---
_id: '2171'
abstract:
- lang: eng
text: We present LS-CRF, a new method for training cyclic Conditional Random Fields
(CRFs) from large datasets that is inspired by classical closed-form expressions
for the maximum likelihood parameters of a generative graphical model with tree
topology. Training a CRF with LS-CRF requires only solving a set of independent
regression problems, each of which can be solved efficiently in closed form or
by an iterative solver. This makes LS-CRF orders of magnitude faster than classical
CRF training based on probabilistic inference, and at the same time more flexible
and easier to implement than other approximate techniques, such as pseudolikelihood
or piecewise training. We apply LS-CRF to the task of semantic image segmentation,
showing that it achieves on par accuracy to other training techniques at higher
speed, thereby allowing efficient CRF training from very large training sets.
For example, training a linearly parameterized pairwise CRF on 150,000 images
requires less than one hour on a modern workstation.
alternative_title:
- LNCS
author:
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
- first_name: Matthieu
full_name: Guillaumin, Matthieu
last_name: Guillaumin
- first_name: Vittorio
full_name: Ferrari, Vittorio
last_name: Ferrari
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Kolesnikov A, Guillaumin M, Ferrari V, Lampert C. Closed-form approximate
CRF training for scalable image segmentation. In: Fleet D, Pajdla T, Schiele B,
Tuytelaars T, eds. Lecture Notes in Computer Science (Including Subseries Lecture
Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol
8691. Springer; 2014:550-565. doi:10.1007/978-3-319-10578-9_36'
apa: 'Kolesnikov, A., Guillaumin, M., Ferrari, V., & Lampert, C. (2014). Closed-form
approximate CRF training for scalable image segmentation. In D. Fleet, T. Pajdla,
B. Schiele, & T. Tuytelaars (Eds.), Lecture Notes in Computer Science (including
subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
(Vol. 8691, pp. 550–565). Zurich, Switzerland: Springer. https://doi.org/10.1007/978-3-319-10578-9_36'
chicago: Kolesnikov, Alexander, Matthieu Guillaumin, Vittorio Ferrari, and Christoph
Lampert. “Closed-Form Approximate CRF Training for Scalable Image Segmentation.”
In Lecture Notes in Computer Science (Including Subseries Lecture Notes in
Artificial Intelligence and Lecture Notes in Bioinformatics), edited by David
Fleet, Tomas Pajdla, Bernt Schiele, and Tinne Tuytelaars, 8691:550–65. Springer,
2014. https://doi.org/10.1007/978-3-319-10578-9_36.
ieee: A. Kolesnikov, M. Guillaumin, V. Ferrari, and C. Lampert, “Closed-form approximate
CRF training for scalable image segmentation,” in Lecture Notes in Computer
Science (including subseries Lecture Notes in Artificial Intelligence and Lecture
Notes in Bioinformatics), Zurich, Switzerland, 2014, vol. 8691, no. PART 3,
pp. 550–565.
ista: 'Kolesnikov A, Guillaumin M, Ferrari V, Lampert C. 2014. Closed-form approximate
CRF training for scalable image segmentation. Lecture Notes in Computer Science
(including subseries Lecture Notes in Artificial Intelligence and Lecture Notes
in Bioinformatics). ECCV: European Conference on Computer Vision, LNCS, vol. 8691,
550–565.'
mla: Kolesnikov, Alexander, et al. “Closed-Form Approximate CRF Training for Scalable
Image Segmentation.” Lecture Notes in Computer Science (Including Subseries
Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics),
edited by David Fleet et al., vol. 8691, no. PART 3, Springer, 2014, pp. 550–65,
doi:10.1007/978-3-319-10578-9_36.
short: A. Kolesnikov, M. Guillaumin, V. Ferrari, C. Lampert, in:, D. Fleet, T. Pajdla,
B. Schiele, T. Tuytelaars (Eds.), Lecture Notes in Computer Science (Including
Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics),
Springer, 2014, pp. 550–565.
conference:
end_date: 2014-09-12
location: Zurich, Switzerland
name: 'ECCV: European Conference on Computer Vision'
start_date: 2014-09-06
date_created: 2018-12-11T11:56:07Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2021-01-12T06:55:46Z
day: '01'
department:
- _id: ChLa
doi: 10.1007/978-3-319-10578-9_36
ec_funded: 1
editor:
- first_name: David
full_name: Fleet, David
last_name: Fleet
- first_name: Tomas
full_name: Pajdla, Tomas
last_name: Pajdla
- first_name: Bernt
full_name: Schiele, Bernt
last_name: Schiele
- first_name: Tinne
full_name: Tuytelaars, Tinne
last_name: Tuytelaars
intvolume: ' 8691'
issue: PART 3
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1403.7057
month: '09'
oa: 1
oa_version: Submitted Version
page: 550 - 565
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication: Lecture Notes in Computer Science (including subseries Lecture Notes
in Artificial Intelligence and Lecture Notes in Bioinformatics)
publication_status: published
publisher: Springer
publist_id: '4813'
quality_controlled: '1'
scopus_import: 1
status: public
title: Closed-form approximate CRF training for scalable image segmentation
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8691
year: '2014'
...
---
_id: '2173'
abstract:
- lang: eng
text: "In this work we introduce a new approach to co-classification, i.e. the task
of jointly classifying multiple, otherwise independent, data samples. The method
we present, named CoConut, is based on the idea of adding a regularizer in the
label space to encode certain priors on the resulting labelings. A regularizer
that encourages labelings that are smooth across the test set, for instance, can
be seen as a test-time variant of the cluster assumption, which has been proven
useful at training time in semi-supervised learning. A regularizer that introduces
a preference for certain class proportions can be regarded as a prior distribution
on the class labels. CoConut can build on existing classifiers without making
any assumptions on how they were obtained and without the need to re-train them.
The use of a regularizer adds a new level of flexibility. It allows the integration
of potentially new information at test time, even in other modalities than what
the classifiers were trained on. We evaluate our framework on six datasets, reporting
a clear performance gain in classification accuracy compared to the standard classification
setup that predicts labels for each test sample separately.\r\n"
author:
- first_name: Sameh
full_name: Khamis, Sameh
last_name: Khamis
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Khamis S, Lampert C. CoConut: Co-classification with output space regularization.
In: Proceedings of the British Machine Vision Conference 2014. BMVA Press;
2014.'
apa: 'Khamis, S., & Lampert, C. (2014). CoConut: Co-classification with output
space regularization. In Proceedings of the British Machine Vision Conference
2014. Nottingham, UK: BMVA Press.'
chicago: 'Khamis, Sameh, and Christoph Lampert. “CoConut: Co-Classification with
Output Space Regularization.” In Proceedings of the British Machine Vision
Conference 2014. BMVA Press, 2014.'
ieee: 'S. Khamis and C. Lampert, “CoConut: Co-classification with output space regularization,”
in Proceedings of the British Machine Vision Conference 2014, Nottingham,
UK, 2014.'
ista: 'Khamis S, Lampert C. 2014. CoConut: Co-classification with output space regularization.
Proceedings of the British Machine Vision Conference 2014. BMVC: British Machine
Vision Conference.'
mla: 'Khamis, Sameh, and Christoph Lampert. “CoConut: Co-Classification with Output
Space Regularization.” Proceedings of the British Machine Vision Conference
2014, BMVA Press, 2014.'
short: S. Khamis, C. Lampert, in:, Proceedings of the British Machine Vision Conference
2014, BMVA Press, 2014.
conference:
end_date: 2014-09-05
location: Nottingham, UK
name: 'BMVC: British Machine Vision Conference'
start_date: 2014-09-01
date_created: 2018-12-11T11:56:08Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2021-01-12T06:55:46Z
day: '01'
ddc:
- '000'
department:
- _id: ChLa
ec_funded: 1
file:
- access_level: open_access
checksum: c4c6d3efdb8ee648faf3e76849839ce2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:23Z
date_updated: 2020-07-14T12:45:31Z
file_id: '4683'
file_name: IST-2016-490-v1+1_khamis-bmvc2014.pdf
file_size: 408172
relation: main_file
file_date_updated: 2020-07-14T12:45:31Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication: Proceedings of the British Machine Vision Conference 2014
publication_status: published
publisher: BMVA Press
publist_id: '4811'
pubrep_id: '490'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'CoConut: Co-classification with output space regularization'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '2172'
abstract:
- lang: eng
text: Fisher Kernels and Deep Learning were two developments with significant impact
on large-scale object categorization in the last years. Both approaches were shown
to achieve state-of-the-art results on large-scale object categorization datasets,
such as ImageNet. Conceptually, however, they are perceived as very different
and it is not uncommon for heated debates to spring up when advocates of both
paradigms meet at conferences or workshops. In this work, we emphasize the similarities
between both architectures rather than their differences and we argue that such
a unified view allows us to transfer ideas from one domain to the other. As a
concrete example we introduce a method for learning a support vector machine classifier
with Fisher kernel at the same time as a task-specific data representation. We
reinterpret the setting as a multi-layer feed forward network. Its final layer
is the classifier, parameterized by a weight vector, and the two previous layers
compute Fisher vectors, parameterized by the coefficients of a Gaussian mixture
model. We introduce a gradient descent based learning algorithm that, in contrast
to other feature learning techniques, is not just derived from intuition or biological
analogy, but has a theoretical justification in the framework of statistical learning
theory. Our experiments show that the new training procedure leads to significant
improvements in classification accuracy while preserving the modularity and geometric
interpretability of a support vector machine setup.
author:
- first_name: Vladyslav
full_name: Sydorov, Vladyslav
last_name: Sydorov
- first_name: Mayu
full_name: Sakurada, Mayu
last_name: Sakurada
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Sydorov V, Sakurada M, Lampert C. Deep Fisher Kernels – End to end learning
of the Fisher Kernel GMM parameters. In: Proceedings of the IEEE Computer Society
Conference on Computer Vision and Pattern Recognition. IEEE; 2014:1402-1409.
doi:10.1109/CVPR.2014.182'
apa: 'Sydorov, V., Sakurada, M., & Lampert, C. (2014). Deep Fisher Kernels –
End to end learning of the Fisher Kernel GMM parameters. In Proceedings of
the IEEE Computer Society Conference on Computer Vision and Pattern Recognition
(pp. 1402–1409). Columbus, USA: IEEE. https://doi.org/10.1109/CVPR.2014.182'
chicago: Sydorov, Vladyslav, Mayu Sakurada, and Christoph Lampert. “Deep Fisher
Kernels – End to End Learning of the Fisher Kernel GMM Parameters.” In Proceedings
of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition,
1402–9. IEEE, 2014. https://doi.org/10.1109/CVPR.2014.182.
ieee: V. Sydorov, M. Sakurada, and C. Lampert, “Deep Fisher Kernels – End to end
learning of the Fisher Kernel GMM parameters,” in Proceedings of the IEEE Computer
Society Conference on Computer Vision and Pattern Recognition, Columbus, USA,
2014, pp. 1402–1409.
ista: 'Sydorov V, Sakurada M, Lampert C. 2014. Deep Fisher Kernels – End to end
learning of the Fisher Kernel GMM parameters. Proceedings of the IEEE Computer
Society Conference on Computer Vision and Pattern Recognition. CVPR: Computer
Vision and Pattern Recognition, 1402–1409.'
mla: Sydorov, Vladyslav, et al. “Deep Fisher Kernels – End to End Learning of the
Fisher Kernel GMM Parameters.” Proceedings of the IEEE Computer Society Conference
on Computer Vision and Pattern Recognition, IEEE, 2014, pp. 1402–09, doi:10.1109/CVPR.2014.182.
short: V. Sydorov, M. Sakurada, C. Lampert, in:, Proceedings of the IEEE Computer
Society Conference on Computer Vision and Pattern Recognition, IEEE, 2014, pp.
1402–1409.
conference:
end_date: 2014-06-28
location: Columbus, USA
name: 'CVPR: Computer Vision and Pattern Recognition'
start_date: 2014-06-23
date_created: 2018-12-11T11:56:08Z
date_published: 2014-09-24T00:00:00Z
date_updated: 2021-01-12T06:55:46Z
day: '24'
department:
- _id: ChLa
doi: 10.1109/CVPR.2014.182
ec_funded: 1
language:
- iso: eng
month: '09'
oa_version: None
page: 1402 - 1409
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication: Proceedings of the IEEE Computer Society Conference on Computer Vision
and Pattern Recognition
publication_status: published
publisher: IEEE
publist_id: '4812'
quality_controlled: '1'
scopus_import: 1
status: public
title: Deep Fisher Kernels – End to end learning of the Fisher Kernel GMM parameters
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '2174'
abstract:
- lang: eng
text: 'When polygenic traits are under stabilizing selection, many different combinations
of alleles allow close adaptation to the optimum. If alleles have equal effects,
all combinations that result in the same deviation from the optimum are equivalent.
Furthermore, the genetic variance that is maintained by mutation-selection balance
is 2μ/S per locus, where μ is the mutation rate and S the strength of stabilizing
selection. In reality, alleles vary in their effects, making the fitness landscape
asymmetric and complicating analysis of the equilibria. We show that that the
resulting genetic variance depends on the fraction of alleles near fixation, which
contribute by 2μ/S, and on the total mutational effects of alleles that are at
intermediate frequency. The inpplayfi between stabilizing selection and mutation
leads to a sharp transition: alleles with effects smaller than a threshold value
of 2 remain polymorphic, whereas those with larger effects are fixed. The genetic
load in equilibrium is less than for traits of equal effects, and the fitness
equilibria are more similar. We find p the optimum is displaced, alleles with
effects close to the threshold value sweep first, and their rate of increase is
bounded by Long-term response leads in general to well-adapted traits, unlike
the case of equal effects that often end up at a suboptimal fitness peak. However,
the particular peaks to which the populations converge are extremely sensitive
to the initial states and to the speed of the shift of the optimum trait value.'
author:
- first_name: Harold
full_name: De Vladar, Harold
last_name: De Vladar
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: De Vladar H, Barton NH. Stability and response of polygenic traits to stabilizing
selection and mutation. Genetics. 2014;197(2):749-767. doi:10.1534/genetics.113.159111
apa: De Vladar, H., & Barton, N. H. (2014). Stability and response of polygenic
traits to stabilizing selection and mutation. Genetics. Genetics Society
of America. https://doi.org/10.1534/genetics.113.159111
chicago: De Vladar, Harold, and Nicholas H Barton. “Stability and Response of Polygenic
Traits to Stabilizing Selection and Mutation.” Genetics. Genetics Society
of America, 2014. https://doi.org/10.1534/genetics.113.159111.
ieee: H. De Vladar and N. H. Barton, “Stability and response of polygenic traits
to stabilizing selection and mutation,” Genetics, vol. 197, no. 2. Genetics
Society of America, pp. 749–767, 2014.
ista: De Vladar H, Barton NH. 2014. Stability and response of polygenic traits to
stabilizing selection and mutation. Genetics. 197(2), 749–767.
mla: De Vladar, Harold, and Nicholas H. Barton. “Stability and Response of Polygenic
Traits to Stabilizing Selection and Mutation.” Genetics, vol. 197, no.
2, Genetics Society of America, 2014, pp. 749–67, doi:10.1534/genetics.113.159111.
short: H. De Vladar, N.H. Barton, Genetics 197 (2014) 749–767.
date_created: 2018-12-11T11:56:08Z
date_published: 2014-06-01T00:00:00Z
date_updated: 2021-01-12T06:55:47Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.113.159111
ec_funded: 1
intvolume: ' 197'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1404.1017
month: '06'
oa: 1
oa_version: Submitted Version
page: 749 - 767
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '4809'
quality_controlled: '1'
scopus_import: 1
status: public
title: Stability and response of polygenic traits to stabilizing selection and mutation
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 197
year: '2014'
...
---
_id: '2179'
abstract:
- lang: eng
text: We extend the proof of the local semicircle law for generalized Wigner matrices
given in MR3068390 to the case when the matrix of variances has an eigenvalue
-1. In particular, this result provides a short proof of the optimal local Marchenko-Pastur
law at the hard edge (i.e. around zero) for sample covariance matrices X*X, where
the variances of the entries of X may vary.
author:
- first_name: Oskari H
full_name: Ajanki, Oskari H
id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87
last_name: Ajanki
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: Ajanki OH, Erdös L, Krüger TH. Local semicircle law with imprimitive variance
matrix. Electronic Communications in Probability. 2014;19. doi:10.1214/ECP.v19-3121
apa: Ajanki, O. H., Erdös, L., & Krüger, T. H. (2014). Local semicircle law
with imprimitive variance matrix. Electronic Communications in Probability.
Institute of Mathematical Statistics. https://doi.org/10.1214/ECP.v19-3121
chicago: Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Local Semicircle
Law with Imprimitive Variance Matrix.” Electronic Communications in Probability.
Institute of Mathematical Statistics, 2014. https://doi.org/10.1214/ECP.v19-3121.
ieee: O. H. Ajanki, L. Erdös, and T. H. Krüger, “Local semicircle law with imprimitive
variance matrix,” Electronic Communications in Probability, vol. 19. Institute
of Mathematical Statistics, 2014.
ista: Ajanki OH, Erdös L, Krüger TH. 2014. Local semicircle law with imprimitive
variance matrix. Electronic Communications in Probability. 19.
mla: Ajanki, Oskari H., et al. “Local Semicircle Law with Imprimitive Variance Matrix.”
Electronic Communications in Probability, vol. 19, Institute of Mathematical
Statistics, 2014, doi:10.1214/ECP.v19-3121.
short: O.H. Ajanki, L. Erdös, T.H. Krüger, Electronic Communications in Probability
19 (2014).
date_created: 2018-12-11T11:56:10Z
date_published: 2014-06-09T00:00:00Z
date_updated: 2021-01-12T06:55:48Z
day: '09'
ddc:
- '570'
department:
- _id: LaEr
doi: 10.1214/ECP.v19-3121
file:
- access_level: open_access
checksum: bd8a041c76d62fe820bf73ff13ce7d1b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:06Z
date_updated: 2020-07-14T12:45:31Z
file_id: '4729'
file_name: IST-2016-426-v1+1_3121-17518-1-PB.pdf
file_size: 327322
relation: main_file
file_date_updated: 2020-07-14T12:45:31Z
has_accepted_license: '1'
intvolume: ' 19'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Electronic Communications in Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '4803'
pubrep_id: '426'
quality_controlled: '1'
scopus_import: 1
status: public
title: Local semicircle law with imprimitive variance matrix
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2014'
...
---
_id: '2176'
abstract:
- lang: eng
text: Electron microscopy (EM) allows for the simultaneous visualization of all
tissue components at high resolution. However, the extent to which conventional
aldehyde fixation and ethanol dehydration of the tissue alter the fine structure
of cells and organelles, thereby preventing detection of subtle structural changes
induced by an experiment, has remained an issue. Attempts have been made to rapidly
freeze tissue to preserve native ultrastructure. Shock-freezing of living tissue
under high pressure (high-pressure freezing, HPF) followed by cryosubstitution
of the tissue water avoids aldehyde fixation and dehydration in ethanol; the tissue
water is immobilized in â ̂1/450 ms, and a close-to-native fine structure of cells,
organelles and molecules is preserved. Here we describe a protocol for HPF that
is useful to monitor ultrastructural changes associated with functional changes
at synapses in the brain but can be applied to many other tissues as well. The
procedure requires a high-pressure freezer and takes a minimum of 7 d but can
be paused at several points.
author:
- first_name: Daniel
full_name: Studer, Daniel
last_name: Studer
- first_name: Shanting
full_name: Zhao, Shanting
last_name: Zhao
- first_name: Xuejun
full_name: Chai, Xuejun
last_name: Chai
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Werner
full_name: Graber, Werner
last_name: Graber
- first_name: Sigrun
full_name: Nestel, Sigrun
last_name: Nestel
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
citation:
ama: Studer D, Zhao S, Chai X, et al. Capture of activity-induced ultrastructural
changes at synapses by high-pressure freezing of brain tissue. Nature Protocols.
2014;9(6):1480-1495. doi:10.1038/nprot.2014.099
apa: Studer, D., Zhao, S., Chai, X., Jonas, P. M., Graber, W., Nestel, S., &
Frotscher, M. (2014). Capture of activity-induced ultrastructural changes at synapses
by high-pressure freezing of brain tissue. Nature Protocols. Nature Publishing
Group. https://doi.org/10.1038/nprot.2014.099
chicago: Studer, Daniel, Shanting Zhao, Xuejun Chai, Peter M Jonas, Werner Graber,
Sigrun Nestel, and Michael Frotscher. “Capture of Activity-Induced Ultrastructural
Changes at Synapses by High-Pressure Freezing of Brain Tissue.” Nature Protocols.
Nature Publishing Group, 2014. https://doi.org/10.1038/nprot.2014.099.
ieee: D. Studer et al., “Capture of activity-induced ultrastructural changes
at synapses by high-pressure freezing of brain tissue,” Nature Protocols,
vol. 9, no. 6. Nature Publishing Group, pp. 1480–1495, 2014.
ista: Studer D, Zhao S, Chai X, Jonas PM, Graber W, Nestel S, Frotscher M. 2014.
Capture of activity-induced ultrastructural changes at synapses by high-pressure
freezing of brain tissue. Nature Protocols. 9(6), 1480–1495.
mla: Studer, Daniel, et al. “Capture of Activity-Induced Ultrastructural Changes
at Synapses by High-Pressure Freezing of Brain Tissue.” Nature Protocols,
vol. 9, no. 6, Nature Publishing Group, 2014, pp. 1480–95, doi:10.1038/nprot.2014.099.
short: D. Studer, S. Zhao, X. Chai, P.M. Jonas, W. Graber, S. Nestel, M. Frotscher,
Nature Protocols 9 (2014) 1480–1495.
date_created: 2018-12-11T11:56:09Z
date_published: 2014-05-29T00:00:00Z
date_updated: 2021-01-12T06:55:47Z
day: '29'
department:
- _id: PeJo
doi: 10.1038/nprot.2014.099
intvolume: ' 9'
issue: '6'
language:
- iso: eng
month: '05'
oa_version: None
page: 1480 - 1495
project:
- _id: 25BDE9A4-B435-11E9-9278-68D0E5697425
grant_number: SFB-TR3-TP10B
name: Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen
publication: Nature Protocols
publication_status: published
publisher: Nature Publishing Group
publist_id: '4807'
quality_controlled: '1'
scopus_import: 1
status: public
title: Capture of activity-induced ultrastructural changes at synapses by high-pressure
freezing of brain tissue
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2014'
...
