---
_id: '6029'
abstract:
- lang: eng
text: Protein micropatterning has become an important tool for many biomedical applications
as well as in academic research. Current techniques that allow to reduce the feature
size of patterns below 1 μm are, however, often costly and require sophisticated
equipment. We present here a straightforward and convenient method to generate
highly condensed nanopatterns of proteins without the need for clean room facilities
or expensive equipment. Our approach is based on nanocontact printing and allows
for the fabrication of protein patterns with feature sizes of 80 nm and periodicities
down to 140 nm. This was made possible by the use of the material X-poly(dimethylsiloxane)
(X-PDMS) in a two-layer stamp layout for protein printing. In a proof of principle,
different proteins at various scales were printed and the pattern quality was
evaluated by atomic force microscopy (AFM) and super-resolution fluorescence microscopy.
article_number: '655'
article_processing_charge: No
author:
- first_name: Marco
full_name: Lindner, Marco
last_name: Lindner
- first_name: Aliz
full_name: Tresztenyak, Aliz
last_name: Tresztenyak
- first_name: Gergö
full_name: Fülöp, Gergö
last_name: Fülöp
- first_name: Wiebke
full_name: Jahr, Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
- first_name: Adrian
full_name: Prinz, Adrian
last_name: Prinz
- first_name: Iris
full_name: Prinz, Iris
last_name: Prinz
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Gerhard J.
full_name: Schütz, Gerhard J.
last_name: Schütz
- first_name: Eva
full_name: Sevcsik, Eva
last_name: Sevcsik
citation:
ama: Lindner M, Tresztenyak A, Fülöp G, et al. A fast and simple contact printing
approach to generate 2D protein nanopatterns. Frontiers in Chemistry. 2019;6.
doi:10.3389/fchem.2018.00655
apa: Lindner, M., Tresztenyak, A., Fülöp, G., Jahr, W., Prinz, A., Prinz, I., …
Sevcsik, E. (2019). A fast and simple contact printing approach to generate 2D
protein nanopatterns. Frontiers in Chemistry. Frontiers Media S.A. https://doi.org/10.3389/fchem.2018.00655
chicago: Lindner, Marco, Aliz Tresztenyak, Gergö Fülöp, Wiebke Jahr, Adrian Prinz,
Iris Prinz, Johann G Danzl, Gerhard J. Schütz, and Eva Sevcsik. “A Fast and Simple
Contact Printing Approach to Generate 2D Protein Nanopatterns.” Frontiers in
Chemistry. Frontiers Media S.A., 2019. https://doi.org/10.3389/fchem.2018.00655.
ieee: M. Lindner et al., “A fast and simple contact printing approach to
generate 2D protein nanopatterns,” Frontiers in Chemistry, vol. 6. Frontiers
Media S.A., 2019.
ista: Lindner M, Tresztenyak A, Fülöp G, Jahr W, Prinz A, Prinz I, Danzl JG, Schütz
GJ, Sevcsik E. 2019. A fast and simple contact printing approach to generate 2D
protein nanopatterns. Frontiers in Chemistry. 6, 655.
mla: Lindner, Marco, et al. “A Fast and Simple Contact Printing Approach to Generate
2D Protein Nanopatterns.” Frontiers in Chemistry, vol. 6, 655, Frontiers
Media S.A., 2019, doi:10.3389/fchem.2018.00655.
short: M. Lindner, A. Tresztenyak, G. Fülöp, W. Jahr, A. Prinz, I. Prinz, J.G. Danzl,
G.J. Schütz, E. Sevcsik, Frontiers in Chemistry 6 (2019).
date_created: 2019-02-17T22:59:24Z
date_published: 2019-01-24T00:00:00Z
date_updated: 2023-08-24T14:45:38Z
day: '24'
ddc:
- '540'
department:
- _id: JoDa
doi: 10.3389/fchem.2018.00655
external_id:
isi:
- '000456718000001'
file:
- access_level: open_access
checksum: 7841301d7c53b56ef873791b4b6f7b24
content_type: application/pdf
creator: dernst
date_created: 2019-02-18T15:10:34Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6039'
file_name: 2019_frontiers_Lindner.pdf
file_size: 1766820
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Frontiers in Chemistry
publication_identifier:
eissn:
- '22962646'
publication_status: published
publisher: Frontiers Media S.A.
quality_controlled: '1'
scopus_import: '1'
status: public
title: A fast and simple contact printing approach to generate 2D protein nanopatterns
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 6
year: '2019'
...
---
_id: '6028'
abstract:
- lang: eng
text: We give a construction allowing us to build local renormalized solutions to
general quasilinear stochastic PDEs within the theory of regularity structures,
thus greatly generalizing the recent results of [1, 5, 11]. Loosely speaking,
our construction covers quasilinear variants of all classes of equations for which
the general construction of [3, 4, 7] applies, including in particular one‐dimensional
systems with KPZ‐type nonlinearities driven by space‐time white noise. In a less
singular and more specific case, we furthermore show that the counterterms introduced
by the renormalization procedure are given by local functionals of the solution.
The main feature of our construction is that it allows exploitation of a number
of existing results developed for the semilinear case, so that the number of additional
arguments it requires is relatively small.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
- first_name: Martin
full_name: Hairer, Martin
last_name: Hairer
citation:
ama: Gerencser M, Hairer M. A solution theory for quasilinear singular SPDEs. Communications
on Pure and Applied Mathematics. 2019;72(9):1983-2005. doi:10.1002/cpa.21816
apa: Gerencser, M., & Hairer, M. (2019). A solution theory for quasilinear singular
SPDEs. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21816
chicago: Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear
Singular SPDEs.” Communications on Pure and Applied Mathematics. Wiley,
2019. https://doi.org/10.1002/cpa.21816.
ieee: M. Gerencser and M. Hairer, “A solution theory for quasilinear singular SPDEs,”
Communications on Pure and Applied Mathematics, vol. 72, no. 9. Wiley,
pp. 1983–2005, 2019.
ista: Gerencser M, Hairer M. 2019. A solution theory for quasilinear singular SPDEs.
Communications on Pure and Applied Mathematics. 72(9), 1983–2005.
mla: Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular
SPDEs.” Communications on Pure and Applied Mathematics, vol. 72, no. 9,
Wiley, 2019, pp. 1983–2005, doi:10.1002/cpa.21816.
short: M. Gerencser, M. Hairer, Communications on Pure and Applied Mathematics 72
(2019) 1983–2005.
date_created: 2019-02-17T22:59:24Z
date_published: 2019-02-08T00:00:00Z
date_updated: 2023-08-24T14:44:31Z
day: '08'
ddc:
- '500'
department:
- _id: JaMa
doi: 10.1002/cpa.21816
external_id:
isi:
- '000475465000003'
file:
- access_level: open_access
checksum: 09aec427eb48c0f96a1cce9ff53f013b
content_type: application/pdf
creator: kschuh
date_created: 2020-01-07T13:25:55Z
date_updated: 2020-07-14T12:47:17Z
file_id: '7237'
file_name: 2019_Wiley_Gerencser.pdf
file_size: 381350
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 72'
isi: 1
issue: '9'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1983-2005
publication: Communications on Pure and Applied Mathematics
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: A solution theory for quasilinear singular SPDEs
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: 72
year: '2019'
...
---
_id: '5948'
abstract:
- lang: eng
text: We study the termination problem for nondeterministic probabilistic programs.
We consider the bounded termination problem that asks whether the supremum of
the expected termination time over all schedulers is bounded. First, we show that
ranking supermartingales (RSMs) are both sound and complete for proving bounded
termination over nondeterministic probabilistic programs. For nondeterministic
probabilistic programs a previous result claimed that RSMs are not complete for
bounded termination, whereas our result corrects the previous flaw and establishes
completeness with a rigorous proof. Second, we present the first sound approach
to establish lower bounds on expected termination time through RSMs.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Fu H, Chatterjee K. Termination of nondeterministic probabilistic programs.
In: International Conference on Verification, Model Checking, and Abstract
Interpretation. Vol 11388. Springer Nature; 2019:468-490. doi:10.1007/978-3-030-11245-5_22'
apa: 'Fu, H., & Chatterjee, K. (2019). Termination of nondeterministic probabilistic
programs. In International Conference on Verification, Model Checking, and
Abstract Interpretation (Vol. 11388, pp. 468–490). Cascais, Portugal: Springer
Nature. https://doi.org/10.1007/978-3-030-11245-5_22'
chicago: Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic
Probabilistic Programs.” In International Conference on Verification, Model
Checking, and Abstract Interpretation, 11388:468–90. Springer Nature, 2019.
https://doi.org/10.1007/978-3-030-11245-5_22.
ieee: H. Fu and K. Chatterjee, “Termination of nondeterministic probabilistic programs,”
in International Conference on Verification, Model Checking, and Abstract Interpretation,
Cascais, Portugal, 2019, vol. 11388, pp. 468–490.
ista: 'Fu H, Chatterjee K. 2019. Termination of nondeterministic probabilistic programs.
