---
_id: '1859'
abstract:
- lang: eng
text: "Structural support vector machines (SSVMs) are amongst the best performing
models for structured computer vision tasks, such as semantic image segmentation
or human pose estimation. Training SSVMs, however, is computationally costly,
because it requires repeated calls to a structured prediction subroutine (called
\\emph{max-oracle}), which has to solve an optimization problem itself, e.g. a
graph cut.\r\nIn this work, we introduce a new algorithm for SSVM training that
is more efficient than earlier techniques when the max-oracle is computationally
expensive, as it is frequently the case in computer vision tasks. The main idea
is to (i) combine the recent stochastic Block-Coordinate Frank-Wolfe algorithm
with efficient hyperplane caching, and (ii) use an automatic selection rule for
deciding whether to call the exact max-oracle or to rely on an approximate one
based on the cached hyperplanes.\r\nWe show experimentally that this strategy
leads to faster convergence to the optimum with respect to the number of requires
oracle calls, and that this translates into faster convergence with respect to
the total runtime when the max-oracle is slow compared to the other steps of the
algorithm. "
author:
- first_name: Neel
full_name: Shah, Neel
id: 31ABAF80-F248-11E8-B48F-1D18A9856A87
last_name: Shah
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Shah N, Kolmogorov V, Lampert C. A multi-plane block-coordinate Frank-Wolfe
algorithm for training structural SVMs with a costly max-oracle. In: IEEE; 2015:2737-2745.
doi:10.1109/CVPR.2015.7298890'
apa: 'Shah, N., Kolmogorov, V., & Lampert, C. (2015). A multi-plane block-coordinate
Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle (pp.
2737–2745). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston,
MA, USA: IEEE. https://doi.org/10.1109/CVPR.2015.7298890'
chicago: Shah, Neel, Vladimir Kolmogorov, and Christoph Lampert. “A Multi-Plane
Block-Coordinate Frank-Wolfe Algorithm for Training Structural SVMs with a Costly
Max-Oracle,” 2737–45. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7298890.
ieee: 'N. Shah, V. Kolmogorov, and C. Lampert, “A multi-plane block-coordinate Frank-Wolfe
algorithm for training structural SVMs with a costly max-oracle,” presented at
the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA, 2015, pp.
2737–2745.'
ista: 'Shah N, Kolmogorov V, Lampert C. 2015. A multi-plane block-coordinate Frank-Wolfe
algorithm for training structural SVMs with a costly max-oracle. CVPR: Computer
Vision and Pattern Recognition, 2737–2745.'
mla: Shah, Neel, et al. A Multi-Plane Block-Coordinate Frank-Wolfe Algorithm
for Training Structural SVMs with a Costly Max-Oracle. IEEE, 2015, pp. 2737–45,
doi:10.1109/CVPR.2015.7298890.
short: N. Shah, V. Kolmogorov, C. Lampert, in:, IEEE, 2015, pp. 2737–2745.
conference:
end_date: 2015-06-12
location: Boston, MA, USA
name: 'CVPR: Computer Vision and Pattern Recognition'
start_date: 2015-06-07
date_created: 2018-12-11T11:54:24Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2021-01-12T06:53:40Z
day: '01'
department:
- _id: VlKo
- _id: ChLa
doi: 10.1109/CVPR.2015.7298890
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1408.6804
month: '06'
oa: 1
oa_version: Preprint
page: 2737 - 2745
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_status: published
publisher: IEEE
publist_id: '5240'
quality_controlled: '1'
scopus_import: 1
status: public
title: A multi-plane block-coordinate Frank-Wolfe algorithm for training structural
SVMs with a costly max-oracle
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1860'
abstract:
- lang: eng
text: Classifiers for object categorization are usually evaluated by their accuracy
on a set of i.i.d. test examples. This provides us with an estimate of the expected
error when applying the classifiers to a single new image. In real application,
however, classifiers are rarely only used for a single image and then discarded.
Instead, they are applied sequentially to many images, and these are typically
not i.i.d. samples from a fixed data distribution, but they carry dependencies
and their class distribution varies over time. In this work, we argue that the
phenomenon of correlated data at prediction time is not a nuisance, but a blessing
in disguise. We describe a probabilistic method for adapting classifiers at prediction
time without having to retrain them. We also introduce a framework for creating
realistically distributed image sequences, which offers a way to benchmark classifier
adaptation methods, such as the one we propose. Experiments on the ILSVRC2010
and ILSVRC2012 datasets show that adapting object classification systems at prediction
time can significantly reduce their error rate, even with no additional human
feedback.
author:
- first_name: Amélie
full_name: Royer, Amélie
last_name: Royer
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Royer A, Lampert C. Classifier adaptation at prediction time. In: IEEE; 2015:1401-1409.
doi:10.1109/CVPR.2015.7298746'
apa: 'Royer, A., & Lampert, C. (2015). Classifier adaptation at prediction time
(pp. 1401–1409). Presented at the CVPR: Computer Vision and Pattern Recognition,
Boston, MA, United States: IEEE. https://doi.org/10.1109/CVPR.2015.7298746'
chicago: Royer, Amélie, and Christoph Lampert. “Classifier Adaptation at Prediction
Time,” 1401–9. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7298746.
ieee: 'A. Royer and C. Lampert, “Classifier adaptation at prediction time,” presented
at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States,
2015, pp. 1401–1409.'
ista: 'Royer A, Lampert C. 2015. Classifier adaptation at prediction time. CVPR:
Computer Vision and Pattern Recognition, 1401–1409.'
mla: Royer, Amélie, and Christoph Lampert. Classifier Adaptation at Prediction
Time. IEEE, 2015, pp. 1401–09, doi:10.1109/CVPR.2015.7298746.
short: A. Royer, C. Lampert, in:, IEEE, 2015, pp. 1401–1409.
conference:
end_date: 2015-06-12
location: Boston, MA, United States
name: 'CVPR: Computer Vision and Pattern Recognition'
start_date: 2015-06-07
date_created: 2018-12-11T11:54:24Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2021-01-12T06:53:41Z
day: '01'
department:
- _id: ChLa
doi: 10.1109/CVPR.2015.7298746
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.cv-foundation.org/openaccess/content_cvpr_2015/papers/Royer_Classifier_Adaptation_at_2015_CVPR_paper.pdf
month: '06'
oa: 1
oa_version: Submitted Version
page: 1401 - 1409
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_status: published
publisher: IEEE
publist_id: '5239'
quality_controlled: '1'
scopus_import: 1
status: public
title: Classifier adaptation at prediction time
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1864'
abstract:
- lang: eng
text: "The Altshuler–Shklovskii formulas (Altshuler and Shklovskii, BZh Eksp Teor
Fiz 91:200, 1986) predict, for any disordered quantum system in the diffusive
regime, a universal power law behaviour for the correlation functions of the mesoscopic
eigenvalue density. In this paper and its companion (Erdős and Knowles, The Altshuler–Shklovskii
formulas for random band matrices I: the unimodular case, 2013), we prove these
formulas for random band matrices. In (Erdős and Knowles, The Altshuler–Shklovskii
formulas for random band matrices I: the unimodular case, 2013) we introduced
a diagrammatic approach and presented robust estimates on general diagrams under
certain simplifying assumptions. In this paper, we remove these assumptions by
giving a general estimate of the subleading diagrams. We also give a precise analysis
of the leading diagrams which give rise to the Altschuler–Shklovskii power laws.
Moreover, we introduce a family of general random band matrices which interpolates
between real symmetric (β = 1) and complex Hermitian (β = 2) models, and track
the transition for the mesoscopic density–density correlation. Finally, we address
the higher-order correlation functions by proving that they behave asymptotically
according to a Gaussian process whose covariance is given by the Altshuler–Shklovskii
formulas.\r\n"
author:
- 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
citation:
ama: 'Erdös L, Knowles A. The Altshuler–Shklovskii formulas for random band matrices
II: The general case. Annales Henri Poincare. 2015;16(3):709-799. doi:10.1007/s00023-014-0333-5'
apa: 'Erdös, L., & Knowles, A. (2015). The Altshuler–Shklovskii formulas for
random band matrices II: The general case. Annales Henri Poincare. Springer.
https://doi.org/10.1007/s00023-014-0333-5'
chicago: 'Erdös, László, and Antti Knowles. “The Altshuler–Shklovskii Formulas for
Random Band Matrices II: The General Case.” Annales Henri Poincare. Springer,
2015. https://doi.org/10.1007/s00023-014-0333-5.'
ieee: 'L. Erdös and A. Knowles, “The Altshuler–Shklovskii formulas for random band
matrices II: The general case,” Annales Henri Poincare, vol. 16, no. 3.