---
_id: '2178'
abstract:
- lang: eng
text: We consider the three-state toric homogeneous Markov chain model (THMC) without
loops and initial parameters. At time T, the size of the design matrix is 6 ×
3 · 2T-1 and the convex hull of its columns is the model polytope. We study the
behavior of this polytope for T ≥ 3 and we show that it is defined by 24 facets
for all T ≥ 5. Moreover, we give a complete description of these facets. From
this, we deduce that the toric ideal associated with the design matrix is generated
by binomials of degree at most 6. Our proof is based on a result due to Sturmfels,
who gave a bound on the degree of the generators of a toric ideal, provided the
normality of the corresponding toric variety. In our setting, we established the
normality of the toric variety associated to the THMC model by studying the geometric
properties of the model polytope.
acknowledgement: Research of Martín del Campo supported in part by NSF Grant DMS-915211.
author:
- first_name: David
full_name: Haws, David
last_name: Haws
- first_name: Abraham
full_name: Martin Del Campo Sanchez, Abraham
id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87
last_name: Martin Del Campo Sanchez
- first_name: Akimichi
full_name: Takemura, Akimichi
last_name: Takemura
- first_name: Ruriko
full_name: Yoshida, Ruriko
last_name: Yoshida
citation:
ama: Haws D, Martin del Campo Sanchez A, Takemura A, Yoshida R. Markov degree of
the three-state toric homogeneous Markov chain model. Beitrage zur Algebra
und Geometrie. 2014;55(1):161-188. doi:10.1007/s13366-013-0178-y
apa: Haws, D., Martin del Campo Sanchez, A., Takemura, A., & Yoshida, R. (2014).
Markov degree of the three-state toric homogeneous Markov chain model. Beitrage
Zur Algebra Und Geometrie. Springer. https://doi.org/10.1007/s13366-013-0178-y
chicago: Haws, David, Abraham Martin del Campo Sanchez, Akimichi Takemura, and Ruriko
Yoshida. “Markov Degree of the Three-State Toric Homogeneous Markov Chain Model.”
Beitrage Zur Algebra Und Geometrie. Springer, 2014. https://doi.org/10.1007/s13366-013-0178-y.
ieee: D. Haws, A. Martin del Campo Sanchez, A. Takemura, and R. Yoshida, “Markov
degree of the three-state toric homogeneous Markov chain model,” Beitrage zur
Algebra und Geometrie, vol. 55, no. 1. Springer, pp. 161–188, 2014.
ista: Haws D, Martin del Campo Sanchez A, Takemura A, Yoshida R. 2014. Markov degree
of the three-state toric homogeneous Markov chain model. Beitrage zur Algebra
und Geometrie. 55(1), 161–188.
mla: Haws, David, et al. “Markov Degree of the Three-State Toric Homogeneous Markov
Chain Model.” Beitrage Zur Algebra Und Geometrie, vol. 55, no. 1, Springer,
2014, pp. 161–88, doi:10.1007/s13366-013-0178-y.
short: D. Haws, A. Martin del Campo Sanchez, A. Takemura, R. Yoshida, Beitrage Zur
Algebra Und Geometrie 55 (2014) 161–188.
date_created: 2018-12-11T11:56:10Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2021-01-12T06:55:48Z
day: '01'
department:
- _id: CaUh
doi: 10.1007/s13366-013-0178-y
intvolume: ' 55'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1204.3070
month: '03'
oa: 1
oa_version: Submitted Version
page: 161 - 188
publication: Beitrage zur Algebra und Geometrie
publication_status: published
publisher: Springer
publist_id: '4804'
quality_controlled: '1'
scopus_import: 1
status: public
title: Markov degree of the three-state toric homogeneous Markov chain model
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2014'
...
---
_id: '2177'
abstract:
- lang: eng
text: We give evidence for the difficulty of computing Betti numbers of simplicial
complexes over a finite field. We do this by reducing the rank computation for
sparse matrices with to non-zero entries to computing Betti numbers of simplicial
complexes consisting of at most a constant times to simplices. Together with the
known reduction in the other direction, this implies that the two problems have
the same computational complexity.
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Salman
full_name: Parsa, Salman
id: 4BDBD4F2-F248-11E8-B48F-1D18A9856A87
last_name: Parsa
citation:
ama: 'Edelsbrunner H, Parsa S. On the computational complexity of betti numbers
reductions from matrix rank. In: Proceedings of the Annual ACM-SIAM Symposium
on Discrete Algorithms. SIAM; 2014:152-160. doi:10.1137/1.9781611973402.11'
apa: 'Edelsbrunner, H., & Parsa, S. (2014). On the computational complexity
of betti numbers reductions from matrix rank. In Proceedings of the Annual
ACM-SIAM Symposium on Discrete Algorithms (pp. 152–160). Portland, USA: SIAM.
https://doi.org/10.1137/1.9781611973402.11'
chicago: Edelsbrunner, Herbert, and Salman Parsa. “On the Computational Complexity
of Betti Numbers Reductions from Matrix Rank.” In Proceedings of the Annual
ACM-SIAM Symposium on Discrete Algorithms, 152–60. SIAM, 2014. https://doi.org/10.1137/1.9781611973402.11.
ieee: H. Edelsbrunner and S. Parsa, “On the computational complexity of betti numbers
reductions from matrix rank,” in Proceedings of the Annual ACM-SIAM Symposium
on Discrete Algorithms, Portland, USA, 2014, pp. 152–160.
ista: 'Edelsbrunner H, Parsa S. 2014. On the computational complexity of betti numbers
reductions from matrix rank. Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms. SODA: Symposium on Discrete Algorithms, 152–160.'
mla: Edelsbrunner, Herbert, and Salman Parsa. “On the Computational Complexity of
Betti Numbers Reductions from Matrix Rank.” Proceedings of the Annual ACM-SIAM
Symposium on Discrete Algorithms, SIAM, 2014, pp. 152–60, doi:10.1137/1.9781611973402.11.
short: H. Edelsbrunner, S. Parsa, in:, Proceedings of the Annual ACM-SIAM Symposium
on Discrete Algorithms, SIAM, 2014, pp. 152–160.
conference:
end_date: 2014-01-07
location: Portland, USA
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2014-01-05
date_created: 2018-12-11T11:56:09Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:55:48Z
day: '01'
department:
- _id: HeEd
doi: 10.1137/1.9781611973402.11
language:
- iso: eng
month: '01'
oa_version: None
page: 152 - 160
publication: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms
publication_status: published
publisher: SIAM
publist_id: '4805'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the computational complexity of betti numbers reductions from matrix rank
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '2185'
abstract:
- lang: eng
text: 'We revisit the classical problem of converting an imperfect source of randomness
into a usable cryptographic key. Assume that we have some cryptographic application
P that expects a uniformly random m-bit key R and ensures that the best attack
(in some complexity class) against P(R) has success probability at most δ. Our
goal is to design a key-derivation function (KDF) h that converts any random source
X of min-entropy k into a sufficiently "good" key h(X), guaranteeing
that P(h(X)) has comparable security δ′ which is ''close'' to δ. Seeded randomness
extractors provide a generic way to solve this problem for all applications P,
with resulting security δ′ = O(δ), provided that we start with entropy k ≥ m +
2 log (1/δ) - O(1). By a result of Radhakrishnan and Ta-Shma, this bound on k
(called the "RT-bound") is also known to be tight in general. Unfortunately,
in many situations the loss of 2 log (1/δ) bits of entropy is unacceptable. This
motivates the study KDFs with less entropy waste by placing some restrictions
on the source X or the application P. In this work we obtain the following new
positive and negative results in this regard: - Efficient samplability of the
source X does not help beat the RT-bound for general applications. This resolves
the SRT (samplable RT) conjecture of Dachman-Soled et al. [DGKM12] in the affirmative,
and also shows that the existence of computationally-secure extractors beating
the RT-bound implies the existence of one-way functions. - We continue in the
line of work initiated by Barak et al. [BDK+11] and construct new information-theoretic
KDFs which beat the RT-bound for large but restricted classes of applications.
Specifically, we design efficient KDFs that work for all unpredictability applications
P (e.g., signatures, MACs, one-way functions, etc.) and can either: (1) extract
all of the entropy k = m with a very modest security loss δ′ = O(δ·log (1/δ)),
or alternatively, (2) achieve essentially optimal security δ′ = O(δ) with a very
modest entropy loss k ≥ m + loglog (1/δ). In comparison, the best prior results
from [BDK+11] for this class of applications would only guarantee δ′ = O(√δ) when
k = m, and would need k ≥ m + log (1/δ) to get δ′ = O(δ). - The weaker bounds
of [BDK+11] hold for a larger class of so-called "square- friendly"
applications (which includes all unpredictability, but also some important indistinguishability,
applications). Unfortunately, we show that these weaker bounds are tight for the
larger class of applications. - We abstract out a clean, information-theoretic
notion of (k,δ,δ′)- unpredictability extractors, which guarantee "induced"
security δ′ for any δ-secure unpredictability application P, and characterize
the parameters achievable for such unpredictability extractors. Of independent
interest, we also relate this notion to the previously-known notion of (min-entropy)
condensers, and improve the state-of-the-art parameters for such condensers.'
alternative_title:
- LNCS
author:
- first_name: Yevgeniy
full_name: Dodis, Yevgeniy
last_name: Dodis
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Daniel
full_name: Wichs, Daniel
last_name: Wichs
citation:
ama: 'Dodis Y, Pietrzak KZ, Wichs D. Key derivation without entropy waste. In: Nguyen
P, Oswald E, eds. Vol 8441. Springer; 2014:93-110. doi:10.1007/978-3-642-55220-5_6'
apa: 'Dodis, Y., Pietrzak, K. Z., & Wichs, D. (2014). Key derivation without
entropy waste. In P. Nguyen & E. Oswald (Eds.) (Vol. 8441, pp. 93–110). Presented
at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Copenhagen,
Denmark: Springer. https://doi.org/10.1007/978-3-642-55220-5_6'
chicago: Dodis, Yevgeniy, Krzysztof Z Pietrzak, and Daniel Wichs. “Key Derivation
without Entropy Waste.” edited by Phong Nguyen and Elisabeth Oswald, 8441:93–110.
Springer, 2014. https://doi.org/10.1007/978-3-642-55220-5_6.
ieee: 'Y. Dodis, K. Z. Pietrzak, and D. Wichs, “Key derivation without entropy waste,”
presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques,
Copenhagen, Denmark, 2014, vol. 8441, pp. 93–110.'
ista: 'Dodis Y, Pietrzak KZ, Wichs D. 2014. Key derivation without entropy waste.
EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 8441,
93–110.'
mla: Dodis, Yevgeniy, et al. Key Derivation without Entropy Waste. Edited
by Phong Nguyen and Elisabeth Oswald, vol. 8441, Springer, 2014, pp. 93–110, doi:10.1007/978-3-642-55220-5_6.
short: Y. Dodis, K.Z. Pietrzak, D. Wichs, in:, P. Nguyen, E. Oswald (Eds.), Springer,
2014, pp. 93–110.
conference:
end_date: 2014-05-15
location: Copenhagen, Denmark
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
start_date: 2014-05-11
date_created: 2018-12-11T11:56:12Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T06:55:51Z
day: '01'
ddc:
- '000'
- '004'
department:
- _id: KrPi
doi: 10.1007/978-3-642-55220-5_6
editor:
- first_name: Phong
full_name: Nguyen, Phong
last_name: Nguyen
- first_name: Elisabeth
full_name: Oswald, Elisabeth
last_name: Oswald
file:
- access_level: open_access
checksum: da1aa01221086083b23c92e547b48ff4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:43Z
date_updated: 2020-07-14T12:45:31Z
file_id: '4705'
file_name: IST-2016-680-v1+1_708.pdf
file_size: 505389
relation: main_file
file_date_updated: 2020-07-14T12:45:31Z
has_accepted_license: '1'
intvolume: ' 8441'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 93 - 110
publication_status: published
publisher: Springer
publist_id: '4795'
pubrep_id: '680'
quality_controlled: '1'
scopus_import: 1
status: public
title: Key derivation without entropy waste
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8441
year: '2014'
...
---
_id: '2180'
abstract:
- lang: eng
text: Weighted majority votes allow one to combine the output of several classifiers
or voters. MinCq is a recent algorithm for optimizing the weight of each voter
based on the minimization of a theoretical bound over the risk of the vote with
elegant PAC-Bayesian generalization guarantees. However, while it has demonstrated
good performance when combining weak classifiers, MinCq cannot make use of the
useful a priori knowledge that one may have when using a mixture of weak and strong
voters. In this paper, we propose P-MinCq, an extension of MinCq that can incorporate
such knowledge in the form of a constraint over the distribution of the weights,
along with general proofs of convergence that stand in the sample compression
setting for data-dependent voters. The approach is applied to a vote of k-NN classifiers
with a specific modeling of the voters' performance. P-MinCq significantly outperforms
the classic k-NN classifier, a symmetric NN and MinCq using the same voters. We
show that it is also competitive with LMNN, a popular metric learning algorithm,
and that combining both approaches further reduces the error.
acknowledgement: 'This work was funded by the French project SoLSTiCe ANR-13-BS02-01
of the ANR. '
author:
- first_name: Aurélien
full_name: Bellet, Aurélien
last_name: Bellet
- first_name: Amaury
full_name: Habrard, Amaury
last_name: Habrard
- first_name: Emilie
full_name: Morvant, Emilie
id: 4BAC2A72-F248-11E8-B48F-1D18A9856A87
last_name: Morvant
orcid: 0000-0002-8301-7240
- first_name: Marc
full_name: Sebban, Marc
last_name: Sebban
citation:
ama: Bellet A, Habrard A, Morvant E, Sebban M. Learning a priori constrained weighted
majority votes. Machine Learning. 2014;97(1-2):129-154. doi:10.1007/s10994-014-5462-z
apa: Bellet, A., Habrard, A., Morvant, E., & Sebban, M. (2014). Learning a priori
constrained weighted majority votes. Machine Learning. Springer. https://doi.org/10.1007/s10994-014-5462-z
chicago: Bellet, Aurélien, Amaury Habrard, Emilie Morvant, and Marc Sebban. “Learning
a Priori Constrained Weighted Majority Votes.” Machine Learning. Springer,
2014. https://doi.org/10.1007/s10994-014-5462-z.
ieee: A. Bellet, A. Habrard, E. Morvant, and M. Sebban, “Learning a priori constrained
weighted majority votes,” Machine Learning, vol. 97, no. 1–2. Springer,
pp. 129–154, 2014.
ista: Bellet A, Habrard A, Morvant E, Sebban M. 2014. Learning a priori constrained
weighted majority votes. Machine Learning. 97(1–2), 129–154.
mla: Bellet, Aurélien, et al. “Learning a Priori Constrained Weighted Majority Votes.”
Machine Learning, vol. 97, no. 1–2, Springer, 2014, pp. 129–54, doi:10.1007/s10994-014-5462-z.
short: A. Bellet, A. Habrard, E. Morvant, M. Sebban, Machine Learning 97 (2014)
129–154.
date_created: 2018-12-11T11:56:10Z
date_published: 2014-10-01T00:00:00Z
date_updated: 2021-01-12T06:55:49Z
day: '01'
department:
- _id: ChLa
doi: 10.1007/s10994-014-5462-z
ec_funded: 1
intvolume: ' 97'
issue: 1-2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-01009578/document
month: '10'
oa: 1
oa_version: Submitted Version
page: 129 - 154
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication: Machine Learning
publication_status: published
publisher: Springer
publist_id: '4802'
quality_controlled: '1'
scopus_import: 1
status: public
title: Learning a priori constrained weighted majority votes
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 97
year: '2014'
...
---
_id: '2184'
abstract:
- lang: eng
text: 'Given topological spaces X,Y, a fundamental problem of algebraic topology
is understanding the structure of all continuous maps X→ Y. We consider a computational
version, where X,Y are given as finite simplicial complexes, and the goal is to
compute [X,Y], that is, all homotopy classes of suchmaps.We solve this problem
in the stable range, where for some d ≥ 2, we have dim X ≤ 2d-2 and Y is (d-1)-connected;
in particular, Y can be the d-dimensional sphere Sd. The algorithm combines classical
tools and ideas from homotopy theory (obstruction theory, Postnikov systems, and
simplicial sets) with algorithmic tools from effective algebraic topology (locally
effective simplicial sets and objects with effective homology). In contrast, [X,Y]
is known to be uncomputable for general X,Y, since for X = S1 it includes a well
known undecidable problem: testing triviality of the fundamental group of Y. In
follow-up papers, the algorithm is shown to run in polynomial time for d fixed,
and extended to other problems, such as the extension problem, where we are given
a subspace A ⊂ X and a map A→ Y and ask whether it extends to a map X → Y, or
computing the Z2-index-everything in the stable range. Outside the stable range,
the extension problem is undecidable.'
acknowledgement: The research by M. K. was supported by project GAUK 49209. The research
by M. K. was also supported by project 1M0545 by the Ministry of Education of the
Czech Republic and by Center of Excellence { Inst. for Theor. Comput. Sci., Prague
(project P202/12/G061 of GACR). The research by U. W. was supported by the Swiss
National Science Foundation (SNF Projects 200021-125309, 200020-138230, and PP00P2-138948).
article_number: '17 '
author:
- first_name: Martin
full_name: Čadek, Martin
last_name: Čadek
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
- first_name: Jiří
full_name: Matoušek, Jiří
last_name: Matoušek
- first_name: Francis
full_name: Sergeraert, Francis
last_name: Sergeraert
- first_name: Lukáš
full_name: Vokřínek, Lukáš
last_name: Vokřínek
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Čadek M, Krcál M, Matoušek J, Sergeraert F, Vokřínek L, Wagner U. Computing
all maps into a sphere. Journal of the ACM. 2014;61(3). doi:10.1145/2597629
apa: Čadek, M., Krcál, M., Matoušek, J., Sergeraert, F., Vokřínek, L., & Wagner,
U. (2014). Computing all maps into a sphere. Journal of the ACM. ACM. https://doi.org/10.1145/2597629
chicago: Čadek, Martin, Marek Krcál, Jiří Matoušek, Francis Sergeraert, Lukáš Vokřínek,
and Uli Wagner. “Computing All Maps into a Sphere.” Journal of the ACM.
ACM, 2014. https://doi.org/10.1145/2597629.
ieee: M. Čadek, M. Krcál, J. Matoušek, F. Sergeraert, L. Vokřínek, and U. Wagner,
“Computing all maps into a sphere,” Journal of the ACM, vol. 61, no. 3.
ACM, 2014.
ista: Čadek M, Krcál M, Matoušek J, Sergeraert F, Vokřínek L, Wagner U. 2014. Computing
all maps into a sphere. Journal of the ACM. 61(3), 17.
mla: Čadek, Martin, et al. “Computing All Maps into a Sphere.” Journal of the
ACM, vol. 61, no. 3, 17, ACM, 2014, doi:10.1145/2597629.
short: M. Čadek, M. Krcál, J. Matoušek, F. Sergeraert, L. Vokřínek, U. Wagner, Journal
of the ACM 61 (2014).
date_created: 2018-12-11T11:56:12Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2021-01-12T06:55:50Z
day: '01'
department:
- _id: UlWa
- _id: HeEd
doi: 10.1145/2597629
intvolume: ' 61'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1105.6257
month: '05'
oa: 1
oa_version: Preprint
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '4797'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computing all maps into a sphere
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2014'
...
---
_id: '2183'
abstract:
- lang: eng
text: 'We describe a simple adaptive network of coupled chaotic maps. The network
reaches a stationary state (frozen topology) for all values of the coupling parameter,
although the dynamics of the maps at the nodes of the network can be nontrivial.
The structure of the network shows interesting hierarchical properties and in
certain parameter regions the dynamics is polysynchronous: Nodes can be divided
in differently synchronized classes but, contrary to cluster synchronization,
nodes in the same class need not be connected to each other. These complicated
synchrony patterns have been conjectured to play roles in systems biology and
circuits. The adaptive system we study describes ways whereby this behavior can
evolve from undifferentiated nodes.'
acknowledgement: "V.B.S. is partially supported by contract MEC (Grant No. AYA2010-22111-C03-02).\r\n"
article_number: '062809'
article_processing_charge: No
author:
- first_name: Vicente
full_name: Botella Soler, Vicente
id: 421234E8-F248-11E8-B48F-1D18A9856A87
last_name: Botella Soler
orcid: 0000-0002-8790-1914
- first_name: Paul
full_name: Glendinning, Paul
last_name: Glendinning
citation:
ama: Botella Soler V, Glendinning P. Hierarchy and polysynchrony in an adaptive
network . Physical Review E Statistical Nonlinear and Soft Matter Physics.
2014;89(6). doi:10.1103/PhysRevE.89.062809
apa: Botella Soler, V., & Glendinning, P. (2014). Hierarchy and polysynchrony
in an adaptive network . Physical Review E Statistical Nonlinear and Soft Matter
Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.062809
chicago: Botella Soler, Vicente, and Paul Glendinning. “Hierarchy and Polysynchrony
in an Adaptive Network .” Physical Review E Statistical Nonlinear and Soft
Matter Physics. American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.062809.
ieee: V. Botella Soler and P. Glendinning, “Hierarchy and polysynchrony in an adaptive
network ,” Physical Review E Statistical Nonlinear and Soft Matter Physics,
vol. 89, no. 6. American Institute of Physics, 2014.
ista: Botella Soler V, Glendinning P. 2014. Hierarchy and polysynchrony in an adaptive
network . Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(6),
062809.
mla: Botella Soler, Vicente, and Paul Glendinning. “Hierarchy and Polysynchrony
in an Adaptive Network .” Physical Review E Statistical Nonlinear and Soft
Matter Physics, vol. 89, no. 6, 062809, American Institute of Physics, 2014,
doi:10.1103/PhysRevE.89.062809.
short: V. Botella Soler, P. Glendinning, Physical Review E Statistical Nonlinear
and Soft Matter Physics 89 (2014).
date_created: 2018-12-11T11:56:11Z
date_published: 2014-06-16T00:00:00Z
date_updated: 2022-08-25T14:04:45Z
day: '16'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.89.062809
ec_funded: 1
intvolume: ' 89'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1403.3209
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '4798'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Hierarchy and polysynchrony in an adaptive network '
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2014'
...
---
_id: '2186'
abstract:
- lang: eng
text: We prove the existence of scattering states for the defocusing cubic Gross-Pitaevskii
(GP) hierarchy in ℝ3. Moreover, we show that an exponential energy growth condition
commonly used in the well-posedness theory of the GP hierarchy is, in a specific
sense, necessary. In fact, we prove that without the latter, there exist initial
data for the focusing cubic GP hierarchy for which instantaneous blowup occurs.
author:
- first_name: Thomas
full_name: Chen, Thomas
last_name: Chen
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Nataša
full_name: Pavlović, Nataša
last_name: Pavlović
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Chen T, Hainzl C, Pavlović N, Seiringer R. On the well-posedness and scattering
for the Gross-Pitaevskii hierarchy via quantum de Finetti. Letters in Mathematical
Physics. 2014;104(7):871-891. doi:10.1007/s11005-014-0693-2
apa: Chen, T., Hainzl, C., Pavlović, N., & Seiringer, R. (2014). On the well-posedness
and scattering for the Gross-Pitaevskii hierarchy via quantum de Finetti. Letters
in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-014-0693-2
chicago: Chen, Thomas, Christian Hainzl, Nataša Pavlović, and Robert Seiringer.
