---
_id: '1474'
abstract:
- lang: eng
text: Cryptographic access control offers selective access to encrypted data via
a combination of key management and functionality-rich cryptographic schemes,
such as attribute-based encryption. Using this approach, publicly available meta-data
may inadvertently leak information on the access policy that is enforced by cryptography,
which renders cryptographic access control unusable in settings where this information
is highly sensitive. We begin to address this problem by presenting rigorous definitions
for policy privacy in cryptographic access control. For concreteness we set our
results in the model of Role-Based Access Control (RBAC), where we identify and
formalize several different flavors of privacy, however, our framework should
serve as inspiration for other models of access control. Based on our insights
we propose a new system which significantly improves on the privacy properties
of state-of-the-art constructions. Our design is based on a novel type of privacy-preserving
attribute-based encryption, which we introduce and show how to instantiate. We
present our results in the context of a cryptographic RBAC system by Ferrara et
al. (CSF'13), which uses cryptography to control read access to files, while write
access is still delegated to trusted monitors. We give an extension of the construction
that permits cryptographic control over write access. Our construction assumes
that key management uses out-of-band channels between the policy enforcer and
the users but eliminates completely the need for monitoring read/write access
to the data.
article_processing_charge: No
author:
- first_name: Anna
full_name: Ferrara, Anna
last_name: Ferrara
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Bin
full_name: Liu, Bin
last_name: Liu
- first_name: Bogdan
full_name: Warinschi, Bogdan
last_name: Warinschi
citation:
ama: 'Ferrara A, Fuchsbauer G, Liu B, Warinschi B. Policy privacy in cryptographic
access control. In: IEEE; 2015:46-60. doi:10.1109/CSF.2015.11'
apa: 'Ferrara, A., Fuchsbauer, G., Liu, B., & Warinschi, B. (2015). Policy privacy
in cryptographic access control (pp. 46–60). Presented at the CSF: Computer Security
Foundations, Verona, Italy: IEEE. https://doi.org/10.1109/CSF.2015.11'
chicago: Ferrara, Anna, Georg Fuchsbauer, Bin Liu, and Bogdan Warinschi. “Policy
Privacy in Cryptographic Access Control,” 46–60. IEEE, 2015. https://doi.org/10.1109/CSF.2015.11.
ieee: 'A. Ferrara, G. Fuchsbauer, B. Liu, and B. Warinschi, “Policy privacy in cryptographic
access control,” presented at the CSF: Computer Security Foundations, Verona,
Italy, 2015, pp. 46–60.'
ista: 'Ferrara A, Fuchsbauer G, Liu B, Warinschi B. 2015. Policy privacy in cryptographic
access control. CSF: Computer Security Foundations, 46–60.'
mla: Ferrara, Anna, et al. Policy Privacy in Cryptographic Access Control.
IEEE, 2015, pp. 46–60, doi:10.1109/CSF.2015.11.
short: A. Ferrara, G. Fuchsbauer, B. Liu, B. Warinschi, in:, IEEE, 2015, pp. 46–60.
conference:
end_date: 2015-07-17
location: Verona, Italy
name: 'CSF: Computer Security Foundations'
start_date: 2015-07-13
date_created: 2018-12-11T11:52:14Z
date_published: 2015-09-04T00:00:00Z
date_updated: 2021-01-12T06:50:59Z
day: '04'
department:
- _id: KrPi
doi: 10.1109/CSF.2015.11
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://epubs.surrey.ac.uk/808055/
month: '09'
oa: 1
oa_version: Submitted Version
page: 46-60
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: IEEE
publist_id: '5722'
quality_controlled: '1'
status: public
title: Policy privacy in cryptographic access control
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1483'
abstract:
- lang: eng
text: Topological data analysis offers a rich source of valuable information to
study vision problems. Yet, so far we lack a theoretically sound connection to
popular kernel-based learning techniques, such as kernel SVMs or kernel PCA. In
this work, we establish such a connection by designing a multi-scale kernel for
persistence diagrams, a stable summary representation of topological features
in data. We show that this kernel is positive definite and prove its stability
with respect to the 1-Wasserstein distance. Experiments on two benchmark datasets
for 3D shape classification/retrieval and texture recognition show considerable
performance gains of the proposed method compared to an alternative approach that
is based on the recently introduced persistence landscapes.
author:
- first_name: Jan
full_name: Reininghaus, Jan
id: 4505473A-F248-11E8-B48F-1D18A9856A87
last_name: Reininghaus
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
- first_name: Roland
full_name: Kwitt, Roland
last_name: Kwitt
citation:
ama: 'Reininghaus J, Huber S, Bauer U, Kwitt R. A stable multi-scale kernel for
topological machine learning. In: IEEE; 2015:4741-4748. doi:10.1109/CVPR.2015.7299106'
apa: 'Reininghaus, J., Huber, S., Bauer, U., & Kwitt, R. (2015). A stable multi-scale
kernel for topological machine learning (pp. 4741–4748). Presented at the CVPR:
Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. https://doi.org/10.1109/CVPR.2015.7299106'
chicago: Reininghaus, Jan, Stefan Huber, Ulrich Bauer, and Roland Kwitt. “A Stable
Multi-Scale Kernel for Topological Machine Learning,” 4741–48. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7299106.
ieee: 'J. Reininghaus, S. Huber, U. Bauer, and R. Kwitt, “A stable multi-scale kernel
for topological machine learning,” presented at the CVPR: Computer Vision and
Pattern Recognition, Boston, MA, USA, 2015, pp. 4741–4748.'
ista: 'Reininghaus J, Huber S, Bauer U, Kwitt R. 2015. A stable multi-scale kernel
for topological machine learning. CVPR: Computer Vision and Pattern Recognition,
4741–4748.'
mla: Reininghaus, Jan, et al. A Stable Multi-Scale Kernel for Topological Machine
Learning. IEEE, 2015, pp. 4741–48, doi:10.1109/CVPR.2015.7299106.
short: J. Reininghaus, S. Huber, U. Bauer, R. Kwitt, in:, IEEE, 2015, pp. 4741–4748.
conference:
end_date: 2015-06-12
location: Boston, MA, USA
name: 'CVPR: Computer Vision and Pattern Recognition'
start_date: 2015-06-07
date_created: 2018-12-11T11:52:17Z
date_published: 2015-10-14T00:00:00Z
date_updated: 2021-01-12T06:51:03Z
day: '14'
department:
- _id: HeEd
doi: 10.1109/CVPR.2015.7299106
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1412.6821
month: '10'
oa: 1
oa_version: Preprint
page: 4741 - 4748
publication_identifier:
eisbn:
- '978-1-4673-6964-0 '
publication_status: published
publisher: IEEE
publist_id: '5709'
scopus_import: 1
status: public
title: A stable multi-scale kernel for topological machine learning
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1498'
abstract:
- lang: eng
text: Fault-tolerant distributed algorithms play an important role in many critical/high-availability
applications. These algorithms are notoriously difficult to implement correctly,
due to asynchronous communication and the occurrence of faults, such as the network
dropping messages or computers crashing. Nonetheless there is surprisingly little
language and verification support to build distributed systems based on fault-tolerant
algorithms. In this paper, we present some of the challenges that a designer has
to overcome to implement a fault-tolerant distributed system. Then we review different
models that have been proposed to reason about distributed algorithms and sketch
how such a model can form the basis for a domain-specific programming language.
Adopting a high-level programming model can simplify the programmer's life and
make the code amenable to automated verification, while still compiling to efficiently
executable code. We conclude by summarizing the current status of an ongoing language
design and implementation project that is based on this idea.
alternative_title:
- LIPIcs
author:
- first_name: Cezara
full_name: Dragoi, Cezara
id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87
last_name: Dragoi
- 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: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: Dragoi C, Henzinger TA, Zufferey D. The need for language support for fault-tolerant
distributed systems. 2015;32:90-102. doi:10.4230/LIPIcs.SNAPL.2015.90
apa: 'Dragoi, C., Henzinger, T. A., & Zufferey, D. (2015). The need for language
support for fault-tolerant distributed systems. Presented at the SNAPL: Summit
oN Advances in Programming Languages, Asilomar, CA, United States: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90'
chicago: Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “The Need for
Language Support for Fault-Tolerant Distributed Systems.” Leibniz International
Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2015. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90.
ieee: C. Dragoi, T. A. Henzinger, and D. Zufferey, “The need for language support
for fault-tolerant distributed systems,” vol. 32. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, pp. 90–102, 2015.
ista: Dragoi C, Henzinger TA, Zufferey D. 2015. The need for language support for
fault-tolerant distributed systems. 32, 90–102.
mla: Dragoi, Cezara, et al. The Need for Language Support for Fault-Tolerant
Distributed Systems. Vol. 32, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2015, pp. 90–102, doi:10.4230/LIPIcs.SNAPL.2015.90.
short: C. Dragoi, T.A. Henzinger, D. Zufferey, 32 (2015) 90–102.
conference:
end_date: 2015-05-06
location: Asilomar, CA, United States
name: 'SNAPL: Summit oN Advances in Programming Languages'
start_date: 2015-05-03
date_created: 2018-12-11T11:52:22Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2020-08-11T10:09:14Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.SNAPL.2015.90
ec_funded: 1
file:
- access_level: open_access
checksum: cf5e94baa89a2dc4c5de01abc676eda8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:02Z
date_updated: 2020-07-14T12:44:58Z
file_id: '5050'
file_name: IST-2016-499-v1+1_9.pdf
file_size: 489362
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 32'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 90 - 102
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
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
isbn:
- '978-3-939897-80-4 '
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5681'
pubrep_id: '499'
quality_controlled: '1'
scopus_import: 1
series_title: Leibniz International Proceedings in Informatics
status: public
title: The need for language support for fault-tolerant distributed systems
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2015'
...
---
_id: '1497'
abstract:
- lang: eng
text: Detecting allelic biases from high-throughput sequencing data requires an
approach that maximises sensitivity while minimizing false positives. Here, we
present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which
uses high-throughput sequencing data from reciprocal crosses of two genetically
distinct mouse strains to detect allele-specific expression and chromatin modifications.
Allelome.PRO extends approaches used in previous studies that exclusively analyzed
imprinted expression to give a complete picture of the ‘allelome’ by automatically
categorising the allelic expression of all genes in a given cell type into imprinted,
strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity
to analyze lowly expressed transcripts, together with a robust false discovery
rate empirically calculated from variation in the sequencing data. We used RNA-seq
data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine
a biologically relevant allelic ratio cutoff, and define for the first time an
entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment
of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This
approach can be easily extended to analyze histone marks of active enhancers,
or transcription factor binding sites and therefore provides a powerful tool to
identify candidate cis regulatory elements genome wide.
acknowledgement: "Austrian Science Fund [FWF P25185-B22, FWF F4302- B09, FWFW1207-B09].
Funding for open access charge: Austrian Science Fund.\r\nWe thank Florian Breitwieser
for advice during the early stages of this project. High-throughput sequencing was
conducted by the Biomedical Sequencing Facility (BSF) at CeMM in Vienna."
article_number: e146
author:
- first_name: Daniel
full_name: Andergassen, Daniel
last_name: Andergassen
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
- first_name: Tomasz
full_name: Kulinski, Tomasz
last_name: Kulinski
- first_name: Philipp
full_name: Guenzl, Philipp
last_name: Guenzl
- first_name: Philipp
full_name: Bammer, Philipp
last_name: Bammer
- first_name: Denise
full_name: Barlow, Denise
last_name: Barlow
- first_name: Florian
full_name: Pauler, Florian
last_name: Pauler
- first_name: Quanah
full_name: Hudson, Quanah
last_name: Hudson
citation:
ama: Andergassen D, Dotter C, Kulinski T, et al. Allelome.PRO, a pipeline to define
allele-specific genomic features from high-throughput sequencing data. Nucleic
Acids Research. 2015;43(21). doi:10.1093/nar/gkv727
apa: Andergassen, D., Dotter, C., Kulinski, T., Guenzl, P., Bammer, P., Barlow,
D., … Hudson, Q. (2015). Allelome.PRO, a pipeline to define allele-specific genomic
features from high-throughput sequencing data. Nucleic Acids Research.
Oxford University Press. https://doi.org/10.1093/nar/gkv727
chicago: Andergassen, Daniel, Christoph Dotter, Tomasz Kulinski, Philipp Guenzl,
Philipp Bammer, Denise Barlow, Florian Pauler, and Quanah Hudson. “Allelome.PRO,
a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing
Data.” Nucleic Acids Research. Oxford University Press, 2015. https://doi.org/10.1093/nar/gkv727.
ieee: D. Andergassen et al., “Allelome.PRO, a pipeline to define allele-specific
genomic features from high-throughput sequencing data,” Nucleic Acids Research,
vol. 43, no. 21. Oxford University Press, 2015.
ista: Andergassen D, Dotter C, Kulinski T, Guenzl P, Bammer P, Barlow D, Pauler
F, Hudson Q. 2015. Allelome.PRO, a pipeline to define allele-specific genomic
features from high-throughput sequencing data. Nucleic Acids Research. 43(21),
e146.
mla: Andergassen, Daniel, et al. “Allelome.PRO, a Pipeline to Define Allele-Specific
Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research,
vol. 43, no. 21, e146, Oxford University Press, 2015, doi:10.1093/nar/gkv727.
short: D. Andergassen, C. Dotter, T. Kulinski, P. Guenzl, P. Bammer, D. Barlow,
F. Pauler, Q. Hudson, Nucleic Acids Research 43 (2015).
date_created: 2018-12-11T11:52:22Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2021-01-12T06:51:09Z
day: '21'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1093/nar/gkv727
file:
- access_level: open_access
checksum: 385b83854fd0eb2e4f386867da2823e2
content_type: application/pdf
creator: dernst
date_created: 2018-12-20T14:18:57Z
date_updated: 2020-07-14T12:44:58Z
file_id: '5768'
file_name: 2015_NucleicAcidsRes_Andergassen.pdf
file_size: 6863297
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 43'
issue: '21'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Nucleic Acids Research
publication_status: published
publisher: Oxford University Press
publist_id: '5682'
quality_controlled: '1'
scopus_import: 1
status: public
title: Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput
sequencing data
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: 43
year: '2015'
...
---
_id: '1499'
abstract:
- lang: eng
text: "We consider weighted automata with both positive and negative integer weights
on edges and\r\nstudy the problem of synchronization using adaptive strategies
that may only observe whether\r\nthe current weight-level is negative or nonnegative.
We show that the synchronization problem is decidable in polynomial time for deterministic
weighted automata."
acknowledgement: "The research leading to these results has received funding from
the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement
601148 (CASSTING), EU FP7 FET project SENSATION, Sino-Danish Basic Research Center
IDAE4CPS, the European Research Council (ERC) under grant agreement 267989 (QUAREM),
the Austrian Science Fund (FWF) project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein
Award), the Czech Science Foundation under grant agreement P202/12/G061, and People
Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme
(FP7/2007-2013) REA Grant No 291734."
alternative_title:
- LIPIcs
author:
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Kim
full_name: Larsen, Kim
last_name: Larsen
- first_name: Simon
full_name: Laursen, Simon
last_name: Laursen
- first_name: Jiří
full_name: Srba, Jiří
last_name: Srba
citation:
ama: 'Kretinsky J, Larsen K, Laursen S, Srba J. Polynomial time decidability of
weighted synchronization under partial observability. In: Vol 42. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik; 2015:142-154. doi:10.4230/LIPIcs.CONCUR.2015.142'
apa: 'Kretinsky, J., Larsen, K., Laursen, S., & Srba, J. (2015). Polynomial
time decidability of weighted synchronization under partial observability (Vol.
42, pp. 142–154). Presented at the CONCUR: Concurrency Theory, Madrid, Spain:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142'
chicago: Kretinsky, Jan, Kim Larsen, Simon Laursen, and Jiří Srba. “Polynomial Time
Decidability of Weighted Synchronization under Partial Observability,” 42:142–54.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142.
ieee: 'J. Kretinsky, K. Larsen, S. Laursen, and J. Srba, “Polynomial time decidability
of weighted synchronization under partial observability,” presented at the CONCUR:
Concurrency Theory, Madrid, Spain, 2015, vol. 42, pp. 142–154.'
ista: 'Kretinsky J, Larsen K, Laursen S, Srba J. 2015. Polynomial time decidability
of weighted synchronization under partial observability. CONCUR: Concurrency Theory,
LIPIcs, vol. 42, 142–154.'
mla: Kretinsky, Jan, et al. Polynomial Time Decidability of Weighted Synchronization
under Partial Observability. Vol. 42, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2015, pp. 142–54, doi:10.4230/LIPIcs.CONCUR.2015.142.
short: J. Kretinsky, K. Larsen, S. Laursen, J. Srba, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2015, pp. 142–154.
conference:
end_date: 2015-09-04
location: Madrid, Spain
name: 'CONCUR: Concurrency Theory'
start_date: 2015-09-01
date_created: 2018-12-11T11:52:22Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:51:10Z
day: '01'
ddc:
- '000'
- '003'
department:
- _id: ToHe
- _id: KrCh
doi: 10.4230/LIPIcs.CONCUR.2015.142
ec_funded: 1
file:
- access_level: open_access
checksum: 49eb5021caafaabe5356c65b9c5f8c9c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:12Z
date_updated: 2020-07-14T12:44:58Z
file_id: '4672'
file_name: IST-2016-498-v1+1_32.pdf
file_size: 623563
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 42'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 142 - 154
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
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5680'
pubrep_id: '498'
quality_controlled: '1'
scopus_import: 1
status: public
title: Polynomial time decidability of weighted synchronization under partial observability
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2015'
...
---
_id: '1495'
abstract:
- lang: eng
text: 'Motivated by biological questions, we study configurations of equal-sized
disks in the Euclidean plane that neither pack nor cover. Measuring the quality
by the probability that a random point lies in exactly one disk, we show that
the regular hexagonal grid gives the maximum among lattice configurations. '
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Mabel
full_name: Iglesias Ham, Mabel
id: 41B58C0C-F248-11E8-B48F-1D18A9856A87
last_name: Iglesias Ham
- first_name: Vitaliy
full_name: Kurlin, Vitaliy
last_name: Kurlin
citation:
ama: 'Edelsbrunner H, Iglesias Ham M, Kurlin V. Relaxed disk packing. In: Proceedings
of the 27th Canadian Conference on Computational Geometry. Vol 2015-August.
Queen’s University; 2015:128-135.'
apa: 'Edelsbrunner, H., Iglesias Ham, M., & Kurlin, V. (2015). Relaxed disk
packing. In Proceedings of the 27th Canadian Conference on Computational Geometry
(Vol. 2015–August, pp. 128–135). Ontario, Canada: Queen’s University.'
chicago: Edelsbrunner, Herbert, Mabel Iglesias Ham, and Vitaliy Kurlin. “Relaxed
Disk Packing.” In Proceedings of the 27th Canadian Conference on Computational
Geometry, 2015–August:128–35. Queen’s University, 2015.
ieee: H. Edelsbrunner, M. Iglesias Ham, and V. Kurlin, “Relaxed disk packing,” in
Proceedings of the 27th Canadian Conference on Computational Geometry,
Ontario, Canada, 2015, vol. 2015–August, pp. 128–135.
ista: 'Edelsbrunner H, Iglesias Ham M, Kurlin V. 2015. Relaxed disk packing. Proceedings
of the 27th Canadian Conference on Computational Geometry. CCCG: Canadian Conference
on Computational Geometry vol. 2015–August, 128–135.'
mla: Edelsbrunner, Herbert, et al. “Relaxed Disk Packing.” Proceedings of the
27th Canadian Conference on Computational Geometry, vol. 2015–August, Queen’s
University, 2015, pp. 128–35.
short: H. Edelsbrunner, M. Iglesias Ham, V. Kurlin, in:, Proceedings of the 27th
Canadian Conference on Computational Geometry, Queen’s University, 2015, pp. 128–135.
conference:
end_date: 2015-08-12
location: Ontario, Canada
name: 'CCCG: Canadian Conference on Computational Geometry'
start_date: 2015-08-10
date_created: 2018-12-11T11:52:21Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:09Z
day: '01'
department:
- _id: HeEd
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1505.03402
month: '08'
oa: 1
oa_version: Submitted Version
page: 128-135
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Proceedings of the 27th Canadian Conference on Computational Geometry
publication_status: published
publisher: Queen's University
publist_id: '5684'
quality_controlled: '1'
scopus_import: 1
status: public
title: Relaxed disk packing
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2015-August
year: '2015'
...
---
_id: '1510'
abstract:
- lang: eng
text: 'The concept of well group in a special but important case captures homological
properties of the zero set of a continuous map f from K to R^n on a compact space
K that are invariant with respect to perturbations of f. The perturbations are
arbitrary continuous maps within L_infty distance r from f for a given r >
0. The main drawback of the approach is that the computability of well groups
was shown only when dim K = n or n = 1. Our contribution to the theory of well
groups is twofold: on the one hand we improve on the computability issue, but
on the other hand we present a range of examples where the well groups are incomplete
invariants, that is, fail to capture certain important robust properties of the
zero set. For the first part, we identify a computable subgroup of the well group
that is obtained by cap product with the pullback of the orientation of R^n by
f. In other words, well groups can be algorithmically approximated from below.
When f is smooth and dim K < 2n-2, our approximation of the (dim K-n)th well
group is exact. For the second part, we find examples of maps f, f'' from K to
R^n with all well groups isomorphic but whose perturbations have different zero
sets. We discuss on a possible replacement of the well groups of vector valued
maps by an invariant of a better descriptive power and computability status. '
alternative_title:
- LIPIcs
author:
- first_name: Peter
full_name: Franek, Peter
id: 473294AE-F248-11E8-B48F-1D18A9856A87
last_name: Franek
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
citation:
ama: 'Franek P, Krcál M. On computability and triviality of well groups. In: Vol
34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:842-856. doi:10.4230/LIPIcs.SOCG.2015.842'
apa: 'Franek, P., & Krcál, M. (2015). On computability and triviality of well
groups (Vol. 34, pp. 842–856). Presented at the SoCG: Symposium on Computational
Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.SOCG.2015.842'
chicago: Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well
Groups,” 34:842–56. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.842.
ieee: 'P. Franek and M. Krcál, “On computability and triviality of well groups,”
presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands,
2015, vol. 34, pp. 842–856.'
ista: 'Franek P, Krcál M. 2015. On computability and triviality of well groups.
SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 842–856.'
mla: Franek, Peter, and Marek Krcál. On Computability and Triviality of Well
Groups. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015,
pp. 842–56, doi:10.4230/LIPIcs.SOCG.2015.842.
short: P. Franek, M. Krcál, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2015, pp. 842–856.
conference:
end_date: 2015-06-25
location: Eindhoven, Netherlands
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2015-06-22
date_created: 2018-12-11T11:52:26Z
date_published: 2015-06-11T00:00:00Z
date_updated: 2023-02-21T17:02:57Z
day: '11'
ddc:
- '510'
department:
- _id: UlWa
- _id: HeEd
doi: 10.4230/LIPIcs.SOCG.2015.842
ec_funded: 1
file:
- access_level: open_access
checksum: 49eb5021caafaabe5356c65b9c5f8c9c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:19Z
date_updated: 2020-07-14T12:44:59Z
file_id: '5001'
file_name: IST-2016-503-v1+1_32.pdf
file_size: 623563
relation: main_file
file_date_updated: 2020-07-14T12:44:59Z
has_accepted_license: '1'
intvolume: ' 34'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 842 - 856
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5667'
pubrep_id: '503'
quality_controlled: '1'
related_material:
record:
- id: '1408'
relation: later_version
status: public
scopus_import: 1
status: public
title: On computability and triviality of well groups
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1505'
abstract:
- lang: eng
text: This paper is aimed at deriving the universality of the largest eigenvalue
of a class of high-dimensional real or complex sample covariance matrices of the
form W N =Σ 1/2XX∗Σ 1/2 . Here, X = (xij )M,N is an M× N random matrix with independent
entries xij , 1 ≤ i M,≤ 1 ≤ j ≤ N such that Exij = 0, E|xij |2 = 1/N . On dimensionality,
we assume that M = M(N) and N/M → d ε (0, ∞) as N ∞→. For a class of general deterministic
positive-definite M × M matrices Σ , under some additional assumptions on the
distribution of xij 's, we show that the limiting behavior of the largest eigenvalue
of W N is universal, via pursuing a Green function comparison strategy raised
in [Probab. Theory Related Fields 154 (2012) 341-407, Adv. Math. 229 (2012) 1435-1515]
by Erd″os, Yau and Yin for Wigner matrices and extended by Pillai and Yin [Ann.
Appl. Probab. 24 (2014) 935-1001] to sample covariance matrices in the null case
(&Epsi = I ). Consequently, in the standard complex case (Ex2 ij = 0), combing
this universality property and the results known for Gaussian matrices obtained
by El Karoui in [Ann. Probab. 35 (2007) 663-714] (nonsingular case) and Onatski
in [Ann. Appl. Probab. 18 (2008) 470-490] (singular case), we show that after
an appropriate normalization the largest eigenvalue of W N converges weakly to
the type 2 Tracy-Widom distribution TW2 . Moreover, in the real case, we show
that whenΣ is spiked with a fixed number of subcritical spikes, the type 1 Tracy-Widom
limit TW1 holds for the normalized largest eigenvalue of W N , which extends a
result of Féral and Péché in [J. Math. Phys. 50 (2009) 073302] to the scenario
of nondiagonal Σ and more generally distributed X . In summary, we establish the
Tracy-Widom type universality for the largest eigenvalue of generally distributed
sample covariance matrices under quite light assumptions on &Sigma . Applications
of these limiting results to statistical signal detection and structure recognition
of separable covariance matrices are also discussed.
acknowledgement: "B.Z. was supported in part by NSFC Grant 11071213, ZJNSF
\ Grant R6090034 and SRFDP Grant 20100101110001. P.G. was supported in part
by the Ministry of Education, Singapore, under Grant ARC 14/11. Z.W. was supported
\ in part by the Ministry of Education, Singapore, under Grant ARC 14/11,
\ and by a Grant R-155-000-131-112 at the National University of Singapore\r\n"
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: Guangming
full_name: Pan, Guangming
last_name: Pan
- first_name: Wang
full_name: Zhou, Wang
last_name: Zhou
citation:
ama: Bao Z, Pan G, Zhou W. Universality for the largest eigenvalue of sample covariance
matrices with general population. Annals of Statistics. 2015;43(1):382-421.
doi:10.1214/14-AOS1281
apa: Bao, Z., Pan, G., & Zhou, W. (2015). Universality for the largest eigenvalue
of sample covariance matrices with general population. Annals of Statistics.
Institute of Mathematical Statistics. https://doi.org/10.1214/14-AOS1281
chicago: Bao, Zhigang, Guangming Pan, and Wang Zhou. “Universality for the Largest
Eigenvalue of Sample Covariance Matrices with General Population.” Annals of
Statistics. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/14-AOS1281.
ieee: Z. Bao, G. Pan, and W. Zhou, “Universality for the largest eigenvalue of sample
covariance matrices with general population,” Annals of Statistics, vol.
43, no. 1. Institute of Mathematical Statistics, pp. 382–421, 2015.
ista: Bao Z, Pan G, Zhou W. 2015. Universality for the largest eigenvalue of sample
covariance matrices with general population. Annals of Statistics. 43(1), 382–421.
mla: Bao, Zhigang, et al. “Universality for the Largest Eigenvalue of Sample Covariance
Matrices with General Population.” Annals of Statistics, vol. 43, no. 1,
Institute of Mathematical Statistics, 2015, pp. 382–421, doi:10.1214/14-AOS1281.
short: Z. Bao, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 382–421.
date_created: 2018-12-11T11:52:25Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T06:51:14Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/14-AOS1281
intvolume: ' 43'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1304.5690
month: '02'
oa: 1
oa_version: Preprint
page: 382 - 421
publication: Annals of Statistics
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '5672'
quality_controlled: '1'
status: public
title: Universality for the largest eigenvalue of sample covariance matrices with
general population
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2015'
...
---
_id: '1508'
abstract:
- lang: eng
text: We consider generalized Wigner ensembles and general β-ensembles with analytic
potentials for any β ≥ 1. The recent universality results in particular assert
that the local averages of consecutive eigenvalue gaps in the bulk of the spectrum
are universal in the sense that they coincide with those of the corresponding
Gaussian β-ensembles. In this article, we show that local averaging is not necessary
for this result, i.e. we prove that the single gap distributions in the bulk are
universal. In fact, with an additional step, our result can be extended to any
C4(ℝ) potential.
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Horng
full_name: Yau, Horng
last_name: Yau
citation:
ama: Erdös L, Yau H. Gap universality of generalized Wigner and β ensembles. Journal
of the European Mathematical Society. 2015;17(8):1927-2036. doi:10.4171/JEMS/548
apa: Erdös, L., & Yau, H. (2015). Gap universality of generalized Wigner and
β ensembles. Journal of the European Mathematical Society. European Mathematical
Society. https://doi.org/10.4171/JEMS/548
chicago: Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and
β Ensembles.” Journal of the European Mathematical Society. European Mathematical
Society, 2015. https://doi.org/10.4171/JEMS/548.
ieee: L. Erdös and H. Yau, “Gap universality of generalized Wigner and β ensembles,”
Journal of the European Mathematical Society, vol. 17, no. 8. European
Mathematical Society, pp. 1927–2036, 2015.
ista: Erdös L, Yau H. 2015. Gap universality of generalized Wigner and β ensembles.
Journal of the European Mathematical Society. 17(8), 1927–2036.
mla: Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β
Ensembles.” Journal of the European Mathematical Society, vol. 17, no.
8, European Mathematical Society, 2015, pp. 1927–2036, doi:10.4171/JEMS/548.
short: L. Erdös, H. Yau, Journal of the European Mathematical Society 17 (2015)
1927–2036.
date_created: 2018-12-11T11:52:26Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:15Z
day: '01'
department:
- _id: LaEr
doi: 10.4171/JEMS/548
intvolume: ' 17'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1211.3786
month: '08'
oa: 1
oa_version: Preprint
page: 1927 - 2036
publication: Journal of the European Mathematical Society
publication_status: published
publisher: European Mathematical Society
publist_id: '5669'
quality_controlled: '1'
scopus_import: 1
status: public
title: Gap universality of generalized Wigner and β ensembles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2015'
...
---
_id: '1506'
abstract:
- lang: eng
text: Consider the square random matrix An = (aij)n,n, where {aij:= a(n)ij , i,
j = 1, . . . , n} is a collection of independent real random variables with means
zero and variances one. Under the additional moment condition supn max1≤i,j ≤n
Ea4ij <∞, we prove Girko's logarithmic law of det An in the sense that as n→∞
log | detAn| ? (1/2) log(n-1)! d/→√(1/2) log n N(0, 1).
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: Guangming
full_name: Pan, Guangming
last_name: Pan
- first_name: Wang
full_name: Zhou, Wang
last_name: Zhou
citation:
ama: Bao Z, Pan G, Zhou W. The logarithmic law of random determinant. Bernoulli.
2015;21(3):1600-1628. doi:10.3150/14-BEJ615
apa: Bao, Z., Pan, G., & Zhou, W. (2015). The logarithmic law of random determinant.
Bernoulli. Bernoulli Society for Mathematical Statistics and Probability.
https://doi.org/10.3150/14-BEJ615
chicago: Bao, Zhigang, Guangming Pan, and Wang Zhou. “The Logarithmic Law of Random
Determinant.” Bernoulli. Bernoulli Society for Mathematical Statistics
and Probability, 2015. https://doi.org/10.3150/14-BEJ615.
ieee: Z. Bao, G. Pan, and W. Zhou, “The logarithmic law of random determinant,”
Bernoulli, vol. 21, no. 3. Bernoulli Society for Mathematical Statistics
and Probability, pp. 1600–1628, 2015.
ista: Bao Z, Pan G, Zhou W. 2015. The logarithmic law of random determinant. Bernoulli.
21(3), 1600–1628.
mla: Bao, Zhigang, et al. “The Logarithmic Law of Random Determinant.” Bernoulli,
vol. 21, no. 3, Bernoulli Society for Mathematical Statistics and Probability,
2015, pp. 1600–28, doi:10.3150/14-BEJ615.
short: Z. Bao, G. Pan, W. Zhou, Bernoulli 21 (2015) 1600–1628.
date_created: 2018-12-11T11:52:25Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:14Z
day: '01'
department:
- _id: LaEr
doi: 10.3150/14-BEJ615
intvolume: ' 21'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1208.5823
month: '08'
oa: 1
oa_version: Preprint
page: 1600 - 1628
publication: Bernoulli
publication_status: published
publisher: Bernoulli Society for Mathematical Statistics and Probability
publist_id: '5671'
quality_controlled: '1'
status: public
title: The logarithmic law of random determinant
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2015'
...
---
_id: '1513'
abstract:
- lang: eng
text: "Insects of the order Hemiptera (true bugs) use a wide range of mechanisms
of sex determination, including genetic sex determination, paternal genome elimination,
and haplodiploidy. Genetic sex determination, the prevalent mode, is generally
controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different
configurations that include additional sex chromosomes are also present. Although
this diversity of sex determining systems has been extensively studied at the
cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon
pisum has been analyzed at the genomic level, and little is known about X chromosome
biology in the rest of the order.\r\n\r\nIn this study, we take advantage of published
DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative
analysis of the gene content and expression of the X chromosome throughout this
clade. We find that, despite showing evidence of dosage compensation, the X chromosomes
of these species show female-biased expression, and a deficit of male-biased genes,
in direct contrast to the pea aphid X. We further detect an excess of shared gene
content between these very distant species, suggesting that despite the diversity
of sex determining systems, the same chromosomal element is used as the X throughout
a large portion of the order. "
article_processing_charge: No
author:
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Pal A, Vicoso B. The X chromosome of hemipteran insects: Conservation, dosage
compensation and sex-biased expression. Genome Biology and Evolution. 2015;7(12):3259-3268.
doi:10.1093/gbe/evv215'
apa: 'Pal, A., & Vicoso, B. (2015). The X chromosome of hemipteran insects:
Conservation, dosage compensation and sex-biased expression. Genome Biology
and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evv215'
chicago: 'Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects:
Conservation, Dosage Compensation and Sex-Biased Expression.” Genome Biology
and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/gbe/evv215.'
ieee: 'A. Pal and B. Vicoso, “The X chromosome of hemipteran insects: Conservation,
dosage compensation and sex-biased expression,” Genome Biology and Evolution,
vol. 7, no. 12. Oxford University Press, pp. 3259–3268, 2015.'
ista: 'Pal A, Vicoso B. 2015. The X chromosome of hemipteran insects: Conservation,
dosage compensation and sex-biased expression. Genome Biology and Evolution. 7(12),
3259–3268.'
mla: 'Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation,
Dosage Compensation and Sex-Biased Expression.” Genome Biology and Evolution,
vol. 7, no. 12, Oxford University Press, 2015, pp. 3259–68, doi:10.1093/gbe/evv215.'
short: A. Pal, B. Vicoso, Genome Biology and Evolution 7 (2015) 3259–3268.
date_created: 2018-12-11T11:52:27Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T06:51:18Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evv215
ec_funded: 1
file:
- access_level: open_access
checksum: 2b56b8c2e2a1d4cc3c9cb8daba26dd9b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:29Z
date_updated: 2020-07-14T12:45:00Z
file_id: '5284'
file_name: IST-2016-496-v1+1_Genome_Biol_Evol-2015-Pal-3259-68.pdf
file_size: 858027
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 3259 - 3268
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '5664'
pubrep_id: '496'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The X chromosome of hemipteran insects: Conservation, dosage compensation
and sex-biased expression'
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: 7
year: '2015'
...
---
_id: '1517'
abstract:
- lang: eng
text: "We study the large deviation rate functional for the empirical distribution
of independent Brownian particles with drift. In one dimension, it has been shown
by Adams, Dirr, Peletier and Zimmer that this functional is asymptotically equivalent
(in the sense of Γ-convergence) to the Jordan-Kinderlehrer-Otto functional arising
in the Wasserstein gradient flow structure of the Fokker-Planck equation. In higher
dimensions, part of this statement (the lower bound) has been recently proved
by Duong, Laschos and Renger, but the upper bound remained open, since the proof
of Duong et al relies on regularity properties of optimal transport maps that
are restricted to one dimension. In this note we present a new proof of the upper
bound, thereby generalising the result of Adams et al to arbitrary dimensions.\r\n"
article_number: '89'
author:
- first_name: Matthias
full_name: Erbar, Matthias
last_name: Erbar
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Michiel
full_name: Renger, Michiel
last_name: Renger
citation:
ama: Erbar M, Maas J, Renger M. From large deviations to Wasserstein gradient flows
in multiple dimensions. Electronic Communications in Probability. 2015;20.
doi:10.1214/ECP.v20-4315
apa: Erbar, M., Maas, J., & Renger, M. (2015). From large deviations to Wasserstein
gradient flows in multiple dimensions. Electronic Communications in Probability.
Institute of Mathematical Statistics. https://doi.org/10.1214/ECP.v20-4315
chicago: Erbar, Matthias, Jan Maas, and Michiel Renger. “From Large Deviations to
Wasserstein Gradient Flows in Multiple Dimensions.” Electronic Communications
in Probability. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/ECP.v20-4315.
ieee: M. Erbar, J. Maas, and M. Renger, “From large deviations to Wasserstein gradient
flows in multiple dimensions,” Electronic Communications in Probability,
vol. 20. Institute of Mathematical Statistics, 2015.
ista: Erbar M, Maas J, Renger M. 2015. From large deviations to Wasserstein gradient
flows in multiple dimensions. Electronic Communications in Probability. 20, 89.
mla: Erbar, Matthias, et al. “From Large Deviations to Wasserstein Gradient Flows
in Multiple Dimensions.” Electronic Communications in Probability, vol.
20, 89, Institute of Mathematical Statistics, 2015, doi:10.1214/ECP.v20-4315.
short: M. Erbar, J. Maas, M. Renger, Electronic Communications in Probability 20
(2015).
date_created: 2018-12-11T11:52:29Z
date_published: 2015-11-29T00:00:00Z
date_updated: 2021-01-12T06:51:19Z
day: '29'
ddc:
- '519'
department:
- _id: JaMa
doi: 10.1214/ECP.v20-4315
file:
- access_level: open_access
checksum: 135741c17d3e1547ca696b6fbdcd559c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:39Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4828'
file_name: IST-2016-494-v1+1_4315-23820-1-PB.pdf
file_size: 230525
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 20'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Electronic Communications in Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '5660'
pubrep_id: '494'
quality_controlled: '1'
scopus_import: 1
status: public
title: From large deviations to Wasserstein gradient flows in multiple dimensions
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: 20
year: '2015'
...
---
_id: '1519'
abstract:
- lang: eng
text: Evolutionary biologists have an array of powerful theoretical techniques that
can accurately predict changes in the genetic composition of populations. Changes
in gene frequencies and genetic associations between loci can be tracked as they
respond to a wide variety of evolutionary forces. However, it is often less clear
how to decompose these various forces into components that accurately reflect
the underlying biology. Here, we present several issues that arise in the definition
and interpretation of selection and selection coefficients, focusing on insights
gained through the examination of selection coefficients in multilocus notation.
Using this notation, we discuss how its flexibility-which allows different biological
units to be identified as targets of selection-is reflected in the interpretation
of the coefficients that the notation generates. In many situations, it can be
difficult to agree on whether loci can be considered to be under "direct"
versus "indirect" selection, or to quantify this selection. We present
arguments for what the terms direct and indirect selection might best encompass,
considering a range of issues, from viability and sexual selection to kin selection.
We show how multilocus notation can discriminate between direct and indirect selection,
and describe when it can do so.
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Maria
full_name: Servedio, Maria
last_name: Servedio
citation:
ama: Barton NH, Servedio M. The interpretation of selection coefficients. Evolution.
2015;69(5):1101-1112. doi:10.1111/evo.12641
apa: Barton, N. H., & Servedio, M. (2015). The interpretation of selection coefficients.
Evolution. Wiley. https://doi.org/10.1111/evo.12641
chicago: Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection
Coefficients.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12641.
ieee: N. H. Barton and M. Servedio, “The interpretation of selection coefficients,”
Evolution, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.
ista: Barton NH, Servedio M. 2015. The interpretation of selection coefficients.
Evolution. 69(5), 1101–1112.
mla: Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.”
Evolution, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:10.1111/evo.12641.
short: N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112.
date_created: 2018-12-11T11:52:29Z
date_published: 2015-03-19T00:00:00Z
date_updated: 2021-01-12T06:51:20Z
day: '19'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.12641
ec_funded: 1
file:
- access_level: open_access
checksum: fd8d23f476bc194419929b72ca265c02
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:34Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4822'
file_name: IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf
file_size: 188872
relation: main_file
- access_level: open_access
checksum: b774911e70044641d556e258efcb52ef
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:35Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4823'
file_name: IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf
file_size: 577415
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 69'
issue: '5'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 1101 - 1112
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution
publication_status: published
publisher: Wiley
publist_id: '5656'
pubrep_id: '560'
quality_controlled: '1'
scopus_import: 1
status: public
title: The interpretation of selection coefficients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 69
year: '2015'
...
---
_id: '1525'
abstract:
- lang: eng
text: 'Based on 16 recommendations, efforts should be made to achieve the following
goal: By 2025, all scholarly publication activity in Austria should be Open Access.
In other words, the final versions of all scholarly publications resulting from
the support of public resources must be freely accessible on the Internet without
delay (Gold Open Access). The resources required to meet this obligation shall
be provided to the authors, or the cost of the publication venues shall be borne
directly by the research organisations.'
article_processing_charge: No
article_type: original
author:
- first_name: Bruno
full_name: Bauer, Bruno
last_name: Bauer
- first_name: Guido
full_name: Blechl, Guido
last_name: Blechl
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
- first_name: Andreas
full_name: Ferus, Andreas
last_name: Ferus
- first_name: Anton
full_name: Graschopf, Anton
last_name: Graschopf
- first_name: Thomas
full_name: König, Thomas
last_name: König
- first_name: Katja
full_name: Mayer, Katja
last_name: Mayer
- first_name: Falk
full_name: Reckling, Falk
last_name: Reckling
- first_name: Katharina
full_name: Rieck, Katharina
last_name: Rieck
- first_name: Peter
full_name: Seitz, Peter
last_name: Seitz
- first_name: Herwig
full_name: Stöger, Herwig
last_name: Stöger
- first_name: Elvira
full_name: Welzig, Elvira
last_name: Welzig
citation:
ama: Bauer B, Blechl G, Bock C, et al. Arbeitsgruppe „Nationale Strategie“ des Open
Access Network Austria OANA. VÖB Mitteilungen. 2015;68(3):580-607. doi:10.5281/zenodo.33178
apa: Bauer, B., Blechl, G., Bock, C., Danowski, P., Ferus, A., Graschopf, A., …
Welzig, E. (2015). Arbeitsgruppe „Nationale Strategie“ des Open Access Network
Austria OANA. VÖB Mitteilungen. Verein Österreichischer Bibliothekare.
https://doi.org/10.5281/zenodo.33178
chicago: Bauer, Bruno, Guido Blechl, Christoph Bock, Patrick Danowski, Andreas Ferus,
Anton Graschopf, Thomas König, et al. “Arbeitsgruppe „Nationale Strategie“ Des
Open Access Network Austria OANA.” VÖB Mitteilungen. Verein Österreichischer
Bibliothekare, 2015. https://doi.org/10.5281/zenodo.33178.
ieee: B. Bauer et al., “Arbeitsgruppe „Nationale Strategie“ des Open Access
Network Austria OANA,” VÖB Mitteilungen, vol. 68, no. 3. Verein Österreichischer
Bibliothekare, pp. 580–607, 2015.
ista: Bauer B, Blechl G, Bock C, Danowski P, Ferus A, Graschopf A, König T, Mayer
K, Reckling F, Rieck K, Seitz P, Stöger H, Welzig E. 2015. Arbeitsgruppe „Nationale
Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. 68(3), 580–607.
mla: Bauer, Bruno, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network
Austria OANA.” VÖB Mitteilungen, vol. 68, no. 3, Verein Österreichischer
Bibliothekare, 2015, pp. 580–607, doi:10.5281/zenodo.33178.
short: B. Bauer, G. Blechl, C. Bock, P. Danowski, A. Ferus, A. Graschopf, T. König,
K. Mayer, F. Reckling, K. Rieck, P. Seitz, H. Stöger, E. Welzig, VÖB Mitteilungen
68 (2015) 580–607.
date_created: 2018-12-11T11:52:31Z
date_published: 2015-11-12T00:00:00Z
date_updated: 2021-01-12T06:51:22Z
day: '12'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.5281/zenodo.33178
file:
- access_level: open_access
checksum: a495fe253bbc7615b1d60e9e85c94408
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:59Z
date_updated: 2020-07-14T12:45:00Z
file_id: '5317'
file_name: IST-2016-720-v1+1_OANA_OA-Empfehlungen_12-11-2015.pdf
file_size: 931707
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 68'
issue: '3'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 580 - 607
publication: VÖB Mitteilungen
publication_status: published
publisher: Verein Österreichischer Bibliothekare
publist_id: '5648'
pubrep_id: '720'
quality_controlled: '1'
scopus_import: 1
status: public
title: Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA
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: 68
year: '2015'
...
