---
_id: '3045'
abstract:
- lang: eng
text: Dynamically polarized membrane proteins define different cell boundaries and
have an important role in intercellular communication - a vital feature of multicellular
development. Efflux carriers for the signalling molecule auxin from the PIN family
are landmarks of cell polarity in plants and have a crucial involvement in auxin
distribution-dependent development including embryo patterning, organogenesis
and tropisms. Polar PIN localization determines the direction of intercellular
auxin flow, yet the mechanisms generating PIN polarity remain unclear. Here we
identify an endocytosis-dependent mechanism of PIN polarity generation and analyse
its developmental implications. Real-time PIN tracking showed that after synthesis,
PINs are initially delivered to the plasma membrane in a non-polar manner and
their polarity is established by subsequent endocytic recycling. Interference
with PIN endocytosis either by auxin or by manipulation of the Arabidopsis Rab5
GTPase pathway prevents PIN polarization. Failure of PIN polarization transiently
alters asymmetric auxin distribution during embryogenesis and increases the local
auxin response in apical embryo regions. This results in ectopic expression of
auxin pathway-associated root-forming master regulators in embryonic leaves and
promotes homeotic transformation of leaves to roots. Our results indicate a two-step
mechanism for the generation of PIN polar localization and the essential role
of endocytosis in this process. It also highlights the link between endocytosis-dependent
polarity of individual cells and auxin distribution-dependent cell fate establishment
for multicellular patterning.
author:
- first_name: Pankaj
full_name: Dhonukshe, Pankaj
last_name: Dhonukshe
- first_name: Hirokazu
full_name: Tanaka, Hirokazu
last_name: Tanaka
- first_name: Tatsuaki
full_name: Goh, Tatsuaki
last_name: Goh
- first_name: Kazuo
full_name: Ebine, Kazuo
last_name: Ebine
- first_name: Ari
full_name: Mähönen, Ari Pekka
last_name: Mähönen
- first_name: Kalika
full_name: Prasad, Kalika
last_name: Prasad
- first_name: Ikram
full_name: Blilou, Ikram
last_name: Blilou
- first_name: Niko
full_name: Geldner, Niko
last_name: Geldner
- first_name: Jian
full_name: Xu, Jian
last_name: Xu
- first_name: Tomohiro
full_name: Uemura, Tomohiro
last_name: Uemura
- first_name: Joanne
full_name: Chory, Joanne
last_name: Chory
- first_name: Takashi
full_name: Ueda, Takashi
last_name: Ueda
- first_name: Akihiko
full_name: Nakano, Akihiko
last_name: Nakano
- first_name: Ben
full_name: Scheres, Ben
last_name: Scheres
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Dhonukshe P, Tanaka H, Goh T, et al. Generation of cell polarity in plants
links endocytosis auxin distribution and cell fate decisions. Nature. 2008;456(7224):962-966.
doi:10.1038/nature07409
apa: Dhonukshe, P., Tanaka, H., Goh, T., Ebine, K., Mähönen, A., Prasad, K., … Friml,
J. (2008). Generation of cell polarity in plants links endocytosis auxin distribution
and cell fate decisions. Nature. Nature Publishing Group. https://doi.org/10.1038/nature07409
chicago: Dhonukshe, Pankaj, Hirokazu Tanaka, Tatsuaki Goh, Kazuo Ebine, Ari Mähönen,
Kalika Prasad, Ikram Blilou, et al. “Generation of Cell Polarity in Plants Links
Endocytosis Auxin Distribution and Cell Fate Decisions.” Nature. Nature
Publishing Group, 2008. https://doi.org/10.1038/nature07409.
ieee: P. Dhonukshe et al., “Generation of cell polarity in plants links endocytosis
auxin distribution and cell fate decisions,” Nature, vol. 456, no. 7224.
Nature Publishing Group, pp. 962–966, 2008.
ista: Dhonukshe P, Tanaka H, Goh T, Ebine K, Mähönen A, Prasad K, Blilou I, Geldner
N, Xu J, Uemura T, Chory J, Ueda T, Nakano A, Scheres B, Friml J. 2008. Generation
of cell polarity in plants links endocytosis auxin distribution and cell fate
decisions. Nature. 456(7224), 962–966.
mla: Dhonukshe, Pankaj, et al. “Generation of Cell Polarity in Plants Links Endocytosis
Auxin Distribution and Cell Fate Decisions.” Nature, vol. 456, no. 7224,
Nature Publishing Group, 2008, pp. 962–66, doi:10.1038/nature07409.
short: P. Dhonukshe, H. Tanaka, T. Goh, K. Ebine, A. Mähönen, K. Prasad, I. Blilou,
N. Geldner, J. Xu, T. Uemura, J. Chory, T. Ueda, A. Nakano, B. Scheres, J. Friml,
Nature 456 (2008) 962–966.
date_created: 2018-12-11T12:01:02Z
date_published: 2008-12-18T00:00:00Z
date_updated: 2021-01-12T07:40:40Z
day: '18'
doi: 10.1038/nature07409
extern: 1
intvolume: ' 456'
issue: '7224'
month: '12'
page: 962 - 966
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '3657'
quality_controlled: 0
status: public
title: Generation of cell polarity in plants links endocytosis auxin distribution
and cell fate decisions
type: journal_article
volume: 456
year: '2008'
...
---
_id: '3194'
abstract:
- lang: eng
text: We consider the problem of optimizing multilabel MRFs, which is in general
NP-hard and ubiquitous in low-level computer vision. One approach for its solution
is to formulate it as an integer linear programming and relax the integrality
constraints. The approach we consider in this paper is to first convert the multi-label
MRF into an equivalent binary-label MRF and then to relax it. The resulting relaxation
can be efficiently solved using a maximum flow algorithm. Its solution provides
us with a partially optimal labelling of the binary variables. This partial labelling
is then easily transferred to the multi-label problem. We study the theoretical
properties of the new relaxation and compare it with the standard one. Specifically,
we compare tightness, and characterize a subclass of problems where the two relaxations
coincide. We propose several combined algorithms based on the technique and demonstrate
their performance on challenging computer vision problems.
author:
- first_name: Pushmeet
full_name: Kohli, Pushmeet
last_name: Kohli
- first_name: Alexander
full_name: Shekhovtsov, Alexander
last_name: Shekhovtsov
- 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: Philip
full_name: Torr, Philip H
last_name: Torr
citation:
ama: 'Kohli P, Shekhovtsov A, Rother C, Kolmogorov V, Torr P. On partial optimality
in multi label MRFs. In: Omnipress; 2008:480-487. doi:10.1145/1390156.1390217'
apa: 'Kohli, P., Shekhovtsov, A., Rother, C., Kolmogorov, V., & Torr, P. (2008).
On partial optimality in multi label MRFs (pp. 480–487). Presented at the ICML:
International Conference on Machine Learning, Omnipress. https://doi.org/10.1145/1390156.1390217'
chicago: Kohli, Pushmeet, Alexander Shekhovtsov, Carsten Rother, Vladimir Kolmogorov,
and Philip Torr. “On Partial Optimality in Multi Label MRFs,” 480–87. Omnipress,
2008. https://doi.org/10.1145/1390156.1390217.
ieee: 'P. Kohli, A. Shekhovtsov, C. Rother, V. Kolmogorov, and P. Torr, “On partial
optimality in multi label MRFs,” presented at the ICML: International Conference
on Machine Learning, 2008, pp. 480–487.'
ista: 'Kohli P, Shekhovtsov A, Rother C, Kolmogorov V, Torr P. 2008. On partial
optimality in multi label MRFs. ICML: International Conference on Machine Learning,
480–487.'
mla: Kohli, Pushmeet, et al. On Partial Optimality in Multi Label MRFs. Omnipress,
2008, pp. 480–87, doi:10.1145/1390156.1390217.
short: P. Kohli, A. Shekhovtsov, C. Rother, V. Kolmogorov, P. Torr, in:, Omnipress,
2008, pp. 480–487.
conference:
name: 'ICML: International Conference on Machine Learning'
date_created: 2018-12-11T12:01:56Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:42Z
day: '01'
doi: 10.1145/1390156.1390217
extern: 1
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/77356/icml08-partoptmrf.pdf
month: '01'
page: 480 - 487
publication_status: published
publisher: Omnipress
publist_id: '3486'
quality_controlled: 0
status: public
title: On partial optimality in multi label MRFs
type: conference
year: '2008'
...