International Conference on Verification, Model Checking, and Abstract Interpretation.
VMCAI: Verification, Model Checking, and Abstract Interpretation, LNCS, vol. 11388,
468–490.'
mla: Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic
Programs.” International Conference on Verification, Model Checking, and Abstract
Interpretation, vol. 11388, Springer Nature, 2019, pp. 468–90, doi:10.1007/978-3-030-11245-5_22.
short: H. Fu, K. Chatterjee, in:, International Conference on Verification, Model
Checking, and Abstract Interpretation, Springer Nature, 2019, pp. 468–490.
conference:
end_date: 2019-01-15
location: Cascais, Portugal
name: 'VMCAI: Verification, Model Checking, and Abstract Interpretation'
start_date: 2019-01-13
date_created: 2019-02-10T22:59:17Z
date_published: 2019-01-11T00:00:00Z
date_updated: 2023-08-24T14:42:22Z
day: '11'
department:
- _id: KrCh
doi: 10.1007/978-3-030-11245-5_22
external_id:
arxiv:
- '1701.02944'
isi:
- '000931943000022'
intvolume: ' 11388'
isi: 1
language:
- iso: eng
main_file_link:
- url: https://arxiv.org/abs/1701.02944
month: '01'
oa_version: Preprint
page: 468-490
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: International Conference on Verification, Model Checking, and Abstract
Interpretation
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Termination of nondeterministic probabilistic programs
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11388
year: '2019'
...
---
_id: '5945'
abstract:
- lang: eng
text: In developing organisms, spatially prescribed cell identities are thought
to be determined by the expression levels of multiple genes. Quantitative tests
of this idea, however, require a theoretical framework capable of exposing the
rules and precision of cell specification over developmental time. We use the
gap gene network in the early fly embryo as an example to show how expression
levels of the four gap genes can be jointly decoded into an optimal specification
of position with 1% accuracy. The decoder correctly predicts, with no free parameters,
the dynamics of pair-rule expression patterns at different developmental time
points and in various mutant backgrounds. Precise cellular identities are thus
available at the earliest stages of development, contrasting the prevailing view
of positional information being slowly refined across successive layers of the
patterning network. Our results suggest that developmental enhancers closely approximate
a mathematically optimal decoding strategy.
article_processing_charge: No
article_type: original
author:
- first_name: Mariela D.
full_name: Petkova, Mariela D.
last_name: Petkova
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Eric F.
full_name: Wieschaus, Eric F.
last_name: Wieschaus
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
citation:
ama: Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal decoding of
cellular identities in a genetic network. Cell. 2019;176(4):844-855.e15.
doi:10.1016/j.cell.2019.01.007
apa: Petkova, M. D., Tkačik, G., Bialek, W., Wieschaus, E. F., & Gregor, T.
(2019). Optimal decoding of cellular identities in a genetic network. Cell.
Cell Press. https://doi.org/10.1016/j.cell.2019.01.007
chicago: Petkova, Mariela D., Gašper Tkačik, William Bialek, Eric F. Wieschaus,
and Thomas Gregor. “Optimal Decoding of Cellular Identities in a Genetic Network.”
Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.01.007.
ieee: M. D. Petkova, G. Tkačik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal
decoding of cellular identities in a genetic network,” Cell, vol. 176,
no. 4. Cell Press, p. 844–855.e15, 2019.
ista: Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. 2019. Optimal decoding
of cellular identities in a genetic network. Cell. 176(4), 844–855.e15.
mla: Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic
Network.” Cell, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:10.1016/j.cell.2019.01.007.
short: M.D. Petkova, G. Tkačik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019)
844–855.e15.
date_created: 2019-02-10T22:59:16Z
date_published: 2019-02-07T00:00:00Z
date_updated: 2023-08-24T14:42:47Z
day: '07'
department:
- _id: GaTk
doi: 10.1016/j.cell.2019.01.007
external_id:
isi:
- '000457969200015'
pmid:
- '30712870'
intvolume: ' 176'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2019.01.007
month: '02'
oa: 1
oa_version: Published Version
page: 844-855.e15
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Cell
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/cells-find-their-identity-using-a-mathematically-optimal-strategy/
scopus_import: '1'
status: public
title: Optimal decoding of cellular identities in a genetic network
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 176
year: '2019'
...
---
_id: '5943'
abstract:
- lang: eng
text: The hairpin instability of a jet in a crossflow (JICF) for a low jet-to-crossflow
velocity ratio is investigated experimentally for a velocity ratio range of R
∈ (0.14, 0.75) and crossflow Reynolds numbers ReD ∈ (260, 640). From spectral
analysis we characterize the Strouhal number and amplitude of the hairpin instability
as a function of R and ReD. We demonstrate that the dynamics of the hairpins is
well described by the Landau model, and, hence, that the instability occurs through
Hopf bifurcation, similarly to other hydrodynamical oscillators such as wake behind
different bluff bodies. Using the Landau model, we determine the precise threshold
values of hairpin shedding. We also study the spatial dependence of this hydrodynamical
instability, which shows a global behaviour.
article_processing_charge: No
article_type: original
author:
- first_name: Lukasz
full_name: Klotz, Lukasz
id: 2C9AF1C2-F248-11E8-B48F-1D18A9856A87
last_name: Klotz
orcid: 0000-0003-1740-7635
- first_name: Konrad
full_name: Gumowski, Konrad
last_name: Gumowski
- first_name: José Eduardo
full_name: Wesfreid, José Eduardo
last_name: Wesfreid
citation:
ama: Klotz L, Gumowski K, Wesfreid JE. Experiments on a jet in a crossflow in the
low-velocity-ratio regime. Journal of Fluid Mechanics. 2019;863:386-406.
doi:10.1017/jfm.2018.974
apa: Klotz, L., Gumowski, K., & Wesfreid, J. E. (2019). Experiments on a jet
in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics.
Cambridge University Press. https://doi.org/10.1017/jfm.2018.974
chicago: Klotz, Lukasz, Konrad Gumowski, and José Eduardo Wesfreid. “Experiments
on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” Journal of Fluid
Mechanics. Cambridge University Press, 2019. https://doi.org/10.1017/jfm.2018.974.
ieee: L. Klotz, K. Gumowski, and J. E. Wesfreid, “Experiments on a jet in a crossflow
in the low-velocity-ratio regime,” Journal of Fluid Mechanics, vol. 863.
Cambridge University Press, pp. 386–406, 2019.
ista: Klotz L, Gumowski K, Wesfreid JE. 2019. Experiments on a jet in a crossflow
in the low-velocity-ratio regime. Journal of Fluid Mechanics. 863, 386–406.
mla: Klotz, Lukasz, et al. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio
Regime.” Journal of Fluid Mechanics, vol. 863, Cambridge University Press,
2019, pp. 386–406, doi:10.1017/jfm.2018.974.
short: L. Klotz, K. Gumowski, J.E. Wesfreid, Journal of Fluid Mechanics 863 (2019)
386–406.
date_created: 2019-02-10T22:59:15Z
date_published: 2019-03-25T00:00:00Z
date_updated: 2023-08-24T14:43:13Z
day: '25'
department:
- _id: BjHo
doi: 10.1017/jfm.2018.974
ec_funded: 1
external_id:
arxiv:
- '1902.07931'
isi:
- '000526029100016'
intvolume: ' 863'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1902.07931
month: '03'
oa: 1
oa_version: Preprint
page: 386-406
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Fluid Mechanics
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Experiments on a jet in a crossflow in the low-velocity-ratio regime
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 863
year: '2019'
...
---
_id: '6042'
abstract:
- lang: eng
text: Static program analyzers are increasingly effective in checking correctness
properties of programs and reporting any errors found, often in the form of error
traces. However, developers still spend a significant amount of time on debugging.
This involves processing long error traces in an effort to localize a bug to a
relatively small part of the program and to identify its cause. In this paper,
we present a technique for automated fault localization that, given a program
and an error trace, efficiently narrows down the cause of the error to a few statements.