“On the Well-Posedness and Scattering for the Gross-Pitaevskii Hierarchy via Quantum
de Finetti.” Letters in Mathematical Physics. Springer, 2014. https://doi.org/10.1007/s11005-014-0693-2.
ieee: T. Chen, C. Hainzl, N. Pavlović, and R. Seiringer, “On the well-posedness
and scattering for the Gross-Pitaevskii hierarchy via quantum de Finetti,” Letters
in Mathematical Physics, vol. 104, no. 7. Springer, pp. 871–891, 2014.
ista: Chen T, Hainzl C, Pavlović N, Seiringer R. 2014. On the well-posedness and
scattering for the Gross-Pitaevskii hierarchy via quantum de Finetti. Letters
in Mathematical Physics. 104(7), 871–891.
mla: Chen, Thomas, et al. “On the Well-Posedness and Scattering for the Gross-Pitaevskii
Hierarchy via Quantum de Finetti.” Letters in Mathematical Physics, vol.
104, no. 7, Springer, 2014, pp. 871–91, doi:10.1007/s11005-014-0693-2.
short: T. Chen, C. Hainzl, N. Pavlović, R. Seiringer, Letters in Mathematical Physics
104 (2014) 871–891.
date_created: 2018-12-11T11:56:12Z
date_published: 2014-05-07T00:00:00Z
date_updated: 2021-01-12T06:55:51Z
day: '07'
department:
- _id: RoSe
doi: 10.1007/s11005-014-0693-2
intvolume: ' 104'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1311.2136
month: '05'
oa: 1
oa_version: Submitted Version
page: 871 - 891
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
publication: Letters in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '4793'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the well-posedness and scattering for the Gross-Pitaevskii hierarchy via
quantum de Finetti
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 104
year: '2014'
...
---
_id: '2187'
abstract:
- lang: eng
text: 'Systems should not only be correct but also robust in the sense that they
behave reasonably in unexpected situations. This article addresses synthesis of
robust reactive systems from temporal specifications. Existing methods allow arbitrary
behavior if assumptions in the specification are violated. To overcome this, we
define two robustness notions, combine them, and show how to enforce them in synthesis.
The first notion applies to safety properties: If safety assumptions are violated
temporarily, we require that the system recovers to normal operation with as few
errors as possible. The second notion requires that, if liveness assumptions are
violated, as many guarantees as possible should be fulfilled nevertheless. We
present a synthesis procedure achieving this for the important class of GR(1)
specifications, and establish complexity bounds. We also present an implementation
of a special case of robustness, and show experimental results.'
article_processing_charge: No
article_type: original
author:
- first_name: Roderick
full_name: Bloem, Roderick
last_name: Bloem
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Karin
full_name: Greimel, Karin
last_name: Greimel
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Georg
full_name: Hofferek, Georg
last_name: Hofferek
- first_name: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
- first_name: Bettina
full_name: Könighofer, Bettina
last_name: Könighofer
- first_name: Robert
full_name: Könighofer, Robert
last_name: Könighofer
citation:
ama: Bloem R, Chatterjee K, Greimel K, et al. Synthesizing robust systems. Acta
Informatica. 2014;51(3-4):193-220. doi:10.1007/s00236-013-0191-5
apa: Bloem, R., Chatterjee, K., Greimel, K., Henzinger, T. A., Hofferek, G., Jobstmann,
B., … Könighofer, R. (2014). Synthesizing robust systems. Acta Informatica.
Springer. https://doi.org/10.1007/s00236-013-0191-5
chicago: Bloem, Roderick, Krishnendu Chatterjee, Karin Greimel, Thomas A Henzinger,
Georg Hofferek, Barbara Jobstmann, Bettina Könighofer, and Robert Könighofer.
“Synthesizing Robust Systems.” Acta Informatica. Springer, 2014. https://doi.org/10.1007/s00236-013-0191-5.
ieee: R. Bloem et al., “Synthesizing robust systems,” Acta Informatica,
vol. 51, no. 3–4. Springer, pp. 193–220, 2014.
ista: Bloem R, Chatterjee K, Greimel K, Henzinger TA, Hofferek G, Jobstmann B, Könighofer
B, Könighofer R. 2014. Synthesizing robust systems. Acta Informatica. 51(3–4),
193–220.
mla: Bloem, Roderick, et al. “Synthesizing Robust Systems.” Acta Informatica,
vol. 51, no. 3–4, Springer, 2014, pp. 193–220, doi:10.1007/s00236-013-0191-5.
short: R. Bloem, K. Chatterjee, K. Greimel, T.A. Henzinger, G. Hofferek, B. Jobstmann,
B. Könighofer, R. Könighofer, Acta Informatica 51 (2014) 193–220.
date_created: 2018-12-11T11:56:13Z
date_published: 2014-06-01T00:00:00Z
date_updated: 2021-01-12T06:55:51Z
day: '01'
ddc:
- '621'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/s00236-013-0191-5
ec_funded: 1
file:
- access_level: open_access
checksum: d7f560f3d923f0f00aa10a0652f83273
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:44Z
date_updated: 2020-07-14T12:45:31Z
file_id: '5234'
file_name: IST-2012-71-v1+1_Synthesizing_robust_systems.pdf
file_size: 169523
relation: main_file
file_date_updated: 2020-07-14T12:45:31Z
has_accepted_license: '1'
intvolume: ' 51'
issue: 3-4
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 193 - 220
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication: Acta Informatica
publication_status: published
publisher: Springer
publist_id: '4787'
pubrep_id: '71'
quality_controlled: '1'
scopus_import: 1
status: public
title: Synthesizing robust systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2014'
...
---
_id: '2188'
abstract:
- lang: eng
text: Although plant and animal cells use a similar core mechanism to deliver proteins
to the plasma membrane, their different lifestyle, body organization and specific
cell structures resulted in the acquisition of regulatory mechanisms that vary
in the two kingdoms. In particular, cell polarity regulators do not seem to be
conserved, because genes encoding key components are absent in plant genomes.
In plants, the broad knowledge on polarity derives from the study of auxin transporters,
the PIN-FORMED proteins, in the model plant Arabidopsis thaliana. In animals,
much information is provided from the study of polarity in epithelial cells that
exhibit basolateral and luminal apical polarities, separated by tight junctions.
In this review, we summarize the similarities and differences of the polarization
mechanisms between plants and animals and survey the main genetic approaches that
have been used to characterize new genes involved in polarity establishment in
plants, including the frequently used forward and reverse genetics screens as
well as a novel chemical genetics approach that is expected to overcome the limitation
of classical genetics methods.
acknowledgement: "This work was supported by a grant from the Research Foundation-Flanders
(Odysseus).\r\n\r\n"
article_number: '140017'
author:
- first_name: Urszula
full_name: Kania, Urszula
id: 4AE5C486-F248-11E8-B48F-1D18A9856A87
last_name: Kania
- first_name: Matyas
full_name: Fendrych, Matyas
last_name: Fendrych
- first_name: Jiřĺ
full_name: Friml, Jiřĺ
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Kania U, Fendrych M, Friml J. Polar delivery in plants; commonalities and differences
to animal epithelial cells. Open Biology. 2014;4(APRIL). doi:10.1098/rsob.140017
apa: Kania, U., Fendrych, M., & Friml, J. (2014). Polar delivery in plants;
commonalities and differences to animal epithelial cells. Open Biology.
Royal Society. https://doi.org/10.1098/rsob.140017
chicago: Kania, Urszula, Matyas Fendrych, and Jiří Friml. “Polar Delivery in Plants;
Commonalities and Differences to Animal Epithelial Cells.” Open Biology.
Royal Society, 2014. https://doi.org/10.1098/rsob.140017.
ieee: U. Kania, M. Fendrych, and J. Friml, “Polar delivery in plants; commonalities
and differences to animal epithelial cells,” Open Biology, vol. 4, no.
APRIL. Royal Society, 2014.
ista: Kania U, Fendrych M, Friml J. 2014. Polar delivery in plants; commonalities
and differences to animal epithelial cells. Open Biology. 4(APRIL), 140017.
mla: Kania, Urszula, et al. “Polar Delivery in Plants; Commonalities and Differences
to Animal Epithelial Cells.” Open Biology, vol. 4, no. APRIL, 140017, Royal
Society, 2014, doi:10.1098/rsob.140017.
short: U. Kania, M. Fendrych, J. Friml, Open Biology 4 (2014).
date_created: 2018-12-11T11:56:13Z
date_published: 2014-04-16T00:00:00Z
date_updated: 2021-01-12T06:55:52Z
day: '16'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1098/rsob.140017
file:
- access_level: open_access
checksum: 2020627feff36cf0799167c84149fa75
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:40Z
date_updated: 2020-07-14T12:45:31Z
file_id: '5025'
file_name: IST-2016-441-v1+1_140017.full.pdf
file_size: 682570
relation: main_file
file_date_updated: 2020-07-14T12:45:31Z
has_accepted_license: '1'
intvolume: ' 4'
issue: APRIL
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Open Biology
publication_status: published
publisher: Royal Society
publist_id: '4786'
pubrep_id: '441'
quality_controlled: '1'
scopus_import: 1
status: public
title: Polar delivery in plants; commonalities and differences to animal epithelial
cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2014'
...
---
_id: '2189'
abstract:
- lang: fre
text: En apprentissage automatique, nous parlons d'adaptation de domaine lorsque
les données de test (cibles) et d'apprentissage (sources) sont générées selon
différentes distributions. Nous devons donc développer des algorithmes de classification
capables de s'adapter à une nouvelle distribution, pour laquelle aucune information
sur les étiquettes n'est disponible. Nous attaquons cette problématique sous l'angle
de l'approche PAC-Bayésienne qui se focalise sur l'apprentissage de modèles définis
comme des votes de majorité sur un ensemble de fonctions. Dans ce contexte, nous
introduisons PV-MinCq une version adaptative de l'algorithme (non adaptatif) MinCq.
PV-MinCq suit le principe suivant. Nous transférons les étiquettes sources aux
points cibles proches pour ensuite appliquer MinCq sur l'échantillon cible ``auto-étiqueté''
(justifié par une borne théorique). Plus précisément, nous définissons un auto-étiquetage
non itératif qui se focalise dans les régions où les distributions marginales
source et cible sont les plus similaires. Dans un second temps, nous étudions
l'influence de notre auto-étiquetage pour en déduire une procédure de validation
des hyperparamètres. Finalement, notre approche montre des résultats empiriques
prometteurs.
article_processing_charge: No
author:
- first_name: Emilie
full_name: Morvant, Emilie
id: 4BAC2A72-F248-11E8-B48F-1D18A9856A87
last_name: Morvant
orcid: 0000-0002-8301-7240
citation:
ama: 'Morvant E. Adaptation de domaine de vote de majorité par auto-étiquetage non
itératif. In: Vol 1. Elsevier; 2014:49-58.'
apa: 'Morvant, E. (2014). Adaptation de domaine de vote de majorité par auto-étiquetage
non itératif (Vol. 1, pp. 49–58). Presented at the CAP: Conférence Francophone
sur l’Apprentissage Automatique (Machine Learning French Conference), Saint-Etienne,
France: Elsevier.'
chicago: Morvant, Emilie. “Adaptation de Domaine de Vote de Majorité Par Auto-Étiquetage
Non Itératif,” 1:49–58. Elsevier, 2014.
ieee: 'E. Morvant, “Adaptation de domaine de vote de majorité par auto-étiquetage
non itératif,” presented at the CAP: Conférence Francophone sur l’Apprentissage
Automatique (Machine Learning French Conference), Saint-Etienne, France, 2014,
vol. 1, pp. 49–58.'
ista: 'Morvant E. 2014. Adaptation de domaine de vote de majorité par auto-étiquetage
non itératif. CAP: Conférence Francophone sur l’Apprentissage Automatique (Machine
Learning French Conference) vol. 1, 49–58.'
mla: Morvant, Emilie. Adaptation de Domaine de Vote de Majorité Par Auto-Étiquetage
Non Itératif. Vol. 1, Elsevier, 2014, pp. 49–58.
short: E. Morvant, in:, Elsevier, 2014, pp. 49–58.
conference:
location: Saint-Etienne, France
name: 'CAP: Conférence Francophone sur l''Apprentissage Automatique (Machine Learning
French Conference)'
date_created: 2018-12-11T11:56:13Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2021-01-12T06:55:52Z
day: '01'
department:
- _id: ChLa
intvolume: ' 1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-01005776/
month: '07'
oa: 1
oa_version: Preprint
page: 49-58
publication_status: published
publisher: Elsevier
publist_id: '4785'
quality_controlled: '1'
status: public
title: Adaptation de domaine de vote de majorité par auto-étiquetage non itératif
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2014'
...
---
_id: '2190'
abstract:
- lang: eng
text: We present a new algorithm to construct a (generalized) deterministic Rabin
automaton for an LTL formula φ. The automaton is the product of a master automaton
and an array of slave automata, one for each G-subformula of φ. The slave automaton
for G ψ is in charge of recognizing whether FG ψ holds. As opposed to standard
determinization procedures, the states of all our automata have a clear logical
structure, which allows for various optimizations. Our construction subsumes former
algorithms for fragments of LTL. Experimental results show improvement in the
sizes of the resulting automata compared to existing methods.
acknowledgement: The author is on leave from Faculty of Informatics, Masaryk University,
Czech Republic, and partially supported by the Czech Science Foundation, grant No.
P202/12/G061.
alternative_title:
- LNCS
author:
- first_name: Javier
full_name: Esparza, Javier
last_name: Esparza
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: 'Esparza J, Kretinsky J. From LTL to deterministic automata: A safraless compositional
approach. In: Vol 8559. Springer; 2014:192-208. doi:10.1007/978-3-319-08867-9_13'
apa: 'Esparza, J., & Kretinsky, J. (2014). From LTL to deterministic automata:
A safraless compositional approach (Vol. 8559, pp. 192–208). Presented at the
CAV: Computer Aided Verification, Springer. https://doi.org/10.1007/978-3-319-08867-9_13'
chicago: 'Esparza, Javier, and Jan Kretinsky. “From LTL to Deterministic Automata:
A Safraless Compositional Approach,” 8559:192–208. Springer, 2014. https://doi.org/10.1007/978-3-319-08867-9_13.'
ieee: 'J. Esparza and J. Kretinsky, “From LTL to deterministic automata: A safraless
compositional approach,” presented at the CAV: Computer Aided Verification, 2014,
vol. 8559, pp. 192–208.'
ista: 'Esparza J, Kretinsky J. 2014. From LTL to deterministic automata: A safraless
compositional approach. CAV: Computer Aided Verification, LNCS, vol. 8559, 192–208.'
mla: 'Esparza, Javier, and Jan Kretinsky. From LTL to Deterministic Automata:
A Safraless Compositional Approach. Vol. 8559, Springer, 2014, pp. 192–208,
doi:10.1007/978-3-319-08867-9_13.'
short: J. Esparza, J. Kretinsky, in:, Springer, 2014, pp. 192–208.
conference:
name: 'CAV: Computer Aided Verification'
date_created: 2018-12-11T11:56:14Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:55:53Z
day: '01'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1007/978-3-319-08867-9_13
ec_funded: 1
intvolume: ' 8559'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1402.3388
month: '01'
oa: 1
oa_version: Submitted Version
page: 192 - 208
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication_status: published
publisher: Springer
publist_id: '4784'
quality_controlled: '1'
status: public
title: 'From LTL to deterministic automata: A safraless compositional approach'
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8559
year: '2014'
...
---
_id: '2208'
abstract:
- lang: eng
text: 'We propose to detect quadrupole interactions of neutral ultracold atoms via
their induced mean-field shift. We consider a Mott insulator state of spin-polarized
atoms in a two-dimensional optical square lattice. The quadrupole moments of the
atoms are aligned by an external magnetic field. As the alignment angle is varied,
the mean-field shift shows a characteristic angular dependence, which constitutes
the defining signature of the quadrupole interaction. For the 3P2 states of Yb
and Sr atoms, we find a frequency shift of the order of tens of Hertz, which can
be realistically detected in experiment with current technology. We compare our
results to the mean-field shift of a spin-polarized quasi-two-dimensional Fermi
gas in continuum. '
article_number: '043616'
author:
- first_name: Martin
full_name: Lahrz, Martin
last_name: Lahrz
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Klaus
full_name: Sengstock, Klaus
last_name: Sengstock
- first_name: Christoph
full_name: Becker, Christoph
last_name: Becker
- first_name: Ludwig
full_name: Mathey, Ludwig
last_name: Mathey
citation:
ama: Lahrz M, Lemeshko M, Sengstock K, Becker C, Mathey L. Detecting quadrupole
interactions in ultracold Fermi gases. Physical Review A - Atomic, Molecular,
and Optical Physics. 2014;89(4). doi:10.1103/PhysRevA.89.043616
apa: Lahrz, M., Lemeshko, M., Sengstock, K., Becker, C., & Mathey, L. (2014).
Detecting quadrupole interactions in ultracold Fermi gases. Physical Review
A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.89.043616
chicago: Lahrz, Martin, Mikhail Lemeshko, Klaus Sengstock, Christoph Becker, and
Ludwig Mathey. “Detecting Quadrupole Interactions in Ultracold Fermi Gases.” Physical
Review A - Atomic, Molecular, and Optical Physics. American Physical Society,
2014. https://doi.org/10.1103/PhysRevA.89.043616.
ieee: M. Lahrz, M. Lemeshko, K. Sengstock, C. Becker, and L. Mathey, “Detecting
quadrupole interactions in ultracold Fermi gases,” Physical Review A - Atomic,
Molecular, and Optical Physics, vol. 89, no. 4. American Physical Society,
2014.
ista: Lahrz M, Lemeshko M, Sengstock K, Becker C, Mathey L. 2014. Detecting quadrupole
interactions in ultracold Fermi gases. Physical Review A - Atomic, Molecular,
and Optical Physics. 89(4), 043616.
mla: Lahrz, Martin, et al. “Detecting Quadrupole Interactions in Ultracold Fermi
Gases.” Physical Review A - Atomic, Molecular, and Optical Physics, vol.
89, no. 4, 043616, American Physical Society, 2014, doi:10.1103/PhysRevA.89.043616.
short: M. Lahrz, M. Lemeshko, K. Sengstock, C. Becker, L. Mathey, Physical Review
A - Atomic, Molecular, and Optical Physics 89 (2014).
date_created: 2018-12-11T11:56:20Z
date_published: 2014-04-23T00:00:00Z
date_updated: 2021-01-12T06:55:59Z
day: '23'
doi: 10.1103/PhysRevA.89.043616
extern: '1'
intvolume: ' 89'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1402.0873
month: '04'
oa: 1
oa_version: Submitted Version
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '4764'
quality_controlled: '1'
status: public
title: Detecting quadrupole interactions in ultracold Fermi gases
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2014'
...
---
_id: '2214'
abstract:
- lang: eng
text: A hallmark of immune cell trafficking is directional guidance via gradients
of soluble or surface bound chemokines. Vascular endothelial cells produce, transport
and deposit either their own chemokines or chemokines produced by the underlying
stroma. Endothelial heparan sulfate (HS) was suggested to be a critical scaffold
for these chemokine pools, but it is unclear how steep chemokine gradients are
sustained between the lumenal and ablumenal aspects of blood vessels. Addressing
this question by semi-quantitative immunostaining of HS moieties around blood
vessels with a pan anti-HS IgM mAb, we found a striking HS enrichment in the basal
lamina of resting and inflamed post capillary skin venules, as well as in high
endothelial venules (HEVs) of lymph nodes. Staining of skin vessels with a glycocalyx
probe further suggested that their lumenal glycocalyx contains much lower HS density
than their basolateral extracellular matrix (ECM). This polarized HS pattern was
observed also in isolated resting and inflamed microvascular dermal cells. Notably,
progressive skin inflammation resulted in massive ECM deposition and in further
HS enrichment around skin post capillary venules and their associated pericytes.
Inflammation-dependent HS enrichment was not compromised in mice deficient in
the main HS degrading enzyme, heparanase. Our results suggest that the blood vasculature
patterns steep gradients of HS scaffolds between their lumenal and basolateral
endothelial aspects, and that inflammatory processes can further enrich the HS
content nearby inflamed vessels. We propose that chemokine gradients between the
lumenal and ablumenal sides of vessels could be favored by these sharp HS scaffold
gradients.
acknowledgement: Michael Sixt's research is supported by the European Research Council
(ERC Starting grant).
article_number: e85699
author:
- first_name: Liat
full_name: Stoler Barak, Liat
last_name: Stoler Barak
- first_name: Christine
full_name: Moussion, Christine
id: 3356F664-F248-11E8-B48F-1D18A9856A87
last_name: Moussion
- first_name: Elias
full_name: Shezen, Elias
last_name: Shezen
- first_name: Miki
full_name: Hatzav, Miki
last_name: Hatzav
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Ronen
full_name: Alon, Ronen
last_name: Alon
citation:
ama: Stoler Barak L, Moussion C, Shezen E, Hatzav M, Sixt MK, Alon R. Blood vessels
pattern heparan sulfate gradients between their apical and basolateral aspects.
PLoS One. 2014;9(1). doi:10.1371/journal.pone.0085699
apa: Stoler Barak, L., Moussion, C., Shezen, E., Hatzav, M., Sixt, M. K., &
Alon, R. (2014). Blood vessels pattern heparan sulfate gradients between their
apical and basolateral aspects. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0085699
chicago: Stoler Barak, Liat, Christine Moussion, Elias Shezen, Miki Hatzav, Michael
K Sixt, and Ronen Alon. “Blood Vessels Pattern Heparan Sulfate Gradients between
Their Apical and Basolateral Aspects.” PLoS One. Public Library of Science,
2014. https://doi.org/10.1371/journal.pone.0085699.
ieee: L. Stoler Barak, C. Moussion, E. Shezen, M. Hatzav, M. K. Sixt, and R. Alon,
“Blood vessels pattern heparan sulfate gradients between their apical and basolateral
aspects,” PLoS One, vol. 9, no. 1. Public Library of Science, 2014.
ista: Stoler Barak L, Moussion C, Shezen E, Hatzav M, Sixt MK, Alon R. 2014. Blood
vessels pattern heparan sulfate gradients between their apical and basolateral
aspects. PLoS One. 9(1), e85699.
mla: Stoler Barak, Liat, et al. “Blood Vessels Pattern Heparan Sulfate Gradients
between Their Apical and Basolateral Aspects.” PLoS One, vol. 9, no. 1,
e85699, Public Library of Science, 2014, doi:10.1371/journal.pone.0085699.
short: L. Stoler Barak, C. Moussion, E. Shezen, M. Hatzav, M.K. Sixt, R. Alon, PLoS
One 9 (2014).
date_created: 2018-12-11T11:56:22Z
date_published: 2014-01-22T00:00:00Z
date_updated: 2021-01-12T06:56:03Z
day: '22'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1371/journal.pone.0085699
ec_funded: 1
file:
- access_level: open_access
checksum: 84a8033bda2e07e39405f5acc85f4eca
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:48Z
date_updated: 2020-07-14T12:45:33Z
file_id: '4646'
file_name: IST-2016-433-v1+1_journal.pone.0085699.pdf
file_size: 12634775
relation: main_file
file_date_updated: 2020-07-14T12:45:33Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25A76F58-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '289720'
name: Stromal Cell-immune Cell Interactions in Health and Disease
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '4756'
pubrep_id: '433'
quality_controlled: '1'
scopus_import: 1
status: public
title: Blood vessels pattern heparan sulfate gradients between their apical and basolateral
aspects
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2014'
...
