---
_id: '1242'
abstract:
- lang: eng
text: A crucial step in the regulation of gene expression is binding of transcription
factor (TF) proteins to regulatory sites along the DNA. But transcription factors
act at nanomolar concentrations, and noise due to random arrival of these molecules
at their binding sites can severely limit the precision of regulation. Recent
work on the optimization of information flow through regulatory networks indicates
that the lower end of the dynamic range of concentrations is simply inaccessible,
overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain
proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest
a scheme in which transcription factors also act as indirect translational regulators,
binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule
acts as an independent sensor of the input concentration, and averaging over these
multiple sensors reduces the noise. We analyze information flow through this scheme
and identify conditions under which it outperforms direct transcriptional regulation.
Our results suggest that the dual role of homeodomain proteins is not just a historical
accident, but a solution to a crucial physics problem in the regulation of gene
expression.
acknowledgement: "We thank T. Gregor, A. Prochaintz, and others for\r\nhelpful discussions.
This work was supported in part by\r\nGrants No. PHY-1305525 and No. CCF-0939370
from the\r\nUS National Science Foundation and by the W.M. Keck\r\nFoundation. A.M.W.
acknowledges the support by European\r\nResearch Council (ERC) Grant No. MCCIG PCIG10–GA-\r\n2011–303561.
G.T. and T.R.S. were supported by Austrian\r\nScience Fund (FWF) Grant No. P28844S."
article_number: '022404'
author:
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Aleksandra
full_name: Walczak, Aleksandra
last_name: Walczak
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of
transcription factor action by translational regulation. Physical Review E
Statistical Nonlinear and Soft Matter Physics. 2016;93(2). doi:10.1103/PhysRevE.93.022404
apa: Sokolowski, T. R., Walczak, A., Bialek, W., & Tkačik, G. (2016). Extending
the dynamic range of transcription factor action by translational regulation.
Physical Review E Statistical Nonlinear and Soft Matter Physics. American
Institute of Physics. https://doi.org/10.1103/PhysRevE.93.022404
chicago: Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik.
“Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.”
Physical Review E Statistical Nonlinear and Soft Matter Physics. American
Institute of Physics, 2016. https://doi.org/10.1103/PhysRevE.93.022404.
ieee: T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic
range of transcription factor action by translational regulation,” Physical
Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2. American
Institute of Physics, 2016.
ista: Sokolowski TR, Walczak A, Bialek W, Tkačik G. 2016. Extending the dynamic
range of transcription factor action by translational regulation. Physical Review
E Statistical Nonlinear and Soft Matter Physics. 93(2), 022404.
mla: Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription
Factor Action by Translational Regulation.” Physical Review E Statistical Nonlinear
and Soft Matter Physics, vol. 93, no. 2, 022404, American Institute of Physics,
2016, doi:10.1103/PhysRevE.93.022404.
short: T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E Statistical
Nonlinear and Soft Matter Physics 93 (2016).
date_created: 2018-12-11T11:50:54Z
date_published: 2016-02-04T00:00:00Z
date_updated: 2021-01-12T06:49:20Z
day: '04'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.93.022404
intvolume: ' 93'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1507.02562
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '6088'
quality_controlled: '1'
scopus_import: 1
status: public
title: Extending the dynamic range of transcription factor action by translational
regulation
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2016'
...
---
_id: '1243'
abstract:
- lang: eng
text: Restriction-modification (RM) systems represent a minimal and ubiquitous biological
system of self/non-self discrimination in prokaryotes [1], which protects hosts
from exogenous DNA [2]. The mechanism is based on the balance between methyltransferase
(M) and cognate restriction endonuclease (R). M tags endogenous DNA as self by
methylating short specific DNA sequences called restriction sites, whereas R recognizes
unmethylated restriction sites as non-self and introduces a double-stranded DNA
break [3]. Restriction sites are significantly underrepresented in prokaryotic
genomes [4-7], suggesting that the discrimination mechanism is imperfect and occasionally
leads to autoimmunity due to self-DNA cleavage (self-restriction) [8]. Furthermore,
RM systems can promote DNA recombination [9] and contribute to genetic variation
in microbial populations, thus facilitating adaptive evolution [10]. However,
cleavage of self-DNA by RM systems as elements shaping prokaryotic genomes has
not been directly detected, and its cause, frequency, and outcome are unknown.
We quantify self-restriction caused by two RM systems of Escherichia coli and
find that, in agreement with levels of restriction site avoidance, EcoRI, but
not EcoRV, cleaves self-DNA at a measurable rate. Self-restriction is a stochastic
process, which temporarily induces the SOS response, and is followed by DNA repair,
maintaining cell viability. We find that RM systems with higher restriction efficiency
against bacteriophage infections exhibit a higher rate of self-restriction, and
that this rate can be further increased by stochastic imbalance between R and
M. Our results identify molecular noise in RM systems as a factor shaping prokaryotic
genomes.
acknowledgement: This work was funded by an HFSP Young Investigators’ grant. M.P.
is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute
of Science and Technology Austria. R.O. and Y.W. were supported by the Platform
for Dynamic Approaches to Living System from MEXT, Japan. We wish to thank I. Kobayashi
for providing us with the EcoRI and EcoRV plasmids, and A. Campbell for providing
us with the λ vir phage. We thank D. Siekhaus and C. Uhler and members of the C.C.G.
and J.P. Bollback laboratories for in-depth discussions. We thank B. Stern for comments
on an earlier version of the manuscript. We especially thank B.R. Levin for advice
and comments, and the anonymous reviewers for significantly improving the manuscript.
author:
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Long
full_name: Qian, Long
last_name: Qian
- first_name: Reiko
full_name: Okura, Reiko
last_name: Okura
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Yuichi
full_name: Wakamoto, Yuichi
last_name: Wakamoto
- first_name: Edo
full_name: Kussell, Edo
last_name: Kussell
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Pleska M, Qian L, Okura R, et al. Bacterial autoimmunity due to a restriction-modification
system. Current Biology. 2016;26(3):404-409. doi:10.1016/j.cub.2015.12.041
apa: Pleska, M., Qian, L., Okura, R., Bergmiller, T., Wakamoto, Y., Kussell, E.,
& Guet, C. C. (2016). Bacterial autoimmunity due to a restriction-modification
system. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2015.12.041
chicago: Pleska, Maros, Long Qian, Reiko Okura, Tobias Bergmiller, Yuichi Wakamoto,
Edo Kussell, and Calin C Guet. “Bacterial Autoimmunity Due to a Restriction-Modification
System.” Current Biology. Cell Press, 2016. https://doi.org/10.1016/j.cub.2015.12.041.
ieee: M. Pleska et al., “Bacterial autoimmunity due to a restriction-modification
system,” Current Biology, vol. 26, no. 3. Cell Press, pp. 404–409, 2016.
ista: Pleska M, Qian L, Okura R, Bergmiller T, Wakamoto Y, Kussell E, Guet CC. 2016.
Bacterial autoimmunity due to a restriction-modification system. Current Biology.
26(3), 404–409.
mla: Pleska, Maros, et al. “Bacterial Autoimmunity Due to a Restriction-Modification
System.” Current Biology, vol. 26, no. 3, Cell Press, 2016, pp. 404–09,
doi:10.1016/j.cub.2015.12.041.
short: M. Pleska, L. Qian, R. Okura, T. Bergmiller, Y. Wakamoto, E. Kussell, C.C.
