---
_id: '3152'
abstract:
- lang: eng
text: The basic concepts of the molecular machinery that mediates cell migration
have been gleaned from cell culture systems. However, the three-dimensional environment
within an organism presents migrating cells with a much greater challenge. They
must move between and among other cells while interpreting multiple attractive
and repulsive cues to choose their proper path. They must coordinate their cell
adhesion with their surroundings and know when to start and stop moving. New insights
into the control of these remaining mysteries have emerged from genetic dissection
and live imaging of germ cell migration in Drosophila, zebrafish, and mouse embryos.
In this review, we first describe germ cell migration in cellular and mechanistic
detail in these different model systems. We then compare these systems to highlight
the emerging principles. Finally, we contrast the migration of germ cells with
that of immune and cancer cells to outline the conserved and different mechanisms.
author:
- first_name: Prabhat
full_name: Kunwar, Prabhat S
last_name: Kunwar
- first_name: Daria E
full_name: Daria Siekhaus
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Ruth
full_name: Lehmann, Ruth
last_name: Lehmann
citation:
ama: Kunwar P, Siekhaus DE, Lehmann R. In vivo migration A germ cell perspective.
Annual Review of Cell and Developmental Biology. 2006;22:237-265. doi:10.1146/annurev.cellbio.22.010305.103337
apa: Kunwar, P., Siekhaus, D. E., & Lehmann, R. (2006). In vivo migration A
germ cell perspective. Annual Review of Cell and Developmental Biology.
Annual Reviews. https://doi.org/10.1146/annurev.cellbio.22.010305.103337
chicago: Kunwar, Prabhat, Daria E Siekhaus, and Ruth Lehmann. “In Vivo Migration
A Germ Cell Perspective.” Annual Review of Cell and Developmental Biology.
Annual Reviews, 2006. https://doi.org/10.1146/annurev.cellbio.22.010305.103337.
ieee: P. Kunwar, D. E. Siekhaus, and R. Lehmann, “In vivo migration A germ cell
perspective,” Annual Review of Cell and Developmental Biology, vol. 22.
Annual Reviews, pp. 237–265, 2006.
ista: Kunwar P, Siekhaus DE, Lehmann R. 2006. In vivo migration A germ cell perspective.
Annual Review of Cell and Developmental Biology. 22, 237–265.
mla: Kunwar, Prabhat, et al. “In Vivo Migration A Germ Cell Perspective.” Annual
Review of Cell and Developmental Biology, vol. 22, Annual Reviews, 2006, pp.
237–65, doi:10.1146/annurev.cellbio.22.010305.103337.
short: P. Kunwar, D.E. Siekhaus, R. Lehmann, Annual Review of Cell and Developmental
Biology 22 (2006) 237–265.
date_created: 2018-12-11T12:01:42Z
date_published: 2006-06-14T00:00:00Z
date_updated: 2021-01-12T07:41:25Z
day: '14'
doi: 10.1146/annurev.cellbio.22.010305.103337
extern: 1
intvolume: ' 22'
month: '06'
page: 237 - 265
publication: Annual Review of Cell and Developmental Biology
publication_status: published
publisher: Annual Reviews
publist_id: '3543'
quality_controlled: 0
status: public
title: In vivo migration A germ cell perspective
type: journal_article
volume: 22
year: '2006'
...
---
_id: '3180'
abstract:
- lang: eng
text: 'One of the most exciting advances in early vision has been the development
of efficient energy minimization algorithms. Many early vision tasks require labeling
each pixel with some quantity such as depth or texture. While many such problems
can be elegantly expressed in the language of Markov Random Fields (MRF''s), the
resulting energy minimization problems were widely viewed as intractable. Recently,
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. Unfortunately, most papers define their own energy
function, which is minimized with a specific algorithm of their choice. As a result,
the tradeoffs among different energy minimization algorithms are not well understood.
In this paper we describe a set of energy minimization benchmarks, which we use
to compare the solution quality and running time of several common energy minimization
algorithms. We investigate three promising recent methods - graph cuts, LBP, and
tree-reweighted message passing - as well as the well-known older iterated conditional
modes (ICM) algorithm. Our benchmark problems are drawn from published energy
functions used for stereo, image stitching and interactive segmentation. We also
provide a general-purpose software interface that allows vision researchers to
easily switch between optimization methods with minimal overhead. We expect that
the availability of our benchmarks and interface will make it significantly easier
for vision researchers to adopt the best method for their specific problems. Benchmarks,
code, results and images 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. In: Vol 3952. Springer; 2006:16-29. doi:10.1007/11744047_2'
apa: 'Szeliski, R., Zabih, R., Scharstein, D., Veksler, O., Kolmogorov, V., Agarwala,
A., … Rother, C. (2006). A comparative study of energy minimization methods for
Markov random fields (Vol. 3952, pp. 16–29). Presented at the ECCV: European Conference
on Computer Vision, Springer. https://doi.org/10.1007/11744047_2'
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,” 3952:16–29. Springer,
2006. https://doi.org/10.1007/11744047_2.
ieee: 'R. Szeliski et al., “A comparative study of energy minimization methods
for Markov random fields,” presented at the ECCV: European Conference on Computer
Vision, 2006, vol. 3952, pp. 16–29.'
ista: 'Szeliski R, Zabih R, Scharstein D, Veksler O, Kolmogorov V, Agarwala A, Tappen
M, Rother C. 2006. A comparative study of energy minimization methods for Markov
random fields. ECCV: European Conference on Computer Vision vol. 3952, 16–29.'
mla: Szeliski, Richard, et al. A Comparative Study of Energy Minimization Methods
for Markov Random Fields. Vol. 3952, Springer, 2006, pp. 16–29, doi:10.1007/11744047_2.
short: R. Szeliski, R. Zabih, D. Scharstein, O. Veksler, V. Kolmogorov, A. Agarwala,
M. Tappen, C. Rother, in:, Springer, 2006, pp. 16–29.
conference:
name: 'ECCV: European Conference on Computer Vision'
date_created: 2018-12-11T12:01:51Z
date_published: 2006-05-03T00:00:00Z
date_updated: 2021-01-12T07:41:37Z
day: '03'
doi: 10.1007/11744047_2
extern: 1
intvolume: ' 3952'
main_file_link:
- open_access: '0'
url: http://research-srv.microsoft.com/pubs/67896/szsvkatr-eccv06.pdf
month: '05'
page: 16 - 29
publication_status: published
publisher: Springer
publist_id: '3499'
quality_controlled: 0
status: public
title: A comparative study of energy minimization methods for Markov random fields
type: conference
volume: 3952
year: '2006'
...
