---
_id: '7804'
abstract:
- lang: eng
text: Besides pro-inflammatory roles, the ancient cytokine interleukin-17 (IL-17)
modulates neural circuit function. We investigate IL-17 signaling in neurons,
and the extent it can alter organismal phenotypes. We combine immunoprecipitation
and mass spectrometry to biochemically characterize endogenous signaling complexes
that function downstream of IL-17 receptors in C. elegans neurons. We identify
the paracaspase MALT-1 as a critical output of the pathway. MALT1 mediates signaling
from many immune receptors in mammals, but was not previously implicated in IL-17
signaling or nervous system function. C. elegans MALT-1 forms a complex with homologs
of Act1 and IRAK and appears to function both as a scaffold and a protease. MALT-1
is expressed broadly in the C. elegans nervous system, and neuronal IL-17–MALT-1
signaling regulates multiple phenotypes, including escape behavior, associative
learning, immunity and longevity. Our data suggest MALT1 has an ancient role modulating
neural circuit function downstream of IL-17 to remodel physiology and behavior.
article_number: '2099'
article_processing_charge: No
article_type: original
author:
- first_name: Sean M.
full_name: Flynn, Sean M.
last_name: Flynn
- first_name: Changchun
full_name: Chen, Changchun
last_name: Chen
- first_name: Murat
full_name: Artan, Murat
id: C407B586-6052-11E9-B3AE-7006E6697425
last_name: Artan
orcid: 0000-0001-8945-6992
- first_name: Stephen
full_name: Barratt, Stephen
last_name: Barratt
- first_name: Alastair
full_name: Crisp, Alastair
last_name: Crisp
- first_name: Geoffrey M.
full_name: Nelson, Geoffrey M.
last_name: Nelson
- first_name: Sew Yeu
full_name: Peak-Chew, Sew Yeu
last_name: Peak-Chew
- first_name: Farida
full_name: Begum, Farida
last_name: Begum
- first_name: Mark
full_name: Skehel, Mark
last_name: Skehel
- first_name: Mario
full_name: De Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: De Bono
orcid: 0000-0001-8347-0443
citation:
ama: Flynn SM, Chen C, Artan M, et al. MALT-1 mediates IL-17 neural signaling to
regulate C. elegans behavior, immunity and longevity. Nature Communications.
2020;11. doi:10.1038/s41467-020-15872-y
apa: Flynn, S. M., Chen, C., Artan, M., Barratt, S., Crisp, A., Nelson, G. M., …
de Bono, M. (2020). MALT-1 mediates IL-17 neural signaling to regulate C. elegans
behavior, immunity and longevity. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-020-15872-y
chicago: Flynn, Sean M., Changchun Chen, Murat Artan, Stephen Barratt, Alastair
Crisp, Geoffrey M. Nelson, Sew Yeu Peak-Chew, Farida Begum, Mark Skehel, and Mario
de Bono. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C. Elegans Behavior,
Immunity and Longevity.” Nature Communications. Springer Nature, 2020.
https://doi.org/10.1038/s41467-020-15872-y.
ieee: S. M. Flynn et al., “MALT-1 mediates IL-17 neural signaling to regulate C.
elegans behavior, immunity and longevity,” Nature Communications, vol.
11. Springer Nature, 2020.
ista: Flynn SM, Chen C, Artan M, Barratt S, Crisp A, Nelson GM, Peak-Chew SY, Begum
F, Skehel M, de Bono M. 2020. MALT-1 mediates IL-17 neural signaling to regulate C.
elegans behavior, immunity and longevity. Nature Communications. 11, 2099.
mla: Flynn, Sean M., et al. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C.
Elegans Behavior, Immunity and Longevity.” Nature Communications, vol.
11, 2099, Springer Nature, 2020, doi:10.1038/s41467-020-15872-y.
short: S.M. Flynn, C. Chen, M. Artan, S. Barratt, A. Crisp, G.M. Nelson, S.Y. Peak-Chew,
F. Begum, M. Skehel, M. de Bono, Nature Communications 11 (2020).
corr_author: '1'
date_created: 2020-05-10T22:00:47Z
date_published: 2020-04-29T00:00:00Z
date_updated: 2026-04-03T09:27:08Z
day: '29'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.1038/s41467-020-15872-y
external_id:
isi:
- '000531855500029'
pmid:
- '32350248'
file:
- access_level: open_access
checksum: dce367abf2c1a1d15f58fe6f7de82893
content_type: application/pdf
creator: dernst
date_created: 2020-05-11T10:36:33Z
date_updated: 2020-07-14T12:48:03Z
file_id: '7817'
file_name: 2020_NatureComm_Flynn.pdf
file_size: 4609120
relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '04'
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: MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity
and longevity
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 11
year: '2020'
...
---
_id: '7805'
abstract:
- lang: eng
text: Plants as non-mobile organisms constantly integrate varying environmental
signals to flexibly adapt their growth and development. Local fluctuations in
water and nutrient availability, sudden changes in temperature or other abiotic
and biotic stresses can trigger changes in the growth of plant organs. Multiple
mutually interconnected hormonal signaling cascades act as essential endogenous
translators of these exogenous signals in the adaptive responses of plants. Although
the molecular backbones of hormone transduction pathways have been identified,
the mechanisms underlying their interactions are largely unknown. Here, using
genome wide transcriptome profiling we identify an auxin and cytokinin cross-talk
component; SYNERGISTIC ON AUXIN AND CYTOKININ 1 (SYAC1), whose expression in roots
is strictly dependent on both of these hormonal pathways. We show that SYAC1 is
a regulator of secretory pathway, whose enhanced activity interferes with deposition
of cell wall components and can fine-tune organ growth and sensitivity to soil
pathogens.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We thank Daria Siekhaus, Jiri Friml and Alexander Johnson for critical
reading of the manuscript, Peter Pimpl, Christian Luschnig and Liwen Jiang for sharing
published material, Lesia Rodriguez Solovey for technical assistance. This work
was supported by the Austrian Science Fund (FWF01_I1774S) to A.H., K.Ö., and E.B.,
the German Research Foundation (DFG; He3424/6-1 to I.H.), by the People Programme
(Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013)
under REA grant agreement n° [291734] (to N.C.), by the EU in the framework of the
Marie-Curie FP7 COFUND People Programme through the award of an AgreenSkills+ fellowship
No. 609398 (to J.S.) and by the Scientific Service Units of IST-Austria through
resources provided by the Bioimaging Facility, the Life Science Facility. The IJPB
benefits from the support of Saclay Plant Sciences-SPS (ANR-17-EUR-0007).
article_number: '2170'
article_processing_charge: No
article_type: original
author:
- first_name: Andrej
full_name: Hurny, Andrej
id: 4DC4AF46-F248-11E8-B48F-1D18A9856A87
last_name: Hurny
orcid: 0000-0003-3638-1426
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Nicola
full_name: Cavallari, Nicola
id: 457160E6-F248-11E8-B48F-1D18A9856A87
last_name: Cavallari
- first_name: Krisztina
full_name: Ötvös, Krisztina
id: 29B901B0-F248-11E8-B48F-1D18A9856A87
last_name: Ötvös
orcid: 0000-0002-5503-4983
- first_name: Jerome
full_name: Duclercq, Jerome
last_name: Duclercq
- first_name: Ladislav
full_name: Dokládal, Ladislav
last_name: Dokládal
- first_name: Juan C
full_name: Montesinos López, Juan C
id: 310A8E3E-F248-11E8-B48F-1D18A9856A87
last_name: Montesinos López
orcid: 0000-0001-9179-6099
- first_name: Marçal
full_name: Gallemi, Marçal
id: 460C6802-F248-11E8-B48F-1D18A9856A87
last_name: Gallemi
orcid: 0000-0003-4675-6893
- first_name: Hana
full_name: Semeradova, Hana
id: 42FE702E-F248-11E8-B48F-1D18A9856A87
last_name: Semeradova
- first_name: Thomas
full_name: Rauter, Thomas
id: A0385D1A-9376-11EA-A47D-9862C5E3AB22
last_name: Rauter
- first_name: Irene
full_name: Stenzel, Irene
last_name: Stenzel
- first_name: Geert
full_name: Persiau, Geert
last_name: Persiau
- first_name: Freia
full_name: Benade, Freia
last_name: Benade
- first_name: Rishikesh
full_name: Bhalearo, Rishikesh
last_name: Bhalearo
- first_name: Eva
full_name: Sýkorová, Eva
last_name: Sýkorová
- first_name: András
full_name: Gorzsás, András
last_name: Gorzsás
- first_name: Julien
full_name: Sechet, Julien
last_name: Sechet
- first_name: Gregory
full_name: Mouille, Gregory
last_name: Mouille
- first_name: Ingo
full_name: Heilmann, Ingo
last_name: Heilmann
- first_name: Geert
full_name: De Jaeger, Geert
last_name: De Jaeger
- first_name: Jutta
full_name: Ludwig-Müller, Jutta
last_name: Ludwig-Müller
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Hurny A, Cuesta C, Cavallari N, et al. Synergistic on Auxin and Cytokinin 1
positively regulates growth and attenuates soil pathogen resistance. Nature
Communications. 2020;11. doi:10.1038/s41467-020-15895-5
apa: Hurny, A., Cuesta, C., Cavallari, N., Ötvös, K., Duclercq, J., Dokládal, L.,
… Benková, E. (2020). Synergistic on Auxin and Cytokinin 1 positively regulates
growth and attenuates soil pathogen resistance. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-020-15895-5
chicago: Hurny, Andrej, Candela Cuesta, Nicola Cavallari, Krisztina Ötvös, Jerome
Duclercq, Ladislav Dokládal, Juan C Montesinos López, et al. “Synergistic on Auxin
and Cytokinin 1 Positively Regulates Growth and Attenuates Soil Pathogen Resistance.”
Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-15895-5.
ieee: A. Hurny et al., “Synergistic on Auxin and Cytokinin 1 positively regulates
growth and attenuates soil pathogen resistance,” Nature Communications,
vol. 11. Springer Nature, 2020.
ista: Hurny A, Cuesta C, Cavallari N, Ötvös K, Duclercq J, Dokládal L, Montesinos
López JC, Gallemi M, Semerádová H, Rauter T, Stenzel I, Persiau G, Benade F, Bhalearo
R, Sýkorová E, Gorzsás A, Sechet J, Mouille G, Heilmann I, De Jaeger G, Ludwig-Müller
J, Benková E. 2020. Synergistic on Auxin and Cytokinin 1 positively regulates
growth and attenuates soil pathogen resistance. Nature Communications. 11, 2170.
mla: Hurny, Andrej, et al. “Synergistic on Auxin and Cytokinin 1 Positively Regulates
Growth and Attenuates Soil Pathogen Resistance.” Nature Communications,
vol. 11, 2170, Springer Nature, 2020, doi:10.1038/s41467-020-15895-5.
short: A. Hurny, C. Cuesta, N. Cavallari, K. Ötvös, J. Duclercq, L. Dokládal, J.C.