Guet, Current Biology 26 (2016) 404–409.
date_created: 2018-12-11T11:50:54Z
date_published: 2016-02-08T00:00:00Z
date_updated: 2023-09-07T11:59:32Z
day: '08'
department:
- _id: CaGu
doi: 10.1016/j.cub.2015.12.041
intvolume: ' 26'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: None
page: 404 - 409
project:
- _id: 251D65D8-B435-11E9-9278-68D0E5697425
grant_number: '24210'
name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems
at the Single-Cell Level (DOC Fellowship)
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '6087'
quality_controlled: '1'
related_material:
record:
- id: '202'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Bacterial autoimmunity due to a restriction-modification system
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2016'
...
---
_id: '1244'
abstract:
- lang: eng
text: Cell polarity refers to a functional spatial organization of proteins that
is crucial for the control of essential cellular processes such as growth and
division. To establish polarity, cells rely on elaborate regulation networks that
control the distribution of proteins at the cell membrane. In fission yeast cells,
a microtubule-dependent network has been identified that polarizes the distribution
of signaling proteins that restricts growth to cell ends and targets the cytokinetic
machinery to the middle of the cell. Although many molecular components have been
shown to play a role in this network, it remains unknown which molecular functionalities
are minimally required to establish a polarized protein distribution in this system.
Here we show that a membrane-binding protein fragment, which distributes homogeneously
in wild-type fission yeast cells, can be made to concentrate at cell ends by attaching
it to a cytoplasmic microtubule end-binding protein. This concentration results
in a polarized pattern of chimera proteins with a spatial extension that is very
reminiscent of natural polarity patterns in fission yeast. However, chimera levels
fluctuate in response to microtubule dynamics, and disruption of microtubules
leads to disappearance of the pattern. Numerical simulations confirm that the
combined functionality of membrane anchoring and microtubule tip affinity is in
principle sufficient to create polarized patterns. Our chimera protein may thus
represent a simple molecular functionality that is able to polarize the membrane,
onto which additional layers of molecular complexity may be built to provide the
temporal robustness that is typical of natural polarity patterns.
acknowledgement: "We thank Sophie Martin, Ken Sawin, Stephen Huisman,\r\nand Damian
Brunner for strains; Julianne\r\nTeapal, Marcel Janson, Sergio Rincon,\r\nand Phong
Tran for technical assistance; Andrew Mugler and Bela Mulder for\r\ndiscussions;
and Sander Tans, Phong Tran,\r\nand Anne Paoletti for critical reading\r\nof the
manuscript. This work is part of the research program of the\r\n“\r\nStichting\r\nvoor
Fundamenteel Onderzoek de Materie,\r\n”\r\nwhich is financially supported by\r\nthe\r\n“\r\nNederlandse
organisatie voor Wete\r\nnschappelijk Onderzoek (NWO).\r\n”"
author:
- first_name: Pierre
full_name: Recouvreux, Pierre
last_name: Recouvreux
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Aristea
full_name: Grammoustianou, Aristea
last_name: Grammoustianou
- first_name: Pieter
full_name: Tenwolde, Pieter
last_name: Tenwolde
- first_name: Marileen
full_name: Dogterom, Marileen
last_name: Dogterom
citation:
ama: Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. Chimera
proteins with affinity for membranes and microtubule tips polarize in the membrane
of fission yeast cells. PNAS. 2016;113(7):1811-1816. doi:10.1073/pnas.1419248113
apa: Recouvreux, P., Sokolowski, T. R., Grammoustianou, A., Tenwolde, P., &
Dogterom, M. (2016). Chimera proteins with affinity for membranes and microtubule
tips polarize in the membrane of fission yeast cells. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.1419248113
chicago: Recouvreux, Pierre, Thomas R Sokolowski, Aristea Grammoustianou, Pieter
Tenwolde, and Marileen Dogterom. “Chimera Proteins with Affinity for Membranes
and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” PNAS.
National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1419248113.
ieee: P. Recouvreux, T. R. Sokolowski, A. Grammoustianou, P. Tenwolde, and M. Dogterom,
“Chimera proteins with affinity for membranes and microtubule tips polarize in
the membrane of fission yeast cells,” PNAS, vol. 113, no. 7. National Academy
of Sciences, pp. 1811–1816, 2016.
ista: Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. 2016.
Chimera proteins with affinity for membranes and microtubule tips polarize in
the membrane of fission yeast cells. PNAS. 113(7), 1811–1816.
mla: Recouvreux, Pierre, et al. “Chimera Proteins with Affinity for Membranes and
Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” PNAS,
vol. 113, no. 7, National Academy of Sciences, 2016, pp. 1811–16, doi:10.1073/pnas.1419248113.
short: P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom,
PNAS 113 (2016) 1811–1816.
date_created: 2018-12-11T11:50:55Z
date_published: 2016-02-16T00:00:00Z
date_updated: 2021-01-12T06:49:21Z
day: '16'
department:
- _id: GaTk
doi: 10.1073/pnas.1419248113
intvolume: ' 113'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763754/
month: '02'
oa: 1
oa_version: Submitted Version
page: 1811 - 1816
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6085'
quality_controlled: '1'
scopus_import: 1
status: public
title: Chimera proteins with affinity for membranes and microtubule tips polarize
in the membrane of fission yeast cells
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '1245'
abstract:
- lang: eng
text: 'To facilitate collaboration in massive online classrooms, instructors must
make many decisions. For instance, the following parameters need to be decided
when designing a peer-feedback system where students review each others'' essays:
the number of students each student must provide feedback to, an algorithm to
map feedback providers to receivers, constraints that ensure students do not become
free-riders (receiving feedback but not providing it), the best times to receive
feedback to improve learning etc. While instructors can answer these questions
by running experiments or invoking past experience, game-theoretic models with
data from online learning platforms can identify better initial designs for further
improvements. As an example, we explore the design space of a peer feedback system
by modeling it using game theory. Our simulations show that incentivizing students
to provide feedback requires the value obtained from receiving a feedback to exceed
the cost of providing it by a large factor (greater than 7). Furthermore, hiding
feedback from low-effort students incentivizes them to provide more feedback.'
acknowledgement: 'ERC Start Grant Graph Games 279307 supported this research. '
author:
- first_name: Vineet
full_name: Pandey, Vineet
last_name: Pandey
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Pandey V, Chatterjee K. Game-theoretic models identify useful principles for
peer collaboration in online learning platforms. In: Proceedings of the ACM
Conference on Computer Supported Cooperative Work. Vol 26. ACM; 2016:365-368.
doi:10.1145/2818052.2869122'
apa: 'Pandey, V., & Chatterjee, K. (2016). Game-theoretic models identify useful
principles for peer collaboration in online learning platforms. In Proceedings
of the ACM Conference on Computer Supported Cooperative Work (Vol. 26, pp.
365–368). San Francisco, CA, USA: ACM. https://doi.org/10.1145/2818052.2869122'
chicago: Pandey, Vineet, and Krishnendu Chatterjee. “Game-Theoretic Models Identify
Useful Principles for Peer Collaboration in Online Learning Platforms.” In Proceedings
of the ACM Conference on Computer Supported Cooperative Work, 26:365–68. ACM,
2016. https://doi.org/10.1145/2818052.2869122.
ieee: V. Pandey and K. Chatterjee, “Game-theoretic models identify useful principles
for peer collaboration in online learning platforms,” in Proceedings of the
ACM Conference on Computer Supported Cooperative Work, San Francisco, CA,
USA, 2016, vol. 26, no. Februar-2016, pp. 365–368.
ista: 'Pandey V, Chatterjee K. 2016. Game-theoretic models identify useful principles
for peer collaboration in online learning platforms. Proceedings of the ACM Conference
on Computer Supported Cooperative Work. CSCW: Computer Supported Cooperative Work
and Social Computing vol. 26, 365–368.'
mla: Pandey, Vineet, and Krishnendu Chatterjee. “Game-Theoretic Models Identify
Useful Principles for Peer Collaboration in Online Learning Platforms.” Proceedings
of the ACM Conference on Computer Supported Cooperative Work, vol. 26, no.
