---
_id: '2922'
author:
- first_name: Sara
full_name: Vicente, Sara
last_name: Vicente
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: 'Vicente S, Kolmogorov V, Rother C. Graph-cut Based Image Segmentation with
Connectivity Priors. In: Blake A, Kohli P, Rother C, eds. Markov Random Fields
for Vision and Image Processing. Massachusetts Institute of Technology Press;
2011.'
apa: Vicente, S., Kolmogorov, V., & Rother, C. (2011). Graph-cut Based Image
Segmentation with Connectivity Priors. In A. Blake, P. Kohli, & C. Rother
(Eds.), Markov Random Fields for Vision and Image Processing. Massachusetts
Institute of Technology Press.
chicago: Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Graph-Cut Based
Image Segmentation with Connectivity Priors.” In Markov Random Fields for Vision
and Image Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten
Rother. Massachusetts Institute of Technology Press, 2011.
ieee: S. Vicente, V. Kolmogorov, and C. Rother, “Graph-cut Based Image Segmentation
with Connectivity Priors,” in Markov Random Fields for Vision and Image Processing,
A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology
Press, 2011.
ista: 'Vicente S, Kolmogorov V, Rother C. 2011.Graph-cut Based Image Segmentation
with Connectivity Priors. In: Markov Random Fields for Vision and Image Processing.
.'
mla: Vicente, Sara, et al. “Graph-Cut Based Image Segmentation with Connectivity
Priors.” Markov Random Fields for Vision and Image Processing, edited by
Andrew Blake et al., Massachusetts Institute of Technology Press, 2011.
short: S. Vicente, V. Kolmogorov, C. Rother, in:, A. Blake, P. Kohli, C. Rother
(Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts Institute
of Technology Press, 2011.
date_created: 2018-12-11T12:00:21Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:43Z
day: '01'
editor:
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Pushmeet
full_name: Kohli, Pushmeet
last_name: Kohli
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
extern: 1
month: '01'
publication: Markov Random Fields for Vision and Image Processing
publication_status: published
publisher: Massachusetts Institute of Technology Press
publist_id: '3815'
quality_controlled: 0
status: public
title: Graph-cut Based Image Segmentation with Connectivity Priors
type: book_chapter
year: '2011'
...
---
_id: '2923'
author:
- first_name: M Pawan
full_name: Kumar, M Pawan
last_name: Kumar
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Philip
full_name: Torr, Philip H
last_name: Torr
citation:
ama: 'Kumar MP, Kolmogorov V, Torr P. Analyzing Convex Relaxations for MAP Estimation.
In: Blake A, Kohli P, Rother C, eds. Markov Random Fields for Vision and Image
Processing. Massachusetts Institute of Technology Press; 2011.'
apa: Kumar, M. P., Kolmogorov, V., & Torr, P. (2011). Analyzing Convex Relaxations
for MAP Estimation. In A. Blake, P. Kohli, & C. Rother (Eds.), Markov Random
Fields for Vision and Image Processing. Massachusetts Institute of Technology
Press.
chicago: Kumar, M Pawan, Vladimir Kolmogorov, and Philip Torr. “Analyzing Convex
Relaxations for MAP Estimation.” In Markov Random Fields for Vision and Image
Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother. Massachusetts
Institute of Technology Press, 2011.
ieee: M. P. Kumar, V. Kolmogorov, and P. Torr, “Analyzing Convex Relaxations for
MAP Estimation,” in Markov Random Fields for Vision and Image Processing,
A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology
Press, 2011.
ista: 'Kumar MP, Kolmogorov V, Torr P. 2011.Analyzing Convex Relaxations for MAP
Estimation. In: Markov Random Fields for Vision and Image Processing. .'
mla: Kumar, M. Pawan, et al. “Analyzing Convex Relaxations for MAP Estimation.”
Markov Random Fields for Vision and Image Processing, edited by Andrew
Blake et al., Massachusetts Institute of Technology Press, 2011.
short: M.P. Kumar, V. Kolmogorov, P. Torr, in:, A. Blake, P. Kohli, C. Rother (Eds.),
Markov Random Fields for Vision and Image Processing, Massachusetts Institute
of Technology Press, 2011.
date_created: 2018-12-11T12:00:21Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:43Z
day: '01'
editor:
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Pushmeet
full_name: Kohli, Pushmeet
last_name: Kohli
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
extern: 1
month: '01'
publication: Markov Random Fields for Vision and Image Processing
publication_status: published
publisher: Massachusetts Institute of Technology Press
publist_id: '3814'
quality_controlled: 0
status: public
title: Analyzing Convex Relaxations for MAP Estimation
type: book_chapter
year: '2011'
...
---
_id: '2924'
author:
- first_name: Antonio
full_name: Criminisi, Antonio
last_name: Criminisi
- first_name: Geoffrey
full_name: Cross, Geoffrey
last_name: Cross
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Criminisi A, Cross G, Blake A, Kolmogorov V. Bilayer Segmentation of Video.
In: Blake A, Kohli P, Rother C, eds. Markov Random Fields for Vision and Image
Processing. Massachusetts Institute of Technology Press; 2011.'
apa: Criminisi, A., Cross, G., Blake, A., & Kolmogorov, V. (2011). Bilayer Segmentation
of Video. In A. Blake, P. Kohli, & C. Rother (Eds.), Markov Random Fields
for Vision and Image Processing. Massachusetts Institute of Technology Press.
chicago: Criminisi, Antonio, Geoffrey Cross, Andrew Blake, and Vladimir Kolmogorov.
“Bilayer Segmentation of Video.” In Markov Random Fields for Vision and Image
Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother. Massachusetts
Institute of Technology Press, 2011.
ieee: A. Criminisi, G. Cross, A. Blake, and V. Kolmogorov, “Bilayer Segmentation
of Video,” in Markov Random Fields for Vision and Image Processing, A.
Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology Press,
2011.
ista: 'Criminisi A, Cross G, Blake A, Kolmogorov V. 2011.Bilayer Segmentation of
Video. In: Markov Random Fields for Vision and Image Processing. .'
mla: Criminisi, Antonio, et al. “Bilayer Segmentation of Video.” Markov Random
Fields for Vision and Image Processing, edited by Andrew Blake et al., Massachusetts
Institute of Technology Press, 2011.
short: A. Criminisi, G. Cross, A. Blake, V. Kolmogorov, in:, A. Blake, P. Kohli,
C. Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts
Institute of Technology Press, 2011.
date_created: 2018-12-11T12:00:22Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:43Z
day: '01'
editor:
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Pushmeet
full_name: Kohli, Pushmeet
last_name: Kohli
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
extern: 1
month: '01'
publication: Markov Random Fields for Vision and Image Processing
publication_status: published
publisher: Massachusetts Institute of Technology Press
publist_id: '3813'
quality_controlled: 0
status: public
title: Bilayer Segmentation of Video
type: book_chapter
year: '2011'
...
---
_id: '2925'
author:
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Yuri
full_name: Boykov, Yuri
last_name: Boykov
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
citation:
ama: 'Rother C, Kolmogorov V, Boykov Y, Blake A. Interactive Foreground Extraction
using graph cut. In: Blake A, Kohli P, Rother C, eds. Markov Random Fields
for Vision and Image Processing. Massachusetts Institute of Technology Press;
2011.'
apa: Rother, C., Kolmogorov, V., Boykov, Y., & Blake, A. (2011). Interactive
Foreground Extraction using graph cut. In A. Blake, P. Kohli, & C. Rother
(Eds.), Markov Random Fields for Vision and Image Processing. Massachusetts
Institute of Technology Press.
chicago: Rother, Carsten, Vladimir Kolmogorov, Yuri Boykov, and Andrew Blake. “Interactive
Foreground Extraction Using Graph Cut.” In Markov Random Fields for Vision
and Image Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten
Rother. Massachusetts Institute of Technology Press, 2011.
ieee: C. Rother, V. Kolmogorov, Y. Boykov, and A. Blake, “Interactive Foreground
Extraction using graph cut,” in Markov Random Fields for Vision and Image Processing,
A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology
Press, 2011.
ista: 'Rother C, Kolmogorov V, Boykov Y, Blake A. 2011.Interactive Foreground Extraction
using graph cut. In: Markov Random Fields for Vision and Image Processing. .'
mla: Rother, Carsten, et al. “Interactive Foreground Extraction Using Graph Cut.”
Markov Random Fields for Vision and Image Processing, edited by Andrew
Blake et al., Massachusetts Institute of Technology Press, 2011.
short: C. Rother, V. Kolmogorov, Y. Boykov, A. Blake, in:, A. Blake, P. Kohli, C.
Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts
Institute of Technology Press, 2011.
date_created: 2018-12-11T12:00:22Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:44Z
day: '01'
editor:
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Pushmeet
full_name: Kohli, Pushmeet
last_name: Kohli
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
extern: 1
month: '01'
publication: Markov Random Fields for Vision and Image Processing
publication_status: published
publisher: Massachusetts Institute of Technology Press
publist_id: '3812'
quality_controlled: 0
status: public
title: Interactive Foreground Extraction using graph cut
type: book_chapter
year: '2011'
...
---
_id: '2935'
author:
- first_name: Yuri
full_name: Boykov, Yuri
last_name: Boykov
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Boykov Y, Kolmogorov V. Basic graph cut algorithms. In: Blake A, Kohli P,
Rother C, eds. Markov Random Fields for Vision and Image Processing. Massachusetts
Institute of Technology Press; 2011:31-50.'
apa: Boykov, Y., & Kolmogorov, V. (2011). Basic graph cut algorithms. In A.
Blake, P. Kohli, & C. Rother (Eds.), Markov Random Fields for Vision and
Image Processing (pp. 31–50). Massachusetts Institute of Technology Press.
chicago: Boykov, Yuri, and Vladimir Kolmogorov. “Basic Graph Cut Algorithms.” In
Markov Random Fields for Vision and Image Processing, edited by Andrew
Blake, Pushmeet Kohli, and Carsten Rother, 31–50. Massachusetts Institute of Technology
Press, 2011.
ieee: Y. Boykov and V. Kolmogorov, “Basic graph cut algorithms,” in Markov Random
Fields for Vision and Image Processing, A. Blake, P. Kohli, and C. Rother,
Eds. Massachusetts Institute of Technology Press, 2011, pp. 31–50.
ista: 'Boykov Y, Kolmogorov V. 2011.Basic graph cut algorithms. In: Markov Random
Fields for Vision and Image Processing. , 31–50.'
mla: Boykov, Yuri, and Vladimir Kolmogorov. “Basic Graph Cut Algorithms.” Markov
Random Fields for Vision and Image Processing, edited by Andrew Blake et al.,
Massachusetts Institute of Technology Press, 2011, pp. 31–50.
short: Y. Boykov, V. Kolmogorov, in:, A. Blake, P. Kohli, C. Rother (Eds.), Markov
Random Fields for Vision and Image Processing, Massachusetts Institute of Technology
Press, 2011, pp. 31–50.
date_created: 2018-12-11T12:00:26Z
date_published: 2011-07-22T00:00:00Z
date_updated: 2021-01-12T07:39:53Z
day: '22'
editor:
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Pushmeet
full_name: Kohli, Pushmeet
last_name: Kohli
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
extern: 1
month: '07'
page: 31 - 50
publication: Markov Random Fields for Vision and Image Processing
publication_status: published
publisher: Massachusetts Institute of Technology Press
publist_id: '3801'
quality_controlled: 0
status: public
title: Basic graph cut algorithms
type: book_chapter
year: '2011'
...
---
_id: '2961'
abstract:
- lang: eng
text: |-
Rapid research progress in genotyping techniques have allowed large genome-wide association studies. Existing methods often focus on determining associations between single loci and a specic phenotype. However, a particular phenotype is usually the result of complex relationships between multiple loci and the environment. In this paper, we describe a two-stage method for detecting epistasis by combining the traditionally used single-locus search with a search for multiway interactions. Our method is based on an extended version of Fisher's exact test. To
perform this test, a Markov chain is constructed on the space of multidimensional contingency tables using the elements of a Markov basis as moves. We test our method on simulated data and compare it to a two-stage logistic regression method and to a fully Bayesian method, showing that we are able to detect the interacting loci when other methods fail to do so. Finally, we apply our method to a genome-wide data set consisting of 685 dogs and identify epistasis associated with canine hair length for four pairs of single nucleotide polymorphisms (SNPs).
acknowledgement: Anna-Sapfo Malaspinas is supported by a Janggen-Poehn Fellowship.
Caroline Uhler is supported by an International Fulbright Science and Technology
Fellowship.
author:
- first_name: Anna
full_name: 'Malaspinas, Anna-Sapfo '
last_name: Malaspinas
- first_name: Caroline
full_name: Caroline Uhler
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: Malaspinas A, Uhler C. Detecting epistasis via Markov bases. Journal of
Algebraic Statistics. 2011;2(1):36-53. doi:http://dx.doi.org/10.18409/jas.v2i1.27
apa: Malaspinas, A., & Uhler, C. (2011). Detecting epistasis via Markov bases.
Journal of Algebraic Statistics. Public Knowledge Project. http://dx.doi.org/10.18409/jas.v2i1.27
chicago: Malaspinas, Anna, and Caroline Uhler. “Detecting Epistasis via Markov Bases.”
Journal of Algebraic Statistics. Public Knowledge Project, 2011. http://dx.doi.org/10.18409/jas.v2i1.27.
ieee: A. Malaspinas and C. Uhler, “Detecting epistasis via Markov bases,” Journal
of Algebraic Statistics, vol. 2, no. 1. Public Knowledge Project, pp. 36–53,
2011.
ista: Malaspinas A, Uhler C. 2011. Detecting epistasis via Markov bases. Journal
of Algebraic Statistics. 2(1), 36–53.
mla: Malaspinas, Anna, and Caroline Uhler. “Detecting Epistasis via Markov Bases.”
Journal of Algebraic Statistics, vol. 2, no. 1, Public Knowledge Project,
2011, pp. 36–53, doi:http://dx.doi.org/10.18409/jas.v2i1.27.
short: A. Malaspinas, C. Uhler, Journal of Algebraic Statistics 2 (2011) 36–53.
date_created: 2018-12-11T12:00:34Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:40:05Z
day: '01'
doi: http://dx.doi.org/10.18409/jas.v2i1.27
extern: 1
intvolume: ' 2'
issue: '1'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1006.4929
month: '01'
oa: 1
page: 36 - 53
publication: Journal of Algebraic Statistics
publication_status: published
publisher: Public Knowledge Project
publist_id: '3764'
quality_controlled: 0
status: public
title: Detecting epistasis via Markov bases
type: journal_article
volume: 2
year: '2011'
...
---
_id: '2960'
abstract:
- lang: eng
text: Traditional statistical methods for the confidentiality protection for statistical
databases do not scale well to deal with GWAS (genome-wide association studies)
databases and external information on them. The more recent concept of differential
privacy, introduced by the cryptographic community, is an approach which provides
a rigorous definition of privacy with meaningful privacy guarantees in the presence
of arbitrary external information. Building on such notions, we propose new methods
to release aggregate GWAS data without compromising an individual's privacy. We
present methods for releasing differentially private minor allele frequencies,
chi-square statistics and p-values. We compare these approaches on simulated data
and on a GWAS study of canine hair length involving 685 dogs. We also propose
a privacy-preserving method for finding genome-wide associations based on a differentially
private approach to penalized logistic regression.
author:
- first_name: Stephen
full_name: Fienberg, Stephen E
last_name: Fienberg
- first_name: Aleksandra
full_name: Slavkovic, Aleksandra
last_name: Slavkovic
- first_name: Caroline
full_name: Caroline Uhler
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: 'Fienberg S, Slavkovic A, Uhler C. Privacy Preserving GWAS Data Sharing. In:
IEEE; 2011. doi:10.1109/ICDMW.2011.140'
apa: Fienberg, S., Slavkovic, A., & Uhler, C. (2011). Privacy Preserving GWAS
Data Sharing. Presented at the Proceedings of the 11th IEEE International Conference
on Data Mining, IEEE. https://doi.org/10.1109/ICDMW.2011.140
chicago: Fienberg, Stephen, Aleksandra Slavkovic, and Caroline Uhler. “Privacy Preserving
GWAS Data Sharing.” IEEE, 2011. https://doi.org/10.1109/ICDMW.2011.140.
ieee: S. Fienberg, A. Slavkovic, and C. Uhler, “Privacy Preserving GWAS Data Sharing,”
presented at the Proceedings of the 11th IEEE International Conference on Data
Mining, 2011.
ista: Fienberg S, Slavkovic A, Uhler C. 2011. Privacy Preserving GWAS Data Sharing.
Proceedings of the 11th IEEE International Conference on Data Mining.
mla: Fienberg, Stephen, et al. Privacy Preserving GWAS Data Sharing. IEEE,
2011, doi:10.1109/ICDMW.2011.140.
short: S. Fienberg, A. Slavkovic, C. Uhler, in:, IEEE, 2011.
conference:
name: Proceedings of the 11th IEEE International Conference on Data Mining
date_created: 2018-12-11T12:00:34Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:40:05Z
day: '01'
doi: 10.1109/ICDMW.2011.140
extern: 1
month: '01'
publication_status: published
publisher: IEEE
publist_id: '3766'
quality_controlled: 0
status: public
title: Privacy Preserving GWAS Data Sharing
type: conference
year: '2011'
...
---
_id: '2975'
abstract:
- lang: eng
text: "Zero-knowledge proofs of knowledge (ZK-PoK) for discrete logarithms and related
problems are indispensable for practical cryptographic protocols. Recently, Camenisch,
Kiayias, and Yung provided a specification language (the CKY-language) for such
protocols which allows for a modular design and protocol analysis: for every zero-knowledge
proof specified in this language, protocol designers are ensured that there exists
an efficient protocol which indeed proves the specified statement.\n\nHowever,
the protocols resulting from their compilation techniques only satisfy the classical
notion of ZK-PoK, which is not retained are when they used as building blocks
for higher-level applications or composed with other protocols.\nThis problem
can be tackled by moving to the Universal Composability (UC) framework, which
guarantees retention of security when composing protocols in arbitrary ways. \nWhile
there exist generic transformations from $\\Sigma$-protocols to UC-secure protocols,
these transformation are often too inefficient for practice.\n \nIn this paper
we introduce a specification language akin to the CKY-language and a compiler
such that the resulting protocols are UC-secure and efficient. \nTo this end,
we propose an extension of the UC-framework addressing the \nissue that UC-secure
zero-knowledge proofs are by definition proofs of knowledge, and state a special
composition theorem which allows one to use the weaker -- but more efficient and
often sufficient -- notion of proofs of membership in the UC-framework. \nWe
believe that our contributions enable the design of practically efficient protocols
that are UC-secure and thus themselves can be used as building blocks."
acknowledgement: This work was in part funded by the Swiss Hasler Foundation, and
the EU FP7 grants 216483 and 216499, as well as by the NSF grant CNS-0716690.
alternative_title:
- LNCS
author:
- first_name: Jan
full_name: Camenisch, Jan
last_name: Camenisch
- first_name: Stephan
full_name: Stephan Krenn
id: 329FCCF0-F248-11E8-B48F-1D18A9856A87
last_name: Krenn
orcid: 0000-0003-2835-9093
- first_name: Victor
full_name: Shoup, Victor
last_name: Shoup
citation:
ama: 'Camenisch J, Krenn S, Shoup V. A Framework for Practical Universally Composable
Zero-Knowledge Protocols. In: Lee D, Wang X, eds. Vol 7073. Springer; 2011:449-467.
doi:10.1007/978-3-642-25385-0'
apa: 'Camenisch, J., Krenn, S., & Shoup, V. (2011). A Framework for Practical
Universally Composable Zero-Knowledge Protocols. In D. Lee & X. Wang (Eds.)
(Vol. 7073, pp. 449–467). Presented at the ASIACRYPT: Theory and Application of
Cryptology and Information Security, Springer. https://doi.org/10.1007/978-3-642-25385-0'
chicago: Camenisch, Jan, Stephan Krenn, and Victor Shoup. “A Framework for Practical
Universally Composable Zero-Knowledge Protocols.” edited by Dong Lee and Xiaoyun
Wang, 7073:449–67. Springer, 2011. https://doi.org/10.1007/978-3-642-25385-0.
ieee: 'J. Camenisch, S. Krenn, and V. Shoup, “A Framework for Practical Universally
Composable Zero-Knowledge Protocols,” presented at the ASIACRYPT: Theory and Application
of Cryptology and Information Security, 2011, vol. 7073, pp. 449–467.'
ista: 'Camenisch J, Krenn S, Shoup V. 2011. A Framework for Practical Universally
Composable Zero-Knowledge Protocols. ASIACRYPT: Theory and Application of Cryptology
and Information Security, LNCS, vol. 7073, 449–467.'
mla: Camenisch, Jan, et al. A Framework for Practical Universally Composable
Zero-Knowledge Protocols. Edited by Dong Lee and Xiaoyun Wang, vol. 7073,
Springer, 2011, pp. 449–67, doi:10.1007/978-3-642-25385-0.
short: J. Camenisch, S. Krenn, V. Shoup, in:, D. Lee, X. Wang (Eds.), Springer,
2011, pp. 449–467.
conference:
name: 'ASIACRYPT: Theory and Application of Cryptology and Information Security'
date_created: 2018-12-11T12:00:39Z
date_published: 2011-11-21T00:00:00Z
date_updated: 2021-01-12T07:40:11Z
day: '21'
doi: 10.1007/978-3-642-25385-0
editor:
- first_name: Dong
full_name: Lee, Dong Hoon
last_name: Lee
- first_name: Xiaoyun
full_name: Wang, Xiaoyun
last_name: Wang
extern: 1
intvolume: ' 7073'
main_file_link:
- open_access: '0'
url: http://eprint.iacr.org/2011/228.pdf
month: '11'
page: 449 - 467
publication_status: published
publisher: Springer
publist_id: '3728'
quality_controlled: 0
status: public
title: A Framework for Practical Universally Composable Zero-Knowledge Protocols
type: conference
volume: 7073
year: '2011'
...
---
_id: '2977'
abstract:
- lang: eng
text: "Cryptographic two-party protocols are used ubiquitously in\n everyday
life. While some of these protocols are easy to\n understand and implement
(e.g., key exchange or transmission of\n encrypted data), many of them are
much more complex (e.g.,\n e-banking and e-voting applications, or anonymous
authentication\n and credential systems).\n\n For a software engineer without
appropriate cryptographic skills\n the implementation of such protocols is
often difficult, time\n consuming and error-prone. For this reason, a number
of compilers\n supporting programmers have been published in recent\n years.
However, they are either designed for very specific\n cryptographic primitives
(e.g., zero-knowledge proofs of\n knowledge), or they only offer a very low
level of abstraction and\n thus again demand substantial mathematical and cryptographic\n
\ skills from the programmer. Finally, some of the existing\n compilers do
not produce executable code, but only metacode which\n has to be instantiated
with mathematical libraries, encryption\n routines, etc. before it can actually
be used.\n \n In this paper we present a cryptographically aware compiler
which\n is equally useful to cryptographers who want to benchmark\n protocols
designed on paper, and to programmers who want to\n implement complex security
sensitive protocols without having to\n understand all subtleties. Our tool
offers a high level of\n abstraction and outputs well-structured and documented
Java\n code. We believe that our compiler can contribute to shortening\n the
development cycles of cryptographic applications and to\n reducing their error-proneness."
acknowledgement: This work was in part funded by the European Community’s Seventh
Framework Programme (FP7) under grant agreement no. 216499 and the Swiss Hasler
Foundation under projects no. 09037 and 10069.
author:
- first_name: Endre
full_name: Bangerter, Endre
last_name: Bangerter
- first_name: Stephan
full_name: Stephan Krenn
id: 329FCCF0-F248-11E8-B48F-1D18A9856A87
last_name: Krenn
orcid: 0000-0003-2835-9093
- first_name: Martial
full_name: Seifriz, Martial
last_name: Seifriz
- first_name: Ulrich
full_name: Ultes-Nitsche, Ulrich
last_name: Ultes Nitsche
citation:
ama: 'Bangerter E, Krenn S, Seifriz M, Ultes Nitsche U. cPLC - A Cryptographic Programming
Language and Compiler. In: Venter H, Coetzee M, Loock M, eds. IEEE; 2011. doi:10.1109/ISSA.2011.6027533'
apa: 'Bangerter, E., Krenn, S., Seifriz, M., & Ultes Nitsche, U. (2011). cPLC
- A Cryptographic Programming Language and Compiler. In H. Venter, M. Coetzee,
& M. Loock (Eds.). Presented at the ISSA: Information Security South Africa,
IEEE. https://doi.org/10.1109/ISSA.2011.6027533'
chicago: Bangerter, Endre, Stephan Krenn, Martial Seifriz, and Ulrich Ultes Nitsche.
“CPLC - A Cryptographic Programming Language and Compiler.” edited by Hein Venter,
Marijke Coetzee, and Marianne Loock. IEEE, 2011. https://doi.org/10.1109/ISSA.2011.6027533.
ieee: 'E. Bangerter, S. Krenn, M. Seifriz, and U. Ultes Nitsche, “cPLC - A Cryptographic
Programming Language and Compiler,” presented at the ISSA: Information Security
South Africa, 2011.'
ista: 'Bangerter E, Krenn S, Seifriz M, Ultes Nitsche U. 2011. cPLC - A Cryptographic
Programming Language and Compiler. ISSA: Information Security South Africa.'
mla: Bangerter, Endre, et al. CPLC - A Cryptographic Programming Language and
Compiler. Edited by Hein Venter et al., IEEE, 2011, doi:10.1109/ISSA.2011.6027533.
short: E. Bangerter, S. Krenn, M. Seifriz, U. Ultes Nitsche, in:, H. Venter, M.
Coetzee, M. Loock (Eds.), IEEE, 2011.
conference:
name: 'ISSA: Information Security South Africa'
date_created: 2018-12-11T12:00:39Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2021-01-12T07:40:12Z
day: '01'
doi: 10.1109/ISSA.2011.6027533
editor:
- first_name: Hein
full_name: Venter, Hein S.
last_name: Venter
- first_name: Marijke
full_name: Coetzee, Marijke
last_name: Coetzee
- first_name: Marianne
full_name: Loock, Marianne
last_name: Loock
extern: 1
month: '08'
publication_status: published
publisher: IEEE
publist_id: '3726'
quality_controlled: 0
status: public
title: cPLC - A Cryptographic Programming Language and Compiler
type: conference
year: '2011'
...
---
_id: '2976'
abstract:
- lang: eng
text: |-
Side channel attacks on cryptographic systems exploit information
gained from physical implementations rather than theoretical
weaknesses of a scheme. In recent years, major achievements were made
for the class of so called access-driven cache attacks. Such attacks
exploit the leakage of the memory locations accessed by a victim
process.
In this paper we consider the AES block cipher and present an attack
which is capable of recovering the full secret key in almost realtime
for AES-128, requiring only a very limited number of observed
encryptions. Unlike previous attacks, we do not require any
information about the plaintext (such as its distribution, etc.).
Moreover, for the first time, we also show how the plaintext can be
recovered without having access to the ciphertext at all. It is the
first working attack on AES implementations using compressed
tables. There, no efficient techniques to identify the beginning
of AES rounds is known, which is the fundamental assumption underlying previous
attacks.
We have a fully working implementation of our attack which is able to
recover AES keys after observing as little as 100 encryptions. It
works against the OpenSSL 0.9.8n implementation of AES on Linux
systems. Our spy process does not require any special privileges
beyond those of a standard Linux user. A contribution of probably
independent interest is a denial of service attack on the task scheduler of
current Linux systems (CFS), which allows one to observe (on average)
every single memory access of a victim process.
acknowledgement: |-
This work was in part funded by the European Community’s Seventh Framework Programme (FP7) under grant agreement no. 216499 and the Swiss Hasler Foundation.
An extended abstract was also accepted for COSADE 2011.
author:
- first_name: David
full_name: Gullasch, David
last_name: Gullasch
- first_name: Endre
full_name: Bangerter, Endre
last_name: Bangerter
- first_name: Stephan
full_name: Stephan Krenn
id: 329FCCF0-F248-11E8-B48F-1D18A9856A87
last_name: Krenn
orcid: 0000-0003-2835-9093
citation:
ama: 'Gullasch D, Bangerter E, Krenn S. Cache Games - Bringing Access-Based Cache
Attacks on AES to Practice. In: IEEE; 2011:490-505. doi:10.1109/SP.2011.22'
apa: 'Gullasch, D., Bangerter, E., & Krenn, S. (2011). Cache Games - Bringing
Access-Based Cache Attacks on AES to Practice (pp. 490–505). Presented at the
S&P: IEEE Symposium on Security and Privacy, IEEE. https://doi.org/10.1109/SP.2011.22'
chicago: Gullasch, David, Endre Bangerter, and Stephan Krenn. “Cache Games - Bringing
Access-Based Cache Attacks on AES to Practice,” 490–505. IEEE, 2011. https://doi.org/10.1109/SP.2011.22.
ieee: 'D. Gullasch, E. Bangerter, and S. Krenn, “Cache Games - Bringing Access-Based
Cache Attacks on AES to Practice,” presented at the S&P: IEEE Symposium on
Security and Privacy, 2011, pp. 490–505.'
ista: 'Gullasch D, Bangerter E, Krenn S. 2011. Cache Games - Bringing Access-Based
Cache Attacks on AES to Practice. S&P: IEEE Symposium on Security and Privacy,
490–505.'
mla: Gullasch, David, et al. Cache Games - Bringing Access-Based Cache Attacks
on AES to Practice. IEEE, 2011, pp. 490–505, doi:10.1109/SP.2011.22.
short: D. Gullasch, E. Bangerter, S. Krenn, in:, IEEE, 2011, pp. 490–505.
conference:
name: 'S&P: IEEE Symposium on Security and Privacy'
date_created: 2018-12-11T12:00:39Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:40:11Z
day: '01'
doi: 10.1109/SP.2011.22
extern: 1
main_file_link:
- open_access: '0'
url: http://eprint.iacr.org/2010/594.pdf
month: '01'
page: 490 - 505
publication_status: published
publisher: IEEE
publist_id: '3727'
quality_controlled: 0
status: public
title: Cache Games - Bringing Access-Based Cache Attacks on AES to Practice
type: conference
year: '2011'
...
---
_id: '3092'
abstract:
- lang: eng
text: The phytohormone auxin is vital to plant growth and development. A unique
property of auxin among all other plant hormones is its cell-to-cell polar transport
that requires activity of polarly localized PIN-FORMED (PIN) auxin efflux transporters.
Despite the substantial molecular insight into the cellular PIN polarization,
the mechanistic understanding for developmentally and environmentally regulated
PIN polarization is scarce. The long-standing belief that auxin modulates its
own transport by means of a positive feedback mechanism has inspired both experimentalists
and theoreticians for more than two decades. Recently, theoretical models for
auxin-dependent patterning in plants include the feedback between auxin transport
and the PIN protein localization. These computer models aid to assess the complexity
of plant development by testing and predicting plausible scenarios for various
developmental processes that occur in planta. Although the majority of these models
rely on purely heuristic principles, the most recent mechanistic models tentatively
integrate biologically testable components into known cellular processes that
underlie the PIN polarity regulation. The existing and emerging computational
approaches to describe PIN polarization are presented and discussed in the light
of recent experimental data on the PIN polar targeting.
author:
- 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: Willy
full_name: Govaerts, Willy
last_name: Govaerts
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jürgen
full_name: Kleine Vehn, Jürgen
last_name: Kleine Vehn
citation:
ama: 'Wabnik KT, Govaerts W, Friml J, Kleine Vehn J. Feedback models for polarized
auxin transport: An emerging trend. Molecular BioSystems. 2011;7(8):2352-2359.
doi:10.1039/c1mb05109a'
apa: 'Wabnik, K. T., Govaerts, W., Friml, J., & Kleine Vehn, J. (2011). Feedback
models for polarized auxin transport: An emerging trend. Molecular BioSystems.
Royal Society of Chemistry. https://doi.org/10.1039/c1mb05109a'
chicago: 'Wabnik, Krzysztof T, Willy Govaerts, Jiří Friml, and Jürgen Kleine Vehn.
“Feedback Models for Polarized Auxin Transport: An Emerging Trend.” Molecular
BioSystems. Royal Society of Chemistry, 2011. https://doi.org/10.1039/c1mb05109a.'
ieee: 'K. T. Wabnik, W. Govaerts, J. Friml, and J. Kleine Vehn, “Feedback models
for polarized auxin transport: An emerging trend,” Molecular BioSystems,
vol. 7, no. 8. Royal Society of Chemistry, pp. 2352–2359, 2011.'
ista: 'Wabnik KT, Govaerts W, Friml J, Kleine Vehn J. 2011. Feedback models for
polarized auxin transport: An emerging trend. Molecular BioSystems. 7(8), 2352–2359.'
mla: 'Wabnik, Krzysztof T., et al. “Feedback Models for Polarized Auxin Transport:
An Emerging Trend.” Molecular BioSystems, vol. 7, no. 8, Royal Society
of Chemistry, 2011, pp. 2352–59, doi:10.1039/c1mb05109a.'
short: K.T. Wabnik, W. Govaerts, J. Friml, J. Kleine Vehn, Molecular BioSystems
7 (2011) 2352–2359.
date_created: 2018-12-11T12:01:20Z
date_published: 2011-06-10T00:00:00Z
date_updated: 2021-01-12T07:41:00Z
day: '10'
doi: 10.1039/c1mb05109a
extern: '1'
external_id:
pmid:
- '21660355'
intvolume: ' 7'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/21660355
month: '06'
oa: 1
oa_version: Published Version
page: 2352 - 2359
pmid: 1
publication: Molecular BioSystems
publication_status: published
publisher: Royal Society of Chemistry
publist_id: '3608'
quality_controlled: '1'
status: public
title: 'Feedback models for polarized auxin transport: An emerging trend'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2011'
...
---
_id: '3089'
abstract:
- lang: eng
text: The phytohormone auxin is an important determinant of plant development. Directional
auxin flow within tissues depends on polar localization of PIN auxin transporters.
To explore regulation of PIN-mediated auxin transport, we screened for suppressors
of PIN1 overexpression (supo) and identified an inositol polyphosphate 1-phosphatase
mutant (supo1), with elevated inositol trisphosphate (InsP 3) and cytosolic Ca
2+ levels. Pharmacological and genetic increases in InsP 3 or Ca 2+ levels also
suppressed the PIN1 gain-of-function phenotypes and caused defects in basal PIN
localization, auxin transport and auxin-mediated development. In contrast, the
reductions in InsP 3 levels and Ca 2+ signaling antagonized the effects of the
supo1 mutation and disrupted preferentially apical PIN localization. InsP 3 and
Ca 2+ are evolutionarily conserved second messengers involved in various cellular
functions, particularly stress responses. Our findings implicate them as modifiers
of cell polarity and polar auxin transport, and highlight a potential integration
point through which Ca 2+ signaling-related stimuli could influence auxin-mediated
development.
author:
- first_name: Jing
full_name: Zhang, Jing
last_name: Zhang
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Philip
full_name: Brewer, Philip B
last_name: Brewer
- first_name: Marta
full_name: Michniewicz, Marta
last_name: Michniewicz
- first_name: Peter
full_name: Peter Grones
id: 399876EC-F248-11E8-B48F-1D18A9856A87
last_name: Grones
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Christian
full_name: Löfke, Christian
last_name: Löfke
- first_name: Thomas
full_name: Teichmann, Thomas
last_name: Teichmann
- first_name: Agnieszka
full_name: Bielach, Agnieszka
last_name: Bielach
- first_name: Bernard
full_name: Cannoot, Bernard
last_name: Cannoot
- first_name: Klára
full_name: Hoyerová, Klára
last_name: Hoyerová
- first_name: Xu
full_name: Xu Chen
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Hong
full_name: Xue, Hong-Wei
last_name: Xue
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Zhang J, Vanneste S, Brewer P, et al. Inositol trisphosphate-induced ca^2+
signaling modulates auxin transport and pin polarity. Developmental Cell.
2011;20(6):855-866. doi:10.1016/j.devcel.2011.05.013
apa: Zhang, J., Vanneste, S., Brewer, P., Michniewicz, M., Grones, P., Kleine Vehn,
J., … Friml, J. (2011). Inositol trisphosphate-induced ca^2+ signaling modulates
auxin transport and pin polarity. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2011.05.013
chicago: Zhang, Jing, Steffen Vanneste, Philip Brewer, Marta Michniewicz, Peter
Grones, Jürgen Kleine Vehn, Christian Löfke, et al. “Inositol Trisphosphate-Induced
Ca^2+ Signaling Modulates Auxin Transport and Pin Polarity.” Developmental
Cell. Cell Press, 2011. https://doi.org/10.1016/j.devcel.2011.05.013.
ieee: J. Zhang et al., “Inositol trisphosphate-induced ca^2+ signaling modulates
auxin transport and pin polarity,” Developmental Cell, vol. 20, no. 6.
Cell Press, pp. 855–866, 2011.
ista: Zhang J, Vanneste S, Brewer P, Michniewicz M, Grones P, Kleine Vehn J, Löfke
C, Teichmann T, Bielach A, Cannoot B, Hoyerová K, Chen X, Xue H, Benková E, Zažímalová
E, Friml J. 2011. Inositol trisphosphate-induced ca^2+ signaling modulates auxin
transport and pin polarity. Developmental Cell. 20(6), 855–866.
mla: Zhang, Jing, et al. “Inositol Trisphosphate-Induced Ca^2+ Signaling Modulates
Auxin Transport and Pin Polarity.” Developmental Cell, vol. 20, no. 6,
Cell Press, 2011, pp. 855–66, doi:10.1016/j.devcel.2011.05.013.
short: J. Zhang, S. Vanneste, P. Brewer, M. Michniewicz, P. Grones, J. Kleine Vehn,
C. Löfke, T. Teichmann, A. Bielach, B. Cannoot, K. Hoyerová, X. Chen, H. Xue,
E. Benková, E. Zažímalová, J. Friml, Developmental Cell 20 (2011) 855–866.
date_created: 2018-12-11T12:01:18Z
date_published: 2011-06-14T00:00:00Z
date_updated: 2021-01-12T07:40:58Z
day: '14'
doi: 10.1016/j.devcel.2011.05.013
extern: 1
intvolume: ' 20'
issue: '6'
month: '06'
page: 855 - 866
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '3612'
quality_controlled: 0
status: public
title: Inositol trisphosphate-induced ca^2+ signaling modulates auxin transport and
pin polarity
type: journal_article
volume: 20
year: '2011'
...
---
_id: '3090'
abstract:
- lang: eng
text: The polarized transport of the phytohormone auxin [1], which is crucial for
the regulation of different stages of plant development [2, 3], depends on the
asymmetric plasma membrane distribution of the PIN-FORMED (PIN) auxin efflux carriers
[4, 5]. The PIN polar localization results from clathrin-mediated endocytosis
(CME) from the plasma membrane and subsequent polar recycling [6]. The Arabidopsis
genome encodes two groups of dynamin-related proteins (DRPs) that show homology
to mammalian dynamin - a protein required for fission of endocytic vesicles during
CME [7, 8]. Here we show by coimmunoprecipitation (coIP), bimolecular fluorescence
complementation (BiFC), and Förster resonance energy transfer (FRET) that members
of the DRP1 group closely associate with PIN proteins at the cell plate. Localization
and phenotypic analysis of novel drp1 mutants revealed a requirement for DRP1
function in correct PIN distribution and in auxin-mediated development. We propose
that rapid and specific internalization of PIN proteins mediated by the DRP1 proteins
and the associated CME machinery from the cell plate membranes during cytokinesis
is an important mechanism for proper polar PIN positioning in interphase cells.
author:
- first_name: Jozef
full_name: Mravec, Jozef
last_name: Mravec
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Na
full_name: Li, Na
last_name: Li
- first_name: Sjef
full_name: Boeren, Sjef
last_name: Boeren
- first_name: Rumyana
full_name: Karlova, Rumyana
last_name: Karlova
- first_name: Saeko
full_name: Kitakura, Saeko
last_name: Kitakura
- first_name: Markéta
full_name: Pařezová, Markéta
last_name: Pařezová
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Thomasz
full_name: Nodzyński, Thomasz
last_name: Nodzyński
- first_name: Pankaj
full_name: Dhonukshe, Pankaj
last_name: Dhonukshe
- first_name: Sebastian
full_name: Bednarek, Sebastian Y
last_name: Bednarek
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Sacco
full_name: De Vries, Sacco
last_name: De Vries
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Mravec J, Petrášek J, Li N, et al. Cell plate restricted association of DRP1A
and PIN proteins is required for cell polarity establishment in arabidopsis. Current
Biology. 2011;21(12):1055-1060. doi:10.1016/j.cub.2011.05.018
apa: Mravec, J., Petrášek, J., Li, N., Boeren, S., Karlova, R., Kitakura, S., …
Friml, J. (2011). Cell plate restricted association of DRP1A and PIN proteins
is required for cell polarity establishment in arabidopsis. Current Biology.
Cell Press. https://doi.org/10.1016/j.cub.2011.05.018
chicago: Mravec, Jozef, Jan Petrášek, Na Li, Sjef Boeren, Rumyana Karlova, Saeko
Kitakura, Markéta Pařezová, et al. “Cell Plate Restricted Association of DRP1A
and PIN Proteins Is Required for Cell Polarity Establishment in Arabidopsis.”
Current Biology. Cell Press, 2011. https://doi.org/10.1016/j.cub.2011.05.018.
ieee: J. Mravec et al., “Cell plate restricted association of DRP1A and PIN
proteins is required for cell polarity establishment in arabidopsis,” Current
Biology, vol. 21, no. 12. Cell Press, pp. 1055–1060, 2011.
ista: Mravec J, Petrášek J, Li N, Boeren S, Karlova R, Kitakura S, Pařezová M, Naramoto
S, Nodzyński T, Dhonukshe P, Bednarek S, Zažímalová E, De Vries S, Friml J. 2011.
Cell plate restricted association of DRP1A and PIN proteins is required for cell
polarity establishment in arabidopsis. Current Biology. 21(12), 1055–1060.
mla: Mravec, Jozef, et al. “Cell Plate Restricted Association of DRP1A and PIN Proteins
Is Required for Cell Polarity Establishment in Arabidopsis.” Current Biology,
vol. 21, no. 12, Cell Press, 2011, pp. 1055–60, doi:10.1016/j.cub.2011.05.018.
short: J. Mravec, J. Petrášek, N. Li, S. Boeren, R. Karlova, S. Kitakura, M. Pařezová,
S. Naramoto, T. Nodzyński, P. Dhonukshe, S. Bednarek, E. Zažímalová, S. De Vries,
J. Friml, Current Biology 21 (2011) 1055–1060.
date_created: 2018-12-11T12:01:19Z
date_published: 2011-06-21T00:00:00Z
date_updated: 2021-01-12T07:40:59Z
day: '21'
doi: 10.1016/j.cub.2011.05.018
extern: 1
intvolume: ' 21'
issue: '12'
month: '06'
page: 1055 - 1060
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '3611'
quality_controlled: 0
status: public
title: Cell plate restricted association of DRP1A and PIN proteins is required for
cell polarity establishment in arabidopsis
type: journal_article
volume: 21
year: '2011'
...
---
_id: '3088'
abstract:
- lang: eng
text: 'Background: Whereas the majority of animals develop toward a predetermined
body plan, plants show iterative growth and continually produce new organs and
structures from actively dividing meristems. This raises an intriguing question:
How are these newly developed organs patterned? In Arabidopsis embryos, radial
symmetry is broken by the bisymmetric specification of the cotyledons in the apical
domain. Subsequently, this bisymmetry is propagated to the root promeristem. Results:
Here we present a mutually inhibitory feedback loop between auxin and cytokinin
that sets distinct boundaries of hormonal output. Cytokinins promote the bisymmetric
distribution of the PIN-FORMED (PIN) auxin efflux proteins, which channel auxin
toward a central domain. High auxin promotes transcription of the cytokinin signaling
inhibitor AHP6, which closes the interaction loop. This bisymmetric auxin response
domain specifies the differentiation of protoxylem in a bisymmetric pattern. In
embryonic roots, cytokinin is required to translate a bisymmetric auxin response
in the cotyledons to a bisymmetric vascular pattern in the root promeristem. Conclusions:
Our results present an interactive feedback loop between hormonal signaling and
transport by which small biases in hormonal input are propagated into distinct
signaling domains to specify the vascular pattern in the root meristem. It is
an intriguing possibility that such a mechanism could transform radial patterns
and allow continuous vascular connections between other newly emerging organs.'
author:
- first_name: Anthony
full_name: Bishopp, Anthony
last_name: Bishopp
- first_name: Hanna
full_name: Help, Hanna
last_name: Help
- first_name: Sedeer
full_name: El-Showk, Sedeer
last_name: El Showk
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Ben
full_name: Scheres, Ben
last_name: Scheres
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Ari
full_name: Mähönen, Ari Pekka
last_name: Mähönen
- first_name: Ykä
full_name: Helariutta, Ykä
last_name: Helariutta
citation:
ama: Bishopp A, Help H, El Showk S, et al. A mutually inhibitory interaction between
auxin and cytokinin specifies vascular pattern in roots. Current Biology.