These statements are then ranked in terms of their suspiciousness. Our technique
relies only on the semantics of the given program and does not require any test
cases or user guidance. In experiments on a set of C benchmarks, we show that
our technique is effective in quickly isolating the cause of error while out-performing
other state-of-the-art fault-localization techniques.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Maria
full_name: Christakis, Maria
last_name: Christakis
- first_name: Matthias
full_name: Heizmann, Matthias
last_name: Heizmann
- first_name: Muhammad Numair
full_name: Mansur, Muhammad Numair
last_name: Mansur
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Valentin
full_name: Wüstholz, Valentin
last_name: Wüstholz
citation:
ama: 'Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. Semantic fault
localization and suspiciousness ranking. In: 25th International Conference
on Tools and Algorithms for the Construction and Analysis of Systems . Vol
11427. Springer Nature; 2019:226-243. doi:10.1007/978-3-030-17462-0_13'
apa: 'Christakis, M., Heizmann, M., Mansur, M. N., Schilling, C., & Wüstholz,
V. (2019). Semantic fault localization and suspiciousness ranking. In 25th
International Conference on Tools and Algorithms for the Construction and Analysis
of Systems (Vol. 11427, pp. 226–243). Prague, Czech Republic: Springer Nature.
https://doi.org/10.1007/978-3-030-17462-0_13'
chicago: Christakis, Maria, Matthias Heizmann, Muhammad Numair Mansur, Christian
Schilling, and Valentin Wüstholz. “Semantic Fault Localization and Suspiciousness
Ranking.” In 25th International Conference on Tools and Algorithms for the
Construction and Analysis of Systems , 11427:226–43. Springer Nature, 2019.
https://doi.org/10.1007/978-3-030-17462-0_13.
ieee: M. Christakis, M. Heizmann, M. N. Mansur, C. Schilling, and V. Wüstholz, “Semantic
fault localization and suspiciousness ranking,” in 25th International Conference
on Tools and Algorithms for the Construction and Analysis of Systems , Prague,
Czech Republic, 2019, vol. 11427, pp. 226–243.
ista: 'Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. 2019. Semantic
fault localization and suspiciousness ranking. 25th 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. 11427,
226–243.'
mla: Christakis, Maria, et al. “Semantic Fault Localization and Suspiciousness Ranking.”
25th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems , vol. 11427, Springer Nature, 2019, pp. 226–43, doi:10.1007/978-3-030-17462-0_13.
short: M. Christakis, M. Heizmann, M.N. Mansur, C. Schilling, V. Wüstholz, in:,
25th International Conference on Tools and Algorithms for the Construction and
Analysis of Systems , Springer Nature, 2019, pp. 226–243.
conference:
end_date: 2019-04-11
location: Prague, Czech Republic
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2019-04-06
date_created: 2019-02-18T16:44:06Z
date_published: 2019-04-04T00:00:00Z
date_updated: 2023-08-24T14:47:45Z
day: '04'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-17462-0_13
ec_funded: 1
external_id:
isi:
- '000681166500013'
file:
- access_level: open_access
checksum: 9998496f6fe202c0a19124b4209154c6
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T14:16:05Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6408'
file_name: 2019_LNCS_Christakis.pdf
file_size: 773083
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 11427'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 226-243
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: '25th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems '
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Semantic fault localization and suspiciousness ranking
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11427
year: '2019'
...
---
_id: '6035'
abstract:
- lang: eng
text: 'We present JuliaReach, a toolbox for set-based reachability analysis of dynamical
systems. JuliaReach consists of two main packages: Reachability, containing implementations
of reachability algorithms for continuous and hybrid systems, and LazySets, a
standalone library that implements state-of-the-art algorithms for calculus with
convex sets. The library offers both concrete and lazy set representations, where
the latter stands for the ability to delay set computations until they are needed.
The choice of the programming language Julia and the accompanying documentation
of our toolbox allow researchers to easily translate set-based algorithms from
mathematics to software in a platform-independent way, while achieving runtime
performance that is comparable to statically compiled languages. Combining lazy
operations in high dimensions and explicit computations in low dimensions, JuliaReach
can be applied to solve complex, large-scale problems.'
article_processing_charge: No
author:
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Marcelo
full_name: Forets, Marcelo
last_name: Forets
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Kostiantyn
full_name: Potomkin, Kostiantyn
last_name: Potomkin
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
citation:
ama: 'Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. JuliaReach: A toolbox
for set-based reachability. In: Proceedings of the 22nd International Conference
on Hybrid Systems: Computation and Control. Vol 22. ACM; 2019:39-44. doi:10.1145/3302504.3311804'
apa: 'Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2019).
JuliaReach: A toolbox for set-based reachability. In Proceedings of the 22nd
International Conference on Hybrid Systems: Computation and Control (Vol.
22, pp. 39–44). Montreal, QC, Canada: ACM. https://doi.org/10.1145/3302504.3311804'
chicago: 'Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin,
and Christian Schilling. “JuliaReach: A Toolbox for Set-Based Reachability.” In
Proceedings of the 22nd International Conference on Hybrid Systems: Computation
and Control, 22:39–44. ACM, 2019. https://doi.org/10.1145/3302504.3311804.'
ieee: 'S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “JuliaReach:
A toolbox for set-based reachability,” in Proceedings of the 22nd International
Conference on Hybrid Systems: Computation and Control, Montreal, QC, Canada,
2019, vol. 22, pp. 39–44.'
ista: 'Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2019. JuliaReach:
A toolbox for set-based reachability. Proceedings of the 22nd International Conference
on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and
Control vol. 22, 39–44.'
mla: 'Bogomolov, Sergiy, et al. “JuliaReach: A Toolbox for Set-Based Reachability.”
Proceedings of the 22nd International Conference on Hybrid Systems: Computation
and Control, vol. 22, ACM, 2019, pp. 39–44, doi:10.1145/3302504.3311804.'
short: 'S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings
of the 22nd International Conference on Hybrid Systems: Computation and Control,
ACM, 2019, pp. 39–44.'
conference:
end_date: 2019-04-18
location: Montreal, QC, Canada
name: 'HSCC: Hybrid Systems Computation and Control'
start_date: 2019-04-16
date_created: 2019-02-18T14:43:28Z
date_published: 2019-04-16T00:00:00Z
date_updated: 2023-08-24T14:47:21Z
day: '16'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/3302504.3311804
ec_funded: 1
external_id:
arxiv:
- '1901.10736'
isi:
- '000516713900005'
file:
- access_level: open_access
checksum: 28ed56439aea5991c3122d4730fd828f
content_type: application/pdf
creator: cschilli
date_created: 2019-03-05T09:27:18Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6067'
file_name: hscc19.pdf
file_size: 3784414
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
keyword:
- reachability analysis
- hybrid systems
- lazy computation
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 39-44
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 'Proceedings of the 22nd International Conference on Hybrid Systems:
Computation and Control'
publication_identifier:
isbn:
- '9781450362825'
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'JuliaReach: A toolbox for set-based reachability'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 22
year: '2019'
...
---
_id: '6052'
abstract:
- lang: eng
text: 'Expansion microscopy is a relatively new approach to super-resolution imaging
that uses expandable hydrogels to isotropically increase the physical distance
between fluorophores in biological samples such as cell cultures or tissue slices.
The classic gel recipe results in an expansion factor of ~4×, with a resolution
of 60–80 nm. We have recently developed X10 microscopy, which uses a gel that
achieves an expansion factor of ~10×, with a resolution of ~25 nm. Here, we provide
a step-by-step protocol for X10 expansion microscopy. A typical experiment consists
of seven sequential stages: (i) immunostaining, (ii) anchoring, (iii) polymerization,
(iv) homogenization, (v) expansion, (vi) imaging, and (vii) validation. The protocol
presented here includes recommendations for optimization, pitfalls and their solutions,
and detailed guidelines that should increase reproducibility. Although our protocol
focuses on X10 expansion microscopy, we detail which of these suggestions are
also applicable to classic fourfold expansion microscopy. We exemplify our protocol
using primary hippocampal neurons from rats, but our approach can be used with
other primary cells or cultured cell lines of interest. This protocol will enable
any researcher with basic experience in immunostainings and access to an epifluorescence
microscope to perform super-resolution microscopy with X10. The procedure takes
3 d and requires ~5 h of actively handling the sample for labeling and expansion,
and another ~3 h for imaging and analysis.'
article_processing_charge: No
article_type: original
author:
- first_name: Sven M
full_name: Truckenbrodt, Sven M
id: 45812BD4-F248-11E8-B48F-1D18A9856A87
last_name: Truckenbrodt
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Silvio O
full_name: Rizzoli, Silvio O
last_name: Rizzoli
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. A practical guide to optimization
in X10 expansion microscopy. Nature Protocols. 2019;14(3):832–863. doi:10.1038/s41596-018-0117-3
apa: Truckenbrodt, S. M., Sommer, C. M., Rizzoli, S. O., & Danzl, J. G. (2019).
A practical guide to optimization in X10 expansion microscopy. Nature Protocols.
Nature Publishing Group. https://doi.org/10.1038/s41596-018-0117-3
chicago: Truckenbrodt, Sven M, Christoph M Sommer, Silvio O Rizzoli, and Johann
G Danzl. “A Practical Guide to Optimization in X10 Expansion Microscopy.” Nature
Protocols. Nature Publishing Group, 2019. https://doi.org/10.1038/s41596-018-0117-3.
ieee: S. M. Truckenbrodt, C. M. Sommer, S. O. Rizzoli, and J. G. Danzl, “A practical
guide to optimization in X10 expansion microscopy,” Nature Protocols, vol.
