---
_id: '3534'
author:
- first_name: David
full_name: Dupret, David
last_name: Dupret
- first_name: Barty
full_name: Pleydell-Bouverie, Barty
last_name: Pleydell Bouverie
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Dupret D, Pleydell Bouverie B, Csicsvari JL. Inhibitory interneurons and network
oscillations. PNAS. 2008;105(47):18079-18080. doi:10.1073/pnas.0810064105
apa: Dupret, D., Pleydell Bouverie, B., & Csicsvari, J. L. (2008). Inhibitory
interneurons and network oscillations. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.0810064105
chicago: Dupret, David, Barty Pleydell Bouverie, and Jozsef L Csicsvari. “Inhibitory
Interneurons and Network Oscillations.” PNAS. National Academy of Sciences,
2008. https://doi.org/10.1073/pnas.0810064105.
ieee: D. Dupret, B. Pleydell Bouverie, and J. L. Csicsvari, “Inhibitory interneurons
and network oscillations,” PNAS, vol. 105, no. 47. National Academy of
Sciences, pp. 18079–18080, 2008.
ista: Dupret D, Pleydell Bouverie B, Csicsvari JL. 2008. Inhibitory interneurons
and network oscillations. PNAS. 105(47), 18079–18080.
mla: Dupret, David, et al. “Inhibitory Interneurons and Network Oscillations.” PNAS,
vol. 105, no. 47, National Academy of Sciences, 2008, pp. 18079–80, doi:10.1073/pnas.0810064105.
short: D. Dupret, B. Pleydell Bouverie, J.L. Csicsvari, PNAS 105 (2008) 18079–18080.
date_created: 2018-12-11T12:03:50Z
date_published: 2008-11-25T00:00:00Z
date_updated: 2021-01-12T07:44:08Z
day: '25'
doi: 10.1073/pnas.0810064105
extern: 1
intvolume: ' 105'
issue: '47'
month: '11'
page: 18079 - 18080
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2852'
quality_controlled: 0
status: public
title: Inhibitory interneurons and network oscillations
type: journal_article
volume: 105
year: '2008'
...
---
_id: '3600'
abstract:
- lang: eng
text: Scalability is one of the most important issues for optimization algorithms
used in wireless sensor networks (WSNs) since there are often many parameters
to be optimized at the same time. In this case it is very hard to ensure that
an optimization algorithm can be smoothly scaled up from a low-dimensional optimization
problem to the one with a high dimensionality. This paper addresses the scalability
issue of a novel optimization algorithm inspired by the Shifting Balance Theory
(SBT) of evolution in population genetics. Toward this end, a cluster-based WSN
is employed in this paper as a benchmark to perform a comparative study. The total
energy consumption is minimized under the required quality of service by jointly
optimizing the transmission power and rate for each sensor node. The results obtained
by the SBT-based algorithm are compared with the Metropolis algorithm (MA) and
currently popular particle swarm optimizer (PSO) to assess the scaling performance
of the three algorithms against the same WSN optimization problem.
alternative_title:
- LNCS
author:
- first_name: Erfu
full_name: Yang, Erfu
last_name: Yang
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Tughrul
full_name: Arslan, Tughrul
last_name: Arslan
- first_name: Ahmet
full_name: Erdogan, Ahmet T
last_name: Erdogan
citation:
ama: 'Yang E, Barton NH, Arslan T, Erdogan A. Scalability of a novel shifting balance
theory-based optimization algorithm: A comparative study on a cluster-based wireless
sensor network. In: Vol 5216. Springer; 2008:249-260. doi:10.1007/978-3-540-85857-7_22'
apa: 'Yang, E., Barton, N. H., Arslan, T., & Erdogan, A. (2008). Scalability
of a novel shifting balance theory-based optimization algorithm: A comparative
study on a cluster-based wireless sensor network (Vol. 5216, pp. 249–260). Presented
at the IECS: International Conference on Evolvable Systems, Springer. https://doi.org/10.1007/978-3-540-85857-7_22'
chicago: 'Yang, Erfu, Nicholas H Barton, Tughrul Arslan, and Ahmet Erdogan. “ Scalability
of a Novel Shifting Balance Theory-Based Optimization Algorithm: A Comparative
Study on a Cluster-Based Wireless Sensor Network,” 5216:249–60. Springer, 2008.
https://doi.org/10.1007/978-3-540-85857-7_22.'
ieee: 'E. Yang, N. H. Barton, T. Arslan, and A. Erdogan, “ Scalability of a novel
shifting balance theory-based optimization algorithm: A comparative study on a
cluster-based wireless sensor network,” presented at the IECS: International Conference
on Evolvable Systems, 2008, vol. 5216, pp. 249–260.'
ista: 'Yang E, Barton NH, Arslan T, Erdogan A. 2008. Scalability of a novel shifting
balance theory-based optimization algorithm: A comparative study on a cluster-based
wireless sensor network. IECS: International Conference on Evolvable Systems,
LNCS, vol. 5216, 249–260.'
mla: 'Yang, Erfu, et al. Scalability of a Novel Shifting Balance Theory-Based
Optimization Algorithm: A Comparative Study on a Cluster-Based Wireless Sensor
Network. Vol. 5216, Springer, 2008, pp. 249–60, doi:10.1007/978-3-540-85857-7_22.'
short: E. Yang, N.H. Barton, T. Arslan, A. Erdogan, in:, Springer, 2008, pp. 249–260.
conference:
name: 'IECS: International Conference on Evolvable Systems'
date_created: 2018-12-11T12:04:10Z
date_published: 2008-09-08T00:00:00Z
date_updated: 2021-01-12T07:44:35Z
day: '08'
doi: 10.1007/978-3-540-85857-7_22
extern: 1
intvolume: ' 5216'
month: '09'
page: 249 - 260
publication_status: published
publisher: Springer
publist_id: '2783'
quality_controlled: 0
status: public
title: ' Scalability of a novel shifting balance theory-based optimization algorithm:
A comparative study on a cluster-based wireless sensor network'
type: conference
volume: 5216
year: '2008'
...
---
_id: '3606'
abstract:
- lang: eng
text: 'Explicit formulae are given for the effects of a barrier to gene flow on
random fluctuations in allele frequency; these formulae can also be seen as generating
functions for the distribution of coalescence times. The formulae are derived
using a continuous diffusion approximation, which is accurate over all but very
small spatial scales. The continuous approximation is confirmed by comparison
with the exact solution to the stepping stone model. In both one and two spatial
dimensions, the variance of fluctuations in allele frequencies increases near
the barrier; when the barrier is very strong, the variance doubles. However, the
effect on fluctuations close to the barrier is much greater when the population
is spread over two spatial dimensions than when it occupies a linear, one-dimensional
habitat: barriers of strength comparable with the dispersal range (B≈σ) can have
an appreciable effect in two dimensions, whereas only barriers with strength comparable
with the characteristic scale (B\! \approx\! L \equals \sigma \sol \sqrt {2 \mu}\hskip2)
are significant in one dimension (μ is the rate of mutation or long-range dispersal).
Thus, in a two-dimensional population, barriers to gene flow can be detected through
their effect on the spatial pattern of genetic marker alleles.'
author:
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. The effect of a barrier to gene flow on patterns of geographic variation.
Genetical Research. 2008;90(1):139-149. doi:10.1017/S0016672307009081
apa: Barton, N. H. (2008). The effect of a barrier to gene flow on patterns of geographic
variation. Genetical Research. Cambridge University Press. https://doi.org/10.1017/S0016672307009081
chicago: Barton, Nicholas H. “The Effect of a Barrier to Gene Flow on Patterns of
Geographic Variation.” Genetical Research. Cambridge University Press,
2008. https://doi.org/10.1017/S0016672307009081.
ieee: N. H. Barton, “The effect of a barrier to gene flow on patterns of geographic
variation,” Genetical Research, vol. 90, no. 1. Cambridge University Press,
pp. 139–149, 2008.
ista: Barton NH. 2008. The effect of a barrier to gene flow on patterns of geographic
variation. Genetical Research. 90(1), 139–149.
mla: Barton, Nicholas H. “The Effect of a Barrier to Gene Flow on Patterns of Geographic
Variation.” Genetical Research, vol. 90, no. 1, Cambridge University Press,
2008, pp. 139–49, doi:10.1017/S0016672307009081.
short: N.H. Barton, Genetical Research 90 (2008) 139–149.
date_created: 2018-12-11T12:04:12Z
date_published: 2008-02-01T00:00:00Z
date_updated: 2021-01-12T07:44:37Z
day: '01'
doi: 10.1017/S0016672307009081
extern: 1
intvolume: ' 90'
issue: '1'
month: '02'
page: 139 - 149
publication: Genetical Research
publication_status: published
publisher: Cambridge University Press
publist_id: '2777'
quality_controlled: 0
status: public
title: The effect of a barrier to gene flow on patterns of geographic variation
type: journal_article
volume: 90
year: '2008'
...
---
_id: '3605'
abstract:
- lang: eng
text: Many animals and plants show a correlation between the traits of the individuals
in the mating pair, implying assortative mating. Given the ubiquity of assortative
mating in nature, why and how it has evolved remain open questions. Here we attempt
to answer these questions in those cases where the trait under assortment is the
same in males and females. We consider the most favorable scenario for assortment
to evolve, where the same trait is under assortment and viability selection. We
find conditions for assortment to evolve using a multilocus formalism in a haploid
population. Our results show how epistasis in fitness between the loci that control
the focal trait is crucial for assortment to evolve. We then assume specific forms
of assortment in haploids and diploids and study the limiting cases of selective
and nonselective mating. We find that selection for increased assortment is weak
and that where increased assortment is costly, it does not invade.
author:
- first_name: Maria
full_name: De Cara, Maria A
last_name: De Cara
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Mark
full_name: Kirkpatrick, Mark
last_name: Kirkpatrick
citation:
ama: De Cara M, Barton NH, Kirkpatrick M. A model for the evolution of assortative
mating. American Naturalist. 2008;171(5):580-596. doi:10.1086/587062
apa: De Cara, M., Barton, N. H., & Kirkpatrick, M. (2008). A model for the evolution
of assortative mating. American Naturalist. University of Chicago Press.
https://doi.org/10.1086/587062
chicago: De Cara, Maria, Nicholas H Barton, and Mark Kirkpatrick. “A Model for the
Evolution of Assortative Mating.” American Naturalist. University of Chicago
Press, 2008. https://doi.org/10.1086/587062.
ieee: M. De Cara, N. H. Barton, and M. Kirkpatrick, “A model for the evolution of
assortative mating,” American Naturalist, vol. 171, no. 5. University of
Chicago Press, pp. 580–596, 2008.
ista: De Cara M, Barton NH, Kirkpatrick M. 2008. A model for the evolution of assortative
mating. American Naturalist. 171(5), 580–596.
mla: De Cara, Maria, et al. “A Model for the Evolution of Assortative Mating.” American
Naturalist, vol. 171, no. 5, University of Chicago Press, 2008, pp. 580–96,
doi:10.1086/587062.
short: M. De Cara, N.H. Barton, M. Kirkpatrick, American Naturalist 171 (2008) 580–596.
date_created: 2018-12-11T12:04:12Z
date_published: 2008-05-01T00:00:00Z
date_updated: 2021-01-12T07:44:36Z
day: '01'
doi: 10.1086/587062
extern: 1
intvolume: ' 171'
issue: '5'
month: '05'
page: 580 - 596
publication: American Naturalist
publication_status: published
publisher: University of Chicago Press
publist_id: '2778'
quality_controlled: 0
status: public
title: A model for the evolution of assortative mating
type: journal_article
volume: 171
year: '2008'
...
---
_id: '3705'
abstract:
- lang: eng
text: 'Sliding window classifiers are among the most successful and widely applied
techniques for object localization. However, training is typically done in a way
that is not specific to the localization task. First a binary classifier is trained
using a sample of positive and negative examples, and this classifier is subsequently
applied to multiple regions within test images. We propose instead to treat object
localization in a principled way by posing it as a problem of predicting structured
data: we model the problem not as binary classification, but as the prediction
of the bounding box of objects located in images. The use of a joint-kernel framework
allows us to formulate the training procedure as a generalization of an SVM, which
can be solved efficiently. We further improve computational efficiency by using
a branch-and-bound strategy for localization during both training and testing.
Experimental evaluation on the PASCAL VOC and TU Darmstadt datasets show that
the structured training procedure improves pe rformance over binary training as
well as the best previously published scores.'
alternative_title:
- LNCS
author:
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Blaschko M, Lampert C. Learning to localize objects with structured output
regression. In: Vol 5302. Springer; 2008:2-15. doi:10.1007/978-3-540-88682-2_2'
apa: 'Blaschko, M., & Lampert, C. (2008). Learning to localize objects with
structured output regression (Vol. 5302, pp. 2–15). Presented at the ECCV: European
Conference on Computer Vision, Springer. https://doi.org/10.1007/978-3-540-88682-2_2'
chicago: Blaschko, Matthew, and Christoph Lampert. “Learning to Localize Objects
with Structured Output Regression,” 5302:2–15. Springer, 2008. https://doi.org/10.1007/978-3-540-88682-2_2.
ieee: 'M. Blaschko and C. Lampert, “Learning to localize objects with structured
output regression,” presented at the ECCV: European Conference on Computer Vision,
2008, vol. 5302, pp. 2–15.'
ista: 'Blaschko M, Lampert C. 2008. Learning to localize objects with structured
output regression. ECCV: European Conference on Computer Vision, LNCS, vol. 5302,
2–15.'
mla: Blaschko, Matthew, and Christoph Lampert. Learning to Localize Objects with
Structured Output Regression. Vol. 5302, Springer, 2008, pp. 2–15, doi:10.1007/978-3-540-88682-2_2.
short: M. Blaschko, C. Lampert, in:, Springer, 2008, pp. 2–15.
conference:
name: 'ECCV: European Conference on Computer Vision'
date_created: 2018-12-11T12:04:43Z
date_published: 2008-11-17T00:00:00Z
date_updated: 2021-01-12T07:51:37Z
day: '17'
doi: 10.1007/978-3-540-88682-2_2
extern: 1
intvolume: ' 5302'
main_file_link:
- open_access: '0'
url: http://www.kyb.mpg.de/fileadmin/user_upload/files/publications/attachments/ECCV2008-Blaschko_5247%5b0%5d.pdf
month: '11'
page: 2 - 15
publication_status: published
publisher: Springer
publist_id: '2653'
quality_controlled: 0
status: public
title: Learning to localize objects with structured output regression
type: conference
volume: 5302
year: '2008'
...
---
_id: '3700'
abstract:
- lang: eng
text: We propose a new method to partition an unlabeled dataset, called Discriminative
Context Partitioning (DCP). It is motivated by the idea of splitting the dataset
based only on how well the resulting parts can be separated from a context class
of disjoint data points. This is in contrast to typical clustering techniques
like K-means that are based on a generative model by implicitly or explicitly
searching for modes in the distribution of samples. The discriminative criterion
in DCP avoids the problems that density based methods have when the a priori assumption
of multimodality is violated, when the number of samples becomes small in relation
to the dimensionality of the feature space, or if the cluster sizes are strongly
unbalanced. We formulate DCP‘s separation
property as a large-margin criterion, and show how the resulting optimization
problem can be solved efficiently. Experiments on the MNIST and USPS datasets
of handwritten digits and on a subset of the Caltech256 dataset show that, given
a suitable context, DCP can achieve good results even in situation where density-based
clustering techniques fail.
acknowledgement: This work was funded in part by the EC project CLASS, IST 027978.
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Lampert C. Partitioning of image datasets using discriminative context information.
In: IEEE; 2008:1-8. doi:10.1109/CVPR.2008.4587448'
apa: 'Lampert, C. (2008). Partitioning of image datasets using discriminative context
information (pp. 1–8). Presented at the CVPR: Computer Vision and Pattern Recognition,
IEEE. https://doi.org/10.1109/CVPR.2008.4587448'
chicago: Lampert, Christoph. “Partitioning of Image Datasets Using Discriminative
Context Information,” 1–8. IEEE, 2008. https://doi.org/10.1109/CVPR.2008.4587448.
ieee: 'C. Lampert, “Partitioning of image datasets using discriminative context
information,” presented at the CVPR: Computer Vision and Pattern Recognition,
2008, pp. 1–8.'
ista: 'Lampert C. 2008. Partitioning of image datasets using discriminative context
information. CVPR: Computer Vision and Pattern Recognition, 1–8.'
mla: Lampert, Christoph. Partitioning of Image Datasets Using Discriminative
Context Information. IEEE, 2008, pp. 1–8, doi:10.1109/CVPR.2008.4587448.
short: C. Lampert, in:, IEEE, 2008, pp. 1–8.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:04:41Z
date_published: 2008-09-18T00:00:00Z
date_updated: 2021-01-12T07:51:35Z
day: '18'
doi: 10.1109/CVPR.2008.4587448
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/~chl/papers/lampert-cvpr2008b.pdf
month: '09'
page: 1 - 8
publication_status: published
publisher: IEEE
publist_id: '2657'
quality_controlled: 0
status: public
title: Partitioning of image datasets using discriminative context information
type: conference
year: '2008'
...
---
_id: '3716'
abstract:
- lang: eng
text: |
Most current methods for multi-class object classification and localization work as independent 1-vs-rest classifiers. They decide whether and where an object is visible in an image purely on a per-class basis. Joint learning of more than one object class would generally be preferable, since this would allow the use of contextual information such as co-occurrence between classes. However, this approach is usually not employed because of its computational cost.
In this paper we propose a method to combine the efficiency of single class localization with a subsequent decision process that works jointly for all given object classes. By following a multiple kernel learning (MKL) approach, we automatically obtain a sparse dependency graph of relevant object classes on which to base the decision. Experiments on the PASCAL VOC 2006 and 2007 datasets show that the subsequent joint decision step clearly improves the accuracy compared to single class detection.
alternative_title:
- LNCS
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
citation:
ama: 'Lampert C, Blaschko M. A multiple kernel learning approach to joint multi-class
object detection. In: Vol 5096. Springer; 2008:31-40. doi:10.1007/978-3-540-69321-5_4'
apa: 'Lampert, C., & Blaschko, M. (2008). A multiple kernel learning approach
to joint multi-class object detection (Vol. 5096, pp. 31–40). Presented at the
DAGM: German Association For Pattern Recognition, Springer. https://doi.org/10.1007/978-3-540-69321-5_4'
chicago: Lampert, Christoph, and Matthew Blaschko. “A Multiple Kernel Learning Approach
to Joint Multi-Class Object Detection,” 5096:31–40. Springer, 2008. https://doi.org/10.1007/978-3-540-69321-5_4.
ieee: 'C. Lampert and M. Blaschko, “A multiple kernel learning approach to joint
multi-class object detection,” presented at the DAGM: German Association For Pattern
Recognition, 2008, vol. 5096, pp. 31–40.'
ista: 'Lampert C, Blaschko M. 2008. A multiple kernel learning approach to joint
multi-class object detection. DAGM: German Association For Pattern Recognition,
LNCS, vol. 5096, 31–40.'
mla: Lampert, Christoph, and Matthew Blaschko. A Multiple Kernel Learning Approach
to Joint Multi-Class Object Detection. Vol. 5096, Springer, 2008, pp. 31–40,
doi:10.1007/978-3-540-69321-5_4.
short: C. Lampert, M. Blaschko, in:, Springer, 2008, pp. 31–40.
conference:
name: 'DAGM: German Association For Pattern Recognition'
date_created: 2018-12-11T12:04:46Z
date_published: 2008-07-07T00:00:00Z
date_updated: 2021-01-12T07:51:41Z
day: '07'
doi: 10.1007/978-3-540-69321-5_4
extern: 1
intvolume: ' 5096'
main_file_link:
- open_access: '0'
url: http://www.kyb.mpg.de/fileadmin/user_upload/files/publications/attachments/DAGM2008-Lampert-Blaschko_5072%5b0%5d.pdf
month: '07'
page: 31 - 40
publication_status: published
publisher: Springer
publist_id: '2641'
quality_controlled: 0
status: public
title: A multiple kernel learning approach to joint multi-class object detection
type: conference
volume: 5096
year: '2008'
...
---
_id: '3714'
abstract:
- lang: eng
text: Most successful object recognition systems rely on binary classification,
deciding only if an object is present or not, but not providing information on
the actual object location. To perform localization, one can take a sliding window
approach, but this strongly increases the computational cost, because the classifier
function has to be evaluated over a large set of candidate subwindows. In this
paper, we propose a simple yet powerful branchand- bound scheme that allows efficient
maximization of a large class of classifier functions over all possible subimages.
It converges to a globally optimal solution typically in sublinear time. We show
how our method is applicable to different object detection and retrieval scenarios.
The achieved speedup allows the use of classifiers for localization that formerly
were considered too slow for this task, such as SVMs with a spatial pyramid kernel
or nearest neighbor classifiers based on the 2-distance. We demonstrate state-of-the-art
performance of the resulting systems on the UIUC Cars dataset, the PASCAL VOC
2006 dataset and in the PASCAL VOC 2007 competition.
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
- first_name: Thomas
full_name: Hofmann,Thomas
last_name: Hofmann
citation:
ama: 'Lampert C, Blaschko M, Hofmann T. Beyond sliding windows: Object localization
by efficient subwindow search. In: IEEE; 2008:1-8. doi:10.1109/CVPR.2008.4587586'
apa: 'Lampert, C., Blaschko, M., & Hofmann, T. (2008). Beyond sliding windows:
Object localization by efficient subwindow search (pp. 1–8). Presented at the
CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2008.4587586'
chicago: 'Lampert, Christoph, Matthew Blaschko, and Thomas Hofmann. “Beyond Sliding
Windows: Object Localization by Efficient Subwindow Search,” 1–8. IEEE, 2008.
https://doi.org/10.1109/CVPR.2008.4587586.'
ieee: 'C. Lampert, M. Blaschko, and T. Hofmann, “Beyond sliding windows: Object
localization by efficient subwindow search,” presented at the CVPR: Computer Vision
and Pattern Recognition, 2008, pp. 1–8.'
ista: 'Lampert C, Blaschko M, Hofmann T. 2008. Beyond sliding windows: Object localization
by efficient subwindow search. CVPR: Computer Vision and Pattern Recognition,
1–8.'
mla: 'Lampert, Christoph, et al. Beyond Sliding Windows: Object Localization
by Efficient Subwindow Search. IEEE, 2008, pp. 1–8, doi:10.1109/CVPR.2008.4587586.'
short: C. Lampert, M. Blaschko, T. Hofmann, in:, IEEE, 2008, pp. 1–8.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:04:46Z
date_published: 2008-09-18T00:00:00Z
date_updated: 2021-01-12T07:51:40Z
day: '18'
doi: 10.1109/CVPR.2008.4587586
extern: 1
main_file_link:
- open_access: '0'
url: http://www.kyb.mpg.de/fileadmin/user_upload/files/publications/pdfs/pdf5070.pdf
month: '09'
page: 1 - 8
publication_status: published
publisher: IEEE
publist_id: '2644'
quality_controlled: 0
status: public
title: 'Beyond sliding windows: Object localization by efficient subwindow search'
type: conference
year: '2008'
...
---
_id: '3734'
abstract:
- lang: eng
text: Gene expression levels fluctuate even under constant external conditions.
Much emphasis has usually been placed on the components of this noise that are
due to randomness in transcription and translation. Here we focus on the role
of noise associated with the inputs to transcriptional regulation; in particular,
we analyze the effects of random arrival times and binding of transcription factors
to their target sites along the genome. This contribution to the total noise sets
a fundamental physical limit to the reliability of genetic control, and has clear
signatures, but we show that these are easily obscured by experimental limitations
and even by conventional methods for plotting the variance vs. mean expression
level. We argue that simple, universal models of noise dominated by transcription
and translation are inconsistent with the embedding of gene expression in a network
of regulatory interactions. Analysis of recent experiments on transcriptional
control in the early Drosophila embryo shows that these results are quantitatively
consistent with the predicted signatures of input noise, and we discuss the experiments
needed to test the importance of input noise more generally.
acknowledgement: NSF Grant PHY-0650617; NIH grants P50 GM071508, R01 GM077599; Burroughs
Wellcome Program in Biological Dynamics
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Tkačik G, Gregor T, Bialek W. The role of input noise in transcriptional regulation.
PLoS One. 2008;3(7). doi:10.1371/journal.pone.0002774
apa: Tkačik, G., Gregor, T., & Bialek, W. (2008). The role of input noise in
transcriptional regulation. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0002774
chicago: Tkačik, Gašper, Thomas Gregor, and William Bialek. “The Role of Input Noise
in Transcriptional Regulation.” PLoS One. Public Library of Science, 2008.
https://doi.org/10.1371/journal.pone.0002774.
ieee: G. Tkačik, T. Gregor, and W. Bialek, “The role of input noise in transcriptional
regulation,” PLoS One, vol. 3, no. 7. Public Library of Science, 2008.
ista: Tkačik G, Gregor T, Bialek W. 2008. The role of input noise in transcriptional
regulation. PLoS One. 3(7).
mla: Tkačik, Gašper, et al. “The Role of Input Noise in Transcriptional Regulation.”
PLoS One, vol. 3, no. 7, Public Library of Science, 2008, doi:10.1371/journal.pone.0002774.
short: G. Tkačik, T. Gregor, W. Bialek, PLoS One 3 (2008).
date_created: 2018-12-11T12:04:52Z
date_published: 2008-07-23T00:00:00Z
date_updated: 2021-01-12T07:51:49Z
day: '23'
doi: 10.1371/journal.pone.0002774
extern: 1
intvolume: ' 3'
issue: '7'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2475664
month: '07'
oa: 1
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '2498'
quality_controlled: 0
status: public
title: The role of input noise in transcriptional regulation
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: 3
year: '2008'
...
---
_id: '3751'
abstract:
- lang: eng
text: 'Revealing the spectrum of combinatorial regulation of transcription at individual
promoters is essential for understanding the complex structure of biological networks.
However, the computations represented by the integration of various molecular
signals at complex promoters are difficult to decipher in the absence of simple
cis regulatory codes. Here we synthetically shuffle the regulatory architecture-operator
sequences binding activators and repressors-of a canonical bacterial promoter.
The resulting library of complex promoters allows for rapid exploration of promoter
encoded logic regulation. Among all possible logic functions, NOR and ANDN promoter
encoded logics predominate. A simple transcriptional cis regulatory code determines
both logics, establishing a straightforward map between promoter structure and
logic phenotype. The regulatory code is determined solely by the type of transcriptional
regulation combinations: two repressors generate a NOR: NOT (a OR b) whereas a
repressor and an activator generate an ANDN: a AND NOT b. Three-input versions
of both logics, having an additional repressor as an input, are also present in
the library. The resulting complex promoters cover a wide dynamic range of transcriptional
strengths. Synthetic promoter shuffling represents a fast and efficient method
for exploring the spectrum of complex regulatory functions that can be encoded
by complex promoters. From an engineering point of view, synthetic promoter shuffling
enables the experimental testing of the functional properties of complex promoters
that cannot necessarily be inferred ab initio from the known properties of the
individual genetic components. Synthetic promoter shuffling may provide a useful
experimental tool for studying naturally occurring promoter shuffling.'
article_number: e2030
author:
- first_name: Ali
full_name: Kinkhabwala, Ali
last_name: Kinkhabwala
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Kinkhabwala A, Guet CC. Uncovering cis regulatory codes using synthetic promoter
shuffling. PLoS One. 2008;3(4). doi:10.1371/journal.pone.0002030
apa: Kinkhabwala, A., & Guet, C. C. (2008). Uncovering cis regulatory codes
using synthetic promoter shuffling. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0002030
chicago: Kinkhabwala, Ali, and Calin C Guet. “Uncovering Cis Regulatory Codes Using
Synthetic Promoter Shuffling.” PLoS One. Public Library of Science, 2008.
https://doi.org/10.1371/journal.pone.0002030.
ieee: A. Kinkhabwala and C. C. Guet, “Uncovering cis regulatory codes using synthetic
promoter shuffling,” PLoS One, vol. 3, no. 4. Public Library of Science,
2008.
ista: Kinkhabwala A, Guet CC. 2008. Uncovering cis regulatory codes using synthetic
promoter shuffling. PLoS One. 3(4), e2030.
mla: Kinkhabwala, Ali, and Calin C. Guet. “Uncovering Cis Regulatory Codes Using
Synthetic Promoter Shuffling.” PLoS One, vol. 3, no. 4, e2030, Public Library
of Science, 2008, doi:10.1371/journal.pone.0002030.
short: A. Kinkhabwala, C.C. Guet, PLoS One 3 (2008).
date_created: 2018-12-11T12:04:58Z
date_published: 2008-04-30T00:00:00Z
date_updated: 2021-01-12T07:51:56Z
day: '30'
ddc:
- '570'
doi: 10.1371/journal.pone.0002030
extern: '1'
external_id:
pmid:
- '18446205'
file:
- access_level: open_access
checksum: 42c26f8337298a9ecadbe34a16139466
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T11:00:36Z
date_updated: 2020-07-14T12:46:15Z
file_id: '6400'
file_name: 2008_PLOS1_Kinkhabwala.PDF
file_size: 679786
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '2477'
quality_controlled: '1'
status: public
title: Uncovering cis regulatory codes using synthetic promoter shuffling
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2008'
...
---
_id: '3754'
abstract:
- lang: eng
text: Fluorescence correlation spectroscopy (FCS) has permitted the characterization
of high concentrations of noncoding RNAs in a single living bacterium. Here, we
extend the use of FCS to low concentrations of coding RNAs in single living cells.
We genetically fuse a red fluorescent protein (RFP) gene and two binding sites
for an RNA-binding protein, whose translated product is the RFP protein alone.
Using this construct, we determine in single cells both the absolute [mRNA] concentration
and the associated [RFP] expressed from an inducible plasmid. We find that the
FCS method allows us to reliably monitor in real-time [mRNA] down to similar to
40 nM (i.e. approximately two transcripts per volume of detection). To validate
these measurements, we show that [mRNA] is proportional to the associated expression
of the RFP protein. This FCS-based technique establishes a framework for minimally
invasive measurements of mRNA concentration in individual living bacteria.
acknowledgement: 'PMCID: PMC2475643 '
author:
- first_name: Calin C
full_name: Calin Guet
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Luke
full_name: Bruneaux,Luke
last_name: Bruneaux
- first_name: Taejin
full_name: Min,Taejin L
last_name: Min
- first_name: Dan
full_name: Siegal-Gaskins,Dan
last_name: Siegal Gaskins
- first_name: Israel
full_name: Figueroa,Israel
last_name: Figueroa
- first_name: Thierry
full_name: Emonet,Thierry
last_name: Emonet
- first_name: Philippe
full_name: Cluzel,Philippe
last_name: Cluzel
citation:
ama: Guet CC, Bruneaux L, Min T, et al. Minimally invasive determination of mRNA
concentration in single living bacteria. Nucleic Acids Research. 2008;36(12).
doi:10.1093/nar/gkn329
apa: Guet, C. C., Bruneaux, L., Min, T., Siegal Gaskins, D., Figueroa, I., Emonet,
T., & Cluzel, P. (2008). Minimally invasive determination of mRNA concentration
in single living bacteria. Nucleic Acids Research. Oxford University Press.
https://doi.org/10.1093/nar/gkn329
chicago: Guet, Calin C, Luke Bruneaux, Taejin Min, Dan Siegal Gaskins, Israel Figueroa,
Thierry Emonet, and Philippe Cluzel. “Minimally Invasive Determination of MRNA
Concentration in Single Living Bacteria.” Nucleic Acids Research. Oxford
University Press, 2008. https://doi.org/10.1093/nar/gkn329.
ieee: C. C. Guet et al., “Minimally invasive determination of mRNA concentration
in single living bacteria,” Nucleic Acids Research, vol. 36, no. 12. Oxford
University Press, 2008.
ista: Guet CC, Bruneaux L, Min T, Siegal Gaskins D, Figueroa I, Emonet T, Cluzel
P. 2008. Minimally invasive determination of mRNA concentration in single living
bacteria. Nucleic Acids Research. 36(12).
mla: Guet, Calin C., et al. “Minimally Invasive Determination of MRNA Concentration
in Single Living Bacteria.” Nucleic Acids Research, vol. 36, no. 12, Oxford
University Press, 2008, doi:10.1093/nar/gkn329.
short: C.C. Guet, L. Bruneaux, T. Min, D. Siegal Gaskins, I. Figueroa, T. Emonet,
P. Cluzel, Nucleic Acids Research 36 (2008).
date_created: 2018-12-11T12:04:59Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:51:57Z
day: '01'
doi: 10.1093/nar/gkn329
extern: 1
intvolume: ' 36'
issue: '12'
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '01'
publication: Nucleic Acids Research
publication_status: published
publisher: Oxford University Press
publist_id: '2474'
quality_controlled: 0
status: public
title: Minimally invasive determination of mRNA concentration in single living bacteria
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
volume: 36
year: '2008'
...
---
_id: '3769'
abstract:
- lang: eng
text: The geometrical representation of the space of phylogenetic trees implies
a metric on the space of weighted trees. This metric, the geodesic distance, is
the length of the shortest path through that space. We present an exact algorithm
to compute this metric. For biologically reasonable trees, the implementation
allows fast computations of the geodesic distance, although the running time of
the algorithm is worst-case exponential. The algorithm was applied to pairs of
118 gene trees of the metazoa. The results show that a special path in tree space,
the cone path, which can be computed in linear time, is a good approximation of
the geodesic distance. The program GeoMeTree is a python implementation of the
geodesic distance, and it is approximations and is available from www.cibiv.at/software/geometree.
acknowledgement: 10.1089/cmb.2008.0068
author:
- first_name: Anne
full_name: Anne Kupczok
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Arndt
full_name: von Haeseler,Arndt
last_name: Von Haeseler
- first_name: Steffen
full_name: Klaere,Steffen
last_name: Klaere
citation:
ama: Kupczok A, Von Haeseler A, Klaere S. An Exact Algorithm for the Geodesic Distance
between Phylogenetic Trees. Journal of Computational Biology. 2008;15(6):577-591.
doi:4200
apa: Kupczok, A., Von Haeseler, A., & Klaere, S. (2008). An Exact Algorithm
for the Geodesic Distance between Phylogenetic Trees. Journal of Computational
Biology. Mary Ann Liebert. https://doi.org/4200
chicago: Kupczok, Anne, Arndt Von Haeseler, and Steffen Klaere. “An Exact Algorithm
for the Geodesic Distance between Phylogenetic Trees.” Journal of Computational
Biology. Mary Ann Liebert, 2008. https://doi.org/4200.
ieee: A. Kupczok, A. Von Haeseler, and S. Klaere, “An Exact Algorithm for the Geodesic
Distance between Phylogenetic Trees.,” Journal of Computational Biology,
vol. 15, no. 6. Mary Ann Liebert, pp. 577–591, 2008.
ista: Kupczok A, Von Haeseler A, Klaere S. 2008. An Exact Algorithm for the Geodesic
Distance between Phylogenetic Trees. Journal of Computational Biology. 15(6),
577–591.
mla: Kupczok, Anne, et al. “An Exact Algorithm for the Geodesic Distance between
Phylogenetic Trees.” Journal of Computational Biology, vol. 15, no. 6,
Mary Ann Liebert, 2008, pp. 577–91, doi:4200.
short: A. Kupczok, A. Von Haeseler, S. Klaere, Journal of Computational Biology
15 (2008) 577–591.
date_created: 2018-12-11T12:05:04Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:04Z
day: '01'
doi: '4200'
extern: 1
intvolume: ' 15'
issue: '6'
month: '01'
page: 577 - 591
publication: Journal of Computational Biology
publication_status: published
publisher: Mary Ann Liebert
publist_id: '2458'
quality_controlled: 0
status: public
title: An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees.
type: journal_article
volume: 15
year: '2008'
...
---
_id: '3826'
abstract:
- lang: eng
text: Gamma frequency (30-100 Hz) oscillations in the mature cortex underlie higher
cognitive functions. Fast signaling in GABAergic interneuron networks plays a
key role in the generation of these oscillations. During development of the rodent
brain, gamma activity appears at the end of the first postnatal week, but frequency
and synchrony reach adult levels only by the fourth week. However, the mechanisms
underlying the maturation of gamma activity are unclear. Here we demonstrate that
hippocampal basket cells (BCs), the proposed cellular substrate of gamma oscillations,
undergo marked changes in their morphological, intrinsic, and synaptic properties
between postnatal day 6 (P6) and P25. During maturation, action potential duration,
propagation time, duration of the release period, and decay time constant of IPSCs
decreases by approximately 30-60%. Thus, postnatal development converts BCs from
slow into fast signaling devices. Computational analysis reveals that BC networks
with young intrinsic and synaptic properties as well as reduced connectivity generate
oscillations with moderate coherence in the lower gamma frequency range. In contrast,
BC networks with mature properties and increased connectivity generate highly
coherent activity in the upper gamma frequency band. Thus, late postnatal maturation
of BCs enhances coherence in neuronal networks and will thereby contribute to
the development of cognitive brain functions.
author:
- first_name: Daniel
full_name: Doischer, Daniel
last_name: Doischer
- first_name: Jonas
full_name: Hosp, Jonas Aurel
last_name: Hosp
- first_name: Yuchio
full_name: Yanagawa, Yuchio
last_name: Yanagawa
- first_name: Kunihiko
full_name: Obata, Kunihiko
last_name: Obata
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Imre
full_name: Vida, Imre
last_name: Vida
- first_name: Marlene
full_name: Bartos, Marlene
last_name: Bartos
citation:
ama: Doischer D, Hosp J, Yanagawa Y, et al. Postnatal differentiation of basket
cells from slow to fast signaling devices. Journal of Neuroscience. 2008;28(48):12956-12968.
doi:10.1523/JNEUROSCI.2890-08.2008
apa: Doischer, D., Hosp, J., Yanagawa, Y., Obata, K., Jonas, P. M., Vida, I., &
Bartos, M. (2008). Postnatal differentiation of basket cells from slow to fast
signaling devices. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2890-08.2008
chicago: Doischer, Daniel, Jonas Hosp, Yuchio Yanagawa, Kunihiko Obata, Peter M
Jonas, Imre Vida, and Marlene Bartos. “Postnatal Differentiation of Basket Cells
from Slow to Fast Signaling Devices.” Journal of Neuroscience. Society
for Neuroscience, 2008. https://doi.org/10.1523/JNEUROSCI.2890-08.2008.
ieee: D. Doischer et al., “Postnatal differentiation of basket cells from
slow to fast signaling devices,” Journal of Neuroscience, vol. 28, no.
48. Society for Neuroscience, pp. 12956–68, 2008.
ista: Doischer D, Hosp J, Yanagawa Y, Obata K, Jonas PM, Vida I, Bartos M. 2008.
Postnatal differentiation of basket cells from slow to fast signaling devices.
Journal of Neuroscience. 28(48), 12956–68.
mla: Doischer, Daniel, et al. “Postnatal Differentiation of Basket Cells from Slow
to Fast Signaling Devices.” Journal of Neuroscience, vol. 28, no. 48, Society
for Neuroscience, 2008, pp. 12956–68, doi:10.1523/JNEUROSCI.2890-08.2008.
short: D. Doischer, J. Hosp, Y. Yanagawa, K. Obata, P.M. Jonas, I. Vida, M. Bartos,
Journal of Neuroscience 28 (2008) 12956–68.
date_created: 2018-12-11T12:05:23Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:28Z
day: '01'
doi: 10.1523/JNEUROSCI.2890-08.2008
extern: 1
intvolume: ' 28'
issue: '48'
month: '01'
page: 12956 - 68
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '2383'
quality_controlled: 0
status: public
title: Postnatal differentiation of basket cells from slow to fast signaling devices
type: journal_article
volume: 28
year: '2008'
...
---
_id: '3827'
abstract:
- lang: eng
text: Previous studies revealed that synaptotagmin 1 is the major Ca(2+) sensor
for fast synchronous transmitter release at excitatory synapses. However, the
molecular identity of the Ca(2+) sensor at hippocampal inhibitory synapses has
not been determined. To address the functional role of synaptotagmin 1 at identified
inhibitory terminals, we made paired recordings from synaptically connected basket
cells (BCs) and granule cells (GCs) in the dentate gyrus in organotypic slice
cultures from wild-type and synaptotagmin 1-deficient mice. As expected, genetic
elimination of synaptotagmin 1 abolished synchronous transmitter release at excitatory
GC-BC synapses. However, synchronous release at inhibitory BC-GC synapses was
maintained. Quantitative analysis revealed that elimination of synaptotagmin 1
reduced release probability and depression but maintained the synchrony of transmitter
release at BC-GC synapses. Elimination of synaptotagmin 1 also increased the frequency
of both miniature excitatory postsynaptic currents (measured in BCs) and miniature
inhibitory postsynaptic currents (recorded in GCs), consistent with a clamping
function of synaptotagmin 1 at both excitatory and inhibitory terminals. Single-cell
reverse-transcription quantitative PCR analysis revealed that single BCs coexpressed
multiple synaptotagmin isoforms, including synaptotagmin 1-5, 7, and 11-13. Our
results indicate that, in contrast to excitatory synapses, synaptotagmin 1 is
not absolutely required for synchronous release at inhibitory BC-GC synapses.
Thus, alternative fast Ca(2+) sensors contribute to synchronous release of the
inhibitory transmitter GABA in cortical circuits.
author:
- first_name: Angharad
full_name: Kerr, Angharad M
last_name: Kerr
- first_name: Ellen
full_name: Reisinger, Ellen
last_name: Reisinger
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Kerr A, Reisinger E, Jonas PM. Differential dependence of phasic transmitter
release on synaptotagmin 1 at GABAergic and glutamatergic hippocampal synapses.
