---
_id: '10220'
abstract:
- lang: eng
text: "We study conditions under which a finite simplicial complex K can be mapped
to ℝd without higher-multiplicity intersections. An almost r-embedding is a map
f: K → ℝd such that the images of any r pairwise disjoint simplices of K do not
have a common point. We show that if r is not a prime power and d ≥ 2r + 1, then
there is a counterexample to the topological Tverberg conjecture, i.e., there
is an almost r-embedding of the (d +1)(r − 1)-simplex in ℝd. This improves on
previous constructions of counterexamples (for d ≥ 3r) based on a series of papers
by M. Özaydin, M. Gromov, P. Blagojević, F. Frick, G. Ziegler, and the second
and fourth present authors.\r\n\r\nThe counterexamples are obtained by proving
the following algebraic criterion in codimension 2: If r ≥ 3 and if K is a finite
2(r − 1)-complex, then there exists an almost r-embedding K → ℝ2r if and only
if there exists a general position PL map f: K → ℝ2r such that the algebraic intersection
number of the f-images of any r pairwise disjoint simplices of K is zero. This
result can be restated in terms of a cohomological obstruction and extends an
analogous codimension 3 criterion by the second and fourth authors. As another
application, we classify ornaments f: S3 ⊔ S3 ⊔ S3 → ℝ5 up to ornament concordance.\r\n\r\nIt
follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous
criterion for r = 2 is false. We prove a lemma on singular higher-dimensional
Borromean rings, yielding an elementary proof of the counterexample."
acknowledgement: Research supported by the Swiss National Science Foundation (Project
SNSF-PP00P2-138948), by the Austrian Science Fund (FWF Project P31312-N35), by the
Russian Foundation for Basic Research (Grants No. 15-01-06302 and 19-01-00169),
by a Simons-IUM Fellowship, and by the D. Zimin Dynasty Foundation Grant. We would
like to thank E. Alkin, A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner
and anonymous referees for helpful comments and discussions.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
- first_name: Arkadiy B.
full_name: Skopenkov, Arkadiy B.
last_name: Skopenkov
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. Eliminating higher-multiplicity
intersections. III. Codimension 2. Israel Journal of Mathematics. 2021;245:501–534.
doi:10.1007/s11856-021-2216-z
apa: Avvakumov, S., Mabillard, I., Skopenkov, A. B., & Wagner, U. (2021). Eliminating
higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics.
Springer Nature. https://doi.org/10.1007/s11856-021-2216-z
chicago: Avvakumov, Sergey, Isaac Mabillard, Arkadiy B. Skopenkov, and Uli Wagner.
“Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” Israel
Journal of Mathematics. Springer Nature, 2021. https://doi.org/10.1007/s11856-021-2216-z.
ieee: S. Avvakumov, I. Mabillard, A. B. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity
intersections. III. Codimension 2,” Israel Journal of Mathematics, vol.
245. Springer Nature, pp. 501–534, 2021.
ista: Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. 2021. Eliminating higher-multiplicity
intersections. III. Codimension 2. Israel Journal of Mathematics. 245, 501–534.
mla: Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections. III.
Codimension 2.” Israel Journal of Mathematics, vol. 245, Springer Nature,
2021, pp. 501–534, doi:10.1007/s11856-021-2216-z.
short: S. Avvakumov, I. Mabillard, A.B. Skopenkov, U. Wagner, Israel Journal of
Mathematics 245 (2021) 501–534.
date_created: 2021-11-07T23:01:24Z
date_published: 2021-10-30T00:00:00Z
date_updated: 2023-08-14T11:43:55Z
day: '30'
department:
- _id: UlWa
doi: 10.1007/s11856-021-2216-z
external_id:
arxiv:
- '1511.03501'
isi:
- '000712942100013'
intvolume: ' 245'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.03501
month: '10'
oa: 1
oa_version: Preprint
page: '501–534 '
project:
- _id: 26611F5C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31312
name: Algorithms for Embeddings and Homotopy Theory
publication: Israel Journal of Mathematics
publication_identifier:
eissn:
- 1565-8511
issn:
- 0021-2172
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8183'
relation: earlier_version
status: public
- id: '9308'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Eliminating higher-multiplicity intersections. III. Codimension 2
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 245
year: '2021'
...
---
_id: '10221'
abstract:
- lang: eng
text: We prove that any deterministic matrix is approximately the identity in the
eigenbasis of a large random Wigner matrix with very high probability and with
an optimal error inversely proportional to the square root of the dimension. Our
theorem thus rigorously verifies the Eigenstate Thermalisation Hypothesis by Deutsch
(Phys Rev A 43:2046–2049, 1991) for the simplest chaotic quantum system, the Wigner
ensemble. In mathematical terms, we prove the strong form of Quantum Unique Ergodicity
(QUE) with an optimal convergence rate for all eigenvectors simultaneously, generalizing
previous probabilistic QUE results in Bourgade and Yau (Commun Math Phys 350:231–278,
2017) and Bourgade et al. (Commun Pure Appl Math 73:1526–1596, 2020).
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: 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. Eigenstate thermalization hypothesis for
Wigner matrices. Communications in Mathematical Physics. 2021;388(2):1005–1048.
doi:10.1007/s00220-021-04239-z
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Eigenstate thermalization
hypothesis for Wigner matrices. Communications in Mathematical Physics.
Springer Nature. https://doi.org/10.1007/s00220-021-04239-z
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Eigenstate Thermalization
Hypothesis for Wigner Matrices.” Communications in Mathematical Physics.
Springer Nature, 2021. https://doi.org/10.1007/s00220-021-04239-z.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Eigenstate thermalization hypothesis
for Wigner matrices,” Communications in Mathematical Physics, vol. 388,
no. 2. Springer Nature, pp. 1005–1048, 2021.
ista: Cipolloni G, Erdös L, Schröder DJ. 2021. Eigenstate thermalization hypothesis
for Wigner matrices. Communications in Mathematical Physics. 388(2), 1005–1048.
mla: Cipolloni, Giorgio, et al. “Eigenstate Thermalization Hypothesis for Wigner
Matrices.” Communications in Mathematical Physics, vol. 388, no. 2, Springer
Nature, 2021, pp. 1005–1048, doi:10.1007/s00220-021-04239-z.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics
388 (2021) 1005–1048.
date_created: 2021-11-07T23:01:25Z
date_published: 2021-10-29T00:00:00Z
date_updated: 2023-08-14T10:29:49Z
day: '29'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00220-021-04239-z
external_id:
arxiv:
- '2012.13215'
isi:
- '000712232700001'
file:
- access_level: open_access
checksum: a2c7b6f5d23b5453cd70d1261272283b
content_type: application/pdf
creator: cchlebak
date_created: 2022-02-02T10:19:55Z
date_updated: 2022-02-02T10:19:55Z
file_id: '10715'
file_name: 2021_CommunMathPhys_Cipolloni.pdf
file_size: 841426
relation: main_file
success: 1
file_date_updated: 2022-02-02T10:19:55Z
has_accepted_license: '1'
intvolume: ' 388'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1005–1048
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
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: Eigenstate thermalization hypothesis 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: 388
year: '2021'
...
---
_id: '10222'
abstract:
- lang: eng
text: Consider a random set of points on the unit sphere in ℝd, which can be either
uniformly sampled or a Poisson point process. Its convex hull is a random inscribed
polytope, whose boundary approximates the sphere. We focus on the case d = 3,
for which there are elementary proofs and fascinating formulas for metric properties.
In particular, we study the fraction of acute facets, the expected intrinsic volumes,
the total edge length, and the distance to a fixed point. Finally we generalize
the results to the ellipsoid with homeoid density.
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme,
grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant
no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization
in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.\r\nWe
are grateful to Dmitry Zaporozhets and Christoph Thäle for valuable comments and
for directing us to relevant references. We also thank to Anton Mellit for a useful
discussion on Bessel functions."
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Anton
full_name: Nikitenko, Anton
id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87
last_name: Nikitenko
orcid: 0000-0002-0659-3201
citation:
ama: Akopyan A, Edelsbrunner H, Nikitenko A. The beauty of random polytopes inscribed
in the 2-sphere. Experimental Mathematics. 2021:1-15. doi:10.1080/10586458.2021.1980459
apa: Akopyan, A., Edelsbrunner, H., & Nikitenko, A. (2021). The beauty of random
polytopes inscribed in the 2-sphere. Experimental Mathematics. Taylor and
Francis. https://doi.org/10.1080/10586458.2021.1980459
chicago: Akopyan, Arseniy, Herbert Edelsbrunner, and Anton Nikitenko. “The Beauty
of Random Polytopes Inscribed in the 2-Sphere.” Experimental Mathematics.
Taylor and Francis, 2021. https://doi.org/10.1080/10586458.2021.1980459.
ieee: A. Akopyan, H. Edelsbrunner, and A. Nikitenko, “The beauty of random polytopes
inscribed in the 2-sphere,” Experimental Mathematics. Taylor and Francis,
pp. 1–15, 2021.
ista: Akopyan A, Edelsbrunner H, Nikitenko A. 2021. The beauty of random polytopes
inscribed in the 2-sphere. Experimental Mathematics., 1–15.
mla: Akopyan, Arseniy, et al. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.”
