---
_id: '3142'
abstract:
- lang: eng
text: Assembly of neuronal circuits is controlled by the sequential acquisition
of neuronal subpopulation-specific identities at progressive developmental steps.
Whereas neuronal features involved in initial phases of differentiation are already
established at cell-cycle exit, recent findings, based mainly on work in the peripheral
nervous system, suggest that the timely integration of signals encountered en
route to targets and from the target region itself is essential to control late
steps in connectivity. As neurons project towards their targets they require target-derived
signals to establish mature axonal projections and acquire neuronal traits such
as the expression of distinct combinations of neurotransmitters. Recent evidence
presented in this review shows that this principle, of a signaling interplay between
target-derived signals and neuronal cell bodies, is often mediated through transcriptional
events and is evolutionarily conserved.
author:
- first_name: Simon
full_name: Simon Hippenmeyer
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Ina
full_name: Kramer, Ina
last_name: Kramer
- first_name: Silvia
full_name: Arber, Silvia
last_name: Arber
citation:
ama: 'Hippenmeyer S, Kramer I, Arber S. Control of neuronal phenotype: What targets
tell the cell bodies. Trends in Neurosciences. 2004;27(8):482-488. doi:10.1016/j.tins.2004.05.012'
apa: 'Hippenmeyer, S., Kramer, I., & Arber, S. (2004). Control of neuronal phenotype:
What targets tell the cell bodies. Trends in Neurosciences. Elsevier. https://doi.org/10.1016/j.tins.2004.05.012'
chicago: 'Hippenmeyer, Simon, Ina Kramer, and Silvia Arber. “Control of Neuronal
Phenotype: What Targets Tell the Cell Bodies.” Trends in Neurosciences.
Elsevier, 2004. https://doi.org/10.1016/j.tins.2004.05.012.'
ieee: 'S. Hippenmeyer, I. Kramer, and S. Arber, “Control of neuronal phenotype:
What targets tell the cell bodies,” Trends in Neurosciences, vol. 27, no.
8. Elsevier, pp. 482–488, 2004.'
ista: 'Hippenmeyer S, Kramer I, Arber S. 2004. Control of neuronal phenotype: What
targets tell the cell bodies. Trends in Neurosciences. 27(8), 482–488.'
mla: 'Hippenmeyer, Simon, et al. “Control of Neuronal Phenotype: What Targets Tell
the Cell Bodies.” Trends in Neurosciences, vol. 27, no. 8, Elsevier, 2004,
pp. 482–88, doi:10.1016/j.tins.2004.05.012.'
short: S. Hippenmeyer, I. Kramer, S. Arber, Trends in Neurosciences 27 (2004) 482–488.
date_created: 2018-12-11T12:01:38Z
date_published: 2004-08-01T00:00:00Z
date_updated: 2019-04-26T07:22:25Z
day: '01'
doi: 10.1016/j.tins.2004.05.012
extern: 1
intvolume: ' 27'
issue: '8'
month: '08'
page: 482 - 488
publication: Trends in Neurosciences
publication_status: published
publisher: Elsevier
publist_id: '3555'
quality_controlled: 0
status: public
title: 'Control of neuronal phenotype: What targets tell the cell bodies'
type: review
volume: 27
year: '2004'
...
---
_id: '3172'
abstract:
- lang: eng
text: The simultaneous multiple volume (SMV) approach in navigator-gated MRI allows
the use of the whole motion range or the entire scan time for the reconstruction
of final images by simultaneously acquiring different image volumes at different
motion states. The motion tolerance range for each volume is kept small, thus
SMV substantially increases the scan efficiency of navigator methods while maintaining
the effectiveness of motion suppression. This article reports a general implementation
of the SMV approach using a multiprocessor scheduling algorithm. Each motion state
is regarded as a processor and each volume is regarded as a job. An efficient
scheduling that completes all jobs in minimal time is maintained even when the
motion pattern changes. Initial experiments demonstrated that SMV significantly
increased the scan efficiency of navigatorgated MRI.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Thành
full_name: Nguyen, Thành D
last_name: Nguyen
- first_name: Anthony
full_name: Nuval, Anthony
last_name: Nuval
- first_name: Pascal
full_name: Spincemaille, Pascal
last_name: Spincemaille
- first_name: Martin
full_name: Prince, Martin R
last_name: Prince
- first_name: Ramin
full_name: Zabih, Ramin
last_name: Zabih
- first_name: Yusu
full_name: Wang, Yusu
last_name: Wang
citation:
ama: Kolmogorov V, Nguyen T, Nuval A, et al. Multiprocessor scheduling implementation
of the simultaneous multiple volume SMV navigator method. Magnetic Resonance
in Medicine. 2004;52(2):362-367. doi:10.1002/mrm.20162
apa: Kolmogorov, V., Nguyen, T., Nuval, A., Spincemaille, P., Prince, M., Zabih,
R., & Wang, Y. (2004). Multiprocessor scheduling implementation of the simultaneous
multiple volume SMV navigator method. Magnetic Resonance in Medicine. Wiley-Blackwell.
https://doi.org/10.1002/mrm.20162
chicago: Kolmogorov, Vladimir, Thành Nguyen, Anthony Nuval, Pascal Spincemaille,
Martin Prince, Ramin Zabih, and Yusu Wang. “Multiprocessor Scheduling Implementation
of the Simultaneous Multiple Volume SMV Navigator Method.” Magnetic Resonance
in Medicine. Wiley-Blackwell, 2004. https://doi.org/10.1002/mrm.20162.
ieee: V. Kolmogorov et al., “Multiprocessor scheduling implementation of
the simultaneous multiple volume SMV navigator method,” Magnetic Resonance
in Medicine, vol. 52, no. 2. Wiley-Blackwell, pp. 362–367, 2004.
ista: Kolmogorov V, Nguyen T, Nuval A, Spincemaille P, Prince M, Zabih R, Wang Y.
2004. Multiprocessor scheduling implementation of the simultaneous multiple volume
SMV navigator method. Magnetic Resonance in Medicine. 52(2), 362–367.
mla: Kolmogorov, Vladimir, et al. “Multiprocessor Scheduling Implementation of the
Simultaneous Multiple Volume SMV Navigator Method.” Magnetic Resonance in Medicine,
vol. 52, no. 2, Wiley-Blackwell, 2004, pp. 362–67, doi:10.1002/mrm.20162.
short: V. Kolmogorov, T. Nguyen, A. Nuval, P. Spincemaille, M. Prince, R. Zabih,
Y. Wang, Magnetic Resonance in Medicine 52 (2004) 362–367.
date_created: 2018-12-11T12:01:48Z
date_published: 2004-08-01T00:00:00Z
date_updated: 2021-01-12T07:41:34Z
day: '01'
doi: 10.1002/mrm.20162
extern: 1
intvolume: ' 52'
issue: '2'
month: '08'
page: 362 - 367
publication: Magnetic Resonance in Medicine
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3508'
quality_controlled: 0
status: public
title: Multiprocessor scheduling implementation of the simultaneous multiple volume
SMV navigator method
type: journal_article
volume: 52
year: '2004'
...
---
_id: '3173'
abstract:
- lang: eng
text: In the last few years, several new algorithms based on graph cuts have been
developed to solve energy minimization problems in computer vision. Each of these
techniques constructs a graph such that the minimum cut on the graph also minimizes
the energy. Yet, because these graph constructions are complex and highly specific
to a particular energy function, graph cuts have seen limited application to date.
In this paper, we give a characterization of the energy functions that can be
minimized by graph cuts. Our results are restricted to functions of binary variables.
However, our work generalizes many previous constructions and is easily applicable
to vision problems that involve large numbers of labels, such as stereo, motion,
image restoration, and scene reconstruction. We give a precise characterization
of what energy functions can be minimized using graph cuts, among the energy functions
that can be written as a sum of terms containing three or fewer binary variables.
We also provide a general-purpose construction to minimize such an energy function.
