---
_id: '9331'
abstract:
- lang: eng
text: 'Quantum entanglement has been generated and verified in cold-atom experiments
and used to make atom-interferometric measurements below the shot-noise limit.
However, current state-of-the-art cold-atom devices exploit separable (i.e., unentangled)
atomic states. This perspective piece asks the question: can entanglement usefully
improve cold-atom sensors, in the sense that it gives new sensing capabilities
unachievable with current state-of-the-art devices? We briefly review the state-of-the-art
in precision cold-atom sensing, focusing on clocks and inertial sensors, identifying
the potential benefits entanglement could bring to these devices, and the challenges
that need to be overcome to realize these benefits. We survey demonstrated methods
of generating metrologically useful entanglement in cold-atom systems, note their
relative strengths and weaknesses, and assess their prospects for near-to-medium
term quantum-enhanced cold-atom sensing.'
acknowledgement: We acknowledge fruitful discussions with John Close, Chris Freier,
Kyle Hardman, Joseph Hope, and Paul Wigley, and insightful suggestions made by Franck
Pereira dos Santos on behalf of the Atom Interferometry and Inertial Sensors team
at SYRTE. S.S.S. was supported by an Australian Research Council Discovery Early
Career Researcher Award (DECRA), Project No. DE200100495. O.H. was supported by
IST Austria.
article_number: '140501'
article_processing_charge: No
article_type: original
author:
- first_name: Stuart S.
full_name: Szigeti, Stuart S.
last_name: Szigeti
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Simon A.
full_name: Haine, Simon A.
last_name: Haine
citation:
ama: 'Szigeti SS, Hosten O, Haine SA. Improving cold-atom sensors with quantum entanglement:
Prospects and challenges. Applied Physics Letters. 2021;118(14). doi:10.1063/5.0050235'
apa: 'Szigeti, S. S., Hosten, O., & Haine, S. A. (2021). Improving cold-atom
sensors with quantum entanglement: Prospects and challenges. Applied Physics
Letters. AIP Publishing. https://doi.org/10.1063/5.0050235'
chicago: 'Szigeti, Stuart S., Onur Hosten, and Simon A. Haine. “Improving Cold-Atom
Sensors with Quantum Entanglement: Prospects and Challenges.” Applied Physics
Letters. AIP Publishing, 2021. https://doi.org/10.1063/5.0050235.'
ieee: 'S. S. Szigeti, O. Hosten, and S. A. Haine, “Improving cold-atom sensors with
quantum entanglement: Prospects and challenges,” Applied Physics Letters,
vol. 118, no. 14. AIP Publishing, 2021.'
ista: 'Szigeti SS, Hosten O, Haine SA. 2021. Improving cold-atom sensors with quantum
entanglement: Prospects and challenges. Applied Physics Letters. 118(14), 140501.'
mla: 'Szigeti, Stuart S., et al. “Improving Cold-Atom Sensors with Quantum Entanglement:
Prospects and Challenges.” Applied Physics Letters, vol. 118, no. 14, 140501,
AIP Publishing, 2021, doi:10.1063/5.0050235.'
short: S.S. Szigeti, O. Hosten, S.A. Haine, Applied Physics Letters 118 (2021).
date_created: 2021-04-18T22:01:40Z
date_published: 2021-04-07T00:00:00Z
date_updated: 2023-08-07T14:36:42Z
day: '07'
department:
- _id: OnHo
doi: 10.1063/5.0050235
external_id:
arxiv:
- '2010.09168'
isi:
- '000637702100001'
intvolume: ' 118'
isi: 1
issue: '14'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2010.09168
month: '04'
oa: 1
oa_version: Preprint
publication: Applied Physics Letters
publication_identifier:
issn:
- '00036951'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Improving cold-atom sensors with quantum entanglement: Prospects and challenges'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 118
year: '2021'
...
---
_id: '9330'
abstract:
- lang: eng
text: In nerve cells the genes encoding for α2δ subunits of voltage-gated calcium
channels have been linked to synaptic functions and neurological disease. Here
we show that α2δ subunits are essential for the formation and organization of
glutamatergic synapses. Using a cellular α2δ subunit triple-knockout/knockdown
model, we demonstrate a failure in presynaptic differentiation evidenced by defective
presynaptic calcium channel clustering and calcium influx, smaller presynaptic
active zones, and a strongly reduced accumulation of presynaptic vesicle-associated
proteins (synapsin and vGLUT). The presynaptic defect is associated with the downscaling
of postsynaptic AMPA receptors and the postsynaptic density. The role of α2δ isoforms
as synaptic organizers is highly redundant, as each individual α2δ isoform can
rescue presynaptic calcium channel trafficking and expression of synaptic proteins.
Moreover, α2δ-2 and α2δ-3 with mutated metal ion-dependent adhesion sites can
fully rescue presynaptic synapsin expression but only partially calcium channel
trafficking, suggesting that the regulatory role of α2δ subunits is independent
from its role as a calcium channel subunit. Our findings influence the current
view on excitatory synapse formation. First, our study suggests that postsynaptic
differentiation is secondary to presynaptic differentiation. Second, the dependence
of presynaptic differentiation on α2δ implicates α2δ subunits as potential nucleation
points for the organization of synapses. Finally, our results suggest that α2δ
subunits act as transsynaptic organizers of glutamatergic synapses, thereby aligning
the synaptic active zone with the postsynaptic density.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "We thank Arnold Schwartz for providing α2δ-1 knockout mice; Ariane
Benedetti, Sabine Baumgartner, Sandra Demetz, and Irene Mahlknecht for technical
support; Nadine Ortner and Andreas Lieb for electrophysiological experiments; the
team of the Electron Microscopy Facility at the Institute of Science and Technology
Austria for technical support related to ultrastructural analysis; Hermann Dietrich
and Anja Beierfuß and her team for animal care; Jutta Engel and Jörg Striessnig
for critical discussions; and Bruno Benedetti and Bernhard Flucher for critical
discussions and reading the manuscript. This study was supported by Austrian Science
Fund Grants P24079, F44060, F44150, and DOC30-B30 (to G.J.O.) and T855 (to M.C.),
European Research Council Grant AdG 694539 (to R.S.), Deutsche Forschungsgemeinschaft\r\nGrant
SFB1348-TP A03 (to M.M.), and Interdisziplinäre Zentrum für Klinische Forschung
Münster Grant Mi3/004/19 (to M.M.). This work is part of the PhD theses of C.L.S.,
S.M.G., and C.A."
article_processing_charge: No
article_type: original
author:
- first_name: Clemens L.
full_name: Schöpf, Clemens L.
last_name: Schöpf
- first_name: Cornelia
full_name: Ablinger, Cornelia
last_name: Ablinger
- first_name: Stefanie M.
full_name: Geisler, Stefanie M.
last_name: Geisler
- first_name: Ruslan I.
full_name: Stanika, Ruslan I.
last_name: Stanika
- first_name: Marta
full_name: Campiglio, Marta
last_name: Campiglio
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Benedikt
full_name: Nimmervoll, Benedikt
last_name: Nimmervoll
- first_name: Bettina
full_name: Schlick, Bettina
last_name: Schlick
- first_name: Johannes
full_name: Brockhaus, Johannes
last_name: Brockhaus
- first_name: Markus
full_name: Missler, Markus
last_name: Missler
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Gerald J.
full_name: Obermair, Gerald J.
last_name: Obermair
citation:
ama: Schöpf CL, Ablinger C, Geisler SM, et al. Presynaptic α2δ subunits are key
organizers of glutamatergic synapses. PNAS. 2021;118(14). doi:10.1073/pnas.1920827118
apa: Schöpf, C. L., Ablinger, C., Geisler, S. M., Stanika, R. I., Campiglio, M.,
Kaufmann, W., … Obermair, G. J. (2021). Presynaptic α2δ subunits are key organizers
of glutamatergic synapses. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1920827118
chicago: Schöpf, Clemens L., Cornelia Ablinger, Stefanie M. Geisler, Ruslan I. Stanika,
Marta Campiglio, Walter Kaufmann, Benedikt Nimmervoll, et al. “Presynaptic Α2δ
Subunits Are Key Organizers of Glutamatergic Synapses.” PNAS. National
Academy of Sciences, 2021. https://doi.org/10.1073/pnas.1920827118.
ieee: C. L. Schöpf et al., “Presynaptic α2δ subunits are key organizers of
glutamatergic synapses,” PNAS, vol. 118, no. 14. National Academy of Sciences,
2021.
ista: Schöpf CL, Ablinger C, Geisler SM, Stanika RI, Campiglio M, Kaufmann W, Nimmervoll
B, Schlick B, Brockhaus J, Missler M, Shigemoto R, Obermair GJ. 2021. Presynaptic
α2δ subunits are key organizers of glutamatergic synapses. PNAS. 118(14).
mla: Schöpf, Clemens L., et al. “Presynaptic Α2δ Subunits Are Key Organizers of
Glutamatergic Synapses.” PNAS, vol. 118, no. 14, National Academy of Sciences,
2021, doi:10.1073/pnas.1920827118.
short: C.L. Schöpf, C. Ablinger, S.M. Geisler, R.I. Stanika, M. Campiglio, W. Kaufmann,
B. Nimmervoll, B. Schlick, J. Brockhaus, M. Missler, R. Shigemoto, G.J. Obermair,
PNAS 118 (2021).
date_created: 2021-04-18T22:01:40Z
date_published: 2021-04-06T00:00:00Z
date_updated: 2023-08-08T13:08:47Z
day: '06'
ddc:
- '570'
department:
- _id: EM-Fac
- _id: RySh
doi: 10.1073/pnas.1920827118
ec_funded: 1
external_id:
isi:
- '000637398300002'
file:
- access_level: open_access
checksum: dd014f68ae9d7d8d8fc4139a24e04506
content_type: application/pdf
creator: dernst
date_created: 2021-04-19T10:10:56Z
date_updated: 2021-04-19T10:10:56Z
file_id: '9340'
file_name: 2021_PNAS_Schoepf.pdf
file_size: 2603911
relation: main_file
success: 1
file_date_updated: 2021-04-19T10:10:56Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '14'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
publication: PNAS
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Presynaptic α2δ subunits are key organizers of glutamatergic synapses
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: 118
year: '2021'
...
---
_id: '9332'
abstract:
- lang: eng
text: Lateral root (LR) formation is an example of a plant post-embryonic organogenesis
event. LRs are issued from non-dividing cells entering consecutive steps of formative
divisions, proliferation and elongation. The chromatin remodeling protein PICKLE
(PKL) negatively regulates auxin-mediated LR formation through a mechanism that
is not yet known. Here we show that PKL interacts with RETINOBLASTOMA-RELATED
1 (RBR1) to repress the LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) promoter activity.
Since LBD16 function is required for the formative division of LR founder cells,
repression mediated by the PKL–RBR1 complex negatively regulates formative division
and LR formation. Inhibition of LR formation by PKL–RBR1 is counteracted by auxin,
indicating that, in addition to auxin-mediated transcriptional responses, the
fine-tuned process of LR formation is also controlled at the chromatin level in
an auxin-signaling dependent manner.
acknowledgement: "This research was supported by a postdoctoral fellowship of the
Carl Tryggers Foundation (to K.Ö.) and by grants from Vetenskapsrådet (Nr.: 621-2004-2921
to L.B.) and VINNOVA (to L.B. and S.R.).\r\nWe thank Frederic Berger, Hidehiro Fukaki,
Malcolm Bennett, Claudia Köhler, Jiri Friml for providing pRBR1::RBR1-RFP, ssl2-1,
slr-1, pPKL::PKL-GFP seeds and the DR5 expressing vector, respectively. Authors
are grateful to Hayashi Kenichiro for providing the auxinol compound and to Rishi
Bhalerao for stimulating discussions. The technical help of Adeline Rigal and Thomas
Vain with the auxinol experiments is much appreciated."
article_number: '3862'
article_processing_charge: No
article_type: original
author:
- first_name: Krisztina
full_name: Ötvös, Krisztina
id: 29B901B0-F248-11E8-B48F-1D18A9856A87
last_name: Ötvös
orcid: 0000-0002-5503-4983
- first_name: Pál
full_name: Miskolczi, Pál
last_name: Miskolczi
- first_name: Peter
full_name: Marhavý, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavý
orcid: 0000-0001-5227-5741
- first_name: Alfredo
full_name: Cruz-Ramírez, Alfredo
last_name: Cruz-Ramírez
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: László
full_name: Bakó, László
last_name: Bakó
citation:
ama: Ötvös K, Miskolczi P, Marhavý P, et al. Pickle recruits retinoblastoma related
1 to control lateral root formation in arabidopsis. International Journal of
Molecular Sciences. 2021;22(8). doi:10.3390/ijms22083862
apa: Ötvös, K., Miskolczi, P., Marhavý, P., Cruz-Ramírez, A., Benková, E., Robert,
S., & Bakó, L. (2021). Pickle recruits retinoblastoma related 1 to control
lateral root formation in arabidopsis. International Journal of Molecular Sciences.
MDPI. https://doi.org/10.3390/ijms22083862
chicago: Ötvös, Krisztina, Pál Miskolczi, Peter Marhavý, Alfredo Cruz-Ramírez, Eva
Benková, Stéphanie Robert, and László Bakó. “Pickle Recruits Retinoblastoma Related
1 to Control Lateral Root Formation in Arabidopsis.” International Journal
of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22083862.
ieee: K. Ötvös et al., “Pickle recruits retinoblastoma related 1 to control
lateral root formation in arabidopsis,” International Journal of Molecular
Sciences, vol. 22, no. 8. MDPI, 2021.
ista: Ötvös K, Miskolczi P, Marhavý P, Cruz-Ramírez A, Benková E, Robert S, Bakó
L. 2021. Pickle recruits retinoblastoma related 1 to control lateral root formation
in arabidopsis. International Journal of Molecular Sciences. 22(8), 3862.
mla: Ötvös, Krisztina, et al. “Pickle Recruits Retinoblastoma Related 1 to Control
Lateral Root Formation in Arabidopsis.” International Journal of Molecular
Sciences, vol. 22, no. 8, 3862, MDPI, 2021, doi:10.3390/ijms22083862.
short: K. Ötvös, P. Miskolczi, P. Marhavý, A. Cruz-Ramírez, E. Benková, S. Robert,
L. Bakó, International Journal of Molecular Sciences 22 (2021).
date_created: 2021-04-18T22:01:41Z
date_published: 2021-04-08T00:00:00Z
date_updated: 2023-08-08T13:09:58Z
day: '08'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.3390/ijms22083862
external_id:
isi:
- '000644394800001'
file:
- access_level: open_access
checksum: 26ada2531ad1f9c01a1664de0431f1fe
content_type: application/pdf
creator: dernst
date_created: 2021-04-19T10:54:55Z
date_updated: 2021-04-19T10:54:55Z
file_id: '9342'
file_name: 2021_JourMolecularScience_Oetvoes.pdf
file_size: 2769717
relation: main_file
success: 1
file_date_updated: 2021-04-19T10:54:55Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '8'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- 1422-0067
issn:
- 1661-6596
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pickle recruits retinoblastoma related 1 to control lateral root formation
in arabidopsis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 22
year: '2021'
...
---
_id: '9333'
abstract:
- lang: eng
text: We revise a previous result about the Fröhlich dynamics in the strong coupling
limit obtained in Griesemer (Rev Math Phys 29(10):1750030, 2017). In the latter
it was shown that the Fröhlich time evolution applied to the initial state φ0⊗ξα,
where φ0 is the electron ground state of the Pekar energy functional and ξα the
associated coherent state of the phonons, can be approximated by a global phase
for times small compared to α2. In the present note we prove that a similar approximation
holds for t=O(α2) if one includes a nontrivial effective dynamics for the phonons
that is generated by an operator proportional to α−2 and quadratic in creation
and annihilation operators. Our result implies that the electron ground state
remains close to its initial state for times of order α2, while the phonon fluctuations
around the coherent state ξα can be described by a time-dependent Bogoliubov transformation.
acknowledgement: 'I thank Marcel Griesemer for many interesting discussions about
the Fröhlich polaron and also for valuable comments on this manuscript. Helpful
discussions with Nikolai Leopold and Robert Seiringer are also gratefully acknowledged.
This work was partially supported by the Deutsche Forschungsgemeinschaft (DFG) through
the Research Training Group 1838: Spectral Theory and Dynamics of Quantum Systems.
Open Access funding enabled and organized by Projekt DEAL.'
article_number: '45'
article_processing_charge: No
article_type: original
author:
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
citation:
ama: Mitrouskas DJ. A note on the Fröhlich dynamics in the strong coupling limit.
Letters in Mathematical Physics. 2021;111. doi:10.1007/s11005-021-01380-7
apa: Mitrouskas, D. J. (2021). A note on the Fröhlich dynamics in the strong coupling
limit. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-021-01380-7
chicago: Mitrouskas, David Johannes. “A Note on the Fröhlich Dynamics in the Strong
Coupling Limit.” Letters in Mathematical Physics. Springer Nature, 2021.
https://doi.org/10.1007/s11005-021-01380-7.
ieee: D. J. Mitrouskas, “A note on the Fröhlich dynamics in the strong coupling
limit,” Letters in Mathematical Physics, vol. 111. Springer Nature, 2021.
ista: Mitrouskas DJ. 2021. A note on the Fröhlich dynamics in the strong coupling
limit. Letters in Mathematical Physics. 111, 45.
mla: Mitrouskas, David Johannes. “A Note on the Fröhlich Dynamics in the Strong
Coupling Limit.” Letters in Mathematical Physics, vol. 111, 45, Springer
Nature, 2021, doi:10.1007/s11005-021-01380-7.
short: D.J. Mitrouskas, Letters in Mathematical Physics 111 (2021).
date_created: 2021-04-18T22:01:41Z
date_published: 2021-04-05T00:00:00Z
date_updated: 2023-08-08T13:09:28Z
day: '05'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s11005-021-01380-7
external_id:
isi:
- '000637359300002'
file:
- access_level: open_access
checksum: be56c0845a43c0c5c772ee0b5053f7d7
content_type: application/pdf
creator: dernst
date_created: 2021-04-19T10:40:01Z
date_updated: 2021-04-19T10:40:01Z
file_id: '9341'
file_name: 2021_LettersMathPhysics_Mitrouskas.pdf
file_size: 438084
relation: main_file
success: 1
file_date_updated: 2021-04-19T10:40:01Z
has_accepted_license: '1'
intvolume: ' 111'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Letters in Mathematical Physics
publication_identifier:
eissn:
- '15730530'
issn:
- '03779017'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A note on the Fröhlich dynamics in the strong coupling limit
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: 111
year: '2021'
...
---
_id: '9335'
abstract:
- lang: eng
text: 'Various degenerate diffusion equations exhibit a waiting time phenomenon:
depending on the “flatness” of the compactly supported initial datum at the boundary
of the support, the support of the solution may not expand for a certain amount
of time. We show that this phenomenon is captured by particular Lagrangian discretizations
of the porous medium and the thin film equations, and we obtain sufficient criteria
for the occurrence of waiting times that are consistent with the known ones for
the original PDEs. For the spatially discrete solution, the waiting time phenomenon
refers to a deviation of the edge of support from its original position by a quantity
comparable to the mesh width, over a mesh-independent time interval. Our proof
is based on estimates on the fluid velocity in Lagrangian coordinates. Combining
weighted entropy estimates with an iteration technique à la Stampacchia leads
to upper bounds on free boundary propagation. Numerical simulations show that
the phenomenon is already clearly visible for relatively coarse discretizations.'
acknowledgement: This research was supported by the DFG Collaborative Research Center
TRR 109, “Discretization in Geometry and Dynamics”.
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: Daniel
full_name: Matthes, Daniel
last_name: Matthes
citation:
ama: Fischer JL, Matthes D. The waiting time phenomenon in spatially discretized
porous medium and thin film equations. SIAM Journal on Numerical Analysis.
2021;59(1):60-87. doi:10.1137/19M1300017
apa: Fischer, J. L., & Matthes, D. (2021). The waiting time phenomenon in spatially
discretized porous medium and thin film equations. SIAM Journal on Numerical
Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19M1300017
chicago: Fischer, Julian L, and Daniel Matthes. “The Waiting Time Phenomenon in
Spatially Discretized Porous Medium and Thin Film Equations.” SIAM Journal
on Numerical Analysis. Society for Industrial and Applied Mathematics, 2021.
https://doi.org/10.1137/19M1300017.
ieee: J. L. Fischer and D. Matthes, “The waiting time phenomenon in spatially discretized
porous medium and thin film equations,” SIAM Journal on Numerical Analysis,
vol. 59, no. 1. Society for Industrial and Applied Mathematics, pp. 60–87, 2021.
ista: Fischer JL, Matthes D. 2021. The waiting time phenomenon in spatially discretized
porous medium and thin film equations. SIAM Journal on Numerical Analysis. 59(1),
60–87.
mla: Fischer, Julian L., and Daniel Matthes. “The Waiting Time Phenomenon in Spatially
Discretized Porous Medium and Thin Film Equations.” SIAM Journal on Numerical
Analysis, vol. 59, no. 1, Society for Industrial and Applied Mathematics,
2021, pp. 60–87, doi:10.1137/19M1300017.
short: J.L. Fischer, D. Matthes, SIAM Journal on Numerical Analysis 59 (2021) 60–87.
date_created: 2021-04-18T22:01:42Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2023-08-08T13:10:40Z
day: '01'
department:
- _id: JuFi
doi: 10.1137/19M1300017
external_id:
arxiv:
- '1911.04185'
isi:
- '000625044600003'
intvolume: ' 59'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1911.04185
month: '01'
oa: 1
oa_version: Preprint
page: 60-87
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: The waiting time phenomenon in spatially discretized porous medium and thin
film equations
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 59
year: '2021'
...
---
_id: '9349'
abstract:
- lang: eng
text: 'The way in which interactions between mechanics and biochemistry lead to
the emergence of complex cell and tissue organization is an old question that
has recently attracted renewed interest from biologists, physicists, mathematicians
and computer scientists. Rapid advances in optical physics, microscopy and computational
image analysis have greatly enhanced our ability to observe and quantify spatiotemporal
patterns of signalling, force generation, deformation, and flow in living cells
and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation
are allowing us to perturb the underlying machinery that generates these patterns
in increasingly sophisticated ways. Rapid advances in theory and computing have
made it possible to construct predictive models that describe how cell and tissue
organization and dynamics emerge from the local coupling of biochemistry and mechanics.
Together, these advances have opened up a wealth of new opportunities to explore
how mechanochemical patterning shapes organismal development. In this roadmap,
we present a series of forward-looking case studies on mechanochemical patterning
in development, written by scientists working at the interface between the physical
and biological sciences, and covering a wide range of spatial and temporal scales,
organisms, and modes of development. Together, these contributions highlight the
many ways in which the dynamic coupling of mechanics and biochemistry shapes biological
dynamics: from mechanoenzymes that sense force to tune their activity and motor
output, to collectives of cells in tissues that flow and redistribute biochemical
signals during development.'
acknowledgement: The AK group is supported by IST Austria and by the ERC under European
Union Horizon 2020 research and innovation programme Grant 680037. Apologies to
those whose work could not be mentioned due to limited space. We thank all my lab
members, both past and present, for stimulating discussion. This work was funded
by a Singapore Ministry of Education Tier 3 Grant, MOE2016-T3-1-005. We thank Francis
Corson for continuous discussion and collaboration contributing to these views and
for figure 4(A). PC is sponsored by the Institut Pasteur and the European Union's
Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie
Grant Agreement No. 665807. Research in JG's laboratory is funded by the European
Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC
Grant Agreement No. 337635, Institut Pasteur, CNRS, Cercle FSER, Fondation pour
la Recherche Medicale, the Vallee Foundation and the ANR-19-CE-13-0024 Grant. We
thank Erez Braun and Alex Mogilner for comments on the manuscript and Niv Ierushalmi
for help with figure 5. This project has received funding from the European Union's
Horizon 2020 research and innovation programme under Grant Agreement No. ERC-2018-COG
Grant 819174-HydraMechanics awarded to KK. EH thanks all lab members, as well as
Pierre Recho, Tsuyoshi Hirashima, Diana Pinheiro and Carl-Philip Heisenberg, for
fruitful discussions on these topics—and apologize for not being able to cite many
very relevant publications due to the strict 10-reference limit. EH acknowledges
the support of Austrian Science Fund (FWF) (P 31639) and the European Research Council
under the European Union's Horizon 2020 Research and Innovation Programme Grant
Agreements (851288). The authors acknowledge the inspiring scientists whose work
could not be cited in this perspective due to space constraints; the members of
the Gartner Lab for helpful discussions; the Barbara and Gerson Bakar Foundation,
the Chan Zuckerberg Biohub Investigators Programme, the National Institute of Health,
and the Centre for Cellular Construction, an NSF Science and Technology Centre.
The Minc laboratory is currently funded by the CNRS and the European Research Council
(CoG Forcaster No. 647073). Research in the lab of J-LM is supported by the Institut
Curie, the Centre National de la Recherche Scientifique (CNRS), the Institut National
de la Santé Et de la Recherche Médicale (INSERM), and is funded by grants from the
ATIP-Avenir programme, the Fondation Schlumberger pour l'Éducation et la Recherche
via the Fondation pour la Recherche Médicale, the European Research Council Starting
Grant ERC-2017-StG 757557, the European Molecular Biology Organization Young Investigator
programme (EMBO YIP), the INSERM transversal programme Human Development Cell Atlas
(HuDeCA), Paris Sciences Lettres (PSL) 'nouvelle équipe' and QLife (17-CONV-0005)
grants and Labex DEEP (ANR-11-LABX-0044) which are part of the IDEX PSL (ANR-10-IDEX-0001-02).
We acknowledge useful discussions with Massimo Vergassola, Sebastian Streichan and
my lab members. Work in my laboratory on Drosophila embryogenesis is partly supported
by NIH-R01GM122936. The authors acknowledge the support by a grant from the European
Research Council (Grant No. 682161). Lenne group is funded by a grant from the 'Investissements
d'Avenir' French Government programme managed by the French National Research Agency
(ANR-16-CONV-0001) and by the Excellence Initiative of Aix-Marseille University—A*MIDEX,
and ANR projects MechaResp (ANR-17-CE13-0032) and AdGastrulo (ANR-19-CE13-0022).
article_number: '041501'
article_processing_charge: No
article_type: original
author:
- first_name: Pierre François
full_name: Lenne, Pierre François
last_name: Lenne
- first_name: Edwin
full_name: Munro, Edwin
last_name: Munro
- first_name: Idse
full_name: Heemskerk, Idse
last_name: Heemskerk
- first_name: Aryeh
full_name: Warmflash, Aryeh
last_name: Warmflash
- first_name: Laura
full_name: Bocanegra, Laura
id: 4896F754-F248-11E8-B48F-1D18A9856A87
last_name: Bocanegra
- first_name: Kasumi
full_name: Kishi, Kasumi
id: 3065DFC4-F248-11E8-B48F-1D18A9856A87
last_name: Kishi
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Yuchen
full_name: Long, Yuchen
last_name: Long
- first_name: Antoine
full_name: Fruleux, Antoine
last_name: Fruleux
- first_name: Arezki
full_name: Boudaoud, Arezki
last_name: Boudaoud
- first_name: Timothy E.
full_name: Saunders, Timothy E.
last_name: Saunders
- first_name: Paolo
full_name: Caldarelli, Paolo
last_name: Caldarelli
- first_name: Arthur
full_name: Michaut, Arthur
last_name: Michaut
- first_name: Jerome
full_name: Gros, Jerome
last_name: Gros
- first_name: Yonit
full_name: Maroudas-Sacks, Yonit
last_name: Maroudas-Sacks
- first_name: Kinneret
full_name: Keren, Kinneret
last_name: Keren
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Zev J.
full_name: Gartner, Zev J.
last_name: Gartner
- first_name: Benjamin
full_name: Stormo, Benjamin
last_name: Stormo
- first_name: Amy
full_name: Gladfelter, Amy
last_name: Gladfelter
- first_name: Alan
full_name: Rodrigues, Alan
last_name: Rodrigues
- first_name: Amy
full_name: Shyer, Amy
last_name: Shyer
- first_name: Nicolas
full_name: Minc, Nicolas
last_name: Minc
- first_name: Jean Léon
full_name: Maître, Jean Léon
last_name: Maître
- first_name: Stefano
full_name: Di Talia, Stefano
last_name: Di Talia
- first_name: Bassma
full_name: Khamaisi, Bassma
last_name: Khamaisi
- first_name: David
full_name: Sprinzak, David
last_name: Sprinzak
- first_name: Sham
full_name: Tlili, Sham
last_name: Tlili
citation:
ama: Lenne PF, Munro E, Heemskerk I, et al. Roadmap for the multiscale coupling
of biochemical and mechanical signals during development. Physical biology.
