---
_id: '3175'
abstract:
- lang: eng
text: This paper addresses the novel problem of automatically synthesizing an output
image from a large collection of different input images. The synthesized image,
called a digital tapestry, can be viewed as a visual summary or a virtual 'thumbnail'
of all the images in the input collection. The problem of creating the tapestry
is cast as a multi-class labeling problem such that each region in the tapestry
is constructed from input image blocks that are salient and such that neighboring
blocks satisfy spatial compatibility. This is formulated using a Markov Random
Field and optimized via the graph cut based expansion move algorithm. The standard
expansion move algorithm can only handle energies with metric terms, while our
energy contains non-metric (soft and hard) constraints. Therefore we propose two
novel contributions. First, we extend the expansion move algorithm for energy
functions with non-metric hard constraints. Secondly, we modify it for functions
with "almost" metric soft terms, and show that it gives good results
in practice. The proposed framework was tested on several consumer photograph
collections, and the results are presented.
author:
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Sanjiv
full_name: Kumar, Sanjiv
last_name: Kumar
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
citation:
ama: 'Rother C, Kumar S, Kolmogorov V, Blake A. Digital tapestry. In: Vol 1. IEEE;
2005:589-596. doi:10.1109/CVPR.2005.130'
apa: 'Rother, C., Kumar, S., Kolmogorov, V., & Blake, A. (2005). Digital tapestry
(Vol. 1, pp. 589–596). Presented at the CVPR: Computer Vision and Pattern Recognition,
IEEE. https://doi.org/10.1109/CVPR.2005.130'
chicago: Rother, Carsten, Sanjiv Kumar, Vladimir Kolmogorov, and Andrew Blake. “Digital
Tapestry,” 1:589–96. IEEE, 2005. https://doi.org/10.1109/CVPR.2005.130.
ieee: 'C. Rother, S. Kumar, V. Kolmogorov, and A. Blake, “Digital tapestry,” presented
at the CVPR: Computer Vision and Pattern Recognition, 2005, vol. 1, pp. 589–596.'
ista: 'Rother C, Kumar S, Kolmogorov V, Blake A. 2005. Digital tapestry. CVPR: Computer
Vision and Pattern Recognition vol. 1, 589–596.'
mla: Rother, Carsten, et al. Digital Tapestry. Vol. 1, IEEE, 2005, pp. 589–96,
doi:10.1109/CVPR.2005.130.
short: C. Rother, S. Kumar, V. Kolmogorov, A. Blake, in:, IEEE, 2005, pp. 589–596.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:50Z
date_published: 2005-07-25T00:00:00Z
date_updated: 2021-01-12T07:41:35Z
day: '25'
doi: 10.1109/CVPR.2005.130
extern: 1
intvolume: ' 1'
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/en-us/um/people/ablake/papers/ablake/rother_cvpr05.pdf
month: '07'
page: 589 - 596
publication_status: published
publisher: IEEE
publist_id: '3503'
quality_controlled: 0
status: public
title: Digital tapestry
type: conference
volume: 1
year: '2005'
...
---
_id: '3176'
abstract:
- lang: eng
text: |
This paper demonstrates the high quality, real-time segmentation techniques. We achieve real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from colour/contrast or from stereo alone is known to be error-prone. Here, colour, 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 6-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive colour 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 marginalised over foreground and background hypotheses, and fused with a contrast-sensitive colour 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 stereo or colour/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. Bi-layer segmentation
of binocular stereo video. In: IEEE; 2005:1186-1186. doi:10.1109/CVPR.2005.90'
apa: 'Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., & Rother, C. (2005).
Bi-layer segmentation of binocular stereo video (pp. 1186–1186). Presented at
the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2005.90'
chicago: Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross,
and Carsten Rother. “Bi-Layer Segmentation of Binocular Stereo Video,” 1186–1186.
IEEE, 2005. https://doi.org/10.1109/CVPR.2005.90.
ieee: 'V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Bi-layer
segmentation of binocular stereo video,” presented at the CVPR: Computer Vision
and Pattern Recognition, 2005, pp. 1186–1186.'
ista: 'Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2005. Bi-layer segmentation
of binocular stereo video. CVPR: Computer Vision and Pattern Recognition, 1186–1186.'
mla: Kolmogorov, Vladimir, et al. Bi-Layer Segmentation of Binocular Stereo Video.
IEEE, 2005, pp. 1186–1186, doi:10.1109/CVPR.2005.90.
short: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, in:, IEEE, 2005,
pp. 1186–1186.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:50Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:35Z
day: '01'
doi: 10.1109/CVPR.2005.90
extern: 1
month: '01'
page: 1186 - 1186
publication_status: published
publisher: IEEE
publist_id: '3504'
quality_controlled: 0
status: public
title: Bi-layer segmentation of binocular stereo video
type: conference
year: '2005'
...
---
_id: '3181'
abstract:
- lang: eng
text: Tree-reweighted max-product (TRW) message passing [9] is a modified form of
the ordinary max-product algorithm for attempting to find minimal energy configurations
in Markov random field with cycles. For a TRW fixed point satisfying the strong
tree agreement condition, the algorithm outputs a configuration that is provably
optimal. In this paper, we focus on the case of binary variables with pairwise
couplings, and establish stronger properties of TRW fixed points that satisfy
only the milder condition of weak tree agreement (WTA). First, we demonstrate
how it is possible to identify part of the optimal solution - i.e., a provably
optimal solution for a subset of nodes - without knowing a complete solution.
Second, we show that for submodular functions, a WTA fixed point always yields
a globally optimal solution. We establish that for binary variables, any WTA fixed
point always achieves the global maximum of the linear programming relaxation
underlying the TRW method.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Martin
full_name: Wainwright, Martin J
last_name: Wainwright
citation:
ama: 'Kolmogorov V, Wainwright M. On the optimality of tree reweighted max product
message passing. In: AUAI Press; 2005:316-323.'
apa: 'Kolmogorov, V., & Wainwright, M. (2005). On the optimality of tree reweighted
max product message passing (pp. 316–323). Presented at the UAI: Uncertainty in
Artificial Intelligence, AUAI Press.'
chicago: Kolmogorov, Vladimir, and Martin Wainwright. “On the Optimality of Tree
Reweighted Max Product Message Passing,” 316–23. AUAI Press, 2005.
ieee: 'V. Kolmogorov and M. Wainwright, “On the optimality of tree reweighted max
product message passing,” presented at the UAI: Uncertainty in Artificial Intelligence,
2005, pp. 316–323.'
ista: 'Kolmogorov V, Wainwright M. 2005. On the optimality of tree reweighted max
product message passing. UAI: Uncertainty in Artificial Intelligence, 316–323.'
mla: Kolmogorov, Vladimir, and Martin Wainwright. On the Optimality of Tree Reweighted
Max Product Message Passing. AUAI Press, 2005, pp. 316–23.
short: V. Kolmogorov, M. Wainwright, in:, AUAI Press, 2005, pp. 316–323.
conference:
name: 'UAI: Uncertainty in Artificial Intelligence'
date_created: 2018-12-11T12:01:51Z
date_published: 2005-07-01T00:00:00Z
date_updated: 2021-01-12T07:41:38Z
day: '01'
extern: 1
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67405/trw_opt_uai05.pdf
month: '07'
page: 316 - 323
publication_status: published
publisher: AUAI Press
publist_id: '3500'
quality_controlled: 0
status: public
title: On the optimality of tree reweighted max product message passing
type: conference
year: '2005'
...