Finally, we give a necessary condition for any energy function of binary variables
to be minimized by graph cuts. Researchers who are considering the use of graph
cuts to optimize a particular energy function can use our results to determine
if this is possible and then follow our construction to create the appropriate
graph. A software implementation is freely available.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Ramin
full_name: Zabih, Ramin
last_name: Zabih
citation:
ama: Kolmogorov V, Zabih R. What energy functions can be minimized via graph cuts?
. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2004;26(2):147-159.
doi:10.1109/TPAMI.2004.1262177
apa: Kolmogorov, V., & Zabih, R. (2004). What energy functions can be minimized
via graph cuts? . IEEE Transactions on Pattern Analysis and Machine Intelligence.
IEEE. https://doi.org/10.1109/TPAMI.2004.1262177
chicago: Kolmogorov, Vladimir, and Ramin Zabih. “What Energy Functions Can Be Minimized
via Graph Cuts? .” IEEE Transactions on Pattern Analysis and Machine Intelligence.
IEEE, 2004. https://doi.org/10.1109/TPAMI.2004.1262177.
ieee: V. Kolmogorov and R. Zabih, “What energy functions can be minimized via graph
cuts? ,” IEEE Transactions on Pattern Analysis and Machine Intelligence,
vol. 26, no. 2. IEEE, pp. 147–159, 2004.
ista: Kolmogorov V, Zabih R. 2004. What energy functions can be minimized via graph
cuts? . IEEE Transactions on Pattern Analysis and Machine Intelligence. 26(2),
147–159.
mla: Kolmogorov, Vladimir, and Ramin Zabih. “What Energy Functions Can Be Minimized
via Graph Cuts? .” IEEE Transactions on Pattern Analysis and Machine Intelligence,
vol. 26, no. 2, IEEE, 2004, pp. 147–59, doi:10.1109/TPAMI.2004.1262177.
short: V. Kolmogorov, R. Zabih, IEEE Transactions on Pattern Analysis and Machine
Intelligence 26 (2004) 147–159.
date_created: 2018-12-11T12:01:49Z
date_published: 2004-02-01T00:00:00Z
date_updated: 2021-01-12T07:41:34Z
day: '01'
doi: 10.1109/TPAMI.2004.1262177
extern: 1
intvolume: ' 26'
issue: '2'
month: '02'
page: 147 - 159
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '3509'
quality_controlled: 0
status: public
title: 'What energy functions can be minimized via graph cuts? '
type: journal_article
volume: 26
year: '2004'
...
---
_id: '3177'
abstract:
- lang: eng
text: Feature space clustering is a popular approach to image segmentation, in which
a feature vector of local properties (such as intensity, texture or motion) is
computed at each pixel. The feature space is then clustered, and each pixel is
labeled with the cluster that contains its feature vector. A major limitation
of this approach is that feature space clusters generally lack spatial coherence
(i.e., they do not correspond to a compact grouping of pixels). In this paper,
we propose a segmentation algorithm that operates simultaneously in feature space
and in image space. We define an energy function over both a set of clusters and
a labeling of pixels with clusters. In our framework, a pixel is labeled with
a single cluster (rather than, for example, a distribution over clusters). Our
energy function penalizes clusters that are a poor fit to the data in feature
space, and also penalizes clusters whose pixels lack spatial coherence. The energy
function can be efficiently minimized using graph cuts. Our algorithm can incorporate
both parametric and non-parametric clustering methods. It can be applied to many
optimization-based clustering methods, including k-means and k-medians, and can
handle models which are very close in feature space. Preliminary results are presented
on segmenting real and synthetic images, using both parametric and non-parametric
clustering.
author:
- first_name: Ramin
full_name: Zabih, Ramin
last_name: Zabih
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Zabih R, Kolmogorov V. Spatially coherent clustering using graph cuts. In:
Vol 2. IEEE; 2004:437-444. doi:10.1109/CVPR.2004.1315196'
apa: 'Zabih, R., & Kolmogorov, V. (2004). Spatially coherent clustering using
graph cuts (Vol. 2, pp. 437–444). Presented at the CVPR: Computer Vision and Pattern
Recognition, IEEE. https://doi.org/10.1109/CVPR.2004.1315196'
chicago: Zabih, Ramin, and Vladimir Kolmogorov. “Spatially Coherent Clustering Using
Graph Cuts,” 2:437–44. IEEE, 2004. https://doi.org/10.1109/CVPR.2004.1315196.
ieee: 'R. Zabih and V. Kolmogorov, “Spatially coherent clustering using graph cuts,”
presented at the CVPR: Computer Vision and Pattern Recognition, 2004, vol. 2,
pp. 437–444.'
ista: 'Zabih R, Kolmogorov V. 2004. Spatially coherent clustering using graph cuts.
CVPR: Computer Vision and Pattern Recognition vol. 2, 437–444.'
mla: Zabih, Ramin, and Vladimir Kolmogorov. Spatially Coherent Clustering Using
Graph Cuts. Vol. 2, IEEE, 2004, pp. 437–44, doi:10.1109/CVPR.2004.1315196.
short: R. Zabih, V. Kolmogorov, in:, IEEE, 2004, pp. 437–444.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:50Z
date_published: 2004-06-01T00:00:00Z
date_updated: 2021-01-12T07:41:36Z
day: '01'
doi: 10.1109/CVPR.2004.1315196
extern: 1
intvolume: ' 2'
month: '06'
page: 437 - 444
publication_status: published
publisher: IEEE
publist_id: '3506'
quality_controlled: 0
status: public
title: Spatially coherent clustering using graph cuts
type: conference
volume: 2
year: '2004'
...
---
_id: '3178'
abstract:
- lang: eng
text: Minimum cut/maximum flow algorithms on graphs have emerged as an increasingly
useful tool for exactor approximate energy minimization in low-level vision. The
combinatorial optimization literature provides many min-cut/max-flow algorithms
with different polynomial time complexity. Their practical efficiency, however,
has to date been studied mainly outside the scope of computer vision. The goal
of this paper is to provide an experimental comparison of the efficiency of min-cut/max
flow algorithms for applications in vision. We compare the running times of several
standard algorithms, as well as a new algorithm that we have recently developed.
The algorithms we study include both Goldberg-Tarjan style "push -relabel"
methods and algorithms based on Ford-Fulkerson style "augmenting paths."
We benchmark these algorithms on a number of typical graphs in the contexts of
image restoration, stereo, and segmentation. In many cases, our new algorithm
works several times faster than any of the other methods, making near real-time
performance possible. An implementation of our max-flow/min-cut algorithm is available
upon request for research purposes.
author:
- first_name: Yuri
full_name: Boykov, Yuri
last_name: Boykov
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: Boykov Y, Kolmogorov V. An experimental comparison of min-cut/max-flow algorithms
for energy minimization in vision. IEEE Transactions on Pattern Analysis and
Machine Intelligence. 2004;26(9):1124-1137. doi:10.1109/TPAMI.2004.60
apa: Boykov, Y., & Kolmogorov, V. (2004). An experimental comparison of min-cut/max-flow
algorithms for energy minimization in vision. IEEE Transactions on Pattern
Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2004.60
chicago: Boykov, Yuri, and Vladimir Kolmogorov. “An Experimental Comparison of Min-Cut/Max-Flow
Algorithms for Energy Minimization in Vision.” IEEE Transactions on Pattern
Analysis and Machine Intelligence. IEEE, 2004. https://doi.org/10.1109/TPAMI.2004.60.
ieee: Y. Boykov and V. Kolmogorov, “An experimental comparison of min-cut/max-flow
algorithms for energy minimization in vision,” IEEE Transactions on Pattern
Analysis and Machine Intelligence, vol. 26, no. 9. IEEE, pp. 1124–1137, 2004.
ista: Boykov Y, Kolmogorov V. 2004. An experimental comparison of min-cut/max-flow
algorithms for energy minimization in vision. IEEE Transactions on Pattern Analysis
and Machine Intelligence. 26(9), 1124–1137.
mla: Boykov, Yuri, and Vladimir Kolmogorov. “An Experimental Comparison of Min-Cut/Max-Flow
Algorithms for Energy Minimization in Vision.” IEEE Transactions on Pattern
Analysis and Machine Intelligence, vol. 26, no. 9, IEEE, 2004, pp. 1124–37,
doi:10.1109/TPAMI.2004.60.
short: Y. Boykov, V. Kolmogorov, IEEE Transactions on Pattern Analysis and Machine
Intelligence 26 (2004) 1124–1137.
date_created: 2018-12-11T12:01:51Z
date_published: 2004-09-01T00:00:00Z
date_updated: 2021-01-12T07:41:36Z
day: '01'
doi: 10.1109/TPAMI.2004.60
extern: 1
intvolume: ' 26'
issue: '9'
month: '09'
page: 1124 - 1137
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '3507'
quality_controlled: 0
status: public
title: An experimental comparison of min-cut/max-flow algorithms for energy minimization
in vision
type: journal_article
volume: 26
year: '2004'
...
