y.F.C. are supported by the Max Planck Society and a European Research
Council Starting Grant (No. 639096 “HybridMiX”).'
article_number: e2015005118
article_processing_charge: No
article_type: original
author:
- first_name: Joana I.
full_name: Meier, Joana I.
last_name: Meier
- first_name: Patricio A.
full_name: Salazar, Patricio A.
last_name: Salazar
- first_name: Marek
full_name: Kučka, Marek
last_name: Kučka
- first_name: Robert William
full_name: Davies, Robert William
last_name: Davies
- first_name: Andreea
full_name: Dréau, Andreea
last_name: Dréau
- first_name: Ismael
full_name: Aldás, Ismael
last_name: Aldás
- first_name: Olivia Box
full_name: Power, Olivia Box
last_name: Power
- first_name: Nicola J.
full_name: Nadeau, Nicola J.
last_name: Nadeau
- first_name: Jon R.
full_name: Bridle, Jon R.
last_name: Bridle
- first_name: Campbell
full_name: Rolian, Campbell
last_name: Rolian
- 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: W. Owen
full_name: McMillan, W. Owen
last_name: McMillan
- first_name: Chris D.
full_name: Jiggins, Chris D.
last_name: Jiggins
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
citation:
ama: Meier JI, Salazar PA, Kučka M, et al. Haplotype tagging reveals parallel formation
of hybrid races in two butterfly species. PNAS. 2021;118(25). doi:10.1073/pnas.2015005118
apa: Meier, J. I., Salazar, P. A., Kučka, M., Davies, R. W., Dréau, A., Aldás, I.,
… Chan, Y. F. (2021). Haplotype tagging reveals parallel formation of hybrid races
in two butterfly species. PNAS. Proceedings of the National Academy of
Sciences. https://doi.org/10.1073/pnas.2015005118
chicago: Meier, Joana I., Patricio A. Salazar, Marek Kučka, Robert William Davies,
Andreea Dréau, Ismael Aldás, Olivia Box Power, et al. “Haplotype Tagging Reveals
Parallel Formation of Hybrid Races in Two Butterfly Species.” PNAS. Proceedings
of the National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2015005118.
ieee: J. I. Meier et al., “Haplotype tagging reveals parallel formation of
hybrid races in two butterfly species,” PNAS, vol. 118, no. 25. Proceedings
of the National Academy of Sciences, 2021.
ista: Meier JI, Salazar PA, Kučka M, Davies RW, Dréau A, Aldás I, Power OB, Nadeau
NJ, Bridle JR, Rolian C, Barton NH, McMillan WO, Jiggins CD, Chan YF. 2021. Haplotype
tagging reveals parallel formation of hybrid races in two butterfly species. PNAS.
118(25), e2015005118.
mla: Meier, Joana I., et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid
Races in Two Butterfly Species.” PNAS, vol. 118, no. 25, e2015005118, Proceedings
of the National Academy of Sciences, 2021, doi:10.1073/pnas.2015005118.
short: J.I. Meier, P.A. Salazar, M. Kučka, R.W. Davies, A. Dréau, I. Aldás, O.B.
Power, N.J. Nadeau, J.R. Bridle, C. Rolian, N.H. Barton, W.O. McMillan, C.D. Jiggins,
Y.F. Chan, PNAS 118 (2021).
date_created: 2021-05-07T17:10:21Z
date_published: 2021-06-21T00:00:00Z
date_updated: 2023-08-08T13:33:09Z
day: '21'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1073/pnas.2015005118
external_id:
isi:
- '000671755600001'
pmid:
- '34155138'
file:
- access_level: open_access
checksum: cb30c6166b2132ee60d616b31a1a7c29
content_type: application/pdf
creator: dernst
date_created: 2022-03-08T08:18:16Z
date_updated: 2022-03-08T08:18:16Z
file_id: '10835'
file_name: 2021_PNAS_Meier.pdf
file_size: 20592929
relation: main_file
success: 1
file_date_updated: 2022-03-08T08:18:16Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '25'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: PNAS
publication_identifier:
eissn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Haplotype tagging reveals parallel formation of hybrid races in two butterfly
species
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: 118
year: '2021'
...