Montesinos López, M. Gallemi, H. Semerádová, T. Rauter, I. Stenzel, G. Persiau,
F. Benade, R. Bhalearo, E. Sýkorová, A. Gorzsás, J. Sechet, G. Mouille, I. Heilmann,
G. De Jaeger, J. Ludwig-Müller, E. Benková, Nature Communications 11 (2020).
corr_author: '1'
date_created: 2020-05-10T22:00:48Z
date_published: 2020-05-01T00:00:00Z
date_updated: 2026-04-02T14:32:53Z
day: '01'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.1038/s41467-020-15895-5
ec_funded: 1
external_id:
isi:
- '000531425900012'
pmid:
- '32358503'
file:
- access_level: open_access
checksum: 2cba327c9e9416d75cb96be54b0fb441
content_type: application/pdf
creator: dernst
date_created: 2020-10-06T07:47:53Z
date_updated: 2020-10-06T07:47:53Z
file_id: '8614'
file_name: 2020_NatureComm_Hurny.pdf
file_size: 4743576
relation: main_file
success: 1
file_date_updated: 2020-10-06T07:47:53Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates
soil pathogen resistance
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 11
year: '2020'
...
---
_id: '7806'
abstract:
- lang: eng
text: "We consider the following decision problem EMBEDk→d in computational topology
(where k ≤ d are fixed positive integers): Given a finite simplicial complex K
of dimension k, does there exist a (piecewise-linear) embedding of K into ℝd?\r\nThe
special case EMBED1→2 is graph planarity, which is decidable in linear time, as
shown by Hopcroft and Tarjan. In higher dimensions, EMBED2→3 and EMBED3→3 are
known to be decidable (as well as NP-hard), and recent results of Čadek et al.
in computational homotopy theory, in combination with the classical Haefliger–Weber
theorem in geometric topology, imply that EMBEDk→d can be solved in polynomial
time for any fixed pair (k, d) of dimensions in the so-called metastable range
.\r\nHere, by contrast, we prove that EMBEDk→d is algorithmically undecidable
for almost all pairs of dimensions outside the metastable range, namely for .
This almost completely resolves the decidability vs. undecidability of EMBEDk→d
in higher dimensions and establishes a sharp dichotomy between polynomial-time
solvability and undecidability.\r\nOur result complements (and in a wide range
of dimensions strengthens) earlier results of Matoušek, Tancer, and the second
author, who showed that EMBEDk→d is undecidable for 4 ≤ k ϵ {d – 1, d}, and NP-hard
for all remaining pairs (k, d) outside the metastable range and satisfying d ≥
4."
article_processing_charge: No
author:
- first_name: Marek
full_name: Filakovský, Marek
id: 3E8AF77E-F248-11E8-B48F-1D18A9856A87
last_name: Filakovský
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
- first_name: Stephan Y
full_name: Zhechev, Stephan Y
id: 3AA52972-F248-11E8-B48F-1D18A9856A87
last_name: Zhechev
citation:
ama: 'Filakovský M, Wagner U, Zhechev SY. Embeddability of simplicial complexes
is undecidable. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms. Vol 2020-January. SIAM; 2020:767-785. doi:10.1137/1.9781611975994.47'
apa: 'Filakovský, M., Wagner, U., & Zhechev, S. Y. (2020). Embeddability of
simplicial complexes is undecidable. In Proceedings of the Annual ACM-SIAM
Symposium on Discrete Algorithms (Vol. 2020–January, pp. 767–785). Salt Lake
City, UT, United States: SIAM. https://doi.org/10.1137/1.9781611975994.47'
chicago: Filakovský, Marek, Uli Wagner, and Stephan Y Zhechev. “Embeddability of
Simplicial Complexes Is Undecidable.” In Proceedings of the Annual ACM-SIAM
Symposium on Discrete Algorithms, 2020–January:767–85. SIAM, 2020. https://doi.org/10.1137/1.9781611975994.47.
ieee: M. Filakovský, U. Wagner, and S. Y. Zhechev, “Embeddability of simplicial
complexes is undecidable,” in Proceedings of the Annual ACM-SIAM Symposium
on Discrete Algorithms, Salt Lake City, UT, United States, 2020, vol. 2020–January,
pp. 767–785.
ista: 'Filakovský M, Wagner U, Zhechev SY. 2020. Embeddability of simplicial complexes
is undecidable. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms.
SODA: Symposium on Discrete Algorithms vol. 2020–January, 767–785.'
mla: Filakovský, Marek, et al. “Embeddability of Simplicial Complexes Is Undecidable.”
Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, vol.
2020–January, SIAM, 2020, pp. 767–85, doi:10.1137/1.9781611975994.47.
short: M. Filakovský, U. Wagner, S.Y. Zhechev, in:, Proceedings of the Annual ACM-SIAM
Symposium on Discrete Algorithms, SIAM, 2020, pp. 767–785.
conference:
end_date: 2020-01-08
location: Salt Lake City, UT, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2020-01-05
date_created: 2020-05-10T22:00:48Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2026-06-18T19:27:16Z
day: '01'
ddc:
- '500'
department:
- _id: UlWa
doi: 10.1137/1.9781611975994.47
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1137/1.9781611975994.47
month: '01'
oa: 1
oa_version: Published Version
page: 767-785
project:
- _id: 26611F5C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31312
name: Algorithms for Embeddings and Homotopy Theory
publication: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
isbn:
- '9781611975994'
publication_status: published
publisher: SIAM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Embeddability of simplicial complexes is undecidable
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2020-January
year: '2020'
...
---
_id: '7807'
abstract:
- lang: eng
text: "In a straight-line embedded triangulation of a point set P in the plane,
removing an inner edge and—provided the resulting quadrilateral is convex—adding
the other diagonal is called an edge flip. The (edge) flip graph has all triangulations
as vertices, and a pair of triangulations is adjacent if they can be obtained
from each other by an edge flip. The goal of this paper is to contribute to a
better understanding of the flip graph, with an emphasis on its connectivity.\r\nFor
sets in general position, it is known that every triangulation allows at least
edge flips (a tight bound) which gives the minimum degree of any flip graph for
n points. We show that for every point set P in general position, the flip graph
is at least -vertex connected. Somewhat more strongly, we show that the vertex
connectivity equals the minimum degree occurring in the flip graph, i.e. the minimum
number of flippable edges in any triangulation of P, provided P is large enough.
Finally, we exhibit some of the geometry of the flip graph by showing that the
flip graph can be covered by 1-skeletons of polytopes of dimension (products of
associahedra).\r\nA corresponding result ((n – 3)-vertex connectedness) can be
shown for the bistellar flip graph of partial triangulations, i.e. the set of
all triangulations of subsets of P which contain all extreme points of P. This
will be treated separately in a second part."
article_processing_charge: No
arxiv: 1
author:
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
- first_name: Emo
full_name: Welzl, Emo
last_name: Welzl
citation:
ama: 'Wagner U, Welzl E. Connectivity of triangulation flip graphs in the plane
(Part I: Edge flips). In: Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms. Vol 2020-January. SIAM; 2020:2823-2841. doi:10.1137/1.9781611975994.172'
apa: 'Wagner, U., & Welzl, E. (2020). Connectivity of triangulation flip graphs
in the plane (Part I: Edge flips). In Proceedings of the Annual ACM-SIAM Symposium
on Discrete Algorithms (Vol. 2020–January, pp. 2823–2841). Salt Lake City,
UT, United States: SIAM. https://doi.org/10.1137/1.9781611975994.172'
chicago: 'Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs
in the Plane (Part I: Edge Flips).” In Proceedings of the Annual ACM-SIAM Symposium
on Discrete Algorithms, 2020–January:2823–41. SIAM, 2020. https://doi.org/10.1137/1.9781611975994.172.'
ieee: 'U. Wagner and E. Welzl, “Connectivity of triangulation flip graphs in the
plane (Part I: Edge flips),” in Proceedings of the Annual ACM-SIAM Symposium
on Discrete Algorithms, Salt Lake City, UT, United States, 2020, vol. 2020–January,
pp. 2823–2841.'
ista: 'Wagner U, Welzl E. 2020. Connectivity of triangulation flip graphs in the
plane (Part I: Edge flips). Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms. SODA: Symposium on Discrete Algorithms vol. 2020–January, 2823–2841.'
mla: 'Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs in
the Plane (Part I: Edge Flips).” Proceedings of the Annual ACM-SIAM Symposium
on Discrete Algorithms, vol. 2020–January, SIAM, 2020, pp. 2823–41, doi:10.1137/1.9781611975994.172.'
short: U. Wagner, E. Welzl, in:, Proceedings of the Annual ACM-SIAM Symposium on
Discrete Algorithms, SIAM, 2020, pp. 2823–2841.
conference:
end_date: 2020-01-08
location: Salt Lake City, UT, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2020-01-05
date_created: 2020-05-10T22:00:48Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2024-10-09T21:03:33Z
day: '01'
department:
- _id: UlWa
doi: 10.1137/1.9781611975994.172
external_id:
arxiv:
- '2003.13557'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1137/1.9781611975994.172
month: '01'
oa: 1
oa_version: Submitted Version
page: 2823-2841
publication: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
isbn:
- '9781611975994'
publication_status: published
publisher: SIAM
quality_controlled: '1'
related_material:
record:
- id: '12129'
relation: later_version
status: public
scopus_import: 1
status: public
title: 'Connectivity of triangulation flip graphs in the plane (Part I: Edge flips)'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2020-January
year: '2020'
...
---
_id: '7808'
abstract:
- lang: eng
text: Quantization converts neural networks into low-bit fixed-point computations
which can be carried out by efficient integer-only hardware, and is standard practice
for the deployment of neural networks on real-time embedded devices. However,
like their real-numbered counterpart, quantized networks are not immune to malicious
misclassification caused by adversarial attacks. We investigate how quantization
affects a network’s robustness to adversarial attacks, which is a formal verification
question. We show that neither robustness nor non-robustness are monotonic with
changing the number of bits for the representation and, also, neither are preserved
by quantization from a real-numbered network. For this reason, we introduce a
verification method for quantized neural networks which, using SMT solving over
bit-vectors, accounts for their exact, bit-precise semantics. We built a tool
and analyzed the effect of quantization on a classifier for the MNIST dataset.
We demonstrate that, compared to our method, existing methods for the analysis
of real-numbered networks often derive false conclusions about their quantizations,
both when determining robustness and when detecting attacks, and that existing
methods for quantized networks often miss attacks. Furthermore, we applied our
method beyond robustness, showing how the number of bits in quantization enlarges
the gender bias of a predictor for students’ grades.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
citation:
ama: 'Giacobbe M, Henzinger TA, Lechner M. How many bits does it take to quantize
your neural network? In: International Conference on Tools and Algorithms for
the Construction and Analysis of Systems. Vol 12079. Springer Nature; 2020:79-97.
doi:10.1007/978-3-030-45237-7_5'
apa: 'Giacobbe, M., Henzinger, T. A., & Lechner, M. (2020). How many bits does
it take to quantize your neural network? In International Conference on Tools
and Algorithms for the Construction and Analysis of Systems (Vol. 12079, pp.
79–97). Dublin, Ireland: Springer Nature. https://doi.org/10.1007/978-3-030-45237-7_5'
chicago: Giacobbe, Mirco, Thomas A Henzinger, and Mathias Lechner. “How Many Bits
Does It Take to Quantize Your Neural Network?” In International Conference
on Tools and Algorithms for the Construction and Analysis of Systems, 12079:79–97.