---
_id: '3179'
abstract:
- lang: eng
text: The problem of efficient, interactive foreground/background segmentation in
still images is of great practical importance in image editing. Classical image
segmentation tools use either texture (colour) information, e.g. Magic Wand, or
edge (contrast) information, e.g. Intelligent Scissors. Recently, an approach
based on optimization by graph-cut has been developed which successfully combines
both types of information. In this paper we extend the graph-cut approach in three
respects. First, we have developed a more powerful, iterative version of the optimisation.
Secondly, the power of the iterative algorithm is used to simplify substantially
the user interaction needed for a given quality of result. Thirdly, a robust algorithm
for "border matting" has been developed to estimate simultaneously the
alpha-matte around an object boundary and the colours of foreground pixels. We
show that for moderately difficult examples the proposed method outperforms competitive
tools.
author:
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
citation:
ama: 'Rother C, Kolmogorov V, Blake A. "GrabCut" - Interactive
foreground extraction using iterated graph cuts . In: Vol 23. ACM; 2004:309-314.
doi:10.1145/1015706.1015720'
apa: 'Rother, C., Kolmogorov, V., & Blake, A. (2004). "GrabCut"
- Interactive foreground extraction using iterated graph cuts (Vol. 23, pp. 309–314).
Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques, ACM. https://doi.org/10.1145/1015706.1015720'
chicago: Rother, Carsten, Vladimir Kolmogorov, and Andrew Blake. “"GrabCut"
- Interactive Foreground Extraction Using Iterated Graph Cuts ,” 23:309–14. ACM,
2004. https://doi.org/10.1145/1015706.1015720.
ieee: 'C. Rother, V. Kolmogorov, and A. Blake, “"GrabCut" - Interactive
foreground extraction using iterated graph cuts ,” presented at the SIGGRAPH:
Special Interest Group on Computer Graphics and Interactive Techniques, 2004,
vol. 23, no. 3, pp. 309–314.'
ista: 'Rother C, Kolmogorov V, Blake A. 2004. "GrabCut" - Interactive
foreground extraction using iterated graph cuts . SIGGRAPH: Special Interest Group
on Computer Graphics and Interactive Techniques vol. 23, 309–314.'
mla: Rother, Carsten, et al. "GrabCut" - Interactive Foreground
Extraction Using Iterated Graph Cuts . Vol. 23, no. 3, ACM, 2004, pp. 309–14,
doi:10.1145/1015706.1015720.
short: C. Rother, V. Kolmogorov, A. Blake, in:, ACM, 2004, pp. 309–314.
conference:
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
date_created: 2018-12-11T12:01:51Z
date_published: 2004-08-01T00:00:00Z
date_updated: 2021-01-12T07:41:36Z
day: '01'
doi: 10.1145/1015706.1015720
extern: 1
intvolume: ' 23'
issue: '3'
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67890/siggraph04-grabcut.pdf
month: '08'
page: 309 - 314
publication_status: published
publisher: ACM
publist_id: '3505'
quality_controlled: 0
status: public
title: '"GrabCut" - Interactive foreground extraction using iterated graph
cuts '
type: conference
volume: 23
year: '2004'
...
---
_id: '3208'
abstract:
- lang: eng
text: |-
A new technique for proving the adaptive indistinguishability of two systems, each composed of some component systems, is presented, using only the fact that corresponding component systems are non-adaptively indistinguishable. The main tool is the definition of a special monotone condition for a random system F, relative to another random system G, whose probability of occurring for a given distinguisher D is closely related to the distinguishing advantage ε of D for F and G, namely it is lower and upper bounded by ε and (1+ln1), respectively.
A concrete instantiation of this result shows that the cascade of two random permutations (with the second one inverted) is indistinguishable from a uniform random permutation by adaptive distinguishers which may query the system from both sides, assuming the components’ security only against non-adaptive one-sided distinguishers.
As applications we provide some results in various fields as almost k-wise independent probability spaces, decorrelation theory and computational indistinguishability (i.e., pseudo-randomness).
alternative_title:
- LNCS
author:
- first_name: Ueli
full_name: Maurer, Ueli M
last_name: Maurer
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Maurer U, Pietrzak KZ. Composition of random systems: When two weak make one
strong. In: Vol 2951. Springer; 2004:410-427. doi:10.1007/978-3-540-24638-1_23'
apa: 'Maurer, U., & Pietrzak, K. Z. (2004). Composition of random systems: When
two weak make one strong (Vol. 2951, pp. 410–427). Presented at the TCC: Theory
of Cryptography Conference, Springer. https://doi.org/10.1007/978-3-540-24638-1_23'
chicago: 'Maurer, Ueli, and Krzysztof Z Pietrzak. “Composition of Random Systems:
When Two Weak Make One Strong,” 2951:410–27. Springer, 2004. https://doi.org/10.1007/978-3-540-24638-1_23.'
ieee: 'U. Maurer and K. Z. Pietrzak, “Composition of random systems: When two weak
make one strong,” presented at the TCC: Theory of Cryptography Conference, 2004,
vol. 2951, pp. 410–427.'
ista: 'Maurer U, Pietrzak KZ. 2004. Composition of random systems: When two weak
make one strong. TCC: Theory of Cryptography Conference, LNCS, vol. 2951, 410–427.'
mla: 'Maurer, Ueli, and Krzysztof Z. Pietrzak. Composition of Random Systems:
When Two Weak Make One Strong. Vol. 2951, Springer, 2004, pp. 410–27, doi:10.1007/978-3-540-24638-1_23.'
short: U. Maurer, K.Z. Pietrzak, in:, Springer, 2004, pp. 410–427.
conference:
name: 'TCC: Theory of Cryptography Conference'
date_created: 2018-12-11T12:02:01Z
date_published: 2004-03-19T00:00:00Z
date_updated: 2021-01-12T07:41:48Z
day: '19'
doi: 10.1007/978-3-540-24638-1_23
extern: 1
intvolume: ' 2951'
month: '03'
page: 410 - 427
publication_status: published
publisher: Springer
publist_id: '3471'
quality_controlled: 0
status: public
title: 'Composition of random systems: When two weak make one strong'
type: conference
volume: 2951
year: '2004'
...
---
_id: '11762'
abstract:
- lang: eng
text: 'In this paper, we describe six algorithmic problems that arise in web search
engines and that are not or only partially solved: (1) Uniformly sampling of web
pages; (2) modeling the web graph; (3) finding duplicate hosts; (4) finding top
gainers and losers in data streams; (5) finding large dense bipartite graphs; and
(6) understanding how eigenvectors partition the web.'
article_processing_charge: No
article_type: original
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: Henzinger MH. Algorithmic challenges in web search engines. Internet Mathematics.