Experimental Mathematics, Taylor and Francis, 2021, pp. 1–15, doi:10.1080/10586458.2021.1980459.
short: A. Akopyan, H. Edelsbrunner, A. Nikitenko, Experimental Mathematics (2021)
1–15.
date_created: 2021-11-07T23:01:25Z
date_published: 2021-10-25T00:00:00Z
date_updated: 2023-08-14T11:57:07Z
day: '25'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1080/10586458.2021.1980459
ec_funded: 1
external_id:
arxiv:
- '2007.07783'
isi:
- '000710893500001'
file:
- access_level: open_access
checksum: 3514382e3a1eb87fa6c61ad622874415
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T11:55:10Z
date_updated: 2023-08-14T11:55:10Z
file_id: '14053'
file_name: 2023_ExperimentalMath_Akopyan.pdf
file_size: 1966019
relation: main_file
success: 1
file_date_updated: 2023-08-14T11:55:10Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1-15
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
- _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316
grant_number: I4887
name: Discretization in Geometry and Dynamics
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Experimental Mathematics
publication_identifier:
eissn:
- 1944-950X
issn:
- 1058-6458
publication_status: published
publisher: Taylor and Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: The beauty of random polytopes inscribed in the 2-sphere
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10223'
abstract:
- lang: eng
text: Growth regulation tailors development in plants to their environment. A prominent
example of this is the response to gravity, in which shoots bend up and roots
bend down1. This paradox is based on opposite effects of the phytohormone auxin,
which promotes cell expansion in shoots while inhibiting it in roots via a yet
unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic
engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding
of how auxin inhibits root growth. We show that auxin activates two distinct,
antagonistically acting signalling pathways that converge on rapid regulation
of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE
KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma
membrane H+-ATPases for apoplast acidification, while intracellular canonical
auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization.
Simultaneous activation of these two counteracting mechanisms poises roots for
rapid, fine-tuned growth modulation in navigating complex soil environments.
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
- _id: Bio
acknowledgement: We thank N. Gnyliukh and L. Hörmayer for technical assistance and
N. Paris for sharing PM-Cyto seeds. We gratefully acknowledge the Life Science,
Machine Shop and Bioimaging Facilities of IST Austria. This project has received
funding from the European Research Council Advanced Grant (ETAP-742985) and the
Austrian Science Fund (FWF) under I 3630-B25 to J.F., the National Institutes of
Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research
(NWO; VIDI-864.13.001), Research Foundation-Flanders (FWO; Odysseus II G0D0515N)
and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R.,
the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research
to M.R. and D.W., the Australian Research Council and China National Distinguished
Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685)
and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and
innovation programme under Marie Skłodowska-Curie grant agreement no. 665385 and
the DOC Fellowship of the Austrian Academy of Sciences to L.L., and the China Scholarship
Council to J.C.
article_processing_charge: No
article_type: original
author:
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Mark
full_name: Roosjen, Mark
last_name: Roosjen
- first_name: Koji
full_name: Takahashi, Koji
last_name: Takahashi
- first_name: Lesia
full_name: Rodriguez Solovey, Lesia
id: 3922B506-F248-11E8-B48F-1D18A9856A87
last_name: Rodriguez Solovey
orcid: 0000-0002-7244-7237
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Jian
full_name: Chen, Jian
last_name: Chen
- first_name: Lana
full_name: Shabala, Lana
last_name: Shabala
- first_name: Wouter
full_name: Smet, Wouter
last_name: Smet
- first_name: Hong
full_name: Ren, Hong
last_name: Ren
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Sergey
full_name: Shabala, Sergey
last_name: Shabala
- first_name: Bert
full_name: De Rybel, Bert
last_name: De Rybel
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Toshinori
full_name: Kinoshita, Toshinori
last_name: Kinoshita
- first_name: William M.
full_name: Gray, William M.
last_name: Gray
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin
signalling for H+ fluxes in root growth. Nature. 2021;599(7884):273-277.
doi:10.1038/s41586-021-04037-6
apa: Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L.,
Merrin, J., … Friml, J. (2021). Cell surface and intracellular auxin signalling
for H+ fluxes in root growth. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-04037-6
chicago: Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez
Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin
Signalling for H+ Fluxes in Root Growth.” Nature. Springer Nature,
2021. https://doi.org/10.1038/s41586-021-04037-6.
ieee: L. Li et al., “Cell surface and intracellular auxin signalling for
H+ fluxes in root growth,” Nature, vol. 599, no. 7884. Springer
Nature, pp. 273–277, 2021.
ista: Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J,
Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D,
Kinoshita T, Gray WM, Friml J. 2021. Cell surface and intracellular auxin signalling
for H+ fluxes in root growth. Nature. 599(7884), 273–277.
mla: Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+
Fluxes in Root Growth.” Nature, vol. 599, no. 7884, Springer Nature, 2021,
pp. 273–77, doi:10.1038/s41586-021-04037-6.
short: L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J.
Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel,
D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Nature 599 (2021) 273–277.
date_created: 2021-11-07T23:01:25Z
date_published: 2021-11-11T00:00:00Z
date_updated: 2024-10-29T10:22:45Z
day: '11'
department:
- _id: JiFr
- _id: NanoFab
doi: 10.1038/s41586-021-04037-6
ec_funded: 1
external_id:
isi:
- '000713338100006'
pmid:
- '34707283'
intvolume: ' 599'
isi: 1
issue: '7884'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.doi.org/10.21203/rs.3.rs-266395/v3
month: '11'
oa: 1
oa_version: Preprint
page: 273-277
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
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 26B4D67E-B435-11E9-9278-68D0E5697425
grant_number: '25351'
name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated
Rapid Growth Inhibition in Arabidopsis Root'
publication: Nature
publication_identifier:
eissn:
- '14764687'
issn:
- '00280836'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/stop-and-grow/
record:
- id: '10095'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Cell surface and intracellular auxin signalling for H+ fluxes in
root growth
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 599
year: '2021'
...
---
_id: '10224'
abstract:
- lang: eng
text: We investigate the Fröhlich polaron model on a three-dimensional torus, and
give a proof of the second-order quantum corrections to its ground-state energy
in the strong-coupling limit. Compared to previous work in the confined case,
the translational symmetry (and its breaking in the Pekar approximation) makes
the analysis substantially more challenging.
acknowledgement: "Funding from the European Union’s Horizon 2020 research and innovation
programme under the ERC grant agreement No 694227 is gratefully acknowledged. We
would also like to thank Rupert Frank for many helpful discussions, especially related
to the Gross coordinate transformation defined in Def. 4.7.\r\nOpen access funding
provided by Institute of Science and Technology (IST Austria)."
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum
corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis.
2021;242(3):1835–1906. doi:10.1007/s00205-021-01715-7'
apa: 'Feliciangeli, D., & Seiringer, R. (2021). The strongly coupled polaron
on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational
Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01715-7'
chicago: 'Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron
on the Torus: Quantum Corrections to the Pekar Asymptotics.” Archive for Rational
Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01715-7.'
ieee: 'D. Feliciangeli and R. Seiringer, “The strongly coupled polaron on the torus:
Quantum corrections to the Pekar asymptotics,” Archive for Rational Mechanics
and Analysis, vol. 242, no. 3. Springer Nature, pp. 1835–1906, 2021.'
ista: 'Feliciangeli D, Seiringer R. 2021. The strongly coupled polaron on the torus:
Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and
Analysis. 242(3), 1835–1906.'
mla: 'Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on
the Torus: Quantum Corrections to the Pekar Asymptotics.” Archive for Rational
Mechanics and Analysis, vol. 242, no. 3, Springer Nature, 2021, pp. 1835–1906,
doi:10.1007/s00205-021-01715-7.'
short: D. Feliciangeli, R. Seiringer, Archive for Rational Mechanics and Analysis
242 (2021) 1835–1906.
date_created: 2021-11-07T23:01:26Z
date_published: 2021-10-25T00:00:00Z
date_updated: 2023-08-14T10:32:19Z
day: '25'
ddc:
- '530'
department:
- _id: RoSe
doi: 10.1007/s00205-021-01715-7
ec_funded: 1
external_id:
arxiv:
- '2101.12566'
isi:
- '000710850600001'
file:
- access_level: open_access
checksum: 672e9c21b20f1a50854b7c821edbb92f
content_type: application/pdf
creator: alisjak
date_created: 2021-12-14T08:35:42Z
date_updated: 2021-12-14T08:35:42Z
file_id: '10544'
file_name: 2021_Springer_Feliciangeli.pdf
file_size: 990529
relation: main_file
success: 1
file_date_updated: 2021-12-14T08:35:42Z
has_accepted_license: '1'
intvolume: ' 242'
isi: 1
issue: '3'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1835–1906
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Archive for Rational Mechanics and Analysis
publication_identifier:
eissn:
- 1432-0673
issn:
- 0003-9527
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '9787'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'The strongly coupled polaron on the torus: Quantum corrections to the Pekar
asymptotics'
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: 242
year: '2021'
...
---
_id: '10267'
abstract:
- lang: eng
text: Tropisms are among the most important growth responses for plant adaptation
to the surrounding environment. One of the most common tropisms is root gravitropism.
Root gravitropism enables the plant to anchor securely to the soil enabling the
absorption of water and nutrients. Most of the knowledge related to the plant
gravitropism has been acquired from the flowering plants, due to limited research
in non-seed plants. Limited research on non-seed plants is due in large part to
the lack of standard research methods. Here, we describe the experimental methods
to evaluate gravitropism in representative non-seed plant species, including the
non-vascular plant moss Physcomitrium patens, the early diverging extant vascular
plant lycophyte Selaginella moellendorffii and fern Ceratopteris richardii. In
addition, we introduce the methods used for statistical analysis of the root gravitropism
in non-seed plant species.
acknowledgement: The Ceratopteris richardii spores were obtained from the lab of Jo
Ann Banks at Purdue University. This work was supported by funding from the European
Union’s Horizon 2020 research and innovation program (ERC grant agreement number
742985), Austrian Science Fund (FWF, grant number I 3630-B25), IST Fellow program
and DOC Fellowship of the Austrian Academy of Sciences.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Yuzhou
full_name: Zhang, Yuzhou
id: 3B6137F2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-2627-6956
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Zhang Y, Li L, Friml J. Evaluation of gravitropism in non-seed plants. In:
Blancaflor EB, ed. Plant Gravitropism. Vol 2368. MIMB. Springer Nature;
2021:43-51. doi:10.1007/978-1-0716-1677-2_2'
apa: Zhang, Y., Li, L., & Friml, J. (2021). Evaluation of gravitropism in non-seed
plants. In E. B. Blancaflor (Ed.), Plant Gravitropism (Vol. 2368, pp. 43–51).