2021;18(4). doi:10.1088/1478-3975/abd0db
apa: Lenne, P. F., Munro, E., Heemskerk, I., Warmflash, A., Bocanegra, L., Kishi,
K., … Tlili, S. (2021). Roadmap for the multiscale coupling of biochemical and
mechanical signals during development. Physical Biology. IOP Publishing.
https://doi.org/10.1088/1478-3975/abd0db
chicago: Lenne, Pierre François, Edwin Munro, Idse Heemskerk, Aryeh Warmflash, Laura
Bocanegra, Kasumi Kishi, Anna Kicheva, et al. “Roadmap for the Multiscale Coupling
of Biochemical and Mechanical Signals during Development.” Physical Biology.
IOP Publishing, 2021. https://doi.org/10.1088/1478-3975/abd0db.
ieee: P. F. Lenne et al., “Roadmap for the multiscale coupling of biochemical
and mechanical signals during development,” Physical biology, vol. 18,
no. 4. IOP Publishing, 2021.
ista: Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra L, Kishi K, Kicheva
A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J,
Maroudas-Sacks Y, Keren K, Hannezo EB, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues
A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. 2021.
Roadmap for the multiscale coupling of biochemical and mechanical signals during
development. Physical biology. 18(4), 041501.
mla: Lenne, Pierre François, et al. “Roadmap for the Multiscale Coupling of Biochemical
and Mechanical Signals during Development.” Physical Biology, vol. 18,
no. 4, 041501, IOP Publishing, 2021, doi:10.1088/1478-3975/abd0db.
short: P.F. Lenne, E. Munro, I. Heemskerk, A. Warmflash, L. Bocanegra, K. Kishi,
A. Kicheva, Y. Long, A. Fruleux, A. Boudaoud, T.E. Saunders, P. Caldarelli, A.
Michaut, J. Gros, Y. Maroudas-Sacks, K. Keren, E.B. Hannezo, Z.J. Gartner, B.
Stormo, A. Gladfelter, A. Rodrigues, A. Shyer, N. Minc, J.L. Maître, S. Di Talia,
B. Khamaisi, D. Sprinzak, S. Tlili, Physical Biology 18 (2021).
date_created: 2021-04-25T22:01:29Z
date_published: 2021-04-14T00:00:00Z
date_updated: 2023-08-08T13:15:46Z
day: '14'
ddc:
- '570'
department:
- _id: AnKi
- _id: EdHa
doi: 10.1088/1478-3975/abd0db
ec_funded: 1
external_id:
isi:
- '000640396400001'
pmid:
- '33276350'
file:
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checksum: 4f52082549d3561c4c15d4d8d84ca5d8
content_type: application/pdf
creator: cziletti
date_created: 2021-04-27T08:38:35Z
date_updated: 2021-04-27T08:38:35Z
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file_name: 2021_PhysBio_Lenne.pdf
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relation: main_file
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has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
- _id: 268294B6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31639
name: Active mechano-chemical description of the cell cytoskeleton
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Physical biology
publication_identifier:
eissn:
- 1478-3975
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
related_material:
record:
- id: '13081'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Roadmap for the multiscale coupling of biochemical and mechanical signals during
development
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2021'
...
---
_id: '9334'
abstract:
- lang: eng
text: 'Polaritons with directional in-plane propagation and ultralow losses in van
der Waals (vdW) crystals promise unprecedented manipulation of light at the nanoscale.
However, these polaritons present a crucial limitation: their directional propagation
is intrinsically determined by the crystal structure of the host material, imposing
forbidden directions of propagation. Here, we demonstrate that directional polaritons
(in-plane hyperbolic phonon polaritons) in a vdW crystal (α-phase molybdenum trioxide)
can be directed along forbidden directions by inducing an optical topological
transition, which emerges when the slab is placed on a substrate with a given
negative permittivity (4H–silicon carbide). By visualizing the transition in real
space, we observe exotic polaritonic states between mutually orthogonal hyperbolic
regimes, which unveil the topological origin of the transition: a gap opening
in the dispersion. This work provides insights into optical topological transitions
in vdW crystals, which introduce a route to direct light at the nanoscale.'
acknowledgement: 'G.Á.-P. and J.T.-G. acknowledge support through the Severo Ochoa
Program from the government of the Principality of Asturias (grant nos. PA20-PF-BP19-053
and PA-18-PF-BP17-126, respectively). K.V.V. and V.S.V. acknowledge the Ministry
of Science and Higher Education of the Russian Federation (no. 0714-2020-0002).
J. M.-S. acknowledges financial support through the Ramón y Cajal Program from the
government of Spain and FSE (RYC2018-026196-I). A.Y.N. acknowledges the Spanish
Ministry of Science, Innovation and Universities (national project no. MAT201788358-C3-3-R),
and the Basque Department of Education (PIBA-2020-1-0014). P.A.-G. acknowledges
support from the European Research Council under starting grant no. 715496, 2DNANOPTICA. '
article_number: eabf2690
article_processing_charge: No
article_type: original
author:
- first_name: J.
full_name: Duan, J.
last_name: Duan
- first_name: G.
full_name: Álvarez-Pérez, G.
last_name: Álvarez-Pérez
- first_name: K. V.
full_name: Voronin, K. V.
last_name: Voronin
- first_name: Ivan
full_name: Prieto Gonzalez, Ivan
id: 2A307FE2-F248-11E8-B48F-1D18A9856A87
last_name: Prieto Gonzalez
orcid: 0000-0002-7370-5357
- first_name: J.
full_name: Taboada-Gutiérrez, J.
last_name: Taboada-Gutiérrez
- first_name: V. S.
full_name: Volkov, V. S.
last_name: Volkov
- first_name: J.
full_name: Martín-Sánchez, J.
last_name: Martín-Sánchez
- first_name: A. Y.
full_name: Nikitin, A. Y.
last_name: Nikitin
- first_name: P.
full_name: Alonso-González, P.
last_name: Alonso-González
citation:
ama: Duan J, Álvarez-Pérez G, Voronin KV, et al. Enabling propagation of anisotropic
polaritons along forbidden directions via a topological transition. Science
Advances. 2021;7(14). doi:10.1126/sciadv.abf2690
apa: Duan, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., Taboada-Gutiérrez,
J., Volkov, V. S., … Alonso-González, P. (2021). Enabling propagation of anisotropic
polaritons along forbidden directions via a topological transition. Science
Advances. AAAS. https://doi.org/10.1126/sciadv.abf2690
chicago: Duan, J., G. Álvarez-Pérez, K. V. Voronin, Ivan Prieto Gonzalez, J. Taboada-Gutiérrez,
V. S. Volkov, J. Martín-Sánchez, A. Y. Nikitin, and P. Alonso-González. “Enabling
Propagation of Anisotropic Polaritons along Forbidden Directions via a Topological
Transition.” Science Advances. AAAS, 2021. https://doi.org/10.1126/sciadv.abf2690.
ieee: J. Duan et al., “Enabling propagation of anisotropic polaritons along
forbidden directions via a topological transition,” Science Advances, vol.
7, no. 14. AAAS, 2021.
ista: Duan J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Taboada-Gutiérrez
J, Volkov VS, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2021. Enabling
propagation of anisotropic polaritons along forbidden directions via a topological
transition. Science Advances. 7(14), eabf2690.
mla: Duan, J., et al. “Enabling Propagation of Anisotropic Polaritons along Forbidden
Directions via a Topological Transition.” Science Advances, vol. 7, no.
14, eabf2690, AAAS, 2021, doi:10.1126/sciadv.abf2690.
short: J. Duan, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, J. Taboada-Gutiérrez,
V.S. Volkov, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Science Advances
7 (2021).
date_created: 2021-04-18T22:01:42Z
date_published: 2021-04-02T00:00:00Z
date_updated: 2023-08-08T13:11:31Z
day: '02'
ddc:
- '530'
department:
- _id: NanoFab
doi: 10.1126/sciadv.abf2690
external_id:
isi:
- '000636455600027'
pmid:
- '33811076'
file:
- access_level: open_access
checksum: 4b383d4a1d484a71bbc64ecf401bbdbb
content_type: application/pdf
creator: dernst
date_created: 2021-04-19T11:17:29Z
date_updated: 2021-04-19T11:17:29Z
file_id: '9343'
file_name: 2021_ScienceAdv_Duan.pdf
file_size: 717489
relation: main_file
success: 1
file_date_updated: 2021-04-19T11:17:29Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '14'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Science Advances
publication_identifier:
eissn:
- '23752548'
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Enabling propagation of anisotropic polaritons along forbidden directions via
a topological transition
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: 7
year: '2021'
...
---
_id: '9351'
abstract:
- lang: eng
text: 'We consider the many-body quantum evolution of a factorized initial data,
in the mean-field regime. We show that fluctuations around the limiting Hartree
dynamics satisfy large deviation estimates that are consistent with central limit
theorems that have been established in the last years. '
acknowledgement: The authors gratefully acknowledge Gérard Ben Arous for suggesting
this kind of result. K.L.K. was partially supported by NSF CAREER Award DMS-125479
and a Simons Sabbatical Fellowship. S.R. acknowledges funding from the European
Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 754411. B. S. gratefully acknowledges partial support from the
NCCR SwissMAP, from the Swiss National Science Foundation through the Grant “Dynamical
and energetic properties of Bose–Einstein condensates” and from the European Research
Council through the ERC-AdG CLaQS. Funding Open access funding provided by Institute
of Science and Technology (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Kay
full_name: Kirkpatrick, Kay
last_name: Kirkpatrick
- first_name: Simone Anna Elvira
full_name: Rademacher, Simone Anna Elvira
id: 856966FE-A408-11E9-977E-802DE6697425
last_name: Rademacher
orcid: 0000-0001-5059-4466
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
citation:
ama: Kirkpatrick K, Rademacher SAE, Schlein B. A large deviation principle in many-body
quantum dynamics. Annales Henri Poincare. 2021;22:2595-2618. doi:10.1007/s00023-021-01044-1
apa: Kirkpatrick, K., Rademacher, S. A. E., & Schlein, B. (2021). A large deviation
principle in many-body quantum dynamics. Annales Henri Poincare. Springer
Nature. https://doi.org/10.1007/s00023-021-01044-1
chicago: Kirkpatrick, Kay, Simone Anna Elvira Rademacher, and Benjamin Schlein.
“A Large Deviation Principle in Many-Body Quantum Dynamics.” Annales Henri
Poincare. Springer Nature, 2021. https://doi.org/10.1007/s00023-021-01044-1.
ieee: K. Kirkpatrick, S. A. E. Rademacher, and B. Schlein, “A large deviation principle
in many-body quantum dynamics,” Annales Henri Poincare, vol. 22. Springer
Nature, pp. 2595–2618, 2021.
ista: Kirkpatrick K, Rademacher SAE, Schlein B. 2021. A large deviation principle
in many-body quantum dynamics. Annales Henri Poincare. 22, 2595–2618.
mla: Kirkpatrick, Kay, et al. “A Large Deviation Principle in Many-Body Quantum
Dynamics.” Annales Henri Poincare, vol. 22, Springer Nature, 2021, pp.
2595–618, doi:10.1007/s00023-021-01044-1.
short: K. Kirkpatrick, S.A.E. Rademacher, B. Schlein, Annales Henri Poincare 22
(2021) 2595–2618.
date_created: 2021-04-25T22:01:30Z
date_published: 2021-04-08T00:00:00Z
date_updated: 2023-08-08T13:14:40Z
day: '08'
ddc:
- '530'
department:
- _id: RoSe
doi: 10.1007/s00023-021-01044-1
ec_funded: 1
external_id:
arxiv:
- '2010.13754'
isi:
- '000638022600001'
file:
- access_level: open_access
checksum: 1a0fb963f2f415ba470881a794f20eb6
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-15T11:15:40Z
date_updated: 2021-10-15T11:15:40Z
file_id: '10143'
file_name: 2021_Annales_Kirkpatrick.pdf
file_size: 522669
relation: main_file
success: 1
file_date_updated: 2021-10-15T11:15:40Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 2595-2618
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Annales Henri Poincare
publication_identifier:
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A large deviation principle in many-body quantum dynamics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 22
year: '2021'
...
---
_id: '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:
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checksum: cb30c6166b2132ee60d616b31a1a7c29
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license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '06'
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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:
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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'
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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: '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
checksum: e39164ce7ea228d287cf8924e1a0f9fe
content_type: application/pdf
creator: cziletti
date_created: 2021-07-19T11:47:16Z
date_updated: 2021-07-19T11:47:16Z
file_id: '9690'
file_name: 2021_NewJPhys_Huber.pdf
file_size: 3868445
relation: main_file
success: 1
file_date_updated: 2021-07-19T11:47:16Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
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'
...
---
_id: '9778'
abstract:
- lang: eng
text: The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit.
Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this
synaptic connection. It is widely believed that mossy fiber PTP is an entirely
presynaptic phenomenon, implying that PTP induction is input-specific, and requires
neither activity of multiple inputs nor stimulation of postsynaptic neurons. To
directly test cooperativity and associativity, we made paired recordings between
single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain
slices. By stimulating non-overlapping mossy fiber inputs converging onto single
CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly,
mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only
minimal PTP after combined pre- and postsynaptic high-frequency stimulation with
intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic
spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP
is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels,
group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde
vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire
of synaptic computations, implementing a brake on mossy fiber detonation and a
“smart teacher” function of hippocampal mossy fiber synapses.
acknowledged_ssus:
- _id: SSU
acknowledgement: We thank Drs. Carolina Borges-Merjane and Jose Guzman for critically
reading the manuscript, and Pablo Castillo for discussions. We are grateful to Alois
Schlögl for help with analysis, Florian Marr for excellent technical assistance
and cell reconstruction, Christina Altmutter for technical help, Eleftheria Kralli-Beller
for manuscript editing, and the Scientific Service Units of IST Austria for support.
This project received funding from the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation program (grant agreement No
692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27,
Wittgenstein award), both to P.J.
article_number: '2912'
article_processing_charge: No
article_type: original
author:
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Yuji
full_name: Okamoto, Yuji
id: 3337E116-F248-11E8-B48F-1D18A9856A87
last_name: Okamoto
orcid: 0000-0003-0408-6094
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Vandael DH, Okamoto Y, Jonas PM. Transsynaptic modulation of presynaptic short-term
plasticity in hippocampal mossy fiber synapses. Nature Communications.
2021;12(1). doi:10.1038/s41467-021-23153-5
apa: Vandael, D. H., Okamoto, Y., & Jonas, P. M. (2021). Transsynaptic modulation
of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature
Communications. Springer. https://doi.org/10.1038/s41467-021-23153-5
chicago: Vandael, David H, Yuji Okamoto, and Peter M Jonas. “Transsynaptic Modulation
of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” Nature
Communications. Springer, 2021. https://doi.org/10.1038/s41467-021-23153-5.
ieee: D. H. Vandael, Y. Okamoto, and P. M. Jonas, “Transsynaptic modulation of presynaptic
short-term plasticity in hippocampal mossy fiber synapses,” Nature Communications,
vol. 12, no. 1. Springer, 2021.
ista: Vandael DH, Okamoto Y, Jonas PM. 2021. Transsynaptic modulation of presynaptic
short-term plasticity in hippocampal mossy fiber synapses. Nature Communications.
12(1), 2912.
mla: Vandael, David H., et al. “Transsynaptic Modulation of Presynaptic Short-Term
Plasticity in Hippocampal Mossy Fiber Synapses.” Nature Communications,
vol. 12, no. 1, 2912, Springer, 2021, doi:10.1038/s41467-021-23153-5.
short: D.H. Vandael, Y. Okamoto, P.M. Jonas, Nature Communications 12 (2021).
date_created: 2021-08-06T07:22:55Z
date_published: 2021-05-18T00:00:00Z
date_updated: 2023-08-10T14:16:16Z
day: '18'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/s41467-021-23153-5
ec_funded: 1
external_id:
isi:
- '000655481800014'
file:
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checksum: 6036a8cdae95e1707c2a04d54e325ff4
content_type: application/pdf
creator: kschuh
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date_updated: 2021-12-17T11:34:50Z
file_id: '10563'
file_name: 2021_NatureCommunications_Vandael.pdf
file_size: 3108845
relation: main_file
success: 1
file_date_updated: 2021-12-17T11:34:50Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- general physics and astronomy
- general biochemistry
- genetics and molecular biology
- general chemistry
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/synaptic-transmission-not-a-one-way-street/
scopus_import: '1'
status: public
title: Transsynaptic modulation of presynaptic short-term plasticity in hippocampal
mossy fiber synapses
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: '9647'
abstract:
- lang: eng
text: 'Gene expression is regulated by the set of transcription factors (TFs) that
bind to the promoter. The ensuing regulating function is often represented as
a combinational logic circuit, where output (gene expression) is determined by
current input values (promoter bound TFs) only. However, the simultaneous arrival
of TFs is a strong assumption, since transcription and translation of genes introduce
intrinsic time delays and there is no global synchronisation among the arrival
times of different molecular species at their targets. We present an experimentally
implementable genetic circuit with two inputs and one output, which in the presence
of small delays in input arrival, exhibits qualitatively distinct population-level
phenotypes, over timescales that are longer than typical cell doubling times.
From a dynamical systems point of view, these phenotypes represent long-lived
transients: although they converge to the same value eventually, they do so after
a very long time span. The key feature of this toy model genetic circuit is that,
despite having only two inputs and one output, it is regulated by twenty-three
distinct DNA-TF configurations, two of which are more stable than others (DNA
looped states), one promoting and another blocking the expression of the output
gene. Small delays in input arrival time result in a majority of cells in the
population quickly reaching the stable state associated with the first input,
while exiting of this stable state occurs at a slow timescale. In order to mechanistically
model the behaviour of this genetic circuit, we used a rule-based modelling language,
and implemented a grid-search to find parameter combinations giving rise to long-lived
transients. Our analysis shows that in the absence of feedback, there exist path-dependent
gene regulatory mechanisms based on the long timescale of transients. The behaviour
of this toy model circuit suggests that gene regulatory networks can exploit event
timing to create phenotypes, and it opens the possibility that they could use
event timing to memorise events, without regulatory feedback. The model reveals
the importance of (i) mechanistically modelling the transitions between the different
DNA-TF states, and (ii) employing transient analysis thereof.'
acknowledgement: 'Tatjana Petrov’s research was supported in part by SNSF Advanced
Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science,
Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence
2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia
Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences.
Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund
(FWF) under grant Z211-N23 (Wittgenstein Award).'
article_processing_charge: No
article_type: original
author:
- first_name: Tatjana
full_name: Petrov, Tatjana
last_name: Petrov
- first_name: Claudia
full_name: Igler, Claudia
id: 46613666-F248-11E8-B48F-1D18A9856A87
last_name: Igler
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
- 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: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in
gene regulation. Theoretical Computer Science. 2021;893:1-16. doi:10.1016/j.tcs.2021.05.023
apa: Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., & Guet, C. C. (2021).
Long lived transients in gene regulation. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2021.05.023
chicago: Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin
C Guet. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science.
Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.05.023.
ieee: T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived
transients in gene regulation,” Theoretical Computer Science, vol. 893.
Elsevier, pp. 1–16, 2021.
ista: Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients
in gene regulation. Theoretical Computer Science. 893, 1–16.
mla: Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” Theoretical
Computer Science, vol. 893, Elsevier, 2021, pp. 1–16, doi:10.1016/j.tcs.2021.05.023.
short: T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer
Science 893 (2021) 1–16.
date_created: 2021-07-11T22:01:18Z
date_published: 2021-06-04T00:00:00Z
date_updated: 2023-08-10T14:11:19Z
day: '04'
ddc:
- '004'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1016/j.tcs.2021.05.023
external_id:
isi:
- '000710180500002'
file:
- access_level: open_access
checksum: d3aef34cfb13e53bba4cf44d01680793
content_type: application/pdf
creator: dernst
date_created: 2022-05-12T12:13:27Z
date_updated: 2022-05-12T12:13:27Z
file_id: '11364'
file_name: 2021_TheoreticalComputerScience_Petrov.pdf
file_size: 2566504
relation: main_file
success: 1
file_date_updated: 2022-05-12T12:13:27Z
has_accepted_license: '1'
intvolume: ' 893'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1-16
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long lived transients in gene regulation
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: 893
year: '2021'
...
---
_id: '9761'
abstract:
- lang: eng
text: 'The important roles of mitochondrial function and dysfunction in the process
of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear
to be a highly vulnerable neuronal cell type in the central nervous system with
respect to mitochondrial dysfunction but the actual reasons for this are still
incompletely understood. These cells have a unique circumstance where unmyelinated
axons must bend nearly 90° to exit the eye and then cross a translaminar pressure
gradient before becoming myelinated in the optic nerve. This region, the optic
nerve head, contains some of the highest density of mitochondria present in these
cells. Glaucoma represents a perfect storm of events occurring at this location,
with a combination of changes in the translaminar pressure gradient and reassignment
of the metabolic support functions of supporting glia, which appears to apply
increased metabolic stress to the RGC axons leading to a failure of axonal transport
mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations,
particularly in genes affecting mitochondrial dynamics and mitochondrial clearance.
These mutations, which systemically affect the mitochondria in every cell, often
lead to an optic neuropathy as the sole pathologic defect in affected patients.
This review summarizes knowledge of mitochondrial structure and function, the
known energy demands of neurons in general, and places these in the context of
normal and pathological characteristics of mitochondria attributed to RGCs. '
acknowledgement: The authors are grateful to Kazuya Oikawa and Gillian McLellan for
generously sharing some of their data for this review, and to Janis Eells for helpful
comments on the manuscript.
article_number: '1593'
article_processing_charge: Yes
article_type: original
author:
- first_name: Nicole A.
full_name: Muench, Nicole A.
last_name: Muench
- first_name: Sonia
full_name: Patel, Sonia
last_name: Patel
- 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: Ryan J.
full_name: Donahue, Ryan J.
last_name: Donahue
- first_name: Akihiro
full_name: Ikeda, Akihiro
last_name: Ikeda
- first_name: Robert W.
full_name: Nickells, Robert W.
last_name: Nickells
citation:
ama: Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence
of mitochondrial dynamics and function on retinal ganglion cell susceptibility
in optic nerve disease. Cells. 2021;10(7). doi:10.3390/cells10071593
apa: Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., & Nickells,
R. W. (2021). The influence of mitochondrial dynamics and function on retinal
ganglion cell susceptibility in optic nerve disease. Cells. MDPI. https://doi.org/10.3390/cells10071593
chicago: Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro
Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function
on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells.
MDPI, 2021. https://doi.org/10.3390/cells10071593.
ieee: N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells,
“The influence of mitochondrial dynamics and function on retinal ganglion cell
susceptibility in optic nerve disease,” Cells, vol. 10, no. 7. MDPI, 2021.
ista: Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence
of mitochondrial dynamics and function on retinal ganglion cell susceptibility
in optic nerve disease. Cells. 10(7), 1593.
mla: Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function
on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells,
vol. 10, no. 7, 1593, MDPI, 2021, doi:10.3390/cells10071593.
short: N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells,
Cells 10 (2021).
date_created: 2021-08-01T22:01:22Z
date_published: 2021-06-25T00:00:00Z
date_updated: 2023-08-10T14:14:53Z
day: '25'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.3390/cells10071593
external_id:
isi:
- '000678193300001'
pmid:
- '34201955'
file:
- access_level: open_access
checksum: e0497ce5c77fa3b65a538c7d6e0f6c66
content_type: application/pdf
creator: cziletti
date_created: 2021-08-04T14:01:30Z
date_updated: 2021-08-04T14:01:30Z
file_id: '9768'
file_name: 2021_Cells_Muench.pdf
file_size: 4555611
relation: main_file
success: 1
file_date_updated: 2021-08-04T14:01:30Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '7'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cells
publication_identifier:
eissn:
- '20734409'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: The influence of mitochondrial dynamics and function on retinal ganglion cell
susceptibility in optic nerve 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: 10
year: '2021'
...
---
_id: '9641'
abstract:
- lang: eng
text: At the encounter with a novel environment, contextual memory formation is
greatly enhanced, accompanied with increased arousal and active exploration. Although
this phenomenon has been widely observed in animal and human daily life, how the
novelty in the environment is detected and contributes to contextual memory formation
has lately started to be unveiled. The hippocampus has been studied for many decades
for its largely known roles in encoding spatial memory, and a growing body of
evidence indicates a differential involvement of dorsal and ventral hippocampal
divisions in novelty detection. In this brief review article, we discuss the recent
findings of the role of mossy cells in the ventral hippocampal moiety in novelty
detection and put them in perspective with other novelty-related pathways in the
hippocampus. We propose a mechanism for novelty-driven memory acquisition in the
dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate
granule cells. By this projection, the ventral hippocampus sends novelty signals
to the dorsal hippocampus, opening a gate for memory encoding in dentate granule
cells based on information coming from the entorhinal cortex. We conclude that,
contrary to the presently accepted functional independence, the dorsal and ventral
hippocampi cooperate to link the novelty and contextual information, and this
dorso-ventral interaction is crucial for the novelty-dependent memory formation.
acknowledgement: This work was supported by a European Research Council Advanced Grant
694539 to Ryuichi Shigemoto.
article_number: '107486'
article_processing_charge: No
article_type: original
author:
- first_name: Felipe
full_name: Fredes, Felipe
last_name: Fredes
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Fredes F, Shigemoto R. The role of hippocampal mossy cells in novelty detection.
