---
_id: '1256'
abstract:
- lang: eng
text: Simulink is widely used for model driven development (MDD) of industrial software
systems. Typically, the Simulink based development is initiated from Stateflow
modeling, followed by simulation, validation and code generation mapped to physical
execution platforms. However, recent industrial trends have raised the demands
of rigorous verification on safety-critical applications, which is unfortunately
challenging for Simulink. In this paper, we present an approach to bridge the
Stateflow based model driven development and a well- defined rigorous verification.
First, we develop a self- contained toolkit to translate Stateflow model into
timed automata, where major advanced modeling features in Stateflow are supported.
Taking advantage of the strong verification capability of Uppaal, we can not only
find bugs in Stateflow models which are missed by Simulink Design Verifier, but
also check more important temporal properties. Next, we customize a runtime verifier
for the generated nonintrusive VHDL and C code of Stateflow model for monitoring.
The major strength of the customization is the flexibility to collect and analyze
runtime properties with a pure software monitor, which opens more opportunities
for engineers to achieve high reliability of the target system compared with the
traditional act that only relies on Simulink Polyspace. We incorporate these two
parts into original Stateflow based MDD seamlessly. In this way, safety-critical
properties are both verified at the model level, and at the consistent system
implementation level with physical execution environment in consideration. We
apply our approach on a train controller design, and the verified implementation
is tested and deployed on a real hardware platform.
acknowledgement: This work is supported in part by NSF CNS 13-30077, NSF CNS 13-29886,
NSF CNS 15-45002, NSFC 61303014, NSFC 61202010, and NSFC 91218302.
article_number: '7461337'
author:
- first_name: Yu
full_name: Jiang, Yu
last_name: Jiang
- first_name: Yixiao
full_name: Yang, Yixiao
last_name: Yang
- first_name: Han
full_name: Liu, Han
last_name: Liu
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Ming
full_name: Gu, Ming
last_name: Gu
- first_name: Jiaguang
full_name: Sun, Jiaguang
last_name: Sun
- first_name: Lui
full_name: Sha, Lui
last_name: Sha
citation:
ama: 'Jiang Y, Yang Y, Liu H, et al. From stateflow simulation to verified implementation:
A verification approach and a real-time train controller design. In: IEEE; 2016.
doi:10.1109/RTAS.2016.7461337'
apa: 'Jiang, Y., Yang, Y., Liu, H., Kong, H., Gu, M., Sun, J., & Sha, L. (2016).
From stateflow simulation to verified implementation: A verification approach
and a real-time train controller design. Presented at the RTAS: Real-time and
Embedded Technology and Applications Symposium, Vienna, Austria: IEEE. https://doi.org/10.1109/RTAS.2016.7461337'
chicago: 'Jiang, Yu, Yixiao Yang, Han Liu, Hui Kong, Ming Gu, Jiaguang Sun, and
Lui Sha. “From Stateflow Simulation to Verified Implementation: A Verification
Approach and a Real-Time Train Controller Design.” IEEE, 2016. https://doi.org/10.1109/RTAS.2016.7461337.'
ieee: 'Y. Jiang et al., “From stateflow simulation to verified implementation:
A verification approach and a real-time train controller design,” presented at
the RTAS: Real-time and Embedded Technology and Applications Symposium, Vienna,
Austria, 2016.'
ista: 'Jiang Y, Yang Y, Liu H, Kong H, Gu M, Sun J, Sha L. 2016. From stateflow
simulation to verified implementation: A verification approach and a real-time
train controller design. RTAS: Real-time and Embedded Technology and Applications
Symposium, 7461337.'
mla: 'Jiang, Yu, et al. From Stateflow Simulation to Verified Implementation:
A Verification Approach and a Real-Time Train Controller Design. 7461337,
IEEE, 2016, doi:10.1109/RTAS.2016.7461337.'
short: Y. Jiang, Y. Yang, H. Liu, H. Kong, M. Gu, J. Sun, L. Sha, in:, IEEE, 2016.
conference:
end_date: 2016-04-14
location: Vienna, Austria
name: 'RTAS: Real-time and Embedded Technology and Applications Symposium'
start_date: 2016-04-11
date_created: 2018-12-11T11:50:58Z
date_published: 2016-04-27T00:00:00Z
date_updated: 2021-01-12T06:49:26Z
day: '27'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1109/RTAS.2016.7461337
file:
- access_level: open_access
checksum: 42f0462911cc9957f2356b12fb33b4b6
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:31Z
date_updated: 2020-07-14T12:44:41Z
file_id: '4949'
file_name: IST-2017-780-v1+1_RTAS-42-Camera-Ready.pdf
file_size: 1293599
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
publication_status: published
publisher: IEEE
publist_id: '6069'
pubrep_id: '780'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'From stateflow simulation to verified implementation: A verification approach
and a real-time train controller design'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1257'
abstract:
- lang: eng
text: We consider products of random matrices that are small, independent identically
distributed perturbations of a fixed matrix (Formula presented.). Focusing on
the eigenvalues of (Formula presented.) of a particular size we obtain a limit
to a SDE in a critical scaling. Previous results required (Formula presented.)
to be a (conjugated) unitary matrix so it could not have eigenvalues of different
modulus. From the result we can also obtain a limit SDE for the Markov process
given by the action of the random products on the flag manifold. Applying the
result to random Schrödinger operators we can improve some results by Valko and
Virag showing GOE statistics for the rescaled eigenvalue process of a sequence
of Anderson models on long boxes. In particular, we solve a problem posed in their
work.
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria). The work of C. Sadel was supported by NSERC Discovery Grant 92997-2010
RGPIN and by the People Programme (Marie Curie Actions) of the EU 7th Framework
Programme FP7/2007-2013, REA Grant 291734.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Christian
full_name: Sadel, Christian
id: 4760E9F8-F248-11E8-B48F-1D18A9856A87
last_name: Sadel
orcid: 0000-0001-8255-3968
- first_name: Bálint
full_name: Virág, Bálint
last_name: Virág
citation:
ama: Sadel C, Virág B. A central limit theorem for products of random matrices and
GOE statistics for the Anderson model on long boxes. Communications in Mathematical
Physics. 2016;343(3):881-919. doi:10.1007/s00220-016-2600-4
apa: Sadel, C., & Virág, B. (2016). A central limit theorem for products of
random matrices and GOE statistics for the Anderson model on long boxes. Communications
in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-016-2600-4
chicago: Sadel, Christian, and Bálint Virág. “A Central Limit Theorem for Products
of Random Matrices and GOE Statistics for the Anderson Model on Long Boxes.” Communications
in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s00220-016-2600-4.
ieee: C. Sadel and B. Virág, “A central limit theorem for products of random matrices
and GOE statistics for the Anderson model on long boxes,” Communications in
Mathematical Physics, vol. 343, no. 3. Springer, pp. 881–919, 2016.
ista: Sadel C, Virág B. 2016. A central limit theorem for products of random matrices
and GOE statistics for the Anderson model on long boxes. Communications in Mathematical
Physics. 343(3), 881–919.
mla: Sadel, Christian, and Bálint Virág. “A Central Limit Theorem for Products of
Random Matrices and GOE Statistics for the Anderson Model on Long Boxes.” Communications
in Mathematical Physics, vol. 343, no. 3, Springer, 2016, pp. 881–919, doi:10.1007/s00220-016-2600-4.
short: C. Sadel, B. Virág, Communications in Mathematical Physics 343 (2016) 881–919.
date_created: 2018-12-11T11:50:59Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2021-01-12T06:49:26Z
day: '01'
ddc:
- '510'
- '539'
department:
- _id: LaEr
doi: 10.1007/s00220-016-2600-4
ec_funded: 1
file:
- access_level: open_access
checksum: 4fb2411d9c2f56676123165aad46c828
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:02Z
date_updated: 2020-07-14T12:44:42Z
file_id: '5119'
file_name: IST-2016-703-v1+1_s00220-016-2600-4.pdf
file_size: 800792
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 343'
issue: '3'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 881 - 919
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '6067'
pubrep_id: '703'
quality_controlled: '1'
scopus_import: 1
status: public
title: A central limit theorem for products of random matrices and GOE statistics
for the Anderson model on long boxes
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 343
year: '2016'
...
---
_id: '1258'
abstract:
- lang: eng
text: When plants grow in close proximity basic resources such as light can become
limiting. Under such conditions plants respond to anticipate and/or adapt to the
light shortage, a process known as the shade avoidance syndrome (SAS). Following
genetic screening using a shade-responsive luciferase reporter line (PHYB:LUC),
we identified DRACULA2 (DRA2), which encodes an Arabidopsis homolog of mammalian
nucleoporin 98, a component of the nuclear pore complex (NPC). DRA2, together
with other nucleoporins, participates positively in the control of the hypocotyl
elongation response to plant proximity, a role that can be considered dependent
on the nucleocytoplasmic transport of macromolecules (i.e. is transport dependent).
In addition, our results reveal a specific role for DRA2 in controlling shade-induced
gene expression. We suggest that this novel regulatory role of DRA2 is transport
independent and that it might rely on its dynamic localization within and outside
of the NPC. These results provide mechanistic insights in to how SAS responses
are rapidly established by light conditions. They also indicate that nucleoporins
have an active role in plant signaling.
acknowledgement: M.G. received an FPI fellowship from the Spanish Ministerio de Economía
y Competitividad (MINECO). A.G. and A.F.-A. received FPU fellowships from the Spanish
Ministerio de Educación. S.P. received an FI fellowship from the Agència de Gestió
D'ajuts Universitaris i de Recerca (AGAUR - Generalitat de Catalunya). C.T. received
a Marie Curie IEF postdoctoral contract funded by the European Commission. I.R.-V.
received initially an FPI fellowship from the Spanish MINECO and later a Beatriu
de Pinós contract from AGAUR. Our research is supported by grants from the Spanish
MINECO-FEDER [BIO2008-00169, BIO2011-23489 and BIO2014-59895-P] and Generalitat
de Catalunya [2011-SGR447 and Xarba] to J.F.M.-G., and Generalitat Valenciana [PROMETEO/2009/112,
PROMETEOII/2014/006] to M.R.P. and J.L.M. We acknowledge the support of the Spanish
MINECO for the ‘Centro de Excelencia Severo Ochoa 2016-2019’ [award SEV-2015-0533].