PNAS. 2008;105(40):15581-15586. doi:10.1073/pnas.0800621105
apa: Kerr, A., Reisinger, E., & Jonas, P. M. (2008). Differential dependence
of phasic transmitter release on synaptotagmin 1 at GABAergic and glutamatergic
hippocampal synapses. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0800621105
chicago: Kerr, Angharad, Ellen Reisinger, and Peter M Jonas. “Differential Dependence
of Phasic Transmitter Release on Synaptotagmin 1 at GABAergic and Glutamatergic
Hippocampal Synapses.” PNAS. National Academy of Sciences, 2008. https://doi.org/10.1073/pnas.0800621105.
ieee: A. Kerr, E. Reisinger, and P. M. Jonas, “Differential dependence of phasic
transmitter release on synaptotagmin 1 at GABAergic and glutamatergic hippocampal
synapses,” PNAS, vol. 105, no. 40. National Academy of Sciences, pp. 15581–6,
2008.
ista: Kerr A, Reisinger E, Jonas PM. 2008. Differential dependence of phasic transmitter
release on synaptotagmin 1 at GABAergic and glutamatergic hippocampal synapses.
PNAS. 105(40), 15581–6.
mla: Kerr, Angharad, et al. “Differential Dependence of Phasic Transmitter Release
on Synaptotagmin 1 at GABAergic and Glutamatergic Hippocampal Synapses.” PNAS,
vol. 105, no. 40, National Academy of Sciences, 2008, pp. 15581–86, doi:10.1073/pnas.0800621105.
short: A. Kerr, E. Reisinger, P.M. Jonas, PNAS 105 (2008) 15581–6.
date_created: 2018-12-11T12:05:23Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:29Z
day: '01'
doi: 10.1073/pnas.0800621105
extern: 1
intvolume: ' 105'
issue: '40'
month: '01'
page: 15581 - 6
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2384'
quality_controlled: 0
status: public
title: Differential dependence of phasic transmitter release on synaptotagmin 1 at
GABAergic and glutamatergic hippocampal synapses
type: journal_article
volume: 105
year: '2008'
...
---
_id: '3504'
abstract:
- lang: eng
text: "Simulation and bisimulation metrics for stochastic systems provide a quantitative
gen- eralization of the classical simulation and bisimulation relations. These
metrics capture the similarity of states with respect to quantitative specifications
written in the quantitative μ-calculus and related probabilistic logics.\r\nWe
present algorithms for computing the metrics on Markov decision processes (MDPs),
turn- based stochastic games, and concurrent games. For turn-based games and MDPs,
we provide a polynomial-time algorithm based on linear programming for the computation
of the one-step metric distance between states. The algorithm improves on the
previously known exponential-time algo- rithm based on a reduction to the theory
of reals. We then present PSPACE algorithms for both the decision problem and
the problem of approximating the metric distance between two states, matching
the best known bound for Markov chains. For the bisimulation kernel of the metric,
which corresponds to probabilistic bisimulation, our algorithm works in time O(n4)
for both turn-based games and MDPs; improving the previously best known O(n9 ·
log(n)) time algorithm for MDPs. For a concurrent game G, we show that computing
the exact distance between states is at least as hard as computing the value of
concurrent reachability games and the square-root-sum problem in computational
geometry. We show that checking whether the metric distance is bounded by a rational
r, can be accomplished via a reduction to the theory of real closed fields, involving
a\r\nformula with three quantifier alternations, yielding O(|G|O(|G|5)) time complexity,
improving the previously known reduction with O(|G|O(|G|7)) time complexity. These
algorithms can be iterated\r\nto approximate the metrics using binary search."
acknowledgement: This research was supported in part by the NSF grants CCR-0132780
and CNS-0720884.
alternative_title:
- LIPIcs
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: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
- first_name: Vishwanath
full_name: Raman, Vishwanath
last_name: Raman
citation:
ama: 'Chatterjee K, De Alfaro L, Majumdar R, Raman V. Algorithms for game metrics.
In: Vol 2. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2008:107-118. doi:10.4230/LIPIcs.FSTTCS.2008.1745'
apa: 'Chatterjee, K., De Alfaro, L., Majumdar, R., & Raman, V. (2008). Algorithms
for game metrics (Vol. 2, pp. 107–118). Presented at the FSTTCS: Foundations of
Software Technology and Theoretical Computer Science, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2008.1745'
chicago: Chatterjee, Krishnendu, Luca De Alfaro, Ritankar Majumdar, and Vishwanath
Raman. “Algorithms for Game Metrics,” 2:107–18. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2008. https://doi.org/10.4230/LIPIcs.FSTTCS.2008.1745.
ieee: 'K. Chatterjee, L. De Alfaro, R. Majumdar, and V. Raman, “Algorithms for game
metrics,” presented at the FSTTCS: Foundations of Software Technology and Theoretical
Computer Science, 2008, vol. 2, pp. 107–118.'
ista: 'Chatterjee K, De Alfaro L, Majumdar R, Raman V. 2008. Algorithms for game
metrics. FSTTCS: Foundations of Software Technology and Theoretical Computer Science,
LIPIcs, vol. 2, 107–118.'
mla: Chatterjee, Krishnendu, et al. Algorithms for Game Metrics. Vol. 2,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 107–18, doi:10.4230/LIPIcs.FSTTCS.2008.1745.
short: K. Chatterjee, L. De Alfaro, R. Majumdar, V. Raman, in:, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2008, pp. 107–118.
conference:
name: 'FSTTCS: Foundations of Software Technology and Theoretical Computer Science'
date_created: 2018-12-11T12:03:40Z
date_published: 2008-12-05T00:00:00Z
date_updated: 2023-02-23T11:46:14Z
day: '05'
ddc:
- '000'
doi: 10.4230/LIPIcs.FSTTCS.2008.1745
extern: '1'
file:
- access_level: open_access
checksum: 0a447454a24e273f7ddf51dbfe47f877
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T10:01:21Z
date_updated: 2020-07-14T12:46:12Z
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file_name: 2008_LIPIcs_Chatterjee.pdf
file_size: 442139
relation: main_file
file_date_updated: 2020-07-14T12:46:12Z
has_accepted_license: '1'
intvolume: ' 2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: 107 - 118
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '2883'
quality_controlled: '1'
related_material:
record:
- id: '3868'
relation: later_version
status: public
status: public
title: Algorithms for game metrics
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2008'
...
---
_id: '3875'
abstract:
- lang: eng
text: We study the problem of model checking Interval-valued Discrete-time Markov
Chains (IDTMC). IDTMCs are discrete-time finite Markov Chains for which the exact
transition probabilities are riot known. Instead in IDTMCs, each transition is
associated with an interval in which the actual transition probability must lie.
We consider two semantic interpretations for the uncertainty in the transition
probabilities of an IDTMC. In the first interpretation, we think of an IDTMC as
representing a (possibly uncountable) family of (classical) discrete-time Markov
Chains, where each member of the family is a Markov Chain whose transition probabilities
lie within the interval range given in the IDTMC. We call this semantic interpretation
Uncertain Markov Chains (UMC). In the second semantics for an IDTMC, which we
call Interval Markov Decision Process (IMDP), we view the uncertainty as being
resolved through non-determinism. In other words, each time a state is visited,
we adversarially pick a transition distribution that respects the interval constraints,
and take a probabilistic step according to the chosen distribution. We introduce
a logic omega-PCTL that can express liveness, strong fairness, and omega-regular
properties (such properties cannot be expressed in PCTL). We show that the omega-PCTL
model checking problem for Uncertain Markov Chain semantics is decidable in PSPACE
(same as the best known upper bound for PCTL) and for Interval Markov Decision
Process semantics is decidable in coNP (improving the previous known PSPACE bound
for PCTL). We also show that the qualitative fragment of the logic can lie solved
in coNP for the UMC interpretation, and can be solved in polynomial time for a
sub-class of UMCs. We also prove lower bounds for these model checking problems.
We show that the model checking problem of IDTMCs with LTL formulas can be solved
for both UMC and IMDP semantics by reduction to the model checking problem of
IDTMC with omega-PcTL formulas.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Koushik
full_name: Sen, Koushik
last_name: Sen
citation:
ama: 'Chatterjee K, Henzinger TA, Sen K. Model-checking omega-regular properties
of interval Markov chains. In: Vol 4962. Springer; 2008:302-317. doi:10.1007/978-3-540-78499-9_22'
apa: 'Chatterjee, K., Henzinger, T. A., & Sen, K. (2008). Model-checking omega-regular
properties of interval Markov chains (Vol. 4962, pp. 302–317). Presented at the
FoSSaCS: Foundations of Software Science and Computation Structures, Springer.
https://doi.org/10.1007/978-3-540-78499-9_22'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Koushik Sen. “Model-Checking
Omega-Regular Properties of Interval Markov Chains,” 4962:302–17. Springer, 2008.
https://doi.org/10.1007/978-3-540-78499-9_22.
ieee: 'K. Chatterjee, T. A. Henzinger, and K. Sen, “Model-checking omega-regular
properties of interval Markov chains,” presented at the FoSSaCS: Foundations of
Software Science and Computation Structures, 2008, vol. 4962, pp. 302–317.'
ista: 'Chatterjee K, Henzinger TA, Sen K. 2008. Model-checking omega-regular properties
of interval Markov chains. FoSSaCS: Foundations of Software Science and Computation
Structures, LNCS, vol. 4962, 302–317.'
mla: Chatterjee, Krishnendu, et al. Model-Checking Omega-Regular Properties of
Interval Markov Chains. Vol. 4962, Springer, 2008, pp. 302–17, doi:10.1007/978-3-540-78499-9_22.
short: K. Chatterjee, T.A. Henzinger, K. Sen, in:, Springer, 2008, pp. 302–317.
conference:
name: 'FoSSaCS: Foundations of Software Science and Computation Structures'
date_created: 2018-12-11T12:05:39Z
date_published: 2008-03-01T00:00:00Z
date_updated: 2021-01-12T07:52:52Z
day: '01'
doi: 10.1007/978-3-540-78499-9_22
extern: 1
intvolume: ' 4962'
month: '03'
page: 302 - 317
publication_status: published
publisher: Springer
publist_id: '2298'
quality_controlled: 0
status: public
title: Model-checking omega-regular properties of interval Markov chains
type: conference
volume: 4962
year: '2008'
...
---
_id: '3873'
abstract:
- lang: eng
text: We study the controller synthesis problem under budget constraints. In this
problem, there is a cost associated with making an observation, and a controller
can make only a limited number of observations in each round so that the total
cost of the observations does not exceed a given fixed budget. The controller
must ensure some omega-regular requirement subject to the budget constraint. Budget
constraints arise in designing and implementing controllers for resource-constrained
embedded systems, where a controller may not have enough power, time, or bandwidth
to obtain data from all sensors in each round. They lead to games of imperfect
information, where the unknown information is not fixed a priori, but can vary
from round to round, based on the choices made by the controller how to allocate
its budget. We show that the budget-constrained synthesis problem for W-regular
objectives is complete for exponential time. In addition to studying synthesis
under a fixed budget constraint, we study the budget optimization problem, where
given a plant, an objective, and observation costs, we have to find a controller
that achieves the objective with minimal average accumulated cost (or minimal
peak cost). We show that this problem is reducible to a game of imperfect information
where the winning objective is a conjunction of an omega-regular condition and
a long-run average condition (or a least max-cost condition), and this again leads
to an exponential-time algorithm. Finally, we extend our results to games over
infinite state spaces, and show that the budget-constrained synthesis problem
is decidable for infinite state games with stable quotients of finite index. Consequently,
the discrete time budget-constrained synthesis problem is decidable for rectangular
hybrid automata.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Chatterjee K, Majumdar R, Henzinger TA. Controller synthesis with budget constraints.
In: Vol 4981. Springer; 2008:72-86. doi:DOI:
10.1007/978-3-540-78929-1_6'
apa: 'Chatterjee, K., Majumdar, R., & Henzinger, T. A. (2008). Controller synthesis
with budget constraints (Vol. 4981, pp. 72–86). Presented at the HSCC: Hybrid
Systems - Computation and Control, Springer. https://doi.org/DOI:
10.1007/978-3-540-78929-1_6'
chicago: 'Chatterjee, Krishnendu, Ritankar Majumdar, and Thomas A Henzinger. “Controller
Synthesis with Budget Constraints,” 4981:72–86. Springer, 2008. https://doi.org/DOI: 10.1007/978-3-540-78929-1_6.'
ieee: 'K. Chatterjee, R. Majumdar, and T. A. Henzinger, “Controller synthesis with
budget constraints,” presented at the HSCC: Hybrid Systems - Computation and Control,
2008, vol. 4981, pp. 72–86.'
ista: 'Chatterjee K, Majumdar R, Henzinger TA. 2008. Controller synthesis with budget
constraints. HSCC: Hybrid Systems - Computation and Control, LNCS, vol. 4981,
72–86.'
mla: 'Chatterjee, Krishnendu, et al. Controller Synthesis with Budget Constraints.
Vol. 4981, Springer, 2008, pp. 72–86, doi:DOI:
10.1007/978-3-540-78929-1_6.'
short: K. Chatterjee, R. Majumdar, T.A. Henzinger, in:, Springer, 2008, pp. 72–86.
conference:
name: 'HSCC: Hybrid Systems - Computation and Control'
date_created: 2018-12-11T12:05:38Z
date_published: 2008-04-03T00:00:00Z
date_updated: 2021-01-12T07:52:51Z
day: '03'
doi: 'DOI: 10.1007/978-3-540-78929-1_6'
extern: 1
intvolume: ' 4981'
month: '04'
page: 72 - 86
publication_status: published
publisher: Springer
publist_id: '2296'
quality_controlled: 0
status: public
title: Controller synthesis with budget constraints
type: conference
volume: 4981
year: '2008'
...
---
_id: '3876'
abstract:
- lang: eng
text: We consider two-player games played in real time on game structures with clocks
and parity objectives. 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 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., nonconcurrent) finite-state (i.e., untimed) parity games. The
states of the resulting game are pairs of clock regions of the original game.
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. 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 strategies. Using a limit-robust 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. We show that exact strategies
are more powerful than limit-robust strategies, which are more powerful than bounded-robust
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.
acknowledgement: This research was supported in part by the NSF grants CCR-0132780,
CNS-0720884, and CCR-0225610, and by the European COMBEST project.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Vinayak
full_name: Prabhu, Vinayak S
last_name: Prabhu
citation:
ama: 'Chatterjee K, Henzinger TA, Prabhu V. Timed parity games: complexity and robustness.
In: Vol 5215. Springer; 2008:124-140. doi:10.1007/978-3-540-85778-5_10'
apa: 'Chatterjee, K., Henzinger, T. A., & Prabhu, V. (2008). Timed parity games:
complexity and robustness (Vol. 5215, pp. 124–140). Presented at the FORMATS:
Formal Modeling and Analysis of Timed Systems, Springer. https://doi.org/10.1007/978-3-540-85778-5_10'
chicago: 'Chatterjee, Krishnendu, Thomas A Henzinger, and Vinayak Prabhu. “Timed
Parity Games: Complexity and Robustness,” 5215:124–40. Springer, 2008. https://doi.org/10.1007/978-3-540-85778-5_10.'
ieee: 'K. Chatterjee, T. A. Henzinger, and V. Prabhu, “Timed parity games: complexity
and robustness,” presented at the FORMATS: Formal Modeling and Analysis of Timed
Systems, 2008, vol. 5215, pp. 124–140.'
ista: 'Chatterjee K, Henzinger TA, Prabhu V. 2008. Timed parity games: complexity
and robustness. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS,
vol. 5215, 124–140.'
mla: 'Chatterjee, Krishnendu, et al. Timed Parity Games: Complexity and Robustness.
Vol. 5215, Springer, 2008, pp. 124–40, doi:10.1007/978-3-540-85778-5_10.'
short: K. Chatterjee, T.A. Henzinger, V. Prabhu, in:, Springer, 2008, pp. 124–140.
conference:
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
date_created: 2018-12-11T12:05:39Z
date_published: 2008-10-01T00:00:00Z
date_updated: 2023-02-23T11:21:54Z
day: '01'
doi: 10.1007/978-3-540-85778-5_10
extern: 1
intvolume: ' 5215'
month: '10'
page: 124 - 140
publication_status: published
publisher: Springer
publist_id: '2294'
quality_controlled: 0
related_material:
record:
- id: '3315'
relation: later_version
status: public
status: public
title: 'Timed parity games: complexity and robustness'
type: conference
volume: 5215
year: '2008'
...
---
_id: '3877'
abstract:
- lang: eng
text: The synthesis problem asks to construct a reactive finite-state system from
an omega-regular specification. Initial specifications are often unrealizable,
which means that there is no system that implements the specification. A common
reason for unrealizability is that assumptions on the environment of the system
are incomplete. We study the problem of correcting an unrealizable specification
phi by computing an environment assumption psi such that the new specification
psi -> phi is realizable. Our aim is to construct an assumption psi that constrains
only the environment and is as weak as possible. We present a two-step algorithm
for computing assumptions. The algorithm operates on the game graph that is used
to answer the realizability question. First, we compute a safety assumption that
removes a minimal set of environment edges from the graph. Second, we compute
a liveness assumption that puts fairness conditions on some of the remaining environment
edges. We show that the problem of finding a minimal set of fair edges is computationally
hard, and we use probabilistic games to compute a locally minimal fairness assumption.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Thomas Henzinger
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: 'Chatterjee K, Henzinger TA, Jobstmann B. Environment assumptions for synthesis.
In: Vol 5201. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2008:147-161.
doi:10.1007/978-3-540-85361-9_14'
apa: 'Chatterjee, K., Henzinger, T. A., & Jobstmann, B. (2008). Environment
assumptions for synthesis (Vol. 5201, pp. 147–161). Presented at the CONCUR: Concurrency
Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-540-85361-9_14'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Barbara Jobstmann. “Environment
Assumptions for Synthesis,” 5201:147–61. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2008. https://doi.org/10.1007/978-3-540-85361-9_14.
ieee: 'K. Chatterjee, T. A. Henzinger, and B. Jobstmann, “Environment assumptions
for synthesis,” presented at the CONCUR: Concurrency Theory, 2008, vol. 5201,
pp. 147–161.'
ista: 'Chatterjee K, Henzinger TA, Jobstmann B. 2008. Environment assumptions for
synthesis. CONCUR: Concurrency Theory, LNCS, vol. 5201, 147–161.'
mla: Chatterjee, Krishnendu, et al. Environment Assumptions for Synthesis.
Vol. 5201, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 147–61,
doi:10.1007/978-3-540-85361-9_14.
short: K. Chatterjee, T.A. Henzinger, B. Jobstmann, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2008, pp. 147–161.
conference:
name: 'CONCUR: Concurrency Theory'
date_created: 2018-12-11T12:05:39Z
date_published: 2008-07-30T00:00:00Z
date_updated: 2021-01-12T07:52:53Z
day: '30'
doi: 10.1007/978-3-540-85361-9_14
extern: 1
intvolume: ' 5201'
month: '07'
page: 147 - 161
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '2295'
quality_controlled: 0
status: public
title: Environment assumptions for synthesis
type: conference
volume: 5201
year: '2008'
...
---
_id: '3878'
abstract:
- lang: eng
text: We study the problem of generating a test sequence that achieves maximal coverage
for a reactive system under test. We formulate the problem as a repeated game
between the tester and the system, where the system state space is partitioned
according to some coverage criterion and the objective of the tester is to maximize
the set of partitions (or coverage goals) visited during the game. We show the
complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete,
but is NP-complete for deterministic systems. For the special case of non-deterministic
systems with a re-initializing “reset” action, which represent running a new test
input on a re-initialized system, we show that the complexity is coNP-complete.
Our proof technique for reset games uses randomized testing strategies that circumvent
the exponentially large memory requirement of deterministic testing strategies.
acknowledgement: This research was supported in part by the NSF grants CCR-0132780
and CNS-0720884.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
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: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
citation:
ama: 'Chatterjee K, De Alfaro L, Majumdar R. The complexity of coverage. In: Vol
5356. Springer; 2008:91-106. doi:10.1007/978-3-540-89330-1_7'
apa: 'Chatterjee, K., De Alfaro, L., & Majumdar, R. (2008). The complexity of
coverage (Vol. 5356, pp. 91–106). Presented at the APLAS: Asian Symposium on Programming
Languages and Systems, Springer. https://doi.org/10.1007/978-3-540-89330-1_7'
chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Ritankar Majumdar. “The Complexity
of Coverage,” 5356:91–106. Springer, 2008. https://doi.org/10.1007/978-3-540-89330-1_7.
ieee: 'K. Chatterjee, L. De Alfaro, and R. Majumdar, “The complexity of coverage,”
presented at the APLAS: Asian Symposium on Programming Languages and Systems,
2008, vol. 5356, pp. 91–106.'
ista: 'Chatterjee K, De Alfaro L, Majumdar R. 2008. The complexity of coverage.
APLAS: Asian Symposium on Programming Languages and Systems, LNCS, vol. 5356,
91–106.'
mla: Chatterjee, Krishnendu, et al. The Complexity of Coverage. Vol. 5356,
Springer, 2008, pp. 91–106, doi:10.1007/978-3-540-89330-1_7.
short: K. Chatterjee, L. De Alfaro, R. Majumdar, in:, Springer, 2008, pp. 91–106.
conference:
name: 'APLAS: Asian Symposium on Programming Languages and Systems'
date_created: 2018-12-11T12:05:40Z
date_published: 2008-12-03T00:00:00Z
date_updated: 2021-01-12T07:52:53Z
day: '03'
doi: 10.1007/978-3-540-89330-1_7
extern: 1
intvolume: ' 5356'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0804.4525
month: '12'
oa: 1
page: 91 - 106
publication_status: published
publisher: Springer
publist_id: '2292'
quality_controlled: 0
status: public
title: The complexity of coverage
type: conference
volume: 5356
year: '2008'
...
---
_id: '3874'
abstract:
- lang: eng
text: We consider concurrent two-player timed automaton games with omega-regular
objectives specified as parity conditions. These games offer an appropriate model
for the synthesis of real-time controllers. Earlier works on timed games focused
on pure strategies for each player. We study, for the first time, the use of randomized
strategies in such games. While pure (i.e., nonrandomized) strategies in timed
games require infinite memory for winning even with respect to reachability objectives,
we show that randomized strategies can win with finite memory with respect to
all parity objectives. Also, the synthesized randomized real-time controllers
are much simpler in structure than the corresponding pure controllers, and therefore
easier to implement. For safety objectives we prove the existence of pure finite-memory
winning strategies. Finally, while randomization helps in simplifying the strategies
required for winning timed parity games, we prove that randomization does not
help in winning at more states.
acknowledgement: This research was supported in part by the NSF grants CCR-0208875,
CCR-0225610, CCR-0234690, by the Swiss National Science Foundation, and by the Artist2
European Network of Excellence.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Vinayak
full_name: Prabhu, Vinayak S
last_name: Prabhu
citation:
ama: 'Chatterjee K, Henzinger TA, Prabhu V. Trading infinite memory for uniform
randomness in timed games. In: Vol 4981. Springer; 2008:87-100. doi:10.1007/978-3-540-78929-1_7'
apa: 'Chatterjee, K., Henzinger, T. A., & Prabhu, V. (2008). Trading infinite
memory for uniform randomness in timed games (Vol. 4981, pp. 87–100). Presented
at the HSCC: Hybrid Systems - Computation and Control, Springer. https://doi.org/10.1007/978-3-540-78929-1_7'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Vinayak Prabhu. “Trading
Infinite Memory for Uniform Randomness in Timed Games,” 4981:87–100. Springer,
2008. https://doi.org/10.1007/978-3-540-78929-1_7.
ieee: 'K. Chatterjee, T. A. Henzinger, and V. Prabhu, “Trading infinite memory for
uniform randomness in timed games,” presented at the HSCC: Hybrid Systems - Computation
and Control, 2008, vol. 4981, pp. 87–100.'
ista: 'Chatterjee K, Henzinger TA, Prabhu V. 2008. Trading infinite memory for uniform
randomness in timed games. HSCC: Hybrid Systems - Computation and Control, LNCS,
vol. 4981, 87–100.'
mla: Chatterjee, Krishnendu, et al. Trading Infinite Memory for Uniform Randomness
in Timed Games. Vol. 4981, Springer, 2008, pp. 87–100, doi:10.1007/978-3-540-78929-1_7.
short: K. Chatterjee, T.A. Henzinger, V. Prabhu, in:, Springer, 2008, pp. 87–100.
conference:
name: 'HSCC: Hybrid Systems - Computation and Control'
date_created: 2018-12-11T12:05:38Z
date_published: 2008-04-03T00:00:00Z
date_updated: 2021-01-12T07:52:51Z
day: '03'
doi: 10.1007/978-3-540-78929-1_7
extern: 1
intvolume: ' 4981'
month: '04'
page: 87 - 100
publication_status: published
publisher: Springer
publist_id: '2297'
quality_controlled: 0
status: public
title: Trading infinite memory for uniform randomness in timed games
type: conference
volume: 4981
year: '2008'
...
---
_id: '3879'
abstract:
- lang: eng
text: Quantitative generalizations of classical languages, which assign to each
word a real number instead of a boolean value, have applications in modeling resource-constrained
computation. We use weighted automata (finite automata with transition weights)
to define several natural classes of quantitative languages over finite and infinite
words; in particular, the real value of an infinite run is computed as the maximum,
limsup, liminf, limit average, or discounted sum of the transition weights. We
define the classical decision problems of automata theory (emptiness, universality,
language inclusion, and language equivalence) in the quantitative setting and
study their computational complexity. As the decidability of language inclusion
remains open for some classes of weighted automata, we introduce a notion of quantitative
simulation that is decidable and implies language inclusion. We also give a complete
characterization of the expressive power of the various classes of weighted automata.
In particular, we show that most classes of weighted automata cannot be determinized.
acknowledgement: Research supported in part by the NSF grants CCR-0132780, CNS-0720884,
and CCR-0225610, by the Swiss National Science Foundation, and by the European COMBEST
project.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
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: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Chatterjee K, Doyen L, Henzinger TA. Quantitative languages. In: Vol 5213.
Springer; 2008:385-400. doi:10.1007/978-3-540-87531-4_28'
apa: 'Chatterjee, K., Doyen, L., & Henzinger, T. A. (2008). Quantitative languages
(Vol. 5213, pp. 385–400). Presented at the CSL: Computer Science Logic, Springer.
https://doi.org/10.1007/978-3-540-87531-4_28'
chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Quantitative
Languages,” 5213:385–400. Springer, 2008. https://doi.org/10.1007/978-3-540-87531-4_28.
ieee: 'K. Chatterjee, L. Doyen, and T. A. Henzinger, “Quantitative languages,” presented
at the CSL: Computer Science Logic, 2008, vol. 5213, pp. 385–400.'
ista: 'Chatterjee K, Doyen L, Henzinger TA. 2008. Quantitative languages. CSL: Computer
Science Logic, LNCS, vol. 5213, 385–400.'
mla: Chatterjee, Krishnendu, et al. Quantitative Languages. Vol. 5213, Springer,
2008, pp. 385–400, doi:10.1007/978-3-540-87531-4_28.
short: K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2008, pp. 385–400.
conference:
name: 'CSL: Computer Science Logic'
date_created: 2018-12-11T12:05:40Z
date_published: 2008-09-10T00:00:00Z
date_updated: 2021-01-12T07:52:54Z
day: '10'
doi: 10.1007/978-3-540-87531-4_28
extern: 1
intvolume: ' 5213'
month: '09'
page: 385 - 400
publication_status: published
publisher: Springer
publist_id: '2293'
quality_controlled: 0
status: public
title: Quantitative languages
type: conference
volume: 5213
year: '2008'
...
---
_id: '3872'
abstract:
- lang: eng
text: We survey value iteration algorithms on graphs. Such algorithms can be used
for determining the existence of certain paths (model checking), the existence
of certain strategies (game solving), and the probabilities of certain events
(performance analysis). We classify the algorithms according to the value domain
(boolean, probabilistic, or quantitative); according to the graph structure (nondeterministic,
probabilistic, or multi-player); according to the desired property of paths (Borel
level 1, 2, or 3); and according to the alternation depth and convergence rate
of fixpoint computations.
acknowledgement: This research was supported in part by the Swiss National Science
Foundation and by the NSF grants CCR-0225610 and CCR-0234690.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Chatterjee K, Henzinger TA. Value iteration. In: 25 Years in Model Checking.
Vol 5000. Springer; 2008:107-138. doi:10.1007/978-3-540-69850-0_7'
apa: Chatterjee, K., & Henzinger, T. A. (2008). Value iteration. In 25 Years
in Model Checking (Vol. 5000, pp. 107–138). Springer. https://doi.org/10.1007/978-3-540-69850-0_7
chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Value Iteration.” In 25
Years in Model Checking, 5000:107–38. Springer, 2008. https://doi.org/10.1007/978-3-540-69850-0_7.
ieee: K. Chatterjee and T. A. Henzinger, “Value iteration,” in 25 Years in Model
Checking, vol. 5000, Springer, 2008, pp. 107–138.
ista: 'Chatterjee K, Henzinger TA. 2008.Value iteration. In: 25 Years in Model Checking.
LNCS, vol. 5000, 107–138.'
mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. “Value Iteration.” 25 Years
in Model Checking, vol. 5000, Springer, 2008, pp. 107–38, doi:10.1007/978-3-540-69850-0_7.
short: K. Chatterjee, T.A. Henzinger, in:, 25 Years in Model Checking, Springer,
2008, pp. 107–138.
date_created: 2018-12-11T12:05:38Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:51Z
day: '01'
doi: 10.1007/978-3-540-69850-0_7
extern: 1
intvolume: ' 5000'
month: '01'
page: 107 - 138
publication: 25 Years in Model Checking
publication_status: published
publisher: Springer
publist_id: '2299'
quality_controlled: 0
status: public
title: Value iteration
type: book_chapter
volume: 5000
year: '2008'
...
---
_id: '3945'
abstract:
- lang: eng
text: Langerhans cells and dermal dendritic cells migrate to the draining lymph
nodes through dermal lymphatic vessels. They do so in the steady-state and under
inflammatory conditions. Peripheral T cell tolerance or T cell priming, respectively,
are the consequences of migration. The nature of dendritic cell-containing vessels
was mostly defined by electron microscopy or by their lack of blood endothelial
markers. Selective markers for murine lymph endothelium were hitherto rare or
not available. Here, we utilised recently developed antibodies against the murine
hyaluronan receptor, LYVE-1, to study the lymph vessel network in mouse skin in
more detail. In hairless skin from the ears, lymph vessels were spread out in
a horizontal plane. They formed anastomoses, and they possessed frequent blind
endings that were occasionally open. Lymph vessels were wider than blood vessels,
which were identified by their strong CD31 expression. In body wall skin LYVE-1
reactive vessels did not extend laterally but they dived straight down into the
deeper dermis. There, they are connected to each other and formed a network similar
to ear skin. The number and width of lymph vessels did not grossly change upon
inflammatory stimuli such as skin explant culture or tape stripping. There were
also no marked changes in caliber in response to the TLR 7/8 ligand Imiquimod.
Double-labelling experiments of cultured skin showed that most of the strongly
cell surface MHC II-expressing (i.e. activated) dendritic cells were confined
to the lymph vessels. Langerin/CD207(+) cells within this population appeared
later than dermal dendritic cells, i.e. langerin-negative cells. Comparable results
were obtained after stimulating the skin in vivo with the TLR 7/8 ligand Imiquimod
or by tape stripping. In untreated skin (i.e. steady state) a few MHC II(+) and
Langerin/CD207(+) cells, presumably migrating skin dendritic cells including epidermal
Langerhans cells, were consistently observed within the lymph vessels. The novel
antibody reagents may serve as important tools to further study the dendritic
cell traffic in the skin under physiological conditions as well as in conditions
of adoptive dendritic cell transfer in immunotherapy.
author:
- first_name: Christoph
full_name: Tripp, Christoph H
last_name: Tripp
- first_name: Bernhard
full_name: Haid, Bernhard
last_name: Haid
- first_name: Vincent
full_name: Flacher, Vincent
last_name: Flacher
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Hannes
full_name: Peter, Hannes
last_name: Peter
- first_name: Julia
full_name: Farkas, Julia
last_name: Farkas
- first_name: Robert
full_name: Gschwentner, Robert
last_name: Gschwentner
- first_name: Lydia
full_name: Sorokin, Lydia
last_name: Sorokin
- first_name: Nikolaus
full_name: Romani, Nikolaus
last_name: Romani
- first_name: Patrizia
full_name: Stoitzner, Patrizia
last_name: Stoitzner
citation:
ama: Tripp C, Haid B, Flacher V, et al. The lymph vessel network in mouse skin visualised
with antibodies against the hyaluronan receptor LYVE-1. Immunobiology.
2008;213(9-10):715-728. doi:10.1016/j.imbio.2008.07.025
apa: Tripp, C., Haid, B., Flacher, V., Sixt, M. K., Peter, H., Farkas, J., … Stoitzner,
P. (2008). The lymph vessel network in mouse skin visualised with antibodies against
the hyaluronan receptor LYVE-1. Immunobiology. Elsevier. https://doi.org/10.1016/j.imbio.2008.07.025
chicago: Tripp, Christoph, Bernhard Haid, Vincent Flacher, Michael K Sixt, Hannes
Peter, Julia Farkas, Robert Gschwentner, Lydia Sorokin, Nikolaus Romani, and Patrizia
Stoitzner. “The Lymph Vessel Network in Mouse Skin Visualised with Antibodies
against the Hyaluronan Receptor LYVE-1.” Immunobiology. Elsevier, 2008.
https://doi.org/10.1016/j.imbio.2008.07.025.
ieee: C. Tripp et al., “The lymph vessel network in mouse skin visualised
with antibodies against the hyaluronan receptor LYVE-1,” Immunobiology,
vol. 213, no. 9–10. Elsevier, pp. 715–28, 2008.
ista: Tripp C, Haid B, Flacher V, Sixt MK, Peter H, Farkas J, Gschwentner R, Sorokin
L, Romani N, Stoitzner P. 2008. The lymph vessel network in mouse skin visualised
with antibodies against the hyaluronan receptor LYVE-1. Immunobiology. 213(9–10),
715–28.
mla: Tripp, Christoph, et al. “The Lymph Vessel Network in Mouse Skin Visualised
with Antibodies against the Hyaluronan Receptor LYVE-1.” Immunobiology,
vol. 213, no. 9–10, Elsevier, 2008, pp. 715–28, doi:10.1016/j.imbio.2008.07.025.
short: C. Tripp, B. Haid, V. Flacher, M.K. Sixt, H. Peter, J. Farkas, R. Gschwentner,
L. Sorokin, N. Romani, P. Stoitzner, Immunobiology 213 (2008) 715–28.
date_created: 2018-12-11T12:06:02Z
date_published: 2008-08-30T00:00:00Z
date_updated: 2021-01-12T07:53:23Z
day: '30'
doi: 10.1016/j.imbio.2008.07.025
extern: 1
intvolume: ' 213'
issue: 9-10
month: '08'
page: 715 - 28
publication: Immunobiology
publication_status: published
publisher: Elsevier
publist_id: '2182'
quality_controlled: 0
status: public
title: The lymph vessel network in mouse skin visualised with antibodies against the
hyaluronan receptor LYVE-1
type: journal_article
volume: 213
year: '2008'
...
---
_id: '3942'
abstract:
- lang: eng
text: Recent in vitro studies have suggested a role for sialylation in chemokine
receptor binding to its ligand (Bannert, N., S. Craig, M. Farzan, D. Sogah, N.V.
Santo, H. Choe, and J. Sodroski. 2001. J. Exp. Med. 194:1661-1673). This prompted
us to investigate chemokine-induced leukocyte adhesion in inflamed cremaster muscle
venules of alpha2,3 sialyltransferase (ST3Gal-IV)-deficient mice. We found a marked
reduction in leukocyte adhesion to inflamed microvessels upon injection of the
CXCR2 ligands CXCL1 (keratinocyte-derived chemokine) or CXCL8 (interleukin 8).
In addition, extravasation of ST3Gal-IV(-/-) neutrophils into thioglycollate-pretreated
peritoneal cavities was significantly decreased. In vitro assays revealed that
CXCL8 binding to isolated ST3Gal-IV(-/-) neutrophils was markedly impaired. Furthermore,
CXCL1-mediated adhesion of ST3Gal-IV(-/-) leukocytes at physiological flow conditions,
as well as transendothelial migration of ST3Gal-IV(-/-) leukocytes in response
to CXCL1, was significantly reduced. In human neutrophils, enzymatic desialylation
decreased binding of CXCR2 ligands to the neutrophil surface and diminished neutrophil
degranulation in response to these chemokines. In addition, binding of alpha2,3-linked
sialic acid-specific Maackia amurensis lectin II to purified CXCR2 from neuraminidase-treated
CXCR2-transfected HEK293 cells was markedly impaired. Collectively, we provide
substantial evidence that sialylation by ST3Gal-IV significantly contributes to
CXCR2-mediated leukocyte adhesion during inflammation in vivo.
author:
- first_name: David
full_name: Frommhold, David
last_name: Frommhold
- first_name: Andreas
full_name: Ludwig, Andreas
last_name: Ludwig
- first_name: M Gabriele
full_name: Bixel, M Gabriele
last_name: Bixel
- first_name: Alexander
full_name: Zarbock, Alexander
last_name: Zarbock
- first_name: Inna
full_name: Babushkina, Inna
last_name: Babushkina
- first_name: Melitta
full_name: Weissinger, Melitta
last_name: Weissinger
- first_name: Sandra
full_name: Cauwenberghs, Sandra
last_name: Cauwenberghs
- first_name: Lesley
full_name: Ellies, Lesley G
last_name: Ellies
- first_name: Jamey
full_name: Marth, Jamey D
last_name: Marth
- first_name: Annette
full_name: Beck-Sickinger, Annette G
last_name: Beck Sickinger
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Bärbel
full_name: Lange-Sperandio, Bärbel
last_name: Lange Sperandio
- first_name: Alma
full_name: Zernecke, Alma
last_name: Zernecke
- first_name: Ernst
full_name: Brandt, Ernst
last_name: Brandt
- first_name: Christian
full_name: Weber, Christian
last_name: Weber
- first_name: Dietmar
full_name: Vestweber, Dietmar
last_name: Vestweber
- first_name: Klaus
full_name: Ley, Klaus
last_name: Ley
- first_name: Markus
full_name: Sperandio, Markus
last_name: Sperandio
citation:
ama: Frommhold D, Ludwig A, Bixel MG, et al. Sialyltransferase ST3Gal-IV controls
CXCR2-mediated firm leukocyte arrest during inflammation. The Journal of Experimental
Medicine. 2008;205(6):1435-1446. doi:10.1084/jem.20070846
apa: Frommhold, D., Ludwig, A., Bixel, M. G., Zarbock, A., Babushkina, I., Weissinger,
M., … Sperandio, M. (2008). Sialyltransferase ST3Gal-IV controls CXCR2-mediated
firm leukocyte arrest during inflammation. The Journal of Experimental Medicine.
Rockefeller University Press. https://doi.org/10.1084/jem.20070846
chicago: Frommhold, David, Andreas Ludwig, M Gabriele Bixel, Alexander Zarbock,
Inna Babushkina, Melitta Weissinger, Sandra Cauwenberghs, et al. “Sialyltransferase
ST3Gal-IV Controls CXCR2-Mediated Firm Leukocyte Arrest during Inflammation.”
The Journal of Experimental Medicine. Rockefeller University Press, 2008.
https://doi.org/10.1084/jem.20070846.
ieee: D. Frommhold et al., “Sialyltransferase ST3Gal-IV controls CXCR2-mediated
firm leukocyte arrest during inflammation,” The Journal of Experimental Medicine,
vol. 205, no. 6. Rockefeller University Press, pp. 1435–1446, 2008.
ista: Frommhold D, Ludwig A, Bixel MG, Zarbock A, Babushkina I, Weissinger M, Cauwenberghs
S, Ellies L, Marth J, Beck Sickinger A, Sixt MK, Lange Sperandio B, Zernecke A,
Brandt E, Weber C, Vestweber D, Ley K, Sperandio M. 2008. Sialyltransferase ST3Gal-IV
controls CXCR2-mediated firm leukocyte arrest during inflammation. The Journal
of Experimental Medicine. 205(6), 1435–1446.
mla: Frommhold, David, et al. “Sialyltransferase ST3Gal-IV Controls CXCR2-Mediated
Firm Leukocyte Arrest during Inflammation.” The Journal of Experimental Medicine,
vol. 205, no. 6, Rockefeller University Press, 2008, pp. 1435–46, doi:10.1084/jem.20070846.
short: D. Frommhold, A. Ludwig, M.G. Bixel, A. Zarbock, I. Babushkina, M. Weissinger,
S. Cauwenberghs, L. Ellies, J. Marth, A. Beck Sickinger, M.K. Sixt, B. Lange Sperandio,
A. Zernecke, E. Brandt, C. Weber, D. Vestweber, K. Ley, M. Sperandio, The Journal
of Experimental Medicine 205 (2008) 1435–1446.
date_created: 2018-12-11T12:06:01Z
date_published: 2008-06-02T00:00:00Z
date_updated: 2021-01-12T07:53:21Z
day: '02'
doi: 10.1084/jem.20070846
extern: 1
intvolume: ' 205'
issue: '6'
month: '06'
page: 1435 - 1446
publication: The Journal of Experimental Medicine
publication_status: published
publisher: Rockefeller University Press
publist_id: '2185'
quality_controlled: 0
status: public
title: Sialyltransferase ST3Gal-IV controls CXCR2-mediated firm leukocyte arrest during
inflammation
type: journal_article
volume: 205
year: '2008'
...
---
_id: '3943'
abstract:
- lang: eng
text: Neutrophil granulocytes form the body's first line of antibacterial defense,
but they also contribute to tissue injury and noninfectious, chronic inflammation.
Proteinase 3 (PR3) and neutrophil elastase (NE) are 2 abundant neutrophil serine
proteases implicated in antimicrobial defense with overlapping and potentially
redundant substrate specificity. Here, we unraveled a cooperative role for PR3
and NE in neutrophil activation and noninfectious inflammation in vivo, which
we believe to be novel. Mice lacking both PR3 and NE demonstrated strongly diminished
immune complex-mediated (IC-mediated) neutrophil infiltration in vivo as well
as reduced activation of isolated neutrophils by ICs in vitro. In contrast, in
mice lacking just NE, neutrophil recruitment to ICs was only marginally impaired.