2004;1(1):115-123. doi:10.1080/15427951.2004.10129079
apa: Henzinger, M. H. (2004). Algorithmic challenges in web search engines. Internet
Mathematics. Internet Mathematics. https://doi.org/10.1080/15427951.2004.10129079
chicago: Henzinger, Monika H. “Algorithmic Challenges in Web Search Engines.” Internet
Mathematics. Internet Mathematics, 2004. https://doi.org/10.1080/15427951.2004.10129079.
ieee: M. H. Henzinger, “Algorithmic challenges in web search engines,” Internet
Mathematics, vol. 1, no. 1. Internet Mathematics, pp. 115–123, 2004.
ista: Henzinger MH. 2004. Algorithmic challenges in web search engines. Internet
Mathematics. 1(1), 115–123.
mla: Henzinger, Monika H. “Algorithmic Challenges in Web Search Engines.” Internet
Mathematics, vol. 1, no. 1, Internet Mathematics, 2004, pp. 115–23, doi:10.1080/15427951.2004.10129079.
short: M.H. Henzinger, Internet Mathematics 1 (2004) 115–123.
date_created: 2022-08-08T11:55:53Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2023-02-10T07:47:21Z
day: '01'
doi: 10.1080/15427951.2004.10129079
extern: '1'
intvolume: ' 1'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1080/15427951.2004.10129079
month: '01'
oa: 1
oa_version: Published Version
page: 115-123
publication: Internet Mathematics
publication_identifier:
eissn:
- 1944-9488
issn:
- 1542-7951
publication_status: published
publisher: Internet Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Algorithmic challenges in web search engines
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2004'
...
---
_id: '8517'
abstract:
- lang: eng
text: We consider the evolution of a connected set on the plane carried by a space
periodic incompressible stochastic flow. While for almost every realization of
the stochastic flow at time t most of the particles are at a distance of order
equation image away from the origin, there is a measure zero set of points that
escape to infinity at the linear rate. We study the set of points visited by the
original set by time t and show that such a set, when scaled down by the factor
of t, has a limiting nonrandom shape.
article_processing_charge: No
article_type: original
author:
- first_name: Dmitry
full_name: Dolgopyat, Dmitry
last_name: Dolgopyat
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Leonid
full_name: Koralov, Leonid
last_name: Koralov
citation:
ama: Dolgopyat D, Kaloshin V, Koralov L. A limit shape theorem for periodic stochastic
dispersion. Communications on Pure and Applied Mathematics. 2004;57(9):1127-1158.
doi:10.1002/cpa.20032
apa: Dolgopyat, D., Kaloshin, V., & Koralov, L. (2004). A limit shape theorem
for periodic stochastic dispersion. Communications on Pure and Applied Mathematics.
Wiley. https://doi.org/10.1002/cpa.20032
chicago: Dolgopyat, Dmitry, Vadim Kaloshin, and Leonid Koralov. “A Limit Shape Theorem
for Periodic Stochastic Dispersion.” Communications on Pure and Applied Mathematics.
Wiley, 2004. https://doi.org/10.1002/cpa.20032.
ieee: D. Dolgopyat, V. Kaloshin, and L. Koralov, “A limit shape theorem for periodic
stochastic dispersion,” Communications on Pure and Applied Mathematics,
vol. 57, no. 9. Wiley, pp. 1127–1158, 2004.
ista: Dolgopyat D, Kaloshin V, Koralov L. 2004. A limit shape theorem for periodic
stochastic dispersion. Communications on Pure and Applied Mathematics. 57(9),
1127–1158.
mla: Dolgopyat, Dmitry, et al. “A Limit Shape Theorem for Periodic Stochastic Dispersion.”
Communications on Pure and Applied Mathematics, vol. 57, no. 9, Wiley,
2004, pp. 1127–58, doi:10.1002/cpa.20032.
short: D. Dolgopyat, V. Kaloshin, L. Koralov, Communications on Pure and Applied
Mathematics 57 (2004) 1127–1158.
date_created: 2020-09-18T10:49:12Z
date_published: 2004-09-01T00:00:00Z
date_updated: 2021-01-12T08:19:50Z
day: '01'
doi: 10.1002/cpa.20032
extern: '1'
intvolume: ' 57'
issue: '9'
keyword:
- Applied Mathematics
- General Mathematics
language:
- iso: eng
month: '09'
oa_version: None
page: 1127-1158
publication: Communications on Pure and Applied Mathematics
publication_identifier:
issn:
- 0010-3640
- 1097-0312
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: A limit shape theorem for periodic stochastic dispersion
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2004'
...
---
_id: '8518'
article_processing_charge: No
article_type: original
author:
- first_name: Leonid
full_name: Koralov, Leonid
last_name: Koralov
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Dmitry
full_name: Dolgopyat, Dmitry
last_name: Dolgopyat
citation:
ama: Koralov L, Kaloshin V, Dolgopyat D. Sample path properties of the stochastic
flows. The Annals of Probability. 2004;32(1A):1-27. doi:10.1214/aop/1078415827
apa: Koralov, L., Kaloshin, V., & Dolgopyat, D. (2004). Sample path properties
of the stochastic flows. The Annals of Probability. Institute of Mathematical
Statistics. https://doi.org/10.1214/aop/1078415827
chicago: Koralov, Leonid, Vadim Kaloshin, and Dmitry Dolgopyat. “Sample Path Properties
of the Stochastic Flows.” The Annals of Probability. Institute of Mathematical
Statistics, 2004. https://doi.org/10.1214/aop/1078415827.
ieee: L. Koralov, V. Kaloshin, and D. Dolgopyat, “Sample path properties of the
stochastic flows,” The Annals of Probability, vol. 32, no. 1A. Institute
of Mathematical Statistics, pp. 1–27, 2004.
ista: Koralov L, Kaloshin V, Dolgopyat D. 2004. Sample path properties of the stochastic
flows. The Annals of Probability. 32(1A), 1–27.
mla: Koralov, Leonid, et al. “Sample Path Properties of the Stochastic Flows.” The
Annals of Probability, vol. 32, no. 1A, Institute of Mathematical Statistics,
2004, pp. 1–27, doi:10.1214/aop/1078415827.
short: L. Koralov, V. Kaloshin, D. Dolgopyat, The Annals of Probability 32 (2004)
1–27.
date_created: 2020-09-18T10:49:19Z
date_published: 2004-03-04T00:00:00Z
date_updated: 2021-01-12T08:19:50Z
day: '04'
doi: 10.1214/aop/1078415827
extern: '1'
intvolume: ' 32'
issue: 1A
language:
- iso: eng
month: '03'
oa_version: None
page: 1-27
publication: The Annals of Probability
publication_identifier:
issn:
- 0091-1798
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
status: public
title: Sample path properties of the stochastic flows
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2004'
...
---
_id: '864'
abstract:
- lang: eng
text: 'We present a method for prediction of functional sites in a set of aligned
protein sequences. The method selects sites which are both well conserved and
clustered together in space, as inferred from the 3D structures of proteins included
in the alignment. We tested the method using 86 alignments from the NCBI CDD database,
where the sites of experimentally determined ligand and/or macromolecular interactions
are annotated. In agreement with earlier investigations, we found that functional
site predictions are most successful when overall background sequence conservation
is low, such that sites under evolutionary constraint become apparent. In addition,
we found that averaging of conservation values across spatially clustered sites
improves predictions under certain conditions: that is, when overall conservation
is relatively high and when the site in question involves a large macromolecular
binding interface. Under these conditions it is better to look for clusters of
conserved sites than to look for particular conserved sites.'
acknowledgement: We thank John Spouge, Ben Shoemaker, and Michael Galperin forhelpful
suggestions, and the NIH Intramural Research Program forsupport.
author:
- first_name: Anna
full_name: Panchenko, Anna R
last_name: Panchenko
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Stephen
full_name: Bryant, Stephen H
last_name: Bryant
citation:
ama: Panchenko A, Kondrashov F, Bryant S. Prediction of functional sites by analysis
of sequence and structure conservation. Protein Science. 2004;13(4):884-892.
doi:10.1110/ps.03465504
apa: Panchenko, A., Kondrashov, F., & Bryant, S. (2004). Prediction of functional
sites by analysis of sequence and structure conservation. Protein Science.