Springer, pp. 709–799, 2015.'
ista: 'Erdös L, Knowles A. 2015. The Altshuler–Shklovskii formulas for random band
matrices II: The general case. Annales Henri Poincare. 16(3), 709–799.'
mla: 'Erdös, László, and Antti Knowles. “The Altshuler–Shklovskii Formulas for Random
Band Matrices II: The General Case.” Annales Henri Poincare, vol. 16, no.
3, Springer, 2015, pp. 709–99, doi:10.1007/s00023-014-0333-5.'
short: L. Erdös, A. Knowles, Annales Henri Poincare 16 (2015) 709–799.
date_created: 2018-12-11T11:54:26Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2021-01-12T06:53:42Z
day: '01'
department:
- _id: LaEr
doi: 10.1007/s00023-014-0333-5
ec_funded: 1
intvolume: ' 16'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1309.5107
month: '03'
oa: 1
oa_version: Preprint
page: 709 - 799
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Annales Henri Poincare
publication_status: published
publisher: Springer
publist_id: '5233'
scopus_import: 1
status: public
title: 'The Altshuler–Shklovskii formulas for random band matrices II: The general
case'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2015'
...
---
_id: '1871'
abstract:
- lang: eng
text: The plant hormone auxin is a key regulator of plant growth and development.
Differences in auxin distribution within tissues are mediated by the polar auxin
transport machinery, and cellular auxin responses occur depending on changes in
cellular auxin levels. Multiple receptor systems at the cell surface and in the
interior operate to sense and interpret fluctuations in auxin distribution that
occur during plant development. Until now, three proteins or protein complexes
that can bind auxin have been identified. SCFTIR1 [a SKP1-cullin-1-F-box complex
that contains transport inhibitor response 1 (TIR1) as the F-box protein] and
S-phase-kinaseassociated protein 2 (SKP2) localize to the nucleus, whereas auxinbinding
protein 1 (ABP1), predominantly associates with the endoplasmic reticulum and
cell surface. In this Cell Science at a Glance article, we summarize recent discoveries
in the field of auxin transport and signaling that have led to the identification
of new components of these pathways, as well as their mutual interaction.
acknowledgement: This work was supported by the European Research Council [project
ERC-2011-StG-20101109-PSDP]; European Social Fund [grant number CZ.1.07/2.3.00/20.0043]
and the Czech Science Foundation GAČR [grant number GA13-40637S]
author:
- first_name: Peter
full_name: Grones, Peter
id: 399876EC-F248-11E8-B48F-1D18A9856A87
last_name: Grones
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Grones P, Friml J. Auxin transporters and binding proteins at a glance. Journal
of Cell Science. 2015;128(1):1-7. doi:10.1242/jcs.159418
apa: Grones, P., & Friml, J. (2015). Auxin transporters and binding proteins
at a glance. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.159418
chicago: Grones, Peter, and Jiří Friml. “Auxin Transporters and Binding Proteins
at a Glance.” Journal of Cell Science. Company of Biologists, 2015. https://doi.org/10.1242/jcs.159418.
ieee: P. Grones and J. Friml, “Auxin transporters and binding proteins at a glance,”
Journal of Cell Science, vol. 128, no. 1. Company of Biologists, pp. 1–7,
2015.
ista: Grones P, Friml J. 2015. Auxin transporters and binding proteins at a glance.
Journal of Cell Science. 128(1), 1–7.
mla: Grones, Peter, and Jiří Friml. “Auxin Transporters and Binding Proteins at
a Glance.” Journal of Cell Science, vol. 128, no. 1, Company of Biologists,
2015, pp. 1–7, doi:10.1242/jcs.159418.
short: P. Grones, J. Friml, Journal of Cell Science 128 (2015) 1–7.
date_created: 2018-12-11T11:54:28Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:45Z
day: '01'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1242/jcs.159418
file:
- access_level: open_access
checksum: 24c779f4cd9d549ca6833e26f486be27
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:00Z
date_updated: 2020-07-14T12:45:19Z
file_id: '4852'
file_name: IST-2016-563-v1+1_1.full.pdf
file_size: 1688844
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 128'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 1 - 7
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '5225'
pubrep_id: '563'
quality_controlled: '1'
scopus_import: 1
status: public
title: Auxin transporters and binding proteins at a glance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 128
year: '2015'
...
---
_id: '1873'
abstract:
- lang: eng
text: 'We consider partially observable Markov decision processes (POMDPs) with
limit-average payoff, where a reward value in the interval [0,1] is associated
with every transition, and the payoff of an infinite path is the long-run average
of the rewards. We consider two types of path constraints: (i) a quantitative
constraint defines the set of paths where the payoff is at least a given threshold
λ1ε(0,1]; and (ii) a qualitative constraint which is a special case of the quantitative
constraint with λ1=1. We consider the computation of the almost-sure winning set,
where the controller needs to ensure that the path constraint is satisfied with
probability 1. Our main results for qualitative path constraints are as follows:
(i) the problem of deciding the existence of a finite-memory controller is EXPTIME-complete;
and (ii) the problem of deciding the existence of an infinite-memory controller
is undecidable. For quantitative path constraints we show that the problem of
deciding the existence of a finite-memory controller is undecidable. We also present
a prototype implementation of our EXPTIME algorithm and experimental results on
several examples.'
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
citation:
ama: Chatterjee K, Chmelik M. POMDPs under probabilistic semantics. Artificial
Intelligence. 2015;221:46-72. doi:10.1016/j.artint.2014.12.009
apa: Chatterjee, K., & Chmelik, M. (2015). POMDPs under probabilistic semantics.
Artificial Intelligence. Elsevier. https://doi.org/10.1016/j.artint.2014.12.009
chicago: Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic
Semantics.” Artificial Intelligence. Elsevier, 2015. https://doi.org/10.1016/j.artint.2014.12.009.
ieee: K. Chatterjee and M. Chmelik, “POMDPs under probabilistic semantics,” Artificial
Intelligence, vol. 221. Elsevier, pp. 46–72, 2015.
ista: Chatterjee K, Chmelik M. 2015. POMDPs under probabilistic semantics. Artificial
Intelligence. 221, 46–72.
mla: Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic Semantics.”
Artificial Intelligence, vol. 221, Elsevier, 2015, pp. 46–72, doi:10.1016/j.artint.2014.12.009.
short: K. Chatterjee, M. Chmelik, Artificial Intelligence 221 (2015) 46–72.
date_created: 2018-12-11T11:54:28Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2021-01-12T06:53:46Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.artint.2014.12.009
external_id:
arxiv:
- '1408.2058'
intvolume: ' 221'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1408.2058
month: '04'
oa: 1
oa_version: Preprint
page: 46 - 72
publication: Artificial Intelligence
publication_status: published
publisher: Elsevier
publist_id: '5224'
quality_controlled: '1'
scopus_import: 1
status: public
title: POMDPs under probabilistic semantics
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 221
year: '2015'
...
---
_id: '1879'
abstract:
- lang: eng
text: When electron microscopy (EM) was introduced in the 1930s it gave scientists
their first look into the nanoworld of cells. Over the last 80 years EM has vastly
increased our understanding of the complex cellular structures that underlie the
diverse functions that cells need to maintain life. One drawback that has been
difficult to overcome was the inherent lack of volume information, mainly due
to the limit on the thickness of sections that could be viewed in a transmission
electron microscope (TEM). For many years scientists struggled to achieve three-dimensional
(3D) EM using serial section reconstructions, TEM tomography, and scanning EM
(SEM) techniques such as freeze-fracture. Although each technique yielded some
special information, they required a significant amount of time and specialist
expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists
began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning
of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and
subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists
were able to collect large volumes of 3D EM information at resolutions that could
address many important biological questions, and do so in an efficient manner.