We thank the CRAG greenhouse service for plant care; Chus Burillo for technical
help; Sergi Portolés and Carles Rentero for assistance with mutagenesis; Mark Estelle
(UCSD, USA) for providing sar1-4, sar3-1 and sar3-3 seeds; Juanjo López-Moya (CRAG,
Barcelona; 35S:HcPro plasmid) and Dolors Ludevid (CRAG; C307 plasmid) for providing
DNA plasmids; and Manuel Rodríguez-Concepción (CRAG) and Miguel Blázquez (IBMCP,
Valencia, Spain) for comments on the manuscript.
author:
- first_name: Marcal
full_name: Gallemi Rovira, Marcal
id: 460C6802-F248-11E8-B48F-1D18A9856A87
last_name: Gallemi Rovira
- first_name: Anahit
full_name: Galstyan, Anahit
last_name: Galstyan
- first_name: Sandi
full_name: Paulišić, Sandi
last_name: Paulišić
- first_name: Christiane
full_name: Then, Christiane
last_name: Then
- first_name: Almudena
full_name: Ferrández Ayela, Almudena
last_name: Ferrández Ayela
- first_name: Laura
full_name: Lorenzo Orts, Laura
last_name: Lorenzo Orts
- first_name: Irma
full_name: Roig Villanova, Irma
last_name: Roig Villanova
- first_name: Xuewen
full_name: Wang, Xuewen
last_name: Wang
- first_name: José
full_name: Micol, José
last_name: Micol
- first_name: Maria
full_name: Ponce, Maria
last_name: Ponce
- first_name: Paul
full_name: Devlin, Paul
last_name: Devlin
- first_name: Jaime
full_name: Martínez García, Jaime
last_name: Martínez García
citation:
ama: Gallemi M, Galstyan A, Paulišić S, et al. DRACULA2 is a dynamic nucleoporin
with a role in regulating the shade avoidance syndrome in Arabidopsis. Development.
2016;143(9):1623-1631. doi:10.1242/dev.130211
apa: Gallemi, M., Galstyan, A., Paulišić, S., Then, C., Ferrández Ayela, A., Lorenzo
Orts, L., … Martínez García, J. (2016). DRACULA2 is a dynamic nucleoporin with
a role in regulating the shade avoidance syndrome in Arabidopsis. Development.
Company of Biologists. https://doi.org/10.1242/dev.130211
chicago: Gallemi, Marçal, Anahit Galstyan, Sandi Paulišić, Christiane Then, Almudena
Ferrández Ayela, Laura Lorenzo Orts, Irma Roig Villanova, et al. “DRACULA2 Is
a Dynamic Nucleoporin with a Role in Regulating the Shade Avoidance Syndrome in
Arabidopsis.” Development. Company of Biologists, 2016. https://doi.org/10.1242/dev.130211.
ieee: M. Gallemi et al., “DRACULA2 is a dynamic nucleoporin with a role in
regulating the shade avoidance syndrome in Arabidopsis,” Development, vol.
143, no. 9. Company of Biologists, pp. 1623–1631, 2016.
ista: Gallemi M, Galstyan A, Paulišić S, Then C, Ferrández Ayela A, Lorenzo Orts
L, Roig Villanova I, Wang X, Micol J, Ponce M, Devlin P, Martínez García J. 2016.
DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance
syndrome in Arabidopsis. Development. 143(9), 1623–1631.
mla: Gallemi, Marçal, et al. “DRACULA2 Is a Dynamic Nucleoporin with a Role in Regulating
the Shade Avoidance Syndrome in Arabidopsis.” Development, vol. 143, no.
9, Company of Biologists, 2016, pp. 1623–31, doi:10.1242/dev.130211.
short: M. Gallemi, A. Galstyan, S. Paulišić, C. Then, A. Ferrández Ayela, L. Lorenzo
Orts, I. Roig Villanova, X. Wang, J. Micol, M. Ponce, P. Devlin, J. Martínez García,
Development 143 (2016) 1623–1631.
date_created: 2018-12-11T11:50:59Z
date_published: 2016-05-03T00:00:00Z
date_updated: 2021-01-12T06:49:27Z
day: '03'
department:
- _id: EvBe
doi: 10.1242/dev.130211
intvolume: ' 143'
issue: '9'
language:
- iso: eng
month: '05'
oa_version: None
page: 1623 - 1631
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '6068'
quality_controlled: '1'
scopus_import: 1
status: public
title: DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance
syndrome in Arabidopsis
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 143
year: '2016'
...
---
_id: '1259'
abstract:
- lang: eng
text: We consider the Bogolubov–Hartree–Fock functional for a fermionic many-body
system with two-body interactions. For suitable interaction potentials that have
a strong enough attractive tail in order to allow for two-body bound states, but
are otherwise sufficiently repulsive to guarantee stability of the system, we
show that in the low-density limit the ground state of this model consists of
a Bose–Einstein condensate of fermion pairs. The latter can be described by means
of the Gross–Pitaevskii energy functional.
acknowledgement: Partial financial support from the DFG grant GRK 1838, as well as
the Austrian Science Fund (FWF), project Nr. P 27533-N27 (R.S.), is gratefully acknowledged.
article_number: '13'
article_processing_charge: Yes (via OA deal)
author:
- first_name: Gerhard
full_name: Bräunlich, Gerhard
last_name: Bräunlich
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Bräunlich G, Hainzl C, Seiringer R. Bogolubov–Hartree–Fock theory for strongly
interacting fermions in the low density limit. Mathematical Physics, Analysis
and Geometry. 2016;19(2). doi:10.1007/s11040-016-9209-x
apa: Bräunlich, G., Hainzl, C., & Seiringer, R. (2016). Bogolubov–Hartree–Fock
theory for strongly interacting fermions in the low density limit. Mathematical
Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-016-9209-x
chicago: Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “Bogolubov–Hartree–Fock
Theory for Strongly Interacting Fermions in the Low Density Limit.” Mathematical
Physics, Analysis and Geometry. Springer, 2016. https://doi.org/10.1007/s11040-016-9209-x.
ieee: G. Bräunlich, C. Hainzl, and R. Seiringer, “Bogolubov–Hartree–Fock theory
for strongly interacting fermions in the low density limit,” Mathematical Physics,
Analysis and Geometry, vol. 19, no. 2. Springer, 2016.
ista: Bräunlich G, Hainzl C, Seiringer R. 2016. Bogolubov–Hartree–Fock theory for
strongly interacting fermions in the low density limit. Mathematical Physics,
Analysis and Geometry. 19(2), 13.
mla: Bräunlich, Gerhard, et al. “Bogolubov–Hartree–Fock Theory for Strongly Interacting
Fermions in the Low Density Limit.” Mathematical Physics, Analysis and Geometry,
vol. 19, no. 2, 13, Springer, 2016, doi:10.1007/s11040-016-9209-x.
short: G. Bräunlich, C. Hainzl, R. Seiringer, Mathematical Physics, Analysis and
Geometry 19 (2016).
date_created: 2018-12-11T11:50:59Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:49:27Z
day: '01'
ddc:
- '510'
- '539'
department:
- _id: RoSe
doi: 10.1007/s11040-016-9209-x
file:
- access_level: open_access
checksum: 9954f685cc25c58d7f1712c67b47ad8d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:13Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4736'
file_name: IST-2016-702-v1+1_s11040-016-9209-x.pdf
file_size: 506242
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 19'
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Mathematical Physics, Analysis and Geometry
publication_status: published
publisher: Springer
publist_id: '6066'
pubrep_id: '702'
quality_controlled: '1'
scopus_import: 1
status: public
title: Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low
density limit
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2016'
...
---
_id: '1260'
abstract:
- lang: eng
text: In this work, the Gardner problem of inferring interactions and fields for
an Ising neural network from given patterns under a local stability hypothesis
is addressed under a dual perspective. By means of duality arguments, an integer
linear system is defined whose solution space is the dual of the Gardner space
and whose solutions represent mutually unstable patterns. We propose and discuss
Monte Carlo methods in order to find and remove unstable patterns and uniformly
sample the space of interactions thereafter. We illustrate the problem on a set
of real data and perform ensemble calculation that shows how the emergence of
phase dominated by unstable patterns can be triggered in a nonlinear discontinuous
way.
article_number: '1650067'
article_processing_charge: No
article_type: original
arxiv: 1
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. The dual of the space of interactions in neural network models.
International Journal of Modern Physics C. 2016;27(6). doi:10.1142/S0129183116500674
apa: De Martino, D. (2016). The dual of the space of interactions in neural network
models. International Journal of Modern Physics C. World Scientific Publishing.
https://doi.org/10.1142/S0129183116500674
chicago: De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network
Models.” International Journal of Modern Physics C. World Scientific Publishing,
2016. https://doi.org/10.1142/S0129183116500674.
ieee: D. De Martino, “The dual of the space of interactions in neural network models,”
International Journal of Modern Physics C, vol. 27, no. 6. World Scientific
Publishing, 2016.
ista: De Martino D. 2016. The dual of the space of interactions in neural network
models. International Journal of Modern Physics C. 27(6), 1650067.
mla: De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network
Models.” International Journal of Modern Physics C, vol. 27, no. 6, 1650067,
World Scientific Publishing, 2016, doi:10.1142/S0129183116500674.
short: D. De Martino, International Journal of Modern Physics C 27 (2016).
date_created: 2018-12-11T11:51:00Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:49:28Z
day: '01'
department:
- _id: GaTk
doi: 10.1142/S0129183116500674
external_id:
arxiv:
- '1505.02963'
intvolume: ' 27'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1505.02963
month: '06'
oa: 1
oa_version: Preprint
publication: International Journal of Modern Physics C
publication_status: published
publisher: World Scientific Publishing
publist_id: '6065'
quality_controlled: '1'
scopus_import: 1
status: public
title: The dual of the space of interactions in neural network models
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2016'
...