---
_id: '3195'
abstract:
- lang: eng
text: 'Graph cut is a popular technique for interactive image segmentation. However,
it has certain shortcomings. In particular, graph cut has problems with segmenting
thin elongated objects due to the ldquoshrinking biasrdquo. To overcome this problem,
we propose to impose an additional connectivity prior, which is a very natural
assumption about objects. We formulate several versions of the connectivity constraint
and show that the corresponding optimization problems are all NP-hard. For some
of these versions we propose two optimization algorithms: (i) a practical heuristic
technique which we call DijkstraGC, and (ii) a slow method based on problem decomposition
which provides a lower bound on the problem. We use the second technique to verify
that for some practical examples DijkstraGC is able to find the global minimum.'
author:
- first_name: Sara
full_name: Vicente, Sara
last_name: Vicente
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: 'Vicente S, Kolmogorov V, Rother C. Graph cut based image segmentation with
connectivity priors. In: IEEE; 2008. doi:10.1109/CVPR.2008.4587440'
apa: 'Vicente, S., Kolmogorov, V., & Rother, C. (2008). Graph cut based image
segmentation with connectivity priors. Presented at the CVPR: Computer Vision
and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2008.4587440'
chicago: Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Graph Cut Based
Image Segmentation with Connectivity Priors.” IEEE, 2008. https://doi.org/10.1109/CVPR.2008.4587440.
ieee: 'S. Vicente, V. Kolmogorov, and C. Rother, “Graph cut based image segmentation
with connectivity priors,” presented at the CVPR: Computer Vision and Pattern
Recognition, 2008.'
ista: 'Vicente S, Kolmogorov V, Rother C. 2008. Graph cut based image segmentation
with connectivity priors. CVPR: Computer Vision and Pattern Recognition.'
mla: Vicente, Sara, et al. Graph Cut Based Image Segmentation with Connectivity
Priors. IEEE, 2008, doi:10.1109/CVPR.2008.4587440.
short: S. Vicente, V. Kolmogorov, C. Rother, in:, IEEE, 2008.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:57Z
date_published: 2008-08-05T00:00:00Z
date_updated: 2021-01-12T07:41:43Z
day: '05'
doi: 10.1109/CVPR.2008.4587440
extern: 1
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/80485/CVPR08-ConnectedGC.pdf
month: '08'
publication_status: published
publisher: IEEE
publist_id: '3487'
quality_controlled: 0
status: public
title: Graph cut based image segmentation with connectivity priors
type: conference
year: '2008'
...
---
_id: '3196'
abstract:
- lang: eng
text: 'Among the most exciting advances in early vision has been the development
of efficient energy minimization algorithms for pixel-labeling tasks such as depth
or texture computation. It has been known for decades that such problems can be
elegantly expressed as Markov random fields, yet the resulting energy minimization
problems have been widely viewed as intractable. Algorithms such as graph cuts
and loopy belief propagation (LBP) have proven to be very powerful: For example,
such methods form the basis for almost all the top-performing stereo methods.
However, the trade-offs among different energy minimization algorithms are still
not well understood. In this paper, we describe a set of energy minimization benchmarks
and use them to compare the solution quality and runtime of several common energy
minimization algorithms. We investigate three promising methods-graph cuts, LBP,
and tree-reweighted message passing-in addition to the well-known older iterated
conditional mode (ICM) algorithm. Our benchmark problems are drawn from published
energy functions used for stereo, image stitching, interactive segmentation, and
denoising. We also provide a general-purpose software interface that allows vision
researchers to easily switch between optimization methods. The benchmarks, code,
images, and results are available at http://vision.middlebury.edu/MRF/.'
author:
- first_name: Richard
full_name: Szeliski, Richard S
last_name: Szeliski
- first_name: Ramin
full_name: Zabih, Ramin
last_name: Zabih
- first_name: Daniel
full_name: Scharstein, Daniel
last_name: Scharstein
- first_name: Olga
full_name: Veksler, Olga
last_name: Veksler
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Aseem
full_name: Agarwala, Aseem
last_name: Agarwala
- first_name: Marshall
full_name: Tappen, Marshall F
last_name: Tappen
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: Szeliski R, Zabih R, Scharstein D, et al. A comparative study of energy minimization
methods for Markov random fields with smoothness-based priors. IEEE Transactions
on Pattern Analysis and Machine Intelligence. 2008;30(6):1068-1080. doi:10.1109/TPAMI.2007.70844
apa: Szeliski, R., Zabih, R., Scharstein, D., Veksler, O., Kolmogorov, V., Agarwala,
A., … Rother, C. (2008). A comparative study of energy minimization methods for
Markov random fields with smoothness-based priors. IEEE Transactions on Pattern
Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2007.70844
chicago: Szeliski, Richard, Ramin Zabih, Daniel Scharstein, Olga Veksler, Vladimir
Kolmogorov, Aseem Agarwala, Marshall Tappen, and Carsten Rother. “A Comparative
Study of Energy Minimization Methods for Markov Random Fields with Smoothness-Based
Priors.” IEEE Transactions on Pattern Analysis and Machine Intelligence.
IEEE, 2008. https://doi.org/10.1109/TPAMI.2007.70844.
ieee: R. Szeliski et al., “A comparative study of energy minimization methods
for Markov random fields with smoothness-based priors,” IEEE Transactions on
Pattern Analysis and Machine Intelligence, vol. 30, no. 6. IEEE, pp. 1068–1080,
2008.
ista: Szeliski R, Zabih R, Scharstein D, Veksler O, Kolmogorov V, Agarwala A, Tappen
M, Rother C. 2008. A comparative study of energy minimization methods for Markov
random fields with smoothness-based priors. IEEE Transactions on Pattern Analysis
and Machine Intelligence. 30(6), 1068–1080.
mla: Szeliski, Richard, et al. “A Comparative Study of Energy Minimization Methods
for Markov Random Fields with Smoothness-Based Priors.” IEEE Transactions on
Pattern Analysis and Machine Intelligence, vol. 30, no. 6, IEEE, 2008, pp.
1068–80, doi:10.1109/TPAMI.2007.70844.
short: R. Szeliski, R. Zabih, D. Scharstein, O. Veksler, V. Kolmogorov, A. Agarwala,
M. Tappen, C. Rother, IEEE Transactions on Pattern Analysis and Machine Intelligence
30 (2008) 1068–1080.
date_created: 2018-12-11T12:01:57Z
date_published: 2008-06-01T00:00:00Z
date_updated: 2021-01-12T07:41:43Z
day: '01'
doi: 10.1109/TPAMI.2007.70844
extern: 1
intvolume: ' 30'
issue: '6'
month: '06'
page: 1068 - 1080
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '3488'
quality_controlled: 0
status: public
title: A comparative study of energy minimization methods for Markov random fields
with smoothness-based priors
type: journal_article
volume: 30
year: '2008'
...
---
_id: '3198'
abstract:
- lang: eng
text: 'In this paper we present a new approach for establishing correspondences
between sparse image features related by an unknown non-rigid mapping and corrupted
by clutter and occlusion, such as points extracted from a pair of images containing
a human figure in distinct poses. We formulate this matching task as an energy
minimization problem by defining a complex objective function of the appearance
and the spatial arrangement of the features. Optimization of this energy is an
instance of graph matching, which is in general a NP-hard problem. We describe
a novel graph matching optimization technique, which we refer to as dual decomposition
(DD), and demonstrate on a variety of examples that this method outperforms existing
graph matching algorithms. In the majority of our examples DD is able to find
the global minimum within a minute. The ability to globally optimize the objective
allows us to accurately learn the parameters of our matching model from training
examples. We show on several matching tasks that our learned model yields results
superior to those of state-of-the-art methods. '
alternative_title:
- LNCS
author:
- first_name: Lorenzo
full_name: Torresani, Lorenzo
last_name: Torresani
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: 'Torresani L, Kolmogorov V, Rother C. Feature correspondence via graph matching:
Models and global optimization. In: Vol 5303. Springer; 2008:596-609. doi:10.1007/978-3-540-88688-4_44'
apa: 'Torresani, L., Kolmogorov, V., & Rother, C. (2008). Feature correspondence
via graph matching: Models and global optimization (Vol. 5303, pp. 596–609). Presented
at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/978-3-540-88688-4_44'
chicago: 'Torresani, Lorenzo, Vladimir Kolmogorov, and Carsten Rother. “Feature
Correspondence via Graph Matching: Models and Global Optimization,” 5303:596–609.
Springer, 2008. https://doi.org/10.1007/978-3-540-88688-4_44.'
ieee: 'L. Torresani, V. Kolmogorov, and C. Rother, “Feature correspondence via graph
matching: Models and global optimization,” presented at the ECCV: European Conference
on Computer Vision, 2008, vol. 5303, pp. 596–609.'
ista: 'Torresani L, Kolmogorov V, Rother C. 2008. Feature correspondence via graph
matching: Models and global optimization. ECCV: European Conference on Computer
Vision, LNCS, vol. 5303, 596–609.'
mla: 'Torresani, Lorenzo, et al. Feature Correspondence via Graph Matching: Models
and Global Optimization. Vol. 5303, Springer, 2008, pp. 596–609, doi:10.1007/978-3-540-88688-4_44.'
short: L. Torresani, V. Kolmogorov, C. Rother, in:, Springer, 2008, pp. 596–609.
conference:
name: 'ECCV: European Conference on Computer Vision'
date_created: 2018-12-11T12:01:58Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:44Z
day: '01'
doi: 10.1007/978-3-540-88688-4_44
extern: 1
intvolume: ' 5303'
main_file_link:
- open_access: '0'
url: http://research-srv.microsoft.com/pubs/70610/eccv08-MatchingMRF.pdf
month: '01'
page: 596 - 609
publication_status: published
publisher: Springer
publist_id: '3485'
quality_controlled: 0
status: public
title: 'Feature correspondence via graph matching: Models and global optimization'
type: conference
volume: 5303
year: '2008'
...
