---
_id: '9336'
abstract:
- lang: eng
text: Mentorship is experience and/or knowledge‐based guidance. Mentors support,
sponsor and advocate for mentees. Having one or more mentors when you seek advice
can significantly influence and improve your research endeavours, well‐being and
career development. Positive mentee–mentor relationships are vital for maintaining
work–life balance and success in careers. Early‐career researchers (ECRs), in
particular, can benefit from mentorship to navigate challenges in academic and
nonacademic life and careers. Yet, strategies for selecting mentors and maintaining
interactions with them are often underdiscussed within research environments.
In this Words of Advice, we provide recommendations for ECRs to seek and manage
mentorship interactions. Our article draws from our experiences as ECRs and published
work, to provide suggestions for mentees to proactively promote beneficial mentorship
interactions. The recommended practices highlight the importance of identifying
mentorship needs, planning and selecting multiple and diverse mentors, setting
goals, and maintaining constructive, and mutually beneficial working relationships
with mentors.
acknowledgement: The authors thank Nicholas Asby of the University of Chicago for
valuable comments on an earlier version of this work. A.P.S. was partially supported
by the NARSAD Young Investigator Grant 27705. S.J.H was supported by the National
Institutes of Health grant R35GM133732.
alternative_title:
- Words of Advice
article_processing_charge: No
article_type: original
author:
- first_name: Sarvenaz
full_name: Sarabipour, Sarvenaz
last_name: Sarabipour
- first_name: Sarah J.
full_name: Hainer, Sarah J.
last_name: Hainer
- 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: Charlotte M.
full_name: De Winde, Charlotte M.
last_name: De Winde
- first_name: Emily
full_name: Furlong, Emily
last_name: Furlong
- first_name: Natalia
full_name: Bielczyk, Natalia
last_name: Bielczyk
- first_name: Nafisa M.
full_name: Jadavji, Nafisa M.
last_name: Jadavji
- first_name: Aparna P.
full_name: Shah, Aparna P.
last_name: Shah
- first_name: Sejal
full_name: Davla, Sejal
last_name: Davla
citation:
ama: Sarabipour S, Hainer SJ, Arslan FN, et al. Building and sustaining mentor interactions
as a mentee. FEBS Journal. 2021. doi:10.1111/febs.15823
apa: Sarabipour, S., Hainer, S. J., Arslan, F. N., De Winde, C. M., Furlong, E.,
Bielczyk, N., … Davla, S. (2021). Building and sustaining mentor interactions
as a mentee. FEBS Journal. Wiley. https://doi.org/10.1111/febs.15823
chicago: Sarabipour, Sarvenaz, Sarah J. Hainer, Feyza N Arslan, Charlotte M. De
Winde, Emily Furlong, Natalia Bielczyk, Nafisa M. Jadavji, Aparna P. Shah, and
Sejal Davla. “Building and Sustaining Mentor Interactions as a Mentee.” FEBS
Journal. Wiley, 2021. https://doi.org/10.1111/febs.15823.
ieee: S. Sarabipour et al., “Building and sustaining mentor interactions
as a mentee,” FEBS Journal. Wiley, 2021.
ista: Sarabipour S, Hainer SJ, Arslan FN, De Winde CM, Furlong E, Bielczyk N, Jadavji
NM, Shah AP, Davla S. 2021. Building and sustaining mentor interactions as a mentee.
FEBS Journal.
mla: Sarabipour, Sarvenaz, et al. “Building and Sustaining Mentor Interactions as
a Mentee.” FEBS Journal, Wiley, 2021, doi:10.1111/febs.15823.
short: S. Sarabipour, S.J. Hainer, F.N. Arslan, C.M. De Winde, E. Furlong, N. Bielczyk,
N.M. Jadavji, A.P. Shah, S. Davla, FEBS Journal (2021).
date_created: 2021-04-18T22:01:43Z
date_published: 2021-04-05T00:00:00Z
date_updated: 2023-08-08T13:12:55Z
day: '05'
department:
- _id: CaHe
doi: 10.1111/febs.15823
external_id:
isi:
- '000636678800001'
pmid:
- '33818917'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/febs.15823
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: FEBS Journal
publication_identifier:
eissn:
- 1742-4658
issn:
- 1742-464X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Building and sustaining mentor interactions as a mentee
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
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:
- open_access: '1'
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: '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
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: '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
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: '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: '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: '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
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: '9361'
abstract:
- lang: eng
text: The multimeric matrix (M) protein of clinically relevant paramyxoviruses orchestrates
assembly and budding activity of viral particles at the plasma membrane (PM).
We identified within the canine distemper virus (CDV) M protein two microdomains,
potentially assuming α-helix structures, which are essential for membrane budding
activity. Remarkably, while two rationally designed microdomain M mutants (E89R,
microdomain 1 and L239D, microdomain 2) preserved proper folding, dimerization,
interaction with the nucleocapsid protein, localization at and deformation of
the PM, the virus-like particle formation, as well as production of infectious
virions (as monitored using a membrane budding-complementation system), were,
in sharp contrast, strongly impaired. Of major importance, raster image correlation
spectroscopy (RICS) revealed that both microdomains contributed to finely tune
M protein mobility specifically at the PM. Collectively, our data highlighted
the cornerstone membrane budding-priming activity of two spatially discrete M
microdomains, potentially by coordinating the assembly of productive higher oligomers
at the PM.
acknowledgement: This work was supported by the Swiss National Science Foundation
(referencenumber 310030_173185 to P. P.).
article_number: e01024-20
article_processing_charge: No
author:
- first_name: Matthieu
full_name: Gast, Matthieu
last_name: Gast
- first_name: Nicole P.
full_name: Kadzioch, Nicole P.
last_name: Kadzioch
- first_name: Doreen
full_name: Milius, Doreen
id: 384050BC-F248-11E8-B48F-1D18A9856A87
last_name: Milius
- first_name: Francesco
full_name: Origgi, Francesco
last_name: Origgi
- first_name: Philippe
full_name: Plattet, Philippe
last_name: Plattet
citation:
ama: Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. Oligomerization and cell
egress controlled by two microdomains of canine distemper virus matrix protein.
mSphere. 2021;6(2). doi:10.1128/mSphere.01024-20
apa: Gast, M., Kadzioch, N. P., Milius, D., Origgi, F., & Plattet, P. (2021).
Oligomerization and cell egress controlled by two microdomains of canine distemper
virus matrix protein. MSphere. American Society for Microbiology. https://doi.org/10.1128/mSphere.01024-20
chicago: Gast, Matthieu, Nicole P. Kadzioch, Doreen Milius, Francesco Origgi, and
Philippe Plattet. “Oligomerization and Cell Egress Controlled by Two Microdomains
of Canine Distemper Virus Matrix Protein.” MSphere. American Society for
Microbiology, 2021. https://doi.org/10.1128/mSphere.01024-20.
ieee: M. Gast, N. P. Kadzioch, D. Milius, F. Origgi, and P. Plattet, “Oligomerization
and cell egress controlled by two microdomains of canine distemper virus matrix
protein,” mSphere, vol. 6, no. 2. American Society for Microbiology, 2021.
ista: Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. 2021. Oligomerization
and cell egress controlled by two microdomains of canine distemper virus matrix
protein. mSphere. 6(2), e01024-20.
mla: Gast, Matthieu, et al. “Oligomerization and Cell Egress Controlled by Two Microdomains
of Canine Distemper Virus Matrix Protein.” MSphere, vol. 6, no. 2, e01024-20,
American Society for Microbiology, 2021, doi:10.1128/mSphere.01024-20.
short: M. Gast, N.P. Kadzioch, D. Milius, F. Origgi, P. Plattet, MSphere 6 (2021).
date_created: 2021-05-02T22:01:28Z
date_published: 2021-04-14T00:00:00Z
date_updated: 2023-08-08T13:26:12Z
day: '14'
ddc:
- '570'
department:
- _id: Bio
doi: 10.1128/mSphere.01024-20
external_id:
isi:
- '000663823400025'
pmid:
- '33853875'
file:
- access_level: open_access
checksum: 310748d140c8838335c1314431095898
content_type: application/pdf
creator: kschuh
date_created: 2021-05-04T12:41:38Z
date_updated: 2021-05-04T12:41:38Z
file_id: '9370'
file_name: 2021_mSphere_Gast.pdf
file_size: 3379349
relation: main_file
success: 1
file_date_updated: 2021-05-04T12:41:38Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: mSphere
publication_identifier:
eissn:
- '23795042'
publication_status: published
publisher: American Society for Microbiology
quality_controlled: '1'
scopus_import: '1'
status: public
title: Oligomerization and cell egress controlled by two microdomains of canine distemper
virus matrix protein
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: 6
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: '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
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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: '9394'
abstract:
- lang: eng
text: 'Chromosomal inversions have long been recognized for their role in local
adaptation. By suppressing recombination in heterozygous individuals, they can
maintain coadapted gene complexes and protect them from homogenizing effects of
gene flow. However, to fully understand their importance for local adaptation
we need to know their influence on phenotypes under divergent selection. For this,
the marine snail Littorina saxatilis provides an ideal study system. Divergent
ecotypes adapted to wave action and crab predation occur in close proximity on
intertidal shores with gene flow between them. Here, we used F2 individuals obtained
from crosses between the ecotypes to test for associations between genomic regions
and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape,
shell thickness, and behavior. We show that most of these traits are influenced
by two previously detected inversion regions that are divergent between ecotypes.
We thus gain a better understanding of one important underlying mechanism responsible
for the rapid and repeated formation of ecotypes: divergent selection acting on
inversions. We also found that some inversions contributed to more than one trait
suggesting that they may contain several loci involved in adaptation, consistent
with the hypothesis that suppression of recombination within inversions facilitates
differentiation in the presence of gene flow.'
acknowledgement: 'We are very grateful to Irena Senčić for technical assistance and
to Michelle Kortyna and Sean Holland at the Center for Anchored Phylogenomics for
assistance with data collection. RKB was funded by the Natural Environment Research
Council and by the European Research Council. KJ was funded by the Swedish Research
Councils VR and Formas (Linnaeus Grant: 217‐2008‐1719). JL was funded by a studentship
from the Leverhulme Centre for Advanced Biological Modelling. AMW was funded by
the European Union''s Horizon 2020 research and innovation program under Marie Skłodowska‐Curie
Grant agreement no. 797747. RF was funded by the European Union''s Horizon 2020
research and innovation programme under the Marie Sklodowska‐Curie Grant agreement
No. 706376 and by FEDER Funds through the Operational Competitiveness Factors Program—COMPETE
and by National Funds through FCT—Foundation for Science and Technology within the
scope of the project “Hybrabbid” (PTDC/BIA‐EVL/30628/2017‐ POCI‐01‐0145‐FEDER‐030628).
We are grateful to other members of the Littorina research group for helpful discussions.
We thank Claire Mérot and an anonymous referee for insightful comments on an earlier
version. '
article_processing_charge: No
article_type: original
author:
- first_name: Eva L.
full_name: Koch, Eva L.
last_name: Koch
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Jenny
full_name: Larsson, Jenny
last_name: Larsson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Alan R.
full_name: Lemmon, Alan R.
last_name: Lemmon
- first_name: E. Moriarty
full_name: Lemmon, E. Moriarty
last_name: Lemmon
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: Koch EL, Morales HE, Larsson J, et al. Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis. Evolution
Letters. 2021;5(3):196-213. doi:10.1002/evl3.227
apa: Koch, E. L., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon,
A. R., … Butlin, R. K. (2021). Genetic variation for adaptive traits is associated
with polymorphic inversions in Littorina saxatilis. Evolution Letters.
Wiley. https://doi.org/10.1002/evl3.227
chicago: Koch, Eva L., Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria,
Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin.
“Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions
in Littorina Saxatilis.” Evolution Letters. Wiley, 2021. https://doi.org/10.1002/evl3.227.
ieee: E. L. Koch et al., “Genetic variation for adaptive traits is associated
with polymorphic inversions in Littorina saxatilis,” Evolution Letters,
vol. 5, no. 3. Wiley, pp. 196–213, 2021.
ista: Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM,
Johannesson K, Butlin RK. 2021. Genetic variation for adaptive traits is associated
with polymorphic inversions in Littorina saxatilis. Evolution Letters. 5(3), 196–213.
mla: Koch, Eva L., et al. “Genetic Variation for Adaptive Traits Is Associated with
Polymorphic Inversions in Littorina Saxatilis.” Evolution Letters, vol.
5, no. 3, Wiley, 2021, pp. 196–213, doi:10.1002/evl3.227.
short: E.L. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon,
E.M. Lemmon, K. Johannesson, R.K. Butlin, Evolution Letters 5 (2021) 196–213.
date_created: 2021-05-16T22:01:47Z
date_published: 2021-05-07T00:00:00Z
date_updated: 2023-08-08T13:34:08Z
day: '07'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/evl3.227
ec_funded: 1
external_id:
isi:
- '000647846200001'
file:
- access_level: open_access
checksum: 023b1608e311f0fda30593ba3d0a4e0b
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-15T08:26:02Z
date_updated: 2021-10-15T08:26:02Z
file_id: '10142'
file_name: 2021_EvolutionLetters_Koch.pdf
file_size: 3021108
relation: main_file
success: 1
file_date_updated: 2021-10-15T08:26:02Z
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intvolume: ' 5'
isi: 1
issue: '3'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 196-213
project:
- _id: 265B41B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '797747'
name: Theoretical and empirical approaches to understanding Parallel Adaptation
publication: Evolution Letters
publication_identifier:
eissn:
- 2056-3744
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '12987'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Genetic variation for adaptive traits is associated with polymorphic inversions
in Littorina saxatilis
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: 5
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: 2023-08-08T13:31:08Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1008523
ec_funded: 1
external_id:
isi:
- '000639711200001'
file:
- access_level: open_access
checksum: a94ebe0c4116f5047eaa6029e54d2dac
content_type: application/pdf
creator: kschuh
date_created: 2021-05-11T13:50:06Z
date_updated: 2021-05-11T13:50:06Z
file_id: '9385'
file_name: 2021_pcbi_Kleshnina.pdf
file_size: 1323820
relation: main_file
success: 1
file_date_updated: 2021-05-11T13:50:06Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '4'
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
- _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:
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: '9392'
abstract:
- lang: eng
text: 'Humans conceptualize the diversity of life by classifying individuals into
types we call ‘species’1. The species we recognize influence political and financial
decisions and guide our understanding of how units of diversity evolve and interact.
Although the idea of species may seem intuitive, a debate about the best way to
define them has raged even before Darwin2. So much energy has been devoted to
the so-called ‘species problem’ that no amount of discourse will ever likely solve
it2,3. Dozens of species concepts are currently recognized3, but we lack a concrete
understanding of how much researchers actually disagree and the factors that cause
them to think differently1,2. To address this, we used a survey to quantify the
species problem for the first time. The results indicate that the disagreement
is extensive: two randomly chosen respondents will most likely disagree on the
nature of species. The probability of disagreement is not predicted by researcher
experience or broad study system, but tended to be lower among researchers with
similar focus, training and who study the same organism. Should we see this diversity
of perspectives as a problem? We argue that we should not.'
acknowledgement: We thank Christopher Cooney, Martin Garlovsky, Anja M. Westram, Carina
Baskett, Stefanie Belohlavy, Michal Hledik, Arka Pal, Nicholas H. Barton, Roger
K. Butlin and members of the University of Sheffield Speciation Journal Club for
feedback on draft survey questions and/or comments on a draft manuscript. Three
anonymous reviewers gave thoughtful feedback that improved the manuscript. We thank
Ahmad Nadeem, who was paid to build the Shiny app. We are especially grateful to
everyone who took part in the survey. Ethical approval for the survey was obtained
through the University of Sheffield Ethics Review Procedure (Application 029768).
S.S. was supported by a NERC grant awarded to Roger K. Butlin.
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. Quantifying the use of species concepts. Current
Biology. 2021;31(9):R428-R429. doi:10.1016/j.cub.2021.03.060
apa: Stankowski, S., & Ravinet, M. (2021). Quantifying the use of species concepts.
Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2021.03.060
chicago: Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.”
Current Biology. Cell Press, 2021. https://doi.org/10.1016/j.cub.2021.03.060.
ieee: S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” Current
Biology, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021.
ista: Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current
Biology. 31(9), R428–R429.
mla: Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.”
Current Biology, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:10.1016/j.cub.2021.03.060.
short: S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429.
date_created: 2021-05-16T22:01:46Z
date_published: 2021-05-10T00:00:00Z
date_updated: 2023-08-08T13:34:38Z
day: '10'
department:
- _id: NiBa
doi: 10.1016/j.cub.2021.03.060
external_id:
isi:
- '000654741200004'
pmid:
- '33974865'
intvolume: ' 31'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2021.03.060
month: '05'
oa: 1
oa_version: Published Version
page: R428-R429
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- '18790445'
issn:
- '09609822'
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantifying the use of species concepts
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 31
year: '2021'
...
---
_id: '9387'
abstract:
- lang: eng
text: We report the complete analysis of a deterministic model of deleterious mutations
and negative selection against them at two haploid loci without recombination.
As long as mutation is a weaker force than selection, mutant alleles remain rare
at the only stable equilibrium, and otherwise, a variety of dynamics are possible.
If the mutation-free genotype is absent, generally the only stable equilibrium
is the one that corresponds to fixation of the mutant allele at the locus where
it is less deleterious. This result suggests that fixation of a deleterious allele
that follows a click of the Muller’s ratchet is governed by natural selection,
instead of random drift.
acknowledgement: This work was supported by the Russian Science Foundation grant N
16-14-10173.
article_number: '110729'
article_processing_charge: No
article_type: original
author:
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
- first_name: Tatiana Yu.
full_name: Neretina, Tatiana Yu.
last_name: Neretina
- first_name: Alexey S.
full_name: Kondrashov, Alexey S.
last_name: Kondrashov
citation:
ama: Khudiakova K, Neretina TY, Kondrashov AS. Two linked loci under mutation-selection
balance and Muller’s ratchet. Journal of Theoretical Biology. 2021;524.
doi:10.1016/j.jtbi.2021.110729
apa: Khudiakova, K., Neretina, T. Y., & Kondrashov, A. S. (2021). Two linked
loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical
Biology. Elsevier . https://doi.org/10.1016/j.jtbi.2021.110729
chicago: Khudiakova, Kseniia, Tatiana Yu. Neretina, and Alexey S. Kondrashov. “Two
Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” Journal
of Theoretical Biology. Elsevier , 2021. https://doi.org/10.1016/j.jtbi.2021.110729.
ieee: K. Khudiakova, T. Y. Neretina, and A. S. Kondrashov, “Two linked loci under
mutation-selection balance and Muller’s ratchet,” Journal of Theoretical Biology,
vol. 524. Elsevier , 2021.
ista: Khudiakova K, Neretina TY, Kondrashov AS. 2021. Two linked loci under mutation-selection
balance and Muller’s ratchet. Journal of Theoretical Biology. 524, 110729.
mla: Khudiakova, Kseniia, et al. “Two Linked Loci under Mutation-Selection Balance
and Muller’s Ratchet.” Journal of Theoretical Biology, vol. 524, 110729,
Elsevier , 2021, doi:10.1016/j.jtbi.2021.110729.
short: K. Khudiakova, T.Y. Neretina, A.S. Kondrashov, Journal of Theoretical Biology
524 (2021).
date_created: 2021-05-12T05:58:42Z
date_published: 2021-04-24T00:00:00Z
date_updated: 2023-08-08T13:32:40Z
day: '24'
department:
- _id: GradSch
doi: 10.1016/j.jtbi.2021.110729
external_id:
isi:
- '000659161500002'
intvolume: ' 524'
isi: 1
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- Modelling and Simulation
- Statistics and Probability
- General Immunology and Microbiology
- Applied Mathematics
- General Agricultural and Biological Sciences
- General Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/477489v1
month: '04'
oa: 1
oa_version: Preprint
publication: Journal of Theoretical Biology
publication_identifier:
issn:
- 0022-5193
publication_status: published
publisher: 'Elsevier '
quality_controlled: '1'
status: public
title: Two linked loci under mutation-selection balance and Muller’s ratchet
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 524
year: '2021'
...
---
_id: '12987'
abstract:
- lang: eng
text: Chromosomal inversion polymorphisms, segments of chromosomes that are flipped
in orientation and occur in reversed order in some individuals, have long been
recognized to play an important role in local adaptation. They can reduce recombination
in heterozygous individuals and thus help to maintain sets of locally adapted
alleles. In a wide range of organisms, populations adapted to different habitats
differ in frequency of inversion arrangements. However, getting a full understanding
of the importance of inversions for adaptation requires confirmation of their
influence on traits under divergent selection. Here, we studied a marine snail,
Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab
predation. These two types occur in close proximity on different parts of the
shore. Gene flow between them exists in contact zones. However, they exhibit strong
phenotypic divergence in several traits under habitat-specific selection, including
size, shape and behaviour. We used crosses between these ecotypes to identify
genomic regions that explain variation in these traits by using QTL analysis and
variance partitioning across linkage groups. We could show that previously detected
inversion regions contribute to adaptive divergence. Some inversions influenced
multiple traits suggesting that they contain sets of locally adaptive alleles.