We present here some examples of 3D EM taken from the many diverse specimens that
have been imaged in our core facility. We propose that the next major step forward
will be to efficiently correlate functional information obtained using light microscopy
(LM) with 3D EM datasets to more completely investigate the important links between
cell structures and their functions.
acknowledgement: The Zeiss Merlin with Gatan 3View2XP and Zeiss Auriga were acquired
through a CLEM grant from Minister Ingrid Lieten to the VIB Bio-Imaging-Core. Michiel
Krols and Saskia Lippens are the recipients of a fellowship from the FWO (Fonds
Wetenschappelijk Onderzoek) of Flanders.
author:
- first_name: A
full_name: Kremer, A
last_name: Kremer
- first_name: Stefaan
full_name: Lippens, Stefaan
last_name: Lippens
- first_name: Sonia
full_name: Bartunkova, Sonia
last_name: Bartunkova
- first_name: Bob
full_name: Asselbergh, Bob
last_name: Asselbergh
- first_name: Cendric
full_name: Blanpain, Cendric
last_name: Blanpain
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: A
full_name: Goossens, A
last_name: Goossens
- first_name: Matthew
full_name: Holt, Matthew
last_name: Holt
- first_name: Sophie
full_name: Janssens, Sophie
last_name: Janssens
- first_name: Michiel
full_name: Krols, Michiel
last_name: Krols
- first_name: Jean
full_name: Larsimont, Jean
last_name: Larsimont
- first_name: Conor
full_name: Mc Guire, Conor
last_name: Mc Guire
- first_name: Moritz
full_name: Nowack, Moritz
last_name: Nowack
- first_name: Xavier
full_name: Saelens, Xavier
last_name: Saelens
- first_name: Andreas
full_name: Schertel, Andreas
last_name: Schertel
- first_name: B
full_name: Schepens, B
last_name: Schepens
- first_name: M
full_name: Slezak, M
last_name: Slezak
- first_name: Vincent
full_name: Timmerman, Vincent
last_name: Timmerman
- first_name: Clara
full_name: Theunis, Clara
last_name: Theunis
- first_name: Ronald
full_name: Van Brempt, Ronald
last_name: Van Brempt
- first_name: Y
full_name: Visser, Y
last_name: Visser
- first_name: Christophe
full_name: Guérin, Christophe
last_name: Guérin
citation:
ama: Kremer A, Lippens S, Bartunkova S, et al. Developing 3D SEM in a broad biological
context. Journal of Microscopy. 2015;259(2):80-96. doi:10.1111/jmi.12211
apa: Kremer, A., Lippens, S., Bartunkova, S., Asselbergh, B., Blanpain, C., Fendrych,
M., … Guérin, C. (2015). Developing 3D SEM in a broad biological context. Journal
of Microscopy. Wiley-Blackwell. https://doi.org/10.1111/jmi.12211
chicago: Kremer, A, Stefaan Lippens, Sonia Bartunkova, Bob Asselbergh, Cendric Blanpain,
Matyas Fendrych, A Goossens, et al. “Developing 3D SEM in a Broad Biological Context.”
Journal of Microscopy. Wiley-Blackwell, 2015. https://doi.org/10.1111/jmi.12211.
ieee: A. Kremer et al., “Developing 3D SEM in a broad biological context,”
Journal of Microscopy, vol. 259, no. 2. Wiley-Blackwell, pp. 80–96, 2015.
ista: Kremer A, Lippens S, Bartunkova S, Asselbergh B, Blanpain C, Fendrych M, Goossens
A, Holt M, Janssens S, Krols M, Larsimont J, Mc Guire C, Nowack M, Saelens X,
Schertel A, Schepens B, Slezak M, Timmerman V, Theunis C, Van Brempt R, Visser
Y, Guérin C. 2015. Developing 3D SEM in a broad biological context. Journal of
Microscopy. 259(2), 80–96.
mla: Kremer, A., et al. “Developing 3D SEM in a Broad Biological Context.” Journal
of Microscopy, vol. 259, no. 2, Wiley-Blackwell, 2015, pp. 80–96, doi:10.1111/jmi.12211.
short: A. Kremer, S. Lippens, S. Bartunkova, B. Asselbergh, C. Blanpain, M. Fendrych,
A. Goossens, M. Holt, S. Janssens, M. Krols, J. Larsimont, C. Mc Guire, M. Nowack,
X. Saelens, A. Schertel, B. Schepens, M. Slezak, V. Timmerman, C. Theunis, R.
Van Brempt, Y. Visser, C. Guérin, Journal of Microscopy 259 (2015) 80–96.
date_created: 2018-12-11T11:54:30Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:53:48Z
day: '01'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1111/jmi.12211
file:
- access_level: open_access
checksum: 3649c5372d1644062d728ea9287e367f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:19Z
date_updated: 2020-07-14T12:45:19Z
file_id: '4872'
file_name: IST-2016-459-v1+1_KREMER_et_al-2015-Journal_of_Microscopy.pdf
file_size: 2899898
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 259'
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '08'
oa: 1
oa_version: Published Version
page: 80 - 96
publication: Journal of Microscopy
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5218'
pubrep_id: '459'
quality_controlled: '1'
scopus_import: 1
status: public
title: Developing 3D SEM in a broad biological context
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: 259
year: '2015'
...
---
_id: '1880'
abstract:
- lang: eng
text: We investigate the relation between Bose-Einstein condensation (BEC) and superfluidity
in the ground state of a one-dimensional model of interacting bosons in a strong
random potential. We prove rigorously that in a certain parameter regime the superfluid
fraction can be arbitrarily small while complete BEC prevails. In another regime
there is both complete BEC and complete superfluidity, despite the strong disorder
acknowledgement: Support from the Natural Sciences and Engineering Research Council
of Canada NSERC (MK and RS) and from the Austrian Science Fund FWF (JY, under project
P 22929-N16) is gratefully acknowledged
article_number: '013022'
author:
- first_name: Martin
full_name: Könenberg, Martin
last_name: Könenberg
- first_name: Thomas
full_name: Moser, Thomas
id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87
last_name: Moser
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jakob
full_name: Yngvason, Jakob
last_name: Yngvason
citation:
ama: Könenberg M, Moser T, Seiringer R, Yngvason J. Superfluid behavior of a Bose-Einstein
condensate in a random potential. New Journal of Physics. 2015;17. doi:10.1088/1367-2630/17/1/013022
apa: Könenberg, M., Moser, T., Seiringer, R., & Yngvason, J. (2015). Superfluid
behavior of a Bose-Einstein condensate in a random potential. New Journal of
Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/17/1/013022
chicago: Könenberg, Martin, Thomas Moser, Robert Seiringer, and Jakob Yngvason.
“Superfluid Behavior of a Bose-Einstein Condensate in a Random Potential.” New
Journal of Physics. IOP Publishing Ltd., 2015. https://doi.org/10.1088/1367-2630/17/1/013022.
ieee: M. Könenberg, T. Moser, R. Seiringer, and J. Yngvason, “Superfluid behavior
of a Bose-Einstein condensate in a random potential,” New Journal of Physics,
vol. 17. IOP Publishing Ltd., 2015.
ista: Könenberg M, Moser T, Seiringer R, Yngvason J. 2015. Superfluid behavior of
a Bose-Einstein condensate in a random potential. New Journal of Physics. 17,
013022.
mla: Könenberg, Martin, et al. “Superfluid Behavior of a Bose-Einstein Condensate
in a Random Potential.” New Journal of Physics, vol. 17, 013022, IOP Publishing
Ltd., 2015, doi:10.1088/1367-2630/17/1/013022.
short: M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, New Journal of Physics
17 (2015).
date_created: 2018-12-11T11:54:30Z
date_published: 2015-01-15T00:00:00Z
date_updated: 2021-01-12T06:53:48Z
day: '15'
ddc:
- '530'
department:
- _id: RoSe
doi: 10.1088/1367-2630/17/1/013022
file:
- access_level: open_access
checksum: 38fdf2b5ac30445e26a5d613abd84b16
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:44Z
date_updated: 2020-07-14T12:45:20Z
file_id: '4963'
file_name: IST-2016-447-v1+1_document_1_.pdf
file_size: 768108
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
intvolume: ' 17'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
publication: New Journal of Physics
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '5214'
pubrep_id: '447'
quality_controlled: '1'
scopus_import: 1
status: public
title: Superfluid behavior of a Bose-Einstein condensate in a random potential
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: 17
year: '2015'
...