---
_id: '3224'
abstract:
- lang: eng
text: 'We propose a new mode of operation, enciphered CBC, for domain extension
of length-preserving functions (like block ciphers), which is a variation on the
popular CBC mode of operation. Our new mode is twice slower than CBC, but has
many (property-preserving) properties not enjoyed by CBC and other known modes.
Most notably, it yields the first constant-rate Variable Input Length (VIL) MAC
from any length preserving Fixed Input Length (FIL) MAC. This answers the question
of Dodis and Puniya from Eurocrypt 2007. Further, our mode is a secure domain
extender for PRFs (with basically the same security as encrypted CBC). This provides
a hedge against the security of the block cipher: if the block cipher is pseudorandom,
one gets a VIL-PRF, while if it is "only" unpredictable, one "at
least" gets a VIL-MAC. Additionally, our mode yields a VIL random oracle
(and, hence, a collision-resistant hash function) when instantiated with length-preserving
random functions, or even random permutations (which can be queried from both
sides). This means that one does not have to re-key the block cipher during the
computation, which was critically used in most previous constructions (analyzed
in the ideal cipher model). '
alternative_title:
- LNCS
author:
- first_name: Yevgeniy
full_name: Dodis, Yevgeniy
last_name: Dodis
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Prashant
full_name: Puniya, Prashant
last_name: Puniya
citation:
ama: 'Dodis Y, Pietrzak KZ, Puniya P. A new mode of operation for block ciphers
and length preserving MACs. In: Vol 4965. Springer; 2008:198-219. doi:10.1007/978-3-540-78967-3_12'
apa: 'Dodis, Y., Pietrzak, K. Z., & Puniya, P. (2008). A new mode of operation
for block ciphers and length preserving MACs (Vol. 4965, pp. 198–219). Presented
at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer.
https://doi.org/10.1007/978-3-540-78967-3_12'
chicago: Dodis, Yevgeniy, Krzysztof Z Pietrzak, and Prashant Puniya. “A New Mode
of Operation for Block Ciphers and Length Preserving MACs,” 4965:198–219. Springer,
2008. https://doi.org/10.1007/978-3-540-78967-3_12.
ieee: 'Y. Dodis, K. Z. Pietrzak, and P. Puniya, “A new mode of operation for block
ciphers and length preserving MACs,” presented at the EUROCRYPT: Theory and Applications
of Cryptographic Techniques, 2008, vol. 4965, pp. 198–219.'
ista: 'Dodis Y, Pietrzak KZ, Puniya P. 2008. A new mode of operation for block ciphers
and length preserving MACs. EUROCRYPT: Theory and Applications of Cryptographic
Techniques, LNCS, vol. 4965, 198–219.'
mla: Dodis, Yevgeniy, et al. A New Mode of Operation for Block Ciphers and Length
Preserving MACs. Vol. 4965, Springer, 2008, pp. 198–219, doi:10.1007/978-3-540-78967-3_12.
short: Y. Dodis, K.Z. Pietrzak, P. Puniya, in:, Springer, 2008, pp. 198–219.
conference:
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
date_created: 2018-12-11T12:02:07Z
date_published: 2008-04-28T00:00:00Z
date_updated: 2021-01-12T07:41:55Z
day: '28'
doi: 10.1007/978-3-540-78967-3_12
extern: 1
intvolume: ' 4965'
month: '04'
page: 198 - 219
publication_status: published
publisher: Springer
publist_id: '3456'
quality_controlled: 0
status: public
title: A new mode of operation for block ciphers and length preserving MACs
type: conference
volume: 4965
year: '2008'
...
---
_id: '3225'
abstract:
- lang: eng
text: 'A robust multi-property combiner for a set of security properties merges
two hash functions such that the resulting function satisfies each of the properties
which at least one of the two starting functions has. Fischlin and Lehmann (TCC
2008) recently constructed a combiner which simultaneously preserves collision-resistance,
target collision-resistance, message authentication, pseudorandomness and indifferentiability
from a random oracle (IRO). Their combiner produces outputs of 5n bits, where
n denotes the output length of the underlying hash functions. In this paper we
propose improved combiners with shorter outputs. By sacrificing the indifferentiability
from random oracles we obtain a combiner which preserves all of the other aforementioned
properties but with output length 2n only. This matches a lower bound for black-box
combiners for collision-resistance as the only property, showing that the other
properties can be achieved without penalizing the length of the hash values. We
then propose a combiner which also preserves the IRO property, slightly increasing
the output length to 2n + ω(logn). Finally, we show that a twist on our combiners
also makes them robust for one-wayness (but at the price of a fixed input length). '
alternative_title:
- LNCS
author:
- first_name: Marc
full_name: Fischlin, Marc
last_name: Fischlin
- first_name: Anja
full_name: Lehmann, Anja
last_name: Lehmann
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Fischlin M, Lehmann A, Pietrzak KZ. Robust multi property combiners for hash
functions revisited. In: Vol 5126. Springer; 2008:655-666. doi:10.1007/978-3-540-70583-3_53'
apa: 'Fischlin, M., Lehmann, A., & Pietrzak, K. Z. (2008). Robust multi property
combiners for hash functions revisited (Vol. 5126, pp. 655–666). Presented at
the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/978-3-540-70583-3_53'
chicago: Fischlin, Marc, Anja Lehmann, and Krzysztof Z Pietrzak. “Robust Multi Property
Combiners for Hash Functions Revisited,” 5126:655–66. Springer, 2008. https://doi.org/10.1007/978-3-540-70583-3_53.
ieee: 'M. Fischlin, A. Lehmann, and K. Z. Pietrzak, “Robust multi property combiners
for hash functions revisited,” presented at the ICALP: Automata, Languages and
Programming, 2008, vol. 5126, no. PART 2, pp. 655–666.'
ista: 'Fischlin M, Lehmann A, Pietrzak KZ. 2008. Robust multi property combiners
for hash functions revisited. ICALP: Automata, Languages and Programming, LNCS,
vol. 5126, 655–666.'
mla: Fischlin, Marc, et al. Robust Multi Property Combiners for Hash Functions
Revisited. Vol. 5126, no. PART 2, Springer, 2008, pp. 655–66, doi:10.1007/978-3-540-70583-3_53.
short: M. Fischlin, A. Lehmann, K.Z. Pietrzak, in:, Springer, 2008, pp. 655–666.
conference:
name: 'ICALP: Automata, Languages and Programming'
date_created: 2018-12-11T12:02:07Z
date_published: 2008-08-06T00:00:00Z
date_updated: 2023-02-23T11:01:10Z
day: '06'
doi: 10.1007/978-3-540-70583-3_53
extern: 1
intvolume: ' 5126'
issue: PART 2
month: '08'
page: 655 - 666
publication_status: published
publisher: Springer
publist_id: '3454'
quality_controlled: 0
related_material:
record:
- id: '2852'
relation: later_version
status: public
status: public
title: Robust multi property combiners for hash functions revisited
type: conference
volume: 5126
year: '2008'
...
---
_id: '3226'
abstract:
- lang: eng
text: 'A family of functions is weakly pseudorandom if a random member of the family
is indistinguishable from a uniform random function when queried on random inputs.
We point out a subtle ambiguity in the definition of weak PRFs: there are natural
weak PRFs whose security breaks down if the randomness used to sample the inputs
is revealed. To capture this ambiguity we distinguish between public-coin and
secret-coin weak PRFs. We show that the existence of a secret-coin weak PRF which
is not also a public-coin weak PRF implies the existence of two pass key-agreement
(i.e. public-key encryption). So in Minicrypt, i.e. under the assumption that
one-way functions exist but public-key cryptography does not, the notion of public-
and secret-coin weak PRFs coincide. Previous to this paper all positive cryptographic
statements known to hold exclusively in Minicrypt concerned the adaptive security
of constructions using non-adaptively secure components. Weak PRFs give rise to
a new set of statements having this property. As another example we consider the
problem of range extension for weak PRFs. We show that in Minicrypt one can beat
the best possible range expansion factor (using a fixed number of distinct keys)
for a very general class of constructions (in particular, this class contains
all constructions that are known today). '
acknowledgement: This work was partially supported by the Zurich Information Security
Center.
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
- first_name: Johan
full_name: Sjödin, Johan
last_name: Sjödin
citation:
ama: 'Pietrzak KZ, Sjödin J. Weak pseudorandom functions in minicrypt. In: Vol 5126.