---
_id: '3182'
abstract:
- lang: eng
text: In the work of the authors (2003), we showed that graph cuts can find hypersurfaces
of globally minimal length (or area) under any Riemannian metric. Here we show
that graph cuts on directed regular grids can approximate a significantly more
general class of continuous non-symmetric metrics. Using submodularity condition
(Boros and Hammer, 2002 and Kolmogorov and Zabih, 2004), we obtain a tight characterization
of graph-representable metrics. Such "submodular" metrics have an elegant
geometric interpretation via hypersurface functionals combining length/area and
flux. Practically speaking, we attend 'geo-cuts' algorithm to a wider class of
geometrically motivated hypersurface functionals and show how to globally optimize
any combination of length/area and flux of a given vector field. The concept of
flux was recently introduced into computer vision by Vasilevskiy and Siddiqi (2002)
but it was mainly studied within variational framework so far. We are first to
show that flux can be integrated into graph cuts as well. Combining geometric
concepts of flux and length/area within the global optimization framework of graph
cuts allows principled discrete segmentation models and advances the slate of
the art for the graph cuts methods in vision. In particular we address the "shrinking"
problem of graph cuts, improve segmentation of long thin objects, and introduce
useful shape constraints.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Yuri
full_name: Boykov, Yuri
last_name: Boykov
citation:
ama: 'Kolmogorov V, Boykov Y. What metrics can be approximated by geo cuts or global
optimization of length area and flux. In: Vol 1. IEEE; 2005:564-571. doi:10.1109/ICCV.2005.252'
apa: 'Kolmogorov, V., & Boykov, Y. (2005). What metrics can be approximated
by geo cuts or global optimization of length area and flux (Vol. 1, pp. 564–571).
Presented at the ICCV: International Conference on Computer Vision, IEEE. https://doi.org/10.1109/ICCV.2005.252'
chicago: Kolmogorov, Vladimir, and Yuri Boykov. “What Metrics Can Be Approximated
by Geo Cuts or Global Optimization of Length Area and Flux,” 1:564–71. IEEE, 2005.
https://doi.org/10.1109/ICCV.2005.252.
ieee: 'V. Kolmogorov and Y. Boykov, “What metrics can be approximated by geo cuts
or global optimization of length area and flux,” presented at the ICCV: International
Conference on Computer Vision, 2005, vol. 1, pp. 564–571.'
ista: 'Kolmogorov V, Boykov Y. 2005. What metrics can be approximated by geo cuts
or global optimization of length area and flux. ICCV: International Conference
on Computer Vision vol. 1, 564–571.'
mla: Kolmogorov, Vladimir, and Yuri Boykov. What Metrics Can Be Approximated
by Geo Cuts or Global Optimization of Length Area and Flux. Vol. 1, IEEE,
2005, pp. 564–71, doi:10.1109/ICCV.2005.252.
short: V. Kolmogorov, Y. Boykov, in:, IEEE, 2005, pp. 564–571.
conference:
name: 'ICCV: International Conference on Computer Vision'
date_created: 2018-12-11T12:01:52Z
date_published: 2005-12-05T00:00:00Z
date_updated: 2021-01-12T07:41:38Z
day: '05'
doi: 10.1109/ICCV.2005.252
extern: 1
intvolume: ' 1'
month: '12'
page: 564 - 571
publication_status: published
publisher: IEEE
publist_id: '3501'
quality_controlled: 0
status: public
title: What metrics can be approximated by geo cuts or global optimization of length
area and flux
type: conference
volume: 1
year: '2005'
...
---
_id: '3183'
abstract:
- lang: eng
text: This paper describes two algorithms capable of real-time segmentation of foreground
from background layers in stereo video sequences. Automatic separation of layers
from colour/contrast or from stereo alone is known to be error-prone. Here, colour,
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 6-state space that represents both foreground/background
layers and occluded regions. The stereo-match likelihood is then fused with a
contrast-sensitive colour 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 marginalised
over foreground and background hypotheses, and fused with a contrast-sensitive
colour 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 perfomance, substantially better than stereo or colour/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. Bi-layer segmentation
of binocular stereo video. In: Vol 2. IEEE; 2005:407-414. doi:10.1109/CVPR.2005.91'
apa: 'Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., & Rother, C. (2005).
Bi-layer segmentation of binocular stereo video (Vol. 2, pp. 407–414). Presented
at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2005.91'
chicago: Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross,
and Carsten Rother. “Bi-Layer Segmentation of Binocular Stereo Video,” 2:407–14.
IEEE, 2005. https://doi.org/10.1109/CVPR.2005.91.
ieee: 'V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Bi-layer
segmentation of binocular stereo video,” presented at the CVPR: Computer Vision
and Pattern Recognition, 2005, vol. 2, pp. 407–414.'
ista: 'Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2005. Bi-layer segmentation
of binocular stereo video. CVPR: Computer Vision and Pattern Recognition vol.
2, 407–414.'
mla: Kolmogorov, Vladimir, et al. Bi-Layer Segmentation of Binocular Stereo Video.
Vol. 2, IEEE, 2005, pp. 407–14, doi:10.1109/CVPR.2005.91.
short: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, in:, IEEE, 2005,
pp. 407–414.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:52Z
date_published: 2005-07-25T00:00:00Z
date_updated: 2021-01-12T07:41:38Z
day: '25'
doi: 10.1109/CVPR.2005.91
extern: 1
intvolume: ' 2'
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67281/criminisi_cvpr2005.pdf
month: '07'
page: 407 - 414
publication_status: published
publisher: IEEE
publist_id: '3502'
quality_controlled: 0
status: public
title: Bi-layer segmentation of binocular stereo video
type: conference
volume: 2
year: '2005'
...
---
_id: '3211'
abstract:
- lang: eng
text: We present an improved bound on the advantage of any q-query adversary at
distinguishing between the CBC MAC over a random n-bit permutation and a random
function outputting n bits. The result assumes that no message queried is a prefix
of any other, as is the case when all messages to be MACed have the same length.
We go on to give an improved analysis of the encrypted CBC MAC, where there is
no restriction on queried messages. Letting m be the block length of the longest
query, our bounds are about mq2/2n for the basic CBC MAC and mo(1)q2/2n for the
encrypted CBC MAC, improving prior bounds of m2q2/2n. The new bounds translate
into improved guarantees on the probability of forging these MACs.
acknowledgement: Pietrzak was supported by the Swiss National Science Foundation,
project No. 200020-103847/1.
alternative_title:
- LNCS
author:
- first_name: Mihir
full_name: Bellare, Mihir
last_name: Bellare
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Phillip
full_name: Rogaway, Phillip
last_name: Rogaway
citation:
ama: 'Bellare M, Pietrzak KZ, Rogaway P. Improved security analyses for CBC MACs.