Our study also identified regions without known inversions that are important
for phenotypic divergence. Thus, we provide a more complete overview of the importance
of inversions in relation to the remaining genome.
article_processing_charge: No
author:
- first_name: Eva
full_name: Koch, Eva
last_name: Koch
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Jenny
full_name: Larsson, Jenny
last_name: Larsson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Alan R.
full_name: Lemmon, Alan R.
last_name: Lemmon
- first_name: E. Moriarty
full_name: Lemmon, E. Moriarty
last_name: Lemmon
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive
traits is associated with polymorphic inversions in Littorina saxatilis. 2021.
doi:10.5061/DRYAD.ZGMSBCCB4'
apa: 'Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon,
A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4'
chicago: 'Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria,
Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin.
“Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic
Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4.'
ieee: 'E. Koch et al., “Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.'
ista: 'Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM,
Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.'
mla: 'Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated
with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4.'
short: E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M.
Lemmon, K. Johannesson, R.K. Butlin, (2021).
date_created: 2023-05-16T12:34:09Z
date_published: 2021-04-10T00:00:00Z
date_updated: 2023-08-08T13:34:07Z
day: '10'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.ZGMSBCCB4
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.zgmsbccb4
month: '04'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9394'
relation: used_in_publication
status: public
status: public
title: 'Data from: Genetic variation for adaptive traits is associated with polymorphic
inversions in Littorina saxatilis'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9408'
abstract:
- lang: eng
text: We present a computational design system that assists users to model, optimize,
and fabricate quad-robots with soft skins. Our system addresses the challenging
task of predicting their physical behavior by fully integrating the multibody
dynamics of the mechanical skeleton and the elastic behavior of the soft skin.
The developed motion control strategy uses an alternating optimization scheme
to avoid expensive full space time-optimization, interleaving space-time optimization
for the skeleton, and frame-by-frame optimization for the full dynamics. The output
are motor torques to drive the robot to achieve a user prescribed motion trajectory.
We also provide a collection of convenient engineering tools and empirical manufacturing
guidance to support the fabrication of the designed quad-robot. We validate the
feasibility of designs generated with our system through physics simulations and
with a physically-fabricated prototype.
acknowledgement: The authors would like to thank anonymous reviewers for their constructive
comments. Weiwei Xu is partially supported by Zhejiang Lab. Yin Yang is partially
spported by NSF under Grant Nos. CHS 1845024 and 1717972. Weiwei Xu and Hujun Bao
are supported by Fundamental Research Funds for the Central Universities. This project
has received funding from the European Research Council (ERC) under the European
Unions Horizon 2020 research and innovation programme (Grant agreement No 715767).
article_number: 2881-2895
article_processing_charge: No
author:
- first_name: Xudong
full_name: Feng, Xudong
last_name: Feng
- first_name: Jiafeng
full_name: Liu, Jiafeng
last_name: Liu
- first_name: Huamin
full_name: Wang, Huamin
last_name: Wang
- first_name: Yin
full_name: Yang, Yin
last_name: Yang
- first_name: Hujun
full_name: Bao, Hujun
last_name: Bao
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Weiwei
full_name: Xu, Weiwei
last_name: Xu
citation:
ama: Feng X, Liu J, Wang H, et al. Computational design of skinned Quad-Robots.
IEEE Transactions on Visualization and Computer Graphics. 2021;27(6). doi:10.1109/TVCG.2019.2957218
apa: Feng, X., Liu, J., Wang, H., Yang, Y., Bao, H., Bickel, B., & Xu, W. (2021).
Computational design of skinned Quad-Robots. IEEE Transactions on Visualization
and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2019.2957218
chicago: Feng, Xudong, Jiafeng Liu, Huamin Wang, Yin Yang, Hujun Bao, Bernd Bickel,
and Weiwei Xu. “Computational Design of Skinned Quad-Robots.” IEEE Transactions
on Visualization and Computer Graphics. IEEE, 2021. https://doi.org/10.1109/TVCG.2019.2957218.
ieee: X. Feng et al., “Computational design of skinned Quad-Robots,” IEEE
Transactions on Visualization and Computer Graphics, vol. 27, no. 6. IEEE,
2021.
ista: Feng X, Liu J, Wang H, Yang Y, Bao H, Bickel B, Xu W. 2021. Computational
design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer
Graphics. 27(6), 2881–2895.
mla: Feng, Xudong, et al. “Computational Design of Skinned Quad-Robots.” IEEE
Transactions on Visualization and Computer Graphics, vol. 27, no. 6, 2881–2895,
IEEE, 2021, doi:10.1109/TVCG.2019.2957218.
short: X. Feng, J. Liu, H. Wang, Y. Yang, H. Bao, B. Bickel, W. Xu, IEEE Transactions
on Visualization and Computer Graphics 27 (2021).
date_created: 2021-05-23T22:01:42Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-08T13:45:46Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1109/TVCG.2019.2957218
ec_funded: 1
external_id:
isi:
- '000649620700009'
pmid:
- '31804937'
file:
- access_level: open_access
checksum: a78e6ac94e33ade4ffaea66943d5f7dc
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T15:08:49Z
date_updated: 2021-05-25T15:08:49Z
file_id: '9427'
file_name: 2021_TVCG_Feng.pdf
file_size: 6183002
relation: main_file
success: 1
file_date_updated: 2021-05-25T15:08:49Z
has_accepted_license: '1'
intvolume: ' 27'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: IEEE Transactions on Visualization and Computer Graphics
publication_identifier:
eissn:
- '10772626'
issn:
- '19410506'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computational design of skinned Quad-Robots
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: 27
year: '2021'
...
---
_id: '9410'
abstract:
- lang: eng
text: Antibiotic concentrations vary dramatically in the body and the environment.
Hence, understanding the dynamics of resistance evolution along antibiotic concentration
gradients is critical for predicting and slowing the emergence and spread of resistance.
While it has been shown that increasing the concentration of an antibiotic slows
resistance evolution, how adaptation to one antibiotic concentration correlates
with fitness at other points along the gradient has not received much attention.
Here, we selected populations of Escherichia coli at several points along a concentration
gradient for three different antibiotics, asking how rapidly resistance evolved
and whether populations became specialized to the antibiotic concentration they
were selected on. Populations selected at higher concentrations evolved resistance
more slowly but exhibited equal or higher fitness across the whole gradient. Populations
selected at lower concentrations evolved resistance rapidly, but overall fitness
in the presence of antibiotics was lower. However, these populations readily adapted
to higher concentrations upon subsequent selection. Our results indicate that
resistance management strategies must account not only for the rates of resistance
evolution but also for the fitness of evolved strains.
acknowledgement: We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton,
Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall,
Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and
Michael Whitlock for insightful support.
article_number: '20200913'
article_processing_charge: No
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Hildegard
full_name: Uecker, Hildegard
id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87
last_name: Uecker
orcid: 0000-0001-9435-2813
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
citation:
ama: Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic
concentration gradients. Biology letters. 2021;17(5). doi:10.1098/rsbl.2020.0913
apa: Lagator, M., Uecker, H., & Neve, P. (2021). Adaptation at different points
along antibiotic concentration gradients. Biology Letters. Royal Society
of London. https://doi.org/10.1098/rsbl.2020.0913
chicago: Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different
Points along Antibiotic Concentration Gradients.” Biology Letters. Royal
Society of London, 2021. https://doi.org/10.1098/rsbl.2020.0913.
ieee: M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along
antibiotic concentration gradients,” Biology letters, vol. 17, no. 5. Royal
Society of London, 2021.
ista: Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic
concentration gradients. Biology letters. 17(5), 20200913.
mla: Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration
Gradients.” Biology Letters, vol. 17, no. 5, 20200913, Royal Society of
London, 2021, doi:10.1098/rsbl.2020.0913.
short: M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021).
date_created: 2021-05-23T22:01:43Z
date_published: 2021-05-12T00:00:00Z
date_updated: 2023-08-08T13:44:35Z
day: '12'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1098/rsbl.2020.0913
ec_funded: 1
external_id:
isi:
- '000651501400001'
pmid:
- ' 33975485'
file:
- access_level: open_access
checksum: 9c13c1f5af7609c97c741f11d293188a
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T14:09:03Z
date_updated: 2021-05-25T14:09:03Z
file_id: '9425'
file_name: 2021_BiologyLetters_Lagator.pdf
file_size: 726759
relation: main_file
success: 1
file_date_updated: 2021-05-25T14:09:03Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Biology letters
publication_identifier:
eissn:
- 1744957X
publication_status: published
publisher: Royal Society of London
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adaptation at different points along antibiotic concentration gradients
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: '9412'
abstract:
- lang: eng
text: We extend our recent result [22] on the central limit theorem for the linear
eigenvalue statistics of non-Hermitian matrices X with independent, identically
distributed complex entries to the real symmetry class. We find that the expectation
and variance substantially differ from their complex counterparts, reflecting
(i) the special spectral symmetry of real matrices onto the real axis; and (ii)
the fact that real i.i.d. matrices have many real eigenvalues. Our result generalizes
the previously known special cases where either the test function is analytic
[49] or the first four moments of the matrix elements match the real Gaussian
[59, 44]. The key element of the proof is the analysis of several weakly dependent
Dyson Brownian motions (DBMs). The conceptual novelty of the real case compared
with [22] is that the correlation structure of the stochastic differentials in
each individual DBM is non-trivial, potentially even jeopardising its well-posedness.
article_number: '24'
article_processing_charge: No
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. Fluctuation around the circular law for
random matrices with real entries. Electronic Journal of Probability. 2021;26.
doi:10.1214/21-EJP591
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Fluctuation around
the circular law for random matrices with real entries. Electronic Journal
of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/21-EJP591
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Fluctuation
around the Circular Law for Random Matrices with Real Entries.” Electronic
Journal of Probability. Institute of Mathematical Statistics, 2021. https://doi.org/10.1214/21-EJP591.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Fluctuation around the circular
law for random matrices with real entries,” Electronic Journal of Probability,
vol. 26. Institute of Mathematical Statistics, 2021.
ista: Cipolloni G, Erdös L, Schröder DJ. 2021. Fluctuation around the circular law
for random matrices with real entries. Electronic Journal of Probability. 26,
24.
mla: Cipolloni, Giorgio, et al. “Fluctuation around the Circular Law for Random
Matrices with Real Entries.” Electronic Journal of Probability, vol. 26,
24, Institute of Mathematical Statistics, 2021, doi:10.1214/21-EJP591.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability
26 (2021).
date_created: 2021-05-23T22:01:44Z
date_published: 2021-03-23T00:00:00Z
date_updated: 2023-08-08T13:39:19Z
day: '23'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1214/21-EJP591
ec_funded: 1
external_id:
arxiv:
- '2002.02438'
isi:
- '000641855600001'
file:
- access_level: open_access
checksum: 864ab003ad4cffea783f65aa8c2ba69f
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T13:24:19Z
date_updated: 2021-05-25T13:24:19Z
file_id: '9423'
file_name: 2021_EJP_Cipolloni.pdf
file_size: 865148
relation: main_file
success: 1
file_date_updated: 2021-05-25T13:24:19Z
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Electronic Journal of Probability
publication_identifier:
eissn:
- '10836489'
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fluctuation around the circular law for random matrices with real entries
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: 26
year: '2021'
...
---
_id: '9407'
abstract:
- lang: eng
text: 'High impact epidemics constitute one of the largest threats humanity is facing
in the 21st century. In the absence of pharmaceutical interventions, physical
distancing together with testing, contact tracing and quarantining are crucial
in slowing down epidemic dynamics. Yet, here we show that if testing capacities
are limited, containment may fail dramatically because such combined countermeasures
drastically change the rules of the epidemic transition: Instead of continuous,
the response to countermeasures becomes discontinuous. Rather than following the
conventional exponential growth, the outbreak that is initially strongly suppressed
eventually accelerates and scales faster than exponential during an explosive
growth period. As a consequence, containment measures either suffice to stop the
outbreak at low total case numbers or fail catastrophically if marginally too
weak, thus implying large uncertainties in reliably estimating overall epidemic
dynamics, both during initial phases and during second wave scenarios.'
acknowledgement: The authors thank Malte Schröder for valuable discussions and creating
the scale-free network topologies. B.H. thanks Mukund Vasudevan for helpful discussion.
The research by M.T. was supported by the Deutsche Forschungsgemeinschaft (DFG,
German Research Foundation) under Germany´s Excellence Strategy–EXC-2068–390729961–Cluster
of Excellence Physics of Life of TU Dresden.
article_number: '2586'
article_processing_charge: No
article_type: original
author:
- first_name: Davide
full_name: Scarselli, Davide
id: 40315C30-F248-11E8-B48F-1D18A9856A87
last_name: Scarselli
orcid: 0000-0001-5227-4271
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Marc
full_name: Timme, Marc
last_name: Timme
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Scarselli D, Budanur NB, Timme M, Hof B. Discontinuous epidemic transition
due to limited testing. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-22725-9
apa: Scarselli, D., Budanur, N. B., Timme, M., & Hof, B. (2021). Discontinuous
epidemic transition due to limited testing. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-021-22725-9
chicago: Scarselli, Davide, Nazmi B Budanur, Marc Timme, and Björn Hof. “Discontinuous
Epidemic Transition Due to Limited Testing.” Nature Communications. Springer
Nature, 2021. https://doi.org/10.1038/s41467-021-22725-9.
ieee: D. Scarselli, N. B. Budanur, M. Timme, and B. Hof, “Discontinuous epidemic
transition due to limited testing,” Nature Communications, vol. 12, no.
1. Springer Nature, 2021.
ista: Scarselli D, Budanur NB, Timme M, Hof B. 2021. Discontinuous epidemic transition
due to limited testing. Nature Communications. 12(1), 2586.
mla: Scarselli, Davide, et al. “Discontinuous Epidemic Transition Due to Limited
Testing.” Nature Communications, vol. 12, no. 1, 2586, Springer Nature,
2021, doi:10.1038/s41467-021-22725-9.
short: D. Scarselli, N.B. Budanur, M. Timme, B. Hof, Nature Communications 12 (2021).
date_created: 2021-05-23T22:01:42Z
date_published: 2021-05-10T00:00:00Z
date_updated: 2023-08-08T13:45:13Z
day: '10'
ddc:
- '570'
department:
- _id: BjHo
doi: 10.1038/s41467-021-22725-9
external_id:
isi:
- '000687305500044'
file:
- access_level: open_access
checksum: fe26c1b8a7da1ae07a6c03f80ff06ea1
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T14:18:40Z
date_updated: 2021-05-25T14:18:40Z
file_id: '9426'
file_name: 2021_NatureCommunications_Scarselli.pdf
file_size: 1176573
relation: main_file
success: 1
file_date_updated: 2021-05-25T14:18:40Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/smashing-the-covid-curve/
scopus_import: '1'
status: public
title: Discontinuous epidemic transition due to limited testing
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: '9411'
abstract:
- lang: eng
text: The dynamics of a triangular magnetocapillary swimmer is studied using the
lattice Boltzmann method. We extend on our previous work, which deals with the
self-assembly and a specific type of the swimmer motion characterized by the swimmer’s
maximum velocity centred around the particle’s inverse viscous time. Here, we
identify additional regimes of motion. First, modifying the ratio of surface tension
and magnetic forces allows to study the swimmer propagation in the regime of significantly
lower frequencies mainly defined by the strength of the magnetocapillary potential.
Second, introducing a constant magnetic contribution in each of the particles
in addition to their magnetic moment induced by external fields leads to another
regime characterized by strong in-plane swimmer reorientations that resemble experimental
observations.
acknowledgement: This work was financially supported by the DFG Priority Programme
SPP 1726 “Microswimmers–From Single Particle Motion to Collective Behaviour” (HA
4382/5-1). We further acknowledge the Jülich Supercomputing Centre (JSC) and the
High Performance Computing Centre Stuttgart (HLRS) for the allocation of computing
time.
article_number: '59'
article_processing_charge: No
author:
- first_name: Alexander
full_name: Sukhov, Alexander
last_name: Sukhov
- first_name: Maxime
full_name: Hubert, Maxime
last_name: Hubert
- first_name: Galien M
full_name: Grosjean, Galien M
id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425
last_name: Grosjean
orcid: 0000-0001-5154-417X
- first_name: Oleg
full_name: Trosman, Oleg
last_name: Trosman
- first_name: Sebastian
full_name: Ziegler, Sebastian
last_name: Ziegler
- first_name: Ylona
full_name: Collard, Ylona
last_name: Collard
- first_name: Nicolas
full_name: Vandewalle, Nicolas
last_name: Vandewalle
- first_name: Ana Sunčana
full_name: Smith, Ana Sunčana
last_name: Smith
- first_name: Jens
full_name: Harting, Jens
last_name: Harting
citation:
ama: Sukhov A, Hubert M, Grosjean GM, et al. Regimes of motion of magnetocapillary
swimmers. European Physical Journal E. 2021;44(4). doi:10.1140/epje/s10189-021-00065-2
apa: Sukhov, A., Hubert, M., Grosjean, G. M., Trosman, O., Ziegler, S., Collard,
Y., … Harting, J. (2021). Regimes of motion of magnetocapillary swimmers. European
Physical Journal E. Springer. https://doi.org/10.1140/epje/s10189-021-00065-2
chicago: Sukhov, Alexander, Maxime Hubert, Galien M Grosjean, Oleg Trosman, Sebastian
Ziegler, Ylona Collard, Nicolas Vandewalle, Ana Sunčana Smith, and Jens Harting.
“Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal
E. Springer, 2021. https://doi.org/10.1140/epje/s10189-021-00065-2.
ieee: A. Sukhov et al., “Regimes of motion of magnetocapillary swimmers,”
European Physical Journal E, vol. 44, no. 4. Springer, 2021.
ista: Sukhov A, Hubert M, Grosjean GM, Trosman O, Ziegler S, Collard Y, Vandewalle
N, Smith AS, Harting J. 2021. Regimes of motion of magnetocapillary swimmers.
European Physical Journal E. 44(4), 59.
mla: Sukhov, Alexander, et al. “Regimes of Motion of Magnetocapillary Swimmers.”
European Physical Journal E, vol. 44, no. 4, 59, Springer, 2021, doi:10.1140/epje/s10189-021-00065-2.
short: A. Sukhov, M. Hubert, G.M. Grosjean, O. Trosman, S. Ziegler, Y. Collard,
N. Vandewalle, A.S. Smith, J. Harting, European Physical Journal E 44 (2021).
date_created: 2021-05-23T22:01:44Z
date_published: 2021-04-24T00:00:00Z
date_updated: 2023-08-08T13:36:28Z
day: '24'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1140/epje/s10189-021-00065-2
external_id:
isi:
- '000643251300001'
file:
- access_level: open_access
checksum: 0ef342d011afbe3c5cb058fda9a3f395
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T11:32:14Z
date_updated: 2021-05-25T11:32:14Z
file_id: '9422'
file_name: 2021_EPJE_Sukhov.pdf
file_size: 2507870
relation: main_file
success: 1
file_date_updated: 2021-05-25T11:32:14Z
has_accepted_license: '1'
intvolume: ' 44'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: European Physical Journal E
publication_identifier:
eissn:
- 1292895X
issn:
- '12928941'
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Regimes of motion of magnetocapillary swimmers
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: 44
year: '2021'
...
---
_id: '9414'
abstract:
- lang: eng
text: Microtubule plus-end depolymerization rate is a potentially important target
of physiological regulation, but it has been challenging to measure, so its role
in spatial organization is poorly understood. Here we apply a method for tracking
plus ends based on time difference imaging to measure depolymerization rates in
large interphase asters growing in Xenopus egg extract. We observed strong spatial
regulation of depolymerization rates, which were higher in the aster interior
compared with the periphery, and much less regulation of polymerization or catastrophe
rates. We interpret these data in terms of a limiting component model, where aster
growth results in lower levels of soluble tubulin and microtubule-associated proteins
(MAPs) in the interior cytosol compared with that at the periphery. The steady-state
polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the
aster interior. We propose that the limiting component for microtubule assembly
is a MAP that inhibits depolymerization, and that egg asters are tuned to low
microtubule density.
acknowledgement: The authors thank the members of Mitchison, Brugués, and Jay Gatlin
groups (University of Wyoming) for discussions. We thank Heino Andreas (MPI-CBG)
for frog maintenance. We thank Nikon for microscopy support at Marine Biological
Laboratory (MBL). K.I. was supported by fellowships from the Honjo International
Scholarship Foundation and Center of Systems Biology Dresden. F.D. was supported
by the DIGGS-BB fellowship provided by the German Research Foundation (DFG). P.C.
is supported by a Boehringer Ingelheim Fonds PhD fellowship. J.F.P. was supported
by a fellowship from the Fannie and John Hertz Foundation. M.L.’s research is supported
by European Research Council (ERC) Grant no. ERC-2015-StG-679239. J.B.’s research
is supported by the Human Frontiers Science Program (CDA00074/2014). T.J.M.’s research
is supported by National Institutes of Health Grant no. R35GM131753.
article_processing_charge: No
article_type: original
author:
- first_name: Keisuke
full_name: Ishihara, Keisuke
last_name: Ishihara
- first_name: Franziska
full_name: Decker, Franziska
last_name: Decker
- first_name: Paulo R
full_name: Dos Santos Caldas, Paulo R
id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87
last_name: Dos Santos Caldas
orcid: 0000-0001-6730-4461
- first_name: James F.
full_name: Pelletier, James F.
last_name: Pelletier
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Jan
full_name: Brugués, Jan
last_name: Brugués
- first_name: Timothy J.
full_name: Mitchison, Timothy J.
last_name: Mitchison
citation:
ama: Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule
depolymerization in large asters. Molecular Biology of the Cell. 2021;32(9):869-879.
doi:10.1091/MBC.E20-11-0723
apa: Ishihara, K., Decker, F., Dos Santos Caldas, P. R., Pelletier, J. F., Loose,
M., Brugués, J., & Mitchison, T. J. (2021). Spatial variation of microtubule
depolymerization in large asters. Molecular Biology of the Cell. American
Society for Cell Biology. https://doi.org/10.1091/MBC.E20-11-0723
chicago: Ishihara, Keisuke, Franziska Decker, Paulo R Dos Santos Caldas, James F.