Springer Nature. https://doi.org/10.1007/978-1-0716-1677-2_2
chicago: Zhang, Yuzhou, Lanxin Li, and Jiří Friml. “Evaluation of Gravitropism in
Non-Seed Plants.” In Plant Gravitropism, edited by Elison B Blancaflor,
2368:43–51. MIMB. Springer Nature, 2021. https://doi.org/10.1007/978-1-0716-1677-2_2.
ieee: Y. Zhang, L. Li, and J. Friml, “Evaluation of gravitropism in non-seed plants,”
in Plant Gravitropism, vol. 2368, E. B. Blancaflor, Ed. Springer Nature,
2021, pp. 43–51.
ista: 'Zhang Y, Li L, Friml J. 2021.Evaluation of gravitropism in non-seed plants.
In: Plant Gravitropism. Methods in Molecular Biology, vol. 2368, 43–51.'
mla: Zhang, Yuzhou, et al. “Evaluation of Gravitropism in Non-Seed Plants.” Plant
Gravitropism, edited by Elison B Blancaflor, vol. 2368, Springer Nature, 2021,
pp. 43–51, doi:10.1007/978-1-0716-1677-2_2.
short: Y. Zhang, L. Li, J. Friml, in:, E.B. Blancaflor (Ed.), Plant Gravitropism,
Springer Nature, 2021, pp. 43–51.
date_created: 2021-11-11T09:26:10Z
date_published: 2021-10-14T00:00:00Z
date_updated: 2022-08-26T09:13:00Z
day: '14'
department:
- _id: JiFr
doi: 10.1007/978-1-0716-1677-2_2
ec_funded: 1
editor:
- first_name: Elison B
full_name: Blancaflor, Elison B
last_name: Blancaflor
external_id:
pmid:
- '34647246'
intvolume: ' 2368'
language:
- iso: eng
month: '10'
oa_version: None
page: 43-51
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: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: Plant Gravitropism
publication_identifier:
eisbn:
- 978-1-0716-1677-2
isbn:
- 978-1-0716-1676-5
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Evaluation of gravitropism in non-seed plants
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2368
year: '2021'
...
---
_id: '10268'
abstract:
- lang: eng
text: The analysis of dynamic cellular processes such as plant cytokinesis stands
and falls with live-cell time-lapse confocal imaging. Conventional approaches
to time-lapse imaging of cell division in Arabidopsis root tips are tedious and
have low throughput. Here, we describe a protocol for long-term time-lapse simultaneous
imaging of multiple root tips on a vertical-stage confocal microscope with automated
root tracking. We also provide modifications of the basic protocol to implement
this imaging method in the analysis of genetic, pharmacological or laser ablation
wounding-mediated experimental manipulations. Our method dramatically improves
the efficiency of cell division time-lapse imaging by increasing the throughput,
while reducing the person-hour requirements of such experiments.
acknowledged_ssus:
- _id: Bio
acknowledgement: We thank B. De Rybel for allowing M.G. to work on this manuscript
during a postdoc in his laboratory, and EMBO for supporting M.G. with a Long-Term
fellowship (ALTF 1005-2019) during this time. We acknowledge the service and support
by the Bioimaging Facility at IST Austria, and finally, we thank A. Mally for proofreading
and correcting the manuscript.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
citation:
ama: 'Hörmayer L, Friml J, Glanc M. Automated time-lapse imaging and manipulation
of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy.
In: Plant Cell Division. Vol 2382. MIMB. Humana Press; 2021:105-114. doi:10.1007/978-1-0716-1744-1_6'
apa: Hörmayer, L., Friml, J., & Glanc, M. (2021). Automated time-lapse imaging
and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal
microscopy. In Plant Cell Division (Vol. 2382, pp. 105–114). Humana Press.
https://doi.org/10.1007/978-1-0716-1744-1_6
chicago: Hörmayer, Lukas, Jiří Friml, and Matous Glanc. “Automated Time-Lapse Imaging
and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal
Microscopy.” In Plant Cell Division, 2382:105–14. MIMB. Humana Press, 2021.
https://doi.org/10.1007/978-1-0716-1744-1_6.
ieee: L. Hörmayer, J. Friml, and M. Glanc, “Automated time-lapse imaging and manipulation
of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy,”
in Plant Cell Division, vol. 2382, Humana Press, 2021, pp. 105–114.
ista: 'Hörmayer L, Friml J, Glanc M. 2021.Automated time-lapse imaging and manipulation
of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy.
In: Plant Cell Division. Methods in Molecular Biology, vol. 2382, 105–114.'
mla: Hörmayer, Lukas, et al. “Automated Time-Lapse Imaging and Manipulation of Cell
Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” Plant
Cell Division, vol. 2382, Humana Press, 2021, pp. 105–14, doi:10.1007/978-1-0716-1744-1_6.
short: L. Hörmayer, J. Friml, M. Glanc, in:, Plant Cell Division, Humana Press,
2021, pp. 105–114.
date_created: 2021-11-11T10:03:30Z
date_published: 2021-10-28T00:00:00Z
date_updated: 2022-06-03T06:47:06Z
day: '28'
department:
- _id: JiFr
doi: 10.1007/978-1-0716-1744-1_6
external_id:
pmid:
- '34705235'
intvolume: ' 2382'
language:
- iso: eng
month: '10'
oa_version: None
page: 105-114
pmid: 1
publication: Plant Cell Division
publication_identifier:
eisbn:
- 978-1-0716-1744-1
eissn:
- 1940-6029
isbn:
- 978-1-0716-1743-4
issn:
- 1064-3745
publication_status: published
publisher: Humana Press
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis
roots by vertical-stage confocal microscopy
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2382
year: '2021'
...
---
_id: '10270'
abstract:
- lang: eng
text: Plants develop new organs to adjust their bodies to dynamic changes in the
environment. How independent organs achieve anisotropic shapes and polarities
is poorly understood. To address this question, we constructed a mechano-biochemical
model for Arabidopsis root meristem growth that integrates biologically plausible
principles. Computer model simulations demonstrate how differential growth of
neighboring tissues results in the initial symmetry-breaking leading to anisotropic
root growth. Furthermore, the root growth feeds back on a polar transport network
of the growth regulator auxin. Model, predictions are in close agreement with
in vivo patterns of anisotropic growth, auxin distribution, and cell polarity,
as well as several root phenotypes caused by chemical, mechanical, or genetic
perturbations. Our study demonstrates that the combination of tissue mechanics
and polar auxin transport organizes anisotropic root growth and cell polarities
during organ outgrowth. Therefore, a mobile auxin signal transported through immobile
cells drives polarity and growth mechanics to coordinate complex organ development.
acknowledgement: 'e are grateful Richard Smith, Anne-Lise Routier, Crisanto Gutierrez
and Juergen Kleine-Vehn for providing critical comments on the manuscript. Funding:
This work was supported by the Programa de Atraccion de Talento 2017 (Comunidad
de Madrid, 2017-T1/BIO-5654 to KW), Severo Ochoa (SO) Programme for Centres of Excellence
in R&D from the Agencia Estatal de Investigacion of Spain (grant SEV-2016–0672 (2017–2021)
to KW via the CBGP). In the frame of SEV-2016–0672 funding MM is supported with
a postdoctoral contract. KW was supported by Programa Estatal de Generacion del
Conocimiento y Fortalecimiento Cientıfico y Tecnologico del Sistema de I + D + I
2019 (PGC2018-093387-A-I00) from MICIU (to KW). MG is recipient of an IST Interdisciplinary
Project (IC1022IPC03).'
article_number: '72132'
article_processing_charge: Yes
article_type: original
author:
- first_name: Marco
full_name: Marconi, Marco
last_name: Marconi
- first_name: Marçal
full_name: Gallemi, Marçal
id: 460C6802-F248-11E8-B48F-1D18A9856A87
last_name: Gallemi
orcid: 0000-0003-4675-6893
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Krzysztof
full_name: Wabnik, Krzysztof
last_name: Wabnik
citation:
ama: Marconi M, Gallemi M, Benková E, Wabnik K. A coupled mechano-biochemical model
for cell polarity guided anisotropic root growth. eLife. 2021;10. doi:10.7554/elife.72132
apa: Marconi, M., Gallemi, M., Benková, E., & Wabnik, K. (2021). A coupled mechano-biochemical
model for cell polarity guided anisotropic root growth. ELife. eLife Sciences
Publications. https://doi.org/10.7554/elife.72132
chicago: Marconi, Marco, Marçal Gallemi, Eva Benková, and Krzysztof Wabnik. “A Coupled
Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” ELife.
eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72132.
ieee: M. Marconi, M. Gallemi, E. Benková, and K. Wabnik, “A coupled mechano-biochemical
model for cell polarity guided anisotropic root growth,” eLife, vol. 10.
eLife Sciences Publications, 2021.
ista: Marconi M, Gallemi M, Benková E, Wabnik K. 2021. A coupled mechano-biochemical
model for cell polarity guided anisotropic root growth. eLife. 10, 72132.
mla: Marconi, Marco, et al. “A Coupled Mechano-Biochemical Model for Cell Polarity
Guided Anisotropic Root Growth.” ELife, vol. 10, 72132, eLife Sciences
Publications, 2021, doi:10.7554/elife.72132.
short: M. Marconi, M. Gallemi, E. Benková, K. Wabnik, ELife 10 (2021).
date_created: 2021-11-11T10:05:18Z
date_published: 2021-11-01T00:00:00Z
date_updated: 2023-08-14T11:49:23Z
day: '01'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.7554/elife.72132
external_id:
isi:
- '000734671200001'
pmid:
- '34723798'
file:
- access_level: open_access
checksum: fad13c509b53bb7a2bef9c946a7ca60a
content_type: application/pdf
creator: dernst
date_created: 2022-05-13T09:00:29Z
date_updated: 2022-05-13T09:00:29Z
file_id: '11372'
file_name: 2021_eLife_Marconi.pdf
file_size: 14137503
relation: main_file
success: 1
file_date_updated: 2022-05-13T09:00:29Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: A coupled mechano-biochemical model for cell polarity guided anisotropic root
growth
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: '10271'
abstract:
- lang: eng
text: Understanding interactions between antibiotics used in combination is an important
theme in microbiology. Using the interactions between the antifolate drug trimethoprim
and the ribosome-targeting antibiotic erythromycin in Escherichia coli as a model,
we applied a transcriptomic approach for dissecting interactions between two antibiotics
with different modes of action. When trimethoprim and erythromycin were combined,
the transcriptional response of genes from the sulfate reduction pathway deviated
from the dominant effect of trimethoprim on the transcriptome. We successfully
altered the drug interaction from additivity to suppression by increasing the
sulfate level in the growth environment and identified sulfate reduction as an
important metabolic determinant that shapes the interaction between the two drugs.