The defects in mice lacking both PR3 and NE were directly linked to the accumulation
of antiinflammatory progranulin (PGRN). Both PR3 and NE cleaved PGRN in vitro
and during neutrophil activation and inflammation in vivo. Local administration
of recombinant PGRN potently inhibited neutrophilic inflammation in vivo, demonstrating
that PGRN represents a crucial inflammation-suppressing mediator. We conclude
that PR3 and NE enhance neutrophil-dependent inflammation by eliminating the local
antiinflammatory activity of PGRN. Our results support the use of serine protease
inhibitors as antiinflammatory agents.
author:
- first_name: Kai
full_name: Kessenbrock, Kai
last_name: Kessenbrock
- first_name: Leopold
full_name: Fröhlich, Leopold
last_name: Fröhlich
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Heiko
full_name: Pfister, Heiko
last_name: Pfister
- first_name: Andrew
full_name: Bateman, Andrew
last_name: Bateman
- first_name: Azzaq
full_name: Belaaouaj, Azzaq
last_name: Belaaouaj
- first_name: Johannes
full_name: Ring, Johannes
last_name: Ring
- first_name: Markus
full_name: Ollert, Markus
last_name: Ollert
- first_name: Reinhard
full_name: Fässler, Reinhard
last_name: Fässler
- first_name: Dieter
full_name: Jenne, Dieter E
last_name: Jenne
citation:
ama: Kessenbrock K, Fröhlich L, Sixt MK, et al. Proteinase 3 and neutrophil elastase
enhance inflammation in mice by inactivating antiinflammatory progranulin. The
Journal of Clinical Investigation. 2008;118(7):2438-2447. doi:10.1172/JCI34694
apa: Kessenbrock, K., Fröhlich, L., Sixt, M. K., Lämmermann, T., Pfister, H., Bateman,
A., … Jenne, D. (2008). Proteinase 3 and neutrophil elastase enhance inflammation
in mice by inactivating antiinflammatory progranulin. The Journal of Clinical
Investigation. American Society for Clinical Investigation. https://doi.org/10.1172/JCI34694
chicago: Kessenbrock, Kai, Leopold Fröhlich, Michael K Sixt, Tim Lämmermann, Heiko
Pfister, Andrew Bateman, Azzaq Belaaouaj, et al. “Proteinase 3 and Neutrophil
Elastase Enhance Inflammation in Mice by Inactivating Antiinflammatory Progranulin.”
The Journal of Clinical Investigation. American Society for Clinical Investigation,
2008. https://doi.org/10.1172/JCI34694.
ieee: K. Kessenbrock et al., “Proteinase 3 and neutrophil elastase enhance
inflammation in mice by inactivating antiinflammatory progranulin,” The Journal
of Clinical Investigation, vol. 118, no. 7. American Society for Clinical
Investigation, pp. 2438–2447, 2008.
ista: Kessenbrock K, Fröhlich L, Sixt MK, Lämmermann T, Pfister H, Bateman A, Belaaouaj
A, Ring J, Ollert M, Fässler R, Jenne D. 2008. Proteinase 3 and neutrophil elastase
enhance inflammation in mice by inactivating antiinflammatory progranulin. The
Journal of Clinical Investigation. 118(7), 2438–2447.
mla: Kessenbrock, Kai, et al. “Proteinase 3 and Neutrophil Elastase Enhance Inflammation
in Mice by Inactivating Antiinflammatory Progranulin.” The Journal of Clinical
Investigation, vol. 118, no. 7, American Society for Clinical Investigation,
2008, pp. 2438–47, doi:10.1172/JCI34694.
short: K. Kessenbrock, L. Fröhlich, M.K. Sixt, T. Lämmermann, H. Pfister, A. Bateman,
A. Belaaouaj, J. Ring, M. Ollert, R. Fässler, D. Jenne, The Journal of Clinical
Investigation 118 (2008) 2438–2447.
date_created: 2018-12-11T12:06:01Z
date_published: 2008-07-01T00:00:00Z
date_updated: 2021-01-12T07:53:22Z
day: '01'
doi: 10.1172/JCI34694
extern: 1
intvolume: ' 118'
issue: '7'
month: '07'
page: 2438 - 2447
publication: The Journal of Clinical Investigation
publication_status: published
publisher: American Society for Clinical Investigation
publist_id: '2183'
quality_controlled: 0
status: public
title: Proteinase 3 and neutrophil elastase enhance inflammation in mice by inactivating
antiinflammatory progranulin
type: journal_article
volume: 118
year: '2008'
...
---
_id: '3941'
abstract:
- lang: eng
text: All metazoan cells carry transmembrane receptors of the integrin family, which
couple the contractile force of the actomyosin cytoskeleton to the extracellular
environment. In agreement with this principle, rapidly migrating leukocytes use
integrin-mediated adhesion when moving over two-dimensional surfaces. As migration
on two-dimensional substrates naturally overemphasizes the role of adhesion, the
contribution of integrins during three-dimensional movement of leukocytes within
tissues has remained controversial. We studied the interplay between adhesive,
contractile and protrusive forces during interstitial leukocyte chemotaxis in
vivo and in vitro. We ablated all integrin heterodimers from murine leukocytes,
and show here that functional integrins do not contribute to migration in three-dimensional
environments. Instead, these cells migrate by the sole force of actin-network
expansion, which promotes protrusive flowing of the leading edge. Myosin II-dependent
contraction is only required on passage through narrow gaps, where a squeezing
contraction of the trailing edge propels the rigid nucleus.
author:
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Bernhard
full_name: Bader, Bernhard L
last_name: Bader
- first_name: Susan
full_name: Monkley, Susan J
last_name: Monkley
- first_name: Tim
full_name: Worbs, Tim
last_name: Worbs
- first_name: Roland
full_name: Wedlich-Söldner, Roland
last_name: Wedlich Söldner
- first_name: Karin
full_name: Hirsch, Karin
last_name: Hirsch
- first_name: Markus
full_name: Keller, Markus
last_name: Keller
- first_name: Reinhold
full_name: Förster, Reinhold
last_name: Förster
- first_name: David
full_name: Critchley, David R
last_name: Critchley
- first_name: Reinhard
full_name: Fässler, Reinhard
last_name: Fässler
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Lämmermann T, Bader B, Monkley S, et al. Rapid leukocyte migration by integrin-independent
flowing and squeezing. Nature. 2008;453(7191):51-55. doi:10.1038/nature06887
apa: Lämmermann, T., Bader, B., Monkley, S., Worbs, T., Wedlich Söldner, R., Hirsch,
K., … Sixt, M. K. (2008). Rapid leukocyte migration by integrin-independent flowing
and squeezing. Nature. Nature Publishing Group. https://doi.org/10.1038/nature06887
chicago: Lämmermann, Tim, Bernhard Bader, Susan Monkley, Tim Worbs, Roland Wedlich
Söldner, Karin Hirsch, Markus Keller, et al. “Rapid Leukocyte Migration by Integrin-Independent
Flowing and Squeezing.” Nature. Nature Publishing Group, 2008. https://doi.org/10.1038/nature06887.
ieee: T. Lämmermann et al., “Rapid leukocyte migration by integrin-independent
flowing and squeezing,” Nature, vol. 453, no. 7191. Nature Publishing Group,
pp. 51–55, 2008.
ista: Lämmermann T, Bader B, Monkley S, Worbs T, Wedlich Söldner R, Hirsch K, Keller
M, Förster R, Critchley D, Fässler R, Sixt MK. 2008. Rapid leukocyte migration
by integrin-independent flowing and squeezing. Nature. 453(7191), 51–55.
mla: Lämmermann, Tim, et al. “Rapid Leukocyte Migration by Integrin-Independent
Flowing and Squeezing.” Nature, vol. 453, no. 7191, Nature Publishing Group,
2008, pp. 51–55, doi:10.1038/nature06887.
short: T. Lämmermann, B. Bader, S. Monkley, T. Worbs, R. Wedlich Söldner, K. Hirsch,
M. Keller, R. Förster, D. Critchley, R. Fässler, M.K. Sixt, Nature 453 (2008)
51–55.
date_created: 2018-12-11T12:06:00Z
date_published: 2008-05-01T00:00:00Z
date_updated: 2021-01-12T07:53:21Z
day: '01'
doi: 10.1038/nature06887
extern: 1
intvolume: ' 453'
issue: '7191'
month: '05'
page: 51 - 55
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '2186'
quality_controlled: 0
status: public
title: Rapid leukocyte migration by integrin-independent flowing and squeezing
type: journal_article
volume: 453
year: '2008'
...
---
_id: '3944'
abstract:
- lang: eng
text: Live imaging of the actin cytoskeleton is crucial for the study of many fundamental
biological processes, but current approaches to visualize actin have several limitations.
Here we describe Lifeact, a 17-amino-acid peptide, which stained filamentous actin
(F-actin) structures in eukaryotic cells and tissues. Lifeact did not interfere
with actin dynamics in vitro and in vivo and in its chemically modified peptide
form allowed visualization of actin dynamics in nontransfectable cells.
author:
- first_name: Julia
full_name: Riedl, Julia
last_name: Riedl
- first_name: Alvaro
full_name: Crevenna, Alvaro H
last_name: Crevenna
- first_name: Kai
full_name: Kessenbrock, Kai
last_name: Kessenbrock
- first_name: Jerry
full_name: Yu, Jerry Haochen
last_name: Yu
- first_name: Dorothee
full_name: Neukirchen, Dorothee
last_name: Neukirchen
- first_name: Michal
full_name: Bista, Michal
last_name: Bista
- first_name: Frank
full_name: Bradke, Frank
last_name: Bradke
- first_name: Dieter
full_name: Jenne, Dieter
last_name: Jenne
- first_name: Tad
full_name: Holak, Tad A
last_name: Holak
- first_name: Zena
full_name: Werb, Zena
last_name: Werb
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Roland
full_name: Wedlich-Soldner, Roland
last_name: Wedlich Soldner
citation:
ama: 'Riedl J, Crevenna A, Kessenbrock K, et al. Lifeact: a versatile marker to
visualize F-actin. Nature Methods. 2008;5(7):605-607. doi:10.1038/nmeth.1220'
apa: 'Riedl, J., Crevenna, A., Kessenbrock, K., Yu, J., Neukirchen, D., Bista, M.,
… Wedlich Soldner, R. (2008). Lifeact: a versatile marker to visualize F-actin.
Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth.1220'
chicago: 'Riedl, Julia, Alvaro Crevenna, Kai Kessenbrock, Jerry Yu, Dorothee Neukirchen,
Michal Bista, Frank Bradke, et al. “Lifeact: A Versatile Marker to Visualize F-Actin.”
Nature Methods. Nature Publishing Group, 2008. https://doi.org/10.1038/nmeth.1220.'
ieee: 'J. Riedl et al., “Lifeact: a versatile marker to visualize F-actin,”
Nature Methods, vol. 5, no. 7. Nature Publishing Group, pp. 605–607, 2008.'
ista: 'Riedl J, Crevenna A, Kessenbrock K, Yu J, Neukirchen D, Bista M, Bradke F,
Jenne D, Holak T, Werb Z, Sixt MK, Wedlich Soldner R. 2008. Lifeact: a versatile
marker to visualize F-actin. Nature Methods. 5(7), 605–607.'
mla: 'Riedl, Julia, et al. “Lifeact: A Versatile Marker to Visualize F-Actin.” Nature
Methods, vol. 5, no. 7, Nature Publishing Group, 2008, pp. 605–07, doi:10.1038/nmeth.1220.'
short: J. Riedl, A. Crevenna, K. Kessenbrock, J. Yu, D. Neukirchen, M. Bista, F.
Bradke, D. Jenne, T. Holak, Z. Werb, M.K. Sixt, R. Wedlich Soldner, Nature Methods
5 (2008) 605–607.
date_created: 2018-12-11T12:06:02Z
date_published: 2008-06-08T00:00:00Z
date_updated: 2021-01-12T07:53:22Z
day: '08'
doi: 10.1038/nmeth.1220
extern: 1
intvolume: ' 5'
issue: '7'
month: '06'
page: 605 - 607
publication: Nature Methods
publication_status: published
publisher: Nature Publishing Group
publist_id: '2184'
quality_controlled: 0
status: public
title: 'Lifeact: a versatile marker to visualize F-actin'
type: journal_article
volume: 5
year: '2008'
...
---
_id: '3974'
abstract:
- lang: eng
text: Generalizing the concept of a Reeb graph, the Reeb space of a multivariate
continuous mapping identifies points of the domain that belong to a common component
of the preimage of a point in the range. We study the local and global structure
of this space for generic, piecewise linear mappings on a combinatorial manifold.
author:
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Amit
full_name: Amit Patel
id: 34A254A0-F248-11E8-B48F-1D18A9856A87
last_name: Patel
citation:
ama: 'Edelsbrunner H, Harer J, Patel A. Reeb spaces of piecewise linear mappings.
In: ACM; 2008:242-250. doi:10.1145/1377676.1377720'
apa: 'Edelsbrunner, H., Harer, J., & Patel, A. (2008). Reeb spaces of piecewise
linear mappings (pp. 242–250). Presented at the SCG: Symposium on Computational
Geometry, ACM. https://doi.org/10.1145/1377676.1377720'
chicago: Edelsbrunner, Herbert, John Harer, and Amit Patel. “Reeb Spaces of Piecewise
Linear Mappings,” 242–50. ACM, 2008. https://doi.org/10.1145/1377676.1377720.
ieee: 'H. Edelsbrunner, J. Harer, and A. Patel, “Reeb spaces of piecewise linear
mappings,” presented at the SCG: Symposium on Computational Geometry, 2008, pp.
242–250.'
ista: 'Edelsbrunner H, Harer J, Patel A. 2008. Reeb spaces of piecewise linear mappings.
SCG: Symposium on Computational Geometry, 242–250.'
mla: Edelsbrunner, Herbert, et al. Reeb Spaces of Piecewise Linear Mappings.
ACM, 2008, pp. 242–50, doi:10.1145/1377676.1377720.
short: H. Edelsbrunner, J. Harer, A. Patel, in:, ACM, 2008, pp. 242–250.
conference:
name: 'SCG: Symposium on Computational Geometry'
date_created: 2018-12-11T12:06:13Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:35Z
day: '01'
doi: 10.1145/1377676.1377720
extern: 1
month: '01'
page: 242 - 250
publication_status: published
publisher: ACM
publist_id: '2155'
quality_controlled: 0
status: public
title: Reeb spaces of piecewise linear mappings
type: conference
year: '2008'
...
---
_id: '4135'
author:
- first_name: D.
full_name: Storch,D.
last_name: Storch
- first_name: A.
full_name: Šizling,A. L
last_name: Šizling
- first_name: J.
full_name: Reif,J.
last_name: Reif
- first_name: Jitka
full_name: Jitka Polechova
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: E.
full_name: Šizlingová,E.
last_name: Šizlingová
- first_name: K.
full_name: Gaston,K. J
last_name: Gaston
citation:
ama: 'Storch D, Šizling A, Reif J, Polechova J, Šizlingová E, Gaston K. The quest
for a null model for macroecological patterns: geometry of species distributions
at multiple spatial scales. Ecology Letters. 2008;11(8):771-784. doi:3817'
apa: 'Storch, D., Šizling, A., Reif, J., Polechova, J., Šizlingová, E., & Gaston,
K. (2008). The quest for a null model for macroecological patterns: geometry of
species distributions at multiple spatial scales. Ecology Letters. Wiley-Blackwell.
https://doi.org/3817'
chicago: 'Storch, D., A. Šizling, J. Reif, Jitka Polechova, E. Šizlingová, and K.
Gaston. “The Quest for a Null Model for Macroecological Patterns: Geometry of
Species Distributions at Multiple Spatial Scales.” Ecology Letters. Wiley-Blackwell,
2008. https://doi.org/3817.'
ieee: 'D. Storch, A. Šizling, J. Reif, J. Polechova, E. Šizlingová, and K. Gaston,
“The quest for a null model for macroecological patterns: geometry of species
distributions at multiple spatial scales,” Ecology Letters, vol. 11, no.
8. Wiley-Blackwell, pp. 771–784, 2008.'
ista: 'Storch D, Šizling A, Reif J, Polechova J, Šizlingová E, Gaston K. 2008. The
quest for a null model for macroecological patterns: geometry of species distributions
at multiple spatial scales. Ecology Letters. 11(8), 771–784.'
mla: 'Storch, D., et al. “The Quest for a Null Model for Macroecological Patterns:
Geometry of Species Distributions at Multiple Spatial Scales.” Ecology Letters,
vol. 11, no. 8, Wiley-Blackwell, 2008, pp. 771–84, doi:3817.'
short: D. Storch, A. Šizling, J. Reif, J. Polechova, E. Šizlingová, K. Gaston, Ecology
Letters 11 (2008) 771–784.
date_created: 2018-12-11T12:07:09Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:54:46Z
day: '01'
doi: '3817'
extern: 1
intvolume: ' 11'
issue: '8'
month: '01'
page: 771 - 784
publication: Ecology Letters
publication_status: published
publisher: Wiley-Blackwell
publist_id: '1985'
quality_controlled: 0
status: public
title: 'The quest for a null model for macroecological patterns: geometry of species
distributions at multiple spatial scales'
type: journal_article
volume: 11
year: '2008'
...
---
_id: '4137'
author:
- first_name: Jon
full_name: Bridle, Jon R
last_name: Bridle
- first_name: Jitka
full_name: Jitka Polechova
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: Timothy
full_name: Vines, Timothy H
last_name: Vines
citation:
ama: 'Bridle J, Polechova J, Vines T. Patterns of biodiversity and limits to adaptation
in time and space. In: R. K. Butlin JR, Schluter D, eds. Evolution and Speciation.
Cambridge University Press; 2008:77-101. doi:3816'
apa: Bridle, J., Polechova, J., & Vines, T. (2008). Patterns of biodiversity
and limits to adaptation in time and space. In J. R. R. K. Butlin & D. Schluter
(Eds.), Evolution and Speciation (pp. 77–101). Cambridge University Press.
https://doi.org/3816
chicago: Bridle, Jon, Jitka Polechova, and Timothy Vines. “Patterns of Biodiversity
and Limits to Adaptation in Time and Space.” In Evolution and Speciation,
edited by J.R. R. K. Butlin and D. Schluter, 77–101. Cambridge University Press,
2008. https://doi.org/3816.
ieee: J. Bridle, J. Polechova, and T. Vines, “Patterns of biodiversity and limits
to adaptation in time and space,” in Evolution and Speciation, J. R. R.
K. Butlin and D. Schluter, Eds. Cambridge University Press, 2008, pp. 77–101.
ista: 'Bridle J, Polechova J, Vines T. 2008.Patterns of biodiversity and limits
to adaptation in time and space. In: Evolution and Speciation. , 77–101.'
mla: Bridle, Jon, et al. “Patterns of Biodiversity and Limits to Adaptation in Time
and Space.” Evolution and Speciation, edited by J.R. R. K. Butlin and D.
Schluter, Cambridge University Press, 2008, pp. 77–101, doi:3816.
short: J. Bridle, J. Polechova, T. Vines, in:, J.R. R. K. Butlin, D. Schluter (Eds.),
Evolution and Speciation, Cambridge University Press, 2008, pp. 77–101.
date_created: 2018-12-11T12:07:09Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:54:46Z
day: '01'
doi: '3816'
editor:
- first_name: J.R.
full_name: R. K. Butlin,J.R. Bridle
last_name: R. K. Butlin
- first_name: D.
full_name: Schluter,D.
last_name: Schluter
extern: 1
month: '01'
page: 77 - 101
publication: Evolution and Speciation
publication_status: published
publisher: Cambridge University Press
publist_id: '1984'
quality_controlled: 0
status: public
title: Patterns of biodiversity and limits to adaptation in time and space
type: book_chapter
year: '2008'
...
---
_id: '4150'
abstract:
- lang: eng
text: This study provides direct functional evidence that differential adhesion,
measurable as quantitative differences in tissue surface tension, influences spatial
positioning between zebrafish germ layer tissues. We show that embryonic ectodermal
and mesendodermal tissues generated by mRNA-overexpression behave on long-time
scales like immiscible fluids. When mixed in hanging drop culture, their cells
segregate into discrete phases with ectoderm adopting an internal position relative
to the mesendoderm. The position adopted directly correlates with differences
in tissue surface tension. We also show that germ layer tissues from untreated
embryos, when extirpated and placed in culture, adopt a configuration similar
to those of their mRNA-overexpressing counterparts. Down-regulating E-cadherin
expression in the ectoderm leads to reduced surface tension and results in phase
reversal with E-cadherin-depleted ectoderm cells now adopting an external position
relative to the mesendoderm. These results show that in vitro cell sorting of
zebrafish mesendoderm and ectoderm tissues is specified by tissue interfacial
tensions. We perform a mathematical analysis indicating that tissue interfacial
tension between actively motile cells contributes to the spatial organization
and dynamics of these zebrafish germ layers in vivo.
article_processing_charge: No
author:
- first_name: Eva
full_name: Schötz, Eva
last_name: Schötz
- first_name: Rebecca
full_name: Burdine, Rebecca
last_name: Burdine
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
- first_name: Malcolm
full_name: Steinberg, Malcolm
last_name: Steinberg
- 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: Ramsey
full_name: Foty, Ramsey
last_name: Foty
citation:
ama: Schötz E, Burdine R, Julicher F, Steinberg M, Heisenberg C-PJ, Foty R. Quantitative
differences in tissue surface tension influence zebrafish germ layer positioning.
HFSP Journal. 2008;2(1):42-56. doi:10.2976/1.2834817
apa: Schötz, E., Burdine, R., Julicher, F., Steinberg, M., Heisenberg, C.-P. J.,
& Foty, R. (2008). Quantitative differences in tissue surface tension influence
zebrafish germ layer positioning. HFSP Journal. HFSP Publishing. https://doi.org/10.2976/1.2834817
chicago: Schötz, Eva, Rebecca Burdine, Frank Julicher, Malcolm Steinberg, Carl-Philipp
J Heisenberg, and Ramsey Foty. “Quantitative Differences in Tissue Surface Tension
Influence Zebrafish Germ Layer Positioning.” HFSP Journal. HFSP Publishing,
2008. https://doi.org/10.2976/1.2834817.
ieee: E. Schötz, R. Burdine, F. Julicher, M. Steinberg, C.-P. J. Heisenberg, and
R. Foty, “Quantitative differences in tissue surface tension influence zebrafish
germ layer positioning,” HFSP Journal, vol. 2, no. 1. HFSP Publishing,
pp. 42–56, 2008.
ista: Schötz E, Burdine R, Julicher F, Steinberg M, Heisenberg C-PJ, Foty R. 2008.
Quantitative differences in tissue surface tension influence zebrafish germ layer
positioning. HFSP Journal. 2(1), 42–56.
mla: Schötz, Eva, et al. “Quantitative Differences in Tissue Surface Tension Influence
Zebrafish Germ Layer Positioning.” HFSP Journal, vol. 2, no. 1, HFSP Publishing,
2008, pp. 42–56, doi:10.2976/1.2834817.
short: E. Schötz, R. Burdine, F. Julicher, M. Steinberg, C.-P.J. Heisenberg, R.
Foty, HFSP Journal 2 (2008) 42–56.
date_created: 2018-12-11T12:07:14Z
date_published: 2008-02-01T00:00:00Z
date_updated: 2021-01-12T07:54:52Z
day: '01'
doi: 10.2976/1.2834817
extern: '1'
intvolume: ' 2'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 42 - 56
publication: HFSP Journal
publication_status: published
publisher: HFSP Publishing
publist_id: '1969'
status: public
title: Quantitative differences in tissue surface tension influence zebrafish germ
layer positioning
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2008'
...
---
_id: '4181'
abstract:
- lang: eng
text: Understanding the factors that direct tissue organization during development
is one of the most fundamental goals in developmental biology. Various hypotheses
explain cell sorting and tissue organization on the basis of the adhesive and
mechanical properties of the constituent cells(1). However, validating these hypotheses
has been difficult due to the lack of appropriate tools to measure these parameters.
Here we use atomic force microscopy ( AFM) to quantify the adhesive and mechanical
properties of individual ectoderm, mesoderm and endoderm progenitor cells from
gastrulating zebrafish embryos. Combining these data with tissue self-assembly
in vitro and the sorting behaviour of progenitors in vivo, we have shown that
differential actomyosin-dependent cell-cortex tension, regulated by Nodal/ TGF
beta-signalling ( transforming growth factor beta), constitutes a key factor that
directs progenitor-cell sorting. These results demonstrate a previously unrecognized
role for Nodal-controlled cell-cortex tension in germ-layer organization during
gastrulation.
article_processing_charge: No
author:
- first_name: Michael
full_name: Krieg, Michael
last_name: Krieg
- first_name: Yohanna
full_name: Arboleda Estudillo, Yohanna
last_name: Arboleda Estudillo
- first_name: Pierre
full_name: Puech, Pierre
last_name: Puech
- first_name: Jos
full_name: Käfer, Jos
last_name: Käfer
- first_name: François
full_name: Graner, François
last_name: Graner
- first_name: Daniel
full_name: Mueller, Daniel
last_name: Mueller
- 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: Krieg M, Arboleda Estudillo Y, Puech P, et al. Tensile forces govern germ-layer
organization in zebrafish. Nature Cell Biology. 2008;10(4):429-436. doi:10.1038/ncb1705
apa: Krieg, M., Arboleda Estudillo, Y., Puech, P., Käfer, J., Graner, F., Mueller,
D., & Heisenberg, C.-P. J. (2008). Tensile forces govern germ-layer organization
in zebrafish. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb1705
chicago: Krieg, Michael, Yohanna Arboleda Estudillo, Pierre Puech, Jos Käfer, François
Graner, Daniel Mueller, and Carl-Philipp J Heisenberg. “Tensile Forces Govern
Germ-Layer Organization in Zebrafish.” Nature Cell Biology. Nature Publishing
Group, 2008. https://doi.org/10.1038/ncb1705.
ieee: M. Krieg et al., “Tensile forces govern germ-layer organization in
zebrafish,” Nature Cell Biology, vol. 10, no. 4. Nature Publishing Group,
pp. 429–436, 2008.
ista: Krieg M, Arboleda Estudillo Y, Puech P, Käfer J, Graner F, Mueller D, Heisenberg
C-PJ. 2008. Tensile forces govern germ-layer organization in zebrafish. Nature
Cell Biology. 10(4), 429–436.
mla: Krieg, Michael, et al. “Tensile Forces Govern Germ-Layer Organization in Zebrafish.”
Nature Cell Biology, vol. 10, no. 4, Nature Publishing Group, 2008, pp.
429–36, doi:10.1038/ncb1705.
short: M. Krieg, Y. Arboleda Estudillo, P. Puech, J. Käfer, F. Graner, D. Mueller,
C.-P.J. Heisenberg, Nature Cell Biology 10 (2008) 429–436.
date_created: 2018-12-11T12:07:26Z
date_published: 2008-03-23T00:00:00Z
date_updated: 2021-01-12T07:55:07Z
day: '23'
doi: 10.1038/ncb1705
extern: '1'
intvolume: ' 10'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 429 - 436
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '1938'
status: public
title: Tensile forces govern germ-layer organization in zebrafish
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2008'
...
---
_id: '4180'
abstract:
- lang: eng
text: '(Figure Presented) The name''s Bond: Separated cells form membranous nanotubes
whose tips are tethered by adhesive bonds (see picture). The lifetime of receptor-ligand
interactions can be measured by using membrane nanotubes of living cells as constant
force actuators. Because the nanotubes are extruded from living cells at conditions
approaching the physiological, cellular processes can be both studied and utilized. '
article_processing_charge: No
author:
- first_name: Michael
full_name: Krieg, Michael
last_name: Krieg
- first_name: Jonne
full_name: Helenius, Jonne
last_name: Helenius
- 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: Daniel
full_name: Mueller, Daniel
last_name: Mueller
citation:
ama: 'Krieg M, Helenius J, Heisenberg C-PJ, Mueller D. A Bond for a Lifetime: Employing
Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics. Angewandte
Chemie - International Edition. 2008;47(50):9775-9777. doi:10.1002/anie.200803552'
apa: 'Krieg, M., Helenius, J., Heisenberg, C.-P. J., & Mueller, D. (2008). A
Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine
Receptor-Ligand Kinetics. Angewandte Chemie - International Edition. Wiley-Blackwell.
https://doi.org/10.1002/anie.200803552'
chicago: 'Krieg, Michael, Jonne Helenius, Carl-Philipp J Heisenberg, and Daniel
Mueller. “A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells
to Determine Receptor-Ligand Kinetics.” Angewandte Chemie - International Edition.
Wiley-Blackwell, 2008. https://doi.org/10.1002/anie.200803552.'
ieee: 'M. Krieg, J. Helenius, C.-P. J. Heisenberg, and D. Mueller, “A Bond for a
Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand
Kinetics,” Angewandte Chemie - International Edition, vol. 47, no. 50.
Wiley-Blackwell, pp. 9775–9777, 2008.'
ista: 'Krieg M, Helenius J, Heisenberg C-PJ, Mueller D. 2008. A Bond for a Lifetime:
Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics.
Angewandte Chemie - International Edition. 47(50), 9775–9777.'
mla: 'Krieg, Michael, et al. “A Bond for a Lifetime: Employing Membrane Nanotubes
from Living Cells to Determine Receptor-Ligand Kinetics.” Angewandte Chemie
- International Edition, vol. 47, no. 50, Wiley-Blackwell, 2008, pp. 9775–77,
doi:10.1002/anie.200803552.'
short: M. Krieg, J. Helenius, C.-P.J. Heisenberg, D. Mueller, Angewandte Chemie
- International Edition 47 (2008) 9775–9777.
date_created: 2018-12-11T12:07:26Z
date_published: 2008-12-01T00:00:00Z
date_updated: 2021-01-12T07:55:06Z
day: '01'
doi: 10.1002/anie.200803552
extern: '1'
intvolume: ' 47'
issue: '50'
language:
- iso: eng
month: '12'
oa_version: None
page: 9775 - 9777
publication: Angewandte Chemie - International Edition
publication_status: published
publisher: Wiley-Blackwell
publist_id: '1939'
status: public
title: 'A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine
Receptor-Ligand Kinetics'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2008'
...
---
_id: '4193'
abstract:
- lang: eng
text: The controlled adhesion of cells to each other and to the extracellular matrix
is crucial for tissue development and maintenance. Numerous assays have been developed
to quantify cell adhesion. Among these, the use of atomic force microscopy (AFM)
for single-cell force spectroscopy (SCFS) has recently been established. This
assay permits the adhesion of living cells to be studied in near-physiological
conditions. This implementation of AFM allows unrivaled spatial and temporal control
of cells, as well as highly quantitative force actuation and force measurement
that is sufficiently sensitive to characterize the interaction of single molecules.
Therefore, not only overall cell adhesion but also the properties of single adhesion-receptor-ligand
interactions can be studied. Here we describe current implementations and applications
of SCFS, as well as potential pitfalls, and outline how developments will provide
insight into the forces, energetics and kinetics of cell-adhesion processes.
article_processing_charge: No
author:
- first_name: Jonne
full_name: Helenius, Jonne
last_name: Helenius
- 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: Hermann
full_name: Gaub, Hermann
last_name: Gaub
- first_name: Daniel
full_name: Mueller, Daniel
last_name: Mueller
citation:
ama: Helenius J, Heisenberg C-PJ, Gaub H, Mueller D. Single-cell force spectroscopy.
Journal of Cell Science. 2008;121(11):1785-1791. doi:10.1242/jcs.030999
apa: Helenius, J., Heisenberg, C.-P. J., Gaub, H., & Mueller, D. (2008). Single-cell
force spectroscopy. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.030999
chicago: Helenius, Jonne, Carl-Philipp J Heisenberg, Hermann Gaub, and Daniel Mueller.
“Single-Cell Force Spectroscopy.” Journal of Cell Science. Company of Biologists,
2008. https://doi.org/10.1242/jcs.030999.
ieee: J. Helenius, C.-P. J. Heisenberg, H. Gaub, and D. Mueller, “Single-cell force
spectroscopy,” Journal of Cell Science, vol. 121, no. 11. Company of Biologists,
pp. 1785–1791, 2008.
ista: Helenius J, Heisenberg C-PJ, Gaub H, Mueller D. 2008. Single-cell force spectroscopy.
Journal of Cell Science. 121(11), 1785–1791.
mla: Helenius, Jonne, et al. “Single-Cell Force Spectroscopy.” Journal of Cell
Science, vol. 121, no. 11, Company of Biologists, 2008, pp. 1785–91, doi:10.1242/jcs.030999.
short: J. Helenius, C.-P.J. Heisenberg, H. Gaub, D. Mueller, Journal of Cell Science
121 (2008) 1785–1791.
date_created: 2018-12-11T12:07:30Z
date_published: 2008-06-01T00:00:00Z
date_updated: 2021-01-12T07:55:12Z
day: '01'
doi: 10.1242/jcs.030999
extern: '1'
intvolume: ' 121'
issue: '11'
language:
- iso: eng
month: '06'
oa_version: None
page: 1785 - 1791
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '1924'
status: public
title: Single-cell force spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2008'
...
---
_id: '4198'
abstract:
- lang: eng
text: Animal body plan arises during gastrulation and organogenesis by the coordination
of inductive events and cell movements. Several signaling pathways, such as BMP,
FGF, Hedgehog, Nodal, and Wnt have well-recognized instructive roles in cell fate
specification during vertebrate embryogenesis. Growing evidence indicates that
BMP, Nodal, and FGF signaling also regulate cell movements, and that they do so
through mechanisms distinct from those that specify cell fates. Moreover, pathways
controlling cell movements can also indirectly influence cell fate specification
by regulating dimensions and relative positions of interacting tissues. The current
challenge is to delineate the molecular mechanisms via which the major signaling
pathways regulate cell fate specification and movements, and how these two processes
are coordinated to ensure normal development.
article_processing_charge: No
author:
- 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: Lilianna
full_name: Solnica Krezel, Lilianna
last_name: Solnica Krezel
citation:
ama: Heisenberg C-PJ, Solnica Krezel L. Back and forth between cell fate specification
and movement during vertebrate gastrulation. Current Opinion in Genetics &
Development. 2008;18(4):311-316. doi:10.1016/j.gde.2008.07.011
apa: Heisenberg, C.-P. J., & Solnica Krezel, L. (2008). Back and forth between
cell fate specification and movement during vertebrate gastrulation. Current
Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2008.07.011
chicago: Heisenberg, Carl-Philipp J, and Lilianna Solnica Krezel. “Back and Forth
between Cell Fate Specification and Movement during Vertebrate Gastrulation.”
Current Opinion in Genetics & Development. Elsevier, 2008. https://doi.org/10.1016/j.gde.2008.07.011.
ieee: C.-P. J. Heisenberg and L. Solnica Krezel, “Back and forth between cell fate
specification and movement during vertebrate gastrulation,” Current Opinion
in Genetics & Development, vol. 18, no. 4. Elsevier, pp. 311–316, 2008.
ista: Heisenberg C-PJ, Solnica Krezel L. 2008. Back and forth between cell fate
specification and movement during vertebrate gastrulation. Current Opinion in
Genetics & Development. 18(4), 311–316.
mla: Heisenberg, Carl-Philipp J., and Lilianna Solnica Krezel. “Back and Forth between
Cell Fate Specification and Movement during Vertebrate Gastrulation.” Current
Opinion in Genetics & Development, vol. 18, no. 4, Elsevier, 2008, pp.
311–16, doi:10.1016/j.gde.2008.07.011.
short: C.-P.J. Heisenberg, L. Solnica Krezel, Current Opinion in Genetics &
Development 18 (2008) 311–316.
date_created: 2018-12-11T12:07:32Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:14Z
day: '01'
doi: 10.1016/j.gde.2008.07.011
extern: '1'
intvolume: ' 18'
issue: '4'
language:
- iso: eng
month: '01'
oa_version: None
page: 311 - 316
publication: Current Opinion in Genetics & Development
publication_status: published
publisher: Elsevier
publist_id: '1918'
status: public
title: Back and forth between cell fate specification and movement during vertebrate
gastrulation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2008'
...
---
_id: '4227'
abstract:
- lang: eng
text: 'Morphogen concentration gradients provide positional information by activating
target genes in a concentration-dependent manner. Recent reports show that the
gradient of the syncytial morphogen Bicoid seems to provide precise positional
information to determine target gene domains. For secreted morphogenetic ligands,
the precision of the gradients, the signal transduction and the reliability of
target gene expression domains have not been studied. Here we investigate these
issues for the TGF-beta-type morphogen Dpp. We first studied theoretically how
cell-to-cell variability in the source, the target tissue, or both, contribute
to the variations of the gradient. Fluctuations in the source and target generate
a local maximum of precision at a finite distance to the source. We then determined
experimentally in the wing epithelium: (1) the precision of the Dpp concentration
gradient; (2) the precision of the Dpp signaling activity profile; and (3) the
precision of activation of the Dpp target gene spalt. As captured by our theoretical
description, the Dpp gradient provides positional information with a maximal precision
a few cells away from the source. This maximal precision corresponds to a positional
uncertainly of about a single cell diameter. The precision of the Dpp gradient
accounts for the precision of the spalt expression range, implying that Dpp can
act as a morphogen to coarsely determine the expression pattern of target genes.'
author:
- first_name: Tobias
full_name: Bollenbach, Tobias
last_name: Bollenbach
- first_name: Periklis
full_name: Pantazis, Periklis
last_name: Pantazis
- first_name: Anna
full_name: Anna Kicheva
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Christian
full_name: Bokel, Christian
last_name: Bokel
- first_name: Marcos
full_name: González-Gaitán, Marcos
last_name: González Gaitán
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
citation:
ama: Bollenbach T, Pantazis P, Kicheva A, Bokel C, González Gaitán M, Julicher F.
Precision of the Dpp gradient. Development. 2008;135(6):1137-1146. doi:10.1242/dev.012062
apa: Bollenbach, T., Pantazis, P., Kicheva, A., Bokel, C., González Gaitán, M.,
& Julicher, F. (2008). Precision of the Dpp gradient. Development.
Company of Biologists. https://doi.org/10.1242/dev.012062
chicago: Bollenbach, Tobias, Periklis Pantazis, Anna Kicheva, Christian Bokel, Marcos
González Gaitán, and Frank Julicher. “Precision of the Dpp Gradient.” Development.
Company of Biologists, 2008. https://doi.org/10.1242/dev.012062.
ieee: T. Bollenbach, P. Pantazis, A. Kicheva, C. Bokel, M. González Gaitán, and
F. Julicher, “Precision of the Dpp gradient,” Development, vol. 135, no.
6. Company of Biologists, pp. 1137–1146, 2008.
ista: Bollenbach T, Pantazis P, Kicheva A, Bokel C, González Gaitán M, Julicher
F. 2008. Precision of the Dpp gradient. Development. 135(6), 1137–1146.
mla: Bollenbach, Tobias, et al. “Precision of the Dpp Gradient.” Development,
vol. 135, no. 6, Company of Biologists, 2008, pp. 1137–46, doi:10.1242/dev.012062.
short: T. Bollenbach, P. Pantazis, A. Kicheva, C. Bokel, M. González Gaitán, F.
Julicher, Development 135 (2008) 1137–1146.
date_created: 2018-12-11T12:07:42Z
date_published: 2008-03-15T00:00:00Z
date_updated: 2021-01-12T07:55:27Z
day: '15'
doi: 10.1242/dev.012062
extern: 1
intvolume: ' 135'
issue: '6'
month: '03'
page: 1137 - 1146
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '1889'
quality_controlled: 0
status: public
title: Precision of the Dpp gradient
type: journal_article
volume: 135
year: '2008'
...
---
_id: '4245'
abstract:
- lang: eng
text: Sex allocation theory has proved extremely successful at predicting when individuals
should adjust the sex of their offspring in response to environmental conditions.
However, we know rather little about the underlying genetics of sex ratio or how
genetic architecture might constrain adaptive sex-ratio behavior. We examined
how mutation influenced genetic variation in the sex ratios produced by the parasitoid
wasp Nasonia vitripennis. In a mutation accumulation experiment, we determined
the mutability of sex ratio, and compared this with the amount of genetic variation
observed in natural populations. We found that the mutability (h2m) ranges from
0.001 to 0.002, similar to estimates for life-history traits in other organisms.
These estimates suggest one mutation every 5–60 generations, which shift the sex
ratio by approximately 0.01 (proportion males). In this and other studies, the
genetic variation in N. vitripennis sex ratio ranged from 0.02 to 0.17 (broad-sense
heritability, H2). If sex ratio is maintained by mutation–selection balance, a
higher genetic variance would be expected given our mutational parameters. Instead,
the observed genetic variance perhaps suggests additional selection against sex-ratio
mutations with deleterious effects on other fitness traits as well as sex ratio
(i.e., pleiotropy), as has been argued to be the case more generally.
author:
- first_name: Bart
full_name: Pannebakker, Bart A
last_name: Pannebakker
- first_name: Daniel
full_name: Halligan, Daniel
last_name: Halligan
- first_name: K Tracy
full_name: Reynolds, K Tracy
last_name: Reynolds
- first_name: Gavin
full_name: Ballantyne, Gavin A
last_name: Ballantyne
- first_name: David
full_name: Shuker, David M
last_name: Shuker
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Stuart
full_name: West, Stuart A
last_name: West
citation:
ama: Pannebakker B, Halligan D, Reynolds KT, et al. Effects of spontaneous mutation
accumulation on sex ratio traits. Evolution; International Journal of Organic
Evolution. 2008;62(8):1921-1935. doi:10.1111/j.1558-5646.2008.00434.x
apa: Pannebakker, B., Halligan, D., Reynolds, K. T., Ballantyne, G., Shuker, D.,
Barton, N. H., & West, S. (2008). Effects of spontaneous mutation accumulation
on sex ratio traits. Evolution; International Journal of Organic Evolution.
Wiley-Blackwell. https://doi.org/10.1111/j.1558-5646.2008.00434.x
chicago: Pannebakker, Bart, Daniel Halligan, K Tracy Reynolds, Gavin Ballantyne,
David Shuker, Nicholas H Barton, and Stuart West. “Effects of Spontaneous Mutation
Accumulation on Sex Ratio Traits.” Evolution; International Journal of Organic
Evolution. Wiley-Blackwell, 2008. https://doi.org/10.1111/j.1558-5646.2008.00434.x.
ieee: B. Pannebakker et al., “Effects of spontaneous mutation accumulation
on sex ratio traits,” Evolution; International Journal of Organic Evolution,
vol. 62, no. 8. Wiley-Blackwell, pp. 1921–1935, 2008.
ista: Pannebakker B, Halligan D, Reynolds KT, Ballantyne G, Shuker D, Barton NH,
West S. 2008. Effects of spontaneous mutation accumulation on sex ratio traits.