---
_id: '9376'
abstract:
- lang: eng
text: This paper presents a method for designing planar multistable compliant structures.
Given a sequence of desired stable states and the corresponding poses of the structure,
we identify the topology and geometric realization of a mechanism—consisting of
bars and joints—that is able to physically reproduce the desired multistable behavior.
In order to solve this problem efficiently, we build on insights from minimally
rigid graph theory to identify simple but effective topologies for the mechanism.
We then optimize its geometric parameters, such as joint positions and bar lengths,
to obtain correct transitions between the given poses. Simultaneously, we ensure
adequate stability of each pose based on an effective approximate error metric
related to the elastic energy Hessian of the bars in the mechanism. As demonstrated
by our results, we obtain functional multistable mechanisms of manageable complexity
that can be fabricated using 3D printing. Further, we evaluated the effectiveness
of our method on a large number of examples in the simulation and fabricated several
physical prototypes.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: 'We would like to thank everyone who contributed to this paper, the
authors of artworks for all the examples, including @macrovec-tor_official and Wikimedia
for the FLAG semaphore, and @pikisuper-star for the FIGURINE. The photos of iconic
poses in the teaser were supplied by (from left to right): Mike Hewitt/Olympics
Day 8 - Athletics/Gettty Images, Oneinchpunch/Basketball player training on acourt
in New york city/Shutterstock, and Andrew Redington/TigerWoods/Getty Images. We
also want to express our gratitude to Christian Hafner for insightful discussions,
the IST Austria machine shop SSU, all proof-readers, and anonymous reviewers. This
project has received funding from the European Union’s Horizon 2020 research and
innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841
(DISTRO), and under the European Research Council grant agreement No 715767 (MATERIALIZABLE).'
article_number: '186'
article_processing_charge: No
article_type: original
author:
- first_name: Ran
full_name: Zhang, Ran
id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0002-3808-281X
- first_name: Thomas
full_name: Auzinger, Thomas
id: 4718F954-F248-11E8-B48F-1D18A9856A87
last_name: Auzinger
orcid: 0000-0002-1546-3265
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: Zhang R, Auzinger T, Bickel B. Computational design of planar multistable compliant
structures. ACM Transactions on Graphics. 2021;40(5). doi:10.1145/3453477
apa: Zhang, R., Auzinger, T., & Bickel, B. (2021). Computational design of planar
multistable compliant structures. ACM Transactions on Graphics. Association
for Computing Machinery. https://doi.org/10.1145/3453477
chicago: Zhang, Ran, Thomas Auzinger, and Bernd Bickel. “Computational Design of
Planar Multistable Compliant Structures.” ACM Transactions on Graphics.
Association for Computing Machinery, 2021. https://doi.org/10.1145/3453477.
ieee: R. Zhang, T. Auzinger, and B. Bickel, “Computational design of planar multistable
compliant structures,” ACM Transactions on Graphics, vol. 40, no. 5. Association
for Computing Machinery, 2021.
ista: Zhang R, Auzinger T, Bickel B. 2021. Computational design of planar multistable
compliant structures. ACM Transactions on Graphics. 40(5), 186.
mla: Zhang, Ran, et al. “Computational Design of Planar Multistable Compliant Structures.”
ACM Transactions on Graphics, vol. 40, no. 5, 186, Association for Computing
Machinery, 2021, doi:10.1145/3453477.
short: R. Zhang, T. Auzinger, B. Bickel, ACM Transactions on Graphics 40 (2021).