---
_id: '1520'
abstract:
- lang: eng
text: Creating mechanical automata that can walk in stable and pleasing manners
is a challenging task that requires both skill and expertise. We propose to use
computational design to offset the technical difficulties of this process. A simple
drag-and-drop interface allows casual users to create personalized walking toys
from a library of pre-defined template mechanisms. Provided with this input, our
method leverages physical simulation and evolutionary optimization to refine the
mechanical designs such that the resulting toys are able to walk. The optimization
process is guided by an intuitive set of objectives that measure the quality of
the walking motions. We demonstrate our approach on a set of simulated mechanical
toys with different numbers of legs and various distinct gaits. Two fabricated
prototypes showcase the feasibility of our designs.
author:
- first_name: Gaurav
full_name: Bharaj, Gaurav
last_name: Bharaj
- first_name: Stelian
full_name: Coros, Stelian
last_name: Coros
- first_name: Bernhard
full_name: Thomaszewski, Bernhard
last_name: Thomaszewski
- first_name: James
full_name: Tompkin, James
last_name: Tompkin
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Hanspeter
full_name: Pfister, Hanspeter
last_name: Pfister
citation:
ama: 'Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. Computational
design of walking automata. In: ACM; 2015:93-100. doi:10.1145/2786784.2786803'
apa: 'Bharaj, G., Coros, S., Thomaszewski, B., Tompkin, J., Bickel, B., & Pfister,
H. (2015). Computational design of walking automata (pp. 93–100). Presented at
the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Los Angeles,
CA, United States: ACM. https://doi.org/10.1145/2786784.2786803'
chicago: Bharaj, Gaurav, Stelian Coros, Bernhard Thomaszewski, James Tompkin, Bernd
Bickel, and Hanspeter Pfister. “Computational Design of Walking Automata,” 93–100.
ACM, 2015. https://doi.org/10.1145/2786784.2786803.
ieee: 'G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, and H. Pfister,
“Computational design of walking automata,” presented at the SCA: ACM SIGGRAPH/Eurographics
Symposium on Computer animation, Los Angeles, CA, United States, 2015, pp. 93–100.'
ista: 'Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. 2015.
Computational design of walking automata. SCA: ACM SIGGRAPH/Eurographics Symposium
on Computer animation, 93–100.'
mla: Bharaj, Gaurav, et al. Computational Design of Walking Automata. ACM,
2015, pp. 93–100, doi:10.1145/2786784.2786803.
short: G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, H. Pfister,
in:, ACM, 2015, pp. 93–100.
conference:
end_date: 2015-08-09
location: Los Angeles, CA, United States
name: 'SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation'
start_date: 2015-08-07
date_created: 2018-12-11T11:52:30Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:21Z
day: '01'
department:
- _id: BeBi
doi: 10.1145/2786784.2786803
language:
- iso: eng
month: '08'
oa_version: None
page: 93 - 100
publication_identifier:
isbn:
- 978-1-4503-3496-9
publication_status: published
publisher: ACM
publist_id: '5655'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computational design of walking automata
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1532'
abstract:
- lang: eng
text: Ammonium is the major nitrogen source in some plant ecosystems but is toxic
at high concentrations, especially when available as the exclusive nitrogen source.
Ammonium stress rapidly leads to various metabolic and hormonal imbalances that
ultimately inhibit root and shoot growth in many plant species, including Arabidopsis
thaliana (L.) Heynh. To identify molecular and genetic factors involved in seedling
survival with prolonged exclusive NH4+ nutrition, a transcriptomic analysis with
microarrays was used. Substantial transcriptional differences were most pronounced
in (NH4)2SO4-grown seedlings, compared with plants grown on KNO3 or NH4NO3. Consistent
with previous physiological analyses, major differences in the expression modules
of photosynthesis-related genes, an altered mitochondrial metabolism, differential
expression of the primary NH4+ assimilation, alteration of transporter gene expression
and crucial changes in cell wall biosynthesis were found. A major difference in
plant hormone responses, particularly of auxin but not cytokinin, was striking.
The activity of the DR5::GUS reporter revealed a dramatically decreased auxin
response in (NH4)2SO4-grown primary roots. The impaired root growth on (NH4)2SO4
was partially rescued by exogenous auxin or in specific mutants in the auxin pathway.
The data suggest that NH4+-induced nutritional and metabolic imbalances can be
partially overcome by elevated auxin levels.
article_processing_charge: No
article_type: original
author:
- first_name: Huaiyu
full_name: Yang, Huaiyu
last_name: Yang
- first_name: Jenny
full_name: Von Der Fecht Bartenbach, Jenny
last_name: Von Der Fecht Bartenbach
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jan
full_name: Lohmann, Jan
last_name: Lohmann
- first_name: Benjamin
full_name: Neuhäuser, Benjamin
last_name: Neuhäuser
- first_name: Uwe
full_name: Ludewig, Uwe
last_name: Ludewig
citation:
ama: Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig
U. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with
ammonium as the sole nitrogen source. Functional Plant Biology. 2015;42(3):239-251.
doi:10.1071/FP14171
apa: Yang, H., Von Der Fecht Bartenbach, J., Friml, J., Lohmann, J., Neuhäuser,
B., & Ludewig, U. (2015). Auxin-modulated root growth inhibition in Arabidopsis
thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant
Biology. CSIRO. https://doi.org/10.1071/FP14171
chicago: Yang, Huaiyu, Jenny Von Der Fecht Bartenbach, Jiří Friml, Jan Lohmann,
Benjamin Neuhäuser, and Uwe Ludewig. “Auxin-Modulated Root Growth Inhibition in
Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” Functional
Plant Biology. CSIRO, 2015. https://doi.org/10.1071/FP14171.
ieee: H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser,
and U. Ludewig, “Auxin-modulated root growth inhibition in Arabidopsis thaliana
seedlings with ammonium as the sole nitrogen source,” Functional Plant Biology,
vol. 42, no. 3. CSIRO, pp. 239–251, 2015.
ista: Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig
U. 2015. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings
with ammonium as the sole nitrogen source. Functional Plant Biology. 42(3), 239–251.
mla: Yang, Huaiyu, et al. “Auxin-Modulated Root Growth Inhibition in Arabidopsis
Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” Functional Plant
Biology, vol. 42, no. 3, CSIRO, 2015, pp. 239–51, doi:10.1071/FP14171.
short: H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser,
U. Ludewig, Functional Plant Biology 42 (2015) 239–251.
date_created: 2018-12-11T11:52:34Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2022-05-24T09:02:24Z
day: '01'
department:
- _id: JiFr
doi: 10.1071/FP14171
external_id:
pmid:
- '32480670'
intvolume: ' 42'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 239 - 251
pmid: 1
publication: Functional Plant Biology
publication_identifier:
issn:
- 1445-4408
publication_status: published
publisher: CSIRO
publist_id: '5639'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with
ammonium as the sole nitrogen source
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2015'
...
---
_id: '1531'
abstract:
- lang: eng
text: The Heat Kernel Signature (HKS) is a scalar quantity which is derived from
the heat kernel of a given shape. Due to its robustness, isometry invariance,
and multiscale nature, it has been successfully applied in many geometric applications.
From a more general point of view, the HKS can be considered as a descriptor of
the metric of a Riemannian manifold. Given a symmetric positive definite tensor
field we may interpret it as the metric of some Riemannian manifold and thereby
apply the HKS to visualize and analyze the given tensor data. In this paper, we
propose a generalization of this approach that enables the treatment of indefinite
tensor fields, like the stress tensor, by interpreting them as a generator of
a positive definite tensor field. To investigate the usefulness of this approach
we consider the stress tensor from the two-point-load model example and from a
mechanical work piece.
alternative_title:
- Mathematics and Visualization
article_processing_charge: No
author:
- first_name: Valentin
full_name: Zobel, Valentin
last_name: Zobel
- first_name: Jan
full_name: Reininghaus, Jan
id: 4505473A-F248-11E8-B48F-1D18A9856A87
last_name: Reininghaus
- first_name: Ingrid
full_name: Hotz, Ingrid
last_name: Hotz
citation:
ama: 'Zobel V, Reininghaus J, Hotz I. Visualizing symmetric indefinite 2D tensor
fields using The Heat Kernel Signature. In: Hotz I, Schultz T, eds. Visualization
and Processing of Higher Order Descriptors for Multi-Valued Data. Vol 40.
1st ed. Springer; 2015:257-267. doi:10.1007/978-3-319-15090-1_13'
apa: Zobel, V., Reininghaus, J., & Hotz, I. (2015). Visualizing symmetric indefinite
2D tensor fields using The Heat Kernel Signature. In I. Hotz & T. Schultz
(Eds.), Visualization and Processing of Higher Order Descriptors for Multi-Valued
Data (1st ed., Vol. 40, pp. 257–267). Springer. https://doi.org/10.1007/978-3-319-15090-1_13
chicago: Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualizing Symmetric
Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” In Visualization
and Processing of Higher Order Descriptors for Multi-Valued Data, edited by
Ingrid Hotz and Thomas Schultz, 1st ed., 40:257–67. Springer, 2015. https://doi.org/10.1007/978-3-319-15090-1_13.
ieee: V. Zobel, J. Reininghaus, and I. Hotz, “Visualizing symmetric indefinite 2D
tensor fields using The Heat Kernel Signature,” in Visualization and Processing
of Higher Order Descriptors for Multi-Valued Data, 1st ed., vol. 40, I. Hotz
and T. Schultz, Eds. Springer, 2015, pp. 257–267.
ista: 'Zobel V, Reininghaus J, Hotz I. 2015.Visualizing symmetric indefinite 2D
tensor fields using The Heat Kernel Signature. In: Visualization and Processing
of Higher Order Descriptors for Multi-Valued Data. Mathematics and Visualization,
vol. 40, 257–267.'
mla: Zobel, Valentin, et al. “Visualizing Symmetric Indefinite 2D Tensor Fields
Using The Heat Kernel Signature.” Visualization and Processing of Higher Order
Descriptors for Multi-Valued Data, edited by Ingrid Hotz and Thomas Schultz,
1st ed., vol. 40, Springer, 2015, pp. 257–67, doi:10.1007/978-3-319-15090-1_13.
short: V. Zobel, J. Reininghaus, I. Hotz, in:, I. Hotz, T. Schultz (Eds.), Visualization
and Processing of Higher Order Descriptors for Multi-Valued Data, 1st ed., Springer,
2015, pp. 257–267.
date_created: 2018-12-11T11:52:33Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2022-06-10T09:50:14Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-319-15090-1_13
edition: '1'
editor:
- first_name: Ingrid
full_name: Hotz, Ingrid
last_name: Hotz
- first_name: Thomas
full_name: Schultz, Thomas
last_name: Schultz
intvolume: ' 40'
language:
- iso: eng
month: '01'
oa_version: None
page: 257 - 267
publication: Visualization and Processing of Higher Order Descriptors for Multi-Valued
Data
publication_identifier:
isbn:
- 978-3-319-15089-5
publication_status: published
publisher: Springer
publist_id: '5640'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2015'
...
---
_id: '1530'
abstract:
- lang: eng
text: In growing cells, protein synthesis and cell growth are typically not synchronous,
and, thus, protein concentrations vary over the cell division cycle. We have developed
a theoretical description of genetic regulatory systems in bacteria that explicitly
considers the cell division cycle to investigate its impact on gene expression.
We calculate the cell-to-cell variations arising from cells being at different
stages in the division cycle for unregulated genes and for basic regulatory mechanisms.
These variations contribute to the extrinsic noise observed in single-cell experiments,
and are most significant for proteins with short lifetimes. Negative autoregulation
buffers against variation of protein concentration over the division cycle, but
the effect is found to be relatively weak. Stronger buffering is achieved by an
increased protein lifetime. Positive autoregulation can strongly amplify such
variation if the parameters are set to values that lead to resonance-like behaviour.
For cooperative positive autoregulation, the concentration variation over the
division cycle diminishes the parameter region of bistability and modulates the
switching times between the two stable states. The same effects are seen for a
two-gene mutual-repression toggle switch. By contrast, an oscillatory circuit,
the repressilator, is only weakly affected by the division cycle.
article_number: '066003'
author:
- first_name: Veronika
full_name: Bierbaum, Veronika
id: 3FD04378-F248-11E8-B48F-1D18A9856A87
last_name: Bierbaum
- first_name: Stefan
full_name: Klumpp, Stefan
last_name: Klumpp
citation:
ama: Bierbaum V, Klumpp S. Impact of the cell division cycle on gene circuits. Physical
Biology. 2015;12(6). doi:10.1088/1478-3975/12/6/066003
apa: Bierbaum, V., & Klumpp, S. (2015). Impact of the cell division cycle on
gene circuits. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/12/6/066003
chicago: Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle
on Gene Circuits.” Physical Biology. IOP Publishing Ltd., 2015. https://doi.org/10.1088/1478-3975/12/6/066003.
ieee: V. Bierbaum and S. Klumpp, “Impact of the cell division cycle on gene circuits,”
Physical Biology, vol. 12, no. 6. IOP Publishing Ltd., 2015.
ista: Bierbaum V, Klumpp S. 2015. Impact of the cell division cycle on gene circuits.
Physical Biology. 12(6), 066003.
mla: Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on
Gene Circuits.” Physical Biology, vol. 12, no. 6, 066003, IOP Publishing
Ltd., 2015, doi:10.1088/1478-3975/12/6/066003.
short: V. Bierbaum, S. Klumpp, Physical Biology 12 (2015).
date_created: 2018-12-11T11:52:33Z
date_published: 2015-09-25T00:00:00Z
date_updated: 2021-01-12T06:51:25Z
day: '25'
department:
- _id: MiSi
doi: 10.1088/1478-3975/12/6/066003
intvolume: ' 12'
issue: '6'
language:
- iso: eng
month: '09'
oa_version: None
publication: Physical Biology
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '5641'
quality_controlled: '1'
scopus_import: 1
status: public
title: Impact of the cell division cycle on gene circuits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2015'
...
---
_id: '1539'
abstract:
- lang: eng
text: 'Many stochastic models of biochemical reaction networks contain some chemical
species for which the number of molecules that are present in the system can only
be finite (for instance due to conservation laws), but also other species that
can be present in arbitrarily large amounts. The prime example of such networks
are models of gene expression, which typically contain a small and finite number
of possible states for the promoter but an infinite number of possible states
for the amount of mRNA and protein. One of the main approaches to analyze such
models is through the use of equations for the time evolution of moments of the
chemical species. Recently, a new approach based on conditional moments of the
species with infinite state space given all the different possible states of the
finite species has been proposed. It was argued that this approach allows one
to capture more details about the full underlying probability distribution with
a smaller number of equations. Here, I show that the result that less moments
provide more information can only stem from an unnecessarily complicated description
of the system in the classical formulation. The foundation of this argument will
be the derivation of moment equations that describe the complete probability distribution
over the finite state space but only low-order moments over the infinite state
space. I will show that the number of equations that is needed is always less
than what was previously claimed and always less than the number of conditional
moment equations up to the same order. To support these arguments, a symbolic
algorithm is provided that can be used to derive minimal systems of unconditional
moment equations for models with partially finite state space. '
article_number: '244103'
author:
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
citation:
ama: Ruess J. Minimal moment equations for stochastic models of biochemical reaction
networks with partially finite state space. Journal of Chemical Physics.
2015;143(24). doi:10.1063/1.4937937
apa: Ruess, J. (2015). Minimal moment equations for stochastic models of biochemical
reaction networks with partially finite state space. Journal of Chemical Physics.
American Institute of Physics. https://doi.org/10.1063/1.4937937
chicago: Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical
Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics.
American Institute of Physics, 2015. https://doi.org/10.1063/1.4937937.
ieee: J. Ruess, “Minimal moment equations for stochastic models of biochemical reaction
networks with partially finite state space,” Journal of Chemical Physics,
vol. 143, no. 24. American Institute of Physics, 2015.
ista: Ruess J. 2015. Minimal moment equations for stochastic models of biochemical
reaction networks with partially finite state space. Journal of Chemical Physics.
143(24), 244103.
mla: Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical
Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics,
vol. 143, no. 24, 244103, American Institute of Physics, 2015, doi:10.1063/1.4937937.
short: J. Ruess, Journal of Chemical Physics 143 (2015).
date_created: 2018-12-11T11:52:36Z
date_published: 2015-12-22T00:00:00Z
date_updated: 2021-01-12T06:51:28Z
day: '22'
ddc:
- '000'
department:
- _id: ToHe
- _id: GaTk
doi: 10.1063/1.4937937
ec_funded: 1
file:
- access_level: open_access
checksum: 838657118ae286463a2b7737319f35ce
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:43Z
date_updated: 2020-07-14T12:45:01Z
file_id: '4641'
file_name: IST-2016-593-v1+1_Minimal_moment_equations.pdf
file_size: 605355
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 143'
issue: '24'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
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
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal of Chemical Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5632'
pubrep_id: '593'
quality_controlled: '1'
scopus_import: 1
status: public
title: Minimal moment equations for stochastic models of biochemical reaction networks
with partially finite state space
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 143
year: '2015'
...
---
_id: '1534'
abstract:
- lang: eng
text: PIN proteins are auxin export carriers that direct intercellular auxin flow
and in turn regulate many aspects of plant growth and development including responses
to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS
(FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development,
as well as female reproductive development and stress responses. Here we show
that FLP and MYB88 act redundantly but differentially in regulating the transcription
of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the
one hand, FLP is involved in responses to gravity stimulation in primary roots,
whereas on the other, FLP and MYB88 function complementarily in establishing the
gravitropic set-point angles of lateral roots. Our results support a model in
which FLP and MYB88 expression specifically determines the temporal-spatial patterns
of PIN3 and PIN7 transcription that are closely associated with their preferential
functions during root responses to gravity.
article_number: '8822'
author:
- first_name: Hongzhe
full_name: Wang, Hongzhe
last_name: Wang
- first_name: Kezhen
full_name: Yang, Kezhen
last_name: Yang
- first_name: Junjie
full_name: Zou, Junjie
last_name: Zou
- first_name: Lingling
full_name: Zhu, Lingling
last_name: Zhu
- first_name: Zidian
full_name: Xie, Zidian
last_name: Xie
- first_name: Miyoterao
full_name: Morita, Miyoterao
last_name: Morita
- first_name: Masao
full_name: Tasaka, Masao
last_name: Tasaka
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Erich
full_name: Grotewold, Erich
last_name: Grotewold
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Fred
full_name: Sack, Fred
last_name: Sack
- first_name: Jie
full_name: Le, Jie
last_name: Le
citation:
ama: Wang H, Yang K, Zou J, et al. Transcriptional regulation of PIN genes by FOUR
LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications.
2015;6. doi:10.1038/ncomms9822
apa: Wang, H., Yang, K., Zou, J., Zhu, L., Xie, Z., Morita, M., … Le, J. (2015).
Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis
root gravitropism. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9822
chicago: Wang, Hongzhe, Kezhen Yang, Junjie Zou, Lingling Zhu, Zidian Xie, Miyoterao
Morita, Masao Tasaka, et al. “Transcriptional Regulation of PIN Genes by FOUR
LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications.
Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9822.
ieee: H. Wang et al., “Transcriptional regulation of PIN genes by FOUR LIPS
and MYB88 during Arabidopsis root gravitropism,” Nature Communications,
vol. 6. Nature Publishing Group, 2015.
ista: Wang H, Yang K, Zou J, Zhu L, Xie Z, Morita M, Tasaka M, Friml J, Grotewold
E, Beeckman T, Vanneste S, Sack F, Le J. 2015. Transcriptional regulation of PIN
genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications.
6, 8822.
mla: Wang, Hongzhe, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS
and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications,
vol. 6, 8822, Nature Publishing Group, 2015, doi:10.1038/ncomms9822.
short: H. Wang, K. Yang, J. Zou, L. Zhu, Z. Xie, M. Morita, M. Tasaka, J. Friml,
E. Grotewold, T. Beeckman, S. Vanneste, F. Sack, J. Le, Nature Communications
6 (2015).
date_created: 2018-12-11T11:52:34Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2021-01-12T06:51:26Z
day: '18'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1038/ncomms9822
ec_funded: 1
file:
- access_level: open_access
checksum: 3c06735fc7cd7e482ca830cbd26001bf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:07Z
date_updated: 2020-07-14T12:45:01Z
file_id: '5259'
file_name: IST-2016-485-v1+1_ncomms9822.pdf
file_size: 1852268
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5637'
pubrep_id: '485'
quality_controlled: '1'
scopus_import: 1
status: public
title: Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis
root gravitropism
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '1538'
abstract:
- lang: eng
text: Systems biology rests on the idea that biological complexity can be better
unraveled through the interplay of modeling and experimentation. However, the
success of this approach depends critically on the informativeness of the chosen
experiments, which is usually unknown a priori. Here, we propose a systematic
scheme based on iterations of optimal experiment design, flow cytometry experiments,
and Bayesian parameter inference to guide the discovery process in the case of
stochastic biochemical reaction networks. To illustrate the benefit of our methodology,
we apply it to the characterization of an engineered light-inducible gene expression
circuit in yeast and compare the performance of the resulting model with models
identified from nonoptimal experiments. In particular, we compare the parameter
posterior distributions and the precision to which the outcome of future experiments
can be predicted. Moreover, we illustrate how the identified stochastic model
can be used to determine light induction patterns that make either the average
amount of protein or the variability in a population of cells follow a desired
profile. Our results show that optimal experiment design allows one to derive
models that are accurate enough to precisely predict and regulate the protein
expression in heterogeneous cell populations over extended periods of time.
acknowledgement: 'J.R., F.P., and J.L. acknowledge support from the European Commission
under the Network of Excellence HYCON2 (highly-complex and networked control systems)
and SystemsX.ch under the SignalX Project. J.R. acknowledges support from the People
Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme
FP7/2007-2013 under REA (Research Executive Agency) Grant 291734. M.K. acknowledges
support from Human Frontier Science Program Grant RP0061/2011 (www.hfsp.org). '
author:
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
- first_name: Francesca
full_name: Parise, Francesca
last_name: Parise
- first_name: Andreas
full_name: Milias Argeitis, Andreas
last_name: Milias Argeitis
- first_name: Mustafa
full_name: Khammash, Mustafa
last_name: Khammash
- first_name: John
full_name: Lygeros, John
last_name: Lygeros
citation:
ama: Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. Iterative experiment
design guides the characterization of a light-inducible gene expression circuit.
PNAS. 2015;112(26):8148-8153. doi:10.1073/pnas.1423947112
apa: Ruess, J., Parise, F., Milias Argeitis, A., Khammash, M., & Lygeros, J.
(2015). Iterative experiment design guides the characterization of a light-inducible
gene expression circuit. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1423947112
chicago: Ruess, Jakob, Francesca Parise, Andreas Milias Argeitis, Mustafa Khammash,
and John Lygeros. “Iterative Experiment Design Guides the Characterization of
a Light-Inducible Gene Expression Circuit.” PNAS. National Academy of Sciences,
2015. https://doi.org/10.1073/pnas.1423947112.
ieee: J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, and J. Lygeros, “Iterative
experiment design guides the characterization of a light-inducible gene expression
circuit,” PNAS, vol. 112, no. 26. National Academy of Sciences, pp. 8148–8153,
2015.
ista: Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. 2015. Iterative
experiment design guides the characterization of a light-inducible gene expression
circuit. PNAS. 112(26), 8148–8153.
mla: Ruess, Jakob, et al. “Iterative Experiment Design Guides the Characterization
of a Light-Inducible Gene Expression Circuit.” PNAS, vol. 112, no. 26,
National Academy of Sciences, 2015, pp. 8148–53, doi:10.1073/pnas.1423947112.
short: J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112
(2015) 8148–8153.
date_created: 2018-12-11T11:52:36Z
date_published: 2015-06-30T00:00:00Z
date_updated: 2021-01-12T06:51:27Z
day: '30'
department:
- _id: ToHe
- _id: GaTk
doi: 10.1073/pnas.1423947112
ec_funded: 1
external_id:
pmid:
- '26085136'
intvolume: ' 112'
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491780/
month: '06'
oa: 1
oa_version: Submitted Version
page: 8148 - 8153
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5633'
quality_controlled: '1'
scopus_import: 1
status: public
title: Iterative experiment design guides the characterization of a light-inducible
gene expression circuit
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1535'
abstract:
- lang: eng
text: Neuronal and neuroendocrine L-type calcium channels (Cav1.2, Cav1.3) open
readily at relatively low membrane potentials and allow Ca2+ to enter the cells
near resting potentials. In this way, Cav1.2 and Cav1.3 shape the action potential
waveform, contribute to gene expression, synaptic plasticity, neuronal differentiation,
hormone secretion and pacemaker activity. In the chromaffin cells (CCs) of the
adrenal medulla, Cav1.3 is highly expressed and is shown to support most of the
pacemaking current that sustains action potential (AP) firings and part of the
catecholamine secretion. Cav1.3 forms Ca2+-nanodomains with the fast inactivating
BK channels and drives the resting SK currents. These latter set the inter-spike
interval duration between consecutive spikes during spontaneous firing and the
rate of spike adaptation during sustained depolarizations. Cav1.3 plays also a
primary role in the switch from “tonic” to “burst” firing that occurs in mouse
CCs when either the availability of voltage-gated Na channels (Nav) is reduced
or the β2 subunit featuring the fast inactivating BK channels is deleted. Here,
we discuss the functional role of these “neuronlike” firing modes in CCs and how
Cav1.3 contributes to them. The open issue is to understand how these novel firing
patterns are adapted to regulate the quantity of circulating catecholamines during
resting condition or in response to acute and chronic stress.
acknowledgement: This work was supported by the Italian MIUR (PRIN 2010/2011 project
2010JFYFY2) and the University of Torino.
article_processing_charge: No
article_type: original
author:
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Andrea
full_name: Marcantoni, Andrea
last_name: Marcantoni
- first_name: Emilio
full_name: Carbone, Emilio
last_name: Carbone
citation:
ama: Vandael DH, Marcantoni A, Carbone E. Cav1.3 channels as key regulators of neuron-like
firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology.
2015;8(2):149-161. doi:10.2174/1874467208666150507105443
apa: Vandael, D. H., Marcantoni, A., & Carbone, E. (2015). Cav1.3 channels as
key regulators of neuron-like firings and catecholamine release in chromaffin
cells. Current Molecular Pharmacology. Bentham Science Publishers. https://doi.org/10.2174/1874467208666150507105443
chicago: Vandael, David H, Andrea Marcantoni, and Emilio Carbone. “Cav1.3 Channels
as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin
Cells.” Current Molecular Pharmacology. Bentham Science Publishers, 2015.
https://doi.org/10.2174/1874467208666150507105443.
ieee: D. H. Vandael, A. Marcantoni, and E. Carbone, “Cav1.3 channels as key regulators
of neuron-like firings and catecholamine release in chromaffin cells,” Current
Molecular Pharmacology, vol. 8, no. 2. Bentham Science Publishers, pp. 149–161,
2015.
ista: Vandael DH, Marcantoni A, Carbone E. 2015. Cav1.3 channels as key regulators
of neuron-like firings and catecholamine release in chromaffin cells. Current
Molecular Pharmacology. 8(2), 149–161.
mla: Vandael, David H., et al. “Cav1.3 Channels as Key Regulators of Neuron-like
Firings and Catecholamine Release in Chromaffin Cells.” Current Molecular Pharmacology,
vol. 8, no. 2, Bentham Science Publishers, 2015, pp. 149–61, doi:10.2174/1874467208666150507105443.
short: D.H. Vandael, A. Marcantoni, E. Carbone, Current Molecular Pharmacology 8
(2015) 149–161.
date_created: 2018-12-11T11:52:35Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2021-01-12T06:51:26Z
day: '01'
department:
- _id: PeJo
doi: 10.2174/1874467208666150507105443
external_id:
pmid:
- '25966692'
intvolume: ' 8'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384372/
month: '10'
oa: 1
oa_version: Submitted Version
page: 149 - 161
pmid: 1
publication: Current Molecular Pharmacology
publication_status: published
publisher: Bentham Science Publishers
publist_id: '5636'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cav1.3 channels as key regulators of neuron-like firings and catecholamine
release in chromaffin cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2015'
...
---
_id: '1536'
abstract:
- lang: eng
text: Strigolactones, first discovered as germination stimulants for parasitic weeds
[1], are carotenoid-derived phytohormones that play major roles in inhibiting
lateral bud outgrowth and promoting plant-mycorrhizal symbiosis [2-4]. Furthermore,
strigolactones are involved in the regulation of lateral and adventitious root
development, root cell division [5, 6], secondary growth [7], and leaf senescence
[8]. Recently, we discovered the strigolactone transporter Petunia axillaris PLEIOTROPIC
DRUG RESISTANCE 1 (PaPDR1), which is required for efficient mycorrhizal colonization
and inhibition of lateral bud outgrowth [9]. However, how strigolactones are transported
through the plant remained unknown. Here we show that PaPDR1 exhibits a cell-type-specific
asymmetric localization in different root tissues. In root tips, PaPDR1 is co-expressed
with the strigolactone biosynthetic gene DAD1 (CCD8), and it is localized at the
apical membrane of root hypodermal cells, presumably mediating the shootward transport
of strigolactone. Above the root tip, in the hypodermal passage cells that form
gates for the entry of mycorrhizal fungi, PaPDR1 is present in the outer-lateral
membrane, compatible with its postulated function as strigolactone exporter from
root to soil. Transport studies are in line with our localization studies since
(1) a papdr1 mutant displays impaired transport of strigolactones out of the root
tip to the shoot as well as into the rhizosphere and (2) DAD1 expression and PIN1/PIN2
levels change in plants deregulated for PDR1 expression, suggestive of variations
in endogenous strigolactone contents. In conclusion, our results indicate that
the polar localizations of PaPDR1 mediate directional shootward strigolactone
transport as well as localized exudation into the soil.
acknowledgement: "This work was funded by a grant of the Swiss National Foundation
to E.M.\r\nWe thank Dr. José María Mateos (University of Zurich) for providing us
with the vibratome, Prof. Dolf Weijers (Wageningen University, the Netherlands)
for shipping us his set of ligation-independent cloning vectors, Prof. Bruno Humbel
(University of Lausanne) for suggestions on GFP-PDR1 detection, and Dr. Undine Krügel
(University of Zurich) and Prof. Michal Jasinski (Polish Academy of Science) for
hints on protein quantification."
author:
- first_name: Joëlle
full_name: Sasse, Joëlle
last_name: Sasse
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Christian
full_name: Gübeli, Christian
last_name: Gübeli
- first_name: Guowei
full_name: Liu, Guowei
last_name: Liu
- first_name: Xi
full_name: Cheng, Xi
last_name: Cheng
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Harro
full_name: Bouwmeester, Harro
last_name: Bouwmeester
- first_name: Enrico
full_name: Martinoia, Enrico
last_name: Martinoia
- first_name: Lorenzo
full_name: Borghi, Lorenzo
last_name: Borghi
citation:
ama: Sasse J, Simon S, Gübeli C, et al. Asymmetric localizations of the ABC transporter
PaPDR1 trace paths of directional strigolactone transport. Current Biology.
2015;25(5):647-655. doi:10.1016/j.cub.2015.01.015
apa: Sasse, J., Simon, S., Gübeli, C., Liu, G., Cheng, X., Friml, J., … Borghi,
L. (2015). Asymmetric localizations of the ABC transporter PaPDR1 trace paths
of directional strigolactone transport. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2015.01.015
chicago: Sasse, Joëlle, Sibu Simon, Christian Gübeli, Guowei Liu, Xi Cheng, Jiří
Friml, Harro Bouwmeester, Enrico Martinoia, and Lorenzo Borghi. “Asymmetric Localizations
of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.”
Current Biology. Cell Press, 2015. https://doi.org/10.1016/j.cub.2015.01.015.
ieee: J. Sasse et al., “Asymmetric localizations of the ABC transporter PaPDR1
trace paths of directional strigolactone transport,” Current Biology, vol.
25, no. 5. Cell Press, pp. 647–655, 2015.
ista: Sasse J, Simon S, Gübeli C, Liu G, Cheng X, Friml J, Bouwmeester H, Martinoia
E, Borghi L. 2015. Asymmetric localizations of the ABC transporter PaPDR1 trace
paths of directional strigolactone transport. Current Biology. 25(5), 647–655.
mla: Sasse, Joëlle, et al. “Asymmetric Localizations of the ABC Transporter PaPDR1
Trace Paths of Directional Strigolactone Transport.” Current Biology, vol.
25, no. 5, Cell Press, 2015, pp. 647–55, doi:10.1016/j.cub.2015.01.015.
short: J. Sasse, S. Simon, C. Gübeli, G. Liu, X. Cheng, J. Friml, H. Bouwmeester,
E. Martinoia, L. Borghi, Current Biology 25 (2015) 647–655.
date_created: 2018-12-11T11:52:35Z
date_published: 2015-02-12T00:00:00Z
date_updated: 2021-01-12T06:51:27Z
day: '12'
department:
- _id: JiFr
doi: 10.1016/j.cub.2015.01.015
intvolume: ' 25'
issue: '5'
language:
- iso: eng
month: '02'
oa_version: None
page: 647 - 655
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '5635'
quality_controlled: '1'
scopus_import: 1
status: public
title: Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional
strigolactone transport
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2015'
...
---
_id: '1533'
abstract:
- lang: eng
text: This paper addresses the problem of semantic segmentation, where the possible
class labels are from a predefined set. We exploit top-down guidance, i.e., the
coarse localization of the objects and their class labels provided by object detectors.
For each detected bounding box, figure-ground segmentation is performed and the
final result is achieved by merging the figure-ground segmentations. The main
idea of the proposed approach, which is presented in our preliminary work, is
to reformulate the figure-ground segmentation problem as sparse reconstruction
pursuing the object mask in a nonparametric manner. The latent segmentation mask
should be coherent subject to sparse error caused by intra-category diversity;
thus, the object mask is inferred by making use of sparse representations over
the training set. To handle local spatial deformations, local patch-level masks
are also considered and inferred by sparse representations over the spatially
nearby patches. The sparse reconstruction coefficients and the latent mask are
alternately optimized by applying the Lasso algorithm and the accelerated proximal
gradient method. The proposed formulation results in a convex optimization problem;
thus, the global optimal solution is achieved. In this paper, we provide theoretical
analysis of the convergence and optimality. We also give an extended numerical
analysis of the proposed algorithm and a comprehensive comparison with the related
semantic segmentation methods on the challenging PASCAL visual object class object
segmentation datasets and the Weizmann horse dataset. The experimental results
demonstrate that the proposed algorithm achieves a competitive performance when
compared with the state of the arts.
author:
- first_name: Wei
full_name: Xia, Wei
last_name: Xia
- first_name: Csaba
full_name: Domokos, Csaba
id: 492DACF8-F248-11E8-B48F-1D18A9856A87
last_name: Domokos
- first_name: Junjun
full_name: Xiong, Junjun
last_name: Xiong
- first_name: Loongfah
full_name: Cheong, Loongfah
last_name: Cheong
- first_name: Shuicheng
full_name: Yan, Shuicheng
last_name: Yan
citation:
ama: Xia W, Domokos C, Xiong J, Cheong L, Yan S. Segmentation over detection via
optimal sparse reconstructions. IEEE Transactions on Circuits and Systems for
Video Technology. 2015;25(8):1295-1308. doi:10.1109/TCSVT.2014.2379972
apa: Xia, W., Domokos, C., Xiong, J., Cheong, L., & Yan, S. (2015). Segmentation
over detection via optimal sparse reconstructions. IEEE Transactions on Circuits
and Systems for Video Technology. IEEE. https://doi.org/10.1109/TCSVT.2014.2379972
chicago: Xia, Wei, Csaba Domokos, Junjun Xiong, Loongfah Cheong, and Shuicheng Yan.
“Segmentation over Detection via Optimal Sparse Reconstructions.” IEEE Transactions
on Circuits and Systems for Video Technology. IEEE, 2015. https://doi.org/10.1109/TCSVT.2014.2379972.
ieee: W. Xia, C. Domokos, J. Xiong, L. Cheong, and S. Yan, “Segmentation over detection
via optimal sparse reconstructions,” IEEE Transactions on Circuits and Systems
for Video Technology, vol. 25, no. 8. IEEE, pp. 1295–1308, 2015.
ista: Xia W, Domokos C, Xiong J, Cheong L, Yan S. 2015. Segmentation over detection
via optimal sparse reconstructions. IEEE Transactions on Circuits and Systems
for Video Technology. 25(8), 1295–1308.
mla: Xia, Wei, et al. “Segmentation over Detection via Optimal Sparse Reconstructions.”
IEEE Transactions on Circuits and Systems for Video Technology, vol. 25,
no. 8, IEEE, 2015, pp. 1295–308, doi:10.1109/TCSVT.2014.2379972.
short: W. Xia, C. Domokos, J. Xiong, L. Cheong, S. Yan, IEEE Transactions on Circuits
and Systems for Video Technology 25 (2015) 1295–1308.
date_created: 2018-12-11T11:52:34Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:26Z
day: '01'
department:
- _id: ChLa
doi: 10.1109/TCSVT.2014.2379972
intvolume: ' 25'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 1295 - 1308
publication: IEEE Transactions on Circuits and Systems for Video Technology
publication_status: published
publisher: IEEE
publist_id: '5638'
quality_controlled: '1'
scopus_import: 1
status: public
title: Segmentation over detection via optimal sparse reconstructions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2015'
...
---
_id: '1542'
abstract:
- lang: eng
text: 'The theory of population genetics and evolutionary computation have been
evolving separately for nearly 30 years. Many results have been independently
obtained in both fields and many others are unique to its respective field. We
aim to bridge this gap by developing a unifying framework for evolutionary processes
that allows both evolutionary algorithms and population genetics models to be
cast in the same formal framework. The framework we present here decomposes the
evolutionary process into its several components in order to facilitate the identification
of similarities between different models. In particular, we propose a classification
of evolutionary operators based on the defining properties of the different components.
We cast several commonly used operators from both fields into this common framework.
Using this, we map different evolutionary and genetic algorithms to different
evolutionary regimes and identify candidates with the most potential for the translation
of results between the fields. This provides a unified description of evolutionary
processes and represents a stepping stone towards new tools and results to both
fields. '
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Golnaz
full_name: Badkobeh, Golnaz
last_name: Badkobeh
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Doğan
full_name: Çörüş, Doğan
last_name: Çörüş
- first_name: Duccuong
full_name: Dang, Duccuong
last_name: Dang
- first_name: Tobias
full_name: Friedrich, Tobias
last_name: Friedrich
- first_name: Per
full_name: Lehre, Per
last_name: Lehre
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Andrew
full_name: Sutton, Andrew
last_name: Sutton
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary
processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011
apa: Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T.,
… Trubenova, B. (2015). Toward a unifying framework for evolutionary processes.
Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.07.011
chicago: Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong
Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova.
“Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical
Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.07.011.
ieee: T. Paixao et al., “Toward a unifying framework for evolutionary processes,”
Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015.
ista: Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt
D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal
of Theoretical Biology. 383, 28–43.
mla: Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.”
Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011.
short: T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P.
Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383
(2015) 28–43.
date_created: 2018-12-11T11:52:37Z
date_published: 2015-10-21T00:00:00Z
date_updated: 2021-01-12T06:51:29Z
day: '21'
ddc:
- '570'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1016/j.jtbi.2015.07.011
ec_funded: 1
file:
- access_level: open_access
checksum: 33b60ecfea60764756a9ee9df5eb65ca
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:53Z
date_updated: 2020-07-14T12:45:01Z
file_id: '5244'
file_name: IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf
file_size: 595307
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 383'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: 28 - 43
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: ' Journal of Theoretical Biology'
publication_status: published
publisher: Elsevier
publist_id: '5629'
pubrep_id: '483'
quality_controlled: '1'
scopus_import: 1
status: public
title: Toward a unifying framework for evolutionary processes
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: 383
year: '2015'
...
---
_id: '1546'
abstract:
- lang: eng
text: Synaptic efficacy and precision are influenced by the coupling of voltage-gated
Ca2+ channels (VGCCs) to vesicles. But because the topography of VGCCs and their
proximity to vesicles is unknown, a quantitative understanding of the determinants
of vesicular release at nanometer scale is lacking. To investigate this, we combined
freeze-fracture replica immunogold labeling of Cav2.1 channels, local [Ca2+] imaging,
and patch pipette perfusion of EGTA at the calyx of Held. Between postnatal day
7 and 21, VGCCs formed variable sized clusters and vesicular release became less
sensitive to EGTA, whereas fixed Ca2+ buffer properties remained constant. Experimentally
constrained reaction-diffusion simulations suggest that Ca2+ sensors for vesicular
release are located at the perimeter of VGCC clusters (<30nm) and predict that
VGCC number per cluster determines vesicular release probability without altering
release time course. This "perimeter release model" provides a unifying
framework accounting for developmental changes in both synaptic efficacy and time
course.
acknowledgement: This work was supported by the Core Research for Evolutional Science
and Technology (CREST) of Japan Science and Technology Agency to T.T. and R.S.;
by the funding provided by Okinawa Institute of Science and Technology (OIST) to
T.T. and Y.N.; by JSPS Core-to-Core Program, A. Advanced Networks to T.T.; by the
Grant-in-Aid for Young Scientists from the Japanese Ministry of Education, Culture,
Sports, Science and Technology (#23700474) to Y.N.; by the Centre National de la
Recherche Scientifique through the Actions Thematiques et Initatives sur Programme,
Fondation Fyssen, Fondation pour la Recherche Medicale, Federation pour la Recherche
sur le Cerveau, Agence Nationale de la Recherche (ANR-2007-Neuro-008-01 and ANR-2010-BLAN-1411-01)
to D.D. and Y.N.; and by the European Commission Coordination Action ENINET (LSHM-CT-2005-19063)
to D.D. and R.A.S. R.A.S. and J.S.R. were funded by Wellcome Trust Senior (064413)
and Principal (095667) Research Fellowship and an ERC advance grant (294667) to
RAS.
author:
- first_name: Yukihiro
full_name: Nakamura, Yukihiro
last_name: Nakamura
- first_name: Harumi
full_name: Harada, Harumi
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Naomi
full_name: Kamasawa, Naomi
last_name: Kamasawa
- first_name: Ko
full_name: Matsui, Ko
last_name: Matsui
- first_name: Jason
full_name: Rothman, Jason
last_name: Rothman
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: R Angus
full_name: Silver, R Angus
last_name: Silver
- first_name: David
full_name: Digregorio, David
last_name: Digregorio
- first_name: Tomoyuki
full_name: Takahashi, Tomoyuki
last_name: Takahashi
citation:
ama: Nakamura Y, Harada H, Kamasawa N, et al. Nanoscale distribution of presynaptic
Ca2+ channels and its impact on vesicular release during development. Neuron.
2015;85(1):145-158. doi:10.1016/j.neuron.2014.11.019
apa: Nakamura, Y., Harada, H., Kamasawa, N., Matsui, K., Rothman, J., Shigemoto,
R., … Takahashi, T. (2015). Nanoscale distribution of presynaptic Ca2+ channels
and its impact on vesicular release during development. Neuron. Elsevier.
https://doi.org/10.1016/j.neuron.2014.11.019
chicago: Nakamura, Yukihiro, Harumi Harada, Naomi Kamasawa, Ko Matsui, Jason Rothman,
Ryuichi Shigemoto, R Angus Silver, David Digregorio, and Tomoyuki Takahashi. “Nanoscale
Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release
during Development.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2014.11.019.
ieee: Y. Nakamura et al., “Nanoscale distribution of presynaptic Ca2+ channels
and its impact on vesicular release during development,” Neuron, vol. 85,
no. 1. Elsevier, pp. 145–158, 2015.
ista: Nakamura Y, Harada H, Kamasawa N, Matsui K, Rothman J, Shigemoto R, Silver
RA, Digregorio D, Takahashi T. 2015. Nanoscale distribution of presynaptic Ca2+
channels and its impact on vesicular release during development. Neuron. 85(1),
145–158.
mla: Nakamura, Yukihiro, et al. “Nanoscale Distribution of Presynaptic Ca2+ Channels
and Its Impact on Vesicular Release during Development.” Neuron, vol. 85,
no. 1, Elsevier, 2015, pp. 145–58, doi:10.1016/j.neuron.2014.11.019.
short: Y. Nakamura, H. Harada, N. Kamasawa, K. Matsui, J. Rothman, R. Shigemoto,
R.A. Silver, D. Digregorio, T. Takahashi, Neuron 85 (2015) 145–158.
date_created: 2018-12-11T11:52:39Z
date_published: 2015-01-07T00:00:00Z
date_updated: 2021-01-12T06:51:31Z
day: '07'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1016/j.neuron.2014.11.019
file:
- access_level: open_access
checksum: 725f4d5be2dbb44b283ce722645ef37d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:47Z
date_updated: 2020-07-14T12:45:01Z
file_id: '5170'
file_name: IST-2016-482-v1+1_1-s2.0-S0896627314010472-main.pdf
file_size: 3080111
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 85'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 145 - 158
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '5625'
pubrep_id: '482'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular
release during development
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: 85
year: '2015'
...