Pelletier, Martin Loose, Jan Brugués, and Timothy J. Mitchison. “Spatial Variation
of Microtubule Depolymerization in Large Asters.” Molecular Biology of the
Cell. American Society for Cell Biology, 2021. https://doi.org/10.1091/MBC.E20-11-0723.
ieee: K. Ishihara et al., “Spatial variation of microtubule depolymerization
in large asters,” Molecular Biology of the Cell, vol. 32, no. 9. American
Society for Cell Biology, pp. 869–879, 2021.
ista: Ishihara K, Decker F, Dos Santos Caldas PR, Pelletier JF, Loose M, Brugués
J, Mitchison TJ. 2021. Spatial variation of microtubule depolymerization in large
asters. Molecular Biology of the Cell. 32(9), 869–879.
mla: Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization
in Large Asters.” Molecular Biology of the Cell, vol. 32, no. 9, American
Society for Cell Biology, 2021, pp. 869–79, doi:10.1091/MBC.E20-11-0723.
short: K. Ishihara, F. Decker, P.R. Dos Santos Caldas, J.F. Pelletier, M. Loose,
J. Brugués, T.J. Mitchison, Molecular Biology of the Cell 32 (2021) 869–879.
date_created: 2021-05-23T22:01:45Z
date_published: 2021-04-19T00:00:00Z
date_updated: 2023-08-08T13:36:02Z
day: '19'
department:
- _id: MaLo
doi: 10.1091/MBC.E20-11-0723
ec_funded: 1
external_id:
isi:
- '000641574700005'
intvolume: ' 32'
isi: 1
issue: '9'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/3.0/
main_file_link:
- open_access: '1'
url: https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723
month: '04'
oa: 1
oa_version: Published Version
page: 869-879
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: 260D98C8-B435-11E9-9278-68D0E5697425
name: Reconstitution of Bacterial Cell Division Using Purified Components
publication: Molecular Biology of the Cell
publication_identifier:
eissn:
- 1939-4586
issn:
- 1059-1524
publication_status: published
publisher: American Society for Cell Biology
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spatial variation of microtubule depolymerization in large asters
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA
3.0)
short: CC BY-NC-SA (3.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 32
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
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: '9439'
abstract:
- lang: eng
text: The ability to adapt to changes in stimulus statistics is a hallmark of sensory
systems. Here, we developed a theoretical framework that can account for the dynamics
of adaptation from an information processing perspective. We use this framework
to optimize and analyze adaptive sensory codes, and we show that codes optimized
for stationary environments can suffer from prolonged periods of poor performance
when the environment changes. To mitigate the adversarial effects of these environmental
changes, sensory systems must navigate tradeoffs between the ability to accurately
encode incoming stimuli and the ability to rapidly detect and adapt to changes
in the distribution of these stimuli. We derive families of codes that balance
these objectives, and we demonstrate their close match to experimentally observed
neural dynamics during mean and variance adaptation. Our results provide a unifying
perspective on adaptation across a range of sensory systems, environments, and
sensory tasks.
acknowledgement: We thank D. Kastner and T. Münch for generously providing figures
from their work. We also thank V. Jayaraman, M. Noorman, T. Ma, and K. Krishnamurthy
for useful discussions and feedback on the manuscript. W.F.M. was funded by the
European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie
Grant Agreement No. 754411. A.M.H. was supported by the Howard Hughes Medical Institute.
article_processing_charge: No
article_type: original
author:
- first_name: Wiktor F
full_name: Mlynarski, Wiktor F
id: 358A453A-F248-11E8-B48F-1D18A9856A87
last_name: Mlynarski
- first_name: Ann M.
full_name: Hermundstad, Ann M.
last_name: Hermundstad
citation:
ama: Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. Nature
Neuroscience. 2021;24:998-1009. doi:10.1038/s41593-021-00846-0
apa: Mlynarski, W. F., & Hermundstad, A. M. (2021). Efficient and adaptive sensory
codes. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-021-00846-0
chicago: Mlynarski, Wiktor F, and Ann M. Hermundstad. “Efficient and Adaptive Sensory
Codes.” Nature Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41593-021-00846-0.
ieee: W. F. Mlynarski and A. M. Hermundstad, “Efficient and adaptive sensory codes,”
Nature Neuroscience, vol. 24. Springer Nature, pp. 998–1009, 2021.
ista: Mlynarski WF, Hermundstad AM. 2021. Efficient and adaptive sensory codes.
Nature Neuroscience. 24, 998–1009.
mla: Mlynarski, Wiktor F., and Ann M. Hermundstad. “Efficient and Adaptive Sensory
Codes.” Nature Neuroscience, vol. 24, Springer Nature, 2021, pp. 998–1009,
doi:10.1038/s41593-021-00846-0.
short: W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009.
date_created: 2021-05-30T22:01:24Z
date_published: 2021-05-20T00:00:00Z
date_updated: 2023-08-08T13:51:14Z
day: '20'
department:
- _id: GaTk
doi: 10.1038/s41593-021-00846-0
ec_funded: 1
external_id:
isi:
- '000652577300003'
intvolume: ' 24'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/669200 '
month: '05'
oa: 1
oa_version: Preprint
page: 998-1009
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature Neuroscience
publication_identifier:
eissn:
- 1546-1726
issn:
- 1097-6256
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient and adaptive sensory codes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 24
year: '2021'
...
---
_id: '9443'
abstract:
- lang: eng
text: Endoplasmic reticulum–plasma membrane contact sites (ER–PM CS) play fundamental
roles in all eukaryotic cells. Arabidopsis thaliana mutants lacking the ER–PM
protein tether synaptotagmin1 (SYT1) exhibit decreased PM integrity under multiple
abiotic stresses, such as freezing, high salt, osmotic stress, and mechanical
damage. Here, we show that, together with SYT1, the stress-induced SYT3 is an
ER–PM tether that also functions in maintaining PM integrity. The ER–PM CS localization
of SYT1 and SYT3 is dependent on PM phosphatidylinositol-4-phosphate and is regulated
by abiotic stress. Lipidomic analysis revealed that cold stress increased the
accumulation of diacylglycerol at the PM in a syt1/3 double mutant relative to
wild-type while the levels of most glycerolipid species remain unchanged. In addition,
the SYT1-green fluorescent protein fusion preferentially binds diacylglycerol
in vivo with little affinity for polar glycerolipids. Our work uncovers a SYT-dependent
mechanism of stress adaptation counteracting the detrimental accumulation of diacylglycerol
at the PM produced during episodes of abiotic stress.
acknowledgement: "We would also like to thank Lothar Willmitzer for the lipidomic
analysis at the Max Planck Institute of Molecular Plant Physiology (Potsdam, Germany).
We thank Manuela Vega from SCI for her technical assistance in image analysis. We
thank John R. Pearson and the Bionand Nanoimaging Unit, F. David Navas Fernández
and the SCAI Imaging Facility and The Plant Cell Biology facility at the Shanghai
Center for Plant Stress Biology for assistance with confocal microscopy. The FaFAH1
clone was a gift from Iraida Amaya Saavedra (IFAPA-Centro de Churriana, Málaga,
Spain). The AHA3 antibody against the H+-ATPase was a gift from Ramón Serrano Salom
(Instituto de Biología Molecular y Celular de Plantas, Valencia, Spain). The MAP-mTU2-SAC1
construct was provided by Yvon Jaillais (Laboratoire Reproduction et Développement
des Plantes, Univ Lyon, France). The pGWB5 from the pGWB vector series, was provided
by Tsuyoshi Nakagawa (Department of Molecular and Functional Genomics, Shimane University).
We thank Plan Propio from the University of Málaga for financial support.\r\nFunding"
article_processing_charge: No
article_type: original
author:
- first_name: N
full_name: Ruiz-Lopez, N
last_name: Ruiz-Lopez
- first_name: J
full_name: Pérez-Sancho, J
last_name: Pérez-Sancho
- first_name: A
full_name: Esteban Del Valle, A
last_name: Esteban Del Valle
- first_name: RP
full_name: Haslam, RP
last_name: Haslam
- first_name: S
full_name: Vanneste, S
last_name: Vanneste
- first_name: R
full_name: Catalá, R
last_name: Catalá
- first_name: C
full_name: Perea-Resa, C
last_name: Perea-Resa
- first_name: D
full_name: Van Damme, D
last_name: Van Damme
- first_name: S
full_name: García-Hernández, S
last_name: García-Hernández
- first_name: A
full_name: Albert, A
last_name: Albert
- first_name: J
full_name: Vallarino, J
last_name: Vallarino
- first_name: J
full_name: Lin, J
last_name: Lin
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: AP
full_name: Macho, AP
last_name: Macho
- first_name: J
full_name: Salinas, J
last_name: Salinas
- first_name: A
full_name: Rosado, A
last_name: Rosado
- first_name: JA
full_name: Napier, JA
last_name: Napier
- first_name: V
full_name: Amorim-Silva, V
last_name: Amorim-Silva
- first_name: MA
full_name: Botella, MA
last_name: Botella
citation:
ama: Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, et al. Synaptotagmins at
the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol
homeostasis during abiotic stress. Plant Cell. 2021;33(7):2431-2453. doi:10.1093/plcell/koab122
apa: Ruiz-Lopez, N., Pérez-Sancho, J., Esteban Del Valle, A., Haslam, R., Vanneste,
S., Catalá, R., … Botella, M. (2021). Synaptotagmins at the endoplasmic reticulum-plasma
membrane contact sites maintain diacylglycerol homeostasis during abiotic stress.
Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab122
chicago: Ruiz-Lopez, N, J Pérez-Sancho, A Esteban Del Valle, RP Haslam, S Vanneste,
R Catalá, C Perea-Resa, et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma
Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.”
Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab122.
ieee: N. Ruiz-Lopez et al., “Synaptotagmins at the endoplasmic reticulum-plasma
membrane contact sites maintain diacylglycerol homeostasis during abiotic stress,”
Plant Cell, vol. 33, no. 7. American Society of Plant Biologists, pp. 2431–2453,
2021.
ista: Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, Haslam R, Vanneste S, Catalá
R, Perea-Resa C, Van Damme D, García-Hernández S, Albert A, Vallarino J, Lin J,
Friml J, Macho A, Salinas J, Rosado A, Napier J, Amorim-Silva V, Botella M. 2021.
Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain
diacylglycerol homeostasis during abiotic stress. Plant Cell. 33(7), 2431–2453.
mla: Ruiz-Lopez, N., et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma
Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.”
Plant Cell, vol. 33, no. 7, American Society of Plant Biologists, 2021,
pp. 2431–53, doi:10.1093/plcell/koab122.
short: N. Ruiz-Lopez, J. Pérez-Sancho, A. Esteban Del Valle, R. Haslam, S. Vanneste,
R. Catalá, C. Perea-Resa, D. Van Damme, S. García-Hernández, A. Albert, J. Vallarino,
J. Lin, J. Friml, A. Macho, J. Salinas, A. Rosado, J. Napier, V. Amorim-Silva,
M. Botella, Plant Cell 33 (2021) 2431–2453.
date_created: 2021-06-02T13:13:58Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-08T13:54:32Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1093/plcell/koab122
ec_funded: 1
external_id:
isi:
- '000703938100026'
pmid:
- '33944955'
file:
- access_level: open_access
checksum: 22d596678d00310d793611864a6d0fcd
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-14T13:36:38Z
date_updated: 2021-10-14T13:36:38Z
file_id: '10141'
file_name: 2021_PlantCell_RuizLopez.pdf
file_size: 2952028
relation: main_file
success: 1
file_date_updated: 2021-10-14T13:36:38Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 2431-2453
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Plant Cell
publication_identifier:
eissn:
- 1532-298x
issn:
- 1040-4651
publication_status: published
publisher: American Society of Plant Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain
diacylglycerol homeostasis during abiotic stress
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: 33
year: '2021'
...
---
_id: '9431'
abstract:
- lang: eng
text: Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report
here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus
from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid
protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces
infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram
averaging, mature capsid-like particles show an IP6-like density in the CA hexamer,
coordinated by rings of six lysines and six arginines. Phosphate and IP6 have
opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons
and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer
formation. Subtomogram averaging and classification optimized for analysis of
pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA
polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast,
the CA pentamer forms rigid units organizing the local architecture. These different
features of hexamers and pentamers determine the structural mechanism to form
CA polyhedrons of variable shape in mature RSV particles.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: EM-Fac
acknowledgement: This work was funded by the National Institute of Allergy and Infectious
Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in
support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S.
Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported
by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European
Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support
in cryo-ET data acquisition. This work made use of the Cornell Center for Materials
Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875).
This research was also supported by the Scientific Service Units (SSUs) of IST Austria
through resources provided by Scientific Computing (SciComp), the Life Science Facility
(LSF), and the Electron Microscopy Facility (EMF).
article_number: '3226'
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
- first_name: Clifton L.
full_name: Ricana, Clifton L.
last_name: Ricana
- first_name: Nadia
full_name: Nikulin, Nadia
last_name: Nikulin
- first_name: Jon-Philip R.
full_name: Feathers, Jon-Philip R.
last_name: Feathers
- first_name: Marco
full_name: Klanschnig, Marco
last_name: Klanschnig
- first_name: Andreas
full_name: Thader, Andreas
id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87
last_name: Thader
- first_name: Marc C.
full_name: Johnson, Marc C.
last_name: Johnson
- first_name: Volker M.
full_name: Vogt, Volker M.
last_name: Vogt
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Robert A.
full_name: Dick, Robert A.
last_name: Dick
citation:
ama: Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus
lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature
Communications. 2021;12(1). doi:10.1038/s41467-021-23506-0
apa: Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader,
A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals
a role for IP6 in the formation of the capsid hexamer. Nature Communications.
Nature Research. https://doi.org/10.1038/s41467-021-23506-0
chicago: Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers,
Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM
Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice
Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications.
Nature Research, 2021. https://doi.org/10.1038/s41467-021-23506-0.
ieee: M. Obr et al., “Structure of the mature Rous sarcoma virus lattice
reveals a role for IP6 in the formation of the capsid hexamer,” Nature Communications,
vol. 12, no. 1. Nature Research, 2021.
ista: Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson
MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus
lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature
Communications. 12(1), 3226.
mla: Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals
a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications,
vol. 12, no. 1, 3226, Nature Research, 2021, doi:10.1038/s41467-021-23506-0.
short: M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader,
M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021).
date_created: 2021-05-28T14:25:50Z
date_published: 2021-05-28T00:00:00Z
date_updated: 2023-08-08T13:53:53Z
day: '28'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1038/s41467-021-23506-0
external_id:
isi:
- '000659145000011'
file:
- access_level: open_access
checksum: 53ccc53d09a9111143839dbe7784e663
content_type: application/pdf
creator: kschuh
date_created: 2021-06-09T15:21:14Z
date_updated: 2021-06-09T15:21:14Z
file_id: '9538'
file_name: 2021_NatureCommunications_Obr.pdf
file_size: 6166295
relation: main_file
success: 1
file_date_updated: 2021-06-09T15:21:14Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Nature Research
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/how-retroviruses-become-infectious/
scopus_import: '1'
status: public
title: Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in
the formation of the capsid hexamer
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: '9467'
abstract:
- lang: eng
text: "Turbulence in the flow of fluid through a pipe can be suppressed by buoyancy
forces. As the suppression of turbulence leads to severe heat transfer deterioration,
this is an important and undesirable phenomenon in both heating and cooling applications.
Vertical flow is often considered, as the axial buoyancy force can help drive
the flow. With heating measured by the buoyancy parameter \U0001D436, our direct
numerical simulations show that shear-driven turbulence may either be completely
laminarised or it transitions to a relatively quiescent convection-driven state.
Buoyancy forces cause a flattening of the base flow profile, which in isothermal
pipe flow has recently been linked to complete suppression of turbulence (Kühnen
et al., Nat. Phys., vol. 14, 2018, pp. 386–390), and the flattened laminar base
profile has enhanced nonlinear stability (Marensi et al., J. Fluid Mech., vol.
863, 2019, pp. 50–875). In agreement with these findings, the nonlinear lower-branch
travelling-wave solution analysed here, which is believed to mediate transition
to turbulence in isothermal pipe flow, is shown to be suppressed by buoyancy.
A linear instability of the laminar base flow is responsible for the appearance
of the relatively quiescent convection driven state for \U0001D436≳4 across the
range of Reynolds numbers considered. In the suppression of turbulence, however,
i.e. in the transition from turbulence, we find clearer association with the analysis
of He et al. (J. Fluid Mech., vol. 809, 2016, pp. 31–71) than with the above dynamical
systems approach, which describes better the transition to turbulence. The laminarisation
criterion He et al. propose, based on an apparent Reynolds number of the flow
as measured by its driving pressure gradient, is found to capture the critical
\U0001D436=\U0001D436\U0001D450\U0001D45F(\U0001D445\U0001D452) above which the
flow will be laminarised or switch to the convection-driven type. Our analysis
suggests that it is the weakened rolls, rather than the streaks, which appear
to be critical for laminarisation."
acknowledgement: The anonymous referees are kindly acknowledged for their useful suggestions
andcomments.
article_number: A17
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Elena
full_name: Marensi, Elena
id: 0BE7553A-1004-11EA-B805-18983DDC885E
last_name: Marensi
- first_name: Shuisheng
full_name: He, Shuisheng
last_name: He
- first_name: Ashley P.
full_name: Willis, Ashley P.
last_name: Willis
citation:
ama: Marensi E, He S, Willis AP. Suppression of turbulence and travelling waves
in a vertical heated pipe. Journal of Fluid Mechanics. 2021;919. doi:10.1017/jfm.2021.371
apa: Marensi, E., He, S., & Willis, A. P. (2021). Suppression of turbulence
and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics.
Cambridge University Press. https://doi.org/10.1017/jfm.2021.371
chicago: Marensi, Elena, Shuisheng He, and Ashley P. Willis. “Suppression of Turbulence
and Travelling Waves in a Vertical Heated Pipe.” Journal of Fluid Mechanics.
Cambridge University Press, 2021. https://doi.org/10.1017/jfm.2021.371.
ieee: E. Marensi, S. He, and A. P. Willis, “Suppression of turbulence and travelling
waves in a vertical heated pipe,” Journal of Fluid Mechanics, vol. 919.
Cambridge University Press, 2021.
ista: Marensi E, He S, Willis AP. 2021. Suppression of turbulence and travelling
waves in a vertical heated pipe. Journal of Fluid Mechanics. 919, A17.
mla: Marensi, Elena, et al. “Suppression of Turbulence and Travelling Waves in a
Vertical Heated Pipe.” Journal of Fluid Mechanics, vol. 919, A17, Cambridge
University Press, 2021, doi:10.1017/jfm.2021.371.
short: E. Marensi, S. He, A.P. Willis, Journal of Fluid Mechanics 919 (2021).
date_created: 2021-06-06T22:01:30Z
date_published: 2021-07-25T00:00:00Z
date_updated: 2023-08-08T13:58:41Z
day: '25'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1017/jfm.2021.371
external_id:
arxiv:
- '2008.13486'
isi:
- '000653785000001'
file:
- access_level: open_access
checksum: 867ad077e45c181c2c5ec1311ba27c41
content_type: application/pdf
creator: kschuh
date_created: 2021-08-03T09:53:28Z
date_updated: 2021-08-03T09:53:28Z
file_id: '9766'
file_name: 2021_JournalFluidMechanics_Marensi.pdf
file_size: 4087358
relation: main_file
success: 1
file_date_updated: 2021-08-03T09:53:28Z
has_accepted_license: '1'
intvolume: ' 919'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- '14697645'
issn:
- '00221120'
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Suppression of turbulence and travelling waves in a vertical heated pipe
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: 919
year: '2021'
...