Evolution; International Journal of Organic Evolution. 62(8), 1921–1935.
mla: Pannebakker, Bart, et al. “Effects of Spontaneous Mutation Accumulation on
Sex Ratio Traits.” Evolution; International Journal of Organic Evolution,
vol. 62, no. 8, Wiley-Blackwell, 2008, pp. 1921–35, doi:10.1111/j.1558-5646.2008.00434.x.
short: B. Pannebakker, D. Halligan, K.T. Reynolds, G. Ballantyne, D. Shuker, N.H.
Barton, S. West, Evolution; International Journal of Organic Evolution 62 (2008)
1921–1935.
date_created: 2018-12-11T12:07:49Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2021-01-12T07:55:34Z
day: '01'
doi: 10.1111/j.1558-5646.2008.00434.x
extern: 1
intvolume: ' 62'
issue: '8'
month: '08'
page: 1921 - 1935
publication: Evolution; International Journal of Organic Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '1860'
quality_controlled: 0
status: public
title: Effects of spontaneous mutation accumulation on sex ratio traits
type: journal_article
volume: 62
year: '2008'
...
---
_id: '4244'
abstract:
- lang: eng
text: This paper presents a new approach to optimization of an energy-constrained
modulation scheme for wireless sensor networks by taking advantage of a novel
bio-inspired optimization algorithm. The algorithm is inspired by Wrightpsilas
shifting balance theory (SBT) of evolution in population genetics. The total energy
consumption of an energy-constrained modulation scheme is minimized by using the
new SBT-based optimization algorithm. The results obtained by this new algorithm
are compared with other popular optimization algorithms. Numerical experiments
are performed to demonstrate that the SBT-based algorithm could be used as an
efficient optimizer for solving the optimization problems arising from currently
emerging energy-efficient wireless sensor networks.
author:
- first_name: Erfu
full_name: Yang, Erfu
last_name: Yang
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Tughrul
full_name: Arslan, Tughrul
last_name: Arslan
- first_name: Ahmet
full_name: Erdogan, Ahmet T
last_name: Erdogan
citation:
ama: 'Yang E, Barton NH, Arslan T, Erdogan A. A novel shifting balance theory-based
approach to optimization of an energy-constrained modulation scheme for wireless
sensor networks. In: IEEE; 2008:2749-2756. doi:10.1109/CEC.2008.4631167'
apa: 'Yang, E., Barton, N. H., Arslan, T., & Erdogan, A. (2008). A novel shifting
balance theory-based approach to optimization of an energy-constrained modulation
scheme for wireless sensor networks (pp. 2749–2756). Presented at the WCCI: IEEE
World Congress on Computational Intelligence, IEEE. https://doi.org/10.1109/CEC.2008.4631167'
chicago: Yang, Erfu, Nicholas H Barton, Tughrul Arslan, and Ahmet Erdogan. “A Novel
Shifting Balance Theory-Based Approach to Optimization of an Energy-Constrained
Modulation Scheme for Wireless Sensor Networks,” 2749–56. IEEE, 2008. https://doi.org/10.1109/CEC.2008.4631167.
ieee: 'E. Yang, N. H. Barton, T. Arslan, and A. Erdogan, “A novel shifting balance
theory-based approach to optimization of an energy-constrained modulation scheme
for wireless sensor networks,” presented at the WCCI: IEEE World Congress on Computational
Intelligence, 2008, pp. 2749–2756.'
ista: 'Yang E, Barton NH, Arslan T, Erdogan A. 2008. A novel shifting balance theory-based
approach to optimization of an energy-constrained modulation scheme for wireless
sensor networks. WCCI: IEEE World Congress on Computational Intelligence, 2749–2756.'
mla: Yang, Erfu, et al. A Novel Shifting Balance Theory-Based Approach to Optimization
of an Energy-Constrained Modulation Scheme for Wireless Sensor Networks. IEEE,
2008, pp. 2749–56, doi:10.1109/CEC.2008.4631167.
short: E. Yang, N.H. Barton, T. Arslan, A. Erdogan, in:, IEEE, 2008, pp. 2749–2756.
conference:
name: 'WCCI: IEEE World Congress on Computational Intelligence'
date_created: 2018-12-11T12:07:49Z
date_published: 2008-09-23T00:00:00Z
date_updated: 2021-01-12T07:55:34Z
day: '23'
doi: 10.1109/CEC.2008.4631167
extern: 1
month: '09'
page: 2749 - 2756
publication_status: published
publisher: IEEE
publist_id: '1861'
quality_controlled: 0
status: public
title: A novel shifting balance theory-based approach to optimization of an energy-constrained
modulation scheme for wireless sensor networks
type: conference
year: '2008'
...
---
_id: '4371'
abstract:
- lang: eng
text: We survey some of the problems associated with checking whether a given behavior
(a sequence, a Boolean signal or a continuous signal) satisfies a property specified
in an appropriate temporal logic and describe two such monitoring algorithms for
the real-time logic MITL.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Amir
full_name: Pnueli, Amir
last_name: Pnueli
citation:
ama: 'Maler O, Nickovic D, Pnueli A. Checking Temporal Properties of Discrete, Timed
and Continuous Behaviors. In: Pillars of Computer Science: Essays Dedicated
To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday. Springer;
2008:475-505. doi:10.1007/978-3-540-78127-1_26'
apa: 'Maler, O., Nickovic, D., & Pnueli, A. (2008). Checking Temporal Properties
of Discrete, Timed and Continuous Behaviors. In Pillars of Computer science:
Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday
(pp. 475–505). Springer. https://doi.org/10.1007/978-3-540-78127-1_26'
chicago: 'Maler, Oded, Dejan Nickovic, and Amir Pnueli. “Checking Temporal Properties
of Discrete, Timed and Continuous Behaviors.” In Pillars of Computer Science:
Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday,
475–505. Springer, 2008. https://doi.org/10.1007/978-3-540-78127-1_26.'
ieee: 'O. Maler, D. Nickovic, and A. Pnueli, “Checking Temporal Properties of Discrete,
Timed and Continuous Behaviors,” in Pillars of Computer science: Essays Dedicated
To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday, Springer,
2008, pp. 475–505.'
ista: 'Maler O, Nickovic D, Pnueli A. 2008.Checking Temporal Properties of Discrete,
Timed and Continuous Behaviors. In: Pillars of Computer science: Essays Dedicated
To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday. LNCS, , 475–505.'
mla: 'Maler, Oded, et al. “Checking Temporal Properties of Discrete, Timed and Continuous
Behaviors.” Pillars of Computer Science: Essays Dedicated To Boris (Boaz) Trakhtenbrot
on the Occasion of His 85th Birthday, Springer, 2008, pp. 475–505, doi:10.1007/978-3-540-78127-1_26.'
short: 'O. Maler, D. Nickovic, A. Pnueli, in:, Pillars of Computer Science: Essays
Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday, Springer,
2008, pp. 475–505.'
date_created: 2018-12-11T12:08:30Z
date_published: 2008-03-11T00:00:00Z
date_updated: 2023-02-14T10:42:38Z
day: '11'
doi: 10.1007/978-3-540-78127-1_26
extern: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 475 - 505
publication: 'Pillars of Computer science: Essays Dedicated To Boris (Boaz) Trakhtenbrot
on the Occasion of His 85th Birthday'
publication_identifier:
isbn:
- '9783540781264'
publication_status: published
publisher: Springer
publist_id: '1087'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Checking Temporal Properties of Discrete, Timed and Continuous Behaviors
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2008'
...
---
_id: '4366'
abstract:
- lang: eng
text: Termination of a heap-manipulating program generally depends on preconditions
that express heap assumptions (i.e., assertions describing reachability, aliasing,
separation and sharing in the heap). We present an algorithm for the inference
of such preconditions. The algorithm exploits a unique interplay between counterexample-producing
abstract termination checker and shape analysis. The shape analysis produces heap
assumptions on demand to eliminate counterexamples, i.e., non-terminating abstract
computations. The experiments with our prototype implementation indicate its practical
potential.
alternative_title:
- LNCS
author:
- first_name: Andreas
full_name: Podelski,Andreas
last_name: Podelski
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
- first_name: Thomas
full_name: Thomas Wies
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
citation:
ama: 'Podelski A, Rybalchenko A, Wies T. Heap Assumptions on Demand. In: Vol 5123.
Springer; 2008:314-327. doi:10.1007/978-3-540-70545-1_31'
apa: 'Podelski, A., Rybalchenko, A., & Wies, T. (2008). Heap Assumptions on
Demand (Vol. 5123, pp. 314–327). Presented at the CAV: Computer Aided Verification,
Springer. https://doi.org/10.1007/978-3-540-70545-1_31'
chicago: Podelski, Andreas, Andrey Rybalchenko, and Thomas Wies. “Heap Assumptions
on Demand,” 5123:314–27. Springer, 2008. https://doi.org/10.1007/978-3-540-70545-1_31.
ieee: 'A. Podelski, A. Rybalchenko, and T. Wies, “Heap Assumptions on Demand,” presented
at the CAV: Computer Aided Verification, 2008, vol. 5123, pp. 314–327.'
ista: 'Podelski A, Rybalchenko A, Wies T. 2008. Heap Assumptions on Demand. CAV:
Computer Aided Verification, LNCS, vol. 5123, 314–327.'
mla: Podelski, Andreas, et al. Heap Assumptions on Demand. Vol. 5123, Springer,
2008, pp. 314–27, doi:10.1007/978-3-540-70545-1_31.
short: A. Podelski, A. Rybalchenko, T. Wies, in:, Springer, 2008, pp. 314–327.
conference:
name: 'CAV: Computer Aided Verification'
date_created: 2018-12-11T12:08:29Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:26Z
day: '01'
doi: 10.1007/978-3-540-70545-1_31
extern: 1
intvolume: ' 5123'
month: '01'
page: 314 - 327
publication_status: published
publisher: Springer
publist_id: '1091'
quality_controlled: 0
status: public
title: Heap Assumptions on Demand
type: conference
volume: 5123
year: '2008'
...
---
_id: '3038'
abstract:
- lang: eng
text: Lateral roots originate deep within the parental root from a small number
of founder cells at the periphery of vascular tissues and must emerge through
intervening layers of tissues. We describe how the hormone auxin, which originates
from the developing lateral root, acts as a local inductive signal which re-programmes
adjacent cells. Auxin induces the expression of a previously uncharacterized auxin
influx carrier LAX3 in cortical and epidermal cells directly overlaying new primordia.
Increased LAX3 activity reinforces the auxin-dependent induction of a selection
of cell-wall-remodelling enzymes, which are likely to promote cell separation
in advance of developing lateral root primordia.
author:
- first_name: Kamal
full_name: Swarup, Kamal
last_name: Swarup
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Ranjan
full_name: Swarup, Ranjan
last_name: Swarup
- first_name: Ilda
full_name: Casimiro, Ilda
last_name: Casimiro
- first_name: Benjamin
full_name: Péret, Benjamin
last_name: Péret
- first_name: Yaodong
full_name: Yang, Yaodong
last_name: Yang
- first_name: Geraint
full_name: Parry, Geraint
last_name: Parry
- first_name: Erik
full_name: Nielsen, Erik
last_name: Nielsen
- first_name: Ive
full_name: De Smet, Ive
last_name: De Smet
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Mitchell
full_name: Levesque, Mitchell P
last_name: Levesque
- first_name: David
full_name: Carrier, David
last_name: Carrier
- first_name: Nicholas
full_name: James, Nicholas
last_name: James
- first_name: Vanessa
full_name: Calvo, Vanessa
last_name: Calvo
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Eric
full_name: Kramer, Eric
last_name: Kramer
- first_name: Rebecca
full_name: Roberts, Rebecca
last_name: Roberts
- first_name: Neil
full_name: Graham, Neil
last_name: Graham
- first_name: Sylvestre
full_name: Marillonnet, Sylvestre
last_name: Marillonnet
- first_name: Kanu
full_name: Patel, Kanu
last_name: Patel
- first_name: Jonathan
full_name: Jones, Jonathan D
last_name: Jones
- first_name: Christopher
full_name: Taylor, Christopher G
last_name: Taylor
- first_name: Daniel
full_name: Schachtman, Daniel P
last_name: Schachtman
- first_name: Sean
full_name: May, Sean
last_name: May
- first_name: Göran
full_name: Sandberg, Göran
last_name: Sandberg
- first_name: Philip
full_name: Benfey, Philip N
last_name: Benfey
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Ian
full_name: Kerr, Ian
last_name: Kerr
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Laurent
full_name: Laplaze, Laurent
last_name: Laplaze
- first_name: Malcolm
full_name: Bennett, Malcolm J
last_name: Bennett
citation:
ama: Swarup K, Benková E, Swarup R, et al. The auxin influx carrier LAX3 promotes
lateral root emergence. Nature Cell Biology. 2008;10(8):946-954. doi:10.1038/ncb1754
apa: Swarup, K., Benková, E., Swarup, R., Casimiro, I., Péret, B., Yang, Y., … Bennett,
M. (2008). The auxin influx carrier LAX3 promotes lateral root emergence. Nature
Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb1754
chicago: Swarup, Kamal, Eva Benková, Ranjan Swarup, Ilda Casimiro, Benjamin Péret,
Yaodong Yang, Geraint Parry, et al. “The Auxin Influx Carrier LAX3 Promotes Lateral
Root Emergence.” Nature Cell Biology. Nature Publishing Group, 2008. https://doi.org/10.1038/ncb1754.
ieee: K. Swarup et al., “The auxin influx carrier LAX3 promotes lateral root
emergence,” Nature Cell Biology, vol. 10, no. 8. Nature Publishing Group,
pp. 946–954, 2008.
ista: Swarup K, Benková E, Swarup R, Casimiro I, Péret B, Yang Y, Parry G, Nielsen
E, De Smet I, Vanneste S, Levesque M, Carrier D, James N, Calvo V, Ljung K, Kramer
E, Roberts R, Graham N, Marillonnet S, Patel K, Jones J, Taylor C, Schachtman
D, May S, Sandberg G, Benfey P, Friml J, Kerr I, Beeckman T, Laplaze L, Bennett
M. 2008. The auxin influx carrier LAX3 promotes lateral root emergence. Nature
Cell Biology. 10(8), 946–954.
mla: Swarup, Kamal, et al. “The Auxin Influx Carrier LAX3 Promotes Lateral Root
Emergence.” Nature Cell Biology, vol. 10, no. 8, Nature Publishing Group,
2008, pp. 946–54, doi:10.1038/ncb1754.
short: K. Swarup, E. Benková, R. Swarup, I. Casimiro, B. Péret, Y. Yang, G. Parry,
E. Nielsen, I. De Smet, S. Vanneste, M. Levesque, D. Carrier, N. James, V. Calvo,
K. Ljung, E. Kramer, R. Roberts, N. Graham, S. Marillonnet, K. Patel, J. Jones,
C. Taylor, D. Schachtman, S. May, G. Sandberg, P. Benfey, J. Friml, I. Kerr, T.
Beeckman, L. Laplaze, M. Bennett, Nature Cell Biology 10 (2008) 946–954.
date_created: 2018-12-11T12:01:00Z
date_published: 2008-07-11T00:00:00Z
date_updated: 2021-01-12T07:40:37Z
day: '11'
doi: 10.1038/ncb1754
extern: 1
intvolume: ' 10'
issue: '8'
month: '07'
page: 946 - 954
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3665'
quality_controlled: 0
status: public
title: The auxin influx carrier LAX3 promotes lateral root emergence
type: journal_article
volume: 10
year: '2008'
...
---
_id: '3036'
abstract:
- lang: eng
text: Plants exhibit an exceptional adaptability to different environmental conditions.
To a large extent, this adaptability depends on their ability to initiate and
form new organs throughout their entire postembryonic life. Plant shoot and root
systems unceasingly branch and form axillary shoots or lateral roots, respectively.
The first event in the formation of a new organ is specification of founder cells.
Several plant hormones, prominent among them auxin, have been implicated in the
acquisition of founder cell identity by differentiated cells, but the mechanisms
underlying this process are largely elusive. Here, we show that auxin and its
local accumulation in root pericycle cells is a necessary and sufficient signal
to respecify these cells into lateral root founder cells. Analysis of the alf4-1
mutant suggests that specification of founder cells and the subsequent activation
of cell division leading to primordium formation represent two genetically separable
events. Time-lapse experiments show that the activation of an auxin response is
the earliest detectable event in founder cell specification. Accordingly, local
activation of auxin response correlates absolutely with the acquisition of founder
cell identity and precedes the actual formation of a lateral root primordium through
patterned cell division. Local production and subsequent accumulation of auxin
in single pericycle cells induced by Cre-Lox-based activation of auxin synthesis
converts them into founder cells. Thus, auxin is the local instructive signal
that is sufficient for acquisition of founder cell identity and can be considered
a morphogenetic trigger in postembryonic plant organogenesis.
author:
- first_name: Joseph
full_name: Dubrovsky, Joseph G
last_name: Dubrovsky
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Selene
full_name: Napsucialy-Mendivil, Selene
last_name: Napsucialy Mendivil
- 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: Svetlana
full_name: Shishkova, Svetlana
last_name: Shishkova
- first_name: John
full_name: Celenza, John
last_name: Celenza
- 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, Sauer M, Napsucialy Mendivil S, et al. Auxin acts as a local morphogenetic
trigger to specify lateral root founder cells. PNAS. 2008;105(25):8790-8794.
doi:10.1073/pnas.0712307105
apa: Dubrovsky, J., Sauer, M., Napsucialy Mendivil, S., Ivanchenko, M., Friml, J.,
Shishkova, S., … Benková, E. (2008). Auxin acts as a local morphogenetic trigger
to specify lateral root founder cells. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.0712307105
chicago: Dubrovsky, Joseph, Michael Sauer, Selene Napsucialy Mendivil, Maria Ivanchenko,
Jiří Friml, Svetlana Shishkova, John Celenza, and Eva Benková. “Auxin Acts as
a Local Morphogenetic Trigger to Specify Lateral Root Founder Cells.” PNAS.
National Academy of Sciences, 2008. https://doi.org/10.1073/pnas.0712307105.
ieee: J. Dubrovsky et al., “Auxin acts as a local morphogenetic trigger to
specify lateral root founder cells,” PNAS, vol. 105, no. 25. National Academy
of Sciences, pp. 8790–8794, 2008.
ista: Dubrovsky J, Sauer M, Napsucialy Mendivil S, Ivanchenko M, Friml J, Shishkova
S, Celenza J, Benková E. 2008. Auxin acts as a local morphogenetic trigger to
specify lateral root founder cells. PNAS. 105(25), 8790–8794.
mla: Dubrovsky, Joseph, et al. “Auxin Acts as a Local Morphogenetic Trigger to Specify
Lateral Root Founder Cells.” PNAS, vol. 105, no. 25, National Academy of
Sciences, 2008, pp. 8790–94, doi:10.1073/pnas.0712307105.
short: J. Dubrovsky, M. Sauer, S. Napsucialy Mendivil, M. Ivanchenko, J. Friml,
S. Shishkova, J. Celenza, E. Benková, PNAS 105 (2008) 8790–8794.
date_created: 2018-12-11T12:00:59Z
date_published: 2008-06-24T00:00:00Z
date_updated: 2021-01-12T07:40:36Z
day: '24'
doi: 10.1073/pnas.0712307105
extern: 1
intvolume: ' 105'
issue: '25'
month: '06'
page: 8790 - 8794
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3666'
quality_controlled: 0
status: public
title: Auxin acts as a local morphogenetic trigger to specify lateral root founder
cells
type: journal_article
volume: 105
year: '2008'
...
---
_id: '3030'
abstract:
- lang: eng
text: Telomeres in many eukaryotes are maintained by telomerase in whose absence
telomere shortening occurs. However, telomerase-deficient Arabidopsis thaliana
mutants (Attert -/-) show extremely low rates of telomere shortening per plant
generation (250-500 bp), which does not correspond to the expected outcome of
replicative telomere shortening resulting from ca. 1,000 meristem cell divisions
per seed-to-seed generation. To investigate the influence of the number of cell
divisions per seed-to-seed generation, Attert -/- mutant plants were propagated
from seeds coming either from the lower-most or the upper-most siliques (L- and
U-plants) and the length of their telomeres were followed over several generations.
The rate of telomere shortening was faster in U-plants, than in L-plants, as would
be expected from their higher number of cell divisions per generation. However,
this trend was observed only in telomeres whose initial length is relatively high
and the differences decreased with progressive general telomere shortening over
generations. But in generation 4, the L-plants frequently show a net telomere
elongation, while the U-plants fail to do so. We propose that this is due to the
activation of alternative telomere lengthening (ALT), a process which is activated
in early embryonic development in both U- and L-plants, but is overridden in U-plants
due to their higher number of cell divisions per generation. These data demonstrate
what so far has only been speculated, that in the absence of telomerase, the number
of cell divisions within one generation influences the control of telomere lengths.
These results also reveal a fast and efficient activation of ALT mechanism(s)
in response to the loss of telomerase activity and imply that ALT is probably
involved also in normal plant development.
author:
- first_name: Eva
full_name: Růčková, Eva
last_name: Růčková
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Petra
full_name: Procházková Schrumpfová, Petra
last_name: Procházková Schrumpfová
- first_name: Jiří
full_name: Fajkus, Jiří
last_name: Fajkus
citation:
ama: Růčková E, Friml J, Procházková Schrumpfová P, Fajkus J. Role of alternative
telomere lengthening unmasked in telomerase knock-out mutant plants. Plant
Molecular Biology. 2008;66(6):637-646. doi:10.1007/s11103-008-9295-7
apa: Růčková, E., Friml, J., Procházková Schrumpfová, P., & Fajkus, J. (2008).
Role of alternative telomere lengthening unmasked in telomerase knock-out mutant
plants. Plant Molecular Biology. Springer. https://doi.org/10.1007/s11103-008-9295-7
chicago: Růčková, Eva, Jiří Friml, Petra Procházková Schrumpfová, and Jiří Fajkus.
“Role of Alternative Telomere Lengthening Unmasked in Telomerase Knock-out Mutant
Plants.” Plant Molecular Biology. Springer, 2008. https://doi.org/10.1007/s11103-008-9295-7.
ieee: E. Růčková, J. Friml, P. Procházková Schrumpfová, and J. Fajkus, “Role of
alternative telomere lengthening unmasked in telomerase knock-out mutant plants,”
Plant Molecular Biology, vol. 66, no. 6. Springer, pp. 637–646, 2008.
ista: Růčková E, Friml J, Procházková Schrumpfová P, Fajkus J. 2008. Role of alternative
telomere lengthening unmasked in telomerase knock-out mutant plants. Plant Molecular
Biology. 66(6), 637–646.
mla: Růčková, Eva, et al. “Role of Alternative Telomere Lengthening Unmasked in
Telomerase Knock-out Mutant Plants.” Plant Molecular Biology, vol. 66,
no. 6, Springer, 2008, pp. 637–46, doi:10.1007/s11103-008-9295-7.
short: E. Růčková, J. Friml, P. Procházková Schrumpfová, J. Fajkus, Plant Molecular
Biology 66 (2008) 637–646.
date_created: 2018-12-11T12:00:57Z
date_published: 2008-04-01T00:00:00Z
date_updated: 2021-01-12T07:40:34Z
day: '01'
doi: 10.1007/s11103-008-9295-7
extern: 1
intvolume: ' 66'
issue: '6'
month: '04'
page: 637 - 646
publication: Plant Molecular Biology
publication_status: published
publisher: Springer
publist_id: '3671'
quality_controlled: 0
status: public
title: Role of alternative telomere lengthening unmasked in telomerase knock-out mutant
plants
type: journal_article
volume: 66
year: '2008'
...
---
_id: '3032'
abstract:
- lang: eng
text: |2-
Cell polarity manifested by the polar cargo delivery to different plasma-membrane domains is a fundamental feature of multicellular organisms. Pathways for polar delivery have been identified in animals; prominent among them is transcytosis, which involves cargo movement between different sides of the cell [1]. PIN transporters are prominent polar cargoes in plants, whose polar subcellular localization determines the directional flow of the signaling molecule auxin [2, 3]. In this study, we address the cellular mechanisms of PIN polar targeting and dynamic polarity changes. We show that apical and basal PIN targeting pathways are interconnected but molecularly distinct by means of ARF GEF vesicle-trafficking regulators. Pharmacological or genetic interference with the Arabidopsis ARF GEF GNOM leads specifically to apicalization of basal cargoes such as PIN1. We visualize the translocation of PIN proteins between the opposite sides of polarized cells in vivo and show that this PIN transcytosis occurs by endocytic recycling and alternative recruitment of the same cargo molecules by apical and basal targeting machineries. Our data suggest that an ARF GEF-dependent transcytosis-like mechanism is operational in plants and provides a plausible mechanism to trigger changes in PIN polarity and hence auxin fluxes during embryogenesis and organogenesis.
author:
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Pankaj
full_name: Dhonukshe, Pankaj
last_name: Dhonukshe
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Philip
full_name: Brewer, Philip B
last_name: Brewer
- first_name: Justyna
full_name: Wiśniewska, Justyna
last_name: Wiśniewska
- first_name: Tomasz
full_name: Paciorek, Tomasz
last_name: Paciorek
- 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: Kleine Vehn J, Dhonukshe P, Sauer M, et al. ARF GEF dependent transcytosis
and polar delivery of PIN auxin carriers in Arabidopsis. Current Biology.
2008;18(7):526-531. doi:10.1016/j.cub.2008.03.021
apa: Kleine Vehn, J., Dhonukshe, P., Sauer, M., Brewer, P., Wiśniewska, J., Paciorek,
T., … Friml, J. (2008). ARF GEF dependent transcytosis and polar delivery of PIN
auxin carriers in Arabidopsis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2008.03.021
chicago: Kleine Vehn, Jürgen, Pankaj Dhonukshe, Michael Sauer, Philip Brewer, Justyna
Wiśniewska, Tomasz Paciorek, Eva Benková, and Jiří Friml. “ARF GEF Dependent Transcytosis
and Polar Delivery of PIN Auxin Carriers in Arabidopsis.” Current Biology.
Cell Press, 2008. https://doi.org/10.1016/j.cub.2008.03.021.
ieee: J. Kleine Vehn et al., “ARF GEF dependent transcytosis and polar delivery
of PIN auxin carriers in Arabidopsis,” Current Biology, vol. 18, no. 7.
Cell Press, pp. 526–531, 2008.
ista: Kleine Vehn J, Dhonukshe P, Sauer M, Brewer P, Wiśniewska J, Paciorek T, Benková
E, Friml J. 2008. ARF GEF dependent transcytosis and polar delivery of PIN auxin
carriers in Arabidopsis. Current Biology. 18(7), 526–531.
mla: Kleine Vehn, Jürgen, et al. “ARF GEF Dependent Transcytosis and Polar Delivery
of PIN Auxin Carriers in Arabidopsis.” Current Biology, vol. 18, no. 7,
Cell Press, 2008, pp. 526–31, doi:10.1016/j.cub.2008.03.021.
short: J. Kleine Vehn, P. Dhonukshe, M. Sauer, P. Brewer, J. Wiśniewska, T. Paciorek,
E. Benková, J. Friml, Current Biology 18 (2008) 526–531.
date_created: 2018-12-11T12:00:58Z
date_published: 2008-04-08T00:00:00Z
date_updated: 2021-01-12T07:40:34Z
day: '08'
doi: 10.1016/j.cub.2008.03.021
extern: 1
intvolume: ' 18'
issue: '7'
month: '04'
page: 526 - 531
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '3670'
quality_controlled: 0
status: public
title: ARF GEF dependent transcytosis and polar delivery of PIN auxin carriers in
Arabidopsis
type: journal_article
volume: 18
year: '2008'
...
---
_id: '3035'
abstract:
- lang: eng
text: Embryogenesis of Arabidopsis thaliana follows a nearly invariant cell division
pattern and provides an ideal system for studies of early plant development. However,
experimental manipulation with embryogenesis is difficult, as the embryo develops
deeply inside maternal tissues. Here, we present a method to culture zygotic Arabidopsis
embryos in vitro. It enables culturing for prolonged periods of time from the
first developmental stages on. The technique omits excision of the embryo by culturing
the entire ovule, which facilitates the manual procedure. It allows pharmacological
manipulation of embryo development and does not interfere with standard techniques
for localizing gene expression and protein localization in the cultivated embryos.
alternative_title:
- Methods In Molecular Biology
author:
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Sauer M, Friml J. In vitro culture of Arabidopsis embryos . In: Suárez M,
Bozhkov P, eds. Plant Embryogenesis. Vol 427. Humana Press; 2008:71-76.
doi:10.1007/978-1-59745-273-1_5'
apa: Sauer, M., & Friml, J. (2008). In vitro culture of Arabidopsis embryos
. In M. Suárez & P. Bozhkov (Eds.), Plant Embryogenesis (Vol. 427,
pp. 71–76). Humana Press. https://doi.org/10.1007/978-1-59745-273-1_5
chicago: Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos
.” In Plant Embryogenesis, edited by María Suárez and Peter Bozhkov, 427:71–76.
Humana Press, 2008. https://doi.org/10.1007/978-1-59745-273-1_5.
ieee: M. Sauer and J. Friml, “In vitro culture of Arabidopsis embryos ,” in Plant
Embryogenesis, vol. 427, M. Suárez and P. Bozhkov, Eds. Humana Press, 2008,
pp. 71–76.
ista: 'Sauer M, Friml J. 2008.In vitro culture of Arabidopsis embryos . In: Plant
Embryogenesis. Methods In Molecular Biology, vol. 427, 71–76.'
mla: Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos .”
Plant Embryogenesis, edited by María Suárez and Peter Bozhkov, vol. 427,
Humana Press, 2008, pp. 71–76, doi:10.1007/978-1-59745-273-1_5.
short: M. Sauer, J. Friml, in:, M. Suárez, P. Bozhkov (Eds.), Plant Embryogenesis,
Humana Press, 2008, pp. 71–76.
date_created: 2018-12-11T12:00:59Z
date_published: 2008-03-07T00:00:00Z
date_updated: 2021-01-12T07:40:35Z
day: '07'
doi: 10.1007/978-1-59745-273-1_5
editor:
- first_name: María
full_name: Suárez, María F
last_name: Suárez
- first_name: Peter
full_name: Bozhkov, Peter V
last_name: Bozhkov
extern: 1
intvolume: ' 427'
month: '03'
page: 71 - 76
publication: Plant Embryogenesis
publication_status: published
publisher: Humana Press
publist_id: '3667'
quality_controlled: 0
status: public
title: 'In vitro culture of Arabidopsis embryos '
type: book_chapter
volume: 427
year: '2008'
...
---
_id: '3033'
abstract:
- lang: eng
text: |2-
Embryogenesis in Arabidopsis thaliana depends on the proper establishment and maintenance of local auxin accumulation. In the course of elucidating the connections between developmental progress and auxin distribution, several techniques have been developed to investigate spatial and temporal distribution of auxin response or accumulation in Arabidopsis embryos. This chapter reviews and describes two independent methods, the detection of the activity of auxin responsive transgenes and immunolocalization of auxin itself.
alternative_title:
- Methods In Molecular Biology
author:
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Sauer M, Friml J. Visualization of auxin gradients in embryogenesis . In:
Suárez M, Bozhkov P, eds. Plant Embryogenesis. Vol 427. Humana Press; 2008:137-144.
doi:10.1007/978-1-59745-273-1_11'
apa: Sauer, M., & Friml, J. (2008). Visualization of auxin gradients in embryogenesis
. In M. Suárez & P. Bozhkov (Eds.), Plant Embryogenesis (Vol. 427,
pp. 137–144). Humana Press. https://doi.org/10.1007/978-1-59745-273-1_11
chicago: Sauer, Michael, and Jiří Friml. “Visualization of Auxin Gradients in Embryogenesis
.” In Plant Embryogenesis, edited by María Suárez and Peter Bozhkov, 427:137–44.
Humana Press, 2008. https://doi.org/10.1007/978-1-59745-273-1_11.
ieee: M. Sauer and J. Friml, “Visualization of auxin gradients in embryogenesis
,” in Plant Embryogenesis, vol. 427, M. Suárez and P. Bozhkov, Eds. Humana
Press, 2008, pp. 137–144.
ista: 'Sauer M, Friml J. 2008.Visualization of auxin gradients in embryogenesis
. In: Plant Embryogenesis. Methods In Molecular Biology, vol. 427, 137–144.'
mla: Sauer, Michael, and Jiří Friml. “Visualization of Auxin Gradients in Embryogenesis
.” Plant Embryogenesis, edited by María Suárez and Peter Bozhkov, vol.
427, Humana Press, 2008, pp. 137–44, doi:10.1007/978-1-59745-273-1_11.
short: M. Sauer, J. Friml, in:, M. Suárez, P. Bozhkov (Eds.), Plant Embryogenesis,
Humana Press, 2008, pp. 137–144.
date_created: 2018-12-11T12:00:58Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:40:35Z
day: '01'
doi: 10.1007/978-1-59745-273-1_11
editor:
- first_name: María
full_name: Suárez, María F
last_name: Suárez
- first_name: Peter
full_name: Bozhkov, Peter V
last_name: Bozhkov
extern: 1
intvolume: ' 427'
month: '01'
page: 137 - 144
publication: Plant Embryogenesis
publication_status: published
publisher: Humana Press
publist_id: '3668'
quality_controlled: 0
status: public
title: 'Visualization of auxin gradients in embryogenesis '
type: book_chapter
volume: 427
year: '2008'
...
---
_id: '3037'
author:
- first_name: Elena
full_name: Feraru, Elena
last_name: Feraru
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Feraru E, Friml J. PIN polar targeting. Plant Physiology. 2008;147(4):1553-1559.
doi:10.1104/pp.108.121756
apa: Feraru, E., & Friml, J. (2008). PIN polar targeting. Plant Physiology.
American Society of Plant Biologists. https://doi.org/10.1104/pp.108.121756
chicago: Feraru, Elena, and Jiří Friml. “PIN Polar Targeting.” Plant Physiology.
American Society of Plant Biologists, 2008. https://doi.org/10.1104/pp.108.121756.
ieee: E. Feraru and J. Friml, “PIN polar targeting,” Plant Physiology, vol.
147, no. 4. American Society of Plant Biologists, pp. 1553–1559, 2008.
ista: Feraru E, Friml J. 2008. PIN polar targeting. Plant Physiology. 147(4), 1553–1559.
mla: Feraru, Elena, and Jiří Friml. “PIN Polar Targeting.” Plant Physiology,
vol. 147, no. 4, American Society of Plant Biologists, 2008, pp. 1553–59, doi:10.1104/pp.108.121756.
short: E. Feraru, J. Friml, Plant Physiology 147 (2008) 1553–1559.
date_created: 2018-12-11T12:01:00Z
date_published: 2008-08-04T00:00:00Z
date_updated: 2021-01-12T07:40:36Z
day: '04'
doi: 10.1104/pp.108.121756
extern: '1'
external_id:
pmid:
- '18678746'
intvolume: ' 147'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2492634/
month: '08'
oa: 1
oa_version: Published Version
page: 1553 - 1559
pmid: 1
publication: Plant Physiology
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3664'
quality_controlled: '1'
status: public
title: PIN polar targeting
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 147
year: '2008'
...
---
_id: '3034'
abstract:
- lang: eng
text: 'They can''t move away from shade, so plants resort to a molecular solution
to find a place in the sun. The action they take is quite radical, and involves
a reprogramming of their development. '
article_type: letter_note
author:
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
citation:
ama: 'Friml J, Sauer M. Plant biology: In their neighbour’s shadow. Nature.
2008;453(7193):298-299. doi:10.1038/453298a'
apa: 'Friml, J., & Sauer, M. (2008). Plant biology: In their neighbour’s shadow.
Nature. Nature Publishing Group. https://doi.org/10.1038/453298a'
chicago: 'Friml, Jiří, and Michael Sauer. “Plant Biology: In Their Neighbour’s Shadow.”
Nature. Nature Publishing Group, 2008. https://doi.org/10.1038/453298a.'
ieee: 'J. Friml and M. Sauer, “Plant biology: In their neighbour’s shadow,” Nature,
vol. 453, no. 7193. Nature Publishing Group, pp. 298–299, 2008.'
ista: 'Friml J, Sauer M. 2008. Plant biology: In their neighbour’s shadow. Nature.
453(7193), 298–299.'
mla: 'Friml, Jiří, and Michael Sauer. “Plant Biology: In Their Neighbour’s Shadow.”
Nature, vol. 453, no. 7193, Nature Publishing Group, 2008, pp. 298–99,
doi:10.1038/453298a.'
short: J. Friml, M. Sauer, Nature 453 (2008) 298–299.
date_created: 2018-12-11T12:00:59Z
date_published: 2008-05-15T00:00:00Z
date_updated: 2021-01-12T07:40:35Z
day: '15'
doi: 10.1038/453298a
extern: '1'
intvolume: ' 453'
issue: '7193'
language:
- iso: eng
month: '05'
oa_version: None
page: 298 - 299
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '3669'
quality_controlled: '1'
status: public
title: 'Plant biology: In their neighbour''s shadow'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 453
year: '2008'
...
---
_id: '3196'
abstract:
- lang: eng
text: 'Among the most exciting advances in early vision has been the development
of efficient energy minimization algorithms for pixel-labeling tasks such as depth
or texture computation. It has been known for decades that such problems can be
elegantly expressed as Markov random fields, yet the resulting energy minimization
problems have been widely viewed as intractable. Algorithms such as graph cuts
and loopy belief propagation (LBP) have proven to be very powerful: For example,
such methods form the basis for almost all the top-performing stereo methods.
However, the trade-offs among different energy minimization algorithms are still
not well understood. In this paper, we describe a set of energy minimization benchmarks
and use them to compare the solution quality and runtime of several common energy
minimization algorithms. We investigate three promising methods-graph cuts, LBP,
and tree-reweighted message passing-in addition to the well-known older iterated
conditional mode (ICM) algorithm. Our benchmark problems are drawn from published
energy functions used for stereo, image stitching, interactive segmentation, and
denoising. We also provide a general-purpose software interface that allows vision
researchers to easily switch between optimization methods. The benchmarks, code,
images, and results are available at http://vision.middlebury.edu/MRF/.'
author:
- first_name: Richard
full_name: Szeliski, Richard S
last_name: Szeliski
- first_name: Ramin
full_name: Zabih, Ramin
last_name: Zabih
- first_name: Daniel
full_name: Scharstein, Daniel
last_name: Scharstein
- first_name: Olga
full_name: Veksler, Olga
last_name: Veksler
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Aseem
full_name: Agarwala, Aseem
last_name: Agarwala
- first_name: Marshall
full_name: Tappen, Marshall F
last_name: Tappen
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: Szeliski R, Zabih R, Scharstein D, et al. A comparative study of energy minimization
methods for Markov random fields with smoothness-based priors. IEEE Transactions
on Pattern Analysis and Machine Intelligence. 2008;30(6):1068-1080. doi:10.1109/TPAMI.2007.70844
apa: Szeliski, R., Zabih, R., Scharstein, D., Veksler, O., Kolmogorov, V., Agarwala,
A., … Rother, C. (2008). A comparative study of energy minimization methods for
Markov random fields with smoothness-based priors. IEEE Transactions on Pattern
Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2007.70844
chicago: Szeliski, Richard, Ramin Zabih, Daniel Scharstein, Olga Veksler, Vladimir
Kolmogorov, Aseem Agarwala, Marshall Tappen, and Carsten Rother. “A Comparative
Study of Energy Minimization Methods for Markov Random Fields with Smoothness-Based
Priors.” IEEE Transactions on Pattern Analysis and Machine Intelligence.
IEEE, 2008. https://doi.org/10.1109/TPAMI.2007.70844.
ieee: R. Szeliski et al., “A comparative study of energy minimization methods
for Markov random fields with smoothness-based priors,” IEEE Transactions on
Pattern Analysis and Machine Intelligence, vol. 30, no. 6. IEEE, pp. 1068–1080,
2008.
ista: Szeliski R, Zabih R, Scharstein D, Veksler O, Kolmogorov V, Agarwala A, Tappen
M, Rother C. 2008. A comparative study of energy minimization methods for Markov
random fields with smoothness-based priors. IEEE Transactions on Pattern Analysis
and Machine Intelligence. 30(6), 1068–1080.
mla: Szeliski, Richard, et al. “A Comparative Study of Energy Minimization Methods
for Markov Random Fields with Smoothness-Based Priors.” IEEE Transactions on
Pattern Analysis and Machine Intelligence, vol. 30, no. 6, IEEE, 2008, pp.
1068–80, doi:10.1109/TPAMI.2007.70844.
short: R. Szeliski, R. Zabih, D. Scharstein, O. Veksler, V. Kolmogorov, A. Agarwala,
M. Tappen, C. Rother, IEEE Transactions on Pattern Analysis and Machine Intelligence
30 (2008) 1068–1080.
date_created: 2018-12-11T12:01:57Z
date_published: 2008-06-01T00:00:00Z
date_updated: 2021-01-12T07:41:43Z
day: '01'
doi: 10.1109/TPAMI.2007.70844
extern: 1
intvolume: ' 30'
issue: '6'
month: '06'
page: 1068 - 1080
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '3488'
quality_controlled: 0
status: public
title: A comparative study of energy minimization methods for Markov random fields
with smoothness-based priors
type: journal_article
volume: 30
year: '2008'
...