Wiley-Blackwell. https://doi.org/10.1110/ps.03465504
chicago: Panchenko, Anna, Fyodor Kondrashov, and Stephen Bryant. “Prediction of
Functional Sites by Analysis of Sequence and Structure Conservation.” Protein
Science. Wiley-Blackwell, 2004. https://doi.org/10.1110/ps.03465504.
ieee: A. Panchenko, F. Kondrashov, and S. Bryant, “Prediction of functional sites
by analysis of sequence and structure conservation,” Protein Science, vol.
13, no. 4. Wiley-Blackwell, pp. 884–892, 2004.
ista: Panchenko A, Kondrashov F, Bryant S. 2004. Prediction of functional sites
by analysis of sequence and structure conservation. Protein Science. 13(4), 884–892.
mla: Panchenko, Anna, et al. “Prediction of Functional Sites by Analysis of Sequence
and Structure Conservation.” Protein Science, vol. 13, no. 4, Wiley-Blackwell,
2004, pp. 884–92, doi:10.1110/ps.03465504.
short: A. Panchenko, F. Kondrashov, S. Bryant, Protein Science 13 (2004) 884–892.
date_created: 2018-12-11T11:48:55Z
date_published: 2004-04-01T00:00:00Z
date_updated: 2021-01-12T08:20:22Z
day: '01'
doi: 10.1110/ps.03465504
extern: 1
intvolume: ' 13'
issue: '4'
month: '04'
page: 884 - 892
publication: Protein Science
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6786'
quality_controlled: 0
status: public
title: Prediction of functional sites by analysis of sequence and structure conservation
type: journal_article
volume: 13
year: '2004'
...
---
_id: '870'
abstract:
- lang: eng
text: Only a fraction of eukaryotic genes affect the phenotype drastically. We compared
18 parameters in 1273 human morbid genes, known to cause diseases, and in the
remaining 16 580 unambiguous human genes. Morbid genes evolve more slowly, have
wider phylogenetic distributions, are more similar to essential genes of Drosophila
melanogaster, code for longer proteins containing more alanine and glycine and
less histidine, lysine and methionine, possess larger numbers of longer introns
with more accurate splicing signals and have higher and broader expressions. These
differences make it possible to classify as non-morbid 34% of human genes with
unknown morbidity, when only 5% of known morbid genes are incorrectly classified
as non-morbid. This classification can help to identify disease-causing genes
among multiple candidates.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Aleksey
full_name: Ogurtsov, Aleksey Yu
last_name: Ogurtsov
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
citation:
ama: Kondrashov F, Ogurtsov A, Kondrashov A. Bioinformatical assay of human gene
morbidity. Nucleic Acids Research. 2004;32(5):1731-1737. doi:10.1093/nar/gkh330
apa: Kondrashov, F., Ogurtsov, A., & Kondrashov, A. (2004). Bioinformatical
assay of human gene morbidity. Nucleic Acids Research. Oxford University
Press. https://doi.org/10.1093/nar/gkh330
chicago: Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Bioinformatical
Assay of Human Gene Morbidity.” Nucleic Acids Research. Oxford University
Press, 2004. https://doi.org/10.1093/nar/gkh330.
ieee: F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Bioinformatical assay of human
gene morbidity,” Nucleic Acids Research, vol. 32, no. 5. Oxford University
Press, pp. 1731–1737, 2004.
ista: Kondrashov F, Ogurtsov A, Kondrashov A. 2004. Bioinformatical assay of human
gene morbidity. Nucleic Acids Research. 32(5), 1731–1737.
mla: Kondrashov, Fyodor, et al. “Bioinformatical Assay of Human Gene Morbidity.”
Nucleic Acids Research, vol. 32, no. 5, Oxford University Press, 2004,
pp. 1731–37, doi:10.1093/nar/gkh330.
short: F. Kondrashov, A. Ogurtsov, A. Kondrashov, Nucleic Acids Research 32 (2004)
1731–1737.
date_created: 2018-12-11T11:48:56Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:37Z
day: '01'
doi: 10.1093/nar/gkh330
extern: 1
intvolume: ' 32'
issue: '5'
month: '01'
page: 1731 - 1737
publication: Nucleic Acids Research
publication_status: published
publisher: Oxford University Press
publist_id: '6780'
quality_controlled: 0
status: public
title: Bioinformatical assay of human gene morbidity
type: journal_article
volume: 32
year: '2004'
...
---
_id: '875'
abstract:
- lang: eng
text: The dominance of wild-type alleles and the concomitant recessivity of deleterious
mutant alleles might have evolved by natural selection or could be a by-product
of the molecular and physiological mechanisms of gene action. We compared the
properties of human haplosufficient genes, whose wild-type alleles are dominant
over loss-of-function alleles, with haploinsufficient (recessive wild-type) genes,
which produce an abnormal phenotype when heterozygous for a loss-of-function allele.
The fraction of haplosufficient genes is the highest among the genes that encode
enzymes, which is best compatible with the physiological theory. Haploinsufficient
genes, on average, have more paralogs than haplosufficient genes, supporting the
idea that gene dosage could be important for the initial fixation of duplications.
Thus, haplo(in)sufficiency of a gene and its propensity for duplication might
have a common evolutionary basis.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Eugene
full_name: Koonin, Eugene V
last_name: Koonin
citation:
ama: Kondrashov F, Koonin E. A common framework for understanding the origin of
genetic dominance and evolutionary fates of gene duplications. Trends in Genetics.
2004;20(7):287-291. doi:10.1016/j.tig.2004.05.001
apa: Kondrashov, F., & Koonin, E. (2004). A common framework for understanding
the origin of genetic dominance and evolutionary fates of gene duplications. Trends
in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2004.05.001
chicago: Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding
the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.”
Trends in Genetics. Elsevier, 2004. https://doi.org/10.1016/j.tig.2004.05.001.
ieee: F. Kondrashov and E. Koonin, “A common framework for understanding the origin
of genetic dominance and evolutionary fates of gene duplications,” Trends in
Genetics, vol. 20, no. 7. Elsevier, pp. 287–291, 2004.
ista: Kondrashov F, Koonin E. 2004. A common framework for understanding the origin
of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics.
20(7), 287–291.
mla: Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding
the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.”
Trends in Genetics, vol. 20, no. 7, Elsevier, 2004, pp. 287–91, doi:10.1016/j.tig.2004.05.001.
short: F. Kondrashov, E. Koonin, Trends in Genetics 20 (2004) 287–291.
date_created: 2018-12-11T11:48:58Z
date_published: 2004-07-01T00:00:00Z
date_updated: 2021-01-12T08:20:54Z
day: '01'
doi: 10.1016/j.tig.2004.05.001
extern: 1
intvolume: ' 20'
issue: '7'
month: '07'
page: 287 - 291
publication: Trends in Genetics
publication_status: published
publisher: Elsevier
publist_id: '6775'
quality_controlled: 0
status: public
title: A common framework for understanding the origin of genetic dominance and evolutionary
fates of gene duplications
type: journal_article
volume: 20
year: '2004'
...
---
_id: '889'
abstract:
- lang: eng
text: 'The function of protein and RNA molecules depends on complex epistatic interactions
between sites. Therefore, the deleterious effect of a mutation can be suppressed
by a compensatory second-site substitution. In relating a list of 86 pathogenic
mutations in human IRNAs encoded by mitochondrial genes to the sequences of their
mammalian orthologs, we noted that 52 pathogenic mutations were present in normal
tRNAs of one or several nonhuman mammals. We found at least five mechanisms of
compensation for 32 pathogenic mutations that destroyed a Watson-Crick pair in
one of the four tRNA stems: restoration of the affected Watson-Crick interaction
(25 cases), strengthening of another pair (4 cases), creation of a new pair (8
cases), changes of multiple interactions in the affected stem (11 cases) and changes
involving the interaction between the loop and stem structures (3 cases). A pathogenic
mutation and its compensating substitution are fixed in a lineage in rapid succession,
and often a compensatory interaction evolves convergently in different clades.
