---
_id: '3150'
abstract:
- lang: eng
text: Tripartite G-protein-coupled receptors (GPCRs) represent one of the largest
groups of signal transducers, transmitting signals from hormones, neuropeptides,
odorants, food and light. Ligand-bound receptors catalyse GDP/GTP exchange on
the G-protein α-subunit (Gα), leading to α-GTP separation from the βγ subunits
and pathway activation. Activating mutations in the receptors or G proteins underlie
many human diseases, including some cancers, dwarfism and premature puberty. Regulators
of G-protein signalling (RGS proteins) are known to modulate the level and duration
of ligand-induced signalling by accelerating the intrinsic GTPase activity of
the Gα subunit, and thus reformation of the inactive GDP-bound Gα. Here we find
that even in the absence of receptor, mutation of the RGS family member Sst2 (refs
6-9) permits spontaneous activation of the G-protein-coupled mating pathway in
Saccharomyces cerevisiae at levels normally seen only in the presence of ligand.
Our work demonstrates the occurence of spontaneous tripartite G-protein signalling
in vivo and identifies a requirement for RGS proteins in preventing such receptor-independent
activation.
author:
- first_name: Daria E
full_name: Daria Siekhaus
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: David
full_name: Drubin, David G
last_name: Drubin
citation:
ama: Siekhaus DE, Drubin D. Spontaneous receptor-independent heterotrimeric G-protein
signalling in an RGS mutant. Nature Cell Biology. 2003;5(3):231-235. doi:10.1038/ncb941
apa: Siekhaus, D. E., & Drubin, D. (2003). Spontaneous receptor-independent
heterotrimeric G-protein signalling in an RGS mutant. Nature Cell Biology.
Nature Publishing Group. https://doi.org/10.1038/ncb941
chicago: Siekhaus, Daria E, and David Drubin. “Spontaneous Receptor-Independent
Heterotrimeric G-Protein Signalling in an RGS Mutant.” Nature Cell Biology.
Nature Publishing Group, 2003. https://doi.org/10.1038/ncb941.
ieee: D. E. Siekhaus and D. Drubin, “Spontaneous receptor-independent heterotrimeric
G-protein signalling in an RGS mutant,” Nature Cell Biology, vol. 5, no.
3. Nature Publishing Group, pp. 231–235, 2003.
ista: Siekhaus DE, Drubin D. 2003. Spontaneous receptor-independent heterotrimeric
G-protein signalling in an RGS mutant. Nature Cell Biology. 5(3), 231–235.
mla: Siekhaus, Daria E., and David Drubin. “Spontaneous Receptor-Independent Heterotrimeric
G-Protein Signalling in an RGS Mutant.” Nature Cell Biology, vol. 5, no.
3, Nature Publishing Group, 2003, pp. 231–35, doi:10.1038/ncb941.
short: D.E. Siekhaus, D. Drubin, Nature Cell Biology 5 (2003) 231–235.
date_created: 2018-12-11T12:01:41Z
date_published: 2003-03-01T00:00:00Z
date_updated: 2021-01-12T07:41:24Z
day: '01'
doi: 10.1038/ncb941
extern: 1
intvolume: ' 5'
issue: '3'
month: '03'
page: 231 - 235
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3544'
quality_controlled: 0
status: public
title: Spontaneous receptor-independent heterotrimeric G-protein signalling in an
RGS mutant
type: journal_article
volume: 5
year: '2003'
...
---
_id: '3151'
abstract:
- lang: eng
text: Biosynthesis of most peptide hormones and neuropeptides requires proteolytic
excision of the active peptide from inactive proprotein precursors, an activity
carried out by subtilisin-like proprotein convertases (SPCs) in constitutive or
regulated secretory pathways. The Drosophila amontillado (amon) gene encodes a
homolog of the mammalian PC2 protein, an SPC that functions in the regulated secretory
pathway in neuroendocrine tissues. We have identified amon mutants by isolating
ethylmethanesulfonate (EMS)-induced lethal and visible mutations that define two
complementation groups in the amon interval at 97D1 of the third chromosome. DNA
sequencing identified the amon complementation group and the DNA sequence change
for each of the nine amon alleles isolated. amon mutants display partial embryonic
lethality, are defective in larval growth, and arrest during the first to second
instar larval molt. Mutant larvae can be rescued by heat-shock-induced expression
of the amon protein. Rescued larvae arrest at the subsequent larval molt, suggesting
that amon is also required for the second to third instar larval molt. Our data
indicate that the amon proprotein convertase is required during embryogenesis
and larval development in Drosophila and support the hypothesis that AMON acts
to proteolytically process peptide hormones that regulate hatching, larval growth,
and larval ecdysis.
author:
- first_name: Lowell
full_name: Rayburn, Lowell Y
last_name: Rayburn
- first_name: Holly
full_name: Gooding, Holly C
last_name: Gooding
- first_name: Semil
full_name: Choksi, Semil P
last_name: Choksi
- first_name: Dhea
full_name: Maloney, Dhea
last_name: Maloney
- first_name: Ambrose
full_name: Kidd, Ambrose R
last_name: Kidd
- first_name: Daria E
full_name: Daria Siekhaus
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Michael
full_name: Bender, Michael
last_name: Bender
citation:
ama: Rayburn L, Gooding H, Choksi S, et al. Amontillado, the Drosophila homolog
of the prohormone processing protease PC2, is required during embryogenesis and
early larval development. Genetics. 2003;163(1):227-237.
apa: Rayburn, L., Gooding, H., Choksi, S., Maloney, D., Kidd, A., Siekhaus, D. E.,
& Bender, M. (2003). Amontillado, the Drosophila homolog of the prohormone
processing protease PC2, is required during embryogenesis and early larval development.