---
_id: '3198'
abstract:
- lang: eng
text: 'In this paper we present a new approach for establishing correspondences
between sparse image features related by an unknown non-rigid mapping and corrupted
by clutter and occlusion, such as points extracted from a pair of images containing
a human figure in distinct poses. We formulate this matching task as an energy
minimization problem by defining a complex objective function of the appearance
and the spatial arrangement of the features. Optimization of this energy is an
instance of graph matching, which is in general a NP-hard problem. We describe
a novel graph matching optimization technique, which we refer to as dual decomposition
(DD), and demonstrate on a variety of examples that this method outperforms existing
graph matching algorithms. In the majority of our examples DD is able to find
the global minimum within a minute. The ability to globally optimize the objective
allows us to accurately learn the parameters of our matching model from training
examples. We show on several matching tasks that our learned model yields results
superior to those of state-of-the-art methods. '
alternative_title:
- LNCS
author:
- first_name: Lorenzo
full_name: Torresani, Lorenzo
last_name: Torresani
- 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: 'Torresani L, Kolmogorov V, Rother C. Feature correspondence via graph matching:
Models and global optimization. In: Vol 5303. Springer; 2008:596-609. doi:10.1007/978-3-540-88688-4_44'
apa: 'Torresani, L., Kolmogorov, V., & Rother, C. (2008). Feature correspondence
via graph matching: Models and global optimization (Vol. 5303, pp. 596–609). Presented
at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/978-3-540-88688-4_44'
chicago: 'Torresani, Lorenzo, Vladimir Kolmogorov, and Carsten Rother. “Feature
Correspondence via Graph Matching: Models and Global Optimization,” 5303:596–609.
Springer, 2008. https://doi.org/10.1007/978-3-540-88688-4_44.'
ieee: 'L. Torresani, V. Kolmogorov, and C. Rother, “Feature correspondence via graph
matching: Models and global optimization,” presented at the ECCV: European Conference
on Computer Vision, 2008, vol. 5303, pp. 596–609.'
ista: 'Torresani L, Kolmogorov V, Rother C. 2008. Feature correspondence via graph
matching: Models and global optimization. ECCV: European Conference on Computer
Vision, LNCS, vol. 5303, 596–609.'
mla: 'Torresani, Lorenzo, et al. Feature Correspondence via Graph Matching: Models
and Global Optimization. Vol. 5303, Springer, 2008, pp. 596–609, doi:10.1007/978-3-540-88688-4_44.'
short: L. Torresani, V. Kolmogorov, C. Rother, in:, Springer, 2008, pp. 596–609.
conference:
name: 'ECCV: European Conference on Computer Vision'
date_created: 2018-12-11T12:01:58Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:44Z
day: '01'
doi: 10.1007/978-3-540-88688-4_44
extern: 1
intvolume: ' 5303'
main_file_link:
- open_access: '0'
url: http://research-srv.microsoft.com/pubs/70610/eccv08-MatchingMRF.pdf
month: '01'
page: 596 - 609
publication_status: published
publisher: Springer
publist_id: '3485'
quality_controlled: 0
status: public
title: 'Feature correspondence via graph matching: Models and global optimization'
type: conference
volume: 5303
year: '2008'
...
---
_id: '3195'
abstract:
- lang: eng
text: 'Graph cut is a popular technique for interactive image segmentation. However,
it has certain shortcomings. In particular, graph cut has problems with segmenting
thin elongated objects due to the ldquoshrinking biasrdquo. To overcome this problem,
we propose to impose an additional connectivity prior, which is a very natural
assumption about objects. We formulate several versions of the connectivity constraint
and show that the corresponding optimization problems are all NP-hard. For some
of these versions we propose two optimization algorithms: (i) a practical heuristic
technique which we call DijkstraGC, and (ii) a slow method based on problem decomposition
which provides a lower bound on the problem. We use the second technique to verify
that for some practical examples DijkstraGC is able to find the global minimum.'
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: IEEE; 2008. doi:10.1109/CVPR.2008.4587440'
apa: 'Vicente, S., Kolmogorov, V., & Rother, C. (2008). Graph cut based image
segmentation with connectivity priors. Presented at the CVPR: Computer Vision
and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2008.4587440'
chicago: Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Graph Cut Based
Image Segmentation with Connectivity Priors.” IEEE, 2008. https://doi.org/10.1109/CVPR.2008.4587440.
ieee: 'S. Vicente, V. Kolmogorov, and C. Rother, “Graph cut based image segmentation
with connectivity priors,” presented at the CVPR: Computer Vision and Pattern
Recognition, 2008.'
ista: 'Vicente S, Kolmogorov V, Rother C. 2008. Graph cut based image segmentation
with connectivity priors. CVPR: Computer Vision and Pattern Recognition.'
mla: Vicente, Sara, et al. Graph Cut Based Image Segmentation with Connectivity
Priors. IEEE, 2008, doi:10.1109/CVPR.2008.4587440.
short: S. Vicente, V. Kolmogorov, C. Rother, in:, IEEE, 2008.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:57Z
date_published: 2008-08-05T00:00:00Z
date_updated: 2021-01-12T07:41:43Z
day: '05'
doi: 10.1109/CVPR.2008.4587440
extern: 1
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/80485/CVPR08-ConnectedGC.pdf
month: '08'
publication_status: published
publisher: IEEE
publist_id: '3487'
quality_controlled: 0
status: public
title: Graph cut based image segmentation with connectivity priors
type: conference
year: '2008'
...
---
_id: '3224'
abstract:
- lang: eng
text: 'We propose a new mode of operation, enciphered CBC, for domain extension
of length-preserving functions (like block ciphers), which is a variation on the
popular CBC mode of operation. Our new mode is twice slower than CBC, but has
many (property-preserving) properties not enjoyed by CBC and other known modes.
Most notably, it yields the first constant-rate Variable Input Length (VIL) MAC
from any length preserving Fixed Input Length (FIL) MAC. This answers the question
of Dodis and Puniya from Eurocrypt 2007. Further, our mode is a secure domain
extender for PRFs (with basically the same security as encrypted CBC). This provides
a hedge against the security of the block cipher: if the block cipher is pseudorandom,
one gets a VIL-PRF, while if it is "only" unpredictable, one "at
least" gets a VIL-MAC. Additionally, our mode yields a VIL random oracle
(and, hence, a collision-resistant hash function) when instantiated with length-preserving
random functions, or even random permutations (which can be queried from both
sides). This means that one does not have to re-key the block cipher during the
computation, which was critically used in most previous constructions (analyzed
in the ideal cipher model). '
alternative_title:
- LNCS
author:
- first_name: Yevgeniy
full_name: Dodis, Yevgeniy
last_name: Dodis
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Prashant
full_name: Puniya, Prashant
last_name: Puniya
citation:
ama: 'Dodis Y, Pietrzak KZ, Puniya P. A new mode of operation for block ciphers
and length preserving MACs. In: Vol 4965. Springer; 2008:198-219. doi:10.1007/978-3-540-78967-3_12'
apa: 'Dodis, Y., Pietrzak, K. Z., & Puniya, P. (2008). A new mode of operation
for block ciphers and length preserving MACs (Vol. 4965, pp. 198–219). Presented
at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer.
https://doi.org/10.1007/978-3-540-78967-3_12'
chicago: Dodis, Yevgeniy, Krzysztof Z Pietrzak, and Prashant Puniya. “A New Mode
of Operation for Block Ciphers and Length Preserving MACs,” 4965:198–219. Springer,
2008. https://doi.org/10.1007/978-3-540-78967-3_12.
ieee: 'Y. Dodis, K. Z. Pietrzak, and P. Puniya, “A new mode of operation for block
ciphers and length preserving MACs,” presented at the EUROCRYPT: Theory and Applications
of Cryptographic Techniques, 2008, vol. 4965, pp. 198–219.'
ista: 'Dodis Y, Pietrzak KZ, Puniya P. 2008. A new mode of operation for block ciphers
and length preserving MACs. EUROCRYPT: Theory and Applications of Cryptographic
Techniques, LNCS, vol. 4965, 198–219.'
mla: Dodis, Yevgeniy, et al. A New Mode of Operation for Block Ciphers and Length
Preserving MACs. Vol. 4965, Springer, 2008, pp. 198–219, doi:10.1007/978-3-540-78967-3_12.
short: Y. Dodis, K.Z. Pietrzak, P. Puniya, in:, Springer, 2008, pp. 198–219.
conference:
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
date_created: 2018-12-11T12:02:07Z
date_published: 2008-04-28T00:00:00Z
date_updated: 2021-01-12T07:41:55Z
day: '28'
doi: 10.1007/978-3-540-78967-3_12
extern: 1
intvolume: ' 4965'
month: '04'
page: 198 - 219
publication_status: published
publisher: Springer
publist_id: '3456'
quality_controlled: 0
status: public
title: A new mode of operation for block ciphers and length preserving MACs
type: conference
volume: 4965
year: '2008'
...
---
_id: '3225'
abstract:
- lang: eng
text: 'A robust multi-property combiner for a set of security properties merges
two hash functions such that the resulting function satisfies each of the properties
which at least one of the two starting functions has. Fischlin and Lehmann (TCC
2008) recently constructed a combiner which simultaneously preserves collision-resistance,
target collision-resistance, message authentication, pseudorandomness and indifferentiability
from a random oracle (IRO). Their combiner produces outputs of 5n bits, where
n denotes the output length of the underlying hash functions. In this paper we
propose improved combiners with shorter outputs. By sacrificing the indifferentiability
from random oracles we obtain a combiner which preserves all of the other aforementioned
properties but with output length 2n only. This matches a lower bound for black-box
combiners for collision-resistance as the only property, showing that the other
properties can be achieved without penalizing the length of the hash values. We
then propose a combiner which also preserves the IRO property, slightly increasing
the output length to 2n + ω(logn). Finally, we show that a twist on our combiners
also makes them robust for one-wayness (but at the price of a fixed input length). '
alternative_title:
- LNCS
author:
- first_name: Marc
full_name: Fischlin, Marc
last_name: Fischlin
- first_name: Anja
full_name: Lehmann, Anja
last_name: Lehmann
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Fischlin M, Lehmann A, Pietrzak KZ. Robust multi property combiners for hash
functions revisited. In: Vol 5126. Springer; 2008:655-666. doi:10.1007/978-3-540-70583-3_53'
apa: 'Fischlin, M., Lehmann, A., & Pietrzak, K. Z. (2008). Robust multi property
combiners for hash functions revisited (Vol. 5126, pp. 655–666). Presented at
the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/978-3-540-70583-3_53'
chicago: Fischlin, Marc, Anja Lehmann, and Krzysztof Z Pietrzak. “Robust Multi Property
Combiners for Hash Functions Revisited,” 5126:655–66. Springer, 2008. https://doi.org/10.1007/978-3-540-70583-3_53.
ieee: 'M. Fischlin, A. Lehmann, and K. Z. Pietrzak, “Robust multi property combiners
for hash functions revisited,” presented at the ICALP: Automata, Languages and
Programming, 2008, vol. 5126, no. PART 2, pp. 655–666.'
ista: 'Fischlin M, Lehmann A, Pietrzak KZ. 2008. Robust multi property combiners
for hash functions revisited. ICALP: Automata, Languages and Programming, LNCS,
vol. 5126, 655–666.'
mla: Fischlin, Marc, et al. Robust Multi Property Combiners for Hash Functions
Revisited. Vol. 5126, no. PART 2, Springer, 2008, pp. 655–66, doi:10.1007/978-3-540-70583-3_53.
short: M. Fischlin, A. Lehmann, K.Z. Pietrzak, in:, Springer, 2008, pp. 655–666.
conference:
name: 'ICALP: Automata, Languages and Programming'
date_created: 2018-12-11T12:02:07Z
date_published: 2008-08-06T00:00:00Z
date_updated: 2023-02-23T11:01:10Z
day: '06'
doi: 10.1007/978-3-540-70583-3_53
extern: 1
intvolume: ' 5126'
issue: PART 2
month: '08'
page: 655 - 666
publication_status: published
publisher: Springer
publist_id: '3454'
quality_controlled: 0
related_material:
record:
- id: '2852'
relation: later_version
status: public
status: public
title: Robust multi property combiners for hash functions revisited
type: conference
volume: 5126
year: '2008'
...
---
_id: '3291'
abstract:
- lang: eng
text: 'The filamentous fungus Aspergillus fumigatus is responsible for a lethal
disease called Invasive Aspergillosis that affects immunocompromised patients.
This disease, like other human fungal diseases, is generally treated by compounds
targeting the primary fungal cell membrane sterol. Recently, glucan synthesis
inhibitors were added to the limited antifungal arsenal and encouraged the search
for novel targets in cell wall biosynthesis. Although galactomannan is a major
component of the A. fumigatus cell wall and extracellular matrix, the biosynthesis
and role of galactomannan are currently unknown. By a targeted gene deletion approach,
we demonstrate that UDP-galactopyranose mutase, a key enzyme of galactofuranose
metabolism, controls the biosynthesis of galactomannan and galactofuranose containing
glycoconjugates. The glfA deletion mutant generated in this study is devoid of
galactofuranose and displays attenuated virulence in a low-dose mouse model of
invasive aspergillosis that likely reflects the impaired growth of the mutant
at mammalian body temperature. Furthermore, the absence of galactofuranose results
in a thinner cell wall that correlates with an increased susceptibility to several
antifungal agents. The UDP-galactopyranose mutase thus appears to be an appealing
adjunct therapeutic target in combination with other drugs against A. fumigatus.
Its absence from mammalian cells indeed offers a considerable advantage to achieve
therapeutic selectivity. '
author:
- first_name: Philipp S
full_name: Philipp Schmalhorst
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Sven
full_name: Krappmann, Sven
last_name: Krappmann
- first_name: Wouter
full_name: Vervecken, Wouter
last_name: Vervecken
- first_name: Manfred
full_name: Rohde, Manfred
last_name: Rohde
- first_name: Meike
full_name: Müller, Meike
last_name: Müller
- first_name: Gerhard
full_name: Braus, Gerhard H.
last_name: Braus
- first_name: Roland
full_name: Contreras, Roland
last_name: Contreras
- first_name: Armin
full_name: Braun, Armin
last_name: Braun
- first_name: Hans
full_name: Bakker, Hans
last_name: Bakker
- first_name: Françoise
full_name: Routier, Françoise H
last_name: Routier
citation:
ama: Schmalhorst PS, Krappmann S, Vervecken W, et al. Contribution of galactofuranose
to the virulence of the opportunistic pathogen Aspergillus fumigatus. Eukaryotic
Cell. 2008;7(8):1268-1277. doi:10.1128/EC.00065-08
apa: Schmalhorst, P. S., Krappmann, S., Vervecken, W., Rohde, M., Müller, M., Braus,
G., … Routier, F. (2008). Contribution of galactofuranose to the virulence of
the opportunistic pathogen Aspergillus fumigatus. Eukaryotic Cell. American
Society for Microbiology. https://doi.org/10.1128/EC.00065-08
chicago: Schmalhorst, Philipp S, Sven Krappmann, Wouter Vervecken, Manfred Rohde,
Meike Müller, Gerhard Braus, Roland Contreras, Armin Braun, Hans Bakker, and Françoise
Routier. “Contribution of Galactofuranose to the Virulence of the Opportunistic
Pathogen Aspergillus Fumigatus.” Eukaryotic Cell. American Society for
Microbiology, 2008. https://doi.org/10.1128/EC.00065-08.
ieee: P. S. Schmalhorst et al., “Contribution of galactofuranose to the virulence
of the opportunistic pathogen Aspergillus fumigatus,” Eukaryotic Cell,
vol. 7, no. 8. American Society for Microbiology, pp. 1268–1277, 2008.
ista: Schmalhorst PS, Krappmann S, Vervecken W, Rohde M, Müller M, Braus G, Contreras
R, Braun A, Bakker H, Routier F. 2008. Contribution of galactofuranose to the
virulence of the opportunistic pathogen Aspergillus fumigatus. Eukaryotic Cell.
7(8), 1268–1277.
mla: Schmalhorst, Philipp S., et al. “Contribution of Galactofuranose to the Virulence
of the Opportunistic Pathogen Aspergillus Fumigatus.” Eukaryotic Cell,
vol. 7, no. 8, American Society for Microbiology, 2008, pp. 1268–77, doi:10.1128/EC.00065-08.
short: P.S. Schmalhorst, S. Krappmann, W. Vervecken, M. Rohde, M. Müller, G. Braus,
R. Contreras, A. Braun, H. Bakker, F. Routier, Eukaryotic Cell 7 (2008) 1268–1277.
date_created: 2018-12-11T12:02:29Z
date_published: 2008-06-13T00:00:00Z
date_updated: 2021-01-12T07:42:26Z
day: '13'
doi: 10.1128/EC.00065-08
extern: 1
intvolume: ' 7'
issue: '8'
month: '06'
page: 1268 - 1277
publication: Eukaryotic Cell
publication_status: published
publisher: American Society for Microbiology
publist_id: '3354'
quality_controlled: 0
status: public
title: Contribution of galactofuranose to the virulence of the opportunistic pathogen
Aspergillus fumigatus
type: journal_article
volume: 7
year: '2008'
...
---
_id: '3307'
abstract:
- lang: eng
text: A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000
year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8
Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally
establishes that the Neandertal mtDNA falls outside the variation of extant human
mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages
of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2
of cytochrome c oxidase of the mitochondrial electron transport chain has experienced
the largest number of amino acid substitutions in human ancestors since the separation
from Neandertals. There is evidence that purifying selection in the Neandertal
mtDNA was reduced compared with other primate lineages, suggesting that the effective
population size of Neandertals was small.
author:
- first_name: Richard
full_name: Green, Richard E
last_name: Green
- first_name: Anna
full_name: 'Malaspinas, Anna-Sapfo '
last_name: Malaspinas
- first_name: Johannes
full_name: Krause, Johannes
last_name: Krause
- first_name: Adrian
full_name: Briggs, Adrian W
last_name: Briggs
- first_name: Philip
full_name: Johnson, Philip L
last_name: Johnson
- first_name: Caroline
full_name: Caroline Uhler
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Matthias
full_name: Meyer, Matthias
last_name: Meyer
- first_name: Jeffrey
full_name: Good, Jeffrey M
last_name: Good
- first_name: Tomislav
full_name: Maricic, Tomislav
last_name: Maricic
- first_name: Udo
full_name: Stenzel, Udo
last_name: Stenzel
- first_name: Kay
full_name: Prüfer, Kay
last_name: Prüfer
- first_name: Michael
full_name: Siebauer, Michael F
last_name: Siebauer
- first_name: Hernän
full_name: Burbano, Hernän A
last_name: Burbano
- first_name: Michael
full_name: Ronan, Michael T
last_name: Ronan
- first_name: Jonathan
full_name: Rothberg, Jonathan M
last_name: Rothberg
- first_name: Michael
full_name: Egholm, Michael
last_name: Egholm
- first_name: Pavao
full_name: Rudan, Pavao
last_name: Rudan
- first_name: Dejana
full_name: Brajković, Dejana
last_name: Brajković
- first_name: Željko
full_name: Kućan, Željko
last_name: Kućan
- first_name: Ivan
full_name: Gušić, Ivan
last_name: Gušić
- first_name: Mårten
full_name: Wikström, Mårten K
last_name: Wikström
- first_name: Liisa
full_name: Laakkonen, Liisa J
last_name: Laakkonen
- first_name: Janet
full_name: Kelso, Janet F
last_name: Kelso
- first_name: Montgomery
full_name: Slatkin, Montgomery
last_name: Slatkin
- first_name: Svante
full_name: Pääbo, Svante H
last_name: Pääbo
citation:
ama: Green R, Malaspinas A, Krause J, et al. A complete neandertal mitochondrial
genome sequence determined by highhhroughput sequencing. Cell. 2008;134:416-426.
doi:10.1016/j.cell.2008.06.021
apa: Green, R., Malaspinas, A., Krause, J., Briggs, A., Johnson, P., Uhler, C.,
… Pääbo, S. (2008). A complete neandertal mitochondrial genome sequence determined
by highhhroughput sequencing. Cell. Cell Press. https://doi.org/10.1016/j.cell.2008.06.021
chicago: Green, Richard, Anna Malaspinas, Johannes Krause, Adrian Briggs, Philip
Johnson, Caroline Uhler, Matthias Meyer, et al. “A Complete Neandertal Mitochondrial
Genome Sequence Determined by Highhhroughput Sequencing.” Cell. Cell Press,
2008. https://doi.org/10.1016/j.cell.2008.06.021.
ieee: R. Green et al., “A complete neandertal mitochondrial genome sequence
determined by highhhroughput sequencing,” Cell, vol. 134. Cell Press, pp.
416–426, 2008.
ista: Green R, Malaspinas A, Krause J, Briggs A, Johnson P, Uhler C, Meyer M, Good
J, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano H, Ronan M, Rothberg J,
Egholm M, Rudan P, Brajković D, Kućan Ž, Gušić I, Wikström M, Laakkonen L, Kelso
J, Slatkin M, Pääbo S. 2008. A complete neandertal mitochondrial genome sequence
determined by highhhroughput sequencing. Cell. 134, 416–426.
mla: Green, Richard, et al. “A Complete Neandertal Mitochondrial Genome Sequence
Determined by Highhhroughput Sequencing.” Cell, vol. 134, Cell Press, 2008,
pp. 416–26, doi:10.1016/j.cell.2008.06.021.
short: R. Green, A. Malaspinas, J. Krause, A. Briggs, P. Johnson, C. Uhler, M. Meyer,
J. Good, T. Maricic, U. Stenzel, K. Prüfer, M. Siebauer, H. Burbano, M. Ronan,
J. Rothberg, M. Egholm, P. Rudan, D. Brajković, Ž. Kućan, I. Gušić, M. Wikström,
L. Laakkonen, J. Kelso, M. Slatkin, S. Pääbo, Cell 134 (2008) 416–426.
date_created: 2018-12-11T12:02:35Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2021-01-12T07:42:32Z
day: '01'
doi: 10.1016/j.cell.2008.06.021
extern: 1
intvolume: ' 134'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2602844/
month: '08'
oa: 1
page: 416 - 426
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3333'
quality_controlled: 0
status: public
title: A complete neandertal mitochondrial genome sequence determined by highhhroughput
sequencing
type: journal_article
volume: 134
year: '2008'
...
---
_id: '3435'
abstract:
- lang: eng
text: We develop a new method for estimating effective population sizes, Ne, and
selection coefficients, s, from time-series data of allele frequencies sampled
from a single diallelic locus. The method is based on calculating transition probabilities,
using a numerical solution of the diffusion process, and assuming independent
binomial sampling from this diffusion process at each time point. We apply the
method in two example applications. First, we estimate selection coefficients
acting on the CCR5-Δ32 mutation on the basis of published samples of contemporary
and ancient human DNA. We show that the data are compatible with the assumption
of s = 0, although moderate amounts of selection acting on this mutation cannot
be excluded. In our second example, we estimate the selection coefficient acting
on a mutation segregating in an experimental phage population. We show that the
selection coefficient acting on this mutation is ~0.43.
author:
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Thomas
full_name: York, Thomas L
last_name: York
- first_name: Rasmus
full_name: Nielsen, Rasmus
last_name: Nielsen
citation:
ama: Bollback JP, York T, Nielsen R. Estimation of 2Nes From Temporal Allele Frequency
Data. Genetics. 2008;179(1):497-502. doi:10.1534/genetics.107.085019
apa: Bollback, J. P., York, T., & Nielsen, R. (2008). Estimation of 2Nes From
Temporal Allele Frequency Data. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.107.085019
chicago: Bollback, Jonathan P, Thomas York, and Rasmus Nielsen. “Estimation of 2Nes
From Temporal Allele Frequency Data.” Genetics. Genetics Society of America,
2008. https://doi.org/10.1534/genetics.107.085019.
ieee: J. P. Bollback, T. York, and R. Nielsen, “Estimation of 2Nes From Temporal
Allele Frequency Data,” Genetics, vol. 179, no. 1. Genetics Society of
America, pp. 497–502, 2008.
ista: Bollback JP, York T, Nielsen R. 2008. Estimation of 2Nes From Temporal Allele
Frequency Data. Genetics. 179(1), 497–502.
mla: Bollback, Jonathan P., et al. “Estimation of 2Nes From Temporal Allele Frequency
Data.” Genetics, vol. 179, no. 1, Genetics Society of America, 2008, pp.
497–502, doi:10.1534/genetics.107.085019.
short: J.P. Bollback, T. York, R. Nielsen, Genetics 179 (2008) 497–502.
date_created: 2018-12-11T12:03:19Z
date_published: 2008-05-01T00:00:00Z
date_updated: 2021-01-12T07:43:27Z
day: '01'
doi: 10.1534/genetics.107.085019
extern: 1
intvolume: ' 179'
issue: '1'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390626
month: '05'
oa: 1
page: 497 - 502
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '2965'
quality_controlled: 0
status: public
title: Estimation of 2Nes From Temporal Allele Frequency Data
type: journal_article
volume: 179
year: '2008'
...
---
_id: '3516'
abstract:
- lang: eng
text: Temporal coding is a means of representing information by the time, as opposed
to the rate, at which neurons fire. Evidence of temporal coding in the hippocampus
comes from place cells, whose spike times relative to theta oscillations reflect
a rat's position while running along stereotyped trajectories. This arises from
the backwards shift in cell firing relative to local theta oscillations (phase
precession). Here we demonstrate phase precession during place-field crossings
in an open-field foraging task. This produced spike sequences in each theta cycle
that disambiguate the rat's trajectory through two-dimensional space and can be
used to predict movement direction. Furthermore, position and movement direction
were maximally predicted from firing in the early and late portions of the theta
cycle, respectively. This represents the first direct evidence of a combined representation
of position, trajectory and heading in the hippocampus, organized on a fine temporal
scale by theta oscillations.
author:
- first_name: John
full_name: Huxter,John R
last_name: Huxter
- first_name: Timothy
full_name: Senior,Timothy J
last_name: Senior
- first_name: Kevin
full_name: Allen, Kevin
last_name: Allen
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Huxter J, Senior T, Allen K, Csicsvari JL. Theta phase-specific codes for two-dimensional
position, trajectory and heading in the hippocampus. Nature Neuroscience.
2008;11(5):587-594. doi:10.1038/nn.2106
apa: Huxter, J., Senior, T., Allen, K., & Csicsvari, J. L. (2008). Theta phase-specific
codes for two-dimensional position, trajectory and heading in the hippocampus.
Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.2106
chicago: Huxter, John, Timothy Senior, Kevin Allen, and Jozsef L Csicsvari. “Theta
Phase-Specific Codes for Two-Dimensional Position, Trajectory and Heading in the
Hippocampus.” Nature Neuroscience. Nature Publishing Group, 2008. https://doi.org/10.1038/nn.2106.
ieee: J. Huxter, T. Senior, K. Allen, and J. L. Csicsvari, “Theta phase-specific
codes for two-dimensional position, trajectory and heading in the hippocampus,”
Nature Neuroscience, vol. 11, no. 5. Nature Publishing Group, pp. 587–594,
2008.
ista: Huxter J, Senior T, Allen K, Csicsvari JL. 2008. Theta phase-specific codes
for two-dimensional position, trajectory and heading in the hippocampus. Nature
Neuroscience. 11(5), 587–594.
mla: Huxter, John, et al. “Theta Phase-Specific Codes for Two-Dimensional Position,
Trajectory and Heading in the Hippocampus.” Nature Neuroscience, vol. 11,
no. 5, Nature Publishing Group, 2008, pp. 587–94, doi:10.1038/nn.2106.
short: J. Huxter, T. Senior, K. Allen, J.L. Csicsvari, Nature Neuroscience 11 (2008)
587–594.
date_created: 2018-12-11T12:03:44Z
date_published: 2008-05-29T00:00:00Z
date_updated: 2021-01-12T07:44:00Z
day: '29'
doi: 10.1038/nn.2106
extern: 1
intvolume: ' 11'
issue: '5'
month: '05'
page: 587 - 594
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '2869'
quality_controlled: 0
status: public
title: Theta phase-specific codes for two-dimensional position, trajectory and heading
in the hippocampus
type: journal_article
volume: 11
year: '2008'
...
---
_id: '3530'
abstract:
- lang: eng
text: In the cerebral cortex, GABAergic interneurons are often regarded as fast-spiking
cells. We have identified a type of slow-spiking interneuron that offers distinct
contributions to network activity. “Ivy” cells, named after their dense and fine
axons innervating mostly basal and oblique pyramidal cell dendrites, are more
numerous than the parvalbumin-expressing basket, bistratified, or axo-axonic cells.
Ivy cells express nitric oxide synthase, neuropeptide Y, and high levels of GABA(A)
receptor alpha 1 subunit; they discharge at a low frequency with wide spikes in
vivo, yet are distinctively phase-locked to behaviorally relevant network rhythms
including theta, gamma, and ripple oscillations. Paired recordings in vitro showed
that Ivy cells receive depressing EPSPs from pyramidal cells, which in turn receive
slowly rising and decaying inhibitory input from Ivy cells. In contrast to fast-spiking
interneurons operating with millisecond precision, the highly abundant Ivy cells
express presynaptically acting neuromodulators and regulate the excitability of
pyramidal cell dendrites through slowly rising and decaying GABAergic inputs.
author:
- first_name: Pablo
full_name: Fuentealba,Pablo
last_name: Fuentealba
- first_name: Rahima
full_name: Begum,Rahima
last_name: Begum
- first_name: Marco
full_name: Capogna,Marco
last_name: Capogna
- first_name: Shozo
full_name: Jinno,Shozo
last_name: Jinno
- first_name: Laszlo
full_name: Marton,Laszlo F
last_name: Marton
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Alex
full_name: Thomson,Alex
last_name: Thomson
- first_name: Péter
full_name: Somogyi, Péter
last_name: Somogyi
- first_name: Thomas
full_name: Klausberger,Thomas
last_name: Klausberger
citation:
ama: 'Fuentealba P, Begum R, Capogna M, et al. Ivy cells: A population of nitric-oxide-producing,
slow-spiking GABAergic neurons and their involvement in hippocampal network activity.
Neuron. 2008;57(6):917-929. doi:10.1016/j.neuron.2008.01.034'
apa: 'Fuentealba, P., Begum, R., Capogna, M., Jinno, S., Marton, L., Csicsvari,
J. L., … Klausberger, T. (2008). Ivy cells: A population of nitric-oxide-producing,
slow-spiking GABAergic neurons and their involvement in hippocampal network activity.
Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2008.01.034'
chicago: 'Fuentealba, Pablo, Rahima Begum, Marco Capogna, Shozo Jinno, Laszlo Marton,
Jozsef L Csicsvari, Alex Thomson, Péter Somogyi, and Thomas Klausberger. “Ivy
Cells: A Population of Nitric-Oxide-Producing, Slow-Spiking GABAergic Neurons
and Their Involvement in Hippocampal Network Activity.” Neuron. Elsevier,
2008. https://doi.org/10.1016/j.neuron.2008.01.034.'
ieee: 'P. Fuentealba et al., “Ivy cells: A population of nitric-oxide-producing,
slow-spiking GABAergic neurons and their involvement in hippocampal network activity,”
Neuron, vol. 57, no. 6. Elsevier, pp. 917–929, 2008.'
ista: 'Fuentealba P, Begum R, Capogna M, Jinno S, Marton L, Csicsvari JL, Thomson
A, Somogyi P, Klausberger T. 2008. Ivy cells: A population of nitric-oxide-producing,
slow-spiking GABAergic neurons and their involvement in hippocampal network activity.
Neuron. 57(6), 917–929.'
mla: 'Fuentealba, Pablo, et al. “Ivy Cells: A Population of Nitric-Oxide-Producing,
Slow-Spiking GABAergic Neurons and Their Involvement in Hippocampal Network Activity.”
Neuron, vol. 57, no. 6, Elsevier, 2008, pp. 917–29, doi:10.1016/j.neuron.2008.01.034.'
short: P. Fuentealba, R. Begum, M. Capogna, S. Jinno, L. Marton, J.L. Csicsvari,
A. Thomson, P. Somogyi, T. Klausberger, Neuron 57 (2008) 917–929.
date_created: 2018-12-11T12:03:49Z
date_published: 2008-03-27T00:00:00Z
date_updated: 2021-01-12T07:44:06Z
day: '27'
doi: 10.1016/j.neuron.2008.01.034
extern: 1
intvolume: ' 57'
issue: '6'
month: '03'
page: 917 - 929
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2855'
quality_controlled: 0
status: public
title: 'Ivy cells: A population of nitric-oxide-producing, slow-spiking GABAergic
neurons and their involvement in hippocampal network activity'
type: journal_article
volume: 57
year: '2008'
...
---
_id: '3544'
abstract:
- lang: eng
text: In the subthalamic nucleus (STN) of Parkinson's disease (PD) patients, a pronounced
synchronization of oscillatory activity at beta frequencies (15-30 Hz) accompanies
movement difficulties. Abnormal beta oscillations and motor symptoms are concomitantly
and acutely suppressed by dopaminergic therapies, suggesting that these inappropriate
rhythms might also emerge acutely from disrupted dopamine transmission. The neural
basis of these abnormal beta oscillations is unclear, and how they might compromise
information processing, or how they arise, is unknown. Using a 6-hydroxydopamine-lesioned
rodent model of PD, we demonstrate that beta oscillations are inappropriately
exaggerated, compared with controls, in a brain-state-dependent manner after chronic
dopamine loss. Exaggerated beta oscillations are expressed at the levels of single
neurons and small neuronal ensembles, and are focally present and spatially distributed
within STN. They are also expressed in synchronous population activities, as evinced
by oscillatory local field potentials, in STN and cortex. Excessively synchronized
beta oscillations reduce the information coding capacity of STN neuronal ensembles,
which may contribute to parkinsonian motor impairment. Acute disruption of dopamine
transmission in control animals with antagonists of D-1/D-2 receptors did not
exaggerate STN or cortical beta oscillations. Moreover, beta oscillations were
not exaggerated until several days after 6-hydroxydopamine injections. Thus, contrary
to predictions, abnormally amplified beta oscillations in cortico-STN circuits
do not result simply from an acute absence of dopamine receptor stimulation, but
are instead delayed sequelae of chronic dopamine depletion. Targeting the plastic
processes underlying the delayed emergence of pathological beta oscillations after
continuing dopaminergic dysfunction may offer considerable therapeutic promise.
author:
- first_name: Nicolas
full_name: Mallet,Nicolas
last_name: Mallet
- first_name: Alek
full_name: Pogosyan,Alek
last_name: Pogosyan
- first_name: Andrew
full_name: Sharott,Andrew
last_name: Sharott
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: John
full_name: Bolam, John Paul
last_name: Bolam
- first_name: Peter
full_name: Brown,Peter
last_name: Brown
- first_name: Peter
full_name: Magill,Peter J
last_name: Magill
citation:
ama: Mallet N, Pogosyan A, Sharott A, et al. Disrupted dopamine transmission and
the emergence of exaggerated beta oscillations in subthalamic nucleus and cerebral
cortex. Journal of Neuroscience. 2008;28(18):4795-4806. doi:10.1523/JNEUROSCI.0123-08.2008
apa: Mallet, N., Pogosyan, A., Sharott, A., Csicsvari, J. L., Bolam, J., Brown,
P., & Magill, P. (2008). Disrupted dopamine transmission and the emergence
of exaggerated beta oscillations in subthalamic nucleus and cerebral cortex. Journal
of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0123-08.2008
chicago: Mallet, Nicolas, Alek Pogosyan, Andrew Sharott, Jozsef L Csicsvari, John
Bolam, Peter Brown, and Peter Magill. “Disrupted Dopamine Transmission and the
Emergence of Exaggerated Beta Oscillations in Subthalamic Nucleus and Cerebral
Cortex.” Journal of Neuroscience. Society for Neuroscience, 2008. https://doi.org/10.1523/JNEUROSCI.0123-08.2008.
ieee: N. Mallet et al., “Disrupted dopamine transmission and the emergence
of exaggerated beta oscillations in subthalamic nucleus and cerebral cortex,”
Journal of Neuroscience, vol. 28, no. 18. Society for Neuroscience, pp.
4795–4806, 2008.
ista: Mallet N, Pogosyan A, Sharott A, Csicsvari JL, Bolam J, Brown P, Magill P.
2008. Disrupted dopamine transmission and the emergence of exaggerated beta oscillations
in subthalamic nucleus and cerebral cortex. Journal of Neuroscience. 28(18), 4795–4806.
mla: Mallet, Nicolas, et al. “Disrupted Dopamine Transmission and the Emergence
of Exaggerated Beta Oscillations in Subthalamic Nucleus and Cerebral Cortex.”
Journal of Neuroscience, vol. 28, no. 18, Society for Neuroscience, 2008,
pp. 4795–806, doi:10.1523/JNEUROSCI.0123-08.2008.
short: N. Mallet, A. Pogosyan, A. Sharott, J.L. Csicsvari, J. Bolam, P. Brown, P.
Magill, Journal of Neuroscience 28 (2008) 4795–4806.
date_created: 2018-12-11T12:03:53Z
date_published: 2008-04-30T00:00:00Z
date_updated: 2021-01-12T07:44:12Z
day: '30'
doi: 10.1523/JNEUROSCI.0123-08.2008
extern: 1
intvolume: ' 28'
issue: '18'
month: '04'
page: 4795 - 4806
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '2842'
quality_controlled: 0
status: public
title: Disrupted dopamine transmission and the emergence of exaggerated beta oscillations
in subthalamic nucleus and cerebral cortex
type: journal_article
volume: 28
year: '2008'
...
---
_id: '3577'
alternative_title:
- Mathematics and Visualization
author:
- first_name: Silvia
full_name: Biasotti, Silvia
last_name: Biasotti
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: Jean
full_name: Boissonnat, Jean-Daniel
last_name: Boissonnat
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Gershon
full_name: Elber, Gershon
last_name: Elber
- first_name: Michela
full_name: Mortara, Michela
last_name: Mortara
- first_name: Gabriella
full_name: Sanniti di Baja, Gabriella
last_name: Sanniti Di Baja
- first_name: Michela
full_name: Spagnuolo, Michela
last_name: Spagnuolo
- first_name: Mirela
full_name: Tanase, Mirela
last_name: Tanase
- first_name: Remco
full_name: Veltkam, Remco
last_name: Veltkam
citation:
ama: 'Biasotti S, Attali D, Boissonnat J, et al. Skeletal structures. In: Shape
Analysis and Structuring. Springer; 2008:145-183. doi:10.1007/978-3-540-33265-7_5'
apa: Biasotti, S., Attali, D., Boissonnat, J., Edelsbrunner, H., Elber, G., Mortara,
M., … Veltkam, R. (2008). Skeletal structures. In Shape Analysis and Structuring
(pp. 145–183). Springer. https://doi.org/10.1007/978-3-540-33265-7_5
chicago: Biasotti, Silvia, Dominique Attali, Jean Boissonnat, Herbert Edelsbrunner,
Gershon Elber, Michela Mortara, Gabriella Sanniti Di Baja, Michela Spagnuolo,
Mirela Tanase, and Remco Veltkam. “Skeletal Structures.” In Shape Analysis
and Structuring, 145–83. Springer, 2008. https://doi.org/10.1007/978-3-540-33265-7_5.
ieee: S. Biasotti et al., “Skeletal structures,” in Shape Analysis and
Structuring, Springer, 2008, pp. 145–183.
ista: 'Biasotti S, Attali D, Boissonnat J, Edelsbrunner H, Elber G, Mortara M, Sanniti
Di Baja G, Spagnuolo M, Tanase M, Veltkam R. 2008.Skeletal structures. In: Shape
Analysis and Structuring. Mathematics and Visualization, , 145–183.'
mla: Biasotti, Silvia, et al. “Skeletal Structures.” Shape Analysis and Structuring,
Springer, 2008, pp. 145–83, doi:10.1007/978-3-540-33265-7_5.
short: S. Biasotti, D. Attali, J. Boissonnat, H. Edelsbrunner, G. Elber, M. Mortara,
G. Sanniti Di Baja, M. Spagnuolo, M. Tanase, R. Veltkam, in:, Shape Analysis and
Structuring, Springer, 2008, pp. 145–183.
date_created: 2018-12-11T12:04:03Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:44:25Z
day: '01'
doi: 10.1007/978-3-540-33265-7_5
extern: 1
month: '01'
page: 145 - 183
publication: Shape Analysis and Structuring
publication_status: published
publisher: Springer
publist_id: '2808'
quality_controlled: 0
status: public
title: Skeletal structures
type: book_chapter
year: '2008'
...
---
_id: '3591'
abstract:
- lang: eng
text: The controlled internalization of membrane receptors and lipids is crucial
for cells to control signaling pathways and interact with their environment. During
clathrin-mediated endocytosis, membrane constituents are transported via endocytic
vesicles into early endosomes, from which they are further distributed within
the cell. The small guanosine triphosphatase (GTPase) Rab5 is both required and
sufficient for the formation of these early endosomes and can be used to experimentally
address endocytic processes. Recent evidence shows that endocytic turnover of
E-cadherin regulates the migration of mesendodermal cells during zebrafish gastrulation
by modulating their adhesive interactions with neighboring cells. This in turn
leads to effective and synchronized movement within the embryo. In this review,
we discuss techniques to manipulate E-cadherin endocytosis by morpholino-mediated
knockdown of rab5 during zebrafish gastrulation. We describe the use of antibodies
specifically directed against zebrafish E-cadherin to detect its intracellular
localization and of in situ hybridization and primary cell culture to reveal patterns
of cell migration and adhesion, respectively
article_processing_charge: No
author:
- first_name: Florian
full_name: Ulrich, Florian
last_name: Ulrich
- 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: Ulrich F, Heisenberg C-PJ. Probing E-cadherin endocytosis by morpholino-mediated
Rab5 knock-down in zebrafish. Methods in Molecular Biology. 2008;440:371-387.
doi:10.1007/978-1-59745-178-9_27
apa: Ulrich, F., & Heisenberg, C.-P. J. (2008). Probing E-cadherin endocytosis
by morpholino-mediated Rab5 knock-down in zebrafish. Methods in Molecular Biology.
Springer. https://doi.org/10.1007/978-1-59745-178-9_27
chicago: Ulrich, Florian, and Carl-Philipp J Heisenberg. “Probing E-Cadherin Endocytosis
by Morpholino-Mediated Rab5 Knock-down in Zebrafish.” Methods in Molecular
Biology. Springer, 2008. https://doi.org/10.1007/978-1-59745-178-9_27.
ieee: F. Ulrich and C.-P. J. Heisenberg, “Probing E-cadherin endocytosis by morpholino-mediated
Rab5 knock-down in zebrafish.,” Methods in Molecular Biology, vol. 440.