Februar-2016, ACM, 2016, pp. 365–68, doi:10.1145/2818052.2869122.
short: V. Pandey, K. Chatterjee, in:, Proceedings of the ACM Conference on Computer
Supported Cooperative Work, ACM, 2016, pp. 365–368.
conference:
end_date: 2016-03-02
location: San Francisco, CA, USA
name: 'CSCW: Computer Supported Cooperative Work and Social Computing'
start_date: 2016-02-26
date_created: 2018-12-11T11:50:55Z
date_published: 2016-02-27T00:00:00Z
date_updated: 2021-01-12T06:49:22Z
day: '27'
department:
- _id: KrCh
doi: 10.1145/2818052.2869122
ec_funded: 1
intvolume: ' 26'
issue: Februar-2016
language:
- iso: eng
month: '02'
oa_version: None
page: 365 - 368
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the ACM Conference on Computer Supported Cooperative Work
publication_status: published
publisher: ACM
publist_id: '6083'
quality_controlled: '1'
scopus_import: 1
status: public
title: Game-theoretic models identify useful principles for peer collaboration in
online learning platforms
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2016'
...
---
_id: '1246'
abstract:
- lang: eng
text: Near-field imaging is a powerful tool to investigate the complex structure
of light at the nanoscale. Recent advances in near-field imaging have indicated
the possibility for the complete reconstruction of both electric and magnetic
components of the evanescent field. Here we study the electro-magnetic field structure
of surface plasmon polariton waves propagating along subwavelength gold nanowires
by performing phase- and polarization-resolved near-field microscopy in collection
mode. By applying the optical reciprocity theorem, we describe the signal collected
by the probe as an overlap integral of the nanowire's evanescent field and the
probe's response function. As a result, we find that the probe's sensitivity to
the magnetic field is approximately equal to its sensitivity to the electric field.
Through rigorous modeling of the nanowire mode as well as the aperture probe response
function, we obtain a good agreement between experimentally measured signals and
a numerical model. Our findings provide a better understanding of aperture-based
near-field imaging of the nanoscopic plasmonic and photonic structures and are
helpful for the interpretation of future near-field experiments.
acknowledgement: 'This work is supported part of the research program of the Netherlands
Foundation for Fundamental Research on Matter (FOM) and the Netherlands Organization
for Scientific Research (NWO), and part of this work has been funded by the project
‘SPANGL4Q’, which acknowledges the financial support of the Future and Emerging
Technologies (FET) program within the Seventh Framework Programme for Research of
the European Commission, under FETOpen grant number: FP7-284743. L.K. acknowledges
funding from ERC Advanced, Investigator Grant (no. 240438-CONSTANS).'
article_number: '22665'
author:
- first_name: Irina
full_name: Kabakova, Irina
last_name: Kabakova
- first_name: Anouk
full_name: De Hoogh, Anouk
last_name: De Hoogh
- first_name: Ruben
full_name: Van Der Wel, Ruben
last_name: Van Der Wel
- first_name: Matthias
full_name: Wulf, Matthias
id: 45598606-F248-11E8-B48F-1D18A9856A87
last_name: Wulf
orcid: 0000-0001-6613-1378
- first_name: Boris
full_name: Le Feber, Boris
last_name: Le Feber
- first_name: Laurens
full_name: Kuipers, Laurens
last_name: Kuipers
citation:
ama: Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. Imaging
of electric and magnetic fields near plasmonic nanowires. Scientific Reports.
2016;6. doi:10.1038/srep22665
apa: Kabakova, I., De Hoogh, A., Van Der Wel, R., Wulf, M., Le Feber, B., &
Kuipers, L. (2016). Imaging of electric and magnetic fields near plasmonic nanowires.
Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep22665
chicago: Kabakova, Irina, Anouk De Hoogh, Ruben Van Der Wel, Matthias Wulf, Boris
Le Feber, and Laurens Kuipers. “Imaging of Electric and Magnetic Fields near Plasmonic
Nanowires.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep22665.
ieee: I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, and L. Kuipers,
“Imaging of electric and magnetic fields near plasmonic nanowires,” Scientific
Reports, vol. 6. Nature Publishing Group, 2016.
ista: Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. 2016.
Imaging of electric and magnetic fields near plasmonic nanowires. Scientific Reports.
6, 22665.
mla: Kabakova, Irina, et al. “Imaging of Electric and Magnetic Fields near Plasmonic
Nanowires.” Scientific Reports, vol. 6, 22665, Nature Publishing Group,
2016, doi:10.1038/srep22665.
short: I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, L. Kuipers,
Scientific Reports 6 (2016).
date_created: 2018-12-11T11:50:55Z
date_published: 2016-03-07T00:00:00Z
date_updated: 2021-01-12T06:49:22Z
day: '07'
ddc:
- '539'
department:
- _id: JoFi
doi: 10.1038/srep22665
file:
- access_level: open_access
checksum: ca76236cb1aae22cb90c65313e2c5e98
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:11Z
date_updated: 2020-07-14T12:44:41Z
file_id: '5061'
file_name: IST-2016-707-v1+1_srep22665.pdf
file_size: 1425165
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6082'
pubrep_id: '707'
quality_controlled: '1'
scopus_import: 1
status: public
title: Imaging of electric and magnetic fields near plasmonic nanowires
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: 6
year: '2016'
...
---
_id: '1247'
abstract:
- lang: eng
text: The shaping of organs in plants depends on the intercellular flow of the phytohormone
auxin, of which the directional signaling is determined by the polar subcellular
localization of PIN-FORMED (PIN) auxin transport proteins. Phosphorylation dynamics
of PIN proteins are affected by the protein phosphatase 2A (PP2A) and the PINOID
kinase, which act antagonistically to mediate their apical-basal polar delivery.
Here, we identified the ROTUNDA3 (RON3) protein as a regulator of the PP2A phosphatase
activity in Arabidopsis thaliana. The RON3 gene was map-based cloned starting
from the ron3-1 leaf mutant and found to be a unique, plant-specific gene coding
for a protein with high and dispersed proline content. The ron3-1 and ron3-2 mutant
phenotypes [i.e., reduced apical dominance, primary root length, lateral root
emergence, and growth; increased ectopic stages II, IV, and V lateral root primordia;
decreased auxin maxima in indole-3-acetic acid (IAA)-treated root apical meristems;
hypergravitropic root growth and response; increased IAA levels in shoot apices;
and reduced auxin accumulation in root meristems] support a role for RON3 in auxin
biology. The affinity-purified PP2A complex with RON3 as bait suggested that RON3
might act in PIN transporter trafficking. Indeed, pharmacological interference
with vesicle trafficking processes revealed that single ron3-2 and double ron3-2
rcn1 mutants have altered PIN polarity and endocytosis in specific cells. Our
data indicate that RON3 contributes to auxin-mediated development by playing a
role in PIN recycling and polarity establishment through regulation of the PP2A
complex activity.
acknowledgement: "This work was supported by the Ghent University Special Research
Fund (M.K.), the European Research Council (Project ERC-2011-StG-20101109-PSDP)
(to J.F.), and the Körber European Science Foun-\r\ndation (J.F.). S.D.G. is indebted
to the Agency for Science and Technology for\r\na predoctoral fellowship."
author:
- first_name: Michael
full_name: Karampelias, Michael
last_name: Karampelias
- first_name: Pia
full_name: Neyt, Pia
last_name: Neyt
- first_name: Steven
full_name: De Groeve, Steven
last_name: De Groeve
- first_name: Stijn
full_name: Aesaert, Stijn
last_name: Aesaert
- first_name: Griet
full_name: Coussens, Griet
last_name: Coussens
- first_name: Jakub
full_name: Rolčík, Jakub
last_name: Rolčík
- first_name: Leonardo
full_name: Bruno, Leonardo
last_name: Bruno
- first_name: Nancy
full_name: De Winne, Nancy
last_name: De Winne
- first_name: Annemie
full_name: Van Minnebruggen, Annemie
last_name: Van Minnebruggen
- first_name: Marc
full_name: Van Montagu, Marc
last_name: Van Montagu
- first_name: Maria
full_name: Ponce, Maria
last_name: Ponce
- first_name: José
full_name: Micol, José
last_name: Micol
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Geert
full_name: De Jaeger, Geert
last_name: De Jaeger
- first_name: Mieke
full_name: Van Lijsebettens, Mieke
last_name: Van Lijsebettens
citation:
ama: Karampelias M, Neyt P, De Groeve S, et al. ROTUNDA3 function in plant development
by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS.