Genetics. Genetics Society of America.
chicago: Rayburn, Lowell, Holly Gooding, Semil Choksi, Dhea Maloney, Ambrose Kidd,
Daria E Siekhaus, and Michael Bender. “Amontillado, the Drosophila Homolog of
the Prohormone Processing Protease PC2, Is Required during Embryogenesis and Early
Larval Development.” Genetics. Genetics Society of America, 2003.
ieee: L. Rayburn et al., “Amontillado, the Drosophila homolog of the prohormone
processing protease PC2, is required during embryogenesis and early larval development,”
Genetics, vol. 163, no. 1. Genetics Society of America, pp. 227–237, 2003.
ista: Rayburn L, Gooding H, Choksi S, Maloney D, Kidd A, Siekhaus DE, Bender M.
2003. Amontillado, the Drosophila homolog of the prohormone processing protease
PC2, is required during embryogenesis and early larval development. Genetics.
163(1), 227–237.
mla: Rayburn, Lowell, et al. “Amontillado, the Drosophila Homolog of the Prohormone
Processing Protease PC2, Is Required during Embryogenesis and Early Larval Development.”
Genetics, vol. 163, no. 1, Genetics Society of America, 2003, pp. 227–37.
short: L. Rayburn, H. Gooding, S. Choksi, D. Maloney, A. Kidd, D.E. Siekhaus, M.
Bender, Genetics 163 (2003) 227–237.
date_created: 2018-12-11T12:01:41Z
date_published: 2003-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:25Z
day: '01'
extern: 1
intvolume: ' 163'
issue: '1'
month: '01'
page: 227 - 237
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3545'
quality_controlled: 0
status: public
title: Amontillado, the Drosophila homolog of the prohormone processing protease PC2,
is required during embryogenesis and early larval development
type: journal_article
volume: 163
year: '2003'
...
---
_id: '3170'
abstract:
- lang: eng
text: Geodesic active contours and graph cuts are two standard image segmentation
techniques. We introduce a new segmentation method combining some of their benefits.
Our main intuition is that any cut on a graph embedded in some continuous space
can be interpreted as a contour (in 2D) or a surface (in 3D). We show how to build
a grid graph and set its edge weights so that the cost of cuts is arbitrarily
close to the length (area) of the corresponding contours (surfaces) for any anisotropic
Riemannian metric. There are two interesting consequences of this technical result.
First, graph cut algorithms can be used to find globally minimum geodesic contours
(minimal surfaces in 3D) under arbitrary Riemannian metric for a given set of
boundary conditions. Second, we show how to minimize metrication artifacts in
existing graph-cut based methods in vision. Theoretically speaking, our work provides
an interesting link between several branches of mathematics -differential geometry,
integral geometry, and combinatorial optimization. The main technical problem
is solved using Cauchy-Crofton formula from integral geometry.
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. Computing geodesics and minimal surfaces via graph
cuts. In: Vol 1. IEEE; 2003:26-33. doi:10.1109/ICCV.2003.1238310'
apa: 'Boykov, Y., & Kolmogorov, V. (2003). Computing geodesics and minimal surfaces
via graph cuts (Vol. 1, pp. 26–33). Presented at the ICCV: International Conference
on Computer Vision, IEEE. https://doi.org/10.1109/ICCV.2003.1238310'
chicago: Boykov, Yuri, and Vladimir Kolmogorov. “Computing Geodesics and Minimal
Surfaces via Graph Cuts,” 1:26–33. IEEE, 2003. https://doi.org/10.1109/ICCV.2003.1238310.
ieee: 'Y. Boykov and V. Kolmogorov, “Computing geodesics and minimal surfaces via
graph cuts,” presented at the ICCV: International Conference on Computer Vision,
2003, vol. 1, pp. 26–33.'
ista: 'Boykov Y, Kolmogorov V. 2003. Computing geodesics and minimal surfaces via
graph cuts. ICCV: International Conference on Computer Vision vol. 1, 26–33.'
mla: Boykov, Yuri, and Vladimir Kolmogorov. Computing Geodesics and Minimal Surfaces
via Graph Cuts. Vol. 1, IEEE, 2003, pp. 26–33, doi:10.1109/ICCV.2003.1238310.
short: Y. Boykov, V. Kolmogorov, in:, IEEE, 2003, pp. 26–33.
conference:
name: 'ICCV: International Conference on Computer Vision'
date_created: 2018-12-11T12:01:48Z
date_published: 2003-09-30T00:00:00Z
date_updated: 2021-01-12T07:41:33Z
day: '30'
doi: 10.1109/ICCV.2003.1238310
extern: 1
intvolume: ' 1'
month: '09'
page: 26 - 33
publication_status: published
publisher: IEEE
publist_id: '3511'
quality_controlled: 0
status: public
title: Computing geodesics and minimal surfaces via graph cuts
type: conference
volume: 1
year: '2003'
...