Neurobiology of Learning and Memory. 2021;183. doi:10.1016/j.nlm.2021.107486
apa: Fredes, F., & Shigemoto, R. (2021). The role of hippocampal mossy cells
in novelty detection. Neurobiology of Learning and Memory. Elsevier. https://doi.org/10.1016/j.nlm.2021.107486
chicago: Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells
in Novelty Detection.” Neurobiology of Learning and Memory. Elsevier, 2021.
https://doi.org/10.1016/j.nlm.2021.107486.
ieee: F. Fredes and R. Shigemoto, “The role of hippocampal mossy cells in novelty
detection,” Neurobiology of Learning and Memory, vol. 183. Elsevier, 2021.
ista: Fredes F, Shigemoto R. 2021. The role of hippocampal mossy cells in novelty
detection. Neurobiology of Learning and Memory. 183, 107486.
mla: Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells
in Novelty Detection.” Neurobiology of Learning and Memory, vol. 183, 107486,
Elsevier, 2021, doi:10.1016/j.nlm.2021.107486.
short: F. Fredes, R. Shigemoto, Neurobiology of Learning and Memory 183 (2021).
date_created: 2021-07-11T22:01:16Z
date_published: 2021-06-30T00:00:00Z
date_updated: 2023-08-10T14:10:37Z
day: '30'
ddc:
- '610'
department:
- _id: RySh
doi: 10.1016/j.nlm.2021.107486
ec_funded: 1
external_id:
isi:
- '000677694900004'
pmid:
- '34214666'
file:
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checksum: 8e8298a9e8c7df146ad23f32c2a63929
content_type: application/pdf
creator: cziletti
date_created: 2021-07-19T13:46:06Z
date_updated: 2021-07-19T13:46:06Z
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file_name: 2021_NeurobLearnMemory_Fredes.pdf
file_size: 1994793
relation: main_file
success: 1
file_date_updated: 2021-07-19T13:46:06Z
has_accepted_license: '1'
intvolume: ' 183'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
publication: Neurobiology of Learning and Memory
publication_identifier:
eissn:
- '10959564'
issn:
- '10747427'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The role of hippocampal mossy cells in novelty detection
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: 183
year: '2021'
...
---
_id: '9646'
abstract:
- lang: eng
text: We consider the fundamental problem of deriving quantitative bounds on the
probability that a given assertion is violated in a probabilistic program. We
provide automated algorithms that obtain both lower and upper bounds on the assertion
violation probability. The main novelty of our approach is that we prove new and
dedicated fixed-point theorems which serve as the theoretical basis of our algorithms
and enable us to reason about assertion violation bounds in terms of pre and post
fixed-point functions. To synthesize such fixed-points, we devise algorithms that
utilize a wide range of mathematical tools, including repulsing ranking supermartingales,
Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization.
On the theoretical side, we provide (i) the first automated algorithm for lower-bounds
on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds
of exponential form in affine programs, and (iii) provably and significantly tighter
upper-bounds than the previous approaches. On the practical side, we show our
algorithms can handle a wide variety of programs from the literature and synthesize
bounds that are remarkably tighter than previous results, in some cases by thousands
of orders of magnitude.
acknowledgement: 'We are very thankful to the anonymous reviewers for the helpful
and valuable comments. The work was partially supported by the National Natural
Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research
Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and
DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW).'
article_processing_charge: No
author:
- first_name: Jinyi
full_name: Wang, Jinyi
last_name: Wang
- first_name: Yican
full_name: Sun, Yican
last_name: Sun
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: 'Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of
assertion violations in probabilistic programs. In: Proceedings of the 42nd
ACM SIGPLAN International Conference on Programming Language Design and Implementation.
Association for Computing Machinery; 2021:1171-1186. doi:10.1145/3453483.3454102'
apa: 'Wang, J., Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2021).
Quantitative analysis of assertion violations in probabilistic programs. In Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation (pp. 1171–1186). Online: Association for Computing Machinery.
https://doi.org/10.1145/3453483.3454102'
chicago: Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar
Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.”
In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, 1171–86. Association for Computing Machinery,
2021. https://doi.org/10.1145/3453483.3454102.
ieee: J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative
analysis of assertion violations in probabilistic programs,” in Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Online, 2021, pp. 1171–1186.
ista: 'Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis
of assertion violations in probabilistic programs. Proceedings of the 42nd ACM
SIGPLAN International Conference on Programming Language Design and Implementation.
PLDI: Programming Language Design and Implementation, 1171–1186.'
mla: Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic
Programs.” Proceedings of the 42nd ACM SIGPLAN International Conference on
Programming Language Design and Implementation, Association for Computing
Machinery, 2021, pp. 1171–86, doi:10.1145/3453483.3454102.
short: J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186.
conference:
end_date: 2021-06-26
location: Online
name: 'PLDI: Programming Language Design and Implementation'
start_date: 2021-06-20
date_created: 2021-07-11T22:01:18Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-10T14:14:08Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3453483.3454102
ec_funded: 1
external_id:
arxiv:
- '2011.14617'
isi:
- '000723661700076'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2011.14617
month: '06'
oa: 1
oa_version: Preprint
page: 1171-1186
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450383912'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantitative analysis of assertion violations in probabilistic programs
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9645'
abstract:
- lang: eng
text: "We consider the fundamental problem of reachability analysis over imperative
programs with real variables. Previous works that tackle reachability are either
unable to handle programs consisting of general loops (e.g. symbolic execution),
or lack completeness guarantees (e.g. abstract interpretation), or are not automated
(e.g. incorrectness logic). In contrast, we propose a novel approach for reachability
analysis that can handle general and complex loops, is complete, and can be entirely
automated for a wide family of programs. Through the notion of Inductive Reachability
Witnesses (IRWs), our approach extends ideas from both invariant generation and
termination to reachability analysis.\r\n\r\nWe first show that our IRW-based
approach is sound and complete for reachability analysis of imperative programs.
Then, we focus on linear and polynomial programs and develop automated methods
for synthesizing linear and polynomial IRWs. In the linear case, we follow the
well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial
case, where we present a push-button semi-complete algorithm. We achieve this
using a novel combination of classical theorems in real algebraic geometry, such
as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally,
our experimental results show we can prove complex reachability objectives over
various benchmarks that were beyond the reach of previous methods."
acknowledgement: This research was partially supported by the ERC CoG 863818 (ForM-SMArt),
the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the
Huawei Innovation Research Program, the Facebook PhD Fellowship Program, and DOC
Fellowship No. 24956 of the Austrian Academy of Sciences (ÖAW).
article_processing_charge: No
author:
- first_name: Ali
full_name: Asadi, Ali
last_name: Asadi
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Mohammad
full_name: Mahdavi, Mohammad
last_name: Mahdavi
citation:
ama: 'Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability
witnesses via Stellensätze. In: Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation. Association
for Computing Machinery; 2021:772-787. doi:10.1145/3453483.3454076'
apa: 'Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., & Mahdavi, M. (2021).
Polynomial reachability witnesses via Stellensätze. In Proceedings of the 42nd
ACM SIGPLAN International Conference on Programming Language Design and Implementation
(pp. 772–787). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454076'
chicago: Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady,
and Mohammad Mahdavi. “Polynomial Reachability Witnesses via Stellensätze.” In
Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, 772–87. Association for Computing Machinery,
2021. https://doi.org/10.1145/3453483.3454076.
ieee: A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial
reachability witnesses via Stellensätze,” in Proceedings of the 42nd ACM SIGPLAN
International Conference on Programming Language Design and Implementation,
Online, 2021, pp. 772–787.
ista: 'Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability
witnesses via Stellensätze. Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation. PLDI: Programming
Language Design and Implementation, 772–787.'
mla: Asadi, Ali, et al. “Polynomial Reachability Witnesses via Stellensätze.” Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 772–87,
doi:10.1145/3453483.3454076.
short: A. Asadi, K. Chatterjee, H. Fu, A.K. Goharshady, M. Mahdavi, in:, Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 772–787.
conference:
end_date: 2021-06-26
location: Online
name: ' PLDI: Programming Language Design and Implementation'
start_date: 2021-06-20
date_created: 2021-07-11T22:01:17Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-10T14:13:39Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3453483.3454076
ec_funded: 1
external_id:
isi:
- '000723661700050'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-03183862/
month: '06'
oa: 1
oa_version: Submitted Version
page: 772-787
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450383912'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Polynomial reachability witnesses via Stellensätze
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9759'
acknowledgement: The authors thank Inez Lam of Johns Hopkins University for valuable
comments on an earlier version of the manuscript. We also thank the facilitators
of the 2019–2020 eLife Community Ambassador program.
article_number: e1009124
article_processing_charge: Yes
article_type: letter_note
author:
- first_name: Michael John
full_name: Bartlett, Michael John
last_name: Bartlett
- 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: Adriana
full_name: Bankston, Adriana
last_name: Bankston
- first_name: Sarvenaz
full_name: Sarabipour, Sarvenaz
last_name: Sarabipour
citation:
ama: Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve
academic work- life balance. PLoS Computational Biology. 2021;17(7). doi:10.1371/journal.pcbi.1009124
apa: Bartlett, M. J., Arslan, F. N., Bankston, A., & Sarabipour, S. (2021).
Ten simple rules to improve academic work- life balance. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009124
chicago: Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz
Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS
Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009124.
ieee: M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple
rules to improve academic work- life balance,” PLoS Computational Biology,
vol. 17, no. 7. Public Library of Science, 2021.
ista: Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to
improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124.
mla: Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work-
Life Balance.” PLoS Computational Biology, vol. 17, no. 7, e1009124, Public
Library of Science, 2021, doi:10.1371/journal.pcbi.1009124.
short: M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational
Biology 17 (2021).
date_created: 2021-08-01T22:01:21Z
date_published: 2021-07-15T00:00:00Z
date_updated: 2023-08-10T14:16:46Z
day: '15'
ddc:
- '613'
department:
- _id: CaHe
doi: 10.1371/journal.pcbi.1009124
external_id:
isi:
- '000677713500008'
pmid:
- '34264932'
file:
- access_level: open_access
checksum: e56d91f0eeadb36f143a90e2c1b3ab63
content_type: application/pdf
creator: cchlebak
date_created: 2021-08-05T12:06:49Z
date_updated: 2021-08-05T12:06:49Z
file_id: '9771'
file_name: 2021_PlosCompBio_Bartlett.pdf
file_size: 693633
relation: main_file
file_date_updated: 2021-08-05T12:06:49Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Computational Biology
publication_identifier:
eissn:
- '15537358'
issn:
- 1553734X
publication_status: published
publisher: Public Library of Science
scopus_import: '1'
status: public
title: Ten simple rules to improve academic work- life balance
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: '9822'
abstract:
- lang: eng
text: Attachment of adhesive molecules on cell culture surfaces to restrict cell
adhesion to defined areas and shapes has been vital for the progress of in vitro
research. In currently existing patterning methods, a combination of pattern properties
such as stability, precision, specificity, high-throughput outcome, and spatiotemporal
control is highly desirable but challenging to achieve. Here, we introduce a versatile
and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent
patterning step and a subsequent functionalization of the pattern via click chemistry.
This two-step process is feasible on arbitrary surfaces and allows for generation
of sustainable patterns and gradients. The method is validated in different biological
systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining
the growth and migration of cells to the designated areas. We then implement a
sequential photopatterning approach by adding a second switchable patterning step,
allowing for spatiotemporal control over two distinct surface patterns. As a proof
of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis.
Our results show that the spatiotemporal control provided by our “sequential photopatterning”
system is essential for mimicking dynamic biological processes and that our innovative
approach has great potential for further applications in cell science.
acknowledgement: We would like to thank Charlott Leu for the production of our chromium
wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh
Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim
Rädler for his valuable scientific guidance.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Themistoklis
full_name: Zisis, Themistoklis
last_name: Zisis
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Miriam
full_name: Balles, Miriam
last_name: Balles
- first_name: Maibritt
full_name: Kretschmer, Maibritt
last_name: Kretschmer
- first_name: Maria
full_name: Nemethova, Maria
id: 34E27F1C-F248-11E8-B48F-1D18A9856A87
last_name: Nemethova
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Janina
full_name: Lange, Janina
last_name: Lange
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-4561-241X
- first_name: Stefan
full_name: Zahler, Stefan
last_name: Zahler
citation:
ama: Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for
studying cellular processes under spatiotemporal control. ACS Applied Materials
and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850
apa: Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R.
P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular
processes under spatiotemporal control. ACS Applied Materials and Interfaces.
American Chemical Society. https://doi.org/10.1021/acsami.1c09850
chicago: Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria
Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning
for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied
Materials and Interfaces. American Chemical Society, 2021. https://doi.org/10.1021/acsami.1c09850.
ieee: T. Zisis et al., “Sequential and switchable patterning for studying
cellular processes under spatiotemporal control,” ACS Applied Materials and
Interfaces, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.
ista: Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild
R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning
for studying cellular processes under spatiotemporal control. ACS Applied Materials
and Interfaces. 13(30), 35545–35560.
mla: Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying
Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and
Interfaces, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560,
doi:10.1021/acsami.1c09850.
short: T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait,
R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials
and Interfaces 13 (2021) 35545–35560.
date_created: 2021-08-08T22:01:28Z
date_published: 2021-08-04T00:00:00Z
date_updated: 2023-08-10T14:22:48Z
day: '04'
ddc:
- '620'
- '570'
department:
- _id: MiSi
- _id: GaTk
- _id: Bio
- _id: CaGu
doi: 10.1021/acsami.1c09850
ec_funded: 1
external_id:
isi:
- '000683741400026'
pmid:
- '34283577'
file:
- access_level: open_access
checksum: b043a91d9f9200e467b970b692687ed3
content_type: application/pdf
creator: asandaue
date_created: 2021-08-09T09:44:03Z
date_updated: 2021-08-09T09:44:03Z
file_id: '9833'
file_name: 2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf
file_size: 7123293
relation: main_file
success: 1
file_date_updated: 2021-08-09T09:44:03Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '30'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 35545–35560
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
publication: ACS Applied Materials and Interfaces
publication_identifier:
eissn:
- '19448252'
issn:
- '19448244'
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sequential and switchable patterning for studying cellular processes under
spatiotemporal control
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: 13
year: '2021'
...
---
_id: '9819'
abstract:
- lang: eng
text: Photorealistic editing of head portraits is a challenging task as humans are
very sensitive to inconsistencies in faces. We present an approach for high-quality
intuitive editing of the camera viewpoint and scene illumination (parameterised
with an environment map) in a portrait image. This requires our method to capture
and control the full reflectance field of the person in the image. Most editing
approaches rely on supervised learning using training data captured with setups
such as light and camera stages. Such datasets are expensive to acquire, not readily
available and do not capture all the rich variations of in-the-wild portrait images.
In addition, most supervised approaches only focus on relighting, and do not allow
camera viewpoint editing. Thus, they only capture and control a subset of the
reflectance field. Recently, portrait editing has been demonstrated by operating
in the generative model space of StyleGAN. While such approaches do not require
direct supervision, there is a significant loss of quality when compared to the
supervised approaches. In this paper, we present a method which learns from limited
supervised training data. The training images only include people in a fixed neutral
expression with eyes closed, without much hair or background variations. Each
person is captured under 150 one-light-at-a-time conditions and under 8 camera
poses. Instead of training directly in the image space, we design a supervised
problem which learns transformations in the latent space of StyleGAN. This combines
the best of supervised learning and generative adversarial modeling. We show that
the StyleGAN prior allows for generalisation to different expressions, hairstyles
and backgrounds. This produces high-quality photorealistic results for in-the-wild
images and significantly outperforms existing methods. Our approach can edit the
illumination and pose simultaneously, and runs at interactive rates.
acknowledgement: This work was supported by the ERC Consolidator Grant 4DReply (770784).
We also acknowledge support from Technicolor and InterDigital. We thank Tiancheng
Sun for kindly helping us with the comparisons with Sun et al. [2019].
article_number: '44'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: B. R.
full_name: Mallikarjun, B. R.
last_name: Mallikarjun
- first_name: Ayush
full_name: Tewari, Ayush
last_name: Tewari
- first_name: Abdallah
full_name: Dib, Abdallah
last_name: Dib
- first_name: Tim
full_name: Weyrich, Tim
last_name: Weyrich
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Hans Peter
full_name: Seidel, Hans Peter
last_name: Seidel
- first_name: Hanspeter
full_name: Pfister, Hanspeter
last_name: Pfister
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
- first_name: Louis
full_name: Chevallier, Louis
last_name: Chevallier
- first_name: Mohamed A.
full_name: Elgharib, Mohamed A.
last_name: Elgharib
- first_name: Christian
full_name: Theobalt, Christian
last_name: Theobalt
citation:
ama: 'Mallikarjun BR, Tewari A, Dib A, et al. PhotoApp: Photorealistic appearance
editing of head portraits. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459765'
apa: 'Mallikarjun, B. R., Tewari, A., Dib, A., Weyrich, T., Bickel, B., Seidel,
H. P., … Theobalt, C. (2021). PhotoApp: Photorealistic appearance editing of head
portraits. ACM Transactions on Graphics. Association for Computing Machinery.
https://doi.org/10.1145/3450626.3459765'
chicago: 'Mallikarjun, B. R., Ayush Tewari, Abdallah Dib, Tim Weyrich, Bernd Bickel,
Hans Peter Seidel, Hanspeter Pfister, et al. “PhotoApp: Photorealistic Appearance
Editing of Head Portraits.” ACM Transactions on Graphics. Association for
Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459765.'
ieee: 'B. R. Mallikarjun et al., “PhotoApp: Photorealistic appearance editing
of head portraits,” ACM Transactions on Graphics, vol. 40, no. 4. Association
for Computing Machinery, 2021.'
ista: 'Mallikarjun BR, Tewari A, Dib A, Weyrich T, Bickel B, Seidel HP, Pfister
H, Matusik W, Chevallier L, Elgharib MA, Theobalt C. 2021. PhotoApp: Photorealistic
appearance editing of head portraits. ACM Transactions on Graphics. 40(4), 44.'
mla: 'Mallikarjun, B. R., et al. “PhotoApp: Photorealistic Appearance Editing of
Head Portraits.” ACM Transactions on Graphics, vol. 40, no. 4, 44, Association
for Computing Machinery, 2021, doi:10.1145/3450626.3459765.'
short: B.R. Mallikarjun, A. Tewari, A. Dib, T. Weyrich, B. Bickel, H.P. Seidel,
H. Pfister, W. Matusik, L. Chevallier, M.A. Elgharib, C. Theobalt, ACM Transactions
on Graphics 40 (2021).
date_created: 2021-08-08T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-10T14:25:08Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3450626.3459765
external_id:
arxiv:
- '2103.07658'
isi:
- '000674930900011'
file:
- access_level: open_access
checksum: 51b61b7e5c175e2d7ed8fa3b35f7525a
content_type: application/pdf
creator: asandaue
date_created: 2021-08-09T11:41:50Z
date_updated: 2021-08-09T11:41:50Z
file_id: '9834'
file_name: 2021_ACMTransactionsOnGraphics_Mallikarjun.pdf
file_size: 49840741
relation: main_file
success: 1
file_date_updated: 2021-08-09T11:41:50Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'PhotoApp: Photorealistic appearance editing of head portraits'
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: '9816'
abstract:
- lang: eng
text: "Aims: Mass antigen testing programs have been challenged because of an alleged
insufficient specificity, leading to a large number of false positives. The objective
of this study is to derive a lower bound of the specificity of the SD Biosensor
Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data
from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020
we calculate a lower confidence bound for the specificity. As positive test results
were not systematically verified by PCR tests, we base the lower bound on a worst
case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332
persons from 79 counties were tested. The lowest positivity rate was observed
in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This
implies a test specificity of at least 99.6% (97.5% one-sided lower confidence
bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests
a higher specificity compared to earlier studies in spite of the underlying worst
case assumption and the application in a mass testing setting. The actual specificity
is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible
at the time of testing. To our knowledge, this estimate constitutes the first
bound obtained from large scale practical use of an antigen test."
acknowledgement: We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová
for very helpful comments. We also thank Matej Mišík for discussion and information
regarding the Slovak testing data and Ag-Test used.
article_number: e0255267
article_processing_charge: Yes
article_type: original
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: Mathias
full_name: Beiglböck, Mathias
last_name: Beiglböck
- first_name: Anna Nele
full_name: Herdina, Anna Nele
last_name: Herdina
- first_name: Robert
full_name: Strassl, Robert
last_name: Strassl
- first_name: Martin
full_name: Posch, Martin
last_name: Posch
citation:
ama: Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis
of the specificity of a COVID-19 antigen test in the Slovak mass testing program.
PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0255267
apa: Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., &
Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the
Slovak mass testing program. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0255267
chicago: Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina,
Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen
Test in the Slovak Mass Testing Program.” PLoS ONE. Public Library of Science,
2021. https://doi.org/10.1371/journal.pone.0255267.
ieee: M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch,
“Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing
program,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021.
ista: Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021.
Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing
program. PLoS ONE. 16(7), e0255267.
mla: Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test
in the Slovak Mass Testing Program.” PLoS ONE, vol. 16, no. 7, e0255267,
Public Library of Science, 2021, doi:10.1371/journal.pone.0255267.
short: M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch,
PLoS ONE 16 (2021).
date_created: 2021-08-08T22:01:26Z
date_published: 2021-07-29T00:00:00Z
date_updated: 2023-08-10T14:26:32Z
day: '29'
ddc:
- '610'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0255267
external_id:
isi:
- '000685248200095'
pmid:
- '34324553'
file:
- access_level: open_access
checksum: ae4df60eb62f4491278588548d0c1f93
content_type: application/pdf
creator: asandaue
date_created: 2021-08-09T11:52:14Z
date_updated: 2021-08-09T11:52:14Z
file_id: '9835'
file_name: 2021_PLoSONE_Hledík.pdf
file_size: 773921
relation: main_file
success: 1
file_date_updated: 2021-08-09T11:52:14Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS ONE
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing
program
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: 16
year: '2021'
...
---
_id: '9821'
abstract:
- lang: eng
text: Heart rate variability (hrv) is a physiological phenomenon of the variation
in the length of the time interval between consecutive heartbeats. In many cases
it could be an indicator of the development of pathological states. The classical
approach to the analysis of hrv includes time domain methods and frequency domain
methods. However, attempts are still being made to define new and more effective
hrv assessment tools. Persistent homology is a novel data analysis tool developed
in the recent decades that is rooted at algebraic topology. The Topological Data
Analysis (TDA) approach focuses on examining the shape of the data in terms of
connectedness and holes, and has recently proved to be very effective in various
fields of research. In this paper we propose the use of persistent homology to
the hrv analysis. We recall selected topological descriptors used in the literature
and we introduce some new topological descriptors that reflect the specificity
of hrv, and we discuss their relation to the standard hrv measures. In particular,
we show that this novel approach provides a collection of indices that might be
at least as useful as the classical parameters in differentiating between series
of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering
from a stroke episode.
acknowledgement: We express our gratitude to the anonymous referees who provided constructive
comments that helped us improve the quality of the paper.
article_number: e0253851
article_processing_charge: Yes
article_type: original
author:
- first_name: Grzegorz
full_name: Graff, Grzegorz
last_name: Graff
- first_name: Beata
full_name: Graff, Beata
last_name: Graff
- first_name: Pawel
full_name: Pilarczyk, Pawel
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
- first_name: Grzegorz
full_name: Jablonski, Grzegorz
id: 4483EF78-F248-11E8-B48F-1D18A9856A87
last_name: Jablonski
orcid: 0000-0002-3536-9866
- first_name: Dariusz
full_name: Gąsecki, Dariusz
last_name: Gąsecki
- first_name: Krzysztof
full_name: Narkiewicz, Krzysztof
last_name: Narkiewicz
citation:
ama: Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. Persistent
homology as a new method of the assessment of heart rate variability. PLoS
ONE. 2021;16(7). doi:10.1371/journal.pone.0253851
apa: Graff, G., Graff, B., Pilarczyk, P., Jablonski, G., Gąsecki, D., & Narkiewicz,
K. (2021). Persistent homology as a new method of the assessment of heart rate
variability. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0253851
chicago: Graff, Grzegorz, Beata Graff, Pawel Pilarczyk, Grzegorz Jablonski, Dariusz
Gąsecki, and Krzysztof Narkiewicz. “Persistent Homology as a New Method of the
Assessment of Heart Rate Variability.” PLoS ONE. Public Library of Science,
2021. https://doi.org/10.1371/journal.pone.0253851.
ieee: G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, and K. Narkiewicz,
“Persistent homology as a new method of the assessment of heart rate variability,”
PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021.
ista: Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. 2021.
Persistent homology as a new method of the assessment of heart rate variability.
PLoS ONE. 16(7), e0253851.
mla: Graff, Grzegorz, et al. “Persistent Homology as a New Method of the Assessment
of Heart Rate Variability.” PLoS ONE, vol. 16, no. 7, e0253851, Public
Library of Science, 2021, doi:10.1371/journal.pone.0253851.
short: G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz,
PLoS ONE 16 (2021).
date_created: 2021-08-08T22:01:28Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-10T14:21:42Z
day: '01'
ddc:
- '006'
department:
- _id: HeEd
doi: 10.1371/journal.pone.0253851
external_id:
isi:
- '000678124900050'
pmid:
- '34292957'
file:
- access_level: open_access
checksum: 0277aa155d5db1febd2cb384768bba5f
content_type: application/pdf
creator: asandaue
date_created: 2021-08-09T09:25:41Z
date_updated: 2021-08-09T09:25:41Z
file_id: '9832'
file_name: 2021_PLoSONE_Graff.pdf
file_size: 2706919
relation: main_file
success: 1
file_date_updated: 2021-08-09T09:25:41Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS ONE
publication_identifier:
eissn:
- '19326203'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Persistent homology as a new method of the assessment of heart rate variability
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: 16
year: '2021'
...
---
_id: '9820'
abstract:
- lang: eng
text: Material appearance hinges on material reflectance properties but also surface
geometry and illumination. The unlimited number of potential combinations between
these factors makes understanding and predicting material appearance a very challenging
task. In this work, we collect a large-scale dataset of perceptual ratings of
appearance attributes with more than 215,680 responses for 42,120 distinct combinations
of material, shape, and illumination. The goal of this dataset is twofold. First,
we analyze for the first time the effects of illumination and geometry in material
perception across such a large collection of varied appearances. We connect our
findings to those of the literature, discussing how previous knowledge generalizes
across very diverse materials, shapes, and illuminations. Second, we use the collected
dataset to train a deep learning architecture for predicting perceptual attributes
that correlate with human judgments. We demonstrate the consistent and robust
behavior of our predictor in various challenging scenarios, which, for the first
time, enables estimating perceived material attributes from general 2D images.
Since our predictor relies on the final appearance in an image, it can compare
appearance properties across different geometries and illumination conditions.
Finally, we demonstrate several applications that use our predictor, including
appearance reproduction using 3D printing, BRDF editing by integrating our predictor
in a differentiable renderer, illumination design, or material recommendations
for scene design.
acknowledgement: This project has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie, grant agreement
Nº 765911 (RealVision) and from the European Research Council (ERC), grant agreement
Nº 804226 (PERDY).
article_number: '125'
article_processing_charge: No
article_type: original
author:
- first_name: Ana
full_name: Serrano, Ana
last_name: Serrano
- first_name: Bin
full_name: Chen, Bin
last_name: Chen
- first_name: Chao
full_name: Wang, Chao
last_name: Wang
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
orcid: 0000-0002-5062-4474
- first_name: Hans Peter
full_name: Seidel, Hans Peter
last_name: Seidel
- first_name: Piotr
full_name: Didyk, Piotr
last_name: Didyk
- first_name: Karol
full_name: Myszkowski, Karol
last_name: Myszkowski
citation:
ama: 'Serrano A, Chen B, Wang C, et al. The effect of shape and illumination on
material perception: Model and applications. ACM Transactions on Graphics.