2011;21(11):917-926. doi:10.1016/j.cub.2011.04.017
apa: Bishopp, A., Help, H., El Showk, S., Weijers, D., Scheres, B., Friml, J., …
Helariutta, Y. (2011). A mutually inhibitory interaction between auxin and cytokinin
specifies vascular pattern in roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2011.04.017
chicago: Bishopp, Anthony, Hanna Help, Sedeer El Showk, Dolf Weijers, Ben Scheres,
Jiří Friml, Eva Benková, Ari Mähönen, and Ykä Helariutta. “A Mutually Inhibitory
Interaction between Auxin and Cytokinin Specifies Vascular Pattern in Roots.”
Current Biology. Cell Press, 2011. https://doi.org/10.1016/j.cub.2011.04.017.
ieee: A. Bishopp et al., “A mutually inhibitory interaction between auxin
and cytokinin specifies vascular pattern in roots,” Current Biology, vol.
21, no. 11. Cell Press, pp. 917–926, 2011.
ista: Bishopp A, Help H, El Showk S, Weijers D, Scheres B, Friml J, Benková E, Mähönen
A, Helariutta Y. 2011. A mutually inhibitory interaction between auxin and cytokinin
specifies vascular pattern in roots. Current Biology. 21(11), 917–926.
mla: Bishopp, Anthony, et al. “A Mutually Inhibitory Interaction between Auxin and
Cytokinin Specifies Vascular Pattern in Roots.” Current Biology, vol. 21,
no. 11, Cell Press, 2011, pp. 917–26, doi:10.1016/j.cub.2011.04.017.
short: A. Bishopp, H. Help, S. El Showk, D. Weijers, B. Scheres, J. Friml, E. Benková,
A. Mähönen, Y. Helariutta, Current Biology 21 (2011) 917–926.
date_created: 2018-12-11T12:01:18Z
date_published: 2011-06-07T00:00:00Z
date_updated: 2021-01-12T07:40:58Z
day: '07'
doi: 10.1016/j.cub.2011.04.017
extern: 1
intvolume: ' 21'
issue: '11'
month: '06'
page: 917 - 926
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '3613'
quality_controlled: 0
status: public
title: A mutually inhibitory interaction between auxin and cytokinin specifies vascular
pattern in roots
type: journal_article
volume: 21
year: '2011'
...
---
_id: '3093'
abstract:
- lang: eng
text: |2-
Plants take up iron from the soil using the IRON-REGULATED TRANSPORTER 1 (IRT1) high-affinity iron transporter at the root surface. Sophisticated regulatory mechanisms allow plants to tightly control the levels of IRT1, ensuring optimal absorption of essential but toxic iron. Here, we demonstrate that overexpression of Arabidopsis thaliana IRT1 leads to constitutive IRT1 protein accumulation, metal overload, and oxidative stress. IRT1 is unexpectedly found in trans-Golgi network/early endosomes of root hair cells, and its levels and localization are unaffected by iron nutrition. Using pharmacological approaches, we show that IRT1 cycles to the plasma membrane to perform iron and metal uptake at the cell surface and is sent to the vacuole for proper turnover. We also prove that IRT1 is monoubiquitinated on several cytosol-exposed residues in vivo and that mutation of two putative monoubiquitination target residues in IRT1 triggers stabilization at the plasma membrane and leads to extreme lethality. Together, these data suggest a model in which monoubiquitin-dependent internalization/sorting and turnover keep the plasma membrane pool of IRT1 low to ensure proper iron uptake and to prevent metal toxicity. More generally, our work demonstrates the existence of monoubiquitin-dependent trafficking to lytic vacuoles in plants and points to proteasome-independent turnover of plasma membrane proteins.
author:
- first_name: Marie
full_name: Barberon, Marie
last_name: Barberon
- first_name: Enric
full_name: Zelazny, Enric
last_name: Zelazny
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Geneviève
full_name: Conéjéro, Geneviève
last_name: Conéjéro
- first_name: Cathy
full_name: Curie, Cathy
last_name: Curie
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Grégory
full_name: Vert, Grégory
last_name: Vert
citation:
ama: Barberon M, Zelazny E, Robert S, et al. Monoubiquitin dependent endocytosis
of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants.
PNAS. 2011;108(32):E450-E458. doi:10.1073/pnas.1100659108
apa: Barberon, M., Zelazny, E., Robert, S., Conéjéro, G., Curie, C., Friml, J.,
& Vert, G. (2011). Monoubiquitin dependent endocytosis of the Iron Regulated
Transporter 1 IRT1 transporter controls iron uptake in plants. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1100659108
chicago: Barberon, Marie, Enric Zelazny, Stéphanie Robert, Geneviève Conéjéro, Cathy
Curie, Jiří Friml, and Grégory Vert. “Monoubiquitin Dependent Endocytosis of the
Iron Regulated Transporter 1 IRT1 Transporter Controls Iron Uptake in Plants.”
PNAS. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1100659108.
ieee: M. Barberon et al., “Monoubiquitin dependent endocytosis of the Iron
Regulated Transporter 1 IRT1 transporter controls iron uptake in plants,” PNAS,
vol. 108, no. 32. National Academy of Sciences, pp. E450–E458, 2011.
ista: Barberon M, Zelazny E, Robert S, Conéjéro G, Curie C, Friml J, Vert G. 2011.
Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter
controls iron uptake in plants. PNAS. 108(32), E450–E458.
mla: Barberon, Marie, et al. “Monoubiquitin Dependent Endocytosis of the Iron Regulated
Transporter 1 IRT1 Transporter Controls Iron Uptake in Plants.” PNAS, vol.
108, no. 32, National Academy of Sciences, 2011, pp. E450–58, doi:10.1073/pnas.1100659108.
short: M. Barberon, E. Zelazny, S. Robert, G. Conéjéro, C. Curie, J. Friml, G. Vert,
PNAS 108 (2011) E450–E458.
date_created: 2018-12-11T12:01:20Z
date_published: 2011-08-09T00:00:00Z
date_updated: 2021-01-12T07:41:00Z
day: '09'
doi: 10.1073/pnas.1100659108
extern: 1
intvolume: ' 108'
issue: '32'
month: '08'
page: E450 - E458
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3607'
quality_controlled: 0
status: public
title: Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1
transporter controls iron uptake in plants
type: journal_article
volume: 108
year: '2011'
...
---
_id: '3094'
abstract:
- lang: eng
text: Summary Gravitropism aligns plant growth with gravity. It involves gravity
perception and the asymmetric distribution of the phytohormone auxin. Here we
provide insights into the mechanism for hypocotyl gravitropic growth. We show
that the Arabidopsis thaliana PIN3 auxin transporter is required for the asymmetric
auxin distribution for the gravitropic response. Gravistimulation polarizes PIN3
to the bottom side of hypocotyl endodermal cells, which correlates with an increased
auxin response at the lower hypocotyl side. Both PIN3 polarization and hypocotyl
bending require the activity of the trafficking regulator GNOM and the protein
kinase PINOID. Our data suggest that gravity-induced PIN3 polarization diverts
the auxin flow to mediate the asymmetric distribution of auxin for gravitropic
shoot bending.
author:
- first_name: Hana
full_name: Rakusová, Hana
last_name: Rakusová
- first_name: Javier
full_name: Gallego-Bartolomé, Javier
last_name: Gallego Bartolomé
- first_name: Marleen
full_name: Vanstraelen, Marleen
last_name: Vanstraelen
- first_name: Hélène
full_name: Robert, Hélène S
last_name: Robert
- first_name: David
full_name: Alabadí, David
last_name: Alabadí
- first_name: Miguel
full_name: Blázquez, Miguel A
last_name: Blázquez
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Rakusová H, Gallego Bartolomé J, Vanstraelen M, et al. Polarization of PIN3
dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana.
Plant Journal. 2011;67(5):817-826. doi:10.1111/j.1365-313X.2011.04636.x
apa: Rakusová, H., Gallego Bartolomé, J., Vanstraelen, M., Robert, H., Alabadí,
D., Blázquez, M., … Friml, J. (2011). Polarization of PIN3 dependent auxin transport
for hypocotyl gravitropic response in Arabidopsis thaliana. Plant Journal.
Wiley-Blackwell. https://doi.org/10.1111/j.1365-313X.2011.04636.x
chicago: Rakusová, Hana, Javier Gallego Bartolomé, Marleen Vanstraelen, Hélène Robert,
David Alabadí, Miguel Blázquez, Eva Benková, and Jiří Friml. “Polarization of
PIN3 Dependent Auxin Transport for Hypocotyl Gravitropic Response in Arabidopsis
Thaliana.” Plant Journal. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1365-313X.2011.04636.x.
ieee: H. Rakusová et al., “Polarization of PIN3 dependent auxin transport
for hypocotyl gravitropic response in Arabidopsis thaliana,” Plant Journal,
vol. 67, no. 5. Wiley-Blackwell, pp. 817–826, 2011.
ista: Rakusová H, Gallego Bartolomé J, Vanstraelen M, Robert H, Alabadí D, Blázquez
M, Benková E, Friml J. 2011. Polarization of PIN3 dependent auxin transport for
hypocotyl gravitropic response in Arabidopsis thaliana. Plant Journal. 67(5),
817–826.
mla: Rakusová, Hana, et al. “Polarization of PIN3 Dependent Auxin Transport for
Hypocotyl Gravitropic Response in Arabidopsis Thaliana.” Plant Journal,
vol. 67, no. 5, Wiley-Blackwell, 2011, pp. 817–26, doi:10.1111/j.1365-313X.2011.04636.x.
short: H. Rakusová, J. Gallego Bartolomé, M. Vanstraelen, H. Robert, D. Alabadí,
M. Blázquez, E. Benková, J. Friml, Plant Journal 67 (2011) 817–826.
date_created: 2018-12-11T12:01:21Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2021-01-12T07:41:01Z
day: '01'
doi: 10.1111/j.1365-313X.2011.04636.x
extern: 1
intvolume: ' 67'
issue: '5'
month: '09'
page: 817 - 826
publication: Plant Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3606'
quality_controlled: 0
status: public
title: Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response
in Arabidopsis thaliana
type: journal_article
volume: 67
year: '2011'
...
---
_id: '3091'
author:
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Sauer M, Friml J. Fleeting hormone cues get stabilized for plant organogenesis.
Molecular Systems Biology. 2011;7. doi:10.1038/msb.2011.45
apa: Sauer, M., & Friml, J. (2011). Fleeting hormone cues get stabilized for
plant organogenesis. Molecular Systems Biology. Nature Publishing Group.
https://doi.org/10.1038/msb.2011.45
chicago: Sauer, Michael, and Jiří Friml. “Fleeting Hormone Cues Get Stabilized for
Plant Organogenesis.” Molecular Systems Biology. Nature Publishing Group,
2011. https://doi.org/10.1038/msb.2011.45.
ieee: M. Sauer and J. Friml, “Fleeting hormone cues get stabilized for plant organogenesis,”
Molecular Systems Biology, vol. 7. Nature Publishing Group, 2011.
ista: Sauer M, Friml J. 2011. Fleeting hormone cues get stabilized for plant organogenesis.
Molecular Systems Biology. 7.
mla: Sauer, Michael, and Jiří Friml. “Fleeting Hormone Cues Get Stabilized for Plant
Organogenesis.” Molecular Systems Biology, vol. 7, Nature Publishing Group,
2011, doi:10.1038/msb.2011.45.
short: M. Sauer, J. Friml, Molecular Systems Biology 7 (2011).
date_created: 2018-12-11T12:01:19Z
date_published: 2011-07-05T00:00:00Z
date_updated: 2021-01-12T07:41:00Z
day: '05'
doi: 10.1038/msb.2011.45
extern: '1'
external_id:
pmid:
- '21734646'
intvolume: ' 7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159970/
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Systems Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3610'
quality_controlled: '1'
status: public
title: Fleeting hormone cues get stabilized for plant organogenesis
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2011'
...
---
_id: '3102'
abstract:
- lang: eng
text: 'Multicellular organisms depend on cell production, cell fate specification,
and correct patterning to shape their adult body. In plants, auxin plays a prominent
role in the timely coordination of these different cellular processes. A well-studied
example is lateral root initiation, in which auxin triggers founder cell specification
and cell cycle activation of xylem pole–positioned pericycle cells. Here, we report
that the E2Fa transcription factor of Arabidopsis thaliana is an essential component
that regulates the asymmetric cell division marking lateral root initiation. Moreover,
we demonstrate that E2Fa expression is regulated by the LATERAL ORGAN BOUNDARY
DOMAIN18/LATERAL ORGAN BOUNDARY DOMAIN33 (LBD18/LBD33) dimer that is, in turn,
regulated by the auxin signaling pathway. LBD18/LBD33 mediates lateral root organogenesis
through E2Fa transcriptional activation, whereas E2Fa expression under control
of the LBD18 promoter eliminates the need for LBD18. Besides lateral root initiation,
vascular patterning is disrupted in E2Fa knockout plants, similarly as it is affected
in auxin signaling and lbd mutants, indicating that the transcriptional induction
of E2Fa through LBDs represents a general mechanism for auxin-dependent cell cycle
activation. Our data illustrate how a conserved mechanism driving cell cycle entry
has been adapted evolutionarily to connect auxin signaling with control of processes
determining plant architecture. '
author:
- first_name: Barbara
full_name: Berckmans, Barbara
last_name: Berckmans
- first_name: Valya
full_name: Vassileva, Valya
last_name: Vassileva
- first_name: Stephan
full_name: Schmid, Stephan P
last_name: Schmid
- first_name: Sara
full_name: Maes, Sara
last_name: Maes
- first_name: Boris
full_name: Parizot, Boris
last_name: Parizot
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Zoltan
full_name: Magyar, Zoltan
last_name: Magyar
- first_name: Claire
full_name: Lessa Alvim Kamei, Claire
last_name: Lessa Alvim Kamei
- first_name: Csaba
full_name: Koncz, Csaba
last_name: Koncz
- first_name: Laszlo
full_name: Bögre, Laszlo
last_name: Bögre
- first_name: Geert
full_name: Persiau, Geert
last_name: Persiau
- first_name: Geert
full_name: De Jaeger, Geert
last_name: De Jaeger
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Rüdiger
full_name: Simon, Rüdiger
last_name: Simon
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Lieven
full_name: de Veyldera, Lieven
last_name: De Veyldera
citation:
ama: Berckmans B, Vassileva V, Schmid S, et al. Auxin Dependent cell cycle reactivation
through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary
proteins. Plant Cell. 2011;23(10):3671-3683. doi:10.1105/tpc.111.088377
apa: Berckmans, B., Vassileva, V., Schmid, S., Maes, S., Parizot, B., Naramoto,
S., … De Veyldera, L. (2011). Auxin Dependent cell cycle reactivation through
transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins.
Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.111.088377
chicago: Berckmans, Barbara, Valya Vassileva, Stephan Schmid, Sara Maes, Boris Parizot,
Satoshi Naramoto, Zoltan Magyar, et al. “Auxin Dependent Cell Cycle Reactivation
through Transcriptional Regulation of Arabidopsis E2Fa by Lateral Organ Boundary
Proteins.” Plant Cell. American Society of Plant Biologists, 2011. https://doi.org/10.1105/tpc.111.088377.
ieee: B. Berckmans et al., “Auxin Dependent cell cycle reactivation through
transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins,”
Plant Cell, vol. 23, no. 10. American Society of Plant Biologists, pp.
3671–3683, 2011.
ista: Berckmans B, Vassileva V, Schmid S, Maes S, Parizot B, Naramoto S, Magyar
Z, Lessa Alvim Kamei C, Koncz C, Bögre L, Persiau G, De Jaeger G, Friml J, Simon
R, Beeckman T, De Veyldera L. 2011. Auxin Dependent cell cycle reactivation through
transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins.
Plant Cell. 23(10), 3671–3683.
mla: Berckmans, Barbara, et al. “Auxin Dependent Cell Cycle Reactivation through
Transcriptional Regulation of Arabidopsis E2Fa by Lateral Organ Boundary Proteins.”
Plant Cell, vol. 23, no. 10, American Society of Plant Biologists, 2011,
pp. 3671–83, doi:10.1105/tpc.111.088377.
short: B. Berckmans, V. Vassileva, S. Schmid, S. Maes, B. Parizot, S. Naramoto,
Z. Magyar, C. Lessa Alvim Kamei, C. Koncz, L. Bögre, G. Persiau, G. De Jaeger,
J. Friml, R. Simon, T. Beeckman, L. De Veyldera, Plant Cell 23 (2011) 3671–3683.
date_created: 2018-12-11T12:01:24Z
date_published: 2011-10-14T00:00:00Z
date_updated: 2021-01-12T07:41:04Z
day: '14'
doi: 10.1105/tpc.111.088377
extern: 1
intvolume: ' 23'
issue: '10'
month: '10'
page: 3671 - 3683
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3598'
quality_controlled: 0
status: public
title: Auxin Dependent cell cycle reactivation through transcriptional regulation
of arabidopsis E2Fa by lateral organ boundary proteins
type: journal_article
volume: 23
year: '2011'
...
---
_id: '3103'
abstract:
- lang: eng
text: Endocytosis in plants has an essential role not only for basic cellular functions
but also for growth and development, hormonal signaling and communication with
the environment including nutrient delivery, toxin avoidance, and pathogen defense.
The major endocytic mechanism in plants depends on the coat protein clathrin.
It starts by clathrin-coated vesicle formation at the plasma membrane, where specific
cargoes are recognized and packaged for internalization. Recently, genetic, biochemical
and advanced microscopy studies provided initial insights into mechanisms and
roles of clathrin-mediated endocytosis in plants. Here we summarize the present
state of knowledge and compare mechanisms of clathrin-mediated endocytosis in
plants with animal and yeast paradigms as well as review plant-specific regulations
and roles of this process.
author:
- first_name: Xu
full_name: Chen, Xu
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Niloufer
full_name: Irani, Niloufer
last_name: Irani
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Chen X, Irani N, Friml J. Clathrin-mediated endocytosis: The gateway into
plant cells. Current Opinion in Plant Biology. 2011;14(6):674-682. doi:10.1016/j.pbi.2011.08.006'
apa: 'Chen, X., Irani, N., & Friml, J. (2011). Clathrin-mediated endocytosis:
The gateway into plant cells. Current Opinion in Plant Biology. Elsevier.
https://doi.org/10.1016/j.pbi.2011.08.006'
chicago: 'Chen, Xu, Niloufer Irani, and Jiří Friml. “Clathrin-Mediated Endocytosis:
The Gateway into Plant Cells.” Current Opinion in Plant Biology. Elsevier,
2011. https://doi.org/10.1016/j.pbi.2011.08.006.'
ieee: 'X. Chen, N. Irani, and J. Friml, “Clathrin-mediated endocytosis: The gateway
into plant cells,” Current Opinion in Plant Biology, vol. 14, no. 6. Elsevier,
pp. 674–682, 2011.'
ista: 'Chen X, Irani N, Friml J. 2011. Clathrin-mediated endocytosis: The gateway
into plant cells. Current Opinion in Plant Biology. 14(6), 674–682.'
mla: 'Chen, Xu, et al. “Clathrin-Mediated Endocytosis: The Gateway into Plant Cells.”
Current Opinion in Plant Biology, vol. 14, no. 6, Elsevier, 2011, pp. 674–82,
doi:10.1016/j.pbi.2011.08.006.'
short: X. Chen, N. Irani, J. Friml, Current Opinion in Plant Biology 14 (2011) 674–682.
date_created: 2018-12-11T12:01:24Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2021-01-12T07:41:05Z
day: '01'
doi: 10.1016/j.pbi.2011.08.006
extern: '1'
intvolume: ' 14'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 674 - 682
publication: Current Opinion in Plant Biology
publication_status: published
publisher: Elsevier
publist_id: '3596'
quality_controlled: '1'
status: public
title: 'Clathrin-mediated endocytosis: The gateway into plant cells'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2011'
...
---
_id: '3147'
abstract:
- lang: eng
text: Cancer cell of origin is difficult to identify by analyzing cells within terminal
stage tumors, whose identity could be concealed by the acquired plasticity. Thus,
an ideal approach to identify the cell of origin is to analyze proliferative abnormalities
in distinct lineages prior to malignancy. Here, we use mosaic analysis with double
markers (MADM) in mice to model gliomagenesis by initiating concurrent p53/Nf1
mutations sporadically in neural stem cells (NSCs). Surprisingly, MADM-based lineage
tracing revealed significant aberrant growth prior to malignancy only in oligodendrocyte
precursor cells (OPCs), but not in any other NSC-derived lineages or NSCs themselves.
Upon tumor formation, phenotypic and transcriptome analyses of tumor cells revealed
salient OPC features. Finally, introducing the same p53/Nf1 mutations directly
into OPCs consistently led to gliomagenesis. Our findings suggest OPCs as the
cell of origin in this model, even when initial mutations occur in NSCs, and highlight
the importance of analyzing premalignant stages to identify the cancer cell of
origin.
author:
- first_name: Chong
full_name: Liu, Chong
last_name: Liu
- first_name: Jonathan
full_name: Sage, Jonathan C
last_name: Sage
- first_name: Michael
full_name: Miller, Michael R
last_name: Miller
- first_name: Roel
full_name: Verhaak, Roel G
last_name: Verhaak
- first_name: Simon
full_name: Simon Hippenmeyer
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Hannes
full_name: Vogel, Hannes
last_name: Vogel
- first_name: Oded
full_name: Foreman, Oded
last_name: Foreman
- first_name: Roderick
full_name: Bronson, Roderick T
last_name: Bronson
- first_name: Akiko
full_name: Nishiyama, Akiko
last_name: Nishiyama
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
- first_name: Hui
full_name: Zong, Hui
last_name: Zong
citation:
ama: Liu C, Sage J, Miller M, et al. Mosaic analysis with double markers reveals
tumor cell of origin in glioma. Cell. 2011;146(2):209-221. doi:10.1016/j.cell.2011.06.014
apa: Liu, C., Sage, J., Miller, M., Verhaak, R., Hippenmeyer, S., Vogel, H., … Zong,
H. (2011). Mosaic analysis with double markers reveals tumor cell of origin in
glioma. Cell. Cell Press. https://doi.org/10.1016/j.cell.2011.06.014
chicago: Liu, Chong, Jonathan Sage, Michael Miller, Roel Verhaak, Simon Hippenmeyer,
Hannes Vogel, Oded Foreman, et al. “Mosaic Analysis with Double Markers Reveals
Tumor Cell of Origin in Glioma.” Cell. Cell Press, 2011. https://doi.org/10.1016/j.cell.2011.06.014.
ieee: C. Liu et al., “Mosaic analysis with double markers reveals tumor cell
of origin in glioma,” Cell, vol. 146, no. 2. Cell Press, pp. 209–221, 2011.
ista: Liu C, Sage J, Miller M, Verhaak R, Hippenmeyer S, Vogel H, Foreman O, Bronson
R, Nishiyama A, Luo L, Zong H. 2011. Mosaic analysis with double markers reveals
tumor cell of origin in glioma. Cell. 146(2), 209–221.
mla: Liu, Chong, et al. “Mosaic Analysis with Double Markers Reveals Tumor Cell
of Origin in Glioma.” Cell, vol. 146, no. 2, Cell Press, 2011, pp. 209–21,
doi:10.1016/j.cell.2011.06.014.
short: C. Liu, J. Sage, M. Miller, R. Verhaak, S. Hippenmeyer, H. Vogel, O. Foreman,
R. Bronson, A. Nishiyama, L. Luo, H. Zong, Cell 146 (2011) 209–221.
date_created: 2018-12-11T12:01:40Z
date_published: 2011-07-22T00:00:00Z
date_updated: 2021-01-12T07:41:23Z
day: '22'
doi: 10.1016/j.cell.2011.06.014
extern: 1
intvolume: ' 146'
issue: '2'
month: '07'
page: 209 - 221
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3548'
quality_controlled: 0
status: public
title: Mosaic analysis with double markers reveals tumor cell of origin in glioma
type: journal_article
volume: 146
year: '2011'
...
---
_id: '3204'
abstract:
- lang: eng
text: 'We introduce a new class of functions that can be minimized in polynomial
time in the value oracle model. These are functions f satisfying f(x) + f(y) ≥
f(x ∏ y) + f(x ∐ y) where the domain of each variable x i corresponds to nodes
of a rooted binary tree, and operations ∏,∐ are defined with respect to this tree.
Special cases include previously studied L-convex and bisubmodular functions,
which can be obtained with particular choices of trees. We present a polynomial-time
algorithm for minimizing functions in the new class. It combines Murota''s steepest
descent algorithm for L-convex functions with bisubmodular minimization algorithms. '
alternative_title:
- LNCS
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Kolmogorov V. Submodularity on a tree: Unifying Submodularity on a tree: Unifying
L-convex and bisubmodular functions convex and bisubmodular functions. In: Vol
6907. Springer; 2011:400-411. doi:10.1007/978-3-642-22993-0_37'
apa: 'Kolmogorov, V. (2011). Submodularity on a tree: Unifying Submodularity on
a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions
(Vol. 6907, pp. 400–411). Presented at the MFCS: Mathematical Foundations of Computer
Science, Springer. https://doi.org/10.1007/978-3-642-22993-0_37'
chicago: 'Kolmogorov, Vladimir. “Submodularity on a Tree: Unifying Submodularity
on a Tree: Unifying L-Convex and Bisubmodular Functions Convex and Bisubmodular
Functions,” 6907:400–411. Springer, 2011. https://doi.org/10.1007/978-3-642-22993-0_37.'
ieee: 'V. Kolmogorov, “Submodularity on a tree: Unifying Submodularity on a tree:
Unifying L-convex and bisubmodular functions convex and bisubmodular functions,”
presented at the MFCS: Mathematical Foundations of Computer Science, 2011, vol.
6907, pp. 400–411.'
ista: 'Kolmogorov V. 2011. Submodularity on a tree: Unifying Submodularity on a
tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions.
MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 6907, 400–411.'
mla: 'Kolmogorov, Vladimir. Submodularity on a Tree: Unifying Submodularity on
a Tree: Unifying L-Convex and Bisubmodular Functions Convex and Bisubmodular Functions.
Vol. 6907, Springer, 2011, pp. 400–11, doi:10.1007/978-3-642-22993-0_37.'
short: V. Kolmogorov, in:, Springer, 2011, pp. 400–411.
conference:
name: 'MFCS: Mathematical Foundations of Computer Science'
date_created: 2018-12-11T12:02:00Z
date_published: 2011-08-09T00:00:00Z
date_updated: 2021-01-12T07:41:47Z
day: '09'
doi: 10.1007/978-3-642-22993-0_37
extern: 1
intvolume: ' 6907'
main_file_link:
- open_access: '0'
url: http://arxiv.org/pdf/1007.1229v3
month: '08'
page: 400 - 411
publication_status: published
publisher: Springer
publist_id: '3478'
quality_controlled: 0
status: public
title: 'Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex
and bisubmodular functions convex and bisubmodular functions'
type: conference
volume: 6907
year: '2011'
...
---
_id: '3206'
abstract:
- lang: eng
text: In this paper we address the problem of finding the most probable state of
discrete Markov random field (MRF) with associative pairwise terms. Although of
practical importance, this problem is known to be NP-hard in general. We propose
a new type of MRF decomposition, submod-ular decomposition (SMD). Unlike existing
decomposition approaches SMD decomposes the initial problem into sub-problems
corresponding to a specific class label while preserving the graph structure of
each subproblem. Such decomposition enables us to take into account several types
of global constraints in an efficient manner. We study theoretical properties
of the proposed approach and demonstrate its applicability on a number of problems.
author:
- first_name: Anton
full_name: Osokin, Anton
last_name: Osokin
- first_name: Dmitry
full_name: Vetrov, Dmitry
last_name: Vetrov
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Osokin A, Vetrov D, Kolmogorov V. Submodular decomposition framework for inference
in associative Markov networks with global constraints. In: IEEE; 2011:1889-1896.
doi:10.1109/CVPR.2011.5995361'
apa: 'Osokin, A., Vetrov, D., & Kolmogorov, V. (2011). Submodular decomposition
framework for inference in associative Markov networks with global constraints
(pp. 1889–1896). Presented at the CVPR: Computer Vision and Pattern Recognition,
IEEE. https://doi.org/10.1109/CVPR.2011.5995361'
chicago: Osokin, Anton, Dmitry Vetrov, and Vladimir Kolmogorov. “Submodular Decomposition
Framework for Inference in Associative Markov Networks with Global Constraints,”
1889–96. IEEE, 2011. https://doi.org/10.1109/CVPR.2011.5995361.
ieee: 'A. Osokin, D. Vetrov, and V. Kolmogorov, “Submodular decomposition framework
for inference in associative Markov networks with global constraints,” presented
at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 1889–1896.'
ista: 'Osokin A, Vetrov D, Kolmogorov V. 2011. Submodular decomposition framework
for inference in associative Markov networks with global constraints. CVPR: Computer
Vision and Pattern Recognition, 1889–1896.'
mla: Osokin, Anton, et al. Submodular Decomposition Framework for Inference in
Associative Markov Networks with Global Constraints. IEEE, 2011, pp. 1889–96,
doi:10.1109/CVPR.2011.5995361.
short: A. Osokin, D. Vetrov, V. Kolmogorov, in:, IEEE, 2011, pp. 1889–1896.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:02:00Z
date_published: 2011-08-22T00:00:00Z
date_updated: 2021-01-12T07:41:47Z
day: '22'
doi: 10.1109/CVPR.2011.5995361
extern: 1
main_file_link:
- open_access: '0'
url: http://arxiv.org/pdf/1103.1077v1
month: '08'
page: 1889 - 1896
publication_status: published
publisher: IEEE
publist_id: '3476'
quality_controlled: 0
status: public
title: Submodular decomposition framework for inference in associative Markov networks
with global constraints
type: conference
year: '2011'
...
---
_id: '3205'
abstract:
- lang: eng
text: This paper proposes a novel Linear Programming (LP) based algorithm, called
Dynamic Tree-Block Coordinate Ascent (DT-BCA), for performing maximum a posteriori
(MAP) inference in probabilistic graphical models. Unlike traditional message
passing algorithms, which operate uniformly on the whole factor graph, our method
dynamically chooses regions of the factor graph on which to focus message-passing
efforts. We propose two criteria for selecting regions, including an efficiently
computable upper-bound on the increase in the objective possible by passing messages
in any particular region. This bound is derived from the theory of primal-dual
methods from combinatorial optimization, and the forest that maximizes the bounds
can be chosen efficiently using a maximum-spanning-tree-like algorithm. Experimental
results show that our dynamic schedules significantly speed up state-of-the-art
LP-based message-passing algorithms on a wide variety of real-world problems.
author:
- first_name: Daniel
full_name: Tarlow, Daniel
last_name: Tarlow
- first_name: Druv
full_name: Batra, Druv
last_name: Batra
- first_name: Pushmeet
full_name: Kohli, Pushmeet
last_name: Kohli
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Tarlow D, Batra D, Kohli P, Kolmogorov V. Dynamic tree block coordinate ascent.
In: Omnipress; 2011:113-120.'
apa: 'Tarlow, D., Batra, D., Kohli, P., & Kolmogorov, V. (2011). Dynamic tree
block coordinate ascent (pp. 113–120). Presented at the ICML: International Conference
on Machine Learning, Omnipress.'
chicago: Tarlow, Daniel, Druv Batra, Pushmeet Kohli, and Vladimir Kolmogorov. “Dynamic
Tree Block Coordinate Ascent,” 113–20. Omnipress, 2011.
ieee: 'D. Tarlow, D. Batra, P. Kohli, and V. Kolmogorov, “Dynamic tree block coordinate
ascent,” presented at the ICML: International Conference on Machine Learning,
2011, pp. 113–120.'
ista: 'Tarlow D, Batra D, Kohli P, Kolmogorov V. 2011. Dynamic tree block coordinate
ascent. ICML: International Conference on Machine Learning, 113–120.'
mla: Tarlow, Daniel, et al. Dynamic Tree Block Coordinate Ascent. Omnipress,
2011, pp. 113–20.
short: D. Tarlow, D. Batra, P. Kohli, V. Kolmogorov, in:, Omnipress, 2011, pp. 113–120.
conference:
name: 'ICML: International Conference on Machine Learning'
date_created: 2018-12-11T12:02:00Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:47Z
day: '01'
extern: 1
main_file_link:
- open_access: '0'
url: http://ttic.uchicago.edu/~dbatra/publications/assets/tbkk_icml11.pdf
month: '01'
page: 113 - 120
publication_status: published
publisher: Omnipress
publist_id: '3475'
quality_controlled: 0
status: public
title: Dynamic tree block coordinate ascent
type: conference
year: '2011'
...
---
_id: '3207'
abstract:
- lang: eng
text: 'Cosegmentation is typically defined as the task of jointly segmenting something
similar in a given set of images. Existing methods are too generic and so far
have not demonstrated competitive results for any specific task. In this paper
we overcome this limitation by adding two new aspects to cosegmentation: (1) the
"something" has to be an object, and (2) the "similarity"
measure is learned. In this way, we are able to achieve excellent results on the
recently introduced iCoseg dataset, which contains small sets of images of either
the same object instance or similar objects of the same class. The challenge of
this dataset lies in the extreme changes in viewpoint, lighting, and object deformations
within each set. We are able to considerably outperform several competitors. To
achieve this performance, we borrow recent ideas from object recognition: the
use of powerful features extracted from a pool of candidate object-like segmentations.
We believe that our work will be beneficial to several application areas, such
as image retrieval.'
author:
- first_name: Sara
full_name: Vicente, Sara
last_name: Vicente
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Vicente S, Rother C, Kolmogorov V. Object cosegmentation. In: IEEE; 2011:2217-2224.
doi:10.1109/CVPR.2011.5995530'
apa: 'Vicente, S., Rother, C., & Kolmogorov, V. (2011). Object cosegmentation
(pp. 2217–2224). Presented at the CVPR: Computer Vision and Pattern Recognition,
IEEE. https://doi.org/10.1109/CVPR.2011.5995530'
chicago: Vicente, Sara, Carsten Rother, and Vladimir Kolmogorov. “Object Cosegmentation,”
2217–24. IEEE, 2011. https://doi.org/10.1109/CVPR.2011.5995530.
ieee: 'S. Vicente, C. Rother, and V. Kolmogorov, “Object cosegmentation,” presented
at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 2217–2224.'
ista: 'Vicente S, Rother C, Kolmogorov V. 2011. Object cosegmentation. CVPR: Computer
Vision and Pattern Recognition, 2217–2224.'
mla: Vicente, Sara, et al. Object Cosegmentation. IEEE, 2011, pp. 2217–24,
doi:10.1109/CVPR.2011.5995530.
short: S. Vicente, C. Rother, V. Kolmogorov, in:, IEEE, 2011, pp. 2217–2224.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:02:01Z
date_published: 2011-08-22T00:00:00Z
date_updated: 2021-01-12T07:41:48Z
day: '22'
doi: 10.1109/CVPR.2011.5995530
extern: 1
month: '08'
page: 2217 - 2224
publication_status: published
publisher: IEEE
publist_id: '3477'
quality_controlled: 0
status: public
title: Object cosegmentation
type: conference
year: '2011'
...
---
_id: '3240'
abstract:
- lang: eng
text: 'The famous Leftover Hash Lemma (LHL) states that (almost) universal hash
functions are good randomness extractors. Despite its numerous applications, LHL-based
extractors suffer from the following two limitations: - Large Entropy Loss: to
extract v bits from distribution X of min-entropy m which are ε-close to uniform,
one must set v ≤ m - 2log(1/ε), meaning that the entropy loss L = def m - v ≥
2 log(1/ε). For many applications, such entropy loss is too large. - Large Seed
Length: the seed length n of (almost) universal hash function required by the
LHL must be at least n ≥ min (u - v, v + 2log(1/ε)) - O(1), where u is the length
of the source, and must grow with the number of extracted bits. Quite surprisingly,
we show that both limitations of the LHL - large entropy loss and large seed -
can be overcome (or, at least, mitigated) in various important scenarios. First,
we show that entropy loss could be reduced to L = log(1/ε) for the setting of
deriving secret keys for a wide range of cryptographic applications. Specifically,
the security of these schemes with an LHL-derived key gracefully degrades from
ε to at most ε + √ε2-L. (Notice that, unlike standard LHL, this bound is meaningful
even when one extracts more bits than the min-entropy we have!) Based on these
results we build a general computational extractor that enjoys low entropy loss
and can be used to instantiate a generic key derivation function for any cryptographic
application. Second, we study the soundness of the natural expand-then-extract
approach, where one uses a pseudorandom generator (PRG) to expand a short "input
seed" S into a longer "output seed" S′, and then use the resulting
S′ as the seed required by the LHL (or, more generally, by any randomness extractor).
We show that, in general, the expand-then-extract approach is not sound if the
Decisional Diffie-Hellman assumption is true. Despite that, we show that it is
sound either: (1) when extracting a "small" (logarithmic in the security
of the PRG) number of bits; or (2) in minicrypt. Implication (2) suggests that
the expand-then-extract approach is likely secure when used with "practical"
PRGs, despite lacking a reductionist proof of security! © 2011 International Association
for Cryptologic Research.'
alternative_title:
- LNCS
author:
- first_name: Boaz
full_name: Barak, Boaz
last_name: Barak
- first_name: Yevgeniy
full_name: Dodis, Yevgeniy
last_name: Dodis
- first_name: Hugo
full_name: Krawczyk, Hugo
last_name: Krawczyk
- first_name: Olivier
full_name: Pereira, Olivier
last_name: Pereira
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: François
full_name: Standaert, François-Xavier
last_name: Standaert
- first_name: Yu
full_name: Yu, Yu
last_name: Yu
citation:
ama: 'Barak B, Dodis Y, Krawczyk H, et al. Leftover hash lemma revisited. In: Vol
6841. Springer; 2011:1-20. doi:
10.1007/978-3-642-22792-9_1'
apa: 'Barak, B., Dodis, Y., Krawczyk, H., Pereira, O., Pietrzak, K. Z., Standaert,
F., & Yu, Y. (2011). Leftover hash lemma revisited (Vol. 6841, pp. 1–20).
Presented at the CRYPTO: International Cryptology Conference, Springer. https://doi.org/ 10.1007/978-3-642-22792-9_1'
chicago: Barak, Boaz, Yevgeniy Dodis, Hugo Krawczyk, Olivier Pereira, Krzysztof
Z Pietrzak, François Standaert, and Yu Yu. “Leftover Hash Lemma Revisited,” 6841:1–20.
Springer, 2011. https://doi.org/
10.1007/978-3-642-22792-9_1.
ieee: 'B. Barak et al., “Leftover hash lemma revisited,” presented at the
CRYPTO: International Cryptology Conference, 2011, vol. 6841, pp. 1–20.'
ista: 'Barak B, Dodis Y, Krawczyk H, Pereira O, Pietrzak KZ, Standaert F, Yu Y.
2011. Leftover hash lemma revisited. CRYPTO: International Cryptology Conference,
LNCS, vol. 6841, 1–20.'
mla: Barak, Boaz, et al. Leftover Hash Lemma Revisited. Vol. 6841, Springer,
2011, pp. 1–20, doi: 10.1007/978-3-642-22792-9_1.
short: B. Barak, Y. Dodis, H. Krawczyk, O. Pereira, K.Z. Pietrzak, F. Standaert,
Y. Yu, in:, Springer, 2011, pp. 1–20.
conference:
name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:12Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:03Z
day: '01'
doi: ' 10.1007/978-3-642-22792-9_1'
extern: 1
intvolume: ' 6841'
month: '01'
page: 1 - 20
publication_status: published
publisher: Springer
publist_id: '3440'
quality_controlled: 0
status: public
title: Leftover hash lemma revisited
type: conference
volume: 6841
year: '2011'
...
---
_id: '3264'
abstract:
- lang: eng
text: Verification of programs with procedures, multi-threaded programs, and higher-order
functional programs can be effectively au- tomated using abstraction and refinement
schemes that rely on spurious counterexamples for abstraction discovery. The analysis
of counterexam- ples can be automated by a series of interpolation queries, or,
alterna- tively, as a constraint solving query expressed by a set of recursion
free Horn clauses. (A set of interpolation queries can be formulated as a single
constraint over Horn clauses with linear dependency structure between the unknown
relations.) In this paper we present an algorithm for solving recursion free Horn
clauses over a combined theory of linear real/rational arithmetic and uninterpreted
functions. Our algorithm performs resolu- tion to deal with the clausal structure
and relies on partial solutions to deal with (non-local) instances of functionality
axioms.
alternative_title:
- LNCS
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Corneliu
full_name: Popeea, Corneliu
last_name: Popeea
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
citation:
ama: 'Gupta A, Popeea C, Rybalchenko A. Solving recursion-free Horn clauses over
LI+UIF. In: Yang H, ed. Vol 7078. Springer; 2011:188-203. doi:10.1007/978-3-642-25318-8_16'
apa: 'Gupta, A., Popeea, C., & Rybalchenko, A. (2011). Solving recursion-free
Horn clauses over LI+UIF. In H. Yang (Ed.) (Vol. 7078, pp. 188–203). Presented
at the APLAS: Asian Symposium on Programming Languages and Systems, Kenting, Taiwan:
Springer. https://doi.org/10.1007/978-3-642-25318-8_16'
chicago: Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Solving Recursion-Free
Horn Clauses over LI+UIF.” edited by Hongseok Yang, 7078:188–203. Springer, 2011.
https://doi.org/10.1007/978-3-642-25318-8_16.
ieee: 'A. Gupta, C. Popeea, and A. Rybalchenko, “Solving recursion-free Horn clauses
over LI+UIF,” presented at the APLAS: Asian Symposium on Programming Languages
and Systems, Kenting, Taiwan, 2011, vol. 7078, pp. 188–203.'
ista: 'Gupta A, Popeea C, Rybalchenko A. 2011. Solving recursion-free Horn clauses
over LI+UIF. APLAS: Asian Symposium on Programming Languages and Systems, LNCS,
vol. 7078, 188–203.'
mla: Gupta, Ashutosh, et al. Solving Recursion-Free Horn Clauses over LI+UIF.
Edited by Hongseok Yang, vol. 7078, Springer, 2011, pp. 188–203, doi:10.1007/978-3-642-25318-8_16.
short: A. Gupta, C. Popeea, A. Rybalchenko, in:, H. Yang (Ed.), Springer, 2011,
pp. 188–203.
conference:
end_date: 2011-12-07
location: Kenting, Taiwan
name: 'APLAS: Asian Symposium on Programming Languages and Systems'
start_date: 2011-12-05
date_created: 2018-12-11T12:02:20Z
date_published: 2011-12-05T00:00:00Z
date_updated: 2021-01-12T07:42:15Z
day: '05'
department:
- _id: ToHe
doi: 10.1007/978-3-642-25318-8_16
ec_funded: 1
editor:
- first_name: Hongseok
full_name: Yang, Hongseok
last_name: Yang
intvolume: ' 7078'
language:
- iso: eng
month: '12'
oa_version: None
page: 188 - 203
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: Springer
publist_id: '3383'
quality_controlled: '1'
status: public
title: Solving recursion-free Horn clauses over LI+UIF
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 7078
year: '2011'
...