---
_id: '9470'
abstract:
- lang: eng
text: A key step in understanding the genetic basis of different evolutionary outcomes
(e.g., adaptation) is to determine the roles played by different mutation types
(e.g., SNPs, translocations and inversions). To do this we must simultaneously
consider different mutation types in an evolutionary framework. Here, we propose
a research framework that directly utilizes the most important characteristics
of mutations, their population genetic effects, to determine their relative evolutionary
significance in a given scenario. We review known population genetic effects of
different mutation types and show how these may be connected to different evolutionary
outcomes. We provide examples of how to implement this framework and pinpoint
areas where more data, theory and synthesis are needed. Linking experimental and
theoretical approaches to examine different mutation types simultaneously is a
critical step towards understanding their evolutionary significance.
acknowledgement: We thank the editor, two helpful reviewers, Roger Butlin, Kerstin
Johannesson, Valentina Peona, Rike Stelkens, Julie Blommaert, Nick Barton, and João
Alpedrinha for helpful comments that improved the manuscript. The authors acknowledge
funding from the Swedish Research Council Formas (2017-01597 to AS), the Swedish
Research Council Vetenskapsrådet (2016-05139 to AS, 2019-04452 to TS) and from the
European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation programme (grant agreement no. 757451 to TS). ELB was funded by a
Carl Tryggers grant awarded to Tanja Slotte. Anja M. Westram was funded by the European
Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie
grant agreement No 797747. Inês Fragata was funded by a Junior Researcher contract
from FCT (CEECIND/02616/2018).
article_processing_charge: No
author:
- first_name: Emma L.
full_name: Berdan, Emma L.
last_name: Berdan
- first_name: Alexandre
full_name: Blanckaert, Alexandre
last_name: Blanckaert
- first_name: Tanja
full_name: Slotte, Tanja
last_name: Slotte
- first_name: Alexander
full_name: Suh, Alexander
last_name: Suh
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Inês
full_name: Fragata, Inês
last_name: Fragata
citation:
ama: 'Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing
mutations: Connecting mutation types with evolutionary consequences. Molecular
Ecology. 2021;30(12):2710-2723. doi:10.1111/mec.15936'
apa: 'Berdan, E. L., Blanckaert, A., Slotte, T., Suh, A., Westram, A. M., &
Fragata, I. (2021). Unboxing mutations: Connecting mutation types with evolutionary
consequences. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15936'
chicago: 'Berdan, Emma L., Alexandre Blanckaert, Tanja Slotte, Alexander Suh, Anja
M Westram, and Inês Fragata. “Unboxing Mutations: Connecting Mutation Types with
Evolutionary Consequences.” Molecular Ecology. Wiley, 2021. https://doi.org/10.1111/mec.15936.'
ieee: 'E. L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A. M. Westram, and I. Fragata,
“Unboxing mutations: Connecting mutation types with evolutionary consequences,”
Molecular Ecology, vol. 30, no. 12. Wiley, pp. 2710–2723, 2021.'
ista: 'Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. 2021. Unboxing
mutations: Connecting mutation types with evolutionary consequences. Molecular
Ecology. 30(12), 2710–2723.'
mla: 'Berdan, Emma L., et al. “Unboxing Mutations: Connecting Mutation Types with
Evolutionary Consequences.” Molecular Ecology, vol. 30, no. 12, Wiley,
2021, pp. 2710–23, doi:10.1111/mec.15936.'
short: E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata,
Molecular Ecology 30 (2021) 2710–2723.
date_created: 2021-06-06T22:01:31Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-08T13:59:18Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.15936
ec_funded: 1
external_id:
isi:
- '000652056400001'
file:
- access_level: open_access
checksum: e6f4731365bde2614b333040a08265d8
content_type: application/pdf
creator: kschuh
date_created: 2021-06-11T15:34:53Z
date_updated: 2021-06-11T15:34:53Z
file_id: '9545'
file_name: 2021_MolecularEcology_Berdan.pdf
file_size: 1031978
relation: main_file
success: 1
file_date_updated: 2021-06-11T15:34:53Z
has_accepted_license: '1'
intvolume: ' 30'
isi: 1
issue: '12'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 2710-2723
project:
- _id: 265B41B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '797747'
name: Theoretical and empirical approaches to understanding Parallel Adaptation
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365294X
issn:
- '09621083'
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Unboxing mutations: Connecting mutation types with evolutionary consequences'
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 30
year: '2021'
...
---
_id: '9468'
abstract:
- lang: eng
text: "Motivated by the successful application of geometry to proving the Harary--Hill
conjecture for “pseudolinear” drawings of $K_n$, we introduce “pseudospherical”
drawings of graphs. A spherical drawing of a graph $G$ is a drawing in the unit
sphere $\\mathbb{S}^2$ in which the vertices of $G$ are represented as points---no
three on a great circle---and the edges of $G$ are shortest-arcs in $\\mathbb{S}^2$
connecting pairs of vertices. Such a drawing has three properties: (1) every edge
$e$ is contained in a simple closed curve $\\gamma_e$ such that the only vertices
in $\\gamma_e$ are the ends of $e$; (2) if $e\\ne f$, then $\\gamma_e\\cap\\gamma_f$
has precisely two crossings; and (3) if $e\\ne f$, then $e$ intersects $\\gamma_f$
at most once, in either a crossing or an end of $e$. We use properties (1)--(3)
to define a pseudospherical drawing of $G$. Our main result is that for the complete
graph, properties (1)--(3) are equivalent to the same three properties but with
“precisely two crossings” in (2) replaced by “at most two crossings.” The proof
requires a result in the geometric transversal theory of arrangements of pseudocircles.
This is proved using the surprising result that the absence of special arcs (coherent
spirals) in an arrangement of simple closed curves characterizes the fact that
any two curves in the arrangement have at most two crossings. Our studies provide
the necessary ideas for exhibiting a drawing of $K_{10}$ that has no extension
to an arrangement of pseudocircles and a drawing of $K_9$ that does extend to
an arrangement of pseudocircles, but no such extension has all pairs of pseudocircles
crossing twice.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Alan M
full_name: Arroyo Guevara, Alan M
id: 3207FDC6-F248-11E8-B48F-1D18A9856A87
last_name: Arroyo Guevara
orcid: 0000-0003-2401-8670
- first_name: R. Bruce
full_name: Richter, R. Bruce
last_name: Richter
- first_name: Matthew
full_name: Sunohara, Matthew
last_name: Sunohara
citation:
ama: Arroyo Guevara AM, Richter RB, Sunohara M. Extending drawings of complete graphs
into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics.
2021;35(2):1050-1076. doi:10.1137/20M1313234
apa: Arroyo Guevara, A. M., Richter, R. B., & Sunohara, M. (2021). Extending
drawings of complete graphs into arrangements of pseudocircles. SIAM Journal
on Discrete Mathematics. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1313234
chicago: Arroyo Guevara, Alan M, R. Bruce Richter, and Matthew Sunohara. “Extending
Drawings of Complete Graphs into Arrangements of Pseudocircles.” SIAM Journal
on Discrete Mathematics. Society for Industrial and Applied Mathematics, 2021.
https://doi.org/10.1137/20M1313234.
ieee: A. M. Arroyo Guevara, R. B. Richter, and M. Sunohara, “Extending drawings
of complete graphs into arrangements of pseudocircles,” SIAM Journal on Discrete
Mathematics, vol. 35, no. 2. Society for Industrial and Applied Mathematics,
pp. 1050–1076, 2021.
ista: Arroyo Guevara AM, Richter RB, Sunohara M. 2021. Extending drawings of complete
graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics.
35(2), 1050–1076.
mla: Arroyo Guevara, Alan M., et al. “Extending Drawings of Complete Graphs into
Arrangements of Pseudocircles.” SIAM Journal on Discrete Mathematics, vol.
35, no. 2, Society for Industrial and Applied Mathematics, 2021, pp. 1050–76,
doi:10.1137/20M1313234.
short: A.M. Arroyo Guevara, R.B. Richter, M. Sunohara, SIAM Journal on Discrete
Mathematics 35 (2021) 1050–1076.
date_created: 2021-06-06T22:01:30Z
date_published: 2021-05-20T00:00:00Z
date_updated: 2023-08-08T13:58:12Z
day: '20'
department:
- _id: UlWa
doi: 10.1137/20M1313234
ec_funded: 1
external_id:
arxiv:
- '2001.06053'
isi:
- '000674142200022'
intvolume: ' 35'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2001.06053
month: '05'
oa: 1
oa_version: Preprint
page: 1050-1076
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: SIAM Journal on Discrete Mathematics
publication_identifier:
issn:
- '08954801'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extending drawings of complete graphs into arrangements of pseudocircles
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 35
year: '2021'
...
---
_id: '9462'
abstract:
- lang: eng
text: We consider a system of N trapped bosons with repulsive interactions in a
combined semiclassical mean-field limit at positive temperature. We show that
the free energy is well approximated by the minimum of the Hartree free energy
functional – a natural extension of the Hartree energy functional to positive
temperatures. The Hartree free energy functional converges in the same limit to
a semiclassical free energy functional, and we show that the system displays Bose–Einstein
condensation if and only if it occurs in the semiclassical free energy functional.
This allows us to show that for weak coupling the critical temperature decreases
due to the repulsive interactions.
acknowledgement: Funding from the European Union's Horizon 2020 research and innovation
programme under the ERC grant agreement No 694227 (R.S.) and under the Marie Sklodowska-Curie
grant agreement No 836146 (A.D.) is gratefully acknowledged. A.D. acknowledges support
of the Swiss National Science Foundation through the Ambizione grant PZ00P2 185851.
article_number: '109096'
article_processing_charge: No
article_type: original
author:
- first_name: Andreas
full_name: Deuchert, Andreas
last_name: Deuchert
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Deuchert A, Seiringer R. Semiclassical approximation and critical temperature
shift for weakly interacting trapped bosons. Journal of Functional Analysis.
2021;281(6). doi:10.1016/j.jfa.2021.109096
apa: Deuchert, A., & Seiringer, R. (2021). Semiclassical approximation and critical
temperature shift for weakly interacting trapped bosons. Journal of Functional
Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109096
chicago: Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and
Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal
of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109096.
ieee: A. Deuchert and R. Seiringer, “Semiclassical approximation and critical temperature
shift for weakly interacting trapped bosons,” Journal of Functional Analysis,
vol. 281, no. 6. Elsevier, 2021.
ista: Deuchert A, Seiringer R. 2021. Semiclassical approximation and critical temperature
shift for weakly interacting trapped bosons. Journal of Functional Analysis. 281(6),
109096.
mla: Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical
Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional
Analysis, vol. 281, no. 6, 109096, Elsevier, 2021, doi:10.1016/j.jfa.2021.109096.
short: A. Deuchert, R. Seiringer, Journal of Functional Analysis 281 (2021).
date_created: 2021-06-06T22:01:28Z
date_published: 2021-09-15T00:00:00Z
date_updated: 2023-08-08T13:56:27Z
day: '15'
department:
- _id: RoSe
doi: 10.1016/j.jfa.2021.109096
ec_funded: 1
external_id:
arxiv:
- '2009.00992'
isi:
- '000656508600008'
intvolume: ' 281'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2009.00992
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
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: Semiclassical approximation and critical temperature shift for weakly interacting
trapped bosons
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 281
year: '2021'
...
---
_id: '9469'
abstract:
- lang: eng
text: In this paper, we consider reflected three-operator splitting methods for
monotone inclusion problems in real Hilbert spaces. To do this, we first obtain
weak convergence analysis and nonasymptotic O(1/n) convergence rate of the reflected
Krasnosel'skiĭ-Mann iteration for finding a fixed point of nonexpansive mapping
in real Hilbert spaces under some seemingly easy to implement conditions on the
iterative parameters. We then apply our results to three-operator splitting for
the monotone inclusion problem and consequently obtain the corresponding convergence
analysis. Furthermore, we derive reflected primal-dual algorithms for highly structured
monotone inclusion problems. Some numerical implementations are drawn from splitting
methods to support the theoretical analysis.
acknowledgement: The authors are grateful to the anonymous referees and the handling
Editor for their insightful comments which have improved the earlier version of
the manuscript greatly. The second author is grateful to the University of Hafr
Al Batin. The last 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: Olaniyi S.
full_name: Iyiola, Olaniyi S.
last_name: Iyiola
- first_name: Cyril D.
full_name: Enyi, Cyril D.
last_name: Enyi
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
citation:
ama: Iyiola OS, Enyi CD, Shehu Y. Reflected three-operator splitting method for
monotone inclusion problem. Optimization Methods and Software. 2021. doi:10.1080/10556788.2021.1924715
apa: Iyiola, O. S., Enyi, C. D., & Shehu, Y. (2021). Reflected three-operator
splitting method for monotone inclusion problem. Optimization Methods and Software.
Taylor and Francis. https://doi.org/10.1080/10556788.2021.1924715
chicago: Iyiola, Olaniyi S., Cyril D. Enyi, and Yekini Shehu. “Reflected Three-Operator
Splitting Method for Monotone Inclusion Problem.” Optimization Methods and
Software. Taylor and Francis, 2021. https://doi.org/10.1080/10556788.2021.1924715.
ieee: O. S. Iyiola, C. D. Enyi, and Y. Shehu, “Reflected three-operator splitting
method for monotone inclusion problem,” Optimization Methods and Software.
Taylor and Francis, 2021.
ista: Iyiola OS, Enyi CD, Shehu Y. 2021. Reflected three-operator splitting method
for monotone inclusion problem. Optimization Methods and Software.
mla: Iyiola, Olaniyi S., et al. “Reflected Three-Operator Splitting Method for Monotone
Inclusion Problem.” Optimization Methods and Software, Taylor and Francis,
2021, doi:10.1080/10556788.2021.1924715.
short: O.S. Iyiola, C.D. Enyi, Y. Shehu, Optimization Methods and Software (2021).
date_created: 2021-06-06T22:01:30Z
date_published: 2021-05-12T00:00:00Z
date_updated: 2023-08-08T13:57:43Z
day: '12'
department:
- _id: VlKo
doi: 10.1080/10556788.2021.1924715
ec_funded: 1
external_id:
isi:
- '000650507600001'
isi: 1
language:
- iso: eng
month: '05'
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 Methods and Software
publication_identifier:
eissn:
- 1029-4937
issn:
- 1055-6788
publication_status: published
publisher: Taylor and Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reflected three-operator splitting method for monotone inclusion problem
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9540'
abstract:
- lang: eng
text: The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis
and initiates cytoplasmic maturation of the large ribosomal subunit by releasing
the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1
and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug
diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown.
Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism.
Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining
its specificity for this site. As a consequence, the D2 domain is locked in a
rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms
identified include abolished drug binding and altered positioning of the nucleotide.
Our results suggest nucleotide-modifying compounds as potential novel inhibitors
for AAA-ATPases.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: We are deeply grateful to the late Gregor Högenauer who built the
foundation for this study with his visionary work on the inhibitor diazaborine and
its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron
chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of
the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS
adduct. We thank the team of the VBCF for support during early phases of this work
and the IST Austria Electron Microscopy Facility for providing equipment. The lab
of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects
P32536 and P32977 (to H.B.).
article_number: '3483'
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Prattes, Michael
last_name: Prattes
- first_name: Irina
full_name: Grishkovskaya, Irina
last_name: Grishkovskaya
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Ingrid
full_name: Rössler, Ingrid
last_name: Rössler
- first_name: Isabella
full_name: Klein, Isabella
last_name: Klein
- first_name: Christina
full_name: Hetzmannseder, Christina
last_name: Hetzmannseder
- first_name: Gertrude
full_name: Zisser, Gertrude
last_name: Zisser
- first_name: Christian C.
full_name: Gruber, Christian C.
last_name: Gruber
- first_name: Karl
full_name: Gruber, Karl
last_name: Gruber
- first_name: David
full_name: Haselbach, David
last_name: Haselbach
- first_name: Helmut
full_name: Bergler, Helmut
last_name: Bergler
citation:
ama: Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition
of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 2021;12(1).
doi:10.1038/s41467-021-23854-x
apa: Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder,
C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1
by diazaborine. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23854-x
chicago: Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid
Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural
Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23854-x.
ieee: M. Prattes et al., “Structural basis for inhibition of the AAA-ATPase
Drg1 by diazaborine,” Nature Communications, vol. 12, no. 1. Springer Nature,
2021.
ista: Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder
C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis
for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1),
3483.
mla: Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase
Drg1 by Diazaborine.” Nature Communications, vol. 12, no. 1, 3483, Springer
Nature, 2021, doi:10.1038/s41467-021-23854-x.
short: M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder,
G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications
12 (2021).
date_created: 2021-06-10T14:57:45Z
date_published: 2021-06-09T00:00:00Z
date_updated: 2023-08-08T14:05:26Z
day: '09'
ddc:
- '570'
department:
- _id: EM-Fac
doi: 10.1038/s41467-021-23854-x
external_id:
isi:
- '000664874700014'
pmid:
- '34108481'
file:
- access_level: open_access
checksum: 40fc24c1310930990b52a8ad1142ee97
content_type: application/pdf
creator: cziletti
date_created: 2021-06-15T18:55:59Z
date_updated: 2021-06-15T18:55:59Z
file_id: '9556'
file_name: 2021_NatureComm_Prattes.pdf
file_size: 3397292
relation: main_file
success: 1
file_date_updated: 2021-06-15T18:55:59Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine
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: '9549'
abstract:
- lang: eng
text: 'AMPA receptors (AMPARs) mediate the majority of excitatory transmission in
the brain and enable the synaptic plasticity that underlies learning1. A diverse
array of AMPAR signalling complexes are established by receptor auxiliary subunits,
which associate with the AMPAR in various combinations to modulate trafficking,
gating and synaptic strength2. However, their mechanisms of action are poorly
understood. Here we determine cryo-electron microscopy structures of the heteromeric
GluA1–GluA2 receptor assembled with both TARP-γ8 and CNIH2, the predominant AMPAR
complex in the forebrain, in both resting and active states. Two TARP-γ8 and two
CNIH2 subunits insert at distinct sites beneath the ligand-binding domains of
the receptor, with site-specific lipids shaping each interaction and affecting
the gating regulation of the AMPARs. Activation of the receptor leads to asymmetry
between GluA1 and GluA2 along the ion conduction path and an outward expansion
of the channel triggers counter-rotations of both auxiliary subunit pairs, promoting
the active-state conformation. In addition, both TARP-γ8 and CNIH2 pivot towards
the pore exit upon activation, extending their reach for cytoplasmic receptor
elements. CNIH2 achieves this through its uniquely extended M2 helix, which has
transformed this endoplasmic reticulum-export factor into a powerful AMPAR modulator
that is capable of providing hippocampal pyramidal neurons with their integrative
synaptic properties. '
acknowledgement: We thank members of the Greger laboratory, B. Herguedas, J. Krieger
and J.-N. Dohrke for comments on the manuscript; J. Krieger and J.-N. Dohrke for
discussion, J. Krieger for help with the normal mode analysis, B. Köhegyi for help
with cryo-EM imaging, V. Chang and K. Suzuki for helping to generate the CNIH2-1D4-HA
stable cell line, M. Carvalho for assistance at early stages of this project, the
LMB scientific computing and the cryo-EM facility for support, P. Emsley for help
with model building, T. Nakane for helpful comments with RELION 3.1 and R. Warshamanage
for helping with EMDA cryo-EM-map processing. We acknowledge the Diamond Light Source
for access and support of the Cryo-EM facilities at the UK national electron bio10
imaging centre (eBIC), proposal EM17434, funded by the Wellcome Trust, MRC and BBSRC.
This work was supported by grants from the Medical Research Council, as part of
United Kingdom Research and Innovation (also known as UK Research and Innovation)
(MC_U105174197) and BBSRC (BB/N002113/1) to I.H.G.
article_processing_charge: No
article_type: original
author:
- first_name: Danyang
full_name: Zhang, Danyang
last_name: Zhang
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Peter M.
full_name: Matthews, Peter M.
last_name: Matthews
- first_name: Ondrej
full_name: Cais, Ondrej
last_name: Cais
- first_name: Ingo H.
full_name: Greger, Ingo H.
last_name: Greger
citation:
ama: Zhang D, Watson J, Matthews PM, Cais O, Greger IH. Gating and modulation of
a hetero-octameric AMPA glutamate receptor. Nature. 2021;594:454-458. doi:10.1038/s41586-021-03613-0
apa: Zhang, D., Watson, J., Matthews, P. M., Cais, O., & Greger, I. H. (2021).
Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature.
Springer Nature. https://doi.org/10.1038/s41586-021-03613-0
chicago: Zhang, Danyang, Jake Watson, Peter M. Matthews, Ondrej Cais, and Ingo H.
Greger. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate Receptor.”
Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03613-0.
ieee: D. Zhang, J. Watson, P. M. Matthews, O. Cais, and I. H. Greger, “Gating and
modulation of a hetero-octameric AMPA glutamate receptor,” Nature, vol.
594. Springer Nature, pp. 454–458, 2021.
ista: Zhang D, Watson J, Matthews PM, Cais O, Greger IH. 2021. Gating and modulation
of a hetero-octameric AMPA glutamate receptor. Nature. 594, 454–458.
mla: Zhang, Danyang, et al. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate
Receptor.” Nature, vol. 594, Springer Nature, 2021, pp. 454–58, doi:10.1038/s41586-021-03613-0.
short: D. Zhang, J. Watson, P.M. Matthews, O. Cais, I.H. Greger, Nature 594 (2021)
454–458.
date_created: 2021-06-13T22:01:33Z
date_published: 2021-06-02T00:00:00Z
date_updated: 2023-08-08T13:59:51Z
day: '02'
department:
- _id: PeJo
doi: 10.1038/s41586-021-03613-0
external_id:
isi:
- '000657238100003'
pmid:
- '34079129'
intvolume: ' 594'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41586-021-03613-0
month: '06'
oa: 1
oa_version: Published Version
page: 454-458
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gating and modulation of a hetero-octameric AMPA glutamate receptor
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 594
year: '2021'
...