---
_id: '3184'
abstract:
- lang: eng
text: 'Algorithms for discrete energy minimization play a fundamental role for low-level
vision. Known techniques include graph cuts, belief propagation (BP) and recently
introduced tree-reweighted message passing (TRW). So far, the standard benchmark
for their comparison has been a 4-connected grid-graph arising in pixel-labelling
stereo. This minimization problem, however, has been largely solved: recent work
shows that for many scenes TRW finds the global optimum. Furthermore, it is known
that a 4-connecled grid-graph is a poor stereo model since it does not take occlusions
into account. We propose the problem of stereo with occlusions as a new test bed
for minimization algorithms. This is a more challenging graph since it has much
larger connectivity, and it also serves as a better stereo model. An attractive
feature of this problem is that increased connectivity does not result in increased
complexity of message passing algorithms. Indeed, one contribution of this paper
is to show that sophisticated implementations of BP and TRW have the same time
and memory complexity as that of 4-connecled grid-graph stereo. The main conclusion
of our experimental study is that for our problem graph cut outperforms both TRW
and BP considerably. TRW achieves consistently a lower energy than BP. However,
as connectivity increases the speed of convergence of TRW becomes slower. Unlike
4-connected grids, the difference between the energy of the best optimization
method and the lower bound of TRW appears significant. This shows the hardness
of the problem and motivates future research.'
alternative_title:
- LNCS
author:
- 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: 'Kolmogorov V, Rother C. Comparison of energy minimization algorithms for highly
connected graphs. In: Vol 3952 LNCS. Springer; 2006:1-15. doi:10.1007/11744047_1'
apa: 'Kolmogorov, V., & Rother, C. (2006). Comparison of energy minimization
algorithms for highly connected graphs (Vol. 3952 LNCS, pp. 1–15). Presented at
the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744047_1'
chicago: Kolmogorov, Vladimir, and Carsten Rother. “Comparison of Energy Minimization
Algorithms for Highly Connected Graphs,” 3952 LNCS:1–15. Springer, 2006. https://doi.org/10.1007/11744047_1.
ieee: 'V. Kolmogorov and C. Rother, “Comparison of energy minimization algorithms
for highly connected graphs,” presented at the ECCV: European Conference on Computer
Vision, 2006, vol. 3952 LNCS, pp. 1–15.'
ista: 'Kolmogorov V, Rother C. 2006. Comparison of energy minimization algorithms
for highly connected graphs. ECCV: European Conference on Computer Vision, LNCS,
vol. 3952 LNCS, 1–15.'
mla: Kolmogorov, Vladimir, and Carsten Rother. Comparison of Energy Minimization
Algorithms for Highly Connected Graphs. Vol. 3952 LNCS, Springer, 2006, pp.
1–15, doi:10.1007/11744047_1.
short: V. Kolmogorov, C. Rother, in:, Springer, 2006, pp. 1–15.
conference:
name: 'ECCV: European Conference on Computer Vision'
date_created: 2018-12-11T12:01:52Z
date_published: 2006-05-03T00:00:00Z
date_updated: 2021-01-12T07:41:39Z
day: '03'
doi: 10.1007/11744047_1
extern: 1
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67889/paper_eccv06-trw.pdf
month: '05'
page: 1 - 15
publication_status: published
publisher: Springer
publist_id: '3498'
quality_controlled: 0
status: public
title: Comparison of energy minimization algorithms for highly connected graphs
type: conference
volume: 3952 LNCS
year: '2006'
...
---
_id: '3185'
abstract:
- lang: eng
text: This paper describes models and algorithms for the real-time segmentation
of foreground from background layers in stereo video sequences. Automatic separation
of layers from color/contrast or from stereo alone is known to be error-prone.
Here, color, contrast, and stereo matching information are fused to infer layers
accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP),
solves stereo in an extended six-state space that represents both foreground/background
layers and occluded regions. The stereo-match likelihood is then fused with a
contrast-sensitive color model that is learned on-the-fly and stereo disparities
are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC),
does not directly solve stereo. Instead, the stereo match likelihood is marginalized
over disparities to evaluate foreground and background hypotheses and then fused
with a contrast-sensitive color model like the one used in LDP. Segmentation is
solved efficiently by ternary graph cut. Both algorithms are evaluated with respect
to ground truth data and found to have similar performance, substantially better
than either stereo or color/contrast alone. However, their characteristics with
respect to computational efficiency are rather different. The algorithms are demonstrated
in the application of background substitution and shown to give good quality composite
video output.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Antonio
full_name: Criminisi, Antonio
last_name: Criminisi
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Geoffrey
full_name: Cross, Geoffrey
last_name: Cross
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Probabilistic fusion
of stereo with color and contrast for bilayer segmentation. IEEE Transactions
on Pattern Analysis and Machine Intelligence. 2006;28(9):1480-1492. doi:10.1109/TPAMI.2006.193
apa: Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., & Rother, C. (2006).
Probabilistic fusion of stereo with color and contrast for bilayer segmentation.
IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2006.193
chicago: Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross,
and Carsten Rother. “Probabilistic Fusion of Stereo with Color and Contrast for
Bilayer Segmentation.” IEEE Transactions on Pattern Analysis and Machine Intelligence.
IEEE, 2006. https://doi.org/10.1109/TPAMI.2006.193.
ieee: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Probabilistic
fusion of stereo with color and contrast for bilayer segmentation,” IEEE Transactions
on Pattern Analysis and Machine Intelligence, vol. 28, no. 9. IEEE, pp. 1480–1492,
2006.
ista: Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2006. Probabilistic
fusion of stereo with color and contrast for bilayer segmentation. IEEE Transactions
on Pattern Analysis and Machine Intelligence. 28(9), 1480–1492.
mla: Kolmogorov, Vladimir, et al. “Probabilistic Fusion of Stereo with Color and
Contrast for Bilayer Segmentation.” IEEE Transactions on Pattern Analysis and
Machine Intelligence, vol. 28, no. 9, IEEE, 2006, pp. 1480–92, doi:10.1109/TPAMI.2006.193.
short: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, IEEE Transactions
on Pattern Analysis and Machine Intelligence 28 (2006) 1480–1492.
date_created: 2018-12-11T12:01:53Z
date_published: 2006-09-01T00:00:00Z
date_updated: 2021-01-12T07:41:39Z
day: '01'
doi: 10.1109/TPAMI.2006.193
extern: 1
intvolume: ' 28'
issue: '9'
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67414/criminisi_pami2006.pdf
month: '09'
page: 1480 - 1492
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '3496'
quality_controlled: 0
status: public
title: Probabilistic fusion of stereo with color and contrast for bilayer segmentation
type: journal_article
volume: 28
year: '2006'
...
---
_id: '3186'
abstract:
- lang: eng
text: We introduce a new approach to modelling gradient flows of contours and surfaces.
While standard variational methods (e.g. level sets) compute local interface motion
in a differential fashion by estimating local contour velocity via energy derivatives,
we propose to solve surface evolution PDEs by explicitly estimating integral motion
of the whole surface. We formulate an optimization problem directly based on an
integral characterization of gradient flow as an infinitesimal move of the (whole)
surface giving the largest energy decrease among all moves of equal size. We show
that this problem can be efficiently solved using recent advances in algorithms
for global hypersurface optimization [4, 2, 11]. In particular, we employ the
geo-cuts method [4] that uses ideas from integral geometry to represent continuous
surfaces as cuts on discrete graphs. The resulting interface evolution algorithm
is validated on some 2D and 3D examples similar to typical demonstrations of level-set
methods. Our method can compute gradient flows of hypersurfaces with respect to
a fairly general class of continuous functional and it is flexible with respect
to distance metrics on the space of contours/surfaces. Preliminary tests for standard
L2 distance metric demonstrate numerical stability, topological changes and an
absence of any oscillatory motion.
alternative_title:
- LNCS
author:
- first_name: Yuri
full_name: Boykov, Yuri
last_name: Boykov
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Daniel
full_name: Cremers, Daniel
last_name: Cremers
- first_name: Andrew
full_name: Delong, Andrew
last_name: Delong
citation:
ama: 'Boykov Y, Kolmogorov V, Cremers D, Delong A. An integral solution to surface
evolution PDEs via geo cuts. In: Vol 3953. Springer; 2006:409-422. doi:10.1007/11744078_32'
apa: 'Boykov, Y., Kolmogorov, V., Cremers, D., & Delong, A. (2006). An integral
solution to surface evolution PDEs via geo cuts (Vol. 3953, pp. 409–422). Presented
at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744078_32'
chicago: Boykov, Yuri, Vladimir Kolmogorov, Daniel Cremers, and Andrew Delong. “An
Integral Solution to Surface Evolution PDEs via Geo Cuts,” 3953:409–22. Springer,
2006. https://doi.org/10.1007/11744078_32.
ieee: 'Y. Boykov, V. Kolmogorov, D. Cremers, and A. Delong, “An integral solution
to surface evolution PDEs via geo cuts,” presented at the ECCV: European Conference
on Computer Vision, 2006, vol. 3953, pp. 409–422.'
ista: 'Boykov Y, Kolmogorov V, Cremers D, Delong A. 2006. An integral solution to
surface evolution PDEs via geo cuts. ECCV: European Conference on Computer Vision,
LNCS, vol. 3953, 409–422.'
mla: Boykov, Yuri, et al. An Integral Solution to Surface Evolution PDEs via
Geo Cuts. Vol. 3953, Springer, 2006, pp. 409–22, doi:10.1007/11744078_32.
short: Y. Boykov, V. Kolmogorov, D. Cremers, A. Delong, in:, Springer, 2006, pp.