Springer Nature, 2020. https://doi.org/10.1007/978-3-030-45237-7_5.
ieee: M. Giacobbe, T. A. Henzinger, and M. Lechner, “How many bits does it take
to quantize your neural network?,” in International Conference on Tools and
Algorithms for the Construction and Analysis of Systems, Dublin, Ireland,
2020, vol. 12079, pp. 79–97.
ista: 'Giacobbe M, Henzinger TA, Lechner M. 2020. How many bits does it take to
quantize your neural network? International Conference on Tools and Algorithms
for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for
the Construction and Analysis of Systems, LNCS, vol. 12079, 79–97.'
mla: Giacobbe, Mirco, et al. “How Many Bits Does It Take to Quantize Your Neural
Network?” International Conference on Tools and Algorithms for the Construction
and Analysis of Systems, vol. 12079, Springer Nature, 2020, pp. 79–97, doi:10.1007/978-3-030-45237-7_5.
short: M. Giacobbe, T.A. Henzinger, M. Lechner, in:, International Conference on
Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature,
2020, pp. 79–97.
conference:
end_date: 2020-04-30
location: Dublin, Ireland
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2020-04-25
corr_author: '1'
date_created: 2020-05-10T22:00:49Z
date_published: 2020-04-17T00:00:00Z
date_updated: 2026-04-16T09:46:07Z
day: '17'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-45237-7_5
external_id:
isi:
- '001288734300005'
file:
- access_level: open_access
checksum: f19905a42891fe5ce93d69143fa3f6fb
content_type: application/pdf
creator: dernst
date_created: 2020-05-26T12:48:15Z
date_updated: 2020-07-14T12:48:03Z
file_id: '7893'
file_name: 2020_TACAS_Giacobbe.pdf
file_size: 2744030
relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
has_accepted_license: '1'
intvolume: ' 12079'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 79-97
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication: International Conference on Tools and Algorithms for the Construction
and Analysis of Systems
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030452360'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '11362'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: How many bits does it take to quantize your neural network?
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 12079
year: '2020'
...
---
_id: '7814'
abstract:
- lang: eng
text: 'Scientific research is to date largely restricted to wealthy laboratories
in developed nations due to the necessity of complex and expensive equipment.
This inequality limits the capacity of science to be used as a diplomatic channel.
Maker movements use open-source technologies including additive manufacturing
(3D printing) and laser cutting, together with low-cost computers for developing
novel products. This movement is setting the groundwork for a revolution, allowing
scientific equipment to be sourced at a fraction of the cost and has the potential
to increase the availability of equipment for scientists around the world. Science
education is increasingly recognized as another channel for science diplomacy.
In this perspective, we introduce the idea that the Maker movement and open-source
technologies have the potential to revolutionize science, technology, engineering
and mathematics (STEM) education worldwide. We present an open-source STEM didactic
tool called SCOPES (Sparking Curiosity through Open-source Platforms in Education
and Science). SCOPES is self-contained, independent of local resources, and cost-effective.
SCOPES can be adapted to communicate complex subjects from genetics to neurobiology,
perform real-world biological experiments and explore digitized scientific samples.
We envision such platforms will enhance science diplomacy by providing a means
for scientists to share their findings with classrooms and for educators to incorporate
didactic concepts into STEM lessons. By providing students the opportunity to
design, perform, and share scientific experiments, students also experience firsthand
the benefits of a multinational scientific community. We provide instructions
on how to build and use SCOPES on our webpage: http://scopeseducation.org.'
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
- _id: EM-Fac
article_number: '48'
article_processing_charge: No
article_type: original
author:
- first_name: Robert J
full_name: Beattie, Robert J
id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
last_name: Beattie
orcid: 0000-0002-8483-8753
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
citation:
ama: 'Beattie RJ, Hippenmeyer S, Pauler F. SCOPES: Sparking curiosity through Open-Source
platforms in education and science. Frontiers in Education. 2020;5. doi:10.3389/feduc.2020.00048'
apa: 'Beattie, R. J., Hippenmeyer, S., & Pauler, F. (2020). SCOPES: Sparking
curiosity through Open-Source platforms in education and science. Frontiers
in Education. Frontiers Media. https://doi.org/10.3389/feduc.2020.00048'
chicago: 'Beattie, Robert J, Simon Hippenmeyer, and Florian Pauler. “SCOPES: Sparking
Curiosity through Open-Source Platforms in Education and Science.” Frontiers
in Education. Frontiers Media, 2020. https://doi.org/10.3389/feduc.2020.00048.'
ieee: 'R. J. Beattie, S. Hippenmeyer, and F. Pauler, “SCOPES: Sparking curiosity
through Open-Source platforms in education and science,” Frontiers in Education,
vol. 5. Frontiers Media, 2020.'
ista: 'Beattie RJ, Hippenmeyer S, Pauler F. 2020. SCOPES: Sparking curiosity through
Open-Source platforms in education and science. Frontiers in Education. 5, 48.'
mla: 'Beattie, Robert J., et al. “SCOPES: Sparking Curiosity through Open-Source
Platforms in Education and Science.” Frontiers in Education, vol. 5, 48,
Frontiers Media, 2020, doi:10.3389/feduc.2020.00048.'
short: R.J. Beattie, S. Hippenmeyer, F. Pauler, Frontiers in Education 5 (2020).
corr_author: '1'
date_created: 2020-05-11T08:18:48Z
date_published: 2020-05-08T00:00:00Z
date_updated: 2024-10-22T10:46:38Z
day: '08'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.3389/feduc.2020.00048
ec_funded: 1
file:
- access_level: open_access
checksum: a24ec24e38d843341ae620ec76c53688
content_type: application/pdf
creator: dernst
date_created: 2020-05-11T11:34:08Z
date_updated: 2020-07-14T12:48:03Z
file_id: '7818'
file_name: 2020_FrontiersEduc_Beattie.pdf
file_size: 1402146
relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 264E56E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02416
name: Molecular Mechanisms Regulating Gliogenesis in the Neocortex
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Frontiers in Education
publication_identifier:
issn:
- 2504-284X
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'SCOPES: Sparking curiosity through Open-Source platforms in education and
science'
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: 5
year: '2020'
...
---
_id: '7847'
abstract:
- lang: eng
text: 'Water-in-salt electrolytes based on highly concentrated bis(trifluoromethyl)sulfonimide
(TFSI) promise aqueous electrolytes with stabilities nearing 3 V. However, especially
with an electrode approaching the cathodic (reductive) stability, cycling stability
is insufficient. While stability critically relies on a solid electrolyte interphase
(SEI), the mechanism behind the cathodic stability limit remains unclear. Here,
we reveal two distinct reduction potentials for the chemical environments of ''free''
and ''bound'' water and that both contribute to SEI formation. Free-water is reduced
~1V above bound water in a hydrogen evolution reaction (HER) and responsible for
SEI formation via reactive intermediates of the HER; concurrent LiTFSI precipitation/dissolution
establishes a dynamic interface. The free-water population emerges, therefore,
as the handle to extend the cathodic limit of aqueous electrolytes and the battery
cycling stability. '
article_processing_charge: No
article_type: original
author:
- first_name: Roza
full_name: Bouchal, Roza
last_name: Bouchal
- first_name: Zhujie
full_name: Li, Zhujie
last_name: Li
- first_name: Chandra
full_name: Bongu, Chandra
last_name: Bongu
- first_name: Steven
full_name: Le Vot, Steven
last_name: Le Vot
- first_name: Romain
full_name: Berthelot, Romain
last_name: Berthelot
- first_name: Benjamin
full_name: Rotenberg, Benjamin
last_name: Rotenberg
- first_name: Fréderic
full_name: Favier, Fréderic
last_name: Favier
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Mathieu
full_name: Salanne, Mathieu
last_name: Salanne
- first_name: Olivier
full_name: Fontaine, Olivier
last_name: Fontaine
citation:
ama: Bouchal R, Li Z, Bongu C, et al. Competitive salt precipitation/dissolution
during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie
International Edition. 2020;59(37):15913-1591. doi:10.1002/anie.202005378
apa: Bouchal, R., Li, Z., Bongu, C., Le Vot, S., Berthelot, R., Rotenberg, B., …
Fontaine, O. (2020). Competitive salt precipitation/dissolution during free‐water
reduction in water‐in‐salt electrolyte. Angewandte Chemie International Edition.
Wiley. https://doi.org/10.1002/anie.202005378
chicago: Bouchal, Roza, Zhujie Li, Chandra Bongu, Steven Le Vot, Romain Berthelot,
Benjamin Rotenberg, Fréderic Favier, Stefan Alexander Freunberger, Mathieu Salanne,
and Olivier Fontaine. “Competitive Salt Precipitation/Dissolution during Free‐water
Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie International Edition.
Wiley, 2020. https://doi.org/10.1002/anie.202005378.
ieee: R. Bouchal et al., “Competitive salt precipitation/dissolution during
free‐water reduction in water‐in‐salt electrolyte,” Angewandte Chemie International
Edition, vol. 59, no. 37. Wiley, pp. 15913–1591, 2020.
ista: Bouchal R, Li Z, Bongu C, Le Vot S, Berthelot R, Rotenberg B, Favier F, Freunberger
SA, Salanne M, Fontaine O. 2020. Competitive salt precipitation/dissolution during
free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie International
Edition. 59(37), 15913–1591.
mla: Bouchal, Roza, et al. “Competitive Salt Precipitation/Dissolution during Free‐water
Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie International Edition,
vol. 59, no. 37, Wiley, 2020, pp. 15913–1591, doi:10.1002/anie.202005378.
short: R. Bouchal, Z. Li, C. Bongu, S. Le Vot, R. Berthelot, B. Rotenberg, F. Favier,
S.A. Freunberger, M. Salanne, O. Fontaine, Angewandte Chemie International Edition
59 (2020) 15913–1591.
date_created: 2020-05-14T21:00:30Z
date_published: 2020-09-07T00:00:00Z
date_updated: 2023-09-05T16:02:53Z
day: '07'
ddc:
- '540'
- '546'
department:
- _id: StFr
doi: 10.1002/anie.202005378
external_id:
isi:
- '000541488700001'
pmid:
- '32390281'
file:
- access_level: open_access
checksum: 7b6c2fc20e9b0ff4353352f7a7004e2d
content_type: application/pdf
creator: dernst
date_created: 2020-09-17T08:57:16Z
date_updated: 2020-09-17T08:57:16Z
file_id: '8400'
file_name: 2020_AngChemieINT_Buchal.pdf
file_size: 1966184
relation: main_file
success: 1
file_date_updated: 2020-09-17T08:57:16Z
has_accepted_license: '1'
intvolume: ' 59'
isi: 1
issue: '37'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 15913-1591
pmid: 1
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt
electrolyte
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 59
year: '2020'
...
---
_id: '7866'
abstract:
- lang: eng
text: In this paper, we establish convergence to equilibrium for a drift–diffusion–recombination
system modelling the charge transport within certain semiconductor devices. More
precisely, we consider a two-level system for electrons and holes which is augmented
by an intermediate energy level for electrons in so-called trapped states. The
recombination dynamics use the mass action principle by taking into account this
additional trap level. The main part of the paper is concerned with the derivation
of an entropy–entropy production inequality, which entails exponential convergence
to the equilibrium via the so-called entropy method. The novelty of our approach
lies in the fact that the entropy method is applied uniformly in a fast-reaction
parameter which governs the lifetime of electrons on the trap level. Thus, the
resulting decay estimate for the densities of electrons and holes extends to the
corresponding quasi-steady-state approximation.
acknowledgement: Open access funding provided by Austrian Science Fund (FWF). The
second author has been supported by the International Research Training Group IGDK
1754 “Optimization and Numerical Analysis for Partial Differential Equations with
Nonsmooth Structures”, funded by the German Research Council (DFG) and the Austrian
Science Fund (FWF) under grant number [W 1244-N18].
article_processing_charge: No
article_type: original
author:
- first_name: Klemens
full_name: Fellner, Klemens
last_name: Fellner
- first_name: Michael
full_name: Kniely, Michael
id: 2CA2C08C-F248-11E8-B48F-1D18A9856A87
last_name: Kniely
orcid: 0000-0001-5645-4333
citation:
ama: Fellner K, Kniely M. Uniform convergence to equilibrium for a family of drift–diffusion
models with trap-assisted recombination and the limiting Shockley–Read–Hall model.