---
_id: '3171'
abstract:
- lang: eng
text: 'Reconstructing a 3-D scene from more than one camera is a classical problem
in computer vision. One of the major sources of difficulty is the fact that not
all scene elements are visible from all cameras. In the last few years, two promising
approaches have been developed 11,12 that formulate the scene reconstruction problem
in terms of energy minimization, and minimize the energy using graph cuts. These
energy minimization approaches treat the input images symmetrically, handle visibility
constraints correctly, and allow spatial smoothness to be enforced. However, these
algorithm propose different problem formulations, and handle a limited class of
smoothness terms. One algorithm 11 uses a problem formulation that is restricted
to two-camera stereo, and imposes smoothness between a pair of cameras. The other
algorithm 12 can handle an arbitrary number of cameras, but imposes smoothness
only with respect to a single camera. In this paper we give a more general energy
minimization formulation for the problem, which allows a larger class of spatial
smoothness constraints. We show that our formulation includes both of the previous
approaches as special cases, as well as permitting new energy functions. Experimental
results on real data with ground truth are also included. '
alternative_title:
- LNCS
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
- first_name: Steven
full_name: Gortler, Steven
last_name: Gortler
citation:
ama: 'Kolmogorov V, Zabih R, Gortler S. Generalized multi camera scene reconstruction
using graph cuts. In: Vol 2683. Springer; 2003:501-516. doi:10.1007/978-3-540-45063-4_32'
apa: 'Kolmogorov, V., Zabih, R., & Gortler, S. (2003). Generalized multi camera
scene reconstruction using graph cuts (Vol. 2683, pp. 501–516). Presented at the
EMMCVPR: Energy Minimization Methods in Computer Vision and Pattern Recognition,
Springer. https://doi.org/10.1007/978-3-540-45063-4_32'
chicago: Kolmogorov, Vladimir, Ramin Zabih, and Steven Gortler. “Generalized Multi
Camera Scene Reconstruction Using Graph Cuts,” 2683:501–16. Springer, 2003. https://doi.org/10.1007/978-3-540-45063-4_32.
ieee: 'V. Kolmogorov, R. Zabih, and S. Gortler, “Generalized multi camera scene
reconstruction using graph cuts,” presented at the EMMCVPR: Energy Minimization
Methods in Computer Vision and Pattern Recognition, 2003, vol. 2683, pp. 501–516.'
ista: 'Kolmogorov V, Zabih R, Gortler S. 2003. Generalized multi camera scene reconstruction
using graph cuts. EMMCVPR: Energy Minimization Methods in Computer Vision and
Pattern Recognition, LNCS, vol. 2683, 501–516.'
mla: Kolmogorov, Vladimir, et al. Generalized Multi Camera Scene Reconstruction
Using Graph Cuts. Vol. 2683, Springer, 2003, pp. 501–16, doi:10.1007/978-3-540-45063-4_32.
short: V. Kolmogorov, R. Zabih, S. Gortler, in:, Springer, 2003, pp. 501–516.
conference:
name: 'EMMCVPR: Energy Minimization Methods in Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:48Z
date_published: 2003-06-26T00:00:00Z
date_updated: 2021-01-12T07:41:34Z
day: '26'
doi: 10.1007/978-3-540-45063-4_32
extern: 1
intvolume: ' 2683'
month: '06'
page: 501 - 516
publication_status: published
publisher: Springer
publist_id: '3512'
quality_controlled: 0
status: public
title: Generalized multi camera scene reconstruction using graph cuts
type: conference
volume: 2683
year: '2003'
...
---
_id: '3174'
abstract:
- lang: eng
text: We address visual correspondence problems without assuming that scene points
have similar intensities in different views. This situation is common, usually
due to non-lambertian scenes or to differences between cameras. We use maximization
of mutual information, a powerful technique for registering images that requires
no a priori model of the relationship between scene intensities in different views.
However, it has proven difficult to use mutual information to compute dense visual
correspondence. Comparing fixed-size windows via mutual information suffers from
the well-known problems of fixed windows, namely poor performance at discontinuities
and in low-texture regions. In this paper, we show how to compute visual correspondence
using mutual information without suffering from these problems. Using 'a simple
approximation, mutual information can be incorporated into the standard energy
minimization framework used in early vision. The energy can then be efficiently
minimized using graph cuts, which preserve discontinuities and handle low-texture
regions. The resulting algorithm combines the accurate disparity maps that come
from graph cuts with the tolerance for intensity changes that comes from mutual
information.
author:
- first_name: Junhwan
full_name: Kim, Junhwan
last_name: Kim
- 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: 'Kim J, Kolmogorov V, Zabih R. Visual correspondence using energy minimization
and mutual information. In: Vol 2. IEEE; 2003:1033-1040. doi:10.1109/ICCV.2003.1238463'
apa: 'Kim, J., Kolmogorov, V., & Zabih, R. (2003). Visual correspondence using
energy minimization and mutual information (Vol. 2, pp. 1033–1040). Presented
at the ICCV: International Conference on Computer Vision, IEEE. https://doi.org/10.1109/ICCV.2003.1238463'
chicago: Kim, Junhwan, Vladimir Kolmogorov, and Ramin Zabih. “Visual Correspondence
Using Energy Minimization and Mutual Information,” 2:1033–40. IEEE, 2003. https://doi.org/10.1109/ICCV.2003.1238463.
ieee: 'J. Kim, V. Kolmogorov, and R. Zabih, “Visual correspondence using energy
minimization and mutual information,” presented at the ICCV: International Conference
on Computer Vision, 2003, vol. 2, pp. 1033–1040.'
ista: 'Kim J, Kolmogorov V, Zabih R. 2003. Visual correspondence using energy minimization
and mutual information. ICCV: International Conference on Computer Vision vol.
2, 1033–1040.'
mla: Kim, Junhwan, et al. Visual Correspondence Using Energy Minimization and
Mutual Information. Vol. 2, IEEE, 2003, pp. 1033–40, doi:10.1109/ICCV.2003.1238463.
short: J. Kim, V. Kolmogorov, R. Zabih, in:, IEEE, 2003, pp. 1033–1040.
conference:
name: 'ICCV: International Conference on Computer Vision'
date_created: 2018-12-11T12:01:49Z
date_published: 2003-09-30T00:00:00Z
date_updated: 2021-01-12T07:41:35Z
day: '30'
doi: 10.1109/ICCV.2003.1238463
extern: 1
intvolume: ' 2'
month: '09'
page: 1033 - 1040
publication_status: published
publisher: IEEE
publist_id: '3510'
quality_controlled: 0
status: public
title: Visual correspondence using energy minimization and mutual information
type: conference
volume: 2
year: '2003'
...