In: Vol 3621. Springer; 2005:527-545. doi:10.1007/11535218_32'
apa: 'Bellare, M., Pietrzak, K. Z., & Rogaway, P. (2005). Improved security
analyses for CBC MACs (Vol. 3621, pp. 527–545). Presented at the CRYPTO: International
Cryptology Conference, Springer. https://doi.org/10.1007/11535218_32'
chicago: Bellare, Mihir, Krzysztof Z Pietrzak, and Phillip Rogaway. “Improved Security
Analyses for CBC MACs,” 3621:527–45. Springer, 2005. https://doi.org/10.1007/11535218_32.
ieee: 'M. Bellare, K. Z. Pietrzak, and P. Rogaway, “Improved security analyses for
CBC MACs,” presented at the CRYPTO: International Cryptology Conference, 2005,
vol. 3621, pp. 527–545.'
ista: 'Bellare M, Pietrzak KZ, Rogaway P. 2005. Improved security analyses for CBC
MACs. CRYPTO: International Cryptology Conference, LNCS, vol. 3621, 527–545.'
mla: Bellare, Mihir, et al. Improved Security Analyses for CBC MACs. Vol.
3621, Springer, 2005, pp. 527–45, doi:10.1007/11535218_32.
short: M. Bellare, K.Z. Pietrzak, P. Rogaway, in:, Springer, 2005, pp. 527–545.
conference:
name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:02Z
date_published: 2005-09-12T00:00:00Z
date_updated: 2021-01-12T07:41:50Z
day: '12'
doi: 10.1007/11535218_32
extern: 1
intvolume: ' 3621'
month: '09'
page: 527 - 545
publication_status: published
publisher: Springer
publist_id: '3469'
quality_controlled: 0
status: public
title: Improved security analyses for CBC MACs
type: conference
volume: 3621
year: '2005'
...
---
_id: '3212'
abstract:
- lang: eng
text: |-
The Full-Domain Hash (FDH) signature scheme [3] forms one the most basic usages of random oracles. It works with a family F of trapdoor permutations (TDP), where the signature of m is computed as f−1(h(m)) (here f ∈R F and h is modelled as a random oracle). It is known to be existentially unforgeable for any TDP family F [3], although a much tighter security reduction is known for a restrictive class of TDP’s [10,14] — namely, those induced by a family of claw-free permutations (CFP) pairs. The latter result was shown [11] to match the best possible “black-box” security reduction in the random oracle model, irrespective of the TDP family F (e.g., RSA) one might use.
In this work we investigate the question if it is possible to instantiate the random oracle h with a “real” family of hash functions H such that the corresponding schemes can be proven secure in the standard model, under some natural assumption on the family F. Our main result rules out the existence of such instantiations for any assumption on F which (1) is satisfied by a family of random permutations; and (2) does not allow the attacker to invert f ∈R F on an a-priori unbounded number of points. Moreover, this holds even if the choice of H can arbitrarily depend on f. As an immediate corollary, we rule out instantiating FDH based on general claw-free permutations, which shows that in order to prove the security of FDH in the standard model one must utilize significantly more structure on F than what is sufficient for the best proof of security in the random oracle model.
acknowledgement: Supported by NSF CAREER Award CCR-0133806 and TC Grant No.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: Roberto
full_name: Oliveira, Roberto
last_name: Oliveira
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Dodis Y, Oliveira R, Pietrzak KZ. On the generic insecurity of the full domain
hash. In: Vol 3621. Springer; 2005:449-466. doi:10.1007/11535218_27'
apa: 'Dodis, Y., Oliveira, R., & Pietrzak, K. Z. (2005). On the generic insecurity
of the full domain hash (Vol. 3621, pp. 449–466). Presented at the CRYPTO: International
Cryptology Conference, Springer. https://doi.org/10.1007/11535218_27'
chicago: Dodis, Yevgeniy, Roberto Oliveira, and Krzysztof Z Pietrzak. “On the Generic
Insecurity of the Full Domain Hash,” 3621:449–66. Springer, 2005. https://doi.org/10.1007/11535218_27.
ieee: 'Y. Dodis, R. Oliveira, and K. Z. Pietrzak, “On the generic insecurity of
the full domain hash,” presented at the CRYPTO: International Cryptology Conference,
2005, vol. 3621, pp. 449–466.'
ista: 'Dodis Y, Oliveira R, Pietrzak KZ. 2005. On the generic insecurity of the
full domain hash. CRYPTO: International Cryptology Conference, LNCS, vol. 3621,
449–466.'
mla: Dodis, Yevgeniy, et al. On the Generic Insecurity of the Full Domain Hash.
Vol. 3621, Springer, 2005, pp. 449–66, doi:10.1007/11535218_27.
short: Y. Dodis, R. Oliveira, K.Z. Pietrzak, in:, Springer, 2005, pp. 449–466.
conference:
name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:03Z
date_published: 2005-09-12T00:00:00Z
date_updated: 2021-01-12T07:41:50Z
day: '12'
doi: 10.1007/11535218_27
extern: 1
intvolume: ' 3621'
month: '09'
page: 449 - 466
publication_status: published
publisher: Springer
publist_id: '3470'
quality_controlled: 0
status: public
title: On the generic insecurity of the full domain hash
type: conference
volume: 3621
year: '2005'
...
---
_id: '3213'
abstract:
- lang: eng
text: |-
We study the question whether the sequential or parallel composition of two functions, each indistinguishable from a random function by non-adaptive distinguishers is secure against adaptive distinguishers. The sequential composition of F and G is the function G(F()), the parallel composition is F G where ⋆ is some group operation. It has been shown that composition indeed gives adaptive security in the information theoretic setting, but unfortunately the proof does not translate into the more interesting computational case.
In this work we show that in the computational setting composition does not imply adaptive security: If there is a prime order cyclic group where the decisional Diffie-Hellman assumption holds, then there are functions F and G which are indistinguishable by non-adaptive polynomially time-bounded adversaries, but whose parallel composition can be completely broken (i.e. we recover the key) with only three adaptive queries. We give a similar result for sequential composition. Interestingly, we need a standard assumption from the asymmetric (aka. public-key) world to prove a negative result for symmetric (aka. private-key) systems.
acknowledgement: Supported by the Swiss National Science Foundation, project No. 200020-103847/1.
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 does not imply adaptive security. In: Vol 3621. Springer;
2005:55-65. doi:10.1007/11535218_4'
apa: 'Pietrzak, K. Z. (2005). Composition does not imply adaptive security (Vol.
3621, pp. 55–65). Presented at the CRYPTO: International Cryptology Conference,
Springer. https://doi.org/10.1007/11535218_4'
chicago: Pietrzak, Krzysztof Z. “Composition Does Not Imply Adaptive Security,”
3621:55–65. Springer, 2005. https://doi.org/10.1007/11535218_4.
ieee: 'K. Z. Pietrzak, “Composition does not imply adaptive security,” presented
at the CRYPTO: International Cryptology Conference, 2005, vol. 3621, pp. 55–65.'
ista: 'Pietrzak KZ. 2005. Composition does not imply adaptive security. CRYPTO:
International Cryptology Conference, LNCS, vol. 3621, 55–65.'
mla: Pietrzak, Krzysztof Z. Composition Does Not Imply Adaptive Security.