---
_id: '1541'
abstract:
- lang: eng
text: We present XSpeed a parallel state-space exploration algorithm for continuous
systems with linear dynamics and nondeterministic inputs. The motivation of having
parallel algorithms is to exploit the computational power of multi-core processors
to speed-up performance. The parallelization is achieved on two fronts. First,
we propose a parallel implementation of the support function algorithm by sampling
functions in parallel. Second, we propose a parallel state-space exploration by
slicing the time horizon and computing the reachable states in the time slices
in parallel. The second method can be however applied only to a class of linear
systems with invertible dynamics and fixed input. A GP-GPU implementation is also
presented following a lazy evaluation strategy on support functions. The parallel
algorithms are implemented in the tool XSpeed. We evaluated the performance on
two benchmarks including an 28 dimension Helicopter model. Comparison with the
sequential counterpart shows a maximum speed-up of almost 7× on a 6 core, 12 thread
Intel Xeon CPU E5-2420 processor. Our GP-GPU implementation shows a maximum speed-up
of 12× over the sequential implementation and 53× over SpaceEx (LGG scenario),
the state of the art tool for reachability analysis of linear hybrid systems.
Experiments illustrate that our parallel algorithm with time slicing not only
speeds-up performance but also improves precision.
acknowledgement: This work was supported in part by the European Research Council
(ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants
S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).
alternative_title:
- LNCS
author:
- first_name: Rajarshi
full_name: Ray, Rajarshi
last_name: Ray
- first_name: Amit
full_name: Gurung, Amit
last_name: Gurung
- first_name: Binayak
full_name: Das, Binayak
last_name: Das
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: 'Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. XSpeed: Accelerating
reachability analysis on multi-core processors. 2015;9434:3-18. doi:10.1007/978-3-319-26287-1_1'
apa: 'Ray, R., Gurung, A., Das, B., Bartocci, E., Bogomolov, S., & Grosu, R.
(2015). XSpeed: Accelerating reachability analysis on multi-core processors. Presented
at the HVC: Haifa Verification Conference, Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-26287-1_1'
chicago: 'Ray, Rajarshi, Amit Gurung, Binayak Das, Ezio Bartocci, Sergiy Bogomolov,
and Radu Grosu. “XSpeed: Accelerating Reachability Analysis on Multi-Core Processors.”
Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-26287-1_1.'
ieee: 'R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, and R. Grosu, “XSpeed:
Accelerating reachability analysis on multi-core processors,” vol. 9434. Springer,
pp. 3–18, 2015.'
ista: 'Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. 2015. XSpeed: Accelerating
reachability analysis on multi-core processors. 9434, 3–18.'
mla: 'Ray, Rajarshi, et al. XSpeed: Accelerating Reachability Analysis on Multi-Core
Processors. Vol. 9434, Springer, 2015, pp. 3–18, doi:10.1007/978-3-319-26287-1_1.'
short: R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, R. Grosu, 9434 (2015)
3–18.
conference:
end_date: 2015-11-19
location: Haifa, Israel
name: 'HVC: Haifa Verification Conference'
start_date: 2015-11-17
date_created: 2018-12-11T11:52:37Z
date_published: 2015-11-28T00:00:00Z
date_updated: 2020-08-11T10:09:17Z
day: '28'
department:
- _id: ToHe
doi: 10.1007/978-3-319-26287-1_1
ec_funded: 1
intvolume: ' 9434'
language:
- iso: eng
month: '11'
oa_version: None
page: 3 - 18
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
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_status: published
publisher: Springer
publist_id: '5630'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: 'XSpeed: Accelerating reachability analysis on multi-core processors'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9434
year: '2015'
...
---
_id: '1543'
abstract:
- lang: eng
text: A plethora of diverse programmed cell death (PCD) processes has been described
in living organisms. In animals and plants, different forms of PCD play crucial
roles in development, immunity, and responses to the environment. While the molecular
control of some animal PCD forms such as apoptosis is known in great detail, we
still know comparatively little about the regulation of the diverse types of plant
PCD. In part, this deficiency in molecular understanding is caused by the lack
of reliable reporters to detect PCD processes. Here, we addressed this issue by
using a combination of bioinformatics approaches to identify commonly regulated
genes during diverse plant PCD processes in Arabidopsis (Arabidopsis thaliana).
Our results indicate that the transcriptional signatures of developmentally controlled
cell death are largely distinct from the ones associated with environmentally
induced cell death. Moreover, different cases of developmental PCD share a set
of cell death-associated genes. Most of these genes are evolutionary conserved
within the green plant lineage, arguing for an evolutionary conserved core machinery
of developmental PCD. Based on this information, we established an array of specific
promoter-reporter lines for developmental PCD in Arabidopsis. These PCD indicators
represent a powerful resource that can be used in addition to established morphological
and biochemical methods to detect and analyze PCD processes in vivo and in planta.
author:
- first_name: Yadira
full_name: Olvera Carrillo, Yadira
last_name: Olvera Carrillo
- first_name: Michiel
full_name: Van Bel, Michiel
last_name: Van Bel
- first_name: Tom
full_name: Van Hautegem, Tom
last_name: Van Hautegem
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Marlies
full_name: Huysmans, Marlies
last_name: Huysmans
- first_name: Mária
full_name: Šimášková, Mária
last_name: Šimášková
- first_name: Matthias
full_name: Van Durme, Matthias
last_name: Van Durme
- first_name: Pierre
full_name: Buscaill, Pierre
last_name: Buscaill
- first_name: Susana
full_name: Rivas, Susana
last_name: Rivas
- first_name: Núria
full_name: Coll, Núria
last_name: Coll
- first_name: Frederik
full_name: Coppens, Frederik
last_name: Coppens
- first_name: Steven
full_name: Maere, Steven
last_name: Maere
- first_name: Moritz
full_name: Nowack, Moritz
last_name: Nowack
citation:
ama: Olvera Carrillo Y, Van Bel M, Van Hautegem T, et al. A conserved core of programmed
cell death indicator genes discriminates developmentally and environmentally induced
programmed cell death in plants. Plant Physiology. 2015;169(4):2684-2699.
doi:10.1104/pp.15.00769
apa: Olvera Carrillo, Y., Van Bel, M., Van Hautegem, T., Fendrych, M., Huysmans,
M., Šimášková, M., … Nowack, M. (2015). A conserved core of programmed cell death
indicator genes discriminates developmentally and environmentally induced programmed
cell death in plants. Plant Physiology. American Society of Plant Biologists.
https://doi.org/10.1104/pp.15.00769
chicago: Olvera Carrillo, Yadira, Michiel Van Bel, Tom Van Hautegem, Matyas Fendrych,
Marlies Huysmans, Mária Šimášková, Matthias Van Durme, et al. “A Conserved Core
of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally
Induced Programmed Cell Death in Plants.” Plant Physiology. American Society
of Plant Biologists, 2015. https://doi.org/10.1104/pp.15.00769.
ieee: Y. Olvera Carrillo et al., “A conserved core of programmed cell death
indicator genes discriminates developmentally and environmentally induced programmed
cell death in plants,” Plant Physiology, vol. 169, no. 4. American Society
of Plant Biologists, pp. 2684–2699, 2015.
ista: Olvera Carrillo Y, Van Bel M, Van Hautegem T, Fendrych M, Huysmans M, Šimášková
M, Van Durme M, Buscaill P, Rivas S, Coll N, Coppens F, Maere S, Nowack M. 2015.
A conserved core of programmed cell death indicator genes discriminates developmentally
and environmentally induced programmed cell death in plants. Plant Physiology.
169(4), 2684–2699.
mla: Olvera Carrillo, Yadira, et al. “A Conserved Core of Programmed Cell Death
Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed
Cell Death in Plants.” Plant Physiology, vol. 169, no. 4, American Society
of Plant Biologists, 2015, pp. 2684–99, doi:10.1104/pp.15.00769.
short: Y. Olvera Carrillo, M. Van Bel, T. Van Hautegem, M. Fendrych, M. Huysmans,
M. Šimášková, M. Van Durme, P. Buscaill, S. Rivas, N. Coll, F. Coppens, S. Maere,
M. Nowack, Plant Physiology 169 (2015) 2684–2699.
date_created: 2018-12-11T11:52:38Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T06:51:30Z
day: '01'
department:
- _id: JiFr
doi: 10.1104/pp.15.00769
intvolume: ' 169'
issue: '4'
language:
- iso: eng
month: '12'
oa_version: None
page: 2684 - 2699
publication: Plant Physiology
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '5628'
scopus_import: 1
status: public
title: A conserved core of programmed cell death indicator genes discriminates developmentally
and environmentally induced programmed cell death in plants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 169
year: '2015'
...
---
_id: '1544'
abstract:
- lang: eng
text: 'Cell division in prokaryotes and eukaryotes is commonly initiated by the
well-controlled binding of proteins to the cytoplasmic side of the cell membrane.
However, a precise characterization of the spatiotemporal dynamics of membrane-bound
proteins is often difficult to achieve in vivo. Here, we present protocols for
the use of supported lipid bilayers to rebuild the cytokinetic machineries of
cells with greatly different dimensions: the bacterium Escherichia coli and eggs
of the vertebrate Xenopus laevis. Combined with total internal reflection fluorescence
microscopy, these experimental setups allow for precise quantitative analyses
of membrane-bound proteins. The protocols described to obtain glass-supported
membranes from bacterial and vertebrate lipids can be used as starting points
for other reconstitution experiments. We believe that similar biochemical assays
will be instrumental to study the biochemistry and biophysics underlying a variety
of complex cellular tasks, such as signaling, vesicle trafficking, and cell motility.'
author:
- first_name: Phuong
full_name: Nguyen, Phuong
last_name: Nguyen
- first_name: Christine
full_name: Field, Christine
last_name: Field
- first_name: Aaron
full_name: Groen, Aaron
last_name: Groen
- first_name: Timothy
full_name: Mitchison, Timothy
last_name: Mitchison
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: 'Nguyen P, Field C, Groen A, Mitchison T, Loose M. Using supported bilayers
to study the spatiotemporal organization of membrane-bound proteins. In: Building
a Cell from Its Components Parts. Vol 128. Academic Press; 2015:223-241. doi:10.1016/bs.mcb.2015.01.007'
apa: Nguyen, P., Field, C., Groen, A., Mitchison, T., & Loose, M. (2015). Using
supported bilayers to study the spatiotemporal organization of membrane-bound
proteins. In Building a Cell from its Components Parts (Vol. 128, pp. 223–241).
Academic Press. https://doi.org/10.1016/bs.mcb.2015.01.007
chicago: Nguyen, Phuong, Christine Field, Aaron Groen, Timothy Mitchison, and Martin
Loose. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound
Proteins.” In Building a Cell from Its Components Parts, 128:223–41. Academic
Press, 2015. https://doi.org/10.1016/bs.mcb.2015.01.007.
ieee: P. Nguyen, C. Field, A. Groen, T. Mitchison, and M. Loose, “Using supported
bilayers to study the spatiotemporal organization of membrane-bound proteins,”
in Building a Cell from its Components Parts, vol. 128, Academic Press,
2015, pp. 223–241.
ista: 'Nguyen P, Field C, Groen A, Mitchison T, Loose M. 2015.Using supported bilayers
to study the spatiotemporal organization of membrane-bound proteins. In: Building
a Cell from its Components Parts. vol. 128, 223–241.'
mla: Nguyen, Phuong, et al. “Using Supported Bilayers to Study the Spatiotemporal
Organization of Membrane-Bound Proteins.” Building a Cell from Its Components
Parts, vol. 128, Academic Press, 2015, pp. 223–41, doi:10.1016/bs.mcb.2015.01.007.
short: P. Nguyen, C. Field, A. Groen, T. Mitchison, M. Loose, in:, Building a Cell
from Its Components Parts, Academic Press, 2015, pp. 223–241.
date_created: 2018-12-11T11:52:38Z
date_published: 2015-04-08T00:00:00Z
date_updated: 2021-01-12T06:51:30Z
day: '08'
department:
- _id: MaLo
doi: 10.1016/bs.mcb.2015.01.007
external_id:
pmid:
- '25997350'
intvolume: ' 128'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578691/
month: '04'
oa: 1
oa_version: Submitted Version
page: 223 - 241
pmid: 1
publication: Building a Cell from its Components Parts
publication_status: published
publisher: Academic Press
publist_id: '5627'
quality_controlled: '1'
scopus_import: 1
status: public
title: Using supported bilayers to study the spatiotemporal organization of membrane-bound
proteins
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 128
year: '2015'
...
---
_id: '1540'
abstract:
- lang: eng
text: 'Plant sexual reproduction involves highly structured and specialized organs:
stamens (male) and gynoecia (female, containing ovules). These organs synchronously
develop within protective flower buds, until anthesis, via tightly coordinated
mechanisms that are essential for effective fertilization and production of viable
seeds. The phytohormone auxin is one of the key endogenous signalling molecules
controlling initiation and development of these, and other, plant organs. In particular,
its uneven distribution, resulting from tightly controlled production, metabolism
and directional transport, is an important morphogenic factor. In this review
we discuss how developmentally controlled and localized auxin biosynthesis and
transport contribute to the coordinated development of plants'' reproductive organs,
and their fertilized derivatives (embryos) via the regulation of auxin levels
and distribution within and around them. Current understanding of the links between
de novo local auxin biosynthesis, auxin transport and/or signalling is presented
to highlight the importance of the non-cell autonomous action of auxin production
on development and morphogenesis of reproductive organs and embryos. An overview
of transcription factor families, which spatiotemporally define local auxin production
by controlling key auxin biosynthetic enzymes, is also presented.'
acknowledgement: 'The work was supported by grants from: the Employment of Best Young
Scientists for International Cooperation Empowerment/OPVKII programme (CZ.1.07/2.3.00/30.0037)
to HSR and LCK; the Czech Science Foundation (GA13-39982S) to EB, LCK and SM; and
the SoMoPro II programme (3SGA5602), cofinanced by the South-Moravian Region and
the EU (FP7/2007–2013 People Programme), to HSR.'
author:
- first_name: Hélène
full_name: Robert, Hélène
last_name: Robert
- first_name: Lucie
full_name: Crhák Khaitová, Lucie
last_name: Crhák Khaitová
- first_name: Souad
full_name: Mroue, Souad
last_name: Mroue
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Robert H, Crhák Khaitová L, Mroue S, Benková E. The importance of localized
auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis.
Journal of Experimental Botany. 2015;66(16):5029-5042. doi:10.1093/jxb/erv256
apa: Robert, H., Crhák Khaitová, L., Mroue, S., & Benková, E. (2015). The importance
of localized auxin production for morphogenesis of reproductive organs and embryos
in Arabidopsis. Journal of Experimental Botany. Oxford University Press.
https://doi.org/10.1093/jxb/erv256
chicago: Robert, Hélène, Lucie Crhák Khaitová, Souad Mroue, and Eva Benková. “The
Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs
and Embryos in Arabidopsis.” Journal of Experimental Botany. Oxford University
Press, 2015. https://doi.org/10.1093/jxb/erv256.
ieee: H. Robert, L. Crhák Khaitová, S. Mroue, and E. Benková, “The importance of
localized auxin production for morphogenesis of reproductive organs and embryos
in Arabidopsis,” Journal of Experimental Botany, vol. 66, no. 16. Oxford
University Press, pp. 5029–5042, 2015.
ista: Robert H, Crhák Khaitová L, Mroue S, Benková E. 2015. The importance of localized
auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis.
Journal of Experimental Botany. 66(16), 5029–5042.
mla: Robert, Hélène, et al. “The Importance of Localized Auxin Production for Morphogenesis
of Reproductive Organs and Embryos in Arabidopsis.” Journal of Experimental
Botany, vol. 66, no. 16, Oxford University Press, 2015, pp. 5029–42, doi:10.1093/jxb/erv256.
short: H. Robert, L. Crhák Khaitová, S. Mroue, E. Benková, Journal of Experimental
Botany 66 (2015) 5029–5042.
date_created: 2018-12-11T11:52:36Z
date_published: 2015-05-05T00:00:00Z
date_updated: 2021-01-12T06:51:29Z
day: '05'
department:
- _id: EvBe
doi: 10.1093/jxb/erv256
intvolume: ' 66'
issue: '16'
language:
- iso: eng
month: '05'
oa_version: None
page: 5029 - 5042
publication: Journal of Experimental Botany
publication_status: published
publisher: Oxford University Press
publist_id: '5631'
quality_controlled: '1'
scopus_import: 1
status: public
title: The importance of localized auxin production for morphogenesis of reproductive
organs and embryos in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 66
year: '2015'
...
---
_id: '1551'
abstract:
- lang: eng
text: 'Reciprocal coevolution between host and pathogen is widely seen as a major
driver of evolution and biological innovation. Yet, to date, the underlying genetic
mechanisms and associated trait functions that are unique to rapid coevolutionary
change are generally unknown. We here combined experimental evolution of the bacterial
biocontrol agent Bacillus thuringiensis and its nematode host Caenorhabditis elegans
with large-scale phenotyping, whole genome analysis, and functional genetics to
demonstrate the selective benefit of pathogen virulence and the underlying toxin
genes during the adaptation process. We show that: (i) high virulence was specifically
favoured during pathogen–host coevolution rather than pathogen one-sided adaptation
to a nonchanging host or to an environment without host; (ii) the pathogen genotype
BT-679 with known nematocidal toxin genes and high virulence specifically swept
to fixation in all of the independent replicate populations under coevolution
but only some under one-sided adaptation; (iii) high virulence in the BT-679-dominated
populations correlated with elevated copy numbers of the plasmid containing the
nematocidal toxin genes; (iv) loss of virulence in a toxin-plasmid lacking BT-679
isolate was reconstituted by genetic reintroduction or external addition of the
toxins.We conclude that sustained coevolution is distinct from unidirectional
selection in shaping the pathogen''s genome and life history characteristics.
To our knowledge, this study is the first to characterize the pathogen genes involved
in coevolutionary adaptation in an animal host–pathogen interaction system.'
acknowledgement: We are very grateful for funding from the German Science Foundation
(DFG) to HS (SCHU 1415/8, SCHU 1415/9), PR (RO 2994/3), EBB (BO 2544/7), HL (LI
1690/2), AT (TE 976/2), RDS (SCHU 2522/1), JK (KU 1929/4); from the Kiel Excellence
Cluster Inflammation at Interfaces to HS and PR; and from the ISTFELLOW program
(Co-fund Marie Curie Actions of the European Commission) to LM.
author:
- first_name: Leila
full_name: El Masri, Leila
id: 349A6E66-F248-11E8-B48F-1D18A9856A87
last_name: El Masri
- first_name: Antoine
full_name: Branca, Antoine
last_name: Branca
- first_name: Anna
full_name: Sheppard, Anna
last_name: Sheppard
- first_name: Andrei
full_name: Papkou, Andrei
last_name: Papkou
- first_name: David
full_name: Laehnemann, David
last_name: Laehnemann
- first_name: Patrick
full_name: Guenther, Patrick
last_name: Guenther
- first_name: Swantje
full_name: Prahl, Swantje
last_name: Prahl
- first_name: Manja
full_name: Saebelfeld, Manja
last_name: Saebelfeld
- first_name: Jacqueline
full_name: Hollensteiner, Jacqueline
last_name: Hollensteiner
- first_name: Heiko
full_name: Liesegang, Heiko
last_name: Liesegang
- first_name: Elzbieta
full_name: Brzuszkiewicz, Elzbieta
last_name: Brzuszkiewicz
- first_name: Rolf
full_name: Daniel, Rolf
last_name: Daniel
- first_name: Nico
full_name: Michiels, Nico
last_name: Michiels
- first_name: Rebecca
full_name: Schulte, Rebecca
last_name: Schulte
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
- first_name: Philip
full_name: Rosenstiel, Philip
last_name: Rosenstiel
- first_name: Arndt
full_name: Telschow, Arndt
last_name: Telschow
- first_name: Erich
full_name: Bornberg Bauer, Erich
last_name: Bornberg Bauer
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
citation:
ama: 'El Masri L, Branca A, Sheppard A, et al. Host–pathogen coevolution: The selective
advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS
Biology. 2015;13(6):1-30. doi:10.1371/journal.pbio.1002169'
apa: 'El Masri, L., Branca, A., Sheppard, A., Papkou, A., Laehnemann, D., Guenther,
P., … Schulenburg, H. (2015). Host–pathogen coevolution: The selective advantage
of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology.
Public Library of Science. https://doi.org/10.1371/journal.pbio.1002169'
chicago: 'El Masri, Leila, Antoine Branca, Anna Sheppard, Andrei Papkou, David Laehnemann,
Patrick Guenther, Swantje Prahl, et al. “Host–Pathogen Coevolution: The Selective
Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS
Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002169.'
ieee: 'L. El Masri et al., “Host–pathogen coevolution: The selective advantage
of Bacillus thuringiensis virulence and its cry toxin genes,” PLoS Biology,
vol. 13, no. 6. Public Library of Science, pp. 1–30, 2015.'
ista: 'El Masri L, Branca A, Sheppard A, Papkou A, Laehnemann D, Guenther P, Prahl
S, Saebelfeld M, Hollensteiner J, Liesegang H, Brzuszkiewicz E, Daniel R, Michiels
N, Schulte R, Kurtz J, Rosenstiel P, Telschow A, Bornberg Bauer E, Schulenburg
H. 2015. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis
virulence and its cry toxin genes. PLoS Biology. 13(6), 1–30.'
mla: 'El Masri, Leila, et al. “Host–Pathogen Coevolution: The Selective Advantage
of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS Biology,
vol. 13, no. 6, Public Library of Science, 2015, pp. 1–30, doi:10.1371/journal.pbio.1002169.'
short: L. El Masri, A. Branca, A. Sheppard, A. Papkou, D. Laehnemann, P. Guenther,
S. Prahl, M. Saebelfeld, J. Hollensteiner, H. Liesegang, E. Brzuszkiewicz, R.
Daniel, N. Michiels, R. Schulte, J. Kurtz, P. Rosenstiel, A. Telschow, E. Bornberg
Bauer, H. Schulenburg, PLoS Biology 13 (2015) 1–30.
date_created: 2018-12-11T11:52:40Z
date_published: 2015-06-04T00:00:00Z
date_updated: 2021-01-12T06:51:33Z
day: '04'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1371/journal.pbio.1002169
ec_funded: 1
file:
- access_level: open_access
checksum: 30dee7a2c11ed09f2f5634655c0146f8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:13Z
date_updated: 2020-07-14T12:45:02Z
file_id: '5063'
file_name: IST-2016-481-v1+1_journal.pbio.1002169.pdf
file_size: 3468956
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1 - 30
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5620'
pubrep_id: '481'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis
virulence and its cry toxin genes'
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: 13
year: '2015'
...
---
_id: '1549'
abstract:
- lang: eng
text: Nature has incorporated small photochromic molecules, colloquially termed
'photoswitches', in photoreceptor proteins to sense optical cues in photo-taxis
and vision. While Nature's ability to employ light-responsive functionalities
has long been recognized, it was not until recently that scientists designed,
synthesized and applied synthetic photochromes to manipulate many of which open
rapidly and locally in their native cell types, biological processes with the
temporal and spatial resolution of light. Ion channels in particular have come
to the forefront of proteins that can be put under the designer control of synthetic
photochromes. Photochromic ion channel controllers are comprised of three classes,
photochromic soluble ligands (PCLs), photochromic tethered ligands (PTLs) and
photochromic crosslinkers (PXs), and in each class ion channel functionality is
controlled through reversible changes in photochrome structure. By acting as light-dependent
ion channel agonists, antagonist or modulators, photochromic controllers effectively
converted a wide range of ion channels, including voltage-gated ion channels,
'leak channels', tri-, tetra- and pentameric ligand-gated ion channels, and temperaturesensitive
ion channels, into man-made photoreceptors. Control by photochromes can be reversible,
unlike in the case of 'caged' compounds, and non-invasive with high spatial precision,
unlike pharmacology and electrical manipulation. Here, we introduce design principles
of emerging photochromic molecules that act on ion channels and discuss the impact
that these molecules are beginning to have on ion channel biophysics and neuronal
physiology.
author:
- first_name: Catherine
full_name: Mckenzie, Catherine
id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87
last_name: Mckenzie
- first_name: Inmaculada
full_name: Sanchez Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez Romero
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: 'Mckenzie C, Sanchez-Romero I, Janovjak HL. Flipping the photoswitch: Ion channels
under light control. In: Novel Chemical Tools to Study Ion Channel Biology.
Vol 869. Advances in Experimental Medicine and Biology. Springer; 2015:101-117.
doi:10.1007/978-1-4939-2845-3_6'
apa: 'Mckenzie, C., Sanchez-Romero, I., & Janovjak, H. L. (2015). Flipping the
photoswitch: Ion channels under light control. In Novel chemical tools to study
ion channel biology (Vol. 869, pp. 101–117). Springer. https://doi.org/10.1007/978-1-4939-2845-3_6'
chicago: 'Mckenzie, Catherine, Inmaculada Sanchez-Romero, and Harald L Janovjak.
“Flipping the Photoswitch: Ion Channels under Light Control.” In Novel Chemical
Tools to Study Ion Channel Biology, 869:101–17. Advances in Experimental Medicine
and Biology. Springer, 2015. https://doi.org/10.1007/978-1-4939-2845-3_6.'
ieee: 'C. Mckenzie, I. Sanchez-Romero, and H. L. Janovjak, “Flipping the photoswitch:
Ion channels under light control,” in Novel chemical tools to study ion channel
biology, vol. 869, Springer, 2015, pp. 101–117.'
ista: 'Mckenzie C, Sanchez-Romero I, Janovjak HL. 2015.Flipping the photoswitch:
Ion channels under light control. In: Novel chemical tools to study ion channel
biology. vol. 869, 101–117.'
mla: 'Mckenzie, Catherine, et al. “Flipping the Photoswitch: Ion Channels under
Light Control.” Novel Chemical Tools to Study Ion Channel Biology, vol.
869, Springer, 2015, pp. 101–17, doi:10.1007/978-1-4939-2845-3_6.'
short: C. Mckenzie, I. Sanchez-Romero, H.L. Janovjak, in:, Novel Chemical Tools
to Study Ion Channel Biology, Springer, 2015, pp. 101–117.
date_created: 2018-12-11T11:52:39Z
date_published: 2015-09-18T00:00:00Z
date_updated: 2021-01-12T06:51:32Z
day: '18'
ddc:
- '571'
- '576'
department:
- _id: HaJa
doi: 10.1007/978-1-4939-2845-3_6
file:
- access_level: open_access
checksum: bd1bfdf2423a0c3b6e7cabfa8b44bc0f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:02Z
date_updated: 2020-07-14T12:45:01Z
file_id: '4854'
file_name: IST-2017-839-v1+1_mckenzie.pdf
file_size: 1919655
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 869'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 101 - 117
publication: Novel chemical tools to study ion channel biology
publication_identifier:
isbn:
- 978-1-4939-2844-6
publication_status: published
publisher: Springer
publist_id: '5622'
pubrep_id: '839'
quality_controlled: '1'
scopus_import: 1
series_title: Advances in Experimental Medicine and Biology
status: public
title: 'Flipping the photoswitch: Ion channels under light control'
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 869
year: '2015'
...
---
_id: '1548'
abstract:
- lang: eng
text: Reproduction within a host and transmission to the next host are crucial for
the virulence and fitness of pathogens. Nevertheless, basic knowledge about such
parameters is often missing from the literature, even for well-studied bacteria,
such as Bacillus thuringiensis, an endospore-forming insect pathogen, which infects
its hosts via the oral route. To characterize bacterial replication success, we
made use of an experimental oral infection system for the red flour beetle Tribolium
castaneum and developed a flow cytometric assay for the quantification of both
spore ingestion by the individual beetle larvae and the resulting spore load after
bacterial replication and resporulation within cadavers. On average, spore numbers
increased 460-fold, showing that Bacillus thuringiensis grows and replicates successfully
in insect cadavers. By inoculating cadaver-derived spores and spores from bacterial
stock cultures into nutrient medium, we next investigated outgrowth characteristics
of vegetative cells and found that cadaver- derived bacteria showed reduced growth
compared to bacteria from the stock cultures. Interestingly, this reduced growth
was a consequence of inhibited spore germination, probably originating from the
host and resulting in reduced host mortality in subsequent infections by cadaver-derived
spores. Nevertheless, we further showed that Bacillus thuringiensis transmission
was possible via larval cannibalism when no other food was offered. These results
contribute to our understanding of the ecology of Bacillus thuringiensis as an
insect pathogen.
author:
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Christina
full_name: Höfling, Christina
last_name: Höfling
- first_name: Momir
full_name: Futo, Momir
last_name: Futo
- first_name: Jörn
full_name: Scharsack, Jörn
last_name: Scharsack
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
citation:
ama: 'Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. Infection of Tribolium
castaneum with Bacillus thuringiensis: Quantification of bacterial replication
within cadavers, transmission via cannibalism, and inhibition of spore germination.
Applied and Environmental Microbiology. 2015;81(23):8135-8144. doi:10.1128/AEM.02051-15'
apa: 'Milutinovic, B., Höfling, C., Futo, M., Scharsack, J., & Kurtz, J. (2015).
Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of
bacterial replication within cadavers, transmission via cannibalism, and inhibition
of spore germination. Applied and Environmental Microbiology. American
Society for Microbiology. https://doi.org/10.1128/AEM.02051-15'
chicago: 'Milutinovic, Barbara, Christina Höfling, Momir Futo, Jörn Scharsack, and
Joachim Kurtz. “Infection of Tribolium Castaneum with Bacillus Thuringiensis:
Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism,
and Inhibition of Spore Germination.” Applied and Environmental Microbiology.
American Society for Microbiology, 2015. https://doi.org/10.1128/AEM.02051-15.'
ieee: 'B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, and J. Kurtz, “Infection
of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial
replication within cadavers, transmission via cannibalism, and inhibition of spore
germination,” Applied and Environmental Microbiology, vol. 81, no. 23.
American Society for Microbiology, pp. 8135–8144, 2015.'
ista: 'Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. 2015. Infection of
Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication
within cadavers, transmission via cannibalism, and inhibition of spore germination.
Applied and Environmental Microbiology. 81(23), 8135–8144.'
mla: 'Milutinovic, Barbara, et al. “Infection of Tribolium Castaneum with Bacillus
Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission
via Cannibalism, and Inhibition of Spore Germination.” Applied and Environmental
Microbiology, vol. 81, no. 23, American Society for Microbiology, 2015, pp.
8135–44, doi:10.1128/AEM.02051-15.'
short: B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, J. Kurtz, Applied and
Environmental Microbiology 81 (2015) 8135–8144.
date_created: 2018-12-11T11:52:39Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T06:51:31Z
day: '01'
department:
- _id: SyCr
doi: 10.1128/AEM.02051-15
external_id:
pmid:
- '26386058'
intvolume: ' 81'
issue: '23'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4651099/
month: '12'
oa: 1
oa_version: Submitted Version
page: 8135 - 8144
pmid: 1
publication: Applied and Environmental Microbiology
publication_status: published
publisher: American Society for Microbiology
publist_id: '5623'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification
of bacterial replication within cadavers, transmission via cannibalism, and inhibition
of spore germination'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 81
year: '2015'
...
---
_id: '1553'
abstract:
- lang: eng
text: Cell movement has essential functions in development, immunity, and cancer.
Various cell migration patterns have been reported, but no general rule has emerged
so far. Here, we show on the basis of experimental data in vitro and in vivo that
cell persistence, which quantifies the straightness of trajectories, is robustly
coupled to cell migration speed. We suggest that this universal coupling constitutes
a generic law of cell migration, which originates in the advection of polarity
cues by an actin cytoskeleton undergoing flows at the cellular scale. Our analysis
relies on a theoretical model that we validate by measuring the persistence of
cells upon modulation of actin flow speeds and upon optogenetic manipulation of
the binding of an actin regulator to actin filaments. Beyond the quantitative
prediction of the coupling, the model yields a generic phase diagram of cellular
trajectories, which recapitulates the full range of observed migration patterns.
author:
- first_name: Paolo
full_name: Maiuri, Paolo
last_name: Maiuri
- first_name: Jean
full_name: Rupprecht, Jean
last_name: Rupprecht
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Olivier
full_name: Bénichou, Olivier
last_name: Bénichou
- first_name: Nicolas
full_name: Carpi, Nicolas
last_name: Carpi
- first_name: Mathieu
full_name: Coppey, Mathieu
last_name: Coppey
- first_name: Simon
full_name: De Beco, Simon
last_name: De Beco
- first_name: Nir
full_name: Gov, Nir
last_name: Gov
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Carolina
full_name: Lage Crespo, Carolina
last_name: Lage Crespo
- first_name: Franziska
full_name: Lautenschlaeger, Franziska
last_name: Lautenschlaeger
- first_name: Maël
full_name: Le Berre, Maël
last_name: Le Berre
- first_name: Ana
full_name: Lennon Duménil, Ana
last_name: Lennon Duménil
- first_name: Matthew
full_name: Raab, Matthew
last_name: Raab
- first_name: Hawa
full_name: Thiam, Hawa
last_name: Thiam
- first_name: Matthieu
full_name: Piel, Matthieu
last_name: Piel
- 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: Raphaël
full_name: Voituriez, Raphaël
last_name: Voituriez
citation:
ama: Maiuri P, Rupprecht J, Wieser S, et al. Actin flows mediate a universal coupling
between cell speed and cell persistence. Cell. 2015;161(2):374-386. doi:10.1016/j.cell.2015.01.056
apa: Maiuri, P., Rupprecht, J., Wieser, S., Ruprecht, V., Bénichou, O., Carpi, N.,
… Voituriez, R. (2015). Actin flows mediate a universal coupling between cell
speed and cell persistence. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.01.056
chicago: Maiuri, Paolo, Jean Rupprecht, Stefan Wieser, Verena Ruprecht, Olivier
Bénichou, Nicolas Carpi, Mathieu Coppey, et al. “Actin Flows Mediate a Universal
Coupling between Cell Speed and Cell Persistence.” Cell. Cell Press, 2015.
https://doi.org/10.1016/j.cell.2015.01.056.
ieee: P. Maiuri et al., “Actin flows mediate a universal coupling between
cell speed and cell persistence,” Cell, vol. 161, no. 2. Cell Press, pp.
374–386, 2015.
ista: Maiuri P, Rupprecht J, Wieser S, Ruprecht V, Bénichou O, Carpi N, Coppey M,
De Beco S, Gov N, Heisenberg C-PJ, Lage Crespo C, Lautenschlaeger F, Le Berre
M, Lennon Duménil A, Raab M, Thiam H, Piel M, Sixt MK, Voituriez R. 2015. Actin
flows mediate a universal coupling between cell speed and cell persistence. Cell.
161(2), 374–386.
mla: Maiuri, Paolo, et al. “Actin Flows Mediate a Universal Coupling between Cell
Speed and Cell Persistence.” Cell, vol. 161, no. 2, Cell Press, 2015, pp.
374–86, doi:10.1016/j.cell.2015.01.056.
short: P. Maiuri, J. Rupprecht, S. Wieser, V. Ruprecht, O. Bénichou, N. Carpi, M.
Coppey, S. De Beco, N. Gov, C.-P.J. Heisenberg, C. Lage Crespo, F. Lautenschlaeger,
M. Le Berre, A. Lennon Duménil, M. Raab, H. Thiam, M. Piel, M.K. Sixt, R. Voituriez,
Cell 161 (2015) 374–386.
date_created: 2018-12-11T11:52:41Z
date_published: 2015-04-09T00:00:00Z
date_updated: 2021-01-12T06:51:33Z
day: '09'
department:
- _id: MiSi
- _id: CaHe
doi: 10.1016/j.cell.2015.01.056
ec_funded: 1
intvolume: ' 161'
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
page: 374 - 386
project:
- _id: 2529486C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T 560-B17
name: Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
- _id: 25ABD200-B435-11E9-9278-68D0E5697425
grant_number: RGP0058/2011
name: 'Cell migration in complex environments: from in vivo experiments to theoretical
models'
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '5618'
quality_controlled: '1'
scopus_import: 1
status: public
title: Actin flows mediate a universal coupling between cell speed and cell persistence
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 161
year: '2015'
...
---
_id: '1550'
abstract:
- lang: eng
text: The medial ganglionic eminence (MGE) gives rise to the majority of mouse forebrain
interneurons. Here, we examine the lineage relationship among MGE-derived interneurons
using a replication-defective retroviral library containing a highly diverse set
of DNA barcodes. Recovering the barcodes from the mature progeny of infected progenitor
cells enabled us to unambiguously determine their respective lineal relationship.
We found that clonal dispersion occurs across large areas of the brain and is
not restricted by anatomical divisions. As such, sibling interneurons can populate
the cortex, hippocampus striatum, and globus pallidus. The majority of interneurons
appeared to be generated from asymmetric divisions of MGE progenitor cells, followed
by symmetric divisions within the subventricular zone. Altogether, our findings
uncover that lineage relationships do not appear to determine interneuron allocation
to particular regions. As such, it is likely that clonally related interneurons
have considerable flexibility as to the particular forebrain circuits to which
they can contribute.
acknowledgement: "Research in the G.F. laboratory is supported by NIH (NS 081297,
MH095147, and P01NS074972) and the Simons Foundation. Research in the S.H. laboratory
is supported by the European Union (FP7-CIG618444). C.M. is supported by EMBO ALTF
(1295-2012). X.H.J. is supported by EMBO (ALTF 303-2010) and HFSP (LT000078/2011-L).\r\n\r\n"
author:
- first_name: Christian
full_name: Mayer, Christian
last_name: Mayer
- first_name: Xavier
full_name: Jaglin, Xavier
last_name: Jaglin
- first_name: Lucy
full_name: Cobbs, Lucy
last_name: Cobbs
- first_name: Rachel
full_name: Bandler, Rachel
last_name: Bandler
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Constance
full_name: Cepko, Constance
last_name: Cepko
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Gord
full_name: Fishell, Gord
last_name: Fishell
citation:
ama: Mayer C, Jaglin X, Cobbs L, et al. Clonally related forebrain interneurons
disperse broadly across both functional areas and structural boundaries. Neuron.
2015;87(5):989-998. doi:10.1016/j.neuron.2015.07.011
apa: Mayer, C., Jaglin, X., Cobbs, L., Bandler, R., Streicher, C., Cepko, C., …
Fishell, G. (2015). Clonally related forebrain interneurons disperse broadly across
both functional areas and structural boundaries. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2015.07.011
chicago: Mayer, Christian, Xavier Jaglin, Lucy Cobbs, Rachel Bandler, Carmen Streicher,
Constance Cepko, Simon Hippenmeyer, and Gord Fishell. “Clonally Related Forebrain
Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.”
Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2015.07.011.
ieee: C. Mayer et al., “Clonally related forebrain interneurons disperse
broadly across both functional areas and structural boundaries,” Neuron,
vol. 87, no. 5. Elsevier, pp. 989–998, 2015.
ista: Mayer C, Jaglin X, Cobbs L, Bandler R, Streicher C, Cepko C, Hippenmeyer S,
Fishell G. 2015. Clonally related forebrain interneurons disperse broadly across
both functional areas and structural boundaries. Neuron. 87(5), 989–998.
mla: Mayer, Christian, et al. “Clonally Related Forebrain Interneurons Disperse
Broadly across Both Functional Areas and Structural Boundaries.” Neuron,
vol. 87, no. 5, Elsevier, 2015, pp. 989–98, doi:10.1016/j.neuron.2015.07.011.
short: C. Mayer, X. Jaglin, L. Cobbs, R. Bandler, C. Streicher, C. Cepko, S. Hippenmeyer,
G. Fishell, Neuron 87 (2015) 989–998.
date_created: 2018-12-11T11:52:40Z
date_published: 2015-09-02T00:00:00Z
date_updated: 2021-01-12T06:51:32Z
day: '02'
department:
- _id: SiHi
doi: 10.1016/j.neuron.2015.07.011
external_id:
pmid:
- '26299473'
intvolume: ' 87'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560602/
month: '09'
oa: 1
oa_version: Submitted Version
page: 989 - 998
pmid: 1
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '5621'
quality_controlled: '1'
scopus_import: 1
status: public
title: Clonally related forebrain interneurons disperse broadly across both functional
areas and structural boundaries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2015'
...
---
_id: '1547'
abstract:
- lang: eng
text: Let G be a graph on the vertex set V(G) = {x1,…,xn} with the edge set E(G),
and let R = K[x1,…, xn] be the polynomial ring over a field K. Two monomial ideals
are associated to G, the edge ideal I(G) generated by all monomials xixj with
{xi,xj} ∈ E(G), and the vertex cover ideal IG generated by monomials ∏xi∈Cxi for
all minimal vertex covers C of G. A minimal vertex cover of G is a subset C ⊂
V(G) such that each edge has at least one vertex in C and no proper subset of
C has the same property. Indeed, the vertex cover ideal of G is the Alexander
dual of the edge ideal of G. In this paper, for an unmixed bipartite graph G we
consider the lattice of vertex covers LG and we explicitly describe the minimal
free resolution of the ideal associated to LG which is exactly the vertex cover
ideal of G. Then we compute depth, projective dimension, regularity and extremal
Betti numbers of R/I(G) in terms of the associated lattice.
author:
- first_name: Fatemeh
full_name: Mohammadi, Fatemeh
id: 2C29581E-F248-11E8-B48F-1D18A9856A87
last_name: Mohammadi
- first_name: Somayeh
full_name: Moradi, Somayeh
last_name: Moradi
citation:
ama: Mohammadi F, Moradi S. Resolution of unmixed bipartite graphs. Bulletin
of the Korean Mathematical Society. 2015;52(3):977-986. doi:10.4134/BKMS.2015.52.3.977
apa: Mohammadi, F., & Moradi, S. (2015). Resolution of unmixed bipartite graphs.
Bulletin of the Korean Mathematical Society. Korean Mathematical Society.
https://doi.org/10.4134/BKMS.2015.52.3.977
chicago: Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite
Graphs.” Bulletin of the Korean Mathematical Society. Korean Mathematical
Society, 2015. https://doi.org/10.4134/BKMS.2015.52.3.977.
ieee: F. Mohammadi and S. Moradi, “Resolution of unmixed bipartite graphs,” Bulletin
of the Korean Mathematical Society, vol. 52, no. 3. Korean Mathematical Society,
pp. 977–986, 2015.
ista: Mohammadi F, Moradi S. 2015. Resolution of unmixed bipartite graphs. Bulletin
of the Korean Mathematical Society. 52(3), 977–986.
mla: Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.”
Bulletin of the Korean Mathematical Society, vol. 52, no. 3, Korean Mathematical
Society, 2015, pp. 977–86, doi:10.4134/BKMS.2015.52.3.977.
short: F. Mohammadi, S. Moradi, Bulletin of the Korean Mathematical Society 52 (2015)
977–986.
date_created: 2018-12-11T11:52:39Z
date_published: 2015-05-31T00:00:00Z
date_updated: 2021-01-12T06:51:31Z
day: '31'
department:
- _id: CaUh
doi: 10.4134/BKMS.2015.52.3.977
intvolume: ' 52'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0901.3015
month: '05'
oa: 1
oa_version: Preprint
page: 977 - 986
publication: Bulletin of the Korean Mathematical Society
publication_identifier:
eissn:
- 2234-3016
publication_status: published
publisher: Korean Mathematical Society
publist_id: '5624'
quality_controlled: '1'
scopus_import: 1
status: public
title: Resolution of unmixed bipartite graphs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2015'
...
---
_id: '1556'
abstract:
- lang: eng
text: The elongator complex subunit 2 (ELP2) protein, one subunit of an evolutionarily
conserved histone acetyltransferase complex, has been shown to participate in
leaf patterning, plant immune and abiotic stress responses in Arabidopsis thaliana.
Here, its role in root development was explored. Compared to the wild type, the
elp2 mutant exhibited an accelerated differentiation of its root stem cells and
cell division was more active in its quiescent centre (QC). The key transcription
factors responsible for maintaining root stem cell and QC identity, such as AP2
transcription factors PLT1 (PLETHORA1) and PLT2 (PLETHORA2), GRAS transcription
factors such as SCR (SCARECROW) and SHR (SHORT ROOT) and WUSCHEL-RELATED HOMEOBOX5
transcription factor WOX5, were all strongly down-regulated in the mutant. On
the other hand, expression of the G2/M transition activator CYCB1 was substantially
induced in elp2. The auxin efflux transporters PIN1 and PIN2 showed decreased
protein levels and PIN1 also displayed mild polarity alterations in elp2, which
resulted in a reduced auxin content in the root tip. Either the acetylation or
methylation level of each of these genes differed between the mutant and the wild
type, suggesting that the ELP2 regulation of root development involves the epigenetic
modification of a range of transcription factors and other developmental regulators.
author:
- first_name: Yuebin
full_name: Jia, Yuebin
last_name: Jia
- first_name: Huiyu
full_name: Tian, Huiyu
last_name: Tian
- first_name: Hongjiang
full_name: Li, Hongjiang
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Qianqian
full_name: Yu, Qianqian
last_name: Yu
- first_name: Lei
full_name: Wang, Lei
last_name: Wang
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Zhaojun
full_name: Ding, Zhaojun
last_name: Ding
citation:
ama: Jia Y, Tian H, Li H, et al. The Arabidopsis thaliana elongator complex subunit
2 epigenetically affects root development. Journal of Experimental Botany.
2015;66(15):4631-4642. doi:10.1093/jxb/erv230
apa: Jia, Y., Tian, H., Li, H., Yu, Q., Wang, L., Friml, J., & Ding, Z. (2015).