2021;40(4). doi:10.1145/3450626.3459813'
apa: 'Serrano, A., Chen, B., Wang, C., Piovarci, M., Seidel, H. P., Didyk, P., &
Myszkowski, K. (2021). The effect of shape and illumination on material perception:
Model and applications. ACM Transactions on Graphics. Association for Computing
Machinery. https://doi.org/10.1145/3450626.3459813'
chicago: 'Serrano, Ana, Bin Chen, Chao Wang, Michael Piovarci, Hans Peter Seidel,
Piotr Didyk, and Karol Myszkowski. “The Effect of Shape and Illumination on Material
Perception: Model and Applications.” ACM Transactions on Graphics. Association
for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459813.'
ieee: 'A. Serrano et al., “The effect of shape and illumination on material
perception: Model and applications,” ACM Transactions on Graphics, vol.
40, no. 4. Association for Computing Machinery, 2021.'
ista: 'Serrano A, Chen B, Wang C, Piovarci M, Seidel HP, Didyk P, Myszkowski K.
2021. The effect of shape and illumination on material perception: Model and applications.
ACM Transactions on Graphics. 40(4), 125.'
mla: 'Serrano, Ana, et al. “The Effect of Shape and Illumination on Material Perception:
Model and Applications.” ACM Transactions on Graphics, vol. 40, no. 4,
125, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459813.'
short: A. Serrano, B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski,
ACM Transactions on Graphics 40 (2021).
date_created: 2021-08-08T22:01:28Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-10T14:20:10Z
day: '01'
department:
- _id: BeBi
doi: 10.1145/3450626.3459813
external_id:
isi:
- '000674930900090'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://zaguan.unizar.es/record/110704/files/texto_completo.pdf
month: '08'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The effect of shape and illumination on material perception: Model and applications'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2021'
...
---
_id: '9818'
abstract:
- lang: eng
text: Triangle mesh-based simulations are able to produce satisfying animations
of knitted and woven cloth; however, they lack the rich geometric detail of yarn-level
simulations. Naive texturing approaches do not consider yarn-level physics, while
full yarn-level simulations may become prohibitively expensive for large garments.
We propose a method to animate yarn-level cloth geometry on top of an underlying
deforming mesh in a mechanics-aware fashion. Using triangle strains to interpolate
precomputed yarn geometry, we are able to reproduce effects such as knit loops
tightening under stretching. In combination with precomputed mesh animation or
real-time mesh simulation, our method is able to animate yarn-level cloth in real-time
at large scales.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We wish to thank the anonymous reviewers and the members of the
Visual Computing Group at IST Austria for their valuable feedback. We also thank
Seddi Labs for providing the garment model with fold-over seams.\r\nThis research
was supported by the Scientific Service Units (SSU) of IST Austria through resources
provided by Scientific\r\nComputing. This project has received funding from the
European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation programme under grant agreement No. 638176. Rahul Narain is supported
by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc."
article_number: '168'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
- first_name: Rahul
full_name: Narain, Rahul
last_name: Narain
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Sperl G, Narain R, Wojtan C. Mechanics-aware deformation of yarn pattern geometry.
ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459816
apa: Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-aware deformation
of yarn pattern geometry. ACM Transactions on Graphics. Association for
Computing Machinery. https://doi.org/10.1145/3450626.3459816
chicago: Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation
of Yarn Pattern Geometry.” ACM Transactions on Graphics. Association for
Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459816.
ieee: G. Sperl, R. Narain, and C. Wojtan, “Mechanics-aware deformation of yarn pattern
geometry,” ACM Transactions on Graphics, vol. 40, no. 4. Association for
Computing Machinery, 2021.
ista: Sperl G, Narain R, Wojtan C. 2021. Mechanics-aware deformation of yarn pattern
geometry. ACM Transactions on Graphics. 40(4), 168.
mla: Sperl, Georg, et al. “Mechanics-Aware Deformation of Yarn Pattern Geometry.”
ACM Transactions on Graphics, vol. 40, no. 4, 168, Association for Computing
Machinery, 2021, doi:10.1145/3450626.3459816.
short: G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 40 (2021).
date_created: 2021-08-08T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-10T14:24:36Z
day: '01'
department:
- _id: GradSch
- _id: ChWo
doi: 10.1145/3450626.3459816
ec_funded: 1
external_id:
isi:
- '000674930900132'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/3450626.3459816
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/knitting-virtual-yarn/
record:
- id: '12358'
relation: dissertation_contains
status: public
- id: '9327'
relation: software
status: public
scopus_import: '1'
status: public
title: Mechanics-aware deformation of yarn pattern geometry
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2021'
...
---
_id: '9828'
abstract:
- lang: eng
text: Amplitude demodulation is a classical operation used in signal processing.
For a long time, its effective applications in practice have been limited to narrowband
signals. In this work, we generalize amplitude demodulation to wideband signals.
We pose demodulation as a recovery problem of an oversampled corrupted signal
and introduce special iterative schemes belonging to the family of alternating
projection algorithms to solve it. Sensibly chosen structural assumptions on the
demodulation outputs allow us to reveal the high inferential accuracy of the method
over a rich set of relevant signals. This new approach surpasses current state-of-the-art
demodulation techniques apt to wideband signals in computational efficiency by
up to many orders of magnitude with no sacrifice in quality. Such performance
opens the door for applications of the amplitude demodulation procedure in new
contexts. In particular, the new method makes online and large-scale offline data
processing feasible, including the calculation of modulator-carrier pairs in higher
dimensions and poor sampling conditions, independent of the signal bandwidth.
We illustrate the utility and specifics of applications of the new method in practice
by using natural speech and synthetic signals.
acknowledgement: The author thanks his colleagues K. Huszár and G. Tkačik for valuable
discussions and comments on the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Mantas
full_name: Gabrielaitis, Mantas
id: 4D5B0CBC-F248-11E8-B48F-1D18A9856A87
last_name: Gabrielaitis
orcid: 0000-0002-7758-2016
citation:
ama: Gabrielaitis M. Fast and accurate amplitude demodulation of wideband signals.
IEEE Transactions on Signal Processing. 2021;69:4039-4054. doi:10.1109/TSP.2021.3087899
apa: Gabrielaitis, M. (2021). Fast and accurate amplitude demodulation of wideband
signals. IEEE Transactions on Signal Processing. Institute of Electrical
and Electronics Engineers. https://doi.org/10.1109/TSP.2021.3087899
chicago: Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband
Signals.” IEEE Transactions on Signal Processing. Institute of Electrical
and Electronics Engineers, 2021. https://doi.org/10.1109/TSP.2021.3087899.
ieee: M. Gabrielaitis, “Fast and accurate amplitude demodulation of wideband signals,”
IEEE Transactions on Signal Processing, vol. 69. Institute of Electrical
and Electronics Engineers, pp. 4039–4054, 2021.
ista: Gabrielaitis M. 2021. Fast and accurate amplitude demodulation of wideband
signals. IEEE Transactions on Signal Processing. 69, 4039–4054.
mla: Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband
Signals.” IEEE Transactions on Signal Processing, vol. 69, Institute of
Electrical and Electronics Engineers, 2021, pp. 4039–54, doi:10.1109/TSP.2021.3087899.
short: M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054.
date_created: 2021-08-08T22:01:31Z
date_published: 2021-06-09T00:00:00Z
date_updated: 2023-08-10T14:19:33Z
day: '09'
department:
- _id: GaTk
doi: 10.1109/TSP.2021.3087899
external_id:
arxiv:
- '2102.04832'
isi:
- '000682123900002'
intvolume: ' 69'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2102.04832
month: '06'
oa: 1
oa_version: Preprint
page: 4039 - 4054
publication: IEEE Transactions on Signal Processing
publication_identifier:
eissn:
- 1941-0476
issn:
- 1053-587X
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast and accurate amplitude demodulation of wideband signals
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 69
year: '2021'
...
---
_id: '9327'
abstract:
- lang: eng
text: "This archive contains the missing sweater mesh animations and displacement
models for the code of \"Mechanics-Aware Deformation of Yarn Pattern Geometry\"\r\n\r\nCode
Repository: https://git.ist.ac.at/gsperl/MADYPG"
author:
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
- first_name: Rahul
full_name: Narain, Rahul
last_name: Narain
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Sperl G, Narain R, Wojtan C. Mechanics-Aware Deformation of Yarn Pattern Geometry
(Additional Animation/Model Data). 2021. doi:10.15479/AT:ISTA:9327
apa: Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-Aware Deformation
of Yarn Pattern Geometry (Additional Animation/Model Data). IST Austria. https://doi.org/10.15479/AT:ISTA:9327
chicago: Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation
of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021.
https://doi.org/10.15479/AT:ISTA:9327.
ieee: G. Sperl, R. Narain, and C. Wojtan, “Mechanics-Aware Deformation of Yarn Pattern
Geometry (Additional Animation/Model Data).” IST Austria, 2021.
ista: Sperl G, Narain R, Wojtan C. 2021. Mechanics-Aware Deformation of Yarn Pattern
Geometry (Additional Animation/Model Data), IST Austria, 10.15479/AT:ISTA:9327.
mla: Sperl, Georg, et al. Mechanics-Aware Deformation of Yarn Pattern Geometry
(Additional Animation/Model Data). IST Austria, 2021, doi:10.15479/AT:ISTA:9327.
short: G. Sperl, R. Narain, C. Wojtan, (2021).
date_created: 2021-04-16T14:26:19Z
date_published: 2021-05-01T00:00:00Z
date_updated: 2023-08-10T14:24:36Z
ddc:
- '005'
department:
- _id: GradSch
- _id: ChWo
doi: 10.15479/AT:ISTA:9327
file:
- access_level: open_access
checksum: 0324cb519273371708743f3282e7c081
content_type: application/zip
creator: gsperl
date_created: 2021-04-16T14:15:12Z
date_updated: 2021-04-16T14:15:12Z
file_id: '9328'
file_name: MADYPG_extra_data.zip
file_size: 802586232
relation: main_file
success: 1
- access_level: open_access
checksum: 4c224551adf852b136ec21a4e13f0c1b
content_type: application/gzip
creator: pub-gitlab-bot
date_created: 2021-04-26T09:33:44Z
date_updated: 2021-04-26T09:33:44Z
file_id: '9353'
file_name: MADYPG.zip
file_size: 64962865
relation: main_file
file_date_updated: 2021-04-26T09:33:44Z
gitlab_commit_id: 6a77e7e22769230ae5f5edaa090fb4b828e57573
gitlab_url: https://git.ist.ac.at/gsperl/MADYPG
has_accepted_license: '1'
license: https://opensource.org/licenses/MIT
month: '05'
oa: 1
publisher: IST Austria
related_material:
record:
- id: '9818'
relation: used_for_analysis_in
status: public
status: public
title: Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model
Data)
tmp:
legal_code_url: https://opensource.org/licenses/MIT
name: The MIT License
short: MIT
type: software
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '9770'
abstract:
- lang: eng
text: We study an effective one-dimensional quantum model that includes friction
and spin-orbit coupling (SOC), and show that the model exhibits spin polarization
when both terms are finite. Most important, strong spin polarization can be observed
even for moderate SOC, provided that the friction is strong. Our findings might
help to explain the pronounced effect of chirality on spin distribution and transport
in chiral molecules. In particular, our model implies static magnetic properties
of a chiral molecule, which lead to Shiba-like states when a molecule is placed
on a superconductor, in accordance with recent experimental data.
acknowledgement: "We thank Rafael Barfknecht for useful discussions. This work has
received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.\r\nand
A.G.V.). M.L. acknowledges support by the European Research Council (ERC) Starting
Grant No. 801770 (ANGULON). Y.P. and O.M. acknowledge funding from the Nidersachsen
Ministry of Science and Culture, and from the\r\nAcademia Sinica Research Program.
O.M. is thankful for support through the Harry de Jur Chair in Applied Science."
article_number: '024430'
article_processing_charge: No
article_type: original
author:
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Hen
full_name: Alpern, Hen
last_name: Alpern
- first_name: Yossi
full_name: Paltiel, Yossi
last_name: Paltiel
- first_name: Oded
full_name: Millo, Oded
last_name: Millo
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
citation:
ama: Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. Interplay
between friction and spin-orbit coupling as a source of spin polarization. Physical
Review B. 2021;104(2). doi:10.1103/physrevb.104.024430
apa: Volosniev, A., Alpern, H., Paltiel, Y., Millo, O., Lemeshko, M., & Ghazaryan,
A. (2021). Interplay between friction and spin-orbit coupling as a source of spin
polarization. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.104.024430
chicago: Volosniev, Artem, Hen Alpern, Yossi Paltiel, Oded Millo, Mikhail Lemeshko,
and Areg Ghazaryan. “Interplay between Friction and Spin-Orbit Coupling as a Source
of Spin Polarization.” Physical Review B. American Physical Society, 2021.
https://doi.org/10.1103/physrevb.104.024430.
ieee: A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, and A. Ghazaryan,
“Interplay between friction and spin-orbit coupling as a source of spin polarization,”
Physical Review B, vol. 104, no. 2. American Physical Society, 2021.
ista: Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. 2021.
Interplay between friction and spin-orbit coupling as a source of spin polarization.
Physical Review B. 104(2), 024430.
mla: Volosniev, Artem, et al. “Interplay between Friction and Spin-Orbit Coupling
as a Source of Spin Polarization.” Physical Review B, vol. 104, no. 2,
024430, American Physical Society, 2021, doi:10.1103/physrevb.104.024430.
short: A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, A. Ghazaryan,
Physical Review B 104 (2021).
date_created: 2021-08-04T15:05:32Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-10T14:27:07Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/physrevb.104.024430
ec_funded: 1
external_id:
arxiv:
- '2101.05173'
isi:
- '000678780800003'
intvolume: ' 104'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2101.05173
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interplay between friction and spin-orbit coupling as a source of spin polarization
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 104
year: '2021'
...
---
_id: '9827'
abstract:
- lang: eng
text: 'The Nearest neighbour search (NNS) is a fundamental problem in many application
domains dealing with multidimensional data. In a concurrent setting, where dynamic
modifications are allowed, a linearizable implementation of the NNS is highly
desirable.This paper introduces the LockFree-kD-tree (LFkD-tree ): a lock-free
concurrent kD-tree, which implements an abstract data type (ADT) that provides
the operations Add, Remove, Contains, and NNS. Our implementation is linearizable.
The operations in the LFkD-tree use single-word read and compare-and-swap (Image
1 ) atomic primitives, which are readily supported on available multi-core processors.
We experimentally evaluate the LFkD-tree using several benchmarks comprising real-world
and synthetic datasets. The experiments show that the presented design is scalable
and achieves significant speed-up compared to the implementations of an existing
sequential kD-tree and a recently proposed multidimensional indexing structure,
PH-tree.'
article_processing_charge: No
article_type: original
author:
- first_name: Bapi
full_name: Chatterjee, Bapi
id: 3C41A08A-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-2742-4028
- first_name: Ivan
full_name: Walulya, Ivan
last_name: Walulya
- first_name: Philippas
full_name: Tsigas, Philippas
last_name: Tsigas
citation:
ama: Chatterjee B, Walulya I, Tsigas P. Concurrent linearizable nearest neighbour
search in LockFree-kD-tree. Theoretical Computer Science. 2021;886:27-48.
doi:10.1016/j.tcs.2021.06.041
apa: Chatterjee, B., Walulya, I., & Tsigas, P. (2021). Concurrent linearizable
nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2021.06.041
chicago: Chatterjee, Bapi, Ivan Walulya, and Philippas Tsigas. “Concurrent Linearizable
Nearest Neighbour Search in LockFree-KD-Tree.” Theoretical Computer Science.
Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.06.041.
ieee: B. Chatterjee, I. Walulya, and P. Tsigas, “Concurrent linearizable nearest
neighbour search in LockFree-kD-tree,” Theoretical Computer Science, vol.
886. Elsevier, pp. 27–48, 2021.
ista: Chatterjee B, Walulya I, Tsigas P. 2021. Concurrent linearizable nearest neighbour
search in LockFree-kD-tree. Theoretical Computer Science. 886, 27–48.
mla: Chatterjee, Bapi, et al. “Concurrent Linearizable Nearest Neighbour Search
in LockFree-KD-Tree.” Theoretical Computer Science, vol. 886, Elsevier,
2021, pp. 27–48, doi:10.1016/j.tcs.2021.06.041.
short: B. Chatterjee, I. Walulya, P. Tsigas, Theoretical Computer Science 886 (2021)
27–48.
date_created: 2021-08-08T22:01:31Z
date_published: 2021-09-13T00:00:00Z
date_updated: 2023-08-10T14:27:43Z
day: '13'
department:
- _id: DaAl
doi: 10.1016/j.tcs.2021.06.041
external_id:
isi:
- '000694718900004'
intvolume: ' 886'
isi: 1
keyword:
- Concurrent data structure
- kD-tree
- Nearest neighbor search
- Similarity search
- Lock-free
- Linearizability
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://publications.lib.chalmers.se/records/fulltext/232185/232185.pdf
month: '09'
oa: 1
oa_version: Submitted Version
page: 27-48
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Concurrent linearizable nearest neighbour search in LockFree-kD-tree
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 886
year: '2021'
...
---
_id: '9877'
abstract:
- lang: eng
text: 'Parent-of-origin–dependent gene expression in mammals and flowering plants
results from differing chromatin imprints (genomic imprinting) between maternally
and paternally inherited alleles. Imprinted gene expression in the endosperm of
seeds is associated with localized hypomethylation of maternally but not paternally
inherited DNA, with certain small RNAs also displaying parent-of-origin–specific
expression. To understand the evolution of imprinting mechanisms in Oryza sativa
(rice), we analyzed imprinting divergence among four cultivars that span both
japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted
genes are imprinted across cultivars and enriched for functions in chromatin and
transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted
genes display divergent imprinting. Analyses of DNA methylation and small RNAs
revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed
DNA methylation, frequently overlap genes, and are imprinted four times more often
than genes. However, imprinting divergence most often correlated with local DNA
methylation epimutations (9 of 17 assessable loci), which were largely stable
within subspecies. Small insertion/deletion events and transposable element insertions
accompanied 4 of the 9 locally epimutated loci and associated with imprinting
divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic
variation occurred at key regulatory regions—the promoter and transcription start
site of maternally biased genes, and the promoter and gene body of paternally
biased genes. Our results reinforce models for the role of maternal-specific DNA
hypomethylation in imprinting of both maternally and paternally biased genes,
and highlight the role of transposition and epimutation in rice imprinting evolution.'
acknowledgement: We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing
team for generating the IR64 genome sequence and initial analysis; L. Bartley and
E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University
of California (UC), Berkeley Sanger sequencing team for technical advice and service.
This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH
Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator
Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright
Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying
Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing
Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.
article_number: e2104445118
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Deling
full_name: Ruan, Deling
last_name: Ruan
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Manoj K.
full_name: Sharma, Manoj K.
last_name: Sharma
- first_name: Rita
full_name: Sharma, Rita
last_name: Sharma
- first_name: XinYi
full_name: Ye, XinYi
last_name: Ye
- first_name: Nicholas D.
full_name: Nguyen, Nicholas D.
last_name: Nguyen
- first_name: Sukhranjan
full_name: Nijjar, Sukhranjan
last_name: Nijjar
- first_name: Pamela C.
full_name: Ronald, Pamela C.
last_name: Ronald
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals
roles for transposition and epimutation in ongoing evolution of genomic imprinting.
Proceedings of the National Academy of Sciences. 2021;118(29). doi:10.1073/pnas.2104445118
apa: Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma,
R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for
transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2104445118
chicago: Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura,
Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars
Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic
Imprinting.” Proceedings of the National Academy of Sciences. National
Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2104445118.
ieee: J. A. Rodrigues et al., “Divergence among rice cultivars reveals roles
for transposition and epimutation in ongoing evolution of genomic imprinting,”
Proceedings of the National Academy of Sciences, vol. 118, no. 29. National
Academy of Sciences, 2021.
ista: Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen
ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice
cultivars reveals roles for transposition and epimutation in ongoing evolution
of genomic imprinting. Proceedings of the National Academy of Sciences. 118(29),
e2104445118.
mla: Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles
for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.”
Proceedings of the National Academy of Sciences, vol. 118, no. 29, e2104445118,
National Academy of Sciences, 2021, doi:10.1073/pnas.2104445118.
short: J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma,
X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings
of the National Academy of Sciences 118 (2021).
date_created: 2021-08-10T19:30:41Z
date_published: 2021-07-16T00:00:00Z
date_updated: 2023-08-11T10:28:10Z
day: '16'
ddc:
- '580'
- '570'
department:
- _id: DaZi
doi: 10.1073/pnas.2104445118
external_id:
isi:
- '000685037700012'
pmid:
- '34272287'
file:
- access_level: open_access
checksum: 19e84ad8c03c60222744ee8e16cd6998
content_type: application/pdf
creator: asandaue
date_created: 2021-08-11T09:31:41Z
date_updated: 2021-08-11T09:31:41Z
file_id: '9879'
file_name: 2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf
file_size: 1898360
relation: main_file
success: 1
file_date_updated: 2021-08-11T09:31:41Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '29'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divergence among rice cultivars reveals roles for transposition and epimutation
in ongoing evolution of genomic imprinting
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: '9874'
abstract:
- lang: eng
text: Myocardial regeneration is restricted to early postnatal life, when mammalian
cardiomyocytes still retain the ability to proliferate. The molecular cues that
induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated
adult heart muscle cells remain obscure. Here we report that the miR-106b~25 cluster
is higher expressed in the early postnatal myocardium and decreases in expression
towards adulthood, especially under conditions of overload, and orchestrates the
transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy
by virtue of its targetome. In line, gene delivery of miR-106b~25 to the mouse
heart provokes cardiomyocyte proliferation by targeting a network of negative
cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted
miR-106b~25 null mice display spontaneous hypertrophic remodeling and exaggerated
remodeling to overload by derepression of the prohypertrophic transcription factors
Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b~25 on
cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b~25
provokes nearly complete regeneration of the adult myocardium after ischemic injury.
Our data demonstrate that exploitation of conserved molecular programs can enhance
the regenerative capacity of the injured heart.
acknowledgement: E.D. is supported by a VENI award 916-150-16 from the Netherlands
Organization for Health Research and Development (ZonMW), an EMBO Long-term Fellowship
(EMBO ALTF 848-2013) and a FP7 Marie Curie Intra-European Fellowship (Project number
627539). V.S.P. was funded by a fellowship from the FCT/ Ministério da Ciência,
Tecnologia e Inovação SFRH/BD/111799/2015. P.D.C.M. is an Established Investigator
of the Dutch Heart Foundation. L.D.W. acknowledges support from the Dutch CardioVascular
Alliance (ARENA-PRIME). L.D.W. was further supported by grant 311549 from the European
Research Council (ERC), a VICI award 918-156-47 from the Dutch Research Council
and Marie Sklodowska-Curie grant agreement no. 813716 (TRAIN-HEART).
article_number: '4808'
article_processing_charge: Yes
article_type: original
author:
- first_name: Andrea
full_name: Raso, Andrea
last_name: Raso
- first_name: Ellen
full_name: Dirkx, Ellen
last_name: Dirkx
- first_name: Vasco
full_name: Sampaio-Pinto, Vasco
last_name: Sampaio-Pinto
- first_name: Hamid
full_name: el Azzouzi, Hamid
last_name: el Azzouzi
- 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: Daniel W.
full_name: Sorensen, Daniel W.
last_name: Sorensen
- first_name: Lara
full_name: Ottaviani, Lara
last_name: Ottaviani
- first_name: Servé
full_name: Olieslagers, Servé
last_name: Olieslagers
- first_name: Manon M.
full_name: Huibers, Manon M.
last_name: Huibers
- first_name: Roel
full_name: de Weger, Roel
last_name: de Weger
- first_name: Sailay
full_name: Siddiqi, Sailay
last_name: Siddiqi
- first_name: Silvia
full_name: Moimas, Silvia
last_name: Moimas
- first_name: Consuelo
full_name: Torrini, Consuelo
last_name: Torrini
- first_name: Lorena
full_name: Zentillin, Lorena
last_name: Zentillin
- first_name: Luca
full_name: Braga, Luca
last_name: Braga
- first_name: Diana S.
full_name: Nascimento, Diana S.
last_name: Nascimento
- first_name: Paula A.
full_name: da Costa Martins, Paula A.
last_name: da Costa Martins
- first_name: Jop H.
full_name: van Berlo, Jop H.
last_name: van Berlo
- first_name: Serena
full_name: Zacchigna, Serena
last_name: Zacchigna
- first_name: Mauro
full_name: Giacca, Mauro
last_name: Giacca
- first_name: Leon J.
full_name: De Windt, Leon J.
last_name: De Windt
citation:
ama: Raso A, Dirkx E, Sampaio-Pinto V, et al. A microRNA program regulates the balance
between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration.
Nature Communications. 2021;12. doi:10.1038/s41467-021-25211-4
apa: Raso, A., Dirkx, E., Sampaio-Pinto, V., el Azzouzi, H., Cubero, R. J., Sorensen,
D. W., … De Windt, L. J. (2021). A microRNA program regulates the balance between
cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-25211-4
chicago: Raso, Andrea, Ellen Dirkx, Vasco Sampaio-Pinto, Hamid el Azzouzi, Ryan
J Cubero, Daniel W. Sorensen, Lara Ottaviani, et al. “A MicroRNA Program Regulates
the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac
Regeneration.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-25211-4.
ieee: A. Raso et al., “A microRNA program regulates the balance between cardiomyocyte
hyperplasia and hypertrophy and stimulates cardiac regeneration,” Nature Communications,
vol. 12. Springer Nature, 2021.
ista: Raso A, Dirkx E, Sampaio-Pinto V, el Azzouzi H, Cubero RJ, Sorensen DW, Ottaviani
L, Olieslagers S, Huibers MM, de Weger R, Siddiqi S, Moimas S, Torrini C, Zentillin
L, Braga L, Nascimento DS, da Costa Martins PA, van Berlo JH, Zacchigna S, Giacca
M, De Windt LJ. 2021. A microRNA program regulates the balance between cardiomyocyte
hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications.
12, 4808.
mla: Raso, Andrea, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte
Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” Nature Communications,
vol. 12, 4808, Springer Nature, 2021, doi:10.1038/s41467-021-25211-4.
short: A. Raso, E. Dirkx, V. Sampaio-Pinto, H. el Azzouzi, R.J. Cubero, D.W. Sorensen,
L. Ottaviani, S. Olieslagers, M.M. Huibers, R. de Weger, S. Siddiqi, S. Moimas,
C. Torrini, L. Zentillin, L. Braga, D.S. Nascimento, P.A. da Costa Martins, J.H.
van Berlo, S. Zacchigna, M. Giacca, L.J. De Windt, Nature Communications 12 (2021).
date_created: 2021-08-10T11:49:20Z
date_published: 2021-08-10T00:00:00Z
date_updated: 2023-08-11T10:27:03Z
day: '10'
ddc:
- '610'
- '570'
department:
- _id: SaSi
doi: 10.1038/s41467-021-25211-4
external_id:
isi:
- '000683910200042'
pmid:
- '34376683'
file:
- access_level: open_access
checksum: 48d8562e8229e4282f3f354b329722c5
content_type: application/pdf
creator: asandaue
date_created: 2021-08-10T12:29:59Z
date_updated: 2021-08-10T12:29:59Z
file_id: '9876'
file_name: 2021_NatureCommunications_Raso.pdf
file_size: 4364333
relation: main_file
success: 1
file_date_updated: 2021-08-10T12:29:59Z
genbank:
- GSE178867
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-022-32785-0
scopus_import: '1'
status: public
title: A microRNA program regulates the balance between cardiomyocyte hyperplasia
and hypertrophy and stimulates cardiac regeneration
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: '9769'
abstract:
- lang: eng
text: A few years ago, flow equations were introduced as a technique for calculating
the ground-state energies of cold Bose gases with and without impurities. In this
paper, we extend this approach to compute observables other than the energy. As
an example, we calculate the densities, and phase fluctuations of one-dimensional
Bose gases with one and two impurities. For a single mobile impurity, we use flow
equations to validate the mean-field results obtained upon the Lee-Low-Pines transformation.