Springer; 2008:423-436. doi:10.1007/978-3-540-70583-3_35'
apa: 'Pietrzak, K. Z., & Sjödin, J. (2008). Weak pseudorandom functions in minicrypt
(Vol. 5126, pp. 423–436). Presented at the ICALP: Automata, Languages and Programming,
Springer. https://doi.org/10.1007/978-3-540-70583-3_35'
chicago: Pietrzak, Krzysztof Z, and Johan Sjödin. “Weak Pseudorandom Functions in
Minicrypt,” 5126:423–36. Springer, 2008. https://doi.org/10.1007/978-3-540-70583-3_35.
ieee: 'K. Z. Pietrzak and J. Sjödin, “Weak pseudorandom functions in minicrypt,”
presented at the ICALP: Automata, Languages and Programming, 2008, vol. 5126,
no. PART 2, pp. 423–436.'
ista: 'Pietrzak KZ, Sjödin J. 2008. Weak pseudorandom functions in minicrypt. ICALP:
Automata, Languages and Programming, LNCS, vol. 5126, 423–436.'
mla: Pietrzak, Krzysztof Z., and Johan Sjödin. Weak Pseudorandom Functions in
Minicrypt. Vol. 5126, no. PART 2, Springer, 2008, pp. 423–36, doi:10.1007/978-3-540-70583-3_35.
short: K.Z. Pietrzak, J. Sjödin, in:, Springer, 2008, pp. 423–436.
conference:
name: 'ICALP: Automata, Languages and Programming'
date_created: 2018-12-11T12:02:07Z
date_published: 2008-08-06T00:00:00Z
date_updated: 2021-01-12T07:41:56Z
day: '06'
doi: 10.1007/978-3-540-70583-3_35
extern: 1
intvolume: ' 5126'
issue: PART 2
month: '08'
page: 423 - 436
publication_status: published
publisher: Springer
publist_id: '3455'
quality_controlled: 0
status: public
title: Weak pseudorandom functions in minicrypt
type: conference
volume: 5126
year: '2008'
...
---
_id: '3227'
abstract:
- lang: eng
text: Large amount of data management can cause a lot of troubles which can be solved
by dedicated computer system. To facilitate management of measurement data which
are gathered in Institute of Power Engineering - Insulation Department a special
system called Elektrowiz® was developed. It allows storing measurement results
which concern partial discharges in insulation of turbo- and hydrogenerators in
power stations. Multilayer architecture of the system allows reaching gathered
data independently on user localization. There are possible different access methods
to the system and dependency on current requirements data exploration can be realized
with read-only or edit rights.
author:
- first_name: Piotr
full_name: Zubielik, Piotr
last_name: Zubielik
- first_name: Jerzy
full_name: Nadaczny, Jerzy
last_name: Nadaczny
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Marcin
full_name: Lawenda, Marcin
last_name: Lawenda
citation:
ama: Zubielik P, Nadaczny J, Pietrzak KZ, Lawenda M. Elektrowiz – system of measurement
data management. Przeglad Elektrotechniczny. 2008;84(10):239-242.
apa: Zubielik, P., Nadaczny, J., Pietrzak, K. Z., & Lawenda, M. (2008). Elektrowiz
– system of measurement data management. Przeglad Elektrotechniczny. SIGMA-NOT.
chicago: Zubielik, Piotr, Jerzy Nadaczny, Krzysztof Z Pietrzak, and Marcin Lawenda.
“Elektrowiz – System of Measurement Data Management.” Przeglad Elektrotechniczny.
SIGMA-NOT, 2008.
ieee: P. Zubielik, J. Nadaczny, K. Z. Pietrzak, and M. Lawenda, “Elektrowiz – system
of measurement data management,” Przeglad Elektrotechniczny, vol. 84, no.
10. SIGMA-NOT, pp. 239–242, 2008.
ista: Zubielik P, Nadaczny J, Pietrzak KZ, Lawenda M. 2008. Elektrowiz – system
of measurement data management. Przeglad Elektrotechniczny. 84(10), 239–242.
mla: Zubielik, Piotr, et al. “Elektrowiz – System of Measurement Data Management.”
Przeglad Elektrotechniczny, vol. 84, no. 10, SIGMA-NOT, 2008, pp. 239–42.
short: P. Zubielik, J. Nadaczny, K.Z. Pietrzak, M. Lawenda, Przeglad Elektrotechniczny
84 (2008) 239–242.
date_created: 2018-12-11T12:02:08Z
date_published: 2008-10-01T00:00:00Z
date_updated: 2021-01-12T07:41:56Z
day: '01'
extern: 1
intvolume: ' 84'
issue: '10'
main_file_link:
- open_access: '0'
url: http://pe.org.pl/abstract_pl.php?nid=1917
month: '10'
page: 239 - 242
publication: Przeglad Elektrotechniczny
publication_status: published
publisher: SIGMA-NOT
publist_id: '3452'
quality_controlled: 0
status: public
title: Elektrowiz – system of measurement data management
type: journal_article
volume: 84
year: '2008'
...
---
_id: '3228'
abstract:
- lang: eng
text: |2-
A black-box combiner for collision resistant hash functions (CRHF) is a construction which given black-box access to two hash functions is collision resistant if at least one of the components is collision resistant. In this paper we prove a lower bound on the output length of black-box combiners for CRHFs. The bound we prove is basically tight as it is achieved by a recent construction of Canetti et al [Crypto'07]. The best previously known lower bounds only ruled out a very restricted class of combiners having a very strong security reduction: the reduction was required to output collisions for both underlying candidate hash-functions given a single collision for the combiner (Canetti et al [Crypto'07] building on Boneh and Boyen [Crypto'06] and Pietrzak [Eurocrypt'07]). Our proof uses a lemma similar to the elegant "reconstruction lemma" of Gennaro and Trevisan [FOCS'00], which states that any function which is not one-way is compressible (and thus uniformly random function must be one-way). In a similar vein we show that a function which is not collision resistant is compressible. We also borrow ideas from recent work by Haitner et al. [FOCS'07], who show that one can prove the reconstruction lemma even relative to some very powerful oracles (in our case this will be an exponential time collision-finding oracle). © 2008 Springer-Verlag Berlin Heidelberg.
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. Compression from collisions or why CRHF combiners have a long
output. In: Vol 5157. Springer; 2008:413-432. doi:10.1007/978-3-540-85174-5_23'
apa: 'Pietrzak, K. Z. (2008). Compression from collisions or why CRHF combiners
have a long output (Vol. 5157, pp. 413–432). Presented at the CRYPTO: International
Cryptology Conference, Springer. https://doi.org/10.1007/978-3-540-85174-5_23'
chicago: Pietrzak, Krzysztof Z. “Compression from Collisions or Why CRHF Combiners
Have a Long Output,” 5157:413–32. Springer, 2008. https://doi.org/10.1007/978-3-540-85174-5_23.
ieee: 'K. Z. Pietrzak, “Compression from collisions or why CRHF combiners have a
long output,” presented at the CRYPTO: International Cryptology Conference, 2008,
vol. 5157, pp. 413–432.'
ista: 'Pietrzak KZ. 2008. Compression from collisions or why CRHF combiners have
a long output. CRYPTO: International Cryptology Conference, LNCS, vol. 5157, 413–432.'
mla: Pietrzak, Krzysztof Z. Compression from Collisions or Why CRHF Combiners
Have a Long Output. Vol. 5157, Springer, 2008, pp. 413–32, doi:10.1007/978-3-540-85174-5_23.
short: K.Z. Pietrzak, in:, Springer, 2008, pp. 413–432.
conference:
name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:08Z
date_published: 2008-09-11T00:00:00Z
date_updated: 2021-01-12T07:41:57Z
day: '11'
doi: 10.1007/978-3-540-85174-5_23
extern: 1
intvolume: ' 5157'
month: '09'
page: 413 - 432
publication_status: published
publisher: Springer
publist_id: '3453'
quality_controlled: 0
status: public
title: Compression from collisions or why CRHF combiners have a long output
type: conference
volume: 5157
year: '2008'
...
---
_id: '3229'
abstract:
- lang: eng
text: 'We construct a stream-cipher S whose implementation is secure even if a bounded
amount of arbitrary (adversarially chosen) information on the internal state ofS
is leaked during computation. This captures all possible side-channel attacks
on S where the amount of information leaked in a given period is bounded, but
overall can be arbitrary large. The only other assumption we make on the implementation
of S is that only data that is accessed during computation leaks information.
The stream-cipher S generates its output in chunks K1, K2, . . . and arbitrary
but bounded information leakage is modeled by allowing the adversary to adaptively
chose a function fl : {0,1}* rarr {0, 1}lambda before Kl is computed, she then
gets fl(taul) where taul is the internal state ofS that is accessed during the
computation of Kg. One notion of security we prove for S is that Kg is indistinguishable
from random when given K1,..., K1-1,f1(tau1 ),..., fl-1(taul-1) and also the complete
internal state of S after Kg has been computed (i.e. S is forward-secure). The
construction is based on alternating extraction (used in the intrusion-resilient
secret-sharing scheme from FOCS''07). We move this concept to the computational
setting by proving a lemma that states that the output of any PRG has high HILLpseudoentropy
(i.e. is indistinguishable from some distribution with high min-entropy) even
if arbitrary information about the seed is leaked. The amount of leakage lambda
that we can tolerate in each step depends on the strength of the underlying PRG,
it is at least logarithmic, but can be as large as a constant fraction of the
internal state of S if the PRG is exponentially hard.'
author:
- first_name: Stefan
full_name: Dziembowski, Stefan
last_name: Dziembowski
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Dziembowski S, Pietrzak KZ. Leakage resilient cryptography. In: IEEE; 2008:293-302.
doi:10.1109/FOCS.2008.56'
apa: 'Dziembowski, S., & Pietrzak, K. Z. (2008). Leakage resilient cryptography
(pp. 293–302). Presented at the FOCS: Foundations of Computer Science, IEEE. https://doi.org/10.1109/FOCS.2008.56'
chicago: Dziembowski, Stefan, and Krzysztof Z Pietrzak. “Leakage Resilient Cryptography,”
293–302. IEEE, 2008. https://doi.org/10.1109/FOCS.2008.56.
ieee: 'S. Dziembowski and K. Z. Pietrzak, “Leakage resilient cryptography,” presented
at the FOCS: Foundations of Computer Science, 2008, pp. 293–302.'
ista: 'Dziembowski S, Pietrzak KZ. 2008. Leakage resilient cryptography. FOCS: Foundations
of Computer Science, 293–302.'
mla: Dziembowski, Stefan, and Krzysztof Z. Pietrzak. Leakage Resilient Cryptography.