---
_id: '9550'
abstract:
- lang: eng
text: 'We prove that the energy of any eigenvector of a sum of several independent
large Wigner matrices is equally distributed among these matrices with very high
precision. This shows a particularly strong microcanonical form of the equipartition
principle for quantum systems whose components are modelled by Wigner matrices. '
acknowledgement: The first author is supported in part by Hong Kong RGC Grant GRF
16301519 and NSFC 11871425. The second author is supported in part by ERC Advanced
Grant RANMAT 338804. The third author is supported in part by Swedish Research Council
Grant VR-2017-05195 and the Knut and Alice Wallenberg Foundation
article_number: e44
article_processing_charge: No
article_type: original
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Bao Z, Erdös L, Schnelli K. Equipartition principle for Wigner matrices. Forum
of Mathematics, Sigma. 2021;9. doi:10.1017/fms.2021.38
apa: Bao, Z., Erdös, L., & Schnelli, K. (2021). Equipartition principle for
Wigner matrices. Forum of Mathematics, Sigma. Cambridge University Press.
https://doi.org/10.1017/fms.2021.38
chicago: Bao, Zhigang, László Erdös, and Kevin Schnelli. “Equipartition Principle
for Wigner Matrices.” Forum of Mathematics, Sigma. Cambridge University
Press, 2021. https://doi.org/10.1017/fms.2021.38.
ieee: Z. Bao, L. Erdös, and K. Schnelli, “Equipartition principle for Wigner matrices,”
Forum of Mathematics, Sigma, vol. 9. Cambridge University Press, 2021.
ista: Bao Z, Erdös L, Schnelli K. 2021. Equipartition principle for Wigner matrices.
Forum of Mathematics, Sigma. 9, e44.
mla: Bao, Zhigang, et al. “Equipartition Principle for Wigner Matrices.” Forum
of Mathematics, Sigma, vol. 9, e44, Cambridge University Press, 2021, doi:10.1017/fms.2021.38.
short: Z. Bao, L. Erdös, K. Schnelli, Forum of Mathematics, Sigma 9 (2021).
date_created: 2021-06-13T22:01:33Z
date_published: 2021-05-27T00:00:00Z
date_updated: 2023-08-08T14:03:40Z
day: '27'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1017/fms.2021.38
ec_funded: 1
external_id:
arxiv:
- '2008.07061'
isi:
- '000654960800001'
file:
- access_level: open_access
checksum: 47c986578de132200d41e6d391905519
content_type: application/pdf
creator: cziletti
date_created: 2021-06-15T14:40:45Z
date_updated: 2021-06-15T14:40:45Z
file_id: '9555'
file_name: 2021_ForumMath_Bao.pdf
file_size: 483458
relation: main_file
success: 1
file_date_updated: 2021-06-15T14:40:45Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Forum of Mathematics, Sigma
publication_identifier:
eissn:
- '20505094'
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Equipartition principle for Wigner matrices
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: 9
year: '2021'
...
---
_id: '9570'
abstract:
- lang: eng
text: We present conductance-matrix measurements in long, three-terminal hybrid
superconductor-semiconductor nanowires, and compare with theoretical predictions
of a magnetic-field-driven, topological quantum phase transition. By examining
the nonlocal conductance, we identify the closure of the excitation gap in the
bulk of the semiconductor before the emergence of zero-bias peaks, ruling out
spurious gap-closure signatures from localized states. We observe that after the
gap closes, nonlocal signals and zero-bias peaks fluctuate strongly at both ends,
inconsistent with a simple picture of clean topological superconductivity.
acknowledgement: We acknowledge insightful discussions with K. Flensberg, E. B. Hansen,
T. Karzig, R. Lutchyn, D. Pikulin, E. Prada, and R. Aguado. This work was supported
by Microsoft Project Q and the Danmarks Grundforskningsfond. C.M.M. acknowledges
support from the Villum Fonden. A.P.H. and L.C. contributed equally to this work.
article_number: '235201'
article_processing_charge: No
article_type: original
author:
- first_name: Denise
full_name: Puglia, Denise
id: 4D495994-AE37-11E9-AC72-31CAE5697425
last_name: Puglia
- first_name: E. A.
full_name: Martinez, E. A.
last_name: Martinez
- first_name: G. C.
full_name: Ménard, G. C.
last_name: Ménard
- first_name: A.
full_name: Pöschl, A.
last_name: Pöschl
- first_name: S.
full_name: Gronin, S.
last_name: Gronin
- first_name: G. C.
full_name: Gardner, G. C.
last_name: Gardner
- first_name: R.
full_name: Kallaher, R.
last_name: Kallaher
- first_name: M. J.
full_name: Manfra, M. J.
last_name: Manfra
- first_name: C. M.
full_name: Marcus, C. M.
last_name: Marcus
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: L.
full_name: Casparis, L.
last_name: Casparis
citation:
ama: Puglia D, Martinez EA, Ménard GC, et al. Closing of the induced gap in a hybrid
superconductor-semiconductor nanowire. Physical Review B. 2021;103(23).
doi:10.1103/PhysRevB.103.235201
apa: Puglia, D., Martinez, E. A., Ménard, G. C., Pöschl, A., Gronin, S., Gardner,
G. C., … Casparis, L. (2021). Closing of the induced gap in a hybrid superconductor-semiconductor
nanowire. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.103.235201
chicago: Puglia, Denise, E. A. Martinez, G. C. Ménard, A. Pöschl, S. Gronin, G.
C. Gardner, R. Kallaher, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/PhysRevB.103.235201.
ieee: D. Puglia et al., “Closing of the induced gap in a hybrid superconductor-semiconductor
nanowire,” Physical Review B, vol. 103, no. 23. American Physical Society,
2021.
ista: Puglia D, Martinez EA, Ménard GC, Pöschl A, Gronin S, Gardner GC, Kallaher
R, Manfra MJ, Marcus CM, Higginbotham AP, Casparis L. 2021. Closing of the induced
gap in a hybrid superconductor-semiconductor nanowire. Physical Review B. 103(23),
235201.
mla: Puglia, Denise, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire.” Physical Review B, vol. 103, no. 23, 235201, American Physical
Society, 2021, doi:10.1103/PhysRevB.103.235201.
short: D. Puglia, E.A. Martinez, G.C. Ménard, A. Pöschl, S. Gronin, G.C. Gardner,
R. Kallaher, M.J. Manfra, C.M. Marcus, A.P. Higginbotham, L. Casparis, Physical
Review B 103 (2021).
date_created: 2021-06-20T22:01:33Z
date_published: 2021-06-15T00:00:00Z
date_updated: 2023-08-08T14:08:08Z
day: '15'
department:
- _id: AnHi
doi: 10.1103/PhysRevB.103.235201
external_id:
arxiv:
- '2006.01275'
isi:
- '000661512500002'
intvolume: ' 103'
isi: 1
issue: '23'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2006.01275
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- '24699969'
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '13080'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Closing of the induced gap in a hybrid superconductor-semiconductor nanowire
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 103
year: '2021'
...
---
_id: '9548'
abstract:
- lang: eng
text: 'We extend the notion of the minimal volume ellipsoid containing a convex
body in Rd to the setting of logarithmically concave functions. We consider a
vast class of logarithmically concave functions whose superlevel sets are concentric
ellipsoids. For a fixed function from this class, we consider the set of all its
“affine” positions. For any log-concave function f on Rd, we consider functions
belonging to this set of “affine” positions, and find the one with the minimal
integral under the condition that it is pointwise greater than or equal to f.
We study the properties of existence and uniqueness of the solution to this problem.
For any s∈[0,+∞), we consider the construction dual to the recently defined John
s-function (Ivanov and Naszódi in Functional John ellipsoids. arXiv preprint:
arXiv:2006.09934, 2020). We prove that such a construction determines a unique
function and call it the Löwner s-function of f. We study the Löwner s-functions
as s tends to zero and to infinity. Finally, extending the notion of the outer
volume ratio, we define the outer integral ratio of a log-concave function and
give an asymptotically tight bound on it.'
acknowledgement: The authors acknowledge the support of the grant of the Russian Government
N 075-15-2019-1926.
article_processing_charge: No
article_type: original
author:
- first_name: Grigory
full_name: Ivanov, Grigory
id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E
last_name: Ivanov
- first_name: Igor
full_name: Tsiutsiurupa, Igor
last_name: Tsiutsiurupa
citation:
ama: Ivanov G, Tsiutsiurupa I. Functional Löwner ellipsoids. Journal of Geometric
Analysis. 2021;31:11493-11528. doi:10.1007/s12220-021-00691-4
apa: Ivanov, G., & Tsiutsiurupa, I. (2021). Functional Löwner ellipsoids. Journal
of Geometric Analysis. Springer. https://doi.org/10.1007/s12220-021-00691-4
chicago: Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.”
Journal of Geometric Analysis. Springer, 2021. https://doi.org/10.1007/s12220-021-00691-4.
ieee: G. Ivanov and I. Tsiutsiurupa, “Functional Löwner ellipsoids,” Journal
of Geometric Analysis, vol. 31. Springer, pp. 11493–11528, 2021.
ista: Ivanov G, Tsiutsiurupa I. 2021. Functional Löwner ellipsoids. Journal of Geometric
Analysis. 31, 11493–11528.
mla: Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.” Journal
of Geometric Analysis, vol. 31, Springer, 2021, pp. 11493–528, doi:10.1007/s12220-021-00691-4.
short: G. Ivanov, I. Tsiutsiurupa, Journal of Geometric Analysis 31 (2021) 11493–11528.
date_created: 2021-06-13T22:01:32Z
date_published: 2021-05-31T00:00:00Z
date_updated: 2023-08-08T14:04:49Z
day: '31'
department:
- _id: UlWa
doi: 10.1007/s12220-021-00691-4
external_id:
arxiv:
- '2008.09543'
isi:
- '000656507500001'
intvolume: ' 31'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2008.09543
month: '05'
oa: 1
oa_version: Preprint
page: 11493-11528
publication: Journal of Geometric Analysis
publication_identifier:
eissn:
- 1559-002X
issn:
- 1050-6926
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Functional Löwner ellipsoids
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 31
year: '2021'
...
---
_id: '13080'
abstract:
- lang: eng
text: "Data for the manuscript 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire' ([2006.01275] Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire (arxiv.org))\r\n\r\nWe upload a pdf with extended data sets, and the
raw data for these extended datasets as well."
article_processing_charge: No
author:
- first_name: Denise
full_name: Puglia, Denise
id: 4D495994-AE37-11E9-AC72-31CAE5697425
last_name: Puglia
- first_name: Esteban
full_name: Martinez, Esteban
last_name: Martinez
- first_name: Gerbold
full_name: Menard, Gerbold
last_name: Menard
- first_name: Andreas
full_name: Pöschl, Andreas
last_name: Pöschl
- first_name: Sergei
full_name: Gronin, Sergei
last_name: Gronin
- first_name: Geoffrey
full_name: Gardner, Geoffrey
last_name: Gardner
- first_name: Ray
full_name: Kallaher, Ray
last_name: Kallaher
- first_name: Michael
full_name: Manfra, Michael
last_name: Manfra
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Lucas
full_name: Casparis, Lucas
last_name: Casparis
citation:
ama: Puglia D, Martinez E, Menard G, et al. Data for ’Closing of the Induced Gap
in a Hybrid Superconductor-Semiconductor Nanowire. 2021. doi:10.5281/ZENODO.4592435
apa: Puglia, D., Martinez, E., Menard, G., Pöschl, A., Gronin, S., Gardner, G.,
… Casparis, L. (2021). Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire. Zenodo. https://doi.org/10.5281/ZENODO.4592435
chicago: Puglia, Denise, Esteban Martinez, Gerbold Menard, Andreas Pöschl, Sergei
Gronin, Geoffrey Gardner, Ray Kallaher, et al. “Data for ’Closing of the Induced
Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.4592435.
ieee: D. Puglia et al., “Data for ’Closing of the Induced Gap in a Hybrid
Superconductor-Semiconductor Nanowire.” Zenodo, 2021.
ista: Puglia D, Martinez E, Menard G, Pöschl A, Gronin S, Gardner G, Kallaher R,
Manfra M, Marcus C, Higginbotham AP, Casparis L. 2021. Data for ’Closing of the
Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire, Zenodo, 10.5281/ZENODO.4592435.
mla: Puglia, Denise, et al. Data for ’Closing of the Induced Gap in a Hybrid
Superconductor-Semiconductor Nanowire. Zenodo, 2021, doi:10.5281/ZENODO.4592435.
short: D. Puglia, E. Martinez, G. Menard, A. Pöschl, S. Gronin, G. Gardner, R. Kallaher,
M. Manfra, C. Marcus, A.P. Higginbotham, L. Casparis, (2021).
date_created: 2023-05-23T17:11:28Z
date_published: 2021-03-09T00:00:00Z
date_updated: 2023-08-08T14:08:07Z
day: '09'
ddc:
- '530'
department:
- _id: AnHi
doi: 10.5281/ZENODO.4592435
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.4592460
month: '03'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
link:
- relation: software
url: https://github.com/caslu85/Induced-Gap-Closing-Shared/tree/1.1.3
record:
- id: '9570'
relation: used_in_publication
status: public
status: public
title: Data for 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9569'
abstract:
- lang: eng
text: We report the synthesis and characterization of graphene functionalized with
iron (Fe3+) oxide (G-Fe3O4) nanohybrids for radio-frequency magnetic hyperthermia
application. We adopted the wet chemical procedure, using various contents of
Fe3O4 (magnetite) from 0–100% for making two-dimensional graphene–Fe3O4 nanohybrids.
The homogeneous dispersal of Fe3O4 nanoparticles decorated on the graphene surface
combined with their biocompatibility and high thermal conductivity make them an
excellent material for magnetic hyperthermia. The morphological and magnetic properties
of the nanohybrids were studied using scanning electron microscopy (SEM) and a
vibrating sample magnetometer (VSM), respectively. The smart magnetic platforms
were exposed to an alternating current (AC) magnetic field of 633 kHz and of strength
9.1 mT for studying their hyperthermic performance. The localized antitumor effects
were investigated with artificial neural network modeling. A neural net time-series
model was developed for the assessment of the best nanohybrid composition to serve
the purpose with an accuracy close to 100%. Six Nonlinear Autoregressive with
External Input (NARX) models were obtained, one for each of the components. The
assessment of the accuracy of the predicted results has been done on the basis
of Mean Squared Error (MSE). The highest Mean Squared Error value was obtained
for the nanohybrid containing 45% magnetite and 55% graphene (F45G55) in the training
phase i.e., 0.44703, which is where the model achieved optimal results after 71
epochs. The F45G55 nanohybrid was found to be the best for hyperthermia applications
in low dosage with the highest specific absorption rate (SAR) and mean squared
error values.
acknowledgement: The research is funded by Higher Education Commission (HEC) Pakistan
under start-up research grant program (SRGP) Project no. 2454.
article_processing_charge: No
article_type: original
author:
- first_name: M. S.
full_name: Dar, M. S.
last_name: Dar
- first_name: Khush Bakhat
full_name: Akram, Khush Bakhat
last_name: Akram
- first_name: Ayesha
full_name: Sohail, Ayesha
last_name: Sohail
- first_name: Fatima
full_name: Arif, Fatima
last_name: Arif
- first_name: Fatemeh
full_name: Zabihi, Fatemeh
last_name: Zabihi
- first_name: Shengyuan
full_name: Yang, Shengyuan
last_name: Yang
- first_name: Shamsa
full_name: Munir, Shamsa
last_name: Munir
- first_name: Meifang
full_name: Zhu, Meifang
last_name: Zhu
- first_name: M.
full_name: Abid, M.
last_name: Abid
- first_name: Muhammad
full_name: Nauman, Muhammad
id: 32c21954-2022-11eb-9d5f-af9f93c24e71
last_name: Nauman
orcid: 0000-0002-2111-4846
citation:
ama: Dar MS, Akram KB, Sohail A, et al. Heat induction in two-dimensional graphene–Fe3O4
nanohybrids for magnetic hyperthermia applications with artificial neural network
modeling. RSC Advances. 2021;11(35):21702-21715. doi:10.1039/d1ra03428f
apa: Dar, M. S., Akram, K. B., Sohail, A., Arif, F., Zabihi, F., Yang, S., … Nauman,
M. (2021). Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic
hyperthermia applications with artificial neural network modeling. RSC Advances.
Royal Society of Chemistry. https://doi.org/10.1039/d1ra03428f
chicago: Dar, M. S., Khush Bakhat Akram, Ayesha Sohail, Fatima Arif, Fatemeh Zabihi,
Shengyuan Yang, Shamsa Munir, Meifang Zhu, M. Abid, and Muhammad Nauman. “Heat
Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids for Magnetic Hyperthermia
Applications with Artificial Neural Network Modeling.” RSC Advances. Royal
Society of Chemistry, 2021. https://doi.org/10.1039/d1ra03428f.
ieee: M. S. Dar et al., “Heat induction in two-dimensional graphene–Fe3O4
nanohybrids for magnetic hyperthermia applications with artificial neural network
modeling,” RSC Advances, vol. 11, no. 35. Royal Society of Chemistry, pp.
21702–21715, 2021.
ista: Dar MS, Akram KB, Sohail A, Arif F, Zabihi F, Yang S, Munir S, Zhu M, Abid
M, Nauman M. 2021. Heat induction in two-dimensional graphene–Fe3O4 nanohybrids
for magnetic hyperthermia applications with artificial neural network modeling.
RSC Advances. 11(35), 21702–21715.
mla: Dar, M. S., et al. “Heat Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids
for Magnetic Hyperthermia Applications with Artificial Neural Network Modeling.”
RSC Advances, vol. 11, no. 35, Royal Society of Chemistry, 2021, pp. 21702–15,
doi:10.1039/d1ra03428f.
short: M.S. Dar, K.B. Akram, A. Sohail, F. Arif, F. Zabihi, S. Yang, S. Munir, M.
Zhu, M. Abid, M. Nauman, RSC Advances 11 (2021) 21702–21715.
date_created: 2021-06-19T07:27:45Z
date_published: 2021-06-18T00:00:00Z
date_updated: 2023-08-08T14:23:21Z
day: '18'
ddc:
- '540'
department:
- _id: KiMo
doi: 10.1039/d1ra03428f
external_id:
isi:
- '000665644000048'
file:
- access_level: open_access
checksum: cd582d67ace7151078e46b3a896871a9
content_type: application/pdf
creator: asandaue
date_created: 2021-06-23T13:09:34Z
date_updated: 2021-06-23T13:09:34Z
file_id: '9596'
file_name: 2021_RSCAdvances_Dar.pdf
file_size: 2114557
relation: main_file
success: 1
file_date_updated: 2021-06-23T13:09:34Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '35'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '06'
oa: 1
oa_version: Published Version
page: 21702-21715
publication: RSC Advances
publication_identifier:
eissn:
- 2046-2069
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia
applications with artificial neural network modeling
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2021'
...
---
_id: '9558'
abstract:
- lang: eng
text: "We show that turbulent dynamics that arise in simulations of the three-dimensional
Navier--Stokes equations in a triply-periodic domain under sinusoidal forcing
can be described as transient visits to the neighborhoods of unstable time-periodic
solutions. Based on this description, we reduce the original system with more
than 10^5 degrees of freedom to a 17-node Markov chain where each node corresponds
to the neighborhood of a periodic orbit. The model accurately reproduces long-term
averages of the system's observables as weighted sums over the periodic orbits.\r\n"
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank the referees for improving this Letter with their comments.
We acknowledge stimulating discussions with\r\nH. Edelsbrunner. This work was supported
by Grant No. 662960 from the Simons Foundation (B. H.). The numerical calculations
were performed at TUBITAK ULAKBIM High Performance and Grid Computing Center (TRUBA
resources) and IST Austria High Performance Computing cluster."
article_number: '244502'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Gökhan
full_name: Yalniz, Gökhan
id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425
last_name: Yalniz
orcid: 0000-0002-8490-9312
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
citation:
ama: Yalniz G, Hof B, Budanur NB. Coarse graining the state space of a turbulent
flow using periodic orbits. Physical Review Letters. 2021;126(24). doi:10.1103/PhysRevLett.126.244502
apa: Yalniz, G., Hof, B., & Budanur, N. B. (2021). Coarse graining the state
space of a turbulent flow using periodic orbits. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.126.244502
chicago: Yalniz, Gökhan, Björn Hof, and Nazmi B Budanur. “Coarse Graining the State
Space of a Turbulent Flow Using Periodic Orbits.” Physical Review Letters.
American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.126.244502.
ieee: G. Yalniz, B. Hof, and N. B. Budanur, “Coarse graining the state space of
a turbulent flow using periodic orbits,” Physical Review Letters, vol.