---
_id: '3209'
abstract:
- lang: eng
text: We show that the fixed alphabet shortest common supersequence (SCS) and the
fixed alphabet longest common subsequence (LCS) problems parameterized in the
number of strings are W[1]-hard. Unless W[1]=FPT, this rules out the existence
of algorithms with time complexity of O(f(k)nα) for those problems. Here n is
the size of the problem instance, α is constant, k is the number of strings and
f is any function of k. The fixed alphabet version of the LCS problem is of particular
interest considering the importance of sequence comparison (e.g. multiple sequence
alignment) in the fixed length alphabet world of DNA and protein sequences.
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. On the parameterized complexity of the fixed alphabet shortest
common supersequence and longest common subsequence problems. Journal of Computer
and System Sciences. 2003;67(4):757-771. doi:10.1016/S0022-0000(03)00078-3
apa: Pietrzak, K. Z. (2003). On the parameterized complexity of the fixed alphabet
shortest common supersequence and longest common subsequence problems. Journal
of Computer and System Sciences. Elsevier. https://doi.org/10.1016/S0022-0000(03)00078-3
chicago: Pietrzak, Krzysztof Z. “On the Parameterized Complexity of the Fixed Alphabet
Shortest Common Supersequence and Longest Common Subsequence Problems.” Journal
of Computer and System Sciences. Elsevier, 2003. https://doi.org/10.1016/S0022-0000(03)00078-3.
ieee: K. Z. Pietrzak, “On the parameterized complexity of the fixed alphabet shortest
common supersequence and longest common subsequence problems,” Journal of Computer
and System Sciences, vol. 67, no. 4. Elsevier, pp. 757–771, 2003.
ista: Pietrzak KZ. 2003. On the parameterized complexity of the fixed alphabet shortest
common supersequence and longest common subsequence problems. Journal of Computer
and System Sciences. 67(4), 757–771.
mla: Pietrzak, Krzysztof Z. “On the Parameterized Complexity of the Fixed Alphabet
Shortest Common Supersequence and Longest Common Subsequence Problems.” Journal
of Computer and System Sciences, vol. 67, no. 4, Elsevier, 2003, pp. 757–71,
doi:10.1016/S0022-0000(03)00078-3.
short: K.Z. Pietrzak, Journal of Computer and System Sciences 67 (2003) 757–771.
date_created: 2018-12-11T12:02:01Z
date_published: 2003-12-01T00:00:00Z
date_updated: 2021-01-12T07:41:49Z
day: '01'
doi: 10.1016/S0022-0000(03)00078-3
extern: 1
intvolume: ' 67'
issue: '4'
month: '12'
page: 757 - 771
publication: Journal of Computer and System Sciences
publication_status: published
publisher: Elsevier
publist_id: '3472'
quality_controlled: 0
status: public
title: On the parameterized complexity of the fixed alphabet shortest common supersequence
and longest common subsequence problems
type: journal_article
volume: 67
year: '2003'
...
---
_id: '3210'
abstract:
- lang: eng
text: 'Luby and Rackoff showed how to construct a (super-)pseudo-random permutation
{0,1}2n→ {0,1}2n from some number r of pseudo-random functions {0,1}n → {0,1}n.
Their construction, motivated by DES, consists of a cascade of r Feistel permutations.
A Feistel permutation 1for a pseudo-random function f is defined as (L, R) → (R,L
⊕ f (R)), where L and R are the left and right part of the input and ⊕ denotes
bitwise XOR or, in this paper, any other group operation on {0,1}n. The only non-trivial
step of the security proof consists of proving that the cascade of r Feistel permutations
with independent uniform random functions {0,1}n → {0,1}n, denoted Ψ2nr is indistinguishable
from a uniform random permutation {0,1}2n → {0,1}2n by any computationally unbounded
adaptive distinguisher making at most O(2cn) combined chosen plaintext/ciphertext
queries for any c < α, where a is a security parameter. Luby and Rackoff proved
α = 1/2 for r = 4. A natural problem, proposed by Pieprzyk is to improve on α
for larger r. The best known result, α = 3/4 for r = 6, is due to Patarin. In
this paper we prove a = 1 -O(1/r), i.e., the trivial upper bound α = 1 can be
approached. The proof uses some new techniques that can be of independent interest. '
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. The security of many round Luby Rackoff pseudo random
permutations. In: Vol 2656. Springer; 2003:544-561. doi:10.1007/3-540-39200-9_34'
apa: 'Maurer, U., & Pietrzak, K. Z. (2003). The security of many round Luby
Rackoff pseudo random permutations (Vol. 2656, pp. 544–561). Presented at the
EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/3-540-39200-9_34'
chicago: Maurer, Ueli, and Krzysztof Z Pietrzak. “The Security of Many Round Luby
Rackoff Pseudo Random Permutations,” 2656:544–61. Springer, 2003. https://doi.org/10.1007/3-540-39200-9_34.
ieee: 'U. Maurer and K. Z. Pietrzak, “The security of many round Luby Rackoff pseudo
random permutations,” presented at the EUROCRYPT: Theory and Applications of Cryptographic
Techniques, 2003, vol. 2656, pp. 544–561.'
ista: 'Maurer U, Pietrzak KZ. 2003. The security of many round Luby Rackoff pseudo
random permutations. EUROCRYPT: Theory and Applications of Cryptographic Techniques,
LNCS, vol. 2656, 544–561.'