At least 10%, and perhaps as many as 50%, of all nucleotide substitutions in evolving
mammalian (RNAs participate in such interactions, indicating that the evolution
of tRNAs proceeds along highly epistatic fitness ridges.'
acknowledgement: We thank J. Gillespie, M. Hahn, L. Horth, A. Kondrashov, A. Kopp,
S. Nuzhdin, M. Turelli and D. Weinreich for their contributions. The authors were
supported by a grant from the US National Institutes of Health to S. Nuzhdin, and
A.D.K. is a Howard Hughes
author:
- first_name: Andrew
full_name: Kern, Andrew D
last_name: Kern
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kern A, Kondrashov F. Mechanisms and convergence of compensatory evolution
in mammalian mitochondrial tRNAs. Nature Genetics. 2004;36(11):1207-1212.
doi:10.1038/ng1451
apa: Kern, A., & Kondrashov, F. (2004). Mechanisms and convergence of compensatory
evolution in mammalian mitochondrial tRNAs. Nature Genetics. Nature Publishing
Group. https://doi.org/10.1038/ng1451
chicago: Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory
Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics. Nature Publishing
Group, 2004. https://doi.org/10.1038/ng1451.
ieee: A. Kern and F. Kondrashov, “Mechanisms and convergence of compensatory evolution
in mammalian mitochondrial tRNAs,” Nature Genetics, vol. 36, no. 11. Nature
Publishing Group, pp. 1207–1212, 2004.
ista: Kern A, Kondrashov F. 2004. Mechanisms and convergence of compensatory evolution
in mammalian mitochondrial tRNAs. Nature Genetics. 36(11), 1207–1212.
mla: Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory
Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics, vol. 36,
no. 11, Nature Publishing Group, 2004, pp. 1207–12, doi:10.1038/ng1451.
short: A. Kern, F. Kondrashov, Nature Genetics 36 (2004) 1207–1212.
date_created: 2018-12-11T11:49:02Z
date_published: 2004-11-01T00:00:00Z
date_updated: 2021-01-12T08:21:17Z
day: '01'
doi: 10.1038/ng1451
extern: 1
intvolume: ' 36'
issue: '11'
month: '11'
page: 1207 - 1212
publication: Nature Genetics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6759'
quality_controlled: 0
status: public
title: Mechanisms and convergence of compensatory evolution in mammalian mitochondrial
tRNAs
type: journal_article
volume: 36
year: '2004'
...
---
_id: '898'
abstract:
- lang: eng
text: New alleles become fixed owing to random drift of nearly neutral mutations
or to positive selection of substantially advantageous mutations. After decades
of debate, the fraction of fixations driven by selection remains uncertain. Within
9,390 genes, we analysed 28,196 codons at which rat and mouse differ from each
other at two nucleotide sites and 1,982 codons with three differences. At codons
where rat-mouse divergence involved two non-synonymous substitutions, both of
them occurred in the same lineage, either rat or mouse, in 64% of cases; however,
independent substitutions would occur in the same lineage with a probability of
only 50%. All three non-synonymous substitutions occurred in the same lineage
for 46% of codons, instead of the 25% expected. Furthermore, comparison of 12
pairs of prokaryotic genomes also shows clumping of multiple non-synonymous substitutions
in the same lineage. This pattern cannot be explained by correlated mutation or
episodes of relaxed negative selection, but instead indicates that positive selection
acts at many sites of rapid, successive amino acid replacement.
acknowledgement: We thank N. Bierne for a number of suggestions. G.A.B. was supported
by a BWF graduate fellowship. S.S. was supported by Genome Canada Foundation.
author:
- first_name: Georgii
full_name: Bazykin, Georgii A
last_name: Bazykin
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Aleksey
full_name: Ogurtsov, Aleksey Yu
last_name: Ogurtsov
- first_name: Shamil
full_name: Sunyaev, Shamil R
last_name: Sunyaev
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
citation:
ama: Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. Positive selection
at sites of multiple amino acid replacements since rat-mouse divergence. Nature.
2004;429(6991):558-562. doi:10.1038/nature02601
apa: Bazykin, G., Kondrashov, F., Ogurtsov, A., Sunyaev, S., & Kondrashov, A.
(2004). Positive selection at sites of multiple amino acid replacements since
rat-mouse divergence. Nature. Nature Publishing Group. https://doi.org/10.1038/nature02601
chicago: Bazykin, Georgii, Fyodor Kondrashov, Aleksey Ogurtsov, Shamil Sunyaev,
and Alexey Kondrashov. “Positive Selection at Sites of Multiple Amino Acid Replacements
since Rat-Mouse Divergence.” Nature. Nature Publishing Group, 2004. https://doi.org/10.1038/nature02601.
ieee: G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, and A. Kondrashov, “Positive
selection at sites of multiple amino acid replacements since rat-mouse divergence,”
Nature, vol. 429, no. 6991. Nature Publishing Group, pp. 558–562, 2004.
ista: Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. 2004. Positive
selection at sites of multiple amino acid replacements since rat-mouse divergence.
Nature. 429(6991), 558–562.
mla: Bazykin, Georgii, et al. “Positive Selection at Sites of Multiple Amino Acid
Replacements since Rat-Mouse Divergence.” Nature, vol. 429, no. 6991, Nature
Publishing Group, 2004, pp. 558–62, doi:10.1038/nature02601.
short: G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, A. Kondrashov, Nature
429 (2004) 558–562.
date_created: 2018-12-11T11:49:05Z
date_published: 2004-06-03T00:00:00Z
date_updated: 2021-01-12T08:21:37Z
day: '03'
doi: 10.1038/nature02601
extern: 1
intvolume: ' 429'
issue: '6991'
month: '06'
page: 558 - 562
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6746'
quality_controlled: 0
status: public
title: Positive selection at sites of multiple amino acid replacements since rat-mouse
divergence
type: journal_article
volume: 429
year: '2004'
...
---
_id: '1963'
abstract:
- lang: eng
text: The mechanism coupling electron transfer and proton pumping in respiratory
complex I (NADH-ubiquinone oxidoreductase) has not been established, but it has
been suggested that it involves conformational changes. Here, the influence of
substrates on the conformation of purified complex I from Escherichia coli was
studied by cross-linking and electron microscopy. When a zero-length cross-linking
reagent was used, the presence of NAD(P)H, in contrast to that of NAD+, prevented
the formation of cross-links between the hydrophilic subunits of the complex,
including NuoB, NuoI, and NuoCD. Comparisons using different cross-linkers suggested
that NuoB, which is likely to coordinate the key iron-sulfur cluster N2, is the
most mobile subunit. The presence of NAD(P)H led also to enhanced proteolysis
of subunit NuoG. These data indicate that upon NAD(P)H binding, the peripheral
arm of the complex adopts a more open conformation, with increased distances between
subunits. Single particle analysis showed the nature of this conformational change.
The enzyme retains its L-shape in the presence of NADH, but exhibits a significantly
more open or expanded structure both in the peripheral arm and, unexpectedly,
in the membrane domain also.
acknowledgement: This work was supported by the Medical Research Council and by a
Royal Society/North Atlantic Treaty Organization postdoctoral fellowship (to A.
A. M.)
author:
- first_name: Aygun
full_name: Mamedova, Aygun A
last_name: Mamedova
- first_name: Peter
full_name: Holt, Peter J
last_name: Holt
- first_name: Joe
full_name: Carroll, Joe D
last_name: Carroll
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Mamedova A, Holt P, Carroll J, Sazanov LA. Substrate-induced conformational
change in bacterial complex I. Journal of Biological Chemistry. 2004;279(22):23830-23836.
doi:10.1074/jbc.M401539200
apa: Mamedova, A., Holt, P., Carroll, J., & Sazanov, L. A. (2004). Substrate-induced
conformational change in bacterial complex I. Journal of Biological Chemistry.