126, no. 24. American Physical Society, 2021.
ista: Yalniz G, Hof B, Budanur NB. 2021. Coarse graining the state space of a turbulent
flow using periodic orbits. Physical Review Letters. 126(24), 244502.
mla: Yalniz, Gökhan, et al. “Coarse Graining the State Space of a Turbulent Flow
Using Periodic Orbits.” Physical Review Letters, vol. 126, no. 24, 244502,
American Physical Society, 2021, doi:10.1103/PhysRevLett.126.244502.
short: G. Yalniz, B. Hof, N.B. Budanur, Physical Review Letters 126 (2021).
date_created: 2021-06-16T15:45:36Z
date_published: 2021-06-18T00:00:00Z
date_updated: 2023-08-08T14:08:36Z
day: '18'
department:
- _id: GradSch
- _id: BjHo
doi: 10.1103/PhysRevLett.126.244502
external_id:
arxiv:
- '2007.02584'
isi:
- '000663310100008'
intvolume: ' 126'
isi: 1
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2007.02584
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 238598C6-32DE-11EA-91FC-C7463DDC885E
grant_number: '662960'
name: 'Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental
Studies on Transitional and Turbulent Flows'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/turbulent-flow-simplified/
status: public
title: Coarse graining the state space of a turbulent flow using periodic orbits
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 126
year: '2021'
...
---
_id: '9607'
abstract:
- lang: eng
text: While high risk of failure is an inherent part of developing innovative therapies,
it can be reduced by adherence to evidence-based rigorous research practices.
Numerous analyses conducted to date have clearly identified measures that need
to be taken to improve research rigor. Supported through the European Union's
Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical
research quality system that can be applied in both public and private sectors
and is free for anyone to use. The EQIPD Quality System was designed to be suited
to boost innovation by ensuring the generation of robust and reliable preclinical
data while being lean, effective and not becoming a burden that could negatively
impact the freedom to explore scientific questions. EQIPD defines research quality
as the extent to which research data are fit for their intended use. Fitness,
in this context, is defined by the stakeholders, who are the scientists directly
involved in the research, but also their funders, sponsors, publishers, research
tool manufacturers and collaboration partners such as peers in a multi-site research
project. The essence of the EQIPD Quality System is the set of 18 core requirements
that can be addressed flexibly, according to user-specific needs and following
a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations
for quality-related measures, defines criteria for adequate processes (i.e., performance
standards) and provides examples of how such measures can be developed and implemented.
However, it does not prescribe any pre-determined solutions. EQIPD has also developed
tools (for optional use) to support users in implementing the system and assessment
services for those research units that successfully implement the quality system
and seek formal accreditation. Building upon the feedback from users and continuous
improvement, a sustainable EQIPD Quality System will ultimately serve the entire
community of scientists conducting non-regulated preclinical research, by helping
them generate reliable data that are fit for their intended use.
acknowledgement: This project has received funding from the Innovative Medicines Initiative
2 Joint Undertaking under grant agreement No 777364. This Joint Undertaking receives
support from the European Union’s Horizon 2020 research and innovation programme
and EFPIA. The authors are very grateful to Martin Heinrich (Abbvie, Ludwigshafen,
Germany) for the exceptional IT support and programming the EQIPD Planning Tool
and the Creator Tool and to Dr Shai Silberberg (NINDS, USA), Dr. Renza Roncarati
(PAASP Italy) and Dr Judith Homberg (Radboud University, Nijmegen) for highly stimulating
contributions to the discussions and comments on earlier versions of this manuscript.
We also wish to express our thanks to Dr. Sara Stöber (concentris research management
GmbH, Fürstenfeldbruck, Germany) for excellent and continuous support of this project.
Creation of the EQIPD Stakeholder group was supported by Noldus Information Technology
bv (Wageningen, the Netherlands).
article_processing_charge: No
article_type: original
author:
- first_name: Anton
full_name: Bespalov, Anton
last_name: Bespalov
- first_name: René
full_name: Bernard, René
last_name: Bernard
- first_name: Anja
full_name: Gilis, Anja
last_name: Gilis
- first_name: Björn
full_name: Gerlach, Björn
last_name: Gerlach
- first_name: Javier
full_name: Guillén, Javier
last_name: Guillén
- first_name: Vincent
full_name: Castagné, Vincent
last_name: Castagné
- first_name: Isabel A.
full_name: Lefevre, Isabel A.
last_name: Lefevre
- first_name: Fiona
full_name: Ducrey, Fiona
last_name: Ducrey
- first_name: Lee
full_name: Monk, Lee
last_name: Monk
- first_name: Sandrine
full_name: Bongiovanni, Sandrine
last_name: Bongiovanni
- first_name: Bruce
full_name: Altevogt, Bruce
last_name: Altevogt
- first_name: María
full_name: Arroyo-Araujo, María
last_name: Arroyo-Araujo
- first_name: Lior
full_name: Bikovski, Lior
last_name: Bikovski
- first_name: Natasja
full_name: De Bruin, Natasja
last_name: De Bruin
- first_name: Esmeralda
full_name: Castaños-Vélez, Esmeralda
last_name: Castaños-Vélez
- first_name: Alexander
full_name: Dityatev, Alexander
last_name: Dityatev
- first_name: Christoph H.
full_name: Emmerich, Christoph H.
last_name: Emmerich
- first_name: Raafat
full_name: Fares, Raafat
last_name: Fares
- first_name: Chantelle
full_name: Ferland-Beckham, Chantelle
last_name: Ferland-Beckham
- first_name: Christelle
full_name: Froger-Colléaux, Christelle
last_name: Froger-Colléaux
- first_name: Valerie
full_name: Gailus-Durner, Valerie
last_name: Gailus-Durner
- first_name: Sabine M.
full_name: Hölter, Sabine M.
last_name: Hölter
- first_name: Martine Cj
full_name: Hofmann, Martine Cj
last_name: Hofmann
- first_name: Patricia
full_name: Kabitzke, Patricia
last_name: Kabitzke
- first_name: Martien Jh
full_name: Kas, Martien Jh
last_name: Kas
- first_name: Claudia
full_name: Kurreck, Claudia
last_name: Kurreck
- first_name: Paul
full_name: Moser, Paul
last_name: Moser
- first_name: Malgorzata
full_name: Pietraszek, Malgorzata
last_name: Pietraszek
- first_name: Piotr
full_name: Popik, Piotr
last_name: Popik
- first_name: Heidrun
full_name: Potschka, Heidrun
last_name: Potschka
- first_name: Ernesto
full_name: Prado Montes De Oca, Ernesto
last_name: Prado Montes De Oca
- first_name: Leonardo
full_name: Restivo, Leonardo
last_name: Restivo
- first_name: Gernot
full_name: Riedel, Gernot
last_name: Riedel
- first_name: Merel
full_name: Ritskes-Hoitinga, Merel
last_name: Ritskes-Hoitinga
- first_name: Janko
full_name: Samardzic, Janko
last_name: Samardzic
- first_name: Michael
full_name: Schunn, Michael
id: 4272DB4A-F248-11E8-B48F-1D18A9856A87
last_name: Schunn
orcid: 0000-0003-4326-5300
- first_name: Claudia
full_name: Stöger, Claudia
last_name: Stöger
- first_name: Vootele
full_name: Voikar, Vootele
last_name: Voikar
- first_name: Jan
full_name: Vollert, Jan
last_name: Vollert
- first_name: Kimberley E.
full_name: Wever, Kimberley E.
last_name: Wever
- first_name: Kathleen
full_name: Wuyts, Kathleen
last_name: Wuyts
- first_name: Malcolm R.
full_name: Macleod, Malcolm R.
last_name: Macleod
- first_name: Ulrich
full_name: Dirnagl, Ulrich
last_name: Dirnagl
- first_name: Thomas
full_name: Steckler, Thomas
last_name: Steckler
citation:
ama: Bespalov A, Bernard R, Gilis A, et al. Introduction to the EQIPD quality system.
eLife. 2021;10. doi:10.7554/eLife.63294
apa: Bespalov, A., Bernard, R., Gilis, A., Gerlach, B., Guillén, J., Castagné, V.,
… Steckler, T. (2021). Introduction to the EQIPD quality system. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.63294
chicago: Bespalov, Anton, René Bernard, Anja Gilis, Björn Gerlach, Javier Guillén,
Vincent Castagné, Isabel A. Lefevre, et al. “Introduction to the EQIPD Quality
System.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.63294.
ieee: A. Bespalov et al., “Introduction to the EQIPD quality system,” eLife,
vol. 10. eLife Sciences Publications, 2021.
ista: Bespalov A, Bernard R, Gilis A, Gerlach B, Guillén J, Castagné V, Lefevre
IA, Ducrey F, Monk L, Bongiovanni S, Altevogt B, Arroyo-Araujo M, Bikovski L,
De Bruin N, Castaños-Vélez E, Dityatev A, Emmerich CH, Fares R, Ferland-Beckham
C, Froger-Colléaux C, Gailus-Durner V, Hölter SM, Hofmann MC, Kabitzke P, Kas
MJ, Kurreck C, Moser P, Pietraszek M, Popik P, Potschka H, Prado Montes De Oca
E, Restivo L, Riedel G, Ritskes-Hoitinga M, Samardzic J, Schunn M, Stöger C, Voikar
V, Vollert J, Wever KE, Wuyts K, Macleod MR, Dirnagl U, Steckler T. 2021. Introduction
to the EQIPD quality system. eLife. 10.
mla: Bespalov, Anton, et al. “Introduction to the EQIPD Quality System.” ELife,
vol. 10, eLife Sciences Publications, 2021, doi:10.7554/eLife.63294.
short: A. Bespalov, R. Bernard, A. Gilis, B. Gerlach, J. Guillén, V. Castagné, I.A.
Lefevre, F. Ducrey, L. Monk, S. Bongiovanni, B. Altevogt, M. Arroyo-Araujo, L.
Bikovski, N. De Bruin, E. Castaños-Vélez, A. Dityatev, C.H. Emmerich, R. Fares,
C. Ferland-Beckham, C. Froger-Colléaux, V. Gailus-Durner, S.M. Hölter, M.C. Hofmann,
P. Kabitzke, M.J. Kas, C. Kurreck, P. Moser, M. Pietraszek, P. Popik, H. Potschka,
E. Prado Montes De Oca, L. Restivo, G. Riedel, M. Ritskes-Hoitinga, J. Samardzic,
M. Schunn, C. Stöger, V. Voikar, J. Vollert, K.E. Wever, K. Wuyts, M.R. Macleod,
U. Dirnagl, T. Steckler, ELife 10 (2021).
date_created: 2021-06-27T22:01:49Z
date_published: 2021-05-24T00:00:00Z
date_updated: 2023-08-10T13:36:50Z
day: '24'
ddc:
- '570'
department:
- _id: PreCl
doi: 10.7554/eLife.63294
external_id:
isi:
- '000661272000001'
pmid:
- '34028353'
file:
- access_level: open_access
checksum: 885b746051a7a6b6e24e3d2781a48fde
content_type: application/pdf
creator: asandaue
date_created: 2021-06-28T11:35:30Z
date_updated: 2021-06-28T11:35:30Z
file_id: '9609'
file_name: 2021_ELife_Bespalov.pdf
file_size: 2500720
relation: main_file
success: 1
file_date_updated: 2021-06-28T11:35:30Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Introduction to the EQIPD quality system
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: 10
year: '2021'
...
---
_id: '9601'
abstract:
- lang: eng
text: 'In mammalian genomes, differentially methylated regions (DMRs) and histone
marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted
genes are asymmetrically inherited to control parentally-biased gene expression.
However, neither parent-of-origin-specific transcription nor imprints have been
comprehensively mapped at the blastocyst stage of preimplantation development.
Here, we address this by integrating transcriptomic and epigenomic approaches
in mouse preimplantation embryos. We find that seventy-one genes exhibit previously
unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted
expressed). Uniparental expression of nBiX genes disappears soon after implantation.
Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts
detects 859 DMRs. We further find that 16% of nBiX genes are associated with a
DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a
role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered:
five clusters contained at least one published imprinted gene, and five clusters
exclusively contained nBiX genes. These data suggest that early development undergoes
a complex program of stage-specific imprinting involving different tiers of regulation.'
acknowledgement: The authors thank Robert Feil and Anton Wutz for helpful discussions
and comments, Samuel Collombet and Peter Fraser for sharing embryo TAD coordinates,
and Andy Riddel at the Cambridge Stem Cell Institute and Thomas Sauer at the Max
Perutz Laboratories FACS facility for flow-sorting. We thank the team of the Biomedical
Sequencing Facility at the CeMM and the Vienna Biocenter Core Facilities (VBCF)
for support with next-generation sequencing. We are grateful to animal care teams
at the University of Bath and MRC Harwell. A.C.F.P. acknowledges support from the
UK Medical Research Council (MR/N000080/1 and MR/N020294/1) and Biotechnology and
Biological Sciences Research Council (BB/P009506/1). L.S. is part of the FWF doctoral
programme SMICH and supported by an Austrian Academy of Sciences DOC Fellowship.
M.L. is funded by a Vienna Research Group for Young Investigators grant (VRG14-006)
by the Vienna Science and Technology Fund (WWTF) and by the Austrian Science Fund
FWF (I3786 and P31334).
article_number: '3804'
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Santini, Laura
last_name: Santini
- first_name: Florian
full_name: Halbritter, Florian
last_name: Halbritter
- first_name: Fabian
full_name: Titz-Teixeira, Fabian
last_name: Titz-Teixeira
- first_name: Toru
full_name: Suzuki, Toru
last_name: Suzuki
- first_name: Maki
full_name: Asami, Maki
last_name: Asami
- first_name: Xiaoyan
full_name: Ma, Xiaoyan
last_name: Ma
- first_name: Julia
full_name: Ramesmayer, Julia
last_name: Ramesmayer
- first_name: Andreas
full_name: Lackner, Andreas
last_name: Lackner
- first_name: Nick
full_name: Warr, Nick
last_name: Warr
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Ernest
full_name: Laue, Ernest
last_name: Laue
- first_name: Matthias
full_name: Farlik, Matthias
last_name: Farlik
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Andreas
full_name: Beyer, Andreas
last_name: Beyer
- first_name: Anthony C.F.
full_name: Perry, Anthony C.F.
last_name: Perry
- first_name: Martin
full_name: Leeb, Martin
last_name: Leeb
citation:
ama: Santini L, Halbritter F, Titz-Teixeira F, et al. Genomic imprinting in mouse
blastocysts is predominantly associated with H3K27me3. Nature Communications.
2021;12(1). doi:10.1038/s41467-021-23510-4
apa: Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ma,
X., … Leeb, M. (2021). Genomic imprinting in mouse blastocysts is predominantly
associated with H3K27me3. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23510-4
chicago: Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki,
Maki Asami, Xiaoyan Ma, Julia Ramesmayer, et al. “Genomic Imprinting in Mouse
Blastocysts Is Predominantly Associated with H3K27me3.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23510-4.
ieee: L. Santini et al., “Genomic imprinting in mouse blastocysts is predominantly
associated with H3K27me3,” Nature Communications, vol. 12, no. 1. Springer
Nature, 2021.
ista: Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ma X, Ramesmayer
J, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer
A, Perry ACF, Leeb M. 2021. Genomic imprinting in mouse blastocysts is predominantly
associated with H3K27me3. Nature Communications. 12(1), 3804.
mla: Santini, Laura, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly
Associated with H3K27me3.” Nature Communications, vol. 12, no. 1, 3804,
Springer Nature, 2021, doi:10.1038/s41467-021-23510-4.
short: L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, X. Ma,
J. Ramesmayer, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik,
C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, Nature Communications 12 (2021).
date_created: 2021-06-27T22:01:46Z
date_published: 2021-07-12T00:00:00Z
date_updated: 2023-08-10T13:53:23Z
day: '12'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1038/s41467-021-23510-4
external_id:
isi:
- '000667248600005'
file:
- access_level: open_access
checksum: 75dd89d09945185b2d14b2434a0bcb50
content_type: application/pdf
creator: asandaue
date_created: 2021-06-28T08:04:22Z
date_updated: 2021-06-28T08:04:22Z
file_id: '9608'
file_name: 2021_NatureCommunications_Santini.pdf
file_size: 2156554
relation: main_file
success: 1
file_date_updated: 2021-06-28T08:04:22Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3
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: '9602'
abstract:
- lang: eng
text: "An ordered graph is a graph with a linear ordering on its vertex set. We
prove that for every positive integer k, there exists a constant ck > 0 such that
any ordered graph G on n vertices with the property that neither G nor its complement
contains an induced monotone path of size k, has either a clique or an independent
set of size at least n^ck . This strengthens a result of Bousquet, Lagoutte, and
Thomassé, who proved the analogous result for unordered graphs.\r\nA key idea
of the above paper was to show that any unordered graph on n vertices that does
not contain an induced path of size k, and whose maximum degree is at most c(k)n
for some small c(k) > 0, contains two disjoint linear size subsets with no edge
between them. This approach fails for ordered graphs, because the analogous statement
is false for k ≥ 3, by a construction of Fox. We provide some further examples
showing that this statement also fails for ordered graphs avoiding other ordered
trees."
acknowledgement: We would like to thank the anonymous referees for their useful comments
and suggestions. János Pach is partially supported by Austrian Science Fund (FWF)
grant Z 342-N31 and by ERC Advanced grant “GeoScape.” István Tomon is partially
supported by Swiss National Science Foundation grant no. 200021_196965, and thanks
the support of MIPT Moscow. Both authors are partially supported by The Russian
Government in the framework of MegaGrant no. 075-15-2019-1926.
article_processing_charge: No
article_type: original
author:
- first_name: János
full_name: Pach, János
id: E62E3130-B088-11EA-B919-BF823C25FEA4
last_name: Pach
- first_name: István
full_name: Tomon, István
last_name: Tomon
citation:
ama: Pach J, Tomon I. Erdős-Hajnal-type results for monotone paths. Journal of
Combinatorial Theory Series B. 2021;151:21-37. doi:10.1016/j.jctb.2021.05.004
apa: Pach, J., & Tomon, I. (2021). Erdős-Hajnal-type results for monotone paths.
Journal of Combinatorial Theory. Series B. Elsevier. https://doi.org/10.1016/j.jctb.2021.05.004
chicago: Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone
Paths.” Journal of Combinatorial Theory. Series B. Elsevier, 2021. https://doi.org/10.1016/j.jctb.2021.05.004.
ieee: J. Pach and I. Tomon, “Erdős-Hajnal-type results for monotone paths,” Journal
of Combinatorial Theory. Series B, vol. 151. Elsevier, pp. 21–37, 2021.
ista: Pach J, Tomon I. 2021. Erdős-Hajnal-type results for monotone paths. Journal
of Combinatorial Theory. Series B. 151, 21–37.
mla: Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.”
Journal of Combinatorial Theory. Series B, vol. 151, Elsevier, 2021, pp.
21–37, doi:10.1016/j.jctb.2021.05.004.
short: J. Pach, I. Tomon, Journal of Combinatorial Theory. Series B 151 (2021) 21–37.
date_created: 2021-06-27T22:01:47Z
date_published: 2021-06-09T00:00:00Z
date_updated: 2023-08-10T13:38:00Z
day: '09'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1016/j.jctb.2021.05.004
external_id:
isi:
- '000702280800002'
file:
- access_level: open_access
checksum: 15fbc9064cd9d1c777ac0043b78c8f12
content_type: application/pdf
creator: asandaue
date_created: 2021-06-28T13:33:23Z
date_updated: 2021-06-28T13:33:23Z
file_id: '9612'
file_name: 2021_JournalOfCombinatorialTheory_Pach.pdf
file_size: 418168
relation: main_file
success: 1
file_date_updated: 2021-06-28T13:33:23Z
has_accepted_license: '1'
intvolume: ' 151'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 21-37
project:
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
publication: Journal of Combinatorial Theory. Series B
publication_identifier:
issn:
- 0095-8956
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Erdős-Hajnal-type results for monotone paths
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: 151
year: '2021'
...
---
_id: '9606'
abstract:
- lang: eng
text: Sound propagation is a macroscopic manifestation of the interplay between
the equilibrium thermodynamics and the dynamical transport properties of fluids.