---
_id: '3266'
abstract:
- lang: eng
text: We present a joint image segmentation and labeling model (JSL) which, given
a bag of figure-ground segment hypotheses extracted at multiple image locations
and scales, constructs a joint probability distribution over both the compatible
image interpretations (tilings or image segmentations) composed from those segments,
and over their labeling into categories. The process of drawing samples from the
joint distribution can be interpreted as first sampling tilings, modeled as maximal
cliques, from a graph connecting spatially non-overlapping segments in the bag
[1], followed by sampling labels for those segments, conditioned on the choice
of a particular tiling. We learn the segmentation and labeling parameters jointly,
based on Maximum Likelihood with a novel Incremental Saddle Point estimation procedure.
The partition function over tilings and labelings is increasingly more accurately
approximated by including incorrect configurations that a not-yet-competent model
rates probable during learning. We show that the proposed methodologymatches the
current state of the art in the Stanford dataset [2], as well as in VOC2010, where
41.7% accuracy on the test set is achieved.
author:
- first_name: Adrian
full_name: Ion, Adrian
id: 29F89302-F248-11E8-B48F-1D18A9856A87
last_name: Ion
- first_name: Joao
full_name: Carreira, Joao
last_name: Carreira
- first_name: Cristian
full_name: Sminchisescu, Cristian
last_name: Sminchisescu
citation:
ama: 'Ion A, Carreira J, Sminchisescu C. Probabilistic joint image segmentation
and labeling. In: NIPS Proceedings. Vol 24. Neural Information Processing
Systems Foundation; 2011:1827-1835.'
apa: 'Ion, A., Carreira, J., & Sminchisescu, C. (2011). Probabilistic joint
image segmentation and labeling. In NIPS Proceedings (Vol. 24, pp. 1827–1835).
Granada, Spain: Neural Information Processing Systems Foundation.'
chicago: Ion, Adrian, Joao Carreira, and Cristian Sminchisescu. “Probabilistic Joint
Image Segmentation and Labeling.” In NIPS Proceedings, 24:1827–35. Neural
Information Processing Systems Foundation, 2011.
ieee: A. Ion, J. Carreira, and C. Sminchisescu, “Probabilistic joint image segmentation
and labeling,” in NIPS Proceedings, Granada, Spain, 2011, vol. 24, pp.
1827–1835.
ista: 'Ion A, Carreira J, Sminchisescu C. 2011. Probabilistic joint image segmentation
and labeling. NIPS Proceedings. NIPS: Neural Information Processing Systems vol.
24, 1827–1835.'
mla: Ion, Adrian, et al. “Probabilistic Joint Image Segmentation and Labeling.”
NIPS Proceedings, vol. 24, Neural Information Processing Systems Foundation,
2011, pp. 1827–35.
short: A. Ion, J. Carreira, C. Sminchisescu, in:, NIPS Proceedings, Neural Information
Processing Systems Foundation, 2011, pp. 1827–1835.
conference:
end_date: 2011-12-14
location: Granada, Spain
name: 'NIPS: Neural Information Processing Systems'
start_date: 2011-12-12
date_created: 2018-12-11T12:02:21Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2021-01-12T07:42:15Z
day: '01'
department:
- _id: HeEd
intvolume: ' 24'
language:
- iso: eng
month: '12'
oa_version: None
page: 1827 - 1835
publication: NIPS Proceedings
publication_status: published
publisher: Neural Information Processing Systems Foundation
publist_id: '3381'
quality_controlled: '1'
scopus_import: 1
status: public
title: Probabilistic joint image segmentation and labeling
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2011'
...
---
_id: '3269'
abstract:
- lang: eng
text: The unintentional scattering of light between neighboring surfaces in complex
projection environments increases the brightness and decreases the contrast, disrupting
the appearance of the desired imagery. To achieve satisfactory projection results,
the inverse problem of global illumination must be solved to cancel this secondary
scattering. In this paper, we propose a global illumination cancellation method
that minimizes the perceptual difference between the desired imagery and the actual
total illumination in the resulting physical environment. Using Gauss-Newton and
active set methods, we design a fast solver for the bound constrained nonlinear
least squares problem raised by the perceptual error metrics. Our solver is further
accelerated with a CUDA implementation and multi-resolution method to achieve
1–2 fps for problems with approximately 3000 variables. We demonstrate the global
illumination cancellation algorithm with our multi-projector system. Results show
that our method preserves the color fidelity of the desired imagery significantly
better than previous methods.
article_processing_charge: No
article_type: original
author:
- first_name: Yu
full_name: Sheng, Yu
last_name: Sheng
- first_name: Barbara
full_name: Cutler, Barbara
last_name: Cutler
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Joshua
full_name: Nasman, Joshua
last_name: Nasman
citation:
ama: Sheng Y, Cutler B, Chen C, Nasman J. Perceptual global illumination cancellation
in complex projection environments. Computer Graphics Forum. 2011;30(4):1261-1268.
doi:10.1111/j.1467-8659.2011.01985.x
apa: Sheng, Y., Cutler, B., Chen, C., & Nasman, J. (2011). Perceptual global
illumination cancellation in complex projection environments. Computer Graphics
Forum. Wiley-Blackwell. https://doi.org/10.1111/j.1467-8659.2011.01985.x
chicago: Sheng, Yu, Barbara Cutler, Chao Chen, and Joshua Nasman. “Perceptual Global
Illumination Cancellation in Complex Projection Environments.” Computer Graphics
Forum. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1467-8659.2011.01985.x.
ieee: Y. Sheng, B. Cutler, C. Chen, and J. Nasman, “Perceptual global illumination
cancellation in complex projection environments,” Computer Graphics Forum,
vol. 30, no. 4. Wiley-Blackwell, pp. 1261–1268, 2011.
ista: Sheng Y, Cutler B, Chen C, Nasman J. 2011. Perceptual global illumination
cancellation in complex projection environments. Computer Graphics Forum. 30(4),
1261–1268.
mla: Sheng, Yu, et al. “Perceptual Global Illumination Cancellation in Complex Projection
Environments.” Computer Graphics Forum, vol. 30, no. 4, Wiley-Blackwell,
2011, pp. 1261–68, doi:10.1111/j.1467-8659.2011.01985.x.
short: Y. Sheng, B. Cutler, C. Chen, J. Nasman, Computer Graphics Forum 30 (2011)
1261–1268.
date_created: 2018-12-11T12:02:22Z
date_published: 2011-07-19T00:00:00Z
date_updated: 2021-01-12T07:42:16Z
day: '19'
department:
- _id: HeEd
doi: 10.1111/j.1467-8659.2011.01985.x
intvolume: ' 30'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.cs.cmu.edu/%7Eshengyu/download/egsr2011_paper.pdf
month: '07'
oa: 1
oa_version: Published Version
page: 1261 - 1268
publication: Computer Graphics Forum
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3377'
quality_controlled: '1'
scopus_import: 1
status: public
title: Perceptual global illumination cancellation in complex projection environments
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2011'
...
---
_id: '3267'
abstract:
- lang: eng
text: 'We address the problem of localizing homology classes, namely, finding the
cycle representing a given class with the most concise geometric measure. We study
the problem with different measures: volume, diameter and radius. For volume,
that is, the 1-norm of a cycle, two main results are presented. First, we prove
that the problem is NP-hard to approximate within any constant factor. Second,
we prove that for homology of dimension two or higher, the problem is NP-hard
to approximate even when the Betti number is O(1). The latter result leads to
the inapproximability of the problem of computing the nonbounding cycle with the
smallest volume and computing cycles representing a homology basis with the minimal
total volume. As for the other two measures defined by pairwise geodesic distance,
diameter and radius, we show that the localization problem is NP-hard for diameter
but is polynomial for radius. Our work is restricted to homology over the ℤ2 field.'
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Daniel
full_name: Freedman, Daniel
last_name: Freedman
citation:
ama: Chen C, Freedman D. Hardness results for homology localization. Discrete
& Computational Geometry. 2011;45(3):425-448. doi:10.1007/s00454-010-9322-8
apa: Chen, C., & Freedman, D. (2011). Hardness results for homology localization.
Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-010-9322-8
chicago: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.”
Discrete & Computational Geometry. Springer, 2011. https://doi.org/10.1007/s00454-010-9322-8.
ieee: C. Chen and D. Freedman, “Hardness results for homology localization,” Discrete
& Computational Geometry, vol. 45, no. 3. Springer, pp. 425–448, 2011.
ista: Chen C, Freedman D. 2011. Hardness results for homology localization. Discrete
& Computational Geometry. 45(3), 425–448.
mla: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.”
Discrete & Computational Geometry, vol. 45, no. 3, Springer, 2011,
pp. 425–48, doi:10.1007/s00454-010-9322-8.
short: C. Chen, D. Freedman, Discrete & Computational Geometry 45 (2011) 425–448.
date_created: 2018-12-11T12:02:21Z
date_published: 2011-01-14T00:00:00Z
date_updated: 2023-02-21T16:07:10Z
day: '14'
department:
- _id: HeEd
doi: 10.1007/s00454-010-9322-8
intvolume: ' 45'
issue: '3'
language:
- iso: eng
month: '01'
oa_version: None
page: 425 - 448
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '3379'
quality_controlled: '1'
related_material:
record:
- id: '10909'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Hardness results for homology localization
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2011'
...
---
_id: '3268'
abstract:
- lang: eng
text: 'Algebraic topology is generally considered one of the purest subfield of
mathematics. However, over the last decade two interesting new lines of research
have emerged, one focusing on algorithms for algebraic topology, and the other
on applications of algebraic topology in engineering and science. Amongst the
new areas in which the techniques have been applied are computer vision and image
processing. In this paper, we survey the results of these endeavours. Because
algebraic topology is an area of mathematics with which most computer vision practitioners
have no experience, we review the machinery behind the theories of homology and
persistent homology; our review emphasizes intuitive explanations. In terms of
applications to computer vision, we focus on four illustrative problems: shape
signatures, natural image statistics, image denoising, and segmentation. Our hope
is that this review will stimulate interest on the part of computer vision researchers
to both use and extend the tools of this new field. '
alternative_title:
- Computer Science, Technology and Applications
author:
- first_name: Daniel
full_name: Freedman, Daniel
last_name: Freedman
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
citation:
ama: 'Freedman D, Chen C. Algebraic topology for computer vision. In: Computer
Vision. Nova Science Publishers; 2011:239-268.'
apa: Freedman, D., & Chen, C. (2011). Algebraic topology for computer vision.
In Computer Vision (pp. 239–268). Nova Science Publishers.
chicago: Freedman, Daniel, and Chao Chen. “Algebraic Topology for Computer Vision.”
In Computer Vision, 239–68. Nova Science Publishers, 2011.
ieee: D. Freedman and C. Chen, “Algebraic topology for computer vision,” in Computer
Vision, Nova Science Publishers, 2011, pp. 239–268.
ista: 'Freedman D, Chen C. 2011.Algebraic topology for computer vision. In: Computer
Vision. Computer Science, Technology and Applications, , 239–268.'
mla: Freedman, Daniel, and Chao Chen. “Algebraic Topology for Computer Vision.”
Computer Vision, Nova Science Publishers, 2011, pp. 239–68.
short: D. Freedman, C. Chen, in:, Computer Vision, Nova Science Publishers, 2011,
pp. 239–268.
date_created: 2018-12-11T12:02:22Z
date_published: 2011-11-30T00:00:00Z
date_updated: 2021-01-12T07:42:16Z
day: '30'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://www.hpl.hp.com/techreports/2009/HPL-2009-375.pdf
month: '11'
oa_version: None
page: 239 - 268
publication: Computer Vision
publication_status: published
publisher: Nova Science Publishers
publist_id: '3378'
quality_controlled: '1'
status: public
title: Algebraic topology for computer vision
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3288'
abstract:
- lang: eng
text: 'The zonula adherens (ZA) of epithelial cells is a site of cell-cell adhesion
where cellular forces are exerted and resisted. Increasing evidence indicates
that E-cadherin adhesion molecules at the ZA serve to sense force applied on the
junctions and coordinate cytoskeletal responses to those forces. Efforts to understand
the role that cadherins play in mechanotransduction have been limited by the lack
of assays to measure the impact of forces on the ZA. In this study we used 4D
imaging of GFP-tagged E-cadherin to analyse the movement of the ZA. Junctions
in confluent epithelial monolayers displayed prominent movements oriented orthogonal
(perpendicular) to the ZA itself. Two components were identified in these movements:
a relatively slow unidirectional (translational) component that could be readily
fitted by least-squares regression analysis, upon which were superimposed more
rapid oscillatory movements. Myosin IIB was a dominant factor responsible for
driving the unilateral translational movements. In contrast, frequency spectrum
analysis revealed that depletion of Myosin IIA increased the power of the oscillatory
movements. This implies that Myosin IIA may serve to dampen oscillatory movements
of the ZA. This extends our recent analysis of Myosin II at the ZA to demonstrate
that Myosin IIA and Myosin IIB make distinct contributions to junctional movement
at the ZA.'
acknowledgement: his work was funded by the National Health and Medical Research Council
(NHMRC) of Australia. M.S. was an Erwin Schroedinger postdoctoral fellow of the
Austrian Science Fund (FWF), S.K.W. is supported by a UQ International Research
Tuition Award and Research Scholarship, S.M .by an ANZ Trustees PhD Scholarship.
A.S.Y. is a Research Fellow of the NHMRC. Confocal imaging was performed at the
Australian Cancer Research Foundation (ACRF) Cancer Biology Imaging Centre at the
Institute for Molecular Bioscience, established with the generous support of the
ACRF.
author:
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Selwin
full_name: Wu, Selwin
last_name: Wu
- first_name: Guillermo
full_name: Gomez, Guillermo
last_name: Gomez
- first_name: Sabine
full_name: Mangold, Sabine
last_name: Mangold
- first_name: Alpha
full_name: Yap, Alpha
last_name: Yap
- first_name: Nicholas
full_name: Hamilton, Nicholas
last_name: Hamilton
citation:
ama: Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. Multicomponent analysis
of junctional movements regulated by Myosin II isoforms at the epithelial zonula
adherens. PLoS One. 2011;6(7). doi:10.1371/journal.pone.0022458
apa: Smutny, M., Wu, S., Gomez, G., Mangold, S., Yap, A., & Hamilton, N. (2011).
Multicomponent analysis of junctional movements regulated by Myosin II isoforms
at the epithelial zonula adherens. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0022458
chicago: Smutny, Michael, Selwin Wu, Guillermo Gomez, Sabine Mangold, Alpha Yap,
and Nicholas Hamilton. “Multicomponent Analysis of Junctional Movements Regulated
by Myosin II Isoforms at the Epithelial Zonula Adherens.” PLoS One. Public
Library of Science, 2011. https://doi.org/10.1371/journal.pone.0022458.
ieee: M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, and N. Hamilton, “Multicomponent
analysis of junctional movements regulated by Myosin II isoforms at the epithelial
zonula adherens,” PLoS One, vol. 6, no. 7. Public Library of Science, 2011.
ista: Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. 2011. Multicomponent
analysis of junctional movements regulated by Myosin II isoforms at the epithelial
zonula adherens. PLoS One. 6(7).
mla: Smutny, Michael, et al. “Multicomponent Analysis of Junctional Movements Regulated
by Myosin II Isoforms at the Epithelial Zonula Adherens.” PLoS One, vol.
6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pone.0022458.
short: M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, N. Hamilton, PLoS One 6 (2011).
date_created: 2018-12-11T12:02:28Z
date_published: 2011-07-22T00:00:00Z
date_updated: 2021-01-12T07:42:25Z
day: '22'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1371/journal.pone.0022458
file:
- access_level: open_access
checksum: 57a5eb11dd05241c48c44f492b3ec3ac
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T10:51:43Z
date_updated: 2020-07-14T12:46:06Z
file_id: '6399'
file_name: 2011_PLOS_Smutny.PDF
file_size: 1984567
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3357'
quality_controlled: '1'
status: public
title: Multicomponent analysis of junctional movements regulated by Myosin II isoforms
at the epithelial zonula adherens
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: '2011'
...
---
_id: '3286'
abstract:
- lang: eng
text: Cationic antimicrobial peptides (CAMPs) selectively target bacterial membranes
by electrostatic interactions with negatively charged lipids. It turned out that
for inhibition of microbial growth a high CAMP membrane concentration is required,
which can be realized by the incorporation of hydrophobic groups within the peptide.
Increasing hydrophobicity, however, reduces the CAMP selectivity for bacterial
over eukaryotic host membranes, thereby causing the risk of detrimental side-effects.
In this study we addressed how cationic amphipathic peptides—in particular a CAMP
with Lysine–Leucine–Lysine repeats (termed KLK)—affect the localization and dynamics
of molecules in eukaryotic membranes. We found KLK to selectively inhibit the
endocytosis of a subgroup of membrane proteins and lipids by electrostatically
interacting with negatively charged sialic acid moieties. Ultrastructural characterization
revealed the formation of membrane invaginations representing fission or fusion
intermediates, in which the sialylated proteins and lipids were immobilized. Experiments
on structurally different cationic amphipathic peptides (KLK, 6-MO-LF11-322 and
NK14-2) indicated a cooperation of electrostatic and hydrophobic forces that selectively
arrest sialylated membrane constituents.
acknowledgement: "This work was funded by the GEN-AU project of the Austrian Research
Promotion Agency, the Austrian Science Fund (FWF; project Y250-B03) and Intercell
AG.\nWe thank the following colleagues for providing plasmids and cells: Daniel
Legler (University of Konstanz, Switzerland), Jennifer Lippincott-Schwartz (NIH,
Bethesda, USA), Hannes Stockinger (Medical University Vienna, Austria), Katharina
Strub (University of Geneva, Switzerland), Lawrence Rajendran (ETH Zurich, Switzerland),
Eileen M. Lafer (UTHSC San Antonio, Texas, USA), Mark McNiven (Mayo Clinic, Minnesota,
USA), John Silvius (McGill University, Montreal, Canada), Christoph Romanin (JKU
Linz, Austria), Herbert Stangl (Medical University Vienna, Austria) and Anton van
der Merwe (Oxford University, Oxford, UK). We thank Harald Kotisch (MFPL, Vienna)
for excellent technical assistance in the processing of samples for electron microscopy
and Sergio Grinstein (Hospital for Sick Children Research Institute, Toronto) for
fruitful discussions. "
author:
- first_name: Julian
full_name: Weghuber, Julian
last_name: Weghuber
- first_name: Michael
full_name: Aichinger, Michael C.
last_name: Aichinger
- first_name: Mario
full_name: Brameshuber, Mario
last_name: Brameshuber
- first_name: Stefan
full_name: Stefan Wieser
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Verena
full_name: Verena Ruprecht
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Birgit
full_name: Plochberger, Birgit
last_name: Plochberger
- first_name: Josef
full_name: Madl, Josef
last_name: Madl
- first_name: Andreas
full_name: Horner, Andreas
last_name: Horner
- first_name: Siegfried
full_name: Reipert, Siegfried
last_name: Reipert
- first_name: Karl
full_name: Lohner, Karl
last_name: Lohner
- first_name: Tamas
full_name: Henics, Tamas
last_name: Henics
- first_name: Gerhard
full_name: Schuetz, Gerhard J
last_name: Schuetz
citation:
ama: Weghuber J, Aichinger M, Brameshuber M, et al. Cationic amphipathic peptides
accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic
host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes. 2011;1808(10):2581-2590.
doi:10.1016/j.bbamem.2011.06.007
apa: Weghuber, J., Aichinger, M., Brameshuber, M., Wieser, S., Ruprecht, V., Plochberger,
B., … Schuetz, G. (2011). Cationic amphipathic peptides accumulate sialylated
proteins and lipids in the plasma membrane of eukaryotic host cells. Biochimica
et Biophysica Acta (BBA) - Biomembranes. Elsevier. https://doi.org/10.1016/j.bbamem.2011.06.007
chicago: Weghuber, Julian, Michael Aichinger, Mario Brameshuber, Stefan Wieser,
Verena Ruprecht, Birgit Plochberger, Josef Madl, et al. “Cationic Amphipathic
Peptides Accumulate Sialylated Proteins and Lipids in the Plasma Membrane of Eukaryotic
Host Cells.” Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier,
2011. https://doi.org/10.1016/j.bbamem.2011.06.007.
ieee: J. Weghuber et al., “Cationic amphipathic peptides accumulate sialylated
proteins and lipids in the plasma membrane of eukaryotic host cells,” Biochimica
et Biophysica Acta (BBA) - Biomembranes, vol. 1808, no. 10. Elsevier, pp.
2581–2590, 2011.
ista: Weghuber J, Aichinger M, Brameshuber M, Wieser S, Ruprecht V, Plochberger
B, Madl J, Horner A, Reipert S, Lohner K, Henics T, Schuetz G. 2011. Cationic
amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane
of eukaryotic host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes.
1808(10), 2581–2590.
mla: Weghuber, Julian, et al. “Cationic Amphipathic Peptides Accumulate Sialylated
Proteins and Lipids in the Plasma Membrane of Eukaryotic Host Cells.” Biochimica
et Biophysica Acta (BBA) - Biomembranes, vol. 1808, no. 10, Elsevier, 2011,
pp. 2581–90, doi:10.1016/j.bbamem.2011.06.007.
short: J. Weghuber, M. Aichinger, M. Brameshuber, S. Wieser, V. Ruprecht, B. Plochberger,
J. Madl, A. Horner, S. Reipert, K. Lohner, T. Henics, G. Schuetz, Biochimica et
Biophysica Acta (BBA) - Biomembranes 1808 (2011) 2581–2590.
date_created: 2018-12-11T12:02:28Z
date_published: 2011-10-01T00:00:00Z
date_updated: 2021-01-12T07:42:24Z
day: '01'
doi: 10.1016/j.bbamem.2011.06.007
extern: 1
intvolume: ' 1808'
issue: '10'
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
page: 2581 - 2590
publication: Biochimica et Biophysica Acta (BBA) - Biomembranes
publication_status: published
publisher: Elsevier
publist_id: '3359'
quality_controlled: 0
status: public
title: Cationic amphipathic peptides accumulate sialylated proteins and lipids in
the plasma membrane of eukaryotic host cells
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
volume: 1808
year: '2011'
...
---
_id: '3287'
abstract:
- lang: eng
text: 'Diffusing membrane constituents are constantly exposed to a variety of forces
that influence their stochastic path. Single molecule experiments allow for resolving
trajectories at extremely high spatial and temporal accuracy, thereby offering
insights into en route interactions of the tracer. In this review we discuss approaches
to derive information about the underlying processes, based on single molecule
tracking experiments. In particular, we focus on a new versatile way to analyze
single molecule diffusion in the absence of a full analytical treatment. The method
is based on comprehensive comparison of an experimental data set against the hypothetical
outcome of multiple experiments performed on the computer. Since Monte Carlo simulations
can be easily and rapidly performed even on state-of-the-art PCs, our method provides
a simple way for testing various - even complicated - diffusion models. We describe
the new method in detail, and show the applicability on two specific examples:
firstly, kinetic rate constants can be derived for the transient interaction of
mobile membrane proteins; secondly, residence time and corral size can be extracted
for confined diffusion.'
author:
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Markus
full_name: Axmann, Markus
last_name: Axmann
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Gerhard
full_name: Schuetz, Gerhard
last_name: Schuetz
citation:
ama: Ruprecht V, Axmann M, Wieser S, Schuetz G. What can we learn from single molecule
trajectories? Current Protein & Peptide Science. 2011;12(8):714-724.
doi:10.2174/138920311798841753
apa: Ruprecht, V., Axmann, M., Wieser, S., & Schuetz, G. (2011). What can we
learn from single molecule trajectories? Current Protein & Peptide Science.
Bentham Science Publishers. https://doi.org/10.2174/138920311798841753
chicago: Ruprecht, Verena, Markus Axmann, Stefan Wieser, and Gerhard Schuetz. “What
Can We Learn from Single Molecule Trajectories?” Current Protein & Peptide
Science. Bentham Science Publishers, 2011. https://doi.org/10.2174/138920311798841753.
ieee: V. Ruprecht, M. Axmann, S. Wieser, and G. Schuetz, “What can we learn from
single molecule trajectories?,” Current Protein & Peptide Science,
vol. 12, no. 8. Bentham Science Publishers, pp. 714–724, 2011.
ista: Ruprecht V, Axmann M, Wieser S, Schuetz G. 2011. What can we learn from single
molecule trajectories? Current Protein & Peptide Science. 12(8), 714–724.
mla: Ruprecht, Verena, et al. “What Can We Learn from Single Molecule Trajectories?”
Current Protein & Peptide Science, vol. 12, no. 8, Bentham Science
Publishers, 2011, pp. 714–24, doi:10.2174/138920311798841753.
short: V. Ruprecht, M. Axmann, S. Wieser, G. Schuetz, Current Protein & Peptide
Science 12 (2011) 714–724.
date_created: 2018-12-11T12:02:28Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2021-01-12T07:42:24Z
day: '01'
department:
- _id: CaHe
- _id: MiSi
doi: 10.2174/138920311798841753
intvolume: ' 12'
issue: '8'
language:
- iso: eng
month: '12'
oa_version: None
page: 714 - 724
publication: Current Protein & Peptide Science
publication_status: published
publisher: Bentham Science Publishers
publist_id: '3358'
quality_controlled: '1'
scopus_import: 1
status: public
title: What can we learn from single molecule trajectories?
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2011'
...
---
_id: '3285'
abstract:
- lang: eng
text: Resolving the dynamical interplay of proteins and lipids in the live-cell
plasma membrane represents a central goal in current cell biology. Superresolution
concepts have introduced a means of capturing spatial heterogeneity at a nanoscopic
length scale. Similar concepts for detecting dynamical transitions (superresolution
chronoscopy) are still lacking. Here, we show that recently introduced spot-variation
fluorescence correlation spectroscopy allows for sensing transient confinement
times of membrane constituents at dramatically improved resolution. Using standard
diffraction-limited optics, spot-variation fluorescence correlation spectroscopy
captures signatures of single retardation events far below the transit time of
the tracer through the focal spot. We provide an analytical description of special
cases of transient binding of a tracer to pointlike traps, or association of a
tracer with nanodomains. The influence of trap mobility and the underlying binding
kinetics are quantified. Experimental approaches are suggested that allow for
gaining quantitative mechanistic insights into the interaction processes of membrane
constituents.
acknowledgement: Y 250-B03/Austrian Science Fund FWF/Austria
author:
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Didier
full_name: Marguet, Didier
last_name: Marguet
- first_name: Gerhard
full_name: Schuetz, Gerhard
last_name: Schuetz
citation:
ama: Ruprecht V, Wieser S, Marguet D, Schuetz G. Spot variation fluorescence correlation
spectroscopy allows for superresolution chronoscopy of confinement times in membranes.
Biophysical Journal. 2011;100(11):2839-2845. doi:10.1016/j.bpj.2011.04.035
apa: Ruprecht, V., Wieser, S., Marguet, D., & Schuetz, G. (2011). Spot variation
fluorescence correlation spectroscopy allows for superresolution chronoscopy of
confinement times in membranes. Biophysical Journal. Biophysical Society.
https://doi.org/10.1016/j.bpj.2011.04.035
chicago: Ruprecht, Verena, Stefan Wieser, Didier Marguet, and Gerhard Schuetz. “Spot
Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy
of Confinement Times in Membranes.” Biophysical Journal. Biophysical Society,
2011. https://doi.org/10.1016/j.bpj.2011.04.035.
ieee: V. Ruprecht, S. Wieser, D. Marguet, and G. Schuetz, “Spot variation fluorescence
correlation spectroscopy allows for superresolution chronoscopy of confinement
times in membranes,” Biophysical Journal, vol. 100, no. 11. Biophysical
Society, pp. 2839–2845, 2011.
ista: Ruprecht V, Wieser S, Marguet D, Schuetz G. 2011. Spot variation fluorescence
correlation spectroscopy allows for superresolution chronoscopy of confinement
times in membranes. Biophysical Journal. 100(11), 2839–2845.
mla: Ruprecht, Verena, et al. “Spot Variation Fluorescence Correlation Spectroscopy
Allows for Superresolution Chronoscopy of Confinement Times in Membranes.” Biophysical
Journal, vol. 100, no. 11, Biophysical Society, 2011, pp. 2839–45, doi:10.1016/j.bpj.2011.04.035.
short: V. Ruprecht, S. Wieser, D. Marguet, G. Schuetz, Biophysical Journal 100 (2011)
2839–2845.
date_created: 2018-12-11T12:02:27Z
date_published: 2011-06-08T00:00:00Z
date_updated: 2021-01-12T07:42:23Z
day: '08'
doi: 10.1016/j.bpj.2011.04.035
extern: '1'
intvolume: ' 100'
issue: '11'
language:
- iso: eng
month: '06'
oa_version: None
page: 2839 - 2845
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '3360'
status: public
title: Spot variation fluorescence correlation spectroscopy allows for superresolution
chronoscopy of confinement times in membranes
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2011'
...
---
_id: '3302'
abstract:
- lang: eng
text: Cloud computing aims to give users virtually unlimited pay-per-use computing
resources without the burden of managing the underlying infrastructure. We present
a new job execution environment Flextic that exploits scal- able static scheduling
techniques to provide the user with a flexible pricing model, such as a tradeoff
between dif- ferent degrees of execution speed and execution price, and at the
same time, reduce scheduling overhead for the cloud provider. We have evaluated
a prototype of Flextic on Amazon EC2 and compared it against Hadoop. For various
data parallel jobs from machine learning, im- age processing, and gene sequencing
that we considered, Flextic has low scheduling overhead and reduces job du- ration
by up to 15% compared to Hadoop, a dynamic cloud scheduler.
author:
- 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: Anmol
full_name: Singh, Anmol
id: 72A86902-E99F-11E9-9F62-915534D1B916
last_name: Singh
- first_name: Vasu
full_name: Singh, Vasu
id: 4DAE2708-F248-11E8-B48F-1D18A9856A87
last_name: Singh
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: 'Henzinger TA, Singh A, Singh V, Wies T, Zufferey D. Static scheduling in clouds.
In: USENIX; 2011:1-6.'
apa: 'Henzinger, T. A., Singh, A., Singh, V., Wies, T., & Zufferey, D. (2011).
Static scheduling in clouds (pp. 1–6). Presented at the HotCloud: Workshop on
Hot Topics in Cloud Computing, USENIX.'
chicago: Henzinger, Thomas A, Anmol Singh, Vasu Singh, Thomas Wies, and Damien Zufferey.
“Static Scheduling in Clouds,” 1–6. USENIX, 2011.
ieee: 'T. A. Henzinger, A. Singh, V. Singh, T. Wies, and D. Zufferey, “Static scheduling
in clouds,” presented at the HotCloud: Workshop on Hot Topics in Cloud Computing,
2011, pp. 1–6.'
ista: 'Henzinger TA, Singh A, Singh V, Wies T, Zufferey D. 2011. Static scheduling
in clouds. HotCloud: Workshop on Hot Topics in Cloud Computing, 1–6.'
mla: Henzinger, Thomas A., et al. Static Scheduling in Clouds. USENIX, 2011,
pp. 1–6.
short: T.A. Henzinger, A. Singh, V. Singh, T. Wies, D. Zufferey, in:, USENIX, 2011,
pp. 1–6.
conference:
end_date: 2011-06-15
name: 'HotCloud: Workshop on Hot Topics in Cloud Computing'
start_date: 2011-06-14
date_created: 2018-12-11T12:02:33Z
date_published: 2011-06-14T00:00:00Z
date_updated: 2021-01-12T07:42:31Z
day: '14'
ddc:
- '000'
- '005'
department:
- _id: ToHe
file:
- access_level: open_access
checksum: 21a461ac004bb535c83320fe79b30375
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:14Z
date_updated: 2020-07-14T12:46:06Z
file_id: '5333'
file_name: IST-2012-90-v1+1_Static_scheduling_in_clouds.pdf
file_size: 232770
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 1 - 6
publication_status: published
publisher: USENIX
publist_id: '3338'
pubrep_id: '90'
quality_controlled: '1'
status: public
title: Static scheduling in clouds
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3301'
abstract:
- lang: eng
text: The chemical master equation is a differential equation describing the time
evolution of the probability distribution over the possible “states” of a biochemical
system. The solution of this equation is of interest within the systems biology
field ever since the importance of the molec- ular noise has been acknowledged.
Unfortunately, most of the systems do not have analytical solutions, and numerical
solutions suffer from the course of dimensionality and therefore need to be approximated.
Here, we introduce the concept of tail approximation, which retrieves an approximation
of the probabilities in the tail of a distribution from the total probability
of the tail and its conditional expectation. This approximation method can then
be used to numerically compute the solution of the chemical master equation on
a subset of the state space, thus fighting the explosion of the state space, for
which this problem is renowned.
author:
- 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: Maria
full_name: Mateescu, Maria
last_name: Mateescu
citation:
ama: 'Henzinger TA, Mateescu M. Tail approximation for the chemical master equation.
In: Tampere International Center for Signal Processing; 2011.'
apa: 'Henzinger, T. A., & Mateescu, M. (2011). Tail approximation for the chemical
master equation. Presented at the WCSB: Workshop on Computational Systems Biology
(TICSP), Tampere International Center for Signal Processing.'
chicago: Henzinger, Thomas A, and Maria Mateescu. “Tail Approximation for the Chemical
Master Equation.” Tampere International Center for Signal Processing, 2011.
ieee: 'T. A. Henzinger and M. Mateescu, “Tail approximation for the chemical master
equation,” presented at the WCSB: Workshop on Computational Systems Biology (TICSP),
2011.'
ista: 'Henzinger TA, Mateescu M. 2011. Tail approximation for the chemical master
equation. WCSB: Workshop on Computational Systems Biology (TICSP).'
mla: Henzinger, Thomas A., and Maria Mateescu. Tail Approximation for the Chemical
Master Equation. Tampere International Center for Signal Processing, 2011.
short: T.A. Henzinger, M. Mateescu, in:, Tampere International Center for Signal
Processing, 2011.
conference:
name: 'WCSB: Workshop on Computational Systems Biology (TICSP)'
date_created: 2018-12-11T12:02:33Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:30Z
day: '01'
ddc:
- '005'
- '570'
department:
- _id: ToHe
file:
- access_level: open_access
checksum: aa4d7a832a5419e6c0090650ebff2b9a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:12Z
date_updated: 2020-07-14T12:46:06Z
file_id: '5331'
file_name: IST-2012-91-v1+1_Tail_approximation_for_the_chemical_master_equation.pdf
file_size: 240820
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
publication_status: published
publisher: Tampere International Center for Signal Processing
publist_id: '3339'
pubrep_id: '91'
quality_controlled: '1'
status: public
title: Tail approximation for the chemical master equation
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3299'
abstract:
- lang: eng
text: 'We introduce propagation models, a formalism designed to support general
and efficient data structures for the transient analysis of biochemical reaction
networks. We give two use cases for propagation abstract data types: the uniformization
method and numerical integration. We also sketch an implementation of a propagation
abstract data type, which uses abstraction to approximate states.'
author:
- 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: Maria
full_name: Mateescu, Maria
last_name: Mateescu
citation:
ama: 'Henzinger TA, Mateescu M. Propagation models for computing biochemical reaction
networks. In: Springer; 2011:1-3. doi:10.1145/2037509.2037510'
apa: 'Henzinger, T. A., & Mateescu, M. (2011). Propagation models for computing
biochemical reaction networks (pp. 1–3). Presented at the CMSB: Computational
Methods in Systems Biology, Paris, France: Springer. https://doi.org/10.1145/2037509.2037510'
chicago: Henzinger, Thomas A, and Maria Mateescu. “Propagation Models for Computing
Biochemical Reaction Networks,” 1–3. Springer, 2011. https://doi.org/10.1145/2037509.2037510.
ieee: 'T. A. Henzinger and M. Mateescu, “Propagation models for computing biochemical
reaction networks,” presented at the CMSB: Computational Methods in Systems Biology,
Paris, France, 2011, pp. 1–3.'
ista: 'Henzinger TA, Mateescu M. 2011. Propagation models for computing biochemical
reaction networks. CMSB: Computational Methods in Systems Biology, 1–3.'
mla: Henzinger, Thomas A., and Maria Mateescu. Propagation Models for Computing
Biochemical Reaction Networks. Springer, 2011, pp. 1–3, doi:10.1145/2037509.2037510.
short: T.A. Henzinger, M. Mateescu, in:, Springer, 2011, pp. 1–3.
conference:
end_date: 2011-09-23
location: Paris, France
name: 'CMSB: Computational Methods in Systems Biology'
start_date: 2011-09-21
date_created: 2018-12-11T12:02:32Z
date_published: 2011-09-21T00:00:00Z
date_updated: 2021-01-12T07:42:29Z
day: '21'
ddc:
- '000'
- '004'
department:
- _id: ToHe
doi: 10.1145/2037509.2037510
file:
- access_level: open_access
checksum: 7f5c65509db1a9fb049abedd9663ed06
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:50Z
date_updated: 2020-07-14T12:46:06Z
file_id: '4649'
file_name: IST-2012-92-v1+1_Propagation_models_for_computing_biochemical_reaction_networks.pdf
file_size: 255780
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 1 - 3
publication_status: published
publisher: Springer
publist_id: '3341'
pubrep_id: '92'
quality_controlled: '1'
scopus_import: 1
status: public
title: Propagation models for computing biochemical reaction networks
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3316'
abstract:
- lang: eng
text: In addition to being correct, a system should be robust, that is, it should
behave reasonably even after receiving unexpected inputs. In this paper, we summarize
two formal notions of robustness that we have introduced previously for reactive
systems. One of the notions is based on assigning costs for failures on a user-provided
notion of incorrect transitions in a specification. Here, we define a system to
be robust if a finite number of incorrect inputs does not lead to an infinite
number of incorrect outputs. We also give a more refined notion of robustness
that aims to minimize the ratio of output failures to input failures. The second
notion is aimed at liveness. In contrast to the previous notion, it has no concept
of recovery from an error. Instead, it compares the ratio of the number of liveness
constraints that the system violates to the number of liveness constraints that
the environment violates.
article_processing_charge: No
author:
- first_name: Roderick
full_name: Bloem, Roderick
last_name: Bloem
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Karin
full_name: Greimel, Karin
last_name: Greimel
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
citation:
ama: 'Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. Specification-centered
robustness. In: 6th IEEE International Symposium on Industrial and Embedded
Systems. IEEE; 2011:176-185. doi:10.1109/SIES.2011.5953660'
apa: 'Bloem, R., Chatterjee, K., Greimel, K., Henzinger, T. A., & Jobstmann,
B. (2011). Specification-centered robustness. In 6th IEEE International Symposium
on Industrial and Embedded Systems (pp. 176–185). Vasteras, Sweden: IEEE.
https://doi.org/10.1109/SIES.2011.5953660'
chicago: Bloem, Roderick, Krishnendu Chatterjee, Karin Greimel, Thomas A Henzinger,
and Barbara Jobstmann. “Specification-Centered Robustness.” In 6th IEEE International
Symposium on Industrial and Embedded Systems, 176–85. IEEE, 2011. https://doi.org/10.1109/SIES.2011.5953660.
ieee: R. Bloem, K. Chatterjee, K. Greimel, T. A. Henzinger, and B. Jobstmann, “Specification-centered
robustness,” in 6th IEEE International Symposium on Industrial and Embedded
Systems, Vasteras, Sweden, 2011, pp. 176–185.
ista: 'Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. 2011. Specification-centered
robustness. 6th IEEE International Symposium on Industrial and Embedded Systems. SIES:
International Symposium on Industrial Embedded Systems, 176–185.'
mla: Bloem, Roderick, et al. “Specification-Centered Robustness.” 6th IEEE International
Symposium on Industrial and Embedded Systems, IEEE, 2011, pp. 176–85, doi:10.1109/SIES.2011.5953660.
short: R. Bloem, K. Chatterjee, K. Greimel, T.A. Henzinger, B. Jobstmann, in:, 6th
IEEE International Symposium on Industrial and Embedded Systems, IEEE, 2011, pp.
176–185.
conference:
end_date: 2011-06-17
location: Vasteras, Sweden
name: ' SIES: International Symposium on Industrial Embedded Systems'
start_date: 2011-06-15
date_created: 2018-12-11T12:02:38Z
date_published: 2011-07-14T00:00:00Z
date_updated: 2021-01-12T07:42:36Z
day: '14'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1109/SIES.2011.5953660
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://openlib.tugraz.at/download.php?id=5cb57c8a49344&location=browse
month: '07'
oa: 1
oa_version: Published Version
page: 176 - 185
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: 6th IEEE International Symposium on Industrial and Embedded Systems
publication_status: published
publisher: IEEE
publist_id: '3323'
quality_controlled: '1'
scopus_import: 1
status: public
title: Specification-centered robustness
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3318'
abstract:
- lang: eng
text: Parvalbumin is thought to act in a manner similar to EGTA, but how a slow
Ca2+ buffer affects nanodomain-coupling regimes at GABAergic synapses is unclear.
Direct measurements of parvalbumin concentration and paired recordings in rodent
hippocampus and cerebellum revealed that parvalbumin affects synaptic dynamics
only when expressed at high levels. Modeling suggests that, in high concentrations,
parvalbumin may exert BAPTA-like effects, modulating nanodomain coupling via competition
with local saturation of endogenous fixed buffers.
author:
- first_name: Emmanuel
full_name: Eggermann, Emmanuel
last_name: Eggermann
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Eggermann E, Jonas PM. How the “slow” Ca(2+) buffer parvalbumin affects transmitter
release in nanodomain coupling regimes at GABAergic synapses. Nature Neuroscience.
2011;15:20-22. doi:10.1038/nn.3002
apa: Eggermann, E., & Jonas, P. M. (2011). How the “slow” Ca(2+) buffer parvalbumin
affects transmitter release in nanodomain coupling regimes at GABAergic synapses.
Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3002
chicago: Eggermann, Emmanuel, and Peter M Jonas. “How the ‘Slow’ Ca(2+) Buffer Parvalbumin
Affects Transmitter Release in Nanodomain Coupling Regimes at GABAergic Synapses.”
Nature Neuroscience. Nature Publishing Group, 2011. https://doi.org/10.1038/nn.3002.
ieee: E. Eggermann and P. M. Jonas, “How the ‘slow’ Ca(2+) buffer parvalbumin affects
transmitter release in nanodomain coupling regimes at GABAergic synapses,” Nature
Neuroscience, vol. 15. Nature Publishing Group, pp. 20–22, 2011.
ista: Eggermann E, Jonas PM. 2011. How the “slow” Ca(2+) buffer parvalbumin affects
transmitter release in nanodomain coupling regimes at GABAergic synapses. Nature
Neuroscience. 15, 20–22.
mla: Eggermann, Emmanuel, and Peter M. Jonas. “How the ‘Slow’ Ca(2+) Buffer Parvalbumin
Affects Transmitter Release in Nanodomain Coupling Regimes at GABAergic Synapses.”
Nature Neuroscience, vol. 15, Nature Publishing Group, 2011, pp. 20–22,
doi:10.1038/nn.3002.
short: E. Eggermann, P.M. Jonas, Nature Neuroscience 15 (2011) 20–22.
date_created: 2018-12-11T12:02:38Z
date_published: 2011-12-04T00:00:00Z
date_updated: 2021-01-12T07:42:37Z
day: '04'
department:
- _id: PeJo
doi: 10.1038/nn.3002
intvolume: ' 15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631701/
month: '12'
oa: 1
oa_version: Submitted Version
page: 20 - 22
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '3321'
quality_controlled: '1'
scopus_import: 1
status: public
title: How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain
coupling regimes at GABAergic synapses
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2011'
...