We show that the mean-field approximation is accurate for all values of the boson-impurity
interaction strength as long as the phase coherence length is much larger than
the healing length of the condensate. For two static impurities, we calculate
impurity-impurity interactions induced by the Bose gas. We find that leading order
perturbation theory fails when boson-impurity interactions are stronger than boson-boson
interactions. The mean-field approximation reproduces the flow equation results
for all values of the boson-impurity interaction strength as long as boson-boson
interactions are weak.
acknowledgement: We thank Matthias Heinz and Volker Karle for helpful comments on
the manuscript; Zoran Ristivojevic for useful correspondence regarding mean-field
calculations of induced impurity-impurity interactions; Fabian Grusdt for sharing
with us the data for the densities presented in Ref. [14]. This work has received
funding from the DFG Project No. 413495248 [VO 2437/1-1] (F. B., H.-W. H., A. G.
V.) and European Union’s Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 754411 (A. G. V.). M. L. acknowledges
support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).
H.-W.H. 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 programme under grant agreement No 824093. H.-W.H. was supported
by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID
279384907 - SFB 1245.
article_number: '008'
article_processing_charge: Yes
article_type: original
author:
- first_name: Fabian
full_name: Brauneis, Fabian
last_name: Brauneis
- first_name: Hans-Werner
full_name: Hammer, Hans-Werner
last_name: Hammer
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: 'Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. Impurities in a one-dimensional
Bose gas: The flow equation approach. SciPost Physics. 2021;11(1). doi:10.21468/scipostphys.11.1.008'
apa: 'Brauneis, F., Hammer, H.-W., Lemeshko, M., & Volosniev, A. (2021). Impurities
in a one-dimensional Bose gas: The flow equation approach. SciPost Physics.
SciPost. https://doi.org/10.21468/scipostphys.11.1.008'
chicago: 'Brauneis, Fabian, Hans-Werner Hammer, Mikhail Lemeshko, and Artem Volosniev.
“Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” SciPost
Physics. SciPost, 2021. https://doi.org/10.21468/scipostphys.11.1.008.'
ieee: 'F. Brauneis, H.-W. Hammer, M. Lemeshko, and A. Volosniev, “Impurities in
a one-dimensional Bose gas: The flow equation approach,” SciPost Physics,
vol. 11, no. 1. SciPost, 2021.'
ista: 'Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. 2021. Impurities in a one-dimensional
Bose gas: The flow equation approach. SciPost Physics. 11(1), 008.'
mla: 'Brauneis, Fabian, et al. “Impurities in a One-Dimensional Bose Gas: The Flow
Equation Approach.” SciPost Physics, vol. 11, no. 1, 008, SciPost, 2021,
doi:10.21468/scipostphys.11.1.008.'
short: F. Brauneis, H.-W. Hammer, M. Lemeshko, A. Volosniev, SciPost Physics 11
(2021).
date_created: 2021-08-04T15:00:55Z
date_published: 2021-07-13T00:00:00Z
date_updated: 2023-08-11T10:25:44Z
day: '13'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.21468/scipostphys.11.1.008
ec_funded: 1
external_id:
arxiv:
- '2101.10958'
isi:
- '000680039500013'
file:
- access_level: open_access
checksum: eaa847346b1a023d97bbb291779610ed
content_type: application/pdf
creator: asandaue
date_created: 2021-08-10T11:44:59Z
date_updated: 2021-08-10T11:44:59Z
file_id: '9875'
file_name: 2021_SciPostPhysics_Brauneis.pdf
file_size: 1085300
relation: main_file
success: 1
file_date_updated: 2021-08-10T11:44:59Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: SciPost Physics
publication_identifier:
eissn:
- 2542-4653
publication_status: published
publisher: SciPost
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Impurities in a one-dimensional Bose gas: The flow equation approach'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2021'
...
---
_id: '9746'
abstract:
- lang: eng
text: Evolutionary adaptation is a major source of antibiotic resistance in bacterial
pathogens. Evolution-informed therapy aims to constrain resistance by accounting
for bacterial evolvability. Sequential treatments with antibiotics that target
different bacterial processes were previously shown to limit adaptation through
genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous
sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly
lead to cross-resistance. We here challenged this assumption by determining the
evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments
involving both heterogenous and homogeneous antibiotic sets. To our surprise,
we found that fast switching between only β-lactam antibiotics resulted in increased
extinction of bacterial populations. We demonstrate that extinction is favored
by low rates of spontaneous resistance emergence and low levels of spontaneous
cross-resistance among the antibiotics in sequence. The uncovered principles may
help to guide the optimized use of available antibiotics in highly potent, evolution-informed
treatment designs.
acknowledgement: We would like to thank Leif Tueffers and João Botelho for discussions
and suggestions as well as Kira Haas and Julia Bunk for technical support. We acknowledge
financial support from the German Science Foundation (grant SCHU 1415/12-2 to HS,
and funding under Germany’s Excellence Strategy EXC 2167–390884018 as well as the
Research Training Group 2501 TransEvo to HS and SN), the Max Planck Society (IMPRS
scholarship to AB; Max-Planck fellowship to HS), and the Leibniz Science Campus
Evolutionary Medicine of the Lung (EvoLUNG, to HS and SN). This work was further
supported by the German Science Foundation Research Infrastructure NGS_CC (project
407495230) as part of the Next Generation Sequencing Competence Network (project
423957469). NGS analyses were carried out at the Competence Centre for Genomic Analysis
Kiel (CCGA Kiel).
article_number: e68876
article_processing_charge: No
article_type: original
author:
- first_name: Aditi
full_name: Batra, Aditi
last_name: Batra
- first_name: Roderich
full_name: Römhild, Roderich
id: 68E56E44-62B0-11EA-B963-444F3DDC885E
last_name: Römhild
orcid: 0000-0001-9480-5261
- first_name: Emilie
full_name: Rousseau, Emilie
last_name: Rousseau
- first_name: Sören
full_name: Franzenburg, Sören
last_name: Franzenburg
- first_name: Stefan
full_name: Niemann, Stefan
last_name: Niemann
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
citation:
ama: Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. High
potency of sequential therapy with only beta-lactam antibiotics. eLife.
2021;10. doi:10.7554/elife.68876
apa: Batra, A., Römhild, R., Rousseau, E., Franzenburg, S., Niemann, S., & Schulenburg,
H. (2021). High potency of sequential therapy with only beta-lactam antibiotics.
ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68876
chicago: Batra, Aditi, Roderich Römhild, Emilie Rousseau, Sören Franzenburg, Stefan
Niemann, and Hinrich Schulenburg. “High Potency of Sequential Therapy with Only
Beta-Lactam Antibiotics.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.68876.
ieee: A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, and H. Schulenburg,
“High potency of sequential therapy with only beta-lactam antibiotics,” eLife,
vol. 10. eLife Sciences Publications, 2021.
ista: Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. 2021.
High potency of sequential therapy with only beta-lactam antibiotics. eLife. 10,
e68876.
mla: Batra, Aditi, et al. “High Potency of Sequential Therapy with Only Beta-Lactam
Antibiotics.” ELife, vol. 10, e68876, eLife Sciences Publications, 2021,
doi:10.7554/elife.68876.
short: A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, H. Schulenburg,
ELife 10 (2021).
date_created: 2021-07-28T13:36:57Z
date_published: 2021-07-28T00:00:00Z
date_updated: 2023-08-11T10:26:29Z
day: '28'
department:
- _id: CaGu
doi: 10.7554/elife.68876
external_id:
isi:
- '000692027800001'
pmid:
- '34318749'
intvolume: ' 10'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.7554/eLife.68876
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: High potency of sequential therapy with only beta-lactam antibiotics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '9911'
abstract:
- lang: eng
text: A modern day light microscope has evolved from a tool devoted to making primarily
empirical observations to what is now a sophisticated , quantitative device that
is an integral part of both physical and life science research. Nowadays, microscopes
are found in nearly every experimental laboratory. However, despite their prevalent
use in capturing and quantifying scientific phenomena, neither a thorough understanding
of the principles underlying quantitative imaging techniques nor appropriate knowledge
of how to calibrate, operate and maintain microscopes can be taken for granted.
This is clearly demonstrated by the well-documented and widespread difficulties
that are routinely encountered in evaluating acquired data and reproducing scientific
experiments. Indeed, studies have shown that more than 70% of researchers have
tried and failed to repeat another scientist's experiments, while more than half
have even failed to reproduce their own experiments. One factor behind the reproducibility
crisis of experiments published in scientific journals is the frequent underreporting
of imaging methods caused by a lack of awareness and/or a lack of knowledge of
the applied technique. Whereas quality control procedures for some methods used
in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry,
have been introduced (e.g. ENCODE), this issue has not been tackled for optical
microscopy instrumentation and images. Although many calibration standards and
protocols have been published, there is a lack of awareness and agreement on common
standards and guidelines for quality assessment and reproducibility. In April
2020, the QUality Assessment and REProducibility for instruments and images in
Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises
imaging scientists from academia and industry who share a common interest in achieving
a better understanding of the performance and limitations of microscopes and improved
quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi
initiative is to establish a set of common QC standards, guidelines, metadata
models and tools, including detailed protocols, with the ultimate aim of improving
reproducible advances in scientific research. This White Paper (1) summarizes
the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi
initiative; (2) identifies the urgent need to address these obstacles in a grassroots
manner, through a community of stakeholders including, researchers, imaging scientists,
bioimage analysts, bioimage informatics developers, corporate partners, funding
agencies, standards organizations, scientific publishers and observers of such;
(3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes
future steps that can be taken to improve the dissemination and acceptance of
the proposed guidelines to manage QC. To summarize, the principal goal of the
QUAREP-LiMi initiative is to improve the overall quality and reproducibility of
light microscope image data by introducing broadly accepted standard practices
and accurately captured image data metrics.
acknowledgement: We thank https://www.somersault1824.com/somersault18:24 BV (Leuven,
Belgium) for help with Figure 1. E. C.-S. was supported by the project PPBI-POCI-01-0145-FEDER-022122,
in the scope of Fundação para a Ciência e Tecnologia, Portugal (FCT) National Roadmap
of Research Infrastructures. R.N. was funded by the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation) Grant number Ni 451/9-1 - MIAP-Freiburg.
article_processing_charge: Yes
article_type: original
author:
- first_name: Glyn
full_name: Nelson, Glyn
last_name: Nelson
- first_name: Ulrike
full_name: Boehm, Ulrike
last_name: Boehm
- first_name: Steve
full_name: Bagley, Steve
last_name: Bagley
- first_name: Peter
full_name: Bajcsy, Peter
last_name: Bajcsy
- first_name: Johanna
full_name: Bischof, Johanna
last_name: Bischof
- first_name: Claire M.
full_name: Brown, Claire M.
last_name: Brown
- first_name: Aurélien
full_name: Dauphin, Aurélien
last_name: Dauphin
- first_name: Ian M.
full_name: Dobbie, Ian M.
last_name: Dobbie
- first_name: John E.
full_name: Eriksson, John E.
last_name: Eriksson
- first_name: Orestis
full_name: Faklaris, Orestis
last_name: Faklaris
- first_name: Julia
full_name: Fernandez-Rodriguez, Julia
last_name: Fernandez-Rodriguez
- first_name: Alexia
full_name: Ferrand, Alexia
last_name: Ferrand
- first_name: Laurent
full_name: Gelman, Laurent
last_name: Gelman
- first_name: Ali
full_name: Gheisari, Ali
last_name: Gheisari
- first_name: Hella
full_name: Hartmann, Hella
last_name: Hartmann
- first_name: Christian
full_name: Kukat, Christian
last_name: Kukat
- first_name: Alex
full_name: Laude, Alex
last_name: Laude
- first_name: Miso
full_name: Mitkovski, Miso
last_name: Mitkovski
- first_name: Sebastian
full_name: Munck, Sebastian
last_name: Munck
- first_name: Alison J.
full_name: North, Alison J.
last_name: North
- first_name: Tobias M.
full_name: Rasse, Tobias M.
last_name: Rasse
- first_name: Ute
full_name: Resch-Genger, Ute
last_name: Resch-Genger
- first_name: Lucas C.
full_name: Schuetz, Lucas C.
last_name: Schuetz
- first_name: Arne
full_name: Seitz, Arne
last_name: Seitz
- first_name: Caterina
full_name: Strambio-De-Castillia, Caterina
last_name: Strambio-De-Castillia
- first_name: Jason R.
full_name: Swedlow, Jason R.
last_name: Swedlow
- first_name: Ioannis
full_name: Alexopoulos, Ioannis
last_name: Alexopoulos
- first_name: Karin
full_name: Aumayr, Karin
last_name: Aumayr
- first_name: Sergiy
full_name: Avilov, Sergiy
last_name: Avilov
- first_name: Gert Jan
full_name: Bakker, Gert Jan
last_name: Bakker
- first_name: Rodrigo R.
full_name: Bammann, Rodrigo R.
last_name: Bammann
- first_name: Andrea
full_name: Bassi, Andrea
last_name: Bassi
- first_name: Hannes
full_name: Beckert, Hannes
last_name: Beckert
- first_name: Sebastian
full_name: Beer, Sebastian
last_name: Beer
- first_name: Yury
full_name: Belyaev, Yury
last_name: Belyaev
- first_name: Jakob
full_name: Bierwagen, Jakob
last_name: Bierwagen
- first_name: Konstantin A.
full_name: Birngruber, Konstantin A.
last_name: Birngruber
- first_name: Manel
full_name: Bosch, Manel
last_name: Bosch
- first_name: Juergen
full_name: Breitlow, Juergen
last_name: Breitlow
- first_name: Lisa A.
full_name: Cameron, Lisa A.
last_name: Cameron
- first_name: Joe
full_name: Chalfoun, Joe
last_name: Chalfoun
- first_name: James J.
full_name: Chambers, James J.
last_name: Chambers
- first_name: Chieh Li
full_name: Chen, Chieh Li
last_name: Chen
- first_name: Eduardo
full_name: Conde-Sousa, Eduardo
last_name: Conde-Sousa
- first_name: Alexander D.
full_name: Corbett, Alexander D.
last_name: Corbett
- first_name: Fabrice P.
full_name: Cordelieres, Fabrice P.
last_name: Cordelieres
- first_name: Elaine Del
full_name: Nery, Elaine Del
last_name: Nery
- first_name: Ralf
full_name: Dietzel, Ralf
last_name: Dietzel
- first_name: Frank
full_name: Eismann, Frank
last_name: Eismann
- first_name: Elnaz
full_name: Fazeli, Elnaz
last_name: Fazeli
- first_name: Andreas
full_name: Felscher, Andreas
last_name: Felscher
- first_name: Hans
full_name: Fried, Hans
last_name: Fried
- first_name: Nathalie
full_name: Gaudreault, Nathalie
last_name: Gaudreault
- first_name: Wah Ing
full_name: Goh, Wah Ing
last_name: Goh
- first_name: Thomas
full_name: Guilbert, Thomas
last_name: Guilbert
- first_name: Roland
full_name: Hadleigh, Roland
last_name: Hadleigh
- first_name: Peter
full_name: Hemmerich, Peter
last_name: Hemmerich
- first_name: Gerhard A.
full_name: Holst, Gerhard A.
last_name: Holst
- first_name: Michelle S.
full_name: Itano, Michelle S.
last_name: Itano
- first_name: Claudia B.
full_name: Jaffe, Claudia B.
last_name: Jaffe
- first_name: Helena K.
full_name: Jambor, Helena K.
last_name: Jambor
- first_name: Stuart C.
full_name: Jarvis, Stuart C.
last_name: Jarvis
- first_name: Antje
full_name: Keppler, Antje
last_name: Keppler
- first_name: David
full_name: Kirchenbuechler, David
last_name: Kirchenbuechler
- first_name: Marcel
full_name: Kirchner, Marcel
last_name: Kirchner
- first_name: Norio
full_name: Kobayashi, Norio
last_name: Kobayashi
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Susanne
full_name: Kunis, Susanne
last_name: Kunis
- first_name: Judith
full_name: Lacoste, Judith
last_name: Lacoste
- first_name: Marco
full_name: Marcello, Marco
last_name: Marcello
- first_name: Gabriel G.
full_name: Martins, Gabriel G.
last_name: Martins
- first_name: Daniel J.
full_name: Metcalf, Daniel J.
last_name: Metcalf
- first_name: Claire A.
full_name: Mitchell, Claire A.
last_name: Mitchell
- first_name: Joshua
full_name: Moore, Joshua
last_name: Moore
- first_name: Tobias
full_name: Mueller, Tobias
last_name: Mueller
- first_name: Michael S.
full_name: Nelson, Michael S.
last_name: Nelson
- first_name: Stephen
full_name: Ogg, Stephen
last_name: Ogg
- first_name: Shuichi
full_name: Onami, Shuichi
last_name: Onami
- first_name: Alexandra L.
full_name: Palmer, Alexandra L.
last_name: Palmer
- first_name: Perrine
full_name: Paul-Gilloteaux, Perrine
last_name: Paul-Gilloteaux
- first_name: Jaime A.
full_name: Pimentel, Jaime A.
last_name: Pimentel
- first_name: Laure
full_name: Plantard, Laure
last_name: Plantard
- first_name: Santosh
full_name: Podder, Santosh
last_name: Podder
- first_name: Elton
full_name: Rexhepaj, Elton
last_name: Rexhepaj
- first_name: Arnaud
full_name: Royon, Arnaud
last_name: Royon
- first_name: Markku A.
full_name: Saari, Markku A.
last_name: Saari
- first_name: Damien
full_name: Schapman, Damien
last_name: Schapman
- first_name: Vincent
full_name: Schoonderwoert, Vincent
last_name: Schoonderwoert
- first_name: Britta
full_name: Schroth-Diez, Britta
last_name: Schroth-Diez
- first_name: Stanley
full_name: Schwartz, Stanley
last_name: Schwartz
- first_name: Michael
full_name: Shaw, Michael
last_name: Shaw
- first_name: Martin
full_name: Spitaler, Martin
last_name: Spitaler
- first_name: Martin T.
full_name: Stoeckl, Martin T.
last_name: Stoeckl
- first_name: Damir
full_name: Sudar, Damir
last_name: Sudar
- first_name: Jeremie
full_name: Teillon, Jeremie
last_name: Teillon
- first_name: Stefan
full_name: Terjung, Stefan
last_name: Terjung
- first_name: Roland
full_name: Thuenauer, Roland
last_name: Thuenauer
- first_name: Christian D.
full_name: Wilms, Christian D.
last_name: Wilms
- first_name: Graham D.
full_name: Wright, Graham D.
last_name: Wright
- first_name: Roland
full_name: Nitschke, Roland
last_name: Nitschke
citation:
ama: 'Nelson G, Boehm U, Bagley S, et al. QUAREP-LiMi: A community-driven initiative
to establish guidelines for quality assessment and reproducibility for instruments
and images in light microscopy. Journal of Microscopy. 2021;284(1):56-73.
doi:10.1111/jmi.13041'
apa: 'Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M.,
… Nitschke, R. (2021). QUAREP-LiMi: A community-driven initiative to establish
guidelines for quality assessment and reproducibility for instruments and images
in light microscopy. Journal of Microscopy. Wiley. https://doi.org/10.1111/jmi.13041'
chicago: 'Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof,
Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative
to Establish Guidelines for Quality Assessment and Reproducibility for Instruments
and Images in Light Microscopy.” Journal of Microscopy. Wiley, 2021. https://doi.org/10.1111/jmi.13041.'
ieee: 'G. Nelson et al., “QUAREP-LiMi: A community-driven initiative to establish
guidelines for quality assessment and reproducibility for instruments and images
in light microscopy,” Journal of Microscopy, vol. 284, no. 1. Wiley, pp.
56–73, 2021.'
ista: 'Nelson G et al. 2021. QUAREP-LiMi: A community-driven initiative to establish
guidelines for quality assessment and reproducibility for instruments and images
in light microscopy. Journal of Microscopy. 284(1), 56–73.'
mla: 'Nelson, Glyn, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish
Guidelines for Quality Assessment and Reproducibility for Instruments and Images
in Light Microscopy.” Journal of Microscopy, vol. 284, no. 1, Wiley, 2021,
pp. 56–73, doi:10.1111/jmi.13041.'
short: G. Nelson, U. Boehm, S. Bagley, P. Bajcsy, J. Bischof, C.M. Brown, A. Dauphin,
I.M. Dobbie, J.E. Eriksson, O. Faklaris, J. Fernandez-Rodriguez, A. Ferrand, L.
Gelman, A. Gheisari, H. Hartmann, C. Kukat, A. Laude, M. Mitkovski, S. Munck,
A.J. North, T.M. Rasse, U. Resch-Genger, L.C. Schuetz, A. Seitz, C. Strambio-De-Castillia,
J.R. Swedlow, I. Alexopoulos, K. Aumayr, S. Avilov, G.J. Bakker, R.R. Bammann,
A. Bassi, H. Beckert, S. Beer, Y. Belyaev, J. Bierwagen, K.A. Birngruber, M. Bosch,
J. Breitlow, L.A. Cameron, J. Chalfoun, J.J. Chambers, C.L. Chen, E. Conde-Sousa,
A.D. Corbett, F.P. Cordelieres, E.D. Nery, R. Dietzel, F. Eismann, E. Fazeli,
A. Felscher, H. Fried, N. Gaudreault, W.I. Goh, T. Guilbert, R. Hadleigh, P. Hemmerich,
G.A. Holst, M.S. Itano, C.B. Jaffe, H.K. Jambor, S.C. Jarvis, A. Keppler, D. Kirchenbuechler,
M. Kirchner, N. Kobayashi, G. Krens, S. Kunis, J. Lacoste, M. Marcello, G.G. Martins,
D.J. Metcalf, C.A. Mitchell, J. Moore, T. Mueller, M.S. Nelson, S. Ogg, S. Onami,
A.L. Palmer, P. Paul-Gilloteaux, J.A. Pimentel, L. Plantard, S. Podder, E. Rexhepaj,
A. Royon, M.A. Saari, D. Schapman, V. Schoonderwoert, B. Schroth-Diez, S. Schwartz,
M. Shaw, M. Spitaler, M.T. Stoeckl, D. Sudar, J. Teillon, S. Terjung, R. Thuenauer,
C.D. Wilms, G.D. Wright, R. Nitschke, Journal of Microscopy 284 (2021) 56–73.
date_created: 2021-08-15T22:01:29Z
date_published: 2021-08-11T00:00:00Z
date_updated: 2023-08-11T10:30:40Z
day: '11'
department:
- _id: Bio
doi: 10.1111/jmi.13041
external_id:
isi:
- '000683702700001'
intvolume: ' 284'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jmi.13041
month: '08'
oa: 1
oa_version: Published Version
page: 56-73
publication: Journal of Microscopy
publication_identifier:
eissn:
- 1365-2818
issn:
- 0022-2720
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'QUAREP-LiMi: A community-driven initiative to establish guidelines for quality
assessment and reproducibility for instruments and images in light microscopy'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 284
year: '2021'
...
---
_id: '9906'
abstract:
- lang: eng
text: Endometriosis is a common gynecological disorder characterized by ectopic
growth of endometrium outside the uterus and is associated with chronic pain and
infertility. We investigated the role of the long intergenic noncoding RNA 01133
(LINC01133) in endometriosis, an lncRNA that has been implicated in several types
of cancer. We found that LINC01133 is upregulated in ectopic endometriotic lesions.
As expression appeared higher in the epithelial endometrial layer, we performed
a siRNA knockdown of LINC01133 in an endometriosis epithelial cell line. Phenotypic
assays indicated that LINC01133 may promote proliferation and suppress cellular
migration, and affect the cytoskeleton and morphology of the cells. Gene ontology
analysis of differentially expressed genes indicated that cell proliferation and
migration pathways were affected in line with the observed phenotype. We validated
upregulation of p21 and downregulation of Cyclin A at the protein level, which
together with the quantification of the DNA content using fluorescence-activated
cell sorting (FACS) analysis indicated that the observed effects on cellular proliferation
may be due to changes in cell cycle. Further, we found testis-specific protein
kinase 1 (TESK1) kinase upregulation corresponding with phosphorylation and inactivation
of actin severing protein Cofilin, which could explain changes in the cytoskeleton
and cellular migration. These results indicate that endometriosis is associated
with LINC01133 upregulation, which may affect pathogenesis via the cellular proliferation
and migration pathways.
acknowledgement: "Open access funding provided by Medical University of Vienna. The
authors would like to thank all the participants and health professionals involved
in the present study. We want to thank our technical assistants Barbara Widmar and
Matthias Witzmann-Stern for their diligent work and constant assistance. We would
like to thank Simon Hippenmeyer for access to\r\nbioinformatic infrastructure and
resources."
article_number: '8385'
article_processing_charge: Yes
article_type: original
author:
- first_name: Iveta
full_name: Yotova, Iveta
last_name: Yotova
- first_name: Quanah J.
full_name: Hudson, Quanah J.
last_name: Hudson
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Katharina
full_name: Proestling, Katharina
last_name: Proestling
- first_name: Isabella
full_name: Haslinger, Isabella
last_name: Haslinger
- first_name: Lorenz
full_name: Kuessel, Lorenz
last_name: Kuessel
- first_name: Alexandra
full_name: Perricos, Alexandra
last_name: Perricos
- first_name: Heinrich
full_name: Husslein, Heinrich
last_name: Husslein
- first_name: René
full_name: Wenzl, René
last_name: Wenzl
citation:
ama: Yotova I, Hudson QJ, Pauler F, et al. LINC01133 inhibits invasion and promotes
proliferation in an endometriosis epithelial cell line. International Journal
of Molecular Sciences. 2021;22(16). doi:10.3390/ijms22168385
apa: Yotova, I., Hudson, Q. J., Pauler, F., Proestling, K., Haslinger, I., Kuessel,
L., … Wenzl, R. (2021). LINC01133 inhibits invasion and promotes proliferation
in an endometriosis epithelial cell line. International Journal of Molecular
Sciences. MDPI. https://doi.org/10.3390/ijms22168385
chicago: Yotova, Iveta, Quanah J. Hudson, Florian Pauler, Katharina Proestling,
Isabella Haslinger, Lorenz Kuessel, Alexandra Perricos, Heinrich Husslein, and
René Wenzl. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis
Epithelial Cell Line.” International Journal of Molecular Sciences. MDPI,
2021. https://doi.org/10.3390/ijms22168385.
ieee: I. Yotova et al., “LINC01133 inhibits invasion and promotes proliferation
in an endometriosis epithelial cell line,” International Journal of Molecular
Sciences, vol. 22, no. 16. MDPI, 2021.
ista: Yotova I, Hudson QJ, Pauler F, Proestling K, Haslinger I, Kuessel L, Perricos
A, Husslein H, Wenzl R. 2021. LINC01133 inhibits invasion and promotes proliferation
in an endometriosis epithelial cell line. International Journal of Molecular Sciences.