---
_id: '1882'
abstract:
- lang: eng
text: We provide a framework for compositional and iterative design and verification
of systems with quantitative information, such as rewards, time or energy. It
is based on disjunctive modal transition systems where we allow actions to bear
various types of quantitative information. Throughout the design process the actions
can be further refined and the information made more precise. We show how to compute
the results of standard operations on the systems, including the quotient (residual),
which has not been previously considered for quantitative non-deterministic systems.
Our quantitative framework has close connections to the modal nu-calculus and
is compositional with respect to general notions of distances between systems
and the standard operations.
acknowledgement: This research was funded in part by the European Research Council
(ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF)
project S11402-N23 (RiSE), and by the Czech Science Foundation, grant No. P202/12/G061.
alternative_title:
- LNCS
author:
- first_name: Uli
full_name: Fahrenberg, Uli
last_name: Fahrenberg
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Axel
full_name: Legay, Axel
last_name: Legay
- first_name: Louis
full_name: Traonouez, Louis
last_name: Traonouez
citation:
ama: 'Fahrenberg U, Kretinsky J, Legay A, Traonouez L. Compositionality for quantitative
specifications. In: Vol 8997. Springer; 2015:306-324. doi:10.1007/978-3-319-15317-9_19'
apa: 'Fahrenberg, U., Kretinsky, J., Legay, A., & Traonouez, L. (2015). Compositionality
for quantitative specifications (Vol. 8997, pp. 306–324). Presented at the FACS:
Formal Aspects of Component Software, Bertinoro, Italy: Springer. https://doi.org/10.1007/978-3-319-15317-9_19'
chicago: Fahrenberg, Uli, Jan Kretinsky, Axel Legay, and Louis Traonouez. “Compositionality
for Quantitative Specifications,” 8997:306–24. Springer, 2015. https://doi.org/10.1007/978-3-319-15317-9_19.
ieee: 'U. Fahrenberg, J. Kretinsky, A. Legay, and L. Traonouez, “Compositionality
for quantitative specifications,” presented at the FACS: Formal Aspects of Component
Software, Bertinoro, Italy, 2015, vol. 8997, pp. 306–324.'
ista: 'Fahrenberg U, Kretinsky J, Legay A, Traonouez L. 2015. Compositionality for
quantitative specifications. FACS: Formal Aspects of Component Software, LNCS,
vol. 8997, 306–324.'
mla: Fahrenberg, Uli, et al. Compositionality for Quantitative Specifications.
Vol. 8997, Springer, 2015, pp. 306–24, doi:10.1007/978-3-319-15317-9_19.
short: U. Fahrenberg, J. Kretinsky, A. Legay, L. Traonouez, in:, Springer, 2015,
pp. 306–324.
conference:
end_date: 2014-09-12
location: Bertinoro, Italy
name: 'FACS: Formal Aspects of Component Software'
start_date: 2014-09-10
date_created: 2018-12-11T11:54:31Z
date_published: 2015-01-30T00:00:00Z
date_updated: 2021-01-12T06:53:49Z
day: '30'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1007/978-3-319-15317-9_19
ec_funded: 1
intvolume: ' 8997'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1408.1256
month: '01'
oa: 1
oa_version: Preprint
page: 306 - 324
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '5216'
quality_controlled: '1'
scopus_import: 1
status: public
title: Compositionality for quantitative specifications
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8997
year: '2015'
...
---
_id: '1883'
abstract:
- lang: eng
text: "We introduce a one-parametric family of tree growth models, in which branching
probabilities decrease with branch age τ as τ-α. Depending on the exponent α,
the scaling of tree depth with tree size n displays a transition between the logarithmic
scaling of random trees and an algebraic growth. At the transition (α=1) tree
depth grows as (logn)2. This anomalous scaling is in good agreement with the trend
observed in evolution of biological species, thus providing a theoretical support
for age-dependent speciation and associating it to the occurrence of a critical
point.\r\n"
article_number: '022803'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Stephanie
full_name: Keller-Schmidt, Stephanie
last_name: Keller-Schmidt
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
- first_name: Víctor
full_name: Eguíluz, Víctor
last_name: Eguíluz
- first_name: Emilio
full_name: Hernandez Garcia, Emilio
last_name: Hernandez Garcia
- first_name: Konstantin
full_name: Klemm, Konstantin
last_name: Klemm
citation:
ama: Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. Anomalous
scaling in an age-dependent branching model. Physical Review E Statistical
Nonlinear and Soft Matter Physics. 2015;91(2). doi:10.1103/PhysRevE.91.022803
apa: Keller-Schmidt, S., Tugrul, M., Eguíluz, V., Hernandez Garcia, E., & Klemm,
K. (2015). Anomalous scaling in an age-dependent branching model. Physical
Review E Statistical Nonlinear and Soft Matter Physics. American Institute
of Physics. https://doi.org/10.1103/PhysRevE.91.022803
chicago: Keller-Schmidt, Stephanie, Murat Tugrul, Víctor Eguíluz, Emilio Hernandez
Garcia, and Konstantin Klemm. “Anomalous Scaling in an Age-Dependent Branching
Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics.
American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.022803.
ieee: S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, and K. Klemm,
“Anomalous scaling in an age-dependent branching model,” Physical Review E
Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 2. American Institute
of Physics, 2015.
ista: Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. 2015.
Anomalous scaling in an age-dependent branching model. Physical Review E Statistical
Nonlinear and Soft Matter Physics. 91(2), 022803.
mla: Keller-Schmidt, Stephanie, et al. “Anomalous Scaling in an Age-Dependent Branching
Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics,
vol. 91, no. 2, 022803, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.022803.
short: S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm,
Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).
date_created: 2018-12-11T11:54:31Z
date_published: 2015-02-02T00:00:00Z
date_updated: 2021-01-12T06:53:49Z
day: '02'
department:
- _id: NiBa
doi: 10.1103/PhysRevE.91.022803
external_id:
arxiv:
- '1012.3298'
intvolume: ' 91'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1012.3298
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5213'
quality_controlled: '1'
scopus_import: 1
status: public
title: Anomalous scaling in an age-dependent branching model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2015'
...
---
_id: '1885'
abstract:
- lang: eng
text: 'The concept of positional information is central to our understanding of
how cells determine their location in a multicellular structure and thereby their
developmental fates. Nevertheless, positional information has neither been defined
mathematically nor quantified in a principled way. Here we provide an information-theoretic
definition in the context of developmental gene expression patterns and examine
the features of expression patterns that affect positional information quantitatively.
We connect positional information with the concept of positional error and develop
tools to directly measure information and error from experimental data. We illustrate
our framework for the case of gap gene expression patterns in the early Drosophila
embryo and show how information that is distributed among only four genes is sufficient
to determine developmental fates with nearly single-cell resolution. Our approach
can be generalized to a variety of different model systems; procedures and examples
are discussed in detail. '
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Julien
full_name: Dubuis, Julien
last_name: Dubuis
- first_name: Mariela
full_name: Petkova, Mariela
last_name: Petkova
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
citation:
ama: 'Tkačik G, Dubuis J, Petkova M, Gregor T. Positional information, positional
error, and readout precision in morphogenesis: A mathematical framework. Genetics.
2015;199(1):39-59. doi:10.1534/genetics.114.171850'
apa: 'Tkačik, G., Dubuis, J., Petkova, M., & Gregor, T. (2015). Positional information,
positional error, and readout precision in morphogenesis: A mathematical framework.
Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.114.171850'
chicago: 'Tkačik, Gašper, Julien Dubuis, Mariela Petkova, and Thomas Gregor. “Positional
Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical
Framework.” Genetics. Genetics Society of America, 2015. https://doi.org/10.1534/genetics.114.171850.'
ieee: 'G. Tkačik, J. Dubuis, M. Petkova, and T. Gregor, “Positional information,
positional error, and readout precision in morphogenesis: A mathematical framework,”
Genetics, vol. 199, no. 1. Genetics Society of America, pp. 39–59, 2015.'
ista: 'Tkačik G, Dubuis J, Petkova M, Gregor T. 2015. Positional information, positional
error, and readout precision in morphogenesis: A mathematical framework. Genetics.