Our work highlights the potential of using prioritization of gene expression patterns
as a tool for identifying key metabolic determinants that shape drug-drug interactions.
We further demonstrated that the sigma factor-binding protein gene crl shapes
the interactions between the two antibiotics, which provides a rare example of
how naturally occurring variations between strains of the same bacterial species
can sometimes generate very different drug interactions.
acknowledgement: High-throughput sequencing data were generated by the Vienna BioCenter
Core Facilities. The authors would like to thank Karin Mitosch, Bor Kavcic, and
Nadine Kraupner for their constructive feedback. The authors would also like to
thank Gertraud Stift, Julia Flor, Renate Srsek, Agnieszka Wiktor, and Booshini Fernando
for technical support.
article_number: '760017'
article_processing_charge: No
article_type: original
author:
- first_name: Qin
full_name: Qi, Qin
id: 3B22D412-F248-11E8-B48F-1D18A9856A87
last_name: Qi
orcid: 0000-0002-6148-2416
- first_name: S. Andreas
full_name: Angermayr, S. Andreas
last_name: Angermayr
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Qi Q, Angermayr SA, Bollenbach MT. Uncovering Key Metabolic Determinants of
the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli.
Frontiers in Microbiology. 2021;12. doi:10.3389/fmicb.2021.760017
apa: Qi, Q., Angermayr, S. A., & Bollenbach, M. T. (2021). Uncovering Key Metabolic
Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in
Escherichia coli. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2021.760017
chicago: Qi, Qin, S. Andreas Angermayr, and Mark Tobias Bollenbach. “Uncovering
Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin
in Escherichia Coli.” Frontiers in Microbiology. Frontiers, 2021. https://doi.org/10.3389/fmicb.2021.760017.
ieee: Q. Qi, S. A. Angermayr, and M. T. Bollenbach, “Uncovering Key Metabolic Determinants
of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia
coli,” Frontiers in Microbiology, vol. 12. Frontiers, 2021.
ista: Qi Q, Angermayr SA, Bollenbach MT. 2021. Uncovering Key Metabolic Determinants
of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia
coli. Frontiers in Microbiology. 12, 760017.
mla: Qi, Qin, et al. “Uncovering Key Metabolic Determinants of the Drug Interactions
Between Trimethoprim and Erythromycin in Escherichia Coli.” Frontiers in Microbiology,
vol. 12, 760017, Frontiers, 2021, doi:10.3389/fmicb.2021.760017.
short: Q. Qi, S.A. Angermayr, M.T. Bollenbach, Frontiers in Microbiology 12 (2021).
date_created: 2021-11-11T10:39:37Z
date_published: 2021-10-20T00:00:00Z
date_updated: 2023-08-14T11:43:23Z
day: '20'
ddc:
- '610'
doi: 10.3389/fmicb.2021.760017
ec_funded: 1
external_id:
isi:
- '000715997300001'
pmid:
- '34745067'
file:
- access_level: open_access
checksum: d41321748e9588dd3cf03e9a7222127f
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-11T10:54:40Z
date_updated: 2021-11-11T10:54:40Z
file_id: '10272'
file_name: 2021_FrontiersMicrob_Qi.pdf
file_size: 2397203
relation: main_file
success: 1
file_date_updated: 2021-11-11T10:54:40Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
keyword:
- microbiology
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
publication: Frontiers in Microbiology
publication_identifier:
eissn:
- 1664-302X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim
and Erythromycin in Escherichia coli
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: '10280'
abstract:
- lang: eng
text: 'Machines enabled the Industrial Revolution and are central to modern technological
progress: A machine’s parts transmit forces, motion, and energy to one another
in a predetermined manner. Today’s engineering frontier, building artificial micromachines
that emulate the biological machinery of living organisms, requires faithful assembly
and energy consumption at the microscale. Here, we demonstrate the programmable
assembly of active particles into autonomous metamachines using optical templates.
Metamachines, or machines made of machines, are stable, mobile and autonomous
architectures, whose dynamics stems from the geometry. We use the interplay between
anisotropic force generation of the active colloids with the control of their
orientation by local geometry. This allows autonomous reprogramming of active
particles of the metamachines to achieve multiple functions. It permits the modular
assembly of metamachines by fusion, reconfiguration of metamachines and, we anticipate,
a shift in focus of self-assembly towards active matter and reprogrammable materials.'
acknowledgement: The authors thank R. Jazzar for useful advice regarding the synthesis
of heterodimers. We thank S. Sacanna for critical reading. This material is based
upon work supported by the National Science Foundation under Grant No. DMR-1554724
and Department of Army Research under grant W911NF-20-1-0112.
article_number: '6398'
article_processing_charge: Yes
article_type: original
author:
- first_name: Antoine
full_name: Aubret, Antoine
last_name: Aubret
- first_name: Quentin
full_name: Martinet, Quentin
id: b37485a8-d343-11eb-a0e9-df8c484ef8ab
last_name: Martinet
orcid: 0000-0002-2916-6632
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: Aubret A, Martinet Q, Palacci JA. Metamachines of pluripotent colloids. Nature
Communications. 2021;12(1). doi:10.1038/s41467-021-26699-6
apa: Aubret, A., Martinet, Q., & Palacci, J. A. (2021). Metamachines of pluripotent
colloids. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26699-6
chicago: Aubret, Antoine, Quentin Martinet, and Jérémie A Palacci. “Metamachines
of Pluripotent Colloids.” Nature Communications. Springer Nature, 2021.
https://doi.org/10.1038/s41467-021-26699-6.
ieee: A. Aubret, Q. Martinet, and J. A. Palacci, “Metamachines of pluripotent colloids,”
Nature Communications, vol. 12, no. 1. Springer Nature, 2021.
ista: Aubret A, Martinet Q, Palacci JA. 2021. Metamachines of pluripotent colloids.
Nature Communications. 12(1), 6398.
mla: Aubret, Antoine, et al. “Metamachines of Pluripotent Colloids.” Nature Communications,
vol. 12, no. 1, 6398, Springer Nature, 2021, doi:10.1038/s41467-021-26699-6.
short: A. Aubret, Q. Martinet, J.A. Palacci, Nature Communications 12 (2021).
date_created: 2021-11-14T23:01:23Z
date_published: 2021-11-04T00:00:00Z
date_updated: 2023-08-14T11:48:37Z
day: '04'
ddc:
- '530'
department:
- _id: JePa
doi: 10.1038/s41467-021-26699-6
external_id:
isi:
- '000714754400010'
pmid:
- '34737315'
file:
- access_level: open_access
checksum: 1c392b12b9b7b615d422d9fabe19cdb9
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-15T13:25:52Z
date_updated: 2021-11-15T13:25:52Z
file_id: '10292'
file_name: 2021_NatComm_Aubret.pdf
file_size: 6282703
relation: main_file
success: 1
file_date_updated: 2021-11-15T13:25:52Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Metamachines of pluripotent colloids
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: '10281'
abstract:
- lang: eng
text: Mutations affecting mTOR or RAS signaling underlie defined syndromes (the
so-called mTORopathies and RASopathies) with high risk for Autism Spectrum Disorder
(ASD). These syndromes show a broad variety of somatic phenotypes including cancers,
skin abnormalities, heart disease and facial dysmorphisms. Less well studied are
the neuropsychiatric symptoms such as ASD. Here, we assess the relevance of these
signalopathies in ASD reviewing genetic, human cell model, rodent studies and
clinical trials. We conclude that signalopathies have an increased liability for
ASD and that, in particular, ASD individuals with dysmorphic features and intellectual
disability (ID) have a higher chance for disruptive mutations in RAS- and mTOR-related
genes. Studies on rodent and human cell models confirm aberrant neuronal development
as the underlying pathology. Human studies further suggest that multiple hits
are necessary to induce the respective phenotypes. Recent clinical trials do only
report improvements for comorbid conditions such as epilepsy or cancer but not
for behavioral aspects. Animal models show that treatment during early development
can rescue behavioral phenotypes. Taken together, we suggest investigating the
differential roles of mTOR and RAS signaling in both human and rodent models,
and to test drug treatment both during and after neuronal development in the available
model systems
acknowledgement: 'This review was funded by the IMI2 Initiative under the grant AIMS-2-TRIALS
No 777394, by the Hessian Ministry for Science and Arts; State of Hesse Ministry
for Science and Arts: LOEWE-Grant to the CePTER-Consortium (www.uni-frankfurt.de/67689811);
Research (BMBF) under the grant RAISE-genic No 779282 all to AGC. This work was
also supported by the European Union’s Horizon 2020 research and innovation program
(ERC) grant 715508 (REVERSEAUTISM) and by the Austrian Science Fund (FWF) (DK W1232-B24)
both to G.N. and both BMBF GeNeRARe 01GM1519A and CRC 1080, project B10, of the
German Research Foundation (DFG) to M.J.S, respectively. We want to thank R. Waltes
for her support in preparing this manuscript.'
alternative_title:
- Special Issue "From Genes to Therapy in Autism Spectrum Disorder"
article_number: '1746'
article_processing_charge: No
article_type: original
author:
- first_name: Verica
full_name: Vasic, Verica
last_name: Vasic
- first_name: Mattson S.O.
full_name: Jones, Mattson S.O.
last_name: Jones
- first_name: Denise
full_name: Haslinger, Denise
id: 76922BDA-3D3B-11EA-90BD-A44F3DDC885E
last_name: Haslinger
- first_name: Lisa
full_name: Knaus, Lisa
id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87
last_name: Knaus
- first_name: Michael J.
full_name: Schmeisser, Michael J.
last_name: Schmeisser
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Andreas G.
full_name: Chiocchetti, Andreas G.
last_name: Chiocchetti
citation:
ama: 'Vasic V, Jones MSO, Haslinger D, et al. Translating the role of mtor-and ras-associated
signalopathies in autism spectrum disorder: Models, mechanisms and treatment.