---
_id: '2215'
abstract:
- lang: eng
text: Homologous recombination is crucial for genome stability and for genetic exchange.
Although our knowledge of the principle steps in recombination and its machinery
is well advanced, homology search, the critical step of exploring the genome for
homologous sequences to enable recombination, has remained mostly enigmatic. However,
recent methodological advances have provided considerable new insights into this
fundamental step in recombination that can be integrated into a mechanistic model.
These advances emphasize the importance of genomic proximity and nuclear organization
for homology search and the critical role of homology search mediators in this
process. They also aid our understanding of how homology search might lead to
unwanted and potentially disease-promoting recombination events.
acknowledgement: J.R. was supported by a Boehringer Ingelheim Fonds PhD stipend.
author:
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Claudio
full_name: Lademann, Claudio
last_name: Lademann
- first_name: Stefan
full_name: Jentsch, Stefan
last_name: Jentsch
citation:
ama: Renkawitz J, Lademann C, Jentsch S. Mechanisms and principles of homology search
during recombination. Nature Reviews Molecular Cell Biology. 2014;15(6):369-383.
doi:10.1038/nrm3805
apa: Renkawitz, J., Lademann, C., & Jentsch, S. (2014). Mechanisms and principles
of homology search during recombination. Nature Reviews Molecular Cell Biology.
Nature Publishing Group. https://doi.org/10.1038/nrm3805
chicago: Renkawitz, Jörg, Claudio Lademann, and Stefan Jentsch. “Mechanisms and
Principles of Homology Search during Recombination.” Nature Reviews Molecular
Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/nrm3805.
ieee: J. Renkawitz, C. Lademann, and S. Jentsch, “Mechanisms and principles of homology
search during recombination,” Nature Reviews Molecular Cell Biology, vol.
15, no. 6. Nature Publishing Group, pp. 369–383, 2014.
ista: Renkawitz J, Lademann C, Jentsch S. 2014. Mechanisms and principles of homology
search during recombination. Nature Reviews Molecular Cell Biology. 15(6), 369–383.
mla: Renkawitz, Jörg, et al. “Mechanisms and Principles of Homology Search during
Recombination.” Nature Reviews Molecular Cell Biology, vol. 15, no. 6,
Nature Publishing Group, 2014, pp. 369–83, doi:10.1038/nrm3805.
short: J. Renkawitz, C. Lademann, S. Jentsch, Nature Reviews Molecular Cell Biology
15 (2014) 369–383.
date_created: 2018-12-11T11:56:22Z
date_published: 2014-05-14T00:00:00Z
date_updated: 2021-01-12T06:56:03Z
day: '14'
department:
- _id: MiSi
doi: 10.1038/nrm3805
intvolume: ' 15'
issue: '6'
language:
- iso: eng
month: '05'
oa_version: None
page: 369 - 383
publication: Nature Reviews Molecular Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '4755'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mechanisms and principles of homology search during recombination
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2014'
...
---
_id: '2223'
abstract:
- lang: eng
text: Correct positioning of membrane proteins is an essential process in eukaryotic
organisms. The plant hormone auxin is distributed through intercellular transport
and triggers various cellular responses. Auxin transporters of the PIN-FORMED
(PIN) family localize asymmetrically at the plasma membrane (PM) and mediate the
directional transport of auxin between cells. A fungal toxin, brefeldin A (BFA),
inhibits a subset of guanine nucleotide exchange factors for ADP-ribosylation
factor small GTPases (ARF GEFs) including GNOM, which plays a major role in localization
of PIN1 predominantly to the basal side of the PM. The Arabidopsis genome encodes
19 ARF-related putative GTPases. However, ARF components involved in PIN1 localization
have been genetically poorly defined. Using a fluorescence imaging-based forward
genetic approach, we identified an Arabidopsis mutant, bfa-visualized exocytic
trafficking defective1 (bex1), in which PM localization of PIN1-green fluorescent
protein (GFP) as well as development is hypersensitive to BFA. We found that in
bex1 a member of the ARF1 gene family, ARF1A1C, was mutated. ARF1A1C localizes
to the trans-Golgi network/early endosome and Golgi apparatus, acts synergistically
to BEN1/MIN7 ARF GEF and is important for PIN recycling to the PM. Consistent
with the developmental importance of PIN proteins, functional interference with
ARF1 resulted in an impaired auxin response gradient and various developmental
defects including embryonic patterning defects and growth arrest. Our results
show that ARF1A1C is essential for recycling of PIN auxin transporters and for
various auxin-dependent developmental processes.
author:
- first_name: Hirokazu
full_name: Tanaka, Hirokazu
last_name: Tanaka
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Saeko
full_name: Kitakura, Saeko
last_name: Kitakura
- first_name: Mugurel
full_name: Feraru, Mugurel
last_name: Feraru
- first_name: Michiko
full_name: Sasabe, Michiko
last_name: Sasabe
- first_name: Tomomi
full_name: Ishikawa, Tomomi
last_name: Ishikawa
- first_name: Jürgen
full_name: Kleine Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Tatsuo
full_name: Kakimoto, Tatsuo
last_name: Kakimoto
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Tanaka H, Nodzyński T, Kitakura S, et al. BEX1/ARF1A1C is required for BFA-sensitive
recycling of PIN auxin transporters and auxin-mediated development in arabidopsis.
Plant and Cell Physiology. 2014;55(4):737-749. doi:10.1093/pcp/pct196
apa: Tanaka, H., Nodzyński, T., Kitakura, S., Feraru, M., Sasabe, M., Ishikawa,
T., … Friml, J. (2014). BEX1/ARF1A1C is required for BFA-sensitive recycling of
PIN auxin transporters and auxin-mediated development in arabidopsis. Plant
and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pct196
chicago: Tanaka, Hirokazu, Tomasz Nodzyński, Saeko Kitakura, Mugurel Feraru, Michiko
Sasabe, Tomomi Ishikawa, Jürgen Kleine Vehn, Tatsuo Kakimoto, and Jiří Friml.
“BEX1/ARF1A1C Is Required for BFA-Sensitive Recycling of PIN Auxin Transporters
and Auxin-Mediated Development in Arabidopsis.” Plant and Cell Physiology.
Oxford University Press, 2014. https://doi.org/10.1093/pcp/pct196.
ieee: H. Tanaka et al., “BEX1/ARF1A1C is required for BFA-sensitive recycling
of PIN auxin transporters and auxin-mediated development in arabidopsis,” Plant
and Cell Physiology, vol. 55, no. 4. Oxford University Press, pp. 737–749,
2014.
ista: Tanaka H, Nodzyński T, Kitakura S, Feraru M, Sasabe M, Ishikawa T, Kleine
Vehn J, Kakimoto T, Friml J. 2014. BEX1/ARF1A1C is required for BFA-sensitive
recycling of PIN auxin transporters and auxin-mediated development in arabidopsis.
Plant and Cell Physiology. 55(4), 737–749.
mla: Tanaka, Hirokazu, et al. “BEX1/ARF1A1C Is Required for BFA-Sensitive Recycling
of PIN Auxin Transporters and Auxin-Mediated Development in Arabidopsis.” Plant
and Cell Physiology, vol. 55, no. 4, Oxford University Press, 2014, pp. 737–49,
doi:10.1093/pcp/pct196.
short: H. Tanaka, T. Nodzyński, S. Kitakura, M. Feraru, M. Sasabe, T. Ishikawa,
J. Kleine Vehn, T. Kakimoto, J. Friml, Plant and Cell Physiology 55 (2014) 737–749.
date_created: 2018-12-11T11:56:25Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T06:56:07Z
day: '01'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1093/pcp/pct196
ec_funded: 1
file:
- access_level: open_access
checksum: b781a76b32ac35a520256453c3ba9433
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:25Z
date_updated: 2020-07-14T12:45:34Z
file_id: '5076'
file_name: IST-2016-431-v1+1_Plant_Cell_Physiol-2014-Tanaka-737-49.pdf
file_size: 2028111
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 55'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://repository.ist.ac.at/id/eprint/431
month: '04'
oa: 1
oa_version: Published Version
page: 737 - 749
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
- _id: 256BDAB0-B435-11E9-9278-68D0E5697425
name: Innovationsförderung in der Grenzregion Österreich – Tschechische Republik
durch die Schaffung von Synergien im Bereich der Forschungsinfrastruktur
publication: Plant and Cell Physiology
publication_identifier:
issn:
- '00320781'
publication_status: published
publisher: Oxford University Press
publist_id: '4741'
pubrep_id: '431'
quality_controlled: '1'
scopus_import: 1
status: public
title: BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters
and auxin-mediated development in arabidopsis
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2014'
...
---
_id: '2225'
abstract:
- lang: eng
text: "We consider sample covariance matrices of the form X∗X, where X is an M×N
matrix with independent random entries. We prove the isotropic local Marchenko-Pastur
law, i.e. we prove that the resolvent (X∗X−z)−1 converges to a multiple of the
identity in the sense of quadratic forms. More precisely, we establish sharp high-probability
bounds on the quantity ⟨v,(X∗X−z)−1w⟩−⟨v,w⟩m(z), where m is the Stieltjes transform
of the Marchenko-Pastur law and v,w∈CN. We require the logarithms of the dimensions
M and N to be comparable. Our result holds down to scales Iz≥N−1+ε and throughout
the entire spectrum away from 0. We also prove analogous results for generalized
Wigner matrices.\r\n"
article_number: '33'
author:
- first_name: Alex
full_name: Bloemendal, Alex
last_name: Bloemendal
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Antti
full_name: Knowles, Antti
last_name: Knowles
- first_name: Horng
full_name: Yau, Horng
last_name: Yau
- first_name: Jun
full_name: Yin, Jun
last_name: Yin
citation:
ama: Bloemendal A, Erdös L, Knowles A, Yau H, Yin J. Isotropic local laws for sample
covariance and generalized Wigner matrices. Electronic Journal of Probability.
2014;19. doi:10.1214/EJP.v19-3054
apa: Bloemendal, A., Erdös, L., Knowles, A., Yau, H., & Yin, J. (2014). Isotropic
local laws for sample covariance and generalized Wigner matrices. Electronic
Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/EJP.v19-3054
chicago: Bloemendal, Alex, László Erdös, Antti Knowles, Horng Yau, and Jun Yin.
“Isotropic Local Laws for Sample Covariance and Generalized Wigner Matrices.”
Electronic Journal of Probability. Institute of Mathematical Statistics,
2014. https://doi.org/10.1214/EJP.v19-3054.
ieee: A. Bloemendal, L. Erdös, A. Knowles, H. Yau, and J. Yin, “Isotropic local
laws for sample covariance and generalized Wigner matrices,” Electronic Journal
of Probability, vol. 19. Institute of Mathematical Statistics, 2014.
ista: Bloemendal A, Erdös L, Knowles A, Yau H, Yin J. 2014. Isotropic local laws
for sample covariance and generalized Wigner matrices. Electronic Journal of Probability.
19, 33.
mla: Bloemendal, Alex, et al. “Isotropic Local Laws for Sample Covariance and Generalized
Wigner Matrices.” Electronic Journal of Probability, vol. 19, 33, Institute
of Mathematical Statistics, 2014, doi:10.1214/EJP.v19-3054.
short: A. Bloemendal, L. Erdös, A. Knowles, H. Yau, J. Yin, Electronic Journal of
Probability 19 (2014).
date_created: 2018-12-11T11:56:25Z
date_published: 2014-03-15T00:00:00Z
date_updated: 2021-01-12T06:56:07Z
day: '15'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1214/EJP.v19-3054
ec_funded: 1
file:
- access_level: open_access
checksum: 7eb297ff367a2ee73b21b6dd1e1948e4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:06Z
date_updated: 2020-07-14T12:45:34Z
file_id: '5055'
file_name: IST-2016-427-v1+1_3054-16624-4-PB.pdf
file_size: 810150
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 19'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Electronic Journal of Probability
publication_identifier:
issn:
- '10836489'
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '4739'
pubrep_id: '427'
quality_controlled: '1'
status: public
title: Isotropic local laws for sample covariance and generalized Wigner matrices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2014'
...
---
_id: '2222'
abstract:
- lang: eng
text: Leaf venation develops complex patterns in angiosperms, but the mechanism
underlying this process is largely unknown. To elucidate the molecular mechanisms
governing vein pattern formation, we previously isolated vascular network defective
(van) mutants that displayed venation discontinuities. Here, we report the phenotypic
analysis of van4 mutants, and we identify and characterize the VAN4 gene. Detailed
phenotypic analysis shows that van4 mutants are defective in procambium cell differentiation
and subsequent vascular cell differentiation. Reduced shoot and root cell growth
is observed in van4 mutants, suggesting that VAN4 function is important for cell
growth and the establishment of venation continuity. Consistent with these phenotypes,
the VAN4 gene is strongly expressed in vascular and meristematic cells. VAN4 encodes
a putative TRS120, which is a known guanine nucleotide exchange factor (GEF) for
Rab GTPase involved in regulating vesicle transport, and a known tethering factor
that determines the specificity of membrane fusion. VAN4 protein localizes at
the trans-Golgi network/early endosome (TGN/EE). Aberrant recycling of the auxin
efflux carrier PIN proteins is observed in van4 mutants. These results suggest
that VAN4-mediated exocytosis at the TGN plays important roles in plant vascular
development and cell growth in shoot and root. Our identification of VAN4 as a
putative TRS120 shows that Rab GTPases are crucial (in addition to ARF GTPases)
for continuous vascular development, and provides further evidence for the importance
of vesicle transport in leaf vascular formation.
author:
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Tomoko
full_name: Dainobu, Tomoko
last_name: Dainobu
- first_name: Hirotomo
full_name: Takatsuka, Hirotomo
last_name: Takatsuka
- first_name: Teruyo
full_name: Okada, Teruyo
last_name: Okada
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Hiroo
full_name: Fukuda, Hiroo
last_name: Fukuda
citation:
ama: Naramoto S, Nodzyński T, Dainobu T, et al. VAN4 encodes a putative TRS120 that
is required for normal cell growth and vein development in arabidopsis. Plant
and Cell Physiology. 2014;55(4):750-763. doi:10.1093/pcp/pcu012
apa: Naramoto, S., Nodzyński, T., Dainobu, T., Takatsuka, H., Okada, T., Friml,
J., & Fukuda, H. (2014). VAN4 encodes a putative TRS120 that is required for
normal cell growth and vein development in arabidopsis. Plant and Cell Physiology.
Oxford University Press. https://doi.org/10.1093/pcp/pcu012
chicago: Naramoto, Satoshi, Tomasz Nodzyński, Tomoko Dainobu, Hirotomo Takatsuka,
Teruyo Okada, Jiří Friml, and Hiroo Fukuda. “VAN4 Encodes a Putative TRS120 That
Is Required for Normal Cell Growth and Vein Development in Arabidopsis.” Plant
and Cell Physiology. Oxford University Press, 2014. https://doi.org/10.1093/pcp/pcu012.
ieee: S. Naramoto et al., “VAN4 encodes a putative TRS120 that is required
for normal cell growth and vein development in arabidopsis,” Plant and Cell
Physiology, vol. 55, no. 4. Oxford University Press, pp. 750–763, 2014.
ista: Naramoto S, Nodzyński T, Dainobu T, Takatsuka H, Okada T, Friml J, Fukuda
H. 2014. VAN4 encodes a putative TRS120 that is required for normal cell growth
and vein development in arabidopsis. Plant and Cell Physiology. 55(4), 750–763.
mla: Naramoto, Satoshi, et al. “VAN4 Encodes a Putative TRS120 That Is Required
for Normal Cell Growth and Vein Development in Arabidopsis.” Plant and Cell
Physiology, vol. 55, no. 4, Oxford University Press, 2014, pp. 750–63, doi:10.1093/pcp/pcu012.
short: S. Naramoto, T. Nodzyński, T. Dainobu, H. Takatsuka, T. Okada, J. Friml,
H. Fukuda, Plant and Cell Physiology 55 (2014) 750–763.
date_created: 2018-12-11T11:56:24Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T06:56:06Z
day: '01'
department:
- _id: JiFr
doi: 10.1093/pcp/pcu012
ec_funded: 1
intvolume: ' 55'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 750 - 763
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Plant and Cell Physiology
publication_identifier:
issn:
- '00320781'
publication_status: published
publisher: Oxford University Press
publist_id: '4742'
quality_controlled: '1'
scopus_import: 1
status: public
title: VAN4 encodes a putative TRS120 that is required for normal cell growth and
vein development in arabidopsis
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2014'
...
---
_id: '2224'
abstract:
- lang: eng
text: This work investigates the transition between different traveling helical
waves (spirals, SPIs) in the setup of differentially independent rotating cylinders.
We use direct numerical simulations to consider an infinite long and periodic
Taylor-Couette apparatus with fixed axial periodicity length. We find so-called
mixed-cross-spirals (MCSs), that can be seen as nonlinear superpositions of SPIs,
to establish stable footbridges connecting SPI states. While bridging the bifurcation
branches of SPIs, the corresponding contributions within the MCS vary continuously
with the control parameters. Here discussed MCSs presenting footbridge solutions
start and end in different SPI branches. Therefore they differ significantly from
the already known MCSs that present bypass solutions (Altmeyer and Hoffmann 2010
New J. Phys. 12 113035). The latter start and end in the same SPI branch, while
they always bifurcate out of those SPI branches with the larger mode amplitude.
Meanwhile, these only appear within the coexisting region of both SPIs. In contrast,
the footbridge solutions can also bifurcate out of the minor SPI contribution.
We also find they exist in regions where only one of the SPIs contributions exists.
In addition, MCS as footbridge solution can appear either stable or unstable.
The latter detected transient solutions offer similar spatio-temporal characteristics
to the flow establishing stable footbridges. Such transition processes are interesting
for pattern-forming systems in general because they accomplish transitions between
traveling waves of different azimuthal wave numbers and have not been described
in the literature yet.
article_number: '025503'
author:
- first_name: Sebastian
full_name: Altmeyer, Sebastian
id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87
last_name: Altmeyer
orcid: 0000-0001-5964-0203
citation:
ama: Altmeyer S. On secondary instabilities generating footbridges between spiral
vortex flow. Fluid Dynamics Research. 2014;46(2). doi:10.1088/0169-5983/46/2/025503
apa: Altmeyer, S. (2014). On secondary instabilities generating footbridges between
spiral vortex flow. Fluid Dynamics Research. IOP Publishing Ltd. https://doi.org/10.1088/0169-5983/46/2/025503
chicago: Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges
between Spiral Vortex Flow.” Fluid Dynamics Research. IOP Publishing Ltd.,
2014. https://doi.org/10.1088/0169-5983/46/2/025503.
ieee: S. Altmeyer, “On secondary instabilities generating footbridges between spiral
vortex flow,” Fluid Dynamics Research, vol. 46, no. 2. IOP Publishing Ltd.,
2014.
ista: Altmeyer S. 2014. On secondary instabilities generating footbridges between
spiral vortex flow. Fluid Dynamics Research. 46(2), 025503.
mla: Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges between
Spiral Vortex Flow.” Fluid Dynamics Research, vol. 46, no. 2, 025503, IOP
Publishing Ltd., 2014, doi:10.1088/0169-5983/46/2/025503.
short: S. Altmeyer, Fluid Dynamics Research 46 (2014).
date_created: 2018-12-11T11:56:25Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T06:56:07Z
day: '01'
department:
- _id: BjHo
doi: 10.1088/0169-5983/46/2/025503
intvolume: ' 46'
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
publication: Fluid Dynamics Research
publication_identifier:
issn:
- '01695983'
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '4740'
quality_controlled: '1'
scopus_import: 1
status: public
title: On secondary instabilities generating footbridges between spiral vortex flow
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2014'
...
---
_id: '2219'
abstract:
- lang: eng
text: Recently, Döttling et al. (ASIACRYPT 2012) proposed the first chosen-ciphertext
(IND-CCA) secure public-key encryption scheme from the learning parity with noise
(LPN) assumption. In this work we give an alternative scheme which is conceptually
simpler and more efficient. At the core of our construction is a trapdoor technique
originally proposed for lattices by Micciancio and Peikert (EUROCRYPT 2012), which
we adapt to the LPN setting. The main technical tool is a new double-trapdoor
mechanism, together with a trapdoor switching lemma based on a computational variant
of the leftover hash lemma.
alternative_title:
- LNCS
author:
- first_name: Eike
full_name: Kiltz, Eike
last_name: Kiltz
- first_name: Daniel
full_name: Masny, Daniel
last_name: Masny
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Kiltz E, Masny D, Pietrzak KZ. Simple chosen-ciphertext security from low
noise LPN. In: Vol 8383. Springer; 2014:1-18. doi:10.1007/978-3-642-54631-0_1'
apa: 'Kiltz, E., Masny, D., & Pietrzak, K. Z. (2014). Simple chosen-ciphertext
security from low noise LPN (Vol. 8383, pp. 1–18). Presented at the IACR: International
Conference on Practice and Theory in Public-Key Cryptography, Springer. https://doi.org/10.1007/978-3-642-54631-0_1'
chicago: Kiltz, Eike, Daniel Masny, and Krzysztof Z Pietrzak. “Simple Chosen-Ciphertext
Security from Low Noise LPN,” 8383:1–18. Springer, 2014. https://doi.org/10.1007/978-3-642-54631-0_1.
ieee: 'E. Kiltz, D. Masny, and K. Z. Pietrzak, “Simple chosen-ciphertext security
from low noise LPN,” presented at the IACR: International Conference on Practice
and Theory in Public-Key Cryptography, 2014, vol. 8383, pp. 1–18.'
ista: 'Kiltz E, Masny D, Pietrzak KZ. 2014. Simple chosen-ciphertext security from
low noise LPN. IACR: International Conference on Practice and Theory in Public-Key
Cryptography, LNCS, vol. 8383, 1–18.'
mla: Kiltz, Eike, et al. Simple Chosen-Ciphertext Security from Low Noise LPN.