Springer, pp. 371–387, 2008.
ista: Ulrich F, Heisenberg C-PJ. 2008. Probing E-cadherin endocytosis by morpholino-mediated
Rab5 knock-down in zebrafish. Methods in Molecular Biology. 440, 371–387.
mla: Ulrich, Florian, and Carl-Philipp J. Heisenberg. “Probing E-Cadherin Endocytosis
by Morpholino-Mediated Rab5 Knock-down in Zebrafish.” Methods in Molecular
Biology, vol. 440, Springer, 2008, pp. 371–87, doi:10.1007/978-1-59745-178-9_27.
short: F. Ulrich, C.-P.J. Heisenberg, Methods in Molecular Biology 440 (2008) 371–387.
date_created: 2018-12-11T12:04:08Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:44:31Z
day: '01'
doi: 10.1007/978-1-59745-178-9_27
extern: '1'
intvolume: ' 440'
language:
- iso: eng
month: '01'
oa_version: None
page: 371 - 387
publication: Methods in Molecular Biology
publication_status: published
publisher: Springer
publist_id: '2792'
status: public
title: Probing E-cadherin endocytosis by morpholino-mediated Rab5 knock-down in zebrafish.
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 440
year: '2008'
...
---
_id: '3599'
abstract:
- lang: eng
text: In this paper, adaptive formation control and bio-inspired optimization are
jointly addressed for a cluster-based satellite wireless sensor network in which
there are multiple satellites flying in formation (MSFF) in the presence of unknown
disturbances. The full nonlinear dynamics model describing the relative positioning
of the MSFF system is used to develop an adaptive formation controller. First,
the original nonlinear system is transformed into a linear controllable system
with aperturbation term by invoking the input-output feedback linearization technique.
Second, by using the integral feedback design scheme, the adaptive formation controller
is presented for improving the steady-state performance of the MSFF system in
the presence of unknown disturbances. Third, as a currently popular bio-inspired
algorithm, PSO (particle swarm optimizer) is employed to minimize the total energy
consumption under the required quality of service by jointly optimizing the transmission
power and rate for each satellite. Simulation results are provided to demonstrate
the effectiveness of the adaptive formation controller and the PSO-based optimization
for saving the total communication energy.
author:
- first_name: Erfu
full_name: Yang, Erfu
last_name: Yang
- first_name: Ahmet
full_name: Erdogan, Ahmet T
last_name: Erdogan
- first_name: Tughrul
full_name: Arslan, Tughrul
last_name: Arslan
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Yang E, Erdogan A, Arslan T, Barton NH. Adaptive formation control and bio-inspired
optimization of a cluster-based satellite wireless sensor network . In: IEEE;
2008:432-439. doi:10.1109/AHS.2008.60'
apa: 'Yang, E., Erdogan, A., Arslan, T., & Barton, N. H. (2008). Adaptive formation
control and bio-inspired optimization of a cluster-based satellite wireless sensor
network (pp. 432–439). Presented at the AHS: NASA/ESA Conference on Adaptive
Hardware and Systems, IEEE. https://doi.org/10.1109/AHS.2008.60'
chicago: Yang, Erfu, Ahmet Erdogan, Tughrul Arslan, and Nicholas H Barton. “Adaptive
Formation Control and Bio-Inspired Optimization of a Cluster-Based Satellite Wireless
Sensor Network ,” 432–39. IEEE, 2008. https://doi.org/10.1109/AHS.2008.60.
ieee: 'E. Yang, A. Erdogan, T. Arslan, and N. H. Barton, “Adaptive formation control
and bio-inspired optimization of a cluster-based satellite wireless sensor network
,” presented at the AHS: NASA/ESA Conference on Adaptive Hardware and Systems,
2008, pp. 432–439.'
ista: 'Yang E, Erdogan A, Arslan T, Barton NH. 2008. Adaptive formation control
and bio-inspired optimization of a cluster-based satellite wireless sensor network
. AHS: NASA/ESA Conference on Adaptive Hardware and Systems, 432–439.'
mla: Yang, Erfu, et al. Adaptive Formation Control and Bio-Inspired Optimization
of a Cluster-Based Satellite Wireless Sensor Network . IEEE, 2008, pp. 432–39,
doi:10.1109/AHS.2008.60.
short: E. Yang, A. Erdogan, T. Arslan, N.H. Barton, in:, IEEE, 2008, pp. 432–439.
conference:
name: 'AHS: NASA/ESA Conference on Adaptive Hardware and Systems'
date_created: 2018-12-11T12:04:10Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2021-01-12T07:44:34Z
day: '01'
doi: 10.1109/AHS.2008.60
extern: 1
month: '08'
page: 432 - 439
publication_status: published
publisher: IEEE
publist_id: '2784'
quality_controlled: 0
status: public
title: 'Adaptive formation control and bio-inspired optimization of a cluster-based
satellite wireless sensor network '
type: conference
year: '2008'
...
---
_id: '3698'
abstract:
- lang: eng
text: Kernel canonical correlation analysis (KCCA) is a dimensionality reduction
technique for paired data. By finding directions that maximize correlation, KCCA
learns representations that are more closely tied to the underlying semantics
of the data rather than noise. However, meaningful directions are not only those
that have high correlation to another modality, but also those that capture the
manifold structure of the data. We propose a method that is simultaneously able
to find highly correlated directions that are also located on high variance directions
along the data manifold. This is achieved by the use of semi-supervised Laplacian
regularization of KCCA. We show experimentally that Laplacian regularized training
improves class separation over KCCA with only Tikhonov regularization, while causing
no degradation in the correlation between modalities. We propose a model selection
criterion based on the Hilbert-Schmidt norm of the semi-supervised Laplacian regularized
cross-covariance operator, which we compute in closed form.
alternative_title:
- LNCS
author:
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Arthur
full_name: Gretton,Arthur
last_name: Gretton
citation:
ama: 'Blaschko M, Lampert C, Gretton A. Semi-supervised Laplacian regularization
of kernel canonical correlation analysis. In: Vol 5211. Springer; 2008:133-145.
doi:10.1007/978-3-540-87479-9_27'
apa: 'Blaschko, M., Lampert, C., & Gretton, A. (2008). Semi-supervised Laplacian
regularization of kernel canonical correlation analysis (Vol. 5211, pp. 133–145).
Presented at the ECML: European Conference on Machine Learning, Springer. https://doi.org/10.1007/978-3-540-87479-9_27'
chicago: Blaschko, Matthew, Christoph Lampert, and Arthur Gretton. “Semi-Supervised
Laplacian Regularization of Kernel Canonical Correlation Analysis,” 5211:133–45.
Springer, 2008. https://doi.org/10.1007/978-3-540-87479-9_27.
ieee: 'M. Blaschko, C. Lampert, and A. Gretton, “Semi-supervised Laplacian regularization
of kernel canonical correlation analysis,” presented at the ECML: European Conference
on Machine Learning, 2008, vol. 5211, no. Part 1, pp. 133–145.'
ista: 'Blaschko M, Lampert C, Gretton A. 2008. Semi-supervised Laplacian regularization
of kernel canonical correlation analysis. ECML: European Conference on Machine
Learning, LNCS, vol. 5211, 133–145.'
mla: Blaschko, Matthew, et al. Semi-Supervised Laplacian Regularization of Kernel
Canonical Correlation Analysis. Vol. 5211, no. Part 1, Springer, 2008, pp.
133–45, doi:10.1007/978-3-540-87479-9_27.
short: M. Blaschko, C. Lampert, A. Gretton, in:, Springer, 2008, pp. 133–145.
conference:
name: 'ECML: European Conference on Machine Learning'
date_created: 2018-12-11T12:04:41Z
date_published: 2008-10-21T00:00:00Z
date_updated: 2021-01-12T07:49:02Z
day: '21'
doi: 10.1007/978-3-540-87479-9_27
extern: 1
intvolume: ' 5211'
issue: Part 1
month: '10'
page: 133 - 145
publication_status: published
publisher: Springer
publist_id: '2662'
quality_controlled: 0
status: public
title: Semi-supervised Laplacian regularization of kernel canonical correlation analysis
type: conference
volume: 5211
year: '2008'
...
---
_id: '3694'
abstract:
- lang: eng
text: Distributed Denial of Service (DDoS) attacks are today the most destabilizing
factor in the global internet and there is a strong need for sophisticated solutions.
We introduce a formal statistical framework and derive a Bayes optimal packet
classifier from it. Our proposed practical algorithm "Adaptive History-Based
IP Filtering" (AHIF) mitigates DDoS attacks near the victim and outperforms
existing methods by at least 32% in terms of collateral damage. Furthermore, it
adjusts to the strength of an ongoing attack and ensures availability of the attacked
server. In contrast to other adaptive solutions, firewall rulesets used to resist
an attack can be precalculated before an attack takes place. This ensures an immediate
response in a DDoS emergency. For evaluation, simulated DDoS attacks and two real-world
user traffic datasets are used.
author:
- first_name: Markus
full_name: Goldstein,Markus
last_name: Goldstein
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Matthias
full_name: Reif,Matthias
last_name: Reif
- first_name: Armin
full_name: Stahl,Armin
last_name: Stahl
- first_name: Thomas
full_name: Breuel,Thomas M
last_name: Breuel
citation:
ama: 'Goldstein M, Lampert C, Reif M, Stahl A, Breuel T. Bayes optimal DDoS mitigation
by adaptive history-based IP filtering. In: IEEE; 2008:174-179. doi:10.1109/ICN.2008.64'
apa: 'Goldstein, M., Lampert, C., Reif, M., Stahl, A., & Breuel, T. (2008).
Bayes optimal DDoS mitigation by adaptive history-based IP filtering (pp. 174–179).
Presented at the ICN: International Conference on Networking, IEEE. https://doi.org/10.1109/ICN.2008.64'
chicago: Goldstein, Markus, Christoph Lampert, Matthias Reif, Armin Stahl, and Thomas
Breuel. “Bayes Optimal DDoS Mitigation by Adaptive History-Based IP Filtering,”
174–79. IEEE, 2008. https://doi.org/10.1109/ICN.2008.64.
ieee: 'M. Goldstein, C. Lampert, M. Reif, A. Stahl, and T. Breuel, “Bayes optimal
DDoS mitigation by adaptive history-based IP filtering,” presented at the ICN:
International Conference on Networking, 2008, pp. 174–179.'
ista: 'Goldstein M, Lampert C, Reif M, Stahl A, Breuel T. 2008. Bayes optimal DDoS
mitigation by adaptive history-based IP filtering. ICN: International Conference
on Networking, 174–179.'
mla: Goldstein, Markus, et al. Bayes Optimal DDoS Mitigation by Adaptive History-Based
IP Filtering. IEEE, 2008, pp. 174–79, doi:10.1109/ICN.2008.64.
short: M. Goldstein, C. Lampert, M. Reif, A. Stahl, T. Breuel, in:, IEEE, 2008,
pp. 174–179.
conference:
name: 'ICN: International Conference on Networking'
date_created: 2018-12-11T12:04:39Z
date_published: 2008-04-13T00:00:00Z
date_updated: 2021-01-12T07:49:01Z
day: '13'
doi: 10.1109/ICN.2008.64
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/~chl/papers/goldstein-icn2008.pdf
month: '04'
page: 174 - 179
publication_status: published
publisher: IEEE
publist_id: '2671'
quality_controlled: 0
status: public
title: Bayes optimal DDoS mitigation by adaptive history-based IP filtering
type: conference
year: '2008'
...
---
_id: '3706'
abstract:
- lang: eng
text: We present a new technique for structured prediction that works in a hybrid
generative/discriminative way, using a one-class support vector machine to model
the joint probability of (input, output)-pairs in a joint reproducing kernel Hilbert
space. Compared to discriminative techniques, like conditional random fields or
structured output SVMs?, the proposed method has the advantage that its training
time depends only on the number of training examples, not on the size of the label
space. Due to its generative aspect, it is also very tolerant against ambiguous,
incomplete or incorrect labels. Experiments on realistic data show that our method
works efficiently and robustly in situations that discriminative techniques have
problems with or that are computationally infeasible for them.
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
citation:
ama: 'Lampert C, Blaschko M. Joint kernel support estimation for structured prediction.
In: Curran Associates, Inc.; 2008:1-4.'
apa: 'Lampert, C., & Blaschko, M. (2008). Joint kernel support estimation for
structured prediction (pp. 1–4). Presented at the NIPS SISO: NIPS Workshop on
“Structured Input - Structured Output,” Curran Associates, Inc.'
chicago: Lampert, Christoph, and Matthew Blaschko. “Joint Kernel Support Estimation
for Structured Prediction,” 1–4. Curran Associates, Inc., 2008.
ieee: 'C. Lampert and M. Blaschko, “Joint kernel support estimation for structured
prediction,” presented at the NIPS SISO: NIPS Workshop on “Structured Input -
Structured Output,” 2008, pp. 1–4.'
ista: 'Lampert C, Blaschko M. 2008. Joint kernel support estimation for structured
prediction. NIPS SISO: NIPS Workshop on ‘Structured Input - Structured Output’,
1–4.'
mla: Lampert, Christoph, and Matthew Blaschko. Joint Kernel Support Estimation
for Structured Prediction. Curran Associates, Inc., 2008, pp. 1–4.
short: C. Lampert, M. Blaschko, in:, Curran Associates, Inc., 2008, pp. 1–4.
conference:
name: 'NIPS SISO: NIPS Workshop on "Structured Input - Structured Output"'
date_created: 2018-12-11T12:04:43Z
date_published: 2008-12-12T00:00:00Z
date_updated: 2021-01-12T07:51:37Z
day: '12'
extern: 1
main_file_link:
- open_access: '0'
url: http://agbs.kyb.tuebingen.mpg.de/wikis/bg/siso2008/Blaschkoetal.pdf
month: '12'
page: 1 - 4
publication_status: published
publisher: Curran Associates, Inc.
publist_id: '2650'
quality_controlled: 0
status: public
title: Joint kernel support estimation for structured prediction
type: conference
year: '2008'
...
---
_id: '3712'
abstract:
- lang: eng
text: We present a new method for spectral clustering with paired data based on
kernel canonical correlation analysis, called correlational spectral clustering.
Paired data are common in real world data sources, such as images with text captions.
Traditional spectral clustering algorithms either assume that data can be represented
by a single similarity measure, or by co-occurrence matrices that are then used
in biclustering. In contrast, the proposed method uses separate similarity measures
for each data representation, and allows for projection of previously unseen data
that are only observed in one representation (e.g. images but not text). We show
that this algorithm generalizes traditional spectral clustering algorithms and
show consistent empirical improvement over spectral clustering on a variety of
datasets of images with associated text.
author:
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Blaschko M, Lampert C. Correlational spectral clustering. In: IEEE; 2008:1-8.
doi:10.1109/CVPR.2008.4587353'
apa: 'Blaschko, M., & Lampert, C. (2008). Correlational spectral clustering
(pp. 1–8). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE.
https://doi.org/10.1109/CVPR.2008.4587353'
chicago: Blaschko, Matthew, and Christoph Lampert. “Correlational Spectral Clustering,”
1–8. IEEE, 2008. https://doi.org/10.1109/CVPR.2008.4587353.
ieee: 'M. Blaschko and C. Lampert, “Correlational spectral clustering,” presented
at the CVPR: Computer Vision and Pattern Recognition, 2008, pp. 1–8.'
ista: 'Blaschko M, Lampert C. 2008. Correlational spectral clustering. CVPR: Computer
Vision and Pattern Recognition, 1–8.'
mla: Blaschko, Matthew, and Christoph Lampert. Correlational Spectral Clustering.
IEEE, 2008, pp. 1–8, doi:10.1109/CVPR.2008.4587353.
short: M. Blaschko, C. Lampert, in:, IEEE, 2008, pp. 1–8.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:04:45Z
date_published: 2008-09-18T00:00:00Z
date_updated: 2021-01-12T07:51:40Z
day: '18'
doi: 10.1109/CVPR.2008.4587353
extern: 1
month: '09'
page: 1 - 8
publication_status: published
publisher: IEEE
publist_id: '2646'
quality_controlled: 0
status: public
title: Correlational spectral clustering
type: conference
year: '2008'
...
---
_id: '3726'
abstract:
- lang: eng
text: Single-molecule atomic force microscopy (AFM) provides novel ways to characterize
the structure-function relationship of native membrane proteins. High-resolution
AFM topographs allow observing the structure of single proteins at sub-nanometer
resolution as well as their conformational changes, oligomeric state, molecular
dynamics and assembly. We will review these feasibilities illustrating examples
of membrane proteins in native and reconstituted membranes. Classification of
individual topographs of single proteins allows understanding the principles of
motions of their extrinsic domains, to learn about their local structural flexibilities
and to find the entropy minima of certain conformations. Combined with the visualization
of functionally related conformational changes these insights allow understanding
why certain flexibilities are required for the protein to function and how structurally
flexible regions allow certain conformational changes. Complementary to AFM imaging,
single-molecule force spectroscopy (SMFS) experiments detect molecular interactions
established within and between membrane proteins. The sensitivity of this method
makes it possible to measure interactions that stabilize secondary structures
such as transmembrane α-helices, polypeptide loops and segments within. Changes
in temperature or protein-protein assembly do not change the locations of stable
structural segments, but influence their stability established by collective molecular
interactions. Such changes alter the probability of proteins to choose a certain
unfolding pathway. Recent examples have elucidated unfolding and refolding pathways
of membrane proteins as well as their energy landscapes.
author:
- first_name: Andreas
full_name: Engel, Andreas
last_name: Engel
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Dimtrios
full_name: Fotiadis, Dimtrios
last_name: Fotiadis
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: David
full_name: Cisneros, David
last_name: Cisneros
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: 'Engel A, Janovjak HL, Fotiadis D, Kedrov A, Cisneros D, Mueller D. Single-molecule
microscopy and force spectroscopy of membrane proteins. In: Single Molecules
and Nanotechnology. Vol 12. Springer; 2008:279-311. doi:10.1007/978-3-540-73924-1_11'
apa: Engel, A., Janovjak, H. L., Fotiadis, D., Kedrov, A., Cisneros, D., & Mueller,
D. (2008). Single-molecule microscopy and force spectroscopy of membrane proteins.
In Single Molecules and Nanotechnology (Vol. 12, pp. 279–311). Springer.
https://doi.org/10.1007/978-3-540-73924-1_11
chicago: Engel, Andreas, Harald L Janovjak, Dimtrios Fotiadis, Alexej Kedrov, David
Cisneros, and Daniel Mueller. “Single-Molecule Microscopy and Force Spectroscopy
of Membrane Proteins.” In Single Molecules and Nanotechnology, 12:279–311.
Springer, 2008. https://doi.org/10.1007/978-3-540-73924-1_11.
ieee: A. Engel, H. L. Janovjak, D. Fotiadis, A. Kedrov, D. Cisneros, and D. Mueller,
“Single-molecule microscopy and force spectroscopy of membrane proteins,” in Single
Molecules and Nanotechnology, vol. 12, Springer, 2008, pp. 279–311.
ista: 'Engel A, Janovjak HL, Fotiadis D, Kedrov A, Cisneros D, Mueller D. 2008.Single-molecule
microscopy and force spectroscopy of membrane proteins. In: Single Molecules and
Nanotechnology. vol. 12, 279–311.'
mla: Engel, Andreas, et al. “Single-Molecule Microscopy and Force Spectroscopy of
Membrane Proteins.” Single Molecules and Nanotechnology, vol. 12, Springer,
2008, pp. 279–311, doi:10.1007/978-3-540-73924-1_11.
short: A. Engel, H.L. Janovjak, D. Fotiadis, A. Kedrov, D. Cisneros, D. Mueller,
in:, Single Molecules and Nanotechnology, Springer, 2008, pp. 279–311.
date_created: 2018-12-11T12:04:50Z
date_published: 2008-01-08T00:00:00Z
date_updated: 2021-01-12T07:51:45Z
day: '08'
doi: 10.1007/978-3-540-73924-1_11
extern: 1
intvolume: ' 12'
month: '01'
page: 279 - 311
publication: Single Molecules and Nanotechnology
publication_status: published
publisher: Springer
publist_id: '2503'
quality_controlled: 0
status: public
title: Single-molecule microscopy and force spectroscopy of membrane proteins
type: book_chapter
volume: 12
year: '2008'
...
---
_id: '3739'
abstract:
- lang: eng
text: 'Changes in a cell''s external or internal conditions are usually reflected
in the concentrations of the relevant transcription factors. These proteins in
turn modulate the expression levels of the genes under their control and sometimes
need to perform nontrivial computations that integrate several inputs and affect
multiple genes. At the same time, the activities of the regulated genes would
fluctuate even if the inputs were held fixed, as a consequence of the intrinsic
noise in the system, and such noise must fundamentally limit the reliability of
any genetic computation. Here we use information theory to formalize the notion
of information transmission in simple genetic regulatory elements in the presence
of physically realistic noise sources. The dependence of this "channel capacity"
on noise parameters, cooperativity and cost of making signaling molecules is explored
systematically. We find that, in the range of parameters probed by recent in vivo
measurements, capacities higher than one bit should be achievable. It is of course
generally accepted that gene regulatory elements must, in order to function properly,
have a capacity of at least one bit. The central point of our analysis is the
demonstration that simple physical models of noisy gene transcription, with realistic
parameters, can indeed achieve this capacity: it was not self-evident that this
should be so. We also demonstrate that capacities significantly greater than one
bit are possible, so that transcriptional regulation need not be limited to simple
"on-off" components. The question whether real systems actually exploit
this richer possibility is beyond the scope of this investigation.'
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Curtis
full_name: Callan,Curtis G
last_name: Callan
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Tkačik G, Callan C, Bialek W. Information capacity of genetic regulatory elements.
Physical Review E Statistical Nonlinear and Soft Matter Physics. 2008;78(1).
doi:10.1103/PhysRevE.78.011910
apa: Tkačik, G., Callan, C., & Bialek, W. (2008). Information capacity of genetic
regulatory elements. Physical Review E Statistical Nonlinear and Soft Matter
Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.78.011910
chicago: Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Capacity
of Genetic Regulatory Elements.” Physical Review E Statistical Nonlinear and
Soft Matter Physics. American Institute of Physics, 2008. https://doi.org/10.1103/PhysRevE.78.011910.
ieee: G. Tkačik, C. Callan, and W. Bialek, “Information capacity of genetic regulatory
elements,” Physical Review E Statistical Nonlinear and Soft Matter Physics,
vol. 78, no. 1. American Institute of Physics, 2008.
ista: Tkačik G, Callan C, Bialek W. 2008. Information capacity of genetic regulatory
elements. Physical Review E Statistical Nonlinear and Soft Matter Physics. 78(1).
mla: Tkačik, Gašper, et al. “Information Capacity of Genetic Regulatory Elements.”
Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 78,
no. 1, American Institute of Physics, 2008, doi:10.1103/PhysRevE.78.011910.
short: G. Tkačik, C. Callan, W. Bialek, Physical Review E Statistical Nonlinear
and Soft Matter Physics 78 (2008).
date_created: 2018-12-11T12:04:54Z
date_published: 2008-07-21T00:00:00Z
date_updated: 2021-01-12T07:51:51Z
day: '21'
doi: 10.1103/PhysRevE.78.011910
extern: 1
intvolume: ' 78'
issue: '1'
month: '07'
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '2488'
quality_controlled: 0
status: public
title: Information capacity of genetic regulatory elements
type: journal_article
volume: 78
year: '2008'
...
---
_id: '3740'
abstract:
- lang: eng
text: In the simplest view of transcriptional regulation, the expression of a gene
is turned on or off by changes in the concentration of a transcription factor
(TF). We use recent data on noise levels in gene expression to show that it should
be possible to transmit much more than just one regulatory bit. Realizing this
optimal information capacity would require that the dynamic range of TF concentrations
used by the cell, the input/output relation of the regulatory module, and the
noise in gene expression satisfy certain matching relations, which we derive.
These results provide parameter-free, quantitative predictions connecting independently
measurable quantities. Although we have considered only the simplified problem
of a single gene responding to a single TF, we find that these predictions are
in surprisingly good agreement with recent experiments on the Bicoid/Hunchback
system in the early Drosophila embryo and that this system achieves approximately
90% of its theoretical maximum information transmission.
acknowledgement: P50 GM071508/GM/NIGMS NIH HHS/United States; R01 GM077599/GM/NIGMS
NIH HHS/United States
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Curtis
full_name: Callan,Curtis G
last_name: Callan
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Tkačik G, Callan C, Bialek W. Information flow and optimization in transcriptional
regulation. PNAS. 2008;105(34):12265-12270. doi:10.1073/pnas.0806077105
apa: Tkačik, G., Callan, C., & Bialek, W. (2008). Information flow and optimization
in transcriptional regulation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0806077105
chicago: Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Flow and
Optimization in Transcriptional Regulation.” PNAS. National Academy of
Sciences, 2008. https://doi.org/10.1073/pnas.0806077105.
ieee: G. Tkačik, C. Callan, and W. Bialek, “Information flow and optimization in
transcriptional regulation,” PNAS, vol. 105, no. 34. National Academy of
Sciences, pp. 12265–12270, 2008.
ista: Tkačik G, Callan C, Bialek W. 2008. Information flow and optimization in transcriptional
regulation. PNAS. 105(34), 12265–12270.
mla: Tkačik, Gašper, et al. “Information Flow and Optimization in Transcriptional
Regulation.” PNAS, vol. 105, no. 34, National Academy of Sciences, 2008,
pp. 12265–70, doi:10.1073/pnas.0806077105.
short: G. Tkačik, C. Callan, W. Bialek, PNAS 105 (2008) 12265–12270.
date_created: 2018-12-11T12:04:54Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:51:52Z
day: '01'
doi: 10.1073/pnas.0806077105
extern: 1
intvolume: ' 105'
issue: '34'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527900
month: '01'
oa: 1
page: 12265 - 12270
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2489'
quality_controlled: 0
status: public
title: Information flow and optimization in transcriptional regulation
type: journal_article
volume: 105
year: '2008'
...
---
_id: '3744'
abstract:
- lang: eng
text: It is widely acknowledged that detailed timing of action potentials is used
to encode information, for example, in auditory pathways; however, the computational
tools required to analyze encoding through timing are still in their infancy.
We present a simple example of encoding, based on a recent model of time-frequency
analysis, in which units fire action potentials when a certain condition is met,
but the timing of the action potential depends also on other features of the stimulus.
We show that, as a result, spike-triggered averages are smoothed so much that
they do not represent the true features of the encoding. Inspired by this example,
we present a simple method, differential reverse correlations, that can separate
an analysis of what causes a neuron to spike, and what controls its timing. We
analyze with this method the leaky integrate-and-fire neuron and show the method
accurately reconstructs the model's kernel.
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Marcelo
full_name: Magnasco, Marcelo O
last_name: Magnasco
citation:
ama: 'Tkačik G, Magnasco M. Decoding spike timing: The differential reverse-correlation
method. Biosystems. 2008;93(1-2):90-100. doi:10.1016/j.biosystems.2008.04.011'
apa: 'Tkačik, G., & Magnasco, M. (2008). Decoding spike timing: The differential
reverse-correlation method. Biosystems. Elsevier. https://doi.org/10.1016/j.biosystems.2008.04.011'
chicago: 'Tkačik, Gašper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential
Reverse-Correlation Method.” Biosystems. Elsevier, 2008. https://doi.org/10.1016/j.biosystems.2008.04.011.'
ieee: 'G. Tkačik and M. Magnasco, “Decoding spike timing: The differential reverse-correlation
method,” Biosystems, vol. 93, no. 1–2. Elsevier, pp. 90–100, 2008.'
ista: 'Tkačik G, Magnasco M. 2008. Decoding spike timing: The differential reverse-correlation
method. Biosystems. 93(1–2), 90–100.'
mla: 'Tkačik, Gašper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential
Reverse-Correlation Method.” Biosystems, vol. 93, no. 1–2, Elsevier, 2008,
pp. 90–100, doi:10.1016/j.biosystems.2008.04.011.'
short: G. Tkačik, M. Magnasco, Biosystems 93 (2008) 90–100.
date_created: 2018-12-11T12:04:56Z
date_published: 2008-07-01T00:00:00Z
date_updated: 2021-01-12T07:51:53Z
day: '01'
doi: 10.1016/j.biosystems.2008.04.011
extern: 1
intvolume: ' 93'
issue: 1-2
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2792887
month: '07'
oa: 1
page: 90 - 100
publication: Biosystems
publication_status: published
publisher: Elsevier
publist_id: '2482'
quality_controlled: 0
status: public
title: 'Decoding spike timing: The differential reverse-correlation method'
type: journal_article
volume: 93
year: '2008'
...
---
_id: '3760'
abstract:
- lang: eng
text: We introduce a method for efficiently animating a wide range of deformable
materials. We combine a high resolution surface mesh with a tetrahedral finite
element simulator that makes use of frequent re-meshing. This combination allows
for fast and detailed simulations of complex elastic and plastic behavior. We
significantly expand the range of physical parameters that can be simulated with
a single technique, and the results are free from common artifacts such as volume-loss,
smoothing, popping, and the absence of thin features like strands and sheets.
Our decision to couple a high resolution surface with low-resolution physics leads
to efficient simulation and detailed surface features, and our approach to creating
the tetrahedral mesh leads to an order-of-magnitude speedup over previous techniques
in the time spent re-meshing. We compute masses, collisions, and surface tension
forces on the scale of the fine mesh, which helps avoid visual artifacts due to
the differing mesh resolutions. The result is a method that can simulate a large
array of different material behaviors with high resolution features in a short
amount of time.
article_processing_charge: No
author:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Greg
full_name: Turk, Greg
last_name: Turk
citation:
ama: Wojtan C, Turk G. Fast viscoelastic behavior with thin features. ACM Transactions
on Graphics. 2008;27(3). doi:10.1145/1360612.1360646
apa: Wojtan, C., & Turk, G. (2008). Fast viscoelastic behavior with thin features.
ACM Transactions on Graphics. ACM. https://doi.org/10.1145/1360612.1360646
chicago: Wojtan, Chris, and Greg Turk. “Fast Viscoelastic Behavior with Thin Features.”
ACM Transactions on Graphics. ACM, 2008. https://doi.org/10.1145/1360612.1360646.
ieee: C. Wojtan and G. Turk, “Fast viscoelastic behavior with thin features,” ACM
Transactions on Graphics, vol. 27, no. 3. ACM, 2008.
ista: Wojtan C, Turk G. 2008. Fast viscoelastic behavior with thin features. ACM
Transactions on Graphics. 27(3).
mla: Wojtan, Chris, and Greg Turk. “Fast Viscoelastic Behavior with Thin Features.”
ACM Transactions on Graphics, vol. 27, no. 3, ACM, 2008, doi:10.1145/1360612.1360646.
short: C. Wojtan, G. Turk, ACM Transactions on Graphics 27 (2008).
date_created: 2018-12-11T12:05:01Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2023-02-23T11:41:29Z
day: '01'
doi: 10.1145/1360612.1360646
extern: '1'
intvolume: ' 27'
issue: '3'
language:
- iso: eng
main_file_link:
- url: http://www.cc.gatech.edu/~turk/my_papers/fast_goop_2008.pdf
month: '08'
oa_version: None
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '2467'
status: public
title: Fast viscoelastic behavior with thin features
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2008'
...
---
_id: '3825'
abstract:
- lang: eng
text: Fast-spiking parvalbumin-expressing basket cells (BCs) represent a major type
of inhibitory interneuron in the hippocampus. These cells inhibit principal cells
in a temporally precise manner and are involved in the generation of network oscillations.
Although BCs show a unique expression profile of Ca(2+)-permeable receptors, Ca(2+)-binding
proteins and Ca(2+)-dependent signalling molecules, physiological Ca(2+) signalling
in these interneurons has not been investigated. To study action potential (AP)-induced
dendritic Ca(2+) influx and buffering, we combined whole-cell patch-clamp recordings
with ratiometric Ca(2+) imaging from the proximal apical dendrites of rigorously
identified BCs in acute slices, using the high-affinity Ca(2+) indicator fura-2
or the low-affinity dye fura-FF. Single APs evoked dendritic Ca(2+) transients
with small amplitude. Bursts of APs evoked Ca(2+) transients with amplitudes that
increased linearly with AP number. Analysis of Ca(2+) transients under steady-state
conditions with different fura-2 concentrations and during loading with 200 microm
fura-2 indicated that the endogenous Ca(2+)-binding ratio was approximately 200
(kappa(S) = 202 +/- 26 for the loading experiments). The peak amplitude of the
Ca(2+) transients measured directly with 100 microm fura-FF was 39 nm AP(-1).
At approximately 23 degrees C, the decay time constant of the Ca(2+) transients
was 390 ms, corresponding to an extrusion rate of approximately 600 s(-1). At
34 degrees C, the decay time constant was 203 ms and the corresponding extrusion
rate was approximately 1100 s(-1). At both temperatures, continuous theta-burst
activity with three to five APs per theta cycle, as occurs in vivo during exploration,
led to a moderate increase in the global Ca(2+) concentration that was proportional
to AP number, whereas more intense stimulation was required to reach micromolar
Ca(2+) concentrations and to shift Ca(2+) signalling into a non-linear regime.
In conclusion, dentate gyrus BCs show a high endogenous Ca(2+)-binding ratio,
a small AP-induced dendritic Ca(2+) influx, and a relatively slow Ca(2+) extrusion.
These specific buffering properties of BCs will sharpen the time course of local
Ca(2+) signals, while prolonging the decay of global Ca(2+) signals.
author:
- first_name: Yexica
full_name: Aponte, Yexica
last_name: Aponte
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Aponte Y, Bischofberger J, Jonas PM. Efficient Ca(2+) buffering in fast-spiking
basket cells of rat hippocampus. Journal of Physiology. 2008;586(8):2061-2075.
doi:10.1113/jphysiol.2007.147298
apa: Aponte, Y., Bischofberger, J., & Jonas, P. M. (2008). Efficient Ca(2+)
buffering in fast-spiking basket cells of rat hippocampus. Journal of Physiology.
Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2007.147298
chicago: Aponte, Yexica, Josef Bischofberger, and Peter M Jonas. “Efficient Ca(2+)
Buffering in Fast-Spiking Basket Cells of Rat Hippocampus.” Journal of Physiology.
Wiley-Blackwell, 2008. https://doi.org/10.1113/jphysiol.2007.147298.
ieee: Y. Aponte, J. Bischofberger, and P. M. Jonas, “Efficient Ca(2+) buffering
in fast-spiking basket cells of rat hippocampus,” Journal of Physiology,
vol. 586, no. 8. Wiley-Blackwell, pp. 2061–75, 2008.
ista: Aponte Y, Bischofberger J, Jonas PM. 2008. Efficient Ca(2+) buffering in fast-spiking
basket cells of rat hippocampus. Journal of Physiology. 586(8), 2061–75.
mla: Aponte, Yexica, et al. “Efficient Ca(2+) Buffering in Fast-Spiking Basket Cells
of Rat Hippocampus.” Journal of Physiology, vol. 586, no. 8, Wiley-Blackwell,
2008, pp. 2061–75, doi:10.1113/jphysiol.2007.147298.
short: Y. Aponte, J. Bischofberger, P.M. Jonas, Journal of Physiology 586 (2008)
2061–75.
date_created: 2018-12-11T12:05:22Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:28Z
day: '01'
doi: 10.1113/jphysiol.2007.147298
extern: 1
intvolume: ' 586'
issue: '8'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2465201/
month: '01'
oa: 1
page: 2061 - 75
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2386'
quality_controlled: 0
status: public
title: Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus
type: journal_article
volume: 586
year: '2008'
...
---
_id: '3822'
abstract:
- lang: eng
text: Dentate gyrus granule cells transmit action potentials (APs) along their unmyelinated
mossy fibre axons to the CA3 region. Although the initiation and propagation of
APs are fundamental steps during neural computation, little is known about the
site of AP initiation and the speed of propagation in mossy fibre axons. To address
these questions, we performed simultaneous somatic and axonal whole-cell recordings
from granule cells in acute hippocampal slices of adult mice at approximately
23 degrees C. Injection of short current pulses or synaptic stimulation evoked
axonal and somatic APs with similar amplitudes. By contrast, the time course was
significantly different, as axonal APs had a higher maximal rate of rise (464
+/- 30 V s(-1) in the axon versus 297 +/- 12 V s(-1) in the soma, mean +/- s.e.m.).
Furthermore, analysis of latencies between the axonal and somatic signals showed
that APs were initiated in the proximal axon at approximately 20-30 mum distance
from the soma, and propagated orthodromically with a velocity of 0.24 m s(-1).
Qualitatively similar results were obtained at a recording temperature of approximately
34 degrees C. Modelling of AP propagation in detailed cable models of granule
cells suggested that a approximately 4 times higher Na(+) channel density ( approximately
1000 pS mum(-2)) in the axon might account for both the higher rate of rise of
axonal APs and the robust AP initiation in the proximal mossy fibre axon. This
may be of critical importance to separate dendritic integration of thousands of
synaptic inputs from the generation and transmission of a common AP output.
author:
- first_name: Christoph
full_name: Schmidt-Hieber, Christoph
last_name: Schmidt Hieber
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
citation:
ama: Schmidt Hieber C, Jonas PM, Bischofberger J. Action potential initiation and
propagation in hippocampal mossy fibre axons. Journal of Physiology. 2008;586(7):1849-1857.
doi:10.1113/jphysiol.2007.150151
apa: Schmidt Hieber, C., Jonas, P. M., & Bischofberger, J. (2008). Action potential
initiation and propagation in hippocampal mossy fibre axons. Journal of Physiology.
Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2007.150151
chicago: Schmidt Hieber, Christoph, Peter M Jonas, and Josef Bischofberger. “Action
Potential Initiation and Propagation in Hippocampal Mossy Fibre Axons.” Journal
of Physiology. Wiley-Blackwell, 2008. https://doi.org/10.1113/jphysiol.2007.150151 .
ieee: C. Schmidt Hieber, P. M. Jonas, and J. Bischofberger, “Action potential initiation
and propagation in hippocampal mossy fibre axons,” Journal of Physiology,
vol. 586, no. 7. Wiley-Blackwell, pp. 1849–57, 2008.
ista: Schmidt Hieber C, Jonas PM, Bischofberger J. 2008. Action potential initiation
and propagation in hippocampal mossy fibre axons. Journal of Physiology. 586(7),
1849–57.
mla: Schmidt Hieber, Christoph, et al. “Action Potential Initiation and Propagation
in Hippocampal Mossy Fibre Axons.” Journal of Physiology, vol. 586, no.
7, Wiley-Blackwell, 2008, pp. 1849–57, doi:10.1113/jphysiol.2007.150151 .
short: C. Schmidt Hieber, P.M. Jonas, J. Bischofberger, Journal of Physiology 586
(2008) 1849–57.
date_created: 2018-12-11T12:05:21Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:27Z
day: '01'
doi: '10.1113/jphysiol.2007.150151 '
extern: 1
intvolume: ' 586'
issue: '7'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375716/
month: '01'
oa: 1
page: 1849 - 57
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2387'
quality_controlled: 0
status: public
title: Action potential initiation and propagation in hippocampal mossy fibre axons
type: journal_article
volume: 586
year: '2008'
...
---
_id: '3824'
abstract:
- lang: eng
text: It is generally thought that transmitter release at mammalian central synapses
is triggered by Ca2+ microdomains, implying loose coupling between presynaptic
Ca2+ channels and Ca2+ sensors of exocytosis. Here we show that Ca2+ channel subunit
immunoreactivity is highly concentrated in the active zone of GABAergic presynaptic
terminals of putative parvalbumin-containing basket cells in the hippocampus.
Paired recording combined with presynaptic patch pipette perfusion revealed that
GABA release at basket cell-granule cell synapses is sensitive to millimolar concentrations
of the fast Ca2+ chelator BAPTA but insensitive to the slow Ca2+ chelator EGTA.
These results show that Ca2+ source and Ca2+ sensor are tightly coupled at this
synapse, with distances in the range of 10-20 nm. Models of Ca2+ inflow-exocytosis
coupling further reveal that the tightness of coupling increases efficacy, speed,
and temporal precision of transmitter release. Thus, tight coupling contributes
to fast feedforward and feedback inhibition in the hippocampal network.
author:
- first_name: Iancu
full_name: Bucurenciu, Iancu
last_name: Bucurenciu
- first_name: Ákos
full_name: Kulik, Ákos
last_name: Kulik
- first_name: Beat
full_name: Schwaller, Beat
last_name: Schwaller
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Bucurenciu I, Kulik Á, Schwaller B, Frotscher M, Jonas PM. Nanodomain coupling
between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter
release at a cortical GABAergic synapse. Neuron. 2008;57(4):536-545. doi:10.1016/j.neuron.2007.12.026
apa: Bucurenciu, I., Kulik, Á., Schwaller, B., Frotscher, M., & Jonas, P. M.
(2008). Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes
fast and efficient transmitter release at a cortical GABAergic synapse. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2007.12.026
chicago: Bucurenciu, Iancu, Ákos Kulik, Beat Schwaller, Michael Frotscher, and Peter
M Jonas. “Nanodomain Coupling between Ca(2+) Channels and Ca2+ Sensors Promotes
Fast and Efficient Transmitter Release at a Cortical GABAergic Synapse.” Neuron.
Elsevier, 2008. https://doi.org/10.1016/j.neuron.2007.12.026.
ieee: I. Bucurenciu, Á. Kulik, B. Schwaller, M. Frotscher, and P. M. Jonas, “Nanodomain
coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient
transmitter release at a cortical GABAergic synapse,” Neuron, vol. 57,
no. 4. Elsevier, pp. 536–45, 2008.
ista: Bucurenciu I, Kulik Á, Schwaller B, Frotscher M, Jonas PM. 2008. Nanodomain
coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient
transmitter release at a cortical GABAergic synapse. Neuron. 57(4), 536–45.
mla: Bucurenciu, Iancu, et al. “Nanodomain Coupling between Ca(2+) Channels and
Ca2+ Sensors Promotes Fast and Efficient Transmitter Release at a Cortical GABAergic
Synapse.” Neuron, vol. 57, no. 4, Elsevier, 2008, pp. 536–45, doi:10.1016/j.neuron.2007.12.026.
short: I. Bucurenciu, Á. Kulik, B. Schwaller, M. Frotscher, P.M. Jonas, Neuron 57
(2008) 536–45.
date_created: 2018-12-11T12:05:22Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:27Z
day: '01'
doi: 10.1016/j.neuron.2007.12.026
extern: 1
intvolume: ' 57'
issue: '4'
month: '01'
page: 536 - 45
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2385'
quality_controlled: 0
status: public
title: Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast
and efficient transmitter release at a cortical GABAergic synapse
type: journal_article
volume: 57
year: '2008'
...