Genes. 2021;12(11). doi:10.3390/genes12111746'
apa: 'Vasic, V., Jones, M. S. O., Haslinger, D., Knaus, L., Schmeisser, M. J., Novarino,
G., & Chiocchetti, A. G. (2021). Translating the role of mtor-and ras-associated
signalopathies in autism spectrum disorder: Models, mechanisms and treatment.
Genes. MDPI. https://doi.org/10.3390/genes12111746'
chicago: 'Vasic, Verica, Mattson S.O. Jones, Denise Haslinger, Lisa Knaus, Michael
J. Schmeisser, Gaia Novarino, and Andreas G. Chiocchetti. “Translating the Role
of Mtor-and Ras-Associated Signalopathies in Autism Spectrum Disorder: Models,
Mechanisms and Treatment.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12111746.'
ieee: 'V. Vasic et al., “Translating the role of mtor-and ras-associated
signalopathies in autism spectrum disorder: Models, mechanisms and treatment,”
Genes, vol. 12, no. 11. MDPI, 2021.'
ista: 'Vasic V, Jones MSO, Haslinger D, Knaus L, Schmeisser MJ, Novarino G, Chiocchetti
AG. 2021. Translating the role of mtor-and ras-associated signalopathies in autism
spectrum disorder: Models, mechanisms and treatment. Genes. 12(11), 1746.'
mla: 'Vasic, Verica, et al. “Translating the Role of Mtor-and Ras-Associated Signalopathies
in Autism Spectrum Disorder: Models, Mechanisms and Treatment.” Genes,
vol. 12, no. 11, 1746, MDPI, 2021, doi:10.3390/genes12111746.'
short: V. Vasic, M.S.O. Jones, D. Haslinger, L. Knaus, M.J. Schmeisser, G. Novarino,
A.G. Chiocchetti, Genes 12 (2021).
date_created: 2021-11-14T23:01:24Z
date_published: 2021-10-30T00:00:00Z
date_updated: 2023-08-14T11:46:12Z
day: '30'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.3390/genes12111746
ec_funded: 1
external_id:
isi:
- '000834044200002'
file:
- access_level: open_access
checksum: 256cb832a9c3051c7dc741f6423b8cbd
content_type: application/pdf
creator: dernst
date_created: 2022-05-16T07:02:27Z
date_updated: 2022-05-16T07:02:27Z
file_id: '11380'
file_name: 2021_Genes_Vasic.pdf
file_size: 1335308
relation: main_file
success: 1
file_date_updated: 2022-05-16T07:02:27Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '11'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Genes
publication_identifier:
eissn:
- 2073-4425
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Translating the role of mtor-and ras-associated signalopathies in autism spectrum
disorder: Models, mechanisms and treatment'
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: '10282'
abstract:
- lang: eng
text: Advanced transcriptome sequencing has revealed that the majority of eukaryotic
genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated
to investigating the functional relevance of particular splicing events, even
those in the key developmental and hormonal regulators. Combining approaches of
genetics, biochemistry and advanced confocal microscopy, we describe the impact
of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana.
PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces
two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing
in a four amino acid stretch, exhibit almost identical expression patterns and
subcellular localization. We reveal that they are closely associated and mutually
influence each other's mobility within the plasma membrane. Phenotypic complementation
tests indicate that the functional contribution of PIN7b per se is minor, but
it markedly reduces the prominent PIN7a activity, which is required for correct
seedling apical hook formation and auxin-mediated tropic responses. Our results
establish alternative splicing of the PIN family as a conserved, functionally
relevant mechanism, revealing an additional regulatory level of auxin-mediated
plant development.
acknowledgement: We thank Claus Schwechheimer for the pin34 and pin347 seeds, Yuliia
Mironova for technical assistance, Ksenia Timofeyenko and Dmitry Konovalov for help
with the evolutional analysis, Konstantin Kutashev and Siarhei Dabravolski for assistance
with FRET-FLIM, Huibin Han for advice with hypocotyl imaging, Karel Müller for the
initial qRT-PCR on the tobacco cell lines, Stano Pekár for suggestions regarding
the statistical analysis of the morphodynamic measurements, and Jozef Mravec, Dolf
Weijers and Lindy Abas for their comments on the manuscript. This work was supported
by the Czech Science Foundation (projects 16-26428S and 19-23773S to IK, MH and
KRůžička, 19-18917S to JHumpolíčková and 18-26981S to JF), and the Ministry of Education,
Youth and Sports of the Czech Republic (MEYS, CZ.02.1.01/0.0/0.0/16_019/0000738)
to KRůžička and JHejátko. The imaging facilities of the Institute of Experimental
Botany and CEITEC are supported by MEYS (LM2018129 – Czech BioImaging and CZ.02.1.01/0.0/0.0/16_013/0001775).
The authors declare no competing interests.
article_processing_charge: No
article_type: original
author:
- first_name: Ivan
full_name: Kashkan, Ivan
last_name: Kashkan
- first_name: Mónika
full_name: Hrtyan, Mónika
id: 45A71A74-F248-11E8-B48F-1D18A9856A87
last_name: Hrtyan
- first_name: Katarzyna
full_name: Retzer, Katarzyna
last_name: Retzer
- first_name: Jana
full_name: Humpolíčková, Jana
last_name: Humpolíčková
- first_name: Aswathy
full_name: Jayasree, Aswathy
last_name: Jayasree
- first_name: Roberta
full_name: Filepová, Roberta
last_name: Filepová
- first_name: Zuzana
full_name: Vondráková, Zuzana
last_name: Vondráková
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Debbie
full_name: Rombaut, Debbie
last_name: Rombaut
- first_name: Thomas B.
full_name: Jacobs, Thomas B.
last_name: Jacobs
- first_name: Mikko J.
full_name: Frilander, Mikko J.
last_name: Frilander
- first_name: Jan
full_name: Hejátko, Jan
last_name: Hejátko
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Kamil
full_name: Růžička, Kamil
last_name: Růžička
citation:
ama: Kashkan I, Hrtyan M, Retzer K, et al. Mutually opposing activity of PIN7 splicing
isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana.
New Phytologist. 2021;233:329-343. doi:10.1111/nph.17792
apa: Kashkan, I., Hrtyan, M., Retzer, K., Humpolíčková, J., Jayasree, A., Filepová,
R., … Růžička, K. (2021). Mutually opposing activity of PIN7 splicing isoforms
is required for auxin-mediated tropic responses in Arabidopsis thaliana. New
Phytologist. Wiley. https://doi.org/10.1111/nph.17792
chicago: Kashkan, Ivan, Mónika Hrtyan, Katarzyna Retzer, Jana Humpolíčková, Aswathy
Jayasree, Roberta Filepová, Zuzana Vondráková, et al. “Mutually Opposing Activity
of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis
Thaliana.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17792.
ieee: I. Kashkan et al., “Mutually opposing activity of PIN7 splicing isoforms
is required for auxin-mediated tropic responses in Arabidopsis thaliana,” New
Phytologist, vol. 233. Wiley, pp. 329–343, 2021.
ista: Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková
Z, Simon S, Rombaut D, Jacobs TB, Frilander MJ, Hejátko J, Friml J, Petrášek J,
Růžička K. 2021. Mutually opposing activity of PIN7 splicing isoforms is required
for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist.
233, 329–343.
mla: Kashkan, Ivan, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms
Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” New
Phytologist, vol. 233, Wiley, 2021, pp. 329–43, doi:10.1111/nph.17792.
short: I. Kashkan, M. Hrtyan, K. Retzer, J. Humpolíčková, A. Jayasree, R. Filepová,
Z. Vondráková, S. Simon, D. Rombaut, T.B. Jacobs, M.J. Frilander, J. Hejátko,
J. Friml, J. Petrášek, K. Růžička, New Phytologist 233 (2021) 329–343.
date_created: 2021-11-14T23:01:24Z
date_published: 2021-11-05T00:00:00Z
date_updated: 2023-08-14T11:46:43Z
day: '05'
department:
- _id: JiFr
doi: 10.1111/nph.17792
external_id:
isi:
- '000714678100001'
pmid:
- '34637542'
intvolume: ' 233'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2020.05.02.074070v2
month: '11'
oa: 1
oa_version: Preprint
page: 329-343
pmid: 1
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: Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated
tropic responses in Arabidopsis thaliana
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 233
year: '2021'
...
---
_id: '10283'
abstract:
- lang: eng
text: 'During the past decade, the scientific community and outside observers have
noted a concerning lack of rigor and transparency in preclinical research that
led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov
& Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed
to address the problem: from better training of scientists to more oversight to
expanded publishing practices such as preregistration of studies. The recently
published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the
largest initiative that aims to establish a systematic approach for increasing
the robustness and reliability of biomedical research (Bespalov et al, 2021).