Vol. 8383, Springer, 2014, pp. 1–18, doi:10.1007/978-3-642-54631-0_1.
short: E. Kiltz, D. Masny, K.Z. Pietrzak, in:, Springer, 2014, pp. 1–18.
conference:
name: 'IACR: International Conference on Practice and Theory in Public-Key Cryptography'
date_created: 2018-12-11T11:56:24Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2021-01-12T06:56:05Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-642-54631-0_1
intvolume: ' 8383'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2015/401
month: '03'
oa: 1
oa_version: Submitted Version
page: 1 - 18
publication_identifier:
isbn:
- 978-364254630-3
publication_status: published
publisher: Springer
publist_id: '4748'
quality_controlled: '1'
scopus_import: 1
status: public
title: Simple chosen-ciphertext security from low noise LPN
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8383
year: '2014'
...
---
_id: '2220'
abstract:
- lang: eng
text: In this issue of Chemistry & Biology, Cokol and colleagues report a systematic
study of drug interactions between antifungal compounds. Suppressive drug interactions
occur more frequently than previously realized and come in different flavors with
interesting implications.
author:
- first_name: Marjon
full_name: De Vos, Marjon
id: 3111FFAC-F248-11E8-B48F-1D18A9856A87
last_name: De Vos
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: de Vos M, Bollenbach MT. Suppressive drug interactions between antifungals.
Chemistry and Biology. 2014;21(4):439-440. doi:10.1016/j.chembiol.2014.04.004
apa: de Vos, M., & Bollenbach, M. T. (2014). Suppressive drug interactions between
antifungals. Chemistry and Biology. Cell Press. https://doi.org/10.1016/j.chembiol.2014.04.004
chicago: Vos, Marjon de, and Mark Tobias Bollenbach. “Suppressive Drug Interactions
between Antifungals.” Chemistry and Biology. Cell Press, 2014. https://doi.org/10.1016/j.chembiol.2014.04.004.
ieee: M. de Vos and M. T. Bollenbach, “Suppressive drug interactions between antifungals,”
Chemistry and Biology, vol. 21, no. 4. Cell Press, pp. 439–440, 2014.
ista: de Vos M, Bollenbach MT. 2014. Suppressive drug interactions between antifungals.
Chemistry and Biology. 21(4), 439–440.
mla: de Vos, Marjon, and Mark Tobias Bollenbach. “Suppressive Drug Interactions
between Antifungals.” Chemistry and Biology, vol. 21, no. 4, Cell Press,
2014, pp. 439–40, doi:10.1016/j.chembiol.2014.04.004.
short: M. de Vos, M.T. Bollenbach, Chemistry and Biology 21 (2014) 439–440.
date_created: 2018-12-11T11:56:24Z
date_published: 2014-04-24T00:00:00Z
date_updated: 2021-01-12T06:56:06Z
day: '24'
department:
- _id: ToBo
doi: 10.1016/j.chembiol.2014.04.004
external_id:
pmid:
- '24766845'
intvolume: ' 21'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/24766845
month: '04'
oa: 1
oa_version: Published Version
page: 439 - 440
pmid: 1
publication: Chemistry and Biology
publication_identifier:
issn:
- '10745521'
publication_status: published
publisher: Cell Press
publist_id: '4747'
quality_controlled: '1'
scopus_import: 1
status: public
title: Suppressive drug interactions between antifungals
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2014'
...
---
_id: '2233'
abstract:
- lang: eng
text: ' A discounted-sum automaton (NDA) is a nondeterministic finite automaton
with edge weights, valuing a run by the discounted sum of visited edge weights.
More precisely, the weight in the i-th position of the run is divided by λi, where
the discount factor λ is a fixed rational number greater than 1. The value of
a word is the minimal value of the automaton runs on it. Discounted summation
is a common and useful measuring scheme, especially for infinite sequences, reflecting
the assumption that earlier weights are more important than later weights. Unfortunately,
determinization of NDAs, which is often essential in formal verification, is,
in general, not possible. We provide positive news, showing that every NDA with
an integral discount factor is determinizable. We complete the picture by proving
that the integers characterize exactly the discount factors that guarantee determinizability:
for every nonintegral rational discount factor λ, there is a nondeterminizable
λ-NDA. We also prove that the class of NDAs with integral discount factors enjoys
closure under the algebraic operations min, max, addition, and subtraction, which
is not the case for general NDAs nor for deterministic NDAs. For general NDAs,
we look into approximate determinization, which is always possible as the influence
of a word''s suffix decays. We show that the naive approach, of unfolding the
automaton computations up to a sufficient level, is doubly exponential in the
discount factor. We provide an alternative construction for approximate determinization,
which is singly exponential in the discount factor, in the precision, and in the
number of states. We also prove matching lower bounds, showing that the exponential
dependency on each of these three parameters cannot be avoided. All our results
hold equally for automata over finite words and for automata over infinite words. '
author:
- first_name: Udi
full_name: Boker, Udi
last_name: Boker
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Boker U, Henzinger TA. Exact and approximate determinization of discounted-sum
automata. Logical Methods in Computer Science. 2014;10(1). doi:10.2168/LMCS-10(1:10)2014
apa: Boker, U., & Henzinger, T. A. (2014). Exact and approximate determinization
of discounted-sum automata. Logical Methods in Computer Science. International
Federation of Computational Logic. https://doi.org/10.2168/LMCS-10(1:10)2014
chicago: Boker, Udi, and Thomas A Henzinger. “Exact and Approximate Determinization
of Discounted-Sum Automata.” Logical Methods in Computer Science. International
Federation of Computational Logic, 2014. https://doi.org/10.2168/LMCS-10(1:10)2014.
ieee: U. Boker and T. A. Henzinger, “Exact and approximate determinization of discounted-sum
automata,” Logical Methods in Computer Science, vol. 10, no. 1. International
Federation of Computational Logic, 2014.
ista: Boker U, Henzinger TA. 2014. Exact and approximate determinization of discounted-sum
automata. Logical Methods in Computer Science. 10(1).
mla: Boker, Udi, and Thomas A. Henzinger. “Exact and Approximate Determinization
of Discounted-Sum Automata.” Logical Methods in Computer Science, vol.
10, no. 1, International Federation of Computational Logic, 2014, doi:10.2168/LMCS-10(1:10)2014.
short: U. Boker, T.A. Henzinger, Logical Methods in Computer Science 10 (2014).
date_created: 2018-12-11T11:56:28Z
date_published: 2014-02-13T00:00:00Z
date_updated: 2021-01-12T06:56:11Z
day: '13'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.2168/LMCS-10(1:10)2014
ec_funded: 1
file:
- access_level: open_access
checksum: 9f6ea2e2d8d4a32ff0becc29d835bbf8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:45Z
date_updated: 2020-07-14T12:45:34Z
file_id: '4643'
file_name: IST-2015-389-v1+1_1401.3957.pdf
file_size: 550936
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication: Logical Methods in Computer Science
publication_identifier:
issn:
- '18605974'
publication_status: published
publisher: International Federation of Computational Logic
publist_id: '4728'
pubrep_id: '389'
quality_controlled: '1'
scopus_import: 1
status: public
title: Exact and approximate determinization of discounted-sum automata
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: 10
year: '2014'
...
---
_id: '2230'
abstract:
- lang: eng
text: Intracellular electrophysiological recordings provide crucial insights into
elementary neuronal signals such as action potentials and synaptic currents. Analyzing
and interpreting these signals is essential for a quantitative understanding of
neuronal information processing, and requires both fast data visualization and
ready access to complex analysis routines. To achieve this goal, we have developed
Stimfit, a free software package for cellular neurophysiology with a Python scripting
interface and a built-in Python shell. The program supports most standard file
formats for cellular neurophysiology and other biomedical signals through the
Biosig library. To quantify and interpret the activity of single neurons and communication
between neurons, the program includes algorithms to characterize the kinetics
of presynaptic action potentials and postsynaptic currents, estimate latencies
between pre- and postsynaptic events, and detect spontaneously occurring events.
We validate and benchmark these algorithms, give estimation errors, and provide
sample use cases, showing that Stimfit represents an efficient, accessible and
extensible way to accurately analyze and interpret neuronal signals.
article_number: '16'
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Christoph
full_name: Schmidt Hieber, Christoph
last_name: Schmidt Hieber
citation:
ama: 'Guzmán J, Schlögl A, Schmidt Hieber C. Stimfit: Quantifying electrophysiological
data with Python. Frontiers in Neuroinformatics. 2014;8(FEB). doi:10.3389/fninf.2014.00016'
apa: 'Guzmán, J., Schlögl, A., & Schmidt Hieber, C. (2014). Stimfit: Quantifying
electrophysiological data with Python. Frontiers in Neuroinformatics. Frontiers
Research Foundation. https://doi.org/10.3389/fninf.2014.00016'
chicago: 'Guzmán, José, Alois Schlögl, and Christoph Schmidt Hieber. “Stimfit: Quantifying
Electrophysiological Data with Python.” Frontiers in Neuroinformatics.
Frontiers Research Foundation, 2014. https://doi.org/10.3389/fninf.2014.00016.'
ieee: 'J. Guzmán, A. Schlögl, and C. Schmidt Hieber, “Stimfit: Quantifying electrophysiological
data with Python,” Frontiers in Neuroinformatics, vol. 8, no. FEB. Frontiers
Research Foundation, 2014.'
ista: 'Guzmán J, Schlögl A, Schmidt Hieber C. 2014. Stimfit: Quantifying electrophysiological
data with Python. Frontiers in Neuroinformatics. 8(FEB), 16.'
mla: 'Guzmán, José, et al. “Stimfit: Quantifying Electrophysiological Data with
Python.” Frontiers in Neuroinformatics, vol. 8, no. FEB, 16, Frontiers
Research Foundation, 2014, doi:10.3389/fninf.2014.00016.'
short: J. Guzmán, A. Schlögl, C. Schmidt Hieber, Frontiers in Neuroinformatics 8
(2014).
date_created: 2018-12-11T11:56:27Z
date_published: 2014-02-21T00:00:00Z
date_updated: 2021-01-12T06:56:09Z
day: '21'
ddc:
- '570'
department:
- _id: ScienComp
- _id: PeJo
doi: 10.3389/fninf.2014.00016
file:
- access_level: open_access
checksum: eeca00bba7232ff7d27db83321f6ea30
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:17Z
date_updated: 2020-07-14T12:45:34Z
file_id: '4935'
file_name: IST-2016-425-v1+1_fninf-08-00016.pdf
file_size: 2883372
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 8'
issue: FEB
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Frontiers in Neuroinformatics
publication_identifier:
issn:
- '16625196'
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '4731'
pubrep_id: '425'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Stimfit: Quantifying electrophysiological data with Python'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2014'
...
---
_id: '2228'
abstract:
- lang: eng
text: Fast-spiking, parvalbumin-expressing GABAergic interneurons, a large proportion
of which are basket cells (BCs), have a key role in feedforward and feedback inhibition,
gamma oscillations and complex information processing. For these functions, fast
propagation of action potentials (APs) from the soma to the presynaptic terminals
is important. However, the functional properties of interneuron axons remain elusive.
We examined interneuron axons by confocally targeted subcellular patch-clamp recording
in rat hippocampal slices. APs were initiated in the proximal axon ∼20 μm from
the soma and propagated to the distal axon with high reliability and speed. Subcellular
mapping revealed a stepwise increase of Na^+ conductance density from the soma
to the proximal axon, followed by a further gradual increase in the distal axon.
Active cable modeling and experiments with partial channel block revealed that
low axonal Na^+ conductance density was sufficient for reliability, but high Na^+
density was necessary for both speed of propagation and fast-spiking AP phenotype.
Our results suggest that a supercritical density of Na^+ channels compensates
for the morphological properties of interneuron axons (small segmental diameter,
extensive branching and high bouton density), ensuring fast AP propagation and
high-frequency repetitive firing.
author:
- first_name: Hua
full_name: Hu, Hua
id: 4AC0145C-F248-11E8-B48F-1D18A9856A87
last_name: Hu
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Hu H, Jonas PM. A supercritical density of Na^+ channels ensures fast signaling
in GABAergic interneuron axons. Nature Neuroscience. 2014;17(5):686-693.
doi:10.1038/nn.3678
apa: Hu, H., & Jonas, P. M. (2014). A supercritical density of Na^+ channels
ensures fast signaling in GABAergic interneuron axons. Nature Neuroscience.
Nature Publishing Group. https://doi.org/10.1038/nn.3678
chicago: Hu, Hua, and Peter M Jonas. “A Supercritical Density of Na^+ Channels Ensures
Fast Signaling in GABAergic Interneuron Axons.” Nature Neuroscience. Nature
Publishing Group, 2014. https://doi.org/10.1038/nn.3678.
ieee: H. Hu and P. M. Jonas, “A supercritical density of Na^+ channels ensures fast
signaling in GABAergic interneuron axons,” Nature Neuroscience, vol. 17,
no. 5. Nature Publishing Group, pp. 686–693, 2014.
ista: Hu H, Jonas PM. 2014. A supercritical density of Na^+ channels ensures fast
signaling in GABAergic interneuron axons. Nature Neuroscience. 17(5), 686–693.
mla: Hu, Hua, and Peter M. Jonas. “A Supercritical Density of Na^+ Channels Ensures
Fast Signaling in GABAergic Interneuron Axons.” Nature Neuroscience, vol.
17, no. 5, Nature Publishing Group, 2014, pp. 686–93, doi:10.1038/nn.3678.
short: H. Hu, P.M. Jonas, Nature Neuroscience 17 (2014) 686–693.
date_created: 2018-12-11T11:56:26Z
date_published: 2014-03-23T00:00:00Z
date_updated: 2021-01-12T06:56:08Z
day: '23'
department:
- _id: PeJo
doi: 10.1038/nn.3678
ec_funded: 1
intvolume: ' 17'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286295/
month: '03'
oa: 1
oa_version: Submitted Version
page: 686-693
project:
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
publication: Nature Neuroscience
publication_identifier:
issn:
- '10976256'
publication_status: published
publisher: Nature Publishing Group
publist_id: '4733'
quality_controlled: '1'
scopus_import: 1
status: public
title: A supercritical density of Na^+ channels ensures fast signaling in GABAergic
interneuron axons
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2014'
...
---
_id: '2229'
abstract:
- lang: eng
text: The distance between Ca^2+ channels and release sensors determines the speed
and efficacy of synaptic transmission. Tight "nanodomain" channel-sensor
coupling initiates transmitter release at synapses in the mature brain, whereas
loose "microdomain" coupling appears restricted to early developmental
stages. To probe the coupling configuration at a plastic synapse in the mature
central nervous system, we performed paired recordings between mossy fiber terminals
and CA3 pyramidal neurons in rat hippocampus. Millimolar concentrations of both
the fast Ca^2+ chelator BAPTA [1,2-bis(2-aminophenoxy)ethane- N,N, N′,N′-tetraacetic
acid] and the slow chelator EGTA efficiently suppressed transmitter release, indicating
loose coupling between Ca^2+ channels and release sensors. Loose coupling enabled
the control of initial release probability by fast endogenous Ca^2+ buffers and
the generation of facilitation by buffer saturation. Thus, loose coupling provides
the molecular framework for presynaptic plasticity.
author:
- first_name: Nicholas
full_name: Vyleta, Nicholas
id: 36C4978E-F248-11E8-B48F-1D18A9856A87
last_name: Vyleta
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Vyleta N, Jonas PM. Loose coupling between Ca^2+ channels and release sensors
at a plastic hippocampal synapse. Science. 2014;343(6171):665-670. doi:10.1126/science.1244811
apa: Vyleta, N., & Jonas, P. M. (2014). Loose coupling between Ca^2+ channels
and release sensors at a plastic hippocampal synapse. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.1244811
chicago: Vyleta, Nicholas, and Peter M Jonas. “Loose Coupling between Ca^2+ Channels
and Release Sensors at a Plastic Hippocampal Synapse.” Science. American
Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1244811.
ieee: N. Vyleta and P. M. Jonas, “Loose coupling between Ca^2+ channels and release
sensors at a plastic hippocampal synapse,” Science, vol. 343, no. 6171.
American Association for the Advancement of Science, pp. 665–670, 2014.
ista: Vyleta N, Jonas PM. 2014. Loose coupling between Ca^2+ channels and release
sensors at a plastic hippocampal synapse. Science. 343(6171), 665–670.
mla: Vyleta, Nicholas, and Peter M. Jonas. “Loose Coupling between Ca^2+ Channels
and Release Sensors at a Plastic Hippocampal Synapse.” Science, vol. 343,
no. 6171, American Association for the Advancement of Science, 2014, pp. 665–70,
doi:10.1126/science.1244811.
short: N. Vyleta, P.M. Jonas, Science 343 (2014) 665–670.
date_created: 2018-12-11T11:56:27Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2021-01-12T06:56:09Z
day: '01'
department:
- _id: PeJo
doi: 10.1126/science.1244811
ec_funded: 1
intvolume: ' 343'
issue: '6171'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617475/
month: '02'
oa: 1
oa_version: Submitted Version
page: 665 - 670
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: Science
publication_identifier:
issn:
- '00368075'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '4732'
quality_controlled: '1'
scopus_import: 1
status: public
title: Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal
synapse
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 343
year: '2014'
...
---
_id: '2232'
abstract:
- lang: eng
text: The purpose of this contribution is to summarize and discuss recent advances
regarding the onset of turbulence in shear flows. The absence of a clear-cut instability
mechanism, the spatio-temporal intermittent character and extremely long lived
transients are some of the major difficulties encountered in these flows and have
hindered progress towards understanding the transition process. We will show for
the case of pipe flow that concepts from nonlinear dynamics and statistical physics
can help to explain the onset of turbulence. In particular, the turbulent structures
(puffs) observed close to onset are spatially localized chaotic transients and
their lifetimes increase super-exponentially with Reynolds number. At the same
time fluctuations of individual turbulent puffs can (although very rarely) lead
to the nucleation of new puffs. The competition between these two stochastic processes
gives rise to a non-equilibrium phase transition where turbulence changes from
a super-transient to a sustained state.
article_number: P02001
article_processing_charge: No
article_type: original
author:
- first_name: Baofang
full_name: Song, Baofang
id: a79e57f5-e8a5-11ec-9dc9-83fb8c81cf72
last_name: Song
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Song B, Hof B. Deterministic and stochastic aspects of the transition to turbulence.
Journal of Statistical Mechanics Theory and Experiment. 2014;2014(2). doi:10.1088/1742-5468/2014/02/P02001
apa: Song, B., & Hof, B. (2014). Deterministic and stochastic aspects of the
transition to turbulence. Journal of Statistical Mechanics Theory and Experiment.
IOP Publishing. https://doi.org/10.1088/1742-5468/2014/02/P02001
chicago: Song, Baofang, and Björn Hof. “Deterministic and Stochastic Aspects of
the Transition to Turbulence.” Journal of Statistical Mechanics Theory and
Experiment. IOP Publishing, 2014. https://doi.org/10.1088/1742-5468/2014/02/P02001.
ieee: B. Song and B. Hof, “Deterministic and stochastic aspects of the transition
to turbulence,” Journal of Statistical Mechanics Theory and Experiment,
vol. 2014, no. 2. IOP Publishing, 2014.
ista: Song B, Hof B. 2014. Deterministic and stochastic aspects of the transition
to turbulence. Journal of Statistical Mechanics Theory and Experiment. 2014(2),
P02001.
mla: Song, Baofang, and Björn Hof. “Deterministic and Stochastic Aspects of the
Transition to Turbulence.” Journal of Statistical Mechanics Theory and Experiment,
vol. 2014, no. 2, P02001, IOP Publishing, 2014, doi:10.1088/1742-5468/2014/02/P02001.
short: B. Song, B. Hof, Journal of Statistical Mechanics Theory and Experiment 2014
(2014).
date_created: 2018-12-11T11:56:28Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2022-06-10T10:13:15Z
day: '01'
department:
- _id: BjHo
doi: 10.1088/1742-5468/2014/02/P02001
external_id:
arxiv:
- '1403.4516'
intvolume: ' 2014'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1403.4516
month: '02'
oa: 1
oa_version: Submitted Version
publication: Journal of Statistical Mechanics Theory and Experiment
publication_identifier:
issn:
- '17425468'
publication_status: published
publisher: IOP Publishing
publist_id: '4729'
quality_controlled: '1'
status: public
title: Deterministic and stochastic aspects of the transition to turbulence
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2014
year: '2014'
...
---
_id: '2231'
abstract:
- lang: eng
text: Based on the measurements of noise in gene expression performed during the
past decade, it has become customary to think of gene regulation in terms of a
two-state model, where the promoter of a gene can stochastically switch between
an ON and an OFF state. As experiments are becoming increasingly precise and the
deviations from the two-state model start to be observable, we ask about the experimental
signatures of complex multistate promoters, as well as the functional consequences
of this additional complexity. In detail, we i), extend the calculations for noise
in gene expression to promoters described by state transition diagrams with multiple
states, ii), systematically compute the experimentally accessible noise characteristics
for these complex promoters, and iii), use information theory to evaluate the
channel capacities of complex promoter architectures and compare them with the
baseline provided by the two-state model. We find that adding internal states
to the promoter generically decreases channel capacity, except in certain cases,
three of which (cooperativity, dual-role regulation, promoter cycling) we analyze
in detail.
author:
- first_name: Georg
full_name: Rieckh, Georg
id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87
last_name: Rieckh
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Rieckh G, Tkačik G. Noise and information transmission in promoters with multiple
internal states. Biophysical Journal. 2014;106(5):1194-1204. doi:10.1016/j.bpj.2014.01.014
apa: Rieckh, G., & Tkačik, G. (2014). Noise and information transmission in
promoters with multiple internal states. Biophysical Journal. Biophysical
Society. https://doi.org/10.1016/j.bpj.2014.01.014
chicago: Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in
Promoters with Multiple Internal States.” Biophysical Journal. Biophysical
Society, 2014. https://doi.org/10.1016/j.bpj.2014.01.014.
ieee: G. Rieckh and G. Tkačik, “Noise and information transmission in promoters
with multiple internal states,” Biophysical Journal, vol. 106, no. 5. Biophysical
Society, pp. 1194–1204, 2014.
ista: Rieckh G, Tkačik G. 2014. Noise and information transmission in promoters
with multiple internal states. Biophysical Journal. 106(5), 1194–1204.
mla: Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters
with Multiple Internal States.” Biophysical Journal, vol. 106, no. 5, Biophysical
Society, 2014, pp. 1194–204, doi:10.1016/j.bpj.2014.01.014.
short: G. Rieckh, G. Tkačik, Biophysical Journal 106 (2014) 1194–1204.
date_created: 2018-12-11T11:56:28Z
date_published: 2014-03-04T00:00:00Z
date_updated: 2021-01-12T06:56:10Z
day: '04'
department:
- _id: GaTk
doi: 10.1016/j.bpj.2014.01.014
external_id:
pmid:
- '24606943'
intvolume: ' 106'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026790/
month: '03'
oa: 1
oa_version: Submitted Version
page: 1194 - 1204
pmid: 1
publication: Biophysical Journal
publication_identifier:
issn:
- '00063495'
publication_status: published
publisher: Biophysical Society
publist_id: '4730'
quality_controlled: '1'
scopus_import: 1
status: public
title: Noise and information transmission in promoters with multiple internal states
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 106
year: '2014'
...