American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M401539200
chicago: Mamedova, Aygun, Peter Holt, Joe Carroll, and Leonid A Sazanov. “Substrate-Induced
Conformational Change in Bacterial Complex I.” Journal of Biological Chemistry.
American Society for Biochemistry and Molecular Biology, 2004. https://doi.org/10.1074/jbc.M401539200.
ieee: A. Mamedova, P. Holt, J. Carroll, and L. A. Sazanov, “Substrate-induced conformational
change in bacterial complex I,” Journal of Biological Chemistry, vol. 279,
no. 22. American Society for Biochemistry and Molecular Biology, pp. 23830–23836,
2004.
ista: Mamedova A, Holt P, Carroll J, Sazanov LA. 2004. Substrate-induced conformational
change in bacterial complex I. Journal of Biological Chemistry. 279(22), 23830–23836.
mla: Mamedova, Aygun, et al. “Substrate-Induced Conformational Change in Bacterial
Complex I.” Journal of Biological Chemistry, vol. 279, no. 22, American
Society for Biochemistry and Molecular Biology, 2004, pp. 23830–36, doi:10.1074/jbc.M401539200.
short: A. Mamedova, P. Holt, J. Carroll, L.A. Sazanov, Journal of Biological Chemistry
279 (2004) 23830–23836.
date_created: 2018-12-11T11:54:56Z
date_published: 2004-05-28T00:00:00Z
date_updated: 2021-01-12T06:54:22Z
day: '28'
doi: 10.1074/jbc.M401539200
extern: 1
intvolume: ' 279'
issue: '22'
month: '05'
page: 23830 - 23836
publication: Journal of Biological Chemistry
publication_status: published
publisher: American Society for Biochemistry and Molecular Biology
publist_id: '5123'
quality_controlled: 0
status: public
title: Substrate-induced conformational change in bacterial complex I
type: journal_article
volume: 279
year: '2004'
...
---
_id: '209'
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Roger
full_name: Heath-Brown, Roger
last_name: Heath Brown
citation:
ama: Browning TD, Heath Brown R. Equal sums of three powers. Inventiones Mathematicae.
2004;157(3):553-573. doi:10.1007/s00222-004-0360-9
apa: Browning, T. D., & Heath Brown, R. (2004). Equal sums of three powers.
Inventiones Mathematicae. Unknown. https://doi.org/10.1007/s00222-004-0360-9
chicago: Browning, Timothy D, and Roger Heath Brown. “Equal Sums of Three Powers.”
Inventiones Mathematicae. Unknown, 2004. https://doi.org/10.1007/s00222-004-0360-9.
ieee: T. D. Browning and R. Heath Brown, “Equal sums of three powers,” Inventiones
Mathematicae, vol. 157, no. 3. Unknown, pp. 553–573, 2004.
ista: Browning TD, Heath Brown R. 2004. Equal sums of three powers. Inventiones
Mathematicae. 157(3), 553–573.
mla: Browning, Timothy D., and Roger Heath Brown. “Equal Sums of Three Powers.”
Inventiones Mathematicae, vol. 157, no. 3, Unknown, 2004, pp. 553–73, doi:10.1007/s00222-004-0360-9.
short: T.D. Browning, R. Heath Brown, Inventiones Mathematicae 157 (2004) 553–573.
date_created: 2018-12-11T11:45:13Z
date_published: 2004-03-17T00:00:00Z
date_updated: 2021-01-12T06:55:14Z
day: '17'
doi: 10.1007/s00222-004-0360-9
extern: 1
intvolume: ' 157'
issue: '3'
month: '03'
page: 553 - 573
publication: Inventiones Mathematicae
publication_status: published
publisher: Unknown
publist_id: '7703'
quality_controlled: 0
status: public
title: Equal sums of three powers
type: journal_article
volume: 157
year: '2004'
...
---
_id: '2308'
abstract:
- lang: eng
text: It is widely believed that the inflammatory events mediated by microglial
activation contribute to several neurodegenerative processes. Alzheimer's disease,
for example, is characterized by an accumulation of β-amyloid protein (Aβ) in
neuritic plaques that are infiltrated by reactive microglia and astrocytes. Although
Aβ and its fragment 25-35 exert a direct toxic effect on neurons, they also activate
microglia. Microglial activation is accompanied by morphological changes, cell
proliferation, and release of various cytokines and growth factors. A number of
scientific reports suggest that the increased proliferation of microglial cells
is dependent on ionic membrane currents and in particular on chloride conductances.
An unusual chloride ion channel known to be associated with macrophage activation
is the chloride intracellular channel-1 (CLIC1). Here we show that Aβ stimulation
of neonatal rat microglia specifically leads to the increase in CLIC1 protein
and to the functional expression of CLIC1 chloride conductance, both barely detectable
on the plasma membrane of quiescent cells. CLIC1 protein expression in microglia
increases after 24 hr of incubation with Aβ, simultaneously with the production
of reactive nitrogen intermediates and of tumor necrosis factor-α (TNF-α). We
demonstrate that reducing CLIC1 chloride conductance by a specific blocker [IAA-94
(R(+)-[(6,7-dichloro-2-cyclopentyl-2,3-dihydro-2-methyl-1-oxo-1H-inden-5yl)-oxy]
acetic acid)] prevents neuronal apoptosis in neurons cocultured with Aβ-treated
microglia. Furthermore, we show that small interfering RNAs used to knock down
CLIC1 expression prevent TNF-α release induced by Aβ stimulation. These results
provide a direct link between Aβ-induced microglial activation and CLIC1 functional
expression.
author:
- first_name: Gaia
full_name: Gaia Novarino
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Cinzia
full_name: Fabrizi, Cinzia
last_name: Fabrizi
- first_name: Raffaella
full_name: Tonini, Raffaella
last_name: Tonini
- first_name: Michela
full_name: Denti, Michela A
last_name: Denti
- first_name: Albedi
full_name: Malchiodi, Albedi F
last_name: Malchiodi
- first_name: Giuliana
full_name: Lauro, Giuliana M
last_name: Lauro
- first_name: Benedetto
full_name: Sacchetti, Benedetto
last_name: Sacchetti
- first_name: Silvia
full_name: Paradisi, Silvia
last_name: Paradisi
- first_name: Arnaldo
full_name: Ferroni, Arnaldo
last_name: Ferroni
- first_name: Paul
full_name: Curmi, Paul M G
last_name: Curmi
- first_name: Samuel
full_name: Breit, Samuel N
last_name: Breit
- first_name: Michele
full_name: Mazzanti, Michele
last_name: Mazzanti
citation:
ama: Novarino G, Fabrizi C, Tonini R, et al. Involvement of the intracellular ion
channel CLIC1 in microglia-mediated β-amyloid-induced neurotoxicity. Journal
of Neuroscience. 2004;24(23):5322-5330. doi:10.1523/JNEUROSCI.1170-04.2004
apa: Novarino, G., Fabrizi, C., Tonini, R., Denti, M., Malchiodi, A., Lauro, G.,
… Mazzanti, M. (2004). Involvement of the intracellular ion channel CLIC1 in microglia-mediated
β-amyloid-induced neurotoxicity. Journal of Neuroscience. Society for Neuroscience.
https://doi.org/10.1523/JNEUROSCI.1170-04.2004
chicago: Novarino, Gaia, Cinzia Fabrizi, Raffaella Tonini, Michela Denti, Albedi
Malchiodi, Giuliana Lauro, Benedetto Sacchetti, et al. “Involvement of the Intracellular
Ion Channel CLIC1 in Microglia-Mediated β-Amyloid-Induced Neurotoxicity.” Journal
of Neuroscience. Society for Neuroscience, 2004. https://doi.org/10.1523/JNEUROSCI.1170-04.2004.
ieee: G. Novarino et al., “Involvement of the intracellular ion channel CLIC1
in microglia-mediated β-amyloid-induced neurotoxicity,” Journal of Neuroscience,
vol. 24, no. 23. Society for Neuroscience, pp. 5322–5330, 2004.
ista: Novarino G, Fabrizi C, Tonini R, Denti M, Malchiodi A, Lauro G, Sacchetti
B, Paradisi S, Ferroni A, Curmi P, Breit S, Mazzanti M. 2004. Involvement of the
intracellular ion channel CLIC1 in microglia-mediated β-amyloid-induced neurotoxicity.