2016;113(10):2768-2773. doi:10.1073/pnas.1501343112
apa: Karampelias, M., Neyt, P., De Groeve, S., Aesaert, S., Coussens, G., Rolčík,
J., … Van Lijsebettens, M. (2016). ROTUNDA3 function in plant development by phosphatase
2A-mediated regulation of auxin transporter recycling. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.1501343112
chicago: Karampelias, Michael, Pia Neyt, Steven De Groeve, Stijn Aesaert, Griet
Coussens, Jakub Rolčík, Leonardo Bruno, et al. “ROTUNDA3 Function in Plant Development
by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” PNAS.
National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1501343112.
ieee: M. Karampelias et al., “ROTUNDA3 function in plant development by phosphatase
2A-mediated regulation of auxin transporter recycling,” PNAS, vol. 113,
no. 10. National Academy of Sciences, pp. 2768–2773, 2016.
ista: Karampelias M, Neyt P, De Groeve S, Aesaert S, Coussens G, Rolčík J, Bruno
L, De Winne N, Van Minnebruggen A, Van Montagu M, Ponce M, Micol J, Friml J, De
Jaeger G, Van Lijsebettens M. 2016. ROTUNDA3 function in plant development by
phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. 113(10),
2768–2773.
mla: Karampelias, Michael, et al. “ROTUNDA3 Function in Plant Development by Phosphatase
2A-Mediated Regulation of Auxin Transporter Recycling.” PNAS, vol. 113,
no. 10, National Academy of Sciences, 2016, pp. 2768–73, doi:10.1073/pnas.1501343112.
short: M. Karampelias, P. Neyt, S. De Groeve, S. Aesaert, G. Coussens, J. Rolčík,
L. Bruno, N. De Winne, A. Van Minnebruggen, M. Van Montagu, M. Ponce, J. Micol,
J. Friml, G. De Jaeger, M. Van Lijsebettens, PNAS 113 (2016) 2768–2773.
date_created: 2018-12-11T11:50:56Z
date_published: 2016-03-08T00:00:00Z
date_updated: 2021-01-12T06:49:22Z
day: '08'
department:
- _id: JiFr
doi: 10.1073/pnas.1501343112
ec_funded: 1
intvolume: ' 113'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791031/
month: '03'
oa: 1
oa_version: Submitted Version
page: 2768 - 2773
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6081'
quality_controlled: '1'
scopus_import: 1
status: public
title: ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation
of auxin transporter recycling
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '1248'
abstract:
- lang: eng
text: Life depends as much on the flow of information as on the flow of energy.
Here we review the many efforts to make this intuition precise. Starting with
the building blocks of information theory, we explore examples where it has been
possible to measure, directly, the flow of information in biological networks,
or more generally where information-theoretic ideas have been used to guide the
analysis of experiments. Systems of interest range from single molecules (the
sequence diversity in families of proteins) to groups of organisms (the distribution
of velocities in flocks of birds), and all scales in between. Many of these analyses
are motivated by the idea that biological systems may have evolved to optimize
the gathering and representation of information, and we review the experimental
evidence for this optimization, again across a wide range of scales.
acknowledgement: "Our work was supported in part by the US\r\nNational Science Foundation
(PHY–1305525 and CCF–\r\n0939370), by the Austrian Science Foundation (FWF\r\nP25651),
by the Human Frontiers Science Program, and\r\nby the Simons and Swartz Foundations."
author:
- 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
citation:
ama: Tkačik G, Bialek W. Information processing in living systems. Annual Review
of Condensed Matter Physics. 2016;7:89-117. doi:10.1146/annurev-conmatphys-031214-014803
apa: Tkačik, G., & Bialek, W. (2016). Information processing in living systems.
Annual Review of Condensed Matter Physics. Annual Reviews. https://doi.org/10.1146/annurev-conmatphys-031214-014803
chicago: Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.”
Annual Review of Condensed Matter Physics. Annual Reviews, 2016. https://doi.org/10.1146/annurev-conmatphys-031214-014803.
ieee: G. Tkačik and W. Bialek, “Information processing in living systems,” Annual
Review of Condensed Matter Physics, vol. 7. Annual Reviews, pp. 89–117, 2016.
ista: Tkačik G, Bialek W. 2016. Information processing in living systems. Annual
Review of Condensed Matter Physics. 7, 89–117.
mla: Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.”
Annual Review of Condensed Matter Physics, vol. 7, Annual Reviews, 2016,
pp. 89–117, doi:10.1146/annurev-conmatphys-031214-014803.
short: G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016)
89–117.
date_created: 2018-12-11T11:50:56Z
date_published: 2016-03-10T00:00:00Z
date_updated: 2021-01-12T06:49:23Z
day: '10'
department:
- _id: GaTk
doi: 10.1146/annurev-conmatphys-031214-014803
intvolume: ' 7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1412.8752
month: '03'
oa: 1
oa_version: Preprint
page: 89 - 117
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: Annual Review of Condensed Matter Physics
publication_status: published
publisher: Annual Reviews
publist_id: '6080'
quality_controlled: '1'
scopus_import: 1
status: public
title: Information processing in living systems
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2016'
...
---
_id: '1249'
abstract:
- lang: eng
text: 'Actin and myosin assemble into a thin layer of a highly dynamic network underneath
the membrane of eukaryotic cells. This network generates the forces that drive
cell- and tissue-scale morphogenetic processes. The effective material properties
of this active network determine large-scale deformations and other morphogenetic
events. For example, the characteristic time of stress relaxation (the Maxwell
time τM) in the actomyosin sets the timescale of large-scale deformation of the
cortex. Similarly, the characteristic length of stress propagation (the hydrodynamic
length λ) sets the length scale of slow deformations, and a large hydrodynamic
length is a prerequisite for long-ranged cortical flows. Here we introduce a method
to determine physical parameters of the actomyosin cortical layer in vivo directly
from laser ablation experiments. For this we investigate the cortical response
to laser ablation in the one-cell-stage Caenorhabditis elegans embryo and in the
gastrulating zebrafish embryo. These responses can be interpreted using a coarse-grained
physical description of the cortex in terms of a two-dimensional thin film of
an active viscoelastic gel. To determine the Maxwell time τM, the hydrodynamic
length λ, the ratio of active stress ζΔμ, and per-area friction γ, we evaluated
the response to laser ablation in two different ways: by quantifying flow and
density fields as a function of space and time, and by determining the time evolution
of the shape of the ablated region. Importantly, both methods provide best-fit
physical parameters that are in close agreement with each other and that are similar
to previous estimates in the two systems. Our method provides an accurate and
robust means for measuring physical parameters of the actomyosin cortical layer.