---
_id: '1261'
abstract:
- lang: eng
text: 'We consider a non-standard finite-volume discretization of a strongly non-linear
fourth order diffusion equation on the d-dimensional cube, for arbitrary . The
scheme preserves two important structural properties of the equation: the first
is the interpretation as a gradient flow in a mass transportation metric, and
the second is an intimate relation to a linear Fokker-Planck equation. Thanks
to these structural properties, the scheme possesses two discrete Lyapunov functionals.
These functionals approximate the entropy and the Fisher information, respectively,
and their dissipation rates converge to the optimal ones in the discrete-to-continuous
limit. Using the dissipation, we derive estimates on the long-time asymptotics
of the discrete solutions. Finally, we present results from numerical experiments
which indicate that our discretization is able to capture significant features
of the complex original dynamics, even with a rather coarse spatial resolution.'
acknowledgement: This research was supported by the DFG Collaborative Research Centers TRR 109, ‘
Discretization in Geometry and Dynamics ’ and 1060 ‘ The Mathematics of Emergent
Effects ’ .
author:
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Daniel
full_name: Matthes, Daniel
last_name: Matthes
citation:
ama: Maas J, Matthes D. Long-time behavior of a finite volume discretization for
a fourth order diffusion equation. Nonlinearity. 2016;29(7):1992-2023.
doi:10.1088/0951-7715/29/7/1992
apa: Maas, J., & Matthes, D. (2016). Long-time behavior of a finite volume discretization
for a fourth order diffusion equation. Nonlinearity. IOP Publishing Ltd.
https://doi.org/10.1088/0951-7715/29/7/1992
chicago: Maas, Jan, and Daniel Matthes. “Long-Time Behavior of a Finite Volume Discretization
for a Fourth Order Diffusion Equation.” Nonlinearity. IOP Publishing Ltd.,
2016. https://doi.org/10.1088/0951-7715/29/7/1992.
ieee: J. Maas and D. Matthes, “Long-time behavior of a finite volume discretization
for a fourth order diffusion equation,” Nonlinearity, vol. 29, no. 7. IOP
Publishing Ltd., pp. 1992–2023, 2016.
ista: Maas J, Matthes D. 2016. Long-time behavior of a finite volume discretization
for a fourth order diffusion equation. Nonlinearity. 29(7), 1992–2023.
mla: Maas, Jan, and Daniel Matthes. “Long-Time Behavior of a Finite Volume Discretization
for a Fourth Order Diffusion Equation.” Nonlinearity, vol. 29, no. 7, IOP
Publishing Ltd., 2016, pp. 1992–2023, doi:10.1088/0951-7715/29/7/1992.
short: J. Maas, D. Matthes, Nonlinearity 29 (2016) 1992–2023.
date_created: 2018-12-11T11:51:00Z
date_published: 2016-06-10T00:00:00Z
date_updated: 2021-01-12T06:49:28Z
day: '10'
department:
- _id: JaMa
doi: 10.1088/0951-7715/29/7/1992
intvolume: ' 29'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1505.03178
month: '06'
oa: 1
oa_version: Preprint
page: 1992 - 2023
publication: Nonlinearity
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '6062'
quality_controlled: '1'
scopus_import: 1
status: public
title: Long-time behavior of a finite volume discretization for a fourth order diffusion
equation
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2016'
...
---
_id: '1262'
abstract:
- lang: eng
text: Emerging infectious diseases (EIDs) have contributed significantly to the
current biodiversity crisis, leading to widespread epidemics and population loss.
Owing to genetic variation in pathogen virulence, a complete understanding of
species decline requires the accurate identification and characterization of EIDs.
We explore this issue in the Western honeybee, where increasing mortality of populations
in the Northern Hemisphere has caused major concern. Specifically, we investigate
the importance of genetic identity of the main suspect in mortality, deformed
wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a
systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B)
is more virulent than the established DWV genotype (DWV-A) and is widespread in
the landscape. Furthermore, we show in a simple model that colonies infected with
DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential
for rapid DWV evolution by revealing extensive genome-wide recombination in vivo.
The emergence of DWV-B in naive honeybee populations, including via recombination
with DWV-A, could be of significant ecological and economic importance. Our findings
emphasize that knowledge of pathogen genetic identity and diversity is critical
to understanding drivers of species decline.
acknowledgement: "This work was supported by the Federal Ministry of Food, Agriculture
and Consumer Protection (Germany): Fit Bee project (grant 511-06.01-28-1-71.007-10),
the EU: BeeDoc (grant 244956), iDiv (2013 NGS-Fast Track grant W47004118) and the
Insect Pollinators Initiative (IPI grant BB/I000100/1 and BB/I000151/1). The IPI
is funded jointly by the Biotechnology and Biological Sciences Research Council,
the Department for Environment, Food and Rural Affairs, the Natural Environment
Research Council, the Scottish Government and the Wellcome Trust, under the Living
with Environmental Change Partnership. We thank A. Abrahams, M. Husemann and A.
Soro\r\nfor support in obtaining\r\nV. destructor\r\n-free honeybees; and BBKA\r\nPresident
D. Aston for access to records of colony overwinter\r\n2011–2012 mortality in the
UK. We also thank the anonymous refe-\r\nrees and Stephen Martin for comments that
led to substantial\r\nimprovement of the manuscript."
article_number: '20160811'
author:
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Myrsini
full_name: Natsopoulou, Myrsini
last_name: Natsopoulou
- first_name: Vincent
full_name: Doublet, Vincent
last_name: Doublet
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Silvio
full_name: Weging, Silvio
last_name: Weging
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Andreas
full_name: Gogol Döring, Andreas
last_name: Gogol Döring
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
citation:
ama: Mcmahon D, Natsopoulou M, Doublet V, et al. Elevated virulence of an emerging
viral genotype as a driver of honeybee loss. Proceedings of the Royal Society
of London Series B Biological Sciences. 2016;283(1833). doi:10.1098/rspb.2016.0811
apa: Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M.,
… Paxton, R. (2016). Elevated virulence of an emerging viral genotype as a driver
of honeybee loss. Proceedings of the Royal Society of London Series B Biological
Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.0811
chicago: Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio
Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Elevated Virulence
of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Proceedings of
the Royal Society of London Series B Biological Sciences. Royal Society, The,
2016. https://doi.org/10.1098/rspb.2016.0811.
ieee: D. Mcmahon et al., “Elevated virulence of an emerging viral genotype
as a driver of honeybee loss,” Proceedings of the Royal Society of London Series
B Biological Sciences, vol. 283, no. 1833. Royal Society, The, 2016.
ista: Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring
A, Paxton R. 2016. Elevated virulence of an emerging viral genotype as a driver
of honeybee loss. Proceedings of the Royal Society of London Series B Biological
Sciences. 283(1833), 20160811.
mla: Mcmahon, Dino, et al. “Elevated Virulence of an Emerging Viral Genotype as
a Driver of Honeybee Loss.” Proceedings of the Royal Society of London Series
B Biological Sciences, vol. 283, no. 1833, 20160811, Royal Society, The, 2016,
doi:10.1098/rspb.2016.0811.
short: D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A.
Gogol Döring, R. Paxton, Proceedings of the Royal Society of London Series B Biological
Sciences 283 (2016).
date_created: 2018-12-11T11:51:00Z
date_published: 2016-06-29T00:00:00Z
date_updated: 2023-02-23T14:05:30Z
day: '29'
ddc:
- '576'
- '592'
department:
- _id: SyCr
doi: 10.1098/rspb.2016.0811
file:
- access_level: open_access
checksum: 0b0d1be38b497d004064650acb3baced
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:46Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4708'
file_name: IST-2016-701-v1+1_20160811.full.pdf
file_size: 796872
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 283'
issue: '1833'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '6060'
pubrep_id: '701'
quality_controlled: '1'
related_material:
record:
- id: '9704'
relation: research_data
status: public
scopus_import: 1
status: public
title: Elevated virulence of an emerging viral genotype as a driver of honeybee loss
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 283
year: '2016'
...
---
_id: '1263'
abstract:
- lang: eng
text: Linking classical microwave electrical circuits to the optical telecommunication
band is at the core of modern communication. Future quantum information networks
will require coherent microwave-to-optical conversion to link electronic quantum
processors and memories via low-loss optical telecommunication networks. Efficient
conversion can be achieved with electro-optical modulators operating at the single
microwave photon level. In the standard electro-optic modulation scheme, this
is impossible because both up- and down-converted sidebands are necessarily present.
Here, we demonstrate true single-sideband up- or down-conversion in a triply resonant
whispering gallery mode resonator by explicitly addressing modes with asymmetric
free spectral range. Compared to previous experiments, we show a 3 orders of magnitude
improvement of the electro-optical conversion efficiency, reaching 0.1% photon
number conversion for a 10 GHz microwave tone at 0.42 mW of optical pump power.