14, no. 3. Nature Publishing Group, pp. 832–863, 2019.
ista: Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. 2019. A practical guide
to optimization in X10 expansion microscopy. Nature Protocols. 14(3), 832–863.
mla: Truckenbrodt, Sven M., et al. “A Practical Guide to Optimization in X10 Expansion
Microscopy.” Nature Protocols, vol. 14, no. 3, Nature Publishing Group,
2019, pp. 832–863, doi:10.1038/s41596-018-0117-3.
short: S.M. Truckenbrodt, C.M. Sommer, S.O. Rizzoli, J.G. Danzl, Nature Protocols
14 (2019) 832–863.
date_created: 2019-02-24T22:59:20Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2023-08-24T14:48:33Z
day: '01'
ddc:
- '570'
department:
- _id: JoDa
- _id: Bio
doi: 10.1038/s41596-018-0117-3
ec_funded: 1
external_id:
isi:
- '000459890700008'
pmid:
- '30778205'
file:
- access_level: open_access
checksum: 7efb9951e7ddf3e3dcc2fb92b859c623
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: kschuh
date_created: 2021-06-29T14:41:46Z
date_updated: 2021-06-29T14:41:46Z
file_id: '9619'
file_name: 181031_Truckenbrodt_ExM_NatProtoc.docx
file_size: 84478958
relation: main_file
success: 1
file_date_updated: 2021-06-29T14:41:46Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 832–863
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
publication: Nature Protocols
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: A practical guide to optimization in X10 expansion microscopy
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2019'
...
---
_id: '6025'
abstract:
- lang: eng
text: Non-canonical Wnt signaling plays a central role for coordinated cell polarization
and directed migration in metazoan development. While spatiotemporally restricted
activation of non-canonical Wnt-signaling drives cell polarization in epithelial
tissues, it remains unclear whether such instructive activity is also critical
for directed mesenchymal cell migration. Here, we developed a light-activated
version of the non-canonical Wnt receptor Frizzled 7 (Fz7) to analyze how restricted
activation of non-canonical Wnt signaling affects directed anterior axial mesendoderm
(prechordal plate, ppl) cell migration within the zebrafish gastrula. We found
that Fz7 signaling is required for ppl cell protrusion formation and migration
and that spatiotemporally restricted ectopic activation is capable of redirecting
their migration. Finally, we show that uniform activation of Fz7 signaling in
ppl cells fully rescues defective directed cell migration in fz7 mutant embryos.
Together, our findings reveal that in contrast to the situation in epithelial
cells, non-canonical Wnt signaling functions permissively rather than instructively
in directed mesenchymal cell migration during gastrulation.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
article_number: e42093
article_processing_charge: No
author:
- first_name: Daniel
full_name: Capek, Daniel
id: 31C42484-F248-11E8-B48F-1D18A9856A87
last_name: Capek
orcid: 0000-0001-5199-9940
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Alexandra Madelaine
full_name: Tichy, Alexandra Madelaine
last_name: Tichy
- first_name: Maurizio
full_name: Morri, Maurizio
id: 4863116E-F248-11E8-B48F-1D18A9856A87
last_name: Morri
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. Light-activated
Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm
cell migration. eLife. 2019;8. doi:10.7554/eLife.42093
apa: Capek, D., Smutny, M., Tichy, A. M., Morri, M., Janovjak, H. L., & Heisenberg,
C.-P. J. (2019). Light-activated Frizzled7 reveals a permissive role of non-canonical
wnt signaling in mesendoderm cell migration. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.42093
chicago: Capek, Daniel, Michael Smutny, Alexandra Madelaine Tichy, Maurizio Morri,
Harald L Janovjak, and Carl-Philipp J Heisenberg. “Light-Activated Frizzled7 Reveals
a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.”
ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42093.
ieee: D. Capek, M. Smutny, A. M. Tichy, M. Morri, H. L. Janovjak, and C.-P. J. Heisenberg,
“Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling
in mesendoderm cell migration,” eLife, vol. 8. eLife Sciences Publications,
2019.
ista: Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. 2019.
Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling
in mesendoderm cell migration. eLife. 8, e42093.
mla: Capek, Daniel, et al. “Light-Activated Frizzled7 Reveals a Permissive Role
of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” ELife, vol.
8, e42093, eLife Sciences Publications, 2019, doi:10.7554/eLife.42093.
short: D. Capek, M. Smutny, A.M. Tichy, M. Morri, H.L. Janovjak, C.-P.J. Heisenberg,
ELife 8 (2019).
date_created: 2019-02-17T22:59:22Z
date_published: 2019-02-06T00:00:00Z
date_updated: 2023-08-24T14:46:01Z
day: '06'
ddc:
- '570'
department:
- _id: CaHe
- _id: HaJa
doi: 10.7554/eLife.42093
ec_funded: 1
external_id:
isi:
- '000458025300001'
file:
- access_level: open_access
checksum: 6cb4ca6d4aa96f6f187a5983aa3e660a
content_type: application/pdf
creator: dernst
date_created: 2019-02-18T15:17:21Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6041'
file_name: 2019_elife_Capek.pdf
file_size: 5500707
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling
in mesendoderm cell migration
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: 8
year: '2019'
...
---
_id: '6022'
abstract:
- lang: eng
text: The evolution of new species is made easier when traits under divergent ecological
selection are also mating cues. Such ecological mating cues are now considered
more common than previously thought, but we still know little about the genetic
changes underlying their evolution or more generally about the genetic basis for
assortative mating behaviors. Both tight physical linkage and the existence of
large-effect preference loci will strengthen genetic associations between behavioral
and ecological barriers, promoting the evolution of assortative mating. The warning
patterns of Heliconius melpomene and H. cydno are under disruptive selection due
to increased predation of nonmimetic hybrids and are used during mate recognition.
We carried out a genome-wide quantitative trait locus (QTL) analysis of preference
behaviors between these species and showed that divergent male preference has
a simple genetic basis. We identify three QTLs that together explain a large proportion
(approximately 60%) of the difference in preference behavior observed between
the parental species. One of these QTLs is just 1.2 (0-4.8) centiMorgans (cM)
from the major color pattern gene optix, and, individually, all three have a large
effect on the preference phenotype. Genomic divergence between H. cydno and H.
melpomene is high but broadly heterogenous, and admixture is reduced at the preference-optix
color pattern locus but not the other preference QTLs. The simple genetic architecture
we reveal will facilitate the evolution and maintenance of new species despite
ongoing gene flow by coupling behavioral and ecological aspects of reproductive
isolation.
article_number: e2005902
article_processing_charge: No
author:
- first_name: Richard M.
full_name: Merrill, Richard M.
last_name: Merrill
- first_name: Pasi
full_name: Rastas, Pasi
last_name: Rastas
- first_name: Simon H.
full_name: Martin, Simon H.
last_name: Martin
- first_name: Maria C
full_name: Melo Hurtado, Maria C
id: 386D7308-F248-11E8-B48F-1D18A9856A87
last_name: Melo Hurtado
- first_name: Sarah
full_name: Barker, Sarah
last_name: Barker
- first_name: John
full_name: Davey, John
last_name: Davey
- first_name: W. Owen
full_name: Mcmillan, W. Owen
last_name: Mcmillan
- first_name: Chris D.
full_name: Jiggins, Chris D.
last_name: Jiggins
citation:
ama: Merrill RM, Rastas P, Martin SH, et al. Genetic dissection of assortative mating
behavior. PLoS Biology. 2019;17(2). doi:10.1371/journal.pbio.2005902
apa: Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S.,
Davey, J., … Jiggins, C. D. (2019). Genetic dissection of assortative mating behavior.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005902
chicago: Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado,
Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Genetic Dissection
of Assortative Mating Behavior.” PLoS Biology. Public Library of Science,
2019. https://doi.org/10.1371/journal.pbio.2005902.
ieee: R. M. Merrill et al., “Genetic dissection of assortative mating behavior,”
PLoS Biology, vol. 17, no. 2. Public Library of Science, 2019.
ista: Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan
WO, Jiggins CD. 2019. Genetic dissection of assortative mating behavior. PLoS
Biology. 17(2), e2005902.
mla: Merrill, Richard M., et al. “Genetic Dissection of Assortative Mating Behavior.”
PLoS Biology, vol. 17, no. 2, e2005902, Public Library of Science, 2019,
doi:10.1371/journal.pbio.2005902.
short: R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey,
W.O. Mcmillan, C.D. Jiggins, PLoS Biology 17 (2019).
date_created: 2019-02-17T22:59:21Z
date_published: 2019-02-07T00:00:00Z
date_updated: 2023-08-24T14:46:23Z
day: '07'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2005902
external_id:
isi:
- '000460317100001'
file:
- access_level: open_access
checksum: 5f34001617ee729314ca520c049b1112
content_type: application/pdf
creator: dernst
date_created: 2019-02-18T14:57:24Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6036'
file_name: 2019_PLOS_Merrill.pdf
file_size: 2005949
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '02'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '9801'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Genetic dissection of assortative mating behavior
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2019'
...