Vol. 3621, Springer, 2005, pp. 55–65, doi:10.1007/11535218_4.
short: K.Z. Pietrzak, in:, Springer, 2005, pp. 55–65.
conference:
name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:03Z
date_published: 2005-09-12T00:00:00Z
date_updated: 2021-01-12T07:41:50Z
day: '12'
doi: 10.1007/11535218_4
extern: 1
intvolume: ' 3621'
month: '09'
page: 55 - 65
publication_status: published
publisher: Springer
publist_id: '3468'
quality_controlled: 0
status: public
title: Composition does not imply adaptive security
type: conference
volume: 3621
year: '2005'
...
---
_id: '3416'
abstract:
- lang: eng
text: In the last decade atomic force microscopy has been used to measure the mechanical
stability of single proteins. These force spectroscopy experiments have shown
that many water-soluble and membrane proteins unfold via one or more intermediates.
Recently, Li and co-workers found a linear correlation between the unfolding force
of the native state and the intermediate in fibronectin, which they suggested
indicated the presence of a molecular memory or multiple unfolding pathways (1).
Here, we apply two independent methods in combination with Monte Carlo simulations
to analyze the unfolding of α-helices E and D of bacteriorhodopsin (BR). We show
that correlation analysis of unfolding forces is very sensitive to errors in force
calibration of the instrument. In contrast, a comparison of relative forces provides
a robust measure for the stability of unfolding intermediates. The proposed approach
detects three energetically different states of α-helices E and D in trimeric
BR. These states are not observed for monomeric BR and indicate that substantial
information is hidden in forced unfolding experiments of single proteins.
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: Tanuj
full_name: Sapra, Tanuj K
last_name: Sapra
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Janovjak HL, Sapra T, Mueller D. Complex stability of single proteins explored
by forced unfolding experiments. Biophysical Journal. 2005;88(5):37-39.
doi:10.1529/biophysj.105.059774
apa: Janovjak, H. L., Sapra, T., & Mueller, D. (2005). Complex stability of
single proteins explored by forced unfolding experiments. Biophysical Journal.
Biophysical Society. https://doi.org/10.1529/biophysj.105.059774
chicago: Janovjak, Harald L, Tanuj Sapra, and Daniel Mueller. “Complex Stability
of Single Proteins Explored by Forced Unfolding Experiments.” Biophysical Journal.
Biophysical Society, 2005. https://doi.org/10.1529/biophysj.105.059774.
ieee: H. L. Janovjak, T. Sapra, and D. Mueller, “Complex stability of single proteins
explored by forced unfolding experiments,” Biophysical Journal, vol. 88,
no. 5. Biophysical Society, pp. 37–39, 2005.
ista: Janovjak HL, Sapra T, Mueller D. 2005. Complex stability of single proteins
explored by forced unfolding experiments. Biophysical Journal. 88(5), 37–39.
mla: Janovjak, Harald L., et al. “Complex Stability of Single Proteins Explored
by Forced Unfolding Experiments.” Biophysical Journal, vol. 88, no. 5,
Biophysical Society, 2005, pp. 37–39, doi:10.1529/biophysj.105.059774.
short: H.L. Janovjak, T. Sapra, D. Mueller, Biophysical Journal 88 (2005) 37–39.
date_created: 2018-12-11T12:03:13Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T07:43:19Z
day: '01'
doi: 10.1529/biophysj.105.059774
extern: 1
intvolume: ' 88'
issue: '5'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305525/
month: '05'
oa: 1
page: 37 - 39
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '2985'
quality_controlled: 0
status: public
title: Complex stability of single proteins explored by forced unfolding experiments
type: journal_article
volume: 88
year: '2005'
...
---
_id: '3417'
abstract:
- lang: eng
text: Recently, direct measurements of forces stabilizing single proteins or individual
receptor–ligand bonds became possible with ultra-sensitive force probe methods
like the atomic force microscope (AFM). In force spectroscopy experiments using
AFM, a single molecule or receptor–ligand pair is tethered between the tip of
a micromachined cantilever and a supporting surface. While the molecule is stretched,
forces are measured by the deflection of the cantilever and plotted against extension,
yielding a force spectrum characteristic for each biomolecular system. In order
to obtain statistically relevant results, several hundred to thousand single-molecule
experiments have to be performed, each resulting in a unique force spectrum. We
developed software and algorithms to analyse large numbers of force spectra. Our
algorithms include the fitting polymer extension models to force peaks as well
as the automatic alignment of spectra. The aligned spectra allowed recognition
of patterns of peaks across different spectra. We demonstrate the capabilities
of our software by analysing force spectra that were recorded by unfolding single
transmembrane proteins such as bacteriorhodopsin and NhaA. Different unfolding
pathways were detected by classifying peak patterns. Deviant spectra, e.g. those
with no attachment or erratic peaks, can be easily identified. The software is
based on the programming language C++, the GNU Scientific Library (GSL), the software
WaveMetrics IGOR Pro and available open-source at http://bioinformatics.org/fskit/.
author:
- first_name: Michael
full_name: Kuhn, Michael
last_name: Kuhn
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Maurice
full_name: Hubain, Maurice
last_name: Hubain
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Kuhn M, Janovjak HL, Hubain M, Mueller D. Automated alignment and pattern recognition
of single-molecule force spectroscopy data. Journal of Microscopy. 2005;218(2):125-132.
doi:10.1111/j.1365-2818.2005.01478.x
apa: Kuhn, M., Janovjak, H. L., Hubain, M., & Mueller, D. (2005). Automated
alignment and pattern recognition of single-molecule force spectroscopy data.
Journal of Microscopy. Wiley-Blackwell. https://doi.org/10.1111/j.1365-2818.2005.01478.x
chicago: Kuhn, Michael, Harald L Janovjak, Maurice Hubain, and Daniel Mueller. “Automated
Alignment and Pattern Recognition of Single-Molecule Force Spectroscopy Data.”
Journal of Microscopy. Wiley-Blackwell, 2005. https://doi.org/10.1111/j.1365-2818.2005.01478.x.
ieee: M. Kuhn, H. L. Janovjak, M. Hubain, and D. Mueller, “Automated alignment and
pattern recognition of single-molecule force spectroscopy data,” Journal of
Microscopy, vol. 218, no. 2. Wiley-Blackwell, pp. 125–132, 2005.
ista: Kuhn M, Janovjak HL, Hubain M, Mueller D. 2005. Automated alignment and pattern
recognition of single-molecule force spectroscopy data. Journal of Microscopy.
218(2), 125–132.
mla: Kuhn, Michael, et al. “Automated Alignment and Pattern Recognition of Single-Molecule
Force Spectroscopy Data.” Journal of Microscopy, vol. 218, no. 2, Wiley-Blackwell,
2005, pp. 125–32, doi:10.1111/j.1365-2818.2005.01478.x.
short: M. Kuhn, H.L. Janovjak, M. Hubain, D. Mueller, Journal of Microscopy 218
(2005) 125–132.
date_created: 2018-12-11T12:03:13Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T07:43:20Z
day: '01'
doi: 10.1111/j.1365-2818.2005.01478.x
extern: 1
intvolume: ' 218'
issue: '2'
month: '05'
page: 125 - 132
publication: Journal of Microscopy
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2984'
quality_controlled: 0
status: public
title: Automated alignment and pattern recognition of single-molecule force spectroscopy
data
type: journal_article
volume: 218
year: '2005'
...