It can be useful for investigations of actomyosin mechanics at the cellular-scale,
but also for providing insights into the active mechanics processes that govern
tissue-scale morphogenesis.'
acknowledgement: S.W.G. acknowledges support by grant no. 281903 from the European
Research Council and by grant No. GR-7271/2-1 from the Deutsche Forschungsgemeinschaft.
S.W.G. and C.-P.H. acknowledge support through a grant from the Fonds zur Förderung
der Wissenschaftlichen Forschung and the Deutsche Forschungsgemeinschaft (No. I930-B20).
We are grateful to Daniel Dickinson for providing the LP133 C. elegans strain. We
thank G. Salbreux, V. K. Krishnamurthy, and J. S. Bois for fruitful discussions.
author:
- first_name: Arnab
full_name: Saha, Arnab
last_name: Saha
- first_name: Masatoshi
full_name: Nishikawa, Masatoshi
last_name: Nishikawa
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- 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: Frank
full_name: Julicher, Frank
last_name: Julicher
- first_name: Stephan
full_name: Grill, Stephan
last_name: Grill
citation:
ama: Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. Determining
physical properties of the cell cortex. Biophysical Journal. 2016;110(6):1421-1429.
doi:10.1016/j.bpj.2016.02.013
apa: Saha, A., Nishikawa, M., Behrndt, M., Heisenberg, C.-P. J., Julicher, F., &
Grill, S. (2016). Determining physical properties of the cell cortex. Biophysical
Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2016.02.013
chicago: Saha, Arnab, Masatoshi Nishikawa, Martin Behrndt, Carl-Philipp J Heisenberg,
Frank Julicher, and Stephan Grill. “Determining Physical Properties of the Cell
Cortex.” Biophysical Journal. Biophysical Society, 2016. https://doi.org/10.1016/j.bpj.2016.02.013.
ieee: A. Saha, M. Nishikawa, M. Behrndt, C.-P. J. Heisenberg, F. Julicher, and S.
Grill, “Determining physical properties of the cell cortex,” Biophysical Journal,
vol. 110, no. 6. Biophysical Society, pp. 1421–1429, 2016.
ista: Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. 2016.
Determining physical properties of the cell cortex. Biophysical Journal. 110(6),
1421–1429.
mla: Saha, Arnab, et al. “Determining Physical Properties of the Cell Cortex.” Biophysical
Journal, vol. 110, no. 6, Biophysical Society, 2016, pp. 1421–29, doi:10.1016/j.bpj.2016.02.013.
short: A. Saha, M. Nishikawa, M. Behrndt, C.-P.J. Heisenberg, F. Julicher, S. Grill,
Biophysical Journal 110 (2016) 1421–1429.
date_created: 2018-12-11T11:50:56Z
date_published: 2016-03-29T00:00:00Z
date_updated: 2021-01-12T06:49:23Z
day: '29'
ddc:
- '572'
- '576'
department:
- _id: CaHe
doi: 10.1016/j.bpj.2016.02.013
file:
- access_level: open_access
checksum: c408cf2e25a25c8d711cffea524bda55
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:54Z
date_updated: 2020-07-14T12:44:41Z
file_id: '4845'
file_name: IST-2016-706-v1+1_1-s2.0-S0006349516001582-main.pdf
file_size: 1965645
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: ' 110'
issue: '6'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 1421 - 1429
project:
- _id: 252ABD0A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 930-B20
name: Control of Epithelial Cell Layer Spreading in Zebrafish
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '6079'
pubrep_id: '706'
quality_controlled: '1'
scopus_import: 1
status: public
title: Determining physical properties of the cell cortex
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: 110
year: '2016'
...
---
_id: '1250'
abstract:
- lang: eng
text: In bacteria, replicative aging manifests as a difference in growth or survival
between the two cells emerging from division. One cell can be regarded as an aging
mother with a decreased potential for future survival and division, the other
as a rejuvenated daughter. Here, we aimed at investigating some of the processes
involved in aging in the bacterium Escherichia coli, where the two types of cells
can be distinguished by the age of their cell poles. We found that certain changes
in the regulation of the carbohydrate metabolism can affect aging. A mutation
in the carbon storage regulator gene, csrA, leads to a dramatically shorter replicative
lifespan; csrA mutants stop dividing once their pole exceeds an age of about five
divisions. These old-pole cells accumulate glycogen at their old cell poles; after
their last division, they do not contain a chromosome, presumably because of spatial
exclusion by the glycogen aggregates. The new-pole daughters produced by these
aging mothers are born young; they only express the deleterious phenotype once
their pole is old. These results demonstrate how manipulations of nutrient allocation
can lead to the exclusion of the chromosome and limit replicative lifespan in
E. coli, and illustrate how mutations can have phenotypic effects that are specific
for cells with old poles. This raises the question how bacteria can avoid the
accumulation of such mutations in their genomes over evolutionary times, and how
they can achieve the long replicative lifespans that have recently been reported.
acknowledgement: This manuscript is dedicated to the memory of Alex Böhm, who was
a great friend and a passionate biologist. Alex passed away after the initial submission
of this manuscript. We thank Vesna Olivera and Ursula Sauder from the Zentrum für
Mikroskopie Uni Basel for excellent service, and Olin Silander, Nikki Freed, and
Nela Nikolic for helpful discussions. This work was supported by the Swiss National
Science Foundation grants to M. Ackermann and Urs Jenal (supporting AB).
article_number: e1005974
author:
- first_name: Alex
full_name: Boehm, Alex
last_name: Boehm
- first_name: Markus
full_name: Arnoldini, Markus
last_name: Arnoldini
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Thomas
full_name: Röösli, Thomas
last_name: Röösli
- first_name: Colette
full_name: Bigosch, Colette
last_name: Bigosch
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Genetic
manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS
Genetics. 2016;12(4). doi:10.1371/journal.pgen.1005974
apa: Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., & Ackermann,
M. (2016). Genetic manipulation of glycogen allocation affects replicative lifespan
in E coli. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005974
chicago: Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette
Bigosch, and Martin Ackermann. “Genetic Manipulation of Glycogen Allocation Affects
Replicative Lifespan in E Coli.” PLoS Genetics. Public Library of Science,
2016. https://doi.org/10.1371/journal.pgen.1005974.
ieee: A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann,
“Genetic manipulation of glycogen allocation affects replicative lifespan in E
coli,” PLoS Genetics, vol. 12, no. 4. Public Library of Science, 2016.
ista: Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016.
Genetic manipulation of glycogen allocation affects replicative lifespan in E
coli. PLoS Genetics. 12(4), e1005974.
mla: Boehm, Alex, et al. “Genetic Manipulation of Glycogen Allocation Affects Replicative
Lifespan in E Coli.” PLoS Genetics, vol. 12, no. 4, e1005974, Public Library
of Science, 2016, doi:10.1371/journal.pgen.1005974.
short: A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann,
PLoS Genetics 12 (2016).
date_created: 2018-12-11T11:50:56Z
date_published: 2016-04-19T00:00:00Z
date_updated: 2023-02-23T14:11:39Z
day: '19'
ddc:
- '576'
- '579'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1005974
file:
- access_level: open_access
checksum: 53d22b2b39e5adc243d34f18b2615a85
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:17Z
date_updated: 2020-07-14T12:44:41Z
file_id: '5067'
file_name: IST-2016-705-v1+1_journal.pgen.1005974.PDF
file_size: 6273249
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '4'
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- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '6077'
pubrep_id: '705'
quality_controlled: '1'
related_material:
record:
- id: '9873'
relation: research_data
status: public
scopus_import: 1
status: public
title: Genetic manipulation of glycogen allocation affects replicative lifespan in
E coli
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2016'
...