199(1), 39–59.'
mla: 'Tkačik, Gašper, et al. “Positional Information, Positional Error, and Readout
Precision in Morphogenesis: A Mathematical Framework.” Genetics, vol. 199,
no. 1, Genetics Society of America, 2015, pp. 39–59, doi:10.1534/genetics.114.171850.'
short: G. Tkačik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59.
date_created: 2018-12-11T11:54:32Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:50Z
day: '01'
department:
- _id: GaTk
doi: 10.1534/genetics.114.171850
intvolume: ' 199'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1404.5599
month: '01'
oa: 1
oa_version: Preprint
page: 39 - 59
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5210'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Positional information, positional error, and readout precision in morphogenesis:
A mathematical framework'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 199
year: '2015'
...
---
_id: '1940'
abstract:
- lang: eng
text: We typically think of cells as responding to external signals independently
by regulating their gene expression levels, yet they often locally exchange information
and coordinate. Can such spatial coupling be of benefit for conveying signals
subject to gene regulatory noise? Here we extend our information-theoretic framework
for gene regulation to spatially extended systems. As an example, we consider
a lattice of nuclei responding to a concentration field of a transcriptional regulator
(the "input") by expressing a single diffusible target gene. When input
concentrations are low, diffusive coupling markedly improves information transmission;
optimal gene activation functions also systematically change. A qualitatively
new regulatory strategy emerges where individual cells respond to the input in
a nearly step-like fashion that is subsequently averaged out by strong diffusion.
While motivated by early patterning events in the Drosophila embryo, our framework
is generically applicable to spatially coupled stochastic gene expression models.
article_number: '062710'
author:
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Sokolowski TR, Tkačik G. Optimizing information flow in small genetic networks.
IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter
Physics. 2015;91(6). doi:10.1103/PhysRevE.91.062710
apa: Sokolowski, T. R., & Tkačik, G. (2015). Optimizing information flow in
small genetic networks. IV. Spatial coupling. Physical Review E Statistical
Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.91.062710
chicago: Sokolowski, Thomas R, and Gašper Tkačik. “Optimizing Information Flow in
Small Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical
Nonlinear and Soft Matter Physics. American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.062710.
ieee: T. R. Sokolowski and G. Tkačik, “Optimizing information flow in small genetic
networks. IV. Spatial coupling,” Physical Review E Statistical Nonlinear and
Soft Matter Physics, vol. 91, no. 6. American Institute of Physics, 2015.
ista: Sokolowski TR, Tkačik G. 2015. Optimizing information flow in small genetic
networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft
Matter Physics. 91(6), 062710.
mla: Sokolowski, Thomas R., and Gašper Tkačik. “Optimizing Information Flow in Small
Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical Nonlinear
and Soft Matter Physics, vol. 91, no. 6, 062710, American Institute of Physics,
2015, doi:10.1103/PhysRevE.91.062710.
short: T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft
Matter Physics 91 (2015).
date_created: 2018-12-11T11:54:49Z
date_published: 2015-06-15T00:00:00Z
date_updated: 2021-01-12T06:54:13Z
day: '15'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.91.062710
intvolume: ' 91'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.04015
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5145'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optimizing information flow in small genetic networks. IV. Spatial coupling
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2015'
...
---
_id: '1992'
abstract:
- lang: eng
text: "We present a method and a tool for generating succinct representations of
sets of concurrent traces. We focus on trace sets that contain all correct or
all incorrect permutations of events from a given trace. We represent trace sets
as HB-Formulas that are Boolean combinations of happens-before constraints between
events. To generate a representation of incorrect interleavings, our method iteratively
explores interleavings that violate the specification and gathers generalizations
of the discovered interleavings into an HB-Formula; its complement yields a representation
of correct interleavings.\r\n\r\nWe claim that our trace set representations can
drive diverse verification, fault localization, repair, and synthesis techniques
for concurrent programs. We demonstrate this by using our tool in three case studies
involving synchronization synthesis, bug summarization, and abstraction refinement
based verification. In each case study, our initial experimental results have
been promising.\r\n\r\nIn the first case study, we present an algorithm for inferring
missing synchronization from an HB-Formula representing correct interleavings
of a given trace. The algorithm applies rules to rewrite specific patterns in
the HB-Formula into locks, barriers, and wait-notify constructs. In the second
case study, we use an HB-Formula representing incorrect interleavings for bug
summarization. While the HB-Formula itself is a concise counterexample summary,
we present additional inference rules to help identify specific concurrency bugs
such as data races, define-use order violations, and two-stage access bugs. In
the final case study, we present a novel predicate learning procedure that uses
HB-Formulas representing abstract counterexamples to accelerate counterexample-guided
abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure
refines the abstraction to eliminate multiple spurious abstract counterexamples
drawn from the HB-Formula."
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- 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
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: 'Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. Succinct representation
of concurrent trace sets. In: ACM; 2015:433-444. doi:10.1145/2676726.2677008'
apa: 'Gupta, A., Henzinger, T. A., Radhakrishna, A., Samanta, R., & Tarrach,
T. (2015). Succinct representation of concurrent trace sets (pp. 433–444). Presented
at the POPL: Principles of Programming Languages, Mumbai, India: ACM. https://doi.org/10.1145/2676726.2677008'
chicago: Gupta, Ashutosh, Thomas A Henzinger, Arjun Radhakrishna, Roopsha Samanta,
and Thorsten Tarrach. “Succinct Representation of Concurrent Trace Sets,” 433–44.
ACM, 2015. https://doi.org/10.1145/2676726.2677008.
ieee: 'A. Gupta, T. A. Henzinger, A. Radhakrishna, R. Samanta, and T. Tarrach, “Succinct
representation of concurrent trace sets,” presented at the POPL: Principles of
Programming Languages, Mumbai, India, 2015, pp. 433–444.'
ista: 'Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. 2015. Succinct
representation of concurrent trace sets. POPL: Principles of Programming Languages,
433–444.'
mla: Gupta, Ashutosh, et al. Succinct Representation of Concurrent Trace Sets.
ACM, 2015, pp. 433–44, doi:10.1145/2676726.2677008.
short: A. Gupta, T.A. Henzinger, A. Radhakrishna, R. Samanta, T. Tarrach, in:, ACM,
2015, pp. 433–444.
conference:
end_date: 2015-01-17
location: Mumbai, India
name: 'POPL: Principles of Programming Languages'
start_date: 2015-01-15
date_created: 2018-12-11T11:55:05Z
date_published: 2015-01-15T00:00:00Z
date_updated: 2021-01-12T06:54:33Z
day: '15'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1145/2676726.2677008
file:
- access_level: open_access
checksum: f0d4395b600f410a191256ac0b73af32
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:56Z
date_updated: 2020-07-14T12:45:22Z
file_id: '5314'
file_name: IST-2015-317-v1+1_author_version.pdf
file_size: 399462
relation: main_file
file_date_updated: 2020-07-14T12:45:22Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 433 - 444
publication_identifier:
isbn:
- 978-1-4503-3300-9
publication_status: published
publisher: ACM
publist_id: '5091'
pubrep_id: '317'
quality_controlled: '1'
scopus_import: 1
status: public
title: Succinct representation of concurrent trace sets
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1993'
abstract:
- lang: eng
text: 'The fitness effects of symbionts on their hosts can be context-dependent,
with usually benign symbionts causing detrimental effects when their hosts are
stressed, or typically parasitic symbionts providing protection towards their
hosts (e.g. against pathogen infection). Here, we studied the novel association
between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia
formicarum for potential costs and benefits. We tested ants with different Laboulbenia
levels for their survival and immunity under resource limitation and exposure
to the obligate killing entomopathogen Metarhizium brunneum. While survival of
L. neglectus workers under starvation was significantly decreased with increasing
Laboulbenia levels, host survival under Metarhizium exposure increased with higher
levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection,
which seems to be driven mechanistically by both improved sanitary behaviours
and an upregulated immune system. Ants with high Laboulbenia levels showed significantly
longer self-grooming and elevated expression of immune genes relevant for wound
repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase),
compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont
Laboulbenia formicarum weakens its ant host by either direct resource exploitation
or the costs of an upregulated behavioural and immunological response, which,
however, provides a prophylactic protection upon later exposure to pathogens. '
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "Funding was obtained by the German Research Foundation (CR 118–2)
and an ERC StG (243071) by the European Research Council (both to S.C.).\r\nWe thank
Line V. Ugelvig for help with ant collection and statistical discussion, Xavier
Espadaler for detailed information on the ant collection site, Birgit Lautenschläger
for the electron microscopy images and Eva Sixt for ant drawings. We further thank
Jørgen Eilenberg for the fungal strain, Meghan L. Vyleta for genetic strain characterization
and immune gene primer development, Paul Schmid-Hempel for discussion, and Line
V. Ugelvig, Xavier Espadaler and Christopher D. Pull for comments on the manuscript.
S.C., M.K. and S.T. conceived the study; M.K. and A.V.G. performed the experiments;
M.K. performed the statistical analysis; S.C. and M.K. wrote the manuscript with
intense contributions of A.V.G. and S.T.; all authors approved the manuscript."
article_number: '20141976'
article_processing_charge: No
article_type: original
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Konrad M, Grasse AV, Tragust S, Cremer S. Anti-pathogen protection versus survival
costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal
Society of London Series B Biological Sciences. 2015;282(1799). doi:10.1098/rspb.2014.1976
apa: Konrad, M., Grasse, A. V., Tragust, S., & Cremer, S. (2015). Anti-pathogen
protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings
of the Royal Society of London Series B Biological Sciences. The Royal Society.
https://doi.org/10.1098/rspb.2014.1976
chicago: Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Anti-Pathogen
Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.”