---
_id: '3418'
abstract:
- lang: eng
text: Atomic force microscopy (AFM) allows the critical forces that unfold single
proteins and rupture individual receptor–ligand bonds to be measured. To derive
the shape of the energy landscape, the dynamic strength of the system is probed
at different force loading rates. This is usually achieved by varying the pulling
speed between a few nm/s and a few mgrm/s, although for a more complete investigation
of the kinetic properties higher speeds are desirable. Above 10 mgrm/s, the hydrodynamic
drag force acting on the AFM cantilever reaches the same order of magnitude as
the molecular forces. This has limited the maximum pulling speed in AFM single-molecule
force spectroscopy experiments. Here, we present an approach for considering these
hydrodynamic effects, thereby allowing a correct evaluation of AFM force measurements
recorded over an extended range of pulling speeds (and thus loading rates). To
support and illustrate our theoretical considerations, we experimentally evaluated
the mechanical unfolding of a multi-domain protein recorded at 30 mgrm/s pulling
speed.
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: Jens
full_name: Struckmeier, Jens
last_name: Struckmeier
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Janovjak HL, Struckmeier J, Mueller D. Hydrodynamic effects in fast AFM single
molecule force measurements. European Biophysics Journal. 2005;34(1):91-96.
doi:10.1007/s00249-004-0430-3
apa: Janovjak, H. L., Struckmeier, J., & Mueller, D. (2005). Hydrodynamic effects
in fast AFM single molecule force measurements. European Biophysics Journal.
Springer. https://doi.org/10.1007/s00249-004-0430-3
chicago: Janovjak, Harald L, Jens Struckmeier, and Daniel Mueller. “Hydrodynamic
Effects in Fast AFM Single Molecule Force Measurements.” European Biophysics
Journal. Springer, 2005. https://doi.org/10.1007/s00249-004-0430-3.
ieee: H. L. Janovjak, J. Struckmeier, and D. Mueller, “Hydrodynamic effects in fast
AFM single molecule force measurements,” European Biophysics Journal, vol.
34, no. 1. Springer, pp. 91–96, 2005.
ista: Janovjak HL, Struckmeier J, Mueller D. 2005. Hydrodynamic effects in fast
AFM single molecule force measurements. European Biophysics Journal. 34(1), 91–96.
mla: Janovjak, Harald L., et al. “Hydrodynamic Effects in Fast AFM Single Molecule
Force Measurements.” European Biophysics Journal, vol. 34, no. 1, Springer,
2005, pp. 91–96, doi:10.1007/s00249-004-0430-3.
short: H.L. Janovjak, J. Struckmeier, D. Mueller, European Biophysics Journal 34
(2005) 91–96.
date_created: 2018-12-11T12:03:14Z
date_published: 2005-02-01T00:00:00Z
date_updated: 2021-01-12T07:43:20Z
day: '01'
doi: 10.1007/s00249-004-0430-3
extern: 1
intvolume: ' 34'
issue: '1'
month: '02'
page: 91 - 96
publication: European Biophysics Journal
publication_status: published
publisher: Springer
publist_id: '2983'
quality_controlled: 0
status: public
title: Hydrodynamic effects in fast AFM single molecule force measurements
type: journal_article
volume: 34
year: '2005'
...
---
_id: '3426'
abstract:
- lang: eng
text: We discuss the formation of graded morphogen profiles in a cell layer by nonlinear
transport phenomena, important for patterning developing organisms. We focus on
a process termed transcytosis, where morphogen transport results from the binding
of ligands to receptors on the cell surface, incorporation into the cell, and
subsequent externalization. Starting from a microscopic model, we derive effective
transport equations. We show that, in contrast to morphogen transport by extracellular
diffusion, transcytosis leads to robust ligand profiles which are insensitive
to the rate of ligand production.
article_processing_charge: No
arxiv: 1
author:
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Karsten
full_name: Kruse, Karsten
last_name: Kruse
- first_name: Periklis
full_name: Pantazis, Periklis
last_name: Pantazis
- first_name: Marcos
full_name: González Gaitán, Marcos
last_name: González Gaitán
- first_name: Frank
full_name: Jülicher, Frank
last_name: Jülicher
citation:
ama: Bollenbach MT, Kruse K, Pantazis P, González Gaitán M, Jülicher F. Robust formation
of morphogen gradients. Physical Review Letters. 2005;94(1). doi:10.1103/PhysRevLett.94.018103
apa: Bollenbach, M. T., Kruse, K., Pantazis, P., González Gaitán, M., & Jülicher,
F. (2005). Robust formation of morphogen gradients. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.94.018103
chicago: Bollenbach, Mark Tobias, Karsten Kruse, Periklis Pantazis, Marcos González
Gaitán, and Frank Jülicher. “Robust Formation of Morphogen Gradients.” Physical
Review Letters. American Physical Society, 2005. https://doi.org/10.1103/PhysRevLett.94.018103.
ieee: M. T. Bollenbach, K. Kruse, P. Pantazis, M. González Gaitán, and F. Jülicher,
“Robust formation of morphogen gradients,” Physical Review Letters, vol.
94, no. 1. American Physical Society, 2005.
ista: Bollenbach MT, Kruse K, Pantazis P, González Gaitán M, Jülicher F. 2005. Robust
formation of morphogen gradients. Physical Review Letters. 94(1).
mla: Bollenbach, Mark Tobias, et al. “Robust Formation of Morphogen Gradients.”
Physical Review Letters, vol. 94, no. 1, American Physical Society, 2005,
doi:10.1103/PhysRevLett.94.018103.
short: M.T. Bollenbach, K. Kruse, P. Pantazis, M. González Gaitán, F. Jülicher,
Physical Review Letters 94 (2005).
date_created: 2018-12-11T12:03:16Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T07:43:23Z
day: '01'
doi: 10.1103/PhysRevLett.94.018103
extern: '1'
external_id:
arxiv:
- q-bio/0412014
intvolume: ' 94'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/q-bio/0412014
month: '01'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '2975'
status: public
title: Robust formation of morphogen gradients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 94
year: '2005'
...
---
_id: '3433'
author:
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: 'Bollback JP. Posterior mapping and posterior predictive distributions. In:
Nielsen R, ed. Statistical Methods in Molecular Evolution. Springer; 2005:439-462.
doi:10.1007/0-387-27733-1'
apa: Bollback, J. P. (2005). Posterior mapping and posterior predictive distributions.
In R. Nielsen (Ed.), Statistical methods in Molecular Evolution (pp. 439–462).
Springer. https://doi.org/10.1007/0-387-27733-1
chicago: Bollback, Jonathan P. “Posterior Mapping and Posterior Predictive Distributions.”
In Statistical Methods in Molecular Evolution, edited by Rasmus Nielsen,
439–62. Springer, 2005. https://doi.org/10.1007/0-387-27733-1.
ieee: J. P. Bollback, “Posterior mapping and posterior predictive distributions,”
in Statistical methods in Molecular Evolution, R. Nielsen, Ed. Springer,
2005, pp. 439–462.
ista: 'Bollback JP. 2005.Posterior mapping and posterior predictive distributions.
In: Statistical methods in Molecular Evolution. , 439–462.'
mla: Bollback, Jonathan P. “Posterior Mapping and Posterior Predictive Distributions.”