Journal of Neuroscience. 24(23), 5322–5330.
mla: Novarino, Gaia, et al. “Involvement of the Intracellular Ion Channel CLIC1
in Microglia-Mediated β-Amyloid-Induced Neurotoxicity.” Journal of Neuroscience,
vol. 24, no. 23, Society for Neuroscience, 2004, pp. 5322–30, doi:10.1523/JNEUROSCI.1170-04.2004.
short: G. Novarino, C. Fabrizi, R. Tonini, M. Denti, A. Malchiodi, G. Lauro, B.
Sacchetti, S. Paradisi, A. Ferroni, P. Curmi, S. Breit, M. Mazzanti, Journal of
Neuroscience 24 (2004) 5322–5330.
date_created: 2018-12-11T11:56:54Z
date_published: 2004-06-09T00:00:00Z
date_updated: 2021-01-12T06:56:41Z
day: '09'
doi: 10.1523/JNEUROSCI.1170-04.2004
extern: 1
intvolume: ' 24'
issue: '23'
month: '06'
page: 5322 - 5330
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '4620'
quality_controlled: 0
status: public
title: Involvement of the intracellular ion channel CLIC1 in microglia-mediated β-amyloid-induced
neurotoxicity
type: journal_article
volume: 24
year: '2004'
...
---
_id: '2355'
abstract:
- lang: eng
text: 'The BMV conjecture for traces, which states that Tr exp(A - λB) is the Laplace
transform of a positive measure, is shown to be equivalent to two other statements:
(i) The polynomial λ → Tr(A + λB) p has only non-negative coefficients for all
A, B ≥ 0, p ∈ ℕ and (ii) λ → Tr(A + λB)-p is the Laplace transform of a positive
measure for A, B ≥ 0, p > 0.'
author:
- first_name: Élliott
full_name: Lieb, Élliott H
last_name: Lieb
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Lieb É, Seiringer R. Equivalent forms of the Bessis-Moussa-Villani conjecture.
Journal of Statistical Physics. 2004;115(1-2):185-190. doi:10.1023/B:JOSS.0000019811.15510.27
apa: Lieb, É., & Seiringer, R. (2004). Equivalent forms of the Bessis-Moussa-Villani
conjecture. Journal of Statistical Physics. Springer. https://doi.org/10.1023/B:JOSS.0000019811.15510.27
chicago: Lieb, Élliott, and Robert Seiringer. “ Equivalent Forms of the Bessis-Moussa-Villani
Conjecture.” Journal of Statistical Physics. Springer, 2004. https://doi.org/10.1023/B:JOSS.0000019811.15510.27.
ieee: É. Lieb and R. Seiringer, “ Equivalent forms of the Bessis-Moussa-Villani
conjecture,” Journal of Statistical Physics, vol. 115, no. 1–2. Springer,
pp. 185–190, 2004.
ista: Lieb É, Seiringer R. 2004. Equivalent forms of the Bessis-Moussa-Villani
conjecture. Journal of Statistical Physics. 115(1–2), 185–190.
mla: Lieb, Élliott, and Robert Seiringer. “ Equivalent Forms of the Bessis-Moussa-Villani
Conjecture.” Journal of Statistical Physics, vol. 115, no. 1–2, Springer,
2004, pp. 185–90, doi:10.1023/B:JOSS.0000019811.15510.27.
short: É. Lieb, R. Seiringer, Journal of Statistical Physics 115 (2004) 185–190.
date_created: 2018-12-11T11:57:11Z
date_published: 2004-04-01T00:00:00Z
date_updated: 2021-01-12T06:56:59Z
day: '01'
doi: 10.1023/B:JOSS.0000019811.15510.27
extern: 1
intvolume: ' 115'
issue: 1-2
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math-ph/0210027
month: '04'
oa: 1
page: 185 - 190
publication: Journal of Statistical Physics
publication_status: published
publisher: Springer
publist_id: '4568'
quality_controlled: 0
status: public
title: ' Equivalent forms of the Bessis-Moussa-Villani conjecture'
type: journal_article
volume: 115
year: '2004'
...
---
_id: '2356'
abstract:
- lang: eng
text: 'Recent experimental and theoretical work has shown that there are conditions
in which a trapped, low-density Bose gas behaves like the one-dimensional delta-function
Bose gas solved years ago by Lieb and Liniger. This is an intrinsically quantum-mechanical
phenomenon because it is not necessary to have a trap width that is the size of
an atom - as might have been supposed - but it suffices merely to have a trap
width such that the energy gap for motion in the transverse direction is large
compared to the energy associated with the motion along the trap. Up to now the
theoretical arguments have been based on variational - perturbative ideas or numerical
investigations. In contrast, this paper gives a rigorous proof of the one-dimensional
behavior as far as the ground state energy and particle density are concerned.
There are four parameters involved: the particle number, N, transverse and longitudinal
dimensions of the trap, r and L, and the scattering length a of the interaction
potential. Our main result is that if r/L → 0 and N → ∞ the ground state energy
and density can be obtained by minimizing a one-dimensional density functional
involving the Lieb-Liniger energy density with coupling constant ∼ a/r 2. This
density functional simplifies in various limiting cases and we identify five asymptotic
parameter regions altogether. Three of these, corresponding to the weak coupling
regime, can also be obtained as limits of a three-dimensional Gross-Pitaevskii
theory. We also show that Bose-Einstein condensation in the ground state persists
in a part of this regime. In the strong coupling regime the longitudinal motion
of the particles is strongly correlated. The Gross-Pitaevskii description is not
valid in this regime and new mathematical methods come into play.'
author:
- first_name: Élliott
full_name: Lieb, Élliott H
last_name: Lieb
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jakob
full_name: Yngvason, Jakob
last_name: Yngvason
citation:
ama: Lieb É, Seiringer R, Yngvason J. One-dimensional behavior of dilute, trapped
Bose gases. Communications in Mathematical Physics. 2004;244(2):347-393.
doi:10.1007/s00220-003-0993-3
apa: Lieb, É., Seiringer, R., & Yngvason, J. (2004). One-dimensional behavior
of dilute, trapped Bose gases. Communications in Mathematical Physics.
Springer. https://doi.org/10.1007/s00220-003-0993-3
chicago: Lieb, Élliott, Robert Seiringer, and Jakob Yngvason. “One-Dimensional Behavior
of Dilute, Trapped Bose Gases.” Communications in Mathematical Physics.
Springer, 2004. https://doi.org/10.1007/s00220-003-0993-3.
ieee: É. Lieb, R. Seiringer, and J. Yngvason, “One-dimensional behavior of dilute,
trapped Bose gases,” Communications in Mathematical Physics, vol. 244,
no. 2. Springer, pp. 347–393, 2004.
ista: Lieb É, Seiringer R, Yngvason J. 2004. One-dimensional behavior of dilute,
trapped Bose gases. Communications in Mathematical Physics. 244(2), 347–393.
mla: Lieb, Élliott, et al. “One-Dimensional Behavior of Dilute, Trapped Bose Gases.”
Communications in Mathematical Physics, vol. 244, no. 2, Springer, 2004,
pp. 347–93, doi:10.1007/s00220-003-0993-3.
short: É. Lieb, R. Seiringer, J. Yngvason, Communications in Mathematical Physics
244 (2004) 347–393.
date_created: 2018-12-11T11:57:11Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:59Z
day: '01'
doi: 10.1007/s00220-003-0993-3
extern: 1
intvolume: ' 244'
issue: '2'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math-ph/0305025
month: '01'
oa: 1
page: 347 - 393
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '4569'
quality_controlled: 0
status: public
title: One-dimensional behavior of dilute, trapped Bose gases
type: journal_article
volume: 244
year: '2004'
...