---
_id: '6023'
abstract:
- lang: eng
text: Multicellular development requires coordinated cell polarization relative
to body axes, and translation to oriented cell division 1–3 . In plants, it is
unknown how cell polarities are connected to organismal axes and translated to
division. Here, we identify Arabidopsis SOSEKI proteins that integrate apical–basal
and radial organismal axes to localize to polar cell edges. Localization does
not depend on tissue context, requires cell wall integrity and is defined by a
transferrable, protein-specific motif. A Domain of Unknown Function in SOSEKI
proteins resembles the DIX oligomerization domain in the animal Dishevelled polarity
regulator. The DIX-like domain self-interacts and is required for edge localization
and for influencing division orientation, together with a second domain that defines
the polar membrane domain. Our work shows that SOSEKI proteins locally interpret
global polarity cues and can influence cell division orientation. Furthermore,
this work reveals that, despite fundamental differences, cell polarity mechanisms
in plants and animals converge on a similar protein domain.
article_processing_charge: No
author:
- first_name: Saiko
full_name: Yoshida, Saiko
id: 2E46069C-F248-11E8-B48F-1D18A9856A87
last_name: Yoshida
- first_name: Alja
full_name: Van Der Schuren, Alja
last_name: Van Der Schuren
- first_name: Maritza
full_name: Van Dop, Maritza
last_name: Van Dop
- first_name: Luc
full_name: Van Galen, Luc
last_name: Van Galen
- first_name: Shunsuke
full_name: Saiga, Shunsuke
last_name: Saiga
- first_name: Milad
full_name: Adibi, Milad
last_name: Adibi
- first_name: Barbara
full_name: Möller, Barbara
last_name: Möller
- first_name: Colette A.
full_name: Ten Hove, Colette A.
last_name: Ten Hove
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Richard
full_name: Smith, Richard
last_name: Smith
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
citation:
ama: Yoshida S, Van Der Schuren A, Van Dop M, et al. A SOSEKI-based coordinate system
interprets global polarity cues in arabidopsis. Nature Plants. 2019;5(2):160-166.
doi:10.1038/s41477-019-0363-6
apa: Yoshida, S., Van Der Schuren, A., Van Dop, M., Van Galen, L., Saiga, S., Adibi,
M., … Weijers, D. (2019). A SOSEKI-based coordinate system interprets global polarity
cues in arabidopsis. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0363-6
chicago: Yoshida, Saiko, Alja Van Der Schuren, Maritza Van Dop, Luc Van Galen, Shunsuke
Saiga, Milad Adibi, Barbara Möller, et al. “A SOSEKI-Based Coordinate System Interprets
Global Polarity Cues in Arabidopsis.” Nature Plants. Springer Nature, 2019.
https://doi.org/10.1038/s41477-019-0363-6.
ieee: S. Yoshida et al., “A SOSEKI-based coordinate system interprets global
polarity cues in arabidopsis,” Nature Plants, vol. 5, no. 2. Springer Nature,
pp. 160–166, 2019.
ista: Yoshida S, Van Der Schuren A, Van Dop M, Van Galen L, Saiga S, Adibi M, Möller
B, Ten Hove CA, Marhavý P, Smith R, Friml J, Weijers D. 2019. A SOSEKI-based coordinate
system interprets global polarity cues in arabidopsis. Nature Plants. 5(2), 160–166.
mla: Yoshida, Saiko, et al. “A SOSEKI-Based Coordinate System Interprets Global
Polarity Cues in Arabidopsis.” Nature Plants, vol. 5, no. 2, Springer Nature,
2019, pp. 160–66, doi:10.1038/s41477-019-0363-6.
short: S. Yoshida, A. Van Der Schuren, M. Van Dop, L. Van Galen, S. Saiga, M. Adibi,
B. Möller, C.A. Ten Hove, P. Marhavý, R. Smith, J. Friml, D. Weijers, Nature Plants
5 (2019) 160–166.
date_created: 2019-02-17T22:59:21Z
date_published: 2019-02-08T00:00:00Z
date_updated: 2023-08-24T14:46:47Z
day: '08'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1038/s41477-019-0363-6
ec_funded: 1
external_id:
isi:
- '000460479600014'
intvolume: ' 5'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/479113v1.abstract
month: '02'
oa: 1
oa_version: Submitted Version
page: 160-166
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature Plants
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2019'
...
---
_id: '6053'
abstract:
- lang: eng
text: Recent technical developments in the fields of quantum electromechanics and
optomechanics have spawned nanoscale mechanical transducers with the sensitivity
to measure mechanical displacements at the femtometre scale and the ability to
convert electromagnetic signals at the single photon level. A key challenge in
this field is obtaining strong coupling between motion and electromagnetic fields
without adding additional decoherence. Here we present an electromechanical transducer
that integrates a high-frequency (0.42 GHz) hypersonic phononic crystal with a
superconducting microwave circuit. The use of a phononic bandgap crystal enables
quantum-level transduction of hypersonic mechanical motion and concurrently eliminates
decoherence caused by acoustic radiation. Devices with hypersonic mechanical frequencies
provide a natural pathway for integration with Josephson junction quantum circuits,
a leading quantum computing technology, and nanophotonic systems capable of optical
networking and distributing quantum information.
article_processing_charge: No
article_type: original
author:
- first_name: Mahmoud
full_name: Kalaee, Mahmoud
last_name: Kalaee
- first_name: Mohammad
full_name: Mirhosseini, Mohammad
last_name: Mirhosseini
- first_name: Paul B.
full_name: Dieterle, Paul B.
last_name: Dieterle
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Oskar
full_name: Painter, Oskar
last_name: Painter
citation:
ama: Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. Quantum
electromechanics of a hypersonic crystal. Nature Nanotechnology. 2019;14(4):334–339.
doi:10.1038/s41565-019-0377-2
apa: Kalaee, M., Mirhosseini, M., Dieterle, P. B., Peruzzo, M., Fink, J. M., &
Painter, O. (2019). Quantum electromechanics of a hypersonic crystal. Nature
Nanotechnology. Springer Nature. https://doi.org/10.1038/s41565-019-0377-2
chicago: Kalaee, Mahmoud, Mohammad Mirhosseini, Paul B. Dieterle, Matilda Peruzzo,
Johannes M Fink, and Oskar Painter. “Quantum Electromechanics of a Hypersonic
Crystal.” Nature Nanotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41565-019-0377-2.
ieee: M. Kalaee, M. Mirhosseini, P. B. Dieterle, M. Peruzzo, J. M. Fink, and O.
Painter, “Quantum electromechanics of a hypersonic crystal,” Nature Nanotechnology,
vol. 14, no. 4. Springer Nature, pp. 334–339, 2019.
ista: Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. 2019.
Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. 14(4),
334–339.
mla: Kalaee, Mahmoud, et al. “Quantum Electromechanics of a Hypersonic Crystal.”
Nature Nanotechnology, vol. 14, no. 4, Springer Nature, 2019, pp. 334–339,
doi:10.1038/s41565-019-0377-2.
short: M. Kalaee, M. Mirhosseini, P.B. Dieterle, M. Peruzzo, J.M. Fink, O. Painter,
Nature Nanotechnology 14 (2019) 334–339.
date_created: 2019-02-24T22:59:21Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-08-24T14:48:08Z
day: '01'
department:
- _id: JoFi
doi: 10.1038/s41565-019-0377-2
external_id:
isi:
- '000463195700014'
intvolume: ' 14'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://authors.library.caltech.edu/92123/
month: '04'
oa: 1
oa_version: Submitted Version
page: 334–339
publication: Nature Nanotechnology
publication_identifier:
eissn:
- 1748-3395
issn:
- 1748-3387
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum electromechanics of a hypersonic crystal
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2019'
...
---
_id: '6050'
abstract:
- lang: eng
text: 'We answer a question of David Hilbert: given two circles it is not possible
in general to construct their centers using only a straightedge. On the other
hand, we give infinitely many families of pairs of circles for which such construction
is possible. '
article_processing_charge: No
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Roman
full_name: Fedorov, Roman
last_name: Fedorov
citation:
ama: Akopyan A, Fedorov R. Two circles and only a straightedge. Proceedings of
the American Mathematical Society. 2019;147:91-102. doi:10.1090/proc/14240
apa: Akopyan, A., & Fedorov, R. (2019). Two circles and only a straightedge.
Proceedings of the American Mathematical Society. AMS. https://doi.org/10.1090/proc/14240
chicago: Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.”
Proceedings of the American Mathematical Society. AMS, 2019. https://doi.org/10.1090/proc/14240.
ieee: A. Akopyan and R. Fedorov, “Two circles and only a straightedge,” Proceedings
of the American Mathematical Society, vol. 147. AMS, pp. 91–102, 2019.
ista: Akopyan A, Fedorov R. 2019. Two circles and only a straightedge. Proceedings
of the American Mathematical Society. 147, 91–102.
mla: Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.”