Journal of Elliptic and Parabolic Equations. 2020;6:529-598. doi:10.1007/s41808-020-00068-8
apa: Fellner, K., & Kniely, M. (2020). Uniform convergence to equilibrium for
a family of drift–diffusion models with trap-assisted recombination and the limiting
Shockley–Read–Hall model. Journal of Elliptic and Parabolic Equations.
Springer Nature. https://doi.org/10.1007/s41808-020-00068-8
chicago: Fellner, Klemens, and Michael Kniely. “Uniform Convergence to Equilibrium
for a Family of Drift–Diffusion Models with Trap-Assisted Recombination and the
Limiting Shockley–Read–Hall Model.” Journal of Elliptic and Parabolic Equations.
Springer Nature, 2020. https://doi.org/10.1007/s41808-020-00068-8.
ieee: K. Fellner and M. Kniely, “Uniform convergence to equilibrium for a family
of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall
model,” Journal of Elliptic and Parabolic Equations, vol. 6. Springer Nature,
pp. 529–598, 2020.
ista: Fellner K, Kniely M. 2020. Uniform convergence to equilibrium for a family
of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall
model. Journal of Elliptic and Parabolic Equations. 6, 529–598.
mla: Fellner, Klemens, and Michael Kniely. “Uniform Convergence to Equilibrium for
a Family of Drift–Diffusion Models with Trap-Assisted Recombination and the Limiting
Shockley–Read–Hall Model.” Journal of Elliptic and Parabolic Equations,
vol. 6, Springer Nature, 2020, pp. 529–98, doi:10.1007/s41808-020-00068-8.
short: K. Fellner, M. Kniely, Journal of Elliptic and Parabolic Equations 6 (2020)
529–598.
corr_author: '1'
date_created: 2020-05-17T22:00:45Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2025-07-17T08:12:24Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s41808-020-00068-8
external_id:
pmid:
- '33195442'
file:
- access_level: open_access
checksum: 6bc6832caacddceee1471291e93dcf1d
content_type: application/pdf
creator: dernst
date_created: 2020-11-25T08:59:59Z
date_updated: 2020-11-25T08:59:59Z
file_id: '8802'
file_name: 2020_JourEllipticParabEquat_Fellner.pdf
file_size: 8408694
relation: main_file
success: 1
file_date_updated: 2020-11-25T08:59:59Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 529-598
pmid: 1
project:
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Journal of Elliptic and Parabolic Equations
publication_identifier:
eissn:
- 2296-9039
issn:
- 2296-9020
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Uniform convergence to equilibrium for a family of drift–diffusion models with
trap-assisted recombination and the limiting Shockley–Read–Hall model
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: 6
year: '2020'
...
---
_id: '7875'
abstract:
- lang: eng
text: 'Cells navigating through complex tissues face a fundamental challenge: while
multiple protrusions explore different paths, the cell needs to avoid entanglement.
How a cell surveys and then corrects its own shape is poorly understood. Here,
we demonstrate that spatially distinct microtubule dynamics regulate amoeboid
cell migration by locally promoting the retraction of protrusions. In migrating
dendritic cells, local microtubule depolymerization within protrusions remote
from the microtubule organizing center triggers actomyosin contractility controlled
by RhoA and its exchange factor Lfc. Depletion of Lfc leads to aberrant myosin
localization, thereby causing two effects that rate-limit locomotion: (1) impaired
cell edge coordination during path finding and (2) defective adhesion resolution.
Compromised shape control is particularly hindering in geometrically complex microenvironments,
where it leads to entanglement and ultimately fragmentation of the cell body.
We thus demonstrate that microtubules can act as a proprioceptive device: they
sense cell shape and control actomyosin retraction to sustain cellular coherence.'
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: PreCl
acknowledgement: "The authors thank the Scientific Service Units (Life Sciences, Bioimaging,
Preclinical) of the Institute of Science and Technology Austria for excellent support.
This work was funded by the European Research Council (ERC StG 281556 and CoG 724373),
two grants from the Austrian\r\nScience Fund (FWF; P29911 and DK Nanocell W1250-B20
to M. Sixt) and by the German Research Foundation (DFG SFB1032 project B09) to O.
Thorn-Seshold and D. Trauner. J. Renkawitz was supported by ISTFELLOW funding from
the People Program (Marie Curie Actions) of the European Union’s Seventh Framework
Programme (FP7/2007-2013) under the Research Executive Agency grant agreement (291734)
and a European Molecular Biology Organization long-term fellowship (ALTF 1396-2014)
co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409), E. Kiermaier
by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s
Excellence Strategy—EXC 2151—390873048, and H. Hacker by the American Lebanese Syrian
Associated ¨Charities. K.-D. Fischer was supported by the Analysis, Imaging and
Modelling of Neuronal and Inflammatory Processes graduate school funded by the Ministry
of Economics, Science, and Digitisation of the State Saxony-Anhalt and by the European
Funds for Social and Regional Development."
article_number: e201907154
article_processing_charge: No
article_type: original
author:
- first_name: Aglaja
full_name: Kopf, Aglaja
id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87
last_name: Kopf
orcid: 0000-0002-2187-6656
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Irute
full_name: Girkontaite, Irute
last_name: Girkontaite
- first_name: Kerry
full_name: Tedford, Kerry
last_name: Tedford
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Oliver
full_name: Thorn-Seshold, Oliver
last_name: Thorn-Seshold
- first_name: Dirk
full_name: Trauner, Dirk
id: E8F27F48-3EBA-11E9-92A1-B709E6697425
last_name: Trauner
- first_name: Hans
full_name: Häcker, Hans
last_name: Häcker
- first_name: Klaus Dieter
full_name: Fischer, Klaus Dieter
last_name: Fischer
- first_name: Eva
full_name: Kiermaier, Eva
id: 3EB04B78-F248-11E8-B48F-1D18A9856A87
last_name: Kiermaier
orcid: 0000-0001-6165-5738
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Kopf A, Renkawitz J, Hauschild R, et al. Microtubules control cellular shape
and coherence in amoeboid migrating cells. The Journal of Cell Biology.
2020;219(6). doi:10.1083/jcb.201907154
apa: Kopf, A., Renkawitz, J., Hauschild, R., Girkontaite, I., Tedford, K., Merrin,
J., … Sixt, M. K. (2020). Microtubules control cellular shape and coherence in
amoeboid migrating cells. The Journal of Cell Biology. Rockefeller University
Press. https://doi.org/10.1083/jcb.201907154
chicago: Kopf, Aglaja, Jörg Renkawitz, Robert Hauschild, Irute Girkontaite, Kerry
Tedford, Jack Merrin, Oliver Thorn-Seshold, et al. “Microtubules Control Cellular
Shape and Coherence in Amoeboid Migrating Cells.” The Journal of Cell Biology.
Rockefeller University Press, 2020. https://doi.org/10.1083/jcb.201907154.
ieee: A. Kopf et al., “Microtubules control cellular shape and coherence
in amoeboid migrating cells,” The Journal of Cell Biology, vol. 219, no.
6. Rockefeller University Press, 2020.
ista: Kopf A, Renkawitz J, Hauschild R, Girkontaite I, Tedford K, Merrin J, Thorn-Seshold
O, Trauner D, Häcker H, Fischer KD, Kiermaier E, Sixt MK. 2020. Microtubules control
cellular shape and coherence in amoeboid migrating cells. The Journal of Cell
Biology. 219(6), e201907154.
mla: Kopf, Aglaja, et al. “Microtubules Control Cellular Shape and Coherence in
Amoeboid Migrating Cells.” The Journal of Cell Biology, vol. 219, no. 6,
e201907154, Rockefeller University Press, 2020, doi:10.1083/jcb.201907154.
short: A. Kopf, J. Renkawitz, R. Hauschild, I. Girkontaite, K. Tedford, J. Merrin,
O. Thorn-Seshold, D. Trauner, H. Häcker, K.D. Fischer, E. Kiermaier, M.K. Sixt,
The Journal of Cell Biology 219 (2020).
corr_author: '1'
date_created: 2020-05-24T22:00:56Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2025-04-14T13:10:03Z
day: '01'
ddc:
- '570'
department:
- _id: MiSi
- _id: Bio
- _id: NanoFab
doi: 10.1083/jcb.201907154
ec_funded: 1
external_id:
isi:
- '000538141100020'
pmid:
- '32379884'
file:
- access_level: open_access
checksum: cb0b9c77842ae1214caade7b77e4d82d
content_type: application/pdf
creator: dernst
date_created: 2020-11-24T13:25:13Z
date_updated: 2020-11-24T13:25:13Z
file_id: '8801'
file_name: 2020_JCellBiol_Kopf.pdf
file_size: 7536712
relation: main_file
success: 1
file_date_updated: 2020-11-24T13:25:13Z
has_accepted_license: '1'
intvolume: ' 219'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular Navigation Along Spatial Gradients
- _id: 26018E70-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29911
name: Mechanical adaptation of lamellipodial actin
- _id: 252C3B08-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1250-B20
name: Nano-Analytics of Cellular Systems
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25A48D24-B435-11E9-9278-68D0E5697425
grant_number: ALTF 1396-2014
name: Molecular and system level view of immune cell migration
publication: The Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Microtubules control cellular shape and coherence in amoeboid migrating cells
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: 219
year: '2020'
...
---
OA_place: publisher
OA_type: free access
_id: '7876'
abstract:
- lang: eng
text: 'In contrast to lymph nodes, the lymphoid regions of the spleen—the white
pulp—are located deep within the organ, yielding the trafficking paths of T cells
in the white pulp largely invisible. In an intravital microscopy tour de force
reported in this issue of Immunity, Chauveau et al. show that T cells perform
unidirectional, perivascular migration through the enigmatic marginal zone bridging
channels. '
article_processing_charge: No
article_type: original
author:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
citation:
ama: 'Sixt MK, Lämmermann T. T cells: Bridge-and-channel commute to the white pulp.
Immunity. 2020;52(5):721-723. doi:10.1016/j.immuni.2020.04.020'
apa: 'Sixt, M. K., & Lämmermann, T. (2020). T cells: Bridge-and-channel commute
to the white pulp. Immunity. Elsevier. https://doi.org/10.1016/j.immuni.2020.04.020'
chicago: 'Sixt, Michael K, and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute
to the White Pulp.” Immunity. Elsevier, 2020. https://doi.org/10.1016/j.immuni.2020.04.020.'
ieee: 'M. K. Sixt and T. Lämmermann, “T cells: Bridge-and-channel commute to the
white pulp,” Immunity, vol. 52, no. 5. Elsevier, pp. 721–723, 2020.'
ista: 'Sixt MK, Lämmermann T. 2020. T cells: Bridge-and-channel commute to the white
pulp. Immunity. 52(5), 721–723.'
mla: 'Sixt, Michael K., and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute
to the White Pulp.” Immunity, vol. 52, no. 5, Elsevier, 2020, pp. 721–23,
doi:10.1016/j.immuni.2020.04.020.'
short: M.K. Sixt, T. Lämmermann, Immunity 52 (2020) 721–723.
date_created: 2020-05-24T22:00:57Z
date_published: 2020-05-19T00:00:00Z
date_updated: 2026-06-18T19:27:52Z
day: '19'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1016/j.immuni.2020.04.020
external_id:
isi:
- '000535371100002'
pmid:
- '32433942'
intvolume: ' 52'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.immuni.2020.04.020
month: '05'
oa: 1
oa_version: Published Version
page: 721-723
pmid: 1
publication: Immunity
publication_identifier:
eissn:
- 1097-4180
issn:
- 1074-7613
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'T cells: Bridge-and-channel commute to the white pulp'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2020'
...