22(16), 8385.
mla: Yotova, Iveta, et al. “LINC01133 Inhibits Invasion and Promotes Proliferation
in an Endometriosis Epithelial Cell Line.” International Journal of Molecular
Sciences, vol. 22, no. 16, 8385, MDPI, 2021, doi:10.3390/ijms22168385.
short: I. Yotova, Q.J. Hudson, F. Pauler, K. Proestling, I. Haslinger, L. Kuessel,
A. Perricos, H. Husslein, R. Wenzl, International Journal of Molecular Sciences
22 (2021).
date_created: 2021-08-15T22:01:27Z
date_published: 2021-08-04T00:00:00Z
date_updated: 2023-08-11T10:34:13Z
day: '04'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.3390/ijms22168385
external_id:
isi:
- '000689147400001'
file:
- access_level: open_access
checksum: be7f0042607ca60549cb27513c19c6af
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:29:17Z
date_updated: 2021-08-16T09:29:17Z
file_id: '9922'
file_name: 2021_InternationalJournalOfMolecularSciences_Yotova.pdf
file_size: 2646018
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:29:17Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '16'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- '14220067'
issn:
- '16616596'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: LINC01133 inhibits invasion and promotes proliferation in an endometriosis
epithelial cell line
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 22
year: '2021'
...
---
_id: '9910'
abstract:
- lang: eng
text: Adult height inspired the first biometrical and quantitative genetic studies
and is a test-case trait for understanding heritability. The studies of height
led to formulation of the classical polygenic model, that has a profound influence
on the way we view and analyse complex traits. An essential part of the classical
model is an assumption of additivity of effects and normality of the distribution
of the residuals. However, it may be expected that the normal approximation will
become insufficient in bigger studies. Here, we demonstrate that when the height
of hundreds of thousands of individuals is analysed, the model complexity needs
to be increased to include non-additive interactions between sex, environment
and genes. Alternatively, the use of log-normal approximation allowed us to still
use the additive effects model. These findings are important for future genetic
and methodologic studies that make use of adult height as an exemplar trait.
acknowledgement: "We are grateful to Marianna Bevova and Pavel Borodin for fruitful
discussion and help with conceptualising our findings and to Lennart C. Karssen
for help with handling the UK Biobank data.\r\n\r\nFunding\r\nThis research has
been conducted using the UK Biobank Resource (project # 41601, “Non-additive effects
in control of complex human traits”). The work of SAS, IAK, and TIS were supported
by Russian Ministry of Science and Education under the 5–100 Excellence Programme.
The work of YSA and TIA was supported by the Ministry of Education and Science of
the RF via the Institute of Cytology and Genetics SB RAS (project number 0324-2019-0040-C-01/AAAA-A17-117092070032-4).
FAK is supported by the ERC Consolidator Grant (ChrFL: 771209)."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Sergei A.
full_name: Slavskii, Sergei A.
last_name: Slavskii
- first_name: Ivan A.
full_name: Kuznetsov, Ivan A.
last_name: Kuznetsov
- first_name: Tatiana I.
full_name: Shashkova, Tatiana I.
last_name: Shashkova
- first_name: Georgii A.
full_name: Bazykin, Georgii A.
last_name: Bazykin
- first_name: Tatiana I.
full_name: Axenovich, Tatiana I.
last_name: Axenovich
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Yurii S.
full_name: Aulchenko, Yurii S.
last_name: Aulchenko
citation:
ama: Slavskii SA, Kuznetsov IA, Shashkova TI, et al. The limits of normal approximation
for adult height. European Journal of Human Genetics. 2021;29(7):1082-1091.
doi:10.1038/s41431-021-00836-7
apa: Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich,
T. I., Kondrashov, F., & Aulchenko, Y. S. (2021). The limits of normal approximation
for adult height. European Journal of Human Genetics. Springer Nature.
https://doi.org/10.1038/s41431-021-00836-7
chicago: Slavskii, Sergei A., Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A.
Bazykin, Tatiana I. Axenovich, Fyodor Kondrashov, and Yurii S. Aulchenko. “The
Limits of Normal Approximation for Adult Height.” European Journal of Human
Genetics. Springer Nature, 2021. https://doi.org/10.1038/s41431-021-00836-7.
ieee: S. A. Slavskii et al., “The limits of normal approximation for adult
height,” European Journal of Human Genetics, vol. 29, no. 7. Springer Nature,
pp. 1082–1091, 2021.
ista: Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov
F, Aulchenko YS. 2021. The limits of normal approximation for adult height. European
Journal of Human Genetics. 29(7), 1082–1091.
mla: Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.”
European Journal of Human Genetics, vol. 29, no. 7, Springer Nature, 2021,
pp. 1082–91, doi:10.1038/s41431-021-00836-7.
short: S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich,
F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091.
date_created: 2021-08-15T22:01:28Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-11T10:33:42Z
day: '01'
ddc:
- '576'
department:
- _id: FyKo
doi: 10.1038/s41431-021-00836-7
ec_funded: 1
external_id:
isi:
- '000625853200001'
pmid:
- '33664501'
file:
- access_level: open_access
checksum: a676d76f91b0dbe0504c63e469129c2a
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:14:36Z
date_updated: 2021-08-16T09:14:36Z
file_id: '9921'
file_name: 2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf
file_size: 1079395
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:14:36Z
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1082-1091
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: European Journal of Human Genetics
publication_identifier:
eissn:
- '14765438'
issn:
- '10184813'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The limits of normal approximation for adult height
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: 29
year: '2021'
...
---
_id: '9912'
abstract:
- lang: eng
text: "In the customary random matrix model for transport in quantum dots with M
internal degrees of freedom coupled to a chaotic environment via \U0001D441≪\U0001D440
channels, the density \U0001D70C of transmission eigenvalues is computed from
a specific invariant ensemble for which explicit formula for the joint probability
density of all eigenvalues is available. We revisit this problem in the large
N regime allowing for (i) arbitrary ratio \U0001D719:=\U0001D441/\U0001D440≤1;
and (ii) general distributions for the matrix elements of the Hamiltonian of the
quantum dot. In the limit \U0001D719→0, we recover the formula for the density
\U0001D70C that Beenakker (Rev Mod Phys 69:731–808, 1997) has derived for a special
matrix ensemble. We also prove that the inverse square root singularity of the
density at zero and full transmission in Beenakker’s formula persists for any
\U0001D719<1 but in the borderline case \U0001D719=1 an anomalous \U0001D706−2/3
singularity arises at zero. To access this level of generality, we develop the
theory of global and local laws on the spectral density of a large class of noncommutative
rational expressions in large random matrices with i.i.d. entries."
acknowledgement: The authors are very grateful to Yan Fyodorov for discussions on
the physical background and for providing references, and to the anonymous referee
for numerous valuable remarks.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
- first_name: Yuriy
full_name: Nemish, Yuriy
id: 4D902E6A-F248-11E8-B48F-1D18A9856A87
last_name: Nemish
orcid: 0000-0002-7327-856X
citation:
ama: Erdös L, Krüger TH, Nemish Y. Scattering in quantum dots via noncommutative
rational functions. Annales Henri Poincaré . 2021;22:4205–4269. doi:10.1007/s00023-021-01085-6
apa: Erdös, L., Krüger, T. H., & Nemish, Y. (2021). Scattering in quantum dots
via noncommutative rational functions. Annales Henri Poincaré . Springer
Nature. https://doi.org/10.1007/s00023-021-01085-6
chicago: Erdös, László, Torben H Krüger, and Yuriy Nemish. “Scattering in Quantum
Dots via Noncommutative Rational Functions.” Annales Henri Poincaré . Springer
Nature, 2021. https://doi.org/10.1007/s00023-021-01085-6.
ieee: L. Erdös, T. H. Krüger, and Y. Nemish, “Scattering in quantum dots via noncommutative
rational functions,” Annales Henri Poincaré , vol. 22. Springer Nature,
pp. 4205–4269, 2021.
ista: Erdös L, Krüger TH, Nemish Y. 2021. Scattering in quantum dots via noncommutative
rational functions. Annales Henri Poincaré . 22, 4205–4269.
mla: Erdös, László, et al. “Scattering in Quantum Dots via Noncommutative Rational
Functions.” Annales Henri Poincaré , vol. 22, Springer Nature, 2021, pp.
4205–4269, doi:10.1007/s00023-021-01085-6.
short: L. Erdös, T.H. Krüger, Y. Nemish, Annales Henri Poincaré 22 (2021) 4205–4269.
date_created: 2021-08-15T22:01:29Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2023-08-11T10:31:48Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00023-021-01085-6
ec_funded: 1
external_id:
arxiv:
- '1911.05112'
isi:
- '000681531500001'
file:
- access_level: open_access
checksum: 8d6bac0e2b0a28539608b0538a8e3b38
content_type: application/pdf
creator: dernst
date_created: 2022-05-12T12:50:27Z
date_updated: 2022-05-12T12:50:27Z
file_id: '11365'
file_name: 2021_AnnHenriPoincare_Erdoes.pdf
file_size: 1162454
relation: main_file
success: 1
file_date_updated: 2022-05-12T12:50:27Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 4205–4269
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: 'Annales Henri Poincaré '
publication_identifier:
eissn:
- 1424-0661
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scattering in quantum dots via noncommutative rational functions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 22
year: '2021'
...
---
_id: '9891'
abstract:
- lang: eng
text: 'Extending on ideas of Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127
(2019)], we present a modified “floating crystal” trial state for jellium (also
known as the classical homogeneous electron gas) with density equal to a characteristic
function. This allows us to show that three definitions of the jellium energy
coincide in dimensions d ≥ 2, thus extending the result of Cotar and Petrache
[“Equality of the Jellium and uniform electron gas next-order asymptotic terms
for Coulomb and Riesz potentials,” arXiv: 1707.07664 (2019)] and Lewin, Lieb,
and Seiringer [Phys. Rev. B 100, 035127 (2019)] that the three definitions coincide
in dimension d ≥ 3. We show that the jellium energy is also equivalent to a “renormalized
energy” studied in a series of papers by Serfaty and others, and thus, by the
work of Bétermin and Sandier [Constr. Approximation 47, 39–74 (2018)], we relate
the jellium energy to the order n term in the logarithmic energy of n points on
the unit 2-sphere. We improve upon known lower bounds for this renormalized energy.
Additionally, we derive formulas for the jellium energy of periodic configurations.'
acknowledgement: The author would like to thank Robert Seiringer for guidance and
many helpful comments on this project. The author would also like to thank Mathieu
Lewin for his comments on the manuscript and Lorenzo Portinale for providing his
lecture notes for the course “Mathematics of quantum many-body systems” in spring
2020, taught by Robert Seiringer. The Proof of Theorem III.1 is inspired by these
lecture notes.
article_number: '083305'
article_processing_charge: No
article_type: original
author:
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
citation:
ama: Lauritsen AB. Floating Wigner crystal and periodic jellium configurations.
Journal of Mathematical Physics. 2021;62(8). doi:10.1063/5.0053494
apa: Lauritsen, A. B. (2021). Floating Wigner crystal and periodic jellium configurations.
Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0053494
chicago: Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium
Configurations.” Journal of Mathematical Physics. AIP Publishing, 2021.
https://doi.org/10.1063/5.0053494.
ieee: A. B. Lauritsen, “Floating Wigner crystal and periodic jellium configurations,”
Journal of Mathematical Physics, vol. 62, no. 8. AIP Publishing, 2021.
ista: Lauritsen AB. 2021. Floating Wigner crystal and periodic jellium configurations.
Journal of Mathematical Physics. 62(8), 083305.
mla: Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium
Configurations.” Journal of Mathematical Physics, vol. 62, no. 8, 083305,
AIP Publishing, 2021, doi:10.1063/5.0053494.
short: A.B. Lauritsen, Journal of Mathematical Physics 62 (2021).
date_created: 2021-08-12T07:08:36Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-11T10:29:48Z
day: '01'
ddc:
- '530'
department:
- _id: GradSch
- _id: RoSe
doi: 10.1063/5.0053494
external_id:
arxiv:
- '2103.07975'
isi:
- '000683960800003'
file:
- access_level: open_access
checksum: d035be2b894c4d50d90ac5ce252e27cd
content_type: application/pdf
creator: cziletti
date_created: 2021-10-27T12:57:06Z
date_updated: 2021-10-27T12:57:06Z
file_id: '10188'
file_name: 2021_JMathPhy_Lauritsen.pdf
file_size: 4352640
relation: main_file
success: 1
file_date_updated: 2021-10-27T12:57:06Z
has_accepted_license: '1'
intvolume: ' 62'
isi: 1
issue: '8'
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Journal of Mathematical Physics
publication_identifier:
eissn:
- 1089-7658
issn:
- 0022-2488
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Floating Wigner crystal and periodic jellium configurations
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: 62
year: '2021'
...
---
_id: '9909'
abstract:
- lang: eng
text: Roots are composed of different root types and, in the dicotyledonous Arabidopsis,
typically consist of a primary root that branches into lateral roots. Adventitious
roots emerge from non-root tissue and are formed upon wounding or other types
of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis
hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously
applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was
less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a
more potent inhibitor at concentrations above 1 µM, suggesting that it was more
selective in triggering a root inhibition response. Analysis of a series of phosphonamide
and phosphonate pyrabactin analogs suggested that adventitious root formation
and lateral root branching are differentially regulated by ABA signaling. ABA
biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and
point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition.
acknowledgement: We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis
mutants and ABA signaling mutants.
article_number: '1141'
article_processing_charge: Yes
article_type: original
author:
- first_name: Yinwei
full_name: Zeng, Yinwei
last_name: Zeng
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Hoang Khai
full_name: Trinh, Hoang Khai
last_name: Trinh
- first_name: Thomas
full_name: Heugebaert, Thomas
last_name: Heugebaert
- first_name: Christian V.
full_name: Stevens, Christian V.
last_name: Stevens
- first_name: Irene
full_name: Garcia-Maquilon, Irene
last_name: Garcia-Maquilon
- first_name: Pedro L.
full_name: Rodriguez, Pedro L.
last_name: Rodriguez
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Danny
full_name: Geelen, Danny
last_name: Geelen
citation:
ama: Zeng Y, Verstraeten I, Trinh HK, et al. Arabidopsis hypocotyl adventitious
root formation is suppressed by ABA signaling. Genes. 2021;12(8). doi:10.3390/genes12081141
apa: Zeng, Y., Verstraeten, I., Trinh, H. K., Heugebaert, T., Stevens, C. V., Garcia-Maquilon,
I., … Geelen, D. (2021). Arabidopsis hypocotyl adventitious root formation is
suppressed by ABA signaling. Genes. MDPI. https://doi.org/10.3390/genes12081141
chicago: Zeng, Yinwei, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian
V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste, and Danny
Geelen. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA
Signaling.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12081141.
ieee: Y. Zeng et al., “Arabidopsis hypocotyl adventitious root formation
is suppressed by ABA signaling,” Genes, vol. 12, no. 8. MDPI, 2021.
ista: Zeng Y, Verstraeten I, Trinh HK, Heugebaert T, Stevens CV, Garcia-Maquilon
I, Rodriguez PL, Vanneste S, Geelen D. 2021. Arabidopsis hypocotyl adventitious
root formation is suppressed by ABA signaling. Genes. 12(8), 1141.
mla: Zeng, Yinwei, et al. “Arabidopsis Hypocotyl Adventitious Root Formation Is
Suppressed by ABA Signaling.” Genes, vol. 12, no. 8, 1141, MDPI, 2021,
doi:10.3390/genes12081141.
short: Y. Zeng, I. Verstraeten, H.K. Trinh, T. Heugebaert, C.V. Stevens, I. Garcia-Maquilon,
P.L. Rodriguez, S. Vanneste, D. Geelen, Genes 12 (2021).
date_created: 2021-08-15T22:01:28Z
date_published: 2021-07-27T00:00:00Z
date_updated: 2023-08-11T10:32:21Z
day: '27'
ddc:
- '580'
- '570'
department:
- _id: JiFr
doi: 10.3390/genes12081141
external_id:
isi:
- '000690558000001'
file:
- access_level: open_access
checksum: 3d99535618cf9a5b14d264408fa52e97
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:02:40Z
date_updated: 2021-08-16T09:02:40Z
file_id: '9919'
file_name: 2021_Genes_Zeng.pdf
file_size: 1340305
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:02:40Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '8'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Genes
publication_identifier:
eissn:
- '20734425'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling
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: '9907'
abstract:
- lang: eng
text: 'DivIVA is a protein initially identified as a spatial regulator of cell division
in the model organism Bacillus subtilis, but its homologues are present in many
other Gram-positive bacteria, including Clostridia species. Besides its role as
topological regulator of the Min system during bacterial cell division, DivIVA
is involved in chromosome segregation during sporulation, genetic competence,
and cell wall synthesis. DivIVA localizes to regions of high membrane curvature,
such as the cell poles and cell division site, where it recruits distinct binding
partners. Previously, it was suggested that negative curvature sensing is the
main mechanism by which DivIVA binds to these specific regions. Here, we show
that Clostridioides difficile DivIVA binds preferably to membranes containing
negatively charged phospholipids, especially cardiolipin. Strikingly, we observed
that upon binding, DivIVA modifies the lipid distribution and induces changes
to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA
might play a more complex and so far unknown active role during the formation
of the cell division septal membrane. '
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "We thank Daniela Krajˇcíkova, Katarína Muchová, Zuzana Chromíkova
and other members of Barák’s laboratory for useful discussions, suggestions and
help. Special thanks also to Emília Chovancová for technical support. We are grateful
to Juraj Labaj for drawing the model and for help with graphics. Many thanks to
all members of Loose’s laboratory: Maria del Mar\r\nLópez, Paulo Caldas, Philipp
Radler, and other members of the Loose’s laboratory for sharing their knowledge
of SLB preparation and TIRF experiment chambers, for sharing coverslips and for
help with the TIRF microscope and data analysis. We also thank the members of the
Dept. of Biochemistry of Biomembranes at the Institute of Animal Biochemistry and
Genetics, CBs SAS for their help with preparing the lipid mixtures. We thank J.
Bauer for critically reading the manuscript."
article_number: '8350'
article_processing_charge: Yes
article_type: original
author:
- first_name: Naďa
full_name: Labajová, Naďa
last_name: Labajová
- first_name: Natalia S.
full_name: Baranova, Natalia S.
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Miroslav
full_name: Jurásek, Miroslav
last_name: Jurásek
- first_name: Robert
full_name: Vácha, Robert
last_name: Vácha
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Imrich
full_name: Barák, Imrich
last_name: Barák
citation:
ama: Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. Cardiolipin-containing
lipid membranes attract the bacterial cell division protein diviva. International
Journal of Molecular Sciences. 2021;22(15). doi:10.3390/ijms22158350
apa: Labajová, N., Baranova, N. S., Jurásek, M., Vácha, R., Loose, M., & Barák,
I. (2021). Cardiolipin-containing lipid membranes attract the bacterial cell division
protein diviva. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22158350
chicago: Labajová, Naďa, Natalia S. Baranova, Miroslav Jurásek, Robert Vácha, Martin
Loose, and Imrich Barák. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial
Cell Division Protein Diviva.” International Journal of Molecular Sciences.
MDPI, 2021. https://doi.org/10.3390/ijms22158350.
ieee: N. Labajová, N. S. Baranova, M. Jurásek, R. Vácha, M. Loose, and I. Barák,
“Cardiolipin-containing lipid membranes attract the bacterial cell division protein
diviva,” International Journal of Molecular Sciences, vol. 22, no. 15.
MDPI, 2021.
ista: Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. 2021. Cardiolipin-containing
lipid membranes attract the bacterial cell division protein diviva. International
Journal of Molecular Sciences. 22(15), 8350.
mla: Labajová, Naďa, et al. “Cardiolipin-Containing Lipid Membranes Attract the
Bacterial Cell Division Protein Diviva.” International Journal of Molecular
Sciences, vol. 22, no. 15, 8350, MDPI, 2021, doi:10.3390/ijms22158350.
short: N. Labajová, N.S. Baranova, M. Jurásek, R. Vácha, M. Loose, I. Barák, International
Journal of Molecular Sciences 22 (2021).
date_created: 2021-08-15T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-11T10:34:44Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.3390/ijms22158350
ec_funded: 1
external_id:
isi:
- '000681815400001'
pmid:
- '34361115'
file:
- access_level: open_access
checksum: a4bc06e9a2c803ceff5a91f10b174054
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:35:56Z
date_updated: 2021-08-16T09:35:56Z
file_id: '9923'
file_name: 2021_InternationalJournalOfMolecularSciences_Labajová .pdf
file_size: 6132410
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:35:56Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '15'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- '14220067'
issn:
- '16616596'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cardiolipin-containing lipid membranes attract the bacterial cell division
protein diviva
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 22
year: '2021'
...
---
_id: '9905'
abstract:
- lang: eng
text: Vaccines are thought to be the best available solution for controlling the
ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains
may come too rapidly for current vaccine developments to alleviate the health,
economic and social consequences of the pandemic. To quantify and characterize
the risk of such a scenario, we created a SIR-derived model with initial stochastic
dynamics of the vaccine-resistant strain to study the probability of its emergence
and establishment. Using parameters realistically resembling SARS-CoV-2 transmission,
we model a wave-like pattern of the pandemic and consider the impact of the rate
of vaccination and the strength of non-pharmaceutical intervention measures on
the probability of emergence of a resistant strain. As expected, we found that
a fast rate of vaccination decreases the probability of emergence of a resistant
strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions
happened at a time when most individuals of the population have already been vaccinated
the probability of emergence of a resistant strain was greatly increased. Consequently,
we show that a period of transmission reduction close to the end of the vaccination
campaign can substantially reduce the probability of resistant strain establishment.
Our results suggest that policymakers and individuals should consider maintaining
non-pharmaceutical interventions and transmission-reducing behaviours throughout
the entire vaccination period.
acknowledgement: We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta,
Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants
of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España
for useful comments. The opinions expressed in this document are exclusively of
the authors and, therefore, do not necessarily coincide with those of the Banco
de España or the Eurosystem. ETD is supported by the Swiss National Science and
Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator
Grant (771209-CharFL).
article_number: '15729'
article_processing_charge: Yes
article_type: original
author:
- first_name: Simon
full_name: Rella, Simon
id: B4765ACA-AA38-11E9-AC9A-0930E6697425
last_name: Rella
- first_name: Yuliya A.
full_name: Kulikova, Yuliya A.
last_name: Kulikova
- first_name: Emmanouil T.
full_name: Dermitzakis, Emmanouil T.
last_name: Dermitzakis
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission
and vaccination impact the fate of vaccine-resistant strains. Scientific Reports.
2021;11(1). doi:10.1038/s41598-021-95025-3
apa: Rella, S., Kulikova, Y. A., Dermitzakis, E. T., & Kondrashov, F. (2021).
Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant
strains. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-95025-3
chicago: Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor
Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate
of Vaccine-Resistant Strains.” Scientific Reports. Springer Nature, 2021.
https://doi.org/10.1038/s41598-021-95025-3.
ieee: S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of
SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,”
Scientific Reports, vol. 11, no. 1. Springer Nature, 2021.
ista: Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2
transmission and vaccination impact the fate of vaccine-resistant strains. Scientific
Reports. 11(1), 15729.
mla: Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact
the Fate of Vaccine-Resistant Strains.” Scientific Reports, vol. 11, no.
1, 15729, Springer Nature, 2021, doi:10.1038/s41598-021-95025-3.
short: S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports
11 (2021).
date_created: 2021-08-15T22:01:26Z
date_published: 2021-07-30T00:00:00Z
date_updated: 2023-08-11T10:42:58Z
day: '30'
ddc:
- '570'
- '610'
department:
- _id: FyKo
doi: 10.1038/s41598-021-95025-3
ec_funded: 1
external_id:
isi:
- '000683329100001'
pmid:
- '34330988'
file:
- access_level: open_access
checksum: ac86892ed17e6724c7251844da5cef5c
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T11:36:49Z
date_updated: 2021-08-16T11:36:49Z
file_id: '9927'
file_name: 2021_ScientificReports_Rella.pdf
file_size: 3432001
relation: main_file
success: 1
file_date_updated: 2021-08-16T11:36:49Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: Scientific Reports
publication_identifier:
eissn:
- '20452322'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/
scopus_import: '1'
status: public
title: Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant
strains
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2021'
...
---
_id: '9903'
abstract:
- lang: eng
text: Eigenstate thermalization in quantum many-body systems implies that eigenstates
at high energy are similar to random vectors. Identifying systems where at least
some eigenstates are nonthermal is an outstanding question. In this Letter we
show that interacting quantum models that have a nullspace—a degenerate subspace
of eigenstates at zero energy (zero modes), which corresponds to infinite temperature,
provide a route to nonthermal eigenstates. We analytically show the existence
of a zero mode which can be represented as a matrix product state for a certain
class of local Hamiltonians. In the more general case we use a subspace disentangling
algorithm to generate an orthogonal basis of zero modes characterized by increasing
entanglement entropy. We show evidence for an area-law entanglement scaling of
the least-entangled zero mode in the broad parameter regime, leading to a conjecture
that all local Hamiltonians with the nullspace feature zero modes with area-law
entanglement scaling and, as such, break the strong thermalization hypothesis.
Finally, we find zero modes in constrained models and propose a setup for observing
their experimental signatures.
acknowledgement: "We acknowledge useful discussions with V. Gritsev and A. Garkun
and suggestions on implementation of the\r\nPPXPP model by D. Bluvstein. A. M. and
M. S. were supported by the European Research Council (ERC) under\r\nthe European
Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899)"
article_number: '060602'
article_processing_charge: Yes (in subscription journal)
article_type: letter_note
author:
- first_name: Volker
full_name: Karle, Volker
id: D7C012AE-D7ED-11E9-95E8-1EC5E5697425
last_name: Karle
orcid: 0000-0002-6963-0129
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
citation:
ama: Karle V, Serbyn M, Michailidis A. Area-law entangled eigenstates from nullspaces
of local Hamiltonians. Physical Review Letters. 2021;127(6). doi:10.1103/physrevlett.127.060602
apa: Karle, V., Serbyn, M., & Michailidis, A. (2021). Area-law entangled eigenstates
from nullspaces of local Hamiltonians. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/physrevlett.127.060602
chicago: Karle, Volker, Maksym Serbyn, and Alexios Michailidis. “Area-Law Entangled
Eigenstates from Nullspaces of Local Hamiltonians.” Physical Review Letters.
American Physical Society, 2021. https://doi.org/10.1103/physrevlett.127.060602.
ieee: V. Karle, M. Serbyn, and A. Michailidis, “Area-law entangled eigenstates from
nullspaces of local Hamiltonians,” Physical Review Letters, vol. 127, no.