The presented scheme is fully compatible with existing superconducting 3D circuit
quantum electrodynamics technology and can be used for nonclassical state conversion
and communication. Our conversion bandwidth is larger than 1 MHz and is not fundamentally
limited.
acknowledgement: Alexander von Humboldt Foundation; Studienstiftung des Deutschen
Volkes. We would like to acknowledge our stimulating discussions with Konrad Lehnert
and Alessandro Pitanti.
article_processing_charge: No
author:
- first_name: Alfredo
full_name: Rueda, Alfredo
last_name: Rueda
- first_name: Florian
full_name: Sedlmeir, Florian
last_name: Sedlmeir
- first_name: Michele
full_name: Collodo, Michele
last_name: Collodo
- first_name: Ulrich
full_name: Vogl, Ulrich
last_name: Vogl
- first_name: Birgit
full_name: Stiller, Birgit
last_name: Stiller
- first_name: Gerhard
full_name: Schunk, Gerhard
last_name: Schunk
- first_name: Dmitry
full_name: Strekalov, Dmitry
last_name: Strekalov
- first_name: Christoph
full_name: Marquardt, Christoph
last_name: Marquardt
- 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
- first_name: Gerd
full_name: Leuchs, Gerd
last_name: Leuchs
- first_name: Harald
full_name: Schwefel, Harald
last_name: Schwefel
citation:
ama: 'Rueda A, Sedlmeir F, Collodo M, et al. Efficient microwave to optical photon
conversion: An electro-optical realization. Optica. 2016;3(6):597-604.
doi:10.1364/OPTICA.3.000597'
apa: 'Rueda, A., Sedlmeir, F., Collodo, M., Vogl, U., Stiller, B., Schunk, G., …
Schwefel, H. (2016). Efficient microwave to optical photon conversion: An electro-optical
realization. Optica. Optica Publishing Group. https://doi.org/10.1364/OPTICA.3.000597'
chicago: 'Rueda, Alfredo, Florian Sedlmeir, Michele Collodo, Ulrich Vogl, Birgit
Stiller, Gerhard Schunk, Dmitry Strekalov, et al. “Efficient Microwave to Optical
Photon Conversion: An Electro-Optical Realization.” Optica. Optica Publishing
Group, 2016. https://doi.org/10.1364/OPTICA.3.000597.'
ieee: 'A. Rueda et al., “Efficient microwave to optical photon conversion:
An electro-optical realization,” Optica, vol. 3, no. 6. Optica Publishing
Group, pp. 597–604, 2016.'
ista: 'Rueda A, Sedlmeir F, Collodo M, Vogl U, Stiller B, Schunk G, Strekalov D,
Marquardt C, Fink JM, Painter O, Leuchs G, Schwefel H. 2016. Efficient microwave
to optical photon conversion: An electro-optical realization. Optica. 3(6), 597–604.'
mla: 'Rueda, Alfredo, et al. “Efficient Microwave to Optical Photon Conversion:
An Electro-Optical Realization.” Optica, vol. 3, no. 6, Optica Publishing
Group, 2016, pp. 597–604, doi:10.1364/OPTICA.3.000597.'
short: A. Rueda, F. Sedlmeir, M. Collodo, U. Vogl, B. Stiller, G. Schunk, D. Strekalov,
C. Marquardt, J.M. Fink, O. Painter, G. Leuchs, H. Schwefel, Optica 3 (2016) 597–604.
date_created: 2018-12-11T11:51:01Z
date_published: 2016-06-20T00:00:00Z
date_updated: 2023-10-17T12:17:15Z
day: '20'
department:
- _id: JoFi
doi: 10.1364/OPTICA.3.000597
intvolume: ' 3'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1364/OPTICA.3.000597
month: '06'
oa: 1
oa_version: Published Version
page: 597 - 604
publication: Optica
publication_status: published
publisher: Optica Publishing Group
publist_id: '6061'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Efficient microwave to optical photon conversion: An electro-optical realization'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2016'
...
---
_id: '1264'
abstract:
- lang: eng
text: n contrast with the wealth of recent reports about the function of μ-adaptins
and clathrin adaptor protein (AP) complexes, there is very little information
about the motifs that determine the sorting of membrane proteins within clathrin-coated
vesicles in plants. Here, we investigated putative sorting signals in the large
cytosolic loop of the Arabidopsis (Arabidopsis thaliana) PIN-FORMED1 (PIN1) auxin
transporter, which are involved in binding μ-adaptins and thus in PIN1 trafficking
and localization. We found that Phe-165 and Tyr-280, Tyr-328, and Tyr-394 are
involved in the binding of different μ-adaptins in vitro. However, only Phe-165,
which binds μA(μ2)- and μD(μ3)-adaptin, was found to be essential for PIN1 trafficking
and localization in vivo. The PIN1:GFP-F165A mutant showed reduced endocytosis
but also localized to intracellular structures containing several layers of membranes
and endoplasmic reticulum (ER) markers, suggesting that they correspond to ER
or ER-derived membranes. While PIN1:GFP localized normally in a μA (μ2)-adaptin
mutant, it accumulated in big intracellular structures containing LysoTracker
in a μD (μ3)-adaptin mutant, consistent with previous results obtained with mutants
of other subunits of the AP-3 complex. Our data suggest that Phe-165, through
the binding of μA (μ2)- and μD (μ3)-adaptin, is important for PIN1 endocytosis
and for PIN1 trafficking along the secretory pathway, respectively.
acknowledgement: "We thank Dr. R. Offringa (Leiden University) for providing the GST-\r\nPIN-CL
construct; Sandra Richter and Gerd Jurgens (University of Tübin-\r\ngen) for providing
the estradiol-inducible PIN1-RFP construct and the\r\ngnl1 mutant expressing BFA-sensitive
GNL1; F.J. Santonja (University of Valencia)\r\nfor help with the statistical analysis;
Jurgen Kleine-Vehn, Elke Barbez, and\r\nEva Benkova for helpful discussions; the
Salk Institute Genomic Analysis\r\nLaboratory for providing the sequence-indexed
Arabidopsis T-DNA in-\r\nsertion mutants; and the greenhouse section and the microscopy
section\r\nof SCSIE (University of Valencia) and Pilar Selvi for excellent technical\r\nassistance."
author:
- first_name: Gloria
full_name: Sancho Andrés, Gloria
last_name: Sancho Andrés
- first_name: Esther
full_name: Soriano Ortega, Esther
last_name: Soriano Ortega
- first_name: Caiji
full_name: Gao, Caiji
last_name: Gao
- first_name: Joan
full_name: Bernabé Orts, Joan
last_name: Bernabé Orts
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: Anna
full_name: Müller, Anna
id: 420AB15A-F248-11E8-B48F-1D18A9856A87
last_name: Müller
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Liwen
full_name: Jiang, Liwen
last_name: Jiang
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Fernando
full_name: Aniento, Fernando
last_name: Aniento
- first_name: Maria
full_name: Marcote, Maria
last_name: Marcote
citation:
ama: Sancho Andrés G, Soriano Ortega E, Gao C, et al. Sorting motifs involved in
the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology.
2016;171(3):1965-1982. doi:10.1104/pp.16.00373
apa: Sancho Andrés, G., Soriano Ortega, E., Gao, C., Bernabé Orts, J., Narasimhan,
M., Müller, A., … Marcote, M. (2016). Sorting motifs involved in the trafficking
and localization of the PIN1 auxin efflux carrier. Plant Physiology. American
Society of Plant Biologists. https://doi.org/10.1104/pp.16.00373
chicago: Sancho Andrés, Gloria, Esther Soriano Ortega, Caiji Gao, Joan Bernabé Orts,
Madhumitha Narasimhan, Anna Müller, Ricardo Tejos, et al. “Sorting Motifs Involved
in the Trafficking and Localization of the PIN1 Auxin Efflux Carrier.” Plant
Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.00373.
ieee: G. Sancho Andrés et al., “Sorting motifs involved in the trafficking
and localization of the PIN1 auxin efflux carrier,” Plant Physiology, vol.
171, no. 3. American Society of Plant Biologists, pp. 1965–1982, 2016.
ista: Sancho Andrés G, Soriano Ortega E, Gao C, Bernabé Orts J, Narasimhan M, Müller
A, Tejos R, Jiang L, Friml J, Aniento F, Marcote M. 2016. Sorting motifs involved
in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology.
171(3), 1965–1982.
mla: Sancho Andrés, Gloria, et al. “Sorting Motifs Involved in the Trafficking and
Localization of the PIN1 Auxin Efflux Carrier.” Plant Physiology, vol.
171, no. 3, American Society of Plant Biologists, 2016, pp. 1965–82, doi:10.1104/pp.16.00373.
short: G. Sancho Andrés, E. Soriano Ortega, C. Gao, J. Bernabé Orts, M. Narasimhan,
A. Müller, R. Tejos, L. Jiang, J. Friml, F. Aniento, M. Marcote, Plant Physiology
171 (2016) 1965–1982.
date_created: 2018-12-11T11:51:01Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:49:29Z
day: '01'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1104/pp.16.00373
ec_funded: 1
intvolume: ' 171'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936568/
month: '07'
oa: 1
oa_version: Submitted Version
page: 1965 - 1982
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Plant Physiology
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '6059'
quality_controlled: '1'
scopus_import: 1
status: public
title: Sorting motifs involved in the trafficking and localization of the PIN1 auxin
efflux carrier
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 171
year: '2016'
...
---
_id: '1265'
abstract:
- lang: eng
text: Extracellular matrices (ECMs) are central to the advent of multicellular life,
and their mechanical propertiesare modulated by and impinge on intracellular signaling
pathways that regulate vital cellular functions. High spatial-resolution mapping
of mechanical properties in live cells is, however, extremely challenging. Thus,
our understanding of how signaling pathways process physiological signals to generate
appropriate mechanical responses is limited. We introduce fluorescence emission-Brillouin
scattering imaging (FBi), a method for the parallel and all-optical measurements
of mechanical properties and fluorescence at the submicrometer scale in living
organisms. Using FBi, we showed thatchanges in cellular hydrostatic pressure and
cytoplasm viscoelasticity modulate the mechanical signatures of plant ECMs. We
further established that the measured "stiffness" of plant ECMs is symmetrically
patternedin hypocotyl cells undergoing directional growth. Finally, application
of this method to Arabidopsis thaliana with photoreceptor mutants revealed that
red and far-red light signals are essential modulators of ECM viscoelasticity.