Proceedings of the American Mathematical Society, vol. 147, AMS, 2019,
pp. 91–102, doi:10.1090/proc/14240.
short: A. Akopyan, R. Fedorov, Proceedings of the American Mathematical Society
147 (2019) 91–102.
date_created: 2019-02-24T22:59:19Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2023-08-24T14:48:59Z
day: '01'
department:
- _id: HeEd
doi: 10.1090/proc/14240
external_id:
arxiv:
- '1709.02562'
isi:
- '000450363900008'
intvolume: ' 147'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1709.02562
month: '01'
oa: 1
oa_version: Preprint
page: 91-102
publication: Proceedings of the American Mathematical Society
publication_status: published
publisher: AMS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Two circles and only a straightedge
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 147
year: '2019'
...
---
_id: '9801'
article_processing_charge: No
author:
- first_name: Richard M.
full_name: Merrill, Richard M.
last_name: Merrill
- first_name: Pasi
full_name: Rastas, Pasi
last_name: Rastas
- first_name: Simon H.
full_name: Martin, Simon H.
last_name: Martin
- first_name: Maria C
full_name: Melo Hurtado, Maria C
id: 386D7308-F248-11E8-B48F-1D18A9856A87
last_name: Melo Hurtado
- first_name: Sarah
full_name: Barker, Sarah
last_name: Barker
- first_name: John
full_name: Davey, John
last_name: Davey
- first_name: W. Owen
full_name: Mcmillan, W. Owen
last_name: Mcmillan
- first_name: Chris D.
full_name: Jiggins, Chris D.
last_name: Jiggins
citation:
ama: Merrill RM, Rastas P, Martin SH, et al. Raw behavioral data. 2019. doi:10.1371/journal.pbio.2005902.s006
apa: Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S.,
Davey, J., … Jiggins, C. D. (2019). Raw behavioral data. Public Library of Science.
https://doi.org/10.1371/journal.pbio.2005902.s006
chicago: Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado,
Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Raw Behavioral
Data.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pbio.2005902.s006.
ieee: R. M. Merrill et al., “Raw behavioral data.” Public Library of Science,
2019.
ista: Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan
WO, Jiggins CD. 2019. Raw behavioral data, Public Library of Science, 10.1371/journal.pbio.2005902.s006.
mla: Merrill, Richard M., et al. Raw Behavioral Data. Public Library of Science,
2019, doi:10.1371/journal.pbio.2005902.s006.
short: R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey,
W.O. Mcmillan, C.D. Jiggins, (2019).
date_created: 2021-08-06T11:34:56Z
date_published: 2019-02-07T00:00:00Z
date_updated: 2023-08-24T14:46:23Z
day: '07'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2005902.s006
month: '02'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '6022'
relation: used_in_publication
status: public
status: public
title: Raw behavioral data
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '6095'
abstract:
- lang: eng
text: Both classical and recent studies suggest that chromosomal inversion polymorphisms
are important in adaptation and speciation. However, biases in discovery and reporting
of inversions make it difficult to assess their prevalence and biological importance.
Here, we use an approach based on linkage disequilibrium among markers genotyped
for samples collected across a transect between contrasting habitats to detect
chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in
a single locality for the coastal marine snail, Littorina saxatilis. Patterns
of diversity in the field and of recombination in controlled crosses provide strong
evidence that at least the majority of these rearrangements are inversions. Most
show clinal changes in frequency between habitats, suggestive of divergent selection,
but only one appears to be fixed for different arrangements in the two habitats.
Consistent with widespread evidence for balancing selection on inversion polymorphisms,
we argue that a combination of heterosis and divergent selection can explain the
observed patterns and should be considered in other systems spanning environmental
gradients.
article_processing_charge: No
author:
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Pragya
full_name: Chaube, Pragya
last_name: Chaube
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Tomas
full_name: Larsson, Tomas
last_name: Larsson
- first_name: Alan R.
full_name: Lemmon, Alan R.
last_name: Lemmon
- first_name: Emily M.
full_name: Lemmon, Emily M.
last_name: Lemmon
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Marina
full_name: Panova, Marina
last_name: Panova
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: Faria R, Chaube P, Morales HE, et al. Multiple chromosomal rearrangements in
a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology.
2019;28(6):1375-1393. doi:10.1111/mec.14972
apa: Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon,
E. M., … Butlin, R. K. (2019). Multiple chromosomal rearrangements in a hybrid
zone between Littorina saxatilis ecotypes. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14972
chicago: Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon,
Emily M. Lemmon, Marina Rafajlović, et al. “Multiple Chromosomal Rearrangements
in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology.
Wiley, 2019. https://doi.org/10.1111/mec.14972.
ieee: R. Faria et al., “Multiple chromosomal rearrangements in a hybrid zone
between Littorina saxatilis ecotypes,” Molecular Ecology, vol. 28, no.
6. Wiley, pp. 1375–1393, 2019.
ista: Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović
M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2019. Multiple chromosomal
rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular
Ecology. 28(6), 1375–1393.
mla: Faria, Rui, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between
Littorina Saxatilis Ecotypes.” Molecular Ecology, vol. 28, no. 6, Wiley,
2019, pp. 1375–93, doi:10.1111/mec.14972.
short: R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon,
M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin,
Molecular Ecology 28 (2019) 1375–1393.
date_created: 2019-03-10T22:59:21Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2023-08-24T14:50:27Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.14972
external_id:
isi:
- '000465219200013'
file:
- access_level: open_access
checksum: f915885756057ec0ca5912a41f46a887
content_type: application/pdf
creator: dernst
date_created: 2019-03-11T16:12:54Z
date_updated: 2020-07-14T12:47:19Z
file_id: '6097'
file_name: 2019_MolecularEcology_Faria.pdf
file_size: 1510715
relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
has_accepted_license: '1'
intvolume: ' 28'
isi: 1
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1375-1393
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '9837'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis
ecotypes
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: 28
year: '2019'
...
---
_id: '6049'
abstract:
- lang: eng
text: 'In this article it is shown that large systems with many interacting units
endowing multiple phases display self-oscillations in the presence of linear feedback
between the control and order parameters, where an Andronov–Hopf bifurcation takes
over the phase transition. This is simply illustrated through the mean field Landau
theory whose feedback dynamics turn out to be described by the Van der Pol equation
and it is then validated for the fully connected Ising model following heat bath
dynamics. Despite its simplicity, this theory accounts potentially for a rich
range of phenomena: here it is applied to describe in a stylized way (i) excess
demand-price cycles due to strong herding in a simple agent-based market model;
(ii) congestion waves in queuing networks triggered by user feedback to delays
in overloaded conditions; and (iii) metabolic network oscillations resulting from
cell growth control in a bistable phenotypic landscape.'
article_number: '045002'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: 'De Martino D. Feedback-induced self-oscillations in large interacting systems
subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical.
2019;52(4). doi:10.1088/1751-8121/aaf2dd'
apa: 'De Martino, D. (2019). Feedback-induced self-oscillations in large interacting
systems subjected to phase transitions. Journal of Physics A: Mathematical
and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/aaf2dd'
chicago: 'De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting
Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical
and Theoretical. IOP Publishing, 2019. https://doi.org/10.1088/1751-8121/aaf2dd.'
ieee: 'D. De Martino, “Feedback-induced self-oscillations in large interacting systems
subjected to phase transitions,” Journal of Physics A: Mathematical and Theoretical,
vol. 52, no. 4. IOP Publishing, 2019.'
ista: 'De Martino D. 2019. Feedback-induced self-oscillations in large interacting
systems subjected to phase transitions. Journal of Physics A: Mathematical and
Theoretical. 52(4), 045002.'
mla: 'De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting
Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical
and Theoretical, vol. 52, no. 4, 045002, IOP Publishing, 2019, doi:10.1088/1751-8121/aaf2dd.'
short: 'D. De Martino, Journal of Physics A: Mathematical and Theoretical 52 (2019).'
date_created: 2019-02-24T22:59:19Z
date_published: 2019-01-07T00:00:00Z
date_updated: 2023-08-24T14:49:23Z
day: '07'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1088/1751-8121/aaf2dd
ec_funded: 1
external_id:
isi:
- '000455379500001'
file:
- access_level: open_access
checksum: 1112304ad363a6d8afaeccece36473cf
content_type: application/pdf
creator: kschuh
date_created: 2019-04-19T12:18:57Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6344'
file_name: 2019_IOP_DeMartino.pdf
file_size: 1804557
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 52'
isi: 1
issue: '4'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: 'Journal of Physics A: Mathematical and Theoretical'
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Feedback-induced self-oscillations in large interacting systems subjected to
phase transitions
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: 52
year: '2019'
...