---
_id: '3335'
abstract:
- lang: eng
text: We study the topology of the Megaparsec Cosmic Web in terms of the scale-dependent
Betti numbers, which formalize the topological information content of the cosmic
mass distribution. While the Betti numbers do not fully quantify topology, they
extend the information beyond conventional cosmological studies of topology in
terms of genus and Euler characteristic. The richer information content of Betti
numbers goes along the availability of fast algorithms to compute them. For continuous
density fields, we determine the scale-dependence of Betti numbers by invoking
the cosmologically familiar filtration of sublevel or superlevel sets defined
by density thresholds. For the discrete galaxy distribution, however, the analysis
is based on the alpha shapes of the particles. These simplicial complexes constitute
an ordered sequence of nested subsets of the Delaunay tessellation, a filtration
defined by the scale parameter, α. As they are homotopy equivalent to the sublevel
sets of the distance field, they are an excellent tool for assessing the topological
structure of a discrete point distribution. In order to develop an intuitive understanding
for the behavior of Betti numbers as a function of α, and their relation to the
morphological patterns in the Cosmic Web, we first study them within the context
of simple heuristic Voronoi clustering models. These can be tuned to consist of
specific morphological elements of the Cosmic Web, i.e. clusters, filaments, or
sheets. To elucidate the relative prominence of the various Betti numbers in different
stages of morphological evolution, we introduce the concept of alpha tracks. Subsequently,
we address the topology of structures emerging in the standard LCDM scenario and
in cosmological scenarios with alternative dark energy content. The evolution
of the Betti numbers is shown to reflect the hierarchical evolution of the Cosmic
Web. We also demonstrate that the scale-dependence of the Betti numbers yields
a promising measure of cosmological parameters, with a potential to help in determining
the nature of dark energy and to probe primordial non-Gaussianities. We also discuss
the expected Betti numbers as a function of the density threshold for superlevel
sets of a Gaussian random field. Finally, we introduce the concept of persistent
homology. It measures scale levels of the mass distribution and allows us to separate
small from large scale features. Within the context of the hierarchical cosmic
structure formation, persistence provides a natural formalism for a multiscale
topology study of the Cosmic Web.
alternative_title:
- LNCS
author:
- first_name: Rien
full_name: Van De Weygaert, Rien
last_name: Van De Weygaert
- first_name: Gert
full_name: Vegter, Gert
last_name: Vegter
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Bernard
full_name: Jones, Bernard
last_name: Jones
- first_name: Pratyush
full_name: Pranav, Pratyush
last_name: Pranav
- first_name: Changbom
full_name: Park, Changbom
last_name: Park
- first_name: Wojciech
full_name: Hellwing, Wojciech
last_name: Hellwing
- first_name: Bob
full_name: Eldering, Bob
last_name: Eldering
- first_name: Nico
full_name: Kruithof, Nico
last_name: Kruithof
- first_name: Patrick
full_name: Bos, Patrick
last_name: Bos
- first_name: Johan
full_name: Hidding, Johan
last_name: Hidding
- first_name: Job
full_name: Feldbrugge, Job
last_name: Feldbrugge
- first_name: Eline
full_name: Ten Have, Eline
last_name: Ten Have
- first_name: Matti
full_name: Van Engelen, Matti
last_name: Van Engelen
- first_name: Manuel
full_name: Caroli, Manuel
last_name: Caroli
- first_name: Monique
full_name: Teillaud, Monique
last_name: Teillaud
citation:
ama: 'Van De Weygaert R, Vegter G, Edelsbrunner H, et al. Alpha, Betti and the Megaparsec
Universe: On the topology of the Cosmic Web. In: Gavrilova M, Tan K, Mostafavi
M, eds. Transactions on Computational Science XIV. Vol 6970. Special Issue
on Voronoi Diagrams and Delaunay Triangulation. Springer; 2011:60-101. doi:10.1007/978-3-642-25249-5_3'
apa: 'Van De Weygaert, R., Vegter, G., Edelsbrunner, H., Jones, B., Pranav, P.,
Park, C., … Teillaud, M. (2011). Alpha, Betti and the Megaparsec Universe: On
the topology of the Cosmic Web. In M. Gavrilova, K. Tan, & M. Mostafavi (Eds.),
Transactions on Computational Science XIV (Vol. 6970, pp. 60–101). Springer.
https://doi.org/10.1007/978-3-642-25249-5_3'
chicago: 'Van De Weygaert, Rien, Gert Vegter, Herbert Edelsbrunner, Bernard Jones,
Pratyush Pranav, Changbom Park, Wojciech Hellwing, et al. “Alpha, Betti and the
Megaparsec Universe: On the Topology of the Cosmic Web.” In Transactions on
Computational Science XIV, edited by Marina Gavrilova, Kenneth Tan, and Mir
Mostafavi, 6970:60–101. Special Issue on Voronoi Diagrams and Delaunay Triangulation.
Springer, 2011. https://doi.org/10.1007/978-3-642-25249-5_3.'
ieee: 'R. Van De Weygaert et al., “Alpha, Betti and the Megaparsec Universe:
On the topology of the Cosmic Web,” in Transactions on Computational Science
XIV, vol. 6970, M. Gavrilova, K. Tan, and M. Mostafavi, Eds. Springer, 2011,
pp. 60–101.'
ista: 'Van De Weygaert R, Vegter G, Edelsbrunner H, Jones B, Pranav P, Park C, Hellwing
W, Eldering B, Kruithof N, Bos P, Hidding J, Feldbrugge J, Ten Have E, Van Engelen
M, Caroli M, Teillaud M. 2011.Alpha, Betti and the Megaparsec Universe: On the
topology of the Cosmic Web. In: Transactions on Computational Science XIV. LNCS,
vol. 6970, 60–101.'
mla: 'Van De Weygaert, Rien, et al. “Alpha, Betti and the Megaparsec Universe: On
the Topology of the Cosmic Web.” Transactions on Computational Science XIV,
edited by Marina Gavrilova et al., vol. 6970, Springer, 2011, pp. 60–101, doi:10.1007/978-3-642-25249-5_3.'
short: R. Van De Weygaert, G. Vegter, H. Edelsbrunner, B. Jones, P. Pranav, C. Park,
W. Hellwing, B. Eldering, N. Kruithof, P. Bos, J. Hidding, J. Feldbrugge, E. Ten
Have, M. Van Engelen, M. Caroli, M. Teillaud, in:, M. Gavrilova, K. Tan, M. Mostafavi
(Eds.), Transactions on Computational Science XIV, Springer, 2011, pp. 60–101.
date_created: 2018-12-11T12:02:44Z
date_published: 2011-11-09T00:00:00Z
date_updated: 2021-01-12T07:42:44Z
day: '09'
department:
- _id: HeEd
doi: 10.1007/978-3-642-25249-5_3
editor:
- first_name: Marina
full_name: Gavrilova, Marina
last_name: Gavrilova
- first_name: Kenneth
full_name: Tan, Kenneth
last_name: Tan
- first_name: Mir
full_name: Mostafavi, Mir
last_name: Mostafavi
external_id:
arxiv:
- '1306.3640'
intvolume: ' 6970'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1306.3640
month: '11'
oa: 1
oa_version: Preprint
page: 60 - 101
publication: Transactions on Computational Science XIV
publication_status: published
publisher: Springer
publist_id: '3295'
quality_controlled: '1'
scopus_import: 1
series_title: Special Issue on Voronoi Diagrams and Delaunay Triangulation
status: public
title: 'Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web'
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6970
year: '2011'
...
---
_id: '3329'
abstract:
- lang: eng
text: 'We consider the offset-deconstruction problem: Given a polygonal shape Q
with n vertices, can it be expressed, up to a tolerance µ in Hausdorff distance,
as the Minkowski sum of another polygonal shape P with a disk of fixed radius?
If it does, we also seek a preferably simple-looking solution shape P; then, P''s
offset constitutes an accurate, vertex-reduced, and smoothened approximation of
Q. We give an O(n log n)-time exact decision algorithm that handles any polygonal
shape, assuming the real-RAM model of computation. An alternative algorithm, based
purely on rational arithmetic, answers the same deconstruction problem, up to
an uncertainty parameter, and its running time depends on the parameter δ (in
addition to the other input parameters: n, δ and the radius of the disk). If the
input shape is found to be approximable, the rational-arithmetic algorithm also
computes an approximate solution shape for the problem. For convex shapes, the
complexity of the exact decision algorithm drops to O(n), which is also the time
required to compute a solution shape P with at most one more vertex than a vertex-minimal
one. Our study is motivated by applications from two different domains. However,
since the offset operation has numerous uses, we anticipate that the reverse question
that we study here will be still more broadly applicable. We present results obtained
with our implementation of the rational-arithmetic algorithm.'
author:
- first_name: Eric
full_name: Berberich, Eric
last_name: Berberich
- first_name: Dan
full_name: Halperin, Dan
last_name: Halperin
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
- first_name: Roza
full_name: Pogalnikova, Roza
last_name: Pogalnikova
citation:
ama: 'Berberich E, Halperin D, Kerber M, Pogalnikova R. Deconstructing approximate
offsets. In: Proceedings of the Twenty-Seventh Annual Symposium on Computational
Geometry. ACM; 2011:187-196. doi:10.1145/1998196.1998225'
apa: 'Berberich, E., Halperin, D., Kerber, M., & Pogalnikova, R. (2011). Deconstructing
approximate offsets. In Proceedings of the twenty-seventh annual symposium
on Computational geometry (pp. 187–196). Paris, France: ACM. https://doi.org/10.1145/1998196.1998225'
chicago: Berberich, Eric, Dan Halperin, Michael Kerber, and Roza Pogalnikova. “Deconstructing
Approximate Offsets.” In Proceedings of the Twenty-Seventh Annual Symposium
on Computational Geometry, 187–96. ACM, 2011. https://doi.org/10.1145/1998196.1998225.
ieee: E. Berberich, D. Halperin, M. Kerber, and R. Pogalnikova, “Deconstructing
approximate offsets,” in Proceedings of the twenty-seventh annual symposium
on Computational geometry, Paris, France, 2011, pp. 187–196.
ista: 'Berberich E, Halperin D, Kerber M, Pogalnikova R. 2011. Deconstructing approximate
offsets. Proceedings of the twenty-seventh annual symposium on Computational geometry.
SCG: Symposium on Computational Geometry, 187–196.'
mla: Berberich, Eric, et al. “Deconstructing Approximate Offsets.” Proceedings
of the Twenty-Seventh Annual Symposium on Computational Geometry, ACM, 2011,
pp. 187–96, doi:10.1145/1998196.1998225.
short: E. Berberich, D. Halperin, M. Kerber, R. Pogalnikova, in:, Proceedings of
the Twenty-Seventh Annual Symposium on Computational Geometry, ACM, 2011, pp.
187–196.
conference:
end_date: 2011-06-15
location: Paris, France
name: 'SCG: Symposium on Computational Geometry'
start_date: 2011-06-13
date_created: 2018-12-11T12:02:42Z
date_published: 2011-06-13T00:00:00Z
date_updated: 2023-02-23T11:12:57Z
day: '13'
department:
- _id: HeEd
doi: 10.1145/1998196.1998225
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1109.2158
month: '06'
oa: 1
oa_version: Preprint
page: 187 - 196
publication: Proceedings of the twenty-seventh annual symposium on Computational geometry
publication_status: published
publisher: ACM
publist_id: '3306'
quality_controlled: '1'
related_material:
record:
- id: '3115'
relation: later_version
status: public
scopus_import: 1
status: public
title: Deconstructing approximate offsets
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3332'
abstract:
- lang: eng
text: Given an algebraic hypersurface O in ℝd, how many simplices are necessary
for a simplicial complex isotopic to O? We address this problem and the variant
where all vertices of the complex must lie on O. We give asymptotically tight
worst-case bounds for algebraic plane curves. Our results gradually improve known
bounds in higher dimensions; however, the question for tight bounds remains unsolved
for d ≥ 3.
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
- first_name: Michael
full_name: Sagraloff, Michael
last_name: Sagraloff
citation:
ama: Kerber M, Sagraloff M. A note on the complexity of real algebraic hypersurfaces.
Graphs and Combinatorics. 2011;27(3):419-430. doi:10.1007/s00373-011-1020-7
apa: Kerber, M., & Sagraloff, M. (2011). A note on the complexity of real algebraic
hypersurfaces. Graphs and Combinatorics. Springer. https://doi.org/10.1007/s00373-011-1020-7
chicago: Kerber, Michael, and Michael Sagraloff. “A Note on the Complexity of Real
Algebraic Hypersurfaces.” Graphs and Combinatorics. Springer, 2011. https://doi.org/10.1007/s00373-011-1020-7.
ieee: M. Kerber and M. Sagraloff, “A note on the complexity of real algebraic hypersurfaces,”
Graphs and Combinatorics, vol. 27, no. 3. Springer, pp. 419–430, 2011.
ista: Kerber M, Sagraloff M. 2011. A note on the complexity of real algebraic hypersurfaces.
Graphs and Combinatorics. 27(3), 419–430.
mla: Kerber, Michael, and Michael Sagraloff. “A Note on the Complexity of Real Algebraic
Hypersurfaces.” Graphs and Combinatorics, vol. 27, no. 3, Springer, 2011,
pp. 419–30, doi:10.1007/s00373-011-1020-7.
short: M. Kerber, M. Sagraloff, Graphs and Combinatorics 27 (2011) 419–430.
date_created: 2018-12-11T12:02:43Z
date_published: 2011-03-17T00:00:00Z
date_updated: 2021-01-12T07:42:43Z
day: '17'
ddc:
- '500'
department:
- _id: HeEd
doi: 10.1007/s00373-011-1020-7
file:
- access_level: open_access
checksum: a63a1e3e885dcc68f1e3dea68dfbe213
content_type: application/pdf
creator: dernst
date_created: 2020-05-19T16:11:36Z
date_updated: 2020-07-14T12:46:08Z
file_id: '7869'
file_name: 2011_GraphsCombi_Kerber.pdf
file_size: 143976
relation: main_file
file_date_updated: 2020-07-14T12:46:08Z
has_accepted_license: '1'
intvolume: ' 27'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 419 - 430
publication: Graphs and Combinatorics
publication_status: published
publisher: Springer
publist_id: '3301'
quality_controlled: '1'
scopus_import: 1
status: public
title: A note on the complexity of real algebraic hypersurfaces
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2011'
...
---
_id: '3330'
abstract:
- lang: eng
text: We consider the problem of approximating all real roots of a square-free polynomial
f. Given isolating intervals, our algorithm refines each of them to a width at
most 2-L, that is, each of the roots is approximated to L bits after the binary
point. Our method provides a certified answer for arbitrary real polynomials,
only requiring finite approximations of the polynomial coefficient and choosing
a suitable working precision adaptively. In this way, we get a correct algorithm
that is simple to implement and practically efficient. Our algorithm uses the
quadratic interval refinement method; we adapt that method to be able to cope
with inaccuracies when evaluating f, without sacrificing its quadratic convergence
behavior. We prove a bound on the bit complexity of our algorithm in terms of
degree, coefficient size and discriminant. Our bound improves previous work on
integer polynomials by a factor of deg f and essentially matches best known theoretical
bounds on root approximation which are obtained by very sophisticated algorithms.
article_processing_charge: No
author:
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
- first_name: Michael
full_name: Sagraloff, Michael
last_name: Sagraloff
citation:
ama: 'Kerber M, Sagraloff M. Root refinement for real polynomials. In: Springer;
2011:209-216. doi:10.1145/1993886.1993920'
apa: 'Kerber, M., & Sagraloff, M. (2011). Root refinement for real polynomials
(pp. 209–216). Presented at the ISSAC: International Symposium on Symbolic and
Algebraic Computation, California, USA: Springer. https://doi.org/10.1145/1993886.1993920'
chicago: Kerber, Michael, and Michael Sagraloff. “Root Refinement for Real Polynomials,”
209–16. Springer, 2011. https://doi.org/10.1145/1993886.1993920.
ieee: 'M. Kerber and M. Sagraloff, “Root refinement for real polynomials,” presented
at the ISSAC: International Symposium on Symbolic and Algebraic Computation, California,
USA, 2011, pp. 209–216.'
ista: 'Kerber M, Sagraloff M. 2011. Root refinement for real polynomials. ISSAC:
International Symposium on Symbolic and Algebraic Computation, 209–216.'
mla: Kerber, Michael, and Michael Sagraloff. Root Refinement for Real Polynomials.
Springer, 2011, pp. 209–16, doi:10.1145/1993886.1993920.
short: M. Kerber, M. Sagraloff, in:, Springer, 2011, pp. 209–216.
conference:
end_date: 2011-06-11
location: California, USA
name: 'ISSAC: International Symposium on Symbolic and Algebraic Computation'
start_date: 2011-06-08
date_created: 2018-12-11T12:02:43Z
date_published: 2011-06-08T00:00:00Z
date_updated: 2021-01-12T07:42:42Z
day: '08'
department:
- _id: HeEd
doi: 10.1145/1993886.1993920
external_id:
arxiv:
- '1104.1362'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1104.1362
month: '06'
oa: 1
oa_version: Preprint
page: 209 - 216
publication_status: published
publisher: Springer
publist_id: '3304'
quality_controlled: '1'
scopus_import: 1
status: public
title: Root refinement for real polynomials
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3328'
abstract:
- lang: eng
text: 'We report on a generic uni- and bivariate algebraic kernel that is publicly
available with CGAL 3.7. It comprises complete, correct, though efficient state-of-the-art
implementations on polynomials, roots of polynomial systems, and the support to
analyze algebraic curves defined by bivariate polynomials. The kernel design is
generic, that is, various number types and substeps can be exchanged. It is accompanied
with a ready-to-use interface to enable arrangements induced by algebraic curves,
that have already been used as basis for various geometric applications, as arrangements
on Dupin cyclides or the triangulation of algebraic surfaces. We present two novel
applications: arrangements of rotated algebraic curves and Boolean set operations
on polygons bounded by segments of algebraic curves. We also provide experiments
showing that our general implementation is competitive and even often clearly
outperforms existing implementations that are explicitly tailored for specific
types of non-linear curves that are available in CGAL.'
article_processing_charge: No
author:
- first_name: Eric
full_name: Berberich, Eric
last_name: Berberich
- first_name: Michael
full_name: Hemmer, Michael
last_name: Hemmer
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
citation:
ama: 'Berberich E, Hemmer M, Kerber M. A generic algebraic kernel for non linear
geometric applications. In: ACM; 2011:179-186. doi:10.1145/1998196.1998224'
apa: 'Berberich, E., Hemmer, M., & Kerber, M. (2011). A generic algebraic kernel
for non linear geometric applications (pp. 179–186). Presented at the SCG: Symposium
on Computational Geometry, Paris, France: ACM. https://doi.org/10.1145/1998196.1998224'
chicago: Berberich, Eric, Michael Hemmer, and Michael Kerber. “A Generic Algebraic
Kernel for Non Linear Geometric Applications,” 179–86. ACM, 2011. https://doi.org/10.1145/1998196.1998224.
ieee: 'E. Berberich, M. Hemmer, and M. Kerber, “A generic algebraic kernel for non
linear geometric applications,” presented at the SCG: Symposium on Computational
Geometry, Paris, France, 2011, pp. 179–186.'
ista: 'Berberich E, Hemmer M, Kerber M. 2011. A generic algebraic kernel for non
linear geometric applications. SCG: Symposium on Computational Geometry, 179–186.'
mla: Berberich, Eric, et al. A Generic Algebraic Kernel for Non Linear Geometric
Applications. ACM, 2011, pp. 179–86, doi:10.1145/1998196.1998224.
short: E. Berberich, M. Hemmer, M. Kerber, in:, ACM, 2011, pp. 179–186.
conference:
end_date: 2011-06-15
location: Paris, France
name: 'SCG: Symposium on Computational Geometry'
start_date: 2011-06-13
date_created: 2018-12-11T12:02:42Z
date_published: 2011-06-13T00:00:00Z
date_updated: 2021-01-12T07:42:41Z
day: '13'
department:
- _id: HeEd
doi: 10.1145/1998196.1998224
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.inria.fr/inria-00480031/file/RR-7274.pdf
month: '06'
oa: 1
oa_version: Published Version
page: 179 - 186
publication_status: published
publisher: ACM
publist_id: '3307'
quality_controlled: '1'
scopus_import: 1
status: public
title: A generic algebraic kernel for non linear geometric applications
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3334'
article_type: letter_note
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: János
full_name: Pach, János
last_name: Pach
- first_name: Günter
full_name: Ziegler, Günter
last_name: Ziegler
citation:
ama: Edelsbrunner H, Pach J, Ziegler G. Letter from the new editors-in-chief. Discrete
& Computational Geometry. 2011;45(1):1-2. doi:10.1007/s00454-010-9313-9
apa: Edelsbrunner, H., Pach, J., & Ziegler, G. (2011). Letter from the new editors-in-chief.
Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-010-9313-9
chicago: Edelsbrunner, Herbert, János Pach, and Günter Ziegler. “Letter from the
New Editors-in-Chief.” Discrete & Computational Geometry. Springer,
2011. https://doi.org/10.1007/s00454-010-9313-9.
ieee: H. Edelsbrunner, J. Pach, and G. Ziegler, “Letter from the new editors-in-chief,”
Discrete & Computational Geometry, vol. 45, no. 1. Springer, pp. 1–2,
2011.
ista: Edelsbrunner H, Pach J, Ziegler G. 2011. Letter from the new editors-in-chief.
Discrete & Computational Geometry. 45(1), 1–2.
mla: Edelsbrunner, Herbert, et al. “Letter from the New Editors-in-Chief.” Discrete
& Computational Geometry, vol. 45, no. 1, Springer, 2011, pp. 1–2, doi:10.1007/s00454-010-9313-9.
short: H. Edelsbrunner, J. Pach, G. Ziegler, Discrete & Computational Geometry
45 (2011) 1–2.
date_created: 2018-12-11T12:02:44Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:44Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s00454-010-9313-9
intvolume: ' 45'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 1 - 2
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '3297'
quality_controlled: '1'
scopus_import: 1
status: public
title: Letter from the new editors-in-chief
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2011'
...
---
_id: '3353'
abstract:
- lang: eng
text: 'Compositional theories are crucial when designing large and complex systems
from smaller components. In this work we propose such a theory for synchronous
concurrent systems. Our approach follows so-called interface theories, which use
game-theoretic interpretations of composition and refinement. These are appropriate
for systems with distinct inputs and outputs, and explicit conditions on inputs
that must be enforced during composition. Our interfaces model systems that execute
in an infinite sequence of synchronous rounds. At each round, a contract must
be satisfied. The contract is simply a relation specifying the set of valid input/output
pairs. Interfaces can be composed by parallel, serial or feedback composition.
A refinement relation between interfaces is defined, and shown to have two main
properties: (1) it is preserved by composition, and (2) it is equivalent to substitutability,
namely, the ability to replace an interface by another one in any context. Shared
refinement and abstraction operators, corresponding to greatest lower and least
upper bounds with respect to refinement, are also defined. Input-complete interfaces,
that impose no restrictions on inputs, and deterministic interfaces, that produce
a unique output for any legal input, are discussed as special cases, and an interesting
duality between the two classes is exposed. A number of illustrative examples
are provided, as well as algorithms to compute compositions, check refinement,
and so on, for finite-state interfaces.'
article_number: '14'
author:
- first_name: Stavros
full_name: Tripakis, Stavros
last_name: Tripakis
- first_name: Ben
full_name: Lickly, Ben
last_name: Lickly
- 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: Edward
full_name: Lee, Edward
last_name: Lee
citation:
ama: Tripakis S, Lickly B, Henzinger TA, Lee E. A theory of synchronous relational
interfaces. ACM Transactions on Programming Languages and Systems (TOPLAS).
2011;33(4). doi:10.1145/1985342.1985345
apa: Tripakis, S., Lickly, B., Henzinger, T. A., & Lee, E. (2011). A theory
of synchronous relational interfaces. ACM Transactions on Programming Languages
and Systems (TOPLAS). ACM. https://doi.org/10.1145/1985342.1985345
chicago: Tripakis, Stavros, Ben Lickly, Thomas A Henzinger, and Edward Lee. “A Theory
of Synchronous Relational Interfaces.” ACM Transactions on Programming Languages
and Systems (TOPLAS). ACM, 2011. https://doi.org/10.1145/1985342.1985345.
ieee: S. Tripakis, B. Lickly, T. A. Henzinger, and E. Lee, “A theory of synchronous
relational interfaces,” ACM Transactions on Programming Languages and Systems
(TOPLAS), vol. 33, no. 4. ACM, 2011.
ista: Tripakis S, Lickly B, Henzinger TA, Lee E. 2011. A theory of synchronous relational
interfaces. ACM Transactions on Programming Languages and Systems (TOPLAS). 33(4),
14.
mla: Tripakis, Stavros, et al. “A Theory of Synchronous Relational Interfaces.”
ACM Transactions on Programming Languages and Systems (TOPLAS), vol. 33,
no. 4, 14, ACM, 2011, doi:10.1145/1985342.1985345.
short: S. Tripakis, B. Lickly, T.A. Henzinger, E. Lee, ACM Transactions on Programming
Languages and Systems (TOPLAS) 33 (2011).
date_created: 2018-12-11T12:02:51Z
date_published: 2011-07-01T00:00:00Z
date_updated: 2021-01-12T07:42:52Z
day: '01'
ddc:
- '000'
- '005'
department:
- _id: ToHe
doi: 10.1145/1985342.1985345
ec_funded: 1
file:
- access_level: open_access
checksum: 5d44a8aa81e33210649beae507602138
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:45Z
date_updated: 2020-07-14T12:46:09Z
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file_name: IST-2012-85-v1+1_A_theory_of_synchronous_relational_interfaces.pdf
file_size: 775662
relation: main_file
file_date_updated: 2020-07-14T12:46:09Z
has_accepted_license: '1'
intvolume: ' 33'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication: ACM Transactions on Programming Languages and Systems (TOPLAS)
publication_status: published
publisher: ACM
publist_id: '3263'
pubrep_id: '85'
quality_controlled: '1'
scopus_import: 1
status: public
title: A theory of synchronous relational interfaces
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2011'
...
---
_id: '3355'
abstract:
- lang: eng
text: Byzantine Fault Tolerant (BFT) protocols aim to improve the reliability of
distributed systems. They enable systems to tolerate arbitrary failures in a bounded
number of nodes. BFT protocols are usually proven correct for certain safety and
liveness properties. However, recent studies have shown that the performance of
state-of-the-art BFT protocols decreases drastically in the presence of even a
single malicious node. This motivates a formal quantitative analysis of BFT protocols
to investigate their performance characteristics under different scenarios. We
present HyPerf, a new hybrid methodology based on model checking and simulation
techniques for evaluating the performance of BFT protocols. We build a transition
system corresponding to a BFT protocol and systematically explore the set of behaviors
allowed by the protocol. We associate certain timing information with different
operations in the protocol, like cryptographic operations and message transmission.
After an elaborate state exploration, we use the time information to evaluate
the performance characteristics of the protocol using simulation techniques. We
integrate our framework in Mace, a tool for building and verifying distributed
systems. We evaluate the performance of PBFT using our framework. We describe
two different use-cases of our methodology. For the benign operation of the protocol,
we use the time information as random variables to compute the probability distribution
of the execution times. In the presence of faults, we estimate the worst-case
performance of the protocol for various attacks that can be employed by malicious
nodes. Our results show the importance of hybrid techniques in systematically
analyzing the performance of large-scale systems.
author:
- first_name: Raluca
full_name: Halalai, Raluca
id: 584C6850-E996-11E9-805B-F01764644770
last_name: Halalai
- 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: Vasu
full_name: Singh, Vasu
id: 4DAE2708-F248-11E8-B48F-1D18A9856A87
last_name: Singh
citation:
ama: 'Halalai R, Henzinger TA, Singh V. Quantitative evaluation of BFT protocols.
In: IEEE; 2011:255-264. doi:10.1109/QEST.2011.40'
apa: 'Halalai, R., Henzinger, T. A., & Singh, V. (2011). Quantitative evaluation
of BFT protocols (pp. 255–264). Presented at the QEST: Quantitative Evaluation
of Systems, Aachen, Germany: IEEE. https://doi.org/10.1109/QEST.2011.40'
chicago: Halalai, Raluca, Thomas A Henzinger, and Vasu Singh. “Quantitative Evaluation
of BFT Protocols,” 255–64. IEEE, 2011. https://doi.org/10.1109/QEST.2011.40.
ieee: 'R. Halalai, T. A. Henzinger, and V. Singh, “Quantitative evaluation of BFT
protocols,” presented at the QEST: Quantitative Evaluation of Systems, Aachen,
Germany, 2011, pp. 255–264.'
ista: 'Halalai R, Henzinger TA, Singh V. 2011. Quantitative evaluation of BFT protocols.
QEST: Quantitative Evaluation of Systems, 255–264.'
mla: Halalai, Raluca, et al. Quantitative Evaluation of BFT Protocols. IEEE,
2011, pp. 255–64, doi:10.1109/QEST.2011.40.
short: R. Halalai, T.A. Henzinger, V. Singh, in:, IEEE, 2011, pp. 255–264.
conference:
end_date: 2011-09-08
location: Aachen, Germany
name: 'QEST: Quantitative Evaluation of Systems'
start_date: 2011-09-05
date_created: 2018-12-11T12:02:51Z
date_published: 2011-10-13T00:00:00Z
date_updated: 2021-01-12T07:42:53Z
day: '13'
ddc:
- '000'
- '004'
department:
- _id: ToHe
doi: 10.1109/QEST.2011.40
file:
- access_level: open_access
checksum: 4dc8750ab7921f51de992000b13d1b01
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:49Z
date_updated: 2020-07-14T12:46:09Z
file_id: '4648'
file_name: IST-2012-84-v1+1_Quantitative_evaluation_of_BFT_protocols.pdf
file_size: 272017
relation: main_file
file_date_updated: 2020-07-14T12:46:09Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 255 - 264
publication_status: published
publisher: IEEE
publist_id: '3260'
pubrep_id: '84'
quality_controlled: '1'
scopus_import: 1
status: public
title: Quantitative evaluation of BFT protocols
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3350'
abstract:
- lang: eng
text: A controller for a discrete game with ω-regular objectives requires attention
if, intuitively, it requires measuring the state and switching from the current
control action. Minimum attention controllers are preferable in modern shared
implementations of cyber-physical systems because they produce the least burden
on system resources such as processor time or communication bandwidth. We give
algorithms to compute minimum attention controllers for ω-regular objectives in
imperfect information discrete two-player games. We show a polynomial-time reduction
from minimum attention controller synthesis to synthesis of controllers for mean-payoff
parity objectives in games of incomplete information. This gives an optimal EXPTIME-complete
synthesis algorithm. We show that the minimum attention controller problem is
decidable for infinite state systems with finite bisimulation quotients. In particular,
the problem is decidable for timed and rectangular automata.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
citation:
ama: 'Chatterjee K, Majumdar R. Minimum attention controller synthesis for omega
regular objectives. In: Fahrenberg U, Tripakis S, eds. Vol 6919. Springer; 2011:145-159.
doi:10.1007/978-3-642-24310-3_11'
apa: 'Chatterjee, K., & Majumdar, R. (2011). Minimum attention controller synthesis
for omega regular objectives. In U. Fahrenberg & S. Tripakis (Eds.) (Vol.
6919, pp. 145–159). Presented at the FORMATS: Formal Modeling and Analysis of
Timed Systems, Aalborg, Denmark: Springer. https://doi.org/10.1007/978-3-642-24310-3_11'
chicago: Chatterjee, Krishnendu, and Ritankar Majumdar. “Minimum Attention Controller
Synthesis for Omega Regular Objectives.” edited by Uli Fahrenberg and Stavros
Tripakis, 6919:145–59. Springer, 2011. https://doi.org/10.1007/978-3-642-24310-3_11.
ieee: 'K. Chatterjee and R. Majumdar, “Minimum attention controller synthesis for
omega regular objectives,” presented at the FORMATS: Formal Modeling and Analysis
of Timed Systems, Aalborg, Denmark, 2011, vol. 6919, pp. 145–159.'
ista: 'Chatterjee K, Majumdar R. 2011. Minimum attention controller synthesis for
omega regular objectives. FORMATS: Formal Modeling and Analysis of Timed Systems,
LNCS, vol. 6919, 145–159.'
mla: Chatterjee, Krishnendu, and Ritankar Majumdar. Minimum Attention Controller
Synthesis for Omega Regular Objectives. Edited by Uli Fahrenberg and Stavros
Tripakis, vol. 6919, Springer, 2011, pp. 145–59, doi:10.1007/978-3-642-24310-3_11.
short: K. Chatterjee, R. Majumdar, in:, U. Fahrenberg, S. Tripakis (Eds.), Springer,
2011, pp. 145–159.
conference:
end_date: 2011-09-23
location: Aalborg, Denmark
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
start_date: 2011-09-21
date_created: 2018-12-11T12:02:49Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:51Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-642-24310-3_11
editor:
- first_name: Uli
full_name: Fahrenberg, Uli
last_name: Fahrenberg
- first_name: Stavros
full_name: Tripakis, Stavros
last_name: Tripakis
intvolume: ' 6919'
language:
- iso: eng
month: '01'
oa_version: None
page: 145 - 159
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '3271'
quality_controlled: '1'
scopus_import: 1
status: public
title: Minimum attention controller synthesis for omega regular objectives
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6919
year: '2011'
...
---
_id: '3351'
abstract:
- lang: eng
text: In two-player games on graph, the players construct an infinite path through
the game graph and get a reward computed by a payoff function over infinite paths.
Over weighted graphs, the typical and most studied payoff functions compute the
limit-average or the discounted sum of the rewards along the path. Besides their
simple definition, these two payoff functions enjoy the property that memoryless
optimal strategies always exist. In an attempt to construct other simple payoff
functions, we define a class of payoff functions which compute an (infinite) weighted
average of the rewards. This new class contains both the limit-average and the
discounted sum functions, and we show that they are the only members of this class
which induce memoryless optimal strategies, showing that there is essentially
no other simple payoff functions.
alternative_title:
- LNCS
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: Rohit
full_name: Singh, Rohit
last_name: Singh
citation:
ama: 'Chatterjee K, Doyen L, Singh R. On memoryless quantitative objectives. In:
Owe O, Steffen M, Telle JA, eds. Vol 6914. Springer; 2011:148-159. doi:10.1007/978-3-642-22953-4_13'
apa: 'Chatterjee, K., Doyen, L., & Singh, R. (2011). On memoryless quantitative
objectives. In O. Owe, M. Steffen, & J. A. Telle (Eds.) (Vol. 6914, pp. 148–159).
Presented at the FCT: Fundamentals of Computation Theory, Oslo, Norway: Springer.
https://doi.org/10.1007/978-3-642-22953-4_13'
chicago: Chatterjee, Krishnendu, Laurent Doyen, and Rohit Singh. “On Memoryless
Quantitative Objectives.” edited by Olaf Owe, Martin Steffen, and Jan Arne Telle,
6914:148–59. Springer, 2011. https://doi.org/10.1007/978-3-642-22953-4_13.
ieee: 'K. Chatterjee, L. Doyen, and R. Singh, “On memoryless quantitative objectives,”
presented at the FCT: Fundamentals of Computation Theory, Oslo, Norway, 2011,
vol. 6914, pp. 148–159.'
ista: 'Chatterjee K, Doyen L, Singh R. 2011. On memoryless quantitative objectives.
FCT: Fundamentals of Computation Theory, LNCS, vol. 6914, 148–159.'
mla: Chatterjee, Krishnendu, et al. On Memoryless Quantitative Objectives.
Edited by Olaf Owe et al., vol. 6914, Springer, 2011, pp. 148–59, doi:10.1007/978-3-642-22953-4_13.
short: K. Chatterjee, L. Doyen, R. Singh, in:, O. Owe, M. Steffen, J.A. Telle (Eds.),
Springer, 2011, pp. 148–159.
conference:
end_date: 2011-08-25
location: Oslo, Norway
name: 'FCT: Fundamentals of Computation Theory'
start_date: 2011-08-22
date_created: 2018-12-11T12:02:50Z
date_published: 2011-04-16T00:00:00Z
date_updated: 2021-01-12T07:42:52Z
day: '16'
department:
- _id: KrCh
doi: 10.1007/978-3-642-22953-4_13
editor:
- first_name: Olaf
full_name: Owe, Olaf
last_name: Owe
- first_name: Martin
full_name: Steffen, Martin
last_name: Steffen
- first_name: Jan Arne
full_name: Telle, Jan Arne
last_name: Telle
intvolume: ' 6914'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1104.3211
month: '04'
oa: 1
oa_version: Submitted Version
page: 148 - 159
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '3270'
quality_controlled: '1'
scopus_import: 1
status: public
title: On memoryless quantitative objectives
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6914
year: '2011'
...
---
_id: '3354'
abstract:
- lang: eng
text: 'We consider two-player games played on a finite state space for an infinite
number of rounds. The games are concurrent: in each round, the two players (player
1 and player 2) choose their moves independently and simultaneously; the current
state and the two moves determine the successor state. We consider ω-regular winning
conditions specified as parity objectives. Both players are allowed to use randomization
when choosing their moves. We study the computation of the limit-winning set of
states, consisting of the states where the sup-inf value of the game for player
1 is 1: in other words, a state is limit-winning if player 1 can ensure a probability
of winning arbitrarily close to 1. We show that the limit-winning set can be computed
in O(n2d+2) time, where n is the size of the game structure and 2d is the number
of priorities (or colors). The membership problem of whether a state belongs to
the limit-winning set can be decided in NP ∩ coNP. While this complexity is the
same as for the simpler class of turn-based parity games, where in each state
only one of the two players has a choice of moves, our algorithms are considerably
more involved than those for turn-based games. This is because concurrent games
do not satisfy two of the most fundamental properties of turn-based parity games.
First, in concurrent games limit-winning strategies require randomization; and
second, they require infinite memory.'
article_number: '28'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Luca
full_name: De Alfaro, Luca
last_name: De Alfaro
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Chatterjee K, De Alfaro L, Henzinger TA. Qualitative concurrent parity games.
ACM Transactions on Computational Logic (TOCL). 2011;12(4). doi:10.1145/1970398.1970404
apa: Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2011). Qualitative concurrent
parity games. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/1970398.1970404
chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Qualitative
Concurrent Parity Games.” ACM Transactions on Computational Logic (TOCL).
ACM, 2011. https://doi.org/10.1145/1970398.1970404.
ieee: K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Qualitative concurrent
parity games,” ACM Transactions on Computational Logic (TOCL), vol. 12,
no. 4. ACM, 2011.
ista: Chatterjee K, De Alfaro L, Henzinger TA. 2011. Qualitative concurrent parity
games. ACM Transactions on Computational Logic (TOCL). 12(4), 28.
mla: Chatterjee, Krishnendu, et al. “Qualitative Concurrent Parity Games.” ACM
Transactions on Computational Logic (TOCL), vol. 12, no. 4, 28, ACM, 2011,
doi:10.1145/1970398.1970404.
short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, ACM Transactions on Computational
Logic (TOCL) 12 (2011).
date_created: 2018-12-11T12:02:51Z
date_published: 2011-07-04T00:00:00Z
date_updated: 2023-02-23T10:26:18Z
day: '04'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1145/1970398.1970404
intvolume: ' 12'
issue: '4'
language:
- iso: eng
month: '07'
oa_version: None
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: ACM Transactions on Computational Logic (TOCL)
publication_status: published
publisher: ACM
publist_id: '3262'
quality_controlled: '1'
related_material:
record:
- id: '2054'
relation: later_version
status: public
scopus_import: 1
status: public
title: Qualitative concurrent parity games
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2011'
...
---
_id: '3349'
abstract:
- lang: eng
text: 'Games on graphs provide a natural model for reactive non-terminating systems.
In such games, the interaction of two players on an arena results in an infinite
path that describes a run of the system. Different settings are used to model
various open systems in computer science, as for instance turn-based or concurrent
moves, and deterministic or stochastic transitions. In this paper, we are interested
in turn-based games, and specifically in deterministic parity games and stochastic
reachability games (also known as simple stochastic games). We present a simple,
direct and efficient reduction from deterministic parity games to simple stochastic
games: it yields an arena whose size is linear up to a logarithmic factor in size
of the original arena.'
alternative_title:
- EPTCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Nathanaël
full_name: Fijalkow, Nathanaël
last_name: Fijalkow
citation:
ama: 'Chatterjee K, Fijalkow N. A reduction from parity games to simple stochastic
games. In: Vol 54. EPTCS; 2011:74-86. doi:10.4204/EPTCS.54.6'
apa: 'Chatterjee, K., & Fijalkow, N. (2011). A reduction from parity games to
simple stochastic games (Vol. 54, pp. 74–86). Presented at the GandALF: Games,
Automata, Logic, and Formal Verification, Minori, Italy: EPTCS. https://doi.org/10.4204/EPTCS.54.6'
chicago: Chatterjee, Krishnendu, and Nathanaël Fijalkow. “A Reduction from Parity
Games to Simple Stochastic Games,” 54:74–86. EPTCS, 2011. https://doi.org/10.4204/EPTCS.54.6.
ieee: 'K. Chatterjee and N. Fijalkow, “A reduction from parity games to simple stochastic
games,” presented at the GandALF: Games, Automata, Logic, and Formal Verification,
Minori, Italy, 2011, vol. 54, pp. 74–86.'
ista: 'Chatterjee K, Fijalkow N. 2011. A reduction from parity games to simple stochastic
games. GandALF: Games, Automata, Logic, and Formal Verification, EPTCS, vol. 54,
74–86.'
mla: Chatterjee, Krishnendu, and Nathanaël Fijalkow. A Reduction from Parity
Games to Simple Stochastic Games. Vol. 54, EPTCS, 2011, pp. 74–86, doi:10.4204/EPTCS.54.6.
short: K. Chatterjee, N. Fijalkow, in:, EPTCS, 2011, pp. 74–86.
conference:
end_date: 2011-06-17
location: Minori, Italy
name: 'GandALF: Games, Automata, Logic, and Formal Verification'
start_date: 2011-06-15
date_created: 2018-12-11T12:02:49Z
date_published: 2011-06-04T00:00:00Z
date_updated: 2021-01-12T07:42:51Z
day: '04'
department:
- _id: KrCh
doi: 10.4204/EPTCS.54.6
intvolume: ' 54'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1106.1232
month: '06'
oa: 1
oa_version: Submitted Version
page: 74 - 86
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: EPTCS
publist_id: '3272'
scopus_import: 1
status: public
title: A reduction from parity games to simple stochastic games
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2011'
...
---
_id: '335'
abstract:
- lang: eng
text: 'Recently reported synthetic routes for the production of hollow nanoparticles
have stimulated significant interest for the possibilities this novel geometry
offers. While advantageous properties have been found and innovative applications
have been proposed, the development of the full potential of these new nanostructures
is still strongly tied to the extent of control that can be accomplished over
their characteristics (e.g., composition, size, shell thickness, and nanocrystalline
structure). In the present work, we investigate the means and limits of control
over these parameters that can be obtained by the Kirkendall effect synthetic
route on cadmium chalcogenide nanocrystalline shells. We demonstrate that the
selection of the reactants and oxidation conditions allows some extent of control
of the nanocrystalline structure and thickness of the shell. However, the tuning
range is limited by the intrinsic restrictions of the synthetic procedure and
by the dependence of the particle geometry on the same reaction conditions. Thus,
we further explore the range of control over the shell parameters that can be
accomplished through post-synthesis processes, such as chemical etching and thermal
annealing. '
article_processing_charge: No
article_type: original
author:
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Jiandong
full_name: Fan, Jiandong
last_name: Fan
- first_name: Wenhua
full_name: Li, Wenhua
last_name: Li
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Raquel
full_name: Nafria, Raquel
last_name: Nafria
- first_name: Alex
full_name: Carrete, Alex
last_name: Carrete
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Ibáñez M, Fan J, Li W, et al. Means and limits of control of the shell parameters
in hollow nanoparticles obtained by the Kirkendall effect. Chemistry of Materials.
2011;23(12):3095-3104. doi:10.1021/cm2006633
apa: Ibáñez, M., Fan, J., Li, W., Cadavid, D., Nafria, R., Carrete, A., & Cabot,
A. (2011). Means and limits of control of the shell parameters in hollow nanoparticles
obtained by the Kirkendall effect. Chemistry of Materials. American Chemical
Society. https://doi.org/10.1021/cm2006633
chicago: Ibáñez, Maria, Jiandong Fan, Wenhua Li, Doris Cadavid, Raquel Nafria, Alex
Carrete, and Andreu Cabot. “Means and Limits of Control of the Shell Parameters
in Hollow Nanoparticles Obtained by the Kirkendall Effect.” Chemistry of Materials.