date_created: 2021-05-08T17:37:08Z
date_published: 2021-10-08T00:00:00Z
date_updated: 2023-08-08T13:31:38Z
day: '08'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3453477
ec_funded: 1
external_id:
isi:
- '000752079300003'
file:
- access_level: open_access
checksum: 8564b3118457d4c8939a8ef2b1a2f16c
content_type: application/pdf
creator: bbickel
date_created: 2021-05-08T17:36:59Z
date_updated: 2021-05-08T17:36:59Z
file_id: '9377'
file_name: Multistable-authorversion.pdf
file_size: 18926557
relation: main_file
- access_level: open_access
checksum: 3b6e874e30bfa1bfc3ad3498710145a1
content_type: video/mp4
creator: bbickel
date_created: 2021-05-08T17:38:22Z
date_updated: 2021-05-08T17:38:22Z
file_id: '9378'
file_name: multistable-video.mp4
file_size: 76542901
relation: main_file
success: 1
- access_level: open_access
checksum: 20dc3bc42e1a912a5b0247c116772098
content_type: application/pdf
creator: bbickel
date_created: 2021-12-17T08:13:51Z
date_updated: 2021-12-17T08:13:51Z
description: This document provides additional results and analyzes the robustness
and limitations of our approach.
file_id: '10562'
file_name: multistable-supplementary material.pdf
file_size: 3367072
relation: supplementary_material
title: Supplementary Material for “Computational Design of Planar Multistable Compliant
Structures”
file_date_updated: 2021-12-17T08:13:51Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '5'
keyword:
- multistability
- mechanism
- computational design
- rigidity
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: Computational design of planar multistable compliant structures
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: 40
year: '2021'
...
---
_id: '9379'
abstract:
- lang: eng
text: When B cells encounter membrane-bound antigens, the formation and coalescence
of B cell antigen receptor (BCR) microclusters amplifies BCR signaling. The ability
of B cells to probe the surface of antigen-presenting cells (APCs) and respond
to APC-bound antigens requires remodeling of the actin cytoskeleton. Initial BCR
signaling stimulates actin-related protein (Arp) 2/3 complex-dependent actin polymerization,
which drives B cell spreading as well as the centripetal movement and coalescence
of BCR microclusters at the B cell-APC synapse. Sustained actin polymerization
depends on concomitant actin filament depolymerization, which enables the recycling
of actin monomers and Arp2/3 complexes. Cofilin-mediated severing of actin filaments
is a rate-limiting step in the morphological changes that occur during immune
synapse formation. Hence, regulators of cofilin activity such as WD repeat-containing
protein 1 (Wdr1), LIM domain kinase (LIMK), and coactosin-like 1 (Cotl1) may also
be essential for actin-dependent processes in B cells. Wdr1 enhances cofilin-mediated
actin disassembly. Conversely, Cotl1 competes with cofilin for binding to actin
and LIMK phosphorylates cofilin and prevents it from binding to actin filaments.
We now show that Wdr1 and LIMK have distinct roles in BCR-induced assembly of
the peripheral actin structures that drive B cell spreading, and that cofilin,
Wdr1, and LIMK all contribute to the actin-dependent amplification of BCR signaling
at the immune synapse. Depleting Cotl1 had no effect on these processes. Thus,
the Wdr1-LIMK-cofilin axis is critical for BCR-induced actin remodeling and for
B cell responses to APC-bound antigens.
acknowledgement: We thank the UBC Life Sciences Institute Imaging Facility andthe
UBC Flow Cytometry Facility.
article_number: '649433'
article_processing_charge: No
article_type: original
author:
- first_name: Madison
full_name: Bolger-Munro, Madison
id: 516F03FA-93A3-11EA-A7C5-D6BE3DDC885E
last_name: Bolger-Munro
orcid: 0000-0002-8176-4824
- first_name: Kate
full_name: Choi, Kate
last_name: Choi
- first_name: Faith
full_name: Cheung, Faith
last_name: Cheung
- first_name: Yi Tian
full_name: Liu, Yi Tian
last_name: Liu
- first_name: May
full_name: Dang-Lawson, May
last_name: Dang-Lawson
- first_name: Nikola
full_name: Deretic, Nikola
last_name: Deretic
- first_name: Connor
full_name: Keane, Connor
last_name: Keane
- first_name: Michael R.
full_name: Gold, Michael R.
last_name: Gold
citation:
ama: Bolger-Munro M, Choi K, Cheung F, et al. The Wdr1-LIMK-Cofilin axis controls
B cell antigen receptor-induced actin remodeling and signaling at the immune synapse.