However, promoting a cultural change in research practices warrants a broad adoption
of the Quality System and its underlying philosophy. It is here that academic
Core Facilities (CF), research service providers at universities and research
institutions, can make a difference. It is fair to assume that a significant fraction
of published data originated from experiments that were designed, run, or analyzed
in CFs. These academic services play an important role in the research ecosystem
by offering access to cutting-edge equipment and by developing and testing novel
techniques and methods that impact research in the academic and private sectors
alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value:
CFs employ competent personnel with profound knowledge and practical experience
of the specific field of interest: animal behavior, imaging, crystallography,
genomics, and so on. Thus, CFs are optimally positioned to address concerns about
the quality and robustness of preclinical research.'
acknowledgement: This EQIPD 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
program and EFPIA. LR was supported by the Faculty of Biology and Medicine, University
of Lausanne. VV was supported by Biocenter Finland and the Jane and Aatos Erkko
Foundation. CP and IKB received funding from the Federal Ministry of Education and
Research (BMBF, grant 01PW18001). SB from the Vienna BioCenter Core Facilities (VBCF)
Preclinical Phenotyping Facility acknowledges funding from the Austrian Federal
Ministry of Education, Science & Research; and the City of Vienna. MT is an incumbent
of the Carolito Stiftung Research Fellow Chair in Neurodegenerative Diseases. We
thank Dr. Katja Kivinen (Helsinki Institute of Life Science) for discussions and
feedback.
article_number: e53824
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Leonardo
full_name: Restivo, Leonardo
last_name: Restivo
- first_name: Björn
full_name: Gerlach, Björn
last_name: Gerlach
- first_name: Michael
full_name: Tsoory, Michael
last_name: Tsoory
- first_name: Lior
full_name: Bikovski, Lior
last_name: Bikovski
- first_name: Sylvia
full_name: Badurek, Sylvia
last_name: Badurek
- first_name: Claudia
full_name: Pitzer, Claudia
last_name: Pitzer
- first_name: Isabelle C.
full_name: Kos-Braun, Isabelle C.
last_name: Kos-Braun
- first_name: Anne Laure Mj
full_name: Mausset-Bonnefont, Anne Laure Mj
last_name: Mausset-Bonnefont
- first_name: Jonathan
full_name: Ward, Jonathan
last_name: Ward
- first_name: Michael
full_name: Schunn, Michael
id: 4272DB4A-F248-11E8-B48F-1D18A9856A87
last_name: Schunn
orcid: 0000-0003-4326-5300
- first_name: Lucas P.J.J.
full_name: Noldus, Lucas P.J.J.
last_name: Noldus
- first_name: Anton
full_name: Bespalov, Anton
last_name: Bespalov
- first_name: Vootele
full_name: Voikar, Vootele
last_name: Voikar
citation:
ama: 'Restivo L, Gerlach B, Tsoory M, et al. Towards best practices in research:
Role of academic core facilities. EMBO Reports. 2021;22. doi:10.15252/embr.202153824'
apa: 'Restivo, L., Gerlach, B., Tsoory, M., Bikovski, L., Badurek, S., Pitzer, C.,
… Voikar, V. (2021). Towards best practices in research: Role of academic core
facilities. EMBO Reports. EMBO Press. https://doi.org/10.15252/embr.202153824'
chicago: 'Restivo, Leonardo, Björn Gerlach, Michael Tsoory, Lior Bikovski, Sylvia
Badurek, Claudia Pitzer, Isabelle C. Kos-Braun, et al. “Towards Best Practices
in Research: Role of Academic Core Facilities.” EMBO Reports. EMBO Press,
2021. https://doi.org/10.15252/embr.202153824.'
ieee: 'L. Restivo et al., “Towards best practices in research: Role of academic
core facilities,” EMBO Reports, vol. 22. EMBO Press, 2021.'
ista: 'Restivo L, Gerlach B, Tsoory M, Bikovski L, Badurek S, Pitzer C, Kos-Braun
IC, Mausset-Bonnefont ALM, Ward J, Schunn M, Noldus LPJJ, Bespalov A, Voikar V.
2021. Towards best practices in research: Role of academic core facilities. EMBO
Reports. 22, e53824.'
mla: 'Restivo, Leonardo, et al. “Towards Best Practices in Research: Role of Academic
Core Facilities.” EMBO Reports, vol. 22, e53824, EMBO Press, 2021, doi:10.15252/embr.202153824.'
short: L. Restivo, B. Gerlach, M. Tsoory, L. Bikovski, S. Badurek, C. Pitzer, I.C.
Kos-Braun, A.L.M. Mausset-Bonnefont, J. Ward, M. Schunn, L.P.J.J. Noldus, A. Bespalov,
V. Voikar, EMBO Reports 22 (2021).
date_created: 2021-11-14T23:01:24Z
date_published: 2021-11-04T00:00:00Z
date_updated: 2023-08-14T11:47:35Z
day: '04'
ddc:
- '570'
department:
- _id: PreCl
doi: 10.15252/embr.202153824
external_id:
isi:
- '000714350000001'
file:
- access_level: open_access
checksum: 74743baa6ef431ef60c3de3bc4da045a
content_type: application/pdf
creator: dernst
date_created: 2022-05-16T07:07:41Z
date_updated: 2022-05-16T07:07:41Z
file_id: '11381'
file_name: 2021_EmboReports_Restivo.pdf
file_size: 488583
relation: main_file
success: 1
file_date_updated: 2022-05-16T07:07:41Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: EMBO Reports
publication_identifier:
eissn:
- 1469-3178
issn:
- 1469-221X
publication_status: published
publisher: EMBO Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Towards best practices in research: Role of academic core facilities'
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: 22
year: '2021'
...
---
_id: '10285'
abstract:
- lang: eng
text: We study the overlaps between right and left eigenvectors for random matrices
of the spherical ensemble, as well as truncated unitary ensembles in the regime
where half of the matrix at least is truncated. These two integrable models exhibit
a form of duality, and the essential steps of our investigation can therefore
be performed in parallel. In every case, conditionally on all eigenvalues, diagonal
overlaps are shown to be distributed as a product of independent random variables
with explicit distributions. This enables us to prove that the scaled diagonal
overlaps, conditionally on one eigenvalue, converge in distribution to a heavy-tail
limit, namely, the inverse of a γ2 distribution. We also provide formulae for
the conditional expectation of diagonal and off-diagonal overlaps, either with
respect to one eigenvalue, or with respect to the whole spectrum. These results,
analogous to what is known for the complex Ginibre ensemble, can be obtained in
these cases thanks to integration techniques inspired from a previous work by
Forrester & Krishnapur.
acknowledgement: We acknowledge partial support from the grants NSF DMS-1812114 of
P. Bourgade (PI) and NSF CAREER DMS-1653602 of L.-P. Arguin (PI). This project has
also received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. We would
like to thank Paul Bourgade and László Erdős for many helpful comments.
article_number: '124'
article_processing_charge: No
article_type: original
author:
- first_name: Guillaume
full_name: Dubach, Guillaume
id: D5C6A458-10C4-11EA-ABF4-A4B43DDC885E
last_name: Dubach
orcid: 0000-0001-6892-8137
citation:
ama: Dubach G. On eigenvector statistics in the spherical and truncated unitary
ensembles. Electronic Journal of Probability. 2021;26. doi:10.1214/21-EJP686
apa: Dubach, G. (2021). On eigenvector statistics in the spherical and truncated
unitary ensembles. Electronic Journal of Probability. Institute of Mathematical
Statistics. https://doi.org/10.1214/21-EJP686
chicago: Dubach, Guillaume. “On Eigenvector Statistics in the Spherical and Truncated
Unitary Ensembles.” Electronic Journal of Probability. Institute of Mathematical
Statistics, 2021. https://doi.org/10.1214/21-EJP686.
ieee: G. Dubach, “On eigenvector statistics in the spherical and truncated unitary
ensembles,” Electronic Journal of Probability, vol. 26. Institute of Mathematical
Statistics, 2021.
ista: Dubach G. 2021. On eigenvector statistics in the spherical and truncated unitary
ensembles. Electronic Journal of Probability. 26, 124.
mla: Dubach, Guillaume. “On Eigenvector Statistics in the Spherical and Truncated
Unitary Ensembles.” Electronic Journal of Probability, vol. 26, 124, Institute
of Mathematical Statistics, 2021, doi:10.1214/21-EJP686.
short: G. Dubach, Electronic Journal of Probability 26 (2021).
date_created: 2021-11-14T23:01:25Z
date_published: 2021-09-28T00:00:00Z
date_updated: 2021-11-15T10:48:46Z
day: '28'
ddc:
- '519'
department:
- _id: LaEr
doi: 10.1214/21-EJP686
ec_funded: 1
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file_id: '10288'
file_name: 2021_ElecJournalProb_Dubach.pdf
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relation: main_file
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file_date_updated: 2021-11-15T10:10:17Z
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intvolume: ' 26'
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: Electronic Journal of Probability
publication_identifier:
eissn:
- 1083-6489
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: On eigenvector statistics in the spherical and truncated unitary ensembles
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 26
year: '2021'
...
---
_id: '10290'
abstract:
- lang: eng
text: A precise quantitative description of the ultrastructural characteristics
underlying biological mechanisms is often key to their understanding. This is
particularly true for dynamic extra- and intracellular filamentous assemblies,
playing a role in cell motility, cell integrity, cytokinesis, tissue formation
and maintenance. For example, genetic manipulation or modulation of actin regulatory
proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural
architecture of actin filament-rich cell peripheral structures, such as lamellipodia
or filopodia. However, the observed ultrastructural effects often remain subtle
and require sufficiently large datasets for appropriate quantitative analysis.