---
_id: '6091'
abstract:
- lang: eng
text: Cortical networks are characterized by sparse connectivity, with synapses
found at only a subset of axo-dendritic contacts. Yet within these networks, neurons
can exhibit high connection probabilities, suggesting that cell-intrinsic factors,
not proximity, determine connectivity. Here, we identify ephrin-B3 (eB3) as a
factor that determines synapse density by mediating a cell-cell competition that
requires ephrin-B-EphB signaling. In a microisland culture system designed to
isolate cell-cell competition, we find that eB3 determines winning and losing
neurons in a contest for synapses. In a Mosaic Analysis with Double Markers (MADM)
genetic mouse model system in vivo the relative levels of eB3 control spine density
in layer 5 and 6 neurons. MADM cortical neurons in vitro reveal that eB3 controls
synapse density independently of action potential-driven activity. Our findings
illustrate a new class of competitive mechanism mediated by trans-synaptic organizing
proteins which control the number of synapses neurons receive relative to neighboring
neurons.
article_number: e41563
article_processing_charge: No
author:
- first_name: Nathan T.
full_name: Henderson, Nathan T.
last_name: Henderson
- first_name: Sylvain J.
full_name: Le Marchand, Sylvain J.
last_name: Le Marchand
- first_name: Martin
full_name: Hruska, Martin
last_name: Hruska
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
- first_name: Matthew B.
full_name: Dalva, Matthew B.
last_name: Dalva
citation:
ama: Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. Ephrin-B3
controls excitatory synapse density through cell-cell competition for EphBs. eLife.
2019;8. doi:10.7554/eLife.41563
apa: Henderson, N. T., Le Marchand, S. J., Hruska, M., Hippenmeyer, S., Luo, L.,
& Dalva, M. B. (2019). Ephrin-B3 controls excitatory synapse density through
cell-cell competition for EphBs. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.41563
chicago: Henderson, Nathan T., Sylvain J. Le Marchand, Martin Hruska, Simon Hippenmeyer,
Liqun Luo, and Matthew B. Dalva. “Ephrin-B3 Controls Excitatory Synapse Density
through Cell-Cell Competition for EphBs.” ELife. eLife Sciences Publications,
2019. https://doi.org/10.7554/eLife.41563.
ieee: N. T. Henderson, S. J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, and
M. B. Dalva, “Ephrin-B3 controls excitatory synapse density through cell-cell
competition for EphBs,” eLife, vol. 8. eLife Sciences Publications, 2019.
ista: Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. 2019.
Ephrin-B3 controls excitatory synapse density through cell-cell competition for
EphBs. eLife. 8, e41563.
mla: Henderson, Nathan T., et al. “Ephrin-B3 Controls Excitatory Synapse Density
through Cell-Cell Competition for EphBs.” ELife, vol. 8, e41563, eLife
Sciences Publications, 2019, doi:10.7554/eLife.41563.
short: N.T. Henderson, S.J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, M.B.
Dalva, ELife 8 (2019).
date_created: 2019-03-10T22:59:20Z
date_published: 2019-02-21T00:00:00Z
date_updated: 2023-08-24T14:50:50Z
day: '21'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.7554/eLife.41563
external_id:
isi:
- '000459380600001'
pmid:
- '30789343'
file:
- access_level: open_access
checksum: 7b0800d003f14cd06b1802dea0c52941
content_type: application/pdf
creator: dernst
date_created: 2019-03-11T16:15:37Z
date_updated: 2020-07-14T12:47:19Z
file_id: '6098'
file_name: 2019_eLife_Henderson.pdf
file_size: 7260753
relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ephrin-B3 controls excitatory synapse density through cell-cell competition
for EphBs
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: 8
year: '2019'
...
---
_id: '6046'
abstract:
- lang: eng
text: Sudden stress often triggers diverse, temporally structured gene expression
responses in microbes, but it is largely unknown how variable in time such responses
are and if genes respond in the same temporal order in every single cell. Here,
we quantified timing variability of individual promoters responding to sublethal
antibiotic stress using fluorescent reporters, microfluidics, and time‐lapse microscopy.
We identified lower and upper bounds that put definite constraints on timing variability,
which varies strongly among promoters and conditions. Timing variability can be
interpreted using results from statistical kinetics, which enable us to estimate
the number of rate‐limiting molecular steps underlying different responses. We
found that just a few critical steps control some responses while others rely
on dozens of steps. To probe connections between different stress responses, we
then tracked the temporal order and response time correlations of promoter pairs
in individual cells. Our results support that, when bacteria are exposed to the
antibiotic nitrofurantoin, the ensuing oxidative stress and SOS responses are
part of the same causal chain of molecular events. In contrast, under trimethoprim,
the acid stress response and the SOS response are part of different chains of
events running in parallel. Our approach reveals fundamental constraints on gene
expression timing and provides new insights into the molecular events that underlie
the timing of stress responses.
acknowledged_ssus:
- _id: Bio
article_number: e8470
article_processing_charge: No
author:
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
- first_name: Georg
full_name: Rieckh, Georg
id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87
last_name: Rieckh
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Mitosch K, Rieckh G, Bollenbach MT. Temporal order and precision of complex
stress responses in individual bacteria. Molecular systems biology. 2019;15(2).
doi:10.15252/msb.20188470
apa: Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2019). Temporal order and
precision of complex stress responses in individual bacteria. Molecular Systems
Biology. Embo Press. https://doi.org/10.15252/msb.20188470
chicago: Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Temporal Order
and Precision of Complex Stress Responses in Individual Bacteria.” Molecular
Systems Biology. Embo Press, 2019. https://doi.org/10.15252/msb.20188470.
ieee: K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Temporal order and precision
of complex stress responses in individual bacteria,” Molecular systems biology,
vol. 15, no. 2. Embo Press, 2019.
ista: Mitosch K, Rieckh G, Bollenbach MT. 2019. Temporal order and precision of
complex stress responses in individual bacteria. Molecular systems biology. 15(2),
e8470.
mla: Mitosch, Karin, et al. “Temporal Order and Precision of Complex Stress Responses
in Individual Bacteria.” Molecular Systems Biology, vol. 15, no. 2, e8470,
Embo Press, 2019, doi:10.15252/msb.20188470.
short: K. Mitosch, G. Rieckh, M.T. Bollenbach, Molecular Systems Biology 15 (2019).
date_created: 2019-02-24T22:59:18Z
date_published: 2019-02-14T00:00:00Z
date_updated: 2023-08-24T14:49:53Z
day: '14'
department:
- _id: GaTk
doi: 10.15252/msb.20188470
external_id:
isi:
- '000459628300003'
pmid:
- '30765425'
intvolume: ' 15'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30765425
month: '02'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
publication: Molecular systems biology
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Temporal order and precision of complex stress responses in individual bacteria
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2019'
...
---
_id: '6105'
abstract:
- lang: eng
text: " Hosts can alter their strategy towards pathogens during their lifetime;
that is, they can show phenotypic plasticity in immunity or life history. Immune
priming is one such example, where a previous encounter with a pathogen confers
enhanced protection upon secondary challenge, resulting in reduced pathogen load
(i.e., resistance) and improved host survival. However, an initial encounter might
also enhance tolerance, particularly to less virulent opportunistic pathogens
that establish persistent infections. In this scenario, individuals are better
able to reduce the negative fecundity consequences that result from a high pathogen
burden. Finally, previous exposure may also lead to life‐history adjustments,
such as terminal investment into reproduction.\r\n Using different Drosophila
melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and
Pseudomonas entomophila, we tested whether previous exposure results in resistance
or tolerance and whether it modifies immune gene expression during an acute‐phase
infection (one day post‐challenge). We then asked whether previous pathogen exposure
affects chronic‐phase pathogen persistence and longer‐term survival (28 days post‐challenge).\r\n
\ We predicted that previous exposure would increase host resistance to an early
stage bacterial infection while it might come at a cost to host fecundity tolerance.
We reasoned that resistance would be due in part to stronger immune gene expression
after challenge. We expected that previous exposure would improve long‐term survival,
that it would reduce infection persistence, and we expected to find genetic variation
in these responses.\r\n We found that previous exposure to P. entomophila weakened
host resistance to a second infection independent of genotype and had no effect
on immune gene expression. Fecundity tolerance showed genotypic variation but
was not influenced by previous exposure. However, L. lactis persisted as a chronic
infection, whereas survivors cleared the more pathogenic P. entomophila infection.\r\n
\ To our knowledge, this is the first study that addresses host tolerance to
bacteria in relation to previous exposure, taking a multi‐faceted approach to
address the topic. Our results suggest that previous exposure comes with transient
costs to resistance during the early stage of infection in this host–pathogen
system and that infection persistence may be bacterium‐specific.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Megan
full_name: Kutzer, Megan
id: 29D0B332-F248-11E8-B48F-1D18A9856A87
last_name: Kutzer
orcid: 0000-0002-8696-6978
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
- first_name: Sophie A.O.
full_name: Armitage, Sophie A.O.
last_name: Armitage
citation:
ama: Kutzer M, Kurtz J, Armitage SAO. A multi-faceted approach testing the effects
of previous bacterial exposure on resistance and tolerance. Journal of Animal
Ecology. 2019;88(4):566-578. doi:10.1111/1365-2656.12953
apa: Kutzer, M., Kurtz, J., & Armitage, S. A. O. (2019). A multi-faceted approach
testing the effects of previous bacterial exposure on resistance and tolerance.