mla: Maurer, Ueli, and Krzysztof Z. Pietrzak. The Security of Many Round Luby
Rackoff Pseudo Random Permutations. Vol. 2656, Springer, 2003, pp. 544–61,
doi:10.1007/3-540-39200-9_34.
short: U. Maurer, K.Z. Pietrzak, in:, Springer, 2003, pp. 544–561.
conference:
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
date_created: 2018-12-11T12:02:02Z
date_published: 2003-06-04T00:00:00Z
date_updated: 2021-01-12T07:41:49Z
day: '04'
doi: 10.1007/3-540-39200-9_34
extern: 1
intvolume: ' 2656'
month: '06'
page: 544 - 561
publication_status: published
publisher: Springer
publist_id: '3473'
quality_controlled: 0
status: public
title: The security of many round Luby Rackoff pseudo random permutations
type: conference
volume: 2656
year: '2003'
...
---
_id: '11121'
abstract:
- lang: eng
text: In metazoa, the nuclear envelope breaks down and reforms during each cell
cycle. Nuclear pore complexes (NPCs), which serve as channels for transport between
the nucleus and cytoplasm1, assemble into the reforming nuclear envelope in a
sequential process involving association of a subset of NPC proteins, nucleoporins,
with chromatin followed by the formation of a closed nuclear envelope fenestrated
by NPCs2,3,4,5,6,7. How chromatin recruitment of nucleoporins and NPC assembly
are regulated is unknown. Here we demonstrate that RanGTP production is required
to dissociate nucleoporins Nup107, Nup153 and Nup358 from Importin β, to target
them to chromatin and to induce association between separate NPC subcomplexes.
Additionally, either an excess of RanGTP or removal of Importin β induces formation
of NPC-containing membrane structures—annulate lamellae—both in vitro in the absence
of chromatin and in vivo. Annulate lamellae formation is strongly and specifically
inhibited by an excess of Importin β. The data demonstrate that RanGTP triggers
distinct steps of NPC assembly, and suggest a mechanism for the spatial restriction
of NPC assembly to the surface of chromatin.
article_processing_charge: No
article_type: original
author:
- first_name: Tobias C.
full_name: Walther, Tobias C.
last_name: Walther
- first_name: Peter
full_name: Askjaer, Peter
last_name: Askjaer
- first_name: Marc
full_name: Gentzel, Marc
last_name: Gentzel
- first_name: Anja
full_name: Habermann, Anja
last_name: Habermann
- first_name: Gareth
full_name: Griffiths, Gareth
last_name: Griffiths
- first_name: Matthias
full_name: Wilm, Matthias
last_name: Wilm
- first_name: Iain W.
full_name: Mattaj, Iain W.
last_name: Mattaj
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Walther TC, Askjaer P, Gentzel M, et al. RanGTP mediates nuclear pore complex
assembly. Nature. 2003;424(6949):689-694. doi:10.1038/nature01898
apa: Walther, T. C., Askjaer, P., Gentzel, M., Habermann, A., Griffiths, G., Wilm,
M., … Hetzer, M. (2003). RanGTP mediates nuclear pore complex assembly. Nature.
Springer Nature. https://doi.org/10.1038/nature01898
chicago: Walther, Tobias C., Peter Askjaer, Marc Gentzel, Anja Habermann, Gareth
Griffiths, Matthias Wilm, Iain W. Mattaj, and Martin Hetzer. “RanGTP Mediates
Nuclear Pore Complex Assembly.” Nature. Springer Nature, 2003. https://doi.org/10.1038/nature01898.
ieee: T. C. Walther et al., “RanGTP mediates nuclear pore complex assembly,”
Nature, vol. 424, no. 6949. Springer Nature, pp. 689–694, 2003.
ista: Walther TC, Askjaer P, Gentzel M, Habermann A, Griffiths G, Wilm M, Mattaj
IW, Hetzer M. 2003. RanGTP mediates nuclear pore complex assembly. Nature. 424(6949),
689–694.
mla: Walther, Tobias C., et al. “RanGTP Mediates Nuclear Pore Complex Assembly.”
Nature, vol. 424, no. 6949, Springer Nature, 2003, pp. 689–94, doi:10.1038/nature01898.
short: T.C. Walther, P. Askjaer, M. Gentzel, A. Habermann, G. Griffiths, M. Wilm,
I.W. Mattaj, M. Hetzer, Nature 424 (2003) 689–694.
date_created: 2022-04-07T07:57:02Z
date_published: 2003-07-30T00:00:00Z
date_updated: 2022-07-18T08:57:40Z
day: '30'
doi: 10.1038/nature01898
extern: '1'
external_id:
pmid:
- '12894213'
intvolume: ' 424'
issue: '6949'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '07'
oa_version: None
page: 689-694
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: RanGTP mediates nuclear pore complex assembly
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 424
year: '2003'
...