The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root
development. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv230
chicago: Jia, Yuebin, Huiyu Tian, Hongjiang Li, Qianqian Yu, Lei Wang, Jiří Friml,
and Zhaojun Ding. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically
Affects Root Development.” Journal of Experimental Botany. Oxford University
Press, 2015. https://doi.org/10.1093/jxb/erv230.
ieee: Y. Jia et al., “The Arabidopsis thaliana elongator complex subunit
2 epigenetically affects root development,” Journal of Experimental Botany,
vol. 66, no. 15. Oxford University Press, pp. 4631–4642, 2015.
ista: Jia Y, Tian H, Li H, Yu Q, Wang L, Friml J, Ding Z. 2015. The Arabidopsis
thaliana elongator complex subunit 2 epigenetically affects root development.
Journal of Experimental Botany. 66(15), 4631–4642.
mla: Jia, Yuebin, et al. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically
Affects Root Development.” Journal of Experimental Botany, vol. 66, no.
15, Oxford University Press, 2015, pp. 4631–42, doi:10.1093/jxb/erv230.
short: Y. Jia, H. Tian, H. Li, Q. Yu, L. Wang, J. Friml, Z. Ding, Journal of Experimental
Botany 66 (2015) 4631–4642.
date_created: 2018-12-11T11:52:42Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:35Z
day: '01'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1093/jxb/erv230
file:
- access_level: open_access
checksum: 257919be0ce3d306185d3891ad7acf39
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:02Z
date_updated: 2020-07-14T12:45:02Z
file_id: '5051'
file_name: IST-2016-480-v1+1_J._Exp._Bot.-2015-Jia-4631-42.pdf
file_size: 7753043
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 66'
issue: '15'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 4631 - 4642
publication: Journal of Experimental Botany
publication_status: published
publisher: Oxford University Press
publist_id: '5615'
pubrep_id: '480'
quality_controlled: '1'
scopus_import: 1
status: public
title: The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects
root development
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: 66
year: '2015'
...
---
_id: '1555'
abstract:
- lang: eng
text: We show that incorporating spatial dispersal of individuals into a simple
vaccination epidemic model may give rise to a model that exhibits rich dynamical
behavior. Using an SIVS (susceptible-infected-vaccinated-susceptible) model as
a basis, we describe the spread of an infectious disease in a population split
into two regions. In each subpopulation, both forward and backward bifurcations
can occur. This implies that for disconnected regions the two-patch system may
admit several steady states. We consider traveling between the regions and investigate
the impact of spatial dispersal of individuals on the model dynamics. We establish
conditions for the existence of multiple nontrivial steady states in the system,
and we study the structure of the equilibria. The mathematical analysis reveals
an unusually rich dynamical behavior, not normally found in the simple epidemic
models. In addition to the disease-free equilibrium, eight endemic equilibria
emerge from backward transcritical and saddle-node bifurcation points, forming
an interesting bifurcation diagram. Stability of steady states, their bifurcations,
and the global dynamics are investigated with analytical tools, numerical simulations,
and rigorous set-oriented numerical computations.
acknowledgement: Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg,
Austria (pawel.pilarczyk@ist.ac.at). This author’s work was partially supported
by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework
Programme (FP7/2007-2013) under REA grant agreement 622033, by Fundo Europeu de
Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de
Competitividade (POFC), by the Portuguese national funds through Funda ̧caoparaaCiˆencia
e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645
(ref. FCT PTDC/MAT/098871/2008), and by European Research Council through StG 259559
in the framework of the EPIDELAY project.
article_processing_charge: No
article_type: original
author:
- first_name: Diána
full_name: Knipl, Diána
last_name: Knipl
- first_name: Pawel
full_name: Pilarczyk, Pawel
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
- first_name: Gergely
full_name: Röst, Gergely
last_name: Röst
citation:
ama: Knipl D, Pilarczyk P, Röst G. Rich bifurcation structure in a two patch vaccination
model. SIAM Journal on Applied Dynamical Systems. 2015;14(2):980-1017.
doi:10.1137/140993934
apa: Knipl, D., Pilarczyk, P., & Röst, G. (2015). Rich bifurcation structure
in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems.
Society for Industrial and Applied Mathematics . https://doi.org/10.1137/140993934
chicago: Knipl, Diána, Pawel Pilarczyk, and Gergely Röst. “Rich Bifurcation Structure
in a Two Patch Vaccination Model.” SIAM Journal on Applied Dynamical Systems.
Society for Industrial and Applied Mathematics , 2015. https://doi.org/10.1137/140993934.
ieee: D. Knipl, P. Pilarczyk, and G. Röst, “Rich bifurcation structure in a two
patch vaccination model,” SIAM Journal on Applied Dynamical Systems, vol.
14, no. 2. Society for Industrial and Applied Mathematics , pp. 980–1017, 2015.
ista: Knipl D, Pilarczyk P, Röst G. 2015. Rich bifurcation structure in a two patch
vaccination model. SIAM Journal on Applied Dynamical Systems. 14(2), 980–1017.
mla: Knipl, Diána, et al. “Rich Bifurcation Structure in a Two Patch Vaccination
Model.” SIAM Journal on Applied Dynamical Systems, vol. 14, no. 2, Society
for Industrial and Applied Mathematics , 2015, pp. 980–1017, doi:10.1137/140993934.
short: D. Knipl, P. Pilarczyk, G. Röst, SIAM Journal on Applied Dynamical Systems
14 (2015) 980–1017.
date_created: 2018-12-11T11:52:42Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:51:34Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1137/140993934
ec_funded: 1
intvolume: ' 14'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://discovery.ucl.ac.uk/1473750/1/99393.pdf
month: '01'
oa: 1
oa_version: Published Version
page: 980 - 1017
project:
- _id: 255F06BE-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '622033'
name: Persistent Homology - Images, Data and Maps
publication: SIAM Journal on Applied Dynamical Systems
publication_identifier:
eissn:
- 1536-0040
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '5616'
quality_controlled: '1'
scopus_import: 1
status: public
title: Rich bifurcation structure in a two patch vaccination model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2015'
...
---
_id: '1558'
abstract:
- lang: eng
text: CyclophilinAis a conserved peptidyl-prolyl cis-trans isomerase (PPIase) best
known as the cellular receptor of the immunosuppressant cyclosporine A. Despite
significant effort, evidence of developmental functions of cyclophilin A in non-plant
systems has remained obscure. Mutations in a tomato (Solanum lycopersicum) cyclophilin
A ortholog, DIAGEOTROPICA (DGT), have been shown to abolish the organogenesis
of lateral roots; however, a mechanistic explanation of the phenotype is lacking.
Here, we show that the dgt mutant lacks auxin maxima relevant to priming and specification
of lateral root founder cells. DGT is expressed in shoot and root, and localizes
to both the nucleus and cytoplasm during lateral root organogenesis. Mutation
of ENTIRE/ IAA9, a member of the auxin-responsive Aux/IAA protein family of transcriptional
repressors, partially restores the inability of dgt to initiate lateral root primordia
but not the primordia outgrowth. By comparison, grafting of a wild-type scion
restores the process of lateral root formation, consistent with participation
of a mobile signal. Antibodies do not detect movement of the DGT protein into
the dgt rootstock; however, experiments with radiolabeled auxin and an auxin-specific
microelectrode demonstrate abnormal auxin fluxes. Functional studies of DGT in
heterologous yeast and tobacco-leaf auxin-transport systems demonstrate that DGT
negatively regulates PIN-FORMED (PIN) auxin efflux transporters by affecting their
plasma membrane localization. Studies in tomato support complex effects of the
dgt mutation on PIN expression level, expression domain and plasma membrane localization.
Our data demonstrate that DGT regulates auxin transport in lateral root formation.
author:
- first_name: Maria
full_name: Ivanchenko, Maria
last_name: Ivanchenko
- first_name: Jinsheng
full_name: Zhu, Jinsheng
last_name: Zhu
- first_name: Bangjun
full_name: Wang, Bangjun
last_name: Wang
- first_name: Eva
full_name: Medvecka, Eva
id: 298814E2-F248-11E8-B48F-1D18A9856A87
last_name: Medvecka
- first_name: Yunlong
full_name: Du, Yunlong
last_name: Du
- first_name: Elisa
full_name: Azzarello, Elisa
last_name: Azzarello
- first_name: Stefano
full_name: Mancuso, Stefano
last_name: Mancuso
- first_name: Molly
full_name: Megraw, Molly
last_name: Megraw
- first_name: Sergei
full_name: Filichkin, Sergei
last_name: Filichkin
- first_name: Joseph
full_name: Dubrovsky, Joseph
last_name: Dubrovsky
- 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: Ivanchenko M, Zhu J, Wang B, et al. The cyclophilin a DIAGEOTROPICA gene affects
auxin transport in both root and shoot to control lateral root formation. Development.
2015;142(4):712-721. doi:10.1242/dev.113225
apa: Ivanchenko, M., Zhu, J., Wang, B., Medvecka, E., Du, Y., Azzarello, E., … Geisler,
M. (2015). The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both
root and shoot to control lateral root formation. Development. Company
of Biologists. https://doi.org/10.1242/dev.113225
chicago: Ivanchenko, Maria, Jinsheng Zhu, Bangjun Wang, Eva Medvecka, Yunlong Du,
Elisa Azzarello, Stefano Mancuso, et al. “The Cyclophilin a DIAGEOTROPICA Gene
Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.”
Development. Company of Biologists, 2015. https://doi.org/10.1242/dev.113225.
ieee: M. Ivanchenko et al., “The cyclophilin a DIAGEOTROPICA gene affects
auxin transport in both root and shoot to control lateral root formation,” Development,
vol. 142, no. 4. Company of Biologists, pp. 712–721, 2015.
ista: Ivanchenko M, Zhu J, Wang B, Medvecka E, Du Y, Azzarello E, Mancuso S, Megraw
M, Filichkin S, Dubrovsky J, Friml J, Geisler M. 2015. The cyclophilin a DIAGEOTROPICA
gene affects auxin transport in both root and shoot to control lateral root formation.
Development. 142(4), 712–721.
mla: Ivanchenko, Maria, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin
Transport in Both Root and Shoot to Control Lateral Root Formation.” Development,
vol. 142, no. 4, Company of Biologists, 2015, pp. 712–21, doi:10.1242/dev.113225.
short: M. Ivanchenko, J. Zhu, B. Wang, E. Medvecka, Y. Du, E. Azzarello, S. Mancuso,
M. Megraw, S. Filichkin, J. Dubrovsky, J. Friml, M. Geisler, Development 142 (2015)
712–721.
date_created: 2018-12-11T11:52:42Z
date_published: 2015-02-15T00:00:00Z
date_updated: 2021-01-12T06:51:35Z
day: '15'
department:
- _id: JiFr
doi: 10.1242/dev.113225
intvolume: ' 142'
issue: '4'
language:
- iso: eng
month: '02'
oa_version: None
page: 712 - 721
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '5613'
quality_controlled: '1'
scopus_import: 1
status: public
title: The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and
shoot to control lateral root formation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 142
year: '2015'
...
---
_id: '1557'
abstract:
- lang: eng
text: γ-Aminobutyric acid (GABA)- and glycine-mediated hyperpolarizing inhibition
is associated with a chloride influx that depends on the inwardly directed chloride
electrochemical gradient. In neurons, the extrusion of chloride from the cytosol
primarily depends on the expression of an isoform of potassium-chloride cotransporters
(KCC2s). KCC2 is crucial in the regulation of the inhibitory tone of neural circuits,
including pain processing neural assemblies. Thus we investigated the cellular
distribution of KCC2 in neurons underlying pain processing in the superficial
spinal dorsal horn of rats by using high-resolution immunocytochemical methods.
We demonstrated that perikarya and dendrites widely expressed KCC2, but axon terminals
proved to be negative for KCC2. In single ultrathin sections, silver deposits
labeling KCC2 molecules showed different densities on the surface of dendritic
profiles, some of which were negative for KCC2. In freeze fracture replicas and
tissue sections double stained for the β3-subunit of GABAA receptors and KCC2,
GABAA receptors were revealed on dendritic segments with high and also with low
KCC2 densities. By measuring the distances between spots immunoreactive for gephyrin
(a scaffolding protein of GABAA and glycine receptors) and KCC2 on the surface
of neurokinin 1 (NK1) receptor-immunoreactive dendrites, we found that gephyrin-immunoreactive
spots were located at various distances from KCC2 cotransporters; 5.7 % of them
were recovered in the middle of 4-10-μm-long dendritic segments that were free
of KCC2 immunostaining. The variable local densities of KCC2 may result in variable
postsynaptic potentials evoked by the activation of GABAA and glycine receptors
along the dendrites of spinal neurons.
acknowledgement: "Funded by:\r\nHungarian Academy of Sciences. Grant Number: MTA-TKI
242\r\nHungarian Brain Research Program. Grant Number: KTIA_NAP_13-1-2013-0001\r\nSolution
Oriented Research for Science and Technology from the Japan Science and Technology
Agency Japanese Ministry of Education, Culture, Sports, Science and Technology"
author:
- first_name: Fariba
full_name: Javdani, Fariba
last_name: Javdani
- first_name: Krisztina
full_name: Holló, Krisztina
last_name: Holló
- first_name: Krisztina
full_name: Hegedűs, Krisztina
last_name: Hegedűs
- first_name: Gréta
full_name: Kis, Gréta
last_name: Kis
- first_name: Zoltán
full_name: Hegyi, Zoltán
last_name: Hegyi
- first_name: Klaudia
full_name: Dócs, Klaudia
last_name: Dócs
- first_name: Yu
full_name: Kasugai, Yu
last_name: Kasugai
- 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: Miklós
full_name: Antal, Miklós
last_name: Antal
citation:
ama: Javdani F, Holló K, Hegedűs K, et al. Differential expression patterns of K+Cl-
cotransporter 2 in neurons within the superficial spinal dorsal horn of rats.
Journal of Comparative Neurology. 2015;523(13):1967-1983. doi:10.1002/cne.23774
apa: Javdani, F., Holló, K., Hegedűs, K., Kis, G., Hegyi, Z., Dócs, K., … Antal,
M. (2015). Differential expression patterns of K+Cl- cotransporter 2 in neurons
within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology.
Wiley-Blackwell. https://doi.org/10.1002/cne.23774
chicago: Javdani, Fariba, Krisztina Holló, Krisztina Hegedűs, Gréta Kis, Zoltán
Hegyi, Klaudia Dócs, Yu Kasugai, Yugo Fukazawa, Ryuichi Shigemoto, and Miklós
Antal. “Differential Expression Patterns of K+Cl- Cotransporter 2 in Neurons within
the Superficial Spinal Dorsal Horn of Rats.” Journal of Comparative Neurology.
Wiley-Blackwell, 2015. https://doi.org/10.1002/cne.23774.
ieee: F. Javdani et al., “Differential expression patterns of K+Cl- cotransporter
2 in neurons within the superficial spinal dorsal horn of rats,” Journal of
Comparative Neurology, vol. 523, no. 13. Wiley-Blackwell, pp. 1967–1983, 2015.
ista: Javdani F, Holló K, Hegedűs K, Kis G, Hegyi Z, Dócs K, Kasugai Y, Fukazawa
Y, Shigemoto R, Antal M. 2015. Differential expression patterns of K+Cl- cotransporter
2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative
Neurology. 523(13), 1967–1983.
mla: Javdani, Fariba, et al. “Differential Expression Patterns of K+Cl- Cotransporter
2 in Neurons within the Superficial Spinal Dorsal Horn of Rats.” Journal of
Comparative Neurology, vol. 523, no. 13, Wiley-Blackwell, 2015, pp. 1967–83,
doi:10.1002/cne.23774.
short: F. Javdani, K. Holló, K. Hegedűs, G. Kis, Z. Hegyi, K. Dócs, Y. Kasugai,
Y. Fukazawa, R. Shigemoto, M. Antal, Journal of Comparative Neurology 523 (2015)
1967–1983.
date_created: 2018-12-11T11:52:42Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2021-01-12T06:51:35Z
day: '01'
department:
- _id: RySh
doi: 10.1002/cne.23774
intvolume: ' 523'
issue: '13'
language:
- iso: eng
month: '09'
oa_version: None
page: 1967 - 1983
publication: Journal of Comparative Neurology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5614'
quality_controlled: '1'
scopus_import: 1
status: public
title: Differential expression patterns of K+Cl- cotransporter 2 in neurons within
the superficial spinal dorsal horn of rats
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 523
year: '2015'
...
---
_id: '1559'
abstract:
- lang: eng
text: 'There are deep, yet largely unexplored, connections between computer science
and biology. Both disciplines examine how information proliferates in time and
space. Central results in computer science describe the complexity of algorithms
that solve certain classes of problems. An algorithm is deemed efficient if it
can solve a problem in polynomial time, which means the running time of the algorithm
is a polynomial function of the length of the input. There are classes of harder
problems for which the fastest possible algorithm requires exponential time. Another
criterion is the space requirement of the algorithm. There is a crucial distinction
between algorithms that can find a solution, verify a solution, or list several
distinct solutions in given time and space. The complexity hierarchy that is generated
in this way is the foundation of theoretical computer science. Precise complexity
results can be notoriously difficult. The famous question whether polynomial time
equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open
problems in computer science and all of mathematics. Here, we consider simple
processes of ecological and evolutionary spatial dynamics. The basic question
is: What is the probability that a new invader (or a new mutant)will take over
a resident population?We derive precise complexity results for a variety of scenarios.
We therefore show that some fundamental questions in this area cannot be answered
by simple equations (assuming that P is not equal to NP).'
author:
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- 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: Nowak, Martin
last_name: Nowak
citation:
ama: Ibsen-Jensen R, Chatterjee K, Nowak M. Computational complexity of ecological
and evolutionary spatial dynamics. PNAS. 2015;112(51):15636-15641. doi:10.1073/pnas.1511366112
apa: Ibsen-Jensen, R., Chatterjee, K., & Nowak, M. (2015). Computational complexity
of ecological and evolutionary spatial dynamics. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.1511366112
chicago: Ibsen-Jensen, Rasmus, Krishnendu Chatterjee, and Martin Nowak. “Computational
Complexity of Ecological and Evolutionary Spatial Dynamics.” PNAS. National
Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511366112.
ieee: R. Ibsen-Jensen, K. Chatterjee, and M. Nowak, “Computational complexity of
ecological and evolutionary spatial dynamics,” PNAS, vol. 112, no. 51.
National Academy of Sciences, pp. 15636–15641, 2015.
ista: Ibsen-Jensen R, Chatterjee K, Nowak M. 2015. Computational complexity of ecological
and evolutionary spatial dynamics. PNAS. 112(51), 15636–15641.
mla: Ibsen-Jensen, Rasmus, et al. “Computational Complexity of Ecological and Evolutionary
Spatial Dynamics.” PNAS, vol. 112, no. 51, National Academy of Sciences,
2015, pp. 15636–41, doi:10.1073/pnas.1511366112.
short: R. Ibsen-Jensen, K. Chatterjee, M. Nowak, PNAS 112 (2015) 15636–15641.
date_created: 2018-12-11T11:52:43Z
date_published: 2015-12-22T00:00:00Z
date_updated: 2021-01-12T06:51:36Z
day: '22'
department:
- _id: KrCh
doi: 10.1073/pnas.1511366112
external_id:
pmid:
- '26644569'
intvolume: ' 112'
issue: '51'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697423/
month: '12'
oa: 1
oa_version: Submitted Version
page: 15636 - 15641
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5612'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computational complexity of ecological and evolutionary spatial dynamics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1561'
abstract:
- lang: eng
text: Replication-deficient recombinant adenoviruses are potent vectors for the
efficient transient expression of exogenous genes in resting immune cells. However,
most leukocytes are refractory to efficient adenoviral transduction as they lack
expression of the coxsackie/adenovirus receptor (CAR). To circumvent this obstacle,
we generated the R26/CAG-CARΔ1StopF (where R26 is ROSA26 and CAG is CMV early
enhancer/chicken β actin promoter) knock-in mouse line. This strain allows monitoring
of in situ Cre recombinase activity through expression of CARΔ1. Simultaneously,
CARΔ1 expression permits selective and highly efficient adenoviral transduction
of immune cell populations, such as mast cells or T cells, directly ex vivo in
bulk cultures without prior cell purification or activation. Furthermore, we show
that CARΔ1 expression dramatically improves adenoviral infection of in vitro differentiated
conventional and plasmacytoid dendritic cells (DCs), basophils, mast cells, as
well as Hoxb8-immortalized hematopoietic progenitor cells. This novel dual function
mouse strain will hence be a valuable tool to rapidly dissect the function of
specific genes in leukocyte physiology.
author:
- first_name: Klaus
full_name: Heger, Klaus
last_name: Heger
- first_name: Maike
full_name: Kober, Maike
last_name: Kober
- first_name: David
full_name: Rieß, David
last_name: Rieß
- first_name: Christoph
full_name: Drees, Christoph
last_name: Drees
- first_name: Ingrid
full_name: De Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: De Vries
- first_name: Arianna
full_name: Bertossi, Arianna
last_name: Bertossi
- first_name: Axel
full_name: Roers, Axel
last_name: Roers
- 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: Marc
full_name: Schmidt Supprian, Marc
last_name: Schmidt Supprian
citation:
ama: Heger K, Kober M, Rieß D, et al. A novel Cre recombinase reporter mouse strain
facilitates selective and efficient infection of primary immune cells with adenoviral
vectors. European Journal of Immunology. 2015;45(6):1614-1620. doi:10.1002/eji.201545457
apa: Heger, K., Kober, M., Rieß, D., Drees, C., de Vries, I., Bertossi, A., … Schmidt
Supprian, M. (2015). A novel Cre recombinase reporter mouse strain facilitates
selective and efficient infection of primary immune cells with adenoviral vectors.
European Journal of Immunology. Wiley. https://doi.org/10.1002/eji.201545457
chicago: Heger, Klaus, Maike Kober, David Rieß, Christoph Drees, Ingrid de Vries,
Arianna Bertossi, Axel Roers, Michael K Sixt, and Marc Schmidt Supprian. “A Novel
Cre Recombinase Reporter Mouse Strain Facilitates Selective and Efficient Infection
of Primary Immune Cells with Adenoviral Vectors.” European Journal of Immunology.
Wiley, 2015. https://doi.org/10.1002/eji.201545457.
ieee: K. Heger et al., “A novel Cre recombinase reporter mouse strain facilitates
selective and efficient infection of primary immune cells with adenoviral vectors,”
European Journal of Immunology, vol. 45, no. 6. Wiley, pp. 1614–1620, 2015.
ista: Heger K, Kober M, Rieß D, Drees C, de Vries I, Bertossi A, Roers A, Sixt MK,
Schmidt Supprian M. 2015. A novel Cre recombinase reporter mouse strain facilitates
selective and efficient infection of primary immune cells with adenoviral vectors.
European Journal of Immunology. 45(6), 1614–1620.
mla: Heger, Klaus, et al. “A Novel Cre Recombinase Reporter Mouse Strain Facilitates
Selective and Efficient Infection of Primary Immune Cells with Adenoviral Vectors.”
European Journal of Immunology, vol. 45, no. 6, Wiley, 2015, pp. 1614–20,
doi:10.1002/eji.201545457.
short: K. Heger, M. Kober, D. Rieß, C. Drees, I. de Vries, A. Bertossi, A. Roers,
M.K. Sixt, M. Schmidt Supprian, European Journal of Immunology 45 (2015) 1614–1620.
date_created: 2018-12-11T11:52:44Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2021-01-12T06:51:36Z
day: '01'
department:
- _id: MiSi
doi: 10.1002/eji.201545457
intvolume: ' 45'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 1614 - 1620
publication: European Journal of Immunology
publication_status: published
publisher: Wiley
publist_id: '5610'
quality_controlled: '1'
scopus_import: 1
status: public
title: A novel Cre recombinase reporter mouse strain facilitates selective and efficient
infection of primary immune cells with adenoviral vectors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2015'
...
---
_id: '1554'
abstract:
- lang: eng
text: The visualization of hormonal signaling input and output is key to understanding
how multicellular development is regulated. The plant signaling molecule auxin
triggers many growth and developmental responses, but current tools lack the sensitivity
or precision to visualize these. We developed a set of fluorescent reporters that
allow sensitive and semiquantitative readout of auxin responses at cellular resolution
in Arabidopsis thaliana. These generic tools are suitable for any transformable
plant species.
author:
- first_name: Cheyang
full_name: Liao, Cheyang
last_name: Liao
- first_name: Wouter
full_name: Smet, Wouter
last_name: Smet
- first_name: Géraldine
full_name: Brunoud, Géraldine
last_name: Brunoud
- first_name: Saiko
full_name: Yoshida, Saiko
id: 2E46069C-F248-11E8-B48F-1D18A9856A87
last_name: Yoshida
- first_name: Teva
full_name: Vernoux, Teva
last_name: Vernoux
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
citation:
ama: Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. Reporters for sensitive
and quantitative measurement of auxin response. Nature Methods. 2015;12(3):207-210.
doi:10.1038/nmeth.3279
apa: Liao, C., Smet, W., Brunoud, G., Yoshida, S., Vernoux, T., & Weijers, D.
(2015). Reporters for sensitive and quantitative measurement of auxin response.
Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth.3279
chicago: Liao, Cheyang, Wouter Smet, Géraldine Brunoud, Saiko Yoshida, Teva Vernoux,
and Dolf Weijers. “Reporters for Sensitive and Quantitative Measurement of Auxin
Response.” Nature Methods. Nature Publishing Group, 2015. https://doi.org/10.1038/nmeth.3279.
ieee: C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, and D. Weijers, “Reporters
for sensitive and quantitative measurement of auxin response,” Nature Methods,
vol. 12, no. 3. Nature Publishing Group, pp. 207–210, 2015.
ista: Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. 2015. Reporters
for sensitive and quantitative measurement of auxin response. Nature Methods.
12(3), 207–210.
mla: Liao, Cheyang, et al. “Reporters for Sensitive and Quantitative Measurement
of Auxin Response.” Nature Methods, vol. 12, no. 3, Nature Publishing Group,
2015, pp. 207–10, doi:10.1038/nmeth.3279.
short: C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, D. Weijers, Nature
Methods 12 (2015) 207–210.
date_created: 2018-12-11T11:52:41Z
date_published: 2015-02-26T00:00:00Z
date_updated: 2021-01-12T06:51:34Z
day: '26'
department:
- _id: JiFr
doi: 10.1038/nmeth.3279
external_id:
pmid:
- '25643149'
intvolume: ' 12'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344836/
month: '02'
oa: 1
oa_version: Submitted Version
page: 207 - 210
pmid: 1
publication: Nature Methods
publication_status: published
publisher: Nature Publishing Group
publist_id: '5617'
quality_controlled: '1'
scopus_import: 1
status: public
title: Reporters for sensitive and quantitative measurement of auxin response
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2015'
...
---
_id: '1560'
abstract:
- lang: eng
text: Stromal cells in the subcapsular sinus of the lymph node 'decide' which cells
and molecules are allowed access to the deeper parenchyma. The glycoprotein PLVAP
is a crucial component of this selector function.
author:
- first_name: Miroslav
full_name: Hons, Miroslav
id: 4167FE56-F248-11E8-B48F-1D18A9856A87
last_name: Hons
orcid: 0000-0002-6625-3348
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Hons M, Sixt MK. The lymph node filter revealed. Nature Immunology.
2015;16(4):338-340. doi:10.1038/ni.3126
apa: Hons, M., & Sixt, M. K. (2015). The lymph node filter revealed. Nature
Immunology. Nature Publishing Group. https://doi.org/10.1038/ni.3126
chicago: Hons, Miroslav, and Michael K Sixt. “The Lymph Node Filter Revealed.” Nature
Immunology. Nature Publishing Group, 2015. https://doi.org/10.1038/ni.3126.
ieee: M. Hons and M. K. Sixt, “The lymph node filter revealed,” Nature Immunology,
vol. 16, no. 4. Nature Publishing Group, pp. 338–340, 2015.
ista: Hons M, Sixt MK. 2015. The lymph node filter revealed. Nature Immunology.
16(4), 338–340.
mla: Hons, Miroslav, and Michael K. Sixt. “The Lymph Node Filter Revealed.” Nature
Immunology, vol. 16, no. 4, Nature Publishing Group, 2015, pp. 338–40, doi:10.1038/ni.3126.
short: M. Hons, M.K. Sixt, Nature Immunology 16 (2015) 338–340.
date_created: 2018-12-11T11:52:43Z
date_published: 2015-03-19T00:00:00Z
date_updated: 2021-01-12T06:51:36Z
day: '19'
department:
- _id: MiSi
doi: 10.1038/ni.3126
intvolume: ' 16'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 338 - 340
publication: Nature Immunology
publication_status: published
publisher: Nature Publishing Group
publist_id: '5611'
quality_controlled: '1'
scopus_import: 1
status: public
title: The lymph node filter revealed
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2015'
...
---
_id: '1565'
abstract:
- lang: eng
text: Leptin is an adipokine produced by the adipose tissue regulating body weight
through its appetite-suppressing effect. Besides being expressed in the hypothalamus
and hippocampus, leptin receptors (ObRs) are also present in chromaffin cells
of the adrenal medulla. In the present study, we report the effect of leptin on
mouse chromaffin cell (MCC) functionality, focusing on cell excitability and catecholamine
secretion. Acute application of leptin (1 nm) on spontaneously firing MCCs caused
a slowly developing membrane hyperpolarization followed by complete blockade of
action potential (AP) firing. This inhibitory effect at rest was abolished by
the BK channel blocker paxilline (1 μm), suggesting the involvement of BK potassium
channels. Single-channel recordings in 'perforated microvesicles' confirmed that
leptin increased BK channel open probability without altering its unitary conductance.
BK channel up-regulation was associated with the phosphoinositide 3-kinase (PI3K)
signalling cascade because the PI3K specific inhibitor wortmannin (100 nm) fully
prevented BK current increase. We also tested the effect of leptin on evoked AP
firing and Ca2+-driven exocytosis. Although leptin preserves well-adapted AP trains
of lower frequency, APs are broader and depolarization-evoked exocytosis is increased
as a result of the larger size of the ready-releasable pool and higher frequency
of vesicle release. The kinetics and quantal size of single secretory events remained
unaltered. Leptin had no effect on firing and secretion in db-/db- mice lacking
the ObR gene, confirming its specificity. In conclusion, leptin exhibits a dual
action on MCC activity. It dampens AP firing at rest but preserves AP firing and
increases catecholamine secretion during sustained stimulation, highlighting the
importance of the adipo-adrenal axis in the leptin-mediated increase of sympathetic
tone and catecholamine release.
acknowledgement: "This work was supported by the Compagnia di San Paolo Foundation
‘Neuroscience Program’ to VC and ‘Progetto di Ateneo 2011-13’ to EC.\r\nWe thank
Dr Claudio Franchino for cell preparation and for providing excellent technical
support."
author:
- first_name: Daniela
full_name: Gavello, Daniela
last_name: Gavello
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Sara
full_name: Gosso, Sara
last_name: Gosso
- first_name: Emilio
full_name: Carbone, Emilio
last_name: Carbone
- first_name: Valentina
full_name: Carabelli, Valentina
last_name: Carabelli
citation:
ama: Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. Dual action of leptin
on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven
BK channel up-regulation in mouse chromaffin cells. Journal of Physiology.
2015;593(22):4835-4853. doi:10.1113/JP271078
apa: Gavello, D., Vandael, D. H., Gosso, S., Carbone, E., & Carabelli, V. (2015).
Dual action of leptin on rest-firing and stimulated catecholamine release via
phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells.
Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/JP271078
chicago: Gavello, Daniela, David H Vandael, Sara Gosso, Emilio Carbone, and Valentina
Carabelli. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine
Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse
Chromaffin Cells.” Journal of Physiology. Wiley-Blackwell, 2015. https://doi.org/10.1113/JP271078.
ieee: D. Gavello, D. H. Vandael, S. Gosso, E. Carbone, and V. Carabelli, “Dual action
of leptin on rest-firing and stimulated catecholamine release via phosphoinositide
3-kinase-riven BK channel up-regulation in mouse chromaffin cells,” Journal
of Physiology, vol. 593, no. 22. Wiley-Blackwell, pp. 4835–4853, 2015.
ista: Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. 2015. Dual action
of leptin on rest-firing and stimulated catecholamine release via phosphoinositide
3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of
Physiology. 593(22), 4835–4853.
mla: Gavello, Daniela, et al. “Dual Action of Leptin on Rest-Firing and Stimulated
Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation
in Mouse Chromaffin Cells.” Journal of Physiology, vol. 593, no. 22, Wiley-Blackwell,
2015, pp. 4835–53, doi:10.1113/JP271078.
short: D. Gavello, D.H. Vandael, S. Gosso, E. Carbone, V. Carabelli, Journal of
Physiology 593 (2015) 4835–4853.
date_created: 2018-12-11T11:52:45Z
date_published: 2015-11-15T00:00:00Z
date_updated: 2021-01-12T06:51:38Z
day: '15'
department:
- _id: PeJo
doi: 10.1113/JP271078
external_id:
pmid:
- '26282459'
intvolume: ' 593'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650409/
month: '11'
oa: 1
oa_version: Submitted Version
page: 4835 - 4853
pmid: 1
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5606'
quality_controlled: '1'
scopus_import: 1
status: public
title: Dual action of leptin on rest-firing and stimulated catecholamine release via
phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 593
year: '2015'
...
---
_id: '1562'
abstract:
- lang: eng
text: The plant hormone auxin is a key regulator of plant growth and development.
Auxin levels are sensed and interpreted by distinct receptor systems that activate
a broad range of cellular responses. The Auxin-Binding Protein1 (ABP1) that has
been identified based on its ability to bind auxin with high affinity is a prime
candidate for the extracellular receptor responsible for mediating a range of
auxin effects, in particular, the fast non-transcriptional ones. Contradictory
genetic studies suggested prominent or no importance of ABP1 in many developmental
processes. However, how crucial the role of auxin binding to ABP1 is for its functions
has not been addressed. Here, we show that the auxin-binding pocket of ABP1 is
essential for its gain-of-function cellular and developmental roles. In total,
16 different abp1 mutants were prepared that possessed substitutions in the metal
core or in the hydrophobic amino acids of the auxin-binding pocket as well as
neutral mutations. Their analysis revealed that an intact auxin-binding pocket
is a prerequisite for ABP1 to activate downstream components of the ABP1 signalling
pathway, such as Rho of Plants (ROPs) and to mediate the clathrin association
with membranes for endocytosis regulation. In planta analyses demonstrated the
importance of the auxin binding pocket for all known ABP1-mediated postembryonic
developmental processes, including morphology of leaf epidermal cells, root growth
and root meristem activity, and vascular tissue differentiation. Taken together,
these findings suggest that auxin binding to ABP1 is central to its function,
supporting the role of ABP1 as auxin receptor.
acknowledgement: This work was supported by ERC Independent Research grant (ERC-2011-StG-
20101109-PSDP to JF); the European Social Fund and the state budget of the Czech
Republic [the project ‘Employment of Newly Graduated Doctors of Science for Scientific
Excellence’ (CZ.1.07/2.3.00/30.0009) to TN]; the Czech Science Foundation (GACR)
[project 13-40637S to JF].
article_type: original
author:
- first_name: Peter
full_name: Grones, Peter
id: 399876EC-F248-11E8-B48F-1D18A9856A87
last_name: Grones
- first_name: Xu
full_name: Chen, Xu
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- 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: Grones P, Chen X, Simon S, et al. Auxin-binding pocket of ABP1 is crucial for
its gain-of-function cellular and developmental roles. Journal of Experimental
Botany. 2015;66(16):5055-5065. doi:10.1093/jxb/erv177
apa: Grones, P., Chen, X., Simon, S., Kaufmann, W., De Rycke, R., Nodzyński, T.,
… Friml, J. (2015). Auxin-binding pocket of ABP1 is crucial for its gain-of-function
cellular and developmental roles. Journal of Experimental Botany. Oxford
University Press. https://doi.org/10.1093/jxb/erv177
chicago: Grones, Peter, Xu Chen, Sibu Simon, Walter Kaufmann, Riet De Rycke, Tomasz
Nodzyński, Eva Zažímalová, and Jiří Friml. “Auxin-Binding Pocket of ABP1 Is Crucial
for Its Gain-of-Function Cellular and Developmental Roles.” Journal of Experimental
Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv177.
ieee: P. Grones et al., “Auxin-binding pocket of ABP1 is crucial for its
gain-of-function cellular and developmental roles,” Journal of Experimental
Botany, vol. 66, no. 16. Oxford University Press, pp. 5055–5065, 2015.
ista: Grones P, Chen X, Simon S, Kaufmann W, De Rycke R, Nodzyński T, Zažímalová
E, Friml J. 2015. Auxin-binding pocket of ABP1 is crucial for its gain-of-function
cellular and developmental roles. Journal of Experimental Botany. 66(16), 5055–5065.
mla: Grones, Peter, et al. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function
Cellular and Developmental Roles.” Journal of Experimental Botany, vol.
66, no. 16, Oxford University Press, 2015, pp. 5055–65, doi:10.1093/jxb/erv177.
short: P. Grones, X. Chen, S. Simon, W. Kaufmann, R. De Rycke, T. Nodzyński, E.
Zažímalová, J. Friml, Journal of Experimental Botany 66 (2015) 5055–5065.
date_created: 2018-12-11T11:52:44Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2023-02-23T10:04:26Z
day: '01'
department:
- _id: JiFr
- _id: EM-Fac
doi: 10.1093/jxb/erv177
ec_funded: 1
intvolume: ' 66'
issue: '16'
language:
- iso: eng
month: '08'
oa_version: None
page: 5055 - 5065
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Journal of Experimental Botany
publication_status: published
publisher: Oxford University Press
publist_id: '5609'
quality_controlled: '1'
scopus_import: 1
status: public
title: Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and
developmental roles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 66
year: '2015'
...
---
_id: '1564'
article_number: '145'
author:
- first_name: Matthieu
full_name: Gilson, Matthieu
last_name: Gilson
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
- first_name: Friedemann
full_name: Zenke, Friedemann
last_name: Zenke
citation:
ama: 'Gilson M, Savin C, Zenke F. Editorial: Emergent neural computation from the
interaction of different forms of plasticity. Frontiers in Computational Neuroscience.
2015;9(11). doi:10.3389/fncom.2015.00145'
apa: 'Gilson, M., Savin, C., & Zenke, F. (2015). Editorial: Emergent neural
computation from the interaction of different forms of plasticity. Frontiers
in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2015.00145'
chicago: 'Gilson, Matthieu, Cristina Savin, and Friedemann Zenke. “Editorial: Emergent
Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers
in Computational Neuroscience. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fncom.2015.00145.'
ieee: 'M. Gilson, C. Savin, and F. Zenke, “Editorial: Emergent neural computation
from the interaction of different forms of plasticity,” Frontiers in Computational
Neuroscience, vol. 9, no. 11. Frontiers Research Foundation, 2015.'
ista: 'Gilson M, Savin C, Zenke F. 2015. Editorial: Emergent neural computation
from the interaction of different forms of plasticity. Frontiers in Computational
Neuroscience. 9(11), 145.'
mla: 'Gilson, Matthieu, et al. “Editorial: Emergent Neural Computation from the
Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience,
vol. 9, no. 11, 145, Frontiers Research Foundation, 2015, doi:10.3389/fncom.2015.00145.'
short: M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9
(2015).
date_created: 2018-12-11T11:52:45Z
date_published: 2015-11-30T00:00:00Z
date_updated: 2021-01-12T06:51:37Z
day: '30'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.3389/fncom.2015.00145
ec_funded: 1
file:
- access_level: open_access
checksum: cea73b6d3ef1579f32da10b82f4de4fd
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:09Z
date_updated: 2020-07-14T12:45:02Z
file_id: '4927'
file_name: IST-2016-479-v1+1_fncom-09-00145.pdf
file_size: 187038
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Frontiers in Computational Neuroscience
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '5607'
pubrep_id: '479'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Editorial: Emergent neural computation from the interaction of different forms
of plasticity'
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: 9
year: '2015'
...
---
_id: '1568'
abstract:
- lang: eng
text: Aiming at the automatic diagnosis of tumors from narrow band imaging (NBI)
magnifying endoscopy (ME) images of the stomach, we combine methods from image
processing, computational topology, and machine learning to classify patterns
into normal, tubular, vessel. Training the algorithm on a small number of images
of each type, we achieve a high rate of correct classifications. The analysis
of the learning algorithm reveals that a handful of geometric and topological
features are responsible for the overwhelming majority of decisions.
acknowledgement: This research is supported by the project No. 477 of P.G. Demidov
Yaroslavl State University within State Assignment for Research.
author:
- first_name: Olga
full_name: Dunaeva, Olga
last_name: Dunaeva
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Anton
full_name: Lukyanov, Anton
last_name: Lukyanov
- first_name: Michael
full_name: Machin, Michael
last_name: Machin
- first_name: Daria
full_name: Malkova, Daria
last_name: Malkova
citation:
ama: 'Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. The classification
of endoscopy images with persistent homology. In: Proceedings - 16th International
Symposium on Symbolic and Numeric Algorithms for Scientific Computing. IEEE;
2015:7034731. doi:10.1109/SYNASC.2014.81'
apa: 'Dunaeva, O., Edelsbrunner, H., Lukyanov, A., Machin, M., & Malkova, D.
(2015). The classification of endoscopy images with persistent homology. In Proceedings
- 16th International Symposium on Symbolic and Numeric Algorithms for Scientific
Computing (p. 7034731). Timisoara, Romania: IEEE. https://doi.org/10.1109/SYNASC.2014.81'
chicago: Dunaeva, Olga, Herbert Edelsbrunner, Anton Lukyanov, Michael Machin, and
Daria Malkova. “The Classification of Endoscopy Images with Persistent Homology.”
In Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms
for Scientific Computing, 7034731. IEEE, 2015. https://doi.org/10.1109/SYNASC.2014.81.
ieee: O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, and D. Malkova, “The
classification of endoscopy images with persistent homology,” in Proceedings
- 16th International Symposium on Symbolic and Numeric Algorithms for Scientific
Computing, Timisoara, Romania, 2015, p. 7034731.
ista: 'Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. 2015. The classification
of endoscopy images with persistent homology. Proceedings - 16th International
Symposium on Symbolic and Numeric Algorithms for Scientific Computing. SYNASC:
Symbolic and Numeric Algorithms for Scientific Computing, 7034731.'
mla: Dunaeva, Olga, et al. “The Classification of Endoscopy Images with Persistent
Homology.” Proceedings - 16th International Symposium on Symbolic and Numeric
Algorithms for Scientific Computing, IEEE, 2015, p. 7034731, doi:10.1109/SYNASC.2014.81.
short: O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, D. Malkova, in:, Proceedings
- 16th International Symposium on Symbolic and Numeric Algorithms for Scientific
Computing, IEEE, 2015, p. 7034731.
conference:
end_date: 2014-09-25
location: Timisoara, Romania
name: 'SYNASC: Symbolic and Numeric Algorithms for Scientific Computing'
start_date: 2014-09-22
date_created: 2018-12-11T11:52:46Z
date_published: 2015-02-05T00:00:00Z
date_updated: 2023-02-21T16:57:29Z
day: '05'
department:
- _id: HeEd
doi: 10.1109/SYNASC.2014.81
language:
- iso: eng
month: '02'
oa_version: None
page: '7034731'
publication: Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms
for Scientific Computing
publication_status: published
publisher: IEEE
publist_id: '5603'
quality_controlled: '1'
related_material:
record:
- id: '1289'
relation: later_version
status: public
scopus_import: 1
status: public
title: The classification of endoscopy images with persistent homology
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1567'
abstract:
- lang: eng
text: My personal journey to the fascinating world of geometric forms started more
than 30 years ago with the invention of alpha shapes in the plane. It took about
10 years before we generalized the concept to higher dimensions, we produced working
software with a graphics interface for the three-dimensional case. At the same
time, we added homology to the computations. Needless to say that this foreshadowed
the inception of persistent homology, because it suggested the study of filtrations
to capture the scale of a shape or data set. Importantly, this method has fast
algorithms. The arguably most useful result on persistent homology is the stability
of its diagrams under perturbations.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Edelsbrunner H. Shape, homology, persistence, and stability. In: 23rd International
Symposium. Vol 9411. Springer Nature; 2015.'
apa: 'Edelsbrunner, H. (2015). Shape, homology, persistence, and stability. In 23rd
International Symposium (Vol. 9411). Los Angeles, CA, United States: Springer
Nature.'
chicago: Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” In
23rd International Symposium, Vol. 9411. Springer Nature, 2015.
ieee: H. Edelsbrunner, “Shape, homology, persistence, and stability,” in 23rd
International Symposium, Los Angeles, CA, United States, 2015, vol. 9411.
ista: 'Edelsbrunner H. 2015. Shape, homology, persistence, and stability. 23rd International
Symposium. GD: Graph Drawing and Network Visualization, LNCS, vol. 9411.'
mla: Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” 23rd
International Symposium, vol. 9411, Springer Nature, 2015.
short: H. Edelsbrunner, in:, 23rd International Symposium, Springer Nature, 2015.
conference:
end_date: 2015-09-26
location: Los Angeles, CA, United States
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2015-09-24
date_created: 2018-12-11T11:52:46Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2022-01-28T08:25:00Z
day: '01'
department:
- _id: HeEd
intvolume: ' 9411'
language:
- iso: eng
month: '01'
oa_version: None
publication: 23rd International Symposium
publication_status: published
publisher: Springer Nature
publist_id: '5604'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Shape, homology, persistence, and stability
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9411
year: '2015'
...