---
_id: '3823'
abstract:
- lang: eng
text: Two studies in this issue of Neuron (Kwon and Castillo and Rebola et al.)
show that the mossy fiber-CA3 pyramidal neuron synapse, a hippocampal synapse
well known for its presynaptic plasticity, exhibits a novel form of long-term
potentiation of NMDAR-mediated currents, which is induced and expressed postsynaptically.
author:
- first_name: Angharad
full_name: Kerr, Angharad M
last_name: Kerr
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Kerr A, Jonas PM. The two sides of hippocampal mossy fiber plasticity (Review).
Neuron. 2008;57(1):5-7. doi:10.1016/j.neuron.2007.12.015
apa: Kerr, A., & Jonas, P. M. (2008). The two sides of hippocampal mossy fiber
plasticity (Review). Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2007.12.015
chicago: Kerr, Angharad, and Peter M Jonas. “The Two Sides of Hippocampal Mossy
Fiber Plasticity (Review).” Neuron. Elsevier, 2008. https://doi.org/10.1016/j.neuron.2007.12.015.
ieee: A. Kerr and P. M. Jonas, “The two sides of hippocampal mossy fiber plasticity
(Review),” Neuron, vol. 57, no. 1. Elsevier, pp. 5–7, 2008.
ista: Kerr A, Jonas PM. 2008. The two sides of hippocampal mossy fiber plasticity
(Review). Neuron. 57(1), 5–7.
mla: Kerr, Angharad, and Peter M. Jonas. “The Two Sides of Hippocampal Mossy Fiber
Plasticity (Review).” Neuron, vol. 57, no. 1, Elsevier, 2008, pp. 5–7,
doi:10.1016/j.neuron.2007.12.015.
short: A. Kerr, P.M. Jonas, Neuron 57 (2008) 5–7.
date_created: 2018-12-11T12:05:22Z
date_published: 2008-01-10T00:00:00Z
date_updated: 2021-01-12T07:52:27Z
day: '10'
doi: 10.1016/j.neuron.2007.12.015
extern: 1
intvolume: ' 57'
issue: '1'
month: '01'
page: 5 - 7
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2388'
quality_controlled: 0
status: public
title: The two sides of hippocampal mossy fiber plasticity (Review)
type: journal_article
volume: 57
year: '2008'
...
---
_id: '3880'
abstract:
- lang: eng
text: We consider imperfect-information parity games in which strategies rely on
observations that provide imperfect information about the history of a play. To
solve such games, i.e., to determine the winning regions of players and corresponding
winning strategies, one can use the subset construction to build an equivalent
perfect-information game. Recently, an algorithm that avoids the inefficient subset
construction has been proposed. The algorithm performs a fixed-point computation
in a lattice of antichains, thus maintaining a succinct representation of state
sets. However, this representation does not allow to recover winning strategies.
In this paper, we build on the antichain approach to develop an algorithm for
constructing the winning strategies in parity games of imperfect information.
We have implemented this algorithm as a prototype. To our knowledge, this is the
first implementation of a procedure for solving imperfect-information parity games
on graphs.
alternative_title:
- LNCS
author:
- first_name: Dietmar
full_name: Berwanger, Dietmar
last_name: Berwanger
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
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: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Sangram
full_name: Raje, Sangram
last_name: Raje
citation:
ama: 'Berwanger D, Chatterjee K, Doyen L, Henzinger TA, Raje S. Strategy construction
for parity games with imperfect information. In: Vol 5201. Schloss Dagstuhl -
Leibniz-Zentrum für Informatik; 2008:325-339. doi:10.1007/978-3-540-85361-9'
apa: 'Berwanger, D., Chatterjee, K., Doyen, L., Henzinger, T. A., & Raje, S.
(2008). Strategy construction for parity games with imperfect information (Vol.
5201, pp. 325–339). Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-540-85361-9'
chicago: Berwanger, Dietmar, Krishnendu Chatterjee, Laurent Doyen, Thomas A Henzinger,
and Sangram Raje. “Strategy Construction for Parity Games with Imperfect Information,”
5201:325–39. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008. https://doi.org/10.1007/978-3-540-85361-9.
ieee: 'D. Berwanger, K. Chatterjee, L. Doyen, T. A. Henzinger, and S. Raje, “Strategy
construction for parity games with imperfect information,” presented at the CONCUR:
Concurrency Theory, 2008, vol. 5201, pp. 325–339.'
ista: 'Berwanger D, Chatterjee K, Doyen L, Henzinger TA, Raje S. 2008. Strategy
construction for parity games with imperfect information. CONCUR: Concurrency
Theory, LNCS, vol. 5201, 325–339.'
mla: Berwanger, Dietmar, et al. Strategy Construction for Parity Games with Imperfect
Information. Vol. 5201, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2008, pp. 325–39, doi:10.1007/978-3-540-85361-9.
short: D. Berwanger, K. Chatterjee, L. Doyen, T.A. Henzinger, S. Raje, in:, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 325–339.
conference:
name: 'CONCUR: Concurrency Theory'
date_created: 2018-12-11T12:05:40Z
date_published: 2008-07-30T00:00:00Z
date_updated: 2023-02-23T11:46:01Z
day: '30'
doi: 10.1007/978-3-540-85361-9
extern: 1
intvolume: ' 5201'
month: '07'
page: 325 - 339
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '2291'
quality_controlled: 0
related_material:
record:
- id: '3863'
relation: later_version
status: public
status: public
title: Strategy construction for parity games with imperfect information
type: conference
volume: 5201
year: '2008'
...
---
_id: '3903'
abstract:
- lang: eng
text: "Background\r\n\r\nThe invasive garden ant, Lasius neglectus, is the most
recently detected pest ant and the first known invasive ant able to become established
and thrive in the temperate regions of Eurasia. In this study, we aim to reconstruct
the invasion history of this ant in Europe analysing 14 populations with three
complementary approaches: genetic microsatellite analysis, chemical analysis of
cuticular hydrocarbon profiles and behavioural observations of aggression behaviour.
We evaluate the relative informative power of the three methodological approaches
and estimate both the number of independent introduction events from a yet unknown
native range somewhere in the Black Sea area, and the invasive potential of the
existing introduced populations.\r\n\r\nResults\r\n\r\nThree clusters of genetically
similar populations were detected, and all but one population had a similar chemical
profile. Aggression between populations could be predicted from their genetic
and chemical distance, and two major clusters of non-aggressive groups of populations
were found. However, populations of L. neglectus did not separate into clear supercolonial
associations, as is typical for other invasive ants.\r\n\r\nConclusion\r\n\r\nThe
three methodological approaches gave consistent and complementary results. All
joint evidence supports the inference that the 14 introduced populations of L.
neglectus in Europe likely arose from only very few independent introductions
from the native range, and that new infestations were typically started through
introductions from other invasive populations. This indicates that existing introduced
populations have a very high invasive potential when the ants are inadvertently
spread by human transport. "
author:
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Falko
full_name: Drijfhout, Falko
last_name: Drijfhout
- first_name: Daniel
full_name: Kronauer, Daniel
last_name: Kronauer
- first_name: Jacobus
full_name: Boomsma, Jacobus
last_name: Boomsma
- first_name: Jes
full_name: Pedersen, Jes
last_name: Pedersen
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Ugelvig LV, Drijfhout F, Kronauer D, Boomsma J, Pedersen J, Cremer S. The
introduction history of invasive garden ants in Europe: integrating genetic, chemical
and behavioural approaches. BMC Biology. 2008;6(11). doi:10.1186/1741-7007-6-11'
apa: 'Ugelvig, L. V., Drijfhout, F., Kronauer, D., Boomsma, J., Pedersen, J., &
Cremer, S. (2008). The introduction history of invasive garden ants in Europe:
integrating genetic, chemical and behavioural approaches. BMC Biology.
BioMed Central. https://doi.org/10.1186/1741-7007-6-11'
chicago: 'Ugelvig, Line V, Falko Drijfhout, Daniel Kronauer, Jacobus Boomsma, Jes
Pedersen, and Sylvia Cremer. “The Introduction History of Invasive Garden Ants
in Europe: Integrating Genetic, Chemical and Behavioural Approaches.” BMC Biology.
BioMed Central, 2008. https://doi.org/10.1186/1741-7007-6-11.'
ieee: 'L. V. Ugelvig, F. Drijfhout, D. Kronauer, J. Boomsma, J. Pedersen, and S.
Cremer, “The introduction history of invasive garden ants in Europe: integrating
genetic, chemical and behavioural approaches,” BMC Biology, vol. 6, no.
11. BioMed Central, 2008.'
ista: 'Ugelvig LV, Drijfhout F, Kronauer D, Boomsma J, Pedersen J, Cremer S. 2008.
The introduction history of invasive garden ants in Europe: integrating genetic,
chemical and behavioural approaches. BMC Biology. 6(11).'
mla: 'Ugelvig, Line V., et al. “The Introduction History of Invasive Garden Ants
in Europe: Integrating Genetic, Chemical and Behavioural Approaches.” BMC Biology,
vol. 6, no. 11, BioMed Central, 2008, doi:10.1186/1741-7007-6-11.'
short: L.V. Ugelvig, F. Drijfhout, D. Kronauer, J. Boomsma, J. Pedersen, S. Cremer,
BMC Biology 6 (2008).
date_created: 2018-12-11T12:05:48Z
date_published: 2008-02-26T00:00:00Z
date_updated: 2021-01-12T07:53:05Z
day: '26'
doi: 10.1186/1741-7007-6-11
extern: '1'
intvolume: ' 6'
issue: '11'
language:
- iso: eng
month: '02'
oa_version: None
publication: BMC Biology
publication_status: published
publisher: BioMed Central
publist_id: '2249'
status: public
title: 'The introduction history of invasive garden ants in Europe: integrating genetic,
chemical and behavioural approaches'
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: '2008'
...
---
_id: '3905'
abstract:
- lang: eng
text: Winged and wingless males coexist in the ant Cardiocondyla obscurior. Wingless
(“ergatoid”) males never leave their maternal colony and fight remorselessly among
each other for the access to emerging females. The peaceful winged males disperse
after about 10 days, but beforehand also mate in the nest. In the first 5 days
of their life, winged males perform a chemical female mimicry that protects them
against attack and even makes them sexually attractive to ergatoid males. When
older, the chemical profile of winged males no longer matches that of virgin females;
nevertheless, they are still tolerated, which so far has been puzzling. Contrasting
this general pattern, we have identified a single aberrant colony in which all
winged males were attacked and killed by the ergatoid males. A comparative analysis
of the morphology and chemical profile of these untypical attacked winged males
and the tolerated males from several normal colonies revealed that normal old
males are still performing some chemical mimicry to the virgin queens, though
less perfect than in their young ages. The anomalous attacked winged males, on
the other hand, had a very different odour to the females. Our study thus exemplifies
that the analysis of rare malfunctioning can add valuable insight on functioning
under normal conditions and allows the conclusion that older winged males from
normal colonies of the ant C. obscurior are guarded through an imperfect chemical
female mimicry, still close enough to protect against attacks by the wingless
fighters yet dissimilar enough not to elicit their sexual interest.
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Patrizia
full_name: D'Ettorre, Patrizia
last_name: D'Ettorre
- first_name: Falko
full_name: Drijfhout, Falko
last_name: Drijfhout
- first_name: Matthew
full_name: Sledge, Matthew
last_name: Sledge
- first_name: Stefano
full_name: Turillazzi, Stefano
last_name: Turillazzi
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
citation:
ama: Cremer S, D’Ettorre P, Drijfhout F, Sledge M, Turillazzi S, Heinze J. Imperfect
chemical female mimicry in males of the ant Cardiocondyla obscurior. Naturwissenschaften.
2008;95(11):1101-1105. doi:10.1007/s00114-008-0430-8
apa: Cremer, S., D’Ettorre, P., Drijfhout, F., Sledge, M., Turillazzi, S., &
Heinze, J. (2008). Imperfect chemical female mimicry in males of the ant Cardiocondyla
obscurior. Naturwissenschaften. Springer. https://doi.org/10.1007/s00114-008-0430-8
chicago: Cremer, Sylvia, Patrizia D’Ettorre, Falko Drijfhout, Matthew Sledge, Stefano
Turillazzi, and Jürgen Heinze. “Imperfect Chemical Female Mimicry in Males of
the Ant Cardiocondyla Obscurior.” Naturwissenschaften. Springer, 2008.
https://doi.org/10.1007/s00114-008-0430-8.
ieee: S. Cremer, P. D’Ettorre, F. Drijfhout, M. Sledge, S. Turillazzi, and J. Heinze,
“Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior,”
Naturwissenschaften, vol. 95, no. 11. Springer, pp. 1101–1105, 2008.
ista: Cremer S, D’Ettorre P, Drijfhout F, Sledge M, Turillazzi S, Heinze J. 2008.
Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior.
Naturwissenschaften. 95(11), 1101–1105.
mla: Cremer, Sylvia, et al. “Imperfect Chemical Female Mimicry in Males of the Ant
Cardiocondyla Obscurior.” Naturwissenschaften, vol. 95, no. 11, Springer,
2008, pp. 1101–05, doi:10.1007/s00114-008-0430-8.
short: S. Cremer, P. D’Ettorre, F. Drijfhout, M. Sledge, S. Turillazzi, J. Heinze,
Naturwissenschaften 95 (2008) 1101–1105.
date_created: 2018-12-11T12:05:48Z
date_published: 2008-08-05T00:00:00Z
date_updated: 2021-01-12T07:53:06Z
day: '05'
doi: 10.1007/s00114-008-0430-8
extern: '1'
intvolume: ' 95'
issue: '11'
language:
- iso: eng
month: '08'
oa_version: None
page: 1101 - 1105
publication: Naturwissenschaften
publication_status: published
publisher: Springer
publist_id: '2246'
status: public
title: Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 95
year: '2008'
...
---
_id: '3907'
abstract:
- lang: eng
text: 'Wingless males of the ant genus Cardiocondyla engage in fatal fighting for
access to female sexual nestmates. Older, heavily sclerotized males are usually
capable of eliminating all younger rivals, whose cuticle is still soft. In Cardiocondyla
sp. A, this type of local mate competition (LMC) has turned the standard pattern
of brood production of social insects upside down, in that mother queens in multi-queen
colonies produce extremely long-lived sons very early in the life cycle of the
colony. Here, we investigated the emergence pattern of sexuals in two species
with LMC, in which males are much less long-lived. Queens of Cardiocondyla obscurior
and Cardiocondyla minutior reared their first sons significantly earlier in multi-queen
than in single-queen societies. In addition, first female sexuals also emerged
earlier in multi-queen colonies, so that early males had mating opportunities.
Hence, the timing of sexual production appears to be well predicted by evolutionary
theory, in particular by local mate and queen–queen competition. '
author:
- first_name: Masaki
full_name: Suefuji, Masaki
last_name: Suefuji
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Jan
full_name: Oettler, Jan
last_name: Oettler
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
citation:
ama: Suefuji M, Cremer S, Oettler J, Heinze J. Queen number influences the timing
of the sexual production in colonies of Cardiocondyla ants. Biology Letters.
2008;4(6):670-673. doi:10.1098/rsbl.2008.0355
apa: Suefuji, M., Cremer, S., Oettler, J., & Heinze, J. (2008). Queen number
influences the timing of the sexual production in colonies of Cardiocondyla ants.
Biology Letters. Royal Society, The. https://doi.org/10.1098/rsbl.2008.0355
chicago: Suefuji, Masaki, Sylvia Cremer, Jan Oettler, and Jürgen Heinze. “Queen
Number Influences the Timing of the Sexual Production in Colonies of Cardiocondyla
Ants.” Biology Letters. Royal Society, The, 2008. https://doi.org/10.1098/rsbl.2008.0355.
ieee: M. Suefuji, S. Cremer, J. Oettler, and J. Heinze, “Queen number influences
the timing of the sexual production in colonies of Cardiocondyla ants,” Biology
Letters, vol. 4, no. 6. Royal Society, The, pp. 670–673, 2008.
ista: Suefuji M, Cremer S, Oettler J, Heinze J. 2008. Queen number influences the
timing of the sexual production in colonies of Cardiocondyla ants. Biology Letters.
4(6), 670–673.
mla: Suefuji, Masaki, et al. “Queen Number Influences the Timing of the Sexual Production
in Colonies of Cardiocondyla Ants.” Biology Letters, vol. 4, no. 6, Royal
Society, The, 2008, pp. 670–73, doi:10.1098/rsbl.2008.0355.
short: M. Suefuji, S. Cremer, J. Oettler, J. Heinze, Biology Letters 4 (2008) 670–673.
date_created: 2018-12-11T12:05:49Z
date_published: 2008-12-23T00:00:00Z
date_updated: 2021-01-12T07:53:07Z
day: '23'
doi: 10.1098/rsbl.2008.0355
extern: '1'
intvolume: ' 4'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 670 - 673
publication: Biology Letters
publication_status: published
publisher: Royal Society, The
publist_id: '2248'
status: public
title: Queen number influences the timing of the sexual production in colonies of
Cardiocondyla ants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2008'
...
---
_id: '3906'
acknowledgement: 'Funding was obtained from the European Community: FP5 EU research-training
network ‘INSECTS’ (JJB SC PD FPD DPH) and FP6 Individual Marie Curie EIF grant (SC),
the Alexander-von-Humboldt Foundation (Feodor-Lynen postdoctoral stipend to SC),
the Danish Natural Science Research Council (JSP), the Danish National Research
Foundation (JJB DRN JSP), and the Austrian Science Fund (BCS FMS CS HK).'
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Falko
full_name: Drijfhout, Falko
last_name: Drijfhout
- first_name: Birgit
full_name: Schlick Steiner, Birgit
last_name: Schlick Steiner
- first_name: Florian
full_name: Steiner, Florian
last_name: Steiner
- first_name: Bernhard
full_name: Seifert, Bernhard
last_name: Seifert
- first_name: David
full_name: Hughes, David
last_name: Hughes
- first_name: Andreas
full_name: Schulz, Andreas
last_name: Schulz
- first_name: Klaus
full_name: Petersen, Klaus
last_name: Petersen
- first_name: Heino
full_name: Konrad, Heino
last_name: Konrad
- first_name: Christian
full_name: Stauffer, Christian
last_name: Stauffer
- first_name: Kadri
full_name: Kiran, Kadri
last_name: Kiran
- first_name: Xavier
full_name: Espadaler, Xavier
last_name: Espadaler
- first_name: Patrizia
full_name: D'Ettorre, Patrizia
last_name: D'Ettorre
- first_name: Nihat
full_name: Aktaç, Nihat
last_name: Aktaç
- first_name: Jørgen
full_name: Eilenberg, Jørgen
last_name: Eilenberg
- first_name: Graeme
full_name: Jones, Graeme
last_name: Jones
- first_name: David
full_name: Nash, David
last_name: Nash
- first_name: Jes
full_name: Pedersen, Jes
last_name: Pedersen
- first_name: Jacobus
full_name: Boomsma, Jacobus
last_name: Boomsma
citation:
ama: Cremer S, Ugelvig LV, Drijfhout F, et al. The evolution of invasiveness in
garden ants. PLoS One. 2008;3(12). doi:10.1371/journal.pone.0003838
apa: Cremer, S., Ugelvig, L. V., Drijfhout, F., Schlick Steiner, B., Steiner, F.,
Seifert, B., … Boomsma, J. (2008). The evolution of invasiveness in garden ants.
PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0003838
chicago: Cremer, Sylvia, Line V Ugelvig, Falko Drijfhout, Birgit Schlick Steiner,
Florian Steiner, Bernhard Seifert, David Hughes, et al. “The Evolution of Invasiveness
in Garden Ants.” PLoS One. Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0003838.
ieee: S. Cremer et al., “The evolution of invasiveness in garden ants,” PLoS
One, vol. 3, no. 12. Public Library of Science, 2008.
ista: Cremer S, Ugelvig LV, Drijfhout F, Schlick Steiner B, Steiner F, Seifert B,
Hughes D, Schulz A, Petersen K, Konrad H, Stauffer C, Kiran K, Espadaler X, D’Ettorre
P, Aktaç N, Eilenberg J, Jones G, Nash D, Pedersen J, Boomsma J. 2008. The evolution
of invasiveness in garden ants. PLoS One. 3(12).
mla: Cremer, Sylvia, et al. “The Evolution of Invasiveness in Garden Ants.” PLoS
One, vol. 3, no. 12, Public Library of Science, 2008, doi:10.1371/journal.pone.0003838.
short: S. Cremer, L.V. Ugelvig, F. Drijfhout, B. Schlick Steiner, F. Steiner, B.
Seifert, D. Hughes, A. Schulz, K. Petersen, H. Konrad, C. Stauffer, K. Kiran,
X. Espadaler, P. D’Ettorre, N. Aktaç, J. Eilenberg, G. Jones, D. Nash, J. Pedersen,
J. Boomsma, PLoS One 3 (2008).
date_created: 2018-12-11T12:05:49Z
date_published: 2008-12-03T00:00:00Z
date_updated: 2021-01-12T07:53:06Z
day: '03'
doi: 10.1371/journal.pone.0003838
extern: '1'
intvolume: ' 3'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '2247'
status: public
title: The evolution of invasiveness in garden ants
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: 3
year: '2008'
...
---
_id: '3939'
abstract:
- lang: eng
text: The priming of a T cell results from its physical interaction with a dendritic
cell (DC) that presents the cognate antigenic peptide. The success rate of such
interactions is extremely low, because the precursor frequency of a naive T cell
recognizing a specific antigen is in the range of 1:10(5)-10(6). To make this
principle practicable, encounter frequencies between DCs and T cells are maximized
within lymph nodes (LNs) that are compact immunological projections of the peripheral
tissue they drain. But LNs are more than passive meeting places for DCs that immigrated
from the tissue and lymphocytes that recirculated via the blood. The microanatomy
of the LN stroma actively organizes the cellular encounters by providing preformed
migration tracks that create dynamic but highly ordered movement patterns. LN
architecture further acts as a sophisticated filtration system that sieves the
incoming interstitial fluid at different levels and guarantees that immunologically
relevant antigens are loaded on DCs or B cells while inert substances are channeled
back into the blood circulation. This review focuses on the non-hematopoietic
infrastructure of the lymph node. We describe the association between fibroblastic
reticular cell, conduit, DC, and T cell as the essential functional unit of the
T-cell cortex.
author:
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Lämmermann T, Sixt MK. The microanatomy of T-cell responses. Immunological
Reviews. 2008;221(1):26-43. doi:10.1111/j.1600-065X.2008.00592.x
apa: Lämmermann, T., & Sixt, M. K. (2008). The microanatomy of T-cell responses.
Immunological Reviews. Wiley-Blackwell. https://doi.org/10.1111/j.1600-065X.2008.00592.x
chicago: Lämmermann, Tim, and Michael K Sixt. “The Microanatomy of T-Cell Responses.”
Immunological Reviews. Wiley-Blackwell, 2008. https://doi.org/10.1111/j.1600-065X.2008.00592.x.
ieee: T. Lämmermann and M. K. Sixt, “The microanatomy of T-cell responses,” Immunological
Reviews, vol. 221, no. 1. Wiley-Blackwell, pp. 26–43, 2008.
ista: Lämmermann T, Sixt MK. 2008. The microanatomy of T-cell responses. Immunological
Reviews. 221(1), 26–43.
mla: Lämmermann, Tim, and Michael K. Sixt. “The Microanatomy of T-Cell Responses.”
Immunological Reviews, vol. 221, no. 1, Wiley-Blackwell, 2008, pp. 26–43,
doi:10.1111/j.1600-065X.2008.00592.x.
short: T. Lämmermann, M.K. Sixt, Immunological Reviews 221 (2008) 26–43.
date_created: 2018-12-11T12:06:00Z
date_published: 2008-02-07T00:00:00Z
date_updated: 2021-01-12T07:53:20Z
day: '07'
doi: 10.1111/j.1600-065X.2008.00592.x
extern: '1'
intvolume: ' 221'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 26 - 43
publication: Immunological Reviews
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2187'
status: public
title: The microanatomy of T-cell responses
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 221
year: '2008'
...
---
_id: '3940'
abstract:
- lang: eng
text: Until recently little information was available on the molecular details of
the extracellular matrix (ECM) of secondary lymphoid tissues. There is now growing
evidence that these ECMs are unique structures, combining characteristics of basement
membranes and interstitial or fibrillar matrices, resulting in scaffolds that
are strong and highly flexible and, in certain secondary lymphoid compartments,
also forming conduit networks for rapid fluid transport. This review will address
the structural characteristics of the ECM of the murine spleen and its potential
role as an organizer of immune cell compartments, with reference to the lymph
node where relevant.
author:
- first_name: Zerina
full_name: Lokmic, Zerina
last_name: Lokmic
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Susanna
full_name: Cardell, Susanna
last_name: Cardell
- first_name: Rupert
full_name: Hallmann, Rupert
last_name: Hallmann
- first_name: Lydia
full_name: Sorokin, Lydia
last_name: Sorokin
citation:
ama: Lokmic Z, Lämmermann T, Sixt MK, Cardell S, Hallmann R, Sorokin L. The extracellular
matrix of the spleen as a potential organizer of immune cell compartments. Seminars
in Immunology. 2008;20(1):4-13. doi:10.1016/j.smim.2007.12.009
apa: Lokmic, Z., Lämmermann, T., Sixt, M. K., Cardell, S., Hallmann, R., & Sorokin,
L. (2008). The extracellular matrix of the spleen as a potential organizer of
immune cell compartments. Seminars in Immunology. Academic Press. https://doi.org/10.1016/j.smim.2007.12.009
chicago: Lokmic, Zerina, Tim Lämmermann, Michael K Sixt, Susanna Cardell, Rupert
Hallmann, and Lydia Sorokin. “The Extracellular Matrix of the Spleen as a Potential
Organizer of Immune Cell Compartments.” Seminars in Immunology. Academic
Press, 2008. https://doi.org/10.1016/j.smim.2007.12.009.
ieee: Z. Lokmic, T. Lämmermann, M. K. Sixt, S. Cardell, R. Hallmann, and L. Sorokin,
“The extracellular matrix of the spleen as a potential organizer of immune cell
compartments,” Seminars in Immunology, vol. 20, no. 1. Academic Press,
pp. 4–13, 2008.
ista: Lokmic Z, Lämmermann T, Sixt MK, Cardell S, Hallmann R, Sorokin L. 2008. The
extracellular matrix of the spleen as a potential organizer of immune cell compartments.
Seminars in Immunology. 20(1), 4–13.
mla: Lokmic, Zerina, et al. “The Extracellular Matrix of the Spleen as a Potential
Organizer of Immune Cell Compartments.” Seminars in Immunology, vol. 20,
no. 1, Academic Press, 2008, pp. 4–13, doi:10.1016/j.smim.2007.12.009.
short: Z. Lokmic, T. Lämmermann, M.K. Sixt, S. Cardell, R. Hallmann, L. Sorokin,
Seminars in Immunology 20 (2008) 4–13.
date_created: 2018-12-11T12:06:00Z
date_published: 2008-02-01T00:00:00Z
date_updated: 2021-01-12T07:53:20Z
day: '01'
doi: 10.1016/j.smim.2007.12.009
extern: 1
intvolume: ' 20'
issue: '1'
month: '02'
page: 4 - 13
publication: Seminars in Immunology
publication_status: published
publisher: Academic Press
publist_id: '2188'
quality_controlled: 0
status: public
title: The extracellular matrix of the spleen as a potential organizer of immune cell
compartments
type: journal_article
volume: 20
year: '2008'
...
---
_id: '3970'
abstract:
- lang: eng
text: 'While genome-wide gene expression data are generated at an increasing rate,
the repertoire of approaches for pattern discovery in these data is still limited.
Identifying subtle patterns of interest in large amounts of data (tens of thousands
of profiles) associated with a certain level of noise remains a challenge. A microarray
time series was recently generated to study the transcriptional program of the
mouse segmentation clock, a biological oscillator associated with the periodic
formation of the segments of the body axis. A method related to Fourier analysis,
the Lomb-Scargle periodogram, was used to detect periodic profiles in the dataset,
leading to the identification of a novel set of cyclic genes associated with the
segmentation clock. Here, we applied to the same microarray time series dataset
four distinct mathematical methods to identify significant patterns in gene expression
profiles. These methods are called: Phase consistency, Address reduction, Cyclohedron
test and Stable persistence, and are based on different conceptual frameworks
that are either hypothesis- or data-driven. Some of the methods, unlike Fourier
transforms, are not dependent on the assumption of periodicity of the pattern
of interest. Remarkably, these methods identified blindly the expression profiles
of known cyclic genes as the most significant patterns in the dataset. Many candidate
genes predicted by more than one approach appeared to be true positive cyclic
genes and will be of particular interest for future research. In addition, these
methods predicted novel candidate cyclic genes that were consistent with previous
biological knowledge and experimental validation in mouse embryos. Our results
demonstrate the utility of these novel pattern detection strategies, notably for
detection of periodic profiles, and suggest that combining several distinct mathematical
approaches to analyze microarray datasets is a valuable strategy for identifying
genes that exhibit novel, interesting transcriptional patterns.'
acknowledgement: This research was partially supported by DARPA grant HR 0011-05-1-0057.
HE and YM mathematical work was supported by DARPA grant HR0011-05-1-0007. AS research
was supported by a Lucent Technologies Bell Labs Graduate Research. Fellowship;
AK and MR research was supported by NIH grant GM U54 GM74942; and SA research was
supported by Association pour la Recherche sur le Cancer (ARC), France. OP, AM,
MLD, EG and GH research was supported by the Stowers Institute for Medical Research.
OP is a Howard Hughes Medical Institute Investigator.
author:
- first_name: Mary
full_name: Dequéant, Mary-Lee
last_name: Dequéant
- first_name: Sebastian
full_name: Ahnert, Sebastian
last_name: Ahnert
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Thomas
full_name: Fink, Thomas M
last_name: Fink
- first_name: Earl
full_name: Glynn, Earl F
last_name: Glynn
- first_name: Gaye
full_name: Hattem, Gaye
last_name: Hattem
- first_name: Andrzej
full_name: Kudlicki, Andrzej
last_name: Kudlicki
- first_name: Yuriy
full_name: Mileyko, Yuriy
last_name: Mileyko
- first_name: Jason
full_name: Morton, Jason
last_name: Morton
- first_name: Arcady
full_name: Mushegian, Arcady R
last_name: Mushegian
- first_name: Lior
full_name: Pachter, Lior
last_name: Pachter
- first_name: Maga
full_name: Rowicka, Maga
last_name: Rowicka
- first_name: Anne
full_name: Shiu, Anne
last_name: Shiu
- first_name: Bernd
full_name: Sturmfels, Bernd
last_name: Sturmfels
- first_name: Olivier
full_name: Pourquie, Olivier
last_name: Pourquie
citation:
ama: Dequéant M, Ahnert S, Edelsbrunner H, et al. Comparison of pattern detection
methods in microarray time series of the segmentation clock. PLoS One.
2008;3(8). doi:10.1371/journal.pone.0002856
apa: Dequéant, M., Ahnert, S., Edelsbrunner, H., Fink, T., Glynn, E., Hattem, G.,
… Pourquie, O. (2008). Comparison of pattern detection methods in microarray time
series of the segmentation clock. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0002856
chicago: Dequéant, Mary, Sebastian Ahnert, Herbert Edelsbrunner, Thomas Fink, Earl
Glynn, Gaye Hattem, Andrzej Kudlicki, et al. “Comparison of Pattern Detection
Methods in Microarray Time Series of the Segmentation Clock.” PLoS One.
Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0002856.
ieee: M. Dequéant et al., “Comparison of pattern detection methods in microarray
time series of the segmentation clock,” PLoS One, vol. 3, no. 8. Public
Library of Science, 2008.
ista: Dequéant M, Ahnert S, Edelsbrunner H, Fink T, Glynn E, Hattem G, Kudlicki
A, Mileyko Y, Morton J, Mushegian A, Pachter L, Rowicka M, Shiu A, Sturmfels B,
Pourquie O. 2008. Comparison of pattern detection methods in microarray time series
of the segmentation clock. PLoS One. 3(8).
mla: Dequéant, Mary, et al. “Comparison of Pattern Detection Methods in Microarray
Time Series of the Segmentation Clock.” PLoS One, vol. 3, no. 8, Public
Library of Science, 2008, doi:10.1371/journal.pone.0002856.
short: M. Dequéant, S. Ahnert, H. Edelsbrunner, T. Fink, E. Glynn, G. Hattem, A.
Kudlicki, Y. Mileyko, J. Morton, A. Mushegian, L. Pachter, M. Rowicka, A. Shiu,
B. Sturmfels, O. Pourquie, PLoS One 3 (2008).
date_created: 2018-12-11T12:06:11Z
date_published: 2008-08-06T00:00:00Z
date_updated: 2021-01-12T07:53:33Z
day: '06'
doi: 10.1371/journal.pone.0002856
extern: 1
intvolume: ' 3'
issue: '8'
month: '08'
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '2157'
quality_controlled: 0
status: public
title: Comparison of pattern detection methods in microarray time series of the segmentation
clock
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: 3
year: '2008'
...
---
_id: '3971'
abstract:
- lang: eng
text: The Reeb graph is a useful tool in visualizing real-valued data obtained from
computational simulations of physical processes. We characterize the evolution
of the Reeb graph of a time-varying continuous function defined in three-dimensional
space. We show how to maintain the Reeb graph over time and compress the entire
sequence of Reeb graphs into a single, partially persistent data structure, and
augment this data structure with Betti numbers to describe the topology of level
sets and with path seeds to assist in the fast extraction of level sets for visualization.
author:
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Ajith
full_name: Mascarenhas, Ajith
last_name: Mascarenhas
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
- first_name: Jack
full_name: Snoeyink, Jack
last_name: Snoeyink
citation:
ama: 'Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. Time-varying
Reeb graphs for continuous space-time data. Computational Geometry: Theory
and Applications. 2008;41(3):149-166. doi:10.1016/j.comgeo.2007.11.001'
apa: 'Edelsbrunner, H., Harer, J., Mascarenhas, A., Pascucci, V., & Snoeyink,
J. (2008). Time-varying Reeb graphs for continuous space-time data. Computational
Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2007.11.001'
chicago: 'Edelsbrunner, Herbert, John Harer, Ajith Mascarenhas, Valerio Pascucci,
and Jack Snoeyink. “Time-Varying Reeb Graphs for Continuous Space-Time Data.”
Computational Geometry: Theory and Applications. Elsevier, 2008. https://doi.org/10.1016/j.comgeo.2007.11.001.'
ieee: 'H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, and J. Snoeyink,
“Time-varying Reeb graphs for continuous space-time data,” Computational Geometry:
Theory and Applications, vol. 41, no. 3. Elsevier, pp. 149–166, 2008.'
ista: 'Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. 2008. Time-varying
Reeb graphs for continuous space-time data. Computational Geometry: Theory and
Applications. 41(3), 149–166.'
mla: 'Edelsbrunner, Herbert, et al. “Time-Varying Reeb Graphs for Continuous Space-Time
Data.” Computational Geometry: Theory and Applications, vol. 41, no. 3,
Elsevier, 2008, pp. 149–66, doi:10.1016/j.comgeo.2007.11.001.'
short: 'H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, J. Snoeyink, Computational
Geometry: Theory and Applications 41 (2008) 149–166.'
date_created: 2018-12-11T12:06:12Z
date_published: 2008-11-01T00:00:00Z
date_updated: 2021-01-12T07:53:34Z
day: '01'
doi: 10.1016/j.comgeo.2007.11.001
extern: 1
intvolume: ' 41'
issue: '3'
month: '11'
page: 149 - 166
publication: 'Computational Geometry: Theory and Applications'
publication_status: published
publisher: Elsevier
publist_id: '2158'
quality_controlled: 0
status: public
title: Time-varying Reeb graphs for continuous space-time data
type: journal_article
volume: 41
year: '2008'
...
---
_id: '3969'
abstract:
- lang: eng
text: Persistent homology is an algebraic tool for measuring topological features
of shapes and functions. It casts the multi-scale organization we frequently observe
in nature into a mathematical formalism. Here we give a record of the short history
of persistent homology and present its basic concepts. Besides the mathematics
we focus on algorithms and mention the various connections to applications, including
to biomolecules, biological networks, data analysis, and geometric modeling.
acknowledgement: Supported in part by DARPA under grants HR0011-05-1-0007 and HR0011-05-0057
and by the NSF under grant DBI-06-06873.
alternative_title:
- Contemporary Mathematics
author:
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
citation:
ama: 'Edelsbrunner H, Harer J. Persistent homology - a survey. In: Surveys on
Discrete and Computational Geometry: Twenty Years Later. American Mathematical
Society; 2008:257-282.'
apa: 'Edelsbrunner, H., & Harer, J. (2008). Persistent homology - a survey.
In Surveys on Discrete and Computational Geometry: Twenty Years Later (pp.
257–282). American Mathematical Society.'
chicago: 'Edelsbrunner, Herbert, and John Harer. “Persistent Homology - a Survey.”
In Surveys on Discrete and Computational Geometry: Twenty Years Later,
257–82. American Mathematical Society, 2008.'
ieee: 'H. Edelsbrunner and J. Harer, “Persistent homology - a survey,” in Surveys
on Discrete and Computational Geometry: Twenty Years Later, American Mathematical
Society, 2008, pp. 257–282.'
ista: 'Edelsbrunner H, Harer J. 2008.Persistent homology - a survey. In: Surveys
on Discrete and Computational Geometry: Twenty Years Later. Contemporary Mathematics,
, 257–282.'
mla: 'Edelsbrunner, Herbert, and John Harer. “Persistent Homology - a Survey.” Surveys
on Discrete and Computational Geometry: Twenty Years Later, American Mathematical
Society, 2008, pp. 257–82.'
short: 'H. Edelsbrunner, J. Harer, in:, Surveys on Discrete and Computational Geometry:
Twenty Years Later, American Mathematical Society, 2008, pp. 257–282.'
date_created: 2018-12-11T12:06:11Z
date_published: 2008-03-28T00:00:00Z
date_updated: 2021-01-12T07:53:33Z
day: '28'
extern: 1
month: '03'
page: 257 - 282
publication: 'Surveys on Discrete and Computational Geometry: Twenty Years Later'
publication_status: published
publisher: American Mathematical Society
publist_id: '2156'
quality_controlled: 0
status: public
title: Persistent homology - a survey
type: book_chapter
year: '2008'
...
---
_id: '4141'
abstract:
- lang: eng
text: The zyxin-related LPP protein is localized at focal adhesions and cell-cell
contacts and is involved in the regulation of smooth muscle cell migration. A
known interaction partner of LPP in human is the tumor suppressor protein SCRIB.
Knocking down scrib expression c uring zebrafish embryonic development results
in defects of convergence and extension (C&E) movements, which occur during
gastrulation and mediate elongation of the anterior-posterior body axis. Mediolateral
cell polarization underlying C&E is regulated by a noncanonical Writ signaling
pathway constituting the vertebrate planar cell polarity (PCP) pathway. Here,
we investigated the role of Lpp during early zebrafish development. We show that
morpholino knockdown of Ipp results in defects of C&E, phenocopying noncanonical
Wnt signaling mutants. Time-lapse analysis associates the defective dorsal convergence
movements with a reduced ability to migrate along straight paths. In addition,
expression of Lpp is significantly reduced in Wnt11 morphants and in embryos overexpressing
Wnt11 or a dominant-negative form of Rho kinase 2, which is a downstream effector
of Wnt11, Suggesting that Lpp expression is dependent on noncanonical Wnt signaling.
Finally, we demonstrate that Lpp interacts with the PCP protein Scrib in zebrafish,
and that Lpp and Scrib cooperate for the mediation of C&E. (C) 2008 Elsevier
Inc. All rights reserved.
article_processing_charge: No
author:
- first_name: Hilke
full_name: Vervenne, Hilke
last_name: Vervenne
- first_name: Koen
full_name: Crombez, Koen
last_name: Crombez
- first_name: Kathleen
full_name: Lambaerts, Kathleen
last_name: Lambaerts
- first_name: Lara
full_name: Carvalho, Lara
last_name: Carvalho
- first_name: Mathias
full_name: Köppen, Mathias
last_name: Köppen
- 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: Wim
full_name: Van De Ven, Wim
last_name: Van De Ven
- first_name: Marleen
full_name: Petit, Marleen
last_name: Petit
citation:
ama: Vervenne H, Crombez K, Lambaerts K, et al. Lpp is involved in Wnt/PCP signaling
and acts together with Scrib to mediate convergence and extension movements during
zebrafish gastrulation. Developmental Biology. 2008;320(1):267-277. doi:10.1016/j.ydbio.2008.05.529
apa: Vervenne, H., Crombez, K., Lambaerts, K., Carvalho, L., Köppen, M., Heisenberg,
C.-P. J., … Petit, M. (2008). Lpp is involved in Wnt/PCP signaling and acts together
with Scrib to mediate convergence and extension movements during zebrafish gastrulation.
Developmental Biology. Elsevier. https://doi.org/10.1016/j.ydbio.2008.05.529
chicago: Vervenne, Hilke, Koen Crombez, Kathleen Lambaerts, Lara Carvalho, Mathias
Köppen, Carl-Philipp J Heisenberg, Wim Van De Ven, and Marleen Petit. “Lpp Is
Involved in Wnt/PCP Signaling and Acts Together with Scrib to Mediate Convergence
and Extension Movements during Zebrafish Gastrulation.” Developmental Biology.
Elsevier, 2008. https://doi.org/10.1016/j.ydbio.2008.05.529.
ieee: H. Vervenne et al., “Lpp is involved in Wnt/PCP signaling and acts
together with Scrib to mediate convergence and extension movements during zebrafish
gastrulation,” Developmental Biology, vol. 320, no. 1. Elsevier, pp. 267–277,
2008.
ista: Vervenne H, Crombez K, Lambaerts K, Carvalho L, Köppen M, Heisenberg C-PJ,
Van De Ven W, Petit M. 2008. Lpp is involved in Wnt/PCP signaling and acts together
with Scrib to mediate convergence and extension movements during zebrafish gastrulation.