409–422.
conference:
name: 'ECCV: European Conference on Computer Vision'
date_created: 2018-12-11T12:01:53Z
date_published: 2006-04-28T00:00:00Z
date_updated: 2021-01-12T07:41:39Z
day: '28'
doi: 10.1007/11744078_32
extern: 1
intvolume: ' 3953'
month: '04'
page: 409 - 422
publication_status: published
publisher: Springer
publist_id: '3497'
quality_controlled: 0
status: public
title: An integral solution to surface evolution PDEs via geo cuts
type: conference
volume: 3953
year: '2006'
...
---
_id: '3188'
abstract:
- lang: eng
text: 'We introduce the term cosegmentation which denotes the task of segmenting
simultaneously the common parts of an image pair. A generative model for cosegmentation
is presented. Inference in the model leads to minimizing an energy with an MRF
term encoding spatial coherency and a global constraint which attempts to match
the appearance histograms of the common parts. This energy has not been proposed
previously and its optimization is challenging and NP-hard. For this problem a
novel optimization scheme which we call trust region graph cuts is presented.
We demonstrate that this framework has the potential to improve a wide range of
research: Object driven image retrieval, video tracking and segmentation, and
interactive image editing. The power of the framework lies in its generality,
the common part can be a rigid/non-rigid object (or scene), observed from different
viewpoints or even similar objects of the same class.'
author:
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Thomas
full_name: Minka, Thomas P
last_name: Minka
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
citation:
ama: 'Rother C, Kolmogorov V, Minka T, Blake A. Cosegmentation of image pairs by
histogram matching - Incorporating a global constraint into MRFs. In: IEEE; 2006:993-1000.
doi:10.1109/CVPR.2006.91'
apa: 'Rother, C., Kolmogorov, V., Minka, T., & Blake, A. (2006). Cosegmentation
of image pairs by histogram matching - Incorporating a global constraint into
MRFs (pp. 993–1000). Presented at the CVPR: Computer Vision and Pattern Recognition,
IEEE. https://doi.org/10.1109/CVPR.2006.91'
chicago: Rother, Carsten, Vladimir Kolmogorov, Thomas Minka, and Andrew Blake. “Cosegmentation
of Image Pairs by Histogram Matching - Incorporating a Global Constraint into
MRFs,” 993–1000. IEEE, 2006. https://doi.org/10.1109/CVPR.2006.91.
ieee: 'C. Rother, V. Kolmogorov, T. Minka, and A. Blake, “Cosegmentation of image
pairs by histogram matching - Incorporating a global constraint into MRFs,” presented
at the CVPR: Computer Vision and Pattern Recognition, 2006, pp. 993–1000.'
ista: 'Rother C, Kolmogorov V, Minka T, Blake A. 2006. Cosegmentation of image pairs
by histogram matching - Incorporating a global constraint into MRFs. CVPR: Computer
Vision and Pattern Recognition, 993–1000.'
mla: Rother, Carsten, et al. Cosegmentation of Image Pairs by Histogram Matching
- Incorporating a Global Constraint into MRFs. IEEE, 2006, pp. 993–1000, doi:10.1109/CVPR.2006.91.
short: C. Rother, V. Kolmogorov, T. Minka, A. Blake, in:, IEEE, 2006, pp. 993–1000.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:54Z
date_published: 2006-07-05T00:00:00Z
date_updated: 2021-01-12T07:41:40Z
day: '05'
doi: 10.1109/CVPR.2006.91
extern: 1
month: '07'
page: 993 - 1000
publication_status: published
publisher: IEEE
publist_id: '3493'
quality_controlled: 0
status: public
title: Cosegmentation of image pairs by histogram matching - Incorporating a global
constraint into MRFs
type: conference
year: '2006'
...
---
_id: '3189'
abstract:
- lang: eng
text: This paper presents an algorithm capable of real-time separation of foreground
from background in monocular video sequences. Automatic segmentation of layers
from colour/contrast or from motion alone is known to be error-prone. Here motion,
colour and contrast cues are probabilistically fused together with spatial and
temporal priors to infer layers accurately and efficiently. Central to our algorithm
is the fact that pixel velocities are not needed, thus removing the need for optical
flow estimation, with its tendency to error and computational expense. Instead,
an efficient motion vs non-motion classifier is trained to operate directly and
jointly on intensity-change and contrast. Its output is then fused with colour
information. The prior on segmentation is represented by a second order, temporal,
Hidden Markov Model, together with a spatial MRF favouring coherence except where
contrast is high. Finally, accurate layer segmentation and explicit occlusion
detection are efficiently achieved by binary graph cut. The segmentation accuracy
of the proposed algorithm is quantitatively evaluated with respect to existing
ground-truth data and found to be comparable to the accuracy of a state of the
art stereo segmentation algorithm. Fore-ground/background segmentation is demonstrated
in the application of live background substitution and shown to generate convincingly
good quality composite video.
author:
- first_name: Antonio
full_name: Criminisi, Antonio
last_name: Criminisi
- first_name: Geoffrey
full_name: Cross, Geoffrey
last_name: Cross
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Criminisi A, Cross G, Blake A, Kolmogorov V. Bilayer segmentation of live
video. In: Vol 1. IEEE; 2006:53-60. doi:10.1109/CVPR.2006.69'
apa: 'Criminisi, A., Cross, G., Blake, A., & Kolmogorov, V. (2006). Bilayer
segmentation of live video (Vol. 1, pp. 53–60). Presented at the CVPR: Computer
Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2006.69'
chicago: Criminisi, Antonio, Geoffrey Cross, Andrew Blake, and Vladimir Kolmogorov.
“Bilayer Segmentation of Live Video,” 1:53–60. IEEE, 2006. https://doi.org/10.1109/CVPR.2006.69.
ieee: 'A. Criminisi, G. Cross, A. Blake, and V. Kolmogorov, “Bilayer segmentation
of live video,” presented at the CVPR: Computer Vision and Pattern Recognition,
2006, vol. 1, pp. 53–60.'
ista: 'Criminisi A, Cross G, Blake A, Kolmogorov V. 2006. Bilayer segmentation of
live video. CVPR: Computer Vision and Pattern Recognition vol. 1, 53–60.'
mla: Criminisi, Antonio, et al. Bilayer Segmentation of Live Video. Vol.
1, IEEE, 2006, pp. 53–60, doi:10.1109/CVPR.2006.69.
short: A. Criminisi, G. Cross, A. Blake, V. Kolmogorov, in:, IEEE, 2006, pp. 53–60.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:54Z
date_published: 2006-07-05T00:00:00Z
date_updated: 2021-01-12T07:41:40Z
day: '05'
doi: 10.1109/CVPR.2006.69
extern: 1
intvolume: ' 1'
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/en-us/um/people/ablake/papers/ablake/criminisi_cvpr06.pdf
month: '07'
page: 53 - 60
publication_status: published
publisher: IEEE
publist_id: '3494'
quality_controlled: 0
status: public
title: Bilayer segmentation of live video
type: conference
volume: 1
year: '2006'
...