By mapping the viscoelastic signatures of a complex ECM, we provide proof of principlefor
the organism-wide applicability of FBi for measuring the mechanical outputs of
intracellular signaling pathways. As such, our work has implications for investigations
of mechanosignaling pathways and developmental biology.
article_number: rs5
author:
- first_name: Kareem
full_name: Elsayad, Kareem
last_name: Elsayad
- first_name: Stephanie
full_name: Werner, Stephanie
last_name: Werner
- first_name: Marcal
full_name: Gallemi Rovira, Marcal
id: 460C6802-F248-11E8-B48F-1D18A9856A87
last_name: Gallemi Rovira
- first_name: Jixiang
full_name: Kong, Jixiang
last_name: Kong
- first_name: Edmundo
full_name: Guajardo, Edmundo
last_name: Guajardo
- first_name: Lijuan
full_name: Zhang, Lijuan
last_name: Zhang
- first_name: Yvon
full_name: Jaillais, Yvon
last_name: Jaillais
- first_name: Thomas
full_name: Greb, Thomas
last_name: Greb
- first_name: Youssef
full_name: Belkhadir, Youssef
last_name: Belkhadir
citation:
ama: Elsayad K, Werner S, Gallemi M, et al. Mapping the subcellular mechanical properties
of live cells in tissues with fluorescence emission-Brillouin imaging. Science
Signaling. 2016;9(435). doi:10.1126/scisignal.aaf6326
apa: Elsayad, K., Werner, S., Gallemi, M., Kong, J., Guajardo, E., Zhang, L., …
Belkhadir, Y. (2016). Mapping the subcellular mechanical properties of live cells
in tissues with fluorescence emission-Brillouin imaging. Science Signaling.
American Association for the Advancement of Science. https://doi.org/10.1126/scisignal.aaf6326
chicago: Elsayad, Kareem, Stephanie Werner, Marçal Gallemi, Jixiang Kong, Edmundo
Guajardo, Lijuan Zhang, Yvon Jaillais, Thomas Greb, and Youssef Belkhadir. “Mapping
the Subcellular Mechanical Properties of Live Cells in Tissues with Fluorescence
Emission-Brillouin Imaging.” Science Signaling. American Association for
the Advancement of Science, 2016. https://doi.org/10.1126/scisignal.aaf6326.
ieee: K. Elsayad et al., “Mapping the subcellular mechanical properties of
live cells in tissues with fluorescence emission-Brillouin imaging,” Science
Signaling, vol. 9, no. 435. American Association for the Advancement of Science,
2016.
ista: Elsayad K, Werner S, Gallemi M, Kong J, Guajardo E, Zhang L, Jaillais Y, Greb
T, Belkhadir Y. 2016. Mapping the subcellular mechanical properties of live cells
in tissues with fluorescence emission-Brillouin imaging. Science Signaling. 9(435),
rs5.
mla: Elsayad, Kareem, et al. “Mapping the Subcellular Mechanical Properties of Live
Cells in Tissues with Fluorescence Emission-Brillouin Imaging.” Science Signaling,
vol. 9, no. 435, rs5, American Association for the Advancement of Science, 2016,
doi:10.1126/scisignal.aaf6326.
short: K. Elsayad, S. Werner, M. Gallemi, J. Kong, E. Guajardo, L. Zhang, Y. Jaillais,
T. Greb, Y. Belkhadir, Science Signaling 9 (2016).
date_created: 2018-12-11T11:51:02Z
date_published: 2016-07-05T00:00:00Z
date_updated: 2021-01-12T06:49:29Z
day: '05'
department:
- _id: EvBe
doi: 10.1126/scisignal.aaf6326
intvolume: ' 9'
issue: '435'
language:
- iso: eng
month: '07'
oa_version: None
publication: Science Signaling
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6057'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mapping the subcellular mechanical properties of live cells in tissues with
fluorescence emission-Brillouin imaging
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2016'
...
---
_id: '1266'
abstract:
- lang: eng
text: 'Cortical networks exhibit ‘global oscillations’, in which neural spike times
are entrained to an underlying oscillatory rhythm, but where individual neurons
fire irregularly, on only a fraction of cycles. While the network dynamics underlying
global oscillations have been well characterised, their function is debated. Here,
we show that such global oscillations are a direct consequence of optimal efficient
coding in spiking networks with synaptic delays and noise. To avoid firing unnecessary
spikes, neurons need to share information about the network state. Ideally, membrane
potentials should be strongly correlated and reflect a ‘prediction error’ while
the spikes themselves are uncorrelated and occur rarely. We show that the most
efficient representation is when: (i) spike times are entrained to a global Gamma
rhythm (implying a consistent representation of the error); but (ii) few neurons
fire on each cycle (implying high efficiency), while (iii) excitation and inhibition
are tightly balanced. This suggests that cortical networks exhibiting such dynamics
are tuned to achieve a maximally efficient population code.'
acknowledgement: Boris Gutkin acknowledges funding by the Russian Academic Excellence
Project '5-100’.
article_number: e13824
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Boris
full_name: Gutkin, Boris
last_name: Gutkin
- first_name: Sophie
full_name: Denève, Sophie
last_name: Denève
citation:
ama: Chalk MJ, Gutkin B, Denève S. Neural oscillations as a signature of efficient
coding in the presence of synaptic delays. eLife. 2016;5(2016JULY). doi:10.7554/eLife.13824
apa: Chalk, M. J., Gutkin, B., & Denève, S. (2016). Neural oscillations as a
signature of efficient coding in the presence of synaptic delays. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.13824
chicago: Chalk, Matthew J, Boris Gutkin, and Sophie Denève. “Neural Oscillations
as a Signature of Efficient Coding in the Presence of Synaptic Delays.” ELife.
eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.13824.
ieee: M. J. Chalk, B. Gutkin, and S. Denève, “Neural oscillations as a signature
of efficient coding in the presence of synaptic delays,” eLife, vol. 5,
no. 2016JULY. eLife Sciences Publications, 2016.
ista: Chalk MJ, Gutkin B, Denève S. 2016. Neural oscillations as a signature of
efficient coding in the presence of synaptic delays. eLife. 5(2016JULY), e13824.
mla: Chalk, Matthew J., et al. “Neural Oscillations as a Signature of Efficient
Coding in the Presence of Synaptic Delays.” ELife, vol. 5, no. 2016JULY,
e13824, eLife Sciences Publications, 2016, doi:10.7554/eLife.13824.
short: M.J. Chalk, B. Gutkin, S. Denève, ELife 5 (2016).
date_created: 2018-12-11T11:51:02Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:49:30Z
day: '01'
ddc:
- '571'
department:
- _id: GaTk
doi: 10.7554/eLife.13824
file:
- access_level: open_access
checksum: dc52d967dc76174477bb258d84be2899
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:20Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4874'
file_name: IST-2016-700-v1+1_e13824-download.pdf
file_size: 2819055
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 5'
issue: 2016JULY
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6056'
pubrep_id: '700'
quality_controlled: '1'
scopus_import: 1
status: public
title: Neural oscillations as a signature of efficient coding in the presence of synaptic
delays
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2016'
...
---
_id: '1267'
abstract:
- lang: eng
text: We give a simplified proof of the nonexistence of large nuclei in the liquid
drop model and provide an explicit bound. Our bound is within a factor of 2.3
of the conjectured value and seems to be the first quantitative result.
acknowledgement: "Open access funding provided by Institute of Science and Technology
Austria.\r\n"
author:
- first_name: Rupert
full_name: Frank, Rupert
last_name: Frank
- first_name: Rowan
full_name: Killip, Rowan
last_name: Killip
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
citation:
ama: Frank R, Killip R, Nam P. Nonexistence of large nuclei in the liquid drop model.
Letters in Mathematical Physics. 2016;106(8):1033-1036. doi:10.1007/s11005-016-0860-8
apa: Frank, R., Killip, R., & Nam, P. (2016). Nonexistence of large nuclei in
the liquid drop model. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-016-0860-8
chicago: Frank, Rupert, Rowan Killip, and Phan Nam. “Nonexistence of Large Nuclei
in the Liquid Drop Model.” Letters in Mathematical Physics. Springer, 2016.
https://doi.org/10.1007/s11005-016-0860-8.
ieee: R. Frank, R. Killip, and P. Nam, “Nonexistence of large nuclei in the liquid
drop model,” Letters in Mathematical Physics, vol. 106, no. 8. Springer,
pp. 1033–1036, 2016.
ista: Frank R, Killip R, Nam P. 2016. Nonexistence of large nuclei in the liquid
drop model. Letters in Mathematical Physics. 106(8), 1033–1036.
mla: Frank, Rupert, et al. “Nonexistence of Large Nuclei in the Liquid Drop Model.”
Letters in Mathematical Physics, vol. 106, no. 8, Springer, 2016, pp. 1033–36,
doi:10.1007/s11005-016-0860-8.
short: R. Frank, R. Killip, P. Nam, Letters in Mathematical Physics 106 (2016) 1033–1036.
date_created: 2018-12-11T11:51:02Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T06:49:30Z
day: '01'
ddc:
- '510'
- '539'
department:
- _id: RoSe
doi: 10.1007/s11005-016-0860-8
file:
- access_level: open_access
checksum: d740a6a226e0f5f864f40e3e269d3cc0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:09Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4863'
file_name: IST-2016-698-v1+1_s11005-016-0860-8.pdf
file_size: 349464
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 106'
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 1033 - 1036
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Letters in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '6054'
pubrep_id: '698'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nonexistence of large nuclei in the liquid drop 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: 106
year: '2016'
...
---
_id: '1268'
acknowledgement: We would like to thank Mihai Netea for inviting us to contribute
to this Theme Issue.
author:
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
citation:
ama: Milutinovic B, Kurtz J. Immune memory in invertebrates. Seminars in Immunology.
2016;28(4):328-342. doi:10.1016/j.smim.2016.05.004
apa: Milutinovic, B., & Kurtz, J. (2016). Immune memory in invertebrates. Seminars
in Immunology. Academic Press. https://doi.org/10.1016/j.smim.2016.05.004
chicago: Milutinovic, Barbara, and Joachim Kurtz. “Immune Memory in Invertebrates.”