IEEE, 2008, pp. 293–302, doi:10.1109/FOCS.2008.56.
short: S. Dziembowski, K.Z. Pietrzak, in:, IEEE, 2008, pp. 293–302.
conference:
name: 'FOCS: Foundations of Computer Science'
date_created: 2018-12-11T12:02:08Z
date_published: 2008-10-28T00:00:00Z
date_updated: 2021-01-12T07:41:57Z
day: '28'
doi: 10.1109/FOCS.2008.56
extern: 1
month: '10'
page: 293 - 302
publication_status: published
publisher: IEEE
publist_id: '3451'
quality_controlled: 0
status: public
title: Leakage resilient cryptography
type: conference
year: '2008'
...
---
_id: '3291'
abstract:
- lang: eng
text: 'The filamentous fungus Aspergillus fumigatus is responsible for a lethal
disease called Invasive Aspergillosis that affects immunocompromised patients.
This disease, like other human fungal diseases, is generally treated by compounds
targeting the primary fungal cell membrane sterol. Recently, glucan synthesis
inhibitors were added to the limited antifungal arsenal and encouraged the search
for novel targets in cell wall biosynthesis. Although galactomannan is a major
component of the A. fumigatus cell wall and extracellular matrix, the biosynthesis
and role of galactomannan are currently unknown. By a targeted gene deletion approach,
we demonstrate that UDP-galactopyranose mutase, a key enzyme of galactofuranose
metabolism, controls the biosynthesis of galactomannan and galactofuranose containing
glycoconjugates. The glfA deletion mutant generated in this study is devoid of
galactofuranose and displays attenuated virulence in a low-dose mouse model of
invasive aspergillosis that likely reflects the impaired growth of the mutant
at mammalian body temperature. Furthermore, the absence of galactofuranose results
in a thinner cell wall that correlates with an increased susceptibility to several
antifungal agents. The UDP-galactopyranose mutase thus appears to be an appealing
adjunct therapeutic target in combination with other drugs against A. fumigatus.
Its absence from mammalian cells indeed offers a considerable advantage to achieve
therapeutic selectivity. '
author:
- first_name: Philipp S
full_name: Philipp Schmalhorst
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Sven
full_name: Krappmann, Sven
last_name: Krappmann
- first_name: Wouter
full_name: Vervecken, Wouter
last_name: Vervecken
- first_name: Manfred
full_name: Rohde, Manfred
last_name: Rohde
- first_name: Meike
full_name: Müller, Meike
last_name: Müller
- first_name: Gerhard
full_name: Braus, Gerhard H.
last_name: Braus
- first_name: Roland
full_name: Contreras, Roland
last_name: Contreras
- first_name: Armin
full_name: Braun, Armin
last_name: Braun
- first_name: Hans
full_name: Bakker, Hans
last_name: Bakker
- first_name: Françoise
full_name: Routier, Françoise H
last_name: Routier
citation:
ama: Schmalhorst PS, Krappmann S, Vervecken W, et al. Contribution of galactofuranose
to the virulence of the opportunistic pathogen Aspergillus fumigatus. Eukaryotic
Cell. 2008;7(8):1268-1277. doi:10.1128/EC.00065-08
apa: Schmalhorst, P. S., Krappmann, S., Vervecken, W., Rohde, M., Müller, M., Braus,
G., … Routier, F. (2008). Contribution of galactofuranose to the virulence of
the opportunistic pathogen Aspergillus fumigatus. Eukaryotic Cell. American
Society for Microbiology. https://doi.org/10.1128/EC.00065-08
chicago: Schmalhorst, Philipp S, Sven Krappmann, Wouter Vervecken, Manfred Rohde,
Meike Müller, Gerhard Braus, Roland Contreras, Armin Braun, Hans Bakker, and Françoise
Routier. “Contribution of Galactofuranose to the Virulence of the Opportunistic
Pathogen Aspergillus Fumigatus.” Eukaryotic Cell. American Society for
Microbiology, 2008. https://doi.org/10.1128/EC.00065-08.
ieee: P. S. Schmalhorst et al., “Contribution of galactofuranose to the virulence
of the opportunistic pathogen Aspergillus fumigatus,” Eukaryotic Cell,
vol. 7, no. 8. American Society for Microbiology, pp. 1268–1277, 2008.
ista: Schmalhorst PS, Krappmann S, Vervecken W, Rohde M, Müller M, Braus G, Contreras
R, Braun A, Bakker H, Routier F. 2008. Contribution of galactofuranose to the
virulence of the opportunistic pathogen Aspergillus fumigatus. Eukaryotic Cell.
7(8), 1268–1277.
mla: Schmalhorst, Philipp S., et al. “Contribution of Galactofuranose to the Virulence
of the Opportunistic Pathogen Aspergillus Fumigatus.” Eukaryotic Cell,
vol. 7, no. 8, American Society for Microbiology, 2008, pp. 1268–77, doi:10.1128/EC.00065-08.
short: P.S. Schmalhorst, S. Krappmann, W. Vervecken, M. Rohde, M. Müller, G. Braus,
R. Contreras, A. Braun, H. Bakker, F. Routier, Eukaryotic Cell 7 (2008) 1268–1277.
date_created: 2018-12-11T12:02:29Z
date_published: 2008-06-13T00:00:00Z
date_updated: 2021-01-12T07:42:26Z
day: '13'
doi: 10.1128/EC.00065-08
extern: 1
intvolume: ' 7'
issue: '8'
month: '06'
page: 1268 - 1277
publication: Eukaryotic Cell
publication_status: published
publisher: American Society for Microbiology
publist_id: '3354'
quality_controlled: 0
status: public
title: Contribution of galactofuranose to the virulence of the opportunistic pathogen
Aspergillus fumigatus
type: journal_article
volume: 7
year: '2008'
...
---
_id: '3307'
abstract:
- lang: eng
text: A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000
year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8
Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally
establishes that the Neandertal mtDNA falls outside the variation of extant human
mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages
of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2
of cytochrome c oxidase of the mitochondrial electron transport chain has experienced
the largest number of amino acid substitutions in human ancestors since the separation
from Neandertals. There is evidence that purifying selection in the Neandertal
mtDNA was reduced compared with other primate lineages, suggesting that the effective
population size of Neandertals was small.
author:
- first_name: Richard
full_name: Green, Richard E
last_name: Green
- first_name: Anna
full_name: 'Malaspinas, Anna-Sapfo '
last_name: Malaspinas
- first_name: Johannes
full_name: Krause, Johannes
last_name: Krause
- first_name: Adrian
full_name: Briggs, Adrian W
last_name: Briggs
- first_name: Philip
full_name: Johnson, Philip L
last_name: Johnson
- first_name: Caroline
full_name: Caroline Uhler
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Matthias
full_name: Meyer, Matthias
last_name: Meyer
- first_name: Jeffrey
full_name: Good, Jeffrey M
last_name: Good
- first_name: Tomislav
full_name: Maricic, Tomislav
last_name: Maricic
- first_name: Udo
full_name: Stenzel, Udo
last_name: Stenzel
- first_name: Kay
full_name: Prüfer, Kay
last_name: Prüfer
- first_name: Michael
full_name: Siebauer, Michael F
last_name: Siebauer
- first_name: Hernän
full_name: Burbano, Hernän A
last_name: Burbano
- first_name: Michael
full_name: Ronan, Michael T
last_name: Ronan
- first_name: Jonathan
full_name: Rothberg, Jonathan M
last_name: Rothberg
- first_name: Michael
full_name: Egholm, Michael
last_name: Egholm
- first_name: Pavao
full_name: Rudan, Pavao
last_name: Rudan
- first_name: Dejana
full_name: Brajković, Dejana
last_name: Brajković
- first_name: Željko
full_name: Kućan, Željko
last_name: Kućan
- first_name: Ivan
full_name: Gušić, Ivan
last_name: Gušić
- first_name: Mårten
full_name: Wikström, Mårten K
last_name: Wikström
- first_name: Liisa
full_name: Laakkonen, Liisa J
last_name: Laakkonen
- first_name: Janet
full_name: Kelso, Janet F
last_name: Kelso
- first_name: Montgomery
full_name: Slatkin, Montgomery
last_name: Slatkin
- first_name: Svante
full_name: Pääbo, Svante H
last_name: Pääbo
citation:
ama: Green R, Malaspinas A, Krause J, et al. A complete neandertal mitochondrial
genome sequence determined by highhhroughput sequencing. Cell. 2008;134:416-426.
doi:10.1016/j.cell.2008.06.021
apa: Green, R., Malaspinas, A., Krause, J., Briggs, A., Johnson, P., Uhler, C.,
… Pääbo, S. (2008). A complete neandertal mitochondrial genome sequence determined
by highhhroughput sequencing. Cell. Cell Press. https://doi.org/10.1016/j.cell.2008.06.021
chicago: Green, Richard, Anna Malaspinas, Johannes Krause, Adrian Briggs, Philip
Johnson, Caroline Uhler, Matthias Meyer, et al. “A Complete Neandertal Mitochondrial
Genome Sequence Determined by Highhhroughput Sequencing.” Cell. Cell Press,
2008. https://doi.org/10.1016/j.cell.2008.06.021.
ieee: R. Green et al., “A complete neandertal mitochondrial genome sequence
determined by highhhroughput sequencing,” Cell, vol. 134. Cell Press, pp.