---
_id: '3190'
abstract:
- lang: eng
text: Algorithms for discrete energy minimization are of fundamental importance
in computer vision. In this paper, we focus on the recent technique proposed by
Wainwright et al. (Nov. 2005)- tree-reweighted max-product message passing (TRW).
It was inspired by the problem of maximizing a lower bound on the energy. However,
the algorithm is not guaranteed to increase this bound - it may actually go down.
In addition, TRW does not always converge. We develop a modification of this algorithm
which we call sequential tree-reweighted message passing. Its main property is
that the bound is guaranteed not to decrease. We also give a weak tree agreement
condition which characterizes local maxima of the bound with respect to TRW algorithms.
We prove that our algorithm has a limit point that achieves weak tree agreement.
Finally, we show that, our algorithm requires half as much memory as traditional
message passing approaches. Experimental results demonstrate that on certain synthetic
and real problems, our algorithm outperforms both the ordinary belief propagation
and tree-reweighted algorithm in (M. J. Wainwright, et al., Nov. 2005). In addition,
on stereo problems with Potts interactions, we obtain a lower energy than graph
cuts.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: Kolmogorov V. Convergent tree reweighted message passing for energy minimization.
IEEE Transactions on Pattern Analysis and Machine Intelligence. 2006;28(10):1568-1583.
doi:10.1109/TPAMI.2006.200
apa: Kolmogorov, V. (2006). Convergent tree reweighted message passing for energy
minimization. IEEE Transactions on Pattern Analysis and Machine Intelligence.
IEEE. https://doi.org/10.1109/TPAMI.2006.200
chicago: Kolmogorov, Vladimir. “Convergent Tree Reweighted Message Passing for Energy
Minimization.” IEEE Transactions on Pattern Analysis and Machine Intelligence.
IEEE, 2006. https://doi.org/10.1109/TPAMI.2006.200.
ieee: V. Kolmogorov, “Convergent tree reweighted message passing for energy minimization,”
IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28,
no. 10. IEEE, pp. 1568–1583, 2006.
ista: Kolmogorov V. 2006. Convergent tree reweighted message passing for energy
minimization. IEEE Transactions on Pattern Analysis and Machine Intelligence.
28(10), 1568–1583.
mla: Kolmogorov, Vladimir. “Convergent Tree Reweighted Message Passing for Energy
Minimization.” IEEE Transactions on Pattern Analysis and Machine Intelligence,
vol. 28, no. 10, IEEE, 2006, pp. 1568–83, doi:10.1109/TPAMI.2006.200.
short: V. Kolmogorov, IEEE Transactions on Pattern Analysis and Machine Intelligence
28 (2006) 1568–1583.
date_created: 2018-12-11T12:01:55Z
date_published: 2006-08-21T00:00:00Z
date_updated: 2021-01-12T07:41:41Z
day: '21'
doi: 10.1109/TPAMI.2006.200
extern: 1
intvolume: ' 28'
issue: '10'
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67371/trw_maxproduct_aistats05.pdf
month: '08'
page: 1568 - 1583
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '3495'
quality_controlled: 0
status: public
title: Convergent tree reweighted message passing for energy minimization
type: journal_article
volume: 28
year: '2006'
...
---
_id: '3214'
abstract:
- lang: eng
text: |-
The Feistel-network is a popular structure underlying many block-ciphers where the cipher is constructed from many simpler rounds, each defined by some function which is derived from the secret key.
Luby and Rackoff showed that the three-round Feistel-network – each round instantiated with a pseudorandom function secure against adaptive chosen plaintext attacks (CPA) – is a CPA secure pseudorandom permutation, thus giving some confidence in the soundness of using a Feistel-network to design block-ciphers.
But the round functions used in actual block-ciphers are – for efficiency reasons – far from being pseudorandom. We investigate the security of the Feistel-network against CPA distinguishers when the only security guarantee we have for the round functions is that they are secure against non-adaptive chosen plaintext attacks (nCPA). We show that in the information-theoretic setting, four rounds with nCPA secure round functions are sufficient (and necessary) to get a CPA secure permutation. Unfortunately, this result does not translate into the more interesting pseudorandom setting. In fact, under the so-called Inverse Decisional Diffie-Hellman assumption the Feistel-network with four rounds, each instantiated with a nCPA secure pseudorandom function, is in general not a CPA secure pseudorandom permutation.
acknowledgement: Most of this work was done while the K. Pietrzak was a PhD student
at ETH where he was supported by the Swiss National Science Foundation, project
No. 200020- 103847/1. Currently he is partially supported by the Commission of the
European Communities through the IST program under contract IST-2002-507932 ECRYPT.
alternative_title:
- LNCS
author:
- first_name: Ueli
full_name: Maurer, Ueli M
last_name: Maurer
- first_name: Yvonne
full_name: Oswald, Yvonne A
last_name: Oswald
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Johan
full_name: Sjödin, Johan
last_name: Sjödin
citation:
ama: 'Maurer U, Oswald Y, Pietrzak KZ, Sjödin J. Luby Rackoff ciphers from weak
round functions . In: Vol 4004. Springer; 2006:391-408. doi:10.1007/11761679_24'
apa: 'Maurer, U., Oswald, Y., Pietrzak, K. Z., & Sjödin, J. (2006). Luby Rackoff
ciphers from weak round functions (Vol. 4004, pp. 391–408). Presented at the
EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/11761679_24'
chicago: Maurer, Ueli, Yvonne Oswald, Krzysztof Z Pietrzak, and Johan Sjödin. “Luby
Rackoff Ciphers from Weak Round Functions ,” 4004:391–408. Springer, 2006. https://doi.org/10.1007/11761679_24.
ieee: 'U. Maurer, Y. Oswald, K. Z. Pietrzak, and J. Sjödin, “Luby Rackoff ciphers
from weak round functions ,” presented at the EUROCRYPT: Theory and Applications
of Cryptographic Techniques, 2006, vol. 4004, pp. 391–408.'
ista: 'Maurer U, Oswald Y, Pietrzak KZ, Sjödin J. 2006. Luby Rackoff ciphers from
weak round functions . EUROCRYPT: Theory and Applications of Cryptographic Techniques,
LNCS, vol. 4004, 391–408.'
mla: Maurer, Ueli, et al. Luby Rackoff Ciphers from Weak Round Functions .
Vol. 4004, Springer, 2006, pp. 391–408, doi:10.1007/11761679_24.
short: U. Maurer, Y. Oswald, K.Z. Pietrzak, J. Sjödin, in:, Springer, 2006, pp.
391–408.
conference:
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
date_created: 2018-12-11T12:02:03Z
date_published: 2006-07-11T00:00:00Z
date_updated: 2021-01-12T07:41:51Z
day: '11'
doi: 10.1007/11761679_24
extern: 1
intvolume: ' 4004'
month: '07'
page: 391 - 408
publication_status: published
publisher: Springer
publist_id: '3465'
quality_controlled: 0
status: public
title: 'Luby Rackoff ciphers from weak round functions '
type: conference
volume: 4004
year: '2006'
...