---
_id: '7877'
abstract:
- lang: eng
text: The NIPBL/MAU2 heterodimer loads cohesin onto chromatin. Mutations inNIPBLaccount
for most cases ofthe rare developmental disorder Cornelia de Lange syndrome (CdLS).
Here we report aMAU2 variant causing CdLS, a deletion of seven amino acids that
impairs the interaction between MAU2 and the NIPBL N terminus.Investigating this
interaction, we discovered that MAU2 and the NIPBL N terminus are largely dispensable
fornormal cohesin and NIPBL function in cells with a NIPBL early truncating mutation.
Despite a predicted fataloutcome of an out-of-frame single nucleotide duplication
inNIPBL, engineered in two different cell lines,alternative translation initiation
yields a form of NIPBL missing N-terminal residues. This form cannot interactwith
MAU2, but binds DNA and mediates cohesin loading. Altogether, our work reveals
that cohesin loading can occur independently of functional NIPBL/MAU2 complexes
and highlights a novel mechanism protectiveagainst out-of-frame mutations that
is potentially relevant for other genetic conditions.
article_number: '107647'
article_processing_charge: No
article_type: original
author:
- first_name: Ilaria
full_name: Parenti, Ilaria
id: D93538B0-5B71-11E9-AC62-02EBE5697425
last_name: Parenti
- first_name: Farah
full_name: Diab, Farah
last_name: Diab
- first_name: Sara Ruiz
full_name: Gil, Sara Ruiz
last_name: Gil
- first_name: Eskeatnaf
full_name: Mulugeta, Eskeatnaf
last_name: Mulugeta
- first_name: Valentina
full_name: Casa, Valentina
last_name: Casa
- first_name: Riccardo
full_name: Berutti, Riccardo
last_name: Berutti
- first_name: Rutger W.W.
full_name: Brouwer, Rutger W.W.
last_name: Brouwer
- first_name: Valerie
full_name: Dupé, Valerie
last_name: Dupé
- first_name: Juliane
full_name: Eckhold, Juliane
last_name: Eckhold
- first_name: Elisabeth
full_name: Graf, Elisabeth
last_name: Graf
- first_name: Beatriz
full_name: Puisac, Beatriz
last_name: Puisac
- first_name: Feliciano
full_name: Ramos, Feliciano
last_name: Ramos
- first_name: Thomas
full_name: Schwarzmayr, Thomas
last_name: Schwarzmayr
- first_name: Macarena Moronta
full_name: Gines, Macarena Moronta
last_name: Gines
- first_name: Thomas
full_name: Van Staveren, Thomas
last_name: Van Staveren
- first_name: Wilfred F.J.
full_name: Van Ijcken, Wilfred F.J.
last_name: Van Ijcken
- first_name: Tim M.
full_name: Strom, Tim M.
last_name: Strom
- first_name: Juan
full_name: Pié, Juan
last_name: Pié
- first_name: Erwan
full_name: Watrin, Erwan
last_name: Watrin
- first_name: Frank J.
full_name: Kaiser, Frank J.
last_name: Kaiser
- first_name: Kerstin S.
full_name: Wendt, Kerstin S.
last_name: Wendt
citation:
ama: Parenti I, Diab F, Gil SR, et al. MAU2 and NIPBL variants impair the heterodimerization
of the cohesin loader subunits and cause Cornelia de Lange syndrome. Cell Reports.
2020;31(7). doi:10.1016/j.celrep.2020.107647
apa: Parenti, I., Diab, F., Gil, S. R., Mulugeta, E., Casa, V., Berutti, R., … Wendt,
K. S. (2020). MAU2 and NIPBL variants impair the heterodimerization of the cohesin
loader subunits and cause Cornelia de Lange syndrome. Cell Reports. Elsevier.
https://doi.org/10.1016/j.celrep.2020.107647
chicago: Parenti, Ilaria, Farah Diab, Sara Ruiz Gil, Eskeatnaf Mulugeta, Valentina
Casa, Riccardo Berutti, Rutger W.W. Brouwer, et al. “MAU2 and NIPBL Variants Impair
the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange
Syndrome.” Cell Reports. Elsevier, 2020. https://doi.org/10.1016/j.celrep.2020.107647.
ieee: I. Parenti et al., “MAU2 and NIPBL variants impair the heterodimerization
of the cohesin loader subunits and cause Cornelia de Lange syndrome,” Cell
Reports, vol. 31, no. 7. Elsevier, 2020.
ista: Parenti I, Diab F, Gil SR, Mulugeta E, Casa V, Berutti R, Brouwer RWW, Dupé
V, Eckhold J, Graf E, Puisac B, Ramos F, Schwarzmayr T, Gines MM, Van Staveren
T, Van Ijcken WFJ, Strom TM, Pié J, Watrin E, Kaiser FJ, Wendt KS. 2020. MAU2
and NIPBL variants impair the heterodimerization of the cohesin loader subunits
and cause Cornelia de Lange syndrome. Cell Reports. 31(7), 107647.
mla: Parenti, Ilaria, et al. “MAU2 and NIPBL Variants Impair the Heterodimerization
of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome.” Cell
Reports, vol. 31, no. 7, 107647, Elsevier, 2020, doi:10.1016/j.celrep.2020.107647.
short: I. Parenti, F. Diab, S.R. Gil, E. Mulugeta, V. Casa, R. Berutti, R.W.W. Brouwer,
V. Dupé, J. Eckhold, E. Graf, B. Puisac, F. Ramos, T. Schwarzmayr, M.M. Gines,
T. Van Staveren, W.F.J. Van Ijcken, T.M. Strom, J. Pié, E. Watrin, F.J. Kaiser,
K.S. Wendt, Cell Reports 31 (2020).
date_created: 2020-05-24T22:00:57Z
date_published: 2020-05-19T00:00:00Z
date_updated: 2026-04-02T14:28:04Z
day: '19'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1016/j.celrep.2020.107647
external_id:
isi:
- '000535655200005'
file:
- access_level: open_access
checksum: 64d8f7467731ee5c166b10b939b8310b
content_type: application/pdf
creator: dernst
date_created: 2020-05-26T11:05:01Z
date_updated: 2020-07-14T12:48:04Z
file_id: '7892'
file_name: 2020_CellReports_Parenti.pdf
file_size: 4695682
relation: main_file
file_date_updated: 2020-07-14T12:48:04Z
has_accepted_license: '1'
intvolume: ' 31'
isi: 1
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader
subunits and cause Cornelia de Lange syndrome
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 31
year: '2020'
...
---
_id: '7878'
abstract:
- lang: eng
text: Type 1 metabotropic glutamate receptors (mGluR1s) are key elements in neuronal
signaling. While their function is well documented in slices, requirements for
their activation in vivo are poorly understood. We examine this question in adult
mice in vivo using 2-photon imaging of cerebellar molecular layer interneurons
(MLIs) expressing GCaMP. In anesthetized mice, parallel fiber activation evokes
beam-like Cai rises in postsynaptic MLIs which depend on co-activation of mGluR1s
and ionotropic glutamate receptors (iGluRs). In awake mice, blocking mGluR1 decreases
Cai rises associated with locomotion. In vitro studies and freeze-fracture electron
microscopy show that the iGluR-mGluR1 interaction is synergistic and favored by
close association of the two classes of receptors. Altogether our results suggest
that mGluR1s, acting in synergy with iGluRs, potently contribute to processing
cerebellar neuronal signaling under physiological conditions.
article_number: e56839
article_processing_charge: No
article_type: original
author:
- first_name: Jin
full_name: Bao, Jin
last_name: Bao
- first_name: Michael
full_name: Graupner, Michael
last_name: Graupner
- first_name: Guadalupe
full_name: Astorga, Guadalupe
last_name: Astorga
- first_name: Thibault
full_name: Collin, Thibault
last_name: Collin
- first_name: Abdelali
full_name: Jalil, Abdelali
last_name: Jalil
- first_name: Dwi Wahyu
full_name: Indriati, Dwi Wahyu
last_name: Indriati
- first_name: Jonathan
full_name: Bradley, Jonathan
last_name: Bradley
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Isabel
full_name: Llano, Isabel
last_name: Llano
citation:
ama: Bao J, Graupner M, Astorga G, et al. Synergism of type 1 metabotropic and ionotropic
glutamate receptors in cerebellar molecular layer interneurons in vivo. eLife.
2020;9. doi:10.7554/eLife.56839
apa: Bao, J., Graupner, M., Astorga, G., Collin, T., Jalil, A., Indriati, D. W.,
… Llano, I. (2020). Synergism of type 1 metabotropic and ionotropic glutamate
receptors in cerebellar molecular layer interneurons in vivo. ELife. eLife
Sciences Publications. https://doi.org/10.7554/eLife.56839
chicago: Bao, Jin, Michael Graupner, Guadalupe Astorga, Thibault Collin, Abdelali
Jalil, Dwi Wahyu Indriati, Jonathan Bradley, Ryuichi Shigemoto, and Isabel Llano.
“Synergism of Type 1 Metabotropic and Ionotropic Glutamate Receptors in Cerebellar
Molecular Layer Interneurons in Vivo.” ELife. eLife Sciences Publications,
2020. https://doi.org/10.7554/eLife.56839.
ieee: J. Bao et al., “Synergism of type 1 metabotropic and ionotropic glutamate
receptors in cerebellar molecular layer interneurons in vivo,” eLife, vol.
9. eLife Sciences Publications, 2020.
ista: Bao J, Graupner M, Astorga G, Collin T, Jalil A, Indriati DW, Bradley J, Shigemoto
R, Llano I. 2020. Synergism of type 1 metabotropic and ionotropic glutamate receptors
in cerebellar molecular layer interneurons in vivo. eLife. 9, e56839.
mla: Bao, Jin, et al. “Synergism of Type 1 Metabotropic and Ionotropic Glutamate
Receptors in Cerebellar Molecular Layer Interneurons in Vivo.” ELife, vol.
9, e56839, eLife Sciences Publications, 2020, doi:10.7554/eLife.56839.
short: J. Bao, M. Graupner, G. Astorga, T. Collin, A. Jalil, D.W. Indriati, J. Bradley,
R. Shigemoto, I. Llano, ELife 9 (2020).
date_created: 2020-05-24T22:00:58Z
date_published: 2020-05-13T00:00:00Z
date_updated: 2026-04-02T14:28:17Z
day: '13'
ddc:
- '570'
department:
- _id: RySh
doi: 10.7554/eLife.56839
external_id:
isi:
- '000535191600001'
pmid:
- '32401196'
file:
- access_level: open_access
checksum: 8ea99bb6660cc407dbdb00c173b01683
content_type: application/pdf
creator: dernst
date_created: 2020-05-26T09:34:54Z
date_updated: 2020-07-14T12:48:04Z
file_id: '7891'
file_name: 2020_eLife_Bao.pdf
file_size: 4832050
relation: main_file
file_date_updated: 2020-07-14T12:48:04Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar
molecular layer interneurons in vivo
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 9
year: '2020'
...