6. American Physical Society, 2021.
ista: Karle V, Serbyn M, Michailidis A. 2021. Area-law entangled eigenstates from
nullspaces of local Hamiltonians. Physical Review Letters. 127(6), 060602.
mla: Karle, Volker, et al. “Area-Law Entangled Eigenstates from Nullspaces of Local
Hamiltonians.” Physical Review Letters, vol. 127, no. 6, 060602, American
Physical Society, 2021, doi:10.1103/physrevlett.127.060602.
short: V. Karle, M. Serbyn, A. Michailidis, Physical Review Letters 127 (2021).
date_created: 2021-08-13T09:27:39Z
date_published: 2021-08-06T00:00:00Z
date_updated: 2023-08-11T10:43:27Z
day: '06'
ddc:
- '539'
department:
- _id: MaSe
- _id: GradSch
- _id: MiLe
doi: 10.1103/physrevlett.127.060602
ec_funded: 1
external_id:
arxiv:
- '2102.13633'
isi:
- '000684276000002'
file:
- access_level: open_access
checksum: 51218f302dcef99d90d1209809fcc874
content_type: application/pdf
creator: mserbyn
date_created: 2021-08-13T09:28:08Z
date_updated: 2021-08-13T09:28:08Z
file_id: '9904'
file_name: PhysRevLett.127.060602_SOM.pdf
file_size: 5064231
relation: main_file
success: 1
file_date_updated: 2021-08-13T09:28:08Z
has_accepted_license: '1'
intvolume: ' 127'
isi: 1
issue: '6'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Area-law entangled eigenstates from nullspaces of local Hamiltonians
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: 127
year: '2021'
...
---
_id: '9952'
abstract:
- lang: eng
text: Proper control of division orientation and symmetry, largely determined by
spindle positioning, is essential to development and homeostasis. Spindle positioning
has been extensively studied in cells dividing in two-dimensional (2D) environments
and in epithelial tissues, where proteins such as NuMA (also known as NUMA1) orient
division along the interphase long axis of the cell. However, little is known
about how cells control spindle positioning in three-dimensional (3D) environments,
such as early mammalian embryos and a variety of adult tissues. Here, we use mouse
embryonic stem cells (ESCs), which grow in 3D colonies, as a model to investigate
division in 3D. We observe that, at the periphery of 3D colonies, ESCs display
high spindle mobility and divide asymmetrically. Our data suggest that enhanced
spindle movements are due to unequal distribution of the cell–cell junction protein
E-cadherin between future daughter cells. Interestingly, when cells progress towards
differentiation, division becomes more symmetric, with more elongated shapes in
metaphase and enhanced cortical NuMA recruitment in anaphase. Altogether, this
study suggests that in 3D contexts, the geometry of the cell and its contacts
with neighbors control division orientation and symmetry.
acknowledgement: We would like to thank the entire Paluch and Baum laboratories at
the MRC-LMCB and the Chalut lab at the Cambridge SCI for discussions and feedback
throughout the project, and the MRC-LMCB microscopy platform, in particular Andrew
Vaughan, for technical support.
article_number: jcs255018
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Agathe
full_name: Chaigne, Agathe
last_name: Chaigne
- first_name: Matthew B.
full_name: Smith, Matthew B.
last_name: Smith
- first_name: R. L.
full_name: Cavestany, R. L.
last_name: Cavestany
- 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: Kevin J.
full_name: Chalut, Kevin J.
last_name: Chalut
- first_name: Ewa K.
full_name: Paluch, Ewa K.
last_name: Paluch
citation:
ama: Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. Three-dimensional
geometry controls division symmetry in stem cell colonies. Journal of Cell
Science. 2021;134(14). doi:10.1242/jcs.255018
apa: Chaigne, A., Smith, M. B., Cavestany, R. L., Hannezo, E. B., Chalut, K. J.,
& Paluch, E. K. (2021). Three-dimensional geometry controls division symmetry
in stem cell colonies. Journal of Cell Science. The Company of Biologists.
https://doi.org/10.1242/jcs.255018
chicago: Chaigne, Agathe, Matthew B. Smith, R. L. Cavestany, Edouard B Hannezo,
Kevin J. Chalut, and Ewa K. Paluch. “Three-Dimensional Geometry Controls Division
Symmetry in Stem Cell Colonies.” Journal of Cell Science. The Company of
Biologists, 2021. https://doi.org/10.1242/jcs.255018.
ieee: A. Chaigne, M. B. Smith, R. L. Cavestany, E. B. Hannezo, K. J. Chalut, and
E. K. Paluch, “Three-dimensional geometry controls division symmetry in stem cell
colonies,” Journal of Cell Science, vol. 134, no. 14. The Company of Biologists,
2021.
ista: Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. 2021.
Three-dimensional geometry controls division symmetry in stem cell colonies. Journal
of Cell Science. 134(14), jcs255018.
mla: Chaigne, Agathe, et al. “Three-Dimensional Geometry Controls Division Symmetry
in Stem Cell Colonies.” Journal of Cell Science, vol. 134, no. 14, jcs255018,
The Company of Biologists, 2021, doi:10.1242/jcs.255018.
short: A. Chaigne, M.B. Smith, R.L. Cavestany, E.B. Hannezo, K.J. Chalut, E.K. Paluch,
Journal of Cell Science 134 (2021).
date_created: 2021-08-22T22:01:20Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-11T10:55:36Z
day: '01'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1242/jcs.255018
external_id:
isi:
- '000681395800008'
file:
- access_level: open_access
checksum: f086f9d7cb63b2474c01921cb060c513
content_type: application/pdf
creator: asandaue
date_created: 2021-08-23T07:32:20Z
date_updated: 2021-08-23T07:32:20Z
file_id: '9954'
file_name: 2021_JournalOfCellScience_Chaigne.pdf
file_size: 8651724
relation: main_file
success: 1
file_date_updated: 2021-08-23T07:32:20Z
has_accepted_license: '1'
intvolume: ' 134'
isi: 1
issue: '14'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Journal of Cell Science
publication_identifier:
eissn:
- '14779137'
issn:
- '00219533'
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Three-dimensional geometry controls division symmetry in stem cell colonies
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: 134
year: '2021'
...
---
_id: '9908'
abstract:
- lang: eng
text: About eight million animal species are estimated to live on Earth, and all
except those belonging to one subphylum are invertebrates. Invertebrates are incredibly
diverse in their morphologies, life histories, and in the range of the ecological
niches that they occupy. A great variety of modes of reproduction and sex determination
systems is also observed among them, and their mosaic-distribution across the
phylogeny shows that transitions between them occur frequently and rapidly. Genetic
conflict in its various forms is a long-standing theory to explain what drives
those evolutionary transitions. Here, we review (1) the different modes of reproduction
among invertebrate species, highlighting sexual reproduction as the probable ancestral
state; (2) the paradoxical diversity of sex determination systems; (3) the different
types of genetic conflicts that could drive the evolution of such different systems.
article_number: '1136'
article_processing_charge: Yes
article_type: review
author:
- first_name: Marion A L
full_name: Picard, Marion A L
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Stéphanie
full_name: Bertrand, Stéphanie
last_name: Bertrand
- first_name: Hector
full_name: Escriva, Hector
last_name: Escriva
citation:
ama: Picard MAL, Vicoso B, Bertrand S, Escriva H. Diversity of modes of reproduction
and sex determination systems in invertebrates, and the putative contribution
of genetic conflict. Genes. 2021;12(8). doi:10.3390/genes12081136
apa: Picard, M. A. L., Vicoso, B., Bertrand, S., & Escriva, H. (2021). Diversity
of modes of reproduction and sex determination systems in invertebrates, and the
putative contribution of genetic conflict. Genes. MDPI. https://doi.org/10.3390/genes12081136
chicago: Picard, Marion A L, Beatriz Vicoso, Stéphanie Bertrand, and Hector Escriva.
“Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates,
and the Putative Contribution of Genetic Conflict.” Genes. MDPI, 2021.
https://doi.org/10.3390/genes12081136.
ieee: M. A. L. Picard, B. Vicoso, S. Bertrand, and H. Escriva, “Diversity of modes
of reproduction and sex determination systems in invertebrates, and the putative
contribution of genetic conflict,” Genes, vol. 12, no. 8. MDPI, 2021.
ista: Picard MAL, Vicoso B, Bertrand S, Escriva H. 2021. Diversity of modes of reproduction
and sex determination systems in invertebrates, and the putative contribution
of genetic conflict. Genes. 12(8), 1136.
mla: Picard, Marion A. L., et al. “Diversity of Modes of Reproduction and Sex Determination
Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.”
Genes, vol. 12, no. 8, 1136, MDPI, 2021, doi:10.3390/genes12081136.
short: M.A.L. Picard, B. Vicoso, S. Bertrand, H. Escriva, Genes 12 (2021).
date_created: 2021-08-15T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-11T10:42:32Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.3390/genes12081136
ec_funded: 1
external_id:
isi:
- '000690475900001'
file:
- access_level: open_access
checksum: 744e60e56d290a96da3c91a9779f886f
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:49:35Z
date_updated: 2021-08-16T09:49:35Z
file_id: '9926'
file_name: 2021_Genes_Picard.pdf
file_size: 2297655
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:49:35Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Genes
publication_identifier:
eissn:
- '20734425'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diversity of modes of reproduction and sex determination systems in invertebrates,
and the putative contribution of genetic conflict
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: '9829'
abstract:
- lang: eng
text: In 2020, many in-person scientific events were canceled due to the COVID-19
pandemic, creating a vacuum in networking and knowledge exchange between scientists.
To fill this void in scientific communication, a group of early career nanocrystal
enthusiasts launched the virtual seminar series, News in Nanocrystals, in the
summer of 2020. By the end of the year, the series had attracted over 850 participants
from 46 countries. In this Nano Focus, we describe the process of organizing the
News in Nanocrystals seminar series; discuss its growth, emphasizing what the
organizers have learned in terms of diversity and accessibility; and provide an
outlook for the next steps and future opportunities. This summary and analysis
of experiences and learned lessons are intended to inform the broader scientific
community, especially those who are looking for avenues to continue fostering
discussion and scientific engagement virtually, both during the pandemic and after.
acknowledgement: K. E. Shulenberger, M. D. Klein, T. Šverko, and H. R. Keller would
like to thank Professors Moungi Bawendi (MIT) and Gordana Dukovic (CU Boulder) for
their feedback and support of the News in Nanocrystals initiative. The authors thank
Madison Jilek (CU Boulder) and Dhananjeya Kumaar (ETH Zurich) for their help in
the organization of the seminar, and Professors Brandi Cossairt (University of Washington)
and Gordana Dukovic for their feedback on an earlier version of this manuscript.
The authors thank all the seminar speakers and attendees for their interest and
continuing participation in the seminar series.
article_processing_charge: No
article_type: original
author:
- first_name: Dmitry
full_name: Baranov, Dmitry
last_name: Baranov
- first_name: Tara
full_name: Šverko, Tara
last_name: Šverko
- first_name: Taylor
full_name: Moot, Taylor
last_name: Moot
- first_name: Helena R.
full_name: Keller, Helena R.
last_name: Keller
- first_name: Megan D.
full_name: Klein, Megan D.
last_name: Klein
- first_name: E. K.
full_name: Vishnu, E. K.
last_name: Vishnu
- first_name: Daniel
full_name: Balazs, Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- first_name: Katherine E.
full_name: Shulenberger, Katherine E.
last_name: Shulenberger
citation:
ama: 'Baranov D, Šverko T, Moot T, et al. News in Nanocrystals seminar: Self-assembly
of early career researchers toward globally accessible nanoscience. ACS Nano.
2021;15(7):10743–10747. doi:10.1021/acsnano.1c03276'
apa: 'Baranov, D., Šverko, T., Moot, T., Keller, H. R., Klein, M. D., Vishnu, E.
K., … Shulenberger, K. E. (2021). News in Nanocrystals seminar: Self-assembly
of early career researchers toward globally accessible nanoscience. ACS Nano.
American Chemical Society. https://doi.org/10.1021/acsnano.1c03276'
chicago: 'Baranov, Dmitry, Tara Šverko, Taylor Moot, Helena R. Keller, Megan D.
Klein, E. K. Vishnu, Daniel Balazs, and Katherine E. Shulenberger. “News in Nanocrystals
Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible
Nanoscience.” ACS Nano. American Chemical Society, 2021. https://doi.org/10.1021/acsnano.1c03276.'
ieee: 'D. Baranov et al., “News in Nanocrystals seminar: Self-assembly of
early career researchers toward globally accessible nanoscience,” ACS Nano,
vol. 15, no. 7. American Chemical Society, pp. 10743–10747, 2021.'
ista: 'Baranov D, Šverko T, Moot T, Keller HR, Klein MD, Vishnu EK, Balazs D, Shulenberger
KE. 2021. News in Nanocrystals seminar: Self-assembly of early career researchers
toward globally accessible nanoscience. ACS Nano. 15(7), 10743–10747.'
mla: 'Baranov, Dmitry, et al. “News in Nanocrystals Seminar: Self-Assembly of Early
Career Researchers toward Globally Accessible Nanoscience.” ACS Nano, vol.
15, no. 7, American Chemical Society, 2021, pp. 10743–10747, doi:10.1021/acsnano.1c03276.'
short: D. Baranov, T. Šverko, T. Moot, H.R. Keller, M.D. Klein, E.K. Vishnu, D.
Balazs, K.E. Shulenberger, ACS Nano 15 (2021) 10743–10747.
date_created: 2021-08-08T22:01:31Z
date_published: 2021-07-06T00:00:00Z
date_updated: 2023-08-11T10:55:08Z
day: '06'
department:
- _id: MaIb
doi: 10.1021/acsnano.1c03276
external_id:
isi:
- '000679406500002'
pmid:
- '34228432'
intvolume: ' 15'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/acsnano.1c03276
month: '07'
oa: 1
oa_version: Published Version
page: 10743–10747
pmid: 1
publication: ACS Nano
publication_identifier:
eissn:
- 1936086X
issn:
- '19360851'
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'News in Nanocrystals seminar: Self-assembly of early career researchers toward
globally accessible nanoscience'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2021'
...
---
_id: '13057'
abstract:
- lang: eng
text: 'This dataset comprises all data shown in the figures of the submitted article
"Geometric superinductance qubits: Controlling phase delocalization across a single
Josephson junction". Additional raw data are available from the corresponding
author on reasonable request.'
article_processing_charge: No
author:
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Grisha
full_name: Szep, Grisha
last_name: Szep
- first_name: Andrea
full_name: Trioni, Andrea
id: 42F71B44-F248-11E8-B48F-1D18A9856A87
last_name: Trioni
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: 'Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling
phase delocalization across a single Josephson junction. 2021. doi:10.5281/ZENODO.5592103'
apa: 'Peruzzo, M., Hassani, F., Szep, G., Trioni, A., Redchenko, E., Zemlicka, M.,
& Fink, J. M. (2021). Geometric superinductance qubits: Controlling phase
delocalization across a single Josephson junction. Zenodo. https://doi.org/10.5281/ZENODO.5592103'
chicago: 'Peruzzo, Matilda, Farid Hassani, Grisha Szep, Andrea Trioni, Elena Redchenko,
Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling
Phase Delocalization across a Single Josephson Junction.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5592103.'
ieee: 'M. Peruzzo et al., “Geometric superinductance qubits: Controlling
phase delocalization across a single Josephson junction.” Zenodo, 2021.'
ista: 'Peruzzo M, Hassani F, Szep G, Trioni A, Redchenko E, Zemlicka M, Fink JM.
2021. Geometric superinductance qubits: Controlling phase delocalization across
a single Josephson junction, Zenodo, 10.5281/ZENODO.5592103.'
mla: 'Peruzzo, Matilda, et al. Geometric Superinductance Qubits: Controlling
Phase Delocalization across a Single Josephson Junction. Zenodo, 2021, doi:10.5281/ZENODO.5592103.'
short: M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M.
Fink, (2021).
date_created: 2023-05-23T13:42:27Z
date_published: 2021-10-22T00:00:00Z
date_updated: 2023-08-11T10:44:21Z
day: '22'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.5281/ZENODO.5592103
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5592104
month: '10'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '9928'
relation: used_in_publication
status: public
status: public
title: 'Geometric superinductance qubits: Controlling phase delocalization across
a single Josephson junction'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9985'
abstract:
- lang: eng
text: AMPA receptor (AMPAR) abundance and positioning at excitatory synapses regulates
the strength of transmission. Changes in AMPAR localisation can enact synaptic
plasticity, allowing long-term information storage, and is therefore tightly controlled.
Multiple mechanisms regulating AMPAR synaptic anchoring have been described, but
with limited coherence or comparison between reports, our understanding of this
process is unclear. Here, combining synaptic recordings from mouse hippocampal
slices and super-resolution imaging in dissociated cultures, we compare the contributions
of three AMPAR interaction domains controlling transmission at hippocampal CA1
synapses. We show that the AMPAR C-termini play only a modulatory role, whereas
the extracellular N-terminal domain (NTD) and PDZ interactions of the auxiliary
subunit TARP γ8 are both crucial, and each is sufficient to maintain transmission.
Our data support a model in which γ8 accumulates AMPARs at the postsynaptic density,
where the NTD further tunes their positioning. This interplay between cytosolic
(TARP γ8) and synaptic cleft (NTD) interactions provides versatility to regulate
synaptic transmission and plasticity.
acknowledgement: The authors are very grateful to Andrew Penn for advice and discussions
on surface receptor labelling in slice tissue, dissociated culture transfection,
and for providing tdTomato and BirAER expression plasmids. This work would not have
been possible without support from the Biological Services teams at both the Laboratory
of Molecular Biology and Ares facilities. We are also very grateful to Nick Barry
and Jerome Boulanger of the LMB Light Microscopy facility for support with confocal
and STORM imaging and analysis, Junichi Takagi for providing scFv-Clasp expression
constructs, Veronica Chang for assistance with scFv-Clasp protein production, and
Nejc Kejzar for assistance with cluster analysis. We would like to thank Teru Nakagawa
and Ole Paulsen for critical reading of the manuscript and constructive feedback.
This work was supported by grants from the Medical Research Council (MC_U105174197)
and BBSRC (BB/N002113/1).
article_number: '5083'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Alexandra
full_name: Pinggera, Alexandra
last_name: Pinggera
- first_name: Hinze
full_name: Ho, Hinze
last_name: Ho
- first_name: Ingo H.
full_name: Greger, Ingo H.
last_name: Greger
citation:
ama: Watson J, Pinggera A, Ho H, Greger IH. AMPA receptor anchoring at CA1 synapses
is determined by N-terminal domain and TARP γ8 interactions. Nature Communications.
2021;12(1). doi:10.1038/s41467-021-25281-4
apa: Watson, J., Pinggera, A., Ho, H., & Greger, I. H. (2021). AMPA receptor
anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions.
Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-021-25281-4
chicago: Watson, Jake, Alexandra Pinggera, Hinze Ho, and Ingo H. Greger. “AMPA Receptor
Anchoring at CA1 Synapses Is Determined by N-Terminal Domain and TARP Γ8 Interactions.”
Nature Communications. Nature Publishing Group, 2021. https://doi.org/10.1038/s41467-021-25281-4.
ieee: J. Watson, A. Pinggera, H. Ho, and I. H. Greger, “AMPA receptor anchoring
at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions,”
Nature Communications, vol. 12, no. 1. Nature Publishing Group, 2021.
ista: Watson J, Pinggera A, Ho H, Greger IH. 2021. AMPA receptor anchoring at CA1
synapses is determined by N-terminal domain and TARP γ8 interactions. Nature Communications.
12(1), 5083.
mla: Watson, Jake, et al. “AMPA Receptor Anchoring at CA1 Synapses Is Determined
by N-Terminal Domain and TARP Γ8 Interactions.” Nature Communications,
vol. 12, no. 1, 5083, Nature Publishing Group, 2021, doi:10.1038/s41467-021-25281-4.
short: J. Watson, A. Pinggera, H. Ho, I.H. Greger, Nature Communications 12 (2021).
date_created: 2021-09-05T22:01:23Z
date_published: 2021-08-23T00:00:00Z
date_updated: 2023-08-11T11:07:51Z
day: '23'
ddc:
- '612'
department:
- _id: PeJo
doi: 10.1038/s41467-021-25281-4
external_id:
isi:
- '000687672000006'
pmid:
- '34426577 '
file:
- access_level: open_access
checksum: 1bf4f6a561f96bc426d754de9cb57710
content_type: application/pdf
creator: cchlebak
date_created: 2021-09-08T12:57:06Z
date_updated: 2021-09-08T12:57:06Z
file_id: '9991'
file_name: 2021_NatureCommunications_Watson.pdf
file_size: 18310502
relation: main_file
success: 1
file_date_updated: 2021-09-08T12:57:06Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain
and TARP γ8 interactions
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: '9981'
abstract:
- lang: eng
text: "The numerical simulation of dynamical phenomena in interacting quantum systems
is a notoriously hard problem. Although a number of promising numerical methods
exist, they often have limited applicability due to the growth of entanglement
or the presence of the so-called sign problem. In this work, we develop an importance
sampling scheme for the simulation of quantum spin dynamics, building on a recent
approach mapping quantum spin systems to classical stochastic processes. The importance
sampling scheme is based on identifying the classical trajectory that yields the
largest contribution to a given quantum observable. An exact transformation is
then carried out to preferentially sample trajectories that are close to the dominant
one. We demonstrate that this approach is capable of reducing the temporal growth
of fluctuations in the stochastic quantities, thus extending the range of accessible
times and system sizes compared to direct sampling. We discuss advantages and
limitations of the proposed approach, outlining directions\r\nfor further developments."
article_number: '048'
article_processing_charge: No
article_type: original
author:
- first_name: Stefano
full_name: De Nicola, Stefano
id: 42832B76-F248-11E8-B48F-1D18A9856A87
last_name: De Nicola
orcid: 0000-0002-4842-6671
citation:
ama: De Nicola S. Importance sampling scheme for the stochastic simulation of quantum
spin dynamics. SciPost Physics. 2021;11(3). doi:10.21468/scipostphys.11.3.048
apa: De Nicola, S. (2021). Importance sampling scheme for the stochastic simulation
of quantum spin dynamics. SciPost Physics. SciPost. https://doi.org/10.21468/scipostphys.11.3.048
chicago: De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation
of Quantum Spin Dynamics.” SciPost Physics. SciPost, 2021. https://doi.org/10.21468/scipostphys.11.3.048.
ieee: S. De Nicola, “Importance sampling scheme for the stochastic simulation of
quantum spin dynamics,” SciPost Physics, vol. 11, no. 3. SciPost, 2021.
ista: De Nicola S. 2021. Importance sampling scheme for the stochastic simulation
of quantum spin dynamics. SciPost Physics. 11(3), 048.
mla: De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation
of Quantum Spin Dynamics.” SciPost Physics, vol. 11, no. 3, 048, SciPost,
2021, doi:10.21468/scipostphys.11.3.048.
short: S. De Nicola, SciPost Physics 11 (2021).
date_created: 2021-09-02T11:49:47Z
date_published: 2021-09-02T00:00:00Z
date_updated: 2023-08-11T10:59:29Z
day: '02'
ddc:
- '519'
department:
- _id: MaSe
doi: 10.21468/scipostphys.11.3.048
ec_funded: 1
external_id:
arxiv:
- '2103.16468'
isi:
- '000692534200001'
file:
- access_level: open_access
checksum: e4ec69d893e31811efc6093cb6ea8eb7
content_type: application/pdf
creator: cchlebak
date_created: 2021-09-02T14:05:43Z
date_updated: 2021-09-02T14:05:43Z
file_id: '9984'
file_name: 2021_SciPostPhys_DeNicola.pdf
file_size: 373833
relation: main_file
success: 1
file_date_updated: 2021-09-02T14:05:43Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '3'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: SciPost Physics
publication_identifier:
eissn:
- 2666-9366
issn:
- 2542-4653
publication_status: published
publisher: SciPost
quality_controlled: '1'
status: public
title: Importance sampling scheme for the stochastic simulation of quantum spin dynamics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2021'
...
---
_id: '9960'
abstract:
- lang: eng
text: The control of many-body quantum dynamics in complex systems is a key challenge
in the quest to reliably produce and manipulate large-scale quantum entangled
states. Recently, quench experiments in Rydberg atom arrays [Bluvstein et al.
Science 371, 1355 (2021)] demonstrated that coherent revivals associated with
quantum many-body scars can be stabilized by periodic driving, generating stable
subharmonic responses over a wide parameter regime. We analyze a simple, related
model where these phenomena originate from spatiotemporal ordering in an effective
Floquet unitary, corresponding to discrete time-crystalline behavior in a prethermal
regime. Unlike conventional discrete time crystals, the subharmonic response exists
only for Néel-like initial states, associated with quantum scars. We predict robustness
to perturbations and identify emergent timescales that could be observed in future
experiments. Our results suggest a route to controlling entanglement in interacting
quantum systems by combining periodic driving with many-body scars.
acknowledgement: We thank Dmitry Abanin, Ehud Altman, Iris Cong, Sepehr Ebadi, Alex
Keesling, Harry Levine, Ahmed Omran, Hannes Pichler, Rhine Samajdar, Guilia Semeghini,
Tout Wang, Norman Yao, and Harry Zhou or stimulating discussions. We acknowledge
support from the Center for Ultracold Atoms, the National Science Foundation, the
Vannevar Bush Faculty Fellowship, the U.S. Department of Energy, the Army Research
Office MURI, and the DARPA ONISQ program (M. L., N. M, W. W. H., D. B.); the European
Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation
Programme Grant Agreement No. 850899 (A. M. and M. S.); the Department of Energy
Computational Science Graduate Fellowship under Awards No. DESC0021110 (N. M.);
the Moore Foundation EPiQS initiative Grant No. GBMF4306, the National University
of Singapore (NUS) Development Grant AY2019/2020 and the Stanford Institute for
Theoretical Physics (W. W. H.); the NSF Graduate Research Fellowship Program (Grant
No. DGE1745303) and The Fannie and John Hertz Foundation (D. B.); the Miller Institute
for Basic Research in Science (S. C.); DOE Quantum Systems Accelerator – Contract
No. 7568717; and DOE Programmable Quantum Simulators for Lattice Gauge Theories
and Gauge-Gravity Correspondence – Grant No. DE-SC0021013.
article_number: '090602'
article_processing_charge: No
article_type: letter_note
author:
- first_name: N.
full_name: Maskara, N.
last_name: Maskara
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: W. W.
full_name: Ho, W. W.
last_name: Ho
- first_name: D.
full_name: Bluvstein, D.
last_name: Bluvstein
- first_name: S.
full_name: Choi, S.
last_name: Choi
- first_name: M. D.
full_name: Lukin, M. D.
last_name: Lukin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: 'Maskara N, Michailidis A, Ho WW, et al. Discrete time-crystalline order enabled
by quantum many-body scars: Entanglement steering via periodic driving. Physical
Review Letters. 2021;127(9). doi:10.1103/PhysRevLett.127.090602'
apa: 'Maskara, N., Michailidis, A., Ho, W. W., Bluvstein, D., Choi, S., Lukin, M.
D., & Serbyn, M. (2021). Discrete time-crystalline order enabled by quantum
many-body scars: Entanglement steering via periodic driving. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.127.090602'
chicago: 'Maskara, N., Alexios Michailidis, W. W. Ho, D. Bluvstein, S. Choi, M.
D. Lukin, and Maksym Serbyn. “Discrete Time-Crystalline Order Enabled by Quantum
Many-Body Scars: Entanglement Steering via Periodic Driving.” Physical Review
Letters. American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.127.090602.'
ieee: 'N. Maskara et al., “Discrete time-crystalline order enabled by quantum
many-body scars: Entanglement steering via periodic driving,” Physical Review
Letters, vol. 127, no. 9. American Physical Society, 2021.'
ista: 'Maskara N, Michailidis A, Ho WW, Bluvstein D, Choi S, Lukin MD, Serbyn M.