416–426, 2008.
ista: Green R, Malaspinas A, Krause J, Briggs A, Johnson P, Uhler C, Meyer M, Good
J, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano H, Ronan M, Rothberg J,
Egholm M, Rudan P, Brajković D, Kućan Ž, Gušić I, Wikström M, Laakkonen L, Kelso
J, Slatkin M, Pääbo S. 2008. A complete neandertal mitochondrial genome sequence
determined by highhhroughput sequencing. Cell. 134, 416–426.
mla: Green, Richard, et al. “A Complete Neandertal Mitochondrial Genome Sequence
Determined by Highhhroughput Sequencing.” Cell, vol. 134, Cell Press, 2008,
pp. 416–26, doi:10.1016/j.cell.2008.06.021.
short: R. Green, A. Malaspinas, J. Krause, A. Briggs, P. Johnson, C. Uhler, M. Meyer,
J. Good, T. Maricic, U. Stenzel, K. Prüfer, M. Siebauer, H. Burbano, M. Ronan,
J. Rothberg, M. Egholm, P. Rudan, D. Brajković, Ž. Kućan, I. Gušić, M. Wikström,
L. Laakkonen, J. Kelso, M. Slatkin, S. Pääbo, Cell 134 (2008) 416–426.
date_created: 2018-12-11T12:02:35Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2021-01-12T07:42:32Z
day: '01'
doi: 10.1016/j.cell.2008.06.021
extern: 1
intvolume: ' 134'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2602844/
month: '08'
oa: 1
page: 416 - 426
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3333'
quality_controlled: 0
status: public
title: A complete neandertal mitochondrial genome sequence determined by highhhroughput
sequencing
type: journal_article
volume: 134
year: '2008'
...
---
_id: '3409'
abstract:
- lang: eng
text: With the introduction of single-molecule force spectroscopy (SMFS) it has
become possible to directly access the interactions of various molecular systems.
A bottleneck in conventional SMFS is collecting the large amount of data required
for statistically meaningful analysis. Currently, atomic force microscopy (AFM)-based
SMFS requires the user to tediously 'fish' for single molecules. In addition,
most experimental and environmental conditions must be manually adjusted. Here,
we developed a fully automated single-molecule force spectroscope. The instrument
is able to perform SMFS while monitoring and regulating experimental conditions
such as buffer composition and temperature. Cantilever alignment and calibration
can also be automatically performed during experiments. This, combined with in-line
data analysis, enables the instrument, once set up, to perform complete SMFS experiments
autonomously.
author:
- first_name: Jens
full_name: Struckmeier, Jens
last_name: Struckmeier
- first_name: Reiner
full_name: Wahl, Reiner
last_name: Wahl
- first_name: Mirko
full_name: Leuschner, Mirko
last_name: Leuschner
- first_name: Joao
full_name: Nunes, Joao
last_name: Nunes
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Ulrich
full_name: Geisler, Ulrich
last_name: Geisler
- first_name: Gerd
full_name: Hofmann, Gerd
last_name: Hofmann
- first_name: Torsten
full_name: Jähnke, Torsten
last_name: Jähnke
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Struckmeier J, Wahl R, Leuschner M, et al. Fully automated single-molecule
force spectroscopy for screening applications. Nanotechnology. 2008;19(38).
doi:10.1088/0957-4484/19/38/384020
apa: Struckmeier, J., Wahl, R., Leuschner, M., Nunes, J., Janovjak, H. L., Geisler,
U., … Mueller, D. (2008). Fully automated single-molecule force spectroscopy for
screening applications. Nanotechnology. IOP Publishing Ltd. https://doi.org/10.1088/0957-4484/19/38/384020
chicago: Struckmeier, Jens, Reiner Wahl, Mirko Leuschner, Joao Nunes, Harald L Janovjak,
Ulrich Geisler, Gerd Hofmann, Torsten Jähnke, and Daniel Mueller. “Fully Automated
Single-Molecule Force Spectroscopy for Screening Applications.” Nanotechnology.
IOP Publishing Ltd., 2008. https://doi.org/10.1088/0957-4484/19/38/384020.
ieee: J. Struckmeier et al., “Fully automated single-molecule force spectroscopy
for screening applications,” Nanotechnology, vol. 19, no. 38. IOP Publishing
Ltd., 2008.
ista: Struckmeier J, Wahl R, Leuschner M, Nunes J, Janovjak HL, Geisler U, Hofmann
G, Jähnke T, Mueller D. 2008. Fully automated single-molecule force spectroscopy
for screening applications. Nanotechnology. 19(38).
mla: Struckmeier, Jens, et al. “Fully Automated Single-Molecule Force Spectroscopy
for Screening Applications.” Nanotechnology, vol. 19, no. 38, IOP Publishing
Ltd., 2008, doi:10.1088/0957-4484/19/38/384020.
short: J. Struckmeier, R. Wahl, M. Leuschner, J. Nunes, H.L. Janovjak, U. Geisler,
G. Hofmann, T. Jähnke, D. Mueller, Nanotechnology 19 (2008).
date_created: 2018-12-11T12:03:11Z
date_published: 2008-08-12T00:00:00Z
date_updated: 2021-01-12T07:43:17Z
day: '12'
doi: 10.1088/0957-4484/19/38/384020
extern: 1
intvolume: ' 19'
issue: '38'
month: '08'
publication: Nanotechnology
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '2993'
quality_controlled: 0
status: public
title: Fully automated single-molecule force spectroscopy for screening applications
type: journal_article
volume: 19
year: '2008'
...
---
_id: '3410'
abstract:
- lang: eng
text: Membrane proteins are involved in essential biological processes such as energy
conversion, signal transduction, solute transport and secretion. All biological
processes, also those involving membrane proteins, are steered by molecular interactions.
Molecular interactions guide the folding and stability of membrane proteins, determine
their assembly, switch their functional states or mediate signal transduction.
The sequential steps of molecular interactions driving these processes can be
described by dynamic energy landscapes. The conceptual energy landscape allows
to follow the complex reaction pathways of membrane proteins while its modifications
describe why and how pathways are changed. Single-molecule force spectroscopy
(SMFS) detects, quantifies and locates interactions within and between membrane
proteins. SMFS helps to determine how these interactions change with temperature,
point mutations, oligomerization and the functional states of membrane proteins.
Applied in different modes, SMFS explores the co-existence and population of reaction
pathways in the energy landscape of the protein and thus reveals detailed insights
into local mechanisms, determining its structural and functional relationships.
Here we review how SMFS extracts the defining parameters of an energy landscape
such as the barrier position, reaction kinetics and roughness with high precision.
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: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: 'Janovjak HL, Sapra T, Kedrov A, Mueller D. From valleys to ridges: Exploring
the energy landscape of single membrane proteins. ChemPhysChem. 2008;9(7):954-966.
doi:10.1002/cphc.200700662'
apa: 'Janovjak, H. L., Sapra, T., Kedrov, A., & Mueller, D. (2008). From valleys
to ridges: Exploring the energy landscape of single membrane proteins. ChemPhysChem.
Wiley-Blackwell. https://doi.org/10.1002/cphc.200700662'
chicago: 'Janovjak, Harald L, Tanuj Sapra, Alexej Kedrov, and Daniel Mueller. “From
Valleys to Ridges: Exploring the Energy Landscape of Single Membrane Proteins.”