---
_id: '7880'
abstract:
- lang: eng
text: 'Following its evoked release, dopamine (DA) signaling is rapidly terminated
by presynaptic reuptake, mediated by the cocaine-sensitive DA transporter (DAT).
DAT surface availability is dynamically regulated by endocytic trafficking, and
direct protein kinase C (PKC) activation acutely diminishes DAT surface expression
by accelerating DAT internalization. Previous cell line studies demonstrated that
PKC-stimulated DAT endocytosis requires both Ack1 inactivation, which releases
a DAT-specific endocytic brake, and the neuronal GTPase, Rit2, which binds DAT.
However, it is unknown whether Rit2 is required for PKC-stimulated DAT endocytosis
in DAergic terminals or whether there are region- and/or sex-dependent differences
in PKC-stimulated DAT trafficking. Moreover, the mechanisms by which Rit2 controls
PKC-stimulated DAT endocytosis are unknown. Here, we directly examined these important
questions. Ex vivo studies revealed that PKC activation acutely decreased DAT
surface expression selectively in ventral, but not dorsal, striatum. AAV-mediated,
conditional Rit2 knockdown in DAergic neurons impacted baseline DAT surface:intracellular
distribution in DAergic terminals from female ventral, but not dorsal, striatum.
Further, Rit2 was required for PKC-stimulated DAT internalization in both male
and female ventral striatum. FRET and surface pulldown studies in cell lines revealed
that PKC activation drives DAT-Rit2 surface dissociation and that the DAT N terminus
is required for both PKC-mediated DAT-Rit2 dissociation and DAT internalization.
Finally, we found that Rit2 and Ack1 independently converge on DAT to facilitate
PKC-stimulated DAT endocytosis. Together, our data provide greater insight into
mechanisms that mediate PKC-regulated DAT internalization and reveal unexpected
region-specific differences in PKC-stimulated DAT trafficking in bona fide DAergic
terminals. '
article_processing_charge: No
article_type: original
author:
- first_name: Rita R.
full_name: Fagan, Rita R.
last_name: Fagan
- first_name: Patrick J.
full_name: Kearney, Patrick J.
last_name: Kearney
- first_name: Carolyn G.
full_name: Sweeney, Carolyn G.
last_name: Sweeney
- first_name: Dino
full_name: Luethi, Dino
last_name: Luethi
- first_name: Florianne E
full_name: Schoot Uiterkamp, Florianne E
id: 3526230C-F248-11E8-B48F-1D18A9856A87
last_name: Schoot Uiterkamp
- first_name: Klaus
full_name: Schicker, Klaus
last_name: Schicker
- first_name: Brian S.
full_name: Alejandro, Brian S.
last_name: Alejandro
- first_name: Lauren C.
full_name: O'Connor, Lauren C.
last_name: O'Connor
- first_name: Harald H.
full_name: Sitte, Harald H.
last_name: Sitte
- first_name: Haley E.
full_name: Melikian, Haley E.
last_name: Melikian
citation:
ama: 'Fagan RR, Kearney PJ, Sweeney CG, et al. Dopamine transporter trafficking
and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of Biological
Chemistry. 2020;295(16):5229-5244. doi:10.1074/jbc.RA120.012628'
apa: 'Fagan, R. R., Kearney, P. J., Sweeney, C. G., Luethi, D., Schoot Uiterkamp,
F. E., Schicker, K., … Melikian, H. E. (2020). Dopamine transporter trafficking
and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of Biological
Chemistry. ASBMB Publications. https://doi.org/10.1074/jbc.RA120.012628'
chicago: 'Fagan, Rita R., Patrick J. Kearney, Carolyn G. Sweeney, Dino Luethi, Florianne
E Schoot Uiterkamp, Klaus Schicker, Brian S. Alejandro, Lauren C. O’Connor, Harald
H. Sitte, and Haley E. Melikian. “Dopamine Transporter Trafficking and Rit2 GTPase:
Mechanism of Action and in Vivo Impact.” Journal of Biological Chemistry.
ASBMB Publications, 2020. https://doi.org/10.1074/jbc.RA120.012628.'
ieee: 'R. R. Fagan et al., “Dopamine transporter trafficking and Rit2 GTPase:
Mechanism of action and in vivo impact,” Journal of Biological Chemistry,
vol. 295, no. 16. ASBMB Publications, pp. 5229–5244, 2020.'
ista: 'Fagan RR, Kearney PJ, Sweeney CG, Luethi D, Schoot Uiterkamp FE, Schicker
K, Alejandro BS, O’Connor LC, Sitte HH, Melikian HE. 2020. Dopamine transporter
trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of
Biological Chemistry. 295(16), 5229–5244.'
mla: 'Fagan, Rita R., et al. “Dopamine Transporter Trafficking and Rit2 GTPase:
Mechanism of Action and in Vivo Impact.” Journal of Biological Chemistry,
vol. 295, no. 16, ASBMB Publications, 2020, pp. 5229–44, doi:10.1074/jbc.RA120.012628.'
short: R.R. Fagan, P.J. Kearney, C.G. Sweeney, D. Luethi, F.E. Schoot Uiterkamp,
K. Schicker, B.S. Alejandro, L.C. O’Connor, H.H. Sitte, H.E. Melikian, Journal
of Biological Chemistry 295 (2020) 5229–5244.
date_created: 2020-05-24T22:00:59Z
date_published: 2020-04-17T00:00:00Z
date_updated: 2025-07-10T11:54:48Z
day: '17'
department:
- _id: SaSi
doi: 10.1074/jbc.RA120.012628
external_id:
isi:
- '000530288000006'
pmid:
- '32132171'
intvolume: ' 295'
isi: 1
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://escholarship.umassmed.edu/oapubs/4187
month: '04'
oa: 1
oa_version: Submitted Version
page: 5229-5244
pmid: 1
publication: Journal of Biological Chemistry
publication_identifier:
eissn:
- 1083-351X
issn:
- 0021-9258
publication_status: published
publisher: ASBMB Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and
in vivo impact'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 295
year: '2020'
...
---
_id: '7882'
abstract:
- lang: eng
text: A few-body cluster is a building block of a many-body system in a gas phase
provided the temperature at most is of the order of the binding energy of this
cluster. Here we illustrate this statement by considering a system of tubes filled
with dipolar distinguishable particles. We calculate the partition function, which
determines the probability to find a few-body cluster at a given temperature.
The input for our calculations—the energies of few-body clusters—is estimated
using the harmonic approximation. We first describe and demonstrate the validity
of our numerical procedure. Then we discuss the results featuring melting of the
zero-temperature many-body state into a gas of free particles and few-body clusters.
For temperature higher than its binding energy threshold, the dimers overwhelmingly
dominate the ensemble, where the remaining probability is in free particles. At
very high temperatures free (harmonic oscillator trap-bound) particle dominance
is eventually reached. This structure evolution appears both for one and two particles
in each layer providing crucial information about the behavior of ultracold dipolar
gases. The investigation addresses the transition region between few- and many-body
physics as a function of temperature using a system of ten dipoles in five tubes.
article_number: '484'
article_processing_charge: No
article_type: original
author:
- first_name: Jeremy R.
full_name: Armstrong, Jeremy R.
last_name: Armstrong
- first_name: Aksel S.
full_name: Jensen, Aksel S.
last_name: Jensen
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Nikolaj T.
full_name: Zinner, Nikolaj T.
last_name: Zinner
citation:
ama: Armstrong JR, Jensen AS, Volosniev A, Zinner NT. Clusters in separated tubes
of tilted dipoles. Mathematics. 2020;8(4). doi:10.3390/math8040484
apa: Armstrong, J. R., Jensen, A. S., Volosniev, A., & Zinner, N. T. (2020).
Clusters in separated tubes of tilted dipoles. Mathematics. MDPI. https://doi.org/10.3390/math8040484
chicago: Armstrong, Jeremy R., Aksel S. Jensen, Artem Volosniev, and Nikolaj T.
Zinner. “Clusters in Separated Tubes of Tilted Dipoles.” Mathematics. MDPI,
2020. https://doi.org/10.3390/math8040484.
ieee: J. R. Armstrong, A. S. Jensen, A. Volosniev, and N. T. Zinner, “Clusters in
separated tubes of tilted dipoles,” Mathematics, vol. 8, no. 4. MDPI, 2020.
ista: Armstrong JR, Jensen AS, Volosniev A, Zinner NT. 2020. Clusters in separated
tubes of tilted dipoles. Mathematics. 8(4), 484.
mla: Armstrong, Jeremy R., et al. “Clusters in Separated Tubes of Tilted Dipoles.”
Mathematics, vol. 8, no. 4, 484, MDPI, 2020, doi:10.3390/math8040484.
short: J.R. Armstrong, A.S. Jensen, A. Volosniev, N.T. Zinner, Mathematics 8 (2020).
date_created: 2020-05-24T22:01:00Z
date_published: 2020-04-01T00:00:00Z
date_updated: 2026-04-02T14:33:47Z
day: '01'
ddc:
- '510'
department:
- _id: MiLe
doi: 10.3390/math8040484
ec_funded: 1
external_id:
isi:
- '000531824100024'
file:
- access_level: open_access
checksum: a05a7df724522203d079673a0d4de4bc
content_type: application/pdf
creator: dernst
date_created: 2020-05-25T14:42:22Z
date_updated: 2020-07-14T12:48:04Z
file_id: '7887'
file_name: 2020_Mathematics_Armstrong.pdf
file_size: 990540
relation: main_file
file_date_updated: 2020-07-14T12:48:04Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Mathematics
publication_identifier:
eissn:
- 2227-7390
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Clusters in separated tubes of tilted dipoles
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 8
year: '2020'
...
---
_id: '7908'
abstract:
- lang: eng
text: Volatile anesthetics are widely used for surgery, but neuronal mechanisms
of anesthesia remain unidentified. At the calyx of Held in brainstem slices from
rats of either sex, isoflurane at clinical doses attenuated EPSCs by decreasing
the release probability and the number of readily releasable vesicles. In presynaptic
recordings of Ca2+ currents and exocytic capacitance changes, isoflurane attenuated
exocytosis by inhibiting Ca2+ currents evoked by a short presynaptic depolarization,
whereas it inhibited exocytosis evoked by a prolonged depolarization via directly
blocking exocytic machinery downstream of Ca2+ influx. Since the length of presynaptic
depolarization can simulate the frequency of synaptic inputs, isoflurane anesthesia
is likely mediated by distinct dual mechanisms, depending on input frequencies.
In simultaneous presynaptic and postsynaptic action potential recordings, isoflurane
impaired the fidelity of repetitive spike transmission, more strongly at higher
frequencies. Furthermore, in the cerebrum of adult mice, isoflurane inhibited
monosynaptic corticocortical spike transmission, preferentially at a higher frequency.