Seminars in Immunology. Academic Press, 2016. https://doi.org/10.1016/j.smim.2016.05.004.
ieee: B. Milutinovic and J. Kurtz, “Immune memory in invertebrates,” Seminars
in Immunology, vol. 28, no. 4. Academic Press, pp. 328–342, 2016.
ista: Milutinovic B, Kurtz J. 2016. Immune memory in invertebrates. Seminars in
Immunology. 28(4), 328–342.
mla: Milutinovic, Barbara, and Joachim Kurtz. “Immune Memory in Invertebrates.”
Seminars in Immunology, vol. 28, no. 4, Academic Press, 2016, pp. 328–42,
doi:10.1016/j.smim.2016.05.004.
short: B. Milutinovic, J. Kurtz, Seminars in Immunology 28 (2016) 328–342.
date_created: 2018-12-11T11:51:03Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T06:49:30Z
day: '01'
department:
- _id: SyCr
doi: 10.1016/j.smim.2016.05.004
intvolume: ' 28'
issue: '4'
language:
- iso: eng
month: '08'
oa_version: None
page: 328 - 342
publication: Seminars in Immunology
publication_status: published
publisher: Academic Press
publist_id: '6053'
quality_controlled: '1'
scopus_import: 1
status: public
title: Immune memory in invertebrates
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2016'
...
---
_id: '1269'
abstract:
- lang: eng
text: Plants are continuously exposed to a myriad of external signals such as fluctuating
nutrients availability, drought, heat, cold, high salinity, or pathogen/pest attacks
that can severely affect their development, growth, and fertility. As sessile
organisms, plants must therefore be able to sense and rapidly react to these external
inputs, activate efficient responses, and adjust development to changing conditions.
In recent years, significant progress has been made towards understanding the
molecular mechanisms underlying the intricate and complex communication between
plants and the environment. It is now becoming increasingly evident that hormones
have an important regulatory role in plant adaptation and defense mechanisms.
author:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Benková E. Plant hormones in interactions with the environment. Plant Molecular
Biology. 2016;91(6):597. doi:10.1007/s11103-016-0501-8
apa: Benková, E. (2016). Plant hormones in interactions with the environment. Plant
Molecular Biology. Springer. https://doi.org/10.1007/s11103-016-0501-8
chicago: Benková, Eva. “Plant Hormones in Interactions with the Environment.” Plant
Molecular Biology. Springer, 2016. https://doi.org/10.1007/s11103-016-0501-8.
ieee: E. Benková, “Plant hormones in interactions with the environment,” Plant
Molecular Biology, vol. 91, no. 6. Springer, p. 597, 2016.
ista: Benková E. 2016. Plant hormones in interactions with the environment. Plant
Molecular Biology. 91(6), 597.
mla: Benková, Eva. “Plant Hormones in Interactions with the Environment.” Plant
Molecular Biology, vol. 91, no. 6, Springer, 2016, p. 597, doi:10.1007/s11103-016-0501-8.
short: E. Benková, Plant Molecular Biology 91 (2016) 597.
date_created: 2018-12-11T11:51:03Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T06:49:31Z
day: '01'
ddc:
- '581'
department:
- _id: EvBe
doi: 10.1007/s11103-016-0501-8
file:
- access_level: open_access
checksum: 0ffb7a15c5336b3a55248cc67021a825
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:28Z
date_updated: 2020-07-14T12:44:42Z
file_id: '5349'
file_name: IST-2016-697-v1+1_s11103-016-0501-8.pdf
file_size: 297282
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 91'
issue: '6'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '597'
publication: Plant Molecular Biology
publication_status: published
publisher: Springer
publist_id: '6052'
pubrep_id: '697'
quality_controlled: '1'
scopus_import: 1
status: public
title: Plant hormones in interactions with the environment
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2016'
...
---
_id: '1270'
abstract:
- lang: eng
text: A crucial step in the early development of multicellular organisms involves
the establishment of spatial patterns of gene expression which later direct proliferating
cells to take on different cell fates. These patterns enable the cells to infer
their global position within a tissue or an organism by reading out local gene
expression levels. The patterning system is thus said to encode positional information,
a concept that was formalized recently in the framework of information theory.
Here we introduce a toy model of patterning in one spatial dimension, which can
be seen as an extension of Wolpert's paradigmatic "French Flag" model,
to patterning by several interacting, spatially coupled genes subject to intrinsic
and extrinsic noise. Our model, a variant of an Ising spin system, allows us to
systematically explore expression patterns that optimally encode positional information.
We find that optimal patterning systems use positional cues, as in the French
Flag model, together with gene-gene interactions to generate combinatorial codes
for position which we call "Counter" patterns. Counter patterns can
also be stabilized against noise and variations in system size or morphogen dosage
by longer-range spatial interactions of the type invoked in the Turing model.
The simple setup proposed here qualitatively captures many of the experimentally
observed properties of biological patterning systems and allows them to be studied
in a single, theoretically consistent framework.
acknowledgement: The authors would like to thank Thomas Sokolowski and Filipe Tostevin
for helpful discussions. PH and UG were funded by the German Excellence Initiative
via the program "Nanosystems Initiative Munich" (https://www.nano-initiative-munich.de)
and the German Research Foundation via the SFB 1032 "Nanoagents for Spatiotemporal
Control of Molecular and Cellular Reactions" (http://www.sfb1032.physik.uni-muenchen.de).
GT was funded by the Austrian Science Fund (FWF P 28844) (http://www.fwf.ac.at).
article_number: e0163628
author:
- first_name: Patrick
full_name: Hillenbrand, Patrick
last_name: Hillenbrand
- first_name: Ulrich
full_name: Gerland, Ulrich
last_name: Gerland
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: 'Hillenbrand P, Gerland U, Tkačik G. Beyond the French flag model: Exploiting
spatial and gene regulatory interactions for positional information. PLoS One.
2016;11(9). doi:10.1371/journal.pone.0163628'
apa: 'Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Beyond the French flag
model: Exploiting spatial and gene regulatory interactions for positional information.
PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628'
chicago: 'Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Beyond the French
Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional
Information.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.'
ieee: 'P. Hillenbrand, U. Gerland, and G. Tkačik, “Beyond the French flag model:
Exploiting spatial and gene regulatory interactions for positional information,”
PLoS One, vol. 11, no. 9. Public Library of Science, 2016.'
ista: 'Hillenbrand P, Gerland U, Tkačik G. 2016. Beyond the French flag model: Exploiting
spatial and gene regulatory interactions for positional information. PLoS One.
11(9), e0163628.'
mla: 'Hillenbrand, Patrick, et al. “Beyond the French Flag Model: Exploiting Spatial
and Gene Regulatory Interactions for Positional Information.” PLoS One,
vol. 11, no. 9, e0163628, Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.'
short: P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016).
date_created: 2018-12-11T11:51:03Z
date_published: 2016-09-27T00:00:00Z
date_updated: 2023-02-23T14:11:37Z
day: '27'
ddc:
- '571'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0163628
file:
- access_level: open_access
checksum: 3d0d55d373096a033bd9cf79288c8586
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:47Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4837'
file_name: IST-2016-696-v1+1_journal.pone.0163628.PDF
file_size: 4950415
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '6050'
pubrep_id: '696'
quality_controlled: '1'
related_material:
record:
- id: '9869'
relation: research_data
status: public
- id: '9870'
relation: research_data
status: public
- id: '9871'
relation: research_data
status: public
scopus_import: 1
status: public
title: 'Beyond the French flag model: Exploiting spatial and gene regulatory interactions
for positional information'
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2016'
...
---
_id: '1271'
abstract:
- lang: eng
text: 'Background: High directional persistence is often assumed to enhance the
efficiency of chemotactic migration. Yet, cells in vivo usually display meandering
trajectories with relatively low directional persistence, and the control and
function of directional persistence during cell migration in three-dimensional
environments are poorly understood. Results: Here, we use mesendoderm progenitors
migrating during zebrafish gastrulation as a model system to investigate the control
of directional persistence during migration in vivo. We show that progenitor cells
alternate persistent run phases with tumble phases that result in cell reorientation.
Runs are characterized by the formation of directed actin-rich protrusions and
tumbles by enhanced blebbing. Increasing the proportion of actin-rich protrusions
or blebs leads to longer or shorter run phases, respectively. Importantly, both
reducing and increasing run phases result in larger spatial dispersion of the
cells, indicative of reduced migration precision. A physical model quantitatively
recapitulating the migratory behavior of mesendoderm progenitors indicates that
the ratio of tumbling to run times, and thus the specific degree of directional
persistence of migration, are critical for optimizing migration precision. Conclusions:
Together, our experiments and model provide mechanistic insight into the control
of migration directionality for cells moving in three-dimensional environments
that combine different protrusion types, whereby the proportion of blebs to actin-rich
protrusions determines the directional persistence and precision of movement by
regulating the ratio of tumbling to run times.'
acknowledged_ssus:
- _id: LifeSc
acknowledgement: "We thank K. Lee, C. Norden, A. Webb, and the members of the Paluch
lab for\r\ncomments on the manuscript. We are grateful to P. Rørth and Peter Dieterich\r\nfor
discussions, S. Ares, Y. Arboleda-Estudillo and S. Schneider for technical help,\r\nM.