Journal of Animal Ecology. Wiley. https://doi.org/10.1111/1365-2656.12953
chicago: Kutzer, Megan, Joachim Kurtz, and Sophie A.O. Armitage. “A Multi-Faceted
Approach Testing the Effects of Previous Bacterial Exposure on Resistance and
Tolerance.” Journal of Animal Ecology. Wiley, 2019. https://doi.org/10.1111/1365-2656.12953.
ieee: M. Kutzer, J. Kurtz, and S. A. O. Armitage, “A multi-faceted approach testing
the effects of previous bacterial exposure on resistance and tolerance,” Journal
of Animal Ecology, vol. 88, no. 4. Wiley, pp. 566–578, 2019.
ista: Kutzer M, Kurtz J, Armitage SAO. 2019. A multi-faceted approach testing the
effects of previous bacterial exposure on resistance and tolerance. Journal of
Animal Ecology. 88(4), 566–578.
mla: Kutzer, Megan, et al. “A Multi-Faceted Approach Testing the Effects of Previous
Bacterial Exposure on Resistance and Tolerance.” Journal of Animal Ecology,
vol. 88, no. 4, Wiley, 2019, pp. 566–78, doi:10.1111/1365-2656.12953.
short: M. Kutzer, J. Kurtz, S.A.O. Armitage, Journal of Animal Ecology 88 (2019)
566–578.
date_created: 2019-03-17T22:59:15Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-08-25T08:04:53Z
day: '01'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1111/1365-2656.12953
ec_funded: 1
external_id:
isi:
- '000467994800007'
file:
- access_level: open_access
checksum: 405cde15120de26018b3bd0dfa29986c
content_type: application/pdf
creator: dernst
date_created: 2019-03-18T07:43:06Z
date_updated: 2020-07-14T12:47:19Z
file_id: '6107'
file_name: 2019_JournalAnimalEcology_Kutzer.pdf
file_size: 1460662
relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
has_accepted_license: '1'
intvolume: ' 88'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 566-578
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal of Animal Ecology
publication_identifier:
eissn:
- '13652656'
issn:
- '00218790'
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '9806'
relation: research_data
status: public
scopus_import: '1'
status: public
title: A multi-faceted approach testing the effects of previous bacterial exposure
on resistance and tolerance
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: 88
year: '2019'
...
---
_id: '6088'
abstract:
- lang: eng
text: P-Glycoprotein (ABCB1) and breast cancer resistance protein (ABCG2) are two
efflux transporters at the blood–brain barrier (BBB), which effectively restrict
brain distribution of diverse drugs, such as tyrosine kinase inhibitors. There
is a crucial need for pharmacological ABCB1 and ABCG2 inhibition protocols for
a more effective treatment of brain diseases. In the present study, seven marketed
drugs (osimertinib, erlotinib, nilotinib, imatinib, lapatinib, pazopanib, and
cyclosporine A) and one nonmarketed drug (tariquidar), with known in vitro ABCB1/ABCG2
inhibitory properties, were screened for their inhibitory potency at the BBB in
vivo. Positron emission tomography (PET) using the model ABCB1/ABCG2 substrate
[11C]erlotinib was performed in mice. Tested inhibitors were administered as i.v.
bolus injections at 30 min before the start of the PET scan, followed by a continuous
i.v. infusion for the duration of the PET scan. Five of the tested drugs increased
total distribution volume of [11C]erlotinib in the brain (VT,brain) compared to
vehicle-treated animals (tariquidar, + 69%; erlotinib, + 19% and +23% for the
21.5 mg/kg and the 43 mg/kg dose, respectively; imatinib, + 22%; lapatinib, +
25%; and cyclosporine A, + 49%). For all drugs, increases in [11C]erlotinib brain
distribution were lower than in Abcb1a/b(−/−)Abcg2(−/−) mice (+149%), which suggested
that only partial ABCB1/ABCG2 inhibition was reached at the mouse BBB. The plasma
concentrations of the tested drugs at the time of the PET scan were higher than
clinically achievable plasma concentrations. Some of the tested drugs led to significant
increases in blood radioactivity concentrations measured at the end of the PET
scan (erlotinib, + 103% and +113% for the 21.5 mg/kg and the 43 mg/kg dose, respectively;
imatinib, + 125%; and cyclosporine A, + 101%), which was most likely caused by
decreased hepatobiliary excretion of radioactivity. Taken together, our data suggest
that some marketed tyrosine kinase inhibitors may be repurposed to inhibit ABCB1
and ABCG2 at the BBB. From a clinical perspective, moderate increases in brain
delivery despite the administration of high i.v. doses as well as peripheral drug–drug
interactions due to transporter inhibition in clearance organs question the translatability
of this concept.
article_processing_charge: No
author:
- first_name: Alexander
full_name: Traxl, Alexander
last_name: Traxl
- first_name: Severin
full_name: Mairinger, Severin
last_name: Mairinger
- first_name: Thomas
full_name: Filip, Thomas
last_name: Filip
- first_name: Michael
full_name: Sauberer, Michael
last_name: Sauberer
- first_name: Johann
full_name: Stanek, Johann
last_name: Stanek
- first_name: Stefan
full_name: Poschner, Stefan
last_name: Poschner
- first_name: Walter
full_name: Jäger, Walter
last_name: Jäger
- first_name: Viktoria
full_name: Zoufal, Viktoria
last_name: Zoufal
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Nicolas
full_name: Tournier, Nicolas
last_name: Tournier
- first_name: Martin
full_name: Bauer, Martin
last_name: Bauer
- first_name: Thomas
full_name: Wanek, Thomas
last_name: Wanek
- first_name: Oliver
full_name: Langer, Oliver
last_name: Langer
citation:
ama: Traxl A, Mairinger S, Filip T, et al. Inhibition of ABCB1 and ABCG2 at the
mouse blood-brain barrier with marketed drugs to improve brain delivery of the
model ABCB1/ABCG2 substrate [11C]erlotinib. Molecular Pharmaceutics. 2019;16(3):1282-1293.
doi:10.1021/acs.molpharmaceut.8b01217
apa: Traxl, A., Mairinger, S., Filip, T., Sauberer, M., Stanek, J., Poschner, S.,
… Langer, O. (2019). Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier
with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate
[11C]erlotinib. Molecular Pharmaceutics. American Chemical Society. https://doi.org/10.1021/acs.molpharmaceut.8b01217
chicago: Traxl, Alexander, Severin Mairinger, Thomas Filip, Michael Sauberer, Johann
Stanek, Stefan Poschner, Walter Jäger, et al. “Inhibition of ABCB1 and ABCG2 at
the Mouse Blood-Brain Barrier with Marketed Drugs to Improve Brain Delivery of
the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Molecular Pharmaceutics.
American Chemical Society, 2019. https://doi.org/10.1021/acs.molpharmaceut.8b01217.
ieee: A. Traxl et al., “Inhibition of ABCB1 and ABCG2 at the mouse blood-brain
barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2
substrate [11C]erlotinib,” Molecular Pharmaceutics, vol. 16, no. 3. American
Chemical Society, pp. 1282–1293, 2019.
ista: Traxl A, Mairinger S, Filip T, Sauberer M, Stanek J, Poschner S, Jäger W,
Zoufal V, Novarino G, Tournier N, Bauer M, Wanek T, Langer O. 2019. Inhibition
of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve
brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Molecular Pharmaceutics.
16(3), 1282–1293.
mla: Traxl, Alexander, et al. “Inhibition of ABCB1 and ABCG2 at the Mouse Blood-Brain
Barrier with Marketed Drugs to Improve Brain Delivery of the Model ABCB1/ABCG2
Substrate [11C]Erlotinib.” Molecular Pharmaceutics, vol. 16, no. 3, American
Chemical Society, 2019, pp. 1282–93, doi:10.1021/acs.molpharmaceut.8b01217.
short: A. Traxl, S. Mairinger, T. Filip, M. Sauberer, J. Stanek, S. Poschner, W.
Jäger, V. Zoufal, G. Novarino, N. Tournier, M. Bauer, T. Wanek, O. Langer, Molecular
Pharmaceutics 16 (2019) 1282–1293.
date_created: 2019-03-10T22:59:19Z
date_published: 2019-03-04T00:00:00Z
date_updated: 2023-08-25T08:02:51Z
day: '04'
department:
- _id: GaNo
doi: 10.1021/acs.molpharmaceut.8b01217
external_id:
isi:
- '000460600400031'
pmid:
- '30694684'
intvolume: ' 16'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 1282-1293
pmid: 1
publication: Molecular Pharmaceutics
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed
drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 16
year: '2019'
...