Statistical Methods in Molecular Evolution, edited by Rasmus Nielsen, Springer,
2005, pp. 439–62, doi:10.1007/0-387-27733-1.
short: J.P. Bollback, in:, R. Nielsen (Ed.), Statistical Methods in Molecular Evolution,
Springer, 2005, pp. 439–462.
date_created: 2018-12-11T12:03:18Z
date_published: 2005-04-21T00:00:00Z
date_updated: 2021-01-12T07:43:26Z
day: '21'
doi: 10.1007/0-387-27733-1
editor:
- first_name: Rasmus
full_name: Nielsen, Rasmus
last_name: Nielsen
extern: 1
month: '04'
page: 439 - 462
publication: Statistical methods in Molecular Evolution
publication_status: published
publisher: Springer
publist_id: '2967'
quality_controlled: 0
status: public
title: Posterior mapping and posterior predictive distributions
type: book_chapter
year: '2005'
...
---
_id: '3443'
abstract:
- lang: eng
text: In the hippocampal CA1 area, a relatively homogenous population of pyramidal
cells is accompanied by a diversity of GABAergic interneurons. Previously, we
found that parvalbumin-expressing basket, axo-axonic, bistratified, and oriens-lacunosum
moleculare cells, innervating different domains of pyramidal cells, have distinct
firing patterns during network oscillations in vivo. A second family of interneurons,
expressing cholecystokinin but not parvalbumin, is known to target the same domains
of pyramidal cells as do the parvalbumin cells. To test the temporal activity
of these independent and parallel GABAergic inputs, we recorded the precise spike
timing of identified cholecystokinin interneurons during hippocampal network oscillations
in anesthetized rats and determined their molecular expression profiles and synaptic
targets. The cells were cannabinoid receptor type 1 immunopositive. Contrary to
the stereotyped firing of parvalbumin interneurons, cholecystokinin-expressing
basket and dendrite-innervating cells discharge, on average, with 1.7 ± 2.0 Hz
during high-frequency ripple oscillations in an episode-dependent manner. During
theta oscillations, cholecystokinin- expressing interneurons fire with 8.8 ± 3.3
Hz at a characteristic time on the ascending phase of theta waves (155 ± 81°),
when place cells start firing in freely moving animals. The firing patterns of
some interneurons recorded in drug-free behaving rats were similar to cholecystokinin
cells in anesthetized animals. Our results demonstrate that cholecystokinin- and
parvalbumin-expressing interneurons make different contributions to network oscillations
and play distinct roles in different brain states. We suggest that the specific
spike timing of cholecystokinin interneurons and their sensitivity to endocannabinoids
might contribute to differentiate subgroups of pyramidal cells forming neuronal
assemblies, whereas parvalbumin interneurons contribute to synchronizing the entire
network. Copyright © 2005 Society for Neuroscience.
author:
- first_name: Thomas
full_name: Klausberger,Thomas
last_name: Klausberger
- first_name: Laszlo
full_name: Marton,Laszlo F
last_name: Marton
- first_name: Joseph
full_name: Joseph O'Neill
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Jojanneke
full_name: Huck, Jojanneke H
last_name: Huck
- first_name: Yannis
full_name: Dalezios, Yannis
last_name: Dalezios
- first_name: Pablo
full_name: Fuentealba,Pablo
last_name: Fuentealba
- first_name: Wai
full_name: Suen, Wai Yee
last_name: Suen
- first_name: Edit
full_name: Papp, Edit Cs
last_name: Papp
- first_name: Takeshi
full_name: Kaneko, Takeshi
last_name: Kaneko
- first_name: Masahiko
full_name: Watanabe, Masahiko
last_name: Watanabe
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Péter
full_name: Somogyi, Péter
last_name: Somogyi
citation:
ama: Klausberger T, Marton L, O’Neill J, et al. Complementary roles of cholecystokinin-
and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations.
Journal of Neuroscience. 2005;25(42):9782-9793. doi:10.1523/JNEUROSCI.3269-05.2005
apa: Klausberger, T., Marton, L., O’Neill, J., Huck, J., Dalezios, Y., Fuentealba,
P., … Somogyi, P. (2005). Complementary roles of cholecystokinin- and parvalbumin-expressing
GABAergic neurons in hippocampal network oscillations. Journal of Neuroscience.
Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.3269-05.2005
chicago: Klausberger, Thomas, Laszlo Marton, Joseph O’Neill, Jojanneke Huck, Yannis
Dalezios, Pablo Fuentealba, Wai Suen, et al. “Complementary Roles of Cholecystokinin-
and Parvalbumin-Expressing GABAergic Neurons in Hippocampal Network Oscillations.”
Journal of Neuroscience. Society for Neuroscience, 2005. https://doi.org/10.1523/JNEUROSCI.3269-05.2005.
ieee: T. Klausberger et al., “Complementary roles of cholecystokinin- and
parvalbumin-expressing GABAergic neurons in hippocampal network oscillations,”
Journal of Neuroscience, vol. 25, no. 42. Society for Neuroscience, pp.
9782–9793, 2005.
ista: Klausberger T, Marton L, O’Neill J, Huck J, Dalezios Y, Fuentealba P, Suen
W, Papp E, Kaneko T, Watanabe M, Csicsvari JL, Somogyi P. 2005. Complementary
roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal
network oscillations. Journal of Neuroscience. 25(42), 9782–9793.
mla: Klausberger, Thomas, et al. “Complementary Roles of Cholecystokinin- and Parvalbumin-Expressing
GABAergic Neurons in Hippocampal Network Oscillations.” Journal of Neuroscience,
vol. 25, no. 42, Society for Neuroscience, 2005, pp. 9782–93, doi:10.1523/JNEUROSCI.3269-05.2005.
short: T. Klausberger, L. Marton, J. O’Neill, J. Huck, Y. Dalezios, P. Fuentealba,
W. Suen, E. Papp, T. Kaneko, M. Watanabe, J.L. Csicsvari, P. Somogyi, Journal
of Neuroscience 25 (2005) 9782–9793.
date_created: 2018-12-11T12:03:21Z
date_published: 2005-10-19T00:00:00Z
date_updated: 2021-01-12T07:43:30Z
day: '19'
doi: 10.1523/JNEUROSCI.3269-05.2005
extern: 1
intvolume: ' 25'
issue: '42'
month: '10'
page: 9782 - 9793
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '2944'
quality_controlled: 0
status: public
title: Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic
neurons in hippocampal network oscillations
type: journal_article
volume: 25
year: '2005'
...