---
_id: '11122'
abstract:
- lang: eng
text: Nuclear pore complexes (NPCs) are large multiprotein assemblies that allow
traffic between the cytoplasm and the nucleus. During mitosis in higher eukaryotes,
the Nuclear Envelope (NE) breaks down and NPCs disassemble. How NPCs reassemble
and incorporate into the NE upon mitotic exit is poorly understood. We demonstrate
a function for the conserved Nup107-160 complex in this process. Partial in vivo
depletion of Nup133 or Nup107 via RNAi in HeLa cells resulted in reduced levels
of multiple nucleoporins and decreased NPC density in the NE. Immunodepletion
of the entire Nup107-160 complex from in vitro nuclear assembly reactions produced
nuclei with a continuous NE but no NPCs. This phenotype was reversible only if
Nup107-160 complex was readded before closed NE formation. Depletion also prevented
association of FG-repeat nucleoporins with chromatin. We propose a stepwise model
in which postmitotic NPC assembly initiates on chromatin via early recruitment
of the Nup107-160 complex.
article_processing_charge: No
article_type: original
author:
- first_name: Tobias C.
full_name: Walther, Tobias C.
last_name: Walther
- first_name: Annabelle
full_name: Alves, Annabelle
last_name: Alves
- first_name: Helen
full_name: Pickersgill, Helen
last_name: Pickersgill
- first_name: Isabelle
full_name: Loı̈odice, Isabelle
last_name: Loı̈odice
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Vincent
full_name: Galy, Vincent
last_name: Galy
- first_name: Bastian B.
full_name: Hülsmann, Bastian B.
last_name: Hülsmann
- first_name: Thomas
full_name: Köcher, Thomas
last_name: Köcher
- first_name: Matthias
full_name: Wilm, Matthias
last_name: Wilm
- first_name: Terry
full_name: Allen, Terry
last_name: Allen
- first_name: Iain W.
full_name: Mattaj, Iain W.
last_name: Mattaj
- first_name: Valérie
full_name: Doye, Valérie
last_name: Doye
citation:
ama: Walther TC, Alves A, Pickersgill H, et al. The conserved Nup107-160 complex
is critical for nuclear pore complex assembly. Cell. 2003;113(2):195-206.
doi:10.1016/s0092-8674(03)00235-6
apa: Walther, T. C., Alves, A., Pickersgill, H., Loı̈odice, I., Hetzer, M., Galy,
V., … Doye, V. (2003). The conserved Nup107-160 complex is critical for nuclear
pore complex assembly. Cell. Elsevier. https://doi.org/10.1016/s0092-8674(03)00235-6
chicago: Walther, Tobias C., Annabelle Alves, Helen Pickersgill, Isabelle Loı̈odice,
Martin Hetzer, Vincent Galy, Bastian B. Hülsmann, et al. “The Conserved Nup107-160
Complex Is Critical for Nuclear Pore Complex Assembly.” Cell. Elsevier,
2003. https://doi.org/10.1016/s0092-8674(03)00235-6.
ieee: T. C. Walther et al., “The conserved Nup107-160 complex is critical
for nuclear pore complex assembly,” Cell, vol. 113, no. 2. Elsevier, pp.
195–206, 2003.
ista: Walther TC, Alves A, Pickersgill H, Loı̈odice I, Hetzer M, Galy V, Hülsmann
BB, Köcher T, Wilm M, Allen T, Mattaj IW, Doye V. 2003. The conserved Nup107-160
complex is critical for nuclear pore complex assembly. Cell. 113(2), 195–206.
mla: Walther, Tobias C., et al. “The Conserved Nup107-160 Complex Is Critical for
Nuclear Pore Complex Assembly.” Cell, vol. 113, no. 2, Elsevier, 2003,
pp. 195–206, doi:10.1016/s0092-8674(03)00235-6.
short: T.C. Walther, A. Alves, H. Pickersgill, I. Loı̈odice, M. Hetzer, V. Galy,
B.B. Hülsmann, T. Köcher, M. Wilm, T. Allen, I.W. Mattaj, V. Doye, Cell 113 (2003)
195–206.
date_created: 2022-04-07T07:57:10Z
date_published: 2003-04-17T00:00:00Z
date_updated: 2022-07-18T08:57:42Z
day: '17'
doi: 10.1016/s0092-8674(03)00235-6
extern: '1'
external_id:
pmid:
- '12705868'
intvolume: ' 113'
issue: '2'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '04'
oa_version: Published Version
page: 195-206
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The conserved Nup107-160 complex is critical for nuclear pore complex assembly
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 113
year: '2003'
...
---
_id: '11764'
abstract:
- lang: eng
text: In this paper we consider the online ftp problem. The goal is to service a
sequence of file transfer requests given bandwidth constraints of the underlying
communication network. The main result of the paper is a technique that leads
to algorithms that optimize several natural metrics, such as max-stretch, total
flow time, max flow time, and total completion time. In particular, we show how
to achieve optimum total flow time and optimum max-stretch if we increase the
capacity of the underlying network by a logarithmic factor. We show that the resource
augmentation is necessary by proving polynomial lower bounds on the max-stretch
and total flow time for the case where online and offline algorithms are using
same-capacity edges. Moreover, we also give polylogarithmic lower bounds on the
resource augmentation factor necessary in order to keep the total flow time and
max-stretch within a constant factor of optimum.
article_processing_charge: No
article_type: original
author:
- first_name: Ashish
full_name: Goel, Ashish
last_name: Goel
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Serge
full_name: Plotkin, Serge
last_name: Plotkin
- first_name: Eva
full_name: Tardos, Eva
last_name: Tardos
citation:
ama: Goel A, Henzinger MH, Plotkin S, Tardos E. Scheduling data transfers in a network
and the set scheduling problem. Journal of Algorithms. 2003;48(2):314-332.
doi:10.1016/s0196-6774(03)00054-3
apa: Goel, A., Henzinger, M. H., Plotkin, S., & Tardos, E. (2003). Scheduling
data transfers in a network and the set scheduling problem. Journal of Algorithms.
Elsevier. https://doi.org/10.1016/s0196-6774(03)00054-3
chicago: Goel, Ashish, Monika H Henzinger, Serge Plotkin, and Eva Tardos. “Scheduling
Data Transfers in a Network and the Set Scheduling Problem.” Journal of Algorithms.
Elsevier, 2003. https://doi.org/10.1016/s0196-6774(03)00054-3.
ieee: A. Goel, M. H. Henzinger, S. Plotkin, and E. Tardos, “Scheduling data transfers
in a network and the set scheduling problem,” Journal of Algorithms, vol.