Biro for help with programming, and the BIOTEC/MPI-CBG and IST zebrafish\r\nand
imaging facilities for help and advice at various stages of this project. This work
was supported by the Max Planck Society, the Medical Research Council UK (core funding
to the MRC LMCB), and by grants from the Polish Ministry of Science and Higher Education
(454/N-MPG/2009/0) to EKP, the Deutsche Forschungsgemeinschaft (HE 3231/6-1 and
PA 1590/1-1) to CPH and EKP, a A*Star JCO career development award (12302FG010)
to WY and a Damon Runyon fellowship award to ADM (DRG 2157-12). This work was also
supported by the Francis Crick Institute which receives its core funding from Cancer
Research UK (FC001317), the UK Medical Research Council (FC001317), and the Wellcome
Trust (FC001317) to GS."
article_number: '74'
author:
- first_name: Alba
full_name: Diz Muñoz, Alba
last_name: Diz Muñoz
- first_name: Pawel
full_name: Romanczuk, Pawel
last_name: Romanczuk
- first_name: Weimiao
full_name: Yu, Weimiao
last_name: Yu
- first_name: Martin
full_name: Bergert, Martin
last_name: Bergert
- first_name: Kenzo
full_name: Ivanovitch, Kenzo
last_name: Ivanovitch
- first_name: Guillame
full_name: Salbreux, Guillame
last_name: Salbreux
- 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
- first_name: Ewa
full_name: Paluch, Ewa
last_name: Paluch
citation:
ama: Diz Muñoz A, Romanczuk P, Yu W, et al. Steering cell migration by alternating
blebs and actin-rich protrusions. BMC Biology. 2016;14(1). doi:10.1186/s12915-016-0294-x
apa: Diz Muñoz, A., Romanczuk, P., Yu, W., Bergert, M., Ivanovitch, K., Salbreux,
G., … Paluch, E. (2016). Steering cell migration by alternating blebs and actin-rich
protrusions. BMC Biology. BioMed Central. https://doi.org/10.1186/s12915-016-0294-x
chicago: Diz Muñoz, Alba, Pawel Romanczuk, Weimiao Yu, Martin Bergert, Kenzo Ivanovitch,
Guillame Salbreux, Carl-Philipp J Heisenberg, and Ewa Paluch. “Steering Cell Migration
by Alternating Blebs and Actin-Rich Protrusions.” BMC Biology. BioMed Central,
2016. https://doi.org/10.1186/s12915-016-0294-x.
ieee: A. Diz Muñoz et al., “Steering cell migration by alternating blebs
and actin-rich protrusions,” BMC Biology, vol. 14, no. 1. BioMed Central,
2016.
ista: Diz Muñoz A, Romanczuk P, Yu W, Bergert M, Ivanovitch K, Salbreux G, Heisenberg
C-PJ, Paluch E. 2016. Steering cell migration by alternating blebs and actin-rich
protrusions. BMC Biology. 14(1), 74.
mla: Diz Muñoz, Alba, et al. “Steering Cell Migration by Alternating Blebs and Actin-Rich
Protrusions.” BMC Biology, vol. 14, no. 1, 74, BioMed Central, 2016, doi:10.1186/s12915-016-0294-x.
short: A. Diz Muñoz, P. Romanczuk, W. Yu, M. Bergert, K. Ivanovitch, G. Salbreux,
C.-P.J. Heisenberg, E. Paluch, BMC Biology 14 (2016).
date_created: 2018-12-11T11:51:04Z
date_published: 2016-09-02T00:00:00Z
date_updated: 2021-01-12T06:49:32Z
day: '02'
ddc:
- '572'
- '576'
department:
- _id: CaHe
doi: 10.1186/s12915-016-0294-x
file:
- access_level: open_access
checksum: 0bfa484ac69a0a560fb9a4589aeda7f6
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:20Z
date_updated: 2020-07-14T12:44:42Z
file_id: '5002'
file_name: IST-2016-695-v1+1_s12915-016-0294-x.pdf
file_size: 1875695
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 14'
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 252064B8-B435-11E9-9278-68D0E5697425
grant_number: HE_3231/6-1
name: Analysis of the Formation and Function of Different Cell Protusion Types During
Cell Migration in Vivo
publication: BMC Biology
publication_status: published
publisher: BioMed Central
publist_id: '6049'
pubrep_id: '695'
quality_controlled: '1'
scopus_import: 1
status: public
title: Steering cell migration by alternating blebs and actin-rich protrusions
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2016'
...
---
_id: '1272'
abstract:
- lang: eng
text: We study different means to extend offsetting based on skeletal structures
beyond the well-known constant-radius and mitered offsets supported by Voronoi
diagrams and straight skeletons, for which the orthogonal distance of offset elements
to their respective input elements is constant and uniform over all input elements.
Our main contribution is a new geometric structure, called variable-radius Voronoi
diagram, which supports the computation of variable-radius offsets, i.e., offsets
whose distance to the input is allowed to vary along the input. We discuss properties
of this structure and sketch a prototype implementation that supports the computation
of variable-radius offsets based on this new variant of Voronoi diagrams.
acknowledgement: 'This work was supported by Austrian Science Fund (FWF): P25816-N15.'
author:
- first_name: Martin
full_name: Held, Martin
last_name: Held
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Peter
full_name: Palfrader, Peter
last_name: Palfrader
citation:
ama: Held M, Huber S, Palfrader P. Generalized offsetting of planar structures using
skeletons. Computer-Aided Design and Applications. 2016;13(5):712-721.
doi:10.1080/16864360.2016.1150718
apa: Held, M., Huber, S., & Palfrader, P. (2016). Generalized offsetting of
planar structures using skeletons. Computer-Aided Design and Applications.
Taylor and Francis. https://doi.org/10.1080/16864360.2016.1150718
chicago: Held, Martin, Stefan Huber, and Peter Palfrader. “Generalized Offsetting
of Planar Structures Using Skeletons.” Computer-Aided Design and Applications.
Taylor and Francis, 2016. https://doi.org/10.1080/16864360.2016.1150718.
ieee: M. Held, S. Huber, and P. Palfrader, “Generalized offsetting of planar structures
using skeletons,” Computer-Aided Design and Applications, vol. 13, no.
5. Taylor and Francis, pp. 712–721, 2016.
ista: Held M, Huber S, Palfrader P. 2016. Generalized offsetting of planar structures
using skeletons. Computer-Aided Design and Applications. 13(5), 712–721.
mla: Held, Martin, et al. “Generalized Offsetting of Planar Structures Using Skeletons.”
Computer-Aided Design and Applications, vol. 13, no. 5, Taylor and Francis,
2016, pp. 712–21, doi:10.1080/16864360.2016.1150718.
short: M. Held, S. Huber, P. Palfrader, Computer-Aided Design and Applications 13
(2016) 712–721.
date_created: 2018-12-11T11:51:04Z
date_published: 2016-09-02T00:00:00Z
date_updated: 2021-01-12T06:49:32Z
day: '02'
ddc:
- '004'
- '516'
department:
- _id: HeEd
doi: 10.1080/16864360.2016.1150718
file:
- access_level: open_access
checksum: c746f3a48edb62b588d92ea5d0fd2c0e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:20Z
date_updated: 2020-07-14T12:44:42Z
file_id: '5206'
file_name: IST-2016-694-v1+1_Generalized_offsetting_of_planar_structures_using_skeletons.pdf
file_size: 1678369
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '5'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 712 - 721
publication: Computer-Aided Design and Applications
publication_status: published
publisher: Taylor and Francis
publist_id: '6048'
pubrep_id: '694'
quality_controlled: '1'
scopus_import: 1
status: public
title: Generalized offsetting of planar structures using skeletons
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2016'
...
---
_id: '1273'
abstract:
- lang: eng
text: Lateral root primordia (LRP) originate from pericycle stem cells located deep
within parental root tissues. LRP emerge through overlying root tissues by inducing
auxin-dependent cell separation and hydraulic changes in adjacent cells. The auxin-inducible
auxin influx carrier LAX3 plays a key role concentrating this signal in cells
overlying LRP. Delimiting LAX3 expression to two adjacent cell files overlying
new LRP is crucial to ensure that auxin-regulated cell separation occurs solely
along their shared walls. Multiscale modeling has predicted that this highly focused
pattern of expression requires auxin to sequentially induce auxin efflux and influx
carriers PIN3 and LAX3, respectively. Consistent with model predictions, we report
that auxin-inducible LAX3 expression is regulated indirectly by AUXIN RESPONSE
FACTOR 7 (ARF7). Yeast one-hybrid screens revealed that the LAX3 promoter is bound
by the transcription factor LBD29, which is a direct target for regulation by
ARF7. Disrupting auxin-inducible LBD29 expression or expressing an LBD29-SRDX
transcriptional repressor phenocopied the lax3 mutant, resulting in delayed lateral
root emergence. We conclude that sequential LBD29 and LAX3 induction by auxin
is required to coordinate cell separation and organ emergence.
acknowledgement: "We acknowledge the support of glasshouse technicians at the University
of\r\nNottingham for help with plant growth and the Nottingham\r\nArabidopsis\r\nStock
Centre\r\n(NASC) for providing\r\nArabidopsis\r\nlines. This research was supported
by the Biotechnology and Biological Sciences Research Council (BBSRC) (to A.B. and
M.J.B.); the European Research Council (ERC) Advanced Grant SysArc (to B.S.) and
FUTUREROOTS (to M.J.B.); The Royal Society for University and Wolfson Research Fellowship
awards (to A.B. and M.J.B.); a Federation of European Biochemical Societies (FEBS)
Long-Term Fellowship (to B.P.); an Intra-European Fellowship for Career Development
under the 7th framework of the European Commission [IEF-2008-220506 to B.P.]; a
European Molecular Biology Organization (EMBO) Long-Term Fellowship (to B.P.); and
a European Reintegration Grant under the 7th framework of the European Commission
[ERG-2010-276662 to B.P.]; Interuniversity Attraction Poles Programme [initiated
by the Belgian Science Policy Office (Federaal Wetenschapsbeleid)] (to M.J.B.);
The Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan:
Grants-in-Aid for Scientific Research on Innovative Areas [25110330 to H.F.] and
a JSPS Research Fellowship for Young Scientists [12J02079 to T.G.]; funds for research
performed by S.M.B. and A.G. were provided by University of California, Davis startup
funds."
author:
- first_name: Silvana
full_name: Porco, Silvana
last_name: Porco
- first_name: Antoine
full_name: Larrieu, Antoine
last_name: Larrieu
- first_name: Yujuan
full_name: Du, Yujuan
last_name: Du
- first_name: Allison
full_name: Gaudinier, Allison
last_name: Gaudinier
- first_name: Tatsuaki
full_name: Goh, Tatsuaki
last_name: Goh
- first_name: Kamal
full_name: Swarup, Kamal
last_name: Swarup
- first_name: Ranjan
full_name: Swarup, Ranjan
last_name: Swarup
- first_name: Britta
full_name: Kuempers, Britta
last_name: Kuempers
- first_name: Anthony
full_name: Bishopp, Anthony
last_name: Bishopp
- first_name: Julien
full_name: Lavenus, Julien
last_name: Lavenus
- first_name: Ilda
full_name: Casimiro, Ilda
last_name: Casimiro
- first_name: Kristine
full_name: Hill, Kristine
last_name: Hill
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Hidehiro
full_name: Fukaki, Hidehiro
last_name: Fukaki
- first_name: Siobhan
full_name: Brady, Siobhan
last_name: Brady
- first_name: Ben
full_name: Scheres, Ben
last_name: Scheres
- first_name: Benjamin
full_name: Peéet, Benjamin
last_name: Peéet
- first_name: Malcolm
full_name: Bennett, Malcolm
last_name: Bennett
citation:
ama: Porco S, Larrieu A, Du Y, et al. Lateral root emergence in Arabidopsis is dependent
on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development.