Here, for a two-dimensional system of ultracold fermions, we calculate the first
and second sound velocities across the whole BCS-BEC crossover, and we analyze
the system response to an external perturbation. In the low-temperature regime
we reproduce the recent measurements [Phys. Rev. Lett. 124, 240403 (2020)] of
the first sound velocity, which, due to the decoupling of density and entropy
fluctuations, is the sole mode excited by a density probe. Conversely, a heat
perturbation excites only the second sound, which, being sensitive to the superfluid
depletion, vanishes in the deep BCS regime and jumps discontinuously to zero at
the Berezinskii-Kosterlitz-Thouless superfluid transition. A mixing between the
modes occurs only in the finite-temperature BEC regime, where our theory converges
to the purely bosonic results.
acknowledgement: "G.B. acknowledges support from the Austrian Science Fund (FWF),
under Project No. M2641-N27. This work was\r\npartially supported by the University
of Padua, BIRD project “Superfluid properties of Fermi gases in optical potentials.”\r\nThe
authors thank Miki Ota, Tomoki Ozawa, Sandro Stringari, Tilman Enss, Hauke Biss,
Henning Moritz, and Nicolò Defenu for fruitful discussions. The authors thank Henning
Moritz and Markus Bohlen for providing their experimental\r\ndata."
article_number: L061303
article_processing_charge: No
article_type: letter_note
author:
- first_name: A.
full_name: Tononi, A.
last_name: Tononi
- first_name: Alberto
full_name: Cappellaro, Alberto
id: 9d13b3cb-30a2-11eb-80dc-f772505e8660
last_name: Cappellaro
orcid: 0000-0001-6110-2359
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: L.
full_name: Salasnich, L.
last_name: Salasnich
citation:
ama: Tononi A, Cappellaro A, Bighin G, Salasnich L. Propagation of first and second
sound in a two-dimensional Fermi superfluid. Physical Review A. 2021;103(6).
doi:10.1103/PhysRevA.103.L061303
apa: Tononi, A., Cappellaro, A., Bighin, G., & Salasnich, L. (2021). Propagation
of first and second sound in a two-dimensional Fermi superfluid. Physical Review
A. American Physical Society. https://doi.org/10.1103/PhysRevA.103.L061303
chicago: Tononi, A., Alberto Cappellaro, Giacomo Bighin, and L. Salasnich. “Propagation
of First and Second Sound in a Two-Dimensional Fermi Superfluid.” Physical
Review A. American Physical Society, 2021. https://doi.org/10.1103/PhysRevA.103.L061303.
ieee: A. Tononi, A. Cappellaro, G. Bighin, and L. Salasnich, “Propagation of first
and second sound in a two-dimensional Fermi superfluid,” Physical Review A,
vol. 103, no. 6. American Physical Society, 2021.
ista: Tononi A, Cappellaro A, Bighin G, Salasnich L. 2021. Propagation of first
and second sound in a two-dimensional Fermi superfluid. Physical Review A. 103(6),
L061303.
mla: Tononi, A., et al. “Propagation of First and Second Sound in a Two-Dimensional
Fermi Superfluid.” Physical Review A, vol. 103, no. 6, L061303, American
Physical Society, 2021, doi:10.1103/PhysRevA.103.L061303.
short: A. Tononi, A. Cappellaro, G. Bighin, L. Salasnich, Physical Review A 103
(2021).
date_created: 2021-06-27T22:01:49Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-10T13:37:25Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.103.L061303
external_id:
arxiv:
- '2009.06491'
isi:
- '000662296700014'
intvolume: ' 103'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2009.06491
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- '24699934'
issn:
- '24699926'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Propagation of first and second sound in a two-dimensional Fermi superfluid
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 103
year: '2021'
...
---
_id: '9642'
abstract:
- lang: eng
text: Perineuronal nets (PNNs), components of the extracellular matrix, preferentially
coat parvalbumin-positive interneurons and constrain critical-period plasticity
in the adult cerebral cortex. Current strategies to remove PNN are long-lasting,
invasive, and trigger neuropsychiatric symptoms. Here, we apply repeated anesthetic
ketamine as a method with minimal behavioral effect. We find that this paradigm
strongly reduces PNN coating in the healthy adult brain and promotes juvenile-like
plasticity. Microglia are critically involved in PNN loss because they engage
with parvalbumin-positive neurons in their defined cortical layer. We identify
external 60-Hz light-flickering entrainment to recapitulate microglia-mediated
PNN removal. Importantly, 40-Hz frequency, which is known to remove amyloid plaques,
does not induce PNN loss, suggesting microglia might functionally tune to distinct
brain frequencies. Thus, our 60-Hz light-entrainment strategy provides an alternative
form of PNN intervention in the healthy adult brain.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: We thank the scientific service units at IST Austria, especially
the IST bioimaging facility, the preclinical facility, and, specifically, Michael
Schunn and Sonja Haslinger for excellent support; Plexxikon for the PLX food; the
Csicsvari group for advice and equipment for in vivo recording; Jürgen Siegert for
the light-entrainment design; Marco Benevento, Soledad Gonzalo Cogno, Pat King,
and all Siegert group members for constant feedback on the project and manuscript;
Lorena Pantano (PILM Bioinformatics Core) for assisting with sample-size determination
for OD plasticity experiments; and Ana Morello from MIT for technical assistance
with VEPs recordings. This research was supported by a DOC Fellowship from the Austrian
Academy of Sciences at the Institute of Science and Technology Austria to R.S.,
from the European Union Horizon 2020 research and innovation program under the Marie
Skłodowska-Curie Actions program (grants 665385 to G.C.; 754411 to R.J.A.C.), the
European Research Council (grant 715571 to S.S.), and the National Eye Institute
of the National Institutes of Health under award numbers R01EY029245 (to M.F.B.)
and R01EY023037 (diversity supplement to H.D.J-C.).
article_number: '109313'
article_processing_charge: No
article_type: original
author:
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Rouven
full_name: Schulz, Rouven
id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87
last_name: Schulz
orcid: 0000-0001-5297-733X
- first_name: Héctor
full_name: De Jesús-Cortés, Héctor
last_name: De Jesús-Cortés
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Balint
full_name: Nagy, Balint
id: 93C65ECC-A6F2-11E9-8DF9-9712E6697425
last_name: Nagy
- first_name: Francis
full_name: Reilly-Andújar, Francis
last_name: Reilly-Andújar
- first_name: Gloria
full_name: Colombo, Gloria
id: 3483CF6C-F248-11E8-B48F-1D18A9856A87
last_name: Colombo
orcid: 0000-0001-9434-8902
- first_name: Ryan J
full_name: Cubero, Ryan J
id: 850B2E12-9CD4-11E9-837F-E719E6697425
last_name: Cubero
orcid: 0000-0003-0002-1867
- first_name: Florianne E
full_name: Schoot Uiterkamp, Florianne E
id: 3526230C-F248-11E8-B48F-1D18A9856A87
last_name: Schoot Uiterkamp
- first_name: Mark F.
full_name: Bear, Mark F.
last_name: Bear
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Venturino A, Schulz R, De Jesús-Cortés H, et al. Microglia enable mature perineuronal
nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment
in the healthy brain. Cell Reports. 2021;36(1). doi:10.1016/j.celrep.2021.109313
apa: Venturino, A., Schulz, R., De Jesús-Cortés, H., Maes, M. E., Nagy, B., Reilly-Andújar,
F., … Siegert, S. (2021). Microglia enable mature perineuronal nets disassembly
upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain.
Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2021.109313
chicago: Venturino, Alessandro, Rouven Schulz, Héctor De Jesús-Cortés, Margaret
E Maes, Balint Nagy, Francis Reilly-Andújar, Gloria Colombo, et al. “Microglia
Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure
or 60-Hz Light Entrainment in the Healthy Brain.” Cell Reports. Elsevier,
2021. https://doi.org/10.1016/j.celrep.2021.109313.
ieee: A. Venturino et al., “Microglia enable mature perineuronal nets disassembly
upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain,”
Cell Reports, vol. 36, no. 1. Elsevier, 2021.
ista: Venturino A, Schulz R, De Jesús-Cortés H, Maes ME, Nagy B, Reilly-Andújar
F, Colombo G, Cubero RJ, Schoot Uiterkamp FE, Bear MF, Siegert S. 2021. Microglia
enable mature perineuronal nets disassembly upon anesthetic ketamine exposure
or 60-Hz light entrainment in the healthy brain. Cell Reports. 36(1), 109313.
mla: Venturino, Alessandro, et al. “Microglia Enable Mature Perineuronal Nets Disassembly
upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.”
Cell Reports, vol. 36, no. 1, 109313, Elsevier, 2021, doi:10.1016/j.celrep.2021.109313.
short: A. Venturino, R. Schulz, H. De Jesús-Cortés, M.E. Maes, B. Nagy, F. Reilly-Andújar,
G. Colombo, R.J. Cubero, F.E. Schoot Uiterkamp, M.F. Bear, S. Siegert, Cell Reports
36 (2021).
date_created: 2021-07-11T22:01:16Z
date_published: 2021-07-06T00:00:00Z
date_updated: 2023-08-10T14:09:39Z
day: '06'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1016/j.celrep.2021.109313
ec_funded: 1
external_id:
isi:
- '000670188500004'
pmid:
- '34233180'
file:
- access_level: open_access
checksum: f056255f6d01fd9a86b5387635928173
content_type: application/pdf
creator: cziletti
date_created: 2021-07-19T13:32:17Z
date_updated: 2021-07-19T13:32:17Z
file_id: '9693'
file_name: 2021_CellReports_Venturino.pdf
file_size: 56388540
relation: main_file
success: 1
file_date_updated: 2021-07-19T13:32:17Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25D4A630-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715571'
name: Microglia action towards neuronal circuit formation and function in health
and disease
publication: Cell Reports
publication_identifier:
eissn:
- '22111247'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/the-twinkle-and-the-brain/
scopus_import: '1'
status: public
title: Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine
exposure or 60-Hz light entrainment in the healthy brain
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: 36
year: '2021'
...
---
_id: '9603'
abstract:
- lang: eng
text: Mosaic analysis with double markers (MADM) offers one approach to visualize
and concomitantly manipulate genetically defined cells in mice with single-cell
resolution. MADM applications include the analysis of lineage, single-cell morphology
and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous
gene functions in vivo in health and disease. Yet, MADM can only be applied to
<25% of all mouse genes on select chromosomes to date. To overcome this limitation,
we generate transgenic mice with knocked-in MADM cassettes near the centromeres
of all 19 autosomes and validate their use across organs. With this resource,
>96% of the entire mouse genome can now be subjected to single-cell genetic mosaic
analysis. Beyond a proof of principle, we apply our MADM library to systematically
trace sister chromatid segregation in distinct mitotic cell lineages. We find
striking chromosome-specific biases in segregation patterns, reflecting a putative
mechanism for the asymmetric segregation of genetic determinants in somatic stem
cell division.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
acknowledgement: We thank the Bioimaging, Life Science, and Pre-Clinical Facilities
at IST Austria; M.P. Postiglione, C. Simbriger, K. Valoskova, C. Schwayer, T. Hussain,
M. Pieber, and V. Wimmer for initial experiments, technical support, and/or assistance;
R. Shigemoto for sharing iv (Dnah11 mutant) mice; and M. Sixt and all members of
the Hippenmeyer lab for discussion. This work was supported by National Institutes
of Health grants ( R01-NS050580 to L.L. and F32MH096361 to L.A.S.). L.L. is an investigator
of HHMI. N.A. received support from FWF Firnberg-Programm ( T 1031 ). A.H.H. is
a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences . This
work also received support from IST Austria institutional funds , FWF SFB F78 to
S.H., the People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme ( FP7/2007-2013 ) under REA grant agreement no 618444 to S.H.,
and the European Research Council (ERC) under the European Union’s Horizon 2020
Research and Innovation Programme (grant agreement no. 725780 LinPro ) to S.H.
article_number: '109274'
article_processing_charge: No
article_type: original
author:
- first_name: Ximena
full_name: Contreras, Ximena
id: 475990FE-F248-11E8-B48F-1D18A9856A87
last_name: Contreras
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Amarbayasgalan
full_name: Davaatseren, Amarbayasgalan
id: 70ADC922-B424-11E9-99E3-BA18E6697425
last_name: Davaatseren
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Johanna
full_name: Sonntag, Johanna
id: 32FE7D7C-F248-11E8-B48F-1D18A9856A87
last_name: Sonntag
- first_name: Lill
full_name: Andersen, Lill
last_name: Andersen
- first_name: Tina
full_name: Bernthaler, Tina
last_name: Bernthaler
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Anna-Magdalena
full_name: Heger, Anna-Magdalena
id: 4B76FFD2-F248-11E8-B48F-1D18A9856A87
last_name: Heger
- first_name: Randy L.
full_name: Johnson, Randy L.
last_name: Johnson
- first_name: Lindsay A.
full_name: Schwarz, Lindsay A.
last_name: Schwarz
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
- first_name: Thomas
full_name: Rülicke, Thomas
last_name: Rülicke
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Contreras X, Amberg N, Davaatseren A, et al. A genome-wide library of MADM
mice for single-cell genetic mosaic analysis. Cell Reports. 2021;35(12).
doi:10.1016/j.celrep.2021.109274
apa: Contreras, X., Amberg, N., Davaatseren, A., Hansen, A. H., Sonntag, J., Andersen,
L., … Hippenmeyer, S. (2021). A genome-wide library of MADM mice for single-cell
genetic mosaic analysis. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2021.109274
chicago: Contreras, Ximena, Nicole Amberg, Amarbayasgalan Davaatseren, Andi H Hansen,
Johanna Sonntag, Lill Andersen, Tina Bernthaler, et al. “A Genome-Wide Library
of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports. Cell
Press, 2021. https://doi.org/10.1016/j.celrep.2021.109274.
ieee: X. Contreras et al., “A genome-wide library of MADM mice for single-cell
genetic mosaic analysis,” Cell Reports, vol. 35, no. 12. Cell Press, 2021.
ista: Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler
T, Streicher C, Heger A-M, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer
S. 2021. A genome-wide library of MADM mice for single-cell genetic mosaic analysis.
Cell Reports. 35(12), 109274.
mla: Contreras, Ximena, et al. “A Genome-Wide Library of MADM Mice for Single-Cell
Genetic Mosaic Analysis.” Cell Reports, vol. 35, no. 12, 109274, Cell Press,
2021, doi:10.1016/j.celrep.2021.109274.
short: X. Contreras, N. Amberg, A. Davaatseren, A.H. Hansen, J. Sonntag, L. Andersen,
T. Bernthaler, C. Streicher, A.-M. Heger, R.L. Johnson, L.A. Schwarz, L. Luo,
T. Rülicke, S. Hippenmeyer, Cell Reports 35 (2021).
date_created: 2021-06-27T22:01:48Z
date_published: 2021-06-22T00:00:00Z
date_updated: 2023-08-10T13:55:00Z
day: '22'
ddc:
- '570'
department:
- _id: SiHi
- _id: LoSw
- _id: PreCl
doi: 10.1016/j.celrep.2021.109274
ec_funded: 1
external_id:
isi:
- '000664463600016'
file:
- access_level: open_access
checksum: d49520fdcbbb5c2f883bddb67cee5d77
content_type: application/pdf
creator: asandaue
date_created: 2021-06-28T14:06:24Z
date_updated: 2021-06-28T14:06:24Z
file_id: '9613'
file_name: 2021_CellReports_Contreras.pdf
file_size: 7653149
relation: main_file
success: 1
file_date_updated: 2021-06-28T14:06:24Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '12'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
grant_number: '24812'
name: Molecular Mechanisms of Radial Neuronal Migration
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Cell Reports
publication_identifier:
eissn:
- '22111247'
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/
scopus_import: '1'
status: public
title: A genome-wide library of MADM mice for single-cell genetic mosaic analysis
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: 35
year: '2021'
...
---
_id: '9618'
abstract:
- lang: eng
text: The control of nonequilibrium quantum dynamics in many-body systems is challenging
because interactions typically lead to thermalization and a chaotic spreading
throughout Hilbert space. We investigate nonequilibrium dynamics after rapid quenches
in a many-body system composed of 3 to 200 strongly interacting qubits in one
and two spatial dimensions. Using a programmable quantum simulator based on Rydberg
atom arrays, we show that coherent revivals associated with so-called quantum
many-body scars can be stabilized by periodic driving, which generates a robust
subharmonic response akin to discrete time-crystalline order. We map Hilbert space
dynamics, geometry dependence, phase diagrams, and system-size dependence of this
emergent phenomenon, demonstrating new ways to steer complex dynamics in many-body
systems and enabling potential applications in quantum information science.
acknowledgement: 'We thank many members of the Harvard AMO community, particularly
E. Urbach, S. Dakoulas, and J. Doyle for their efforts enabling safe and productive
operation of our laboratories during 2020. We thank D. Abanin, I. Cong, F. Machado,
H. Pichler, N. Yao, B. Ye, and H. Zhou for stimulating discussions. Funding: We
acknowledge financial support from the Center for Ultracold Atoms, the National
Science Foundation, the Vannevar Bush Faculty Fellowship, the U.S. Department of
Energy (LBNL QSA Center and grant no. DE-SC0021013), the Office of Naval Research,
the Army Research Office MURI, the DARPA DRINQS program (grant no. D18AC00033),
and the DARPA ONISQ program (grant no. W911NF2010021). The authors acknowledge support
from the NSF Graduate Research Fellowship Program (grant DGE1745303) and The Fannie
and John Hertz Foundation (D.B.); a National Defense Science and Engineering Graduate
(NDSEG) fellowship (H.L.); a fellowship from the Max Planck/Harvard Research Center
for Quantum Optics (G.S.); Gordon College (T.T.W.); the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
agreement no. 850899) (A.A.M. and M.S.); a Department of Energy Computational Science
Graduate Fellowship under award number DE-SC0021110 (N.M.); the Moore Foundation’s
EPiQS Initiative grant no. GBMF4306, the NUS Development grant AY2019/2020, and
the Stanford Institute of Theoretical Physics (W.W.H.); and the Miller Institute
for Basic Research in Science (S.C.). Author contributions: D.B., A.O., H.L., A.K.,
G.S., S.E., and T.T.W. contributed to the building of the experimental setup, performed
the measurements, and analyzed the data. A.A.M., N.M., W.W.H., S.C., and M.S. performed
theoretical analysis. All work was supervised by M.G., V.V., and M.D.L. All authors
discussed the results and contributed to the manuscript. Competing interests: M.G.,
V.V., and M.D.L. are co-founders and shareholders of QuEra Computing. A.O. is a
shareholder of QuEra Computing. Data and materials availability: All data needed
to evaluate the conclusions in the paper are present in the paper and the supplementary
materials.'
article_processing_charge: No
article_type: original
author:
- first_name: D.
full_name: Bluvstein, D.
last_name: Bluvstein
- first_name: A.
full_name: Omran, A.
last_name: Omran
- first_name: H.
full_name: Levine, H.
last_name: Levine
- first_name: A.
full_name: Keesling, A.
last_name: Keesling
- first_name: G.
full_name: Semeghini, G.
last_name: Semeghini
- first_name: S.
full_name: Ebadi, S.
last_name: Ebadi
- first_name: T. T.
full_name: Wang, T. T.
last_name: Wang
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: N.
full_name: Maskara, N.
last_name: Maskara
- first_name: W. W.
full_name: Ho, W. W.
last_name: Ho
- first_name: S.
full_name: Choi, S.
last_name: Choi
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: M.
full_name: Greiner, M.
last_name: Greiner
- first_name: V.
full_name: Vuletić, V.
last_name: Vuletić
- first_name: M. D.
full_name: Lukin, M. D.
last_name: Lukin
citation:
ama: Bluvstein D, Omran A, Levine H, et al. Controlling quantum many-body dynamics
in driven Rydberg atom arrays. Science. 2021;371(6536):1355-1359. doi:10.1126/science.abg2530
apa: Bluvstein, D., Omran, A., Levine, H., Keesling, A., Semeghini, G., Ebadi, S.,
… Lukin, M. D. (2021). Controlling quantum many-body dynamics in driven Rydberg
atom arrays. Science. AAAS. https://doi.org/10.1126/science.abg2530
chicago: Bluvstein, D., A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi,
T. T. Wang, et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom
Arrays.” Science. AAAS, 2021. https://doi.org/10.1126/science.abg2530.
ieee: D. Bluvstein et al., “Controlling quantum many-body dynamics in driven
Rydberg atom arrays,” Science, vol. 371, no. 6536. AAAS, pp. 1355–1359,
2021.
ista: Bluvstein D, Omran A, Levine H, Keesling A, Semeghini G, Ebadi S, Wang TT,
Michailidis A, Maskara N, Ho WW, Choi S, Serbyn M, Greiner M, Vuletić V, Lukin
MD. 2021. Controlling quantum many-body dynamics in driven Rydberg atom arrays.
Science. 371(6536), 1355–1359.
mla: Bluvstein, D., et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg
Atom Arrays.” Science, vol. 371, no. 6536, AAAS, 2021, pp. 1355–59, doi:10.1126/science.abg2530.
short: D. Bluvstein, A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T.T.
Wang, A. Michailidis, N. Maskara, W.W. Ho, S. Choi, M. Serbyn, M. Greiner, V.
Vuletić, M.D. Lukin, Science 371 (2021) 1355–1359.
date_created: 2021-06-29T12:04:05Z
date_published: 2021-03-26T00:00:00Z
date_updated: 2023-08-10T13:57:07Z
day: '26'
ddc:
- '539'
department:
- _id: MaSe
doi: 10.1126/science.abg2530
ec_funded: 1
external_id:
arxiv:
- '2012.12276'
isi:
- '000636043400048'
pmid:
- '33632894'
file:
- access_level: open_access
checksum: 0b356fd10ab9bb95177d4c047d4e9c1a
content_type: application/pdf
creator: patrickd
date_created: 2021-09-23T14:00:05Z
date_updated: 2021-09-23T14:00:05Z
file_id: '10040'
file_name: scars_subharmonic_combined_manuscript_2_11_2021 (2)-1.pdf
file_size: 3671159
relation: main_file
success: 1
file_date_updated: 2021-09-23T14:00:05Z
has_accepted_license: '1'
intvolume: ' 371'
isi: 1
issue: '6536'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '03'
oa: 1
oa_version: Preprint
page: 1355-1359
pmid: 1
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Controlling quantum many-body dynamics in driven Rydberg atom arrays
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 371
year: '2021'
...