American Chemical Society, 2011. https://doi.org/10.1021/cm2006633.
ieee: M. Ibáñez et al., “Means and limits of control of the shell parameters
in hollow nanoparticles obtained by the Kirkendall effect,” Chemistry of Materials,
vol. 23, no. 12. American Chemical Society, pp. 3095–3104, 2011.
ista: Ibáñez M, Fan J, Li W, Cadavid D, Nafria R, Carrete A, Cabot A. 2011. Means
and limits of control of the shell parameters in hollow nanoparticles obtained
by the Kirkendall effect. Chemistry of Materials. 23(12), 3095–3104.
mla: Ibáñez, Maria, et al. “Means and Limits of Control of the Shell Parameters
in Hollow Nanoparticles Obtained by the Kirkendall Effect.” Chemistry of Materials,
vol. 23, no. 12, American Chemical Society, 2011, pp. 3095–104, doi:10.1021/cm2006633.
short: M. Ibáñez, J. Fan, W. Li, D. Cadavid, R. Nafria, A. Carrete, A. Cabot, Chemistry
of Materials 23 (2011) 3095–3104.
date_created: 2018-12-11T11:45:53Z
date_published: 2011-05-24T00:00:00Z
date_updated: 2021-01-12T07:42:51Z
day: '24'
doi: 10.1021/cm2006633
extern: '1'
intvolume: ' 23'
issue: '12'
language:
- iso: eng
month: '05'
oa_version: None
page: 3095 - 3104
publication: Chemistry of Materials
publication_status: published
publisher: American Chemical Society
publist_id: '7492'
quality_controlled: '1'
status: public
title: Means and limits of control of the shell parameters in hollow nanoparticles
obtained by the Kirkendall effect
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2011'
...
---
_id: '3352'
abstract:
- lang: eng
text: Exploring the connection of biology with reactive systems to better understand
living systems.
author:
- first_name: Jasmin
full_name: Fisher, Jasmin
last_name: Fisher
- first_name: David
full_name: Harel, David
last_name: Harel
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Fisher J, Harel D, Henzinger TA. Biology as reactivity. Communications of
the ACM. 2011;54(10):72-82. doi:10.1145/2001269.2001289
apa: Fisher, J., Harel, D., & Henzinger, T. A. (2011). Biology as reactivity.
Communications of the ACM. ACM. https://doi.org/10.1145/2001269.2001289
chicago: Fisher, Jasmin, David Harel, and Thomas A Henzinger. “Biology as Reactivity.”
Communications of the ACM. ACM, 2011. https://doi.org/10.1145/2001269.2001289.
ieee: J. Fisher, D. Harel, and T. A. Henzinger, “Biology as reactivity,” Communications
of the ACM, vol. 54, no. 10. ACM, pp. 72–82, 2011.
ista: Fisher J, Harel D, Henzinger TA. 2011. Biology as reactivity. Communications
of the ACM. 54(10), 72–82.
mla: Fisher, Jasmin, et al. “Biology as Reactivity.” Communications of the ACM,
vol. 54, no. 10, ACM, 2011, pp. 72–82, doi:10.1145/2001269.2001289.
short: J. Fisher, D. Harel, T.A. Henzinger, Communications of the ACM 54 (2011)
72–82.
date_created: 2018-12-11T12:02:50Z
date_published: 2011-10-01T00:00:00Z
date_updated: 2021-01-12T07:42:52Z
day: '01'
department:
- _id: ToHe
doi: 10.1145/2001269.2001289
ec_funded: 1
intvolume: ' 54'
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 72 - 82
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication: Communications of the ACM
publication_status: published
publisher: ACM
publist_id: '3267'
quality_controlled: '1'
status: public
title: Biology as reactivity
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2011'
...
---
_id: '3362'
abstract:
- lang: eng
text: State-transition systems communicating by shared variables have been the underlying
model of choice for applications of model checking. Such formalisms, however,
have difficulty with modeling process creation or death and communication reconfigurability.
Here, we introduce “dynamic reactive modules” (DRM), a state-transition modeling
formalism that supports dynamic reconfiguration and creation/death of processes.
The resulting formalism supports two types of variables, data variables and reference
variables. Reference variables enable changing the connectivity between processes
and referring to instances of processes. We show how this new formalism supports
parallel composition and refinement through trace containment. DRM provide a natural
language for modeling (and ultimately reasoning about) biological systems and
multiple threads communicating through shared variables.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Jasmin
full_name: Fisher, Jasmin
last_name: Fisher
- 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: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Nir
full_name: Piterman, Nir
last_name: Piterman
- first_name: Anmol
full_name: Singh, Anmol
last_name: Singh
- first_name: Moshe
full_name: Vardi, Moshe
last_name: Vardi
citation:
ama: 'Fisher J, Henzinger TA, Nickovic D, Piterman N, Singh A, Vardi M. Dynamic
reactive modules. In: Vol 6901. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2011:404-418. doi:10.1007/978-3-642-23217-6_27'
apa: 'Fisher, J., Henzinger, T. A., Nickovic, D., Piterman, N., Singh, A., &
Vardi, M. (2011). Dynamic reactive modules (Vol. 6901, pp. 404–418). Presented
at the CONCUR: Concurrency Theory, Aachen, Germany: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.1007/978-3-642-23217-6_27'
chicago: Fisher, Jasmin, Thomas A Henzinger, Dejan Nickovic, Nir Piterman, Anmol
Singh, and Moshe Vardi. “Dynamic Reactive Modules,” 6901:404–18. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2011. https://doi.org/10.1007/978-3-642-23217-6_27.
ieee: 'J. Fisher, T. A. Henzinger, D. Nickovic, N. Piterman, A. Singh, and M. Vardi,
“Dynamic reactive modules,” presented at the CONCUR: Concurrency Theory, Aachen,
Germany, 2011, vol. 6901, pp. 404–418.'
ista: 'Fisher J, Henzinger TA, Nickovic D, Piterman N, Singh A, Vardi M. 2011. Dynamic
reactive modules. CONCUR: Concurrency Theory, LNCS, vol. 6901, 404–418.'
mla: Fisher, Jasmin, et al. Dynamic Reactive Modules. Vol. 6901, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2011, pp. 404–18, doi:10.1007/978-3-642-23217-6_27.
short: J. Fisher, T.A. Henzinger, D. Nickovic, N. Piterman, A. Singh, M. Vardi,
in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2011, pp. 404–418.
conference:
end_date: 2011-09-09
location: Aachen, Germany
name: 'CONCUR: Concurrency Theory'
start_date: 2011-09-06
date_created: 2018-12-11T12:02:54Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:57Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-642-23217-6_27
ec_funded: 1
file:
- access_level: open_access
checksum: 6bf2453d8e52e979ddb58d17325bad26
content_type: application/pdf
creator: dernst
date_created: 2020-05-19T16:17:48Z
date_updated: 2020-07-14T12:46:10Z
file_id: '7870'
file_name: 2011_CONCUR_Fisher.pdf
file_size: 337125
relation: main_file
file_date_updated: 2020-07-14T12:46:10Z
has_accepted_license: '1'
intvolume: ' 6901'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 404 - 418
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '3253'
quality_controlled: '1'
scopus_import: 1
status: public
title: Dynamic reactive modules
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6901
year: '2011'
...
---
_id: '3365'
abstract:
- lang: eng
text: We present the tool Quasy, a quantitative synthesis tool. Quasy takes qualitative
and quantitative specifications and automatically constructs a system that satisfies
the qualitative specification and optimizes the quantitative specification, if
such a system exists. The user can choose between a system that satisfies and
optimizes the specifications (a) under all possible environment behaviors or (b)
under the most-likely environment behaviors given as a probability distribution
on the possible input sequences. Quasy solves these two quantitative synthesis
problems by reduction to instances of 2-player games and Markov Decision Processes
(MDPs) with quantitative winning objectives. Quasy can also be seen as a game
solver for quantitative games. Most notable, it can solve lexicographic mean-payoff
games with 2 players, MDPs with mean-payoff objectives, and ergodic MDPs with
mean-payoff parity objectives.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
- first_name: Rohit
full_name: Singh, Rohit
last_name: Singh
citation:
ama: 'Chatterjee K, Henzinger TA, Jobstmann B, Singh R. QUASY: quantitative synthesis
tool. In: Vol 6605. Springer; 2011:267-271. doi:10.1007/978-3-642-19835-9_24'
apa: 'Chatterjee, K., Henzinger, T. A., Jobstmann, B., & Singh, R. (2011). QUASY:
quantitative synthesis tool (Vol. 6605, pp. 267–271). Presented at the TACAS:
Tools and Algorithms for the Construction and Analysis of Systems, Saarbrucken,
Germany: Springer. https://doi.org/10.1007/978-3-642-19835-9_24'
chicago: 'Chatterjee, Krishnendu, Thomas A Henzinger, Barbara Jobstmann, and Rohit
Singh. “QUASY: Quantitative Synthesis Tool,” 6605:267–71. Springer, 2011. https://doi.org/10.1007/978-3-642-19835-9_24.'
ieee: 'K. Chatterjee, T. A. Henzinger, B. Jobstmann, and R. Singh, “QUASY: quantitative
synthesis tool,” presented at the TACAS: Tools and Algorithms for the Construction
and Analysis of Systems, Saarbrucken, Germany, 2011, vol. 6605, pp. 267–271.'
ista: 'Chatterjee K, Henzinger TA, Jobstmann B, Singh R. 2011. QUASY: quantitative
synthesis tool. TACAS: Tools and Algorithms for the Construction and Analysis
of Systems, LNCS, vol. 6605, 267–271.'
mla: 'Chatterjee, Krishnendu, et al. QUASY: Quantitative Synthesis Tool.
Vol. 6605, Springer, 2011, pp. 267–71, doi:10.1007/978-3-642-19835-9_24.'
short: K. Chatterjee, T.A. Henzinger, B. Jobstmann, R. Singh, in:, Springer, 2011,
pp. 267–271.
conference:
end_date: 2011-04-03
location: Saarbrucken, Germany
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2011-03-26
date_created: 2018-12-11T12:02:55Z
date_published: 2011-09-29T00:00:00Z
date_updated: 2021-01-12T07:42:58Z
day: '29'
ddc:
- '000'
- '005'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-642-19835-9_24
file:
- access_level: open_access
checksum: 762e52eb296f6dbfbf2a75d98b8ebaee
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:37Z
date_updated: 2020-07-14T12:46:10Z
file_id: '5022'
file_name: IST-2012-77-v1+1_QUASY-_quantitative_synthesis_tool.pdf
file_size: 475661
relation: main_file
file_date_updated: 2020-07-14T12:46:10Z
has_accepted_license: '1'
intvolume: ' 6605'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 267 - 271
publication_status: published
publisher: Springer
publist_id: '3248'
pubrep_id: '77'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'QUASY: quantitative synthesis tool'
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6605
year: '2011'
...
---
_id: '3367'
abstract:
- lang: eng
text: In this paper, we present the first output-sensitive algorithm to compute
the persistence diagram of a filtered simplicial complex. For any Γ>0, it returns
only those homology classes with persistence at least Γ. Instead of the classical
reduction via column operations, our algorithm performs rank computations on submatrices
of the boundary matrix. For an arbitrary constant δ ∈ (0,1), the running time
is O(C(1-δ)ΓR(n)log n), where C(1-δ)Γ is the number of homology classes with persistence
at least (1-δ)Γ, n is the total number of simplices, and R(n) is the complexity
of computing the rank of an n x n matrix with O(n) nonzero entries. Depending
on the choice of the rank algorithm, this yields a deterministic O(C(1-δ)Γn2.376)
algorithm, a O(C(1-δ)Γn2.28) Las-Vegas algorithm, or a O(C(1-δ)Γn2+ε) Monte-Carlo
algorithm for an arbitrary ε>0.
article_processing_charge: No
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
citation:
ama: 'Chen C, Kerber M. An output sensitive algorithm for persistent homology. In:
ACM; 2011:207-216. doi:10.1145/1998196.1998228'
apa: 'Chen, C., & Kerber, M. (2011). An output sensitive algorithm for persistent
homology (pp. 207–216). Presented at the SoCG: Symposium on Computational Geometry,
Paris, France: ACM. https://doi.org/10.1145/1998196.1998228'
chicago: Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent
Homology,” 207–16. ACM, 2011. https://doi.org/10.1145/1998196.1998228.
ieee: 'C. Chen and M. Kerber, “An output sensitive algorithm for persistent homology,”
presented at the SoCG: Symposium on Computational Geometry, Paris, France, 2011,
pp. 207–216.'
ista: 'Chen C, Kerber M. 2011. An output sensitive algorithm for persistent homology.
SoCG: Symposium on Computational Geometry, 207–216.'
mla: Chen, Chao, and Michael Kerber. An Output Sensitive Algorithm for Persistent
Homology. ACM, 2011, pp. 207–16, doi:10.1145/1998196.1998228.
short: C. Chen, M. Kerber, in:, ACM, 2011, pp. 207–216.
conference:
end_date: 2011-06-15
location: Paris, France
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2011-06-13
date_created: 2018-12-11T12:02:56Z
date_published: 2011-06-13T00:00:00Z
date_updated: 2023-02-23T11:05:04Z
day: '13'
department:
- _id: HeEd
doi: 10.1145/1998196.1998228
language:
- iso: eng
month: '06'
oa_version: None
page: 207 - 216
publication_status: published
publisher: ACM
publist_id: '3245'
quality_controlled: '1'
related_material:
record:
- id: '2939'
relation: later_version
status: public
scopus_import: 1
status: public
title: An output sensitive algorithm for persistent homology
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3363'
abstract:
- lang: eng
text: We consider probabilistic automata on infinite words with acceptance defined
by safety, reachability, Büchi, coBüchi, and limit-average conditions. We consider
quantitative and qualitative decision problems. We present extensions and adaptations
of proofs for probabilistic finite automata and present a complete characterization
of the decidability and undecidability frontier of the quantitative and qualitative
decision problems for probabilistic automata on infinite words.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: Mathieu
full_name: Tracol, Mathieu
id: 3F54FA38-F248-11E8-B48F-1D18A9856A87
last_name: Tracol
citation:
ama: Chatterjee K, Henzinger TA, Tracol M. The decidability frontier for probabilistic
automata on infinite words.
apa: Chatterjee, K., Henzinger, T. A., & Tracol, M. (n.d.). The decidability
frontier for probabilistic automata on infinite words. ArXiv.
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Mathieu Tracol. “The Decidability
Frontier for Probabilistic Automata on Infinite Words.” ArXiv, n.d.
ieee: K. Chatterjee, T. A. Henzinger, and M. Tracol, “The decidability frontier
for probabilistic automata on infinite words.” ArXiv.
ista: Chatterjee K, Henzinger TA, Tracol M. The decidability frontier for probabilistic
automata on infinite words.
mla: Chatterjee, Krishnendu, et al. The Decidability Frontier for Probabilistic
Automata on Infinite Words. ArXiv.
short: K. Chatterjee, T.A. Henzinger, M. Tracol, (n.d.).
date_created: 2018-12-11T12:02:54Z
date_published: 2011-04-01T00:00:00Z
date_updated: 2020-01-21T13:20:24Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
ec_funded: 1
external_id:
arxiv:
- '1104.0127'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1104.0127
month: '04'
oa: 1
oa_version: Preprint
page: '19'
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
publication_status: submitted
publisher: ArXiv
publist_id: '3251'
status: public
title: The decidability frontier for probabilistic automata on infinite words
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3372'
abstract:
- lang: eng
text: Nowak et al.1 argue that inclusive fitness theory has been of little value
in explaining the natural world, and that it has led to negligible progress in
explaining the evolution of eusociality. However, we believe that their arguments
are based upon a misunderstanding of evolutionary theory and a misrepresentation
of the empirical literature. We will focus our comments on three general issues.
author:
- first_name: Patrick
full_name: Abbot, Patrick
last_name: Abbot
- first_name: Jun
full_name: Abe, Jun
last_name: Abe
- first_name: John
full_name: Alcock, John
last_name: Alcock
- first_name: Samuel
full_name: Alizon, Samuel
last_name: Alizon
- first_name: Joao
full_name: Alpedrinha, Joao
last_name: Alpedrinha
- first_name: Malte
full_name: Andersson, Malte
last_name: Andersson
- first_name: Jean
full_name: Andre, Jean
last_name: Andre
- first_name: Minus
full_name: Van Baalen, Minus
last_name: Van Baalen
- first_name: Francois
full_name: Balloux, Francois
last_name: Balloux
- first_name: Sigal
full_name: Balshine, Sigal
last_name: Balshine
- 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: Leo
full_name: Beukeboom, Leo
last_name: Beukeboom
- first_name: Jay
full_name: Biernaskie, Jay
last_name: Biernaskie
- first_name: Trine
full_name: Bilde, Trine
last_name: Bilde
- first_name: Gerald
full_name: Borgia, Gerald
last_name: Borgia
- first_name: Michael
full_name: Breed, Michael
last_name: Breed
- first_name: Sam
full_name: Brown, Sam
last_name: Brown
- first_name: Redouan
full_name: Bshary, Redouan
last_name: Bshary
- first_name: Angus
full_name: Buckling, Angus
last_name: Buckling
- first_name: Nancy
full_name: Burley, Nancy
last_name: Burley
- first_name: Max
full_name: Burton Chellew, Max
last_name: Burton Chellew
- first_name: Michael
full_name: Cant, Michael
last_name: Cant
- first_name: Michel
full_name: Chapuisat, Michel
last_name: Chapuisat
- first_name: Eric
full_name: Charnov, Eric
last_name: Charnov
- first_name: Tim
full_name: Clutton Brock, Tim
last_name: Clutton Brock
- first_name: Andrew
full_name: Cockburn, Andrew
last_name: Cockburn
- first_name: Blaine
full_name: Cole, Blaine
last_name: Cole
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
- first_name: Leda
full_name: Cosmides, Leda
last_name: Cosmides
- first_name: Iain
full_name: Couzin, Iain
last_name: Couzin
- first_name: Jerry
full_name: Coyne, Jerry
last_name: Coyne
- first_name: Scott
full_name: Creel, Scott
last_name: Creel
- first_name: Bernard
full_name: Crespi, Bernard
last_name: Crespi
- first_name: Robert
full_name: Curry, Robert
last_name: Curry
- first_name: Sasha
full_name: Dall, Sasha
last_name: Dall
- first_name: Troy
full_name: Day, Troy
last_name: Day
- first_name: Janis
full_name: Dickinson, Janis
last_name: Dickinson
- first_name: Lee
full_name: Dugatkin, Lee
last_name: Dugatkin
- first_name: Claire
full_name: El Mouden, Claire
last_name: El Mouden
- first_name: Stephen
full_name: Emlen, Stephen
last_name: Emlen
- first_name: Jay
full_name: Evans, Jay
last_name: Evans
- first_name: Regis
full_name: Ferriere, Regis
last_name: Ferriere
- first_name: Jeremy
full_name: Field, Jeremy
last_name: Field
- first_name: Susanne
full_name: Foitzik, Susanne
last_name: Foitzik
- first_name: Kevin
full_name: Foster, Kevin
last_name: Foster
- first_name: William
full_name: Foster, William
last_name: Foster
- first_name: Charles
full_name: Fox, Charles
last_name: Fox
- first_name: Juergen
full_name: Gadau, Juergen
last_name: Gadau
- first_name: Sylvain
full_name: Gandon, Sylvain
last_name: Gandon
- first_name: Andy
full_name: Gardner, Andy
last_name: Gardner
- first_name: Michael
full_name: Gardner, Michael
last_name: Gardner
- first_name: Thomas
full_name: Getty, Thomas
last_name: Getty
- first_name: Michael
full_name: Goodisman, Michael
last_name: Goodisman
- first_name: Alan
full_name: Grafen, Alan
last_name: Grafen
- first_name: Rick
full_name: Grosberg, Rick
last_name: Grosberg
- first_name: Christina
full_name: Grozinger, Christina
last_name: Grozinger
- first_name: Pierre
full_name: Gouyon, Pierre
last_name: Gouyon
- first_name: Darryl
full_name: Gwynne, Darryl
last_name: Gwynne
- first_name: Paul
full_name: Harvey, Paul
last_name: Harvey
- first_name: Ben
full_name: Hatchwell, Ben
last_name: Hatchwell
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Heikki
full_name: Helantera, Heikki
last_name: Helantera
- first_name: Ken
full_name: Helms, Ken
last_name: Helms
- first_name: Kim
full_name: Hill, Kim
last_name: Hill
- first_name: Natalie
full_name: Jiricny, Natalie
last_name: Jiricny
- first_name: Rufus
full_name: Johnstone, Rufus
last_name: Johnstone
- first_name: Alex
full_name: Kacelnik, Alex
last_name: Kacelnik
- first_name: E Toby
full_name: Kiers, E Toby
last_name: Kiers
- first_name: Hanna
full_name: Kokko, Hanna
last_name: Kokko
- first_name: Jan
full_name: Komdeur, Jan
last_name: Komdeur
- first_name: Judith
full_name: Korb, Judith
last_name: Korb
- first_name: Daniel
full_name: Kronauer, Daniel
last_name: Kronauer
- first_name: Rolf
full_name: Kümmerli, Rolf
last_name: Kümmerli
- first_name: Laurent
full_name: Lehmann, Laurent
last_name: Lehmann
- first_name: Timothy
full_name: Linksvayer, Timothy
last_name: Linksvayer
- first_name: Sébastien
full_name: Lion, Sébastien
last_name: Lion
- first_name: Bruce
full_name: Lyon, Bruce
last_name: Lyon
- first_name: James
full_name: Marshall, James
last_name: Marshall
- first_name: Richard
full_name: Mcelreath, Richard
last_name: Mcelreath
- first_name: Yannis
full_name: Michalakis, Yannis
last_name: Michalakis
- first_name: Richard
full_name: Michod, Richard
last_name: Michod
- first_name: Douglas
full_name: Mock, Douglas
last_name: Mock
- first_name: Thibaud
full_name: Monnin, Thibaud
last_name: Monnin
- first_name: Robert
full_name: Montgomerie, Robert
last_name: Montgomerie
- first_name: Allen
full_name: Moore, Allen
last_name: Moore
- first_name: Ulrich
full_name: Mueller, Ulrich
last_name: Mueller
- first_name: Ronald
full_name: Noë, Ronald
last_name: Noë
- first_name: Samir
full_name: Okasha, Samir
last_name: Okasha
- first_name: Pekka
full_name: Pamilo, Pekka
last_name: Pamilo
- first_name: Geoff
full_name: Parker, Geoff
last_name: Parker
- first_name: Jes
full_name: Pedersen, Jes
last_name: Pedersen
- first_name: Ido
full_name: Pen, Ido
last_name: Pen
- first_name: David
full_name: Pfennig, David
last_name: Pfennig
- first_name: David
full_name: Queller, David
last_name: Queller
- first_name: Daniel
full_name: Rankin, Daniel
last_name: Rankin
- first_name: Sarah
full_name: Reece, Sarah
last_name: Reece
- first_name: Hudson
full_name: Reeve, Hudson
last_name: Reeve
- first_name: Max
full_name: Reuter, Max
last_name: Reuter
- first_name: Gilbert
full_name: Roberts, Gilbert
last_name: Roberts
- first_name: Simon
full_name: Robson, Simon
last_name: Robson
- first_name: Denis
full_name: Roze, Denis
last_name: Roze
- first_name: Francois
full_name: Rousset, Francois
last_name: Rousset
- first_name: Olav
full_name: Rueppell, Olav
last_name: Rueppell
- first_name: Joel
full_name: Sachs, Joel
last_name: Sachs
- first_name: Lorenzo
full_name: Santorelli, Lorenzo
last_name: Santorelli
- first_name: Paul
full_name: Schmid Hempel, Paul
last_name: Schmid Hempel
- first_name: Michael
full_name: Schwarz, Michael
last_name: Schwarz
- first_name: Tom
full_name: Scott Phillips, Tom
last_name: Scott Phillips
- first_name: Janet
full_name: Shellmann Sherman, Janet
last_name: Shellmann Sherman
- first_name: Paul
full_name: Sherman, Paul
last_name: Sherman
- first_name: David
full_name: Shuker, David
last_name: Shuker
- first_name: Jeff
full_name: Smith, Jeff
last_name: Smith
- first_name: Joseph
full_name: Spagna, Joseph
last_name: Spagna
- first_name: Beverly
full_name: Strassmann, Beverly
last_name: Strassmann
- first_name: Andrew
full_name: Suarez, Andrew
last_name: Suarez
- first_name: Liselotte
full_name: Sundström, Liselotte
last_name: Sundström
- first_name: Michael
full_name: Taborsky, Michael
last_name: Taborsky
- first_name: Peter
full_name: Taylor, Peter
last_name: Taylor
- first_name: Graham
full_name: Thompson, Graham
last_name: Thompson
- first_name: John
full_name: Tooby, John
last_name: Tooby
- first_name: Neil
full_name: Tsutsui, Neil
last_name: Tsutsui
- first_name: Kazuki
full_name: Tsuji, Kazuki
last_name: Tsuji
- first_name: Stefano
full_name: Turillazzi, Stefano
last_name: Turillazzi
- first_name: Francisco
full_name: Úbeda, Francisco
last_name: Úbeda
- first_name: Edward
full_name: Vargo, Edward
last_name: Vargo
- first_name: Bernard
full_name: Voelkl, Bernard
last_name: Voelkl
- first_name: Tom
full_name: Wenseleers, Tom
last_name: Wenseleers
- first_name: Stuart
full_name: West, Stuart
last_name: West
- first_name: Mary
full_name: West Eberhard, Mary
last_name: West Eberhard
- first_name: David
full_name: Westneat, David
last_name: Westneat
- first_name: Diane
full_name: Wiernasz, Diane
last_name: Wiernasz
- first_name: Geoff
full_name: Wild, Geoff
last_name: Wild
- first_name: Richard
full_name: Wrangham, Richard
last_name: Wrangham
- first_name: Andrew
full_name: Young, Andrew
last_name: Young
- first_name: David
full_name: Zeh, David
last_name: Zeh
- first_name: Jeanne
full_name: Zeh, Jeanne
last_name: Zeh
- first_name: Andrew
full_name: Zink, Andrew
last_name: Zink
citation:
ama: Abbot P, Abe J, Alcock J, et al. Inclusive fitness theory and eusociality.
Nature. 2011;471(7339):E1-E4. doi:10.1038/nature09831
apa: Abbot, P., Abe, J., Alcock, J., Alizon, S., Alpedrinha, J., Andersson, M.,
… Zink, A. (2011). Inclusive fitness theory and eusociality. Nature. Nature
Publishing Group. https://doi.org/10.1038/nature09831
chicago: Abbot, Patrick, Jun Abe, John Alcock, Samuel Alizon, Joao Alpedrinha, Malte
Andersson, Jean Andre, et al. “Inclusive Fitness Theory and Eusociality.” Nature.
Nature Publishing Group, 2011. https://doi.org/10.1038/nature09831.
ieee: P. Abbot et al., “Inclusive fitness theory and eusociality,” Nature,
vol. 471, no. 7339. Nature Publishing Group, pp. E1–E4, 2011.
ista: Abbot P et al. 2011. Inclusive fitness theory and eusociality. Nature. 471(7339),
E1–E4.
mla: Abbot, Patrick, et al. “Inclusive Fitness Theory and Eusociality.” Nature,
vol. 471, no. 7339, Nature Publishing Group, 2011, pp. E1–4, doi:10.1038/nature09831.
short: P. Abbot, J. Abe, J. Alcock, S. Alizon, J. Alpedrinha, M. Andersson, J. Andre,
M. Van Baalen, F. Balloux, S. Balshine, N.H. Barton, L. Beukeboom, J. Biernaskie,
T. Bilde, G. Borgia, M. Breed, S. Brown, R. Bshary, A. Buckling, N. Burley, M.
Burton Chellew, M. Cant, M. Chapuisat, E. Charnov, T. Clutton Brock, A. Cockburn,
B. Cole, N. Colegrave, L. Cosmides, I. Couzin, J. Coyne, S. Creel, B. Crespi,
R. Curry, S. Dall, T. Day, J. Dickinson, L. Dugatkin, C. El Mouden, S. Emlen,
J. Evans, R. Ferriere, J. Field, S. Foitzik, K. Foster, W. Foster, C. Fox, J.
Gadau, S. Gandon, A. Gardner, M. Gardner, T. Getty, M. Goodisman, A. Grafen, R.
Grosberg, C. Grozinger, P. Gouyon, D. Gwynne, P. Harvey, B. Hatchwell, J. Heinze,
H. Helantera, K. Helms, K. Hill, N. Jiricny, R. Johnstone, A. Kacelnik, E.T. Kiers,
H. Kokko, J. Komdeur, J. Korb, D. Kronauer, R. Kümmerli, L. Lehmann, T. Linksvayer,
S. Lion, B. Lyon, J. Marshall, R. Mcelreath, Y. Michalakis, R. Michod, D. Mock,
T. Monnin, R. Montgomerie, A. Moore, U. Mueller, R. Noë, S. Okasha, P. Pamilo,
G. Parker, J. Pedersen, I. Pen, D. Pfennig, D. Queller, D. Rankin, S. Reece, H.
Reeve, M. Reuter, G. Roberts, S. Robson, D. Roze, F. Rousset, O. Rueppell, J.
Sachs, L. Santorelli, P. Schmid Hempel, M. Schwarz, T. Scott Phillips, J. Shellmann
Sherman, P. Sherman, D. Shuker, J. Smith, J. Spagna, B. Strassmann, A. Suarez,
L. Sundström, M. Taborsky, P. Taylor, G. Thompson, J. Tooby, N. Tsutsui, K. Tsuji,
S. Turillazzi, F. Úbeda, E. Vargo, B. Voelkl, T. Wenseleers, S. West, M. West
Eberhard, D. Westneat, D. Wiernasz, G. Wild, R. Wrangham, A. Young, D. Zeh, J.
Zeh, A. Zink, Nature 471 (2011) E1–E4.
date_created: 2018-12-11T12:02:57Z
date_published: 2011-03-23T00:00:00Z
date_updated: 2021-01-12T07:43:02Z
day: '23'
department:
- _id: NiBa
doi: 10.1038/nature09831
external_id:
pmid:
- '21430721'
intvolume: ' 471'
issue: '7339'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/
month: '03'
oa: 1
oa_version: Submitted Version
page: E1 - E4
pmid: 1
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '3237'
quality_controlled: '1'
scopus_import: 1
status: public
title: Inclusive fitness theory and eusociality
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 471
year: '2011'
...
---
_id: '3371'
abstract:
- lang: eng
text: The Minisymposium “Cell Migration and Motility” was attended by approximately
500 visitors and covered a broad range of questions in the field using diverse
model systems. Topics comprised actin dynamics, cell polarity, force transduction,
signal transduction, bar- rier transmigration, and chemotactic guidance.
article_type: original
author:
- 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: Carole
full_name: Parent, Carole
last_name: Parent
citation:
ama: Sixt MK, Parent C. Cells on the move in Philadelphia. Molecular Biology
and Evolution. 2011;22(6):724. doi:10.1091/mbc.E10-12-0958
apa: Sixt, M. K., & Parent, C. (2011). Cells on the move in Philadelphia. Molecular
Biology and Evolution. Oxford University Press. https://doi.org/10.1091/mbc.E10-12-0958
chicago: Sixt, Michael K, and Carole Parent. “Cells on the Move in Philadelphia.”
Molecular Biology and Evolution. Oxford University Press, 2011. https://doi.org/10.1091/mbc.E10-12-0958.
ieee: M. K. Sixt and C. Parent, “Cells on the move in Philadelphia,” Molecular
Biology and Evolution, vol. 22, no. 6. Oxford University Press, p. 724, 2011.
ista: Sixt MK, Parent C. 2011. Cells on the move in Philadelphia. Molecular Biology
and Evolution. 22(6), 724.
mla: Sixt, Michael K., and Carole Parent. “Cells on the Move in Philadelphia.” Molecular
Biology and Evolution, vol. 22, no. 6, Oxford University Press, 2011, p. 724,
doi:10.1091/mbc.E10-12-0958.
short: M.K. Sixt, C. Parent, Molecular Biology and Evolution 22 (2011) 724.
date_created: 2018-12-11T12:02:57Z
date_published: 2011-03-15T00:00:00Z
date_updated: 2021-01-12T07:43:01Z
day: '15'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1091/mbc.E10-12-0958
file:
- access_level: open_access
checksum: 3467986ab7a64e7694ffd1013b5d9da9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:29Z
date_updated: 2020-07-14T12:46:11Z
file_id: '5283'
file_name: IST-2015-373-v1+1_Mol._Biol._Cell-2011-Sixt-724.pdf
file_size: 105421
relation: main_file
file_date_updated: 2020-07-14T12:46:11Z
has_accepted_license: '1'
intvolume: ' 22'
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '724'
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '3238'
pubrep_id: '373'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cells on the move in Philadelphia
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2011'
...
---
_id: '3374'
abstract:
- lang: eng
text: Genetic regulatory networks enable cells to respond to changes in internal
and external conditions by dynamically coordinating their gene expression profiles.
Our ability to make quantitative measurements in these biochemical circuits has
deepened our understanding of what kinds of computations genetic regulatory networks
can perform, and with what reliability. These advances have motivated researchers
to look for connections between the architecture and function of genetic regulatory
networks. Transmitting information between a network's inputs and outputs has
been proposed as one such possible measure of function, relevant in certain biological
contexts. Here we summarize recent developments in the application of information
theory to gene regulatory networks. We first review basic concepts in information
theory necessary for understanding recent work. We then discuss the functional
complexity of gene regulation, which arises from the molecular nature of the regulatory
interactions. We end by reviewing some experiments that support the view that
genetic networks responsible for early development of multicellular organisms
might be maximizing transmitted 'positional information'.
article_number: '153102'
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Aleksandra
full_name: Walczak, Aleksandra
last_name: Walczak
citation:
ama: 'Tkačik G, Walczak A. Information transmission in genetic regulatory networks
a review. Journal of Physics: Condensed Matter. 2011;23(15). doi:10.1088/0953-8984/23/15/153102'
apa: 'Tkačik, G., & Walczak, A. (2011). Information transmission in genetic
regulatory networks a review. Journal of Physics: Condensed Matter. IOP
Publishing Ltd. https://doi.org/10.1088/0953-8984/23/15/153102'
chicago: 'Tkačik, Gašper, and Aleksandra Walczak. “Information Transmission in Genetic
Regulatory Networks a Review.” Journal of Physics: Condensed Matter. IOP
Publishing Ltd., 2011. https://doi.org/10.1088/0953-8984/23/15/153102.'
ieee: 'G. Tkačik and A. Walczak, “Information transmission in genetic regulatory
networks a review,” Journal of Physics: Condensed Matter, vol. 23, no.
15. IOP Publishing Ltd., 2011.'
ista: 'Tkačik G, Walczak A. 2011. Information transmission in genetic regulatory
networks a review. Journal of Physics: Condensed Matter. 23(15), 153102.'
mla: 'Tkačik, Gašper, and Aleksandra Walczak. “Information Transmission in Genetic
Regulatory Networks a Review.” Journal of Physics: Condensed Matter, vol.
23, no. 15, 153102, IOP Publishing Ltd., 2011, doi:10.1088/0953-8984/23/15/153102.'
short: 'G. Tkačik, A. Walczak, Journal of Physics: Condensed Matter 23 (2011).'
date_created: 2018-12-11T12:02:58Z
date_published: 2011-04-01T00:00:00Z
date_updated: 2021-01-12T07:43:03Z
day: '01'
department:
- _id: GaTk
doi: 10.1088/0953-8984/23/15/153102
intvolume: ' 23'
issue: '15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1101.4240
month: '04'
oa: 1
oa_version: Submitted Version
publication: 'Journal of Physics: Condensed Matter'
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '3233'
quality_controlled: '1'
scopus_import: 1
status: public
title: Information transmission in genetic regulatory networks a review
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2011'
...
---
_id: '3368'
abstract:
- lang: eng
text: Tissue surface tension (TST) is an important mechanical property influencing
cell sorting and tissue envelopment. The study by Manning et al. (1) reported
on a mathematical model describing TST on the basis of the balance between adhesive
and tensile properties of the constituent cells. The model predicts that, in high-adhesion
cell aggregates, surface cells will be stretched to maintain the same area of
cell–cell contact as interior bulk cells, resulting in an elongated and flattened
cell shape. The authors (1) observed flat and elongated cells at the surface of
high-adhesion zebrafish germ-layer explants, which they argue are undifferentiated
stretched germ-layer progenitor cells, and they use this observation as a validation
of their model.
author:
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Stephanie
full_name: Möllmert, Stephanie
id: 260FD49C-E911-11E9-B5EA-D9538404589B
last_name: Möllmert
- 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: Krens G, Möllmert S, Heisenberg C-PJ. Enveloping cell layer differentiation
at the surface of zebrafish germ layer tissue explants. PNAS. 2011;108(3):E9-E10.
doi:10.1073/pnas.1010767108
apa: Krens, G., Möllmert, S., & Heisenberg, C.-P. J. (2011). Enveloping cell
layer differentiation at the surface of zebrafish germ layer tissue explants.
PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1010767108
chicago: Krens, Gabriel, Stephanie Möllmert, and Carl-Philipp J Heisenberg. “Enveloping
Cell Layer Differentiation at the Surface of Zebrafish Germ Layer Tissue Explants.”
PNAS. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1010767108.
ieee: G. Krens, S. Möllmert, and C.-P. J. Heisenberg, “Enveloping cell layer differentiation
at the surface of zebrafish germ layer tissue explants,” PNAS, vol. 108,
no. 3. National Academy of Sciences, pp. E9–E10, 2011.
ista: Krens G, Möllmert S, Heisenberg C-PJ. 2011. Enveloping cell layer differentiation
at the surface of zebrafish germ layer tissue explants. PNAS. 108(3), E9–E10.
mla: Krens, Gabriel, et al. “Enveloping Cell Layer Differentiation at the Surface
of Zebrafish Germ Layer Tissue Explants.” PNAS, vol. 108, no. 3, National
Academy of Sciences, 2011, pp. E9–10, doi:10.1073/pnas.1010767108.
short: G. Krens, S. Möllmert, C.-P.J. Heisenberg, PNAS 108 (2011) E9–E10.
date_created: 2018-12-11T12:02:56Z
date_published: 2011-01-18T00:00:00Z
date_updated: 2021-01-12T07:43:00Z
day: '18'
department:
- _id: CaHe
doi: 10.1073/pnas.1010767108
external_id:
pmid:
- '21212360'
intvolume: ' 108'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024655
month: '01'
oa: 1
oa_version: Submitted Version
page: E9 - E10
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3244'
quality_controlled: '1'
scopus_import: 1
status: public
title: Enveloping cell layer differentiation at the surface of zebrafish germ layer
tissue explants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2011'
...
---
_id: '3370'
abstract:
- lang: eng
text: Supertree methods are widely applied and give rise to new conclusions about
phylogenies (e.g., Bininda-Emonds et al. 2007). Although several desiderata for
supertree methods exist (Wilkinson, Thorley, et al. 2004), only few of them have
been studied in greater detail, examples include shape bias (Wilkinson et al.
2005) or pareto properties (Wilkinson et al. 2007). Here I look more closely at
two matrix representation methods, matrix representation with compatibility (MRC)
and matrix representation with parsimony (MRP). Different null models of random
data are studied and the resulting tree shapes are investigated. Thereby I consider
unrooted trees and a bias in tree shape is determined by a tree balance measure.
The measure for unrooted trees is a modification of a tree balance measure for
rooted trees. I observe that depending on the underlying null model of random
data, the methods may resolve conflict in favor of more balanced tree shapes.
The analyses refer only to trees with the same taxon set, also known as the consensus
setting (e.g., Wilkinson et al. 2007), but I will be able to draw conclusions
on how to deal with missing data.
author:
- first_name: Anne
full_name: Kupczok, Anne
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
citation:
ama: Kupczok A. Consequences of different null models on the tree shape bias of
supertree methods. Systematic Biology. 2011;60(2):218-225. doi:10.1093/sysbio/syq086
apa: Kupczok, A. (2011). Consequences of different null models on the tree shape
bias of supertree methods. Systematic Biology. Oxford University Press.
https://doi.org/10.1093/sysbio/syq086
chicago: Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape
Bias of Supertree Methods.” Systematic Biology. Oxford University Press,
2011. https://doi.org/10.1093/sysbio/syq086.
ieee: A. Kupczok, “Consequences of different null models on the tree shape bias
of supertree methods,” Systematic Biology, vol. 60, no. 2. Oxford University
Press, pp. 218–225, 2011.
ista: Kupczok A. 2011. Consequences of different null models on the tree shape bias
of supertree methods. Systematic Biology. 60(2), 218–225.
mla: Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape Bias
of Supertree Methods.” Systematic Biology, vol. 60, no. 2, Oxford University
Press, 2011, pp. 218–25, doi:10.1093/sysbio/syq086.
short: A. Kupczok, Systematic Biology 60 (2011) 218–225.
date_created: 2018-12-11T12:02:57Z
date_published: 2011-03-01T00:00:00Z
date_updated: 2021-01-12T07:43:01Z
day: '01'
department:
- _id: JoBo
doi: 10.1093/sysbio/syq086
intvolume: ' 60'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprints.cs.univie.ac.at/3226/
month: '03'
oa: 1
oa_version: Submitted Version
page: 218 - 225
publication: Systematic Biology
publication_status: published
publisher: Oxford University Press
publist_id: '3241'
quality_controlled: '1'
status: public
title: Consequences of different null models on the tree shape bias of supertree methods
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2011'
...
---
_id: '3369'
abstract:
- lang: eng
text: Rab3 interacting molecules (RIMs) are highly enriched in the active zones
of presynaptic terminals. It is generally thought that they operate as effectors
of the small G protein Rab3. Three recent papers, by Han et al. (this issue of
Neuron), Deng et al. (this issue of Neuron), and Kaeser et al. (a recent issue
of Cell), shed new light on the functional role of RIM in presynaptic terminals.
First, RIM tethers Ca2+ channels to active zones. Second, RIM contributes to priming
of synaptic vesicles by interacting with another presynaptic protein, Munc13.
author:
- first_name: Alejandro
full_name: Pernia-Andrade, Alejandro
id: 36963E98-F248-11E8-B48F-1D18A9856A87
last_name: Pernia-Andrade
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Pernia-Andrade A, Jonas PM. The multiple faces of RIM. Neuron. 2011;69(2):185-187.
doi:10.1016/j.neuron.2011.01.010
apa: Pernia-Andrade, A., & Jonas, P. M. (2011). The multiple faces of RIM. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2011.01.010
chicago: Pernia-Andrade, Alejandro, and Peter M Jonas. “The Multiple Faces of RIM.”
Neuron. Elsevier, 2011. https://doi.org/10.1016/j.neuron.2011.01.010.
ieee: A. Pernia-Andrade and P. M. Jonas, “The multiple faces of RIM,” Neuron,
vol. 69, no. 2. Elsevier, pp. 185–187, 2011.
ista: Pernia-Andrade A, Jonas PM. 2011. The multiple faces of RIM. Neuron. 69(2),
185–187.
mla: Pernia-Andrade, Alejandro, and Peter M. Jonas. “The Multiple Faces of RIM.”
Neuron, vol. 69, no. 2, Elsevier, 2011, pp. 185–87, doi:10.1016/j.neuron.2011.01.010.
short: A. Pernia-Andrade, P.M. Jonas, Neuron 69 (2011) 185–187.
date_created: 2018-12-11T12:02:56Z
date_published: 2011-01-27T00:00:00Z
date_updated: 2021-01-12T07:43:00Z
day: '27'
department:
- _id: PeJo
doi: 10.1016/j.neuron.2011.01.010
intvolume: ' 69'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 185 - 187
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '3243'
quality_controlled: '1'
scopus_import: 1
status: public
title: The multiple faces of RIM
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 69
year: '2011'
...
---
_id: '3396'
abstract:
- lang: eng
text: Facial branchiomotor neurons (FBMNs) in zebrafish and mouse embryonic hindbrain
undergo a characteristic tangential migration from rhombomere (r) 4, where they
are born, to r6/7. Cohesion among neuroepithelial cells (NCs) has been suggested
to function in FBMN migration by inhibiting FBMNs positioned in the basal neuroepithelium
such that they move apically between NCs towards the midline of the neuroepithelium
instead of tangentially along the basal side of the neuroepithelium towards r6/7.
However, direct experimental evaluation of this hypothesis is still lacking. Here,
we have used a combination of biophysical cell adhesion measurements and high-resolution
time-lapse microscopy to determine the role of NC cohesion in FBMN migration.