We conclude that dual presynaptic mechanisms operate for the anesthetic action
of isoflurane, of which direct inhibition of exocytic machinery plays a low-pass
filtering role in spike transmission at central excitatory synapses.
article_processing_charge: No
article_type: original
author:
- first_name: Han Ying
full_name: Wang, Han Ying
last_name: Wang
- first_name: Kohgaku
full_name: Eguchi, Kohgaku
id: 2B7846DC-F248-11E8-B48F-1D18A9856A87
last_name: Eguchi
orcid: 0000-0002-6170-2546
- first_name: Takayuki
full_name: Yamashita, Takayuki
last_name: Yamashita
- first_name: Tomoyuki
full_name: Takahashi, Tomoyuki
last_name: Takahashi
citation:
ama: Wang HY, Eguchi K, Yamashita T, Takahashi T. Frequency-dependent block of excitatory
neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of
Neuroscience. 2020;40(21):4103-4115. doi:10.1523/JNEUROSCI.2946-19.2020
apa: Wang, H. Y., Eguchi, K., Yamashita, T., & Takahashi, T. (2020). Frequency-dependent
block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms.
Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2946-19.2020
chicago: Wang, Han Ying, Kohgaku Eguchi, Takayuki Yamashita, and Tomoyuki Takahashi.
“Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual
Presynaptic Mechanisms.” Journal of Neuroscience. Society for Neuroscience,
2020. https://doi.org/10.1523/JNEUROSCI.2946-19.2020.
ieee: H. Y. Wang, K. Eguchi, T. Yamashita, and T. Takahashi, “Frequency-dependent
block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms,”
Journal of Neuroscience, vol. 40, no. 21. Society for Neuroscience, pp.
4103–4115, 2020.
ista: Wang HY, Eguchi K, Yamashita T, Takahashi T. 2020. Frequency-dependent block
of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms.
Journal of Neuroscience. 40(21), 4103–4115.
mla: Wang, Han Ying, et al. “Frequency-Dependent Block of Excitatory Neurotransmission
by Isoflurane via Dual Presynaptic Mechanisms.” Journal of Neuroscience,
vol. 40, no. 21, Society for Neuroscience, 2020, pp. 4103–15, doi:10.1523/JNEUROSCI.2946-19.2020.
short: H.Y. Wang, K. Eguchi, T. Yamashita, T. Takahashi, Journal of Neuroscience
40 (2020) 4103–4115.
date_created: 2020-05-31T22:00:48Z
date_published: 2020-05-20T00:00:00Z
date_updated: 2025-03-07T08:29:32Z
day: '20'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1523/JNEUROSCI.2946-19.2020
external_id:
isi:
- '000535694700004'
pmid:
- '32327530'
file:
- access_level: open_access
checksum: 6571607ea9036154b67cc78e848a7f7d
content_type: application/pdf
creator: dernst
date_created: 2020-06-02T09:12:16Z
date_updated: 2020-07-14T12:48:05Z
file_id: '7912'
file_name: 2020_JourNeuroscience_Wang.pdf
file_size: 3817360
relation: main_file
file_date_updated: 2020-07-14T12:48:05Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '21'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 4103-4115
pmid: 1
publication: Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: Frequency-dependent block of excitatory neurotransmission by isoflurane via
dual presynaptic mechanisms
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: 40
year: '2020'
...
---
_id: '7909'
abstract:
- lang: eng
text: Cell migration entails networks and bundles of actin filaments termed lamellipodia
and microspikes or filopodia, respectively, as well as focal adhesions, all of
which recruit Ena/VASP family members hitherto thought to antagonize efficient
cell motility. However, we find these proteins to act as positive regulators of
migration in different murine cell lines. CRISPR/Cas9-mediated loss of Ena/VASP
proteins reduced lamellipodial actin assembly and perturbed lamellipodial architecture,
as evidenced by changed network geometry as well as reduction of filament length
and number that was accompanied by abnormal Arp2/3 complex and heterodimeric capping
protein accumulation. Loss of Ena/VASP function also abolished the formation of
microspikes normally embedded in lamellipodia, but not of filopodia capable of
emanating without lamellipodia. Ena/VASP-deficiency also impaired integrin-mediated
adhesion accompanied by reduced traction forces exerted through these structures.
Our data thus uncover novel Ena/VASP functions of these actin polymerases that
are fully consistent with their promotion of cell migration.
article_number: e55351
article_processing_charge: No
article_type: original
author:
- first_name: Julia
full_name: Damiano-Guercio, Julia
last_name: Damiano-Guercio
- first_name: Laëtitia
full_name: Kurzawa, Laëtitia
last_name: Kurzawa
- first_name: Jan
full_name: Müller, Jan
id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D
last_name: Müller
- 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: Matthias
full_name: Schaks, Matthias
last_name: Schaks
- first_name: Maria
full_name: Nemethova, Maria
id: 34E27F1C-F248-11E8-B48F-1D18A9856A87
last_name: Nemethova
- first_name: Thomas
full_name: Pokrant, Thomas
last_name: Pokrant
- first_name: Stefan
full_name: Brühmann, Stefan
last_name: Brühmann
- first_name: Joern
full_name: Linkner, Joern
last_name: Linkner
- first_name: Laurent
full_name: Blanchoin, Laurent
last_name: Blanchoin
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
citation:
ama: Damiano-Guercio J, Kurzawa L, Müller J, et al. Loss of Ena/VASP interferes
with lamellipodium architecture, motility and integrin-dependent adhesion. eLife.
2020;9. doi:10.7554/eLife.55351
apa: Damiano-Guercio, J., Kurzawa, L., Müller, J., Dimchev, G. A., Schaks, M., Nemethova,
M., … Faix, J. (2020). Loss of Ena/VASP interferes with lamellipodium architecture,
motility and integrin-dependent adhesion. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.55351
chicago: Damiano-Guercio, Julia, Laëtitia Kurzawa, Jan Müller, Georgi A Dimchev,
Matthias Schaks, Maria Nemethova, Thomas Pokrant, et al. “Loss of Ena/VASP Interferes
with Lamellipodium Architecture, Motility and Integrin-Dependent Adhesion.” ELife.
eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.55351.
ieee: J. Damiano-Guercio et al., “Loss of Ena/VASP interferes with lamellipodium
architecture, motility and integrin-dependent adhesion,” eLife, vol. 9.
eLife Sciences Publications, 2020.
ista: Damiano-Guercio J, Kurzawa L, Müller J, Dimchev GA, Schaks M, Nemethova M,
Pokrant T, Brühmann S, Linkner J, Blanchoin L, Sixt MK, Rottner K, Faix J. 2020.
Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent
adhesion. eLife. 9, e55351.
mla: Damiano-Guercio, Julia, et al. “Loss of Ena/VASP Interferes with Lamellipodium
Architecture, Motility and Integrin-Dependent Adhesion.” ELife, vol. 9,
e55351, eLife Sciences Publications, 2020, doi:10.7554/eLife.55351.
short: J. Damiano-Guercio, L. Kurzawa, J. Müller, G.A. Dimchev, M. Schaks, M. Nemethova,
T. Pokrant, S. Brühmann, J. Linkner, L. Blanchoin, M.K. Sixt, K. Rottner, J. Faix,
ELife 9 (2020).
date_created: 2020-05-31T22:00:49Z
date_published: 2020-05-11T00:00:00Z
date_updated: 2026-04-02T14:32:12Z
day: '11'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.7554/eLife.55351
ec_funded: 1
external_id:
isi:
- '000537208000001'
pmid:
- '32391788'
file:
- access_level: open_access
checksum: d33bd4441b9a0195718ce1ba5d2c48a6
content_type: application/pdf
creator: dernst
date_created: 2020-06-02T10:35:37Z
date_updated: 2020-07-14T12:48:05Z
file_id: '7914'
file_name: 2020_eLife_Damiano_Guercio.pdf
file_size: 10535713
relation: main_file
file_date_updated: 2020-07-14T12:48:05Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular Navigation Along Spatial Gradients
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent
adhesion
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 9
year: '2020'
...
---
_id: '7910'
abstract:
- lang: eng
text: Quantum illumination uses entangled signal-idler photon pairs to boost the
detection efficiency of low-reflectivity objects in environments with bright thermal
noise. Its advantage is particularly evident at low signal powers, a promising
feature for applications such as noninvasive biomedical scanning or low-power
short-range radar. Here, we experimentally investigate the concept of quantum
illumination at microwave frequencies. We generate entangled fields to illuminate
a room-temperature object at a distance of 1 m in a free-space detection setup.
We implement a digital phase-conjugate receiver based on linear quadrature measurements
that outperforms a symmetric classical noise radar in the same conditions, despite
the entanglement-breaking signal path. Starting from experimental data, we also
simulate the case of perfect idler photon number detection, which results in a
quantum advantage compared with the relative classical benchmark. Our results
highlight the opportunities and challenges in the way toward a first room-temperature
application of microwave quantum circuits.
article_number: eabb0451
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: S.
full_name: Pirandola, S.
last_name: Pirandola
- first_name: D
full_name: Vitali, D
last_name: Vitali
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Barzanjeh S, Pirandola S, Vitali D, Fink JM. Microwave quantum illumination
using a digital receiver. Science Advances. 2020;6(19). doi:10.1126/sciadv.abb0451
apa: Barzanjeh, S., Pirandola, S., Vitali, D., & Fink, J. M. (2020). Microwave
quantum illumination using a digital receiver. Science Advances. AAAS.
https://doi.org/10.1126/sciadv.abb0451
chicago: Barzanjeh, Shabir, S. Pirandola, D Vitali, and Johannes M Fink. “Microwave
Quantum Illumination Using a Digital Receiver.” Science Advances. AAAS,
2020. https://doi.org/10.1126/sciadv.abb0451.
ieee: S. Barzanjeh, S. Pirandola, D. Vitali, and J. M. Fink, “Microwave quantum
illumination using a digital receiver,” Science Advances, vol. 6, no. 19.
AAAS, 2020.
ista: Barzanjeh S, Pirandola S, Vitali D, Fink JM. 2020. Microwave quantum illumination
using a digital receiver. Science Advances. 6(19), eabb0451.
mla: Barzanjeh, Shabir, et al. “Microwave Quantum Illumination Using a Digital Receiver.”
Science Advances, vol. 6, no. 19, eabb0451, AAAS, 2020, doi:10.1126/sciadv.abb0451.
short: S. Barzanjeh, S. Pirandola, D. Vitali, J.M. Fink, Science Advances 6 (2020).
corr_author: '1'
date_created: 2020-05-31T22:00:49Z
date_published: 2020-05-06T00:00:00Z
date_updated: 2026-04-15T06:42:37Z
day: '06'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1126/sciadv.abb0451
ec_funded: 1
external_id:
arxiv:
- '1908.03058'
isi:
- '000531171100045'
pmid:
- '32548249'
file:
- access_level: open_access
checksum: 16fa61cc1951b444ee74c07188cda9da
content_type: application/pdf
creator: dernst
date_created: 2020-06-02T09:18:36Z
date_updated: 2020-07-14T12:48:05Z
file_id: '7913'
file_name: 2020_ScienceAdvances_Barzanjeh.pdf
file_size: 795822
relation: main_file
file_date_updated: 2020-07-14T12:48:05Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '19'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862644'
name: Quantum readout techniques and technologies
- _id: 258047B6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '707438'
name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination
with cavity Optomechanics'
- _id: 257EB838-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '732894'
name: Hybrid Optomechanical Technologies
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
grant_number: F07105
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: AAAS
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/scientists-demonstrate-quantum-radar-prototype/
record:
- id: '9001'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Microwave quantum illumination using a digital receiver
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: 6
year: '2020'
...