2016;143(18):3340-3349. doi:10.1242/dev.136283
apa: Porco, S., Larrieu, A., Du, Y., Gaudinier, A., Goh, T., Swarup, K., … Bennett,
M. (2016). Lateral root emergence in Arabidopsis is dependent on transcription
factor LBD29 regulation of auxin influx carrier LAX3. Development. Company
of Biologists. https://doi.org/10.1242/dev.136283
chicago: Porco, Silvana, Antoine Larrieu, Yujuan Du, Allison Gaudinier, Tatsuaki
Goh, Kamal Swarup, Ranjan Swarup, et al. “Lateral Root Emergence in Arabidopsis
Is Dependent on Transcription Factor LBD29 Regulation of Auxin Influx Carrier
LAX3.” Development. Company of Biologists, 2016. https://doi.org/10.1242/dev.136283.
ieee: S. Porco et al., “Lateral root emergence in Arabidopsis is dependent
on transcription factor LBD29 regulation of auxin influx carrier LAX3,” Development,
vol. 143, no. 18. Company of Biologists, pp. 3340–3349, 2016.
ista: Porco S, Larrieu A, Du Y, Gaudinier A, Goh T, Swarup K, Swarup R, Kuempers
B, Bishopp A, Lavenus J, Casimiro I, Hill K, Benková E, Fukaki H, Brady S, Scheres
B, Peéet B, Bennett M. 2016. Lateral root emergence in Arabidopsis is dependent
on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development.
143(18), 3340–3349.
mla: Porco, Silvana, et al. “Lateral Root Emergence in Arabidopsis Is Dependent
on Transcription Factor LBD29 Regulation of Auxin Influx Carrier LAX3.” Development,
vol. 143, no. 18, Company of Biologists, 2016, pp. 3340–49, doi:10.1242/dev.136283.
short: S. Porco, A. Larrieu, Y. Du, A. Gaudinier, T. Goh, K. Swarup, R. Swarup,
B. Kuempers, A. Bishopp, J. Lavenus, I. Casimiro, K. Hill, E. Benková, H. Fukaki,
S. Brady, B. Scheres, B. Peéet, M. Bennett, Development 143 (2016) 3340–3349.
date_created: 2018-12-11T11:51:04Z
date_published: 2016-09-13T00:00:00Z
date_updated: 2021-01-12T06:49:32Z
day: '13'
department:
- _id: EvBe
doi: 10.1242/dev.136283
intvolume: ' 143'
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-01595056/
month: '09'
oa: 1
oa_version: Preprint
page: 3340 - 3349
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '6044'
quality_controlled: '1'
scopus_import: 1
status: public
title: Lateral root emergence in Arabidopsis is dependent on transcription factor
LBD29 regulation of auxin influx carrier LAX3
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 143
year: '2016'
...
---
_id: '1274'
abstract:
- lang: eng
text: Synchronized tissue polarization during regeneration or de novo vascular tissue
formation is a plant-specific example of intercellular communication and coordinated
development. According to the canalization hypothesis, the plant hormone auxin
serves as polarizing signal that mediates directional channel formation underlying
the spatio-temporal vasculature patterning. A necessary part of canalization is
a positive feedback between auxin signaling and polarity of the intercellular
auxin flow. The cellular and molecular mechanisms of this process are still poorly
understood, not the least, because of a lack of a suitable model system. We show
that the main genetic model plant, Arabidopsis (Arabidopsis thaliana) can be used
to study the canalization during vascular cambium regeneration and new vasculature
formation. We monitored localized auxin responses, directional auxin-transport
channels formation, and establishment of new vascular cambium polarity during
regenerative processes after stem wounding. The increased auxin response above
and around the wound preceded the formation of PIN1 auxin transporter-marked channels
from the primarily homogenous tissue and the transient, gradual changes in PIN1
localization preceded the polarity of newly formed vascular tissue. Thus, Arabidopsis
is a useful model for studies of coordinated tissue polarization and vasculature
formation after wounding allowing for genetic and mechanistic dissection of the
canalization hypothesis.
acknowledgement: We wish to thank Prof. Ewa U. Kurczyńska for initiation of this work
and valuable advices. We thank Martine De Cock for help in preparing the manuscript.
This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP),
the European Social Fund (CZ.1.07/2.3.00/20.0043), and the Czech Science Foundation
GAČR (GA13-40637 S) to J.F., (GA 13-39982S) to E.B. and E.M. and in part by the
European Regional Development Fund (project “CEITEC, Central European Institute
of Technology”, CZ.1.05/1.1.00/02.0068).
article_number: '33754'
article_processing_charge: No
author:
- first_name: Ewa
full_name: Mazur, Ewa
last_name: Mazur
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Mazur E, Benková E, Friml J. Vascular cambium regeneration and vessel formation
in wounded inflorescence stems of Arabidopsis. Scientific Reports. 2016;6.
doi:10.1038/srep33754
apa: Mazur, E., Benková, E., & Friml, J. (2016). Vascular cambium regeneration
and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific
Reports. Nature Publishing Group. https://doi.org/10.1038/srep33754
chicago: Mazur, Ewa, Eva Benková, and Jiří Friml. “Vascular Cambium Regeneration
and Vessel Formation in Wounded Inflorescence Stems of Arabidopsis.” Scientific
Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep33754.
ieee: E. Mazur, E. Benková, and J. Friml, “Vascular cambium regeneration and vessel
formation in wounded inflorescence stems of Arabidopsis,” Scientific Reports,
vol. 6. Nature Publishing Group, 2016.
ista: Mazur E, Benková E, Friml J. 2016. Vascular cambium regeneration and vessel
formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. 6,
33754.
mla: Mazur, Ewa, et al. “Vascular Cambium Regeneration and Vessel Formation in Wounded
Inflorescence Stems of Arabidopsis.” Scientific Reports, vol. 6, 33754,
Nature Publishing Group, 2016, doi:10.1038/srep33754.
short: E. Mazur, E. Benková, J. Friml, Scientific Reports 6 (2016).
date_created: 2018-12-11T11:51:05Z
date_published: 2016-09-21T00:00:00Z
date_updated: 2025-05-07T11:12:28Z
day: '21'
ddc:
- '581'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1038/srep33754
external_id:
pmid:
- '27649687'
file:
- access_level: open_access
checksum: ee371fbc9124ad93157a95829264e4fe
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:25Z
date_updated: 2020-07-14T12:44:42Z
file_id: '5008'
file_name: IST-2016-692-v1+1_srep33754.pdf
file_size: 2895147
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6042'
pubrep_id: '692'
quality_controlled: '1'
related_material:
record:
- id: '545'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Vascular cambium regeneration and vessel formation in wounded inflorescence
stems of Arabidopsis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1275'
article_number: '139802'
author:
- first_name: Andrew
full_name: Callan Jones, Andrew
last_name: Callan Jones
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- 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
- first_name: Raphaël
full_name: Voituriez, Raphaël
last_name: Voituriez
citation:
ama: Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. Callan-Jones
et al. Reply. Physical Review Letters. 2016;117(13). doi:10.1103/PhysRevLett.117.139802
apa: Callan Jones, A., Ruprecht, V., Wieser, S., Heisenberg, C.-P. J., & Voituriez,
R. (2016). Callan-Jones et al. Reply. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.117.139802
chicago: Callan Jones, Andrew, Verena Ruprecht, Stefan Wieser, Carl-Philipp J Heisenberg,
and Raphaël Voituriez. “Callan-Jones et Al. Reply.” Physical Review Letters.
American Physical Society, 2016. https://doi.org/10.1103/PhysRevLett.117.139802.
ieee: A. Callan Jones, V. Ruprecht, S. Wieser, C.-P. J. Heisenberg, and R. Voituriez,
“Callan-Jones et al. Reply,” Physical Review Letters, vol. 117, no. 13.
American Physical Society, 2016.
ista: Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. 2016.
Callan-Jones et al. Reply. Physical Review Letters. 117(13), 139802.
mla: Callan Jones, Andrew, et al. “Callan-Jones et Al. Reply.” Physical Review
Letters, vol. 117, no. 13, 139802, American Physical Society, 2016, doi:10.1103/PhysRevLett.117.139802.
short: A. Callan Jones, V. Ruprecht, S. Wieser, C.-P.J. Heisenberg, R. Voituriez,
Physical Review Letters 117 (2016).
date_created: 2018-12-11T11:51:05Z
date_published: 2016-09-22T00:00:00Z
date_updated: 2021-01-12T06:49:33Z
day: '22'
department:
- _id: CaHe
doi: 10.1103/PhysRevLett.117.139802
intvolume: ' 117'
issue: '13'
language:
- iso: eng
month: '09'
oa_version: None
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6041'
quality_controlled: '1'
scopus_import: 1
status: public
title: Callan-Jones et al. Reply
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2016'
...