Proceedings of the Royal Society of London Series B Biological Sciences.
The Royal Society, 2015. https://doi.org/10.1098/rspb.2014.1976.
ieee: M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Anti-pathogen protection
versus survival costs mediated by an ectosymbiont in an ant host,” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 282, no.
1799. The Royal Society, 2015.
ista: Konrad M, Grasse AV, Tragust S, Cremer S. 2015. Anti-pathogen protection versus
survival costs mediated by an ectosymbiont in an ant host. Proceedings of the
Royal Society of London Series B Biological Sciences. 282(1799), 20141976.
mla: Konrad, Matthias, et al. “Anti-Pathogen Protection versus Survival Costs Mediated
by an Ectosymbiont in an Ant Host.” Proceedings of the Royal Society of London
Series B Biological Sciences, vol. 282, no. 1799, 20141976, The Royal Society,
2015, doi:10.1098/rspb.2014.1976.
short: M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society
of London Series B Biological Sciences 282 (2015).
date_created: 2018-12-11T11:55:06Z
date_published: 2015-01-22T00:00:00Z
date_updated: 2023-02-23T14:06:41Z
day: '22'
department:
- _id: SyCr
doi: 10.1098/rspb.2014.1976
ec_funded: 1
external_id:
pmid:
- '25473011'
intvolume: ' 282'
issue: '1799'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/
month: '01'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
- _id: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_identifier:
eissn:
- 1471-2954
issn:
- 0962-8452
publication_status: published
publisher: The Royal Society
publist_id: '5090'
quality_controlled: '1'
related_material:
record:
- id: '9740'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Anti-pathogen protection versus survival costs mediated by an ectosymbiont
in an ant host
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 282
year: '2015'
...
---
_id: '1997'
abstract:
- lang: eng
text: We prove that the three-state toric homogeneous Markov chain model has Markov
degree two. In algebraic terminology this means, that a certain class of toric
ideals is generated by quadratic binomials. This was conjectured by Haws, Martin
del Campo, Takemura and Yoshida, who proved that they are generated by degree
six binomials.
author:
- first_name: Patrik
full_name: Noren, Patrik
id: 46870C74-F248-11E8-B48F-1D18A9856A87
last_name: Noren
citation:
ama: Noren P. The three-state toric homogeneous Markov chain model has Markov degree
two. Journal of Symbolic Computation. 2015;68/Part 2(May-June):285-296.
doi:10.1016/j.jsc.2014.09.014
apa: Noren, P. (2015). The three-state toric homogeneous Markov chain model has
Markov degree two. Journal of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2014.09.014
chicago: Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has
Markov Degree Two.” Journal of Symbolic Computation. Elsevier, 2015. https://doi.org/10.1016/j.jsc.2014.09.014.
ieee: P. Noren, “The three-state toric homogeneous Markov chain model has Markov
degree two,” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June.
Elsevier, pp. 285–296, 2015.
ista: Noren P. 2015. The three-state toric homogeneous Markov chain model has Markov
degree two. Journal of Symbolic Computation. 68/Part 2(May-June), 285–296.
mla: Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov
Degree Two.” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June,
Elsevier, 2015, pp. 285–96, doi:10.1016/j.jsc.2014.09.014.
short: P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296.
date_created: 2018-12-11T11:55:07Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2021-01-12T06:54:35Z
day: '01'
department:
- _id: CaUh
doi: 10.1016/j.jsc.2014.09.014
issue: May-June
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1207.0077
month: '05'
oa: 1
oa_version: Preprint
page: 285 - 296
publication: Journal of Symbolic Computation
publication_status: published
publisher: Elsevier
publist_id: '5082'
quality_controlled: '1'
scopus_import: 1
status: public
title: The three-state toric homogeneous Markov chain model has Markov degree two
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 68/Part 2
year: '2015'
...
---
_id: '2006'
abstract:
- lang: eng
text: 'The monotone secant conjecture posits a rich class of polynomial systems,
all of whose solutions are real. These systems come from the Schubert calculus
on flag manifolds, and the monotone secant conjecture is a compelling generalization
of the Shapiro conjecture for Grassmannians (Theorem of Mukhin, Tarasov, and Varchenko).
We present some theoretical evidence for this conjecture, as well as computational
evidence obtained by 1.9 teraHertz-years of computing, and we discuss some of
the phenomena we observed in our data. '
article_processing_charge: No
author:
- first_name: Nicolas
full_name: Hein, Nicolas
last_name: Hein
- first_name: Christopher
full_name: Hillar, Christopher
last_name: Hillar
- first_name: Abraham
full_name: Martin Del Campo Sanchez, Abraham
id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87
last_name: Martin Del Campo Sanchez
- first_name: Frank
full_name: Sottile, Frank
last_name: Sottile
- first_name: Zach
full_name: Teitler, Zach
last_name: Teitler
citation:
ama: Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. The monotone
secant conjecture in the real Schubert calculus. Experimental Mathematics.
2015;24(3):261-269. doi:10.1080/10586458.2014.980044
apa: Hein, N., Hillar, C., Martin del Campo Sanchez, A., Sottile, F., & Teitler,
Z. (2015). The monotone secant conjecture in the real Schubert calculus. Experimental
Mathematics. Taylor & Francis. https://doi.org/10.1080/10586458.2014.980044
chicago: Hein, Nicolas, Christopher Hillar, Abraham Martin del Campo Sanchez, Frank
Sottile, and Zach Teitler. “The Monotone Secant Conjecture in the Real Schubert
Calculus.” Experimental Mathematics. Taylor & Francis, 2015. https://doi.org/10.1080/10586458.2014.980044.
ieee: N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, and Z. Teitler,
“The monotone secant conjecture in the real Schubert calculus,” Experimental
Mathematics, vol. 24, no. 3. Taylor & Francis, pp. 261–269, 2015.
ista: Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. 2015.
The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics.
24(3), 261–269.
mla: Hein, Nicolas, et al. “The Monotone Secant Conjecture in the Real Schubert
Calculus.” Experimental Mathematics, vol. 24, no. 3, Taylor & Francis,
2015, pp. 261–69, doi:10.1080/10586458.2014.980044.
short: N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler,
Experimental Mathematics 24 (2015) 261–269.
date_created: 2018-12-11T11:55:10Z
date_published: 2015-06-23T00:00:00Z
date_updated: 2021-01-12T06:54:40Z
day: '23'
department:
- _id: CaUh
doi: 10.1080/10586458.2014.980044
intvolume: ' 24'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1109.3436
month: '06'
oa: 1
oa_version: Preprint
page: 261 - 269
publication: Experimental Mathematics
publication_status: published
publisher: Taylor & Francis
publist_id: '5070'
quality_controlled: '1'
scopus_import: 1
status: public
title: The monotone secant conjecture in the real Schubert calculus
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2015'
...
---
_id: '2008'
abstract:
- lang: eng
text: The paper describes a generalized iterative proportional fitting procedure
that can be used for maximum likelihood estimation in a special class of the general
log-linear model. The models in this class, called relational, apply to multivariate
discrete sample spaces that do not necessarily have a Cartesian product structure
and may not contain an overall effect. When applied to the cell probabilities,
the models without the overall effect are curved exponential families and the
values of the sufficient statistics are reproduced by the MLE only up to a constant
of proportionality. The paper shows that Iterative Proportional Fitting, Generalized
Iterative Scaling, and Improved Iterative Scaling fail to work for such models.