---
_id: '1563'
abstract:
- lang: eng
text: For a given self-map $f$ of $M$, a closed smooth connected and simply-connected
manifold of dimension $m\geq 4$, we provide an algorithm for estimating the values
of the topological invariant $D^m_r[f]$, which equals the minimal number of $r$-periodic
points in the smooth homotopy class of $f$. Our results are based on the combinatorial
scheme for computing $D^m_r[f]$ introduced by G. Graff and J. Jezierski [J. Fixed
Point Theory Appl. 13 (2013), 63-84]. An open-source implementation of the algorithm
programmed in C++ is publicly available at {\tt http://www.pawelpilarczyk.com/combtop/}.
author:
- first_name: Grzegorz
full_name: Graff, Grzegorz
last_name: Graff
- first_name: Pawel
full_name: Pilarczyk, Pawel
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
citation:
ama: Graff G, Pilarczyk P. An algorithmic approach to estimating the minimal number
of periodic points for smooth self-maps of simply-connected manifolds. Topological
Methods in Nonlinear Analysis. 2015;45(1):273-286. doi:10.12775/TMNA.2015.014
apa: Graff, G., & Pilarczyk, P. (2015). An algorithmic approach to estimating
the minimal number of periodic points for smooth self-maps of simply-connected
manifolds. Topological Methods in Nonlinear Analysis. Juliusz Schauder
Center for Nonlinear Studies. https://doi.org/10.12775/TMNA.2015.014
chicago: Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating
the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected
Manifolds.” Topological Methods in Nonlinear Analysis. Juliusz Schauder
Center for Nonlinear Studies, 2015. https://doi.org/10.12775/TMNA.2015.014.
ieee: G. Graff and P. Pilarczyk, “An algorithmic approach to estimating the minimal
number of periodic points for smooth self-maps of simply-connected manifolds,”
Topological Methods in Nonlinear Analysis, vol. 45, no. 1. Juliusz Schauder
Center for Nonlinear Studies, pp. 273–286, 2015.
ista: Graff G, Pilarczyk P. 2015. An algorithmic approach to estimating the minimal
number of periodic points for smooth self-maps of simply-connected manifolds.
Topological Methods in Nonlinear Analysis. 45(1), 273–286.
mla: Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating
the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected
Manifolds.” Topological Methods in Nonlinear Analysis, vol. 45, no. 1,
Juliusz Schauder Center for Nonlinear Studies, 2015, pp. 273–86, doi:10.12775/TMNA.2015.014.
short: G. Graff, P. Pilarczyk, Topological Methods in Nonlinear Analysis 45 (2015)
273–286.
date_created: 2018-12-11T11:52:44Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2021-01-12T06:51:37Z
day: '01'
department:
- _id: HeEd
doi: 10.12775/TMNA.2015.014
intvolume: ' 45'
issue: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 273 - 286
publication: Topological Methods in Nonlinear Analysis
publication_status: published
publisher: Juliusz Schauder Center for Nonlinear Studies
publist_id: '5608'
quality_controlled: '1'
scopus_import: 1
status: public
title: An algorithmic approach to estimating the minimal number of periodic points
for smooth self-maps of simply-connected manifolds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2015'
...
---
_id: '1574'
abstract:
- lang: eng
text: Multiple plant developmental processes, such as lateral root development,
depend on auxin distribution patterns that are in part generated by the PIN-formed
family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7
(ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly
form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription
in planta to steer the early steps of lateral root formation. This regulatory
mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli,
potentially maintaining and enhancing the robustness of the auxin flux directionality
during lateral root development. The cooperative action between canonical auxin
signalling and other transcription factors might constitute a general mechanism
by which transcriptional auxin-sensitivity can be regulated at a tissue-specific
level.
acknowledgement: 'of the European Research Council (project ERC-2011-StG-20101109-PSDP)
(to J.F.), a FEBS long-term fellowship (to P.M.) '
article_number: '8821'
author:
- first_name: Qian
full_name: Chen, Qian
last_name: Chen
- first_name: Yang
full_name: Liu, Yang
last_name: Liu
- first_name: Steven
full_name: Maere, Steven
last_name: Maere
- first_name: Eunkyoung
full_name: Lee, Eunkyoung
last_name: Lee
- first_name: Gert
full_name: Van Isterdael, Gert
last_name: Van Isterdael
- first_name: Zidian
full_name: Xie, Zidian
last_name: Xie
- first_name: Wei
full_name: Xuan, Wei
last_name: Xuan
- first_name: Jessica
full_name: Lucas, Jessica
last_name: Lucas
- first_name: Valya
full_name: Vassileva, Valya
last_name: Vassileva
- first_name: Saeko
full_name: Kitakura, Saeko
last_name: Kitakura
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Niko
full_name: Geldner, Niko
last_name: Geldner
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jie
full_name: Le, Jie
last_name: Le
- first_name: Hidehiro
full_name: Fukaki, Hidehiro
last_name: Fukaki
- first_name: Erich
full_name: Grotewold, Erich
last_name: Grotewold
- first_name: Chuanyou
full_name: Li, Chuanyou
last_name: Li
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Fred
full_name: Sack, Fred
last_name: Sack
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
citation:
ama: Chen Q, Liu Y, Maere S, et al. A coherent transcriptional feed-forward motif
model for mediating auxin-sensitive PIN3 expression during lateral root development.
Nature Communications. 2015;6. doi:10.1038/ncomms9821
apa: Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., … Vanneste,
S. (2015). A coherent transcriptional feed-forward motif model for mediating auxin-sensitive
PIN3 expression during lateral root development. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms9821
chicago: Chen, Qian, Yang Liu, Steven Maere, Eunkyoung Lee, Gert Van Isterdael,
Zidian Xie, Wei Xuan, et al. “A Coherent Transcriptional Feed-Forward Motif Model
for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.”
Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9821.
ieee: Q. Chen et al., “A coherent transcriptional feed-forward motif model
for mediating auxin-sensitive PIN3 expression during lateral root development,”
Nature Communications, vol. 6. Nature Publishing Group, 2015.
ista: Chen Q, Liu Y, Maere S, Lee E, Van Isterdael G, Xie Z, Xuan W, Lucas J, Vassileva
V, Kitakura S, Marhavý P, Wabnik KT, Geldner N, Benková E, Le J, Fukaki H, Grotewold
E, Li C, Friml J, Sack F, Beeckman T, Vanneste S. 2015. A coherent transcriptional
feed-forward motif model for mediating auxin-sensitive PIN3 expression during
lateral root development. Nature Communications. 6, 8821.
mla: Chen, Qian, et al. “A Coherent Transcriptional Feed-Forward Motif Model for
Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature
Communications, vol. 6, 8821, Nature Publishing Group, 2015, doi:10.1038/ncomms9821.
short: Q. Chen, Y. Liu, S. Maere, E. Lee, G. Van Isterdael, Z. Xie, W. Xuan, J.
Lucas, V. Vassileva, S. Kitakura, P. Marhavý, K.T. Wabnik, N. Geldner, E. Benková,
J. Le, H. Fukaki, E. Grotewold, C. Li, J. Friml, F. Sack, T. Beeckman, S. Vanneste,
Nature Communications 6 (2015).
date_created: 2018-12-11T11:52:48Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2021-01-12T06:51:42Z
day: '18'
ddc:
- '580'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1038/ncomms9821
file:
- access_level: open_access
checksum: 8ff5c108899b548806e1cb7a302fe76d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:32Z
date_updated: 2020-07-14T12:45:02Z
file_id: '5085'
file_name: IST-2016-477-v1+1_ncomms9821.pdf
file_size: 1701815
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5597'
pubrep_id: '477'
quality_controlled: '1'
scopus_import: 1
status: public
title: A coherent transcriptional feed-forward motif model for mediating auxin-sensitive
PIN3 expression during lateral root development
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '1575'
abstract:
- lang: eng
text: The immune response relies on the migration of leukocytes and on their ability
to stop in precise anatomical locations to fulfil their task. How leukocyte migration
and function are coordinated is unknown. Here we show that in immature dendritic
cells, which patrol their environment by engulfing extracellular material, cell
migration and antigen capture are antagonistic. This antagonism results from transient
enrichment of myosin IIA at the cell front, which disrupts the back-to-front gradient
of the motor protein, slowing down locomotion but promoting antigen capture. We
further highlight that myosin IIA enrichment at the cell front requires the MHC
class II-associated invariant chain (Ii). Thus, by controlling myosin IIA localization,
Ii imposes on dendritic cells an intermittent antigen capture behaviour that might
facilitate environment patrolling. We propose that the requirement for myosin
II in both cell migration and specific cell functions may provide a general mechanism
for their coordination in time and space.
acknowledgement: M.C. and M.L.H. were supported by fellowships from the Fondation
pour la Recherche Médicale and the Association pour la Recherche contre le Cancer,
respectively. This work was funded by grants from the City of Paris and the European
Research Council to A.-M.L.-D. (Strapacemi 243103), the Association Nationale pour
la Recherche (ANR-09-PIRI-0027-PCVI) and the InnaBiosanté foundation (Micemico)
to A.-M.L.-D., M.P. and R.V., and the DCBIOL Labex from the French Government (ANR-10-IDEX-0001-02-PSL*
and ANR-11-LABX-0043). The super-resolution SIM microscope was funded through an
ERC Advanced Investigator Grant (250367) to Edith Heard (CNRS UMR3215/Inserm U934,
Institut Curie).
article_number: '7526'
author:
- first_name: Mélanie
full_name: Chabaud, Mélanie
last_name: Chabaud
- first_name: Mélina
full_name: Heuzé, Mélina
last_name: Heuzé
- first_name: Marine
full_name: Bretou, Marine
last_name: Bretou
- first_name: Pablo
full_name: Vargas, Pablo
last_name: Vargas
- first_name: Paolo
full_name: Maiuri, Paolo
last_name: Maiuri
- first_name: Paola
full_name: Solanes, Paola
last_name: Solanes
- first_name: Mathieu
full_name: Maurin, Mathieu
last_name: Maurin
- first_name: Emmanuel
full_name: Terriac, Emmanuel
last_name: Terriac
- first_name: Maël
full_name: Le Berre, Maël
last_name: Le Berre
- first_name: Danielle
full_name: Lankar, Danielle
last_name: Lankar
- first_name: Tristan
full_name: Piolot, Tristan
last_name: Piolot
- first_name: Robert
full_name: Adelstein, Robert
last_name: Adelstein
- first_name: Yingfan
full_name: Zhang, Yingfan
last_name: Zhang
- 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: Jordan
full_name: Jacobelli, Jordan
last_name: Jacobelli
- first_name: Olivier
full_name: Bénichou, Olivier
last_name: Bénichou
- first_name: Raphaël
full_name: Voituriez, Raphaël
last_name: Voituriez
- first_name: Matthieu
full_name: Piel, Matthieu
last_name: Piel
- first_name: Ana
full_name: Lennon Duménil, Ana
last_name: Lennon Duménil
citation:
ama: Chabaud M, Heuzé M, Bretou M, et al. Cell migration and antigen capture are
antagonistic processes coupled by myosin II in dendritic cells. Nature Communications.
2015;6. doi:10.1038/ncomms8526
apa: Chabaud, M., Heuzé, M., Bretou, M., Vargas, P., Maiuri, P., Solanes, P., …
Lennon Duménil, A. (2015). Cell migration and antigen capture are antagonistic
processes coupled by myosin II in dendritic cells. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms8526
chicago: Chabaud, Mélanie, Mélina Heuzé, Marine Bretou, Pablo Vargas, Paolo Maiuri,
Paola Solanes, Mathieu Maurin, et al. “Cell Migration and Antigen Capture Are
Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications.
Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms8526.
ieee: M. Chabaud et al., “Cell migration and antigen capture are antagonistic
processes coupled by myosin II in dendritic cells,” Nature Communications,
vol. 6. Nature Publishing Group, 2015.
ista: Chabaud M, Heuzé M, Bretou M, Vargas P, Maiuri P, Solanes P, Maurin M, Terriac
E, Le Berre M, Lankar D, Piolot T, Adelstein R, Zhang Y, Sixt MK, Jacobelli J,
Bénichou O, Voituriez R, Piel M, Lennon Duménil A. 2015. Cell migration and antigen
capture are antagonistic processes coupled by myosin II in dendritic cells. Nature
Communications. 6, 7526.
mla: Chabaud, Mélanie, et al. “Cell Migration and Antigen Capture Are Antagonistic
Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications,
vol. 6, 7526, Nature Publishing Group, 2015, doi:10.1038/ncomms8526.
short: M. Chabaud, M. Heuzé, M. Bretou, P. Vargas, P. Maiuri, P. Solanes, M. Maurin,
E. Terriac, M. Le Berre, D. Lankar, T. Piolot, R. Adelstein, Y. Zhang, M.K. Sixt,
J. Jacobelli, O. Bénichou, R. Voituriez, M. Piel, A. Lennon Duménil, Nature Communications
6 (2015).
date_created: 2018-12-11T11:52:48Z
date_published: 2015-06-25T00:00:00Z
date_updated: 2021-01-12T06:51:42Z
day: '25'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1038/ncomms8526
file:
- access_level: open_access
checksum: bae12e86be2adb28253f890b8bba8315
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:58Z
date_updated: 2020-07-14T12:45:02Z
file_id: '4915'
file_name: IST-2016-476-v1+1_ncomms8526.pdf
file_size: 4530215
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5596'
pubrep_id: '476'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cell migration and antigen capture are antagonistic processes coupled by myosin
II in dendritic 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '1569'
abstract:
- lang: eng
text: Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin)
is essential for plant development. Auxin gradient establishment is mediated by
polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their
localization and abundance at the plasma membrane are tightly regulated by endomembrane
machinery, especially the endocytic and recycling pathways mediated by the ADP
ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed
the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis
thaliana by pharmacological and genetic approaches. We identified the compound
endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without
altering the polarity of apical proteins. ES8 alters the auxin distribution pattern
in the root and induces a strong developmental phenotype, including reduced root
length. The ARF-GEF- defective mutants gnom-like 1 ( gnl1-1) and gnom ( van7)
are significantly resistant to ES8. The compound does not affect recycling or
vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting
in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role
for GNOM in endoplasmic reticulum (ER) - Golgi trafficking and reveal that a GNL1/GNOM-mediated
early secretory pathway selectively regulates PIN1 basal polarity establishment
in a manner essential for normal plant development.
acknowledgement: 'This work was supported by Vetenskapsrådet and Vinnova (Verket för
Innovationssystemet) (S.M.D., T.V., M.Ł., and S.R.), Knut och Alice Wallenbergs
Stiftelse (S.M.D., A.R., and C.V.), Kempestiftelserna (A.H. and Q.M.), Carl Tryggers
Stiftelse för Vetenskaplig Forskning (Q.M.), European Research Council Grant ERC-2011-StG-20101109-PSDP
(to J.F.), US Department of Energy Grant DE-FG02-02ER15295 (to N.V.R.), and National
Science Foundation Grant MCB-0817916 (to N.V.R. and G.R.H.). '
author:
- first_name: Siamsa
full_name: Doyle, Siamsa
last_name: Doyle
- first_name: Ash
full_name: Haegera, Ash
last_name: Haegera
- first_name: Thomas
full_name: Vain, Thomas
last_name: Vain
- first_name: Adeline
full_name: Rigala, Adeline
last_name: Rigala
- first_name: Corrado
full_name: Viotti, Corrado
last_name: Viotti
- first_name: Małgorzata
full_name: Łangowskaa, Małgorzata
last_name: Łangowskaa
- first_name: Qian
full_name: Maa, Qian
last_name: Maa
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Natasha
full_name: Raikhel, Natasha
last_name: Raikhel
- first_name: Glenn
full_name: Hickse, Glenn
last_name: Hickse
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
citation:
ama: Doyle S, Haegera A, Vain T, et al. An early secretory pathway mediated by gnom-like
1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana.
PNAS. 2015;112(7):E806-E815. doi:10.1073/pnas.1424856112
apa: Doyle, S., Haegera, A., Vain, T., Rigala, A., Viotti, C., Łangowskaa, M., …
Robert, S. (2015). An early secretory pathway mediated by gnom-like 1 and gnom
is essential for basal polarity establishment in Arabidopsis thaliana. PNAS.
National Academy of Sciences. https://doi.org/10.1073/pnas.1424856112
chicago: Doyle, Siamsa, Ash Haegera, Thomas Vain, Adeline Rigala, Corrado Viotti,
Małgorzata Łangowskaa, Qian Maa, et al. “An Early Secretory Pathway Mediated by
Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis
Thaliana.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1424856112.
ieee: S. Doyle et al., “An early secretory pathway mediated by gnom-like
1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana,”
PNAS, vol. 112, no. 7. National Academy of Sciences, pp. E806–E815, 2015.
ista: Doyle S, Haegera A, Vain T, Rigala A, Viotti C, Łangowskaa M, Maa Q, Friml
J, Raikhel N, Hickse G, Robert S. 2015. An early secretory pathway mediated by
gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis
thaliana. PNAS. 112(7), E806–E815.
mla: Doyle, Siamsa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and
Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS,
vol. 112, no. 7, National Academy of Sciences, 2015, pp. E806–15, doi:10.1073/pnas.1424856112.
short: S. Doyle, A. Haegera, T. Vain, A. Rigala, C. Viotti, M. Łangowskaa, Q. Maa,
J. Friml, N. Raikhel, G. Hickse, S. Robert, PNAS 112 (2015) E806–E815.
date_created: 2018-12-11T11:52:46Z
date_published: 2015-02-17T00:00:00Z
date_updated: 2021-01-12T06:51:39Z
day: '17'
department:
- _id: JiFr
doi: 10.1073/pnas.1424856112
ec_funded: 1
intvolume: ' 112'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343110/
month: '02'
oa: 1
oa_version: Published Version
page: E806 - E815
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5602'
quality_controlled: '1'
scopus_import: 1
status: public
title: An early secretory pathway mediated by gnom-like 1 and gnom is essential for
basal polarity establishment in Arabidopsis thaliana
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1570'
abstract:
- lang: eng
text: Grounding autonomous behavior in the nervous system is a fundamental challenge
for neuroscience. In particular, self-organized behavioral development provides
more questions than answers. Are there special functional units for curiosity,
motivation, and creativity? This paper argues that these features can be grounded
in synaptic plasticity itself, without requiring any higher-level constructs.
We propose differential extrinsic plasticity (DEP) as a new synaptic rule for
self-learning systems and apply it to a number of complex robotic systems as a
test case. Without specifying any purpose or goal, seemingly purposeful and adaptive
rhythmic behavior is developed, displaying a certain level of sensorimotor intelligence.
These surprising results require no systemspecific modifications of the DEP rule.
They rather arise from the underlying mechanism of spontaneous symmetry breaking,which
is due to the tight brain body environment coupling. The new synaptic rule is
biologically plausible and would be an interesting target for neurobiological
investigation. We also argue that this neuronal mechanism may have been a catalyst
in natural evolution.
author:
- first_name: Ralf
full_name: Der, Ralf
last_name: Der
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
citation:
ama: Der R, Martius GS. Novel plasticity rule can explain the development of sensorimotor
intelligence. PNAS. 2015;112(45):E6224-E6232. doi:10.1073/pnas.1508400112
apa: Der, R., & Martius, G. S. (2015). Novel plasticity rule can explain the
development of sensorimotor intelligence. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1508400112
chicago: Der, Ralf, and Georg S Martius. “Novel Plasticity Rule Can Explain the
Development of Sensorimotor Intelligence.” PNAS. National Academy of Sciences,
2015. https://doi.org/10.1073/pnas.1508400112.
ieee: R. Der and G. S. Martius, “Novel plasticity rule can explain the development
of sensorimotor intelligence,” PNAS, vol. 112, no. 45. National Academy
of Sciences, pp. E6224–E6232, 2015.
ista: Der R, Martius GS. 2015. Novel plasticity rule can explain the development
of sensorimotor intelligence. PNAS. 112(45), E6224–E6232.
mla: Der, Ralf, and Georg S. Martius. “Novel Plasticity Rule Can Explain the Development
of Sensorimotor Intelligence.” PNAS, vol. 112, no. 45, National Academy
of Sciences, 2015, pp. E6224–32, doi:10.1073/pnas.1508400112.
short: R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232.
date_created: 2018-12-11T11:52:47Z
date_published: 2015-11-10T00:00:00Z
date_updated: 2021-01-12T06:51:40Z
day: '10'
department:
- _id: ChLa
- _id: GaTk
doi: 10.1073/pnas.1508400112
ec_funded: 1
external_id:
pmid:
- '26504200'
intvolume: ' 112'
issue: '45'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653169/
month: '11'
oa: 1
oa_version: Submitted Version
page: E6224 - E6232
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5601'
quality_controlled: '1'
scopus_import: 1
status: public
title: Novel plasticity rule can explain the development of sensorimotor intelligence
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1571'
abstract:
- lang: eng
text: Epistatic interactions can frustrate and shape evolutionary change. Indeed,
phenotypes may fail to evolve when essential mutations are only accessible through
positive selection if they are fixed simultaneously. How environmental variability
affects such constraints is poorly understood. Here, we studied genetic constraints
in fixed and fluctuating environments using the Escherichia coli lac operon as
a model system for genotype-environment interactions. We found that, in different
fixed environments, all trajectories that were reconstructed by applying point
mutations within the transcription factor-operator interface became trapped at
suboptima, where no additional improvements were possible. Paradoxically, repeated
switching between these same environments allows unconstrained adaptation by continuous
improvements. This evolutionary mode is explained by pervasive cross-environmental
tradeoffs that reposition the peaks in such a way that trapped genotypes can repeatedly
climb ascending slopes and hence, escape adaptive stasis. Using a Markov approach,
we developed a mathematical framework to quantify the landscape-crossing rates
and show that this ratchet-like adaptive mechanism is robust in a wide spectrum
of fluctuating environments. Overall, this study shows that genetic constraints
can be overcome by environmental change and that crossenvironmental tradeoffs
do not necessarily impede but also, can facilitate adaptive evolution. Because
tradeoffs and environmental variability are ubiquitous in nature, we speculate
this evolutionary mode to be of general relevance.
acknowledgement: This work is part of the research program of the Foundation for Fundamental
Research on Matter, which is part of the Netherlands Organization for Scientific
Research (NWO). M.G.J.d.V. was (partially) funded by NWO Earth and Life Sciences
(ALW), project 863.14.015. We thank D. M. Weinreich, J. A. G. M. de Visser, T. Paixão,
J. Polechová, T. Friedlander, and A. E. Mayo for reading and commenting on earlier
versions of the manuscript and B. Houchmandzadeh, O. Rivoire, and M. Hemery for
discussions and suggestions on the Markov computation. Furthermore, we thank F.
J. Poelwijk for sharing plasmid pCascade5 and pRD007 and Y. Yokobayashi for sharing
plasmid pINV-110. We also thank the anonymous reviewers for remarks on the initial
version of the manuscript.
author:
- first_name: Marjon
full_name: De Vos, Marjon
id: 3111FFAC-F248-11E8-B48F-1D18A9856A87
last_name: De Vos
- first_name: Alexandre
full_name: Dawid, Alexandre
last_name: Dawid
- first_name: Vanda
full_name: Šunderlíková, Vanda
last_name: Šunderlíková
- first_name: Sander
full_name: Tans, Sander
last_name: Tans
citation:
ama: de Vos M, Dawid A, Šunderlíková V, Tans S. Breaking evolutionary constraint
with a tradeoff ratchet. PNAS. 2015;112(48):14906-14911. doi:10.1073/pnas.1510282112
apa: de Vos, M., Dawid, A., Šunderlíková, V., & Tans, S. (2015). Breaking evolutionary
constraint with a tradeoff ratchet. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1510282112
chicago: Vos, Marjon de, Alexandre Dawid, Vanda Šunderlíková, and Sander Tans. “Breaking
Evolutionary Constraint with a Tradeoff Ratchet.” PNAS. National Academy
of Sciences, 2015. https://doi.org/10.1073/pnas.1510282112.
ieee: M. de Vos, A. Dawid, V. Šunderlíková, and S. Tans, “Breaking evolutionary
constraint with a tradeoff ratchet,” PNAS, vol. 112, no. 48. National Academy
of Sciences, pp. 14906–14911, 2015.
ista: de Vos M, Dawid A, Šunderlíková V, Tans S. 2015. Breaking evolutionary constraint
with a tradeoff ratchet. PNAS. 112(48), 14906–14911.
mla: de Vos, Marjon, et al. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.”
PNAS, vol. 112, no. 48, National Academy of Sciences, 2015, pp. 14906–11,
doi:10.1073/pnas.1510282112.
short: M. de Vos, A. Dawid, V. Šunderlíková, S. Tans, PNAS 112 (2015) 14906–14911.
date_created: 2018-12-11T11:52:47Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T06:51:40Z
day: '01'
department:
- _id: ToBo
doi: 10.1073/pnas.1510282112
intvolume: ' 112'
issue: '48'
language:
- iso: eng
month: '12'
oa_version: None
page: 14906 - 14911
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5600'
quality_controlled: '1'
scopus_import: 1
status: public
title: Breaking evolutionary constraint with a tradeoff ratchet
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1572'
abstract:
- lang: eng
text: "We consider the quantum ferromagnetic Heisenberg model in three dimensions,
for all spins S ≥ 1/2. We rigorously prove the validity of the spin-wave approximation
for the excitation spectrum, at the level of the first non-trivial contribution
to the free energy at low temperatures. Our proof comes with explicit, constructive
upper and lower bounds on the error term. It uses in an essential way the bosonic
formulation of the model in terms of the Holstein-Primakoff representation. In
this language, the model describes interacting bosons with a hard-core on-site
repulsion and a nearest-neighbor attraction. This attractive interaction makes
the lower bound on the free energy particularly tricky: the key idea there is
to prove a differential inequality for the two-particle density, which is thereby
shown to be smaller than the probability density of a suitably weighted two-particle
random process on the lattice.\r\n"
author:
- first_name: Michele
full_name: Correggi, Michele
last_name: Correggi
- first_name: Alessandro
full_name: Giuliani, Alessandro
last_name: Giuliani
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Correggi M, Giuliani A, Seiringer R. Validity of the spin-wave approximation
for the free energy of the Heisenberg ferromagnet. Communications in Mathematical
Physics. 2015;339(1):279-307. doi:10.1007/s00220-015-2402-0
apa: Correggi, M., Giuliani, A., & Seiringer, R. (2015). Validity of the spin-wave
approximation for the free energy of the Heisenberg ferromagnet. Communications
in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-015-2402-0
chicago: Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity
of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.”
Communications in Mathematical Physics. Springer, 2015. https://doi.org/10.1007/s00220-015-2402-0.
ieee: M. Correggi, A. Giuliani, and R. Seiringer, “Validity of the spin-wave approximation
for the free energy of the Heisenberg ferromagnet,” Communications in Mathematical
Physics, vol. 339, no. 1. Springer, pp. 279–307, 2015.
ista: Correggi M, Giuliani A, Seiringer R. 2015. Validity of the spin-wave approximation
for the free energy of the Heisenberg ferromagnet. Communications in Mathematical
Physics. 339(1), 279–307.
mla: Correggi, Michele, et al. “Validity of the Spin-Wave Approximation for the
Free Energy of the Heisenberg Ferromagnet.” Communications in Mathematical
Physics, vol. 339, no. 1, Springer, 2015, pp. 279–307, doi:10.1007/s00220-015-2402-0.
short: M. Correggi, A. Giuliani, R. Seiringer, Communications in Mathematical Physics
339 (2015) 279–307.
date_created: 2018-12-11T11:52:47Z
date_published: 2015-06-23T00:00:00Z
date_updated: 2021-01-12T06:51:41Z
day: '23'
department:
- _id: RoSe
doi: 10.1007/s00220-015-2402-0
intvolume: ' 339'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1312.7873
month: '06'
oa: 1
oa_version: Preprint
page: 279 - 307
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '5599'
quality_controlled: '1'
scopus_import: 1
status: public
title: Validity of the spin-wave approximation for the free energy of the Heisenberg
ferromagnet
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 339
year: '2015'
...
---
_id: '1573'
abstract:
- lang: eng
text: We present a new, simpler proof of the unconditional uniqueness of solutions
to the cubic Gross-Pitaevskii hierarchy in ℝ3. One of the main tools in our analysis
is the quantum de Finetti theorem. Our uniqueness result is equivalent to the
one established in the celebrated works of Erdos, Schlein, and Yau.
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. Unconditional uniqueness for the
cubic gross pitaevskii hierarchy via quantum de finetti. Communications on
Pure and Applied Mathematics. 2015;68(10):1845-1884. doi:10.1002/cpa.21552
apa: Chen, T., Hainzl, C., Pavlović, N., & Seiringer, R. (2015). Unconditional
uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications
on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21552
chicago: Chen, Thomas, Christian Hainzl, Nataša Pavlović, and Robert Seiringer.
“Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum
de Finetti.” Communications on Pure and Applied Mathematics. Wiley, 2015.
https://doi.org/10.1002/cpa.21552.
ieee: T. Chen, C. Hainzl, N. Pavlović, and R. Seiringer, “Unconditional uniqueness
for the cubic gross pitaevskii hierarchy via quantum de finetti,” Communications
on Pure and Applied Mathematics, vol. 68, no. 10. Wiley, pp. 1845–1884, 2015.
ista: Chen T, Hainzl C, Pavlović N, Seiringer R. 2015. Unconditional uniqueness
for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications
on Pure and Applied Mathematics. 68(10), 1845–1884.
mla: Chen, Thomas, et al. “Unconditional Uniqueness for the Cubic Gross Pitaevskii
Hierarchy via Quantum de Finetti.” Communications on Pure and Applied Mathematics,
vol. 68, no. 10, Wiley, 2015, pp. 1845–84, doi:10.1002/cpa.21552.
short: T. Chen, C. Hainzl, N. Pavlović, R. Seiringer, Communications on Pure and
Applied Mathematics 68 (2015) 1845–1884.
date_created: 2018-12-11T11:52:48Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2021-01-12T06:51:41Z
day: '01'
department:
- _id: RoSe
doi: 10.1002/cpa.21552
intvolume: ' 68'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1307.3168
month: '10'
oa: 1
oa_version: Preprint
page: 1845 - 1884
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
publication: Communications on Pure and Applied Mathematics
publication_status: published
publisher: Wiley
publist_id: '5598'
quality_controlled: '1'
scopus_import: 1
status: public
title: Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum
de finetti
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 68
year: '2015'
...
---
_id: '1580'
abstract:
- lang: eng
text: Synapsins (Syns) are an evolutionarily conserved family of presynaptic proteins
crucial for the fine-tuning of synaptic function. A large amount of experimental
evidences has shown that Syns are involved in the development of epileptic phenotypes
and several mutations in Syn genes have been associated with epilepsy in humans
and animal models. Syn mutations induce alterations in circuitry and neurotransmitter
release, differentially affecting excitatory and inhibitory synapses, thus causing
an excitation/inhibition imbalance in network excitability toward hyperexcitability
that may be a determinant with regard to the development of epilepsy. Another
approach to investigate epileptogenic mechanisms is to understand how silencing
Syn affects the cellular behavior of single neurons and is associated with the
hyperexcitable phenotypes observed in epilepsy. Here, we examined the functional
effects of antisense-RNA inhibition of Syn expression on individually identified
and isolated serotonergic cells of the Helix land snail. We found that Helix synapsin
silencing increases cell excitability characterized by a slightly depolarized
resting membrane potential, decreases the rheobase, reduces the threshold for
action potential (AP) firing and increases the mean and instantaneous firing rates,
with respect to control cells. The observed increase of Ca2+ and BK currents in
Syn-silenced cells seems to be related to changes in the shape of the AP waveform.
These currents sustain the faster spiking in Syn-deficient cells by increasing
the after hyperpolarization and limiting the Na+ and Ca2+ channel inactivation
during repetitive firing. This in turn speeds up the depolarization phase by reaching
the AP threshold faster. Our results provide evidence that Syn silencing increases
intrinsic cell excitability associated with increased Ca2+ and Ca2+-dependent
BK currents in the absence of excitatory or inhibitory inputs.
article_processing_charge: No
article_type: original
author:
- first_name: Oscar
full_name: Brenes, Oscar
last_name: Brenes
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Emilio
full_name: Carbone, Emilio
last_name: Carbone
- first_name: Pier
full_name: Montarolo, Pier
last_name: Montarolo
- first_name: Mirella
full_name: Ghirardi, Mirella
last_name: Ghirardi
citation:
ama: Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. Knock-down of synapsin
alters cell excitability and action potential waveform by potentiating BK and
voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience.
2015;311:430-443. doi:10.1016/j.neuroscience.2015.10.046
apa: Brenes, O., Vandael, D. H., Carbone, E., Montarolo, P., & Ghirardi, M.
(2015). Knock-down of synapsin alters cell excitability and action potential waveform
by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons.
Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2015.10.046
chicago: Brenes, Oscar, David H Vandael, Emilio Carbone, Pier Montarolo, and Mirella
Ghirardi. “Knock-down of Synapsin Alters Cell Excitability and Action Potential
Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic
Neurons.” Neuroscience. Elsevier, 2015. https://doi.org/10.1016/j.neuroscience.2015.10.046.
ieee: O. Brenes, D. H. Vandael, E. Carbone, P. Montarolo, and M. Ghirardi, “Knock-down
of synapsin alters cell excitability and action potential waveform by potentiating
BK and voltage gated Ca2 currents in Helix serotonergic neurons,” Neuroscience,
vol. 311. Elsevier, pp. 430–443, 2015.
ista: Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. 2015. Knock-down
of synapsin alters cell excitability and action potential waveform by potentiating
BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience.
311, 430–443.
mla: Brenes, Oscar, et al. “Knock-down of Synapsin Alters Cell Excitability and
Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in
Helix Serotonergic Neurons.” Neuroscience, vol. 311, Elsevier, 2015, pp.
430–43, doi:10.1016/j.neuroscience.2015.10.046.
short: O. Brenes, D.H. Vandael, E. Carbone, P. Montarolo, M. Ghirardi, Neuroscience
311 (2015) 430–443.
date_created: 2018-12-11T11:52:50Z
date_published: 2015-12-17T00:00:00Z
date_updated: 2021-01-12T06:51:44Z
day: '17'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.neuroscience.2015.10.046
file:
- access_level: open_access
checksum: af2c4c994718c7be417eba0dc746aac9
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T06:50:20Z
date_updated: 2020-07-14T12:45:02Z
file_id: '7849'
file_name: 2015_Neuroscience_Brenes.pdf
file_size: 5563015
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 311'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
page: 430 - 443
publication: Neuroscience
publication_status: published
publisher: Elsevier
publist_id: '5591'
quality_controlled: '1'
scopus_import: 1
status: public
title: Knock-down of synapsin alters cell excitability and action potential waveform
by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons
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: 311
year: '2015'
...
---
_id: '1577'
abstract:
- lang: eng
text: Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked
genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be
unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y
transposition must be the main source of Drosophila Y-linked genes. Here we show
how these genes were acquired. We found a previously unidentified gene (flagrante
delicto Y, FDY) that originated from a recent duplication of the autosomal gene
vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were
duplicated along with vig2, but they became pseudogenes through the accumulation
of deletions and transposable element insertions, whereas FDY remained functional,
acquired testis-specific expression, and now accounts for ∼20% of the vig2-like
mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and
DNA sequence divergence indicates that the duplication to the Y chromosome occurred
∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the
establishment of a Y-linked gene and demonstrates how the Drosophila Y has been
accumulating autosomal genes.
acknowledgement: "This work was supported by grants from Conselho Nacional de Desenvolvimento
Científico e Tecnológico (CNPq), FAPERJ, and CAPES (to A.B.C.), and National Institutes
of Health Grant R01 GM64590 (to A.G.C. and A.B.C.).\r\nWe thank M. Vibranovski,
C. Bergman, and the Berkeley Drosophila Genome Project for access to unpublished
data; M. Vibranovski, R. Hoskins, S. Celniker, C. Kennedy, J. Carlson, S. Galasinski,
B. Wakimoto, J. Yasuhara, G. Sutton, M. Kuhner, J. Felsenstein, and C. Santos for
help in various steps of the work; and B. Bitner-Mathe, R. Ventura, the members
of the A.B.C. and A.G.C. laboratories, and two reviewers for many valuable comments
on the manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: Antonio
full_name: Carvalho, Antonio
last_name: Carvalho
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Claudia
full_name: Russo, Claudia
last_name: Russo
- first_name: Bonnielin
full_name: Swenor, Bonnielin
last_name: Swenor
- first_name: Andrew
full_name: Clark, Andrew
last_name: Clark
citation:
ama: Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. Birth of a new gene on the
Y chromosome of Drosophila melanogaster. PNAS. 2015;112(40):12450-12455.
doi:10.1073/pnas.1516543112
apa: Carvalho, A., Vicoso, B., Russo, C., Swenor, B., & Clark, A. (2015). Birth
of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1516543112
chicago: Carvalho, Antonio, Beatriz Vicoso, Claudia Russo, Bonnielin Swenor, and
Andrew Clark. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.”
PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1516543112.
ieee: A. Carvalho, B. Vicoso, C. Russo, B. Swenor, and A. Clark, “Birth of a new
gene on the Y chromosome of Drosophila melanogaster,” PNAS, vol. 112, no.
40. National Academy of Sciences, pp. 12450–12455, 2015.
ista: Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. 2015. Birth of a new gene
on the Y chromosome of Drosophila melanogaster. PNAS. 112(40), 12450–12455.
mla: Carvalho, Antonio, et al. “Birth of a New Gene on the Y Chromosome of Drosophila
Melanogaster.” PNAS, vol. 112, no. 40, National Academy of Sciences, 2015,
pp. 12450–55, doi:10.1073/pnas.1516543112.
short: A. Carvalho, B. Vicoso, C. Russo, B. Swenor, A. Clark, PNAS 112 (2015) 12450–12455.
date_created: 2018-12-11T11:52:49Z
date_published: 2015-10-06T00:00:00Z
date_updated: 2021-01-12T06:51:43Z
day: '06'
department:
- _id: BeVi
doi: 10.1073/pnas.1516543112
external_id:
pmid:
- '26385968'
intvolume: ' 112'
issue: '40'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603513/
month: '10'
oa: 1
oa_version: Published Version
page: 12450 - 12455
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5594'
quality_controlled: '1'
scopus_import: 1
status: public
title: Birth of a new gene on the Y chromosome of Drosophila melanogaster
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1579'
abstract:
- lang: eng
text: We show that the Galois group of any Schubert problem involving lines in projective
space contains the alternating group. This constitutes the largest family of enumerative
problems whose Galois groups have been largely determined. Using a criterion of
Vakil and a special position argument due to Schubert, our result follows from
a particular inequality among Kostka numbers of two-rowed tableaux. In most cases,
a combinatorial injection proves the inequality. For the remaining cases, we use
the Weyl integral formulas to obtain an integral formula for these Kostka numbers.
This rewrites the inequality as an integral, which we estimate to establish the
inequality.
acknowledgement: "This research was supported in part by NSF grant DMS-915211 and
the Institut Mittag-Leffler.\r\n"
article_processing_charge: No
author:
- first_name: Christopher
full_name: Brooks, Christopher
last_name: Brooks
- 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
citation:
ama: Brooks C, Martin del Campo Sanchez A, Sottile F. Galois groups of Schubert
problems of lines are at least alternating. Transactions of the American Mathematical
Society. 2015;367(6):4183-4206. doi:10.1090/S0002-9947-2014-06192-8
apa: Brooks, C., Martin del Campo Sanchez, A., & Sottile, F. (2015). Galois
groups of Schubert problems of lines are at least alternating. Transactions
of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/S0002-9947-2014-06192-8
chicago: Brooks, Christopher, Abraham Martin del Campo Sanchez, and Frank Sottile.
“Galois Groups of Schubert Problems of Lines Are at Least Alternating.” Transactions
of the American Mathematical Society. American Mathematical Society, 2015.
https://doi.org/10.1090/S0002-9947-2014-06192-8.
ieee: C. Brooks, A. Martin del Campo Sanchez, and F. Sottile, “Galois groups of
Schubert problems of lines are at least alternating,” Transactions of the American
Mathematical Society, vol. 367, no. 6. American Mathematical Society, pp.
4183–4206, 2015.
ista: Brooks C, Martin del Campo Sanchez A, Sottile F. 2015. Galois groups of Schubert
problems of lines are at least alternating. Transactions of the American Mathematical
Society. 367(6), 4183–4206.
mla: Brooks, Christopher, et al. “Galois Groups of Schubert Problems of Lines Are
at Least Alternating.” Transactions of the American Mathematical Society,
vol. 367, no. 6, American Mathematical Society, 2015, pp. 4183–206, doi:10.1090/S0002-9947-2014-06192-8.
short: C. Brooks, A. Martin del Campo Sanchez, F. Sottile, Transactions of the American
Mathematical Society 367 (2015) 4183–4206.
date_created: 2018-12-11T11:52:50Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2021-01-12T06:51:43Z
day: '01'
department:
- _id: CaUh
doi: 10.1090/S0002-9947-2014-06192-8
intvolume: ' 367'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1207.4280
month: '06'
oa: 1
oa_version: Preprint
page: 4183 - 4206
publication: Transactions of the American Mathematical Society
publication_status: published
publisher: American Mathematical Society
publist_id: '5592'
quality_controlled: '1'
scopus_import: 1
status: public
title: Galois groups of Schubert problems of lines are at least alternating
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 367
year: '2015'
...
---
_id: '1578'
abstract:
- lang: eng
text: We prove that the dual of the digital Voronoi diagram constructed by flooding
the plane from the data points gives a geometrically and topologically correct
dual triangulation. This provides the proof of correctness for recently developed
GPU algorithms that outperform traditional CPU algorithms for constructing two-dimensional
Delaunay triangulations.
acknowledgement: "The research of the second author is partially supported by NSF
under grant DBI-0820624 and by DARPA under grants HR011-05-1-0057 and HR0011-09-006\r\n"
author:
- first_name: Thanhtung
full_name: Cao, Thanhtung
last_name: Cao
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Tiowseng
full_name: Tan, Tiowseng
last_name: Tan
citation:
ama: Cao T, Edelsbrunner H, Tan T. Triangulations from topologically correct digital
Voronoi diagrams. Computational Geometry. 2015;48(7):507-519. doi:10.1016/j.comgeo.2015.04.001
apa: Cao, T., Edelsbrunner, H., & Tan, T. (2015). Triangulations from topologically
correct digital Voronoi diagrams. Computational Geometry. Elsevier. https://doi.org/10.1016/j.comgeo.2015.04.001
chicago: Cao, Thanhtung, Herbert Edelsbrunner, and Tiowseng Tan. “Triangulations
from Topologically Correct Digital Voronoi Diagrams.” Computational Geometry.
Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2015.04.001.
ieee: T. Cao, H. Edelsbrunner, and T. Tan, “Triangulations from topologically correct
digital Voronoi diagrams,” Computational Geometry, vol. 48, no. 7. Elsevier,
pp. 507–519, 2015.
ista: Cao T, Edelsbrunner H, Tan T. 2015. Triangulations from topologically correct
digital Voronoi diagrams. Computational Geometry. 48(7), 507–519.
mla: Cao, Thanhtung, et al. “Triangulations from Topologically Correct Digital Voronoi
Diagrams.” Computational Geometry, vol. 48, no. 7, Elsevier, 2015, pp.
507–19, doi:10.1016/j.comgeo.2015.04.001.
short: T. Cao, H. Edelsbrunner, T. Tan, Computational Geometry 48 (2015) 507–519.
date_created: 2018-12-11T11:52:49Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:43Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.comgeo.2015.04.001
intvolume: ' 48'
issue: '7'
language:
- iso: eng
month: '08'
oa_version: None
page: 507 - 519
publication: Computational Geometry
publication_status: published
publisher: Elsevier
publist_id: '5593'
quality_controlled: '1'
scopus_import: 1
status: public
title: Triangulations from topologically correct digital Voronoi diagrams
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2015'
...
---
_id: '1581'
abstract:
- lang: eng
text: In animal embryos, morphogen gradients determine tissue patterning and morphogenesis.
Shyer et al. provide evidence that, during vertebrate gut formation, tissue folding
generates graded activity of signals required for subsequent steps of gut growth
and differentiation, thereby revealing an intriguing link between tissue morphogenesis
and morphogen gradient formation.
article_processing_charge: No
author:
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Bollenbach MT, Heisenberg C-PJ. Gradients are shaping up. Cell. 2015;161(3):431-432.
doi:10.1016/j.cell.2015.04.009
apa: Bollenbach, M. T., & Heisenberg, C.-P. J. (2015). Gradients are shaping
up. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.04.009
chicago: Bollenbach, Mark Tobias, and Carl-Philipp J Heisenberg. “Gradients Are
Shaping Up.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.04.009.
ieee: M. T. Bollenbach and C.-P. J. Heisenberg, “Gradients are shaping up,” Cell,
vol. 161, no. 3. Cell Press, pp. 431–432, 2015.
ista: Bollenbach MT, Heisenberg C-PJ. 2015. Gradients are shaping up. Cell. 161(3),
431–432.
mla: Bollenbach, Mark Tobias, and Carl-Philipp J. Heisenberg. “Gradients Are Shaping
Up.” Cell, vol. 161, no. 3, Cell Press, 2015, pp. 431–32, doi:10.1016/j.cell.2015.04.009.
short: M.T. Bollenbach, C.-P.J. Heisenberg, Cell 161 (2015) 431–432.
date_created: 2018-12-11T11:52:50Z
date_published: 2015-04-23T00:00:00Z
date_updated: 2022-08-25T13:56:10Z
day: '23'
department:
- _id: ToBo
- _id: CaHe
doi: 10.1016/j.cell.2015.04.009
intvolume: ' 161'
issue: '3'
language:
- iso: eng
month: '04'
oa_version: None
page: 431 - 432
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '5590'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gradients are shaping up
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 161
year: '2015'
...