We show that reducing NC cohesion by interfering with Cadherin 2 (Cdh2) activity
results in FBMNs positioned at the basal side of the neuroepithelium moving apically
towards the neural tube midline instead of tangentially towards r6/7. In embryos
with strongly reduced NC cohesion, ectopic apical FBMN movement frequently results
in fusion of the bilateral FBMN clusters over the apical midline of the neural
tube. By contrast, reducing cohesion among FBMNs by interfering with Contactin
2 (Cntn2) expression in these cells has little effect on apical FBMN movement,
but reduces the fusion of the bilateral FBMN clusters in embryos with strongly
diminished NC cohesion. These data provide direct experimental evidence that NC
cohesion functions in tangential FBMN migration by restricting their apical movement.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
article_type: original
author:
- first_name: Petra
full_name: Stockinger, Petra
id: 261CB030-E90D-11E9-B182-F697D44B663C
last_name: Stockinger
- 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: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
citation:
ama: Stockinger P, Heisenberg C-PJ, Maître J-L. Defective neuroepithelial cell cohesion
affects tangential branchiomotor neuron migration in the zebrafish neural tube.
Development. 2011;138(21):4673-4683. doi:10.1242/dev.071233
apa: Stockinger, P., Heisenberg, C.-P. J., & Maître, J.-L. (2011). Defective
neuroepithelial cell cohesion affects tangential branchiomotor neuron migration
in the zebrafish neural tube. Development. Company of Biologists. https://doi.org/10.1242/dev.071233
chicago: Stockinger, Petra, Carl-Philipp J Heisenberg, and Jean-Léon Maître. “Defective
Neuroepithelial Cell Cohesion Affects Tangential Branchiomotor Neuron Migration
in the Zebrafish Neural Tube.” Development. Company of Biologists, 2011.
https://doi.org/10.1242/dev.071233.
ieee: P. Stockinger, C.-P. J. Heisenberg, and J.-L. Maître, “Defective neuroepithelial
cell cohesion affects tangential branchiomotor neuron migration in the zebrafish
neural tube,” Development, vol. 138, no. 21. Company of Biologists, pp.
4673–4683, 2011.
ista: Stockinger P, Heisenberg C-PJ, Maître J-L. 2011. Defective neuroepithelial
cell cohesion affects tangential branchiomotor neuron migration in the zebrafish
neural tube. Development. 138(21), 4673–4683.
mla: Stockinger, Petra, et al. “Defective Neuroepithelial Cell Cohesion Affects
Tangential Branchiomotor Neuron Migration in the Zebrafish Neural Tube.” Development,
vol. 138, no. 21, Company of Biologists, 2011, pp. 4673–83, doi:10.1242/dev.071233.
short: P. Stockinger, C.-P.J. Heisenberg, J.-L. Maître, Development 138 (2011) 4673–4683.
date_created: 2018-12-11T12:03:06Z
date_published: 2011-09-28T00:00:00Z
date_updated: 2021-01-12T07:43:11Z
day: '28'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1242/dev.071233
file:
- access_level: open_access
checksum: ca12b79e01ef36c1ef1aea31cf7e7139
content_type: application/pdf
creator: dernst
date_created: 2019-10-07T14:19:42Z
date_updated: 2020-07-14T12:46:12Z
file_id: '6930'
file_name: 2011_Development_Stockinger.pdf
file_size: 4672439
relation: main_file
file_date_updated: 2020-07-14T12:46:12Z
has_accepted_license: '1'
intvolume: ' 138'
issue: '21'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 4673 - 4683
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '3210'
quality_controlled: '1'
scopus_import: 1
status: public
title: Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron
migration in the zebrafish neural tube
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 138
year: '2011'
...
---
_id: '3394'
abstract:
- lang: eng
text: 'Random genetic drift shifts clines in space, alters their width, and distorts
their shape. Such random fluctuations complicate inferences from cline width and
position. Notably, the effect of genetic drift on the expected shape of the cline
is opposite to the naive (but quite common) misinterpretation of classic results
on the expected cline. While random drift on average broadens the overall cline
in expected allele frequency, it narrows the width of any particular cline. The
opposing effects arise because locally, drift drives alleles to fixation—but fluctuations
in position widen the expected cline. The effect of genetic drift can be predicted
from standardized variance in allele frequencies, averaged across the habitat:
〈F〉. A cline maintained by spatially varying selection (step change) is expected
to be narrower by a factor of relative to the cline in the absence of drift.
The expected cline is broader by the inverse of this factor. In a tension zone
maintained by underdominance, the expected cline width is narrower by about 1
– 〈F〉relative to the width in the absence of drift. Individual clines can differ
substantially from the expectation, and we give quantitative predictions for the
variance in cline position and width. The predictions apply to clines in almost
one-dimensional circumstances such as hybrid zones in rivers, deep valleys, or
along a coast line and give a guide to what patterns to expect in two dimensions.'
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Polechova J, Barton NH. Genetic drift widens the expected cline but narrows
the expected cline width. Genetics. 2011;189(1):227-235. doi:10.1534/genetics.111.129817
apa: Polechova, J., & Barton, N. H. (2011). Genetic drift widens the expected
cline but narrows the expected cline width. Genetics. Genetics Society
of America. https://doi.org/10.1534/genetics.111.129817
chicago: Polechova, Jitka, and Nicholas H Barton. “Genetic Drift Widens the Expected
Cline but Narrows the Expected Cline Width.” Genetics. Genetics Society
of America, 2011. https://doi.org/10.1534/genetics.111.129817.
ieee: J. Polechova and N. H. Barton, “Genetic drift widens the expected cline but
narrows the expected cline width,” Genetics, vol. 189, no. 1. Genetics
Society of America, pp. 227–235, 2011.
ista: Polechova J, Barton NH. 2011. Genetic drift widens the expected cline but
narrows the expected cline width. Genetics. 189(1), 227–235.
mla: Polechova, Jitka, and Nicholas H. Barton. “Genetic Drift Widens the Expected
Cline but Narrows the Expected Cline Width.” Genetics, vol. 189, no. 1,
Genetics Society of America, 2011, pp. 227–35, doi:10.1534/genetics.111.129817.
short: J. Polechova, N.H. Barton, Genetics 189 (2011) 227–235.
date_created: 2018-12-11T12:03:05Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2021-01-12T07:43:11Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.111.129817
ec_funded: 1
intvolume: ' 189'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176109/
month: '09'
oa: 1
oa_version: Submitted Version
page: 227 - 235
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3213'
quality_controlled: '1'
scopus_import: 1
status: public
title: Genetic drift widens the expected cline but narrows the expected cline width
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 189
year: '2011'
...
---
_id: '3390'
abstract:
- lang: eng
text: 'What determines the genetic contribution that an individual makes to future
generations? With biparental reproduction, each individual leaves a ''pedigree''
of descendants, determined by the biparental relationships in the population.
The pedigree of an individual constrains the lines of descent of each of its genes.
An individual''s reproductive value is the expected number of copies of each of
its genes that is passed on to distant generations conditional on its pedigree.
For the simplest model of biparental reproduction analogous to the Wright-Fisher
model, an individual''s reproductive value is determined within ~10 generations,
independent of population size. Partial selfing and subdivision do not greatly
slow this convergence. Our central result is that the probability that a gene
will survive is proportional to the reproductive value of the individual that
carries it, and that conditional on survival, after a few tens of generations,
the distribution of the number of surviving copies is the same for all individuals,
whatever their reproductive value. These results can be generalized to the joint
distribution of surviving blocks of ancestral genome. Selection on unlinked loci
in the genetic background may greatly increase the variance in reproductive value,
but the above results nevertheless still hold. The almost linear relationship
between survival probability and reproductive value also holds for weakly favored
alleles. Thus, the influence of the complex pedigree of descendants on an individual''s
genetic contribution to the population can be summarized through a single number:
its reproductive value.'
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: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: Barton NH, Etheridge A. The relation between reproductive value and genetic
contribution. Genetics. 2011;188(4):953-973. doi:10.1534/genetics.111.127555
apa: Barton, N. H., & Etheridge, A. (2011). The relation between reproductive
value and genetic contribution. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.111.127555
chicago: Barton, Nicholas H, and Alison Etheridge. “The Relation between Reproductive
Value and Genetic Contribution.” Genetics. Genetics Society of America,
2011. https://doi.org/10.1534/genetics.111.127555.
ieee: N. H. Barton and A. Etheridge, “The relation between reproductive value and
genetic contribution,” Genetics, vol. 188, no. 4. Genetics Society of America,
pp. 953–973, 2011.
ista: Barton NH, Etheridge A. 2011. The relation between reproductive value and
genetic contribution. Genetics. 188(4), 953–973.
mla: Barton, Nicholas H., and Alison Etheridge. “The Relation between Reproductive
Value and Genetic Contribution.” Genetics, vol. 188, no. 4, Genetics Society
of America, 2011, pp. 953–73, doi:10.1534/genetics.111.127555.
short: N.H. Barton, A. Etheridge, Genetics 188 (2011) 953–973.
date_created: 2018-12-11T12:03:04Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2021-01-12T07:43:09Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.111.127555
ec_funded: 1
intvolume: ' 188'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176105/
month: '08'
oa: 1
oa_version: Submitted Version
page: 953 - 973
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3217'
quality_controlled: '1'
scopus_import: 1
status: public
title: The relation between reproductive value and genetic contribution
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 188
year: '2011'
...
---
_id: '3391'
abstract:
- lang: eng
text: 'Evolutionary biology shares many concepts with statistical physics: both
deal with populations, whether of molecules or organisms, and both seek to simplify
evolution in very many dimensions. Often, methodologies have undergone parallel
and independent development, as with stochastic methods in population genetics.
Here, we discuss aspects of population genetics that have embraced methods from
physics: non-equilibrium statistical mechanics, travelling waves and Monte-Carlo
methods, among others, have been used to study polygenic evolution, rates of adaptation
and range expansions. These applications indicate that evolutionary biology can
further benefit from interactions with other areas of statistical physics; for
example, by following the distribution of paths taken by a population through
time'
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: de Vladar H, Barton NH. The contribution of statistical physics to evolutionary
biology. Trends in Ecology and Evolution. 2011;26(8):424-432. doi:10.1016/j.tree.2011.04.002
apa: de Vladar, H., & Barton, N. H. (2011). The contribution of statistical
physics to evolutionary biology. Trends in Ecology and Evolution. Cell
Press. https://doi.org/10.1016/j.tree.2011.04.002
chicago: Vladar, Harold de, and Nicholas H Barton. “The Contribution of Statistical
Physics to Evolutionary Biology.” Trends in Ecology and Evolution. Cell
Press, 2011. https://doi.org/10.1016/j.tree.2011.04.002.
ieee: H. de Vladar and N. H. Barton, “The contribution of statistical physics to
evolutionary biology,” Trends in Ecology and Evolution, vol. 26, no. 8.
Cell Press, pp. 424–432, 2011.
ista: de Vladar H, Barton NH. 2011. The contribution of statistical physics to evolutionary
biology. Trends in Ecology and Evolution. 26(8), 424–432.
mla: de Vladar, Harold, and Nicholas H. Barton. “The Contribution of Statistical
Physics to Evolutionary Biology.” Trends in Ecology and Evolution, vol.
26, no. 8, Cell Press, 2011, pp. 424–32, doi:10.1016/j.tree.2011.04.002.
short: H. de Vladar, N.H. Barton, Trends in Ecology and Evolution 26 (2011) 424–432.
date_created: 2018-12-11T12:03:04Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2021-01-12T07:43:10Z
day: '01'
department:
- _id: NiBa
doi: 10.1016/j.tree.2011.04.002
ec_funded: 1
intvolume: ' 26'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1104.2854
month: '08'
oa: 1
oa_version: Submitted Version
page: 424 - 432
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Trends in Ecology and Evolution
publication_status: published
publisher: Cell Press
publist_id: '3216'
quality_controlled: '1'
scopus_import: 1
status: public
title: The contribution of statistical physics to evolutionary biology
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2011'
...
---
_id: '3397'
abstract:
- lang: eng
text: Recent advances in microscopy techniques and biophysical measurements have
provided novel insight into the molecular, cellular and biophysical basis of cell
adhesion. However, comparably little is known about a core element of cell–cell
adhesion—the energy of adhesion at the cell–cell contact. In this review, we discuss
approaches to understand the nature and regulation of adhesion energy, and propose
strategies to determine adhesion energy between cells in vitro and in vivo.
author:
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
- 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: Maître J-L, Heisenberg C-PJ. The role of adhesion energy in controlling cell-cell
contacts. Current Opinion in Cell Biology. 2011;23(5):508-514. doi:10.1016/j.ceb.2011.07.004
apa: Maître, J.-L., & Heisenberg, C.-P. J. (2011). The role of adhesion energy
in controlling cell-cell contacts. Current Opinion in Cell Biology. Elsevier.
https://doi.org/10.1016/j.ceb.2011.07.004
chicago: Maître, Jean-Léon, and Carl-Philipp J Heisenberg. “The Role of Adhesion
Energy in Controlling Cell-Cell Contacts.” Current Opinion in Cell Biology.
Elsevier, 2011. https://doi.org/10.1016/j.ceb.2011.07.004.
ieee: J.-L. Maître and C.-P. J. Heisenberg, “The role of adhesion energy in controlling
cell-cell contacts,” Current Opinion in Cell Biology, vol. 23, no. 5. Elsevier,
pp. 508–514, 2011.
ista: Maître J-L, Heisenberg C-PJ. 2011. The role of adhesion energy in controlling
cell-cell contacts. Current Opinion in Cell Biology. 23(5), 508–514.
mla: Maître, Jean-Léon, and Carl-Philipp J. Heisenberg. “The Role of Adhesion Energy
in Controlling Cell-Cell Contacts.” Current Opinion in Cell Biology, vol.
23, no. 5, Elsevier, 2011, pp. 508–14, doi:10.1016/j.ceb.2011.07.004.
short: J.-L. Maître, C.-P.J. Heisenberg, Current Opinion in Cell Biology 23 (2011)
508–514.
date_created: 2018-12-11T12:03:06Z
date_published: 2011-10-01T00:00:00Z
date_updated: 2021-01-12T07:43:12Z
day: '01'
department:
- _id: CaHe
doi: 10.1016/j.ceb.2011.07.004
intvolume: ' 23'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188705/
month: '10'
oa: 1
oa_version: Submitted Version
page: 508 - 514
publication: Current Opinion in Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '3211'
quality_controlled: '1'
scopus_import: 1
status: public
title: The role of adhesion energy in controlling cell-cell contacts
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2011'
...
---
_id: '3405'
abstract:
- lang: eng
text: Glutamate is the major excitatory neurotransmitter in the mammalian central
nervous system and gates non-selective cation channels. The origins of glutamate
receptors are not well understood as they differ structurally and functionally
from simple bacterial ligand-gated ion channels. Here we report the discovery
of an ionotropic glutamate receptor that combines the typical eukaryotic domain
architecture with the 'TXVGYG' signature sequence of the selectivity filter found
in K+ channels. This receptor exhibits functional properties intermediate between
bacterial and eukaryotic glutamate-gated ion channels, suggesting a link in the
evolution of ionotropic glutamate receptors.
author:
- 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: Guillaume
full_name: Sandoz, Guillaume
last_name: Sandoz
- first_name: Ehud
full_name: Isacoff, Ehud
last_name: Isacoff
citation:
ama: Janovjak HL, Sandoz G, Isacoff E. Modern ionotropic glutamate receptor with
a K+ selectivity signature sequence. Nature Communications. 2011;2(232):1-6.
doi:10.1038/ncomms1231
apa: Janovjak, H. L., Sandoz, G., & Isacoff, E. (2011). Modern ionotropic glutamate
receptor with a K+ selectivity signature sequence. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms1231
chicago: Janovjak, Harald L, Guillaume Sandoz, and Ehud Isacoff. “Modern Ionotropic
Glutamate Receptor with a K+ Selectivity Signature Sequence.” Nature Communications.
Nature Publishing Group, 2011. https://doi.org/10.1038/ncomms1231.
ieee: H. L. Janovjak, G. Sandoz, and E. Isacoff, “Modern ionotropic glutamate receptor
with a K+ selectivity signature sequence,” Nature Communications, vol.
2, no. 232. Nature Publishing Group, pp. 1–6, 2011.
ista: Janovjak HL, Sandoz G, Isacoff E. 2011. Modern ionotropic glutamate receptor
with a K+ selectivity signature sequence. Nature Communications. 2(232), 1–6.
mla: Janovjak, Harald L., et al. “Modern Ionotropic Glutamate Receptor with a K+
Selectivity Signature Sequence.” Nature Communications, vol. 2, no. 232,
Nature Publishing Group, 2011, pp. 1–6, doi:10.1038/ncomms1231.
short: H.L. Janovjak, G. Sandoz, E. Isacoff, Nature Communications 2 (2011) 1–6.
date_created: 2018-12-11T12:03:09Z
date_published: 2011-03-08T00:00:00Z
date_updated: 2021-01-12T07:43:15Z
day: '08'
ddc:
- '570'
- '571'
department:
- _id: HaJa
doi: 10.1038/ncomms1231
file:
- access_level: open_access
checksum: 6b68d65aadd97c18d663eb117a0a9d35
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:36Z
date_updated: 2020-07-14T12:46:12Z
file_id: '4891'
file_name: IST-2017-832-v1+1_janovjak.pdf
file_size: 387654
relation: main_file
file_date_updated: 2020-07-14T12:46:12Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '232'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 1 - 6
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '2997'
pubrep_id: '832'
quality_controlled: '1'
scopus_import: 1
status: public
title: Modern ionotropic glutamate receptor with a K+ selectivity signature sequence
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2011'
...
---
_id: '341'
abstract:
- lang: eng
text: An oriented attachment and growth mechanism allows an accurate control of
the size and morphology of Cu2-xS nanocrystals, from spheres and disks to tetradecahedrons
and dodecahedrons. The synthesis conditions and the growth mechanism are detailed
here.
acknowledgement: "This work was supported by the Spanish MICINN projects\r\nMAT2008-05779,
MAT2008-03400-E/MAT, ENE2008-03277-E/\r\nCON, MAT2010-15138, MAT-2010-21510, CDS2009-00050
and\r\nCSD2009-00013 and by Generalitat de Catalunya 2009-SGR-770\r\nand XaRMAE."
article_processing_charge: No
article_type: original
author:
- first_name: Wenhua
full_name: Li, Wenhua
last_name: Li
- first_name: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: Roger
full_name: Guzman, Roger
last_name: Guzman
- first_name: Javier
full_name: Rubio Garcia, Javier
last_name: Rubio Garcia
- first_name: Cristina
full_name: Flox, Cristina
last_name: Flox
- first_name: Jiandong
full_name: Fan, Jiandong
last_name: Fan
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Joan
full_name: Morante, Joan
last_name: Morante
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: 'Li W, Shavel A, Guzman R, et al. Morphology evolution of Cu2−xS nanoparticles:
from spheres to dodecahedrons. Chemical Communications. 2011;47(37):10332-10334.
doi:10.1039/c1cc13803k'
apa: 'Li, W., Shavel, A., Guzman, R., Rubio Garcia, J., Flox, C., Fan, J., … Cabot,
A. (2011). Morphology evolution of Cu2−xS nanoparticles: from spheres to dodecahedrons.
Chemical Communications. Royal Society of Chemistry (RSC) . https://doi.org/10.1039/c1cc13803k'
chicago: 'Li, Wenhua, Alexey Shavel, Roger Guzman, Javier Rubio Garcia, Cristina
Flox, Jiandong Fan, Doris Cadavid, et al. “Morphology Evolution of Cu2−xS Nanoparticles:
From Spheres to Dodecahedrons.” Chemical Communications. Royal Society
of Chemistry (RSC) , 2011. https://doi.org/10.1039/c1cc13803k.'
ieee: 'W. Li et al., “Morphology evolution of Cu2−xS nanoparticles: from
spheres to dodecahedrons,” Chemical Communications, vol. 47, no. 37. Royal
Society of Chemistry (RSC) , pp. 10332–10334, 2011.'
ista: 'Li W, Shavel A, Guzman R, Rubio Garcia J, Flox C, Fan J, Cadavid D, Ibáñez
M, Arbiol J, Morante J, Cabot A. 2011. Morphology evolution of Cu2−xS nanoparticles:
from spheres to dodecahedrons. Chemical Communications. 47(37), 10332–10334.'
mla: 'Li, Wenhua, et al. “Morphology Evolution of Cu2−xS Nanoparticles: From Spheres
to Dodecahedrons.” Chemical Communications, vol. 47, no. 37, Royal Society
of Chemistry (RSC) , 2011, pp. 10332–34, doi:10.1039/c1cc13803k.'
short: W. Li, A. Shavel, R. Guzman, J. Rubio Garcia, C. Flox, J. Fan, D. Cadavid,
M. Ibáñez, J. Arbiol, J. Morante, A. Cabot, Chemical Communications 47 (2011)
10332–10334.
date_created: 2018-12-11T11:45:55Z
date_published: 2011-10-07T00:00:00Z
date_updated: 2021-01-12T07:43:17Z
day: '07'
doi: 10.1039/c1cc13803k
extern: '1'
intvolume: ' 47'
issue: '37'
language:
- iso: eng
month: '10'
oa_version: None
page: 10332 - 10334
publication: Chemical Communications
publication_status: published
publisher: 'Royal Society of Chemistry (RSC) '
publist_id: '7491'
quality_controlled: '1'
status: public
title: 'Morphology evolution of Cu2−xS nanoparticles: from spheres to dodecahedrons'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2011'
...
---
_id: '3429'
abstract:
- lang: eng
text: Transcription factors are central to sustaining pluripotency, yet little is
known about transcription factor dynamics in defining pluripotency in the early
mammalian embryo. Here, we establish a fluorescence decay after photoactivation
(FDAP) assay to quantitatively study the kinetic behaviour of Oct4, a key transcription
factor controlling pre-implantation development in the mouse embryo. FDAP measurements
reveal that each cell in a developing embryo shows one of two distinct Oct4 kinetics,
before there are any morphologically distinguishable differences or outward signs
of lineage patterning. The differences revealed by FDAP are due to differences
in the accessibility of Oct4 to its DNA binding sites in the nucleus. Lineage
tracing of the cells in the two distinct sub-populations demonstrates that the
Oct4 kinetics predict lineages of the early embryo. Cells with slower Oct4 kinetics
are more likely to give rise to the pluripotent cell lineage that contributes
to the inner cell mass. Those with faster Oct4 kinetics contribute mostly to the
extra-embryonic lineage. Our findings identify Oct4 kinetics, rather than differences
in total transcription factor expression levels, as a predictive measure of developmental
cell lineage patterning in the early mouse embryo.
acknowledgement: This work was supported by the Beckman Institute and Biological Imaging
Center at the California Institute of Technology and by the NHGRI Center of Excellence
in Genomic Science grant P50HG004071.
author:
- first_name: Nicolas
full_name: Plachta, Nicolas
last_name: Plachta
- 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: Shirley
full_name: Pease, Shirley
last_name: Pease
- first_name: Scott
full_name: Fraser, Scott
last_name: Fraser
- first_name: Periklis
full_name: Pantazis, Periklis
last_name: Pantazis
citation:
ama: Plachta N, Bollenbach MT, Pease S, Fraser S, Pantazis P. Oct4 kinetics predict
cell lineage patterning in the early mammalian embryo. Nature Cell Biology.
2011;13(2):117-123. doi:10.1038/ncb2154
apa: Plachta, N., Bollenbach, M. T., Pease, S., Fraser, S., & Pantazis, P. (2011).
Oct4 kinetics predict cell lineage patterning in the early mammalian embryo. Nature
Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2154
chicago: Plachta, Nicolas, Mark Tobias Bollenbach, Shirley Pease, Scott Fraser,
and Periklis Pantazis. “Oct4 Kinetics Predict Cell Lineage Patterning in the Early
Mammalian Embryo.” Nature Cell Biology. Nature Publishing Group, 2011.
https://doi.org/10.1038/ncb2154.
ieee: N. Plachta, M. T. Bollenbach, S. Pease, S. Fraser, and P. Pantazis, “Oct4
kinetics predict cell lineage patterning in the early mammalian embryo,” Nature
Cell Biology, vol. 13, no. 2. Nature Publishing Group, pp. 117–123, 2011.
ista: Plachta N, Bollenbach MT, Pease S, Fraser S, Pantazis P. 2011. Oct4 kinetics
predict cell lineage patterning in the early mammalian embryo. Nature Cell Biology.
13(2), 117–123.
mla: Plachta, Nicolas, et al. “Oct4 Kinetics Predict Cell Lineage Patterning in
the Early Mammalian Embryo.” Nature Cell Biology, vol. 13, no. 2, Nature
Publishing Group, 2011, pp. 117–23, doi:10.1038/ncb2154.
short: N. Plachta, M.T. Bollenbach, S. Pease, S. Fraser, P. Pantazis, Nature Cell
Biology 13 (2011) 117–123.
date_created: 2018-12-11T12:03:17Z
date_published: 2011-01-23T00:00:00Z
date_updated: 2021-01-12T07:43:24Z
day: '23'
department:
- _id: ToBo
doi: 10.1038/ncb2154
intvolume: ' 13'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 117 - 123
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '2971'
scopus_import: 1
status: public
title: Oct4 kinetics predict cell lineage patterning in the early mammalian embryo
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2011'
...
---
_id: '3505'
abstract:
- lang: eng
text: Cell migration on two-dimensional (2D) substrates follows entirely different
rules than cell migration in three-dimensional (3D) environments. This is especially
relevant for leukocytes that are able to migrate in the absence of adhesion receptors
within the confined geometry of artificial 3D extracellular matrix scaffolds and
within the interstitial space in vivo. Here, we describe in detail a simple and
economical protocol to visualize dendritic cell migration in 3D collagen scaffolds
along chemotactic gradients. This method can be adapted to other cell types and
may serve as a physiologically relevant paradigm for the directed locomotion of
most amoeboid cells.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
article_type: original
author:
- 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: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
citation:
ama: Sixt MK, Lämmermann T. In vitro analysis of chemotactic leukocyte migration
in 3D environments. Cell Migration. 2011;769:149-165. doi:10.1007/978-1-61779-207-6_11
apa: Sixt, M. K., & Lämmermann, T. (2011). In vitro analysis of chemotactic
leukocyte migration in 3D environments. Cell Migration. Springer. https://doi.org/10.1007/978-1-61779-207-6_11
chicago: Sixt, Michael K, and Tim Lämmermann. “In Vitro Analysis of Chemotactic
Leukocyte Migration in 3D Environments.” Cell Migration. Springer, 2011.
https://doi.org/10.1007/978-1-61779-207-6_11.
ieee: M. K. Sixt and T. Lämmermann, “In vitro analysis of chemotactic leukocyte
migration in 3D environments,” Cell Migration, vol. 769. Springer, pp.
149–165, 2011.
ista: Sixt MK, Lämmermann T. 2011. In vitro analysis of chemotactic leukocyte migration
in 3D environments. Cell Migration. 769, 149–165.
mla: Sixt, Michael K., and Tim Lämmermann. “In Vitro Analysis of Chemotactic Leukocyte
Migration in 3D Environments.” Cell Migration, vol. 769, Springer, 2011,
pp. 149–65, doi:10.1007/978-1-61779-207-6_11.
short: M.K. Sixt, T. Lämmermann, Cell Migration 769 (2011) 149–165.
date_created: 2018-12-11T12:03:41Z
date_published: 2011-05-17T00:00:00Z
date_updated: 2021-01-12T07:43:55Z
day: '17'
department:
- _id: MiSi
doi: 10.1007/978-1-61779-207-6_11
intvolume: ' 769'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://pure.mpg.de/pubman/item/item_3219628_1/component/file_3219630/Sixt%20et%20al..pdf
month: '05'
oa: 1
oa_version: Published Version
page: 149 - 165
publication: Cell Migration
publication_status: published
publisher: Springer
publist_id: '2882'
quality_controlled: '1'
status: public
title: In vitro analysis of chemotactic leukocyte migration in 3D environments
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 769
year: '2011'
...
---
_id: '3784'
abstract:
- lang: eng
text: Advanced stages of Scyllarus phyllosoma larvae were collected by demersal
trawling during fishery research surveys in the western Mediterranean Sea in 2003–2005.
Nucleotide sequence analysis of the mitochondrial 16S rDNA gene allowed the final-stage
phyllosoma of Scyllarus arctus to be identified among these larvae. Its morphology
is described and illustrated. This constitutes the second complete description
of a Scyllaridae phyllosoma with its specific identity being validated by molecular
techniques (the first was S. pygmaeus). These results also solved a long lasting
taxonomic anomaly of several species assigned to the ancient genus Phyllosoma
Leach, 1814. Detailed examination indicated that the final-stage phyllosoma of
S. arctus shows closer affinities with the American scyllarid Scyllarus depressus
or with the Australian Scyllarus sp. b (sensu Phillips et al., 1981) than to its
sympatric species S. pygmaeus.
article_processing_charge: No
article_type: original
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Guillermo
full_name: Guerao, Guillermo
last_name: Guerao
- first_name: Paul
full_name: Clark, Paul
last_name: Clark
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
citation:
ama: 'Palero F, Guerao G, Clark P, Abello P. Scyllarus arctus (Crustacea: Decapoda:
Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological
description. Journal of the Marine Biological Association of the United Kingdom.
2011;91(2):485-492. doi:10.1017/S0025315410000287'
apa: 'Palero, F., Guerao, G., Clark, P., & Abello, P. (2011). Scyllarus arctus
(Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis,
with morphological description. Journal of the Marine Biological Association
of the United Kingdom. Cambridge University Press. https://doi.org/10.1017/S0025315410000287'
chicago: 'Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Scyllarus
Arctus (Crustacea: Decapoda: Scyllaridae) Final Stage Phyllosoma Identified by
DNA Analysis, with Morphological Description.” Journal of the Marine Biological
Association of the United Kingdom. Cambridge University Press, 2011. https://doi.org/10.1017/S0025315410000287.'
ieee: 'F. Palero, G. Guerao, P. Clark, and P. Abello, “Scyllarus arctus (Crustacea:
Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with
morphological description,” Journal of the Marine Biological Association of
the United Kingdom, vol. 91, no. 2. Cambridge University Press, pp. 485–492,
2011.'
ista: 'Palero F, Guerao G, Clark P, Abello P. 2011. Scyllarus arctus (Crustacea:
Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with
morphological description. Journal of the Marine Biological Association of the
United Kingdom. 91(2), 485–492.'
mla: 'Palero, Ferran, et al. “Scyllarus Arctus (Crustacea: Decapoda: Scyllaridae)
Final Stage Phyllosoma Identified by DNA Analysis, with Morphological Description.”
Journal of the Marine Biological Association of the United Kingdom, vol.
91, no. 2, Cambridge University Press, 2011, pp. 485–92, doi:10.1017/S0025315410000287.'
short: F. Palero, G. Guerao, P. Clark, P. Abello, Journal of the Marine Biological
Association of the United Kingdom 91 (2011) 485–492.
date_created: 2018-12-11T12:05:09Z
date_published: 2011-03-01T00:00:00Z
date_updated: 2021-01-12T07:52:10Z
day: '01'
department:
- _id: NiBa
doi: 10.1017/S0025315410000287
intvolume: ' 91'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://digital.csic.es/bitstream/10261/32783/3/Palero_et_al_2011.pdf
month: '03'
oa: 1
oa_version: Published Version
page: 485 - 492
publication: Journal of the Marine Biological Association of the United Kingdom
publication_status: published
publisher: Cambridge University Press
publist_id: '2443'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma
identified by DNA analysis, with morphological description'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2011'
...
---
_id: '3781'
abstract:
- lang: eng
text: We bound the difference in length of two curves in terms of their total curvatures
and the Fréchet distance. The bound is independent of the dimension of the ambient
Euclidean space, it improves upon a bound by Cohen-Steiner and Edelsbrunner, and
it generalizes a result by Fáry and Chakerian.
acknowledgement: Funded by Graduate Aid in Areas of National Need (GAANN) Fellowship.
author:
- first_name: Brittany Terese
full_name: Fasy, Brittany Terese
id: F65D502E-E68D-11E9-9252-C644099818F6
last_name: Fasy
citation:
ama: Fasy BT. The difference in length of curves in R^n. Acta Sci Math (Szeged).
2011;77(1-2):359-367.
apa: Fasy, B. T. (2011). The difference in length of curves in R^n. Acta Sci.
Math. (Szeged). Szegedi Tudományegyetem.
chicago: Fasy, Brittany Terese. “The Difference in Length of Curves in R^n.” Acta
Sci. Math. (Szeged). Szegedi Tudományegyetem, 2011.
ieee: B. T. Fasy, “The difference in length of curves in R^n,” Acta Sci. Math.
(Szeged), vol. 77, no. 1–2. Szegedi Tudományegyetem, pp. 359–367, 2011.
ista: Fasy BT. 2011. The difference in length of curves in R^n. Acta Sci. Math.
(Szeged). 77(1–2), 359–367.
mla: Fasy, Brittany Terese. “The Difference in Length of Curves in R^n.” Acta
Sci. Math. (Szeged), vol. 77, no. 1–2, Szegedi Tudományegyetem, 2011, pp.
359–67.
short: B.T. Fasy, Acta Sci. Math. (Szeged) 77 (2011) 359–367.
date_created: 2018-12-11T12:05:08Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:09Z
day: '01'
department:
- _id: HeEd
intvolume: ' 77'
issue: 1-2
language:
- iso: eng
month: '01'
oa_version: None
page: 359 - 367
publication: Acta Sci. Math. (Szeged)
publication_status: published
publisher: Szegedi Tudományegyetem
publist_id: '2446'
quality_controlled: '1'
status: public
title: The difference in length of curves in R^n
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 77
year: '2011'
...
---
_id: '3796'
abstract:
- lang: eng
text: We address the problem of covering ℝ n with congruent balls, while minimizing
the number of balls that contain an average point. Considering the 1-parameter
family of lattices defined by stretching or compressing the integer grid in diagonal
direction, we give a closed formula for the covering density that depends on the
distortion parameter. We observe that our family contains the thinnest lattice
coverings in dimensions 2 to 5. We also consider the problem of packing congruent
balls in ℝ n , for which we give a closed formula for the packing density as well.
Again we observe that our family contains optimal configurations, this time densest
packings in dimensions 2 and 3.
alternative_title:
- LNCS
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
citation:
ama: 'Edelsbrunner H, Kerber M. Covering and packing with spheres by diagonal distortion
in R^n. In: Calude C, Rozenberg G, Salomaa A, eds. Rainbow of Computer Science.
Vol 6570. Dedicated to Hermann Maurer on the Occasion of His 70th Birthday. Springer;
2011:20-35. doi:10.1007/978-3-642-19391-0_2'
apa: Edelsbrunner, H., & Kerber, M. (2011). Covering and packing with spheres
by diagonal distortion in R^n. In C. Calude, G. Rozenberg, & A. Salomaa (Eds.),
Rainbow of Computer Science (Vol. 6570, pp. 20–35). Springer. https://doi.org/10.1007/978-3-642-19391-0_2
chicago: Edelsbrunner, Herbert, and Michael Kerber. “Covering and Packing with Spheres
by Diagonal Distortion in R^n.” In Rainbow of Computer Science, edited
by Cristian Calude, Grzegorz Rozenberg, and Arto Salomaa, 6570:20–35. Dedicated
to Hermann Maurer on the Occasion of His 70th Birthday. Springer, 2011. https://doi.org/10.1007/978-3-642-19391-0_2.
ieee: H. Edelsbrunner and M. Kerber, “Covering and packing with spheres by diagonal
distortion in R^n,” in Rainbow of Computer Science, vol. 6570, C. Calude,
G. Rozenberg, and A. Salomaa, Eds. Springer, 2011, pp. 20–35.
ista: 'Edelsbrunner H, Kerber M. 2011.Covering and packing with spheres by diagonal
distortion in R^n. In: Rainbow of Computer Science. LNCS, vol. 6570, 20–35.'
mla: Edelsbrunner, Herbert, and Michael Kerber. “Covering and Packing with Spheres
by Diagonal Distortion in R^n.” Rainbow of Computer Science, edited by
Cristian Calude et al., vol. 6570, Springer, 2011, pp. 20–35, doi:10.1007/978-3-642-19391-0_2.
short: H. Edelsbrunner, M. Kerber, in:, C. Calude, G. Rozenberg, A. Salomaa (Eds.),
Rainbow of Computer Science, Springer, 2011, pp. 20–35.
date_created: 2018-12-11T12:05:13Z
date_published: 2011-05-03T00:00:00Z
date_updated: 2021-01-12T07:52:15Z
day: '03'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/978-3-642-19391-0_2
editor:
- first_name: Cristian
full_name: Calude, Cristian
last_name: Calude
- first_name: Grzegorz
full_name: Rozenberg, Grzegorz
last_name: Rozenberg
- first_name: Arto
full_name: Salomaa, Arto
last_name: Salomaa
file:
- access_level: open_access
checksum: aaf22b4d7bd4277ffe8db532119cf474
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:42Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4640'
file_name: IST-2016-539-v1+1_2011-B-01-CoveringPacking.pdf
file_size: 436875
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 6570'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 20 - 35
publication: Rainbow of Computer Science
publication_status: published
publisher: Springer
publist_id: '2427'
pubrep_id: '539'
quality_controlled: '1'
series_title: Dedicated to Hermann Maurer on the Occasion of His 70th Birthday
status: public
title: Covering and packing with spheres by diagonal distortion in R^n
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6570
year: '2011'
...
---
_id: '3381'
abstract:
- lang: eng
text: In this survey, we compare several languages for specifying Markovian population
models such as queuing networks and chemical reaction networks. All these languages
— matrix descriptions, stochastic Petri nets, stoichiometric equations, stochastic
process algebras, and guarded command models — describe continuous-time Markov
chains, but they differ according to important properties, such as compositionality,
expressiveness and succinctness, executability, and ease of use. Moreover, they
provide different support for checking the well-formedness of a model and for
analyzing a model.
author:
- 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: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
citation:
ama: 'Henzinger TA, Jobstmann B, Wolf V. Formalisms for specifying Markovian population
models. IJFCS: International Journal of Foundations of Computer Science.
2011;22(4):823-841. doi:10.1142/S0129054111008441'
apa: 'Henzinger, T. A., Jobstmann, B., & Wolf, V. (2011). Formalisms for specifying
Markovian population models. IJFCS: International Journal of Foundations of
Computer Science. World Scientific Publishing. https://doi.org/10.1142/S0129054111008441'
chicago: 'Henzinger, Thomas A, Barbara Jobstmann, and Verena Wolf. “Formalisms for
Specifying Markovian Population Models.” IJFCS: International Journal of Foundations
of Computer Science. World Scientific Publishing, 2011. https://doi.org/10.1142/S0129054111008441.'
ieee: 'T. A. Henzinger, B. Jobstmann, and V. Wolf, “Formalisms for specifying Markovian
population models,” IJFCS: International Journal of Foundations of Computer
Science, vol. 22, no. 4. World Scientific Publishing, pp. 823–841, 2011.'
ista: 'Henzinger TA, Jobstmann B, Wolf V. 2011. Formalisms for specifying Markovian
population models. IJFCS: International Journal of Foundations of Computer Science.
22(4), 823–841.'
mla: 'Henzinger, Thomas A., et al. “Formalisms for Specifying Markovian Population
Models.” IJFCS: International Journal of Foundations of Computer Science,
vol. 22, no. 4, World Scientific Publishing, 2011, pp. 823–41, doi:10.1142/S0129054111008441.'
short: 'T.A. Henzinger, B. Jobstmann, V. Wolf, IJFCS: International Journal of Foundations
of Computer Science 22 (2011) 823–841.'
date_created: 2018-12-11T12:03:00Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2023-02-23T11:45:03Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1142/S0129054111008441
file:
- access_level: open_access
checksum: df88431872586c773fbcfea37d7b36a2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:45Z
date_updated: 2020-07-14T12:46:11Z
file_id: '4707'
file_name: IST-2016-628-v1+1_journals-ijfcs-HenzingerJW11.pdf
file_size: 222840
relation: main_file
file_date_updated: 2020-07-14T12:46:11Z
has_accepted_license: '1'
intvolume: ' 22'
issue: '4'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 823 - 841
publication: 'IJFCS: International Journal of Foundations of Computer Science'
publication_status: published
publisher: World Scientific Publishing
publist_id: '3226'
pubrep_id: '628'
quality_controlled: '1'
related_material:
record:
- id: '3841'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Formalisms for specifying Markovian population models
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2011'
...
---
_id: '386'
abstract:
- lang: eng
text: 'We present a detailed study of the local density of states (LDOS) associated
with the surface-state band near a step edge of the strong topological insulator
Bi2Te3 and reveal a one-dimensional bound state that runs parallel to the step
edge and is bound to it at some characteristic distance. This bound state is clearly
observed in the bulk gap region, while it becomes entangled with the oscillations
of the warped surface band at high energy, and with the valence-band states near
the Dirac point. We obtain excellent fits to theoretical predictions [Alpichshev,
2011] that properly incorporate the three-dimensional nature of the problem to
the surface state. Fitting the data at different energies, we can recalculate
the LDOS originating from the Dirac band without the contribution of the bulk
bands or incoherent tunneling effects. '
article_processing_charge: No
article_type: original
author:
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
- first_name: J G
full_name: Analytis, J G
last_name: Analytis
- first_name: J H
full_name: Chu, J H
last_name: Chu
- first_name: I R
full_name: Fisher, I R
last_name: Fisher
- first_name: A
full_name: Kapitulnik, A
last_name: Kapitulnik
citation:
ama: Alpichshev Z, Analytis JG, Chu JH, Fisher IR, Kapitulnik A. STM imaging of
a bound state along a step on the surface of the topological insulator Bi2Te3.
Physical Review B - Condensed Matter and Materials Physics. 2011;84(4).
doi:10.1103/PhysRevB.84.041104
apa: Alpichshev, Z., Analytis, J. G., Chu, J. H., Fisher, I. R., & Kapitulnik,
A. (2011). STM imaging of a bound state along a step on the surface of the topological
insulator Bi2Te3. Physical Review B - Condensed Matter and Materials Physics.
American Physical Society. https://doi.org/10.1103/PhysRevB.84.041104
chicago: Alpichshev, Zhanybek, J G Analytis, J H Chu, I R Fisher, and A Kapitulnik.
“STM Imaging of a Bound State along a Step on the Surface of the Topological Insulator
Bi2Te3.” Physical Review B - Condensed Matter and Materials Physics. American
Physical Society, 2011. https://doi.org/10.1103/PhysRevB.84.041104.
ieee: Z. Alpichshev, J. G. Analytis, J. H. Chu, I. R. Fisher, and A. Kapitulnik,
“STM imaging of a bound state along a step on the surface of the topological insulator
Bi2Te3,” Physical Review B - Condensed Matter and Materials Physics, vol.
84, no. 4. American Physical Society, 2011.
ista: Alpichshev Z, Analytis JG, Chu JH, Fisher IR, Kapitulnik A. 2011. STM imaging
of a bound state along a step on the surface of the topological insulator Bi2Te3.
Physical Review B - Condensed Matter and Materials Physics. 84(4).
mla: Alpichshev, Zhanybek, et al. “STM Imaging of a Bound State along a Step on
the Surface of the Topological Insulator Bi2Te3.” Physical Review B - Condensed
Matter and Materials Physics, vol. 84, no. 4, American Physical Society, 2011,
doi:10.1103/PhysRevB.84.041104.
short: Z. Alpichshev, J.G. Analytis, J.H. Chu, I.R. Fisher, A. Kapitulnik, Physical
Review B - Condensed Matter and Materials Physics 84 (2011).
date_created: 2018-12-11T11:46:10Z
date_published: 2011-07-21T00:00:00Z
date_updated: 2021-01-12T07:52:44Z
day: '21'
doi: 10.1103/PhysRevB.84.041104
extern: '1'
external_id:
arxiv:
- '1003.2233'
intvolume: ' 84'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1003.2233
month: '07'
oa: 1
oa_version: Preprint
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '7443'
quality_controlled: '1'
status: public
title: STM imaging of a bound state along a step on the surface of the topological
insulator Bi2Te3
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 84
year: '2011'
...