The algorithm proposed here is based on iterated Bregman projections. As a by-product,
estimates of the multiplicative parameters are also obtained. An implementation
of the algorithm is available as an R-package.
acknowledgement: Part of the material presented here was contained in the PhD thesis
of the first author to which the second author and Thomas Richardson were advisers.
The authors wish to thank him for several comments and suggestions. We also thank
the reviewers and the Associate Editor for helpful comments. The proof of Proposition 1
uses the idea of Olga Klimova, to whom the authors are also indebted. The second
author was supported in part by Grant K-106154 from the Hungarian National Scientific
Research Fund (OTKA).
author:
- first_name: Anna
full_name: Klimova, Anna
id: 31934120-F248-11E8-B48F-1D18A9856A87
last_name: Klimova
- first_name: Tamás
full_name: Rudas, Tamás
last_name: Rudas
citation:
ama: Klimova A, Rudas T. Iterative scaling in curved exponential families. Scandinavian
Journal of Statistics. 2015;42(3):832-847. doi:10.1111/sjos.12139
apa: Klimova, A., & Rudas, T. (2015). Iterative scaling in curved exponential
families. Scandinavian Journal of Statistics. Wiley. https://doi.org/10.1111/sjos.12139
chicago: Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential
Families.” Scandinavian Journal of Statistics. Wiley, 2015. https://doi.org/10.1111/sjos.12139.
ieee: A. Klimova and T. Rudas, “Iterative scaling in curved exponential families,”
Scandinavian Journal of Statistics, vol. 42, no. 3. Wiley, pp. 832–847,
2015.
ista: Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families.
Scandinavian Journal of Statistics. 42(3), 832–847.
mla: Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.”
Scandinavian Journal of Statistics, vol. 42, no. 3, Wiley, 2015, pp. 832–47,
doi:10.1111/sjos.12139.
short: A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 832–847.
date_created: 2018-12-11T11:55:11Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2021-01-12T06:54:41Z
day: '01'
department:
- _id: CaUh
doi: 10.1111/sjos.12139
intvolume: ' 42'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1307.3282
month: '09'
oa: 1
oa_version: Preprint
page: 832 - 847
publication: Scandinavian Journal of Statistics
publication_status: published
publisher: Wiley
publist_id: '5068'
quality_controlled: '1'
scopus_import: 1
status: public
title: Iterative scaling in curved exponential families
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2015'
...
---
_id: '2014'
abstract:
- lang: eng
text: The concepts of faithfulness and strong-faithfulness are important for statistical
learning of graphical models. Graphs are not sufficient for describing the association
structure of a discrete distribution. Hypergraphs representing hierarchical log-linear
models are considered instead, and the concept of parametric (strong-) faithfulness
with respect to a hypergraph is introduced. Strong-faithfulness ensures the existence
of uniformly consistent parameter estimators and enables building uniformly consistent
procedures for a hypergraph search. The strength of association in a discrete
distribution can be quantified with various measures, leading to different concepts
of strong-faithfulness. Lower and upper bounds for the proportions of distributions
that do not satisfy strong-faithfulness are computed for different parameterizations
and measures of association.
author:
- first_name: Anna
full_name: Klimova, Anna
id: 31934120-F248-11E8-B48F-1D18A9856A87
last_name: Klimova
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Tamás
full_name: Rudas, Tamás
last_name: Rudas
citation:
ama: Klimova A, Uhler C, Rudas T. Faithfulness and learning hypergraphs from discrete
distributions. Computational Statistics & Data Analysis. 2015;87(7):57-72.
doi:10.1016/j.csda.2015.01.017
apa: Klimova, A., Uhler, C., & Rudas, T. (2015). Faithfulness and learning hypergraphs
from discrete distributions. Computational Statistics & Data Analysis.
Elsevier. https://doi.org/10.1016/j.csda.2015.01.017
chicago: Klimova, Anna, Caroline Uhler, and Tamás Rudas. “Faithfulness and Learning
Hypergraphs from Discrete Distributions.” Computational Statistics & Data
Analysis. Elsevier, 2015. https://doi.org/10.1016/j.csda.2015.01.017.
ieee: A. Klimova, C. Uhler, and T. Rudas, “Faithfulness and learning hypergraphs
from discrete distributions,” Computational Statistics & Data Analysis,
vol. 87, no. 7. Elsevier, pp. 57–72, 2015.
ista: Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from
discrete distributions. Computational Statistics & Data Analysis. 87(7), 57–72.
mla: Klimova, Anna, et al. “Faithfulness and Learning Hypergraphs from Discrete
Distributions.” Computational Statistics & Data Analysis, vol. 87,
no. 7, Elsevier, 2015, pp. 57–72, doi:10.1016/j.csda.2015.01.017.
short: A. Klimova, C. Uhler, T. Rudas, Computational Statistics & Data Analysis
87 (2015) 57–72.
date_created: 2018-12-11T11:55:13Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2021-01-12T06:54:43Z
day: '01'
department:
- _id: CaUh
doi: 10.1016/j.csda.2015.01.017
intvolume: ' 87'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1404.6617
month: '07'
oa: 1
oa_version: Preprint
page: 57 - 72
publication: Computational Statistics & Data Analysis
publication_status: published
publisher: Elsevier
publist_id: '5062'
quality_controlled: '1'
scopus_import: 1
status: public
title: Faithfulness and learning hypergraphs from discrete distributions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2015'
...
---
_id: '2025'
abstract:
- lang: eng
text: Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular
trafficking. Among them, the Rab, Arf, and Rho families function in successive
steps of vesicle transport, in forming vesicles from donor membranes, directing
vesicle trafficking toward target membranes and docking vesicles onto target membranes.
These proteins act as molecular switches that are controlled by a cycle of GTP
binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs)
and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs
in the regulation of the endocytic pathway using fluorescently labeled yeast mating
pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion
of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of
fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells
show defective α-factor binding to the cell surface. Interestingly, Ste2p, the
α-factor receptor, was mis-localized from the plasma membrane to the vacuole in
glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent
function, as well as the GAP activity, of Glo3p is important for both α-factor
binding and Ste2p localization at the cell surface. Additionally, we found that
deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi
compartments and causes a defect in transport from the TGN to the plasma membrane.
Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN
transport pathway, but not in the early endosome-to-TGN transport pathway. These
findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell
surface proteins.
author:
- first_name: Daiki
full_name: Kawada, Daiki
last_name: Kawada
- first_name: Hiromu
full_name: Kobayashi, Hiromu
last_name: Kobayashi
- first_name: Tsuyoshi
full_name: Tomita, Tsuyoshi
last_name: Tomita
- first_name: Eisuke
full_name: Nakata, Eisuke
last_name: Nakata
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Junko
full_name: Toshima, Junko
last_name: Toshima
- first_name: Jiro
full_name: Toshimaa, Jiro
last_name: Toshimaa
citation:
ama: Kawada D, Kobayashi H, Tomita T, et al. The yeast Arf-GAP Glo3p is required
for the endocytic recycling of cell surface proteins. Biochimica et Biophysica
Acta - Molecular Cell Research. 2015;1853(1):144-156. doi:10.1016/j.bbamcr.2014.10.009
apa: Kawada, D., Kobayashi, H., Tomita, T., Nakata, E., Nagano, M., Siekhaus, D.
E., … Toshimaa, J. (2015). The yeast Arf-GAP Glo3p is required for the endocytic
recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular
Cell Research. Elsevier. https://doi.org/10.1016/j.bbamcr.2014.10.009
chicago: Kawada, Daiki, Hiromu Kobayashi, Tsuyoshi Tomita, Eisuke Nakata, Makoto
Nagano, Daria E Siekhaus, Junko Toshima, and Jiro Toshimaa. “The Yeast Arf-GAP
Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” Biochimica
et Biophysica Acta - Molecular Cell Research. Elsevier, 2015. https://doi.org/10.1016/j.bbamcr.2014.10.009.
ieee: D. Kawada et al., “The yeast Arf-GAP Glo3p is required for the endocytic
recycling of cell surface proteins,” Biochimica et Biophysica Acta - Molecular
Cell Research, vol. 1853, no. 1. Elsevier, pp. 144–156, 2015.
ista: Kawada D, Kobayashi H, Tomita T, Nakata E, Nagano M, Siekhaus DE, Toshima
J, Toshimaa J. 2015. The yeast Arf-GAP Glo3p is required for the endocytic recycling
of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research.