---
_id: '2226'
abstract:
- lang: eng
text: Coriolis force effects on shear flows are important in geophysical and astrophysical
contexts. We report a study on the linear stability and the transient energy growth
of the plane Couette flow with system rotation perpendicular to the shear direction.
External rotation causes linear instability. At small rotation rates, the onset
of linear instability scales inversely with the rotation rate and the optimal
transient growth in the linearly stable region is slightly enhanced ∼Re2. The
corresponding optimal initial perturbations are characterized by roll structures
inclined in the streamwise direction and are twisted under external rotation.
At large rotation rates, the transient growth is significantly inhibited and hence
linear stability analysis is a reliable indicator for instability.
article_number: '013001'
author:
- first_name: Liang
full_name: Shi, Liang
last_name: Shi
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Andreas
full_name: Tilgner, Andreas
last_name: Tilgner
citation:
ama: Shi L, Hof B, Tilgner A. Transient growth of Ekman-Couette flow. Physical
Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(1). doi:10.1103/PhysRevE.89.013001
apa: Shi, L., Hof, B., & Tilgner, A. (2014). Transient growth of Ekman-Couette
flow. Physical Review E Statistical Nonlinear and Soft Matter Physics.
American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.013001
chicago: Shi, Liang, Björn Hof, and Andreas Tilgner. “Transient Growth of Ekman-Couette
Flow.” Physical Review E Statistical Nonlinear and Soft Matter Physics.
American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.013001.
ieee: L. Shi, B. Hof, and A. Tilgner, “Transient growth of Ekman-Couette flow,”
Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89,
no. 1. American Institute of Physics, 2014.
ista: Shi L, Hof B, Tilgner A. 2014. Transient growth of Ekman-Couette flow. Physical
Review E Statistical Nonlinear and Soft Matter Physics. 89(1), 013001.
mla: Shi, Liang, et al. “Transient Growth of Ekman-Couette Flow.” Physical Review
E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 1, 013001, American
Institute of Physics, 2014, doi:10.1103/PhysRevE.89.013001.
short: L. Shi, B. Hof, A. Tilgner, Physical Review E Statistical Nonlinear and Soft
Matter Physics 89 (2014).
date_created: 2018-12-11T11:56:26Z
date_published: 2014-01-06T00:00:00Z
date_updated: 2021-01-12T06:56:08Z
day: '06'
department:
- _id: BjHo
doi: 10.1103/PhysRevE.89.013001
intvolume: ' 89'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1312.5095
month: '01'
oa: 1
oa_version: Submitted Version
project:
- _id: 25BDE9A4-B435-11E9-9278-68D0E5697425
grant_number: SFB-TR3-TP10B
name: Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_identifier:
issn:
- '15393755'
publication_status: published
publisher: American Institute of Physics
publist_id: '4737'
quality_controlled: '1'
scopus_import: 1
status: public
title: Transient growth of Ekman-Couette flow
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2014'
...
---
_id: '2227'
abstract:
- lang: eng
text: The Balkan Peninsula, characterized by high rates of endemism, is recognised
as one of the most diverse and species-rich areas of Europe. However, little is
known about the origin of Balkan endemics. The present study addresses the phylogenetic
position of the Balkan endemic Ranunculus wettsteinii, as well as its taxonomic
status and relationship with the widespread R. parnassiifolius, based on nuclear
DNA (internal transcribed spacer, ITS) and plastid regions (rpl32-trnL, rps16-trnQ,
trnK-matK and ycf6-psbM). Maximum parsimony and Bayesian inference analyses revealed
a well-supported clade formed by accessions of R. wettsteinii. Furthermore, our
phylogenetic and network analyses supported previous hypotheses of a likely allopolyploid
origin for R. wettsteinii between R. montenegrinus and R. parnassiifolius, with
the latter as the maternal parent.
article_processing_charge: No
author:
- first_name: Eduardo
full_name: Cires Rodriguez, Eduardo
id: 2AD56A7A-F248-11E8-B48F-1D18A9856A87
last_name: Cires Rodriguez
- first_name: Matthias
full_name: Baltisberger, Matthias
last_name: Baltisberger
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Pablo
full_name: Vargas, Pablo
last_name: Vargas
- first_name: José
full_name: Prieto, José
last_name: Prieto
citation:
ama: Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. Allopolyploid
origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from
nuclear and plastid DNA sequences. Organisms Diversity and Evolution. 2014;14(1):1-10.
doi:10.1007/s13127-013-0150-6
apa: Cires Rodriguez, E., Baltisberger, M., Cuesta, C., Vargas, P., & Prieto,
J. (2014). Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae)
inferred from nuclear and plastid DNA sequences. Organisms Diversity and Evolution.
Springer. https://doi.org/10.1007/s13127-013-0150-6
chicago: Cires Rodriguez, Eduardo, Matthias Baltisberger, Candela Cuesta, Pablo
Vargas, and José Prieto. “Allopolyploid Origin of the Balkan Endemic Ranunculus
Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.”
Organisms Diversity and Evolution. Springer, 2014. https://doi.org/10.1007/s13127-013-0150-6.
ieee: E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, and J. Prieto,
“Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae)
inferred from nuclear and plastid DNA sequences,” Organisms Diversity and Evolution,
vol. 14, no. 1. Springer, pp. 1–10, 2014.
ista: Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. 2014. Allopolyploid
origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from
nuclear and plastid DNA sequences. Organisms Diversity and Evolution. 14(1), 1–10.
mla: Cires Rodriguez, Eduardo, et al. “Allopolyploid Origin of the Balkan Endemic
Ranunculus Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.”
Organisms Diversity and Evolution, vol. 14, no. 1, Springer, 2014, pp.
1–10, doi:10.1007/s13127-013-0150-6.
short: E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, J. Prieto, Organisms
Diversity and Evolution 14 (2014) 1–10.
date_created: 2018-12-11T11:56:26Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2022-08-25T14:42:46Z
day: '01'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1007/s13127-013-0150-6
intvolume: ' 14'
issue: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 1 - 10
publication: Organisms Diversity and Evolution
publication_identifier:
issn:
- '14396092'
publication_status: published
publisher: Springer
publist_id: '4734'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae)
inferred from nuclear and plastid DNA sequences
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2014'
...
---
_id: '2234'
abstract:
- lang: eng
text: We study Markov decision processes (MDPs) with multiple limit-average (or
mean-payoff) functions. We consider two different objectives, namely, expectation
and satisfaction objectives. Given an MDP with κ limit-average functions, in the
expectation objective the goal is to maximize the expected limit-average value,
and in the satisfaction objective the goal is to maximize the probability of runs
such that the limit-average value stays above a given vector. We show that under
the expectation objective, in contrast to the case of one limit-average function,
both randomization and memory are necessary for strategies even for ε-approximation,
and that finite-memory randomized strategies are sufficient for achieving Pareto
optimal values. Under the satisfaction objective, in contrast to the case of one
limit-average function, infinite memory is necessary for strategies achieving
a specific value (i.e. randomized finite-memory strategies are not sufficient),
whereas memoryless randomized strategies are sufficient for ε-approximation, for
all ε > 0. We further prove that the decision problems for both expectation
and satisfaction objectives can be solved in polynomial time and the trade-off
curve (Pareto curve) can be ε-approximated in time polynomial in the size of the
MDP and 1/ε, and exponential in the number of limit-average functions, for all
ε > 0. Our analysis also reveals flaws in previous work for MDPs with multiple
mean-payoff functions under the expectation objective, corrects the flaws, and
allows us to obtain improved results.
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Václav
full_name: Brožek, Václav
last_name: Brožek
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Vojtěch
full_name: Forejt, Vojtěch
last_name: Forejt
- first_name: Antonín
full_name: Kučera, Antonín
last_name: Kučera
citation:
ama: Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. Markov decision processes
with multiple long-run average objectives. Logical Methods in Computer Science.
2014;10(1). doi:10.2168/LMCS-10(1:13)2014
apa: Brázdil, T., Brožek, V., Chatterjee, K., Forejt, V., & Kučera, A. (2014).
Markov decision processes with multiple long-run average objectives. Logical
Methods in Computer Science. International Federation of Computational Logic.
https://doi.org/10.2168/LMCS-10(1:13)2014
chicago: Brázdil, Tomáš, Václav Brožek, Krishnendu Chatterjee, Vojtěch Forejt, and
Antonín Kučera. “Markov Decision Processes with Multiple Long-Run Average Objectives.”
Logical Methods in Computer Science. International Federation of Computational
Logic, 2014. https://doi.org/10.2168/LMCS-10(1:13)2014.
ieee: T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, and A. Kučera, “Markov decision
processes with multiple long-run average objectives,” Logical Methods in Computer
Science, vol. 10, no. 1. International Federation of Computational Logic,
2014.
ista: Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. 2014. Markov decision
processes with multiple long-run average objectives. Logical Methods in Computer
Science. 10(1).
mla: Brázdil, Tomáš, et al. “Markov Decision Processes with Multiple Long-Run Average
Objectives.” Logical Methods in Computer Science, vol. 10, no. 1, International
Federation of Computational Logic, 2014, doi:10.2168/LMCS-10(1:13)2014.
short: T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, A. Kučera, Logical Methods
in Computer Science 10 (2014).
date_created: 2018-12-11T11:56:29Z
date_published: 2014-02-14T00:00:00Z
date_updated: 2021-01-12T06:56:11Z
day: '14'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.2168/LMCS-10(1:13)2014
ec_funded: 1
file:
- access_level: open_access
checksum: 803edcc2d8c1acfba44a9ec43a5eb9f0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:57Z
date_updated: 2020-07-14T12:45:34Z
file_id: '4656'
file_name: IST-2016-428-v1+1_1104.3489.pdf
file_size: 375388
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://repository.ist.ac.at/id/eprint/428
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Logical Methods in Computer Science
publication_identifier:
issn:
- '18605974'
publication_status: published
publisher: International Federation of Computational Logic
publist_id: '4727'
pubrep_id: '428'
quality_controlled: '1'
scopus_import: 1
status: public
title: Markov decision processes with multiple long-run average objectives
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2014'
...
---
_id: '2236'
abstract:
- lang: eng
text: Consider a joint distribution (X,A) on a set. We show that for any family
of distinguishers, there exists a simulator such that 1 no function in can distinguish
(X,A) from (X,h(X)) with advantage ε, 2 h is only O(2 3ℓ ε -2) times less efficient
than the functions in. For the most interesting settings of the parameters (in
particular, the cryptographic case where X has superlogarithmic min-entropy, ε
> 0 is negligible and consists of circuits of polynomial size), we can make
the simulator h deterministic. As an illustrative application of our theorem,
we give a new security proof for the leakage-resilient stream-cipher from Eurocrypt'09.
Our proof is simpler and quantitatively much better than the original proof using
the dense model theorem, giving meaningful security guarantees if instantiated
with a standard blockcipher like AES. Subsequent to this work, Chung, Lui and
Pass gave an interactive variant of our main theorem, and used it to investigate
weak notions of Zero-Knowledge. Vadhan and Zheng give a more constructive version
of our theorem using their new uniform min-max theorem.
alternative_title:
- LNCS
author:
- first_name: Dimitar
full_name: Jetchev, Dimitar
last_name: Jetchev
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Jetchev D, Pietrzak KZ. How to fake auxiliary input. In: Lindell Y, ed. Vol
8349. Springer; 2014:566-590. doi:10.1007/978-3-642-54242-8_24'
apa: 'Jetchev, D., & Pietrzak, K. Z. (2014). How to fake auxiliary input. In
Y. Lindell (Ed.) (Vol. 8349, pp. 566–590). Presented at the TCC: Theory of Cryptography
Conference, San Diego, USA: Springer. https://doi.org/10.1007/978-3-642-54242-8_24'
chicago: Jetchev, Dimitar, and Krzysztof Z Pietrzak. “How to Fake Auxiliary Input.”
edited by Yehuda Lindell, 8349:566–90. Springer, 2014. https://doi.org/10.1007/978-3-642-54242-8_24.
ieee: 'D. Jetchev and K. Z. Pietrzak, “How to fake auxiliary input,” presented at
the TCC: Theory of Cryptography Conference, San Diego, USA, 2014, vol. 8349, pp.
566–590.'
ista: 'Jetchev D, Pietrzak KZ. 2014. How to fake auxiliary input. TCC: Theory of
Cryptography Conference, LNCS, vol. 8349, 566–590.'
mla: Jetchev, Dimitar, and Krzysztof Z. Pietrzak. How to Fake Auxiliary Input.
Edited by Yehuda Lindell, vol. 8349, Springer, 2014, pp. 566–90, doi:10.1007/978-3-642-54242-8_24.
short: D. Jetchev, K.Z. Pietrzak, in:, Y. Lindell (Ed.), Springer, 2014, pp. 566–590.
conference:
end_date: 2014-02-26
location: San Diego, USA
name: 'TCC: Theory of Cryptography Conference'
start_date: 2014-02-24
date_created: 2018-12-11T11:56:29Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2021-01-12T06:56:12Z
day: '01'
ddc:
- '004'
department:
- _id: KrPi
doi: 10.1007/978-3-642-54242-8_24
ec_funded: 1
editor:
- first_name: Yehuda
full_name: Lindell, Yehuda
last_name: Lindell
file:
- access_level: open_access
checksum: 42960325c29dcd8d832edadcc3ce0045
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:21Z
date_updated: 2020-07-14T12:45:34Z
file_id: '5275'
file_name: IST-2016-681-v1+1_869_1_.pdf
file_size: 313528
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 8349'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://repository.ist.ac.at/id/eprint/681
month: '02'
oa: 1
oa_version: Submitted Version
page: 566 - 590
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_identifier:
isbn:
- 978-364254241-1
publication_status: published
publisher: Springer
publist_id: '4725'
pubrep_id: '681'
quality_controlled: '1'
status: public
title: How to fake auxiliary input
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8349
year: '2014'
...
---
_id: '2240'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis is the major mechanism for eukaryotic plasma
membrane-based proteome turn-over. In plants, clathrin-mediated endocytosis is
essential for physiology and development, but the identification and organization
of the machinery operating this process remains largely obscure. Here, we identified
an eight-core-component protein complex, the TPLATE complex, essential for plant
growth via its role as major adaptor module for clathrin-mediated endocytosis.
This complex consists of evolutionarily unique proteins that associate closely
with core endocytic elements. The TPLATE complex is recruited as dynamic foci
at the plasma membrane preceding recruitment of adaptor protein complex 2, clathrin,
and dynamin-related proteins. Reduced function of different complex components
severely impaired internalization of assorted endocytic cargoes, demonstrating
its pivotal role in clathrin-mediated endocytosis. Taken together, the TPLATE
complex is an early endocytic module representing a unique evolutionary plant
adaptation of the canonical eukaryotic pathway for clathrin-mediated endocytosis.
author:
- first_name: Astrid
full_name: Gadeyne, Astrid
last_name: Gadeyne
- first_name: Clara
full_name: Sánchez Rodríguez, Clara
last_name: Sánchez Rodríguez
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Simone
full_name: Di Rubbo, Simone
last_name: Di Rubbo
- first_name: Henrik
full_name: Zauber, Henrik
last_name: Zauber
- first_name: Kevin
full_name: Vanneste, Kevin
last_name: Vanneste
- first_name: Jelle
full_name: Van Leene, Jelle
last_name: Van Leene
- first_name: Nancy
full_name: De Winne, Nancy
last_name: De Winne
- first_name: Dominique
full_name: Eeckhout, Dominique
last_name: Eeckhout
- first_name: Geert
full_name: Persiau, Geert
last_name: Persiau
- first_name: Eveline
full_name: Van De Slijke, Eveline
last_name: Van De Slijke
- first_name: Bernard
full_name: Cannoot, Bernard
last_name: Cannoot
- first_name: Leen
full_name: Vercruysse, Leen
last_name: Vercruysse
- first_name: Jonathan
full_name: Mayers, Jonathan
last_name: Mayers
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Urszula
full_name: Kania, Urszula
id: 4AE5C486-F248-11E8-B48F-1D18A9856A87
last_name: Kania
- first_name: Matthias
full_name: Ehrlich, Matthias
last_name: Ehrlich
- first_name: Alois
full_name: Schweighofer, Alois
last_name: Schweighofer
- first_name: Tijs
full_name: Ketelaar, Tijs
last_name: Ketelaar
- first_name: Steven
full_name: Maere, Steven
last_name: Maere
- first_name: Sebastian
full_name: Bednarek, Sebastian
last_name: Bednarek
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Kris
full_name: Gevaert, Kris
last_name: Gevaert
- first_name: Erwin
full_name: Witters, Erwin
last_name: Witters
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
- first_name: Staffan
full_name: Persson, Staffan
last_name: Persson
- first_name: Geert
full_name: De Jaeger, Geert
last_name: De Jaeger
- first_name: Daniël
full_name: Van Damme, Daniël
last_name: Van Damme
citation:
ama: Gadeyne A, Sánchez Rodríguez C, Vanneste S, et al. The TPLATE adaptor complex
drives clathrin-mediated endocytosis in plants. Cell. 2014;156(4):691-704.
doi:10.1016/j.cell.2014.01.039
apa: Gadeyne, A., Sánchez Rodríguez, C., Vanneste, S., Di Rubbo, S., Zauber, H.,
Vanneste, K., … Van Damme, D. (2014). The TPLATE adaptor complex drives clathrin-mediated
endocytosis in plants. Cell. Cell Press. https://doi.org/10.1016/j.cell.2014.01.039
chicago: Gadeyne, Astrid, Clara Sánchez Rodríguez, Steffen Vanneste, Simone Di Rubbo,
Henrik Zauber, Kevin Vanneste, Jelle Van Leene, et al. “The TPLATE Adaptor Complex
Drives Clathrin-Mediated Endocytosis in Plants.” Cell. Cell Press, 2014.
https://doi.org/10.1016/j.cell.2014.01.039.
ieee: A. Gadeyne et al., “The TPLATE adaptor complex drives clathrin-mediated
endocytosis in plants,” Cell, vol. 156, no. 4. Cell Press, pp. 691–704,
2014.
ista: Gadeyne A, Sánchez Rodríguez C, Vanneste S, Di Rubbo S, Zauber H, Vanneste
K, Van Leene J, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Cannoot B,
Vercruysse L, Mayers J, Adamowski M, Kania U, Ehrlich M, Schweighofer A, Ketelaar
T, Maere S, Bednarek S, Friml J, Gevaert K, Witters E, Russinova E, Persson S,
De Jaeger G, Van Damme D. 2014. The TPLATE adaptor complex drives clathrin-mediated
endocytosis in plants. Cell. 156(4), 691–704.
mla: Gadeyne, Astrid, et al. “The TPLATE Adaptor Complex Drives Clathrin-Mediated
Endocytosis in Plants.” Cell, vol. 156, no. 4, Cell Press, 2014, pp. 691–704,
doi:10.1016/j.cell.2014.01.039.
short: A. Gadeyne, C. Sánchez Rodríguez, S. Vanneste, S. Di Rubbo, H. Zauber, K.
Vanneste, J. Van Leene, N. De Winne, D. Eeckhout, G. Persiau, E. Van De Slijke,
B. Cannoot, L. Vercruysse, J. Mayers, M. Adamowski, U. Kania, M. Ehrlich, A. Schweighofer,
T. Ketelaar, S. Maere, S. Bednarek, J. Friml, K. Gevaert, E. Witters, E. Russinova,
S. Persson, G. De Jaeger, D. Van Damme, Cell 156 (2014) 691–704.
date_created: 2018-12-11T11:56:31Z
date_published: 2014-02-13T00:00:00Z
date_updated: 2021-01-12T06:56:13Z
day: '13'
department:
- _id: JiFr
doi: 10.1016/j.cell.2014.01.039
intvolume: ' 156'
issue: '4'
language:
- iso: eng
month: '02'
oa_version: None
page: 691 - 704
publication: Cell
publication_identifier:
issn:
- '00928674'
publication_status: published
publisher: Cell Press
publist_id: '4721'
quality_controlled: '1'
scopus_import: 1
status: public
title: The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 156
year: '2014'
...
---
_id: '2239'
abstract:
- lang: eng
text: The analysis of the energy consumption of software is an important goal for
quantitative formal methods. Current methods, using weighted transition systems
or energy games, model the energy source as an ideal resource whose status is
characterized by one number, namely the amount of remaining energy. Real batteries,
however, exhibit behaviors that can deviate substantially from an ideal energy
resource. Based on a discretization of a standard continuous battery model, we
introduce battery transition systems. In this model, a battery is viewed as consisting
of two parts-the available-charge tank and the bound-charge tank. Any charge or
discharge is applied to the available-charge tank. Over time, the energy from
each tank diffuses to the other tank. Battery transition systems are infinite
state systems that, being not well-structured, fall into no decidable class that
is known to us. Nonetheless, we are able to prove that the !-regular modelchecking
problem is decidable for battery transition systems. We also present a case study
on the verification of control programs for energy-constrained semi-autonomous
robots.
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
citation:
ama: 'Boker U, Henzinger TA, Radhakrishna A. Battery transition systems. In: Vol
49. ACM; 2014:595-606. doi:10.1145/2535838.2535875'
apa: 'Boker, U., Henzinger, T. A., & Radhakrishna, A. (2014). Battery transition
systems (Vol. 49, pp. 595–606). Presented at the POPL: Principles of Programming
Languages, San Diego, USA: ACM. https://doi.org/10.1145/2535838.2535875'
chicago: Boker, Udi, Thomas A Henzinger, and Arjun Radhakrishna. “Battery Transition
Systems,” 49:595–606. ACM, 2014. https://doi.org/10.1145/2535838.2535875.
ieee: 'U. Boker, T. A. Henzinger, and A. Radhakrishna, “Battery transition systems,”
presented at the POPL: Principles of Programming Languages, San Diego, USA, 2014,
vol. 49, no. 1, pp. 595–606.'
ista: 'Boker U, Henzinger TA, Radhakrishna A. 2014. Battery transition systems.
POPL: Principles of Programming Languages vol. 49, 595–606.'
mla: Boker, Udi, et al. Battery Transition Systems. Vol. 49, no. 1, ACM,
2014, pp. 595–606, doi:10.1145/2535838.2535875.
short: U. Boker, T.A. Henzinger, A. Radhakrishna, in:, ACM, 2014, pp. 595–606.
conference:
end_date: 2014-01-24
location: San Diego, USA
name: 'POPL: Principles of Programming Languages'
start_date: 2014-01-22
date_created: 2018-12-11T11:56:30Z
date_published: 2014-01-13T00:00:00Z
date_updated: 2021-01-12T06:56:13Z
day: '13'
department:
- _id: ToHe
doi: 10.1145/2535838.2535875
ec_funded: 1
intvolume: ' 49'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 595 - 606
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_identifier:
isbn:
- 978-145032544-8
publication_status: published
publisher: ACM
publist_id: '4722'
quality_controlled: '1'
scopus_import: 1
status: public
title: Battery transition systems
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 49
year: '2014'
...