---
_id: '1251'
abstract:
- lang: eng
text: Plant growth and architecture is regulated by the polar distribution of the
hormone auxin. Polarity and flexibility of this process is provided by constant
cycling of auxin transporter vesicles along actin filaments, coordinated by a
positive auxinactin feedback loop. Both polar auxin transport and vesicle cycling
are inhibited by synthetic auxin transport inhibitors, such as 1-Nnaphthylphthalamic
acid (NPA), counteracting the effect of auxin; however, underlying targets and
mechanisms are unclear. Using NMR, we map the NPA binding surface on the Arabidopsis
thaliana ABCB chaperone TWISTED DWARF1 (TWD1).We identify ACTIN7 as a relevant,
although likely indirect, TWD1 interactor, and show TWD1-dependent regulation
of actin filament organization and dynamics and that TWD1 is required for NPA-mediated
actin cytoskeleton remodeling. The TWD1-ACTIN7 axis controls plasma membrane presence
of efflux transporters, and as a consequence act7 and twd1 share developmental
and physiological phenotypes indicative of defects in auxin transport. These can
be phenocopied by NPA treatment or by chemical actin (de)stabilization. We provide
evidence that TWD1 determines downstreamlocations of auxin efflux transporters
by adjusting actin filament debundling and dynamizing processes and mediating
NPA action on the latter. This function appears to be evolutionary conserved since
TWD1 expression in budding yeast alters actin polarization and cell polarity and
provides NPA sensitivity.
acknowledgement: ' This work was supported by grants from the European Social Fund
(CZ.1.07/2.3.00/20.0043), the Czech Science Foundation GAČR (GA13-40637S) to J.F.
and M.Z., the Ministry of Education, Youth, and Sports of the Czech Republic under
the project CEITEC 2020 (LQ1601) to M.Z., the Ministry for Higher Education and
Research of Luxembourg (REC-LOCM-20140703) to C.T., the Partial Funding Program
for Short Stays Abroad of CONICET Argentina (to N.I.B.), Swiss National Funds, the
Pool de Recherche of the University of Fribourg, and the Novartis Foundation (all
to M.G.). '
author:
- first_name: Jinsheng
full_name: Zhu, Jinsheng
last_name: Zhu
- first_name: Aurélien
full_name: Bailly, Aurélien
last_name: Bailly
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Valpuri
full_name: Sovero, Valpuri
last_name: Sovero
- first_name: Martin
full_name: Di Donato, Martin
last_name: Di Donato
- first_name: Pei
full_name: Ge, Pei
last_name: Ge
- first_name: Jacqueline
full_name: Oehri, Jacqueline
last_name: Oehri
- first_name: Bibek
full_name: Aryal, Bibek
last_name: Aryal
- first_name: Pengchao
full_name: Hao, Pengchao
last_name: Hao
- first_name: Miriam
full_name: Linnert, Miriam
last_name: Linnert
- first_name: Noelia
full_name: Burgardt, Noelia
last_name: Burgardt
- first_name: Christian
full_name: Lücke, Christian
last_name: Lücke
- first_name: Matthias
full_name: Weiwad, Matthias
last_name: Weiwad
- first_name: Max
full_name: Michel, Max
last_name: Michel
- first_name: Oliver
full_name: Weiergräber, Oliver
last_name: Weiergräber
- first_name: Stephan
full_name: Pollmann, Stephan
last_name: Pollmann
- first_name: Elisa
full_name: Azzarello, Elisa
last_name: Azzarello
- first_name: Stefano
full_name: Mancuso, Stefano
last_name: Mancuso
- first_name: Noel
full_name: Ferro, Noel
last_name: Ferro
- first_name: Yoichiro
full_name: Fukao, Yoichiro
last_name: Fukao
- first_name: Céline
full_name: Hoffmann, Céline
last_name: Hoffmann
- first_name: Roland
full_name: Wedlich Söldner, Roland
last_name: Wedlich Söldner
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Clément
full_name: Thomas, Clément
last_name: Thomas
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
citation:
ama: Zhu J, Bailly A, Zwiewka M, et al. TWISTED DWARF1 mediates the action of auxin
transport inhibitors on actin cytoskeleton dynamics. Plant Cell. 2016;28(4):930-948.
doi:10.1105/tpc.15.00726
apa: Zhu, J., Bailly, A., Zwiewka, M., Sovero, V., Di Donato, M., Ge, P., … Geisler,
M. (2016). TWISTED DWARF1 mediates the action of auxin transport inhibitors on
actin cytoskeleton dynamics. Plant Cell. American Society of Plant Biologists.
https://doi.org/10.1105/tpc.15.00726
chicago: Zhu, Jinsheng, Aurélien Bailly, Marta Zwiewka, Valpuri Sovero, Martin Di
Donato, Pei Ge, Jacqueline Oehri, et al. “TWISTED DWARF1 Mediates the Action of
Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics.” Plant Cell.
American Society of Plant Biologists, 2016. https://doi.org/10.1105/tpc.15.00726.
ieee: J. Zhu et al., “TWISTED DWARF1 mediates the action of auxin transport
inhibitors on actin cytoskeleton dynamics,” Plant Cell, vol. 28, no. 4.
American Society of Plant Biologists, pp. 930–948, 2016.
ista: Zhu J, Bailly A, Zwiewka M, Sovero V, Di Donato M, Ge P, Oehri J, Aryal B,
Hao P, Linnert M, Burgardt N, Lücke C, Weiwad M, Michel M, Weiergräber O, Pollmann
S, Azzarello E, Mancuso S, Ferro N, Fukao Y, Hoffmann C, Wedlich Söldner R, Friml
J, Thomas C, Geisler M. 2016. TWISTED DWARF1 mediates the action of auxin transport
inhibitors on actin cytoskeleton dynamics. Plant Cell. 28(4), 930–948.
mla: Zhu, Jinsheng, et al. “TWISTED DWARF1 Mediates the Action of Auxin Transport
Inhibitors on Actin Cytoskeleton Dynamics.” Plant Cell, vol. 28, no. 4,
American Society of Plant Biologists, 2016, pp. 930–48, doi:10.1105/tpc.15.00726.
short: J. Zhu, A. Bailly, M. Zwiewka, V. Sovero, M. Di Donato, P. Ge, J. Oehri,
B. Aryal, P. Hao, M. Linnert, N. Burgardt, C. Lücke, M. Weiwad, M. Michel, O.
Weiergräber, S. Pollmann, E. Azzarello, S. Mancuso, N. Ferro, Y. Fukao, C. Hoffmann,
R. Wedlich Söldner, J. Friml, C. Thomas, M. Geisler, Plant Cell 28 (2016) 930–948.
date_created: 2018-12-11T11:50:57Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:49:24Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.15.00726
intvolume: ' 28'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863381/
month: '04'
oa: 1
oa_version: Submitted Version
page: 930 - 948
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '6078'
quality_controlled: '1'
scopus_import: 1
status: public
title: TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton
dynamics
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2016'
...
---
_id: '1252'
abstract:
- lang: eng
text: We study the homomorphism induced in homology by a closed correspondence between
topological spaces, using projections from the graph of the correspondence to
its domain and codomain. We provide assumptions under which the homomorphism induced
by an outer approximation of a continuous map coincides with the homomorphism
induced in homology by the map. In contrast to more classical results we do not
require that the projection to the domain have acyclic preimages. Moreover, we
show that it is possible to retrieve correct homological information from a correspondence
even if some data is missing or perturbed. Finally, we describe an application
to combinatorial maps that are either outer approximations of continuous maps
or reconstructions of such maps from a finite set of data points.
acknowledgement: "The authors gratefully acknowledge the support of the Lorenz Center
which\r\nprovided an opportunity for us to discuss in depth the work of this paper.