Frontiers in Cell and Developmental Biology. 2021;9. doi:10.3389/fcell.2021.649433
apa: Bolger-Munro, M., Choi, K., Cheung, F., Liu, Y. T., Dang-Lawson, M., Deretic,
N., … Gold, M. R. (2021). The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced
actin remodeling and signaling at the immune synapse. Frontiers in Cell and
Developmental Biology. Frontiers Media. https://doi.org/10.3389/fcell.2021.649433
chicago: Bolger-Munro, Madison, Kate Choi, Faith Cheung, Yi Tian Liu, May Dang-Lawson,
Nikola Deretic, Connor Keane, and Michael R. Gold. “The Wdr1-LIMK-Cofilin Axis
Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the
Immune Synapse.” Frontiers in Cell and Developmental Biology. Frontiers
Media, 2021. https://doi.org/10.3389/fcell.2021.649433.
ieee: M. Bolger-Munro et al., “The Wdr1-LIMK-Cofilin axis controls B cell
antigen receptor-induced actin remodeling and signaling at the immune synapse,”
Frontiers in Cell and Developmental Biology, vol. 9. Frontiers Media, 2021.
ista: Bolger-Munro M, Choi K, Cheung F, Liu YT, Dang-Lawson M, Deretic N, Keane
C, Gold MR. 2021. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced
actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental
Biology. 9, 649433.
mla: Bolger-Munro, Madison, et al. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen
Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” Frontiers
in Cell and Developmental Biology, vol. 9, 649433, Frontiers Media, 2021,
doi:10.3389/fcell.2021.649433.
short: M. Bolger-Munro, K. Choi, F. Cheung, Y.T. Liu, M. Dang-Lawson, N. Deretic,
C. Keane, M.R. Gold, Frontiers in Cell and Developmental Biology 9 (2021).
date_created: 2021-05-09T22:01:37Z
date_published: 2021-04-13T00:00:00Z
date_updated: 2023-10-18T08:19:49Z
day: '13'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.3389/fcell.2021.649433
external_id:
isi:
- '000644419500001'
pmid:
- '33928084'
file:
- access_level: open_access
checksum: 8c8a03575d2f7583f88dc3b658b0976b
content_type: application/pdf
creator: kschuh
date_created: 2021-05-11T15:09:23Z
date_updated: 2021-05-11T15:09:23Z
file_id: '9386'
file_name: 2021_Frontiers_Cell_Bolger-Munro.pdf
file_size: 4076024
relation: main_file
success: 1
file_date_updated: 2021-05-11T15:09:23Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
keyword:
- B cell
- actin
- immune synapse
- cell spreading
- cofilin
- WDR1 (AIP1)
- LIM domain kinase
- B cell receptor (BCR)
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Cell and Developmental Biology
publication_identifier:
eissn:
- 2296-634X
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling
and signaling at the immune synapse
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2021'
...
---
_id: '9380'
abstract:
- lang: eng
text: Shigella are pathogens originating within the Escherichia lineage but frequently
classified as a separate genus. Shigella genomes contain numerous insertion sequences
(ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous
recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess
the contribution of genomic rearrangements to Shigella evolution. We found that
Shigella experienced exceptionally high rates of intragenomic rearrangements and
had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic
E. coli. The high rearrangement rate resulted in independent disruption of syntenic
regions and parallel rearrangements in different Shigella lineages. Specifically,
we identified two types of chromosomally encoded E3 ubiquitin-protein ligases
acquired independently by all Shigella strains that also showed a high level of
sequence conservation in the promoter and further in the 5′-intergenic region.
In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic
E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli,
we found a rate of genome rearrangements comparable to those in other E. coli
and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These
data indicate that the accumulation of ISs influenced many aspects of genome evolution
and played an important role in the evolution of intracellular pathogens. Our
research demonstrates the power of comparative genomics-based on synteny block
composition and an important role of non-coding regions in the evolution of genomic
islands.
acknowledgement: We thank Fyodor Kondrashov for valuable advice and manuscript proofreading.