---
_id: '3315'
abstract:
- lang: eng
text: We consider two-player games played in real time on game structures with clocks
where the objectives of players are described using parity conditions. The games
are concurrent in that at each turn, both players independently propose a time
delay and an action, and the action with the shorter delay is chosen. To prevent
a player from winning by blocking time, we restrict each player to play strategies
that ensure that the player cannot be responsible for causing a zeno run. First,
we present an efficient reduction of these games to turn-based (i.e., not concurrent)
finite-state (i.e., untimed) parity games. Our reduction improves the best known
complexity for solving timed parity games. Moreover, the rich class of algorithms
for classical parity games can now be applied to timed parity games. The states
of the resulting game are based on clock regions of the original game, and the
state space of the finite game is linear in the size of the region graph. Second,
we consider two restricted classes of strategies for the player that represents
the controller in a real-time synthesis problem, namely, limit-robust and bounded-robust
winning strategies. Using a limit-robust winning strategy, the controller cannot
choose an exact real-valued time delay but must allow for some nonzero jitter
in each of its actions. If there is a given lower bound on the jitter, then the
strategy is bounded-robust winning. We show that exact strategies are more powerful
than limit-robust strategies, which are more powerful than bounded-robust winning
strategies for any bound. For both kinds of robust strategies, we present efficient
reductions to standard timed automaton games. These reductions provide algorithms
for the synthesis of robust real-time controllers.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: Vinayak
full_name: Prabhu, Vinayak
last_name: Prabhu
citation:
ama: 'Chatterjee K, Henzinger TA, Prabhu V. Timed parity games: Complexity and robustness.
Logical Methods in Computer Science. 2011;7(4). doi:10.2168/LMCS-7(4:8)2011'
apa: 'Chatterjee, K., Henzinger, T. A., & Prabhu, V. (2011). Timed parity games:
Complexity and robustness. Logical Methods in Computer Science. International
Federation of Computational Logic. https://doi.org/10.2168/LMCS-7(4:8)2011'
chicago: 'Chatterjee, Krishnendu, Thomas A Henzinger, and Vinayak Prabhu. “Timed
Parity Games: Complexity and Robustness.” Logical Methods in Computer Science.
International Federation of Computational Logic, 2011. https://doi.org/10.2168/LMCS-7(4:8)2011.'
ieee: 'K. Chatterjee, T. A. Henzinger, and V. Prabhu, “Timed parity games: Complexity
and robustness,” Logical Methods in Computer Science, vol. 7, no. 4. International
Federation of Computational Logic, 2011.'
ista: 'Chatterjee K, Henzinger TA, Prabhu V. 2011. Timed parity games: Complexity
and robustness. Logical Methods in Computer Science. 7(4).'
mla: 'Chatterjee, Krishnendu, et al. “Timed Parity Games: Complexity and Robustness.”
Logical Methods in Computer Science, vol. 7, no. 4, International Federation
of Computational Logic, 2011, doi:10.2168/LMCS-7(4:8)2011.'
short: K. Chatterjee, T.A. Henzinger, V. Prabhu, Logical Methods in Computer Science
7 (2011).
date_created: 2018-12-11T12:02:37Z
date_published: 2011-12-14T00:00:00Z
date_updated: 2023-02-23T11:46:35Z
day: '14'
ddc:
- '000'
- '005'
department:
- _id: KrCh
- _id: ToHe
doi: 10.2168/LMCS-7(4:8)2011
ec_funded: 1
file:
- access_level: open_access
checksum: 3480e1594bbef25ff7462fa93a8a814e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:42Z
date_updated: 2020-07-14T12:46:07Z
file_id: '5231'
file_name: IST-2016-86-v2+1_1011.0688_3_.pdf
file_size: 588863
relation: main_file
file_date_updated: 2020-07-14T12:46:07Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
publication: Logical Methods in Computer Science
publication_status: published
publisher: International Federation of Computational Logic
publist_id: '3324'
pubrep_id: '506'
quality_controlled: '1'
related_material:
record:
- id: '3876'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: 'Timed parity games: Complexity and robustness'
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2011'
...
---
_id: '3965'
abstract:
- lang: eng
text: The elevation function on a smoothly embedded 2-manifold in R-3 reflects the
multiscale topography of cavities and protrusions as local maxima. The function
has been useful in identifying coarse docking configurations for protein pairs.
Transporting the concept from the smooth to the piecewise linear category, this
paper describes an algorithm for finding all local maxima. While its worst-case
running time is the same as of the algorithm used in prior work, its performance
in practice is orders of magnitudes superior. We cast light on this improvement
by relating the running time to the total absolute Gaussian curvature of the 2-manifold.
author:
- first_name: Bei
full_name: Wang, Bei
last_name: Wang
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Dmitriy
full_name: Morozov, Dmitriy
last_name: Morozov
citation:
ama: Wang B, Edelsbrunner H, Morozov D. Computing elevation maxima by searching
the Gauss sphere. Journal of Experimental Algorithmics. 2011;16(2.2):1-13.
doi:10.1145/1963190.1970375
apa: Wang, B., Edelsbrunner, H., & Morozov, D. (2011). Computing elevation maxima
by searching the Gauss sphere. Journal of Experimental Algorithmics. ACM.
https://doi.org/10.1145/1963190.1970375
chicago: Wang, Bei, Herbert Edelsbrunner, and Dmitriy Morozov. “Computing Elevation
Maxima by Searching the Gauss Sphere.” Journal of Experimental Algorithmics.
ACM, 2011. https://doi.org/10.1145/1963190.1970375.
ieee: B. Wang, H. Edelsbrunner, and D. Morozov, “Computing elevation maxima by searching
the Gauss sphere,” Journal of Experimental Algorithmics, vol. 16, no. 2.2.
ACM, pp. 1–13, 2011.
ista: Wang B, Edelsbrunner H, Morozov D. 2011. Computing elevation maxima by searching
the Gauss sphere. Journal of Experimental Algorithmics. 16(2.2), 1–13.
mla: Wang, Bei, et al. “Computing Elevation Maxima by Searching the Gauss Sphere.”
Journal of Experimental Algorithmics, vol. 16, no. 2.2, ACM, 2011, pp.
1–13, doi:10.1145/1963190.1970375.
short: B. Wang, H. Edelsbrunner, D. Morozov, Journal of Experimental Algorithmics
16 (2011) 1–13.
date_created: 2018-12-11T12:06:09Z
date_published: 2011-05-01T00:00:00Z
date_updated: 2021-01-12T07:53:31Z
day: '01'
department:
- _id: HeEd
doi: 10.1145/1963190.1970375
intvolume: ' 16'
issue: '2.2'
language:
- iso: eng
month: '05'
oa_version: None
page: 1 - 13
publication: Journal of Experimental Algorithmics
publication_status: published
publisher: ACM
publist_id: '2161'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computing elevation maxima by searching the Gauss sphere
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2011'
...
---
_id: '3086'
abstract:
- lang: eng
text: PIN-FORMED (PIN)-dependent auxin transport is essential for plant development
and its modulation in response to the environment or endogenous signals. A NON-PHOTOTROPIC
HYPOCOTYL 3 (NPH3)-like protein, MACCHI-BOU 4 (MAB4), has been shown to control
PIN1 localization during organ formation, but its contribution is limited. The
Arabidopsis genome contains four genes, MAB4/ENP/NPY1-LIKE1 (MEL1), MEL2, MEL3
and MEL4, highly homologous to MAB4. Genetic analysis disclosed functional redundancy
between MAB4 and MEL genes in regulation of not only organ formation but also
of root gravitropism, revealing that NPH3 family proteins have a wider range of
functions than previously suspected. Multiple mutants showed severe reduction
in PIN abundance and PIN polar localization, leading to defective expression of
an auxin responsive marker DR5rev::GFP. Pharmacological analyses and fluorescence
recovery after photo-bleaching experiments showed that mel mutations increase
PIN2 internalization from the plasma membrane, but affect neither intracellular
PIN2 trafficking nor PIN2 lateral diffusion at the plasma membrane. Notably, all
MAB4 subfamily proteins show polar localization at the cell periphery in plants.
The MAB4 polarity was almost identical to PIN polarity. Our results suggest that
the MAB4 subfamily proteins specifically retain PIN proteins in a polarized manner
at the plasma membrane, thus controlling directional auxin transport and plant
development.
author:
- first_name: Masahiko
full_name: Furutani, Masahiko
last_name: Furutani
- first_name: Norihito
full_name: Sakamoto, Norihito
last_name: Sakamoto
- first_name: Shuhei
full_name: Yoshida, Shuhei
last_name: Yoshida
- first_name: Takahito
full_name: Kajiwara, Takahito
last_name: Kajiwara
- first_name: Hélène
full_name: Robert, Hélène S
last_name: Robert
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Masao
full_name: Tasaka, Masao
last_name: Tasaka
citation:
ama: Furutani M, Sakamoto N, Yoshida S, et al. Polar localized NPH3-like proteins
regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers. Development.
2011;138(10):2069-2078. doi:10.1242/dev.057745
apa: Furutani, M., Sakamoto, N., Yoshida, S., Kajiwara, T., Robert, H., Friml, J.,
& Tasaka, M. (2011). Polar localized NPH3-like proteins regulate polarity
and endocytosis of PIN-FORMED auxin efflux carriers. Development. Company
of Biologists. https://doi.org/10.1242/dev.057745
chicago: Furutani, Masahiko, Norihito Sakamoto, Shuhei Yoshida, Takahito Kajiwara,
Hélène Robert, Jiří Friml, and Masao Tasaka. “Polar Localized NPH3-like Proteins
Regulate Polarity and Endocytosis of PIN-FORMED Auxin Efflux Carriers.” Development.
Company of Biologists, 2011. https://doi.org/10.1242/dev.057745.
ieee: M. Furutani et al., “Polar localized NPH3-like proteins regulate polarity
and endocytosis of PIN-FORMED auxin efflux carriers,” Development, vol.
138, no. 10. Company of Biologists, pp. 2069–2078, 2011.
ista: Furutani M, Sakamoto N, Yoshida S, Kajiwara T, Robert H, Friml J, Tasaka M.
2011. Polar localized NPH3-like proteins regulate polarity and endocytosis of
PIN-FORMED auxin efflux carriers. Development. 138(10), 2069–2078.
mla: Furutani, Masahiko, et al. “Polar Localized NPH3-like Proteins Regulate Polarity
and Endocytosis of PIN-FORMED Auxin Efflux Carriers.” Development, vol.
138, no. 10, Company of Biologists, 2011, pp. 2069–78, doi:10.1242/dev.057745.
short: M. Furutani, N. Sakamoto, S. Yoshida, T. Kajiwara, H. Robert, J. Friml, M.
Tasaka, Development 138 (2011) 2069–2078.
date_created: 2018-12-11T12:01:17Z
date_published: 2011-05-01T00:00:00Z
date_updated: 2021-01-12T07:40:57Z
day: '01'
doi: 10.1242/dev.057745
extern: 1
intvolume: ' 138'
issue: '10'
month: '05'
page: 2069 - 2078
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '3615'
quality_controlled: 0
status: public
title: Polar localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED
auxin efflux carriers
type: journal_article
volume: 138
year: '2011'
...
---
_id: '3087'
abstract:
- lang: eng
text: Endocytosis is a crucial mechanism by which eukaryotic cells internalize extracellular
and plasma membrane material, and it is required for a multitude of cellular and
developmental processes in unicellular and multicellular organisms. In animals
and yeast, the best characterized pathway for endocytosis depends on the function
of the vesicle coat protein clathrin. Clathrinmediated endocytosis has recently
been demonstrated also in plant cells, but its physiological and developmental
roles remain unclear. Here, we assessed the roles of the clathrin-mediated mechanism
of endocytosis in plants by genetic means. We interfered with clathrin heavy chain
(CHC) function through mutants and dominant-negative approaches in Arabidopsis
thaliana and established tools to manipulate clathrin function in a cell type-specific
manner. The chc2 single mutants and dominant-negative CHC1 (HUB) transgenic lines
were defective in bulk endocytosis as well as in internalization of prominent
plasma membrane proteins. Interference with clathrin-mediated endocytosis led
to defects in constitutive endocytic recycling of PIN auxin transporters and their
polar distribution in embryos and roots. Consistent with this, these lines had
altered auxin distribution patterns and associated auxin transport-related phenotypes,
such as aberrant embryo patterning, imperfect cotyledon specification, agravitropic
growth, and impaired lateral root organogenesis. Together, these data demonstrate
a fundamental role for clathrin function in cell polarity, growth, patterning,
and organogenesis in plants.
author:
- first_name: Saeko
full_name: Kitakura, Saeko
last_name: Kitakura
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Christian
full_name: Löfke, Christian
last_name: Löfke
- first_name: Thomas
full_name: Teichmann, Thomas
last_name: Teichmann
- first_name: Hirokazu
full_name: Tanaka, Hirokazu
last_name: Tanaka
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Kitakura S, Vanneste S, Robert S, et al. Clathrin mediates endocytosis and
polar distribution of PIN auxin transporters in Arabidopsis. Plant Cell.
2011;23(5):1920-1931. doi:10.1105/tpc.111.083030
apa: Kitakura, S., Vanneste, S., Robert, S., Löfke, C., Teichmann, T., Tanaka, H.,
& Friml, J. (2011). Clathrin mediates endocytosis and polar distribution of
PIN auxin transporters in Arabidopsis. Plant Cell. American Society of
Plant Biologists. https://doi.org/10.1105/tpc.111.083030
chicago: Kitakura, Saeko, Steffen Vanneste, Stéphanie Robert, Christian Löfke, Thomas
Teichmann, Hirokazu Tanaka, and Jiří Friml. “Clathrin Mediates Endocytosis and
Polar Distribution of PIN Auxin Transporters in Arabidopsis.” Plant Cell.
American Society of Plant Biologists, 2011. https://doi.org/10.1105/tpc.111.083030.
ieee: S. Kitakura et al., “Clathrin mediates endocytosis and polar distribution
of PIN auxin transporters in Arabidopsis,” Plant Cell, vol. 23, no. 5.
American Society of Plant Biologists, pp. 1920–1931, 2011.
ista: Kitakura S, Vanneste S, Robert S, Löfke C, Teichmann T, Tanaka H, Friml J.
2011. Clathrin mediates endocytosis and polar distribution of PIN auxin transporters
in Arabidopsis. Plant Cell. 23(5), 1920–1931.
mla: Kitakura, Saeko, et al. “Clathrin Mediates Endocytosis and Polar Distribution
of PIN Auxin Transporters in Arabidopsis.” Plant Cell, vol. 23, no. 5,
American Society of Plant Biologists, 2011, pp. 1920–31, doi:10.1105/tpc.111.083030.
short: S. Kitakura, S. Vanneste, S. Robert, C. Löfke, T. Teichmann, H. Tanaka, J.
Friml, Plant Cell 23 (2011) 1920–1931.
date_created: 2018-12-11T12:01:18Z
date_published: 2011-05-01T00:00:00Z
date_updated: 2021-01-12T07:40:57Z
day: '01'
doi: 10.1105/tpc.111.083030
extern: 1
intvolume: ' 23'
issue: '5'
month: '05'
page: 1920 - 1931
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3614'
quality_controlled: 0
status: public
title: Clathrin mediates endocytosis and polar distribution of PIN auxin transporters
in Arabidopsis
type: journal_article
volume: 23
year: '2011'
...
---
_id: '3085'
abstract:
- lang: eng
text: Phototropism is an adaptation response, through which plants grow towards
the light. It involves light perception and asymmetric distribution of the plant
hormone auxin. Here we identify a crucial part of the mechanism for phototropism,
revealing how light perception initiates auxin redistribution that leads to directional
growth. We show that light polarizes the cellular localization of the auxin efflux
carrier PIN3 in hypocotyl endodermis cells, resulting in changes in auxin distribution
and differential growth. In the dark, high expression and activity of the PINOID
(PID) kinase correlates with apolar targeting of PIN3 to all cell sides. Following
illumination, light represses PINOID transcription and PIN3 is polarized specifically
to the inner cell sides by GNOM ARF GTPase GEF (guanine nucleotide exchange factor)-dependent
trafficking. Thus, differential trafficking at the shaded and illuminated hypocotyl
side aligns PIN3 polarity with the light direction, and presumably redirects auxin
flow towards the shaded side, where auxin promotes growth, causing hypocotyls
to bend towards the light. Our results imply that PID phosphorylation-dependent
recruitment of PIN proteins into distinct trafficking pathways is a mechanism
to polarize auxin fluxes in response to different environmental and endogenous
cues.
author:
- first_name: Zhaojun
full_name: Ding, Zhaojun
last_name: Ding
- first_name: Carlos
full_name: Galván-Ampudia, Carlos S
last_name: Galván Ampudia
- first_name: Emilie
full_name: Demarsy, Emilie
last_name: Demarsy
- first_name: Łukasz
full_name: Łangowski, Łukasz
last_name: Łangowski
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Yuanwei
full_name: Fan, Yuanwei
last_name: Fan
- first_name: Miyo
full_name: Morita, Miyo T
last_name: Morita
- first_name: Masao
full_name: Tasaka, Masao
last_name: Tasaka
- first_name: Christian
full_name: Fankhauser, Christian
last_name: Fankhauser
- first_name: Remko
full_name: Offringa, Remko
last_name: Offringa
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Ding Z, Galván Ampudia C, Demarsy E, et al. Light-mediated polarization of
the PIN3 auxin transporter for the phototropic response in Arabidopsis. Nature
Cell Biology. 2011;13(4):447-453. doi:10.1038/ncb2208
apa: Ding, Z., Galván Ampudia, C., Demarsy, E., Łangowski, Ł., Kleine Vehn, J.,
Fan, Y., … Friml, J. (2011). Light-mediated polarization of the PIN3 auxin transporter
for the phototropic response in Arabidopsis. Nature Cell Biology. Nature
Publishing Group. https://doi.org/10.1038/ncb2208
chicago: Ding, Zhaojun, Carlos Galván Ampudia, Emilie Demarsy, Łukasz Łangowski,
Jürgen Kleine Vehn, Yuanwei Fan, Miyo Morita, et al. “Light-Mediated Polarization
of the PIN3 Auxin Transporter for the Phototropic Response in Arabidopsis.” Nature
Cell Biology. Nature Publishing Group, 2011. https://doi.org/10.1038/ncb2208.
ieee: Z. Ding et al., “Light-mediated polarization of the PIN3 auxin transporter
for the phototropic response in Arabidopsis,” Nature Cell Biology, vol.
13, no. 4. Nature Publishing Group, pp. 447–453, 2011.
ista: Ding Z, Galván Ampudia C, Demarsy E, Łangowski Ł, Kleine Vehn J, Fan Y, Morita
M, Tasaka M, Fankhauser C, Offringa R, Friml J. 2011. Light-mediated polarization
of the PIN3 auxin transporter for the phototropic response in Arabidopsis. Nature
Cell Biology. 13(4), 447–453.
mla: Ding, Zhaojun, et al. “Light-Mediated Polarization of the PIN3 Auxin Transporter
for the Phototropic Response in Arabidopsis.” Nature Cell Biology, vol.
13, no. 4, Nature Publishing Group, 2011, pp. 447–53, doi:10.1038/ncb2208.
short: Z. Ding, C. Galván Ampudia, E. Demarsy, Ł. Łangowski, J. Kleine Vehn, Y.
Fan, M. Morita, M. Tasaka, C. Fankhauser, R. Offringa, J. Friml, Nature Cell Biology
13 (2011) 447–453.
date_created: 2018-12-11T12:01:17Z
date_published: 2011-04-01T00:00:00Z
date_updated: 2021-01-12T07:40:57Z
day: '01'
doi: 10.1038/ncb2208
extern: 1
intvolume: ' 13'
issue: '4'
month: '04'
page: 447 - 453
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3616'
quality_controlled: 0
status: public
title: Light-mediated polarization of the PIN3 auxin transporter for the phototropic
response in Arabidopsis
type: journal_article
volume: 13
year: '2011'
...
---
_id: '3084'
abstract:
- lang: eng
text: |2-
A central question in developmental biology concerns the mechanism of generation and maintenance of cell polarity, because these processes are essential for many cellular functions and multicellular development [1]. In plants, cell polarity has an additional role in mediating directional transport of the plant hormone auxin that is crucial for multiple developmental processes [2-4]. In addition, plant cells have a complex extracellular matrix, the cell wall [5, 6], whose role in regulating cellular processes, including cell polarity, is unexplored. We have found that polar distribution of PIN auxin transporters [7] in plant cells is maintained by connections between polar domains at the plasma membrane and the cell wall. Genetic and pharmacological interference with cellulose, the major component of the cell wall, or mechanical interference with the cell wall disrupts these connections and leads to increased lateral diffusion and loss of polar distribution of PIN transporters for the phytohormone auxin. Our results reveal a plant-specific mechanism for cell polarity maintenance and provide a conceptual framework for modulating cell polarity and plant development via endogenous and environmental manipulations of the cellulose-based extracellular matrix.
author:
- first_name: Elena
full_name: Feraru, Elena
last_name: Feraru
- first_name: Mugurel
full_name: Feraru, Mugurel I
last_name: Feraru
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Alexandre
full_name: Martinière, Alexandre
last_name: Martinière
- first_name: Grégory
full_name: Mouille, Grégory
last_name: Mouille
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Samantha
full_name: Vernhettes, Samantha
last_name: Vernhettes
- first_name: John
full_name: Runions, John
last_name: Runions
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Feraru E, Feraru M, Kleine Vehn J, et al. PIN polarity maintenance by the cell
wall in Arabidopsis. Current Biology. 2011;21(4):338-343. doi:10.1016/j.cub.2011.01.036
apa: Feraru, E., Feraru, M., Kleine Vehn, J., Martinière, A., Mouille, G., Vanneste,
S., … Friml, J. (2011). PIN polarity maintenance by the cell wall in Arabidopsis.
Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2011.01.036
chicago: Feraru, Elena, Mugurel Feraru, Jürgen Kleine Vehn, Alexandre Martinière,
Grégory Mouille, Steffen Vanneste, Samantha Vernhettes, John Runions, and Jiří
Friml. “PIN Polarity Maintenance by the Cell Wall in Arabidopsis.” Current
Biology. Cell Press, 2011. https://doi.org/10.1016/j.cub.2011.01.036.
ieee: E. Feraru et al., “PIN polarity maintenance by the cell wall in Arabidopsis,”
Current Biology, vol. 21, no. 4. Cell Press, pp. 338–343, 2011.
ista: Feraru E, Feraru M, Kleine Vehn J, Martinière A, Mouille G, Vanneste S, Vernhettes
S, Runions J, Friml J. 2011. PIN polarity maintenance by the cell wall in Arabidopsis.
Current Biology. 21(4), 338–343.
mla: Feraru, Elena, et al. “PIN Polarity Maintenance by the Cell Wall in Arabidopsis.”
Current Biology, vol. 21, no. 4, Cell Press, 2011, pp. 338–43, doi:10.1016/j.cub.2011.01.036.
short: E. Feraru, M. Feraru, J. Kleine Vehn, A. Martinière, G. Mouille, S. Vanneste,
S. Vernhettes, J. Runions, J. Friml, Current Biology 21 (2011) 338–343.
date_created: 2018-12-11T12:01:17Z
date_published: 2011-02-22T00:00:00Z
date_updated: 2021-01-12T07:40:56Z
day: '22'
doi: 10.1016/j.cub.2011.01.036
extern: 1
intvolume: ' 21'
issue: '4'
month: '02'
page: 338 - 343
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '3618'
quality_controlled: 0
status: public
title: PIN polarity maintenance by the cell wall in Arabidopsis
type: journal_article
volume: 21
year: '2011'
...
---
_id: '3082'
abstract:
- lang: eng
text: Shoot branching is one of the major determinants of plant architecture. Polar
auxin transport in stems is necessary for the control of bud outgrowth by a dominant
apex. Here, we show that following decapitation in pea (Pisum sativum L.), the
axillary buds establish directional auxin export by subcellular polarization of
PIN auxin transporters. Apical auxin application on the decapitated stem prevents
this PIN polarization and canalization of laterally applied auxin. These results
support a model in which the apical and lateral auxin sources compete for primary
channels of auxin transport in the stem to control the outgrowth of axillary buds.
author:
- first_name: Jozef
full_name: Balla, Jozef
last_name: Balla
- first_name: Petr
full_name: Kalousek, Petr
last_name: Kalousek
- first_name: Vilém
full_name: Reinöhl, Vilém
last_name: Reinöhl
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Stanislav
full_name: Procházka, Stanislav
last_name: Procházka
citation:
ama: Balla J, Kalousek P, Reinöhl V, Friml J, Procházka S. Competitive canalization
of PIN dependent auxin flow from axillary buds controls pea bud outgrowth. Plant
Journal. 2011;65(4):571-577. doi:10.1111/j.1365-313X.2010.04443.x
apa: Balla, J., Kalousek, P., Reinöhl, V., Friml, J., & Procházka, S. (2011).
Competitive canalization of PIN dependent auxin flow from axillary buds controls
pea bud outgrowth. Plant Journal. Wiley-Blackwell. https://doi.org/10.1111/j.1365-313X.2010.04443.x
chicago: Balla, Jozef, Petr Kalousek, Vilém Reinöhl, Jiří Friml, and Stanislav Procházka.
“Competitive Canalization of PIN Dependent Auxin Flow from Axillary Buds Controls
Pea Bud Outgrowth.” Plant Journal. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1365-313X.2010.04443.x.
ieee: J. Balla, P. Kalousek, V. Reinöhl, J. Friml, and S. Procházka, “Competitive
canalization of PIN dependent auxin flow from axillary buds controls pea bud outgrowth,”
Plant Journal, vol. 65, no. 4. Wiley-Blackwell, pp. 571–577, 2011.
ista: Balla J, Kalousek P, Reinöhl V, Friml J, Procházka S. 2011. Competitive canalization
of PIN dependent auxin flow from axillary buds controls pea bud outgrowth. Plant
Journal. 65(4), 571–577.
mla: Balla, Jozef, et al. “Competitive Canalization of PIN Dependent Auxin Flow
from Axillary Buds Controls Pea Bud Outgrowth.” Plant Journal, vol. 65,
no. 4, Wiley-Blackwell, 2011, pp. 571–77, doi:10.1111/j.1365-313X.2010.04443.x.
short: J. Balla, P. Kalousek, V. Reinöhl, J. Friml, S. Procházka, Plant Journal
65 (2011) 571–577.
date_created: 2018-12-11T12:01:16Z
date_published: 2011-02-01T00:00:00Z
date_updated: 2021-01-12T07:40:56Z
day: '01'
doi: 10.1111/j.1365-313X.2010.04443.x
extern: 1
intvolume: ' 65'
issue: '4'
month: '02'
page: 571 - 577
publication: Plant Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3619'
quality_controlled: 0
status: public
title: Competitive canalization of PIN dependent auxin flow from axillary buds controls
pea bud outgrowth
type: journal_article
volume: 65
year: '2011'
...
---
_id: '3083'
author:
- first_name: David
full_name: Robinson, David G
last_name: Robinson
- first_name: David
full_name: Scheuring, David
last_name: Scheuring
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Robinson D, Scheuring D, Naramoto S, Friml J. ARF1 localizes to the golgi and
the trans Golgi network. Plant Cell. 2011;23(3):846-849. doi:10.1105/tpc.110.082099
apa: Robinson, D., Scheuring, D., Naramoto, S., & Friml, J. (2011). ARF1 localizes
to the golgi and the trans Golgi network. Plant Cell. American Society
of Plant Biologists. https://doi.org/10.1105/tpc.110.082099
chicago: Robinson, David, David Scheuring, Satoshi Naramoto, and Jiří Friml. “ARF1
Localizes to the Golgi and the Trans Golgi Network.” Plant Cell. American
Society of Plant Biologists, 2011. https://doi.org/10.1105/tpc.110.082099.
ieee: D. Robinson, D. Scheuring, S. Naramoto, and J. Friml, “ARF1 localizes to the
golgi and the trans Golgi network,” Plant Cell, vol. 23, no. 3. American
Society of Plant Biologists, pp. 846–849, 2011.
ista: Robinson D, Scheuring D, Naramoto S, Friml J. 2011. ARF1 localizes to the
golgi and the trans Golgi network. Plant Cell. 23(3), 846–849.
mla: Robinson, David, et al. “ARF1 Localizes to the Golgi and the Trans Golgi Network.”
Plant Cell, vol. 23, no. 3, American Society of Plant Biologists, 2011,
pp. 846–49, doi:10.1105/tpc.110.082099.
short: D. Robinson, D. Scheuring, S. Naramoto, J. Friml, Plant Cell 23 (2011) 846–849.
date_created: 2018-12-11T12:01:16Z
date_published: 2011-03-01T00:00:00Z
date_updated: 2021-01-12T07:40:56Z
day: '01'
doi: 10.1105/tpc.110.082099
extern: 1
intvolume: ' 23'
issue: '3'
month: '03'
page: 846 - 849
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3617'
quality_controlled: 0
status: public
title: ARF1 localizes to the golgi and the trans Golgi network
type: journal_article
volume: 23
year: '2011'
...
---
_id: '3101'
abstract:
- lang: eng
text: Subcellular trafficking is required for a multitude of functions in eukaryotic
cells. It involves regulation of cargo sorting, vesicle formation, trafficking
and fusion processes at multiple levels. Adaptor protein (AP) complexes are key
regulators of cargo sorting into vesicles in yeast and mammals but their existence
and function in plants have not been demonstrated. Here we report the identification
of the protein-affected trafficking 4 (pat4) mutant defective in the putative
δ subunit of the AP-3 complex. pat4 and pat2, a mutant isolated from the same
GFP imaging-based forward genetic screen that lacks a functional putative AP-3
β, as well as dominant negative AP-3 μ transgenic lines display undistinguishable
phenotypes characterized by largely normal morphology and development, but strong
intracellular accumulation of membrane proteins in aberrant vacuolar structures.
All mutants are defective in morphology and function of lytic and protein storage
vacuoles (PSVs) but show normal sorting of reserve proteins to PSVs. Immunoprecipitation
experiments and genetic studies revealed tight functional and physical associations
of putative AP-3 β and AP-3 δ subunits. Furthermore, both proteins are closely
linked with putative AP-3 μ and σ subunits and several components of the clathrin
and dynamin machineries. Taken together, these results demonstrate that AP complexes,
similar to those in other eukaryotes, exist in plants, and that AP-3 plays a specific
role in the regulation of biogenesis and function of vacuoles in plant cells.
© 2011 IBCB, SIBS, CAS All rights reserved
author:
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Elena
full_name: Feraru, Elena
last_name: Feraru
- first_name: Barbara
full_name: Möller, Barbara
last_name: Möller
- first_name: Inhwan
full_name: Hwang, Inhwan
last_name: Hwang
- first_name: Mugurel
full_name: Feraru, Mugurel I
last_name: Feraru
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Zwiewka M, Feraru E, Möller B, et al. The AP 3 adaptor complex is required
for vacuolar function in Arabidopsis. Cell Research. 2011;21(12):1711-1722.
doi:10.1038/cr.2011.99
apa: Zwiewka, M., Feraru, E., Möller, B., Hwang, I., Feraru, M., Kleine Vehn, J.,
… Friml, J. (2011). The AP 3 adaptor complex is required for vacuolar function
in Arabidopsis. Cell Research. Nature Publishing Group. https://doi.org/10.1038/cr.2011.99
chicago: Zwiewka, Marta, Elena Feraru, Barbara Möller, Inhwan Hwang, Mugurel Feraru,
Jürgen Kleine Vehn, Dolf Weijers, and Jiří Friml. “The AP 3 Adaptor Complex Is
Required for Vacuolar Function in Arabidopsis.” Cell Research. Nature Publishing
Group, 2011. https://doi.org/10.1038/cr.2011.99.
ieee: M. Zwiewka et al., “The AP 3 adaptor complex is required for vacuolar
function in Arabidopsis,” Cell Research, vol. 21, no. 12. Nature Publishing
Group, pp. 1711–1722, 2011.
ista: Zwiewka M, Feraru E, Möller B, Hwang I, Feraru M, Kleine Vehn J, Weijers D,
Friml J. 2011. The AP 3 adaptor complex is required for vacuolar function in Arabidopsis.
Cell Research. 21(12), 1711–1722.
mla: Zwiewka, Marta, et al. “The AP 3 Adaptor Complex Is Required for Vacuolar Function
in Arabidopsis.” Cell Research, vol. 21, no. 12, Nature Publishing Group,
2011, pp. 1711–22, doi:10.1038/cr.2011.99.
short: M. Zwiewka, E. Feraru, B. Möller, I. Hwang, M. Feraru, J. Kleine Vehn, D.
Weijers, J. Friml, Cell Research 21 (2011) 1711–1722.
date_created: 2018-12-11T12:01:23Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:04Z
day: '01'
doi: 10.1038/cr.2011.99
extern: 1
intvolume: ' 21'
issue: '12'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357998/
month: '01'
oa: 1
page: 1711 - 1722
publication: Cell Research
publication_status: published
publisher: Nature Publishing Group
publist_id: '3597'
quality_controlled: 0
status: public
title: The AP 3 adaptor complex is required for vacuolar function in Arabidopsis
type: journal_article
volume: 21
year: '2011'
...
---
_id: '3098'
abstract:
- lang: eng
text: Cell polarity reflected by asymmetric distribution of proteins at the plasma
membrane is a fundamental feature of unicellular and multicellular organisms.
It remains conceptually unclear how cell polarity is kept in cell wall-encapsulated
plant cells. We have used super-resolution and semi-quantitative live-cell imaging
in combination with pharmacological, genetic, and computational approaches to
reveal insights into the mechanism of cell polarity maintenance in Arabidopsis
thaliana. We show that polar-competent PIN transporters for the phytohormone auxin
are delivered to the center of polar domains by super-polar recycling. Within
the plasma membrane, PINs are recruited into non-mobile membrane clusters and
their lateral diffusion is dramatically reduced, which ensures longer polar retention.
At the circumventing edges of the polar domain, spatially defined internalization
of escaped cargos occurs by clathrin-dependent endocytosis. Computer simulations
confirm that the combination of these processes provides a robust mechanism for
polarity maintenance in plant cells. Moreover, our study suggests that the regulation
of lateral diffusion and spatially defined endocytosis, but not super-polar exocytosis
have primary importance for PIN polarity maintenance.
author:
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Krzysztof T
full_name: Krzysztof Wabnik
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Alexandre
full_name: Martinière, Alexandre
last_name: Martinière
- first_name: Łukasz
full_name: Łangowski, Łukasz
last_name: Łangowski
- first_name: Katrin
full_name: Willig, Katrin
last_name: Willig
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Johannes
full_name: Leitner, Johannes
last_name: Leitner
- first_name: Hirokazu
full_name: Tanaka, Hirokazu
last_name: Tanaka
- first_name: Stefan
full_name: Jakobs, Stefan
last_name: Jakobs
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
- first_name: Willy
full_name: Govaerts, Willy J
last_name: Govaerts
- first_name: Stefan
full_name: Hell, Stefan W
last_name: Hell
- first_name: John
full_name: Runions, John
last_name: Runions
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Kleine Vehn J, Wabnik KT, Martinière A, et al. Recycling, clustering and endocytosis
jointly maintain PIN auxin carrier polarity at the plasma membrane. Molecular
Systems Biology. 2011;7. doi:10.1038/msb.2011.72
apa: Kleine Vehn, J., Wabnik, K. T., Martinière, A., Łangowski, Ł., Willig, K.,
Naramoto, S., … Friml, J. (2011). Recycling, clustering and endocytosis jointly
maintain PIN auxin carrier polarity at the plasma membrane. Molecular Systems
Biology. Nature Publishing Group. https://doi.org/10.1038/msb.2011.72
chicago: Kleine Vehn, Jürgen, Krzysztof T Wabnik, Alexandre Martinière, Łukasz Łangowski,
Katrin Willig, Satoshi Naramoto, Johannes Leitner, et al. “Recycling, Clustering
and Endocytosis Jointly Maintain PIN Auxin Carrier Polarity at the Plasma Membrane.”
Molecular Systems Biology. Nature Publishing Group, 2011. https://doi.org/10.1038/msb.2011.72.
ieee: J. Kleine Vehn et al., “Recycling, clustering and endocytosis jointly
maintain PIN auxin carrier polarity at the plasma membrane,” Molecular Systems
Biology, vol. 7. Nature Publishing Group, 2011.
ista: Kleine Vehn J, Wabnik KT, Martinière A, Łangowski Ł, Willig K, Naramoto S,
Leitner J, Tanaka H, Jakobs S, Robert S, Luschnig C, Govaerts W, Hell S, Runions
J, Friml J. 2011. Recycling, clustering and endocytosis jointly maintain PIN auxin
carrier polarity at the plasma membrane. Molecular Systems Biology. 7.
mla: Kleine Vehn, Jürgen, et al. “Recycling, Clustering and Endocytosis Jointly
Maintain PIN Auxin Carrier Polarity at the Plasma Membrane.” Molecular Systems
Biology, vol. 7, Nature Publishing Group, 2011, doi:10.1038/msb.2011.72.
short: J. Kleine Vehn, K.T. Wabnik, A. Martinière, Ł. Łangowski, K. Willig, S. Naramoto,
J. Leitner, H. Tanaka, S. Jakobs, S. Robert, C. Luschnig, W. Govaerts, S. Hell,
J. Runions, J. Friml, Molecular Systems Biology 7 (2011).
date_created: 2018-12-11T12:01:22Z
date_published: 2011-10-25T00:00:00Z
date_updated: 2021-01-12T07:41:02Z
day: '25'
doi: 10.1038/msb.2011.72
extern: 1
intvolume: ' 7'
month: '10'
publication: Molecular Systems Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3601'
quality_controlled: 0
status: public
title: Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity
at the plasma membrane
type: journal_article
volume: 7
year: '2011'
...
---
_id: '3100'
abstract:
- lang: eng
text: In multicellular organisms, morphogenesis relies on a strict coordination
in time and space of cell proliferation and differentiation. In contrast to animals,
plant development displays continuous organ formation and adaptive growth responses
during their lifespan relying on a tight coordination of cell proliferation. How
developmental signals interact with the plant cell-cycle machinery is largely
unknown. Here, we characterize plant A2-type cyclins, a small gene family of mitotic
cyclins, and show how they contribute to the fine-tuning of local proliferation
during plant development. Moreover, the timely repression of CYCA2;3 expression
in newly formed guard cells is shown to require the stomatal transcription factors
FOUR LIPS/MYB124 and MYB88, providing a direct link between developmental programming
and cell-cycle exit in plants. Thus, transcriptional downregulation of CYCA2s
represents a critical mechanism to coordinate proliferation during plant development.
author:
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Frederik
full_name: Coppens, Frederik
last_name: Coppens
- first_name: Eunkyoung
full_name: Lee, EunKyoung
last_name: Lee
- first_name: Tyler
full_name: Donner, Tyler J
last_name: Donner
- first_name: Zidian
full_name: Xie, Zidian
last_name: Xie
- first_name: Gert
full_name: Van Isterdael, Gert
last_name: Van Isterdael
- first_name: Stijn
full_name: Dhondt, Stijn
last_name: Dhondt
- first_name: Freya
full_name: De Winter, Freya
last_name: De Winter
- first_name: Bert
full_name: De Rybel, Bert
last_name: De Rybel
- first_name: Marnik
full_name: Vuylsteke, Marnik
last_name: Vuylsteke
- first_name: Lieven
full_name: De Veylder, Lieven
last_name: De Veylder
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Dirk
full_name: Inzé, Dirk
last_name: Inzé
- first_name: Erich
full_name: Grotewold, Erich
last_name: Grotewold
- first_name: Enrico
full_name: Scarpella, Enrico
last_name: Scarpella
- first_name: Fred
full_name: Sack, Fred
last_name: Sack
- first_name: Gerrit
full_name: Beemster, Gerrit T
last_name: Beemster
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
citation:
ama: Vanneste S, Coppens F, Lee E, et al. Developmental regulation of CYCA2s contributes
to tissue-specific proliferation in Arabidopsis . EMBO Journal. 2011;30(16):3430-3441.
doi:10.1038/emboj.2011.240
apa: Vanneste, S., Coppens, F., Lee, E., Donner, T., Xie, Z., Van Isterdael, G.,
… Beeckman, T. (2011). Developmental regulation of CYCA2s contributes to tissue-specific
proliferation in Arabidopsis . EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2011.240
chicago: Vanneste, Steffen, Frederik Coppens, Eunkyoung Lee, Tyler Donner, Zidian
Xie, Gert Van Isterdael, Stijn Dhondt, et al. “Developmental Regulation of CYCA2s
Contributes to Tissue-Specific Proliferation in Arabidopsis .” EMBO Journal.
Wiley-Blackwell, 2011. https://doi.org/10.1038/emboj.2011.240.
ieee: S. Vanneste et al., “Developmental regulation of CYCA2s contributes
to tissue-specific proliferation in Arabidopsis ,” EMBO Journal, vol. 30,
no. 16. Wiley-Blackwell, pp. 3430–3441, 2011.
ista: Vanneste S, Coppens F, Lee E, Donner T, Xie Z, Van Isterdael G, Dhondt S,
De Winter F, De Rybel B, Vuylsteke M, De Veylder L, Friml J, Inzé D, Grotewold
E, Scarpella E, Sack F, Beemster G, Beeckman T. 2011. Developmental regulation
of CYCA2s contributes to tissue-specific proliferation in Arabidopsis . EMBO Journal.
30(16), 3430–3441.
mla: Vanneste, Steffen, et al. “Developmental Regulation of CYCA2s Contributes to
Tissue-Specific Proliferation in Arabidopsis .” EMBO Journal, vol. 30,
no. 16, Wiley-Blackwell, 2011, pp. 3430–41, doi:10.1038/emboj.2011.240.
short: S. Vanneste, F. Coppens, E. Lee, T. Donner, Z. Xie, G. Van Isterdael, S.
Dhondt, F. De Winter, B. De Rybel, M. Vuylsteke, L. De Veylder, J. Friml, D. Inzé,
E. Grotewold, E. Scarpella, F. Sack, G. Beemster, T. Beeckman, EMBO Journal 30
(2011) 3430–3441.
date_created: 2018-12-11T12:01:23Z
date_published: 2011-08-17T00:00:00Z
date_updated: 2021-01-12T07:41:04Z
day: '17'
doi: 10.1038/emboj.2011.240
extern: 1
intvolume: ' 30'
issue: '16'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160660/
month: '08'
oa: 1
page: 3430 - 3441
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3600'
quality_controlled: 0
status: public
title: 'Developmental regulation of CYCA2s contributes to tissue-specific proliferation
in Arabidopsis '
type: journal_article
volume: 30
year: '2011'
...
---
_id: '3099'
abstract:
- lang: eng
text: Endomembrane trafficking relies on the coordination of a highly complex, dynamic
network of intracellular vesicles. Understanding the network will require a dissection
of cargo and vesicle dynamics at the cellular level in vivo. This is also a key
to establishing a link between vesicular networks and their functional roles in
development. We used a high-content intracellular screen to discover small molecules
targeting endomembrane trafficking in vivo in a complex eukaryote, Arabidopsis
thaliana. Tens of thousands of molecules were prescreened and a selected subset
was interrogated against a panel of plasma membrane (PM) and other endomembrane
compartment markers to identify molecules that altered vesicle trafficking. The
extensive image dataset was transformed by a flexible algorithm into a marker-by-phenotype-by-treatment
time matrix and revealed groups of molecules that induced similar subcellular
fingerprints (clusters). This matrix provides a platform for a systems view of
trafficking. Molecules from distinct clusters presented avenues and enabled an
entry point to dissect recycling at the PM, vacuolar sorting, and cell-plate maturation.