The acquisition of such large datasets has been enabled by recent advances in
high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates
the development of complementary approaches to maximize the extraction of relevant
biological information. We have developed a computational toolbox for the semi-automatic
quantification of segmented and vectorized filamentous networks from pre-processed
cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple
experimental conditions. GUI-based components simplify the processing of data
and allow users to obtain a large number of ultrastructural parameters describing
filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing
cryo-ET data of untreated and chemically perturbed branched actin filament networks
and that of parallel actin filament arrays. In principle, the computational toolbox
presented here is applicable for data analysis comprising any type of filaments
in regular (i.e. parallel) or random arrangement. We show that it can ease the
identification of key differences between experimental groups and facilitate the
in-depth analysis of ultrastructural data in a time-efficient manner.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
acknowledgement: 'This research was supported by the Scientific Service Units (SSUs)
of IST Austria through resources provided by Scientific Computing (SciComp), the
Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy
Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data
acquisition. The authors acknowledge support from IST Austria and from the Austrian
Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.'
article_number: '107808'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Behnam
full_name: Amiri, Behnam
last_name: Amiri
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Martin
full_name: Falcke, Martin
last_name: Falcke
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for
ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal
of Structural Biology. 2021;213(4). doi:10.1016/j.jsb.2021.107808
apa: Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2021).
Computational toolbox for ultrastructural quantitative analysis of filament networks
in cryo-ET data. Journal of Structural Biology. Elsevier . https://doi.org/10.1016/j.jsb.2021.107808
chicago: Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian
KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of
Filament Networks in Cryo-ET Data.” Journal of Structural Biology. Elsevier
, 2021. https://doi.org/10.1016/j.jsb.2021.107808.
ieee: G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational
toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET
data,” Journal of Structural Biology, vol. 213, no. 4. Elsevier , 2021.
ista: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox
for ultrastructural quantitative analysis of filament networks in cryo-ET data.
Journal of Structural Biology. 213(4), 107808.
mla: Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative
Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology,
vol. 213, no. 4, 107808, Elsevier , 2021, doi:10.1016/j.jsb.2021.107808.
short: G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural
Biology 213 (2021).
date_created: 2021-11-15T12:21:42Z
date_published: 2021-11-03T00:00:00Z
date_updated: 2023-11-21T08:36:02Z
day: '03'
ddc:
- '572'
department:
- _id: FlSc
doi: 10.1016/j.jsb.2021.107808
external_id:
isi:
- '000720259500002'
file:
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checksum: 6b209e4d44775d4e02b50f78982c15fa
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-15T13:11:27Z
date_updated: 2021-11-15T13:11:27Z
file_id: '10291'
file_name: 2021_JournalStructBiol_Dimchev.pdf
file_size: 16818304
relation: main_file
success: 1
file_date_updated: 2021-11-15T13:11:27Z
has_accepted_license: '1'
intvolume: ' 213'
isi: 1
issue: '4'
keyword:
- Structural Biology
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
- _id: 2674F658-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02495
name: Protein structure and function in filopodia across scales
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: 'Elsevier '
quality_controlled: '1'
related_material:
record:
- id: '14502'
relation: software
status: public
scopus_import: '1'
status: public
title: Computational toolbox for ultrastructural quantitative analysis of filament
networks in cryo-ET data
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 213
year: '2021'
...
---
_id: '10293'
abstract:
- lang: eng
text: "Indirect reciprocity in evolutionary game theory is a prominent mechanism
for explaining the evolution of cooperation among unrelated individuals. In contrast
to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally
cooperating by using their own experiences, indirect reciprocity is based on individuals’
reputations. If a player helps another, this increases the helper’s public standing,
benefitting them in the future. This lets cooperation in the population emerge
without individuals having to meet more than once. While the two modes of reciprocity
are intertwined, they are difficult to compare. Thus, they are usually studied
in isolation. Direct reciprocity can maintain cooperation with simple strategies,
and is robust against noise even when players do not remember more\r\nthan their
partner’s last action. Meanwhile, indirect reciprocity requires its successful
strategies, or social norms, to be more complex. Exhaustive search previously
identified eight such norms, called the “leading eight”, which excel at maintaining
cooperation. However, as the first result of this thesis, we show that the leading
eight break down once we remove the fundamental assumption that information is
synchronized and public, such that everyone agrees on reputations. Once we consider
a more realistic scenario of imperfect information, where reputations are private,
and individuals occasionally misinterpret or miss observations, the leading eight
do not promote cooperation anymore. Instead, minor initial disagreements can proliferate,
fragmenting populations into subgroups. In a next step, we consider ways to mitigate
this issue. We first explore whether introducing “generosity” can stabilize cooperation
when players use the leading eight strategies in noisy environments. This approach
of modifying strategies to include probabilistic elements for coping with errors
is known to work well in direct reciprocity. However, as we show here, it fails
for the more complex norms of indirect reciprocity. Imperfect information still
prevents cooperation from evolving. On the other hand, we succeeded to show in
this thesis that modifying the leading eight to use “quantitative assessment”,
i.e. tracking reputation scores on a scale beyond good and bad, and making overall
judgments of others based on a threshold, is highly successful, even when noise
increases in the environment. Cooperation can flourish when reputations\r\nare
more nuanced, and players have a broader understanding what it means to be “good.”
Finally, we present a single theoretical framework that unites the two modes of
reciprocity despite their differences. Within this framework, we identify a novel
simple and successful strategy for indirect reciprocity, which can cope with noisy
environments and has an analogue in direct reciprocity. We can also analyze decision
making when different sources of information are available. Our results help highlight
that for sustaining cooperation, already the most simple rules of reciprocity
can be sufficient."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
citation:
ama: Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect
information. 2021. doi:10.15479/at:ista:10293
apa: Schmid, L. (2021). Evolution of cooperation via (in)direct reciprocity under
imperfect information. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10293
chicago: Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under
Imperfect Information.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10293.
ieee: L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect
information,” Institute of Science and Technology Austria, 2021.
ista: Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under
imperfect information. Institute of Science and Technology Austria.
mla: Schmid, Laura. Evolution of Cooperation via (in)Direct Reciprocity under
Imperfect Information. Institute of Science and Technology Austria, 2021,
doi:10.15479/at:ista:10293.
short: L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect
Information, Institute of Science and Technology Austria, 2021.
date_created: 2021-11-15T17:12:57Z
date_published: 2021-11-17T00:00:00Z
date_updated: 2025-07-14T09:10:09Z
day: '17'
ddc:
- '519'
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: KrCh
doi: 10.15479/at:ista:10293
ec_funded: 1
file:
- access_level: closed
checksum: 86a05b430756ca12ae8107b6e6f3c1e5
content_type: application/zip
creator: lschmid
date_created: 2021-11-18T12:41:46Z
date_updated: 2022-12-20T23:30:08Z
embargo_to: open_access
file_id: '10305'
file_name: submission_new.zip
file_size: 29703124
relation: source_file
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checksum: d940af042e94660c6b6a7b4f0b184d47
content_type: application/pdf
creator: lschmid
date_created: 2021-11-18T12:59:15Z
date_updated: 2022-12-20T23:30:08Z
embargo: 2022-10-18
file_id: '10306'
file_name: thesis_new_upload.pdf
file_size: 8320985
relation: main_file
file_date_updated: 2022-12-20T23:30:08Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '171'
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: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _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_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9997'
relation: part_of_dissertation
status: public
- id: '2'
relation: part_of_dissertation
status: public
- id: '9402'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: Evolution of cooperation via (in)direct reciprocity under imperfect information
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10299'
abstract:
- lang: eng
text: Turbulence generally arises in shear flows if velocities and hence, inertial
forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit
disordered motion even at vanishing inertia. Intermediate between these cases,
a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed
in a narrow Reynolds number interval. We here determine the origin of EIT in experiments
and show that characteristic EIT structures can be detected across an unexpectedly
wide range of parameters. Close to onset, a pattern of chevron-shaped streaks
emerges in qualitative agreement with linear and weakly nonlinear theory. However,
in experiments, the dynamics remain weakly chaotic, and the instability can be
traced to far lower Reynolds numbers than permitted by theory. For increasing
inertia, the flow undergoes a transformation to a wall mode composed of inclined
near-wall streaks and shear layers. This mode persists to what is known as the
“maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic
flows across more than three orders of magnitude in Reynolds number.
acknowledgement: We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg,
and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge
funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft
research unit FOR 2688.
article_number: e2102350118
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: George H
full_name: Choueiri, George H
id: 448BD5BC-F248-11E8-B48F-1D18A9856A87
last_name: Choueiri
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Sarath
full_name: Sankar, Sarath
last_name: Sankar
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation
of the origin and structure of elastoinertial turbulence. Proceedings of the
National Academy of Sciences. 2021;118(45). doi:10.1073/pnas.2102350118
apa: Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., & Hof,
B. (2021). Experimental observation of the origin and structure of elastoinertial
turbulence. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.2102350118
chicago: Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar,
and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial
Turbulence.” Proceedings of the National Academy of Sciences. National
Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2102350118.
ieee: G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental
observation of the origin and structure of elastoinertial turbulence,” Proceedings
of the National Academy of Sciences, vol. 118, no. 45. National Academy of
Sciences, 2021.
ista: Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental
observation of the origin and structure of elastoinertial turbulence. Proceedings
of the National Academy of Sciences. 118(45), e2102350118.
mla: Choueiri, George H., et al. “Experimental Observation of the Origin and Structure
of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences,
vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:10.1073/pnas.2102350118.
short: G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings
of the National Academy of Sciences 118 (2021).
date_created: 2021-11-17T13:24:24Z
date_published: 2021-11-03T00:00:00Z
date_updated: 2023-08-14T11:50:10Z
day: '03'
department:
- _id: BjHo
doi: 10.1073/pnas.2102350118
external_id:
arxiv:
- '2103.00023'
isi:
- '000720926900019'
pmid:
- ' 34732570'
intvolume: ' 118'
isi: 1
issue: '45'
keyword:
- multidisciplinary
- elastoinertial turbulence
- viscoelastic flows
- elastic instability
- drag reduction
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2103.00023
month: '11'
oa: 1
oa_version: Preprint
pmid: 1
project:
- _id: 238B8092-32DE-11EA-91FC-C7463DDC885E
call_identifier: FWF
grant_number: I04188
name: Instabilities in pulsating pipe flow of Newtonian and complex fluids
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: Experimental observation of the origin and structure of elastoinertial turbulence
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 118
year: '2021'
...