1853(1), 144–156.
mla: Kawada, Daiki, et al. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic
Recycling of Cell Surface Proteins.” Biochimica et Biophysica Acta - Molecular
Cell Research, vol. 1853, no. 1, Elsevier, 2015, pp. 144–56, doi:10.1016/j.bbamcr.2014.10.009.
short: D. Kawada, H. Kobayashi, T. Tomita, E. Nakata, M. Nagano, D.E. Siekhaus,
J. Toshima, J. Toshimaa, Biochimica et Biophysica Acta - Molecular Cell Research
1853 (2015) 144–156.
date_created: 2018-12-11T11:55:17Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:54:48Z
day: '01'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.1016/j.bbamcr.2014.10.009
file:
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checksum: 5bb328edebb6a91337cadd7d63f961b7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:18Z
date_updated: 2020-07-14T12:45:25Z
file_id: '4936'
file_name: IST-2016-615-v1+1_BBAMCR.pdf
file_size: 926685
relation: main_file
file_date_updated: 2020-07-14T12:45:25Z
has_accepted_license: '1'
intvolume: ' 1853'
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '01'
oa: 1
oa_version: Submitted Version
page: 144 - 156
publication: Biochimica et Biophysica Acta - Molecular Cell Research
publication_status: published
publisher: Elsevier
publist_id: '5047'
pubrep_id: '615'
quality_controlled: '1'
scopus_import: 1
status: public
title: The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface
proteins
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1853
year: '2015'
...
---
_id: '2030'
abstract:
- lang: eng
text: A hybrid-parallel direct-numerical-simulation method with application to turbulent
Taylor-Couette flow is presented. The Navier-Stokes equations are discretized
in cylindrical coordinates with the spectral Fourier-Galerkin method in the axial
and azimuthal directions, and high-order finite differences in the radial direction.
Time is advanced by a second-order, semi-implicit projection scheme, which requires
the solution of five Helmholtz/Poisson equations, avoids staggered grids and renders
very small slip velocities. Nonlinear terms are evaluated with the pseudospectral
method. The code is parallelized using a hybrid MPI-OpenMP strategy, which, compared
with a flat MPI parallelization, is simpler to implement, allows to reduce inter-node
communications and MPI overhead that become relevant at high processor-core counts,
and helps to contain the memory footprint. A strong scaling study shows that the
hybrid code maintains scalability up to more than 20,000 processor cores and thus
allows to perform simulations at higher resolutions than previously feasible.
In particular, it opens up the possibility to simulate turbulent Taylor-Couette
flows at Reynolds numbers up to O(105). This enables to probe hydrodynamic turbulence
in Keplerian flows in experimentally relevant regimes.
author:
- first_name: Liang
full_name: Shi, Liang
id: 374A3F1A-F248-11E8-B48F-1D18A9856A87
last_name: Shi
- first_name: Markus
full_name: Rampp, Markus
last_name: Rampp
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
citation:
ama: Shi L, Rampp M, Hof B, Avila M. A hybrid MPI-OpenMP parallel implementation
for pseudospectral simulations with application to Taylor-Couette flow. Computers
and Fluids. 2015;106(1):1-11. doi:10.1016/j.compfluid.2014.09.021
apa: Shi, L., Rampp, M., Hof, B., & Avila, M. (2015). A hybrid MPI-OpenMP parallel
implementation for pseudospectral simulations with application to Taylor-Couette
flow. Computers and Fluids. Elsevier. https://doi.org/10.1016/j.compfluid.2014.09.021
chicago: Shi, Liang, Markus Rampp, Björn Hof, and Marc Avila. “A Hybrid MPI-OpenMP
Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette
Flow.” Computers and Fluids. Elsevier, 2015. https://doi.org/10.1016/j.compfluid.2014.09.021.
ieee: L. Shi, M. Rampp, B. Hof, and M. Avila, “A hybrid MPI-OpenMP parallel implementation
for pseudospectral simulations with application to Taylor-Couette flow,” Computers
and Fluids, vol. 106, no. 1. Elsevier, pp. 1–11, 2015.
ista: Shi L, Rampp M, Hof B, Avila M. 2015. A hybrid MPI-OpenMP parallel implementation
for pseudospectral simulations with application to Taylor-Couette flow. Computers
and Fluids. 106(1), 1–11.
mla: Shi, Liang, et al. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral
Simulations with Application to Taylor-Couette Flow.” Computers and Fluids,
vol. 106, no. 1, Elsevier, 2015, pp. 1–11, doi:10.1016/j.compfluid.2014.09.021.
short: L. Shi, M. Rampp, B. Hof, M. Avila, Computers and Fluids 106 (2015) 1–11.
date_created: 2018-12-11T11:55:18Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:54:51Z
day: '01'
department:
- _id: BjHo
doi: 10.1016/j.compfluid.2014.09.021
intvolume: ' 106'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1311.2481
month: '01'
oa: 1
oa_version: Preprint
page: 1 - 11
publication: Computers and Fluids
publication_status: published
publisher: Elsevier
publist_id: '5042'
quality_controlled: '1'
scopus_import: 1
status: public
title: A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations
with application to Taylor-Couette flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 106
year: '2015'
...
---
_id: '2034'
abstract:
- lang: eng
text: Opacity is a generic security property, that has been defined on (non-probabilistic)
transition systems and later on Markov chains with labels. For a secret predicate,
given as a subset of runs, and a function describing the view of an external observer,
the value of interest for opacity is a measure of the set of runs disclosing the
secret. We extend this definition to the richer framework of Markov decision processes,
where non-deterministicchoice is combined with probabilistic transitions, and
we study related decidability problems with partial or complete observation hypotheses
for the schedulers. We prove that all questions are decidable with complete observation
and ω-regular secrets. With partial observation, we prove that all quantitative
questions are undecidable but the question whether a system is almost surely non-opaquebecomes
decidable for a restricted class of ω-regular secrets, as well as for all ω-regular
secrets under finite-memory schedulers.
author:
- first_name: Béatrice
full_name: Bérard, Béatrice
last_name: Bérard
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Nathalie
full_name: Sznajder, Nathalie
last_name: Sznajder
citation:
ama: Bérard B, Chatterjee K, Sznajder N. Probabilistic opacity for Markov decision
processes. Information Processing Letters. 2015;115(1):52-59. doi:10.1016/j.ipl.2014.09.001
apa: Bérard, B., Chatterjee, K., & Sznajder, N. (2015). Probabilistic opacity
for Markov decision processes. Information Processing Letters. Elsevier.
https://doi.org/10.1016/j.ipl.2014.09.001
chicago: Bérard, Béatrice, Krishnendu Chatterjee, and Nathalie Sznajder. “Probabilistic
Opacity for Markov Decision Processes.” Information Processing Letters.
Elsevier, 2015. https://doi.org/10.1016/j.ipl.2014.09.001.
ieee: B. Bérard, K. Chatterjee, and N. Sznajder, “Probabilistic opacity for Markov
decision processes,” Information Processing Letters, vol. 115, no. 1.
Elsevier, pp. 52–59, 2015.
ista: Bérard B, Chatterjee K, Sznajder N. 2015. Probabilistic opacity for Markov
decision processes. Information Processing Letters. 115(1), 52–59.
mla: Bérard, Béatrice, et al. “Probabilistic Opacity for Markov Decision Processes.”
Information Processing Letters, vol. 115, no. 1, Elsevier, 2015, pp. 52–59,
doi:10.1016/j.ipl.2014.09.001.
short: B. Bérard, K. Chatterjee, N. Sznajder, Information Processing Letters 115
(2015) 52–59.
date_created: 2018-12-11T11:55:20Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:54:52Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.ipl.2014.09.001
ec_funded: 1
intvolume: ' 115'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1407.4225
month: '01'
oa: 1
oa_version: Preprint
page: 52 - 59
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: ' Information Processing Letters'
publication_status: published
publisher: Elsevier
publist_id: '5025'
quality_controlled: '1'
scopus_import: 1
status: public
title: Probabilistic opacity for Markov decision processes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2015'
...