---
_id: '2235'
abstract:
- lang: eng
text: Emerging infectious diseases (EIDs) pose a risk to human welfare, both directly
and indirectly, by affecting managed livestock and wildlife that provide valuable
resources and ecosystem services, such as the pollination of crops. Honeybees
(Apis mellifera), the prevailing managed insect crop pollinator, suffer from a
range of emerging and exotic high-impact pathogens, and population maintenance
requires active management by beekeepers to control them. Wild pollinators such
as bumblebees (Bombus spp.) are in global decline, one cause of which may be pathogen
spillover from managed pollinators like honeybees or commercial colonies of bumblebees.
Here we use a combination of infection experiments and landscape-scale field data
to show that honeybee EIDs are indeed widespread infectious agents within the
pollinator assemblage. The prevalence of deformed wing virus (DWV) and the exotic
parasite Nosema ceranae in honeybees and bumblebees is linked; as honeybees have
higher DWV prevalence, and sympatric bumblebees and honeybees are infected by
the same DWV strains, Apis is the likely source of at least one major EID in wild
pollinators. Lessons learned from vertebrates highlight the need for increased
pathogen control in managed bee species to maintain wild pollinators, as declines
in native pollinators may be caused by interspecies pathogen transmission originating
from managed pollinators.
author:
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Juliet
full_name: Osborne, Juliet
last_name: Osborne
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
citation:
ama: Fürst M, Mcmahon D, Osborne J, Paxton R, Brown M. Disease associations between
honeybees and bumblebees as a threat to wild pollinators. Nature. 2014;506(7488):364-366.
doi:10.1038/nature12977
apa: Fürst, M., Mcmahon, D., Osborne, J., Paxton, R., & Brown, M. (2014). Disease
associations between honeybees and bumblebees as a threat to wild pollinators.
Nature. Nature Publishing Group. https://doi.org/10.1038/nature12977
chicago: Fürst, Matthias, Dino Mcmahon, Juliet Osborne, Robert Paxton, and Mark
Brown. “Disease Associations between Honeybees and Bumblebees as a Threat to Wild
Pollinators.” Nature. Nature Publishing Group, 2014. https://doi.org/10.1038/nature12977.
ieee: M. Fürst, D. Mcmahon, J. Osborne, R. Paxton, and M. Brown, “Disease associations
between honeybees and bumblebees as a threat to wild pollinators,” Nature,
vol. 506, no. 7488. Nature Publishing Group, pp. 364–366, 2014.
ista: Fürst M, Mcmahon D, Osborne J, Paxton R, Brown M. 2014. Disease associations
between honeybees and bumblebees as a threat to wild pollinators. Nature. 506(7488),
364–366.
mla: Fürst, Matthias, et al. “Disease Associations between Honeybees and Bumblebees
as a Threat to Wild Pollinators.” Nature, vol. 506, no. 7488, Nature Publishing
Group, 2014, pp. 364–66, doi:10.1038/nature12977.
short: M. Fürst, D. Mcmahon, J. Osborne, R. Paxton, M. Brown, Nature 506 (2014)
364–366.
date_created: 2018-12-11T11:56:29Z
date_published: 2014-02-20T00:00:00Z
date_updated: 2021-01-12T06:56:11Z
day: '20'
department:
- _id: SyCr
doi: 10.1038/nature12977
intvolume: ' 506'
issue: '7488'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985068/
month: '02'
oa: 1
oa_version: Submitted Version
page: 364 - 366
publication: Nature
publication_identifier:
issn:
- '00280836'
publication_status: published
publisher: Nature Publishing Group
publist_id: '4726'
quality_controlled: '1'
scopus_import: 1
status: public
title: Disease associations between honeybees and bumblebees as a threat to wild pollinators
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 506
year: '2014'
...
---
_id: '2241'
abstract:
- lang: eng
text: 'The brain demands high-energy supply and obstruction of blood flow causes
rapid deterioration of the healthiness of brain cells. Two major events occur
upon ischemia: acidosis and liberation of excess glutamate, which leads to excitotoxicity.
However, cellular source of glutamate and its release mechanism upon ischemia
remained unknown. Here we show a causal relationship between glial acidosis and
neuronal excitotoxicity. As the major cation that flows through channelrhodopsin-2
(ChR2) is proton, this could be regarded as an optogenetic tool for instant intracellular
acidification. Optical activation of ChR2 expressed in glial cells led to glial
acidification and to release of glutamate. On the other hand, glial alkalization
via optogenetic activation of a proton pump, archaerhodopsin (ArchT), led to cessation
of glutamate release and to the relief of ischemic brain damage in vivo. Our results
suggest that controlling glial pH may be an effective therapeutic strategy for
intervention of ischemic brain damage.'
author:
- first_name: Kaoru
full_name: Beppu, Kaoru
last_name: Beppu
- first_name: Takuya
full_name: Sasaki, Takuya
last_name: Sasaki
- first_name: Kenji
full_name: Tanaka, Kenji
last_name: Tanaka
- first_name: Akihiro
full_name: Yamanaka, Akihiro
last_name: Yamanaka
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Ko
full_name: Matsui, Ko
last_name: Matsui
citation:
ama: Beppu K, Sasaki T, Tanaka K, et al. Optogenetic countering of glial acidosis
suppresses glial glutamate release and ischemic brain damage. Neuron. 2014;81(2):314-320.
doi:10.1016/j.neuron.2013.11.011
apa: Beppu, K., Sasaki, T., Tanaka, K., Yamanaka, A., Fukazawa, Y., Shigemoto, R.,
& Matsui, K. (2014). Optogenetic countering of glial acidosis suppresses glial
glutamate release and ischemic brain damage. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.11.011
chicago: Beppu, Kaoru, Takuya Sasaki, Kenji Tanaka, Akihiro Yamanaka, Yugo Fukazawa,
Ryuichi Shigemoto, and Ko Matsui. “Optogenetic Countering of Glial Acidosis Suppresses
Glial Glutamate Release and Ischemic Brain Damage.” Neuron. Elsevier, 2014.
https://doi.org/10.1016/j.neuron.2013.11.011.
ieee: K. Beppu et al., “Optogenetic countering of glial acidosis suppresses
glial glutamate release and ischemic brain damage,” Neuron, vol. 81, no.
2. Elsevier, pp. 314–320, 2014.
ista: Beppu K, Sasaki T, Tanaka K, Yamanaka A, Fukazawa Y, Shigemoto R, Matsui K.
2014. Optogenetic countering of glial acidosis suppresses glial glutamate release
and ischemic brain damage. Neuron. 81(2), 314–320.
mla: Beppu, Kaoru, et al. “Optogenetic Countering of Glial Acidosis Suppresses Glial
Glutamate Release and Ischemic Brain Damage.” Neuron, vol. 81, no. 2, Elsevier,
2014, pp. 314–20, doi:10.1016/j.neuron.2013.11.011.
short: K. Beppu, T. Sasaki, K. Tanaka, A. Yamanaka, Y. Fukazawa, R. Shigemoto, K.
Matsui, Neuron 81 (2014) 314–320.
date_created: 2018-12-11T11:56:31Z
date_published: 2014-01-22T00:00:00Z
date_updated: 2021-01-12T06:56:14Z
day: '22'
department:
- _id: RySh
doi: 10.1016/j.neuron.2013.11.011
intvolume: ' 81'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 314 - 320
publication: Neuron
publication_identifier:
issn:
- '08966273'
publication_status: published
publisher: Elsevier
publist_id: '4715'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optogenetic countering of glial acidosis suppresses glial glutamate release
and ischemic brain damage
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 81
year: '2014'
...
---
_id: '2245'
abstract:
- lang: eng
text: 'Exogenous application of biologically important molecules for plant growth
promotion and/or regulation is very common both in plant research and horticulture.
Plant hormones such as auxins and cytokinins are classes of compounds which are
often applied exogenously. Nevertheless, plants possess a well-established machinery
to regulate the active pool of exogenously applied compounds by converting them
to metabolites and conjugates. Consequently, it is often very useful to know the
in vivo status of applied compounds to connect them with some of the regulatory
events in plant developmental processes. The in vivo status of applied compounds
can be measured by incubating plants with radiolabeled compounds, followed by
extraction, purification, and HPLC metabolic profiling of plant extracts. Recently
we have used this method to characterize the intracellularly localized PIN protein,
PIN5. Here we explain the method in detail, with a focus on general application. '
alternative_title:
- Methods in Molecular Biology
author:
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Petr
full_name: Skůpa, Petr
last_name: Skůpa
- first_name: Petre
full_name: Dobrev, Petre
last_name: Dobrev
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. Analyzing the
in vivo status of exogenously applied auxins: A HPLC-based method to characterize
the intracellularly localized auxin transporters. In: Hicks G, Robert S, eds.
Plant Chemical Genomics. Vol 1056. Methods in Molecular Biology. Springer;
2014:255-264. doi:10.1007/978-1-62703-592-7_23'
apa: 'Simon, S., Skůpa, P., Dobrev, P., Petrášek, J., Zažímalová, E., & Friml,
J. (2014). Analyzing the in vivo status of exogenously applied auxins: A HPLC-based
method to characterize the intracellularly localized auxin transporters. In G.
Hicks & S. Robert (Eds.), Plant Chemical Genomics (Vol. 1056, pp. 255–264).
Springer. https://doi.org/10.1007/978-1-62703-592-7_23'
chicago: 'Simon, Sibu, Petr Skůpa, Petre Dobrev, Jan Petrášek, Eva Zažímalová, and
Jiří Friml. “Analyzing the in Vivo Status of Exogenously Applied Auxins: A HPLC-Based
Method to Characterize the Intracellularly Localized Auxin Transporters.” In Plant
Chemical Genomics, edited by Glenn Hicks and Stéphanie Robert, 1056:255–64.
Methods in Molecular Biology. Springer, 2014. https://doi.org/10.1007/978-1-62703-592-7_23.'
ieee: 'S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, and J. Friml,
“Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method
to characterize the intracellularly localized auxin transporters,” in Plant
Chemical Genomics, vol. 1056, G. Hicks and S. Robert, Eds. Springer, 2014,
pp. 255–264.'
ista: 'Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. 2014.Analyzing
the in vivo status of exogenously applied auxins: A HPLC-based method to characterize
the intracellularly localized auxin transporters. In: Plant Chemical Genomics.
Methods in Molecular Biology, vol. 1056, 255–264.'
mla: 'Simon, Sibu, et al. “Analyzing the in Vivo Status of Exogenously Applied Auxins:
A HPLC-Based Method to Characterize the Intracellularly Localized Auxin Transporters.”
Plant Chemical Genomics, edited by Glenn Hicks and Stéphanie Robert, vol.
1056, Springer, 2014, pp. 255–64, doi:10.1007/978-1-62703-592-7_23.'
short: S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, J. Friml, in:,
G. Hicks, S. Robert (Eds.), Plant Chemical Genomics, Springer, 2014, pp. 255–264.
date_created: 2018-12-11T11:56:32Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:15Z
day: '01'
department:
- _id: JiFr
doi: 10.1007/978-1-62703-592-7_23
editor:
- first_name: Glenn
full_name: Hicks, Glenn
last_name: Hicks
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
intvolume: ' 1056'
language:
- iso: eng
month: '01'
oa_version: None
page: 255 - 264
publication: Plant Chemical Genomics
publication_identifier:
issn:
- '10643745'
publication_status: published
publisher: Springer
publist_id: '4704'
quality_controlled: '1'
scopus_import: 1
series_title: Methods in Molecular Biology
status: public
title: 'Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method
to characterize the intracellularly localized auxin transporters'
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 1056
year: '2014'
...
---
_id: '2246'
abstract:
- lang: eng
text: 'Muller games are played by two players moving a token along a graph; the
winner is determined by the set of vertices that occur infinitely often. The central
algorithmic problem is to compute the winning regions for the players. Different
classes and representations of Muller games lead to problems of varying computational
complexity. One such class are parity games; these are of particular significance
in computational complexity, as they remain one of the few combinatorial problems
known to be in NP ∩ co-NP but not known to be in P. We show that winning regions
for a Muller game can be determined from the alternating structure of its traps.
To every Muller game we then associate a natural number that we call its trap
depth; this parameter measures how complicated the trap structure is. We present
algorithms for parity games that run in polynomial time for graphs of bounded
trap depth, and in general run in time exponential in the trap depth. '
author:
- first_name: Andrey
full_name: Grinshpun, Andrey
last_name: Grinshpun
- first_name: Pakawat
full_name: Phalitnonkiat, Pakawat
last_name: Phalitnonkiat
- first_name: Sasha
full_name: Rubin, Sasha
id: 2EC51194-F248-11E8-B48F-1D18A9856A87
last_name: Rubin
- first_name: Andrei
full_name: Tarfulea, Andrei
last_name: Tarfulea
citation:
ama: Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. Alternating traps in Muller
and parity games. Theoretical Computer Science. 2014;521:73-91. doi:10.1016/j.tcs.2013.11.032
apa: Grinshpun, A., Phalitnonkiat, P., Rubin, S., & Tarfulea, A. (2014). Alternating
traps in Muller and parity games. Theoretical Computer Science. Elsevier.
https://doi.org/10.1016/j.tcs.2013.11.032
chicago: Grinshpun, Andrey, Pakawat Phalitnonkiat, Sasha Rubin, and Andrei Tarfulea.
“Alternating Traps in Muller and Parity Games.” Theoretical Computer Science.
Elsevier, 2014. https://doi.org/10.1016/j.tcs.2013.11.032.
ieee: A. Grinshpun, P. Phalitnonkiat, S. Rubin, and A. Tarfulea, “Alternating traps
in Muller and parity games,” Theoretical Computer Science, vol. 521. Elsevier,
pp. 73–91, 2014.
ista: Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. 2014. Alternating traps
in Muller and parity games. Theoretical Computer Science. 521, 73–91.
mla: Grinshpun, Andrey, et al. “Alternating Traps in Muller and Parity Games.” Theoretical
Computer Science, vol. 521, Elsevier, 2014, pp. 73–91, doi:10.1016/j.tcs.2013.11.032.
short: A. Grinshpun, P. Phalitnonkiat, S. Rubin, A. Tarfulea, Theoretical Computer
Science 521 (2014) 73–91.
date_created: 2018-12-11T11:56:33Z
date_published: 2014-02-13T00:00:00Z
date_updated: 2021-01-12T06:56:16Z
day: '13'
department:
- _id: KrCh
doi: 10.1016/j.tcs.2013.11.032
intvolume: ' 521'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1303.3777
month: '02'
oa: 1
oa_version: Submitted Version
page: 73 - 91
publication: Theoretical Computer Science
publication_identifier:
issn:
- '03043975'
publication_status: published
publisher: Elsevier
publist_id: '4703'
quality_controlled: '1'
scopus_import: 1
status: public
title: Alternating traps in Muller and parity games
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 521
year: '2014'
...
---
_id: '2242'
abstract:
- lang: eng
text: MicroRNAs (miRNAs) are small RNAs that play important regulatory roles in
many cellular pathways. MiRNAs associate with members of the Argonaute protein
family and bind to partially complementary sequences on mRNAs and induce translational
repression or mRNA decay. Using deep sequencing and Northern blotting, we characterized
miRNA expression in wild type and miR-155-deficient dendritic cells (DCs) and
macrophages. Analysis of different stimuli (LPS, LDL, eLDL, oxLDL) reveals a direct
influence of miR-155 on the expression levels of other miRNAs. For example, miR-455
is negatively regulated in miR-155-deficient cells possibly due to inhibition
of the transcription factor C/EBPbeta by miR-155. Based on our comprehensive data
sets, we propose a model of hierarchical miRNA expression dominated by miR-155
in DCs and macrophages.
author:
- first_name: Anne
full_name: Dueck, Anne
last_name: Dueck
- first_name: Alexander
full_name: Eichner, Alexander
id: 4DFA52AE-F248-11E8-B48F-1D18A9856A87
last_name: Eichner
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Gunter
full_name: Meister, Gunter
last_name: Meister
citation:
ama: Dueck A, Eichner A, Sixt MK, Meister G. A miR-155-dependent microRNA hierarchy
in dendritic cell maturation and macrophage activation. FEBS Letters. 2014;588(4):632-640.
doi:10.1016/j.febslet.2014.01.009
apa: Dueck, A., Eichner, A., Sixt, M. K., & Meister, G. (2014). A miR-155-dependent
microRNA hierarchy in dendritic cell maturation and macrophage activation. FEBS
Letters. Elsevier. https://doi.org/10.1016/j.febslet.2014.01.009
chicago: Dueck, Anne, Alexander Eichner, Michael K Sixt, and Gunter Meister. “A
MiR-155-Dependent MicroRNA Hierarchy in Dendritic Cell Maturation and Macrophage
Activation.” FEBS Letters. Elsevier, 2014. https://doi.org/10.1016/j.febslet.2014.01.009.
ieee: A. Dueck, A. Eichner, M. K. Sixt, and G. Meister, “A miR-155-dependent microRNA
hierarchy in dendritic cell maturation and macrophage activation,” FEBS Letters,
vol. 588, no. 4. Elsevier, pp. 632–640, 2014.
ista: Dueck A, Eichner A, Sixt MK, Meister G. 2014. A miR-155-dependent microRNA
hierarchy in dendritic cell maturation and macrophage activation. FEBS Letters.
588(4), 632–640.
mla: Dueck, Anne, et al. “A MiR-155-Dependent MicroRNA Hierarchy in Dendritic Cell
Maturation and Macrophage Activation.” FEBS Letters, vol. 588, no. 4, Elsevier,
2014, pp. 632–40, doi:10.1016/j.febslet.2014.01.009.
short: A. Dueck, A. Eichner, M.K. Sixt, G. Meister, FEBS Letters 588 (2014) 632–640.
date_created: 2018-12-11T11:56:31Z
date_published: 2014-02-14T00:00:00Z
date_updated: 2021-01-12T06:56:14Z
day: '14'
department:
- _id: MiSi
doi: 10.1016/j.febslet.2014.01.009
intvolume: ' 588'
issue: '4'
language:
- iso: eng
month: '02'
oa_version: None
page: 632 - 640
publication: FEBS Letters
publication_identifier:
issn:
- '00145793'
publication_status: published
publisher: Elsevier
publist_id: '4714'
quality_controlled: '1'
scopus_import: 1
status: public
title: A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage
activation
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 588
year: '2014'
...
---
_id: '2250'
abstract:
- lang: eng
text: The genome sequences of new viruses often contain many "orphan"
or "taxon-specific" proteins apparently lacking homologs. However, because
viral proteins evolve very fast, commonly used sequence similarity detection methods
such as BLAST may overlook homologs. We analyzed a data set of proteins from RNA
viruses characterized as "genus specific" by BLAST. More powerful methods
developed recently, such as HHblits or HHpred (available through web-based, user-friendly
interfaces), could detect distant homologs of a quarter of these proteins, suggesting
that these methods should be used to annotate viral genomes. In-depth manual analyses
of a subset of the remaining sequences, guided by contextual information such
as taxonomy, gene order, or domain cooccurrence, identified distant homologs of
another third. Thus, a combination of powerful automated methods and manual analyses
can uncover distant homologs of many proteins thought to be orphans. We expect
these methodological results to be also applicable to cellular organisms, since
they generally evolve much more slowly than RNA viruses. As an application, we
reanalyzed the genome of a bee pathogen, Chronic bee paralysis virus (CBPV). We
could identify homologs of most of its proteins thought to be orphans; in each
case, identifying homologs provided functional clues. We discovered that CBPV
encodes a domain homologous to the Alphavirus methyltransferase-guanylyltransferase;
a putative membrane protein, SP24, with homologs in unrelated insect viruses and
insect-transmitted plant viruses having different morphologies (cileviruses, higreviruses,
blunerviruses, negeviruses); and a putative virion glycoprotein, ORF2, also found
in negeviruses. SP24 and ORF2 are probably major structural components of the
virionsd.
author:
- first_name: Durga
full_name: Kuchibhatla, Durga
last_name: Kuchibhatla
- first_name: Westley
full_name: Sherman, Westley
last_name: Sherman
- first_name: Betty
full_name: Chung, Betty
last_name: Chung
- first_name: Shelley
full_name: Cook, Shelley
last_name: Cook
- first_name: Georg
full_name: Schneider, Georg
id: 329095A0-F248-11E8-B48F-1D18A9856A87
last_name: Schneider
- first_name: Birgit
full_name: Eisenhaber, Birgit
last_name: Eisenhaber
- first_name: David
full_name: Karlin, David
last_name: Karlin
citation:
ama: Kuchibhatla D, Sherman W, Chung B, et al. Powerful sequence similarity search
methods and in-depth manual analyses can identify remote homologs in many apparently
“orphan” viral proteins. Journal of Virology. 2014;88(1):10-20. doi:10.1128/JVI.02595-13
apa: Kuchibhatla, D., Sherman, W., Chung, B., Cook, S., Schneider, G., Eisenhaber,
B., & Karlin, D. (2014). Powerful sequence similarity search methods and in-depth
manual analyses can identify remote homologs in many apparently “orphan” viral
proteins. Journal of Virology. ASM. https://doi.org/10.1128/JVI.02595-13
chicago: Kuchibhatla, Durga, Westley Sherman, Betty Chung, Shelley Cook, Georg Schneider,
Birgit Eisenhaber, and David Karlin. “Powerful Sequence Similarity Search Methods
and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently ‘Orphan’
Viral Proteins.” Journal of Virology. ASM, 2014. https://doi.org/10.1128/JVI.02595-13.
ieee: D. Kuchibhatla et al., “Powerful sequence similarity search methods
and in-depth manual analyses can identify remote homologs in many apparently ‘orphan’
viral proteins,” Journal of Virology, vol. 88, no. 1. ASM, pp. 10–20, 2014.
ista: Kuchibhatla D, Sherman W, Chung B, Cook S, Schneider G, Eisenhaber B, Karlin
D. 2014. Powerful sequence similarity search methods and in-depth manual analyses
can identify remote homologs in many apparently ‘orphan’ viral proteins. Journal
of Virology. 88(1), 10–20.
mla: Kuchibhatla, Durga, et al. “Powerful Sequence Similarity Search Methods and
In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently ‘Orphan’
Viral Proteins.” Journal of Virology, vol. 88, no. 1, ASM, 2014, pp. 10–20,
doi:10.1128/JVI.02595-13.
short: D. Kuchibhatla, W. Sherman, B. Chung, S. Cook, G. Schneider, B. Eisenhaber,
D. Karlin, Journal of Virology 88 (2014) 10–20.
date_created: 2018-12-11T11:56:34Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:17Z
day: '01'
ddc:
- '570'
department:
- _id: MD
doi: 10.1128/JVI.02595-13
file:
- access_level: open_access
checksum: 2c121b5e884992dfec5605bdf4e659da
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:43Z
date_updated: 2020-07-14T12:45:34Z
file_id: '5029'
file_name: IST-2016-417-v1+1_J._Virol.-2014-Kuchibhatla-10-20.pdf
file_size: 825756
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 88'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 10 - 20
publication: Journal of Virology
publication_identifier:
issn:
- 0022538X
publication_status: published
publisher: ASM
publist_id: '4698'
pubrep_id: '417'
quality_controlled: '1'
scopus_import: 1
status: public
title: Powerful sequence similarity search methods and in-depth manual analyses can
identify remote homologs in many apparently "orphan" viral proteins
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 88
year: '2014'
...