---
_id: '3215'
abstract:
- lang: eng
text: 'Most cryptographic primitives such as encryption, authentication or secret
sharing require randomness. Usually one assumes that perfect randomness is available,
but those primitives might also be realized under weaker assumptions. In this
work we continue the study of building secure cryptographic primitives from imperfect
random sources initiated by Dodis and Spencer (FOCS’02). Their main result shows
that there exists a (high-entropy) source of randomness allowing for perfect encryption
of a bit, and yet from which one cannot extract even a single weakly random bit,
separating encryption from extraction. Our main result separates encryption from
2-out-2 secret sharing (both in the information-theoretic and in the computational
settings): any source which can be used to achieve one-bit encryption also can
be used for 2-out-2 secret sharing of one bit, but the converse is false, even
for high-entropy sources. Therefore, possibility of extraction strictly implies
encryption, which in turn strictly implies 2-out-2 secret sharing.'
acknowledgement: Supported in part by NSF career award CCR-0133806 and NSF grant CCR-0311095.
Supported by the Swiss National Science Foundation, project No. 200020-103847/1.
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: Bartosz
full_name: Przydatek, Bartosz
last_name: Przydatek
citation:
ama: 'Dodis Y, Pietrzak KZ, Przydatek B. Separating sources for encryption and secret
sharing. In: Vol 3876. Springer; 2006:601-616. doi:10.1007/11681878_31'
apa: 'Dodis, Y., Pietrzak, K. Z., & Przydatek, B. (2006). Separating sources
for encryption and secret sharing (Vol. 3876, pp. 601–616). Presented at the TCC:
Theory of Cryptography Conference, Springer. https://doi.org/10.1007/11681878_31'
chicago: Dodis, Yevgeniy, Krzysztof Z Pietrzak, and Bartosz Przydatek. “Separating
Sources for Encryption and Secret Sharing,” 3876:601–16. Springer, 2006. https://doi.org/10.1007/11681878_31.
ieee: 'Y. Dodis, K. Z. Pietrzak, and B. Przydatek, “Separating sources for encryption
and secret sharing,” presented at the TCC: Theory of Cryptography Conference,
2006, vol. 3876, pp. 601–616.'
ista: 'Dodis Y, Pietrzak KZ, Przydatek B. 2006. Separating sources for encryption
and secret sharing. TCC: Theory of Cryptography Conference, LNCS, vol. 3876, 601–616.'
mla: Dodis, Yevgeniy, et al. Separating Sources for Encryption and Secret Sharing.
Vol. 3876, Springer, 2006, pp. 601–16, doi:10.1007/11681878_31.
short: Y. Dodis, K.Z. Pietrzak, B. Przydatek, in:, Springer, 2006, pp. 601–616.
conference:
name: 'TCC: Theory of Cryptography Conference'
date_created: 2018-12-11T12:02:04Z
date_published: 2006-04-11T00:00:00Z
date_updated: 2021-01-12T07:41:51Z
day: '11'
doi: 10.1007/11681878_31
extern: 1
intvolume: ' 3876'
month: '04'
page: 601 - 616
publication_status: published
publisher: Springer
publist_id: '3466'
quality_controlled: 0
status: public
title: Separating sources for encryption and secret sharing
type: conference
volume: 3876
year: '2006'
...
---
_id: '3216'
abstract:
- lang: eng
text: |-
We prove a new upper bound on the advantage of any adversary for distinguishing the encrypted CBC-MAC (EMAC) based on random permutations from a random function. Our proof uses techniques recently introduced in [BPR05], which again were inspired by [DGH + 04].
The bound we prove is tight — in the sense that it matches the advantage of known attacks up to a constant factor — for a wide range of the parameters: let n denote the block-size, q the number of queries the adversary is allowed to make and ℓ an upper bound on the length (i.e. number of blocks) of the messages, then for ℓ ≤ 2 n/8 and q≥ł2 the advantage is in the order of q 2/2 n (and in particular independent of ℓ). This improves on the previous bound of q 2ℓΘ(1/ln ln ℓ)/2 n from [BPR05] and matches the trivial attack (which thus is basically optimal) where one simply asks random queries until a collision is found.
acknowledgement: Part of this work is supported by the Commission of the European
Communities through the IST program under contract IST-2002-507932 ECRYPT.
alternative_title:
- LNCS
author:
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Pietrzak KZ. A tight bound for EMAC. In: Vol 4052. Springer; 2006:168-179.
doi:10.1007/11787006_15'
apa: 'Pietrzak, K. Z. (2006). A tight bound for EMAC (Vol. 4052, pp. 168–179). Presented
at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/11787006_15'
chicago: Pietrzak, Krzysztof Z. “A Tight Bound for EMAC,” 4052:168–79. Springer,
2006. https://doi.org/10.1007/11787006_15.
ieee: 'K. Z. Pietrzak, “A tight bound for EMAC,” presented at the ICALP: Automata,
Languages and Programming, 2006, vol. 4052, pp. 168–179.'
ista: 'Pietrzak KZ. 2006. A tight bound for EMAC. ICALP: Automata, Languages and
Programming, LNCS, vol. 4052, 168–179.'
mla: Pietrzak, Krzysztof Z. A Tight Bound for EMAC. Vol. 4052, Springer,
2006, pp. 168–79, doi:10.1007/11787006_15.
short: K.Z. Pietrzak, in:, Springer, 2006, pp. 168–179.
conference:
name: 'ICALP: Automata, Languages and Programming'
date_created: 2018-12-11T12:02:04Z
date_published: 2006-07-28T00:00:00Z
date_updated: 2021-01-12T07:41:52Z
day: '28'
doi: 10.1007/11787006_15
extern: 1
intvolume: ' 4052'
month: '07'
page: 168 - 179
publication_status: published
publisher: Springer
publist_id: '3463'
quality_controlled: 0
status: public
title: A tight bound for EMAC
type: conference
volume: 4052
year: '2006'
...
---
_id: '3217'
abstract:
- lang: eng
text: |-
To prove that a secure key-agreement protocol exists one must at least show P ≠NP. Moreover any proof that the sequential composition of two non-adaptively secure pseudorandom functions is secure against at least two adaptive queries must falsify the decisional Diffie-Hellman assumption, a standard assumption from public-key cryptography. Hence proving any of this two seemingly unrelated statements would require a significant breakthrough. We show that at least one of the two statements is true.
To our knowledge this gives the first positive cryptographic result (namely that composition implies some weak adaptive security) which holds in Minicrypt, but not in Cryptomania, i.e. under the assumption that one-way functions exist, but public-key cryptography does not.
acknowledgement: Author was supported during the writing of this work by the Swiss
National Science Foundation, project No. 200020-103847/1. Part of this work is supported
by the Commission of the European Communities through the IST program under contract
IST-2002-507932
alternative_title:
- LNCS
author:
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Pietrzak KZ. Composition implies adaptive security in minicrypt. In: Vol 4004.
Springer; 2006:328-338. doi:10.1007/11761679_20'
apa: 'Pietrzak, K. Z. (2006). Composition implies adaptive security in minicrypt
(Vol. 4004, pp. 328–338). Presented at the EUROCRYPT: Theory and Applications
of Cryptographic Techniques, Springer. https://doi.org/10.1007/11761679_20'
chicago: Pietrzak, Krzysztof Z. “Composition Implies Adaptive Security in Minicrypt,”
4004:328–38. Springer, 2006. https://doi.org/10.1007/11761679_20.
ieee: 'K. Z. Pietrzak, “Composition implies adaptive security in minicrypt,” presented
at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2006, vol.
4004, pp. 328–338.'
ista: 'Pietrzak KZ. 2006. Composition implies adaptive security in minicrypt. EUROCRYPT:
Theory and Applications of Cryptographic Techniques, LNCS, vol. 4004, 328–338.'
mla: Pietrzak, Krzysztof Z. Composition Implies Adaptive Security in Minicrypt.