---
_id: '1589'
abstract:
- lang: eng
text: We investigate the dynamics of ferrofluidic wavy vortex flows in the counter-rotating
Taylor-Couette system, with a focus on wavy flows with a mixture of the dominant
azimuthal modes. Without external magnetic field flows are stable and pro-grade
with respect to the rotation of the inner cylinder. More complex behaviors can
arise when an axial or a transverse magnetic field is applied. Depending on the
direction and strength of the field, multi-stable wavy states and bifurcations
can occur. We uncover the phenomenon of flow pattern reversal as the strength
of the magnetic field is increased through a critical value. In between the regimes
of pro-grade and retrograde flow rotations, standing waves with zero angular velocities
can emerge. A striking finding is that, under a transverse magnetic field, a second
reversal in the flow pattern direction can occur, where the flow pattern evolves
into pro-grade rotation again from a retrograde state. Flow reversal is relevant
to intriguing phenomena in nature such as geomagnetic reversal. Our results suggest
that, in ferrofluids, flow pattern reversal can be induced by varying a magnetic
field in a controlled manner, which can be realized in laboratory experiments
with potential applications in the development of modern fluid devices.
article_number: '18589'
article_type: original
author:
- first_name: Sebastian
full_name: Altmeyer, Sebastian
id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87
last_name: Altmeyer
orcid: 0000-0001-5964-0203
- first_name: Younghae
full_name: Do, Younghae
last_name: Do
- first_name: Ying
full_name: Lai, Ying
last_name: Lai
citation:
ama: Altmeyer S, Do Y, Lai Y. Magnetic field induced flow pattern reversal in a
ferrofluidic Taylor-Couette system. Scientific Reports. 2015;5. doi:10.1038/srep18589
apa: Altmeyer, S., Do, Y., & Lai, Y. (2015). Magnetic field induced flow pattern
reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. Nature
Publishing Group. https://doi.org/10.1038/srep18589
chicago: Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Magnetic Field Induced
Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” Scientific
Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep18589.
ieee: S. Altmeyer, Y. Do, and Y. Lai, “Magnetic field induced flow pattern reversal
in a ferrofluidic Taylor-Couette system,” Scientific Reports, vol. 5. Nature
Publishing Group, 2015.
ista: Altmeyer S, Do Y, Lai Y. 2015. Magnetic field induced flow pattern reversal
in a ferrofluidic Taylor-Couette system. Scientific Reports. 5, 18589.
mla: Altmeyer, Sebastian, et al. “Magnetic Field Induced Flow Pattern Reversal in
a Ferrofluidic Taylor-Couette System.” Scientific Reports, vol. 5, 18589,
Nature Publishing Group, 2015, doi:10.1038/srep18589.
short: S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).
date_created: 2018-12-11T11:52:53Z
date_published: 2015-12-21T00:00:00Z
date_updated: 2021-01-12T06:51:48Z
day: '21'
ddc:
- '530'
- '540'
department:
- _id: BjHo
doi: 10.1038/srep18589
file:
- access_level: open_access
checksum: 927e151674347661ce36eae2818dafdc
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:49Z
date_updated: 2020-07-14T12:45:03Z
file_id: '5036'
file_name: IST-2016-472-v1+1_srep18589.pdf
file_size: 2771236
relation: main_file
file_date_updated: 2020-07-14T12:45:03Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '5582'
pubrep_id: '472'
quality_controlled: '1'
scopus_import: 1
status: public
title: Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette
system
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: 5
year: '2015'
...
---
_id: '1584'
abstract:
- lang: eng
text: We investigate weighted straight skeletons from a geometric, graph-theoretical,
and combinatorial point of view. We start with a thorough definition and shed
light on some ambiguity issues in the procedural definition. We investigate the
geometry, combinatorics, and topology of faces and the roof model, and we discuss
in which cases a weighted straight skeleton is connected. Finally, we show that
the weighted straight skeleton of even a simple polygon may be non-planar and
may contain cycles, and we discuss under which restrictions on the weights and/or
the input polygon the weighted straight skeleton still behaves similar to its
unweighted counterpart. In particular, we obtain a non-procedural description
and a linear-time construction algorithm for the straight skeleton of strictly
convex polygons with arbitrary weights.
author:
- first_name: Therese
full_name: Biedl, Therese
last_name: Biedl
- first_name: Martin
full_name: Held, Martin
last_name: Held
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Dominik
full_name: Kaaser, Dominik
last_name: Kaaser
- first_name: Peter
full_name: Palfrader, Peter
last_name: Palfrader
citation:
ama: 'Biedl T, Held M, Huber S, Kaaser D, Palfrader P. Reprint of: Weighted straight
skeletons in the plane. Computational Geometry: Theory and Applications.
2015;48(5):429-442. doi:10.1016/j.comgeo.2015.01.004'
apa: 'Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). Reprint
of: Weighted straight skeletons in the plane. Computational Geometry: Theory
and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2015.01.004'
chicago: 'Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader.
“Reprint of: Weighted Straight Skeletons in the Plane.” Computational Geometry:
Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2015.01.004.'
ieee: 'T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “Reprint of: Weighted
straight skeletons in the plane,” Computational Geometry: Theory and Applications,
vol. 48, no. 5. Elsevier, pp. 429–442, 2015.'
ista: 'Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. Reprint of: Weighted
straight skeletons in the plane. Computational Geometry: Theory and Applications.
48(5), 429–442.'
mla: 'Biedl, Therese, et al. “Reprint of: Weighted Straight Skeletons in the Plane.”
Computational Geometry: Theory and Applications, vol. 48, no. 5, Elsevier,
2015, pp. 429–42, doi:10.1016/j.comgeo.2015.01.004.'
short: 'T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry:
Theory and Applications 48 (2015) 429–442.'
date_created: 2018-12-11T11:52:51Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-02-23T10:05:22Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1016/j.comgeo.2015.01.004
file:
- access_level: open_access
checksum: 5b33719a86f7f4c8e5dc62c1b6893f49
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:36Z
date_updated: 2020-07-14T12:45:03Z
file_id: '5292'
file_name: IST-2016-475-v1+1_1-s2.0-S092577211500005X-main.pdf
file_size: 508379
relation: main_file
file_date_updated: 2020-07-14T12:45:03Z
has_accepted_license: '1'
intvolume: ' 48'
issue: '5'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 429 - 442
publication: 'Computational Geometry: Theory and Applications'
publication_status: published
publisher: Elsevier
publist_id: '5587'
pubrep_id: '475'
quality_controlled: '1'
related_material:
record:
- id: '1582'
relation: other
status: public
scopus_import: 1
status: public
title: 'Reprint of: Weighted straight skeletons in the plane'
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: 48
year: '2015'
...
---
_id: '1582'
abstract:
- lang: eng
text: We investigate weighted straight skeletons from a geometric, graph-theoretical,
and combinatorial point of view. We start with a thorough definition and shed
light on some ambiguity issues in the procedural definition. We investigate the
geometry, combinatorics, and topology of faces and the roof model, and we discuss
in which cases a weighted straight skeleton is connected. Finally, we show that
the weighted straight skeleton of even a simple polygon may be non-planar and
may contain cycles, and we discuss under which restrictions on the weights and/or
the input polygon the weighted straight skeleton still behaves similar to its
unweighted counterpart. In particular, we obtain a non-procedural description
and a linear-time construction algorithm for the straight skeleton of strictly
convex polygons with arbitrary weights.
author:
- first_name: Therese
full_name: Biedl, Therese
last_name: Biedl
- first_name: Martin
full_name: Held, Martin
last_name: Held
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Dominik
full_name: Kaaser, Dominik
last_name: Kaaser
- first_name: Peter
full_name: Palfrader, Peter
last_name: Palfrader
citation:
ama: 'Biedl T, Held M, Huber S, Kaaser D, Palfrader P. Weighted straight skeletons
in the plane. Computational Geometry: Theory and Applications. 2015;48(2):120-133.
doi:10.1016/j.comgeo.2014.08.006'
apa: 'Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). Weighted
straight skeletons in the plane. Computational Geometry: Theory and Applications.
Elsevier. https://doi.org/10.1016/j.comgeo.2014.08.006'
chicago: 'Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader.
“Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory
and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2014.08.006.'
ieee: 'T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “Weighted straight
skeletons in the plane,” Computational Geometry: Theory and Applications,
vol. 48, no. 2. Elsevier, pp. 120–133, 2015.'
ista: 'Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. Weighted straight
skeletons in the plane. Computational Geometry: Theory and Applications. 48(2),
120–133.'
mla: 'Biedl, Therese, et al. “Weighted Straight Skeletons in the Plane.” Computational
Geometry: Theory and Applications, vol. 48, no. 2, Elsevier, 2015, pp. 120–33,
doi:10.1016/j.comgeo.2014.08.006.'
short: 'T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry:
Theory and Applications 48 (2015) 120–133.'
date_created: 2018-12-11T11:52:51Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2023-02-23T10:05:27Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1016/j.comgeo.2014.08.006
file:
- access_level: open_access
checksum: c1ef67f6ec925e12f73a96b8fe285ab4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:28Z
date_updated: 2020-07-14T12:45:02Z
file_id: '5215'
file_name: IST-2016-474-v1+1_1-s2.0-S0925772114000807-main.pdf
file_size: 505987
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 48'
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 120 - 133
publication: 'Computational Geometry: Theory and Applications'
publication_status: published
publisher: Elsevier
publist_id: '5589'
pubrep_id: '474'
quality_controlled: '1'
related_material:
record:
- id: '1584'
relation: other
status: public
scopus_import: 1
status: public
title: Weighted straight skeletons in the plane
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: 48
year: '2015'
...
---
_id: '1583'
abstract:
- lang: eng
text: We study the characteristics of straight skeletons of monotone polygonal chains
and use them to devise an algorithm for computing positively weighted straight
skeletons of monotone polygons. Our algorithm runs in O(nlogn) time and O(n) space,
where n denotes the number of vertices of the polygon.
author:
- first_name: Therese
full_name: Biedl, Therese
last_name: Biedl
- first_name: Martin
full_name: Held, Martin
last_name: Held
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Dominik
full_name: Kaaser, Dominik
last_name: Kaaser
- first_name: Peter
full_name: Palfrader, Peter
last_name: Palfrader
citation:
ama: Biedl T, Held M, Huber S, Kaaser D, Palfrader P. A simple algorithm for computing
positively weighted straight skeletons of monotone polygons. Information Processing
Letters. 2015;115(2):243-247. doi:10.1016/j.ipl.2014.09.021
apa: Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). A simple
algorithm for computing positively weighted straight skeletons of monotone polygons.
Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2014.09.021
chicago: Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader.
“A Simple Algorithm for Computing Positively Weighted Straight Skeletons of Monotone
Polygons.” Information Processing Letters. Elsevier, 2015. https://doi.org/10.1016/j.ipl.2014.09.021.
ieee: T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “A simple algorithm
for computing positively weighted straight skeletons of monotone polygons,” Information
Processing Letters, vol. 115, no. 2. Elsevier, pp. 243–247, 2015.
ista: Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. A simple algorithm
for computing positively weighted straight skeletons of monotone polygons. Information
Processing Letters. 115(2), 243–247.
mla: Biedl, Therese, et al. “A Simple Algorithm for Computing Positively Weighted
Straight Skeletons of Monotone Polygons.” Information Processing Letters,
vol. 115, no. 2, Elsevier, 2015, pp. 243–47, doi:10.1016/j.ipl.2014.09.021.
short: T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Information Processing
Letters 115 (2015) 243–247.
date_created: 2018-12-11T11:52:51Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T06:51:45Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1016/j.ipl.2014.09.021
file:
- access_level: open_access
checksum: 2779a648610c9b5c86d0b51a62816d23
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:45Z
date_updated: 2020-07-14T12:45:03Z
file_id: '5367'
file_name: IST-2016-473-v1+1_1-s2.0-S0020019014001987-main.pdf
file_size: 270137
relation: main_file
file_date_updated: 2020-07-14T12:45:03Z
has_accepted_license: '1'
intvolume: ' 115'
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 243 - 247
publication: Information Processing Letters
publication_status: published
publisher: Elsevier
publist_id: '5588'
pubrep_id: '473'
quality_controlled: '1'
scopus_import: 1
status: public
title: A simple algorithm for computing positively weighted straight skeletons of
monotone polygons
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: 115
year: '2015'
...
---
_id: '1587'
abstract:
- lang: eng
text: We investigate the quantum interference shifts between energetically close
states, where the state structure is observed by laser spectroscopy. We report
a compact and analytical expression that models the quantum interference induced
shift for any admixture of circular polarization of the incident laser and angle
of observation. An experimental scenario free of quantum interference can thus
be predicted with this formula. Although this study is exemplified here for muonic
deuterium, it can be applied to any other laser spectroscopy measurement of ns-n′p
frequencies of a nonrelativistic atomic system, via an ns→n′p→n′′s scheme.
article_number: '062506'
article_processing_charge: No
article_type: original
author:
- first_name: Pedro
full_name: Amaro, Pedro
last_name: Amaro
- first_name: Filippo
full_name: Fratini, Filippo
last_name: Fratini
- first_name: Laleh
full_name: Safari, Laleh
id: 3C325E5E-F248-11E8-B48F-1D18A9856A87
last_name: Safari
- first_name: Aldo
full_name: Antognini, Aldo
last_name: Antognini
- first_name: Paul
full_name: Indelicato, Paul
last_name: Indelicato
- first_name: Randolf
full_name: Pohl, Randolf
last_name: Pohl
- first_name: José
full_name: Santos, José
last_name: Santos
citation:
ama: Amaro P, Fratini F, Safari L, et al. Quantum interference shifts in laser spectroscopy
with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical
Physics. 2015;92(6). doi:10.1103/PhysRevA.92.062506
apa: Amaro, P., Fratini, F., Safari, L., Antognini, A., Indelicato, P., Pohl, R.,
& Santos, J. (2015). Quantum interference shifts in laser spectroscopy with
elliptical polarization. Physical Review A - Atomic, Molecular, and Optical
Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.92.062506
chicago: Amaro, Pedro, Filippo Fratini, Laleh Safari, Aldo Antognini, Paul Indelicato,
Randolf Pohl, and José Santos. “Quantum Interference Shifts in Laser Spectroscopy
with Elliptical Polarization.” Physical Review A - Atomic, Molecular, and Optical
Physics. American Physical Society, 2015. https://doi.org/10.1103/PhysRevA.92.062506.
ieee: P. Amaro et al., “Quantum interference shifts in laser spectroscopy
with elliptical polarization,” Physical Review A - Atomic, Molecular, and Optical
Physics, vol. 92, no. 6. American Physical Society, 2015.
ista: Amaro P, Fratini F, Safari L, Antognini A, Indelicato P, Pohl R, Santos J.
2015. Quantum interference shifts in laser spectroscopy with elliptical polarization.
Physical Review A - Atomic, Molecular, and Optical Physics. 92(6), 062506.
mla: Amaro, Pedro, et al. “Quantum Interference Shifts in Laser Spectroscopy with
Elliptical Polarization.” Physical Review A - Atomic, Molecular, and Optical
Physics, vol. 92, no. 6, 062506, American Physical Society, 2015, doi:10.1103/PhysRevA.92.062506.
short: P. Amaro, F. Fratini, L. Safari, A. Antognini, P. Indelicato, R. Pohl, J.
Santos, Physical Review A - Atomic, Molecular, and Optical Physics 92 (2015).
date_created: 2018-12-11T11:52:53Z
date_published: 2015-12-31T00:00:00Z
date_updated: 2021-01-12T06:51:47Z
day: '31'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.92.062506
ec_funded: 1
external_id:
arxiv:
- '1511.03585'
intvolume: ' 92'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.03585
month: '12'
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 A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '5584'
quality_controlled: '1'
scopus_import: 1
status: public
title: Quantum interference shifts in laser spectroscopy with elliptical polarization
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 92
year: '2015'
...
---
_id: '1588'
abstract:
- lang: eng
text: 'We investigate the Taylor-Couette system where the radius ratio is close
to unity. Systematically increasing the Reynolds number, we observe a number of
previously known transitions, such as one from the classical Taylor vortex flow
(TVF) to wavy vortex flow (WVF) and the transition to fully developed turbulence.
Prior to the onset of turbulence, we observe intermittent bursting patterns of
localized turbulent patches, confirming the experimentally observed pattern of
very short wavelength bursts (VSWBs). A striking finding is that, for a Reynolds
number larger than that for the onset of VSWBs, a new type of intermittently bursting
behavior emerges: patterns of azimuthally closed rings of various orders. We call
them ring-bursting patterns, which surround the cylinder completely but remain
localized and separated in the axial direction through nonturbulent wavy structures.
We employ a number of quantitative measures including the cross-flow energy to
characterize the ring-bursting patterns and to distinguish them from the background
flow. These patterns are interesting because they do not occur in the wide-gap
Taylor-Couette flow systems. The narrow-gap regime is less studied but certainly
deserves further attention to gain deeper insights into complex flow dynamics
in fluids.'
article_number: '053018'
author:
- first_name: Sebastian
full_name: Altmeyer, Sebastian
id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87
last_name: Altmeyer
orcid: 0000-0001-5964-0203
- first_name: Younghae
full_name: Do, Younghae
last_name: Do
- first_name: Ying
full_name: Lai, Ying
last_name: Lai
citation:
ama: Altmeyer S, Do Y, Lai Y. Ring-bursting behavior en route to turbulence in narrow-gap
Taylor-Couette flows. Physical Review E. 2015;92(5). doi:10.1103/PhysRevE.92.053018
apa: Altmeyer, S., Do, Y., & Lai, Y. (2015). Ring-bursting behavior en route
to turbulence in narrow-gap Taylor-Couette flows. Physical Review E. American
Physical Society. https://doi.org/10.1103/PhysRevE.92.053018
chicago: Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Ring-Bursting Behavior
En Route to Turbulence in Narrow-Gap Taylor-Couette Flows.” Physical Review
E. American Physical Society, 2015. https://doi.org/10.1103/PhysRevE.92.053018.
ieee: S. Altmeyer, Y. Do, and Y. Lai, “Ring-bursting behavior en route to turbulence
in narrow-gap Taylor-Couette flows,” Physical Review E, vol. 92, no. 5.
American Physical Society, 2015.
ista: Altmeyer S, Do Y, Lai Y. 2015. Ring-bursting behavior en route to turbulence
in narrow-gap Taylor-Couette flows. Physical Review E. 92(5), 053018.
mla: Altmeyer, Sebastian, et al. “Ring-Bursting Behavior En Route to Turbulence
in Narrow-Gap Taylor-Couette Flows.” Physical Review E, vol. 92, no. 5,
053018, American Physical Society, 2015, doi:10.1103/PhysRevE.92.053018.
short: S. Altmeyer, Y. Do, Y. Lai, Physical Review E 92 (2015).
date_created: 2018-12-11T11:52:53Z
date_published: 2015-11-24T00:00:00Z
date_updated: 2021-01-12T06:51:47Z
day: '24'
department:
- _id: BjHo
doi: 10.1103/PhysRevE.92.053018
intvolume: ' 92'
issue: '5'
language:
- iso: eng
month: '11'
oa_version: None
publication: Physical Review E
publication_status: published
publisher: American Physical Society
publist_id: '5583'
quality_controlled: '1'
scopus_import: 1
status: public
title: Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette
flows
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 92
year: '2015'
...
---
_id: '1586'
abstract:
- lang: eng
text: Through metabolic engineering cyanobacteria can be employed in biotechnology.
Combining the capacity for oxygenic photosynthesis and carbon fixation with an
engineered metabolic pathway allows carbon-based product formation from CO2, light,
and water directly. Such cyanobacterial 'cell factories' are constructed to produce
biofuels, bioplastics, and commodity chemicals. Efforts of metabolic engineers
and synthetic biologists allow the modification of the intermediary metabolism
at various branching points, expanding the product range. The new biosynthesis
routes 'tap' the metabolism ever more efficiently, particularly through the engineering
of driving forces and utilization of cofactors generated during the light reactions
of photosynthesis, resulting in higher product titers. High rates of carbon rechanneling
ultimately allow an almost-complete allocation of fixed carbon to product above
biomass.
author:
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Aleix
full_name: Gorchs, Aleix
last_name: Gorchs
- first_name: Klaas
full_name: Hellingwerf, Klaas
last_name: Hellingwerf
citation:
ama: Angermayr A, Gorchs A, Hellingwerf K. Metabolic engineering of cyanobacteria
for the synthesis of commodity products. Trends in Biotechnology. 2015;33(6):352-361.
doi:10.1016/j.tibtech.2015.03.009
apa: Angermayr, A., Gorchs, A., & Hellingwerf, K. (2015). Metabolic engineering
of cyanobacteria for the synthesis of commodity products. Trends in Biotechnology.
Elsevier. https://doi.org/10.1016/j.tibtech.2015.03.009
chicago: Angermayr, Andreas, Aleix Gorchs, and Klaas Hellingwerf. “Metabolic Engineering
of Cyanobacteria for the Synthesis of Commodity Products.” Trends in Biotechnology.
Elsevier, 2015. https://doi.org/10.1016/j.tibtech.2015.03.009.
ieee: A. Angermayr, A. Gorchs, and K. Hellingwerf, “Metabolic engineering of cyanobacteria
for the synthesis of commodity products,” Trends in Biotechnology, vol.
33, no. 6. Elsevier, pp. 352–361, 2015.
ista: Angermayr A, Gorchs A, Hellingwerf K. 2015. Metabolic engineering of cyanobacteria
for the synthesis of commodity products. Trends in Biotechnology. 33(6), 352–361.
mla: Angermayr, Andreas, et al. “Metabolic Engineering of Cyanobacteria for the
Synthesis of Commodity Products.” Trends in Biotechnology, vol. 33, no.
6, Elsevier, 2015, pp. 352–61, doi:10.1016/j.tibtech.2015.03.009.
short: A. Angermayr, A. Gorchs, K. Hellingwerf, Trends in Biotechnology 33 (2015)
352–361.
date_created: 2018-12-11T11:52:52Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2021-01-12T06:51:46Z
day: '01'
department:
- _id: ToBo
doi: 10.1016/j.tibtech.2015.03.009
intvolume: ' 33'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 352 - 361
publication: Trends in Biotechnology
publication_status: published
publisher: Elsevier
publist_id: '5585'
quality_controlled: '1'
scopus_import: 1
status: public
title: Metabolic engineering of cyanobacteria for the synthesis of commodity products
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2015'
...
---
_id: '1585'
abstract:
- lang: eng
text: In this paper, we consider the fluctuation of mutual information statistics
of a multiple input multiple output channel communication systems without assuming
that the entries of the channel matrix have zero pseudovariance. To this end,
we also establish a central limit theorem of the linear spectral statistics for
sample covariance matrices under general moment conditions by removing the restrictions
imposed on the second moment and fourth moment on the matrix entries in Bai and
Silverstein (2004).
acknowledgement: "G. Pan was supported by MOE Tier 2 under Grant 2014-T2-2-060 and
in part by Tier 1 under Grant RG25/14 through the Nanyang Technological University,
Singapore. W. Zhou was supported by the National University of Singapore, Singapore,
under Grant R-155-000-131-112.\r\n"
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: Guangming
full_name: Pan, Guangming
last_name: Pan
- first_name: Wang
full_name: Zhou, Wang
last_name: Zhou
citation:
ama: Bao Z, Pan G, Zhou W. Asymptotic mutual information statistics of MIMO channels
and CLT of sample covariance matrices. IEEE Transactions on Information Theory.
2015;61(6):3413-3426. doi:10.1109/TIT.2015.2421894
apa: Bao, Z., Pan, G., & Zhou, W. (2015). Asymptotic mutual information statistics
of MIMO channels and CLT of sample covariance matrices. IEEE Transactions on
Information Theory. IEEE. https://doi.org/10.1109/TIT.2015.2421894
chicago: Bao, Zhigang, Guangming Pan, and Wang Zhou. “Asymptotic Mutual Information
Statistics of MIMO Channels and CLT of Sample Covariance Matrices.” IEEE Transactions
on Information Theory. IEEE, 2015. https://doi.org/10.1109/TIT.2015.2421894.
ieee: Z. Bao, G. Pan, and W. Zhou, “Asymptotic mutual information statistics of
MIMO channels and CLT of sample covariance matrices,” IEEE Transactions on
Information Theory, vol. 61, no. 6. IEEE, pp. 3413–3426, 2015.
ista: Bao Z, Pan G, Zhou W. 2015. Asymptotic mutual information statistics of MIMO
channels and CLT of sample covariance matrices. IEEE Transactions on Information
Theory. 61(6), 3413–3426.
mla: Bao, Zhigang, et al. “Asymptotic Mutual Information Statistics of MIMO Channels
and CLT of Sample Covariance Matrices.” IEEE Transactions on Information Theory,
vol. 61, no. 6, IEEE, 2015, pp. 3413–26, doi:10.1109/TIT.2015.2421894.
short: Z. Bao, G. Pan, W. Zhou, IEEE Transactions on Information Theory 61 (2015)
3413–3426.
date_created: 2018-12-11T11:52:52Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2021-01-12T06:51:46Z
day: '01'
department:
- _id: LaEr
doi: 10.1109/TIT.2015.2421894
intvolume: ' 61'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 3413 - 3426
publication: IEEE Transactions on Information Theory
publication_status: published
publisher: IEEE
publist_id: '5586'
quality_controlled: '1'
scopus_import: 1
status: public
title: Asymptotic mutual information statistics of MIMO channels and CLT of sample
covariance matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2015'
...
---
_id: '1593'
abstract:
- lang: eng
text: 'Plants are sessile organisms that are permanently restricted to their site
of germination. To compensate for their lack of mobility, plants evolved unique
mechanisms enabling them to rapidly react to ever changing environmental conditions
and flexibly adapt their postembryonic developmental program. A prominent demonstration
of this developmental plasticity is their ability to bend organs in order to reach
the position most optimal for growth and utilization of light, nutrients, and
other resources. Shortly after germination, dicotyledonous seedlings form a bended
structure, the so-called apical hook, to protect the delicate shoot meristem and
cotyledons from damage when penetrating through the soil. Upon perception of a
light stimulus, the apical hook rapidly opens and the photomorphogenic developmental
program is activated. After germination, plant organs are able to align their
growth with the light source and adopt the most favorable orientation through
bending, in a process named phototropism. On the other hand, when roots and shoots
are diverted from their upright orientation, they immediately detect a change
in the gravity vector and bend to maintain a vertical growth direction. Noteworthy,
despite the diversity of external stimuli perceived by different plant organs,
all plant tropic movements share a common mechanistic basis: differential cell
growth. In our review, we will discuss the molecular principles underlying various
tropic responses with the focus on mechanisms mediating the perception of external
signals, transduction cascades and downstream responses that regulate differential
cell growth and consequently, organ bending. In particular, we highlight common
and specific features of regulatory pathways in control of the bending of organs
and a role for the plant hormone auxin as a key regulatory component.'
author:
- first_name: Petra
full_name: Žádníková, Petra
last_name: Žádníková
- first_name: Dajo
full_name: Smet, Dajo
last_name: Smet
- first_name: Qiang
full_name: Zhu, Qiang
id: 40A4B9E6-F248-11E8-B48F-1D18A9856A87
last_name: Zhu
- first_name: Dominique
full_name: Van Der Straeten, Dominique
last_name: Van Der Straeten
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: 'Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. Strategies of seedlings
to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant
Science. 2015;6(4). doi:10.3389/fpls.2015.00218'
apa: 'Žádníková, P., Smet, D., Zhu, Q., Van Der Straeten, D., & Benková, E.
(2015). Strategies of seedlings to overcome their sessile nature: Auxin in mobility
control. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2015.00218'
chicago: 'Žádníková, Petra, Dajo Smet, Qiang Zhu, Dominique Van Der Straeten, and
Eva Benková. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin
in Mobility Control.” Frontiers in Plant Science. Frontiers Research Foundation,
2015. https://doi.org/10.3389/fpls.2015.00218.'
ieee: 'P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, and E. Benková, “Strategies
of seedlings to overcome their sessile nature: Auxin in mobility control,” Frontiers
in Plant Science, vol. 6, no. 4. Frontiers Research Foundation, 2015.'
ista: 'Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. 2015. Strategies
of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers
in Plant Science. 6(4).'
mla: 'Žádníková, Petra, et al. “Strategies of Seedlings to Overcome Their Sessile
Nature: Auxin in Mobility Control.” Frontiers in Plant Science, vol. 6,
no. 4, Frontiers Research Foundation, 2015, doi:10.3389/fpls.2015.00218.'
short: P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, E. Benková, Frontiers
in Plant Science 6 (2015).
date_created: 2018-12-11T11:52:55Z
date_published: 2015-04-14T00:00:00Z
date_updated: 2021-01-12T06:51:50Z
day: '14'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.3389/fpls.2015.00218
ec_funded: 1
file:
- access_level: open_access
checksum: c454d642e18dfa86820b97a86cd6d3cc
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:23Z
date_updated: 2020-07-14T12:45:03Z
file_id: '5142'
file_name: IST-2016-471-v1+1_fpls-06-00218.pdf
file_size: 965690
relation: main_file
file_date_updated: 2020-07-14T12:45:03Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: Frontiers in Plant Science
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '5578'
pubrep_id: '471'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Strategies of seedlings to overcome their sessile nature: Auxin in mobility
control'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '1595'
abstract:
- lang: eng
text: 'A drawing of a graph G is radial if the vertices of G are placed on concentric
circles C1, . . . , Ck with common center c, and edges are drawn radially: every
edge intersects every circle centered at c at most once. G is radial planar if
it has a radial embedding, that is, a crossing- free radial drawing. If the vertices
of G are ordered or partitioned into ordered levels (as they are for leveled graphs),
we require that the assignment of vertices to circles corresponds to the given
ordering or leveling. We show that a graph G is radial planar if G has a radial
drawing in which every two edges cross an even number of times; the radial embedding
has the same leveling as the radial drawing. In other words, we establish the
weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes
a result by Pach and Tóth.'
acknowledgement: The research leading to these results has received funding from the
People Programme (Marie Curie Actions) of the European Union’s Seventh Framework
Programme (FP7/2007-2013) under REA grant agreement no [291734].
alternative_title:
- LNCS
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Michael
full_name: Pelsmajer, Michael
last_name: Pelsmajer
- first_name: Marcus
full_name: Schaefer, Marcus
last_name: Schaefer
citation:
ama: 'Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. In: Vol
9411. Springer; 2015:99-110. doi:10.1007/978-3-319-27261-0_9'
apa: 'Fulek, R., Pelsmajer, M., & Schaefer, M. (2015). Hanani-Tutte for radial
planarity (Vol. 9411, pp. 99–110). Presented at the GD: Graph Drawing and Network
Visualization, Los Angeles, CA, USA: Springer. https://doi.org/10.1007/978-3-319-27261-0_9'
chicago: Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte
for Radial Planarity,” 9411:99–110. Springer, 2015. https://doi.org/10.1007/978-3-319-27261-0_9.
ieee: 'R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,”
presented at the GD: Graph Drawing and Network Visualization, Los Angeles, CA,
USA, 2015, vol. 9411, pp. 99–110.'
ista: 'Fulek R, Pelsmajer M, Schaefer M. 2015. Hanani-Tutte for radial planarity.
GD: Graph Drawing and Network Visualization, LNCS, vol. 9411, 99–110.'
mla: Fulek, Radoslav, et al. Hanani-Tutte for Radial Planarity. Vol. 9411,
Springer, 2015, pp. 99–110, doi:10.1007/978-3-319-27261-0_9.
short: R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2015, pp. 99–110.
conference:
end_date: 2015-09-26
location: Los Angeles, CA, USA
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2015-09-24
date_created: 2018-12-11T11:52:55Z
date_published: 2015-11-27T00:00:00Z
date_updated: 2023-02-21T16:23:36Z
day: '27'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.1007/978-3-319-27261-0_9
ec_funded: 1
file:
- access_level: open_access
checksum: 685f91bd077a951ba067d42cce75409e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:36Z
date_updated: 2020-07-14T12:45:03Z
file_id: '4697'
file_name: IST-2016-594-v1+1_HTCylinder_GD_Revision.pdf
file_size: 330135
relation: main_file
file_date_updated: 2020-07-14T12:45:03Z
has_accepted_license: '1'
intvolume: ' 9411'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 99 - 110
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '5576'
pubrep_id: '594'
quality_controlled: '1'
related_material:
record:
- id: '1113'
relation: later_version
status: public
- id: '1164'
relation: later_version
status: public
scopus_import: 1
status: public
title: Hanani-Tutte for radial planarity
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9411
year: '2015'
...
---
_id: '1590'
abstract:
- lang: eng
text: 'The straight skeleton of a polygon is the geometric graph obtained by tracing
the vertices during a mitered offsetting process. It is known that the straight
skeleton of a simple polygon is a tree, and one can naturally derive directions
on the edges of the tree from the propagation of the shrinking process. In this
paper, we ask the reverse question: Given a tree with directed edges, can it be
the straight skeleton of a polygon? And if so, can we find a suitable simple polygon?
We answer these questions for all directed trees where the order of edges around
each node is fixed.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Oswin
full_name: Aichholzer, Oswin
last_name: Aichholzer
- first_name: Therese
full_name: Biedl, Therese
last_name: Biedl
- first_name: Thomas
full_name: Hackl, Thomas
last_name: Hackl
- first_name: Martin
full_name: Held, Martin
last_name: Held
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Peter
full_name: Palfrader, Peter
last_name: Palfrader
- first_name: Birgit
full_name: Vogtenhuber, Birgit
last_name: Vogtenhuber
citation:
ama: 'Aichholzer O, Biedl T, Hackl T, et al. Representing directed trees as straight
skeletons. In: Graph Drawing and Network Visualization. Vol 9411. Springer
Nature; 2015:335-347. doi:10.1007/978-3-319-27261-0_28'
apa: 'Aichholzer, O., Biedl, T., Hackl, T., Held, M., Huber, S., Palfrader, P.,
& Vogtenhuber, B. (2015). Representing directed trees as straight skeletons.
In Graph Drawing and Network Visualization (Vol. 9411, pp. 335–347). Los
Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-319-27261-0_28'
chicago: Aichholzer, Oswin, Therese Biedl, Thomas Hackl, Martin Held, Stefan Huber,
Peter Palfrader, and Birgit Vogtenhuber. “Representing Directed Trees as Straight
Skeletons.” In Graph Drawing and Network Visualization, 9411:335–47. Springer
Nature, 2015. https://doi.org/10.1007/978-3-319-27261-0_28.
ieee: O. Aichholzer et al., “Representing directed trees as straight skeletons,”
in Graph Drawing and Network Visualization, vol. 9411, Springer Nature,
2015, pp. 335–347.
ista: 'Aichholzer O, Biedl T, Hackl T, Held M, Huber S, Palfrader P, Vogtenhuber
B. 2015.Representing directed trees as straight skeletons. In: Graph Drawing and
Network Visualization. LNCS, vol. 9411, 335–347.'
mla: Aichholzer, Oswin, et al. “Representing Directed Trees as Straight Skeletons.”
Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015,
pp. 335–47, doi:10.1007/978-3-319-27261-0_28.
short: O. Aichholzer, T. Biedl, T. Hackl, M. Held, S. Huber, P. Palfrader, B. Vogtenhuber,
in:, Graph Drawing and Network Visualization, Springer Nature, 2015, pp. 335–347.
conference:
end_date: 2015-09-26
location: Los Angeles, CA, United States
name: 'GD: International Symposium on Graph Drawing'
start_date: 2015-09-24
date_created: 2018-12-11T11:52:54Z
date_published: 2015-11-27T00:00:00Z
date_updated: 2022-01-28T09:10:37Z
day: '27'
department:
- _id: HeEd
doi: 10.1007/978-3-319-27261-0_28
intvolume: ' 9411'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1508.01076
month: '11'
oa: 1
oa_version: Preprint
page: 335 - 347
publication: Graph Drawing and Network Visualization
publication_identifier:
eisbn:
- 978-3-319-27261-0
isbn:
- 978-3-319-27260-3
publication_status: published
publisher: Springer Nature
publist_id: '5581'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Representing directed trees as straight skeletons
type: book_chapter
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9411
year: '2015'
...
---
_id: '1594'
abstract:
- lang: eng
text: Quantitative extensions of temporal logics have recently attracted significant
attention. In this work, we study frequency LTL (fLTL), an extension of LTL which
allows to speak about frequencies of events along an execution. Such an extension
is particularly useful for probabilistic systems that often cannot fulfil strict
qualitative guarantees on the behaviour. It has been recently shown that controller
synthesis for Markov decision processes and fLTL is decidable when all the bounds
on frequencies are 1. As a step towards a complete quantitative solution, we show
that the problem is decidable for the fragment fLTL\GU, where U does not occur
in the scope of G (but still F can). Our solution is based on a novel translation
of such quantitative formulae into equivalent deterministic automata.
acknowledgement: "This work is partly supported by the German Research Council (DFG)
as part of the Transregional Collaborative Research Center AVACS (SFB/TR 14), by
the Czech Science Foundation under grant agreement P202/12/G061, by the EU 7th Framework
Programme under grant agreement no. 295261 (MEALS) and 318490 (SENSATION), by the
CDZ project 1023 (CAP), by the CAS/SAFEA International Partnership Program for Creative
Research Teams, by the EPSRC grant EP/M023656/1, by the People Programme (Marie
Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013)
REA Grant No 291734, by the Austrian Science Fund (FWF) S11407-N23 (RiSE/SHiNE),
and by the ERC Start Grant (279307: Graph Games).\r\n"
alternative_title:
- LNCS
author:
- first_name: Vojtěch
full_name: Forejt, Vojtěch
last_name: Forejt
- first_name: Jan
full_name: Krčál, Jan
last_name: Krčál
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: 'Forejt V, Krčál J, Kretinsky J. Controller synthesis for MDPs and frequency
LTL\GU. In: Vol 9450. Springer; 2015:162-177. doi:10.1007/978-3-662-48899-7_12'
apa: 'Forejt, V., Krčál, J., & Kretinsky, J. (2015). Controller synthesis for
MDPs and frequency LTL\GU (Vol. 9450, pp. 162–177). Presented at the LPAR: Logic
for Programming, Artificial Intelligence, and Reasoning, Suva, Fiji: Springer.
https://doi.org/10.1007/978-3-662-48899-7_12'
chicago: Forejt, Vojtěch, Jan Krčál, and Jan Kretinsky. “Controller Synthesis for
MDPs and Frequency LTL\GU,” 9450:162–77. Springer, 2015. https://doi.org/10.1007/978-3-662-48899-7_12.
ieee: 'V. Forejt, J. Krčál, and J. Kretinsky, “Controller synthesis for MDPs and
frequency LTL\GU,” presented at the LPAR: Logic for Programming, Artificial Intelligence,
and Reasoning, Suva, Fiji, 2015, vol. 9450, pp. 162–177.'
ista: 'Forejt V, Krčál J, Kretinsky J. 2015. Controller synthesis for MDPs and frequency
LTL\GU. LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS,
vol. 9450, 162–177.'
mla: Forejt, Vojtěch, et al. Controller Synthesis for MDPs and Frequency LTL\GU.
Vol. 9450, Springer, 2015, pp. 162–77, doi:10.1007/978-3-662-48899-7_12.
short: V. Forejt, J. Krčál, J. Kretinsky, in:, Springer, 2015, pp. 162–177.
conference:
end_date: 2015-11-28
location: Suva, Fiji
name: 'LPAR: Logic for Programming, Artificial Intelligence, and Reasoning'
start_date: 2015-11-24
date_created: 2018-12-11T11:52:55Z
date_published: 2015-11-22T00:00:00Z
date_updated: 2021-01-12T06:51:50Z
day: '22'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1007/978-3-662-48899-7_12
ec_funded: 1
intvolume: ' 9450'
language:
- iso: eng
month: '11'
oa_version: None
page: 162 - 177
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_status: published
publisher: Springer
publist_id: '5577'
quality_controlled: '1'
scopus_import: 1
status: public
title: Controller synthesis for MDPs and frequency LTL\GU
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9450
year: '2015'
...
---
_id: '1596'
abstract:
- lang: eng
text: Let C={C1,...,Cn} denote a collection of translates of a regular convex k-gon
in the plane with the stacking order. The collection C forms a visibility clique
if for everyi < j the intersection Ci and (Ci ∩ Cj)\⋃i<l<jCl =∅.elements
that are stacked between them, i.e., We show that if C forms a visibility clique
its size is bounded from above by O(k4) thereby improving the upper bound of 22k
from the aforementioned paper. We also obtain an upper bound of 22(k/2)+2 on the
size of a visibility clique for homothetes of a convex (not necessarily regular)
k-gon.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Radoš
full_name: Radoičić, Radoš
last_name: Radoičić
citation:
ama: 'Fulek R, Radoičić R. Vertical visibility among parallel polygons in three
dimensions. In: Graph Drawing and Network Visualization. Vol 9411. Springer
Nature; 2015:373-379. doi:10.1007/978-3-319-27261-0_31'
apa: 'Fulek, R., & Radoičić, R. (2015). Vertical visibility among parallel polygons
in three dimensions. In Graph Drawing and Network Visualization (Vol. 9411,
pp. 373–379). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-319-27261-0_31'
chicago: Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel
Polygons in Three Dimensions.” In Graph Drawing and Network Visualization,
9411:373–79. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-27261-0_31.
ieee: R. Fulek and R. Radoičić, “Vertical visibility among parallel polygons in
three dimensions,” in Graph Drawing and Network Visualization, vol. 9411,
Springer Nature, 2015, pp. 373–379.
ista: 'Fulek R, Radoičić R. 2015.Vertical visibility among parallel polygons in
three dimensions. In: Graph Drawing and Network Visualization. LNCS, vol. 9411,
373–379.'
mla: Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel Polygons
in Three Dimensions.” Graph Drawing and Network Visualization, vol. 9411,
Springer Nature, 2015, pp. 373–79, doi:10.1007/978-3-319-27261-0_31.
short: R. Fulek, R. Radoičić, in:, Graph Drawing and Network Visualization, Springer
Nature, 2015, pp. 373–379.
conference:
end_date: 2015-09-26
location: Los Angeles, CA, United States
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2015-09-24
date_created: 2018-12-11T11:52:56Z
date_published: 2015-11-27T00:00:00Z
date_updated: 2022-01-28T09:20:50Z
day: '27'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.1007/978-3-319-27261-0_31
ec_funded: 1
file:
- access_level: open_access
checksum: eec04f86c5921d04f025d5791db9b965
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:06Z
date_updated: 2020-07-14T12:45:04Z
file_id: '5258'
file_name: IST-2016-595-v1+1_VerticalVisibilityGDRevision.pdf
file_size: 312992
relation: main_file
file_date_updated: 2020-07-14T12:45:04Z
has_accepted_license: '1'
intvolume: ' 9411'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 373 - 379
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Graph Drawing and Network Visualization
publication_identifier:
isbn:
- 978-3-319-27260-3
publication_status: published
publisher: Springer Nature
publist_id: '5575'
pubrep_id: '595'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Vertical visibility among parallel polygons in three dimensions
type: book_chapter
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9411
year: '2015'
...
---
_id: '1601'
abstract:
- lang: eng
text: We propose a flexible exchange format for ω-automata, as typically used in
formal verification, and implement support for it in a range of established tools.
Our aim is to simplify the interaction of tools, helping the research community
to build upon other people’s work. A key feature of the format is the use of very
generic acceptance conditions, specified by Boolean combinations of acceptance
primitives, rather than being limited to common cases such as Büchi, Streett,
or Rabin. Such flexibility in the choice of acceptance conditions can be exploited
in applications, for example in probabilistic model checking, and furthermore
encourages the development of acceptance-agnostic tools for automata manipulations.
The format allows acceptance conditions that are either state-based or transition-based,
and also supports alternating automata.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Tomáš
full_name: Babiak, Tomáš
last_name: Babiak
- first_name: František
full_name: Blahoudek, František
last_name: Blahoudek
- first_name: Alexandre
full_name: Duret Lutz, Alexandre
last_name: Duret Lutz
- first_name: Joachim
full_name: Klein, Joachim
last_name: Klein
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Daniel
full_name: Mueller, Daniel
last_name: Mueller
- first_name: David
full_name: Parker, David
last_name: Parker
- first_name: Jan
full_name: Strejček, Jan
last_name: Strejček
citation:
ama: 'Babiak T, Blahoudek F, Duret Lutz A, et al. The Hanoi omega-automata format.