---
_id: '2254'
abstract:
- lang: eng
text: Theta-gamma network oscillations are thought to represent key reference signals
for information processing in neuronal ensembles, but the underlying synaptic
mechanisms remain unclear. To address this question, we performed whole-cell (WC)
patch-clamp recordings from mature hippocampal granule cells (GCs) in vivo in
the dentate gyrus of anesthetized and awake rats. GCs in vivo fired action potentials
at low frequency, consistent with sparse coding in the dentate gyrus. GCs were
exposed to barrages of fast AMPAR-mediated excitatory postsynaptic currents (EPSCs),
primarily relayed from the entorhinal cortex, and inhibitory postsynaptic currents
(IPSCs), presumably generated by local interneurons. EPSCs exhibited coherence
with the field potential predominantly in the theta frequency band, whereas IPSCs
showed coherence primarily in the gamma range. Action potentials in GCs were phase
locked to network oscillations. Thus, theta-gamma-modulated synaptic currents
may provide a framework for sparse temporal coding of information in the dentate
gyrus.
author:
- first_name: Alejandro
full_name: Pernia-Andrade, Alejandro
id: 36963E98-F248-11E8-B48F-1D18A9856A87
last_name: Pernia-Andrade
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Pernia-Andrade A, Jonas PM. Theta-gamma-modulated synaptic currents in hippocampal
granule cells in vivo define a mechanism for network oscillations. Neuron.
2014;81(1):140-152. doi:10.1016/j.neuron.2013.09.046
apa: Pernia-Andrade, A., & Jonas, P. M. (2014). Theta-gamma-modulated synaptic
currents in hippocampal granule cells in vivo define a mechanism for network oscillations.
Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.09.046
chicago: Pernia-Andrade, Alejandro, and Peter M Jonas. “Theta-Gamma-Modulated Synaptic
Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.”
Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2013.09.046.
ieee: A. Pernia-Andrade and P. M. Jonas, “Theta-gamma-modulated synaptic currents
in hippocampal granule cells in vivo define a mechanism for network oscillations,”
Neuron, vol. 81, no. 1. Elsevier, pp. 140–152, 2014.
ista: Pernia-Andrade A, Jonas PM. 2014. Theta-gamma-modulated synaptic currents
in hippocampal granule cells in vivo define a mechanism for network oscillations.
Neuron. 81(1), 140–152.
mla: Pernia-Andrade, Alejandro, and Peter M. Jonas. “Theta-Gamma-Modulated Synaptic
Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.”
Neuron, vol. 81, no. 1, Elsevier, 2014, pp. 140–52, doi:10.1016/j.neuron.2013.09.046.
short: A. Pernia-Andrade, P.M. Jonas, Neuron 81 (2014) 140–152.
date_created: 2018-12-11T11:56:35Z
date_published: 2014-01-08T00:00:00Z
date_updated: 2021-01-12T06:56:19Z
day: '08'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.neuron.2013.09.046
ec_funded: 1
file:
- access_level: open_access
checksum: 438547cfcd9045a22f065f2019f07849
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:48Z
date_updated: 2020-07-14T12:45:35Z
file_id: '4773'
file_name: IST-2016-422-v1+1_1-s2.0-S0896627313009227-main.pdf
file_size: 4373072
relation: main_file
file_date_updated: 2020-07-14T12:45:35Z
has_accepted_license: '1'
intvolume: ' 81'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 140 - 152
project:
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
publication: Neuron
publication_identifier:
issn:
- '08966273'
publication_status: published
publisher: Elsevier
publist_id: '4692'
pubrep_id: '422'
quality_controlled: '1'
scopus_import: 1
status: public
title: Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo
define a mechanism for network oscillations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 81
year: '2014'
...
---
_id: '2251'
abstract:
- lang: eng
text: 'Sharp wave/ripple (SWR, 150–250 Hz) hippocampal events have long been postulated
to be involved in memory consolidation. However, more recent work has investigated
SWRs that occur during active waking behaviour: findings that suggest that SWRs
may also play a role in cell assembly strengthening or spatial working memory.
Do such theories of SWR function apply to animal learning? This review discusses
how general theories linking SWRs to memory-related function may explain circuit
mechanisms related to rodent spatial learning and to the associated stabilization
of new cognitive maps.'
acknowledgement: CC BY 3.0
article_number: '20120528'
article_processing_charge: No
author:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: David
full_name: Dupret, David
last_name: Dupret
citation:
ama: Csicsvari JL, Dupret D. Sharp wave/ripple network oscillations and learning-associated
hippocampal maps. Philosophical Transactions of the Royal Society of London
Series B, Biological Sciences. 2014;369(1635). doi:10.1098/rstb.2012.0528
apa: Csicsvari, J. L., & Dupret, D. (2014). Sharp wave/ripple network oscillations
and learning-associated hippocampal maps. Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences. Royal Society, The.
https://doi.org/10.1098/rstb.2012.0528
chicago: Csicsvari, Jozsef L, and David Dupret. “Sharp Wave/Ripple Network Oscillations
and Learning-Associated Hippocampal Maps.” Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences. Royal Society, The,
2014. https://doi.org/10.1098/rstb.2012.0528.
ieee: J. L. Csicsvari and D. Dupret, “Sharp wave/ripple network oscillations and
learning-associated hippocampal maps,” Philosophical Transactions of the Royal
Society of London. Series B, Biological Sciences, vol. 369, no. 1635. Royal
Society, The, 2014.
ista: Csicsvari JL, Dupret D. 2014. Sharp wave/ripple network oscillations and learning-associated
hippocampal maps. Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences. 369(1635), 20120528.
mla: Csicsvari, Jozsef L., and David Dupret. “Sharp Wave/Ripple Network Oscillations
and Learning-Associated Hippocampal Maps.” Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences, vol. 369, no. 1635,
20120528, Royal Society, The, 2014, doi:10.1098/rstb.2012.0528.
short: J.L. Csicsvari, D. Dupret, Philosophical Transactions of the Royal Society
of London. Series B, Biological Sciences 369 (2014).
date_created: 2018-12-11T11:56:34Z
date_published: 2014-02-05T00:00:00Z
date_updated: 2021-01-12T06:56:18Z
day: '05'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1098/rstb.2012.0528
external_id:
pmid:
- '24366138'
file:
- access_level: open_access
checksum: 51beb33de71c9c19e0c205a20d206f9a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:24Z
date_updated: 2020-07-14T12:45:34Z
file_id: '5006'
file_name: IST-2016-527-v1+1_20120528.full.pdf
file_size: 771896
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 369'
issue: '1635'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_identifier:
issn:
- '09628436'
publication_status: published
publisher: Royal Society, The
publist_id: '4697'
pubrep_id: '527'
quality_controlled: '1'
scopus_import: 1
status: public
title: Sharp wave/ripple network oscillations and learning-associated hippocampal
maps
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 369
year: '2014'
...
---
_id: '2253'
abstract:
- lang: eng
text: Plant growth is achieved predominantly by cellular elongation, which is thought
to be controlled on several levels by apoplastic auxin. Auxin export into the
apoplast is achieved by plasma membrane efflux catalysts of the PIN-FORMED (PIN)
and ATP-binding cassette protein subfamily B/phosphor- glycoprotein (ABCB/PGP)
classes; the latter were shown to depend on interaction with the FKBP42, TWISTED
DWARF1 (TWD1). Here by using a transgenic approach in combination with phenotypical,
biochemical and cell biological analyses we demonstrate the importance of a putative
C-terminal in-plane membrane anchor of TWD1 in the regulation of ABCB-mediated
auxin transport. In contrast with dwarfed twd1 loss-of-function alleles, TWD1
gain-of-function lines that lack a putative in-plane membrane anchor (HA-TWD1-Ct)
show hypermorphic plant architecture, characterized by enhanced stem length and
leaf surface but reduced shoot branching. Greater hypocotyl length is the result
of enhanced cell elongation that correlates with reduced polar auxin transport
capacity for HA-TWD1-Ct. As a consequence, HA-TWD1-Ct displays higher hypocotyl
auxin accumulation, which is shown to result in elevated auxin-induced cell elongation
rates. Our data highlight the importance of C-terminal membrane anchoring for
TWD1 action, which is required for specific regulation of ABCB-mediated auxin
transport. These data support a model in which TWD1 controls lateral ABCB1-mediated
export into the apoplast, which is required for auxin-mediated cell elongation.
article_processing_charge: No
article_type: original
author:
- first_name: Aurélien
full_name: Bailly, Aurélien
last_name: Bailly
- first_name: Bangjun
full_name: Wang, Bangjun
last_name: Wang
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Stephan
full_name: Pollmann, Stephan
last_name: Pollmann
- first_name: Daniel
full_name: Schenck, Daniel
last_name: Schenck
- first_name: Hartwig
full_name: Lüthen, Hartwig
last_name: Lüthen
- first_name: Alexander
full_name: Schulz, Alexander
last_name: Schulz
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
citation:
ama: Bailly A, Wang B, Zwiewka M, et al. Expression of TWISTED DWARF1 lacking its
in-plane membrane anchor leads to increased cell elongation and hypermorphic growth.
Plant Journal. 2014;77(1):108-118. doi:10.1111/tpj.12369
apa: Bailly, A., Wang, B., Zwiewka, M., Pollmann, S., Schenck, D., Lüthen, H., …
Geisler, M. (2014). Expression of TWISTED DWARF1 lacking its in-plane membrane
anchor leads to increased cell elongation and hypermorphic growth. Plant Journal.
Wiley-Blackwell. https://doi.org/10.1111/tpj.12369
chicago: Bailly, Aurélien, Bangjun Wang, Marta Zwiewka, Stephan Pollmann, Daniel
Schenck, Hartwig Lüthen, Alexander Schulz, Jiří Friml, and Markus Geisler. “Expression
of TWISTED DWARF1 Lacking Its In-Plane Membrane Anchor Leads to Increased Cell
Elongation and Hypermorphic Growth.” Plant Journal. Wiley-Blackwell, 2014.
https://doi.org/10.1111/tpj.12369.
ieee: A. Bailly et al., “Expression of TWISTED DWARF1 lacking its in-plane
membrane anchor leads to increased cell elongation and hypermorphic growth,” Plant
Journal, vol. 77, no. 1. Wiley-Blackwell, pp. 108–118, 2014.
ista: Bailly A, Wang B, Zwiewka M, Pollmann S, Schenck D, Lüthen H, Schulz A, Friml
J, Geisler M. 2014. Expression of TWISTED DWARF1 lacking its in-plane membrane
anchor leads to increased cell elongation and hypermorphic growth. Plant Journal.
77(1), 108–118.
mla: Bailly, Aurélien, et al. “Expression of TWISTED DWARF1 Lacking Its In-Plane
Membrane Anchor Leads to Increased Cell Elongation and Hypermorphic Growth.” Plant
Journal, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 108–18, doi:10.1111/tpj.12369.
short: A. Bailly, B. Wang, M. Zwiewka, S. Pollmann, D. Schenck, H. Lüthen, A. Schulz,
J. Friml, M. Geisler, Plant Journal 77 (2014) 108–118.
date_created: 2018-12-11T11:56:35Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:18Z
day: '01'
department:
- _id: JiFr
doi: 10.1111/tpj.12369
intvolume: ' 77'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/tpj.12369
month: '01'
oa: 1
oa_version: Published Version
page: 108 - 118
project:
- _id: 256BDAB0-B435-11E9-9278-68D0E5697425
name: Innovationsförderung in der Grenzregion Österreich – Tschechische Republik
durch die Schaffung von Synergien im Bereich der Forschungsinfrastruktur
publication: Plant Journal
publication_identifier:
issn:
- '09607412'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4694'
quality_controlled: '1'
scopus_import: 1
status: public
title: Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to
increased cell elongation and hypermorphic growth
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 77
year: '2014'
...
---
_id: '2248'
abstract:
- lang: eng
text: 'Avian forelimb digit homology remains one of the standard themes in comparative
biology and EvoDevo research. In order to resolve the apparent contradictions
between embryological and paleontological evidence a variety of hypotheses have
been presented in recent years. The proposals range from excluding birds from
the dinosaur clade, to assignments of homology by different criteria, or even
assuming a hexadactyl tetrapod limb ground state. At present two approaches prevail:
the frame shift hypothesis and the pyramid reduction hypothesis. While the former
postulates a homeotic shift of digit identities, the latter argues for a gradual
bilateral reduction of phalanges and digits. Here we present a new model that
integrates elements from both hypotheses with the existing experimental and fossil
evidence. We start from the main feature common to both earlier concepts, the
initiating ontogenetic event: reduction and loss of the anterior-most digit. It
is proposed that a concerted mechanism of molecular regulation and developmental
mechanics is capable of shifting the boundaries of hoxD expression in embryonic
forelimb buds as well as changing the digit phenotypes. Based on a distinction
between positional (topological) and compositional (phenotypic) homology criteria,
we argue that the identity of the avian digits is II, III, IV, despite a partially
altered phenotype. Finally, we introduce an alternative digit reduction scheme
that reconciles the current fossil evidence with the presented molecular-morphogenetic
model. Our approach identifies specific experiments that allow to test whether
gene expression can be shifted and digit phenotypes can be altered by induced
digit loss or digit gain.'
author:
- first_name: Daniel
full_name: Capek, Daniel
id: 31C42484-F248-11E8-B48F-1D18A9856A87
last_name: Capek
orcid: 0000-0001-5199-9940
- first_name: Brian
full_name: Metscher, Brian
last_name: Metscher
- first_name: Gerd
full_name: Müller, Gerd
last_name: Müller
citation:
ama: 'Capek D, Metscher B, Müller G. Thumbs down: A molecular-morphogenetic approach
to avian digit homology. Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. 2014;322(1):1-12. doi:10.1002/jez.b.22545'
apa: 'Capek, D., Metscher, B., & Müller, G. (2014). Thumbs down: A molecular-morphogenetic
approach to avian digit homology. Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. Wiley-Blackwell. https://doi.org/10.1002/jez.b.22545'
chicago: 'Capek, Daniel, Brian Metscher, and Gerd Müller. “Thumbs down: A Molecular-Morphogenetic
Approach to Avian Digit Homology.” Journal of Experimental Zoology Part B:
Molecular and Developmental Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1002/jez.b.22545.'
ieee: 'D. Capek, B. Metscher, and G. Müller, “Thumbs down: A molecular-morphogenetic
approach to avian digit homology,” Journal of Experimental Zoology Part B:
Molecular and Developmental Evolution, vol. 322, no. 1. Wiley-Blackwell, pp.
1–12, 2014.'
ista: 'Capek D, Metscher B, Müller G. 2014. Thumbs down: A molecular-morphogenetic
approach to avian digit homology. Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. 322(1), 1–12.'
mla: 'Capek, Daniel, et al. “Thumbs down: A Molecular-Morphogenetic Approach to
Avian Digit Homology.” Journal of Experimental Zoology Part B: Molecular and
Developmental Evolution, vol. 322, no. 1, Wiley-Blackwell, 2014, pp. 1–12,
doi:10.1002/jez.b.22545.'
short: 'D. Capek, B. Metscher, G. Müller, Journal of Experimental Zoology Part B:
Molecular and Developmental Evolution 322 (2014) 1–12.'
date_created: 2018-12-11T11:56:33Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:16Z
day: '01'
department:
- _id: CaHe
doi: 10.1002/jez.b.22545
intvolume: ' 322'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 1 - 12
publication: 'Journal of Experimental Zoology Part B: Molecular and Developmental
Evolution'
publication_identifier:
issn:
- '15525007'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4701'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Thumbs down: A molecular-morphogenetic approach to avian digit homology'
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 322
year: '2014'
...
---
_id: '2249'
abstract:
- lang: eng
text: The unfolded protein response (UPR) is a signaling network triggered by overload
of protein-folding demand in the endoplasmic reticulum (ER), a condition termed
ER stress. The UPR is critical for growth and development; nonetheless, connections
between the UPR and other cellular regulatory processes remain largely unknown.
Here, we identify a link between the UPR and the phytohormone auxin, a master
regulator of plant physiology. We show that ER stress triggers down-regulation
of auxin receptors and transporters in Arabidopsis thaliana. We also demonstrate
that an Arabidopsis mutant of a conserved ER stress sensor IRE1 exhibits defects
in the auxin response and levels. These data not only support that the plant IRE1
is required for auxin homeostasis, they also reveal a species-specific feature
of IRE1 in multicellular eukaryotes. Furthermore, by establishing that UPR activation
is reduced in mutants of ER-localized auxin transporters, including PIN5, we define
a long-neglected biological significance of ER-based auxin regulation. We further
examine the functional relationship of IRE1 and PIN5 by showing that an ire1 pin5
triple mutant enhances defects of UPR activation and auxin homeostasis in ire1
or pin5. Our results imply that the plant UPR has evolved a hormone-dependent
strategy for coordinating ER function with physiological processes.
author:
- first_name: Yani
full_name: Chen, Yani
last_name: Chen
- first_name: Kyaw
full_name: Aung, Kyaw
last_name: Aung
- first_name: Jakub
full_name: Rolčík, Jakub
last_name: Rolčík
- first_name: Kathryn
full_name: Walicki, Kathryn
last_name: Walicki
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Federica
full_name: Brandizzí, Federica
last_name: Brandizzí
citation:
ama: Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. Inter-regulation
of the unfolded protein response and auxin signaling. Plant Journal. 2014;77(1):97-107.
doi:10.1111/tpj.12373
apa: Chen, Y., Aung, K., Rolčík, J., Walicki, K., Friml, J., & Brandizzí, F.
(2014). Inter-regulation of the unfolded protein response and auxin signaling.
Plant Journal. Wiley-Blackwell. https://doi.org/10.1111/tpj.12373
chicago: Chen, Yani, Kyaw Aung, Jakub Rolčík, Kathryn Walicki, Jiří Friml, and Federica
Brandizzí. “Inter-Regulation of the Unfolded Protein Response and Auxin Signaling.”
Plant Journal. Wiley-Blackwell, 2014. https://doi.org/10.1111/tpj.12373.
ieee: Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, and F. Brandizzí, “Inter-regulation
of the unfolded protein response and auxin signaling,” Plant Journal, vol.
77, no. 1. Wiley-Blackwell, pp. 97–107, 2014.
ista: Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. 2014. Inter-regulation
of the unfolded protein response and auxin signaling. Plant Journal. 77(1), 97–107.
mla: Chen, Yani, et al. “Inter-Regulation of the Unfolded Protein Response and Auxin
Signaling.” Plant Journal, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 97–107,
doi:10.1111/tpj.12373.
short: Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, F. Brandizzí, Plant Journal
77 (2014) 97–107.
date_created: 2018-12-11T11:56:34Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:17Z
day: '01'
department:
- _id: JiFr
doi: 10.1111/tpj.12373
intvolume: ' 77'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981873/
month: '01'
oa: 1
oa_version: Submitted Version
page: 97 - 107
publication: Plant Journal
publication_identifier:
issn:
- '09607412'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4699'
quality_controlled: '1'
scopus_import: 1
status: public
title: Inter-regulation of the unfolded protein response and auxin signaling
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 77
year: '2014'
...
---
_id: '2252'
abstract:
- lang: eng
text: The pattern of inheritance and mechanism of sex determination can have important
evolutionary consequences. We studied probabilistic sex determination in the ciliate
Tetrahymena thermophila, which was previously shown to cause evolution of skewed
sex ratios. We find that the genetic background alters the sex determination patterns
of mat alleles in heterozygotes and that allelic interaction can differentially
influence the expression probability of the 7 sexes. We quantify the dominance
relationships between several mat alleles and find that A-type alleles, which
specify sex I, are indeed recessive to B-type alleles, which are unable to specify
that sex. Our results provide additional support for the presence of modifier
loci and raise implications for the dynamics of sex ratios in populations of T.
thermophila.
article_processing_charge: No
author:
- first_name: Sujal
full_name: Phadke, Sujal
last_name: Phadke
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Tuan
full_name: Pham, Tuan
last_name: Pham
- first_name: Stephanie
full_name: Pham, Stephanie
last_name: Pham
- first_name: Rebecca
full_name: Zufall, Rebecca
last_name: Zufall
citation:
ama: Phadke S, Paixao T, Pham T, Pham S, Zufall R. Genetic background alters dominance
relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal
of Heredity. 2014;105(1):130-135. doi:10.1093/jhered/est063
apa: Phadke, S., Paixao, T., Pham, T., Pham, S., & Zufall, R. (2014). Genetic
background alters dominance relationships between mat alleles in the ciliate Tetrahymena
Thermophila. Journal of Heredity. Oxford University Press. https://doi.org/10.1093/jhered/est063
chicago: Phadke, Sujal, Tiago Paixao, Tuan Pham, Stephanie Pham, and Rebecca Zufall.
“Genetic Background Alters Dominance Relationships between Mat Alleles in the
Ciliate Tetrahymena Thermophila.” Journal of Heredity. Oxford University
Press, 2014. https://doi.org/10.1093/jhered/est063.
ieee: S. Phadke, T. Paixao, T. Pham, S. Pham, and R. Zufall, “Genetic background
alters dominance relationships between mat alleles in the ciliate Tetrahymena
Thermophila,” Journal of Heredity, vol. 105, no. 1. Oxford University Press,
pp. 130–135, 2014.
ista: Phadke S, Paixao T, Pham T, Pham S, Zufall R. 2014. Genetic background alters
dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila.
Journal of Heredity. 105(1), 130–135.
mla: Phadke, Sujal, et al. “Genetic Background Alters Dominance Relationships between
Mat Alleles in the Ciliate Tetrahymena Thermophila.” Journal of Heredity,
vol. 105, no. 1, Oxford University Press, 2014, pp. 130–35, doi:10.1093/jhered/est063.
short: S. Phadke, T. Paixao, T. Pham, S. Pham, R. Zufall, Journal of Heredity 105
(2014) 130–135.
date_created: 2018-12-11T11:56:35Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2022-08-25T14:45:42Z
day: '01'
department:
- _id: NiBa
doi: 10.1093/jhered/est063
intvolume: ' 105'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 130 - 135
publication: Journal of Heredity
publication_identifier:
issn:
- '00221503'
publication_status: published
publisher: Oxford University Press
publist_id: '4695'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic background alters dominance relationships between mat alleles in the
ciliate Tetrahymena Thermophila
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 105
year: '2014'
...