2021. Discrete time-crystalline order enabled by quantum many-body scars: Entanglement
steering via periodic driving. Physical Review Letters. 127(9), 090602.'
mla: 'Maskara, N., et al. “Discrete Time-Crystalline Order Enabled by Quantum Many-Body
Scars: Entanglement Steering via Periodic Driving.” Physical Review Letters,
vol. 127, no. 9, 090602, American Physical Society, 2021, doi:10.1103/PhysRevLett.127.090602.'
short: N. Maskara, A. Michailidis, W.W. Ho, D. Bluvstein, S. Choi, M.D. Lukin, M.
Serbyn, Physical Review Letters 127 (2021).
date_created: 2021-08-28T08:08:58Z
date_published: 2021-08-27T00:00:00Z
date_updated: 2023-08-11T10:57:51Z
day: '27'
department:
- _id: MaSe
doi: 10.1103/PhysRevLett.127.090602
ec_funded: 1
external_id:
arxiv:
- '2102.13160'
isi:
- '000692200100002'
intvolume: ' 127'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2102.13160
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'Discrete time-crystalline order enabled by quantum many-body scars: Entanglement
steering via periodic driving'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 127
year: '2021'
...
---
_id: '9961'
abstract:
- lang: eng
text: The notion of Thouless energy plays a central role in the theory of Anderson
localization. We investigate and compare the scaling of Thouless energy across
the many-body localization (MBL) transition in a Floquet model. We use a combination
of methods that are reliable on the ergodic side of the transition (e.g., spectral
form factor) and methods that work on the MBL side (e.g., typical matrix elements
of local operators) to obtain a complete picture of the Thouless energy behavior
across the transition. On the ergodic side, Thouless energy decreases slowly with
the system size, while at the transition it becomes comparable to the level spacing.
Different probes yield consistent estimates of Thouless energy in their overlapping
regime of applicability, giving the location of the transition point nearly free
of finite-size drift. This work establishes a connection between different definitions
of Thouless energy in a many-body setting and yields insights into the MBL transition
in Floquet systems.
acknowledgement: "We thank S. Garratt for useful comments on the manuscript. This
work was supported by the Swiss National Science Foundation (M. Sonner and D.A.A.)
and by the European Research Council (ERC) under the European Union’s Horizon 2020
research and innovation program (M. Serbyn, Grant Agreement No. 850899, and D.A.A.,
Grant Agreement No. 864597). Z.P. acknowledges support from EPSRC Grant No. EP/R020612/1
and from Leverhulme Trust Research Leadership Award No. RL-2019-015. The computations
were performed on the Baobab cluster of the University\r\nof Geneva."
article_number: L081112
article_processing_charge: No
article_type: letter_note
author:
- first_name: Michael
full_name: Sonner, Michael
last_name: Sonner
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
citation:
ama: Sonner M, Serbyn M, Papić Z, Abanin DA. Thouless energy across the many-body
localization transition in Floquet systems. Physical Review B. 2021;104(8).
doi:10.1103/PhysRevB.104.L081112
apa: Sonner, M., Serbyn, M., Papić, Z., & Abanin, D. A. (2021). Thouless energy
across the many-body localization transition in Floquet systems. Physical Review
B. American Physical Society. https://doi.org/10.1103/PhysRevB.104.L081112
chicago: Sonner, Michael, Maksym Serbyn, Zlatko Papić, and Dmitry A. Abanin. “Thouless
Energy across the Many-Body Localization Transition in Floquet Systems.” Physical
Review B. American Physical Society, 2021. https://doi.org/10.1103/PhysRevB.104.L081112.
ieee: M. Sonner, M. Serbyn, Z. Papić, and D. A. Abanin, “Thouless energy across
the many-body localization transition in Floquet systems,” Physical Review
B, vol. 104, no. 8. American Physical Society, 2021.
ista: Sonner M, Serbyn M, Papić Z, Abanin DA. 2021. Thouless energy across the many-body
localization transition in Floquet systems. Physical Review B. 104(8), L081112.
mla: Sonner, Michael, et al. “Thouless Energy across the Many-Body Localization
Transition in Floquet Systems.” Physical Review B, vol. 104, no. 8, L081112,
American Physical Society, 2021, doi:10.1103/PhysRevB.104.L081112.
short: M. Sonner, M. Serbyn, Z. Papić, D.A. Abanin, Physical Review B 104 (2021).
date_created: 2021-08-28T16:44:55Z
date_published: 2021-08-15T00:00:00Z
date_updated: 2023-08-11T10:57:09Z
day: '15'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.104.L081112
ec_funded: 1
external_id:
arxiv:
- '2012.15676'
isi:
- '000689734500009'
intvolume: ' 104'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2012.15676
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Thouless energy across the many-body localization transition in Floquet systems
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 104
year: '2021'
...
---
_id: '9957'
abstract:
- lang: eng
text: The reflectance field of a face describes the reflectance properties responsible
for complex lighting effects including diffuse, specular, inter-reflection and
self shadowing. Most existing methods for estimating the face reflectance from
a monocular image assume faces to be diffuse with very few approaches adding a
specular component. This still leaves out important perceptual aspects of reflectance
as higher-order global illumination effects and self-shadowing are not modeled.
We present a new neural representation for face reflectance where we can estimate
all components of the reflectance responsible for the final appearance from a
single monocular image. Instead of modeling each component of the reflectance
separately using parametric models, our neural representation allows us to generate
a basis set of faces in a geometric deformation-invariant space, parameterized
by the input light direction, viewpoint and face geometry. We learn to reconstruct
this reflectance field of a face just from a monocular image, which can be used
to render the face from any viewpoint in any light condition. Our method is trained
on a light-stage training dataset, which captures 300 people illuminated with
150 light conditions from 8 viewpoints. We show that our method outperforms existing
monocular reflectance reconstruction methods, in terms of photorealism due to
better capturing of physical premitives, such as sub-surface scattering, specularities,
self-shadows and other higher-order effects.
acknowledgement: "We thank Tarun Yenamandra and Duarte David for helping us with the
comparisons. This work was supported by the\r\nERC Consolidator Grant 4DReply (770784).
We also acknowledge support from InterDigital."
article_processing_charge: No
author:
- first_name: Mallikarjun
full_name: B R, Mallikarjun
last_name: B R
- first_name: Ayush
full_name: Tewari, Ayush
last_name: Tewari
- first_name: Tae-Hyun
full_name: Oh, Tae-Hyun
last_name: Oh
- first_name: Tim
full_name: Weyrich, Tim
last_name: Weyrich
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Hans-Peter
full_name: Seidel, Hans-Peter
last_name: Seidel
- first_name: Hanspeter
full_name: Pfister, Hanspeter
last_name: Pfister
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
- first_name: Mohamed
full_name: Elgharib, Mohamed
last_name: Elgharib
- first_name: Christian
full_name: Theobalt, Christian
last_name: Theobalt
citation:
ama: 'B R M, Tewari A, Oh T-H, et al. Monocular reconstruction of neural face reflectance
fields. In: Proceedings of the IEEE Computer Society Conference on Computer
Vision and Pattern Recognition. IEEE; 2021:4791-4800. doi:10.1109/CVPR46437.2021.00476'
apa: 'B R, M., Tewari, A., Oh, T.-H., Weyrich, T., Bickel, B., Seidel, H.-P., …
Theobalt, C. (2021). Monocular reconstruction of neural face reflectance fields.
In Proceedings of the IEEE Computer Society Conference on Computer Vision and
Pattern Recognition (pp. 4791–4800). Nashville, TN, United States; Virtual:
IEEE. https://doi.org/10.1109/CVPR46437.2021.00476'
chicago: B R, Mallikarjun, Ayush Tewari, Tae-Hyun Oh, Tim Weyrich, Bernd Bickel,
Hans-Peter Seidel, Hanspeter Pfister, Wojciech Matusik, Mohamed Elgharib, and
Christian Theobalt. “Monocular Reconstruction of Neural Face Reflectance Fields.”
In Proceedings of the IEEE Computer Society Conference on Computer Vision and
Pattern Recognition, 4791–4800. IEEE, 2021. https://doi.org/10.1109/CVPR46437.2021.00476.
ieee: M. B R et al., “Monocular reconstruction of neural face reflectance
fields,” in Proceedings of the IEEE Computer Society Conference on Computer
Vision and Pattern Recognition, Nashville, TN, United States; Virtual, 2021,
pp. 4791–4800.
ista: 'B R M, Tewari A, Oh T-H, Weyrich T, Bickel B, Seidel H-P, Pfister H, Matusik
W, Elgharib M, Theobalt C. 2021. Monocular reconstruction of neural face reflectance
fields. Proceedings of the IEEE Computer Society Conference on Computer Vision
and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition,
4791–4800.'
mla: B R, Mallikarjun, et al. “Monocular Reconstruction of Neural Face Reflectance
Fields.” Proceedings of the IEEE Computer Society Conference on Computer Vision
and Pattern Recognition, IEEE, 2021, pp. 4791–800, doi:10.1109/CVPR46437.2021.00476.
short: M. B R, A. Tewari, T.-H. Oh, T. Weyrich, B. Bickel, H.-P. Seidel, H. Pfister,
W. Matusik, M. Elgharib, C. Theobalt, in:, Proceedings of the IEEE Computer Society
Conference on Computer Vision and Pattern Recognition, IEEE, 2021, pp. 4791–4800.
conference:
end_date: 2021-06-25
location: Nashville, TN, United States; Virtual
name: 'CVPR: Conference on Computer Vision and Pattern Recognition'
start_date: 2021-06-20
date_created: 2021-08-24T06:03:00Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2023-08-11T11:08:35Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1109/CVPR46437.2021.00476
external_id:
arxiv:
- '2008.10247'
isi:
- '000739917304096'
file:
- access_level: open_access
checksum: 961db0bde76dd87cf833930080bb9f38
content_type: application/pdf
creator: bbickel
date_created: 2021-08-24T06:02:15Z
date_updated: 2021-08-24T06:02:15Z
file_id: '9958'
file_name: R_Monocular_Reconstruction_of_Neural_Face_Reflectance_Fields_CVPR_2021_paper[1].pdf
file_size: 4746649
relation: main_file
file_date_updated: 2021-08-24T06:02:15Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Preprint
page: 4791-4800
publication: Proceedings of the IEEE Computer Society Conference on Computer Vision
and Pattern Recognition
publication_identifier:
isbn:
- 978-166544509-2
issn:
- 1063-6919
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monocular reconstruction of neural face reflectance fields
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9973'
abstract:
- lang: eng
text: In this article we introduce a complete gradient estimate for symmetric quantum
Markov semigroups on von Neumann algebras equipped with a normal faithful tracial
state, which implies semi-convexity of the entropy with respect to the recently
introduced noncommutative 2-Wasserstein distance. We show that this complete gradient
estimate is stable under tensor products and free products and establish its validity
for a number of examples. As an application we prove a complete modified logarithmic
Sobolev inequality with optimal constant for Poisson-type semigroups on free group
factors.
acknowledgement: Both authors would like to thank Jan Maas for fruitful discussions
and helpful comments.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
- first_name: Haonan
full_name: Zhang, Haonan
id: D8F41E38-9E66-11E9-A9E2-65C2E5697425
last_name: Zhang
citation:
ama: Wirth M, Zhang H. Complete gradient estimates of quantum Markov semigroups.
Communications in Mathematical Physics. 2021;387:761–791. doi:10.1007/s00220-021-04199-4
apa: Wirth, M., & Zhang, H. (2021). Complete gradient estimates of quantum Markov
semigroups. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-021-04199-4
chicago: Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum
Markov Semigroups.” Communications in Mathematical Physics. Springer Nature,
2021. https://doi.org/10.1007/s00220-021-04199-4.
ieee: M. Wirth and H. Zhang, “Complete gradient estimates of quantum Markov semigroups,”
Communications in Mathematical Physics, vol. 387. Springer Nature, pp.
761–791, 2021.
ista: Wirth M, Zhang H. 2021. Complete gradient estimates of quantum Markov semigroups.
Communications in Mathematical Physics. 387, 761–791.
mla: Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum
Markov Semigroups.” Communications in Mathematical Physics, vol. 387, Springer
Nature, 2021, pp. 761–791, doi:10.1007/s00220-021-04199-4.
short: M. Wirth, H. Zhang, Communications in Mathematical Physics 387 (2021) 761–791.
date_created: 2021-08-30T10:07:44Z
date_published: 2021-08-30T00:00:00Z
date_updated: 2023-08-11T11:09:07Z
day: '30'
ddc:
- '621'
department:
- _id: JaMa
doi: 10.1007/s00220-021-04199-4
ec_funded: 1
external_id:
arxiv:
- '2007.13506'
isi:
- '000691214200001'
file:
- access_level: open_access
checksum: 8a602f916b1c2b0dc1159708b7cb204b
content_type: application/pdf
creator: cchlebak
date_created: 2021-09-08T07:34:24Z
date_updated: 2021-09-08T09:46:34Z
file_id: '9990'
file_name: 2021_CommunMathPhys_Wirth.pdf
file_size: 505971
relation: main_file
file_date_updated: 2021-09-08T09:46:34Z
has_accepted_license: '1'
intvolume: ' 387'
isi: 1
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 761–791
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- 1432-0916
issn:
- 0010-3616
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Complete gradient estimates of quantum Markov semigroups
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: 387
year: '2021'
...
---
_id: '10000'
abstract:
- lang: eng
text: Inhibition or targeted deletion of histone deacetylase 3 (HDAC3) is neuroprotective
in a variety neurodegenerative conditions, including retinal ganglion cells (RGCs)
after acute optic nerve damage. Consistent with this, induced HDAC3 expression
in cultured cells shows selective toxicity to neurons. Despite an established
role for HDAC3 in neuronal pathology, little is known regarding the mechanism
of this pathology.
acknowledgement: 'The authors thank Joel Dietz for maintaining the mice used in this
study, Satoshi Kinoshita and the Translational Research Initiative in Pathology
Laboratory at the University of Wisconsin-Madison for cutting retinal sections analyzed
in this study, and Mark Banghart for statistical review of the data analysis. Supported
by National Eye Institute Grants R01 EY012223 (RWN), R01 EY030123 (RWN), R01 EY029809
(LWG), R01 EY029809 (LWG) and a Vision Research CORE grant P30 EY016665, NRSA grant
T32 GM081061, by an unrestricted research grant from Research to Prevent Blindness,
Inc., and by a University of Wisconsin-Madison Vilas Life Cycle award and the Frederick
A. Davis Research Chair (RWN). '
article_number: '14'
article_processing_charge: Yes
article_type: original
author:
- first_name: Heather M.
full_name: Schmitt, Heather M.
last_name: Schmitt
- first_name: Rachel L.
full_name: Fehrman, Rachel L.
last_name: Fehrman
- 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: Huan
full_name: Yang, Huan
last_name: Yang
- first_name: Lian Wang
full_name: Guo, Lian Wang
last_name: Guo
- first_name: Cassandra L.
full_name: Schlamp, Cassandra L.
last_name: Schlamp
- first_name: Heather R.
full_name: Pelzel, Heather R.
last_name: Pelzel
- first_name: Robert W.
full_name: Nickells, Robert W.
last_name: Nickells
citation:
ama: Schmitt HM, Fehrman RL, Maes ME, et al. Increased susceptibility and intrinsic
apoptotic signaling in neurons by induced HDAC3 expression. Investigative Ophthalmology
and Visual Science. 2021;62(10). doi:10.1167/IOVS.62.10.14
apa: Schmitt, H. M., Fehrman, R. L., Maes, M. E., Yang, H., Guo, L. W., Schlamp,
C. L., … Nickells, R. W. (2021). Increased susceptibility and intrinsic apoptotic
signaling in neurons by induced HDAC3 expression. Investigative Ophthalmology
and Visual Science. Association for Research in Vision and Ophthalmology.
https://doi.org/10.1167/IOVS.62.10.14
chicago: Schmitt, Heather M., Rachel L. Fehrman, Margaret E Maes, Huan Yang, Lian
Wang Guo, Cassandra L. Schlamp, Heather R. Pelzel, and Robert W. Nickells. “Increased
Susceptibility and Intrinsic Apoptotic Signaling in Neurons by Induced HDAC3 Expression.”
Investigative Ophthalmology and Visual Science. Association for Research
in Vision and Ophthalmology, 2021. https://doi.org/10.1167/IOVS.62.10.14.
ieee: H. M. Schmitt et al., “Increased susceptibility and intrinsic apoptotic
signaling in neurons by induced HDAC3 expression,” Investigative Ophthalmology
and Visual Science, vol. 62, no. 10. Association for Research in Vision and
Ophthalmology, 2021.
ista: Schmitt HM, Fehrman RL, Maes ME, Yang H, Guo LW, Schlamp CL, Pelzel HR, Nickells
RW. 2021. Increased susceptibility and intrinsic apoptotic signaling in neurons
by induced HDAC3 expression. Investigative Ophthalmology and Visual Science. 62(10),
14.
mla: Schmitt, Heather M., et al. “Increased Susceptibility and Intrinsic Apoptotic
Signaling in Neurons by Induced HDAC3 Expression.” Investigative Ophthalmology
and Visual Science, vol. 62, no. 10, 14, Association for Research in Vision
and Ophthalmology, 2021, doi:10.1167/IOVS.62.10.14.
short: H.M. Schmitt, R.L. Fehrman, M.E. Maes, H. Yang, L.W. Guo, C.L. Schlamp, H.R.
Pelzel, R.W. Nickells, Investigative Ophthalmology and Visual Science 62 (2021).
date_created: 2021-09-12T22:01:23Z
date_published: 2021-08-16T00:00:00Z
date_updated: 2023-08-14T06:35:17Z
day: '16'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1167/IOVS.62.10.14
external_id:
isi:
- '000695230000014'
pmid:
- '34398198'
file:
- access_level: open_access
checksum: c430967746f653aa1ae84ee617f62b73
content_type: application/pdf
creator: dernst
date_created: 2022-05-13T07:40:15Z
date_updated: 2022-05-13T07:40:15Z
file_id: '11369'
file_name: 2021_IOVS_Schmitt.pdf
file_size: 19707796
relation: main_file
success: 1
file_date_updated: 2022-05-13T07:40:15Z
has_accepted_license: '1'
intvolume: ' 62'
isi: 1
issue: '10'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Investigative Ophthalmology and Visual Science
publication_identifier:
eissn:
- 1552-5783
issn:
- 0146-0404
publication_status: published
publisher: Association for Research in Vision and Ophthalmology
quality_controlled: '1'
scopus_import: '1'
status: public
title: Increased susceptibility and intrinsic apoptotic signaling in neurons by induced
HDAC3 expression
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: 62
year: '2021'
...
---
_id: '9998'
abstract:
- lang: eng
text: We define quantum equivariant K-theory of Nakajima quiver varieties. We discuss
type A in detail as well as its connections with quantum XXZ spin chains and trigonometric
Ruijsenaars-Schneider models. Finally we study a limit which produces a K-theoretic
version of results of Givental and Kim, connecting quantum geometry of flag varieties
and Toda lattice.
acknowledgement: 'First of all we would like to thank Andrei Okounkov for invaluable
discussions, advises and sharing with us his fantastic viewpoint on modern quantum
geometry. We are also grateful to D. Korb and Z. Zhou for their interest and comments.
The work of A. Smirnov was supported in part by RFBR Grants under Numbers 15-02-04175
and 15-01-04217 and in part by NSF Grant DMS–2054527. The work of P. Koroteev, A.M.
Zeitlin and A. Smirnov is supported in part by AMS Simons travel Grant. A. M. Zeitlin
is partially supported by Simons Collaboration Grant, Award ID: 578501. Open access
funding provided by Institute of Science and Technology (IST Austria).'
article_number: '87'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Peter
full_name: Koroteev, Peter
last_name: Koroteev
- first_name: Petr
full_name: Pushkar, Petr
id: 151DCEB6-9EC3-11E9-8480-ABECE5697425
last_name: Pushkar
- first_name: Andrey V.
full_name: Smirnov, Andrey V.
last_name: Smirnov
- first_name: Anton M.
full_name: Zeitlin, Anton M.
last_name: Zeitlin
citation:
ama: Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. Quantum K-theory of quiver varieties
and many-body systems. Selecta Mathematica. 2021;27(5). doi:10.1007/s00029-021-00698-3
apa: Koroteev, P., Pushkar, P., Smirnov, A. V., & Zeitlin, A. M. (2021). Quantum
K-theory of quiver varieties and many-body systems. Selecta Mathematica.
Springer Nature. https://doi.org/10.1007/s00029-021-00698-3
chicago: Koroteev, Peter, Petr Pushkar, Andrey V. Smirnov, and Anton M. Zeitlin.
“Quantum K-Theory of Quiver Varieties and Many-Body Systems.” Selecta Mathematica.
Springer Nature, 2021. https://doi.org/10.1007/s00029-021-00698-3.
ieee: P. Koroteev, P. Pushkar, A. V. Smirnov, and A. M. Zeitlin, “Quantum K-theory
of quiver varieties and many-body systems,” Selecta Mathematica, vol. 27,
no. 5. Springer Nature, 2021.
ista: Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. 2021. Quantum K-theory of quiver
varieties and many-body systems. Selecta Mathematica. 27(5), 87.
mla: Koroteev, Peter, et al. “Quantum K-Theory of Quiver Varieties and Many-Body
Systems.” Selecta Mathematica, vol. 27, no. 5, 87, Springer Nature, 2021,
doi:10.1007/s00029-021-00698-3.
short: P. Koroteev, P. Pushkar, A.V. Smirnov, A.M. Zeitlin, Selecta Mathematica
27 (2021).
date_created: 2021-09-12T22:01:22Z
date_published: 2021-08-30T00:00:00Z
date_updated: 2023-08-14T06:34:14Z
day: '30'
ddc:
- '530'
department:
- _id: TaHa
doi: 10.1007/s00029-021-00698-3
external_id:
isi:
- '000692795200001'
file:
- access_level: open_access
checksum: beadc5a722ffb48190e1e63ee2dbfee5
content_type: application/pdf
creator: cchlebak
date_created: 2021-09-13T11:31:34Z
date_updated: 2021-09-13T11:31:34Z
file_id: '10010'
file_name: 2021_SelectaMath_Koroteev.pdf
file_size: 584648
relation: main_file
success: 1
file_date_updated: 2021-09-13T11:31:34Z
has_accepted_license: '1'
intvolume: ' 27'
isi: 1
issue: '5'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Selecta Mathematica
publication_identifier:
eissn:
- 1420-9020
issn:
- 1022-1824
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum K-theory of quiver varieties and many-body systems
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: '9999'
abstract:
- lang: eng
text: 'The developmental strategies used by progenitor cells to endure a safe journey
from their induction place towards the site of terminal differentiation are still
poorly understood. Here we uncovered a progenitor cell allocation mechanism that
stems from an incomplete process of epithelial delamination that allows progenitors
to coordinate their movement with adjacent extra-embryonic tissues. Progenitors
of the zebrafish laterality organ originate from the surface epithelial enveloping
layer by an apical constriction process of cell delamination. During this process,
progenitors retain long-term apical contacts that enable the epithelial layer
to pull a subset of progenitors along their way towards the vegetal pole. The
remaining delaminated progenitors follow apically-attached progenitors’ movement
by a co-attraction mechanism, avoiding sequestration by the adjacent endoderm,
ensuring their fate and collective allocation at the differentiation site. Thus,
we reveal that incomplete delamination serves as a cellular platform for coordinated
tissue movements during development. Impact Statement: Incomplete delamination
serves as a cellular platform for coordinated tissue movements during development,
guiding newly formed progenitor cell groups to the differentiation site.'
article_number: e66483
article_processing_charge: Yes
article_type: original
author:
- first_name: Eduardo
full_name: Pulgar, Eduardo
last_name: Pulgar
- first_name: Cornelia
full_name: Schwayer, Cornelia
id: 3436488C-F248-11E8-B48F-1D18A9856A87
last_name: Schwayer
orcid: 0000-0001-5130-2226
- first_name: Néstor
full_name: Guerrero, Néstor
last_name: Guerrero
- first_name: Loreto
full_name: López, Loreto
last_name: López
- first_name: Susana
full_name: Márquez, Susana
last_name: Márquez
- first_name: Steffen
full_name: Härtel, Steffen
last_name: Härtel
- first_name: Rodrigo
full_name: Soto, Rodrigo
last_name: Soto
- first_name: Carl Philipp
full_name: Heisenberg, Carl Philipp
last_name: Heisenberg
- first_name: Miguel L.
full_name: Concha, Miguel L.
last_name: Concha
citation:
ama: Pulgar E, Schwayer C, Guerrero N, et al. Apical contacts stemming from incomplete
delamination guide progenitor cell allocation through a dragging mechanism. eLife.
2021;10. doi:10.7554/eLife.66483
apa: Pulgar, E., Schwayer, C., Guerrero, N., López, L., Márquez, S., Härtel, S.,
… Concha, M. L. (2021). Apical contacts stemming from incomplete delamination
guide progenitor cell allocation through a dragging mechanism. ELife. eLife
Sciences Publications. https://doi.org/10.7554/eLife.66483
chicago: Pulgar, Eduardo, Cornelia Schwayer, Néstor Guerrero, Loreto López, Susana
Márquez, Steffen Härtel, Rodrigo Soto, Carl Philipp Heisenberg, and Miguel L.
Concha. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor
Cell Allocation through a Dragging Mechanism.” ELife. eLife Sciences Publications,
2021. https://doi.org/10.7554/eLife.66483.
ieee: E. Pulgar et al., “Apical contacts stemming from incomplete delamination
guide progenitor cell allocation through a dragging mechanism,” eLife,
vol. 10. eLife Sciences Publications, 2021.
ista: Pulgar E, Schwayer C, Guerrero N, López L, Márquez S, Härtel S, Soto R, Heisenberg
CP, Concha ML. 2021. Apical contacts stemming from incomplete delamination guide
progenitor cell allocation through a dragging mechanism. eLife. 10, e66483.
mla: Pulgar, Eduardo, et al. “Apical Contacts Stemming from Incomplete Delamination
Guide Progenitor Cell Allocation through a Dragging Mechanism.” ELife,
vol. 10, e66483, eLife Sciences Publications, 2021, doi:10.7554/eLife.66483.
short: E. Pulgar, C. Schwayer, N. Guerrero, L. López, S. Márquez, S. Härtel, R.
Soto, C.P. Heisenberg, M.L. Concha, ELife 10 (2021).
date_created: 2021-09-12T22:01:23Z
date_published: 2021-08-27T00:00:00Z
date_updated: 2023-08-14T06:53:33Z
day: '27'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.7554/eLife.66483
ec_funded: 1
external_id:
isi:
- '000700428500001'
pmid:
- '34448451'
file:
- access_level: open_access
checksum: a3f82b0499cc822ac1eab48a01f3f57e
content_type: application/pdf
creator: dernst
date_created: 2022-05-13T08:03:37Z
date_updated: 2022-05-13T08:03:37Z
file_id: '11371'
file_name: 2021_eLife_Pulgar.pdf
file_size: 9010446
relation: main_file
success: 1
file_date_updated: 2022-05-13T08:03:37Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
keyword:
- cell delamination
- apical constriction
- dragging
- mechanical forces
- collective 18 locomotion
- dorsal forerunner cells
- zebrafish
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Apical contacts stemming from incomplete delamination guide progenitor cell
allocation through a dragging mechanism
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'
...