---
_id: '3509'
abstract:
- lang: eng
text: Methods, apparatus and computer program products can generate light weight
but highly realistic and accurate colored models of three-dimensional colored
objects. The colored model may be generated from a second plurality of points
that define a coarse digital representation of the surface and at least one texture
map containing information derived from a first plurality of colored points that
define a fine digital representation of the surface. This derivation is achieved
by mapping points within the texture map to the fine digital representation of
the three-dimensional surface. Colored scan data may be used to construct the
fine digital representation as a triangulated surface (i.e., triangulation) using
a wrapping operation.
applicant:
- Raindrop Geomagic, Inc.
article_processing_charge: No
author:
- first_name: Steven
full_name: Williams, Steven
last_name: Williams
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Ping
full_name: Fu, Ping
last_name: Fu
citation:
ama: Williams S, Edelsbrunner H, Fu P. Methods, apparatus and computer program products
for modeling three-dimensional colored objects. 2005.
apa: Williams, S., Edelsbrunner, H., & Fu, P. (2005). Methods, apparatus and
computer program products for modeling three-dimensional colored objects.
chicago: Williams, Steven, Herbert Edelsbrunner, and Ping Fu. “Methods, Apparatus
and Computer Program Products for Modeling Three-Dimensional Colored Objects,”
2005.
ieee: S. Williams, H. Edelsbrunner, and P. Fu, “Methods, apparatus and computer
program products for modeling three-dimensional colored objects.” 2005.
ista: Williams S, Edelsbrunner H, Fu P. 2005. Methods, apparatus and computer program
products for modeling three-dimensional colored objects.
mla: Williams, Steven, et al. Methods, Apparatus and Computer Program Products
for Modeling Three-Dimensional Colored Objects. 2005.
short: S. Williams, H. Edelsbrunner, P. Fu, (2005).
date_created: 2018-12-11T12:03:42Z
date_published: 2005-02-08T00:00:00Z
date_updated: 2022-01-05T13:59:09Z
day: '08'
extern: '1'
ipc: G06T17/20 ; G06T15/04
ipn: US6853373B2
main_file_link:
- open_access: '1'
url: https://patents.google.com/patent/US6853373B2/
month: '02'
oa: 1
oa_version: Published Version
publication_date: 2005-02-08
publist_id: '2878'
status: public
title: Methods, apparatus and computer program products for modeling three-dimensional
colored objects
type: patent
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2005'
...
---
_id: '3557'
abstract:
- lang: eng
text: A challenging problem in computer-aided geometric design is the decomposition
of a surface into four-sided regions that are then represented by NURBS patches.
There are various approaches published in the literature and implemented as commercially
available software, but all fall short in either automation or quality of the
result. At Raindrop Geomagic, we have recently taken a fresh approach based on
concepts from Morse theory. This by itself is not a new idea, but we have some
novel ingredients that make this work, one being a rational notion of hierarchy
that guides the construction of a simplified decomposition sensitive to only the
major critical points.
author:
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Edelsbrunner H. Surface tiling with differential topology. In: ACM; 2005:9-11.
doi:http://dx.doi.org/10.2312/SGP/SGP05/009-011'
apa: 'Edelsbrunner, H. (2005). Surface tiling with differential topology (pp. 9–11).
Presented at the SGP: Eurographics Symposium on Geometry processing, ACM. http://dx.doi.org/10.2312/SGP/SGP05/009-011'
chicago: Edelsbrunner, Herbert. “Surface Tiling with Differential Topology,” 9–11.
ACM, 2005. http://dx.doi.org/10.2312/SGP/SGP05/009-011.
ieee: 'H. Edelsbrunner, “Surface tiling with differential topology,” presented at
the SGP: Eurographics Symposium on Geometry processing, 2005, pp. 9–11.'
ista: 'Edelsbrunner H. 2005. Surface tiling with differential topology. SGP: Eurographics
Symposium on Geometry processing, 9–11.'
mla: Edelsbrunner, Herbert. Surface Tiling with Differential Topology. ACM,
2005, pp. 9–11, doi:http://dx.doi.org/10.2312/SGP/SGP05/009-011.
short: H. Edelsbrunner, in:, ACM, 2005, pp. 9–11.
conference:
name: 'SGP: Eurographics Symposium on Geometry processing'
date_created: 2018-12-11T12:03:57Z
date_published: 2005-07-01T00:00:00Z
date_updated: 2021-01-12T07:44:17Z
day: '01'
doi: http://dx.doi.org/10.2312/SGP/SGP05/009-011
extern: 1
main_file_link:
- open_access: '0'
url: http://www.cs.duke.edu/~edels/Papers/2005-P-03-SurfaceTiling.pdf
month: '07'
page: 9 - 11
publication_status: published
publisher: ACM
publist_id: '2828'
quality_controlled: 0
status: public
title: Surface tiling with differential topology
type: conference
year: '2005'
...
---
_id: '3558'
abstract:
- lang: eng
text: The tandem algorithm combines the marching cube algorithm for surface extraction
and the edge contraction algorithm for surface simplification in lock-step to
avoid the costly intermediate step of storing the entire extracted surface triangulation.
Beyond this basic strategy, we introduce refinements to prevent artifacts in the
resulting triangulation, first, by carefully monitoring the amount of simplification
during the process and, second, by driving the simplification toward a compromise
between shape approximation and mesh quality. We have implemented the algorithm
and used extensive computational experiments to document the effects of various
design options and to further fine-tune the algorithm.
acknowledgement: 'Partially supported the generated triangulations. Two questions
arise: “how do by NSF grant CCR-00-86013 (BioGeometry).'
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: David
full_name: Cohen-Steiner, David
last_name: Cohen Steiner
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Attali D, Cohen Steiner D, Edelsbrunner H. Extraction and simplification of
iso-surfaces in tandem. In: ACM; 2005:139-148.'
apa: 'Attali, D., Cohen Steiner, D., & Edelsbrunner, H. (2005). Extraction and
simplification of iso-surfaces in tandem (pp. 139–148). Presented at the SGP:
Eurographics Symposium on Geometry processing, ACM.'
chicago: Attali, Dominique, David Cohen Steiner, and Herbert Edelsbrunner. “Extraction
and Simplification of Iso-Surfaces in Tandem,” 139–48. ACM, 2005.
ieee: 'D. Attali, D. Cohen Steiner, and H. Edelsbrunner, “Extraction and simplification
of iso-surfaces in tandem,” presented at the SGP: Eurographics Symposium on Geometry
processing, 2005, pp. 139–148.'
ista: 'Attali D, Cohen Steiner D, Edelsbrunner H. 2005. Extraction and simplification
of iso-surfaces in tandem. SGP: Eurographics Symposium on Geometry processing,
139–148.'
mla: Attali, Dominique, et al. Extraction and Simplification of Iso-Surfaces
in Tandem. ACM, 2005, pp. 139–48.
short: D. Attali, D. Cohen Steiner, H. Edelsbrunner, in:, ACM, 2005, pp. 139–148.
conference:
name: 'SGP: Eurographics Symposium on Geometry processing'
date_created: 2018-12-11T12:03:57Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T07:44:18Z
day: '01'
extern: 1
main_file_link:
- open_access: '0'
url: http://dl.acm.org/citation.cfm?id=1281943
month: '01'
page: 139 - 148
publication_status: published
publisher: ACM
publist_id: '2827'
quality_controlled: 0
status: public
title: Extraction and simplification of iso-surfaces in tandem
type: conference
year: '2005'
...
---
_id: '3576'
abstract:
- lang: eng
text: |-
ears of research in biology have established that all cellular functions are deeply connected to the shape and dynamics of their molec- ular actors. As a response, structural molecular biology has emerged as a new line of experimental research focused on revealing the structure of biomolecules. The analysis of these structures has led to the development of computational biology, whose aim is to predict from molecular simulation properties inaccessible to experimental probes.