Vol. 4004, Springer, 2006, pp. 328–38, doi:10.1007/11761679_20.
short: K.Z. Pietrzak, in:, Springer, 2006, pp. 328–338.
conference:
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
date_created: 2018-12-11T12:02:04Z
date_published: 2006-07-11T00:00:00Z
date_updated: 2021-01-12T07:41:52Z
day: '11'
doi: 10.1007/11761679_20
extern: 1
intvolume: ' 4004'
month: '07'
page: 328 - 338
publication_status: published
publisher: Springer
publist_id: '3464'
quality_controlled: 0
status: public
title: Composition implies adaptive security in minicrypt
type: conference
volume: 4004
year: '2006'
...
---
_id: '3404'
alternative_title:
- Manuals in Biomedical Research
author:
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Ravi
full_name: Sawhney, Ravi K
last_name: Sawhney
- first_name: Martin
full_name: Stark, Martin
last_name: Stark
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: 'Janovjak HL, Sawhney R, Stark M, Mueller D. Atomic force microscopy. In: Techniques
in Microscopy for Biomedical Applications. Vol 2. World Scientific Publishing;
2006:213-284.'
apa: Janovjak, H. L., Sawhney, R., Stark, M., & Mueller, D. (2006). Atomic force
microscopy. In Techniques in Microscopy for Biomedical Applications (Vol.
2, pp. 213–284). World Scientific Publishing.
chicago: Janovjak, Harald L, Ravi Sawhney, Martin Stark, and Daniel Mueller. “Atomic
Force Microscopy.” In Techniques in Microscopy for Biomedical Applications,
2:213–84. World Scientific Publishing, 2006.
ieee: H. L. Janovjak, R. Sawhney, M. Stark, and D. Mueller, “Atomic force microscopy,”
in Techniques in Microscopy for Biomedical Applications, vol. 2, World
Scientific Publishing, 2006, pp. 213–284.
ista: 'Janovjak HL, Sawhney R, Stark M, Mueller D. 2006.Atomic force microscopy.
In: Techniques in Microscopy for Biomedical Applications. Manuals in Biomedical
Research, vol. 2, 213–284.'
mla: Janovjak, Harald L., et al. “Atomic Force Microscopy.” Techniques in Microscopy
for Biomedical Applications, vol. 2, World Scientific Publishing, 2006, pp.
213–84.
short: H.L. Janovjak, R. Sawhney, M. Stark, D. Mueller, in:, Techniques in Microscopy
for Biomedical Applications, World Scientific Publishing, 2006, pp. 213–284.
date_created: 2018-12-11T12:03:09Z
date_published: 2006-09-28T00:00:00Z
date_updated: 2021-01-12T07:43:15Z
day: '28'
extern: 1
intvolume: ' 2'
month: '09'
page: 213 - 284
publication: Techniques in Microscopy for Biomedical Applications
publication_status: published
publisher: World Scientific Publishing
publist_id: '2998'
quality_controlled: 0
status: public
title: Atomic force microscopy
type: book_chapter
volume: 2
year: '2006'
...
---
_id: '3413'
abstract:
- lang: eng
text: |-
Despite their crucial importance for cellular function, little is known about the folding mechanisms of membrane proteins. Recently details of the folding energy landscape were elucidated by atomic force microscope (AFM)-based single molecule force spectroscopy. Upon unfolding and extraction of individual membrane proteins energy barriers in structural elements such as loops and helices were mapped and quantified with the precision of a few amino acids.
Here we report on the next logical step: controlled refolding of single proteins into the membrane. First individual bacteriorhodopsin monomers were partially unfolded and extracted from the purple membrane by pulling at the C-terminal end with an AFM tip. Then by gradually lowering the tip, the protein was allowed to refold into the membrane while the folding force was recorded.
We discovered that upon refolding certain helices are pulled into the membraneagainst a sizable externalforce of several tens of picoNewton. From the mechanical work, which the helix performs on the AFM cantilever, we derive an upper limit for the Gibbs free folding energy. Subsequent unfolding allowed us to analyze the pattern of unfolding barriers and corroborate that the protein had refolded into the native state.
author:
- first_name: Max
full_name: Kessler, Max
last_name: Kessler
- first_name: Kay
full_name: Gottschalk, Kay E
last_name: Gottschalk
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
- first_name: Hermann
full_name: Gaub, Hermann
last_name: Gaub
citation:
ama: Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. Bacteriorhodopsin
folds into the membrane against an external force. Journal of Molecular Biology.
2006;357(2):644-654. doi:10.1016/j.jmb.2005.12.065
apa: Kessler, M., Gottschalk, K., Janovjak, H. L., Mueller, D., & Gaub, H. (2006).
Bacteriorhodopsin folds into the membrane against an external force. Journal
of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2005.12.065
chicago: Kessler, Max, Kay Gottschalk, Harald L Janovjak, Daniel Mueller, and Hermann
Gaub. “Bacteriorhodopsin Folds into the Membrane against an External Force.” Journal
of Molecular Biology. Elsevier, 2006. https://doi.org/10.1016/j.jmb.2005.12.065.
ieee: M. Kessler, K. Gottschalk, H. L. Janovjak, D. Mueller, and H. Gaub, “Bacteriorhodopsin
folds into the membrane against an external force,” Journal of Molecular Biology,
vol. 357, no. 2. Elsevier, pp. 644–654, 2006.
ista: Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. 2006. Bacteriorhodopsin
folds into the membrane against an external force. Journal of Molecular Biology.
357(2), 644–654.
mla: Kessler, Max, et al. “Bacteriorhodopsin Folds into the Membrane against an
External Force.” Journal of Molecular Biology, vol. 357, no. 2, Elsevier,
2006, pp. 644–54, doi:10.1016/j.jmb.2005.12.065.
short: M. Kessler, K. Gottschalk, H.L. Janovjak, D. Mueller, H. Gaub, Journal of
Molecular Biology 357 (2006) 644–654.
date_created: 2018-12-11T12:03:12Z
date_published: 2006-03-24T00:00:00Z
date_updated: 2021-01-12T07:43:18Z
day: '24'
doi: 10.1016/j.jmb.2005.12.065
extern: 1
intvolume: ' 357'
issue: '2'
month: '03'
page: 644 - 654
publication: Journal of Molecular Biology
publication_status: published
publisher: Elsevier
publist_id: '2988'
quality_controlled: 0
status: public
title: Bacteriorhodopsin folds into the membrane against an external force
type: journal_article
volume: 357
year: '2006'
...
---
_id: '3414'
abstract:
- lang: eng
text: Mechanisms of folding and misfolding of membrane proteins are of interest
in cell biology. Recently, we have established single-molecule force spectroscopy
to observe directly the stepwise folding of the Na+/H+antiporter NhaA from Escherichia
coli in vitro. Here, we improved this approach significantly to track the folding
intermediates of asingle NhaA polypeptide forming structural segments such as
the Na+-binding site, transmembrane α-helices, and helical pairs. The folding
rates of structural segments ranged from 0.31 s−1 to 47 s−1, providing detailed
insight into a distinct folding hierarchy of an unfolded polypeptide into the
native membrane protein structure. In some cases, however, the folding chain formed
stable and kinetically trapped non-native structures, which could be assigned
to misfolding events of the antiporter.
author:
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Christine
full_name: Ziegler, Christine
last_name: Ziegler
- first_name: Werner
full_name: Kühlbrandt, Werner
last_name: Kühlbrandt
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. Observing folding
pathways and kinetics of a single sodium-proton antiporter from Escherichia coli.
Journal of Molecular Biology. 2006;355(1):2-8. doi:10.1016/j.jmb.2005.10.028
apa: Kedrov, A., Janovjak, H. L., Ziegler, C., Kühlbrandt, W., & Mueller, D.