Research leading to these results has received funding from Fundo Europeu de Desenvolvimento
Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade
(POFC) and from the Portuguese national funds through Funda¸c˜ao para a Ciˆencia
e a Tecnologia (FCT) in the framework of the research\r\nproject FCOMP-01-0124-FEDER-010645
(ref. FCT PTDC/MAT/098871/2008),\r\nas well as from the People Programme (Marie
Curie Actions) of the European\r\nUnion’s Seventh Framework Programme (FP7/2007-2013)
under REA grant agreement no. 622033 (supporting PP). The work of the first and
third author has\r\nbeen partially supported by NSF grants NSF-DMS-0835621, 0915019,
1125174,\r\n1248071, and contracts from AFOSR and DARPA. The work of the second
author\r\nwas supported by Grant-in-Aid for Scientific Research (No. 25287029),
Ministry of\r\nEducation, Science, Technology, Culture and Sports, Japan."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Shaun
full_name: Harker, Shaun
last_name: Harker
- first_name: Hiroshi
full_name: Kokubu, Hiroshi
last_name: Kokubu
- first_name: Konstantin
full_name: Mischaikow, Konstantin
last_name: Mischaikow
- first_name: Pawel
full_name: Pilarczyk, Pawel
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
citation:
ama: Harker S, Kokubu H, Mischaikow K, Pilarczyk P. Inducing a map on homology from
a correspondence. Proceedings of the American Mathematical Society. 2016;144(4):1787-1801.
doi:10.1090/proc/12812
apa: Harker, S., Kokubu, H., Mischaikow, K., & Pilarczyk, P. (2016). Inducing
a map on homology from a correspondence. Proceedings of the American Mathematical
Society. American Mathematical Society. https://doi.org/10.1090/proc/12812
chicago: Harker, Shaun, Hiroshi Kokubu, Konstantin Mischaikow, and Pawel Pilarczyk.
“Inducing a Map on Homology from a Correspondence.” Proceedings of the American
Mathematical Society. American Mathematical Society, 2016. https://doi.org/10.1090/proc/12812.
ieee: S. Harker, H. Kokubu, K. Mischaikow, and P. Pilarczyk, “Inducing a map on
homology from a correspondence,” Proceedings of the American Mathematical Society,
vol. 144, no. 4. American Mathematical Society, pp. 1787–1801, 2016.
ista: Harker S, Kokubu H, Mischaikow K, Pilarczyk P. 2016. Inducing a map on homology
from a correspondence. Proceedings of the American Mathematical Society. 144(4),
1787–1801.
mla: Harker, Shaun, et al. “Inducing a Map on Homology from a Correspondence.” Proceedings
of the American Mathematical Society, vol. 144, no. 4, American Mathematical
Society, 2016, pp. 1787–801, doi:10.1090/proc/12812.
short: S. Harker, H. Kokubu, K. Mischaikow, P. Pilarczyk, Proceedings of the American
Mathematical Society 144 (2016) 1787–1801.
date_created: 2018-12-11T11:50:57Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2022-05-24T09:35:58Z
day: '01'
department:
- _id: HeEd
doi: 10.1090/proc/12812
ec_funded: 1
external_id:
arxiv:
- '1411.7563'
intvolume: ' 144'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1411.7563
month: '04'
oa: 1
oa_version: Preprint
page: 1787 - 1801
project:
- _id: 255F06BE-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '622033'
name: Persistent Homology - Images, Data and Maps
publication: Proceedings of the American Mathematical Society
publication_identifier:
issn:
- 1088-6826
publication_status: published
publisher: American Mathematical Society
publist_id: '6075'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inducing a map on homology from a correspondence
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 144
year: '2016'
...
---
_id: '1253'
abstract:
- lang: eng
text: This article provides an introduction to the role of microRNAs in the nervous
system and outlines their potential involvement in the pathophysiology of schizophrenia,
which is hypothesized to arise owing to environmental factors and genetic predisposition.
article_processing_charge: No
author:
- first_name: Lihuei
full_name: Tsai, Lihuei
last_name: Tsai
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Tsai L, Siegert S. How MicroRNAs Are involved in splitting the mind. JAMA
Psychiatry. 2016;73(4):409-410. doi:10.1001/jamapsychiatry.2015.3144
apa: Tsai, L., & Siegert, S. (2016). How MicroRNAs Are involved in splitting
the mind. JAMA Psychiatry. American Medical Association. https://doi.org/10.1001/jamapsychiatry.2015.3144
chicago: Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting
the Mind.” JAMA Psychiatry. American Medical Association, 2016. https://doi.org/10.1001/jamapsychiatry.2015.3144.
ieee: L. Tsai and S. Siegert, “How MicroRNAs Are involved in splitting the mind,”
JAMA Psychiatry, vol. 73, no. 4. American Medical Association, pp. 409–410,
2016.
ista: Tsai L, Siegert S. 2016. How MicroRNAs Are involved in splitting the mind.
JAMA Psychiatry. 73(4), 409–410.
mla: Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting
the Mind.” JAMA Psychiatry, vol. 73, no. 4, American Medical Association,
2016, pp. 409–10, doi:10.1001/jamapsychiatry.2015.3144.
short: L. Tsai, S. Siegert, JAMA Psychiatry 73 (2016) 409–410.
date_created: 2018-12-11T11:50:58Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2024-02-14T12:07:22Z
day: '01'
ddc:
- '576'
- '610'
department:
- _id: SaSi
doi: 10.1001/jamapsychiatry.2015.3144
external_id:
pmid:
- '26963490'
file:
- access_level: open_access
checksum: 649aee381f30f7ef7e9efa912d41c2e3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:24Z
date_updated: 2020-07-14T12:44:41Z
file_id: '5278'
file_name: IST-2018-981-v1+1_YNP150011_annotatedproof_FINAL.pdf
file_size: 601679
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: ' 73'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 409 - 410
pmid: 1
publication: JAMA Psychiatry
publication_identifier:
issn:
- 2168-622X
publication_status: published
publisher: American Medical Association
publist_id: '6074'
pubrep_id: '981'
quality_controlled: '1'
scopus_import: '1'
status: public
title: How MicroRNAs Are involved in splitting the mind
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 73
year: '2016'
...
---
_id: '1254'
abstract:
- lang: eng
text: We use rigorous numerical techniques to compute a lower bound for the exponent
of expansivity outside a neighborhood of the critical point for thousands of intervals
of parameter values in the quadratic family. We first compute a radius of the
critical neighborhood outside which the map is uniformly expanding. This radius
is taken as small as possible, yet large enough for our numerical procedure to
succeed in proving that the expansivity exponent outside this neighborhood is
positive. Then, for each of the intervals, we compute a lower bound for this expansivity
exponent, valid for all the parameters in that interval. We illustrate and study
the distribution of the radii and the expansivity exponents. The results of our
computations are mathematically rigorous. The source code of the software and
the results of the computations are made publicly available at http://www.pawelpilarczyk.com/quadratic/.
acknowledgement: "AG and PP were partially supported by Abdus Salam International
Centre for Theoretical Physics (ICTP). Additionally, AG was supported by BREUDS,
and research conducted by PP has received funding from Fundo Europeu de Desenvolvimento
Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade
(POFC) and from the Portuguese national funds through Fundação para a Ciência e
a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645
(ref. FCT PTDC/MAT/098871/2008); and from the People Programme (Marie Curie Actions)
of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant
agreement no. 622033. The authors gratefully acknowledge the Department of\r\nMathematics
\ of Kyoto University for providing access\r\nto their server for conducting
\ computations for this\r\nproject."
author:
- first_name: Ali
full_name: Golmakani, Ali
last_name: Golmakani
- first_name: Stefano
full_name: Luzzatto, Stefano
last_name: Luzzatto
- first_name: Pawel
full_name: Pilarczyk, Pawel
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
citation:
ama: Golmakani A, Luzzatto S, Pilarczyk P. Uniform expansivity outside a critical
neighborhood in the quadratic family. Experimental Mathematics. 2016;25(2):116-124.
doi:10.1080/10586458.2015.1048011
apa: Golmakani, A., Luzzatto, S., & Pilarczyk, P. (2016). Uniform expansivity
outside a critical neighborhood in the quadratic family. Experimental Mathematics.