In: Vol 9206. Springer; 2015:479-486. doi:10.1007/978-3-319-21690-4_31'
apa: 'Babiak, T., Blahoudek, F., Duret Lutz, A., Klein, J., Kretinsky, J., Mueller,
D., … Strejček, J. (2015). The Hanoi omega-automata format (Vol. 9206, pp. 479–486).
Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States:
Springer. https://doi.org/10.1007/978-3-319-21690-4_31'
chicago: Babiak, Tomáš, František Blahoudek, Alexandre Duret Lutz, Joachim Klein,
Jan Kretinsky, Daniel Mueller, David Parker, and Jan Strejček. “The Hanoi Omega-Automata
Format,” 9206:479–86. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_31.
ieee: 'T. Babiak et al., “The Hanoi omega-automata format,” presented at
the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015,
vol. 9206, pp. 479–486.'
ista: 'Babiak T, Blahoudek F, Duret Lutz A, Klein J, Kretinsky J, Mueller D, Parker
D, Strejček J. 2015. The Hanoi omega-automata format. CAV: Computer Aided Verification,
LNCS, vol. 9206, 479–486.'
mla: Babiak, Tomáš, et al. The Hanoi Omega-Automata Format. Vol. 9206, Springer,
2015, pp. 479–86, doi:10.1007/978-3-319-21690-4_31.
short: T. Babiak, F. Blahoudek, A. Duret Lutz, J. Klein, J. Kretinsky, D. Mueller,
D. Parker, J. Strejček, in:, Springer, 2015, pp. 479–486.
conference:
end_date: 2015-07-24
location: San Francisco, CA, United States
name: 'CAV: Computer Aided Verification'
start_date: 2015-07-18
date_created: 2018-12-11T11:52:57Z
date_published: 2015-07-16T00:00:00Z
date_updated: 2021-01-12T06:51:54Z
day: '16'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1007/978-3-319-21690-4_31
ec_funded: 1
file:
- access_level: open_access
checksum: 5885236fa88a439baba9ac6f3e801e93
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T08:38:12Z
date_updated: 2020-07-14T12:45:04Z
file_id: '7850'
file_name: 2015_CAV_Babiak.pdf
file_size: 1651779
relation: main_file
file_date_updated: 2020-07-14T12:45:04Z
has_accepted_license: '1'
intvolume: ' 9206'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 479 - 486
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _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: '5566'
quality_controlled: '1'
scopus_import: 1
status: public
title: The Hanoi omega-automata format
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9206
year: '2015'
...
---
_id: '1605'
abstract:
- lang: eng
text: Multiaffine hybrid automata (MHA) represent a powerful formalism to model
complex dynamical systems. This formalism is particularly suited for the representation
of biological systems which often exhibit highly non-linear behavior. In this
paper, we consider the problem of parameter identification for MHA. We present
an abstraction of MHA based on linear hybrid automata, which can be analyzed by
the SpaceEx model checker. This abstraction enables a precise handling of time-dependent
properties. We demonstrate the potential of our approach on a model of a genetic
regulatory network and a myocyte model.
acknowledgement: This work was partly supported by the European Research Council (ERC)
under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants S11402-N23,
S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), and by
the German Research Foundation (DFG) as part of the Transregional Collaborative
Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR
14 AVACS, http://www.avacs.org/).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Grégory
full_name: Batt, Grégory
last_name: Batt
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: 'Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. Abstraction-based
parameter synthesis for multiaffine systems. In: Vol 9434. Springer; 2015:19-35.
doi:10.1007/978-3-319-26287-1_2'
apa: 'Bogomolov, S., Schilling, C., Bartocci, E., Batt, G., Kong, H., & Grosu,
R. (2015). Abstraction-based parameter synthesis for multiaffine systems (Vol.
9434, pp. 19–35). Presented at the HVC: Haifa Verification Conference, Haifa,
Israel: Springer. https://doi.org/10.1007/978-3-319-26287-1_2'
chicago: Bogomolov, Sergiy, Christian Schilling, Ezio Bartocci, Grégory Batt, Hui
Kong, and Radu Grosu. “Abstraction-Based Parameter Synthesis for Multiaffine Systems,”
9434:19–35. Springer, 2015. https://doi.org/10.1007/978-3-319-26287-1_2.
ieee: 'S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, and R. Grosu,
“Abstraction-based parameter synthesis for multiaffine systems,” presented at
the HVC: Haifa Verification Conference, Haifa, Israel, 2015, vol. 9434, pp. 19–35.'
ista: 'Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. 2015. Abstraction-based
parameter synthesis for multiaffine systems. HVC: Haifa Verification Conference,
LNCS, vol. 9434, 19–35.'
mla: Bogomolov, Sergiy, et al. Abstraction-Based Parameter Synthesis for Multiaffine
Systems. Vol. 9434, Springer, 2015, pp. 19–35, doi:10.1007/978-3-319-26287-1_2.
short: S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, R. Grosu, in:,
Springer, 2015, pp. 19–35.
conference:
end_date: 2015-11-19
location: Haifa, Israel
name: 'HVC: Haifa Verification Conference'
start_date: 2015-11-17
date_created: 2018-12-11T11:52:59Z
date_published: 2015-11-28T00:00:00Z
date_updated: 2021-01-12T06:51:56Z
day: '28'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-26287-1_2
ec_funded: 1
file:
- access_level: open_access
checksum: 3aab260f3f34641d622030ba22645b3e
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T08:43:19Z
date_updated: 2020-07-14T12:45:05Z
file_id: '7851'
file_name: 2015_LNCS_Bogomolov.pdf
file_size: 1053207
relation: main_file
file_date_updated: 2020-07-14T12:45:05Z
has_accepted_license: '1'
intvolume: ' 9434'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 19 - 35
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '5561'
quality_controlled: '1'
scopus_import: 1
status: public
title: Abstraction-based parameter synthesis for multiaffine systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9434
year: '2015'
...
---
_id: '1606'
abstract:
- lang: eng
text: 'In this paper, we present the first steps toward a runtime verification framework
for monitoring hybrid and cyber-physical systems (CPS) development tools based
on randomized differential testing. The development tools include hybrid systems
reachability analysis tools, model-based development environments like Simulink/Stateflow
(SLSF), etc. First, hybrid automaton models are randomly generated. Next, these
hybrid automaton models are translated to a number of different tools (currently,
SpaceEx, dReach, Flow*, HyCreate, and the MathWorks’ Simulink/Stateflow) using
the HyST source transformation and translation tool. Then, the hybrid automaton
models are executed in the different tools and their outputs are parsed. The final
step is the differential comparison: the outputs of the different tools are compared.
If the results do not agree (in the sense that an analysis or verification result
from one tool does not match that of another tool, ignoring timeouts, etc.), a
candidate bug is flagged and the model is saved for future analysis by the user.
The process then repeats and the monitoring continues until the user terminates
the process. We present preliminary results that have been useful in identifying
a few bugs in the analysis methods of different development tools, and in an earlier
version of HyST.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Luan
full_name: Nguyen, Luan
last_name: Nguyen
- first_name: Christian
full_name: Schilling, Christian
last_name: Schilling
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Taylor
full_name: Johnson, Taylor
last_name: Johnson
citation:
ama: 'Nguyen L, Schilling C, Bogomolov S, Johnson T. Runtime verification for hybrid
analysis tools. In: 6th International Conference. Vol 9333. Springer Nature;
2015:281-286. doi:10.1007/978-3-319-23820-3_19'
apa: 'Nguyen, L., Schilling, C., Bogomolov, S., & Johnson, T. (2015). Runtime
verification for hybrid analysis tools. In 6th International Conference
(Vol. 9333, pp. 281–286). Vienna, Austria: Springer Nature. https://doi.org/10.1007/978-3-319-23820-3_19'
chicago: Nguyen, Luan, Christian Schilling, Sergiy Bogomolov, and Taylor Johnson.
“Runtime Verification for Hybrid Analysis Tools.” In 6th International Conference,
9333:281–86. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-23820-3_19.
ieee: L. Nguyen, C. Schilling, S. Bogomolov, and T. Johnson, “Runtime verification
for hybrid analysis tools,” in 6th International Conference, Vienna, Austria,
2015, vol. 9333, pp. 281–286.
ista: 'Nguyen L, Schilling C, Bogomolov S, Johnson T. 2015. Runtime verification
for hybrid analysis tools. 6th International Conference. RV: Runtime Verification,
LNCS, vol. 9333, 281–286.'
mla: Nguyen, Luan, et al. “Runtime Verification for Hybrid Analysis Tools.” 6th
International Conference, vol. 9333, Springer Nature, 2015, pp. 281–86, doi:10.1007/978-3-319-23820-3_19.
short: L. Nguyen, C. Schilling, S. Bogomolov, T. Johnson, in:, 6th International
Conference, Springer Nature, 2015, pp. 281–286.
conference:
end_date: 2015-09-25
location: Vienna, Austria
name: 'RV: Runtime Verification'
start_date: 2015-09-22
date_created: 2018-12-11T11:52:59Z
date_published: 2015-11-15T00:00:00Z
date_updated: 2022-02-01T14:52:59Z
day: '15'
department:
- _id: ToHe
doi: 10.1007/978-3-319-23820-3_19
ec_funded: 1
intvolume: ' 9333'
language:
- iso: eng
month: '11'
oa_version: None
page: 281 - 286
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: 6th International Conference
publication_identifier:
isbn:
- 978-3-319-23819-7
publication_status: published
publisher: Springer Nature
publist_id: '5562'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Runtime verification for hybrid analysis tools
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9333
year: '2015'
...
---
_id: '1609'
abstract:
- lang: eng
text: The synthesis problem asks for the automatic construction of a system from
its specification. In the traditional setting, the system is “constructed from
scratch” rather than composed from reusable components. However, this is rare
in practice, and almost every non-trivial software system relies heavily on the
use of libraries of reusable components. Recently, Lustig and Vardi introduced
dataflow and controlflow synthesis from libraries of reusable components. They
proved that dataflow synthesis is undecidable, while controlflow synthesis is
decidable. The problem of controlflow synthesis from libraries of probabilistic
components was considered by Nain, Lustig and Vardi, and was shown to be decidable
for qualitative analysis (that asks that the specification be satisfied with probability
1). Our main contribution for controlflow synthesis from probabilistic components
is to establish better complexity bounds for the qualitative analysis problem,
and to show that the more general quantitative problem is undecidable. For the
qualitative analysis, we show that the problem (i) is EXPTIME-complete when the
specification is given as a deterministic parity word automaton, improving the
previously known 2EXPTIME upper bound; and (ii) belongs to UP ∩ coUP and is parity-games
hard, when the specification is given directly as a parity condition on the components,
improving the previously known EXPTIME upper bound.
acknowledgement: 'This research was supported by Austrian Science Fund (FWF) Grant
No P23499- N23, FWF NFN Grant No S11407-N23 (SHiNE), ERC Start grant (279307: Graph
Games), EU FP7 Project Cassting, NSF grants CNS 1049862 and CCF-1139011, by NSF
Expeditions in Computing project “ExCAPE: Expeditions in Computer Augmented Program
Engineering”, by BSF grant 9800096, and by gift from Intel.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Moshe
full_name: Vardi, Moshe
last_name: Vardi
citation:
ama: 'Chatterjee K, Doyen L, Vardi M. The complexity of synthesis from probabilistic
components. In: 42nd International Colloquium. Vol 9135. Springer Nature;
2015:108-120. doi:10.1007/978-3-662-47666-6_9'
apa: 'Chatterjee, K., Doyen, L., & Vardi, M. (2015). The complexity of synthesis
from probabilistic components. In 42nd International Colloquium (Vol. 9135,
pp. 108–120). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_9'
chicago: Chatterjee, Krishnendu, Laurent Doyen, and Moshe Vardi. “The Complexity
of Synthesis from Probabilistic Components.” In 42nd International Colloquium,
9135:108–20. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_9.
ieee: K. Chatterjee, L. Doyen, and M. Vardi, “The complexity of synthesis from probabilistic
components,” in 42nd International Colloquium, Kyoto, Japan, 2015, vol.
9135, pp. 108–120.
ista: 'Chatterjee K, Doyen L, Vardi M. 2015. The complexity of synthesis from probabilistic
components. 42nd International Colloquium. ICALP: Automata, Languages and Programming,
LNCS, vol. 9135, 108–120.'
mla: Chatterjee, Krishnendu, et al. “The Complexity of Synthesis from Probabilistic
Components.” 42nd International Colloquium, vol. 9135, Springer Nature,
2015, pp. 108–20, doi:10.1007/978-3-662-47666-6_9.
short: K. Chatterjee, L. Doyen, M. Vardi, in:, 42nd International Colloquium, Springer
Nature, 2015, pp. 108–120.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'ICALP: Automata, Languages and Programming'
start_date: 2015-07-06
date_created: 2018-12-11T11:53:00Z
date_published: 2015-06-20T00:00:00Z
date_updated: 2022-02-01T15:04:44Z
day: '20'
department:
- _id: KrCh
doi: 10.1007/978-3-662-47666-6_9
ec_funded: 1
intvolume: ' 9135'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1502.04844
month: '06'
oa: 1
oa_version: Preprint
page: 108 - 120
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'
publication: 42nd International Colloquium
publication_identifier:
isbn:
- 978-3-662-47665-9
publication_status: published
publisher: Springer Nature
publist_id: '5557'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The complexity of synthesis from probabilistic components
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9135
year: '2015'
...
---
_id: '1615'
abstract:
- lang: eng
text: Loss-of-function mutations in the synaptic adhesion protein Neuroligin-4 are
among the most common genetic abnormalities associated with autism spectrum disorders,
but little is known about the function of Neuroligin-4 and the consequences of
its loss. We assessed synaptic and network characteristics in Neuroligin-4 knockout
mice, focusing on the hippocampus as a model brain region with a critical role
in cognition and memory, and found that Neuroligin-4 deletion causes subtle defects
of the protein composition and function of GABAergic synapses in the hippocampal
CA3 region. Interestingly, these subtle synaptic changes are accompanied by pronounced
perturbations of γ-oscillatory network activity, which has been implicated in
cognitive function and is altered in multiple psychiatric and neurodevelopmental
disorders. Our data provide important insights into the mechanisms by which Neuroligin-4-dependent
GABAergic synapses may contribute to autism phenotypes and indicate new strategies
for therapeutic approaches.
acknowledgement: This work was supported by the Max Planck Society (N.B. and H.E.),
the European Commission (EU-AIMS FP7-115300, N.B. and H.E.; Marie Curie IRG, D.K.-B.),
the German Research Foundation (CNMPB, N.B., H.E., and F.V.), the Alexander von
Humboldt-Foundation (D.K.-B.), and the Austrian Fond zur Förderung der Wissenschaftlichen
Forschung (P 24909-B24, P.J.). M.H. was a student of the doctoral program Molecular
Physiology of the Brain. Dr. J.-M. Fritschy generously provided the GABAARγ2 antibody.
We thank F. Benseler, I. Thanhäuser, D. Schwerdtfeger, A. Ronnenberg, and D. Winkler
for valuable advice and excellent technical support. We are grateful to the staff
at the animal facility of the Max Planck Institute of Experimental Medicine for
mouse husbandry.
author:
- first_name: Matthieu
full_name: Hammer, Matthieu
last_name: Hammer
- first_name: Dilja
full_name: Krueger Burg, Dilja
last_name: Krueger Burg
- first_name: Liam
full_name: Tuffy, Liam
last_name: Tuffy
- first_name: Benjamin
full_name: Cooper, Benjamin
last_name: Cooper
- first_name: Holger
full_name: Taschenberger, Holger
last_name: Taschenberger
- first_name: Sarit
full_name: Goswami, Sarit
id: 3A578F32-F248-11E8-B48F-1D18A9856A87
last_name: Goswami
- first_name: Hannelore
full_name: Ehrenreich, Hannelore
last_name: Ehrenreich
- 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: Frederique
full_name: Varoqueaux, Frederique
last_name: Varoqueaux
- first_name: Jeong
full_name: Rhee, Jeong
last_name: Rhee
- first_name: Nils
full_name: Brose, Nils
last_name: Brose
citation:
ama: Hammer M, Krueger Burg D, Tuffy L, et al. Perturbed hippocampal synaptic inhibition
and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports.
2015;13(3):516-523. doi:10.1016/j.celrep.2015.09.011
apa: Hammer, M., Krueger Burg, D., Tuffy, L., Cooper, B., Taschenberger, H., Goswami,
S., … Brose, N. (2015). Perturbed hippocampal synaptic inhibition and γ-oscillations
in a neuroligin-4 knockout mouse model of autism. Cell Reports. Cell Press.
https://doi.org/10.1016/j.celrep.2015.09.011
chicago: Hammer, Matthieu, Dilja Krueger Burg, Liam Tuffy, Benjamin Cooper, Holger
Taschenberger, Sarit Goswami, Hannelore Ehrenreich, et al. “Perturbed Hippocampal
Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model
of Autism.” Cell Reports. Cell Press, 2015. https://doi.org/10.1016/j.celrep.2015.09.011.
ieee: M. Hammer et al., “Perturbed hippocampal synaptic inhibition and γ-oscillations
in a neuroligin-4 knockout mouse model of autism,” Cell Reports, vol. 13,
no. 3. Cell Press, pp. 516–523, 2015.
ista: Hammer M, Krueger Burg D, Tuffy L, Cooper B, Taschenberger H, Goswami S, Ehrenreich
H, Jonas PM, Varoqueaux F, Rhee J, Brose N. 2015. Perturbed hippocampal synaptic
inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism.
Cell Reports. 13(3), 516–523.
mla: Hammer, Matthieu, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations
in a Neuroligin-4 Knockout Mouse Model of Autism.” Cell Reports, vol. 13,
no. 3, Cell Press, 2015, pp. 516–23, doi:10.1016/j.celrep.2015.09.011.
short: M. Hammer, D. Krueger Burg, L. Tuffy, B. Cooper, H. Taschenberger, S. Goswami,
H. Ehrenreich, P.M. Jonas, F. Varoqueaux, J. Rhee, N. Brose, Cell Reports 13 (2015)
516–523.
date_created: 2018-12-11T11:53:02Z
date_published: 2015-10-20T00:00:00Z
date_updated: 2021-01-12T06:52:01Z
day: '20'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.celrep.2015.09.011
file:
- access_level: open_access
checksum: 44d30fbb543774b076b4938bd36af9d7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:23Z
date_updated: 2020-07-14T12:45:07Z
file_id: '5005'
file_name: IST-2016-470-v1+1_1-s2.0-S2211124715010220-main.pdf
file_size: 2314406
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '3'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 516 - 523
publication: Cell Reports
publication_status: published
publisher: Cell Press
publist_id: '5551'
pubrep_id: '470'
quality_controlled: '1'
scopus_import: 1
status: public
title: Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4
knockout mouse model of autism
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: 13
year: '2015'
...
---
_id: '1614'
abstract:
- lang: eng
text: 'GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively
control the activity of large neuron populations by their wide axonal arborizations.
It is generally assumed that the output of one PII to its target cells is strong
and rapid. Here, we show that, unexpectedly, both strength and time course of
PII-mediated perisomatic inhibition change with distance between synaptically
connected partners in the rodent hippocampus. Synaptic signals become weaker due
to lower contact numbers and decay more slowly with distance, very likely resulting
from changes in GABAA receptor subunit composition. When distance-dependent synaptic
inhibition is introduced to a rhythmically active neuronal network model, randomly
driven principal cell assemblies are strongly synchronized by the PIIs, leading
to higher precision in principal cell spike times than in a network with uniform
synaptic inhibition. '
author:
- first_name: Michael
full_name: Strüber, Michael
last_name: Strüber
- 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: Marlene
full_name: Bartos, Marlene
last_name: Bartos
citation:
ama: Strüber M, Jonas PM, Bartos M. Strength and duration of perisomatic GABAergic
inhibition depend on distance between synaptically connected cells. PNAS.
2015;112(4):1220-1225. doi:10.1073/pnas.1412996112
apa: Strüber, M., Jonas, P. M., & Bartos, M. (2015). Strength and duration of
perisomatic GABAergic inhibition depend on distance between synaptically connected
cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1412996112
chicago: Strüber, Michael, Peter M Jonas, and Marlene Bartos. “Strength and Duration
of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected
Cells.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1412996112.
ieee: M. Strüber, P. M. Jonas, and M. Bartos, “Strength and duration of perisomatic
GABAergic inhibition depend on distance between synaptically connected cells,”
PNAS, vol. 112, no. 4. National Academy of Sciences, pp. 1220–1225, 2015.
ista: Strüber M, Jonas PM, Bartos M. 2015. Strength and duration of perisomatic
GABAergic inhibition depend on distance between synaptically connected cells.
PNAS. 112(4), 1220–1225.
mla: Strüber, Michael, et al. “Strength and Duration of Perisomatic GABAergic Inhibition
Depend on Distance between Synaptically Connected Cells.” PNAS, vol. 112,
no. 4, National Academy of Sciences, 2015, pp. 1220–25, doi:10.1073/pnas.1412996112.
short: M. Strüber, P.M. Jonas, M. Bartos, PNAS 112 (2015) 1220–1225.
date_created: 2018-12-11T11:53:02Z
date_published: 2015-01-27T00:00:00Z
date_updated: 2021-01-12T06:52:01Z
day: '27'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1073/pnas.1412996112
ec_funded: 1
external_id:
pmid:
- '25583495'
file:
- access_level: open_access
checksum: 6703309a1f58493cf5a704211fb6ebed
content_type: application/pdf
creator: dernst
date_created: 2019-01-17T07:52:40Z
date_updated: 2020-07-14T12:45:07Z
file_id: '5838'
file_name: 2015_PNAS_Strueber.pdf
file_size: 1280860
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 112'
issue: '4'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 1220 - 1225
pmid: 1
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: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5552'
quality_controlled: '1'
scopus_import: 1
status: public
title: Strength and duration of perisomatic GABAergic inhibition depend on distance
between synaptically connected cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1611'
abstract:
- lang: eng
text: Biosensors for signaling molecules allow the study of physiological processes
by bringing together the fields of protein engineering, fluorescence imaging,
and cell biology. Construction of genetically encoded biosensors generally relies
on the availability of a binding "core" that is both specific and stable,
which can then be combined with fluorescent molecules to create a sensor. However,
binding proteins with the desired properties are often not available in nature
and substantial improvement to sensors can be required, particularly with regard
to their durability. Ancestral protein reconstruction is a powerful protein-engineering
tool able to generate highly stable and functional proteins. In this work, we
sought to establish the utility of ancestral protein reconstruction to biosensor
development, beginning with the construction of an l-arginine biosensor. l-arginine,
as the immediate precursor to nitric oxide, is an important molecule in many physiological
contexts including brain function. Using a combination of ancestral reconstruction
and circular permutation, we constructed a Förster resonance energy transfer (FRET)
biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity,
with a Kd of ∼14 μM and a maximal dynamic range of 35%. Importantly, cpFLIPR was
highly robust, enabling accurate l-arginine measurement at physiological temperatures.
We established that cpFLIPR is compatible with two-photon excitation fluorescence
microscopy and report l-arginine concentrations in brain tissue.
author:
- first_name: Jason
full_name: Whitfield, Jason
last_name: Whitfield
- first_name: William
full_name: Zhang, William
last_name: Zhang
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Ben
full_name: Clifton, Ben
last_name: Clifton
- first_name: Johanna
full_name: Radziejewski, Johanna
last_name: Radziejewski
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
citation:
ama: Whitfield J, Zhang W, Herde M, et al. Construction of a robust and sensitive
arginine biosensor through ancestral protein reconstruction. Protein Science.
2015;24(9):1412-1422. doi:10.1002/pro.2721
apa: Whitfield, J., Zhang, W., Herde, M., Clifton, B., Radziejewski, J., Janovjak,
H. L., … Jackson, C. (2015). Construction of a robust and sensitive arginine biosensor
through ancestral protein reconstruction. Protein Science. Wiley. https://doi.org/10.1002/pro.2721
chicago: Whitfield, Jason, William Zhang, Michel Herde, Ben Clifton, Johanna Radziejewski,
Harald L Janovjak, Christian Henneberger, and Colin Jackson. “Construction of
a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.”
Protein Science. Wiley, 2015. https://doi.org/10.1002/pro.2721.
ieee: J. Whitfield et al., “Construction of a robust and sensitive arginine
biosensor through ancestral protein reconstruction,” Protein Science, vol.
24, no. 9. Wiley, pp. 1412–1422, 2015.
ista: Whitfield J, Zhang W, Herde M, Clifton B, Radziejewski J, Janovjak HL, Henneberger
C, Jackson C. 2015. Construction of a robust and sensitive arginine biosensor
through ancestral protein reconstruction. Protein Science. 24(9), 1412–1422.
mla: Whitfield, Jason, et al. “Construction of a Robust and Sensitive Arginine Biosensor
through Ancestral Protein Reconstruction.” Protein Science, vol. 24, no.
9, Wiley, 2015, pp. 1412–22, doi:10.1002/pro.2721.
short: J. Whitfield, W. Zhang, M. Herde, B. Clifton, J. Radziejewski, H.L. Janovjak,
C. Henneberger, C. Jackson, Protein Science 24 (2015) 1412–1422.
date_created: 2018-12-11T11:53:01Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2021-01-12T06:52:00Z
day: '01'
department:
- _id: HaJa
doi: 10.1002/pro.2721
external_id:
pmid:
- '26061224'
intvolume: ' 24'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570536/
month: '09'
oa: 1
oa_version: Submitted Version
page: 1412 - 1422
pmid: 1
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors (HFSP Young Investigator)
publication: Protein Science
publication_status: published
publisher: Wiley
publist_id: '5555'
quality_controlled: '1'
scopus_import: 1
status: public
title: Construction of a robust and sensitive arginine biosensor through ancestral
protein reconstruction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2015'
...
---
_id: '1624'
abstract:
- lang: eng
text: Population structure can facilitate evolution of cooperation. In a structured
population, cooperators can form clusters which resist exploitation by defectors.
Recently, it was observed that a shift update rule is an extremely strong amplifier
of cooperation in a one dimensional spatial model. For the shift update rule,
an individual is chosen for reproduction proportional to fecundity; the offspring
is placed next to the parent; a random individual dies. Subsequently, the population
is rearranged (shifted) until all individual cells are again evenly spaced out.
For large population size and a one dimensional population structure, the shift
update rule favors cooperation for any benefit-to-cost ratio greater than one.
But every attempt to generalize shift updating to higher dimensions while maintaining
its strong effect has failed. The reason is that in two dimensions the clusters
are fragmented by the movements caused by rearranging the cells. Here we introduce
the natural phenomenon of a repulsive force between cells of different types.
After a birth and death event, the cells are being rearranged minimizing the overall
energy expenditure. If the repulsive force is sufficiently high, shift becomes
a strong promoter of cooperation in two dimensions.
acknowledgement: 'The research was supported by the Austrian Science Fund (FWF) Grant
No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307:
Graph Games), and Microsoft Faculty Fellows award. Support from the John Templeton
foundation is gratefully acknowledged.'
article_number: '17147'
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ben
full_name: Adlam, Ben
last_name: Adlam
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. Cellular cooperation with shift
updating and repulsion. Scientific Reports. 2015;5. doi:10.1038/srep17147
apa: Pavlogiannis, A., Chatterjee, K., Adlam, B., & Nowak, M. (2015). Cellular
cooperation with shift updating and repulsion. Scientific Reports. Nature
Publishing Group. https://doi.org/10.1038/srep17147
chicago: Pavlogiannis, Andreas, Krishnendu Chatterjee, Ben Adlam, and Martin Nowak.
“Cellular Cooperation with Shift Updating and Repulsion.” Scientific Reports.
Nature Publishing Group, 2015. https://doi.org/10.1038/srep17147.
ieee: A. Pavlogiannis, K. Chatterjee, B. Adlam, and M. Nowak, “Cellular cooperation
with shift updating and repulsion,” Scientific Reports, vol. 5. Nature
Publishing Group, 2015.
ista: Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. 2015. Cellular cooperation
with shift updating and repulsion. Scientific Reports. 5, 17147.
mla: Pavlogiannis, Andreas, et al. “Cellular Cooperation with Shift Updating and
Repulsion.” Scientific Reports, vol. 5, 17147, Nature Publishing Group,
2015, doi:10.1038/srep17147.
short: A. Pavlogiannis, K. Chatterjee, B. Adlam, M. Nowak, Scientific Reports 5
(2015).
date_created: 2018-12-11T11:53:06Z
date_published: 2015-11-25T00:00:00Z
date_updated: 2021-01-12T06:52:05Z
day: '25'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/srep17147
ec_funded: 1
file:
- access_level: open_access
checksum: 38e06d8310d2087cae5f6d4d4bfe082b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:29Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4947'
file_name: IST-2016-466-v1+1_srep17147.pdf
file_size: 1021931
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
month: '11'
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: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _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: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '5536'
pubrep_id: '466'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cellular cooperation with shift updating and repulsion
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: 5
year: '2015'
...
---
_id: '1623'
abstract:
- lang: eng
text: "Background\r\nPhotosynthetic cyanobacteria are attractive for a range of
biotechnological applications including biofuel production. However, due to slow
growth, screening of mutant libraries using microtiter plates is not feasible.\r\nResults\r\nWe
present a method for high-throughput, single-cell analysis and sorting of genetically
engineered l-lactate-producing strains of Synechocystis sp. PCC6803. A microfluidic
device is used to encapsulate single cells in picoliter droplets, assay the droplets
for l-lactate production, and sort strains with high productivity. We demonstrate
the separation of low- and high-producing reference strains, as well as enrichment
of a more productive l-lactate-synthesizing population after UV-induced mutagenesis.
The droplet platform also revealed population heterogeneity in photosynthetic
growth and lactate production, as well as the presence of metabolically stalled
cells.\r\nConclusions\r\nThe workflow will facilitate metabolic engineering and
directed evolution studies and will be useful in studies of cyanobacteria biochemistry
and physiology.\r\n"
article_number: '193'
author:
- first_name: Petter
full_name: Hammar, Petter
last_name: Hammar
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Staffan
full_name: Sjostrom, Staffan
last_name: Sjostrom
- first_name: Josefin
full_name: Van Der Meer, Josefin
last_name: Van Der Meer
- first_name: Klaas
full_name: Hellingwerf, Klaas
last_name: Hellingwerf
- first_name: Elton
full_name: Hudson, Elton
last_name: Hudson
- first_name: Hakaan
full_name: Joensson, Hakaan
last_name: Joensson
citation:
ama: Hammar P, Angermayr A, Sjostrom S, et al. Single-cell screening of photosynthetic
growth and lactate production by cyanobacteria. Biotechnology for Biofuels.
2015;8(1). doi:10.1186/s13068-015-0380-2
apa: Hammar, P., Angermayr, A., Sjostrom, S., Van Der Meer, J., Hellingwerf, K.,
Hudson, E., & Joensson, H. (2015). Single-cell screening of photosynthetic
growth and lactate production by cyanobacteria. Biotechnology for Biofuels.
BioMed Central. https://doi.org/10.1186/s13068-015-0380-2
chicago: Hammar, Petter, Andreas Angermayr, Staffan Sjostrom, Josefin Van Der Meer,
Klaas Hellingwerf, Elton Hudson, and Hakaan Joensson. “Single-Cell Screening of
Photosynthetic Growth and Lactate Production by Cyanobacteria.” Biotechnology
for Biofuels. BioMed Central, 2015. https://doi.org/10.1186/s13068-015-0380-2.
ieee: P. Hammar et al., “Single-cell screening of photosynthetic growth and
lactate production by cyanobacteria,” Biotechnology for Biofuels, vol.
8, no. 1. BioMed Central, 2015.
ista: Hammar P, Angermayr A, Sjostrom S, Van Der Meer J, Hellingwerf K, Hudson E,
Joensson H. 2015. Single-cell screening of photosynthetic growth and lactate production
by cyanobacteria. Biotechnology for Biofuels. 8(1), 193.
mla: Hammar, Petter, et al. “Single-Cell Screening of Photosynthetic Growth and
Lactate Production by Cyanobacteria.” Biotechnology for Biofuels, vol.
8, no. 1, 193, BioMed Central, 2015, doi:10.1186/s13068-015-0380-2.
short: P. Hammar, A. Angermayr, S. Sjostrom, J. Van Der Meer, K. Hellingwerf, E.
Hudson, H. Joensson, Biotechnology for Biofuels 8 (2015).
date_created: 2018-12-11T11:53:05Z
date_published: 2015-11-25T00:00:00Z
date_updated: 2021-01-12T06:52:04Z
day: '25'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1186/s13068-015-0380-2
file:
- access_level: open_access
checksum: 172b0b6f4eb2e5c22b7cec1d57dc0107
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:11Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4796'
file_name: IST-2016-467-v1+1_s13068-015-0380-2.pdf
file_size: 2914089
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Biotechnology for Biofuels
publication_status: published
publisher: BioMed Central
publist_id: '5537'
pubrep_id: '467'
quality_controlled: '1'
scopus_import: 1
status: public
title: Single-cell screening of photosynthetic growth and lactate production by cyanobacteria
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: '2015'
...
---
_id: '1625'
abstract:
- lang: eng
text: In recent years we have seen numerous improvements on 3D scanning and tracking
of human faces, greatly advancing the creation of digital doubles for film and
video games. However, despite the high-resolution quality of the reconstruction
approaches available, current methods are unable to capture one of the most important
regions of the face - the eye region. In this work we present the first method
for detailed spatio-temporal reconstruction of eyelids. Tracking and reconstructing
eyelids is extremely challenging, as this region exhibits very complex and unique
skin deformation where skin is folded under while opening the eye. Furthermore,
eyelids are often only partially visible and obstructed due to selfocclusion and
eyelashes. Our approach is to combine a geometric deformation model with image
data, leveraging multi-view stereo, optical flow, contour tracking and wrinkle
detection from local skin appearance. Our deformation model serves as a prior
that enables reconstruction of eyelids even under strong self-occlusions caused
by rolling and folding skin as the eye opens and closes. The output is a person-specific,
time-varying eyelid reconstruction with anatomically plausible deformations. Our
high-resolution detailed eyelids couple naturally with current facial performance
capture approaches. As a result, our method can largely increase the fidelity
of facial capture and the creation of digital doubles.
article_number: '44'
author:
- first_name: Amit
full_name: Bermano, Amit
last_name: Bermano
- first_name: Thabo
full_name: Beeler, Thabo
last_name: Beeler
- first_name: Yeara
full_name: Kozlov, Yeara
last_name: Kozlov
- first_name: Derek
full_name: Bradley, Derek
last_name: Bradley
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Markus
full_name: Gross, Markus
last_name: Gross
citation:
ama: 'Bermano A, Beeler T, Kozlov Y, Bradley D, Bickel B, Gross M. Detailed spatio-temporal
reconstruction of eyelids. In: Vol 34. ACM; 2015. doi:10.1145/2766924'
apa: 'Bermano, A., Beeler, T., Kozlov, Y., Bradley, D., Bickel, B., & Gross,
M. (2015). Detailed spatio-temporal reconstruction of eyelids (Vol. 34). Presented
at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques,
Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766924'
chicago: Bermano, Amit, Thabo Beeler, Yeara Kozlov, Derek Bradley, Bernd Bickel,
and Markus Gross. “Detailed Spatio-Temporal Reconstruction of Eyelids,” Vol. 34.
ACM, 2015. https://doi.org/10.1145/2766924.
ieee: 'A. Bermano, T. Beeler, Y. Kozlov, D. Bradley, B. Bickel, and M. Gross, “Detailed
spatio-temporal reconstruction of eyelids,” presented at the SIGGRAPH: Special
Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA,
United States, 2015, vol. 34, no. 4.'
ista: 'Bermano A, Beeler T, Kozlov Y, Bradley D, Bickel B, Gross M. 2015. Detailed
spatio-temporal reconstruction of eyelids. SIGGRAPH: Special Interest Group on
Computer Graphics and Interactive Techniques vol. 34, 44.'
mla: Bermano, Amit, et al. Detailed Spatio-Temporal Reconstruction of Eyelids.
Vol. 34, no. 4, 44, ACM, 2015, doi:10.1145/2766924.
short: A. Bermano, T. Beeler, Y. Kozlov, D. Bradley, B. Bickel, M. Gross, in:, ACM,
2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:06Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2021-01-12T06:52:05Z
day: '27'
department:
- _id: BeBi
doi: 10.1145/2766924
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa_version: None
publication_status: published
publisher: ACM
publist_id: '5535'
quality_controlled: '1'
scopus_import: 1
status: public
title: Detailed spatio-temporal reconstruction of eyelids
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1626'
abstract:
- lang: eng
text: This paper introduces "OmniAD," a novel data-driven pipeline to
model and acquire the aerodynamics of three-dimensional rigid objects. Traditionally,
aerodynamics are examined through elaborate wind tunnel experiments or expensive
fluid dynamics computations, and are only measured for a small number of discrete
wind directions. OmniAD allows the evaluation of aerodynamic forces, such as drag
and lift, for any incoming wind direction using a novel representation based on
spherical harmonics. Our datadriven technique acquires the aerodynamic properties
of an object simply by capturing its falling motion using a single camera. Once
model parameters are estimated, OmniAD enables realistic realtime simulation of
rigid bodies, such as the tumbling and gliding of leaves, without simulating the
surrounding air. In addition, we propose an intuitive user interface based on
OmniAD to interactively design three-dimensional kites that actually fly. Various
nontraditional kites were designed to demonstrate the physical validity of our
model.
alternative_title:
- ACM Transactions on Graphics
article_number: '113'
author:
- first_name: Tobias
full_name: Martin, Tobias
last_name: Martin
- first_name: Nobuyuki
full_name: Umetani, Nobuyuki
last_name: Umetani
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: 'Martin T, Umetani N, Bickel B. OmniAD: Data-driven omni-directional aerodynamics.
In: Vol 34. ACM; 2015. doi:10.1145/2766919'
apa: 'Martin, T., Umetani, N., & Bickel, B. (2015). OmniAD: Data-driven omni-directional
aerodynamics (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766919'
chicago: 'Martin, Tobias, Nobuyuki Umetani, and Bernd Bickel. “OmniAD: Data-Driven
Omni-Directional Aerodynamics,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766919.'
ieee: 'T. Martin, N. Umetani, and B. Bickel, “OmniAD: Data-driven omni-directional
aerodynamics,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics
and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no.
4.'
ista: 'Martin T, Umetani N, Bickel B. 2015. OmniAD: Data-driven omni-directional
aerodynamics. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques, ACM Transactions on Graphics, vol. 34, 113.'
mla: 'Martin, Tobias, et al. OmniAD: Data-Driven Omni-Directional Aerodynamics.
Vol. 34, no. 4, 113, ACM, 2015, doi:10.1145/2766919.'
short: T. Martin, N. Umetani, B. Bickel, in:, ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:06Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2021-01-12T06:52:05Z
day: '27'
department:
- _id: BeBi
doi: 10.1145/2766919
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa_version: None
publication_status: published
publisher: ACM
publist_id: '5532'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'OmniAD: Data-driven omni-directional aerodynamics'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1628'
abstract:
- lang: eng
text: We propose a method for fabricating deformable objects with spatially varying
elasticity using 3D printing. Using a single, relatively stiff printer material,
our method designs an assembly of smallscale microstructures that have the effect
of a softer material at the object scale, with properties depending on the microstructure
used in each part of the object. We build on work in the area of metamaterials,
using numerical optimization to design tiled microstructures with desired properties,
but with the key difference that our method designs families of related structures
that can be interpolated to smoothly vary the material properties over a wide
range. To create an object with spatially varying elastic properties, we tile
the object's interior with microstructures drawn from these families, generating
a different microstructure for each cell using an efficient algorithm to select
compatible structures for neighboring cells. We show results computed for both
2D and 3D objects, validating several 2D and 3D printed structures using standard
material tests as well as demonstrating various example applications.
article_number: '136'
article_processing_charge: No
author:
- first_name: Christian
full_name: Schumacher, Christian
last_name: Schumacher
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Jan
full_name: Rys, Jan
last_name: Rys
- first_name: Steve
full_name: Marschner, Steve
last_name: Marschner
- first_name: Chiara
full_name: Daraio, Chiara
last_name: Daraio
- first_name: Markus
full_name: Gross, Markus
last_name: Gross
citation:
ama: 'Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. Microstructures
to control elasticity in 3D printing. In: Vol 34. ACM; 2015. doi:10.1145/2766926'
apa: 'Schumacher, C., Bickel, B., Rys, J., Marschner, S., Daraio, C., & Gross,
M. (2015). Microstructures to control elasticity in 3D printing (Vol. 34). Presented
at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques,
Los Angeles, CA, USA: ACM. https://doi.org/10.1145/2766926'
chicago: Schumacher, Christian, Bernd Bickel, Jan Rys, Steve Marschner, Chiara Daraio,
and Markus Gross. “Microstructures to Control Elasticity in 3D Printing,” Vol.
34. ACM, 2015. https://doi.org/10.1145/2766926.
ieee: 'C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, and M. Gross,
“Microstructures to control elasticity in 3D printing,” presented at the SIGGRAPH:
Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles,
CA, USA, 2015, vol. 34, no. 4.'
ista: 'Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. 2015. Microstructures
to control elasticity in 3D printing. SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques vol. 34, 136.'
mla: Schumacher, Christian, et al. Microstructures to Control Elasticity in 3D
Printing. Vol. 34, no. 4, 136, ACM, 2015, doi:10.1145/2766926.
short: C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, M. Gross, in:,
ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, USA
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:07Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:52:06Z
day: '01'
department:
- _id: BeBi
doi: 10.1145/2766926
intvolume: ' 34'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/2766926
month: '08'
oa: 1
oa_version: Published Version
publication_status: published
publisher: ACM
publist_id: '5529'
quality_controlled: '1'
scopus_import: 1
status: public
title: Microstructures to control elasticity in 3D printing
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1627'
abstract:
- lang: eng
text: We present a computational tool for fabrication-oriented design of flexible
rod meshes. Given a deformable surface and a set of deformed poses as input, our
method automatically computes a printable rod mesh that, once manufactured, closely
matches the input poses under the same boundary conditions. The core of our method
is formed by an optimization scheme that adjusts the cross-sectional profiles
of the rods and their rest centerline in order to best approximate the target
deformations. This approach allows us to locally control the bending and stretching
resistance of the surface with a single material, yielding high design flexibility
and low fabrication cost.
acknowledgement: This work was supported in part by grants from the Spanish Ministry
of Economy (TIN2012-35840), and the European Research Council (ERC Starting Grant
no. 280135 Animetrics).
article_number: '138'
author:
- first_name: Jesús
full_name: Pérez, Jesús
last_name: Pérez
- first_name: Bernhard
full_name: Thomaszewski, Bernhard
last_name: Thomaszewski
- first_name: Stelian
full_name: Coros, Stelian
last_name: Coros
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: José
full_name: Canabal, José
last_name: Canabal
- first_name: Robert
full_name: Sumner, Robert
last_name: Sumner
- first_name: Miguel
full_name: Otaduy, Miguel
last_name: Otaduy
citation:
ama: 'Pérez J, Thomaszewski B, Coros S, et al. Design and fabrication of flexible
rod meshes. In: Vol 34. ACM; 2015. doi:10.1145/2766998'
apa: 'Pérez, J., Thomaszewski, B., Coros, S., Bickel, B., Canabal, J., Sumner, R.,
& Otaduy, M. (2015). Design and fabrication of flexible rod meshes (Vol. 34).
Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766998'
chicago: Pérez, Jesús, Bernhard Thomaszewski, Stelian Coros, Bernd Bickel, José
Canabal, Robert Sumner, and Miguel Otaduy. “Design and Fabrication of Flexible
Rod Meshes,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766998.
ieee: 'J. Pérez et al., “Design and fabrication of flexible rod meshes,”
presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.'
ista: 'Pérez J, Thomaszewski B, Coros S, Bickel B, Canabal J, Sumner R, Otaduy M.
2015. Design and fabrication of flexible rod meshes. SIGGRAPH: Special Interest
Group on Computer Graphics and Interactive Techniques vol. 34, 138.'
mla: Pérez, Jesús, et al. Design and Fabrication of Flexible Rod Meshes.
Vol. 34, no. 4, 138, ACM, 2015, doi:10.1145/2766998.
short: J. Pérez, B. Thomaszewski, S. Coros, B. Bickel, J. Canabal, R. Sumner, M.