(2006). Observing folding pathways and kinetics of a single sodium-proton antiporter
from Escherichia coli. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2005.10.028
chicago: Kedrov, Alexej, Harald L Janovjak, Christine Ziegler, Werner Kühlbrandt,
and Daniel Mueller. “Observing Folding Pathways and Kinetics of a Single Sodium-Proton
Antiporter from Escherichia Coli.” Journal of Molecular Biology. Elsevier,
2006. https://doi.org/10.1016/j.jmb.2005.10.028.
ieee: A. Kedrov, H. L. Janovjak, C. Ziegler, W. Kühlbrandt, and D. Mueller, “Observing
folding pathways and kinetics of a single sodium-proton antiporter from Escherichia
coli,” Journal of Molecular Biology, vol. 355, no. 1. Elsevier, pp. 2–8,
2006.
ista: Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. 2006. Observing
folding pathways and kinetics of a single sodium-proton antiporter from Escherichia
coli. Journal of Molecular Biology. 355(1), 2–8.
mla: Kedrov, Alexej, et al. “Observing Folding Pathways and Kinetics of a Single
Sodium-Proton Antiporter from Escherichia Coli.” Journal of Molecular Biology,
vol. 355, no. 1, Elsevier, 2006, pp. 2–8, doi:10.1016/j.jmb.2005.10.028.
short: A. Kedrov, H.L. Janovjak, C. Ziegler, W. Kühlbrandt, D. Mueller, Journal
of Molecular Biology 355 (2006) 2–8.
date_created: 2018-12-11T12:03:12Z
date_published: 2006-01-06T00:00:00Z
date_updated: 2021-01-12T07:43:19Z
day: '06'
doi: 10.1016/j.jmb.2005.10.028
extern: 1
intvolume: ' 355'
issue: '1'
month: '01'
page: 2 - 8
publication: Journal of Molecular Biology
publication_status: published
publisher: Elsevier
publist_id: '2987'
quality_controlled: 0
status: public
title: Observing folding pathways and kinetics of a single sodium-proton antiporter
from Escherichia coli
type: journal_article
volume: 355
year: '2006'
...
---
_id: '3415'
author:
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: David
full_name: Cisneros, David
last_name: Cisneros
- first_name: Tanuj
full_name: Sapra, Tanuj K
last_name: Sapra
- first_name: Jens
full_name: Struckmeier, Jens
last_name: Struckmeier
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. Imaging
and detecting molecular interactions of single membrane proteins. Neurobiology
of Aging. 2006;27:546-561. doi:10.1016/j.neurobiolaging.2005.03.031
apa: Janovjak, H. L., Kedrov, A., Cisneros, D., Sapra, T., Struckmeier, J., &
Mueller, D. (2006). Imaging and detecting molecular interactions of single membrane
proteins. Neurobiology of Aging. Elsevier. https://doi.org/10.1016/j.neurobiolaging.2005.03.031
chicago: Janovjak, Harald L, Alexej Kedrov, David Cisneros, Tanuj Sapra, Jens Struckmeier,
and Daniel Mueller. “Imaging and Detecting Molecular Interactions of Single Membrane
Proteins.” Neurobiology of Aging. Elsevier, 2006. https://doi.org/10.1016/j.neurobiolaging.2005.03.031.
ieee: H. L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, and D. Mueller,
“Imaging and detecting molecular interactions of single membrane proteins,” Neurobiology
of Aging, vol. 27. Elsevier, pp. 546–561, 2006.
ista: Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. 2006.
Imaging and detecting molecular interactions of single membrane proteins. Neurobiology
of Aging. 27, 546–561.
mla: Janovjak, Harald L., et al. “Imaging and Detecting Molecular Interactions of
Single Membrane Proteins.” Neurobiology of Aging, vol. 27, Elsevier, 2006,
pp. 546–61, doi:10.1016/j.neurobiolaging.2005.03.031.
short: H.L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, D. Mueller,
Neurobiology of Aging 27 (2006) 546–561.
date_created: 2018-12-11T12:03:12Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2019-04-26T07:22:27Z
day: '01'
doi: 10.1016/j.neurobiolaging.2005.03.031
extern: 1
intvolume: ' 27'
month: '01'
page: 546 - 561
publication: Neurobiology of Aging
publication_status: published
publisher: Elsevier
publist_id: '2986'
quality_controlled: 0
status: public
title: Imaging and detecting molecular interactions of single membrane proteins
type: review
volume: 27
year: '2006'
...
---
_id: '3431'
abstract:
- lang: eng
text: Ising models with pairwise interactions are the least structured, or maximum-entropy,
probability distributions that exactly reproduce measured pairwise correlations
between spins. Here we use this equivalence to construct Ising models that describe
the correlated spiking activity of populations of 40 neurons in the retina, and
show that pairwise interactions account for observed higher-order correlations.
By first finding a representative ensemble for observed networks we can create
synthetic networks of 120 neurons, and find that with increasing size the networks
operate closer to a critical point and start exhibiting collective behaviors reminiscent
of spin glasses.
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: E.
full_name: Schneidman, E.
last_name: Schneidman
- first_name: M.
full_name: Berry, M. J.
last_name: Berry
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Tkačik G, Schneidman E, Berry M, Bialek W. Ising models for networks of real
neurons. ArXiv. 2006:1-4.
apa: Tkačik, G., Schneidman, E., Berry, M., & Bialek, W. (2006). Ising models
for networks of real neurons. ArXiv. ArXiv.
chicago: Tkačik, Gašper, E. Schneidman, M. Berry, and William Bialek. “Ising Models
for Networks of Real Neurons.” ArXiv. ArXiv, 2006.
ieee: G. Tkačik, E. Schneidman, M. Berry, and W. Bialek, “Ising models for networks
of real neurons,” ArXiv. ArXiv, pp. 1–4, 2006.
ista: Tkačik G, Schneidman E, Berry M, Bialek W. 2006. Ising models for networks
of real neurons. ArXiv, 1–4, .
mla: Tkačik, Gašper, et al. “Ising Models for Networks of Real Neurons.” ArXiv,
ArXiv, 2006, pp. 1–4.
short: G. Tkačik, E. Schneidman, M. Berry, W. Bialek, ArXiv (2006) 1–4.
date_created: 2018-12-11T12:03:18Z
date_published: 2006-11-22T00:00:00Z
date_updated: 2021-01-12T07:43:25Z
day: '22'
extern: 1
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/q-bio/0611072
month: '11'
oa: 1
page: 1 - 4
publication: ArXiv
publication_status: published
publisher: ArXiv
publist_id: '2969'
quality_controlled: 0
status: public
title: Ising models for networks of real neurons
type: preprint
year: '2006'
...