We also thank Alla Mikheenko for assistance with Circos.
article_number: '628622'
article_processing_charge: No
article_type: original
author:
- first_name: Zaira
full_name: Seferbekova, Zaira
last_name: Seferbekova
- first_name: Alexey
full_name: Zabelkin, Alexey
last_name: Zabelkin
- first_name: Yulia
full_name: Yakovleva, Yulia
last_name: Yakovleva
- first_name: Robert
full_name: Afasizhev, Robert
last_name: Afasizhev
- first_name: Natalia O.
full_name: Dranenko, Natalia O.
last_name: Dranenko
- first_name: Nikita
full_name: Alexeev, Nikita
last_name: Alexeev
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
citation:
ama: Seferbekova Z, Zabelkin A, Yakovleva Y, et al. High rates of genome rearrangements
and pathogenicity of Shigella spp. Frontiers in Microbiology. 2021;12.
doi:10.3389/fmicb.2021.628622
apa: Seferbekova, Z., Zabelkin, A., Yakovleva, Y., Afasizhev, R., Dranenko, N. O.,
Alexeev, N., … Bochkareva, O. (2021). High rates of genome rearrangements and
pathogenicity of Shigella spp. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2021.628622
chicago: Seferbekova, Zaira, Alexey Zabelkin, Yulia Yakovleva, Robert Afasizhev,
Natalia O. Dranenko, Nikita Alexeev, Mikhail S. Gelfand, and Olga Bochkareva.
“High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” Frontiers
in Microbiology. Frontiers, 2021. https://doi.org/10.3389/fmicb.2021.628622.
ieee: Z. Seferbekova et al., “High rates of genome rearrangements and pathogenicity
of Shigella spp,” Frontiers in Microbiology, vol. 12. Frontiers, 2021.
ista: Seferbekova Z, Zabelkin A, Yakovleva Y, Afasizhev R, Dranenko NO, Alexeev
N, Gelfand MS, Bochkareva O. 2021. High rates of genome rearrangements and pathogenicity
of Shigella spp. Frontiers in Microbiology. 12, 628622.
mla: Seferbekova, Zaira, et al. “High Rates of Genome Rearrangements and Pathogenicity
of Shigella Spp.” Frontiers in Microbiology, vol. 12, 628622, Frontiers,
2021, doi:10.3389/fmicb.2021.628622.
short: Z. Seferbekova, A. Zabelkin, Y. Yakovleva, R. Afasizhev, N.O. Dranenko, N.
Alexeev, M.S. Gelfand, O. Bochkareva, Frontiers in Microbiology 12 (2021).
date_created: 2021-05-09T22:01:38Z
date_published: 2021-04-12T00:00:00Z
date_updated: 2023-08-08T13:30:39Z
day: '12'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.3389/fmicb.2021.628622
ec_funded: 1
external_id:
isi:
- '000643713300001'
file:
- access_level: open_access
checksum: 2f856543add59273a482a7f326fc0400
content_type: application/pdf
creator: kschuh
date_created: 2021-05-11T13:05:52Z
date_updated: 2021-05-11T13:05:52Z
file_id: '9384'
file_name: 2021_Frontiers_Microbiology_Seferbekova.pdf
file_size: 14362316
relation: main_file
success: 1
file_date_updated: 2021-05-11T13:05:52Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Frontiers in Microbiology
publication_identifier:
eissn:
- 1664-302X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: High rates of genome rearrangements and pathogenicity of Shigella spp
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: 12
year: '2021'
...
---
_id: '9381'
abstract:
- lang: eng
text: 'A game of rock-paper-scissors is an interesting example of an interaction
where none of the pure strategies strictly dominates all others, leading to a
cyclic pattern. In this work, we consider an unstable version of rock-paper-scissors
dynamics and allow individuals to make behavioural mistakes during the strategy
execution. We show that such an assumption can break a cyclic relationship leading
to a stable equilibrium emerging with only one strategy surviving. We consider
two cases: completely random mistakes when individuals have no bias towards any
strategy and a general form of mistakes. Then, we determine conditions for a strategy
to dominate all other strategies. However, given that individuals who adopt a
dominating strategy are still prone to behavioural mistakes in the observed behaviour,
we may still observe extinct strategies. That is, behavioural mistakes in strategy
execution stabilise evolutionary dynamics leading to an evolutionary stable and,
potentially, mixed co-existence equilibrium.'