Otaduy, in:, ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:07Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2021-01-12T06:52:06Z
day: '27'
department:
- _id: BeBi
doi: 10.1145/2766998
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa_version: None
publication_status: published
publisher: ACM
publist_id: '5530'
quality_controlled: '1'
scopus_import: 1
status: public
title: Design and fabrication of flexible rod meshes
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1634'
abstract:
- lang: eng
text: Simulating the delightful dynamics of soap films, bubbles, and foams has traditionally
required the use of a fully three-dimensional many-phase Navier-Stokes solver,
even though their visual appearance is completely dominated by the thin liquid
surface. We depart from earlier work on soap bubbles and foams by noting that
their dynamics are naturally described by a Lagrangian vortex sheet model in which
circulation is the primary variable. This leads us to derive a novel circulation-preserving
surface-only discretization of foam dynamics driven by surface tension on a non-manifold
triangle mesh. We represent the surface using a mesh-based multimaterial surface
tracker which supports complex bubble topology changes, and evolve the surface
according to the ambient air flow induced by a scalar circulation field stored
on the mesh. Surface tension forces give rise to a simple update rule for circulation,
even at non-manifold Plateau borders, based on a discrete measure of signed scalar
mean curvature. We further incorporate vertex constraints to enable the interaction
of soap films with wires. The result is a method that is at once simple, robust,
and efficient, yet able to capture an array of soap films behaviors including
foam rearrangement, catenoid collapse, blowing bubbles, and double bubbles being
pulled apart.
article_number: '149'
author:
- first_name: Fang
full_name: Da, Fang
last_name: Da
- first_name: Christopher
full_name: Batty, Christopher
last_name: Batty
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Eitan
full_name: Grinspun, Eitan
last_name: Grinspun
citation:
ama: 'Da F, Batty C, Wojtan C, Grinspun E. Double bubbles sans toil and trouble:
discrete circulation-preserving vortex sheets for soap films and foams. In: Vol
34. ACM; 2015. doi:10.1145/2767003'
apa: 'Da, F., Batty, C., Wojtan, C., & Grinspun, E. (2015). Double bubbles sans
toil and trouble: discrete circulation-preserving vortex sheets for soap films
and foams (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2767003'
chicago: 'Da, Fang, Christopher Batty, Chris Wojtan, and Eitan Grinspun. “Double
Bubbles sans Toil and Trouble: Discrete Circulation-Preserving Vortex Sheets for
Soap Films and Foams,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2767003.'
ieee: 'F. Da, C. Batty, C. Wojtan, and E. Grinspun, “Double bubbles sans toil and
trouble: discrete circulation-preserving vortex sheets for soap films and foams,”
presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.'
ista: 'Da F, Batty C, Wojtan C, Grinspun E. 2015. Double bubbles sans toil and trouble:
discrete circulation-preserving vortex sheets for soap films and foams. SIGGRAPH:
Special Interest Group on Computer Graphics and Interactive Techniques vol. 34,
149.'
mla: 'Da, Fang, et al. Double Bubbles sans Toil and Trouble: Discrete Circulation-Preserving
Vortex Sheets for Soap Films and Foams. Vol. 34, no. 4, 149, ACM, 2015, doi:10.1145/2767003.'
short: F. Da, C. Batty, C. Wojtan, E. Grinspun, in:, ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:09Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2023-02-23T10:07:42Z
day: '27'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2767003
ec_funded: 1
file:
- access_level: open_access
checksum: 57b07d78d2d612a8052744b37d4a71fa
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:14Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4867'
file_name: IST-2016-608-v1+1_doublebubbles.pdf
file_size: 8973215
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication_status: published
publisher: ACM
publist_id: '5521'
pubrep_id: '608'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Double bubbles sans toil and trouble: discrete circulation-preserving vortex
sheets for soap films and foams'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1636'
abstract:
- lang: eng
text: "Constraint Satisfaction Problem (CSP) is a fundamental algorithmic problem
that appears in many areas of Computer Science. It can be equivalently stated
as computing a homomorphism R→ΓΓ between two relational structures, e.g. between
two directed graphs. Analyzing its complexity has been a prominent research direction,
especially for the fixed template CSPs where the right side ΓΓ is fixed and the
left side R is unconstrained.\r\n\r\nFar fewer results are known for the hybrid
setting that restricts both sides simultaneously. It assumes that R belongs to
a certain class of relational structures (called a structural restriction in this
paper). We study which structural restrictions are effective, i.e. there exists
a fixed template ΓΓ (from a certain class of languages) for which the problem
is tractable when R is restricted, and NP-hard otherwise. We provide a characterization
for structural restrictions that are closed under inverse homomorphisms. The criterion
is based on the chromatic number of a relational structure defined in this paper;
it generalizes the standard chromatic number of a graph.\r\n\r\nAs our main tool,
we use the algebraic machinery developed for fixed template CSPs. To apply it
to our case, we introduce a new construction called a “lifted language”. We also
give a characterization for structural restrictions corresponding to minor-closed
families of graphs, extend results to certain Valued CSPs (namely conservative
valued languages), and state implications for (valued) CSPs with ordered variables
and for the maximum weight independent set problem on some restricted families
of graphs."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
- first_name: Rustem
full_name: Takhanov, Rustem
last_name: Takhanov
citation:
ama: 'Kolmogorov V, Rolinek M, Takhanov R. Effectiveness of structural restrictions
for hybrid CSPs. In: 26th International Symposium. Vol 9472. Springer Nature;
2015:566-577. doi:10.1007/978-3-662-48971-0_48'
apa: 'Kolmogorov, V., Rolinek, M., & Takhanov, R. (2015). Effectiveness of structural
restrictions for hybrid CSPs. In 26th International Symposium (Vol. 9472,
pp. 566–577). Nagoya, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-48971-0_48'
chicago: Kolmogorov, Vladimir, Michal Rolinek, and Rustem Takhanov. “Effectiveness
of Structural Restrictions for Hybrid CSPs.” In 26th International Symposium,
9472:566–77. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-48971-0_48.
ieee: V. Kolmogorov, M. Rolinek, and R. Takhanov, “Effectiveness of structural restrictions
for hybrid CSPs,” in 26th International Symposium, Nagoya, Japan, 2015,
vol. 9472, pp. 566–577.
ista: 'Kolmogorov V, Rolinek M, Takhanov R. 2015. Effectiveness of structural restrictions
for hybrid CSPs. 26th International Symposium. ISAAC: International Symposium
on Algorithms and Computation, LNCS, vol. 9472, 566–577.'
mla: Kolmogorov, Vladimir, et al. “Effectiveness of Structural Restrictions for
Hybrid CSPs.” 26th International Symposium, vol. 9472, Springer Nature,
2015, pp. 566–77, doi:10.1007/978-3-662-48971-0_48.
short: V. Kolmogorov, M. Rolinek, R. Takhanov, in:, 26th International Symposium,
Springer Nature, 2015, pp. 566–577.
conference:
end_date: 2015-12-11
location: Nagoya, Japan
name: 'ISAAC: International Symposium on Algorithms and Computation'
start_date: 2015-12-09
date_created: 2018-12-11T11:53:10Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2022-02-01T15:12:35Z
day: '01'
department:
- _id: VlKo
doi: 10.1007/978-3-662-48971-0_48
ec_funded: 1
external_id:
arxiv:
- '1504.07067'
intvolume: ' 9472'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1504.07067
month: '12'
oa: 1
oa_version: Preprint
page: 566 - 577
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: 26th International Symposium
publication_identifier:
isbn:
- 978-3-662-48970-3
publication_status: published
publisher: Springer Nature
publist_id: '5519'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effectiveness of structural restrictions for hybrid CSPs
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9472
year: '2015'
...
---
_id: '1632'
abstract:
- lang: eng
text: "This paper presents a liquid simulation technique that enforces the incompressibility
condition using a stream function solve instead of a pressure projection. Previous
methods have used stream function techniques for the simulation of detailed single-phase
flows, but a formulation for liquid simulation has proved elusive in part due
to the free surface boundary conditions. In this paper, we introduce a stream
function approach to liquid simulations with novel boundary conditions for free
surfaces, solid obstacles, and solid-fluid coupling.\r\n\r\nAlthough our approach
increases the dimension of the linear system necessary to enforce incompressibility,
it provides interesting and surprising benefits. First, the resulting flow is
guaranteed to be divergence-free regardless of the accuracy of the solve. Second,
our free-surface boundary conditions guarantee divergence-free motion even in
the un-simulated air phase, which enables two-phase flow simulation by only computing
a single phase. We implemented this method using a variant of FLIP simulation
which only samples particles within a narrow band of the liquid surface, and we
illustrate the effectiveness of our method for detailed two-phase flow simulations
with complex boundaries, detailed bubble interactions, and two-way solid-fluid
coupling."
acknowledgement: The first author was supported by a JSPS Postdoctoral Fellowship
for Research Abroad. This work was also supported by the ERC projects ERC-2014-StG-637014
realFlow and ERC-2014- StG-638176 BigSplash.
alternative_title:
- ACM Transactions on Graphics
article_number: '53'
author:
- first_name: Ryoichi
full_name: Ando, Ryoichi
last_name: Ando
- first_name: Nils
full_name: Thuerey, Nils
last_name: Thuerey
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Ando R, Thuerey N, Wojtan C. A stream function solver for liquid simulations.
In: Vol 34. ACM; 2015. doi:10.1145/2766935'
apa: 'Ando, R., Thuerey, N., & Wojtan, C. (2015). A stream function solver for
liquid simulations (Vol. 34). Presented at the SIGGRAPH: Special Interest Group
on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/2766935'
chicago: Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “A Stream Function Solver
for Liquid Simulations,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766935.
ieee: 'R. Ando, N. Thuerey, and C. Wojtan, “A stream function solver for liquid
simulations,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics
and Interactive Techniques, Los Angeles, CA, USA, 2015, vol. 34, no. 4.'
ista: 'Ando R, Thuerey N, Wojtan C. 2015. A stream function solver for liquid simulations.
SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques,
ACM Transactions on Graphics, vol. 34, 53.'
mla: Ando, Ryoichi, et al. A Stream Function Solver for Liquid Simulations.
Vol. 34, no. 4, 53, ACM, 2015, doi:10.1145/2766935.
short: R. Ando, N. Thuerey, C. Wojtan, in:, ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, USA
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:09Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2023-02-23T10:07:37Z
day: '27'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2766935
file:
- access_level: open_access
checksum: 7a9afdfaba9209157ce19376e15bc90b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:52Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4909'
file_name: IST-2016-610-v1+1_vecpotential.pdf
file_size: 21831121
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
publication_status: published
publisher: ACM
publist_id: '5523'
pubrep_id: '610'
quality_controlled: '1'
scopus_import: 1
status: public
title: A stream function solver for liquid simulations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1630'
abstract:
- lang: eng
text: We present a method to learn and propagate shape placements in 2D polygonal
scenes from a few examples provided by a user. The placement of a shape is modeled
as an oriented bounding box. Simple geometric relationships between this bounding
box and nearby scene polygons define a feature set for the placement. The feature
sets of all example placements are then used to learn a probabilistic model over
all possible placements and scenes. With this model, we can generate a new set
of placements with similar geometric relationships in any given scene. We introduce
extensions that enable propagation and generation of shapes in 3D scenes, as
well as the application of a learned modeling session to large scenes without
additional user interaction. These concepts allow us to generate complex scenes
with thousands of objects with relatively little user interaction.
acknowledgement: This publication is based upon work supported by the KAUST Office
of Competitive Research Funds (OCRF) under Award No. 62140401, the KAUST Visual
Computing Center and the Austrian Science Fund (FWF) projects DEEP PICTURES (no.
P24352-N23) and Data-Driven Procedural Modeling of Interiors (no. P24600-N23).
article_number: '108'
author:
- first_name: Paul
full_name: Guerrero, Paul
last_name: Guerrero
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Michael
full_name: Wimmer, Michael
last_name: Wimmer
- first_name: Peter
full_name: Wonka, Peter
last_name: Wonka
citation:
ama: 'Guerrero P, Jeschke S, Wimmer M, Wonka P. Learning shape placements by example.
In: Vol 34. ACM; 2015. doi:10.1145/2766933'
apa: 'Guerrero, P., Jeschke, S., Wimmer, M., & Wonka, P. (2015). Learning shape
placements by example (Vol. 34). Presented at the SIGGRAPH: Special Interest Group
on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States:
ACM. https://doi.org/10.1145/2766933'
chicago: Guerrero, Paul, Stefan Jeschke, Michael Wimmer, and Peter Wonka. “Learning
Shape Placements by Example,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766933.
ieee: 'P. Guerrero, S. Jeschke, M. Wimmer, and P. Wonka, “Learning shape placements
by example,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics
and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no.
4.'
ista: 'Guerrero P, Jeschke S, Wimmer M, Wonka P. 2015. Learning shape placements
by example. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques vol. 34, 108.'
mla: Guerrero, Paul, et al. Learning Shape Placements by Example. Vol. 34,
no. 4, 108, ACM, 2015, doi:10.1145/2766933.
short: P. Guerrero, S. Jeschke, M. Wimmer, P. Wonka, in:, ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:08Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2021-01-12T06:52:07Z
day: '27'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2766933
file:
- access_level: open_access
checksum: 8b05a51e372c9b0b5af9a00098a9538b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:49Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4647'
file_name: IST-2016-576-v1+1_guerrero-2015-lsp-paper.pdf
file_size: 11902290
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 25357BD2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 24352-N23
name: 'Deep Pictures: Creating Visual and Haptic Vector Images'
publication_status: published
publisher: ACM
publist_id: '5525'
pubrep_id: '576'
quality_controlled: '1'
scopus_import: 1
status: public
title: Learning shape placements by example
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1640'
abstract:
- lang: eng
text: Auxin and cytokinin are key endogenous regulators of plant development. Although
cytokinin-mediated modulation of auxin distribution is a developmentally crucial
hormonal interaction, its molecular basis is largely unknown. Here we show a direct
regulatory link between cytokinin signalling and the auxin transport machinery
uncovering a mechanistic framework for cytokinin-auxin cross-talk. We show that
the CYTOKININ RESPONSE FACTORS (CRFs), transcription factors downstream of cytokinin
perception, transcriptionally control genes encoding PIN-FORMED (PIN) auxin transporters
at a specific PIN CYTOKININ RESPONSE ELEMENT (PCRE) domain. Removal of this cis-regulatory
element effectively uncouples PIN transcription from the CRF-mediated cytokinin
regulation and attenuates plant cytokinin sensitivity. We propose that CRFs represent
a missing cross-talk component that fine-tunes auxin transport capacity downstream
of cytokinin signalling to control plant development.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: This work was supported by the European Research Council Starting
Independent Research grant (ERC-2007-Stg-207362-HCPO to E.B., M.S., C.C.), by the
Ghent University Multidisciplinary Research Partnership ‘Biotechnology for a Sustainable
Economy’ no.01MRB510W, by the Research Foundation—Flanders (grant 3G033711 to J.-A.O.),
by the Austrian Science Fund (FWF01_I1774S) to K.Ö.,E.B., and by the Interuniversity
Attraction Poles Programme (IUAP P7/29 ‘MARS’) initiated by the Belgian Science
Policy Office. I.D.C. and S.V. are post-doctoral fellows of the Research Foundation—Flanders
(FWO). This research was supported by the Scientific Service Units (SSU) of IST-Austria
through resources provided by the Bioimaging Facility (BIF), the Life Science Facility
(LSF).
article_number: '8717'
author:
- first_name: Mária
full_name: Šimášková, Mária
last_name: Šimášková
- first_name: José
full_name: O'Brien, José
last_name: O'Brien
- first_name: Mamoona
full_name: Khan-Djamei, Mamoona
id: 391B5BBC-F248-11E8-B48F-1D18A9856A87
last_name: Khan-Djamei
- first_name: Giel
full_name: Van Noorden, Giel
last_name: Van Noorden
- first_name: Krisztina
full_name: Ötvös, Krisztina
id: 29B901B0-F248-11E8-B48F-1D18A9856A87
last_name: Ötvös
orcid: 0000-0002-5503-4983
- first_name: Anne
full_name: Vieten, Anne
last_name: Vieten
- first_name: Inge
full_name: De Clercq, Inge
last_name: De Clercq
- first_name: Johanna
full_name: Van Haperen, Johanna
last_name: Van Haperen
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Klára
full_name: Hoyerová, Klára
last_name: Hoyerová
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Frank
full_name: Van Breusegem, Frank
last_name: Van Breusegem
- first_name: Moritz
full_name: Nowack, Moritz
last_name: Nowack
- first_name: Angus
full_name: Murphy, Angus
last_name: Murphy
- first_name: Jiřĺ
full_name: Friml, Jiřĺ
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Šimášková M, O’Brien J, Khan-Djamei M, et al. Cytokinin response factors regulate
PIN-FORMED auxin transporters. Nature Communications. 2015;6. doi:10.1038/ncomms9717
apa: Šimášková, M., O’Brien, J., Khan-Djamei, M., Van Noorden, G., Ötvös, K., Vieten,
A., … Benková, E. (2015). Cytokinin response factors regulate PIN-FORMED auxin
transporters. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9717
chicago: Šimášková, Mária, José O’Brien, Mamoona Khan-Djamei, Giel Van Noorden,
Krisztina Ötvös, Anne Vieten, Inge De Clercq, et al. “Cytokinin Response Factors
Regulate PIN-FORMED Auxin Transporters.” Nature Communications. Nature
Publishing Group, 2015. https://doi.org/10.1038/ncomms9717.
ieee: M. Šimášková et al., “Cytokinin response factors regulate PIN-FORMED
auxin transporters,” Nature Communications, vol. 6. Nature Publishing Group,
2015.
ista: Šimášková M, O’Brien J, Khan-Djamei M, Van Noorden G, Ötvös K, Vieten A, De
Clercq I, Van Haperen J, Cuesta C, Hoyerová K, Vanneste S, Marhavý P, Wabnik KT,
Van Breusegem F, Nowack M, Murphy A, Friml J, Weijers D, Beeckman T, Benková E.
2015. Cytokinin response factors regulate PIN-FORMED auxin transporters. Nature
Communications. 6, 8717.
mla: Šimášková, Mária, et al. “Cytokinin Response Factors Regulate PIN-FORMED Auxin
Transporters.” Nature Communications, vol. 6, 8717, Nature Publishing Group,
2015, doi:10.1038/ncomms9717.
short: M. Šimášková, J. O’Brien, M. Khan-Djamei, G. Van Noorden, K. Ötvös, A. Vieten,
I. De Clercq, J. Van Haperen, C. Cuesta, K. Hoyerová, S. Vanneste, P. Marhavý,
K.T. Wabnik, F. Van Breusegem, M. Nowack, A. Murphy, J. Friml, D. Weijers, T.
Beeckman, E. Benková, Nature Communications 6 (2015).
date_created: 2018-12-11T11:53:12Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:11Z
day: '01'
ddc:
- '580'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1038/ncomms9717
ec_funded: 1
file:
- access_level: open_access
checksum: c2c84bca37401435fedf76bad0ba0579
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:36Z
date_updated: 2020-07-14T12:45:08Z
file_id: '5358'
file_name: IST-2018-1020-v1+1_Simaskova_et_al_NatCom_2015.pdf
file_size: 1471217
relation: main_file
file_date_updated: 2020-07-14T12:45:08Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5513'
pubrep_id: '1020'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cytokinin response factors regulate PIN-FORMED auxin transporters
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '1642'
abstract:
- lang: eng
text: The Hanani-Tutte theorem is a classical result proved for the first time in
the 1930s that characterizes planar graphs as graphs that admit a drawing in the
plane in which every pair of edges not sharing a vertex cross an even number of
times. We generalize this result to clustered graphs with two disjoint clusters,
and show that a straightforward extension to flat clustered graphs with three
or more disjoint clusters is not possible. For general clustered graphs we show
a variant of the Hanani-Tutte theorem in the case when each cluster induces a
connected subgraph. Di Battista and Frati proved that clustered planarity of embedded
clustered graphs whose every face is incident to at most five vertices can be
tested in polynomial time. We give a new and short proof of this result, using
the matroid intersection algorithm.
acknowledgement: e research leading to these results has received funding fromthe
People Programme (Marie Curie Actions) of the European Union’s Seventh Framework
Programme(FP7/2007-2013) under REA grant agreement no [291734], and ESF Eurogiga
project GraDR as GAˇCRGIG/11/E023.
article_number: 'P4.24 '
article_processing_charge: No
article_type: original
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Jan
full_name: Kynčl, Jan
last_name: Kynčl
- first_name: Igor
full_name: Malinovič, Igor
last_name: Malinovič
- first_name: Dömötör
full_name: Pálvölgyi, Dömötör
last_name: Pálvölgyi
citation:
ama: Fulek R, Kynčl J, Malinovič I, Pálvölgyi D. Clustered planarity testing revisited.
Electronic Journal of Combinatorics. 2015;22(4). doi:10.37236/5002
apa: Fulek, R., Kynčl, J., Malinovič, I., & Pálvölgyi, D. (2015). Clustered
planarity testing revisited. Electronic Journal of Combinatorics. Electronic
Journal of Combinatorics. https://doi.org/10.37236/5002
chicago: Fulek, Radoslav, Jan Kynčl, Igor Malinovič, and Dömötör Pálvölgyi. “Clustered
Planarity Testing Revisited.” Electronic Journal of Combinatorics. Electronic
Journal of Combinatorics, 2015. https://doi.org/10.37236/5002.
ieee: R. Fulek, J. Kynčl, I. Malinovič, and D. Pálvölgyi, “Clustered planarity testing
revisited,” Electronic Journal of Combinatorics, vol. 22, no. 4. Electronic
Journal of Combinatorics, 2015.
ista: Fulek R, Kynčl J, Malinovič I, Pálvölgyi D. 2015. Clustered planarity testing
revisited. Electronic Journal of Combinatorics. 22(4), P4.24.
mla: Fulek, Radoslav, et al. “Clustered Planarity Testing Revisited.” Electronic
Journal of Combinatorics, vol. 22, no. 4, P4.24, Electronic Journal of Combinatorics,
2015, doi:10.37236/5002.
short: R. Fulek, J. Kynčl, I. Malinovič, D. Pálvölgyi, Electronic Journal of Combinatorics
22 (2015).
date_created: 2018-12-11T11:53:12Z
date_published: 2015-11-13T00:00:00Z
date_updated: 2023-02-21T16:03:02Z
day: '13'
ddc:
- '514'
- '516'
department:
- _id: UlWa
doi: 10.37236/5002
ec_funded: 1
external_id:
arxiv:
- '1305.4519'
file:
- access_level: open_access
checksum: 40b5920b49ee736694f59f39588ee206
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:03Z
date_updated: 2020-07-14T12:45:08Z
file_id: '5120'
file_name: IST-2016-714-v1+1_5002-15499-3-PB.pdf
file_size: 443655
relation: main_file
file_date_updated: 2020-07-14T12:45:08Z
has_accepted_license: '1'
intvolume: ' 22'
issue: '4'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Electronic Journal of Combinatorics
publication_identifier:
eissn:
- 1077-8926
publication_status: published
publisher: Electronic Journal of Combinatorics
publist_id: '5511'
pubrep_id: '714'
quality_controlled: '1'
related_material:
record:
- id: '10793'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Clustered planarity testing revisited
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2015'
...
---
_id: '1639'
abstract:
- lang: eng
text: In this paper the optimal transport and the metamorphosis perspectives are
combined. For a pair of given input images geodesic paths in the space of images
are defined as minimizers of a resulting path energy. To this end, the underlying
Riemannian metric measures the rate of transport cost and the rate of viscous
dissipation. Furthermore, the model is capable to deal with strongly varying image
contrast and explicitly allows for sources and sinks in the transport equations
which are incorporated in the metric related to the metamorphosis approach by
Trouvé and Younes. In the non-viscous case with source term existence of geodesic
paths is proven in the space of measures. The proposed model is explored on the
range from merely optimal transport to strongly dissipative dynamics. For this
model a robust and effective variational time discretization of geodesic paths
is proposed. This requires to minimize a discrete path energy consisting of a
sum of consecutive image matching functionals. These functionals are defined on
corresponding pairs of intensity functions and on associated pairwise matching
deformations. Existence of time discrete geodesics is demonstrated. Furthermore,
a finite element implementation is proposed and applied to instructive test cases
and to real images. In the non-viscous case this is compared to the algorithm
proposed by Benamou and Brenier including a discretization of the source term.
Finally, the model is generalized to define discrete weighted barycentres with
applications to textures and objects.
acknowledgement: The authors acknowledge support of the Collaborative Research Centre
1060 funded by the German Science foundation. This work is further supported by
the King Abdullah University for Science and Technology (KAUST) Award No. KUK-I1-007-43
and the EPSRC grant Nr. EP/M00483X/1.
author:
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Martin
full_name: Rumpf, Martin
last_name: Rumpf
- first_name: Carola
full_name: Schönlieb, Carola
last_name: Schönlieb
- first_name: Stefan
full_name: Simon, Stefan
last_name: Simon
citation:
ama: 'Maas J, Rumpf M, Schönlieb C, Simon S. A generalized model for optimal transport
of images including dissipation and density modulation. ESAIM: Mathematical
Modelling and Numerical Analysis. 2015;49(6):1745-1769. doi:10.1051/m2an/2015043'
apa: 'Maas, J., Rumpf, M., Schönlieb, C., & Simon, S. (2015). A generalized
model for optimal transport of images including dissipation and density modulation.
ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences. https://doi.org/10.1051/m2an/2015043'
chicago: 'Maas, Jan, Martin Rumpf, Carola Schönlieb, and Stefan Simon. “A Generalized
Model for Optimal Transport of Images Including Dissipation and Density Modulation.”
ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences, 2015.
https://doi.org/10.1051/m2an/2015043.'
ieee: 'J. Maas, M. Rumpf, C. Schönlieb, and S. Simon, “A generalized model for optimal
transport of images including dissipation and density modulation,” ESAIM: Mathematical
Modelling and Numerical Analysis, vol. 49, no. 6. EDP Sciences, pp. 1745–1769,
2015.'
ista: 'Maas J, Rumpf M, Schönlieb C, Simon S. 2015. A generalized model for optimal
transport of images including dissipation and density modulation. ESAIM: Mathematical
Modelling and Numerical Analysis. 49(6), 1745–1769.'
mla: 'Maas, Jan, et al. “A Generalized Model for Optimal Transport of Images Including
Dissipation and Density Modulation.” ESAIM: Mathematical Modelling and Numerical
Analysis, vol. 49, no. 6, EDP Sciences, 2015, pp. 1745–69, doi:10.1051/m2an/2015043.'
short: 'J. Maas, M. Rumpf, C. Schönlieb, S. Simon, ESAIM: Mathematical Modelling
and Numerical Analysis 49 (2015) 1745–1769.'
date_created: 2018-12-11T11:53:11Z
date_published: 2015-11-01T00:00:00Z
date_updated: 2021-01-12T06:52:10Z
day: '01'
department:
- _id: JaMa
doi: 10.1051/m2an/2015043
external_id:
arxiv:
- '1504.01988'
intvolume: ' 49'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1504.01988
month: '11'
oa: 1
oa_version: Preprint
page: 1745 - 1769
publication: 'ESAIM: Mathematical Modelling and Numerical Analysis'
publication_status: published
publisher: EDP Sciences
publist_id: '5514'
quality_controlled: '1'
scopus_import: 1
status: public
title: A generalized model for optimal transport of images including dissipation and
density modulation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 49
year: '2015'
...
---
_id: '1638'
abstract:
- lang: eng
text: The mitochondrial respiratory chain, also known as the electron transport
chain (ETC), is crucial to life, and energy production in the form of ATP is the
main mitochondrial function. Three proton-translocating enzymes of the ETC, namely
complexes I, III and IV, generate proton motive force, which in turn drives ATP
synthase (complex V). The atomic structures and basic mechanisms of most respiratory
complexes have previously been established, with the exception of complex I, the
largest complex in the ETC. Recently, the crystal structure of the entire complex
I was solved using a bacterial enzyme. The structure provided novel insights into
the core architecture of the complex, the electron transfer and proton translocation
pathways, as well as the mechanism that couples these two processes.
author:
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: 'Sazanov LA. A giant molecular proton pump: structure and mechanism of respiratory
complex I. Nature Reviews Molecular Cell Biology. 2015;16(6):375-388. doi:10.1038/nrm3997'
apa: 'Sazanov, L. A. (2015). A giant molecular proton pump: structure and mechanism
of respiratory complex I. Nature Reviews Molecular Cell Biology. Nature
Publishing Group. https://doi.org/10.1038/nrm3997'
chicago: 'Sazanov, Leonid A. “A Giant Molecular Proton Pump: Structure and Mechanism
of Respiratory Complex I.” Nature Reviews Molecular Cell Biology. Nature
Publishing Group, 2015. https://doi.org/10.1038/nrm3997.'
ieee: 'L. A. Sazanov, “A giant molecular proton pump: structure and mechanism of
respiratory complex I,” Nature Reviews Molecular Cell Biology, vol. 16,
no. 6. Nature Publishing Group, pp. 375–388, 2015.'
ista: 'Sazanov LA. 2015. A giant molecular proton pump: structure and mechanism
of respiratory complex I. Nature Reviews Molecular Cell Biology. 16(6), 375–388.'
mla: 'Sazanov, Leonid A. “A Giant Molecular Proton Pump: Structure and Mechanism
of Respiratory Complex I.” Nature Reviews Molecular Cell Biology, vol.
16, no. 6, Nature Publishing Group, 2015, pp. 375–88, doi:10.1038/nrm3997.'
short: L.A. Sazanov, Nature Reviews Molecular Cell Biology 16 (2015) 375–388.
date_created: 2018-12-11T11:53:11Z
date_published: 2015-05-22T00:00:00Z
date_updated: 2021-01-12T06:52:10Z
day: '22'
department:
- _id: LeSa
doi: 10.1038/nrm3997
intvolume: ' 16'
issue: '6'
language:
- iso: eng
month: '05'
oa_version: None
page: 375 - 388
publication: Nature Reviews Molecular Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '5517'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'A giant molecular proton pump: structure and mechanism of respiratory complex
I'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2015'
...
---
_id: '1646'
abstract:
- lang: eng
text: 'A pseudorandom function (PRF) is a keyed function F : K × X → Y where, for
a random key k ∈ K, the function F(k, ·) is indistinguishable from a uniformly
random function, given black-box access. A key-homomorphic PRF has the additional
feature that for any keys k, k'' and any input x, we have F(k+k'', x) = F(k, x)⊕F(k'',
x) for some group operations +,⊕ on K and Y, respectively. A constrained PRF for
a family of setsS ⊆ P(X) has the property that, given any key k and set S ∈ S,
one can efficiently compute a “constrained” key kS that enables evaluation of
F(k, x) on all inputs x ∈ S, while the values F(k, x) for x /∈ S remain pseudorandom
even given kS. In this paper we construct PRFs that are simultaneously constrained
and key homomorphic, where the homomorphic property holds even for constrained
keys. We first show that the multilinear map-based bit-fixing and circuit-constrained
PRFs of Boneh and Waters (Asiacrypt 2013) can be modified to also be keyhomomorphic.
We then show that the LWE-based key-homomorphic PRFs of Banerjee and Peikert (Crypto
2014) are essentially already prefix-constrained PRFs, using a (non-obvious) definition
of constrained keys and associated group operation. Moreover, the constrained
keys themselves are pseudorandom, and the constraining and evaluation functions
can all be computed in low depth. As an application of key-homomorphic constrained
PRFs,we construct a proxy re-encryption schemewith fine-grained access control.
This scheme allows storing encrypted data on an untrusted server, where each file
can be encrypted relative to some attributes, so that only parties whose constrained
keys match the attributes can decrypt. Moreover, the server can re-key (arbitrary
subsets of) the ciphertexts without learning anything about the plaintexts, thus
permitting efficient and finegrained revocation.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Abishek
full_name: Banerjee, Abishek
last_name: Banerjee
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Chris
full_name: Peikert, Chris
last_name: Peikert
- 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: Sophie
full_name: Stevens, Sophie
last_name: Stevens
citation:
ama: 'Banerjee A, Fuchsbauer G, Peikert C, Pietrzak KZ, Stevens S. Key-homomorphic
constrained pseudorandom functions. In: 12th Theory of Cryptography Conference.
Vol 9015. Springer Nature; 2015:31-60. doi:10.1007/978-3-662-46497-7_2'
apa: 'Banerjee, A., Fuchsbauer, G., Peikert, C., Pietrzak, K. Z., & Stevens,
S. (2015). Key-homomorphic constrained pseudorandom functions. In 12th Theory
of Cryptography Conference (Vol. 9015, pp. 31–60). Warsaw, Poland: Springer
Nature. https://doi.org/10.1007/978-3-662-46497-7_2'
chicago: Banerjee, Abishek, Georg Fuchsbauer, Chris Peikert, Krzysztof Z Pietrzak,
and Sophie Stevens. “Key-Homomorphic Constrained Pseudorandom Functions.” In 12th
Theory of Cryptography Conference, 9015:31–60. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-46497-7_2.
ieee: A. Banerjee, G. Fuchsbauer, C. Peikert, K. Z. Pietrzak, and S. Stevens, “Key-homomorphic
constrained pseudorandom functions,” in 12th Theory of Cryptography Conference,
Warsaw, Poland, 2015, vol. 9015, pp. 31–60.
ista: 'Banerjee A, Fuchsbauer G, Peikert C, Pietrzak KZ, Stevens S. 2015. Key-homomorphic
constrained pseudorandom functions. 12th Theory of Cryptography Conference. TCC:
Theory of Cryptography Conference, LNCS, vol. 9015, 31–60.'
mla: Banerjee, Abishek, et al. “Key-Homomorphic Constrained Pseudorandom Functions.”
12th Theory of Cryptography Conference, vol. 9015, Springer Nature, 2015,
pp. 31–60, doi:10.1007/978-3-662-46497-7_2.
short: A. Banerjee, G. Fuchsbauer, C. Peikert, K.Z. Pietrzak, S. Stevens, in:, 12th
Theory of Cryptography Conference, Springer Nature, 2015, pp. 31–60.
conference:
end_date: 2015-03-25
location: Warsaw, Poland
name: 'TCC: Theory of Cryptography Conference'
start_date: 2015-03-23
date_created: 2018-12-11T11:53:14Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2022-02-03T08:41:46Z
day: '01'
ddc:
- '000'
- '004'
department:
- _id: KrPi
doi: 10.1007/978-3-662-46497-7_2
ec_funded: 1
file:
- access_level: open_access
checksum: 3c5093bda5783c89beaacabf1aa0e60e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:17Z
date_updated: 2020-07-14T12:45:08Z
file_id: '5136'
file_name: IST-2016-679-v1+1_180.pdf
file_size: 450665
relation: main_file
file_date_updated: 2020-07-14T12:45:08Z
has_accepted_license: '1'
intvolume: ' 9015'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2015/180
month: '03'
oa: 1
oa_version: Submitted Version
page: 31 - 60
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: 12th Theory of Cryptography Conference
publication_identifier:
isbn:
- 978-3-662-46496-0
publication_status: published
publisher: Springer Nature
publist_id: '5505'
pubrep_id: '679'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Key-homomorphic constrained pseudorandom functions
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9015
year: '2015'
...
---
_id: '1648'
abstract:
- lang: eng
text: Generalized Selective Decryption (GSD), introduced by Panjwani [TCC’07], is
a game for a symmetric encryption scheme Enc that captures the difficulty of proving
adaptive security of certain protocols, most notably the Logical Key Hierarchy
(LKH) multicast encryption protocol. In the GSD game there are n keys k1,...,
kn, which the adversary may adaptively corrupt (learn); moreover, it can ask for
encryptions Encki (kj) of keys under other keys. The adversary’s task is to distinguish
keys (which it cannot trivially compute) from random. Proving the hardness of
GSD assuming only IND-CPA security of Enc is surprisingly hard. Using “complexity
leveraging” loses a factor exponential in n, which makes the proof practically
meaningless. We can think of the GSD game as building a graph on n vertices, where
we add an edge i → j when the adversary asks for an encryption of kj under ki.
If restricted to graphs of depth ℓ, Panjwani gave a reduction that loses only
a factor exponential in ℓ (not n). To date, this is the only non-trivial result
known for GSD. In this paper we give almost-polynomial reductions for large classes
of graphs. Most importantly, we prove the security of the GSD game restricted
to trees losing only a quasi-polynomial factor n3 log n+5. Trees are an important
special case capturing real-world protocols like the LKH protocol. Our new bound
improves upon Panjwani’s on some LKH variants proposed in the literature where
the underlying tree is not balanced. Our proof builds on ideas from the “nested
hybrids” technique recently introduced by Fuchsbauer et al. [Asiacrypt’14] for
proving the adaptive security of constrained PRFs.
alternative_title:
- LNCS
author:
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Zahra
full_name: Jafargholi, Zahra
last_name: Jafargholi
- 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: 'Fuchsbauer G, Jafargholi Z, Pietrzak KZ. A quasipolynomial reduction for generalized
selective decryption on trees. In: Vol 9215. Springer; 2015:601-620. doi:10.1007/978-3-662-47989-6_29'
apa: 'Fuchsbauer, G., Jafargholi, Z., & Pietrzak, K. Z. (2015). A quasipolynomial
reduction for generalized selective decryption on trees (Vol. 9215, pp. 601–620).
Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA,
USA: Springer. https://doi.org/10.1007/978-3-662-47989-6_29'
chicago: Fuchsbauer, Georg, Zahra Jafargholi, and Krzysztof Z Pietrzak. “A Quasipolynomial
Reduction for Generalized Selective Decryption on Trees,” 9215:601–20. Springer,
2015. https://doi.org/10.1007/978-3-662-47989-6_29.
ieee: 'G. Fuchsbauer, Z. Jafargholi, and K. Z. Pietrzak, “A quasipolynomial reduction
for generalized selective decryption on trees,” presented at the CRYPTO: International
Cryptology Conference, Santa Barbara, CA, USA, 2015, vol. 9215, pp. 601–620.'
ista: 'Fuchsbauer G, Jafargholi Z, Pietrzak KZ. 2015. A quasipolynomial reduction
for generalized selective decryption on trees. CRYPTO: International Cryptology
Conference, LNCS, vol. 9215, 601–620.'
mla: Fuchsbauer, Georg, et al. A Quasipolynomial Reduction for Generalized Selective
Decryption on Trees. Vol. 9215, Springer, 2015, pp. 601–20, doi:10.1007/978-3-662-47989-6_29.
short: G. Fuchsbauer, Z. Jafargholi, K.Z. Pietrzak, in:, Springer, 2015, pp. 601–620.
conference:
end_date: 2015-08-20
location: Santa Barbara, CA, USA
name: 'CRYPTO: International Cryptology Conference'
start_date: 2015-08-16
date_created: 2018-12-11T11:53:14Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:52:14Z
day: '01'
ddc:
- '004'
department:
- _id: KrPi
doi: 10.1007/978-3-662-47989-6_29
ec_funded: 1
file:
- access_level: open_access
checksum: 99b76b3263d5082554d0a9cbdeca3a22
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:31Z
date_updated: 2020-07-14T12:45:08Z
file_id: '5015'
file_name: IST-2016-674-v1+1_389.pdf
file_size: 505618
relation: main_file
file_date_updated: 2020-07-14T12:45:08Z
has_accepted_license: '1'
intvolume: ' 9215'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 601 - 620
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '5502'
pubrep_id: '674'
quality_controlled: '1'
scopus_import: 1
status: public
title: A quasipolynomial reduction for generalized selective decryption on trees
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9215
year: '2015'
...
---
_id: '1649'
abstract:
- lang: eng
text: 'We extend a commitment scheme based on the learning with errors over rings
(RLWE) problem, and present efficient companion zeroknowledge proofs of knowledge.
Our scheme maps elements from the ring (or equivalently, n elements from '
alternative_title:
- LNCS
author:
- first_name: Fabrice
full_name: Benhamouda, Fabrice
last_name: Benhamouda
- first_name: Stephan
full_name: Krenn, Stephan
last_name: Krenn
- first_name: Vadim
full_name: Lyubashevsky, Vadim
last_name: Lyubashevsky
- 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: Benhamouda F, Krenn S, Lyubashevsky V, Pietrzak KZ. Efficient zero-knowledge
proofs for commitments from learning with errors over rings. 2015;9326:305-325.
doi:10.1007/978-3-319-24174-6_16
apa: 'Benhamouda, F., Krenn, S., Lyubashevsky, V., & Pietrzak, K. Z. (2015).
Efficient zero-knowledge proofs for commitments from learning with errors over
rings. Presented at the ESORICS: European Symposium on Research in Computer Security,
Vienna, Austria: Springer. https://doi.org/10.1007/978-3-319-24174-6_16'
chicago: Benhamouda, Fabrice, Stephan Krenn, Vadim Lyubashevsky, and Krzysztof Z
Pietrzak. “Efficient Zero-Knowledge Proofs for Commitments from Learning with
Errors over Rings.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-24174-6_16.
ieee: F. Benhamouda, S. Krenn, V. Lyubashevsky, and K. Z. Pietrzak, “Efficient zero-knowledge
proofs for commitments from learning with errors over rings,” vol. 9326. Springer,
pp. 305–325, 2015.
ista: Benhamouda F, Krenn S, Lyubashevsky V, Pietrzak KZ. 2015. Efficient zero-knowledge
proofs for commitments from learning with errors over rings. 9326, 305–325.
mla: Benhamouda, Fabrice, et al. Efficient Zero-Knowledge Proofs for Commitments
from Learning with Errors over Rings. Vol. 9326, Springer, 2015, pp. 305–25,
doi:10.1007/978-3-319-24174-6_16.
short: F. Benhamouda, S. Krenn, V. Lyubashevsky, K.Z. Pietrzak, 9326 (2015) 305–325.
conference:
end_date: 2015-09-25
location: Vienna, Austria
name: 'ESORICS: European Symposium on Research in Computer Security'
start_date: 2015-09-21
date_created: 2018-12-11T11:53:15Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:14Z
day: '01'
ddc:
- '000'
- '004'
department:
- _id: KrPi
doi: 10.1007/978-3-319-24174-6_16
ec_funded: 1
file:
- access_level: open_access
checksum: 6eac4a485b2aa644b2d3f753ed0b280b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:28Z
date_updated: 2020-07-14T12:45:08Z
file_id: '4883'
file_name: IST-2016-678-v1+1_889.pdf
file_size: 494239
relation: main_file
file_date_updated: 2020-07-14T12:45:08Z
has_accepted_license: '1'
intvolume: ' 9326'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 305 - 325
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '5501'
pubrep_id: '678'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Efficient zero-knowledge proofs for commitments from learning with errors over
rings
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9326
year: '2015'
...
---
_id: '1644'
abstract:
- lang: eng
text: Increasing the computational complexity of evaluating a hash function, both
for the honest users as well as for an adversary, is a useful technique employed
for example in password-based cryptographic schemes to impede brute-force attacks,
and also in so-called proofs of work (used in protocols like Bitcoin) to show
that a certain amount of computation was performed by a legitimate user. A natural
approach to adjust the complexity of a hash function is to iterate it c times,
for some parameter c, in the hope that any query to the scheme requires c evaluations
of the underlying hash function. However, results by Dodis et al. (Crypto 2012)
imply that plain iteration falls short of achieving this goal, and designing schemes
which provably have such a desirable property remained an open problem. This paper
formalizes explicitly what it means for a given scheme to amplify the query complexity
of a hash function. In the random oracle model, the goal of a secure query-complexity
amplifier (QCA) scheme is captured as transforming, in the sense of indifferentiability,
a random oracle allowing R queries (for the adversary) into one provably allowing
only r < R queries. Turned around, this means that making r queries to the
scheme requires at least R queries to the actual random oracle. Second, a new
scheme, called collision-free iteration, is proposed and proven to achieve c-fold
QCA for both the honest parties and the adversary, for any fixed parameter c.
alternative_title:
- LNCS
author:
- first_name: Grégory
full_name: Demay, Grégory
last_name: Demay
- first_name: Peter
full_name: Gazi, Peter
id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87
last_name: Gazi
- first_name: Ueli
full_name: Maurer, Ueli
last_name: Maurer
- first_name: Björn
full_name: Tackmann, Björn
last_name: Tackmann
citation:
ama: 'Demay G, Gazi P, Maurer U, Tackmann B. Query-complexity amplification for
random oracles. In: Vol 9063. Springer; 2015:159-180. doi:10.1007/978-3-319-17470-9_10'
apa: 'Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2015). Query-complexity
amplification for random oracles (Vol. 9063, pp. 159–180). Presented at the ICITS:
International Conference on Information Theoretic Security, Lugano, Switzerland:
Springer. https://doi.org/10.1007/978-3-319-17470-9_10'
chicago: Demay, Grégory, Peter Gazi, Ueli Maurer, and Björn Tackmann. “Query-Complexity
Amplification for Random Oracles,” 9063:159–80. Springer, 2015. https://doi.org/10.1007/978-3-319-17470-9_10.
ieee: 'G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Query-complexity amplification
for random oracles,” presented at the ICITS: International Conference on Information
Theoretic Security, Lugano, Switzerland, 2015, vol. 9063, pp. 159–180.'
ista: 'Demay G, Gazi P, Maurer U, Tackmann B. 2015. Query-complexity amplification
for random oracles. ICITS: International Conference on Information Theoretic Security,
LNCS, vol. 9063, 159–180.'
mla: Demay, Grégory, et al. Query-Complexity Amplification for Random Oracles.
Vol. 9063, Springer, 2015, pp. 159–80, doi:10.1007/978-3-319-17470-9_10.
short: G. Demay, P. Gazi, U. Maurer, B. Tackmann, in:, Springer, 2015, pp. 159–180.
conference:
end_date: 2015-05-05
location: Lugano, Switzerland
name: 'ICITS: International Conference on Information Theoretic Security'
start_date: 2015-05-02
date_created: 2018-12-11T11:53:13Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:13Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-319-17470-9_10
ec_funded: 1
intvolume: ' 9063'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprint.iacr.org/2015/315
month: '01'
oa: 1
oa_version: Submitted Version
page: 159 - 180
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '5507'
quality_controlled: '1'
scopus_import: 1
status: public
title: Query-complexity amplification for random oracles
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9063
year: '2015'
...