Developmental Biology. 320(1), 267–277.
mla: Vervenne, Hilke, et al. “Lpp Is Involved in Wnt/PCP Signaling and Acts Together
with Scrib to Mediate Convergence and Extension Movements during Zebrafish Gastrulation.”
Developmental Biology, vol. 320, no. 1, Elsevier, 2008, pp. 267–77, doi:10.1016/j.ydbio.2008.05.529.
short: H. Vervenne, K. Crombez, K. Lambaerts, L. Carvalho, M. Köppen, C.-P.J. Heisenberg,
W. Van De Ven, M. Petit, Developmental Biology 320 (2008) 267–277.
date_created: 2018-12-11T12:07:11Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2021-01-12T07:54:48Z
day: '01'
doi: 10.1016/j.ydbio.2008.05.529
extern: '1'
intvolume: ' 320'
issue: '1'
language:
- iso: eng
month: '08'
oa_version: None
page: 267 - 277
publication: Developmental Biology
publication_status: published
publisher: Elsevier
publist_id: '1978'
status: public
title: Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate
convergence and extension movements during zebrafish gastrulation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 320
year: '2008'
...
---
_id: '4161'
abstract:
- lang: eng
text: Handedness of the vertebrate body plan critically depends on transient embryonic
structures/ organs that generate cilia-dependent leftward fluid flow within constrained
extracellular environments. Although the function of ciliated organs in laterality
determination has been extensively studied, how they are formed during embryogenesis
is still poorly understood. Here we show that Kupffer's vesicle (KV), the zebrafish
organ of laterality, arises from a surface epithelium previously thought to adopt
exclusively extra-embryonic fates. Live multi-photon confocal imaging reveals
that surface epithelial cells undergo Nodal/TGF beta signalling-dependent ingression
at the dorsal germ ring margin prior to gastrulation, to give rise to dorsal forerunner
cells (DFCs), the precursors of KV. DFCs then migrate attached to the overlying
surface epithelium and rearrange into rosette-like epithelial structures at the
end of gastrulation. During early somitogenesis, these epithelial rosettes coalesce
into a single rosette that differentiates into the KV with a ciliated lumen at
its apical centre. Our results provide novel insights into the morphogenetic transformations
that shape the laterality organ in zebrafish and suggest a conserved progenitor
role of the surface epithelium during laterality organ formation in vertebrates.
article_processing_charge: No
author:
- first_name: Pablo
full_name: Oteíza, Pablo
last_name: Oteíza
- first_name: Mathias
full_name: Köppen, Mathias
last_name: Köppen
- first_name: Miguel
full_name: Concha, Miguel
last_name: Concha
- 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: Oteíza P, Köppen M, Concha M, Heisenberg C-PJ. Origin and shaping of the laterality
organ in zebrafish. Development. 2008;135(16):2807-2813. doi:10.1242/dev.022228
apa: Oteíza, P., Köppen, M., Concha, M., & Heisenberg, C.-P. J. (2008). Origin
and shaping of the laterality organ in zebrafish. Development. Company
of Biologists. https://doi.org/10.1242/dev.022228
chicago: Oteíza, Pablo, Mathias Köppen, Miguel Concha, and Carl-Philipp J Heisenberg.
“Origin and Shaping of the Laterality Organ in Zebrafish.” Development.
Company of Biologists, 2008. https://doi.org/10.1242/dev.022228.
ieee: P. Oteíza, M. Köppen, M. Concha, and C.-P. J. Heisenberg, “Origin and shaping
of the laterality organ in zebrafish,” Development, vol. 135, no. 16. Company
of Biologists, pp. 2807–2813, 2008.
ista: Oteíza P, Köppen M, Concha M, Heisenberg C-PJ. 2008. Origin and shaping of
the laterality organ in zebrafish. Development. 135(16), 2807–2813.
mla: Oteíza, Pablo, et al. “Origin and Shaping of the Laterality Organ in Zebrafish.”
Development, vol. 135, no. 16, Company of Biologists, 2008, pp. 2807–13,
doi:10.1242/dev.022228.
short: P. Oteíza, M. Köppen, M. Concha, C.-P.J. Heisenberg, Development 135 (2008)
2807–2813.
date_created: 2018-12-11T12:07:19Z
date_published: 2008-08-15T00:00:00Z
date_updated: 2021-01-12T07:54:57Z
day: '15'
doi: 10.1242/dev.022228
extern: '1'
intvolume: ' 135'
issue: '16'
language:
- iso: eng
month: '08'
oa_version: None
page: 2807 - 2813
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '1956'
status: public
title: Origin and shaping of the laterality organ in zebrafish
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 135
year: '2008'
...
---
_id: '4190'
abstract:
- lang: eng
text: During vertebrate gastrulation, cells forming the prechordal plate undergo
directed migration as a cohesive cluster. Recent studies revealed that E-cadherin-mediated
coherence between these cells plays an important role in effective anterior migration,
and that platelet-derived growth factor (Pdgf) appears to act as a guidance cue
in this process. However, the mechanisms underlying this process at the individual
cell level remain poorly understood. We have identified miles apart (mil) as a
suppressor of defective anterior migration of the prospective prechordal plate
in silberblick (slb)/wnt11 mutant embryos, in which E-cadherin-mediated coherence
of cell movement is reduced. mil encodes Edg5, a sphingosine-1-phosphate (S1P)
receptor belonging to a family of five G-protein-coupled receptors (S1PRs). S1P
is a lipid signalling molecule that has been implicated in regulating cytoskeletal
rearrangements, cell motility and cell adhesion in a variety of cell types. We
examined the roles of Mil in anterior migration of prechordal plate progenitor
cells and found that, in slb embryos injected with mil-MO, cells migrate with
increased motility but decreased directionality, without restoring the coherence
of cell migration. This indicates that prechordal plate progenitor cells can migrate
effectively as individuals, as well as in a coherent cluster of cells. Moreover,
we demonstrate that Mil regulates cell motility and polarisation through Pdgf
and its intracellular effecter PI3K, but modulates cell coherence independently
of the Pdgf/PI3K pathway, thus co-ordinating cell motility and coherence. These
results suggest that the net migration of prechordal plate progenitors is determined
by different parameters, including motility, persistence and coherence.
article_processing_charge: No
author:
- first_name: Masatake
full_name: Kai, Masatake
last_name: Kai
- 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: Masazumi
full_name: Tada, Masazumi
last_name: Tada
citation:
ama: Kai M, Heisenberg C-PJ, Tada M. Sphingosine-1-phosphate receptors regulate
individual cell behaviours underlying the directed migration of prechordal plate
progenitor cells during zebrafish gastrulation. Development. 2008;135(18):3043-3051.
doi:10.1242/dev.020396
apa: Kai, M., Heisenberg, C.-P. J., & Tada, M. (2008). Sphingosine-1-phosphate
receptors regulate individual cell behaviours underlying the directed migration
of prechordal plate progenitor cells during zebrafish gastrulation. Development.
Company of Biologists. https://doi.org/10.1242/dev.020396
chicago: Kai, Masatake, Carl-Philipp J Heisenberg, and Masazumi Tada. “Sphingosine-1-Phosphate
Receptors Regulate Individual Cell Behaviours Underlying the Directed Migration
of Prechordal Plate Progenitor Cells during Zebrafish Gastrulation.” Development.
Company of Biologists, 2008. https://doi.org/10.1242/dev.020396.
ieee: M. Kai, C.-P. J. Heisenberg, and M. Tada, “Sphingosine-1-phosphate receptors
regulate individual cell behaviours underlying the directed migration of prechordal
plate progenitor cells during zebrafish gastrulation,” Development, vol.
135, no. 18. Company of Biologists, pp. 3043–3051, 2008.
ista: Kai M, Heisenberg C-PJ, Tada M. 2008. Sphingosine-1-phosphate receptors regulate
individual cell behaviours underlying the directed migration of prechordal plate
progenitor cells during zebrafish gastrulation. Development. 135(18), 3043–3051.
mla: Kai, Masatake, et al. “Sphingosine-1-Phosphate Receptors Regulate Individual
Cell Behaviours Underlying the Directed Migration of Prechordal Plate Progenitor
Cells during Zebrafish Gastrulation.” Development, vol. 135, no. 18, Company
of Biologists, 2008, pp. 3043–51, doi:10.1242/dev.020396.
short: M. Kai, C.-P.J. Heisenberg, M. Tada, Development 135 (2008) 3043–3051.
date_created: 2018-12-11T12:07:29Z
date_published: 2008-09-15T00:00:00Z
date_updated: 2021-01-12T07:55:11Z
day: '15'
doi: 10.1242/dev.020396
extern: '1'
intvolume: ' 135'
issue: '18'
language:
- iso: eng
month: '09'
oa_version: None
page: 3043 - 3051
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '1928'
status: public
title: Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying
the directed migration of prechordal plate progenitor cells during zebrafish gastrulation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 135
year: '2008'
...
---
_id: '4384'
abstract:
- lang: eng
text: |-
Model checking software transactional memories (STMs) is difficult because of the unbounded number, length, and delay of concurrent transactions and the unbounded size of the memory. We show that, under certain conditions, the verification problem can be reduced to a finite-state problem, and we illustrate the use of the method by proving the correctness of several STMs, including two-phase locking, DSTM, TL2, and optimistic concurrency control. The safety properties we consider include strict serializability and opacity; the liveness properties include obstruction freedom, livelock freedom, and wait freedom.
Our main contribution lies in the structure of the proofs, which are largely automated and not restricted to the STMs mentioned above. In a first step we show that every STM that enjoys certain structural properties either violates a safety or liveness requirement on some program with two threads and two shared variables, or satisfies the requirement on all programs. In the second step we use a model checker to prove the requirement for the STM applied to a most general program with two threads and two variables. In the safety case, the model checker constructs a simulation relation between two carefully constructed finite-state transition systems, one representing the given STM applied to a most general program, and the other representing a most liberal safe STM applied to the same program. In the liveness case, the model checker analyzes fairness conditions on the given STM transition system.
author:
- first_name: Rachid
full_name: Guerraoui, Rachid
last_name: Guerraoui
- first_name: Thomas A
full_name: Thomas Henzinger
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: Vasu
full_name: Vasu Singh
id: 4DAE2708-F248-11E8-B48F-1D18A9856A87
last_name: Singh
citation:
ama: 'Guerraoui R, Henzinger TA, Jobstmann B, Singh V. Model checking transactional
memories. In: ACM; 2008:372-382. doi:10.1145/1375581.1375626'
apa: 'Guerraoui, R., Henzinger, T. A., Jobstmann, B., & Singh, V. (2008). Model
checking transactional memories (pp. 372–382). Presented at the PLDI: Programming
Languages Design and Implementation, ACM. https://doi.org/10.1145/1375581.1375626'
chicago: Guerraoui, Rachid, Thomas A Henzinger, Barbara Jobstmann, and Vasu Singh.
“Model Checking Transactional Memories,” 372–82. ACM, 2008. https://doi.org/10.1145/1375581.1375626.
ieee: 'R. Guerraoui, T. A. Henzinger, B. Jobstmann, and V. Singh, “Model checking
transactional memories,” presented at the PLDI: Programming Languages Design and
Implementation, 2008, pp. 372–382.'
ista: 'Guerraoui R, Henzinger TA, Jobstmann B, Singh V. 2008. Model checking transactional
memories. PLDI: Programming Languages Design and Implementation, 372–382.'
mla: Guerraoui, Rachid, et al. Model Checking Transactional Memories. ACM,
2008, pp. 372–82, doi:10.1145/1375581.1375626.
short: R. Guerraoui, T.A. Henzinger, B. Jobstmann, V. Singh, in:, ACM, 2008, pp.
372–382.
conference:
name: 'PLDI: Programming Languages Design and Implementation'
date_created: 2018-12-11T12:08:34Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:34Z
day: '01'
doi: 10.1145/1375581.1375626
extern: 1
file:
- access_level: open_access
checksum: 1238258a27f212fc1a2050a9a246da20
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:05Z
date_updated: 2020-07-14T12:46:28Z
file_id: '5054'
file_name: IST-2012-74-v1+1_Model_checking_transactional_memories.pdf
file_size: 201583
relation: main_file
file_date_updated: 2020-07-14T12:46:28Z
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/model_checking_transactional_memories.pdf
month: '01'
oa: 1
page: 372 - 382
publication_status: published
publisher: ACM
publist_id: '1073'
quality_controlled: 0
status: public
title: Model checking transactional memories
type: conference
year: '2008'
...
---
_id: '4386'
abstract:
- lang: eng
text: We introduce the notion of permissiveness in transactional memories (TM).
Intuitively, a TM is permissive if it never aborts a transaction when it need
not. More specifically, a TM is permissive with respect to a safety property p
if the TM accepts every history that satisfies p. Permissiveness, like safety
and liveness, can be used as a metric to compare TMs. We illustrate that it is
impractical to achieve permissiveness deterministically, and then show how randomization
can be used to achieve permissiveness efficiently. We introduce Adaptive Validation
STM (AVSTM), which is probabilistically permissive with respect to opacity; that
is, every opaque history is accepted by AVSTM with positive probability. Moreover,
AVSTM guarantees lock freedom. Owing to its permissiveness, AVSTM outperforms
other STMs by up to 40% in read dominated workloads in high contention scenarios.
But, in low contention scenarios, the book-keeping done by AVSTM to achieve permissiveness
makes AVSTM, on average, 20-30% worse than existing STMs.
acknowledgement: This research was supported by the Swiss National Science Foundation.
alternative_title:
- LNCS
author:
- first_name: Rachid
full_name: Guerraoui, Rachid
last_name: Guerraoui
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Vasu
full_name: Vasu Singh
id: 4DAE2708-F248-11E8-B48F-1D18A9856A87
last_name: Singh
citation:
ama: 'Guerraoui R, Henzinger TA, Singh V. Permissiveness in transactional memories.
In: Vol 5218. Springer; 2008:305-319. doi:10.1007/978-3-540-87779-0_21'
apa: 'Guerraoui, R., Henzinger, T. A., & Singh, V. (2008). Permissiveness in
transactional memories (Vol. 5218, pp. 305–319). Presented at the DISC: Distributed
Computing, Springer. https://doi.org/10.1007/978-3-540-87779-0_21'
chicago: Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Permissiveness
in Transactional Memories,” 5218:305–19. Springer, 2008. https://doi.org/10.1007/978-3-540-87779-0_21.
ieee: 'R. Guerraoui, T. A. Henzinger, and V. Singh, “Permissiveness in transactional
memories,” presented at the DISC: Distributed Computing, 2008, vol. 5218, pp.
305–319.'
ista: 'Guerraoui R, Henzinger TA, Singh V. 2008. Permissiveness in transactional
memories. DISC: Distributed Computing, LNCS, vol. 5218, 305–319.'
mla: Guerraoui, Rachid, et al. Permissiveness in Transactional Memories.
Vol. 5218, Springer, 2008, pp. 305–19, doi:10.1007/978-3-540-87779-0_21.
short: R. Guerraoui, T.A. Henzinger, V. Singh, in:, Springer, 2008, pp. 305–319.
conference:
name: 'DISC: Distributed Computing'
date_created: 2018-12-11T12:08:35Z
date_published: 2008-09-10T00:00:00Z
date_updated: 2021-01-12T07:56:35Z
day: '10'
doi: 10.1007/978-3-540-87779-0_21
extern: 1
intvolume: ' 5218'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/permissiveness_in_transactional_memories.pdf
month: '09'
page: 305 - 319
publication_status: published
publisher: Springer
publist_id: '1072'
quality_controlled: 0
status: public
title: Permissiveness in transactional memories
type: conference
volume: 5218
year: '2008'
...
---
_id: '4387'
abstract:
- lang: eng
text: Software transactional memory (STM) offers a disciplined concurrent programming
model for exploiting the parallelism of modern processor architectures. This paper
presents the first deterministic specification automata for strict serializability
and opacity in STMs. Using an antichain-based tool, we show our deterministic
specifications to be equivalent to more intuitive, nondeterministic specification
automata (which are too large to be determinized automatically). Using deterministic
specification automata, we obtain a complete verification tool for STMs. We also
show how to model and verify contention management within STMs. We automatically
check the opacity of popular STM algorithms, such as TL2 and DSTM, with a universal
contention manager. The universal contention manager is nondeterministic and establishes
correctness for all possible contention management schemes.
acknowledgement: This research was supported by the Swiss National Science Foundation.
alternative_title:
- LNCS
author:
- first_name: Rachid
full_name: Guerraoui, Rachid
last_name: Guerraoui
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Vasu
full_name: Vasu Singh
id: 4DAE2708-F248-11E8-B48F-1D18A9856A87
last_name: Singh
citation:
ama: 'Guerraoui R, Henzinger TA, Singh V. Completeness and nondeterminism in model
checking transactional memories. In: Vol 5201. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2008:21-35. doi:10.1007/978-3-540-85361-9_6'
apa: 'Guerraoui, R., Henzinger, T. A., & Singh, V. (2008). Completeness and
nondeterminism in model checking transactional memories (Vol. 5201, pp. 21–35).
Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.1007/978-3-540-85361-9_6'
chicago: Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Completeness and
Nondeterminism in Model Checking Transactional Memories,” 5201:21–35. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2008. https://doi.org/10.1007/978-3-540-85361-9_6.
ieee: 'R. Guerraoui, T. A. Henzinger, and V. Singh, “Completeness and nondeterminism
in model checking transactional memories,” presented at the CONCUR: Concurrency
Theory, 2008, vol. 5201, pp. 21–35.'
ista: 'Guerraoui R, Henzinger TA, Singh V. 2008. Completeness and nondeterminism
in model checking transactional memories. CONCUR: Concurrency Theory, LNCS, vol.
5201, 21–35.'
mla: Guerraoui, Rachid, et al. Completeness and Nondeterminism in Model Checking
Transactional Memories. Vol. 5201, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2008, pp. 21–35, doi:10.1007/978-3-540-85361-9_6.
short: R. Guerraoui, T.A. Henzinger, V. Singh, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2008, pp. 21–35.
conference:
name: 'CONCUR: Concurrency Theory'
date_created: 2018-12-11T12:08:35Z
date_published: 2008-07-30T00:00:00Z
date_updated: 2021-01-12T07:56:35Z
day: '30'
doi: 10.1007/978-3-540-85361-9_6
extern: 1
intvolume: ' 5201'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/completeness_and_nondeterminism_in_model_checking_transactional_memories.pdf
month: '07'
page: 21 - 35
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '1071'
quality_controlled: 0
status: public
title: Completeness and nondeterminism in model checking transactional memories
type: conference
volume: 5201
year: '2008'
...
---
_id: '4397'
alternative_title:
- LNCS 5123
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- first_name: Damien
full_name: Damien Zufferey
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
citation:
ama: 'Beyer D, Zufferey D, Majumdar R. CSIsat: Interpolation for LA+EUF. In: Springer;
2008:304-308.'
apa: 'Beyer, D., Zufferey, D., & Majumdar, R. (2008). CSIsat: Interpolation
for LA+EUF (pp. 304–308). Presented at the CAV: Computer Aided Verification, Springer.'
chicago: 'Beyer, Dirk, Damien Zufferey, and Ritankar Majumdar. “CSIsat: Interpolation
for LA+EUF,” 304–8. Springer, 2008.'
ieee: 'D. Beyer, D. Zufferey, and R. Majumdar, “CSIsat: Interpolation for LA+EUF,”
presented at the CAV: Computer Aided Verification, 2008, pp. 304–308.'
ista: 'Beyer D, Zufferey D, Majumdar R. 2008. CSIsat: Interpolation for LA+EUF.
CAV: Computer Aided Verification, LNCS 5123, , 304–308.'
mla: 'Beyer, Dirk, et al. CSIsat: Interpolation for LA+EUF. Springer, 2008,
pp. 304–08.'
short: D. Beyer, D. Zufferey, R. Majumdar, in:, Springer, 2008, pp. 304–308.
conference:
name: 'CAV: Computer Aided Verification'
date_created: 2018-12-11T12:08:38Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:40Z
day: '01'
extern: 1
month: '01'
page: 304 - 308
publication_status: published
publisher: Springer
publist_id: '1060'
quality_controlled: 0
status: public
title: 'CSIsat: Interpolation for LA+EUF'
type: conference
year: '2008'
...
---
_id: '4400'
author:
- first_name: Adam
full_name: Aviv,Adam J.
last_name: Aviv
- first_name: Pavol
full_name: Pavol Cerny
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Sandy
full_name: Clark,Sandy
last_name: Clark
- first_name: Eric
full_name: Cronin,Eric
last_name: Cronin
- first_name: Gaurav
full_name: Shah,Gaurav
last_name: Shah
- first_name: Micah
full_name: Sherr,Micah
last_name: Sherr
- first_name: Matt
full_name: Blaze,Matt
last_name: Blaze
citation:
ama: 'Aviv A, Cerny P, Clark S, et al. Security Evaluation of ES&S Voting
Machines and Election Management System. In: USENIX; 2008. doi:1545'
apa: Aviv, A., Cerny, P., Clark, S., Cronin, E., Shah, G., Sherr, M., & Blaze,
M. (2008). Security Evaluation of ES&S Voting Machines and Election Management
System. Presented at the Usenix/ Accurate Electronic Voting Technology Workshop
(EVT) 08, USENIX. https://doi.org/1545
chicago: Aviv, Adam, Pavol Cerny, Sandy Clark, Eric Cronin, Gaurav Shah, Micah Sherr,
and Matt Blaze. “Security Evaluation of ES&S Voting Machines and Election
Management System.” USENIX, 2008. https://doi.org/1545.
ieee: A. Aviv et al., “Security Evaluation of ES&S Voting Machines
and Election Management System,” presented at the Usenix/ Accurate Electronic
Voting Technology Workshop (EVT) 08, 2008.
ista: Aviv A, Cerny P, Clark S, Cronin E, Shah G, Sherr M, Blaze M. 2008. Security
Evaluation of ES&S Voting Machines and Election Management System. Usenix/
Accurate Electronic Voting Technology Workshop (EVT) 08.
mla: Aviv, Adam, et al. Security Evaluation of ES&S Voting Machines and
Election Management System. USENIX, 2008, doi:1545.
short: A. Aviv, P. Cerny, S. Clark, E. Cronin, G. Shah, M. Sherr, M. Blaze, in:,
USENIX, 2008.
conference:
name: Usenix/ Accurate Electronic Voting Technology Workshop (EVT) 08
date_created: 2018-12-11T12:08:39Z
date_published: 2008-07-29T00:00:00Z
date_updated: 2021-01-12T07:56:42Z
day: '29'
doi: '1545'
extern: 1
main_file_link:
- open_access: '0'
url: http://www.usenix.org/event/evt08/tech/full_papers/aviv/aviv.pdf
month: '07'
publication_status: published
publisher: USENIX
publist_id: '1057'
quality_controlled: 0
status: public
title: Security Evaluation of ES&S Voting Machines and Election Management System
type: conference
year: '2008'
...
---
_id: '4409'
abstract:
- lang: eng
text: "Models of timed systems must incorporate not only the sequence of system
events, but the timings of these events as well to capture the real-time aspects
of physical systems. Timed automata are models of real-time systems in which states
consist of discrete locations and values for real-time clocks. The presence of
real-time clocks leads to an uncountable state space. This thesis studies verification
problems on timed automata in a game theoretic framework.\r\n\r\nFor untimed systems,
two systems are close if every sequence of events of one system is also observable
in the second system. For timed systems, the difference in timings of the two
corresponding sequences is also of importance. We propose the notion of bisimulation
distance which quantifies timing differences; if the bisimulation distance between
two systems is epsilon, then (a) every sequence of events of one system has a
corresponding matching sequence in the other, and (b) the timings of matching
events in between the two corresponding traces do not differ by more than epsilon.
We show that we can compute the bisimulation distance between two timed automata
to within any desired degree of accuracy. We also show that the timed verification
logic TCTL is robust with respect to our notion of quantitative bisimilarity,
in particular, if a system satisfies a formula, then every close system satisfies
a close formula.\r\n\r\nTimed games are used for distinguishing between the actions
of several agents, typically a controller and an environment. The controller must
achieve its objective against all possible choices of the environment. The modeling
of the passage of time leads to the presence of zeno executions, and corresponding
unrealizable strategies of the controller which may achieve objectives by blocking
time. We disallow such unreasonable strategies by restricting all agents to use
only receptive strategies --strategies which while not being required to ensure
time divergence by any agent, are such that no agent is responsible for blocking
time. Time divergence is guaranteed when all players use receptive strategies.
We show that timed automaton games with receptive strategies can be solved by
a reduction to finite state turn based game graphs. We define the logic timed
alternating-time temporal logic for verification of timed automaton games and
show that the logic can be model checked in EXPTIME. We also show that the minimum
time required by an agent to reach a desired location, and the maximum time an
agent can stay safe within a set of locations, against all possible actions of
its adversaries are both computable.\r\n\r\nWe next study the memory requirements
of winning strategies for timed automaton games. We prove that finite memory strategies
suffice for safety objectives, and that winning strategies for reachability objectives
may require infinite memory in general. We introduce randomized strategies in
which an agent can propose a probabilistic distribution of moves and show that
finite memory randomized strategies suffice for all omega-regular objectives.
We also show that while randomization helps in simplifying winning strategies,
and thus allows the construction of simpler controllers, it does not help a player
in winning at more states, and thus does not allow the construction of more powerful
controllers.\r\n\r\nFinally we study robust winning strategies in timed games.
In a physical system, a controller may propose an action together with a time
delay, but the action cannot be assumed to be executed at the exact proposed time
delay. We present robust strategies which incorporate such jitters and show that
the set of states from which an agent can win robustly is computable."
article_processing_charge: No
author:
- first_name: Vinayak
full_name: Prabhu, Vinayak
last_name: Prabhu
citation:
ama: Prabhu V. Games for the verification of timed systems. 2008:1-137.
apa: Prabhu, V. (2008). Games for the verification of timed systems. University
of California, Berkeley.
chicago: Prabhu, Vinayak. “Games for the Verification of Timed Systems.” University
of California, Berkeley, 2008.
ieee: V. Prabhu, “Games for the verification of timed systems,” University of California,
Berkeley, 2008.
ista: Prabhu V. 2008. Games for the verification of timed systems. University of
California, Berkeley.
mla: Prabhu, Vinayak. Games for the Verification of Timed Systems. University
of California, Berkeley, 2008, pp. 1–137.
short: V. Prabhu, Games for the Verification of Timed Systems, University of California,
Berkeley, 2008.
date_created: 2018-12-11T12:08:42Z
date_published: 2008-09-01T00:00:00Z
date_updated: 2022-02-14T14:35:11Z
day: '01'
degree_awarded: PhD
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www2.eecs.berkeley.edu/Pubs/TechRpts/2008/EECS-2008-97.html
month: '09'
oa: 1
oa_version: None
page: 1 - 137
publication_status: published
publisher: University of California, Berkeley
publist_id: '319'
status: public
supervisor:
- 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: John
full_name: Steel, John
last_name: Steel
- first_name: Pravin
full_name: Varaiya, Pravin
last_name: Varaiya
title: Games for the verification of timed systems
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2008'
...
---
_id: '4415'
abstract:
- lang: eng
text: 'Many computing applications, especially those in safety critical embedded
systems, require highly predictable timing properties. However, time is often
not present in the prevailing computing and networking abstractions. In fact,
most advances in computer architecture, software, and networking favor average-case
performance over timing predictability. This thesis studies several methods for
the design of concurrent and/or distributed embedded systems with precise timing
guarantees. The focus is on flexible and compositional methods for programming
and verification of the timing properties. The presented methods together with
related formalisms cover two levels of design: (1) Programming language/model
level. We propose the distributed variant of Giotto, a coordination programming
language with an explicit temporal semantics—the logical execution time (LET)
semantics. The LET of a task is an interval of time that specifies the time instants
at which task inputs and outputs become available (task release and termination
instants). The LET of a task is always non-zero. This allows us to communicate
values across the network without changing the timing information of the task,
and without introducing nondeterminism. We show how this methodology supports
distributed code generation for distributed real-time systems. The method gives
up some performance in favor of composability and predictability. We characterize
the tradeoff by comparing the LET semantics with the semantics used in Simulink.
(2) Abstract task graph level. We study interface-based design and verification
of applications represented with task graphs. We consider task sequence graphs
with general event models, and cyclic graphs with periodic event models with jitter
and phase. Here an interface of a component exposes time and resource constraints
of the component. Together with interfaces we formally define interface composition
operations and the refinement relation. For efficient and flexible composability
checking two properties are important: incremental design and independent refinement.
According to the incremental design property the composition of interfaces can
be performed in any order, even if interfaces for some components are not known.
The refinement relation is defined such that in a design we can always substitute
a refined interface for an abstract one. We show that the framework supports independent
refinement, i.e., the refinement relation is preserved under composition operations.'
acknowledgement: 978-0-549-83480-9
article_processing_charge: No
author:
- first_name: Slobodan
full_name: Matic, Slobodan
last_name: Matic
citation:
ama: Matic S. Compositionality in deterministic real-time embedded systems. 2008:1-148.
apa: Matic, S. (2008). Compositionality in deterministic real-time embedded systems.
University of California, Berkeley.
chicago: Matic, Slobodan. “Compositionality in Deterministic Real-Time Embedded
Systems.” University of California, Berkeley, 2008.
ieee: S. Matic, “Compositionality in deterministic real-time embedded systems,”
University of California, Berkeley, 2008.
ista: Matic S. 2008. Compositionality in deterministic real-time embedded systems.
University of California, Berkeley.
mla: Matic, Slobodan. Compositionality in Deterministic Real-Time Embedded Systems.
University of California, Berkeley, 2008, pp. 1–148.
short: S. Matic, Compositionality in Deterministic Real-Time Embedded Systems, University
of California, Berkeley, 2008.
date_created: 2018-12-11T12:08:44Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2022-02-14T14:08:50Z
day: '01'
degree_awarded: PhD
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 1 - 148
publication_status: published
publisher: University of California, Berkeley
publist_id: '316'
status: public
supervisor:
- 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
- first_name: Raja
full_name: Sengupta, Raja
last_name: Sengupta
title: Compositionality in deterministic real-time embedded systems
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2008'
...
---
_id: '4452'
abstract:
- lang: eng
text: We describe Valigator, a software tool for imperative program verification
that efficiently combines symbolic computation and automated reasoning in a uniform
framework. The system offers support for automatically generating and proving
verification conditions and, most importantly, for automatically inferring loop
invariants and bound assertions by means of symbolic summation, Gröbner basis
computation, and quantifier elimination. We present general principles of the
implementation and illustrate them on examples.
acknowledgement: This research was supported by the Swiss NSF.
alternative_title:
- LNCS
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Thibaud
full_name: Hottelier, Thibaud
last_name: Hottelier
- first_name: Laura
full_name: Kovács, Laura
last_name: Kovács
citation:
ama: 'Henzinger TA, Hottelier T, Kovács L. Valigator: A verification tool with bound
and invariant generation. In: Vol 5330. Springer; 2008:333-342. doi:10.1007/978-3-540-89439-1_24'
apa: 'Henzinger, T. A., Hottelier, T., & Kovács, L. (2008). Valigator: A verification
tool with bound and invariant generation (Vol. 5330, pp. 333–342). Presented at
the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Springer.
https://doi.org/10.1007/978-3-540-89439-1_24'
chicago: 'Henzinger, Thomas A, Thibaud Hottelier, and Laura Kovács. “Valigator:
A Verification Tool with Bound and Invariant Generation,” 5330:333–42. Springer,
2008. https://doi.org/10.1007/978-3-540-89439-1_24.'
ieee: 'T. A. Henzinger, T. Hottelier, and L. Kovács, “Valigator: A verification
tool with bound and invariant generation,” presented at the LPAR: Logic for Programming,
Artificial Intelligence, and Reasoning, 2008, vol. 5330, pp. 333–342.'
ista: 'Henzinger TA, Hottelier T, Kovács L. 2008. Valigator: A verification tool
with bound and invariant generation. LPAR: Logic for Programming, Artificial Intelligence,
and Reasoning, LNCS, vol. 5330, 333–342.'
mla: 'Henzinger, Thomas A., et al. Valigator: A Verification Tool with Bound
and Invariant Generation. Vol. 5330, Springer, 2008, pp. 333–42, doi:10.1007/978-3-540-89439-1_24.'
short: T.A. Henzinger, T. Hottelier, L. Kovács, in:, Springer, 2008, pp. 333–342.
conference:
name: 'LPAR: Logic for Programming, Artificial Intelligence, and Reasoning'
date_created: 2018-12-11T12:08:55Z
date_published: 2008-11-13T00:00:00Z
date_updated: 2021-01-12T07:57:04Z
day: '13'
doi: 10.1007/978-3-540-89439-1_24
extern: 1
intvolume: ' 5330'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/valigator.pdf
month: '11'
page: 333 - 342
publication_status: published
publisher: Springer
publist_id: '277'
quality_controlled: 0
status: public
title: 'Valigator: A verification tool with bound and invariant generation'
type: conference
volume: 5330
year: '2008'
...
---
_id: '4509'
abstract:
- lang: eng
text: 'I discuss two main challenges in embedded systems design: the challenge to
build predictable systems, and that to build robust systems. I suggest how predictability
can be formalized as a form of determinism, and robustness as a form of continuity.'
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Henzinger TA. Two challenges in embedded systems design: Predictability and
robustness. Philosophical Transactions of the Royal Society A Mathematical
Physical and Engineering Sciences. 2008;366(1881):3727-3736. doi:10.1098/rsta.2008.0141'
apa: 'Henzinger, T. A. (2008). Two challenges in embedded systems design: Predictability
and robustness. Philosophical Transactions of the Royal Society A Mathematical
Physical and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rsta.2008.0141'
chicago: 'Henzinger, Thomas A. “Two Challenges in Embedded Systems Design: Predictability
and Robustness.” Philosophical Transactions of the Royal Society A Mathematical
Physical and Engineering Sciences. Royal Society of London, 2008. https://doi.org/10.1098/rsta.2008.0141.'
ieee: 'T. A. Henzinger, “Two challenges in embedded systems design: Predictability
and robustness,” Philosophical Transactions of the Royal Society A Mathematical
Physical and Engineering Sciences, vol. 366, no. 1881. Royal Society of London,
pp. 3727–3736, 2008.'
ista: 'Henzinger TA. 2008. Two challenges in embedded systems design: Predictability
and robustness. Philosophical Transactions of the Royal Society A Mathematical
Physical and Engineering Sciences. 366(1881), 3727–3736.'
mla: 'Henzinger, Thomas A. “Two Challenges in Embedded Systems Design: Predictability
and Robustness.” Philosophical Transactions of the Royal Society A Mathematical
Physical and Engineering Sciences, vol. 366, no. 1881, Royal Society of London,
2008, pp. 3727–36, doi:10.1098/rsta.2008.0141.'
short: T.A. Henzinger, Philosophical Transactions of the Royal Society A Mathematical
Physical and Engineering Sciences 366 (2008) 3727–3736.
date_created: 2018-12-11T12:09:13Z
date_published: 2008-07-31T00:00:00Z
date_updated: 2021-01-12T07:59:19Z
day: '31'
doi: 10.1098/rsta.2008.0141
extern: 1
intvolume: ' 366'
issue: '1881'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/two_challenges_in_embedded_systems_design.pdf
month: '07'
page: 3727 - 3736
publication: Philosophical Transactions of the Royal Society A Mathematical Physical
and Engineering Sciences
publication_status: published
publisher: Royal Society of London
publist_id: '219'
quality_controlled: 0
status: public
title: 'Two challenges in embedded systems design: Predictability and robustness'
type: journal_article
volume: 366
year: '2008'
...
---
_id: '4524'
abstract:
- lang: eng
text: "Complex requirements, time-to-market pressure and regulatory constraints
have made the designing of embedded systems extremely challenging. This is evident
by the increase in effort and expenditure for design of safety-driven real-time
control-dominated applications like automotive and avionic controllers. Design
processes are often challenged by lack of proper programming tools for specifying
and verifying critical requirements (e.g. timing and reliability) of such applications.
Platform based design, an approach for designing embedded systems, addresses the
above concerns by separating requirement from architecture. The requirement specifies
the intended behavior of an application while the architecture specifies the guarantees
(e.g. execution speed, failure rate etc). An implementation, a mapping of the
requirement on the architecture, is then analyzed for correctness. The orthogonalization
of concerns makes the specification and analyses simpler. An effective use of
such design methodology has been proposed in Logical Execution Time (LET) model
of real-time tasks. The model separates the timing requirements (specified by
release and termination instances of a task) from the architecture guarantees
(specified by worst-case execution time of the task).\r\n\r\nThis dissertation
proposes a coordination language, Hierarchical Timing Language (HTL), that captures
the timing and reliability requirements of real-time applications. An implementation
of the program on an architecture is then analyzed to check whether desired timing
and reliability requirements are met or not. The core framework extends the LET
model by accounting for reliability and refinement. The reliability model separates
the reliability requirements of tasks from the reliability guarantees of the architecture.
The requirement expresses the desired long-term reliability while the architecture
provides a short-term reliability guarantee (e.g. failure rate for each iteration).
The analysis checks if the short-term guarantee ensures the desired long-term
reliability. The refinement model allows replacing a task by another task during
program execution. Refinement preserves schedulability and reliability, i.e.,
if a refined task is schedulable and reliable for an implementation, then the
refining task is also schedulable and reliable for the implementation. Refinement
helps in concise specification without overloading analysis.\r\n\r\nThe work presents
the formal model, the analyses (both with and without refinement), and a compiler
for HTL programs. The compiler checks composition and refinement constraints,
performs schedulability and reliability analyses, and generates code for implementation
of an HTL program on a virtual machine. Three real-time controllers, one each
from automatic control, automotive control and avionic control, are used to illustrate
the steps in modeling and analyzing HTL programs."
acknowledgement: 978-0-549-83679-7
article_processing_charge: No
author:
- first_name: Arkadeb
full_name: Ghosal, Arkadeb
last_name: Ghosal
citation:
ama: Ghosal A. A hierarchical coordination language for reliable real-time tasks.
2008:1-210.
apa: Ghosal, A. (2008). A hierarchical coordination language for reliable real-time
tasks. University of California, Berkeley.
chicago: Ghosal, Arkadeb. “A Hierarchical Coordination Language for Reliable Real-Time
Tasks.” University of California, Berkeley, 2008.
ieee: A. Ghosal, “A hierarchical coordination language for reliable real-time tasks,”
University of California, Berkeley, 2008.
ista: Ghosal A. 2008. A hierarchical coordination language for reliable real-time
tasks. University of California, Berkeley.
mla: Ghosal, Arkadeb. A Hierarchical Coordination Language for Reliable Real-Time
Tasks. University of California, Berkeley, 2008, pp. 1–210.
short: A. Ghosal, A Hierarchical Coordination Language for Reliable Real-Time Tasks,
University of California, Berkeley, 2008.
date_created: 2018-12-11T12:09:18Z
date_published: 2008-01-31T00:00:00Z
date_updated: 2021-01-12T07:59:26Z
day: '31'
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 1 - 210
publication_status: published
publisher: University of California, Berkeley
publist_id: '199'
status: public
supervisor:
- first_name: Alberto
full_name: Sangiovanni-Vincentelli, Alberto
last_name: Sangiovanni-Vincentelli
- 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
- first_name: Karl
full_name: Hedrick, Karl
last_name: Hedrick
title: A hierarchical coordination language for reliable real-time tasks
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2008'
...
---
_id: '4521'
abstract:
- lang: eng
text: The search for proof and the search for counterexamples (bugs) are complementary
activities that need to be pursued concurrently in order to maximize the practical
success rate of verification tools.While this is well-understood in safety verification,
the current focus of liveness verification has been almost exclusively on the
search for termination proofs. A counterexample to termination is an infinite
programexecution. In this paper, we propose a method to search for such counterexamples.
The search proceeds in two phases. We first dynamically enumerate lasso-shaped
candidate paths for counterexamples, and then statically prove their feasibility.
We illustrate the utility of our nontermination prover, called TNT, on several
nontrivial examples, some of which require bit-level reasoning about integer representations.
author:
- first_name: Ashutosh
full_name: Ashutosh Gupta
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
- first_name: Ru
full_name: Xu, Ru-Gang
last_name: Xu
citation:
ama: 'Gupta A, Henzinger TA, Majumdar R, Rybalchenko A, Xu R. Proving non-termination.
In: ACM; 2008:147-158. doi:10.1145/1328438.1328459'
apa: 'Gupta, A., Henzinger, T. A., Majumdar, R., Rybalchenko, A., & Xu, R. (2008).
Proving non-termination (pp. 147–158). Presented at the POPL: Principles of Programming
Languages, ACM. https://doi.org/10.1145/1328438.1328459'
chicago: Gupta, Ashutosh, Thomas A Henzinger, Ritankar Majumdar, Andrey Rybalchenko,
and Ru Xu. “Proving Non-Termination,” 147–58. ACM, 2008. https://doi.org/10.1145/1328438.1328459.
ieee: 'A. Gupta, T. A. Henzinger, R. Majumdar, A. Rybalchenko, and R. Xu, “Proving
non-termination,” presented at the POPL: Principles of Programming Languages,
2008, pp. 147–158.'
ista: 'Gupta A, Henzinger TA, Majumdar R, Rybalchenko A, Xu R. 2008. Proving non-termination.
POPL: Principles of Programming Languages, 147–158.'
mla: Gupta, Ashutosh, et al. Proving Non-Termination. ACM, 2008, pp. 147–58,
doi:10.1145/1328438.1328459.
short: A. Gupta, T.A. Henzinger, R. Majumdar, A. Rybalchenko, R. Xu, in:, ACM, 2008,
pp. 147–158.
conference:
name: 'POPL: Principles of Programming Languages'
date_created: 2018-12-11T12:09:17Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:59:25Z
day: '01'
doi: 10.1145/1328438.1328459
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/proving_non-termination.pdf
month: '01'
page: 147 - 158
publication_status: published
publisher: ACM
publist_id: '208'
quality_controlled: 0
status: public
title: Proving non-termination
type: conference
year: '2008'
...