Bioactivity in human cells indicated the value of the approach to identifying
small molecules that are active in diverse organisms for biology and drug discovery.
author:
- first_name: Georgia
full_name: Drakakaki, Georgia
last_name: Drakakaki
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Anna
full_name: Szatmári, Anna-Maria
last_name: Szatmári
- first_name: Michelle
full_name: Brown, Michelle Q
last_name: Brown
- first_name: Shingo
full_name: Nagawa, Shingo
last_name: Nagawa
- first_name: Daniël
full_name: Van Damme, Daniël
last_name: Van Damme
- first_name: Marylin
full_name: Leonard, Marylin
last_name: Leonard
- first_name: Zhenbiao
full_name: Yang, Zhenbiao
last_name: Yang
- first_name: Thomas
full_name: Girke, Thomas
last_name: Girke
- first_name: Sandra
full_name: Schmid, Sandra L
last_name: Schmid
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Natasha
full_name: Raikhel, Natasha V
last_name: Raikhel
- first_name: Glen
full_name: Hicks, Glen R
last_name: Hicks
citation:
ama: Drakakaki G, Robert S, Szatmári A, et al. Clusters of bioactive compounds target
dynamic endomembrane networks in vivo. PNAS. 2011;108(43):17850-17855.
doi:10.1073/pnas.1108581108
apa: Drakakaki, G., Robert, S., Szatmári, A., Brown, M., Nagawa, S., Van Damme,
D., … Hicks, G. (2011). Clusters of bioactive compounds target dynamic endomembrane
networks in vivo. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1108581108
chicago: Drakakaki, Georgia, Stéphanie Robert, Anna Szatmári, Michelle Brown, Shingo
Nagawa, Daniël Van Damme, Marylin Leonard, et al. “Clusters of Bioactive Compounds
Target Dynamic Endomembrane Networks in Vivo.” PNAS. National Academy of
Sciences, 2011. https://doi.org/10.1073/pnas.1108581108.
ieee: G. Drakakaki et al., “Clusters of bioactive compounds target dynamic
endomembrane networks in vivo,” PNAS, vol. 108, no. 43. National Academy
of Sciences, pp. 17850–17855, 2011.
ista: Drakakaki G, Robert S, Szatmári A, Brown M, Nagawa S, Van Damme D, Leonard
M, Yang Z, Girke T, Schmid S, Russinova E, Friml J, Raikhel N, Hicks G. 2011.
Clusters of bioactive compounds target dynamic endomembrane networks in vivo.
PNAS. 108(43), 17850–17855.
mla: Drakakaki, Georgia, et al. “Clusters of Bioactive Compounds Target Dynamic
Endomembrane Networks in Vivo.” PNAS, vol. 108, no. 43, National Academy
of Sciences, 2011, pp. 17850–55, doi:10.1073/pnas.1108581108.
short: G. Drakakaki, S. Robert, A. Szatmári, M. Brown, S. Nagawa, D. Van Damme,
M. Leonard, Z. Yang, T. Girke, S. Schmid, E. Russinova, J. Friml, N. Raikhel,
G. Hicks, PNAS 108 (2011) 17850–17855.
date_created: 2018-12-11T12:01:23Z
date_published: 2011-10-25T00:00:00Z
date_updated: 2021-01-12T07:41:02Z
day: '25'
doi: 10.1073/pnas.1108581108
extern: 1
intvolume: ' 108'
issue: '43'
month: '10'
page: 17850 - 17855
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3602'
quality_controlled: 0
status: public
title: Clusters of bioactive compounds target dynamic endomembrane networks in vivo
type: journal_article
volume: 108
year: '2011'
...
---
_id: '3095'
abstract:
- lang: eng
text: Root system architecture depends on lateral root (LR) initiation that takes
place in a relatively narrow developmental window (DW). Here, we analyzed the
role of auxin gradients established along the parent root in defining this DW
for LR initiation. Correlations between auxin distribution and response, and spatiotemporal
control of LR initiation were analyzed in Arabidopsis thaliana and tomato (Solanum
lycopersicum). In both Arabidopsis and tomato roots, a well defined zone, where
auxin content and response are minimal, demarcates the position of a DW for founder
cell specification and LR initiation. We show that in the zone of auxin minimum
pericycle cells have highest probability to become founder cells and that auxin
perception via the TIR1/AFB pathway, and polar auxin transport, are essential
for the establishment of this zone. Altogether, this study reveals that the same
morphogen-like molecule, auxin, can act simultaneously as a morphogenetic trigger
of LR founder cell identity and as a gradient-dependent signal defining positioning
of the founder cell specification. This auxin minimum zone might represent an
important control mechanism ensuring the LR initiation steadiness and the acropetal
LR initiation pattern. © 2011 The Authors. New Phytologist © 2011 New Phytologist
Trust.
author:
- first_name: Joseph
full_name: Dubrovsky, Joseph G
last_name: Dubrovsky
- first_name: Selene
full_name: Napsucialy-Mendivil, Selene
last_name: Napsucialy Mendivil
- first_name: Jérôme
full_name: Duclercq, Jérôme
last_name: Duclercq
- first_name: Yan
full_name: Cheng, Yan
last_name: Cheng
- first_name: Svetlana
full_name: Shishkova, Svetlana O
last_name: Shishkova
- first_name: Maria
full_name: Ivanchenko, Maria G
last_name: Ivanchenko
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Angus
full_name: Murphy, Angus S
last_name: Murphy
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Dubrovsky J, Napsucialy Mendivil S, Duclercq J, et al. Auxin minimum defines
a developmental window for lateral root initiation. New Phytologist. 2011;191(4):970-983.
doi: 10.1111/j.1469-8137.2011.03757.x
apa: Dubrovsky, J., Napsucialy Mendivil, S., Duclercq, J., Cheng, Y., Shishkova,
S., Ivanchenko, M., … Benková, E. (2011). Auxin minimum defines a developmental
window for lateral root initiation. New Phytologist. Wiley-Blackwell. https://doi.org/ 10.1111/j.1469-8137.2011.03757.x
chicago: Dubrovsky, Joseph, Selene Napsucialy Mendivil, Jérôme Duclercq, Yan Cheng,
Svetlana Shishkova, Maria Ivanchenko, Jiří Friml, Angus Murphy, and Eva Benková.
“Auxin Minimum Defines a Developmental Window for Lateral Root Initiation.” New
Phytologist. Wiley-Blackwell, 2011. https://doi.org/
10.1111/j.1469-8137.2011.03757.x.
ieee: J. Dubrovsky et al., “Auxin minimum defines a developmental window
for lateral root initiation,” New Phytologist, vol. 191, no. 4. Wiley-Blackwell,
pp. 970–983, 2011.
ista: Dubrovsky J, Napsucialy Mendivil S, Duclercq J, Cheng Y, Shishkova S, Ivanchenko
M, Friml J, Murphy A, Benková E. 2011. Auxin minimum defines a developmental window
for lateral root initiation. New Phytologist. 191(4), 970–983.
mla: Dubrovsky, Joseph, et al. “Auxin Minimum Defines a Developmental Window for
Lateral Root Initiation.” New Phytologist, vol. 191, no. 4, Wiley-Blackwell,
2011, pp. 970–83, doi:
10.1111/j.1469-8137.2011.03757.x.
short: J. Dubrovsky, S. Napsucialy Mendivil, J. Duclercq, Y. Cheng, S. Shishkova,
M. Ivanchenko, J. Friml, A. Murphy, E. Benková, New Phytologist 191 (2011) 970–983.
date_created: 2018-12-11T12:01:21Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:01Z
day: '01'
doi: ' 10.1111/j.1469-8137.2011.03757.x'
extern: 1
intvolume: ' 191'
issue: '4'
month: '01'
page: 970 - 983
publication: New Phytologist
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3605'
quality_controlled: 0
status: public
title: Auxin minimum defines a developmental window for lateral root initiation
type: journal_article
volume: 191
year: '2011'
...
---
_id: '3097'
abstract:
- lang: eng
text: Cytokinin is an important regulator of plant growth and development. In Arabidopsis
thaliana, the two-component phosphorelay mediated through a family of histidine
kinases and response regulators is recognized as the principal cytokinin signal
transduction mechanism activating the complex transcriptional response to control
various developmental processes. Here, we identified an alternative mode of cytokinin
action that uses endocytic trafficking as a means to direct plant organogenesis.
This activity occurs downstream of known cytokinin receptors but through a branch
of the cytokinin signaling pathway that does not involve transcriptional regulation.
We show that cytokinin regulates endocytic recycling of the auxin efflux carrier
PINFORMED1 (PIN1) by redirecting it for lytic degradation in vacuoles. Stimulation
of the lytic PIN1 degradation is not a default effect for general downregulation
of proteins from plasma membranes, but a specific mechanism to rapidly modulate
the auxin distribution in cytokinin-mediated developmental processes.
author:
- first_name: Peter
full_name: Peter Marhavy
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Agnieszka
full_name: Bielach, Agnieszka
last_name: Bielach
- first_name: Lindy
full_name: Abas, Lindy
last_name: Abas
- first_name: Anas
full_name: Abuzeineh, Anas
last_name: Abuzeineh
- first_name: Jérôme
full_name: Duclercq, Jérôme
last_name: Duclercq
- first_name: Hirokazu
full_name: Tanaka, Hirokazu
last_name: Tanaka
- first_name: Markéta
full_name: Pařezová, Markéta
last_name: Pařezová
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Marhavý P, Bielach A, Abas L, et al. Cytokinin modulates endocytic trafficking
of PIN1 auxin efflux carrier to control plant organogenesis. Developmental
Cell. 2011;21(4):796-804. doi:10.1016/j.devcel.2011.08.014
apa: Marhavý, P., Bielach, A., Abas, L., Abuzeineh, A., Duclercq, J., Tanaka, H.,
… Benková, E. (2011). Cytokinin modulates endocytic trafficking of PIN1 auxin
efflux carrier to control plant organogenesis. Developmental Cell. Cell
Press. https://doi.org/10.1016/j.devcel.2011.08.014
chicago: Marhavý, Peter, Agnieszka Bielach, Lindy Abas, Anas Abuzeineh, Jérôme Duclercq,
Hirokazu Tanaka, Markéta Pařezová, et al. “Cytokinin Modulates Endocytic Trafficking
of PIN1 Auxin Efflux Carrier to Control Plant Organogenesis.” Developmental
Cell. Cell Press, 2011. https://doi.org/10.1016/j.devcel.2011.08.014.
ieee: P. Marhavý et al., “Cytokinin modulates endocytic trafficking of PIN1
auxin efflux carrier to control plant organogenesis,” Developmental Cell,
vol. 21, no. 4. Cell Press, pp. 796–804, 2011.
ista: Marhavý P, Bielach A, Abas L, Abuzeineh A, Duclercq J, Tanaka H, Pařezová
M, Petrášek J, Friml J, Kleine Vehn J, Benková E. 2011. Cytokinin modulates endocytic
trafficking of PIN1 auxin efflux carrier to control plant organogenesis. Developmental
Cell. 21(4), 796–804.
mla: Marhavý, Peter, et al. “Cytokinin Modulates Endocytic Trafficking of PIN1 Auxin
Efflux Carrier to Control Plant Organogenesis.” Developmental Cell, vol.
21, no. 4, Cell Press, 2011, pp. 796–804, doi:10.1016/j.devcel.2011.08.014.
short: P. Marhavý, A. Bielach, L. Abas, A. Abuzeineh, J. Duclercq, H. Tanaka, M.
Pařezová, J. Petrášek, J. Friml, J. Kleine Vehn, E. Benková, Developmental Cell
21 (2011) 796–804.
date_created: 2018-12-11T12:01:22Z
date_published: 2011-10-18T00:00:00Z
date_updated: 2021-01-12T07:41:02Z
day: '18'
doi: 10.1016/j.devcel.2011.08.014
extern: 1
intvolume: ' 21'
issue: '4'
month: '10'
page: 796 - 804
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '3603'
quality_controlled: 0
status: public
title: Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control
plant organogenesis
type: journal_article
volume: 21
year: '2011'
...
---
_id: '3096'
abstract:
- lang: eng
text: Carrier-dependent, intercellular auxin transport is central to the developmental
patterning of higher plants (tracheophytes). The evolution of this polar auxin
transport might be linked to the translocation of some PIN auxin efflux carriers
from their presumably ancestral localization at the endoplasmic reticulum (ER)
to the polar domains at the plasma membrane. Here we propose an eventually ancient
mechanism of intercellular auxin distribution by ER-localized auxin transporters
involving intracellular auxin retention and switch-like release from the ER. The
proposed model integrates feedback circuits utilizing the conserved nuclear auxin
signaling for the regulation of PIN transcription and a hypothetical ER-based
signaling for the regulation of PIN-dependent transport activity at the ER. Computer
simulations of the model revealed its plausibility for generating auxin channels
and localized auxin maxima highlighting the possibility of this alternative mechanism
for polar auxin transport.
author:
- 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: Jürgen
full_name: Kleine Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Willy
full_name: Govaerts, Willy
last_name: Govaerts
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Wabnik KT, Kleine Vehn J, Govaerts W, Friml J. Prototype cell-to-cell auxin
transport mechanism by intracellular auxin compartmentalization. Trends in
Plant Science. 2011;16(9):468-475. doi:10.1016/j.tplants.2011.05.002
apa: Wabnik, K. T., Kleine Vehn, J., Govaerts, W., & Friml, J. (2011). Prototype
cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization.
Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2011.05.002
chicago: Wabnik, Krzysztof T, Jürgen Kleine Vehn, Willy Govaerts, and Jiří Friml.
“Prototype Cell-to-Cell Auxin Transport Mechanism by Intracellular Auxin Compartmentalization.”
Trends in Plant Science. Cell Press, 2011. https://doi.org/10.1016/j.tplants.2011.05.002.
ieee: K. T. Wabnik, J. Kleine Vehn, W. Govaerts, and J. Friml, “Prototype cell-to-cell
auxin transport mechanism by intracellular auxin compartmentalization,” Trends
in Plant Science, vol. 16, no. 9. Cell Press, pp. 468–475, 2011.
ista: Wabnik KT, Kleine Vehn J, Govaerts W, Friml J. 2011. Prototype cell-to-cell
auxin transport mechanism by intracellular auxin compartmentalization. Trends
in Plant Science. 16(9), 468–475.
mla: Wabnik, Krzysztof T., et al. “Prototype Cell-to-Cell Auxin Transport Mechanism
by Intracellular Auxin Compartmentalization.” Trends in Plant Science,
vol. 16, no. 9, Cell Press, 2011, pp. 468–75, doi:10.1016/j.tplants.2011.05.002.
short: K.T. Wabnik, J. Kleine Vehn, W. Govaerts, J. Friml, Trends in Plant Science
16 (2011) 468–475.
date_created: 2018-12-11T12:01:21Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2021-01-12T07:41:01Z
day: '01'
doi: 10.1016/j.tplants.2011.05.002
extern: '1'
intvolume: ' 16'
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 468 - 475
publication: Trends in Plant Science
publication_status: published
publisher: Cell Press
publist_id: '3604'
quality_controlled: '1'
status: public
title: Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2011'
...
---
_id: '3138'
abstract:
- lang: eng
text: Hippocampal sharp waves (SPWs) and associated fast ("ripple") oscillations
(SPW-Rs) in the CA1 region are among the most synchronous physiological patterns
in the mammalian brain. Using two-dimensional arrays of electrodes for recording
local field potentials and unit discharges in freely moving rats, we studied the
emergence of ripple oscillations (140-220 Hz) and compared their origin and cellular-synaptic
mechanisms with fast gamma oscillations (90-140 Hz). We show that (1) hippocampal
SPW-Rs and fast gamma oscillations are quantitatively distinct patterns but involve
the same networks and share similar mechanisms; (2) both the frequency and magnitude
of fast oscillations are positively correlated with the magnitude of SPWs; (3)
during both ripples and fast gamma oscillations the frequency of network oscillation
is higher in CA1 than in CA3; and (4) the emergence of CA3 population bursts,
a prerequisite for SPW-Rs, is biased by activity patterns in the dentate gyrus
and entorhinal cortex, with the highest probability of ripples associated with
an "optimum" level of dentate gamma power. We hypothesize that each
hippocampal subnetwork possesses distinct resonant properties, tuned by the magnitude
of the excitatory drive.
author:
- first_name: David
full_name: Sullivan, David W
last_name: Sullivan
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Kenji
full_name: Mizuseki, Kenji
last_name: Mizuseki
- first_name: Sean
full_name: Montgomery, Sean M
last_name: Montgomery
- first_name: Kamran
full_name: Diba, Kamran
last_name: Diba
- first_name: György
full_name: Buzsáki, György
last_name: Buzsáki
citation:
ama: Sullivan D, Csicsvari JL, Mizuseki K, Montgomery S, Diba K, Buzsáki G. Relationships
between hippocampal sharp waves ripples and fast gamma oscillation Influence of
dentate and entorhinal cortical activity. Journal of Neuroscience. 2011;31(23):8605-8616.
doi:10.1523/JNEUROSCI.0294-11.2011
apa: Sullivan, D., Csicsvari, J. L., Mizuseki, K., Montgomery, S., Diba, K., &
Buzsáki, G. (2011). Relationships between hippocampal sharp waves ripples and
fast gamma oscillation Influence of dentate and entorhinal cortical activity.
Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0294-11.2011
chicago: Sullivan, David, Jozsef L Csicsvari, Kenji Mizuseki, Sean Montgomery, Kamran
Diba, and György Buzsáki. “Relationships between Hippocampal Sharp Waves Ripples
and Fast Gamma Oscillation Influence of Dentate and Entorhinal Cortical Activity.”
Journal of Neuroscience. Society for Neuroscience, 2011. https://doi.org/10.1523/JNEUROSCI.0294-11.2011.
ieee: D. Sullivan, J. L. Csicsvari, K. Mizuseki, S. Montgomery, K. Diba, and G.
Buzsáki, “Relationships between hippocampal sharp waves ripples and fast gamma
oscillation Influence of dentate and entorhinal cortical activity,” Journal
of Neuroscience, vol. 31, no. 23. Society for Neuroscience, pp. 8605–8616,
2011.
ista: Sullivan D, Csicsvari JL, Mizuseki K, Montgomery S, Diba K, Buzsáki G. 2011.
Relationships between hippocampal sharp waves ripples and fast gamma oscillation
Influence of dentate and entorhinal cortical activity. Journal of Neuroscience.
31(23), 8605–8616.
mla: Sullivan, David, et al. “Relationships between Hippocampal Sharp Waves Ripples
and Fast Gamma Oscillation Influence of Dentate and Entorhinal Cortical Activity.”
Journal of Neuroscience, vol. 31, no. 23, Society for Neuroscience, 2011,
pp. 8605–16, doi:10.1523/JNEUROSCI.0294-11.2011.
short: D. Sullivan, J.L. Csicsvari, K. Mizuseki, S. Montgomery, K. Diba, G. Buzsáki,
Journal of Neuroscience 31 (2011) 8605–8616.
date_created: 2018-12-11T12:01:36Z
date_published: 2011-06-08T00:00:00Z
date_updated: 2021-01-12T07:41:19Z
day: '08'
doi: 10.1523/JNEUROSCI.0294-11.2011
extern: 1
intvolume: ' 31'
issue: '23'
month: '06'
page: 8605 - 8616
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '3559'
quality_controlled: 0
status: public
title: Relationships between hippocampal sharp waves ripples and fast gamma oscillation
Influence of dentate and entorhinal cortical activity
type: journal_article
volume: 31
year: '2011'
...
---
_id: '3145'
abstract:
- lang: eng
text: Microinjection of recombinant DNA into zygotic pronuclei has been widely used
for producing transgenic mice. However, with this method, the insertion site,
integrity, and copy number of the transgene cannot be controlled. Here, we present
an integrase-based approach to produce transgenic mice via pronuclear injection,
whereby an intact single-copy transgene can be inserted into predetermined chromosomal
loci with high efficiency (up to 40%), and faithfully transmitted through generations.
We show that neighboring transgenic elements and bacterial DNA within the transgene
cause profound silencing and expression variability of the transgenic marker.
Removal of these undesirable elements leads to global high-level marker expression
from transgenes driven by a ubiquitous promoter. We also obtained faithful marker
expression from a tissue-specific promoter. The technique presented here will
greatly facilitate murine transgenesis and precise structure/function dissection
of mammalian gene function and regulation in vivo.
author:
- first_name: Bosiljka
full_name: Tasic, Bosiljka
last_name: Tasic
- first_name: Simon
full_name: Simon Hippenmeyer
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Charlene
full_name: Wang, Charlene
last_name: Wang
- first_name: Matthew
full_name: Gamboa, Matthew
last_name: Gamboa
- first_name: Hui
full_name: Zong, Hui
last_name: Zong
- first_name: Yanru
full_name: Chen-Tsai, Yanru
last_name: Chen Tsai
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
citation:
ama: Tasic B, Hippenmeyer S, Wang C, et al. Site specific integrase mediated transgenesis
in mice via pronuclear injection. PNAS. 2011;108(19):7902-7907. doi:10.1073/pnas.1019507108
apa: Tasic, B., Hippenmeyer, S., Wang, C., Gamboa, M., Zong, H., Chen Tsai, Y.,
& Luo, L. (2011). Site specific integrase mediated transgenesis in mice via
pronuclear injection. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1019507108
chicago: Tasic, Bosiljka, Simon Hippenmeyer, Charlene Wang, Matthew Gamboa, Hui
Zong, Yanru Chen Tsai, and Liqun Luo. “Site Specific Integrase Mediated Transgenesis
in Mice via Pronuclear Injection.” PNAS. National Academy of Sciences,
2011. https://doi.org/10.1073/pnas.1019507108.
ieee: B. Tasic et al., “Site specific integrase mediated transgenesis in
mice via pronuclear injection,” PNAS, vol. 108, no. 19. National Academy
of Sciences, pp. 7902–7907, 2011.
ista: Tasic B, Hippenmeyer S, Wang C, Gamboa M, Zong H, Chen Tsai Y, Luo L. 2011.
Site specific integrase mediated transgenesis in mice via pronuclear injection.
PNAS. 108(19), 7902–7907.
mla: Tasic, Bosiljka, et al. “Site Specific Integrase Mediated Transgenesis in Mice
via Pronuclear Injection.” PNAS, vol. 108, no. 19, National Academy of
Sciences, 2011, pp. 7902–07, doi:10.1073/pnas.1019507108.
short: B. Tasic, S. Hippenmeyer, C. Wang, M. Gamboa, H. Zong, Y. Chen Tsai, L. Luo,
PNAS 108 (2011) 7902–7907.
date_created: 2018-12-11T12:01:39Z
date_published: 2011-05-10T00:00:00Z
date_updated: 2021-01-12T07:41:22Z
day: '10'
doi: 10.1073/pnas.1019507108
extern: 1
intvolume: ' 108'
issue: '19'
month: '05'
page: 7902 - 7907
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3549'
quality_controlled: 0
status: public
title: Site specific integrase mediated transgenesis in mice via pronuclear injection
type: journal_article
volume: 108
year: '2011'
...
---
_id: '3154'
abstract:
- lang: eng
text: Regulated adhesion between cells and their environment is critical for normal
cell migration. We have identified mutations in a gene encoding the Drosophila
hydrogen peroxide (H2O2)-degrading enzyme Jafrac1, which lead to germ cell adhesion
defects. During gastrulation, primordial germ cells (PGCs) associate tightly with
the invaginating midgut primordium as it enters the embryo; however, in embryos
from jafrac1 mutant mothers this association is disrupted, leaving some PGCs trailing
on the outside of the embryo. We observed similar phenotypes in embryos from DE-cadherin/shotgun
(shg) mutant mothers and were able to rescue the jafrac1 phenotype by increasing
DE-cadherin levels. This and our biochemical evidence strongly suggest that Jafrac1-mediated
reduction of H2O2 is required to maintain DE-cadherin protein levels in the early
embryo. Our results present in vivo evidence of a peroxiredoxin regulating DE-cadherin-mediated
adhesion.
author:
- first_name: Matthew
full_name: DeGennaro, Matthew
last_name: Degennaro
- first_name: Thomas
full_name: Hurd, Thomas R
last_name: Hurd
- first_name: Daria E
full_name: Daria Siekhaus
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Benoit
full_name: Biteau, Benoit
last_name: Biteau
- first_name: Heinrich
full_name: Jasper, Heinrich
last_name: Jasper
- first_name: Ruth
full_name: Lehmann, Ruth
last_name: Lehmann
citation:
ama: Degennaro M, Hurd T, Siekhaus DE, Biteau B, Jasper H, Lehmann R. Peroxiredoxin
stabilization of DE-cadherin promotes primordial germ cell adhesion. Developmental
Cell. 2011;20(2):233-243. doi:10.1016/j.devcel.2010.12.007
apa: Degennaro, M., Hurd, T., Siekhaus, D. E., Biteau, B., Jasper, H., & Lehmann,
R. (2011). Peroxiredoxin stabilization of DE-cadherin promotes primordial germ
cell adhesion. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2010.12.007
chicago: Degennaro, Matthew, Thomas Hurd, Daria E Siekhaus, Benoit Biteau, Heinrich
Jasper, and Ruth Lehmann. “Peroxiredoxin Stabilization of DE-Cadherin Promotes
Primordial Germ Cell Adhesion.” Developmental Cell. Cell Press, 2011. https://doi.org/10.1016/j.devcel.2010.12.007.
ieee: M. Degennaro, T. Hurd, D. E. Siekhaus, B. Biteau, H. Jasper, and R. Lehmann,
“Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion,”
Developmental Cell, vol. 20, no. 2. Cell Press, pp. 233–243, 2011.
ista: Degennaro M, Hurd T, Siekhaus DE, Biteau B, Jasper H, Lehmann R. 2011. Peroxiredoxin
stabilization of DE-cadherin promotes primordial germ cell adhesion. Developmental
Cell. 20(2), 233–243.
mla: Degennaro, Matthew, et al. “Peroxiredoxin Stabilization of DE-Cadherin Promotes
Primordial Germ Cell Adhesion.” Developmental Cell, vol. 20, no. 2, Cell
Press, 2011, pp. 233–43, doi:10.1016/j.devcel.2010.12.007.
short: M. Degennaro, T. Hurd, D.E. Siekhaus, B. Biteau, H. Jasper, R. Lehmann, Developmental
Cell 20 (2011) 233–243.
date_created: 2018-12-11T12:01:42Z
date_published: 2011-02-15T00:00:00Z
date_updated: 2021-01-12T07:41:26Z
day: '15'
doi: 10.1016/j.devcel.2010.12.007
extern: 1
intvolume: ' 20'
issue: '2'
month: '02'
page: 233 - 243
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '3541'
quality_controlled: 0
status: public
title: Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion
type: journal_article
volume: 20
year: '2011'
...
---
_id: '3239'
abstract:
- lang: eng
text: Tampering attacks are cryptanalytic attacks on the implementation of cryptographic
algorithms (e.g., smart cards), where an adversary introduces faults with the
hope that the tampered device will reveal secret information. Inspired by the
work of Ishai et al. [Eurocrypt'06], we propose a compiler that transforms any
circuit into a new circuit with the same functionality, but which is resilient
against a well-defined and powerful tampering adversary. More concretely, our
transformed circuits remain secure even if the adversary can adaptively tamper
with every wire in the circuit as long as the tampering fails with some probability
δ>0. This additional requirement is motivated by practical tampering attacks,
where it is often difficult to guarantee the success of a specific attack. Formally,
we show that a q-query tampering attack against the transformed circuit can be
"simulated" with only black-box access to the original circuit and log(q)
bits of additional auxiliary information. Thus, if the implemented cryptographic
scheme is secure against log(q) bits of leakage, then our implementation is tamper-proof
in the above sense. Surprisingly, allowing for this small amount of information
leakage allows for much more efficient compilers, which moreover do not require
randomness during evaluation. Similar to earlier works our compiler requires small,
stateless and computation-independent tamper-proof gadgets. Thus, our result can
be interpreted as reducing the problem of shielding arbitrary complex computation
to protecting simple components. © 2011 Springer-Verlag.
alternative_title:
- LNCS
author:
- first_name: Sebastian
full_name: Faust, Sebastian
last_name: Faust
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Daniele
full_name: Venturi, Daniele
last_name: Venturi
citation:
ama: 'Faust S, Pietrzak KZ, Venturi D. Tamper proof circuits How to trade leakage
for tamper resilience. In: Vol 6755. Springer; 2011:391-402. doi:10.1007/978-3-642-22006-7_33'
apa: 'Faust, S., Pietrzak, K. Z., & Venturi, D. (2011). Tamper proof circuits
How to trade leakage for tamper resilience (Vol. 6755, pp. 391–402). Presented
at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/978-3-642-22006-7_33'
chicago: Faust, Sebastian, Krzysztof Z Pietrzak, and Daniele Venturi. “Tamper Proof
Circuits How to Trade Leakage for Tamper Resilience,” 6755:391–402. Springer,
2011. https://doi.org/10.1007/978-3-642-22006-7_33.
ieee: 'S. Faust, K. Z. Pietrzak, and D. Venturi, “Tamper proof circuits How to trade
leakage for tamper resilience,” presented at the ICALP: Automata, Languages and
Programming, 2011, vol. 6755, no. Part 1, pp. 391–402.'
ista: 'Faust S, Pietrzak KZ, Venturi D. 2011. Tamper proof circuits How to trade
leakage for tamper resilience. ICALP: Automata, Languages and Programming, LNCS,
vol. 6755, 391–402.'
mla: Faust, Sebastian, et al. Tamper Proof Circuits How to Trade Leakage for
Tamper Resilience. Vol. 6755, no. Part 1, Springer, 2011, pp. 391–402, doi:10.1007/978-3-642-22006-7_33.
short: S. Faust, K.Z. Pietrzak, D. Venturi, in:, Springer, 2011, pp. 391–402.
conference:
name: 'ICALP: Automata, Languages and Programming'
date_created: 2018-12-11T12:02:12Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:02Z
day: '01'
doi: 10.1007/978-3-642-22006-7_33
extern: 1
issue: Part 1
month: '01'
page: 391 - 402
publication_status: published
publisher: Springer
publist_id: '3441'
quality_controlled: 0
status: public
title: Tamper proof circuits How to trade leakage for tamper resilience
type: conference
volume: '6755 '
year: '2011'
...
---
_id: '3236'
abstract:
- lang: eng
text: 'If a cryptographic primitive remains secure even if ℓ bits about the secret
key are leaked to the adversary, one would expect that at least one of n independent
instantiations of the scheme remains secure given n·ℓ bits of leakage. This intuition
has been proven true for schemes satisfying some special information-theoretic
properties by Alwen et al. [Eurocrypt''10]. On the negative side, Lewko and Waters
[FOCS''10] construct a CPA secure public-key encryption scheme for which this
intuition fails. The counterexample of Lewko and Waters leaves open the interesting
possibility that for any scheme there exists a constant c>0, such that n fold
repetition remains secure against c·n·ℓ bits of leakage. Furthermore, their counterexample
requires the n copies of the encryption scheme to share a common reference parameter,
leaving open the possibility that the intuition is true for all schemes without
common setup. In this work we give a stronger counterexample ruling out these
possibilities. We construct a signature scheme such that: 1. a single instantiation
remains secure given ℓ = log(k) bits of leakage where k is a security parameter.
2. any polynomial number of independent instantiations can be broken (in the strongest
sense of key-recovery) given ℓ′ = poly(k) bits of leakage. Note that ℓ does not
depend on the number of instances. The computational assumption underlying our
counterexample is that non-interactive computationally sound proofs exist. Moreover,
under a stronger (non-standard) assumption about such proofs, our counterexample
does not require a common reference parameter. The underlying idea of our counterexample
is rather generic and can be applied to other primitives like encryption schemes.
© 2011 International Association for Cryptologic Research.'
alternative_title:
- LNCS
author:
- first_name: Abhishek
full_name: Jain, Abhishek
last_name: Jain
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Jain A, Pietrzak KZ. Parallel repetition for leakage resilience amplification
revisited. In: Vol 6597. Springer; 2011:58-69. doi:10.1007/978-3-642-19571-6_5'
apa: 'Jain, A., & Pietrzak, K. Z. (2011). Parallel repetition for leakage resilience
amplification revisited (Vol. 6597, pp. 58–69). Presented at the TCC: Theory of
Cryptography Conference, Springer. https://doi.org/10.1007/978-3-642-19571-6_5'
chicago: Jain, Abhishek, and Krzysztof Z Pietrzak. “Parallel Repetition for Leakage
Resilience Amplification Revisited,” 6597:58–69. Springer, 2011. https://doi.org/10.1007/978-3-642-19571-6_5.
ieee: 'A. Jain and K. Z. Pietrzak, “Parallel repetition for leakage resilience amplification
revisited,” presented at the TCC: Theory of Cryptography Conference, 2011, vol.
6597, pp. 58–69.'
ista: 'Jain A, Pietrzak KZ. 2011. Parallel repetition for leakage resilience amplification
revisited. TCC: Theory of Cryptography Conference, LNCS, vol. 6597, 58–69.'
mla: Jain, Abhishek, and Krzysztof Z. Pietrzak. Parallel Repetition for Leakage
Resilience Amplification Revisited. Vol. 6597, Springer, 2011, pp. 58–69,
doi:10.1007/978-3-642-19571-6_5.
short: A. Jain, K.Z. Pietrzak, in:, Springer, 2011, pp. 58–69.
conference:
name: 'TCC: Theory of Cryptography Conference'
date_created: 2018-12-11T12:02:11Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:00Z
day: '01'
doi: 10.1007/978-3-642-19571-6_5
extern: 1
month: '01'
page: 58 - 69
publication_status: published
publisher: Springer
publist_id: '3443'
quality_controlled: 0
status: public
title: Parallel repetition for leakage resilience amplification revisited
type: conference
volume: '6597 '
year: '2011'
...
---
_id: '3276'
abstract:
- lang: eng
text: 'We present an algorithm to identify individual neural spikes observed on
high-density multi-electrode arrays (MEAs). Our method can distinguish large numbers
of distinct neural units, even when spikes overlap, and accounts for intrinsic
variability of spikes from each unit. As MEAs grow larger, it is important to
find spike-identification methods that are scalable, that is, the computational
cost of spike fitting should scale well with the number of units observed. Our
algorithm accomplishes this goal, and is fast, because it exploits the spatial
locality of each unit and the basic biophysics of extracellular signal propagation.
Human interaction plays a key role in our method; but effort is minimized and
streamlined via a graphical interface. We illustrate our method on data from guinea
pig retinal ganglion cells and document its performance on simulated data consisting
of spikes added to experimentally measured background noise. We present several
tests demonstrating that the algorithm is highly accurate: it exhibits low error
rates on fits to synthetic data, low refractory violation rates, good receptive
field coverage, and consistency across users.'
acknowledgement: |+
This work was supported by National Science Foundation (NSF) grants IBN-0344678, EF-0928048, National Institutes of Health (NIH) grant RO1 EY08124, NIH training grant T32-07035, and NIH training grant 5T90DA022763-04.
Michael Berry and Olivier Marre have developed an algorithm similar to, but different from, ours (manuscript in preparation). We thank them for discussions of their work, and specifically thank Olivier Marre for suggesting to us that the most complete subtraction of a spike can be obtained by refitting the spike without a prior.
author:
- first_name: Jason
full_name: Prentice, Jason S
last_name: Prentice
- first_name: Jan
full_name: Homann, Jan
last_name: Homann
- first_name: Kristina
full_name: Simmons, Kristina D
last_name: Simmons
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Vijay
full_name: Balasubramanian, Vijay
last_name: Balasubramanian
- first_name: Philip
full_name: Nelson, Philip C
last_name: Nelson
citation:
ama: Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. Fast,
scalable, Bayesian spike identification for multi-electrode arrays. PLoS One.
2011;6(7). doi:10.1371/journal.pone.0019884
apa: Prentice, J., Homann, J., Simmons, K., Tkačik, G., Balasubramanian, V., &
Nelson, P. (2011). Fast, scalable, Bayesian spike identification for multi-electrode
arrays. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0019884
chicago: Prentice, Jason, Jan Homann, Kristina Simmons, Gašper Tkačik, Vijay Balasubramanian,
and Philip Nelson. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode
Arrays.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0019884.
ieee: J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, and P.
Nelson, “Fast, scalable, Bayesian spike identification for multi-electrode arrays,”
PLoS One, vol. 6, no. 7. Public Library of Science, 2011.
ista: Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. 2011.
Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS
One. 6(7).
mla: Prentice, Jason, et al. “Fast, Scalable, Bayesian Spike Identification for
Multi-Electrode Arrays.” PLoS One, vol. 6, no. 7, Public Library of Science,
2011, doi:10.1371/journal.pone.0019884.
short: J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, P. Nelson,
PLoS One 6 (2011).
date_created: 2018-12-11T12:02:24Z
date_published: 2011-07-20T00:00:00Z
date_updated: 2021-01-12T07:42:19Z
day: '20'
doi: 10.1371/journal.pone.0019884
extern: 1
file:
- access_level: open_access
checksum: 654464e99683b55a699734213d5356f1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:38Z
date_updated: 2020-07-14T12:46:06Z
file_id: '4894'
file_name: IST-2015-381-v1+1_journal.pone.0019884.pdf
file_size: 885464
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
intvolume: ' 6'
issue: '7'
month: '07'
oa: 1
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3370'
pubrep_id: '381'
quality_controlled: 0
status: public
title: Fast, scalable, Bayesian spike identification for multi-electrode arrays
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
volume: 6
year: '2011'
...
...
---
_id: '3271'
abstract:
- lang: eng
text: In this paper we present an efficient framework for computation of persis-
tent homology of cubical data in arbitrary dimensions. An existing algorithm using
simplicial complexes is adapted to the setting of cubical complexes. The proposed
approach enables efficient application of persistent homology in domains where
the data is naturally given in a cubical form. By avoiding triangulation of the
data, we significantly reduce the size of the complex. We also present a data-structure
de- signed to compactly store and quickly manipulate cubical complexes. By means
of numerical experiments, we show high speed and memory efficiency of our ap-
proach. We compare our framework to other available implementations, showing its
superiority. Finally, we report performance on selected 3D and 4D data-sets.
alternative_title:
- Theory, Algorithms, and Applications
author:
- first_name: Hubert
full_name: Wagner, Hubert
last_name: Wagner
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Erald
full_name: Vuçini, Erald
last_name: Vuçini
citation:
ama: 'Wagner H, Chen C, Vuçini E. Efficient computation of persistent homology for
cubical data. In: Peikert R, Hauser H, Carr H, Fuchs R, eds. Topological Methods
in Data Analysis and Visualization II. Springer; 2011:91-106. doi:10.1007/978-3-642-23175-9_7'
apa: Wagner, H., Chen, C., & Vuçini, E. (2011). Efficient computation of persistent
homology for cubical data. In R. Peikert, H. Hauser, H. Carr, & R. Fuchs (Eds.),
Topological Methods in Data Analysis and Visualization II (pp. 91–106).
Springer. https://doi.org/10.1007/978-3-642-23175-9_7
chicago: Wagner, Hubert, Chao Chen, and Erald Vuçini. “Efficient Computation of
Persistent Homology for Cubical Data.” In Topological Methods in Data Analysis
and Visualization II, edited by Ronald Peikert, Helwig Hauser, Hamish Carr,
and Raphael Fuchs, 91–106. Springer, 2011. https://doi.org/10.1007/978-3-642-23175-9_7.
ieee: H. Wagner, C. Chen, and E. Vuçini, “Efficient computation of persistent homology
for cubical data,” in Topological Methods in Data Analysis and Visualization
II, R. Peikert, H. Hauser, H. Carr, and R. Fuchs, Eds. Springer, 2011, pp.
91–106.
ista: 'Wagner H, Chen C, Vuçini E. 2011.Efficient computation of persistent homology
for cubical data. In: Topological Methods in Data Analysis and Visualization II.
Theory, Algorithms, and Applications, , 91–106.'
mla: Wagner, Hubert, et al. “Efficient Computation of Persistent Homology for Cubical
Data.” Topological Methods in Data Analysis and Visualization II, edited
by Ronald Peikert et al., Springer, 2011, pp. 91–106, doi:10.1007/978-3-642-23175-9_7.
short: H. Wagner, C. Chen, E. Vuçini, in:, R. Peikert, H. Hauser, H. Carr, R. Fuchs
(Eds.), Topological Methods in Data Analysis and Visualization II, Springer, 2011,
pp. 91–106.
date_created: 2018-12-11T12:02:23Z
date_published: 2011-11-14T00:00:00Z
date_updated: 2021-01-12T07:42:18Z
day: '14'
department:
- _id: HeEd
doi: 10.1007/978-3-642-23175-9_7
editor:
- first_name: Ronald
full_name: Peikert, Ronald
last_name: Peikert
- first_name: Helwig
full_name: Hauser, Helwig
last_name: Hauser
- first_name: Hamish
full_name: Carr, Hamish
last_name: Carr
- first_name: Raphael
full_name: Fuchs, Raphael
last_name: Fuchs
language:
- iso: eng
month: '11'
oa_version: None
page: 91 - 106
publication: Topological Methods in Data Analysis and Visualization II
publication_status: published
publisher: Springer
publist_id: '3375'
quality_controlled: '1'
scopus_import: 1
status: public
title: Efficient computation of persistent homology for cubical data
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3278'
abstract:
- lang: eng
text: |-
Despite much research on the socially parasitic large blue butterflies (genus Maculinea) in the past 40 years, their relationship to their closest relatives, Phengaris, is controversial and the relationships among the remaining genera in the Glaucopsyche section are largely unresolved. The evolutionary history of this butterfly section is particularly important to understand the evolution of life history diversity con- nected to food-plant and host-ant associations in the larval stage. In the present study, we use a combi- nation of four nuclear and two mitochondrial genes to reconstruct the phylogeny of the Glaucopsyche section, and in particular, to study the relationships among and within the Phengaris–Maculinea species.
We find a clear pattern between the clades recovered in the Glaucopsyche section phylogeny and their food-plant associations, with only the Phengaris–Maculinea clade utilising more than one plant family. Maculinea is, for the first time, recovered with strong support as a monophyletic group nested within Phengaris, with the closest relative being the rare genus Caerulea. The genus Glaucopsyche is polyphyletic, including the genera Sinia and Iolana. Interestingly, we find evidence for additional potential cryptic spe- cies within the highly endangered Maculinea, which has long been suspected from morphological, ecolog- ical and molecular studies.
author:
- first_name: Roger
full_name: Vila, Roger
last_name: Vila
- first_name: Naomi
full_name: Pierce, Naomi E
last_name: Pierce
- first_name: David
full_name: Nash, David R
last_name: Nash
- first_name: Line V
full_name: Line Ugelvig
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
citation:
ama: 'Vila R, Pierce N, Nash D, Ugelvig LV. A phylogenetic revision of the Glaucopsyche
section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea
clade. Molecular Phylogenetics and Evolution. 2011;61(1):237-243. doi:10.1016/j.ympev.2011.05.016'
apa: 'Vila, R., Pierce, N., Nash, D., & Ugelvig, L. V. (2011). A phylogenetic
revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus
on the Phengaris-Maculinea clade. Molecular Phylogenetics and Evolution.
Elsevier. https://doi.org/10.1016/j.ympev.2011.05.016'
chicago: 'Vila, Roger, Naomi Pierce, David Nash, and Line V Ugelvig. “A Phylogenetic
Revision of the Glaucopsyche Section (Lepidoptera: Lycaenidae), with Special Focus
on the Phengaris-Maculinea Clade.” Molecular Phylogenetics and Evolution.
Elsevier, 2011. https://doi.org/10.1016/j.ympev.2011.05.016.'
ieee: 'R. Vila, N. Pierce, D. Nash, and L. V. Ugelvig, “A phylogenetic revision
of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the
Phengaris-Maculinea clade,” Molecular Phylogenetics and Evolution, vol.
61, no. 1. Elsevier, pp. 237–243, 2011.'
ista: 'Vila R, Pierce N, Nash D, Ugelvig LV. 2011. A phylogenetic revision of the
Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea
clade. Molecular Phylogenetics and Evolution. 61(1), 237–243.'
mla: 'Vila, Roger, et al. “A Phylogenetic Revision of the Glaucopsyche Section (Lepidoptera:
Lycaenidae), with Special Focus on the Phengaris-Maculinea Clade.” Molecular
Phylogenetics and Evolution, vol. 61, no. 1, Elsevier, 2011, pp. 237–43, doi:10.1016/j.ympev.2011.05.016.'
short: R. Vila, N. Pierce, D. Nash, L.V. Ugelvig, Molecular Phylogenetics and Evolution
61 (2011) 237–243.
date_created: 2018-12-11T12:02:25Z
date_published: 2011-10-01T00:00:00Z
date_updated: 2021-01-12T07:42:20Z
day: '01'
doi: 10.1016/j.ympev.2011.05.016
extern: 1
intvolume: ' 61'
issue: '1'
month: '10'
page: 237 - 243
publication: Molecular Phylogenetics and Evolution
publication_status: published
publisher: Elsevier
publist_id: '3368'
quality_controlled: 0
status: public
title: 'A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae),
with special focus on the Phengaris-Maculinea clade'
type: journal_article
volume: 61
year: '2011'
...