---
_id: '3437'
abstract:
- lang: eng
text: The mutational landscape model is a theoretical model describing sequence
evolution in natural populations. However, recent experimental work has begun
to test its predictions in laboratory populations of microbes. Several of these
studies have focused on testing the prediction that the effects of beneficial
mutations should be roughly exponentially distributed. The prediction appears
to be borne out by most of these studies, at least qualitatively. Another study
showed that a modified version of the model was able to predict, with reasonable
accuracy, which of a ranked set of beneficial alleles will be fixed next. Although
it remains to be seen whether the mutational landscape model adequately describes
adaptation in organisms other than microbes, together these studies suggest that
adaptive evolution has surprisingly general properties that can be successfully
captured by theoretical models.
author:
- first_name: Andrea
full_name: Betancourt, Andrea J
last_name: Betancourt
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: 'Betancourt A, Bollback JP. Fitness effects of beneficial mutations: the mutational
landscape model in experimental evolution. Current Opinion in Genetics &
Development. 2006;16(6):618-623. doi:10.1016/j.gde.2006.10.006'
apa: 'Betancourt, A., & Bollback, J. P. (2006). Fitness effects of beneficial
mutations: the mutational landscape model in experimental evolution. Current
Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2006.10.006'
chicago: 'Betancourt, Andrea, and Jonathan P Bollback. “Fitness Effects of Beneficial
Mutations: The Mutational Landscape Model in Experimental Evolution.” Current
Opinion in Genetics & Development. Elsevier, 2006. https://doi.org/10.1016/j.gde.2006.10.006.'
ieee: 'A. Betancourt and J. P. Bollback, “Fitness effects of beneficial mutations:
the mutational landscape model in experimental evolution,” Current Opinion
in Genetics & Development, vol. 16, no. 6. Elsevier, pp. 618–623, 2006.'
ista: 'Betancourt A, Bollback JP. 2006. Fitness effects of beneficial mutations:
the mutational landscape model in experimental evolution. Current Opinion in Genetics
& Development. 16(6), 618–623.'
mla: 'Betancourt, Andrea, and Jonathan P. Bollback. “Fitness Effects of Beneficial
Mutations: The Mutational Landscape Model in Experimental Evolution.” Current
Opinion in Genetics & Development, vol. 16, no. 6, Elsevier, 2006, pp.
618–23, doi:10.1016/j.gde.2006.10.006.'
short: A. Betancourt, J.P. Bollback, Current Opinion in Genetics & Development
16 (2006) 618–623.
date_created: 2018-12-11T12:03:19Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2021-01-12T07:43:27Z
day: '01'
doi: 10.1016/j.gde.2006.10.006
extern: 1
intvolume: ' 16'
issue: '6'
month: '12'
page: 618 - 623
publication: Current Opinion in Genetics & Development
publication_status: published
publisher: Elsevier
publist_id: '2963'
quality_controlled: 0
status: public
title: 'Fitness effects of beneficial mutations: the mutational landscape model in
experimental evolution'
type: journal_article
volume: 16
year: '2006'
...
---
_id: '3449'
abstract:
- lang: eng
text: We argue that games are expressive enough to encompass (history-based) access
control, (resource) usage control (e.g., dynamic adaptive access control of reputation
systems), accountability based controls (e.g., insurance), controls derived from
rationality assumptions on participants (e.g., network mechanisms), and their
composition. Building on the extensive research into games, we demonstrate that
this expressive power coexists with a formal analysis framework comparable to
that available for access control.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rhada
full_name: Jagadeesan, Rhada
last_name: Jagadeesan
- first_name: Corin
full_name: Pitcher, Corin
last_name: Pitcher
citation:
ama: 'Chatterjee K, Jagadeesan R, Pitcher C. Games for controls. In: IEEE; 2006:70-82.
doi:10.1109/CSFW.2006.14'
apa: 'Chatterjee, K., Jagadeesan, R., & Pitcher, C. (2006). Games for controls
(pp. 70–82). Presented at the CSF: Computer Security Foundations, IEEE. https://doi.org/10.1109/CSFW.2006.14'
chicago: Chatterjee, Krishnendu, Rhada Jagadeesan, and Corin Pitcher. “Games for
Controls,” 70–82. IEEE, 2006. https://doi.org/10.1109/CSFW.2006.14.
ieee: 'K. Chatterjee, R. Jagadeesan, and C. Pitcher, “Games for controls,” presented
at the CSF: Computer Security Foundations, 2006, pp. 70–82.'
ista: 'Chatterjee K, Jagadeesan R, Pitcher C. 2006. Games for controls. CSF: Computer
Security Foundations, 70–82.'
mla: Chatterjee, Krishnendu, et al. Games for Controls. IEEE, 2006, pp. 70–82,
doi:10.1109/CSFW.2006.14.
short: K. Chatterjee, R. Jagadeesan, C. Pitcher, in:, IEEE, 2006, pp. 70–82.
conference:
name: 'CSF: Computer Security Foundations'
date_created: 2018-12-11T12:03:23Z
date_published: 2006-07-31T00:00:00Z
date_updated: 2021-01-12T07:43:32Z
day: '31'
doi: 10.1109/CSFW.2006.14
extern: 1
month: '07'
page: 70 - 82
publication_status: published
publisher: IEEE
publist_id: '2938'
quality_controlled: 0
status: public
title: Games for controls
type: conference
year: '2006'
...
---
_id: '3463'
abstract:
- lang: eng
text: It is widely accepted that the hippocampus plays a major role in learning
and memory. The mossy fiber synapse between granule cells in the dentate gyrus
and pyramidal neurons in the CA3 region is a key component of the hippocampal
trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp
recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms
of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+)
channel density in mossy fiber boutons leads to a large amplitude of the presynaptic
action potential. Together with the fast gating of presynaptic Ca(2+) channels,
this generates a large and brief presynaptic Ca(2+) influx, which can trigger
transmitter release with high efficiency and temporal precision. The large number
of release sites, the large size of the releasable pool of vesicles, and the huge
extent of presynaptic plasticity confer unique strength to this synapse, suggesting
a large impact onto the CA3 pyramidal cell network under specific behavioral conditions.
The characteristic properties of the hippocampal mossy fiber synapse may be important
for pattern separation and information storage in the dentate gyrus-CA3 cell network.
author:
- first_name: Joseph
full_name: Bischofberger, Joseph
last_name: Bischofberger
- first_name: Dominique
full_name: Engel, Dominique
last_name: Engel
- 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: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. Timing and efficacy of transmitter
release at mossy fiber synapses in the hippocampal network. (Review). Pflugers
Archiv : European Journal of Physiology. 2006;453(3):361-372. doi:10.1007/s00424-006-0093-2'
apa: 'Bischofberger, J., Engel, D., Frotscher, M., & Jonas, P. M. (2006). Timing
and efficacy of transmitter release at mossy fiber synapses in the hippocampal
network. (Review). Pflugers Archiv : European Journal of Physiology. Springer.
https://doi.org/10.1007/s00424-006-0093-2'
chicago: 'Bischofberger, Joseph, Dominique Engel, Michael Frotscher, and Peter M
Jonas. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in
the Hippocampal Network. (Review).” Pflugers Archiv : European Journal of Physiology.
Springer, 2006. https://doi.org/10.1007/s00424-006-0093-2.'
ieee: 'J. Bischofberger, D. Engel, M. Frotscher, and P. M. Jonas, “Timing and efficacy
of transmitter release at mossy fiber synapses in the hippocampal network. (Review),”
Pflugers Archiv : European Journal of Physiology, vol. 453, no. 3. Springer,
pp. 361–372, 2006.'
ista: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. 2006. Timing and efficacy
of transmitter release at mossy fiber synapses in the hippocampal network. (Review).
Pflugers Archiv : European Journal of Physiology. 453(3), 361–372.'
mla: 'Bischofberger, Joseph, et al. “Timing and Efficacy of Transmitter Release
at Mossy Fiber Synapses in the Hippocampal Network. (Review).” Pflugers Archiv :
European Journal of Physiology, vol. 453, no. 3, Springer, 2006, pp. 361–72,
doi:10.1007/s00424-006-0093-2.'
short: 'J. Bischofberger, D. Engel, M. Frotscher, P.M. Jonas, Pflugers Archiv :
European Journal of Physiology 453 (2006) 361–372.'
date_created: 2018-12-11T12:03:28Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2019-04-26T07:22:28Z
day: '01'
doi: 10.1007/s00424-006-0093-2
extern: 1
intvolume: ' 453'
issue: '3'
month: '12'
page: 361 - 372
publication: 'Pflugers Archiv : European Journal of Physiology'
publication_status: published
publisher: Springer
publist_id: '2924'
quality_controlled: 0
status: public
title: Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal
network. (Review)
type: review
volume: 453
year: '2006'
...