acknowledgement: Authors would like to thank Christian Hilbe and Martin Nowak for
their inspiring and very helpful feedback on the manuscript.
article_number: e1008523
article_processing_charge: No
article_type: original
author:
- first_name: Maria
full_name: Kleshnina, Maria
id: 4E21749C-F248-11E8-B48F-1D18A9856A87
last_name: Kleshnina
- first_name: Sabrina S.
full_name: Streipert, Sabrina S.
last_name: Streipert
- first_name: Jerzy A.
full_name: Filar, Jerzy A.
last_name: Filar
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Kleshnina M, Streipert SS, Filar JA, Chatterjee K. Mistakes can stabilise the
dynamics of rock-paper-scissors games. PLoS Computational Biology. 2021;17(4).
doi:10.1371/journal.pcbi.1008523
apa: Kleshnina, M., Streipert, S. S., Filar, J. A., & Chatterjee, K. (2021).
Mistakes can stabilise the dynamics of rock-paper-scissors games. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008523
chicago: Kleshnina, Maria, Sabrina S. Streipert, Jerzy A. Filar, and Krishnendu
Chatterjee. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors Games.”
PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008523.
ieee: M. Kleshnina, S. S. Streipert, J. A. Filar, and K. Chatterjee, “Mistakes can
stabilise the dynamics of rock-paper-scissors games,” PLoS Computational Biology,
vol. 17, no. 4. Public Library of Science, 2021.
ista: Kleshnina M, Streipert SS, Filar JA, Chatterjee K. 2021. Mistakes can stabilise
the dynamics of rock-paper-scissors games. PLoS Computational Biology. 17(4),
e1008523.
mla: Kleshnina, Maria, et al. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors
Games.” PLoS Computational Biology, vol. 17, no. 4, e1008523, Public Library
of Science, 2021, doi:10.1371/journal.pcbi.1008523.
short: M. Kleshnina, S.S. Streipert, J.A. Filar, K. Chatterjee, PLoS Computational
Biology 17 (2021).
date_created: 2021-05-09T22:01:38Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2025-07-14T09:10:04Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1008523
ec_funded: 1
external_id:
isi:
- '000639711200001'
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checksum: a94ebe0c4116f5047eaa6029e54d2dac
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success: 1
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isi: 1
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language:
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month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: PLoS Computational Biology
publication_identifier:
eissn:
- '15537358'
issn:
- 1553734X
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mistakes can stabilise the dynamics of rock-paper-scissors games
tmp:
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
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type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
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year: '2021'
...
---
_id: '9383'
abstract:
- lang: eng
text: A primary roadblock to our understanding of speciation is that it usually
occurs over a timeframe that is too long to study from start to finish. The idea
of a speciation continuum provides something of a solution to this problem; rather
than observing the entire process, we can simply reconstruct it from the multitude
of speciation events that surround us. But what do we really mean when we talk
about the speciation continuum, and can it really help us understand speciation?
We explored these questions using a literature review and online survey of speciation
researchers. Although most researchers were familiar with the concept and thought
it was useful, our survey revealed extensive disagreement about what the speciation
continuum actually tells us. This is due partly to the lack of a clear definition.
Here, we provide an explicit definition that is compatible with the Biological
Species Concept. That is, the speciation continuum is a continuum of reproductive
isolation. After outlining the logic of the definition in light of alternatives,
we explain why attempts to reconstruct the speciation process from present‐day
populations will ultimately fail. We then outline how we think the speciation
continuum concept can continue to act as a foundation for understanding the continuum
of reproductive isolation that surrounds us.