Here we focus on the representation of biomolecules used in these sim- ulations, and in particular on the hard sphere models. We review how the geometry of the union of such spheres is used to model their interactions with their environment, and how it has been included in simulations of molecular dynamics.
In parallel, we review our own developments in mathematics and com- puter science on understanding the geometry of unions of balls, and their applications in molecular simulation.
alternative_title:
- Mathematical Sciences Research Institute Publications
author:
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Patrice
full_name: Koehl, Patrice
last_name: Koehl
citation:
ama: 'Edelsbrunner H, Koehl P. The geometry of biomolecular solvation. In: Combinatorial
and Computational Geometry. Vol 52. Cambridge University Press; 2005:243-275.'
apa: Edelsbrunner, H., & Koehl, P. (2005). The geometry of biomolecular solvation.
In Combinatorial and Computational Geometry (Vol. 52, pp. 243–275). Cambridge
University Press.
chicago: Edelsbrunner, Herbert, and Patrice Koehl. “The Geometry of Biomolecular
Solvation.” In Combinatorial and Computational Geometry, 52:243–75. Cambridge
University Press, 2005.
ieee: H. Edelsbrunner and P. Koehl, “The geometry of biomolecular solvation,” in
Combinatorial and Computational Geometry, vol. 52, Cambridge University
Press, 2005, pp. 243–275.
ista: 'Edelsbrunner H, Koehl P. 2005.The geometry of biomolecular solvation. In:
Combinatorial and Computational Geometry. Mathematical Sciences Research Institute
Publications, vol. 52, 243–275.'
mla: Edelsbrunner, Herbert, and Patrice Koehl. “The Geometry of Biomolecular Solvation.”
Combinatorial and Computational Geometry, vol. 52, Cambridge University
Press, 2005, pp. 243–75.
short: H. Edelsbrunner, P. Koehl, in:, Combinatorial and Computational Geometry,
Cambridge University Press, 2005, pp. 243–275.
date_created: 2018-12-11T12:04:03Z
date_published: 2005-08-08T00:00:00Z
date_updated: 2021-01-12T07:44:25Z
day: '08'
extern: 1
intvolume: ' 52'
main_file_link:
- open_access: '0'
url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.117.3732
month: '08'
page: 243 - 275
publication: Combinatorial and Computational Geometry
publication_status: published
publisher: Cambridge University Press
publist_id: '2809'
quality_controlled: 0
status: public
title: The geometry of biomolecular solvation
type: book_chapter
volume: 52
year: '2005'
...
---
_id: '3588'
article_processing_charge: No
author:
- first_name: Irinka
full_name: Castanon Ortega, Irinka
last_name: Castanon Ortega
- 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: 'Castanon Ortega I, Heisenberg C-PJ. Cell migration during zebrafish gastrulation.
In: Wedlich D, ed. Cell Migration in Development and Disease. Wiley-VCH;
2005:71-105. doi:10.1002/3527604669'
apa: Castanon Ortega, I., & Heisenberg, C.-P. J. (2005). Cell migration during
zebrafish gastrulation. In D. Wedlich (Ed.), Cell Migration in Development
and Disease (pp. 71–105). Wiley-VCH. https://doi.org/10.1002/3527604669
chicago: Castanon Ortega, Irinka, and Carl-Philipp J Heisenberg. “Cell Migration
during Zebrafish Gastrulation.” In Cell Migration in Development and Disease,
edited by Doris Wedlich, 71–105. Wiley-VCH, 2005. https://doi.org/10.1002/3527604669.
ieee: I. Castanon Ortega and C.-P. J. Heisenberg, “Cell migration during zebrafish
gastrulation,” in Cell Migration in Development and Disease, D. Wedlich,
Ed. Wiley-VCH, 2005, pp. 71–105.
ista: 'Castanon Ortega I, Heisenberg C-PJ. 2005.Cell migration during zebrafish
gastrulation. In: Cell Migration in Development and Disease. , 71–105.'
mla: Castanon Ortega, Irinka, and Carl-Philipp J. Heisenberg. “Cell Migration during
Zebrafish Gastrulation.” Cell Migration in Development and Disease, edited
by Doris Wedlich, Wiley-VCH, 2005, pp. 71–105, doi:10.1002/3527604669.
short: I. Castanon Ortega, C.-P.J. Heisenberg, in:, D. Wedlich (Ed.), Cell Migration
in Development and Disease, Wiley-VCH, 2005, pp. 71–105.
date_created: 2018-12-11T12:04:07Z
date_published: 2005-03-14T00:00:00Z
date_updated: 2021-01-12T07:44:29Z
day: '14'
doi: 10.1002/3527604669
editor:
- first_name: Doris
full_name: Wedlich, Doris
last_name: Wedlich
extern: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 71 - 105
publication: Cell Migration in Development and Disease
publication_status: published
publisher: Wiley-VCH
publist_id: '2795'
status: public
title: Cell migration during zebrafish gastrulation
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2005'
...
---
_id: '3589'
abstract:
- lang: eng
text: During zebrafish gastrulation, the interplay between patterning events and
morphogenesis creates an embryo out of a seemingly unstructured blastula stage
embryo, an embryo with distinct polarities along its anterior–posterior, dorsoventral
and left–right axes at the end of gastrulation.
article_processing_charge: No
author:
- 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
citation:
ama: 'Köppen M, Heisenberg C-PJ. Cleavage and gastrulation in zebrafish embryos.
In: Encyclopedia of Life Sciences. Wiley-Blackwell; 2005. doi:10.1038/npg.els.0001072'
apa: Köppen, M., & Heisenberg, C.-P. J. (2005). Cleavage and gastrulation in
zebrafish embryos. In Encyclopedia of Life Sciences. Wiley-Blackwell. https://doi.org/10.1038/npg.els.0001072
chicago: Köppen, Mathias, and Carl-Philipp J Heisenberg. “Cleavage and Gastrulation
in Zebrafish Embryos.” In Encyclopedia of Life Sciences. Wiley-Blackwell,
2005. https://doi.org/10.1038/npg.els.0001072.
ieee: M. Köppen and C.-P. J. Heisenberg, “Cleavage and gastrulation in zebrafish
embryos,” in Encyclopedia of Life Sciences, Wiley-Blackwell, 2005.
ista: 'Köppen M, Heisenberg C-PJ. 2005.Cleavage and gastrulation in zebrafish embryos.
In: Encyclopedia of Life Sciences. .'
mla: Köppen, Mathias, and Carl-Philipp J. Heisenberg. “Cleavage and Gastrulation
in Zebrafish Embryos.” Encyclopedia of Life Sciences, Wiley-Blackwell,
2005, doi:10.1038/npg.els.0001072.
short: M. Köppen, C.-P.J. Heisenberg, in:, Encyclopedia of Life Sciences, Wiley-Blackwell,
2005.
date_created: 2018-12-11T12:04:07Z
date_published: 2005-09-23T00:00:00Z
date_updated: 2021-01-12T07:44:30Z
day: '23'
doi: 10.1038/npg.els.0001072
extern: '1'
language:
- iso: eng
month: '09'
oa_version: None
publication: Encyclopedia of Life Sciences
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2794'
status: public
title: Cleavage and gastrulation in zebrafish embryos
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2005'
...