ChemPhysChem. Wiley-Blackwell, 2008. https://doi.org/10.1002/cphc.200700662.'
ieee: 'H. L. Janovjak, T. Sapra, A. Kedrov, and D. Mueller, “From valleys to ridges:
Exploring the energy landscape of single membrane proteins,” ChemPhysChem,
vol. 9, no. 7. Wiley-Blackwell, pp. 954–966, 2008.'
ista: 'Janovjak HL, Sapra T, Kedrov A, Mueller D. 2008. From valleys to ridges:
Exploring the energy landscape of single membrane proteins. ChemPhysChem. 9(7),
954–966.'
mla: 'Janovjak, Harald L., et al. “From Valleys to Ridges: Exploring the Energy
Landscape of Single Membrane Proteins.” ChemPhysChem, vol. 9, no. 7, Wiley-Blackwell,
2008, pp. 954–66, doi:10.1002/cphc.200700662.'
short: H.L. Janovjak, T. Sapra, A. Kedrov, D. Mueller, ChemPhysChem 9 (2008) 954–966.
date_created: 2018-12-11T12:03:11Z
date_published: 2008-05-02T00:00:00Z
date_updated: 2019-04-26T07:22:27Z
day: '02'
doi: 10.1002/cphc.200700662
extern: 1
intvolume: ' 9'
issue: '7'
month: '05'
page: 954 - 966
publication: ChemPhysChem
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2992'
quality_controlled: 0
status: public
title: 'From valleys to ridges: Exploring the energy landscape of single membrane
proteins'
type: review
volume: 9
year: '2008'
...
---
_id: '3435'
abstract:
- lang: eng
text: We develop a new method for estimating effective population sizes, Ne, and
selection coefficients, s, from time-series data of allele frequencies sampled
from a single diallelic locus. The method is based on calculating transition probabilities,
using a numerical solution of the diffusion process, and assuming independent
binomial sampling from this diffusion process at each time point. We apply the
method in two example applications. First, we estimate selection coefficients
acting on the CCR5-Δ32 mutation on the basis of published samples of contemporary
and ancient human DNA. We show that the data are compatible with the assumption
of s = 0, although moderate amounts of selection acting on this mutation cannot
be excluded. In our second example, we estimate the selection coefficient acting
on a mutation segregating in an experimental phage population. We show that the
selection coefficient acting on this mutation is ~0.43.
author:
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Thomas
full_name: York, Thomas L
last_name: York
- first_name: Rasmus
full_name: Nielsen, Rasmus
last_name: Nielsen
citation:
ama: Bollback JP, York T, Nielsen R. Estimation of 2Nes From Temporal Allele Frequency
Data. Genetics. 2008;179(1):497-502. doi:10.1534/genetics.107.085019
apa: Bollback, J. P., York, T., & Nielsen, R. (2008). Estimation of 2Nes From
Temporal Allele Frequency Data. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.107.085019
chicago: Bollback, Jonathan P, Thomas York, and Rasmus Nielsen. “Estimation of 2Nes
From Temporal Allele Frequency Data.” Genetics. Genetics Society of America,
2008. https://doi.org/10.1534/genetics.107.085019.
ieee: J. P. Bollback, T. York, and R. Nielsen, “Estimation of 2Nes From Temporal
Allele Frequency Data,” Genetics, vol. 179, no. 1. Genetics Society of
America, pp. 497–502, 2008.
ista: Bollback JP, York T, Nielsen R. 2008. Estimation of 2Nes From Temporal Allele
Frequency Data. Genetics. 179(1), 497–502.
mla: Bollback, Jonathan P., et al. “Estimation of 2Nes From Temporal Allele Frequency
Data.” Genetics, vol. 179, no. 1, Genetics Society of America, 2008, pp.
497–502, doi:10.1534/genetics.107.085019.
short: J.P. Bollback, T. York, R. Nielsen, Genetics 179 (2008) 497–502.
date_created: 2018-12-11T12:03:19Z
date_published: 2008-05-01T00:00:00Z
date_updated: 2021-01-12T07:43:27Z
day: '01'
doi: 10.1534/genetics.107.085019
extern: 1
intvolume: ' 179'
issue: '1'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390626
month: '05'
oa: 1
page: 497 - 502
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '2965'
quality_controlled: 0
status: public
title: Estimation of 2Nes From Temporal Allele Frequency Data
type: journal_article
volume: 179
year: '2008'
...
---
_id: '3501'
abstract:
- lang: eng
text: |-
The Wikipedia is a collaborative encyclopedia: anyone can contribute to its articles simply by clicking on an "edit" button. The open nature of the Wikipedia has been key to its success, but has also created a challenge: how can readers develop an informed opinion on its reliability? We propose a system that computes quantitative values of trust for the text in Wikipedia articles; these trust values provide an indication of text reliability.
The system uses as input the revision history of each article, as well as information about the reputation of the contributing authors, as provided by a reputation system. The trust of a word in an article is computed on the basis of the reputation of the original author of the word, as well as the reputation of all authors who edited text near the word. The algorithm computes word trust values that vary smoothly across the text; the trust values can be visualized using varying text-background colors. The algorithm ensures that all changes to an article's text are reflected in the trust values, preventing surreptitious content changes.
We have implemented the proposed system, and we have used it to compute and display the trust of the text of thousands of articles of the English Wikipedia. To validate our trust-computation algorithms, we show that text labeled as low-trust has a significantly higher probability of being edited in the future than text labeled as high-trust.
acknowledgement: 'This research has been partially supported by the CITRIS: Center
for Information Technology Research in the Interest of Society.'
author:
- first_name: B Thomas
full_name: Adler, B Thomas
last_name: Adler
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Luca
full_name: de Alfaro, Luca
last_name: De Alfaro
- first_name: Marco
full_name: Faella, Marco
last_name: Faella
- first_name: Ian
full_name: Pye, Ian
last_name: Pye
- first_name: Vishwanath
full_name: Raman, Vishwanath
last_name: Raman
citation:
ama: 'Adler BT, Chatterjee K, De Alfaro L, Faella M, Pye I, Raman V. Assigning trust
to Wikipedia content. In: ACM; 2008. doi:10.1145/1822258.1822293'
apa: 'Adler, B. T., Chatterjee, K., De Alfaro, L., Faella, M., Pye, I., & Raman,
V. (2008). Assigning trust to Wikipedia content. Presented at the WikiSym: International
Symposium on Wikis, ACM. https://doi.org/10.1145/1822258.1822293'
chicago: Adler, B Thomas, Krishnendu Chatterjee, Luca De Alfaro, Marco Faella, Ian
Pye, and Vishwanath Raman. “Assigning Trust to Wikipedia Content.” ACM, 2008.
https://doi.org/10.1145/1822258.1822293.
ieee: 'B. T. Adler, K. Chatterjee, L. De Alfaro, M. Faella, I. Pye, and V. Raman,
“Assigning trust to Wikipedia content,” presented at the WikiSym: International
Symposium on Wikis, 2008.'
ista: 'Adler BT, Chatterjee K, De Alfaro L, Faella M, Pye I, Raman V. 2008. Assigning
trust to Wikipedia content. WikiSym: International Symposium on Wikis.'
mla: Adler, B. Thomas, et al. Assigning Trust to Wikipedia Content. ACM,
2008, doi:10.1145/1822258.1822293.
short: B.T. Adler, K. Chatterjee, L. De Alfaro, M. Faella, I. Pye, V. Raman, in:,
ACM, 2008.
conference:
name: 'WikiSym: International Symposium on Wikis'
date_created: 2018-12-11T12:03:40Z
date_published: 2008-09-10T00:00:00Z
date_updated: 2021-01-12T07:43:53Z
day: '10'
doi: 10.1145/1822258.1822293
extern: 1
month: '09'
publication_status: published
publisher: ACM
publist_id: '2886'
quality_controlled: 0
status: public
title: Assigning trust to Wikipedia content
type: conference
year: '2008'
...
---
_id: '3502'
abstract:
- lang: eng
text: 'In content-driven reputation systems for collaborative content, users gain
or lose reputation according to how their contributions fare: authors of long-lived
contributions gain reputation, while authors of reverted contributions lose reputation.
Existing content-driven systems are prone to Sybil attacks, in which multiple
identities, controlled by the same person, perform coordinated actions to increase
their reputation. We show that content-driven reputation systems can be made resistant
to such attacks by taking advantage of thefact that the reputation increments
and decrements depend on content modifications, which are visible to all. We present
an algorithm for content-driven reputation that prevents a set of identities from
increasing their maximum reputation without doing any useful work. Here, work
is considered useful if it causes content to evolve in a direction that is consistent
with the actions of high-reputation users. We argue that the content modifications
that require no effort, such as the insertion or deletion of arbitrary text, are
invariably non-useful. We prove a truthfullness result for the resulting system,
stating that users who wish to perform a contribution do not gain by employing
complex contribution schemes, compared to simply performing the contribution at
once. In particular, splitting the contribution in multiple portions, or employing
the coordinated actions of multiple identities, do not yield additional reputation.
Taken together, these results indicate that content-driven systems can be made
robust with respect to Sybil attacks. Copyright 2008 ACM.'
acknowledgement: 'This research has been partially supported by the CITRIS: Center
for Information Technology Research in the Interest of Society.'