48, no. 2. Elsevier, pp. 314–332, 2003.
ista: Goel A, Henzinger MH, Plotkin S, Tardos E. 2003. Scheduling data transfers
in a network and the set scheduling problem. Journal of Algorithms. 48(2), 314–332.
mla: Goel, Ashish, et al. “Scheduling Data Transfers in a Network and the Set Scheduling
Problem.” Journal of Algorithms, vol. 48, no. 2, Elsevier, 2003, pp. 314–32,
doi:10.1016/s0196-6774(03)00054-3.
short: A. Goel, M.H. Henzinger, S. Plotkin, E. Tardos, Journal of Algorithms 48
(2003) 314–332.
date_created: 2022-08-08T12:09:32Z
date_published: 2003-09-01T00:00:00Z
date_updated: 2022-09-12T09:45:06Z
day: '01'
doi: 10.1016/s0196-6774(03)00054-3
extern: '1'
intvolume: ' 48'
issue: '2'
language:
- iso: eng
month: '09'
oa_version: None
page: 314-332
publication: Journal of Algorithms
publication_identifier:
issn:
- 0196-6774
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scheduling data transfers in a network and the set scheduling problem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2003'
...
---
_id: '11766'
abstract:
- lang: eng
text: 'This paper studies the multicast routing and admission control problem on
unit-capacity tree and mesh topologies in the throughput model. The problem is
a generalization of the edge-disjoint paths problem and is NP-hard both on trees
and meshes. We study both the offline and the online version of the problem: In
the offline setting, we give the first constant-factor approximation algorithm
for trees, and an -factor approximation algorithm for meshes. In the online setting,
we give the first polylogarithmic competitive online algorithm for tree and mesh
topologies. No polylogarithmic-competitive algorithm is possible on general network
topologies (Lower bounds for on-line graph problems with application to on-line
circuits and optical routing, in: Proceedings of the 28th ACM Symposium on Theory
of Computing, 1996, pp. 531–540) and there exists a polylogarithmic lower bound
on the competitive ratio of any online algorithm on tree topologies (Making commitments
in the face of uncertainity: how to pick a winner almost every time, in: Proceedings
of the 28th Annual ACM Symposium on Theory of Computing, 1996, pp. 519–530). We
prove the same lower bound for meshes.'
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
- first_name: Stefano
full_name: Leonardi, Stefano
last_name: Leonardi
citation:
ama: Henzinger MH, Leonardi S. Scheduling multicasts on unit-capacity trees and
meshes. Journal of Computer and System Sciences. 2003;66(3):567-611. doi:10.1016/s0022-0000(03)00043-6
apa: Henzinger, M. H., & Leonardi, S. (2003). Scheduling multicasts on unit-capacity
trees and meshes. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/s0022-0000(03)00043-6
chicago: Henzinger, Monika H, and Stefano Leonardi. “Scheduling Multicasts on Unit-Capacity
Trees and Meshes.” Journal of Computer and System Sciences. Elsevier, 2003.
https://doi.org/10.1016/s0022-0000(03)00043-6.
ieee: M. H. Henzinger and S. Leonardi, “Scheduling multicasts on unit-capacity trees
and meshes,” Journal of Computer and System Sciences, vol. 66, no. 3. Elsevier,
pp. 567–611, 2003.
ista: Henzinger MH, Leonardi S. 2003. Scheduling multicasts on unit-capacity trees
and meshes. Journal of Computer and System Sciences. 66(3), 567–611.
mla: Henzinger, Monika H., and Stefano Leonardi. “Scheduling Multicasts on Unit-Capacity
Trees and Meshes.” Journal of Computer and System Sciences, vol. 66, no.
3, Elsevier, 2003, pp. 567–611, doi:10.1016/s0022-0000(03)00043-6.
short: M.H. Henzinger, S. Leonardi, Journal of Computer and System Sciences 66 (2003)
567–611.
date_created: 2022-08-08T12:24:35Z
date_published: 2003-05-01T00:00:00Z
date_updated: 2023-02-10T08:03:31Z
day: '01'
doi: 10.1016/s0022-0000(03)00043-6
extern: '1'
intvolume: ' 66'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/S0022-0000(03)00043-6
month: '05'
oa: 1
oa_version: Published Version
page: 567-611
publication: Journal of Computer and System Sciences
publication_identifier:
issn:
- 0022-0000
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scheduling multicasts on unit-capacity trees and meshes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 66
year: '2003'
...
---
_id: '847'
abstract:
- lang: eng
text: The accumulation of genome-wide information on single nucleotide polymorphisms
in humans provides an unprecedented opportunity to detect the evolutionary forces
responsible for heterogeneity of the level of genetic variability across loci.
Previous studies have shown that history of recombination events has produced
long haplotype blocks in the human genome, which contribute to this heterogeneity.
Other factors, however, such as natural selection or the heterogeneity of mutation
rates across loci, may also lead to heterogeneity of genetic variability. We compared
synonymous and non-synonymous variability within human genes with their divergence
from murine orthologs. We separately analyzed the non-synonymous variants predicted
to damage protein structure or function and the variants predicted to be functionally
benign. The predictions were based on comparative sequence analysis and, in some
cases, on the analysis of protein structure. A strong correlation between non-synonymous,
benign variability and non-synonymous human-mouse divergence suggests that selection
played an important role in shaping the pattern of variability in coding regions
of human genes. However, the lack of correlation between deleterious variability
and evolutionary divergence shows that a substantial proportion of the observed
non-synonymous single-nucleotide polymorphisms reduces fitness and never reaches
fixation. Evolutionary and medical implications of the impact of selection on
human polymorphisms are discussed.
acknowledgement: We are grateful to Alexey Kondrashov and Alison Wellman for the careful
reading of the manuscript and providing us with their valuable comments.
author:
- first_name: Shamil
full_name: Sunyaev, Shamil R
last_name: Sunyaev
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Peer
full_name: Bork, Peer
last_name: Bork
- first_name: Vasily
full_name: Ramensky, Vasily
last_name: Ramensky
citation:
ama: Sunyaev S, Kondrashov F, Bork P, Ramensky V. Impact of selection, mutation
rate and genetic drift on human genetic variation. Human Molecular Genetics.