---
_id: '10301'
abstract:
- lang: eng
text: De novo protein synthesis is required for synapse modifications underlying
stable memory encoding. Yet neurons are highly compartmentalized cells and how
protein synthesis can be regulated at the synapse level is unknown. Here, we characterize
neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mechanistic
target of rapamycin (mTOR) kinase, and Raptor that couple synaptic stimuli to
mTOR-dependent protein synthesis; and identify NMDA receptors containing GluN3A
subunits as key negative regulators of GIT1 binding to mTOR. Disruption of GIT1/mTOR
complexes by enhancing GluN3A expression or silencing GIT1 inhibits synaptic mTOR
activation and restricts the mTOR-dependent translation of specific activity-regulated
mRNAs. Conversely, GluN3A removal enables complex formation, potentiates mTOR-dependent
protein synthesis, and facilitates the consolidation of associative and spatial
memories in mice. The memory enhancement becomes evident with light or spaced
training, can be achieved by selectively deleting GluN3A from excitatory neurons
during adulthood, and does not compromise other aspects of cognition such as memory
flexibility or extinction. Our findings provide mechanistic insight into synaptic
translational control and reveal a potentially selective target for cognitive
enhancement.
acknowledgement: We thank Stuart Lipton and Nobuki Nakanishi for providing the Grin3a
knockout mice, Beverly Davidson for the AAV-caRheb, Jose Esteban for help with behavioral
and biochemical experiments, and Noelia Campillo, Rebeca Martínez-Turrillas, and
Ana Navarro for expert technical help. Work was funded by the UTE project CIMA;
fellowships from the Fundación Tatiana Pérez de Guzmán el Bueno, FEBS, and IBRO
(to M.J.C.D.), Generalitat Valenciana (to O.E.-Z.), Juan de la Cierva (to L.G.R.),
FPI-MINECO (to E.R.V., to S.N.) and Intertalentum postdoctoral program (to V.B.);
ANR (GluBrain3A) and ERC Advanced Grants (#693021) (to P.P.); Ramón y Cajal program
RYC2014-15784, RETOS-MINECO SAF2016-76565-R, ERANET-Neuron JTC 2019 ISCIII AC19/00077
FEDER funds (to R.A.); RETOS-MINECO SAF2017-87928-R (to A.B.); an NIH grant (NS76637)
and UTHSC College of Medicine funds (to S.J.T.); and NARSAD Independent Investigator
Award and grants from the MINECO (CSD2008-00005, SAF2013-48983R, SAF2016-80895-R),
Generalitat Valenciana (PROMETEO 2019/020)(to I.P.O.) and Severo-Ochoa Excellence
Awards (SEV-2013-0317, SEV-2017-0723).
article_number: e71575
article_processing_charge: No
article_type: original
author:
- first_name: María J
full_name: Conde-Dusman, María J
last_name: Conde-Dusman
- first_name: Partha N
full_name: Dey, Partha N
last_name: Dey
- first_name: Óscar
full_name: Elía-Zudaire, Óscar
last_name: Elía-Zudaire
- first_name: Luis E
full_name: Garcia Rabaneda, Luis E
id: 33D1B084-F248-11E8-B48F-1D18A9856A87
last_name: Garcia Rabaneda
- first_name: Carmen
full_name: García-Lira, Carmen
last_name: García-Lira
- first_name: Teddy
full_name: Grand, Teddy
last_name: Grand
- first_name: Victor
full_name: Briz, Victor
last_name: Briz
- first_name: Eric R
full_name: Velasco, Eric R
last_name: Velasco
- first_name: Raül
full_name: Andero Galí, Raül
last_name: Andero Galí
- first_name: Sergio
full_name: Niñerola, Sergio
last_name: Niñerola
- first_name: Angel
full_name: Barco, Angel
last_name: Barco
- first_name: Pierre
full_name: Paoletti, Pierre
last_name: Paoletti
- first_name: John F
full_name: Wesseling, John F
last_name: Wesseling
- first_name: Fabrizio
full_name: Gardoni, Fabrizio
last_name: Gardoni
- first_name: Steven J
full_name: Tavalin, Steven J
last_name: Tavalin
- first_name: Isabel
full_name: Perez-Otaño, Isabel
last_name: Perez-Otaño
citation:
ama: Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, et al. Control of protein synthesis
and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly.
eLife. 2021;10. doi:10.7554/elife.71575
apa: Conde-Dusman, M. J., Dey, P. N., Elía-Zudaire, Ó., Garcia Rabaneda, L. E.,
García-Lira, C., Grand, T., … Perez-Otaño, I. (2021). Control of protein synthesis
and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly.
ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.71575
chicago: Conde-Dusman, María J, Partha N Dey, Óscar Elía-Zudaire, Luis E Garcia
Rabaneda, Carmen García-Lira, Teddy Grand, Victor Briz, et al. “Control of Protein
Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1
Assembly.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.71575.
ieee: M. J. Conde-Dusman et al., “Control of protein synthesis and memory
by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly,” eLife,
vol. 10. eLife Sciences Publications, 2021.
ista: Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, Garcia Rabaneda LE, García-Lira C,
Grand T, Briz V, Velasco ER, Andero Galí R, Niñerola S, Barco A, Paoletti P, Wesseling
JF, Gardoni F, Tavalin SJ, Perez-Otaño I. 2021. Control of protein synthesis and
memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife.
10, e71575.
mla: Conde-Dusman, María J., et al. “Control of Protein Synthesis and Memory by
GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife,
vol. 10, e71575, eLife Sciences Publications, 2021, doi:10.7554/elife.71575.
short: M.J. Conde-Dusman, P.N. Dey, Ó. Elía-Zudaire, L.E. Garcia Rabaneda, C. García-Lira,
T. Grand, V. Briz, E.R. Velasco, R. Andero Galí, S. Niñerola, A. Barco, P. Paoletti,
J.F. Wesseling, F. Gardoni, S.J. Tavalin, I. Perez-Otaño, ELife 10 (2021).
date_created: 2021-11-18T06:59:45Z
date_published: 2021-11-17T00:00:00Z
date_updated: 2023-08-14T11:50:50Z
day: '17'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.7554/elife.71575
external_id:
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intvolume: ' 10'
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keyword:
- general immunology and microbiology
- general biochemistry
- genetics and molecular biology
- general medicine
- general neuroscience
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
status: public
title: Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition
of GIT1/mTORC1 assembly
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: '10303'
abstract:
- lang: eng
text: 'Nitrogen is an essential macronutrient determining plant growth, development
and affecting agricultural productivity. Root, as a hub that perceives and integrates
local and systemic signals on the plant’s external and endogenous nitrogen resources,
communicates with other plant organs to consolidate their physiology and development
in accordance with actual nitrogen balance. Over the last years, numerous studies
demonstrated that these comprehensive developmental adaptations rely on the interaction
between pathways controlling nitrogen homeostasis and hormonal networks acting
globally in the plant body. However, molecular insights into how the information
about the nitrogen status is translated through hormonal pathways into specific
developmental output are lacking. In my work, I addressed so far poorly understood
mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment
of shoot growth and development after nitrate provision. Applying a combination
of molecular, cell, and developmental biology approaches, genetics and grafting
experiments as well as hormonal analytics, I identified and characterized an unknown
molecular framework orchestrating shoot development with a root nitrate sensory
system. '
acknowledged_ssus:
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- _id: Bio
alternative_title:
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article_processing_charge: No
author:
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full_name: Abualia, Rashed
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last_name: Abualia
orcid: 0000-0002-9357-9415
citation:
ama: Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303
apa: Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303
chicago: Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute
of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10303.
ieee: R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science
and Technology Austria, 2021.
ista: Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of
Science and Technology Austria.
mla: Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute
of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303.
short: R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science
and Technology Austria, 2021.
date_created: 2021-11-18T11:20:59Z
date_published: 2021-11-22T00:00:00Z
date_updated: 2023-09-19T14:42:45Z
day: '22'
ddc:
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degree_awarded: PhD
department:
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doi: 10.15479/at:ista:10303
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publisher: Institute of Science and Technology Austria
related_material:
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relation: part_of_dissertation
status: public
- id: '9913'
relation: part_of_dissertation
status: public
- id: '47'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
title: Role of hormones in nitrate regulated growth
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10307'
abstract:
- lang: eng
text: Bacteria-host interactions represent a continuous trade-off between benefit
and risk. Thus, the host immune response is faced with a non-trivial problem –
accommodate beneficial commensals and remove harmful pathogens. This is especially
difficult as molecular patterns, such as lipopolysaccharide or specific surface
organelles such as pili, are conserved in both, commensal and pathogenic bacteria.
Type 1 pili, tightly regulated by phase variation, are considered an important
virulence factor of pathogenic bacteria as they facilitate invasion into host
cells. While invasion represents a de facto passive mechanism for pathogens to
escape the host immune response, we demonstrate a fundamental role of type 1 pili
as active modulators of the innate and adaptive immune response.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: PreCl
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
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full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
citation:
ama: Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021.
doi:10.15479/at:ista:10307
apa: Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307
chicago: Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307.
ieee: K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,”
Institute of Science and Technology Austria, 2021.
ista: Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response.
Institute of Science and Technology Austria.
mla: Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307.
short: K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response,
Institute of Science and Technology Austria, 2021.
date_created: 2021-11-18T15:05:06Z
date_published: 2021-11-18T00:00:00Z
date_updated: 2023-09-07T13:34:38Z
day: '18'
ddc:
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degree_awarded: PhD
department:
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- _id: CaGu
- _id: GradSch
doi: 10.15479/at:ista:10307
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supervisor:
- 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: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: Pathogenic Escherichia coli hijack the host immune response
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
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...