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Luca
full_name: de Alfaro, Luca
last_name: De Alfaro
- first_name: Ian
full_name: Pye, Ian
last_name: Pye
citation:
ama: 'Chatterjee K, De Alfaro L, Pye I. Robust content-driven reputation. In: ACM;
2008:33-42. doi:10.1145/1456377.1456387
'
apa: 'Chatterjee, K., De Alfaro, L., & Pye, I. (2008). Robust content-driven
reputation (pp. 33–42). Presented at the AISec: Artificial Intelligence and Security,
ACM. https://doi.org/10.1145/1456377.1456387
'
chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Ian Pye. “Robust Content-Driven
Reputation,” 33–42. ACM, 2008. https://doi.org/10.1145/1456377.1456387 .
ieee: 'K. Chatterjee, L. De Alfaro, and I. Pye, “Robust content-driven reputation,”
presented at the AISec: Artificial Intelligence and Security, 2008, pp. 33–42.'
ista: 'Chatterjee K, De Alfaro L, Pye I. 2008. Robust content-driven reputation.
AISec: Artificial Intelligence and Security, 33–42.'
mla: Chatterjee, Krishnendu, et al. Robust Content-Driven Reputation. ACM,
2008, pp. 33–42, doi:10.1145/1456377.1456387
.
short: K. Chatterjee, L. De Alfaro, I. Pye, in:, ACM, 2008, pp. 33–42.
conference:
name: 'AISec: Artificial Intelligence and Security'
date_created: 2018-12-11T12:03:40Z
date_published: 2008-10-31T00:00:00Z
date_updated: 2021-01-12T07:43:54Z
day: '31'
doi: '10.1145/1456377.1456387 '
extern: 1
month: '10'
page: 33 - 42
publication_status: published
publisher: ACM
publist_id: '2885'
quality_controlled: 0
status: public
title: Robust content-driven reputation
type: conference
year: '2008'
...
---
_id: '3504'
abstract:
- lang: eng
text: "Simulation and bisimulation metrics for stochastic systems provide a quantitative
gen- eralization of the classical simulation and bisimulation relations. These
metrics capture the similarity of states with respect to quantitative specifications
written in the quantitative μ-calculus and related probabilistic logics.\r\nWe
present algorithms for computing the metrics on Markov decision processes (MDPs),
turn- based stochastic games, and concurrent games. For turn-based games and MDPs,
we provide a polynomial-time algorithm based on linear programming for the computation
of the one-step metric distance between states. The algorithm improves on the
previously known exponential-time algo- rithm based on a reduction to the theory
of reals. We then present PSPACE algorithms for both the decision problem and
the problem of approximating the metric distance between two states, matching
the best known bound for Markov chains. For the bisimulation kernel of the metric,
which corresponds to probabilistic bisimulation, our algorithm works in time O(n4)
for both turn-based games and MDPs; improving the previously best known O(n9 ·
log(n)) time algorithm for MDPs. For a concurrent game G, we show that computing
the exact distance between states is at least as hard as computing the value of
concurrent reachability games and the square-root-sum problem in computational
geometry. We show that checking whether the metric distance is bounded by a rational
r, can be accomplished via a reduction to the theory of real closed fields, involving
a\r\nformula with three quantifier alternations, yielding O(|G|O(|G|5)) time complexity,
improving the previously known reduction with O(|G|O(|G|7)) time complexity. These
algorithms can be iterated\r\nto approximate the metrics using binary search."
acknowledgement: This research was supported in part by the NSF grants CCR-0132780
and CNS-0720884.
alternative_title:
- LIPIcs
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Luca
full_name: De Alfaro, Luca
last_name: De Alfaro
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
- first_name: Vishwanath
full_name: Raman, Vishwanath
last_name: Raman
citation:
ama: 'Chatterjee K, De Alfaro L, Majumdar R, Raman V. Algorithms for game metrics.
In: Vol 2. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2008:107-118. doi:10.4230/LIPIcs.FSTTCS.2008.1745'
apa: 'Chatterjee, K., De Alfaro, L., Majumdar, R., & Raman, V. (2008). Algorithms
for game metrics (Vol. 2, pp. 107–118). Presented at the FSTTCS: Foundations of
Software Technology and Theoretical Computer Science, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2008.1745'
chicago: Chatterjee, Krishnendu, Luca De Alfaro, Ritankar Majumdar, and Vishwanath
Raman. “Algorithms for Game Metrics,” 2:107–18. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2008. https://doi.org/10.4230/LIPIcs.FSTTCS.2008.1745.
ieee: 'K. Chatterjee, L. De Alfaro, R. Majumdar, and V. Raman, “Algorithms for game
metrics,” presented at the FSTTCS: Foundations of Software Technology and Theoretical
Computer Science, 2008, vol. 2, pp. 107–118.'
ista: 'Chatterjee K, De Alfaro L, Majumdar R, Raman V. 2008. Algorithms for game
metrics. FSTTCS: Foundations of Software Technology and Theoretical Computer Science,
LIPIcs, vol. 2, 107–118.'
mla: Chatterjee, Krishnendu, et al. Algorithms for Game Metrics. Vol. 2,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 107–18, doi:10.4230/LIPIcs.FSTTCS.2008.1745.
short: K. Chatterjee, L. De Alfaro, R. Majumdar, V. Raman, in:, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2008, pp. 107–118.
conference:
name: 'FSTTCS: Foundations of Software Technology and Theoretical Computer Science'
date_created: 2018-12-11T12:03:40Z
date_published: 2008-12-05T00:00:00Z
date_updated: 2023-02-23T11:46:14Z
day: '05'
ddc:
- '000'
doi: 10.4230/LIPIcs.FSTTCS.2008.1745
extern: '1'
file:
- access_level: open_access
checksum: 0a447454a24e273f7ddf51dbfe47f877
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T10:01:21Z
date_updated: 2020-07-14T12:46:12Z
file_id: '6398'
file_name: 2008_LIPIcs_Chatterjee.pdf
file_size: 442139
relation: main_file
file_date_updated: 2020-07-14T12:46:12Z
has_accepted_license: '1'
intvolume: ' 2'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 107 - 118
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '2883'
quality_controlled: '1'
related_material:
record:
- id: '3868'
relation: later_version
status: public
status: public
title: Algorithms for game metrics
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2008'
...
---
_id: '3516'
abstract:
- lang: eng
text: Temporal coding is a means of representing information by the time, as opposed
to the rate, at which neurons fire. Evidence of temporal coding in the hippocampus
comes from place cells, whose spike times relative to theta oscillations reflect
a rat's position while running along stereotyped trajectories. This arises from
the backwards shift in cell firing relative to local theta oscillations (phase
precession). Here we demonstrate phase precession during place-field crossings
in an open-field foraging task. This produced spike sequences in each theta cycle
that disambiguate the rat's trajectory through two-dimensional space and can be
used to predict movement direction. Furthermore, position and movement direction
were maximally predicted from firing in the early and late portions of the theta
cycle, respectively. This represents the first direct evidence of a combined representation
of position, trajectory and heading in the hippocampus, organized on a fine temporal
scale by theta oscillations.
author:
- first_name: John
full_name: Huxter,John R
last_name: Huxter
- first_name: Timothy
full_name: Senior,Timothy J
last_name: Senior
- first_name: Kevin
full_name: Allen, Kevin
last_name: Allen
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Huxter J, Senior T, Allen K, Csicsvari JL. Theta phase-specific codes for two-dimensional
position, trajectory and heading in the hippocampus. Nature Neuroscience.
2008;11(5):587-594. doi:10.1038/nn.2106
apa: Huxter, J., Senior, T., Allen, K., & Csicsvari, J. L. (2008). Theta phase-specific
codes for two-dimensional position, trajectory and heading in the hippocampus.
Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.2106
chicago: Huxter, John, Timothy Senior, Kevin Allen, and Jozsef L Csicsvari. “Theta
Phase-Specific Codes for Two-Dimensional Position, Trajectory and Heading in the
Hippocampus.” Nature Neuroscience. Nature Publishing Group, 2008. https://doi.org/10.1038/nn.2106.
ieee: J. Huxter, T. Senior, K. Allen, and J. L. Csicsvari, “Theta phase-specific
codes for two-dimensional position, trajectory and heading in the hippocampus,”
Nature Neuroscience, vol. 11, no. 5. Nature Publishing Group, pp. 587–594,
2008.
ista: Huxter J, Senior T, Allen K, Csicsvari JL. 2008. Theta phase-specific codes
for two-dimensional position, trajectory and heading in the hippocampus. Nature
Neuroscience. 11(5), 587–594.
mla: Huxter, John, et al. “Theta Phase-Specific Codes for Two-Dimensional Position,
Trajectory and Heading in the Hippocampus.” Nature Neuroscience, vol. 11,
no. 5, Nature Publishing Group, 2008, pp. 587–94, doi:10.1038/nn.2106.
short: J. Huxter, T. Senior, K. Allen, J.L. Csicsvari, Nature Neuroscience 11 (2008)
587–594.
date_created: 2018-12-11T12:03:44Z
date_published: 2008-05-29T00:00:00Z
date_updated: 2021-01-12T07:44:00Z
day: '29'
doi: 10.1038/nn.2106
extern: 1
intvolume: ' 11'
issue: '5'
month: '05'
page: 587 - 594
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '2869'
quality_controlled: 0
status: public
title: Theta phase-specific codes for two-dimensional position, trajectory and heading
in the hippocampus
type: journal_article
volume: 11
year: '2008'
...