acknowledgement: We thank M. Garlovsky, S. Martin, C. Cooney, C. Roux, J. Larson,
and J. Mallet for critical feedback and for discussion. K. Lohse, M. de la Cámara,
J. Cerca, M. A. Chase, C. Baskett, A. M. Westram, and N. H. Barton gave feedback
on a draft of the manuscript. O. Seehausen, two anonymous reviewers, and the AE
(Michael Kopp) provided comments that greatly improved the manuscript. V. Holzmann
made many corrections to the proofs. G. Bisschop and K. Lohse kindly contributed
the simulations and analyses presented in Box 3. We would also like to extend our
thanks to everyone who took part in the speciation survey, which received ethical
approval through the University of Sheffield Ethics Review Procedure (Application
029768). We are especially grateful to R. K. Butlin for stimulating discussion throughout
the writing of the manuscript and for feedback on an earlier draft.
article_processing_charge: No
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
citation:
ama: Stankowski S, Ravinet M. Defining the speciation continuum. Evolution.
2021;75(6):1256-1273. doi:10.1111/evo.14215
apa: Stankowski, S., & Ravinet, M. (2021). Defining the speciation continuum.
Evolution. Oxford University Press. https://doi.org/10.1111/evo.14215
chicago: Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.”
Evolution. Oxford University Press, 2021. https://doi.org/10.1111/evo.14215.
ieee: S. Stankowski and M. Ravinet, “Defining the speciation continuum,” Evolution,
vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021.
ista: Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution.
75(6), 1256–1273.
mla: Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution,
vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:10.1111/evo.14215.
short: S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273.
date_created: 2021-05-09T22:01:39Z
date_published: 2021-03-22T00:00:00Z
date_updated: 2023-10-18T08:16:01Z
day: '22'
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department:
- _id: NiBa
doi: 10.1111/evo.14215
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creator: kschuh
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file_size: 719991
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file_date_updated: 2022-03-25T12:02:04Z
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intvolume: ' 75'
isi: 1
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1256-1273
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Defining the speciation continuum
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type: journal_article
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volume: 75
year: '2021'
...
---
_id: '9389'
abstract:
- lang: eng
text: "This .zip File contains the transport data for \"Non-topological zero bias
peaks in full-shell nanowires induced by flux tunable Andreev states\" by M. Valentini,
et. al. \r\nThe measurements were done using Labber Software and the data is
stored in the hdf5 file format.\r\nInstructions of how to read the data are in
\"Notebook_Valentini.pdf\"."
acknowledged_ssus:
- _id: NanoFab
article_processing_charge: No
author:
- first_name: Marco
full_name: Valentini, Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
citation:
ama: Valentini M. Research data for “Non-topological zero bias peaks in full-shell
nanowires induced by flux tunable Andreev states.” 2021. doi:10.15479/AT:ISTA:9389
apa: Valentini, M. (2021). Research data for “Non-topological zero bias peaks in
full-shell nanowires induced by flux tunable Andreev states.” Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:9389
chicago: Valentini, Marco. “Research Data for ‘Non-Topological Zero Bias Peaks in
Full-Shell Nanowires Induced by Flux Tunable Andreev States.’” Institute of Science
and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9389.
ieee: M. Valentini, “Research data for ‘Non-topological zero bias peaks in full-shell
nanowires induced by flux tunable Andreev states.’” Institute of Science and Technology
Austria, 2021.
ista: Valentini M. 2021. Research data for ‘Non-topological zero bias peaks in full-shell
nanowires induced by flux tunable Andreev states’, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:9389.
mla: Valentini, Marco. Research Data for “Non-Topological Zero Bias Peaks in
Full-Shell Nanowires Induced by Flux Tunable Andreev States.” Institute of
Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9389.
short: M. Valentini, (2021).
contributor:
- contributor_type: contact_person
first_name: Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
date_created: 2021-05-14T12:07:53Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2024-02-21T12:40:09Z
ddc:
- '530'
department:
- _id: GradSch
- _id: GeKa
doi: 10.15479/AT:ISTA:9389
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date_updated: 2021-05-14T11:56:48Z
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publisher: Institute of Science and Technology Austria
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title: Research data for "Non-topological zero bias peaks in full-shell nanowires
induced by flux tunable Andreev states"
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short: CC0 (1.0)
type: research_data
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