---
_id: '9657'
abstract:
- lang: eng
text: To overcome nitrogen deficiency, legume roots establish symbiotic interactions
with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules).
Similar to other organs, nodule formation is determined by a local maximum of
the phytohormone auxin at the primordium site. However, how auxin regulates nodule
development remains poorly understood. Here, we found that in soybean, (Glycine
max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is
involved in nodule primordium formation. GmPIN1 was specifically expressed in
nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation
regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical
cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated
with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems
and aberrant divisions in the nodule primordium cells. Moreover, overexpression
of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis
thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally
transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement.
Our findings reveal how PIN-dependent auxin transport modulates different aspects
of soybean nodule development and suggest that establishment of auxin gradient
is a prerequisite for the proper interaction between legumes and rhizobia.
article_processing_charge: No
article_type: original
author:
- first_name: Z
full_name: Gao, Z
last_name: Gao
- first_name: Z
full_name: Chen, Z
last_name: Chen
- first_name: Y
full_name: Cui, Y
last_name: Cui
- first_name: M
full_name: Ke, M
last_name: Ke
- first_name: H
full_name: Xu, H
last_name: Xu
- first_name: Q
full_name: Xu, Q
last_name: Xu
- first_name: J
full_name: Chen, J
last_name: Chen
- first_name: Y
full_name: Li, Y
last_name: Li
- first_name: L
full_name: Huang, L
last_name: Huang
- first_name: H
full_name: Zhao, H
last_name: Zhao
- first_name: D
full_name: Huang, D
last_name: Huang
- first_name: S
full_name: Mai, S
last_name: Mai
- first_name: T
full_name: Xu, T
last_name: Xu
- first_name: X
full_name: Liu, X
last_name: Liu
- first_name: S
full_name: Li, S
last_name: Li
- first_name: Y
full_name: Guan, Y
last_name: Guan
- first_name: W
full_name: Yang, W
last_name: Yang
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: J
full_name: Petrášek, J
last_name: Petrášek
- first_name: J
full_name: Zhang, J
last_name: Zhang
- first_name: X
full_name: Chen, X
last_name: Chen
citation:
ama: Gao Z, Chen Z, Cui Y, et al. GmPIN-dependent polar auxin transport is involved
in soybean nodule development. Plant Cell. 2021;33(9):2981–3003. doi:10.1093/plcell/koab183
apa: Gao, Z., Chen, Z., Cui, Y., Ke, M., Xu, H., Xu, Q., … Chen, X. (2021). GmPIN-dependent
polar auxin transport is involved in soybean nodule development. Plant Cell.
American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab183
chicago: Gao, Z, Z Chen, Y Cui, M Ke, H Xu, Q Xu, J Chen, et al. “GmPIN-Dependent
Polar Auxin Transport Is Involved in Soybean Nodule Development.” Plant Cell.
American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab183.
ieee: Z. Gao et al., “GmPIN-dependent polar auxin transport is involved in
soybean nodule development,” Plant Cell, vol. 33, no. 9. American Society
of Plant Biologists, pp. 2981–3003, 2021.
ista: Gao Z, Chen Z, Cui Y, Ke M, Xu H, Xu Q, Chen J, Li Y, Huang L, Zhao H, Huang
D, Mai S, Xu T, Liu X, Li S, Guan Y, Yang W, Friml J, Petrášek J, Zhang J, Chen
X. 2021. GmPIN-dependent polar auxin transport is involved in soybean nodule development.
Plant Cell. 33(9), 2981–3003.
mla: Gao, Z., et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean
Nodule Development.” Plant Cell, vol. 33, no. 9, American Society of Plant
Biologists, 2021, pp. 2981–3003, doi:10.1093/plcell/koab183.
short: Z. Gao, Z. Chen, Y. Cui, M. Ke, H. Xu, Q. Xu, J. Chen, Y. Li, L. Huang, H.
Zhao, D. Huang, S. Mai, T. Xu, X. Liu, S. Li, Y. Guan, W. Yang, J. Friml, J. Petrášek,
J. Zhang, X. Chen, Plant Cell 33 (2021) 2981–3003.
date_created: 2021-07-14T15:32:43Z
date_published: 2021-07-07T00:00:00Z
date_updated: 2023-08-10T14:01:41Z
day: '07'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1093/plcell/koab183
external_id:
isi:
- '000702165300012'
pmid:
- '34240197'
file:
- access_level: open_access
checksum: 6715712ec306c321f0204c817b7f8ae7
content_type: application/pdf
creator: cziletti
date_created: 2021-07-19T12:13:34Z
date_updated: 2021-07-19T12:13:34Z
file_id: '9691'
file_name: 2021_PlantCell_Gao.pdf
file_size: 10566921
relation: main_file
success: 1
file_date_updated: 2021-07-19T12:13:34Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '9'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 2981–3003
pmid: 1
publication: Plant Cell
publication_identifier:
eissn:
- 1532-298x
issn:
- 1040-4651
publication_status: published
publisher: American Society of Plant Biologists
quality_controlled: '1'
status: public
title: GmPIN-dependent polar auxin transport is involved in soybean nodule development
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: 33
year: '2021'
...
---
_id: '9640'
abstract:
- lang: eng
text: 'Selection and random drift determine the probability that novel mutations
fixate in a population. Population structure is known to affect the dynamics of
the evolutionary process. Amplifiers of selection are population structures that
increase the fixation probability of beneficial mutants compared to well-mixed
populations. Over the past 15 years, extensive research has produced remarkable
structures called strong amplifiers which guarantee that every beneficial mutation
fixates with high probability. But strong amplification has come at the cost of
considerably delaying the fixation event, which can slow down the overall rate
of evolution. However, the precise relationship between fixation probability and
time has remained elusive. Here we characterize the slowdown effect of strong
amplification. First, we prove that all strong amplifiers must delay the fixation
event at least to some extent. Second, we construct strong amplifiers that delay
the fixation event only marginally as compared to the well-mixed populations.
Our results thus establish a tight relationship between fixation probability and
time: Strong amplification always comes at a cost of a slowdown, but more than
a marginal slowdown is not needed.'
acknowledgement: 'K.C. acknowledges support from ERC Start grant no. (279307: Graph
Games), ERC Consolidator grant no. (863818: ForM-SMart), Austrian Science Fund (FWF)
grant no. P23499-N23 and S11407-N23 (RiSE). M.A.N. acknowledges support from Office
of Naval Research grant N00014-16-1-2914 and from the John Templeton Foundation.'
article_number: '4009'
article_processing_charge: No
article_type: original
author:
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin A.
full_name: Nowak, Martin A.
last_name: Nowak
citation:
ama: Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Fast and strong amplifiers
of natural selection. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-24271-w
apa: Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2021). Fast
and strong amplifiers of natural selection. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-021-24271-w
chicago: Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin
A. Nowak. “Fast and Strong Amplifiers of Natural Selection.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-24271-w.
ieee: J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Fast and strong
amplifiers of natural selection,” Nature Communications, vol. 12, no. 1.
Springer Nature, 2021.
ista: Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2021. Fast and strong amplifiers
of natural selection. Nature Communications. 12(1), 4009.
mla: Tkadlec, Josef, et al. “Fast and Strong Amplifiers of Natural Selection.” Nature
Communications, vol. 12, no. 1, 4009, Springer Nature, 2021, doi:10.1038/s41467-021-24271-w.
short: J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Nature Communications
12 (2021).
date_created: 2021-07-11T22:01:15Z
date_published: 2021-06-29T00:00:00Z
date_updated: 2023-08-10T14:05:09Z
day: '29'
ddc:
- '510'
department:
- _id: KrCh
doi: 10.1038/s41467-021-24271-w
ec_funded: 1
external_id:
isi:
- '000671752100003'
pmid:
- '34188036'
file:
- access_level: open_access
checksum: 5767418926a7f7fb76151de29473dae0
content_type: application/pdf
creator: cziletti
date_created: 2021-07-19T13:02:20Z
date_updated: 2021-07-19T13:02:20Z
file_id: '9692'
file_name: 2021_NatCoom_Tkadlec.pdf
file_size: 628992
relation: main_file
success: 1
file_date_updated: 2021-07-19T13:02:20Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast and strong amplifiers of natural selection
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: '9656'
abstract:
- lang: eng
text: Tropisms, growth responses to environmental stimuli such as light or gravity,
are spectacular examples of adaptive plant development. The plant hormone auxin
serves as a major coordinative signal. The PIN auxin exporters, through their
dynamic polar subcellular localizations, redirect auxin fluxes in response to
environmental stimuli and the resulting auxin gradients across organs underly
differential cell elongation and bending. In this review, we discuss recent advances
concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation
and trafficking. We also cover how environmental cues regulate PIN actions during
tropisms, and a crucial role of auxin feedback on PIN polarity during bending
termination. Finally, the interactions between different tropisms are reviewed
to understand plant adaptive growth in the natural environment.
acknowledgement: We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and
Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript.
We apologize to those researchers whose great work was not cited. This work is supported
by the European Research Council under the European Union’s Horizon 2020 research
and innovation Programme (ERC grant agreement number 742985), and the Austrian Science
Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship
Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture
University (9232308314).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Linlin
full_name: Qi, Linlin
id: 44B04502-A9ED-11E9-B6FC-583AE6697425
last_name: Qi
orcid: 0000-0001-5187-8401
- first_name: SS
full_name: Alotaibi, SS
last_name: Alotaibi
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport
regulations in plant tropic responses. New Phytologist. 2021;232(2):510-522.
doi:10.1111/nph.17617
apa: Han, H., Adamowski, M., Qi, L., Alotaibi, S., & Friml, J. (2021). PIN-mediated
polar auxin transport regulations in plant tropic responses. New Phytologist.
Wiley. https://doi.org/10.1111/nph.17617
chicago: Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiří Friml.
“PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New
Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17617.
ieee: H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar
auxin transport regulations in plant tropic responses,” New Phytologist,
vol. 232, no. 2. Wiley, pp. 510–522, 2021.
ista: Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin
transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522.
mla: Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant
Tropic Responses.” New Phytologist, vol. 232, no. 2, Wiley, 2021, pp. 510–22,
doi:10.1111/nph.17617.
short: H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021)
510–522.
date_created: 2021-07-14T15:29:14Z
date_published: 2021-10-01T00:00:00Z
date_updated: 2023-08-10T14:02:41Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/nph.17617
ec_funded: 1
external_id:
isi:
- '000680587100001'
pmid:
- '34254313'
file:
- access_level: open_access
checksum: 6422a6eb329b52d96279daaee0fcf189
content_type: application/pdf
creator: kschuh
date_created: 2021-10-07T13:42:47Z
date_updated: 2021-10-07T13:42:47Z
file_id: '10105'
file_name: 2021_NewPhytologist_Han.pdf
file_size: 1939800
relation: main_file
success: 1
file_date_updated: 2021-10-07T13:42:47Z
has_accepted_license: '1'
intvolume: ' 232'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 510-522
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646x
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: PIN-mediated polar auxin transport regulations in plant tropic responses
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: 232
year: '2021'
...
---
_id: '9679'
abstract:
- lang: eng
text: The relative motion of three impenetrable particles on a ring, in our case
two identical fermions and one impurity, is isomorphic to a triangular quantum
billiard. Depending on the ratio κ of the impurity and fermion masses, the billiards
can be integrable or non-integrable (also referred to in the main text as chaotic).
To set the stage, we first investigate the energy level distributions of the billiards
as a function of 1/κ ∈ [0, 1] and find no evidence of integrable cases beyond
the limiting values 1/κ = 1 and 1/κ = 0. Then, we use machine learning tools to
analyze properties of probability distributions of individual quantum states.
We find that convolutional neural networks can correctly classify integrable and
non-integrable states. The decisive features of the wave functions are the normalization
and a large number of zero elements, corresponding to the existence of a nodal
line. The network achieves typical accuracies of 97%, suggesting that machine
learning tools can be used to analyze and classify the morphology of probability
densities obtained in theory or experiment.
acknowledgement: We thank Aidan Tracy for his input during the initial stages of this
project. We thank Nathan Harshman, Achim Richter, Wojciech Rzadkowski, and Dane
Hudson Smith for helpful discussions and comments on the manuscript. This work has
been supported by European Union's Horizon 2020 research and innovation program
under the Marie Skłodowska-Curie Grant Agreement No. 754411 (AGV); by the German
Aeronautics and Space Administration (DLR) through Grant No. 50 WM 1957 (OVM); by
the Deutsche Forschungsgemeinschaft through Project VO 2437/1-1 (Project No. 413495248)
(AGV and HWH); by the Deutsche Forschungsgemeinschaft through Collaborative Research
Center SFB 1245 (Project No. 279384907) and by the Bundesministerium für Bildung
und Forschung under Contract 05P18RDFN1 (HWH). HWH also thanks the ECT* for hospitality
during the workshop 'Universal physics in Many-Body Quantum Systems—From Atoms to
Quarks'. This infrastructure is part of a project that has received funding from
the European Union's Horizon 2020 research and innovation program under Grant Agreement
No. 824093. We acknowledge support by the Deutsche Forschungsgemeinschaft and the
Open Access Publishing Fund of Technische Universität Darmstadt.
article_number: '065009'
article_processing_charge: Yes
article_type: original
author:
- first_name: David
full_name: Huber, David
last_name: Huber
- first_name: Oleksandr V.
full_name: Marchukov, Oleksandr V.
last_name: Marchukov
- first_name: Hans Werner
full_name: Hammer, Hans Werner
last_name: Hammer
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Huber D, Marchukov OV, Hammer HW, Volosniev A. Morphology of three-body quantum
states from machine learning. New Journal of Physics. 2021;23(6). doi:10.1088/1367-2630/ac0576
apa: Huber, D., Marchukov, O. V., Hammer, H. W., & Volosniev, A. (2021). Morphology
of three-body quantum states from machine learning. New Journal of Physics.
IOP Publishing. https://doi.org/10.1088/1367-2630/ac0576
chicago: Huber, David, Oleksandr V. Marchukov, Hans Werner Hammer, and Artem Volosniev.
“Morphology of Three-Body Quantum States from Machine Learning.” New Journal
of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac0576.
ieee: D. Huber, O. V. Marchukov, H. W. Hammer, and A. Volosniev, “Morphology of
three-body quantum states from machine learning,” New Journal of Physics,
vol. 23, no. 6. IOP Publishing, 2021.
ista: Huber D, Marchukov OV, Hammer HW, Volosniev A. 2021. Morphology of three-body
quantum states from machine learning. New Journal of Physics. 23(6), 065009.
mla: Huber, David, et al. “Morphology of Three-Body Quantum States from Machine
Learning.” New Journal of Physics, vol. 23, no. 6, 065009, IOP Publishing,
2021, doi:10.1088/1367-2630/ac0576.
short: D. Huber, O.V. Marchukov, H.W. Hammer, A. Volosniev, New Journal of Physics
23 (2021).
date_created: 2021-07-18T22:01:22Z
date_published: 2021-06-23T00:00:00Z
date_updated: 2023-08-10T13:58:09Z
day: '23'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1088/1367-2630/ac0576
ec_funded: 1
external_id:
arxiv:
- '2102.04961'
isi:
- '000664736300001'
file:
- access_level: open_access
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creator: cziletti
date_created: 2021-07-19T11:47:16Z
date_updated: 2021-07-19T11:47:16Z
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file_name: 2021_NewJPhys_Huber.pdf
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intvolume: ' 23'
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issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: New Journal of Physics
publication_identifier:
eissn:
- '13672630'
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Morphology of three-body quantum states from machine learning
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: 23
year: '2021'
...
---
_id: '9629'
abstract:
- lang: eng
text: Intestinal organoids derived from single cells undergo complex crypt–villus
patterning and morphogenesis. However, the nature and coordination of the underlying
forces remains poorly characterized. Here, using light-sheet microscopy and large-scale
imaging quantification, we demonstrate that crypt formation coincides with a stark
reduction in lumen volume. We develop a 3D biophysical model to computationally
screen different mechanical scenarios of crypt morphogenesis. Combining this with
live-imaging data and multiple mechanical perturbations, we show that actomyosin-driven
crypt apical contraction and villus basal tension work synergistically with lumen
volume reduction to drive crypt morphogenesis, and demonstrate the existence of
a critical point in differential tensions above which crypt morphology becomes
robust to volume changes. Finally, we identified a sodium/glucose cotransporter
that is specific to differentiated enterocytes that modulates lumen volume reduction
through cell swelling in the villus region. Together, our study uncovers the cellular
basis of how cell fate modulates osmotic and actomyosin forces to coordinate robust
morphogenesis.
acknowledgement: 'We acknowledge the members of the Lennon-Duménil laboratory for
sharing the mouse line of Myh9-GFP. We are grateful to the members of the Liberali
laboratory and the FMI facilities for their support. We thank E. Tagliavini for
IT support; L. Gelman for assistance and training; S. Bichet and A. Bogucki for
helping with histology of mouse tissues; H. Kohler for fluorescence-activated cell
sorting; G. Q. G. de Medeiros for maintenance of light-sheet microscopy; M. G. Stadler
for scRNA-seq analysis; G. Gay for discussions on the 3D vertex model; the members
of the Liberali laboratory, C. P. Heisenberg and C. Tsiairis for reading and providing
feedback on the manuscript. Funding: Q.Y. is supported by a Postdoc fellowship from
Peter und Taul Engelhorn Stiftung (PTES). This work received funding from the European
Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme
Grant Agreement no. 758617 (to P.L.), the Swiss National Foundation (SNF) (POOP3_157531,
to P.L.) and from the ERC under the EU Horizon 2020 Research and Innovation Program
Grant Agreements 851288 (to E.H.) and the Austrian Science Fund (FWF) (P31639, to
E.H.).'
article_processing_charge: No
article_type: original
author:
- first_name: Qiutan
full_name: Yang, Qiutan
last_name: Yang
- first_name: Shi-lei
full_name: Xue, Shi-lei
id: 31D2C804-F248-11E8-B48F-1D18A9856A87
last_name: Xue
- first_name: Chii Jou
full_name: Chan, Chii Jou
last_name: Chan
- first_name: Markus
full_name: Rempfler, Markus
last_name: Rempfler
- first_name: Dario
full_name: Vischi, Dario
last_name: Vischi
- first_name: Francisca
full_name: Maurer-Gutierrez, Francisca
last_name: Maurer-Gutierrez
- first_name: Takashi
full_name: Hiiragi, Takashi
last_name: Hiiragi
- 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: Prisca
full_name: Liberali, Prisca
last_name: Liberali
citation:
ama: Yang Q, Xue S, Chan CJ, et al. Cell fate coordinates mechano-osmotic forces
in intestinal crypt formation. Nature Cell Biology. 2021;23:733–744. doi:10.1038/s41556-021-00700-2
apa: Yang, Q., Xue, S., Chan, C. J., Rempfler, M., Vischi, D., Maurer-Gutierrez,
F., … Liberali, P. (2021). Cell fate coordinates mechano-osmotic forces in intestinal
crypt formation. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-021-00700-2
chicago: Yang, Qiutan, Shi-lei Xue, Chii Jou Chan, Markus Rempfler, Dario Vischi,
Francisca Maurer-Gutierrez, Takashi Hiiragi, Edouard B Hannezo, and Prisca Liberali.
“Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.”
Nature Cell Biology. Springer Nature, 2021. https://doi.org/10.1038/s41556-021-00700-2.
ieee: Q. Yang et al., “Cell fate coordinates mechano-osmotic forces in intestinal
crypt formation,” Nature Cell Biology, vol. 23. Springer Nature, pp. 733–744,
2021.
ista: Yang Q, Xue S, Chan CJ, Rempfler M, Vischi D, Maurer-Gutierrez F, Hiiragi
T, Hannezo EB, Liberali P. 2021. Cell fate coordinates mechano-osmotic forces
in intestinal crypt formation. Nature Cell Biology. 23, 733–744.
mla: Yang, Qiutan, et al. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal
Crypt Formation.” Nature Cell Biology, vol. 23, Springer Nature, 2021,
pp. 733–744, doi:10.1038/s41556-021-00700-2.
short: Q. Yang, S. Xue, C.J. Chan, M. Rempfler, D. Vischi, F. Maurer-Gutierrez,
T. Hiiragi, E.B. Hannezo, P. Liberali, Nature Cell Biology 23 (2021) 733–744.
date_created: 2021-07-04T22:01:25Z
date_published: 2021-06-21T00:00:00Z
date_updated: 2023-08-10T13:57:36Z
day: '21'
department:
- _id: EdHa
doi: 10.1038/s41556-021-00700-2
ec_funded: 1
external_id:
isi:
- '000664016300003'
pmid:
- '34155381'
intvolume: ' 23'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2020.05.13.094359
month: '06'
oa: 1
oa_version: Preprint
page: 733–744
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 268294B6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31639
name: Active mechano-chemical description of the cell cytoskeleton
publication: Nature Cell Biology
publication_identifier:
eissn:
- 1476-4679
issn:
- 1465-7392
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell fate coordinates mechano-osmotic forces in intestinal crypt formation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 23
year: '2021'
...