---
_id: '7919'
abstract:
- lang: eng
text: We explore the time evolution of two impurities in a trapped one-dimensional
Bose gas that follows a change of the boson-impurity interaction. We study the
induced impurity-impurity interactions and their effect on the quench dynamics.
In particular, we report on the size of the impurity cloud, the impurity-impurity
entanglement, and the impurity-impurity correlation function. The presented numerical
simulations are based upon the variational multilayer multiconfiguration time-dependent
Hartree method for bosons. To analyze and quantify induced impurity-impurity correlations,
we employ an effective two-body Hamiltonian with a contact interaction. We show
that the effective model consistent with the mean-field attraction of two heavy
impurities explains qualitatively our results for weak interactions. Our findings
suggest that the quench dynamics in cold-atom systems can be a tool for studying
impurity-impurity correlations.
article_number: '023154 '
article_processing_charge: No
article_type: original
author:
- first_name: S. I.
full_name: Mistakidis, S. I.
last_name: Mistakidis
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: P.
full_name: Schmelcher, P.
last_name: Schmelcher
citation:
ama: Mistakidis SI, Volosniev A, Schmelcher P. Induced correlations between impurities
in a one-dimensional quenched Bose gas. Physical Review Research. 2020;2.
doi:10.1103/physrevresearch.2.023154
apa: Mistakidis, S. I., Volosniev, A., & Schmelcher, P. (2020). Induced correlations
between impurities in a one-dimensional quenched Bose gas. Physical Review
Research. American Physical Society. https://doi.org/10.1103/physrevresearch.2.023154
chicago: Mistakidis, S. I., Artem Volosniev, and P. Schmelcher. “Induced Correlations
between Impurities in a One-Dimensional Quenched Bose Gas.” Physical Review
Research. American Physical Society, 2020. https://doi.org/10.1103/physrevresearch.2.023154.
ieee: S. I. Mistakidis, A. Volosniev, and P. Schmelcher, “Induced correlations between
impurities in a one-dimensional quenched Bose gas,” Physical Review Research,
vol. 2. American Physical Society, 2020.
ista: Mistakidis SI, Volosniev A, Schmelcher P. 2020. Induced correlations between
impurities in a one-dimensional quenched Bose gas. Physical Review Research. 2,
023154.
mla: Mistakidis, S. I., et al. “Induced Correlations between Impurities in a One-Dimensional
Quenched Bose Gas.” Physical Review Research, vol. 2, 023154, American
Physical Society, 2020, doi:10.1103/physrevresearch.2.023154.
short: S.I. Mistakidis, A. Volosniev, P. Schmelcher, Physical Review Research 2
(2020).
date_created: 2020-06-03T11:30:10Z
date_published: 2020-05-11T00:00:00Z
date_updated: 2024-10-21T06:02:23Z
day: '11'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/physrevresearch.2.023154
ec_funded: 1
file:
- access_level: open_access
checksum: e1c362fe094d6b246b3cd4a49722e78b
content_type: application/pdf
creator: dernst
date_created: 2020-06-04T13:51:59Z
date_updated: 2020-07-14T12:48:05Z
file_id: '7926'
file_name: 2020_PhysRevResearch_Mistakidis.pdf
file_size: 1741098
relation: main_file
file_date_updated: 2020-07-14T12:48:05Z
has_accepted_license: '1'
intvolume: ' 2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Induced correlations between impurities in a one-dimensional quenched Bose
gas
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: 2
year: '2020'
...
---
_id: '7931'
abstract:
- lang: eng
text: In the course of sample preparation for Next Generation Sequencing (NGS),
DNA is fragmented by various methods. Fragmentation shows a persistent bias with
regard to the cleavage rates of various dinucleotides. With the exception of CpG
dinucleotides the previously described biases were consistent with results of
the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides
including the methylated CpG and unmethylated CpG dinucleotides using data of
the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that
the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides.
Using this information, we developed a classifier for distinguishing cancer and
healthy tissues based on their CpG islands statuses of the fragmentation. A simple
Support Vector Machine classifier based on this algorithm shows an accuracy of
84%. The proposed method allows the detection of epigenetic markers purely based
on mechanochemical DNA fragmentation, which can be detected by a simple analysis
of the NGS sequencing data.
article_number: '8635'
article_processing_charge: No
article_type: original
author:
- first_name: Leonid A.
full_name: Uroshlev, Leonid A.
last_name: Uroshlev
- first_name: Eldar T.
full_name: Abdullaev, Eldar T.
last_name: Abdullaev
- first_name: Iren R.
full_name: Umarova, Iren R.
last_name: Umarova
- first_name: Irina A.
full_name: Il’Icheva, Irina A.
last_name: Il’Icheva
- first_name: Larisa A.
full_name: Panchenko, Larisa A.
last_name: Panchenko
- first_name: Robert V.
full_name: Polozov, Robert V.
last_name: Polozov
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Yury D.
full_name: Nechipurenko, Yury D.
last_name: Nechipurenko
- first_name: Sergei L.
full_name: Grokhovsky, Sergei L.
last_name: Grokhovsky
citation:
ama: Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of
the methylation level of CpG islands from NGS data. Scientific Reports.
2020;10. doi:10.1038/s41598-020-65406-1
apa: Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko,
L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification
of the methylation level of CpG islands from NGS data. Scientific Reports.
Springer Nature. https://doi.org/10.1038/s41598-020-65406-1
chicago: Uroshlev, Leonid A., Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il’Icheva,
Larisa A. Panchenko, Robert V. Polozov, Fyodor Kondrashov, Yury D. Nechipurenko,
and Sergei L. Grokhovsky. “A Method for Identification of the Methylation Level
of CpG Islands from NGS Data.” Scientific Reports. Springer Nature, 2020.
https://doi.org/10.1038/s41598-020-65406-1.
ieee: L. A. Uroshlev et al., “A method for identification of the methylation
level of CpG islands from NGS data,” Scientific Reports, vol. 10. Springer
Nature, 2020.
ista: Uroshlev LA, Abdullaev ET, Umarova IR, Il’Icheva IA, Panchenko LA, Polozov
RV, Kondrashov F, Nechipurenko YD, Grokhovsky SL. 2020. A method for identification
of the methylation level of CpG islands from NGS data. Scientific Reports. 10,
8635.
mla: Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation
Level of CpG Islands from NGS Data.” Scientific Reports, vol. 10, 8635,
Springer Nature, 2020, doi:10.1038/s41598-020-65406-1.
short: L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko,
R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports
10 (2020).
date_created: 2020-06-07T22:00:51Z
date_published: 2020-05-25T00:00:00Z
date_updated: 2026-04-03T09:26:06Z
day: '25'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41598-020-65406-1
external_id:
isi:
- '000560774200007'
pmid:
- '32451390'
file:
- access_level: open_access
checksum: 099e51611a5b7ca04244d03b2faddf33
content_type: application/pdf
creator: dernst
date_created: 2020-06-08T06:27:32Z
date_updated: 2020-07-14T12:48:05Z
file_id: '7947'
file_name: 2020_ScientificReports_Uroshlev.pdf
file_size: 1001724
relation: main_file
file_date_updated: 2020-07-14T12:48:05Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
eissn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A method for identification of the methylation level of CpG islands from NGS
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 10
year: '2020'
...
---
_id: '7932'
abstract:
- lang: eng
text: Pulsating flows through tubular geometries are laminar provided that velocities
are moderate. This in particular is also believed to apply to cardiovascular flows
where inertial forces are typically too low to sustain turbulence. On the other
hand, flow instabilities and fluctuating shear stresses are held responsible for
a variety of cardiovascular diseases. Here we report a nonlinear instability mechanism
for pulsating pipe flow that gives rise to bursts of turbulence at low flow rates.
Geometrical distortions of small, yet finite, amplitude are found to excite a
state consisting of helical vortices during flow deceleration. The resulting flow
pattern grows rapidly in magnitude, breaks down into turbulence, and eventually
returns to laminar when the flow accelerates. This scenario causes shear stress
fluctuations and flow reversal during each pulsation cycle. Such unsteady conditions
can adversely affect blood vessels and have been shown to promote inflammation
and dysfunction of the shear stress-sensitive endothelial cell layer.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Duo
full_name: Xu, Duo
id: 3454D55E-F248-11E8-B48F-1D18A9856A87
last_name: Xu
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Xingyu
full_name: Ma, Xingyu
id: 34BADBA6-F248-11E8-B48F-1D18A9856A87
last_name: Ma
orcid: 0000-0002-0179-9737
- first_name: Baofang
full_name: Song, Baofang
last_name: Song
- first_name: Michael
full_name: Riedl, Michael
id: 3BE60946-F248-11E8-B48F-1D18A9856A87
last_name: Riedl
orcid: 0000-0003-4844-6311
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Xu D, Varshney A, Ma X, et al. Nonlinear hydrodynamic instability and turbulence
in pulsatile flow. Proceedings of the National Academy of Sciences of the United
States of America. 2020;117(21):11233-11239. doi:10.1073/pnas.1913716117
apa: Xu, D., Varshney, A., Ma, X., Song, B., Riedl, M., Avila, M., & Hof, B.
(2020). Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences. https://doi.org/10.1073/pnas.1913716117
chicago: Xu, Duo, Atul Varshney, Xingyu Ma, Baofang Song, Michael Riedl, Marc Avila,
and Björn Hof. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile
Flow.” Proceedings of the National Academy of Sciences of the United States
of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1913716117.
ieee: D. Xu et al., “Nonlinear hydrodynamic instability and turbulence in
pulsatile flow,” Proceedings of the National Academy of Sciences of the United
States of America, vol. 117, no. 21. National Academy of Sciences, pp. 11233–11239,
2020.
ista: Xu D, Varshney A, Ma X, Song B, Riedl M, Avila M, Hof B. 2020. Nonlinear hydrodynamic
instability and turbulence in pulsatile flow. Proceedings of the National Academy
of Sciences of the United States of America. 117(21), 11233–11239.
mla: Xu, Duo, et al. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile
Flow.” Proceedings of the National Academy of Sciences of the United States
of America, vol. 117, no. 21, National Academy of Sciences, 2020, pp. 11233–39,
doi:10.1073/pnas.1913716117.
short: D. Xu, A. Varshney, X. Ma, B. Song, M. Riedl, M. Avila, B. Hof, Proceedings
of the National Academy of Sciences of the United States of America 117 (2020)
11233–11239.
date_created: 2020-06-07T22:00:51Z
date_published: 2020-05-26T00:00:00Z
date_updated: 2026-04-07T13:29:13Z
day: '26'
department:
- _id: BjHo
doi: 10.1073/pnas.1913716117
ec_funded: 1
external_id:
arxiv:
- '2005.11190'
isi:
- '000536797100014'
pmid:
- '32393637'
intvolume: ' 117'
isi: 1
issue: '21'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2005.11190
month: '05'
oa: 1
oa_version: Preprint
page: 11233-11239
pmid: 1
project:
- _id: 238B8092-32DE-11EA-91FC-C7463DDC885E
call_identifier: FWF
grant_number: I04188
name: Instabilities in pulsating pipe flow in complex fluids
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/blood-flows-more-turbulent-than-previously-expected/
record:
- id: '12726'
relation: dissertation_contains
status: public
- id: '14530'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Nonlinear hydrodynamic instability and turbulence in pulsatile flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2020'
...