Taylor and Francis. https://doi.org/10.1080/10586458.2015.1048011
chicago: Golmakani, Ali, Stefano Luzzatto, and Pawel Pilarczyk. “Uniform Expansivity
Outside a Critical Neighborhood in the Quadratic Family.” Experimental Mathematics.
Taylor and Francis, 2016. https://doi.org/10.1080/10586458.2015.1048011.
ieee: A. Golmakani, S. Luzzatto, and P. Pilarczyk, “Uniform expansivity outside
a critical neighborhood in the quadratic family,” Experimental Mathematics,
vol. 25, no. 2. Taylor and Francis, pp. 116–124, 2016.
ista: Golmakani A, Luzzatto S, Pilarczyk P. 2016. Uniform expansivity outside a
critical neighborhood in the quadratic family. Experimental Mathematics. 25(2),
116–124.
mla: Golmakani, Ali, et al. “Uniform Expansivity Outside a Critical Neighborhood
in the Quadratic Family.” Experimental Mathematics, vol. 25, no. 2, Taylor
and Francis, 2016, pp. 116–24, doi:10.1080/10586458.2015.1048011.
short: A. Golmakani, S. Luzzatto, P. Pilarczyk, Experimental Mathematics 25 (2016)
116–124.
date_created: 2018-12-11T11:50:58Z
date_published: 2016-04-02T00:00:00Z
date_updated: 2021-01-12T06:49:25Z
day: '02'
department:
- _id: HeEd
doi: 10.1080/10586458.2015.1048011
ec_funded: 1
intvolume: ' 25'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.00116
month: '04'
oa: 1
oa_version: Preprint
page: 116 - 124
project:
- _id: 255F06BE-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '622033'
name: Persistent Homology - Images, Data and Maps
publication: Experimental Mathematics
publication_status: published
publisher: Taylor and Francis
publist_id: '6071'
quality_controlled: '1'
scopus_import: 1
status: public
title: Uniform expansivity outside a critical neighborhood in the quadratic family
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2016'
...
---
_id: '1255'
abstract:
- lang: eng
text: Down syndrome cell adhesion molecule 1 (Dscam1) has widereaching and vital
neuronal functions although the role it plays in insect and crustacean immunity
is less well understood. In this study, we combine different approaches to understand
the roles that Dscam1 plays in fitness-related contexts in two model insect species.
Contrary to our expectations, we found no short-term modulation of Dscam1 gene
expression after haemocoelic or oral bacterial exposure in Tribolium castaneum,
or after haemocoelic bacterial exposure in Drosophila melanogaster. Furthermore,
RNAi-mediated Dscam1 knockdown and subsequent bacterial exposure did not reduce
T. castaneum survival. However, Dscam1 knockdown in larvae resulted in adult locomotion
defects, as well as dramatically reduced fecundity in males and females. We suggest
that Dscam1 does not always play a straightforward role in immunity, but strongly
influences behaviour and fecundity. This study takes a step towards understanding
more about the role of this intriguing gene from different phenotypic perspectives.
acknowledgement: "We thank Dietmar Schmucker for reading a draft of this manuscript
and thank him and his group for\r\nhelpful discussions. We thank Barbara Hasert,
Kevin Ferro and Manuel F. Talarico for technical support and helpful\r\ndiscussions.
We also thank two anonymous reviewers for their comments. This study was supported
by grants from the Volkswagen Stiftung (1/83 516 and AZ 86020: both to S.A.O.A.)
and from the DFG priority programme 1399 ‘Host parasite coevolution’ (KU 1929/4-2
to R.P. and J.K.)."
article_number: '160138'
author:
- first_name: Robert
full_name: Peuß, Robert
last_name: Peuß
- first_name: Kristina
full_name: Wensing, Kristina
last_name: Wensing
- first_name: Luisa
full_name: Woestmann, Luisa
last_name: Woestmann
- first_name: Hendrik
full_name: Eggert, Hendrik
last_name: Eggert
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Marlene
full_name: Sroka, Marlene
last_name: Sroka
- first_name: Jörn
full_name: Scharsack, Jörn
last_name: Scharsack
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
- first_name: Sophie
full_name: Armitage, Sophie
last_name: Armitage
citation:
ama: 'Peuß R, Wensing K, Woestmann L, et al. Down syndrome cell adhesion molecule
1: Testing for a role in insect immunity, behaviour and reproduction. Royal
Society Open Science. 2016;3(4). doi:10.1098/rsos.160138'
apa: 'Peuß, R., Wensing, K., Woestmann, L., Eggert, H., Milutinovic, B., Sroka,
M., … Armitage, S. (2016). Down syndrome cell adhesion molecule 1: Testing for
a role in insect immunity, behaviour and reproduction. Royal Society Open Science.
Royal Society, The. https://doi.org/10.1098/rsos.160138'
chicago: 'Peuß, Robert, Kristina Wensing, Luisa Woestmann, Hendrik Eggert, Barbara
Milutinovic, Marlene Sroka, Jörn Scharsack, Joachim Kurtz, and Sophie Armitage.
“Down Syndrome Cell Adhesion Molecule 1: Testing for a Role in Insect Immunity,
Behaviour and Reproduction.” Royal Society Open Science. Royal Society,
The, 2016. https://doi.org/10.1098/rsos.160138.'
ieee: 'R. Peuß et al., “Down syndrome cell adhesion molecule 1: Testing for
a role in insect immunity, behaviour and reproduction,” Royal Society Open
Science, vol. 3, no. 4. Royal Society, The, 2016.'
ista: 'Peuß R, Wensing K, Woestmann L, Eggert H, Milutinovic B, Sroka M, Scharsack
J, Kurtz J, Armitage S. 2016. Down syndrome cell adhesion molecule 1: Testing
for a role in insect immunity, behaviour and reproduction. Royal Society Open
Science. 3(4), 160138.'
mla: 'Peuß, Robert, et al. “Down Syndrome Cell Adhesion Molecule 1: Testing for
a Role in Insect Immunity, Behaviour and Reproduction.” Royal Society Open
Science, vol. 3, no. 4, 160138, Royal Society, The, 2016, doi:10.1098/rsos.160138.'
short: R. Peuß, K. Wensing, L. Woestmann, H. Eggert, B. Milutinovic, M. Sroka, J.
Scharsack, J. Kurtz, S. Armitage, Royal Society Open Science 3 (2016).
date_created: 2018-12-11T11:50:58Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:49:25Z
day: '01'
ddc:
- '576'
- '592'
department:
- _id: SyCr
doi: 10.1098/rsos.160138
file:
- access_level: open_access
checksum: c3cd84666c8dc0ce6a784f1c82c1cf68
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:01Z
date_updated: 2020-07-14T12:44:41Z
file_id: '5049'
file_name: IST-2016-704-v1+1_160138.full.pdf
file_size: 627377
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Royal Society Open Science
publication_status: published
publisher: Royal Society, The
publist_id: '6070'
pubrep_id: '704'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity,
behaviour and reproduction'
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: 3
year: '2016'
...
---
_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'
...