2003;12(24):3325-3330. doi:10.1093/hmg/ddg359
apa: Sunyaev, S., Kondrashov, F., Bork, P., & Ramensky, V. (2003). Impact of
selection, mutation rate and genetic drift on human genetic variation. Human
Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/ddg359
chicago: Sunyaev, Shamil, Fyodor Kondrashov, Peer Bork, and Vasily Ramensky. “Impact
of Selection, Mutation Rate and Genetic Drift on Human Genetic Variation.” Human
Molecular Genetics. Oxford University Press, 2003. https://doi.org/10.1093/hmg/ddg359.
ieee: S. Sunyaev, F. Kondrashov, P. Bork, and V. Ramensky, “Impact of selection,
mutation rate and genetic drift on human genetic variation,” Human Molecular
Genetics, vol. 12, no. 24. Oxford University Press, pp. 3325–3330, 2003.
ista: Sunyaev S, Kondrashov F, Bork P, Ramensky V. 2003. Impact of selection, mutation
rate and genetic drift on human genetic variation. Human Molecular Genetics. 12(24),
3325–3330.
mla: Sunyaev, Shamil, et al. “Impact of Selection, Mutation Rate and Genetic Drift
on Human Genetic Variation.” Human Molecular Genetics, vol. 12, no. 24,
Oxford University Press, 2003, pp. 3325–30, doi:10.1093/hmg/ddg359.
short: S. Sunyaev, F. Kondrashov, P. Bork, V. Ramensky, Human Molecular Genetics
12 (2003) 3325–3330.
date_created: 2018-12-11T11:48:49Z
date_published: 2003-12-15T00:00:00Z
date_updated: 2021-01-12T08:19:29Z
day: '15'
doi: 10.1093/hmg/ddg359
extern: 1
intvolume: ' 12'
issue: '24'
month: '12'
page: 3325 - 3330
publication: Human Molecular Genetics
publication_status: published
publisher: Oxford University Press
publist_id: '6803'
quality_controlled: 0
status: public
title: Impact of selection, mutation rate and genetic drift on human genetic variation
type: journal_article
volume: 12
year: '2003'
...
---
_id: '8519'
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Kaloshin V. The existential Hilbert 16-th problem and an estimate for cyclicity
of elementary polycycles. Inventiones mathematicae. 2003;151(3):451-512.
doi:10.1007/s00222-002-0244-9
apa: Kaloshin, V. (2003). The existential Hilbert 16-th problem and an estimate
for cyclicity of elementary polycycles. Inventiones Mathematicae. Springer
Nature. https://doi.org/10.1007/s00222-002-0244-9
chicago: Kaloshin, Vadim. “The Existential Hilbert 16-Th Problem and an Estimate
for Cyclicity of Elementary Polycycles.” Inventiones Mathematicae. Springer
Nature, 2003. https://doi.org/10.1007/s00222-002-0244-9.
ieee: V. Kaloshin, “The existential Hilbert 16-th problem and an estimate for cyclicity
of elementary polycycles,” Inventiones mathematicae, vol. 151, no. 3. Springer
Nature, pp. 451–512, 2003.
ista: Kaloshin V. 2003. The existential Hilbert 16-th problem and an estimate for
cyclicity of elementary polycycles. Inventiones mathematicae. 151(3), 451–512.
mla: Kaloshin, Vadim. “The Existential Hilbert 16-Th Problem and an Estimate for
Cyclicity of Elementary Polycycles.” Inventiones Mathematicae, vol. 151,
no. 3, Springer Nature, 2003, pp. 451–512, doi:10.1007/s00222-002-0244-9.
short: V. Kaloshin, Inventiones Mathematicae 151 (2003) 451–512.
date_created: 2020-09-18T10:49:26Z
date_published: 2003-03-01T00:00:00Z
date_updated: 2021-01-12T08:19:50Z
day: '01'
doi: 10.1007/s00222-002-0244-9
extern: '1'
intvolume: ' 151'
issue: '3'
keyword:
- General Mathematics
language:
- iso: eng
month: '03'
oa_version: None
page: 451-512
publication: Inventiones mathematicae
publication_identifier:
issn:
- 0020-9910
- 1432-1297
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: The existential Hilbert 16-th problem and an estimate for cyclicity of elementary
polycycles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 151
year: '2003'
...
---
_id: '876'
abstract:
- lang: eng
text: Alternative splicing is thought to be a major source of functional diversity
in animal proteins. We analyzed the evolutionary conservation of proteins encoded
by alternatively spliced genes and predicted the ancestral state for 73 cases
of alternative splicing (25 insertions and 48 deletions). The amino acid sequences
of most of the inserts in proteins produced by alternative splicing are as conserved
as the surrounding sequences. Thus, alternative splicing often creates novel isoforms
by the insertion of new, functional protein sequences that probably originated
from noncoding sequences of introns.
acknowledgement: We thank Peer Bork, Mikhail Gelfand, Alexey Kondrashov, David Lipman
and Shamil Sunyaev for critical reading of the manuscript and useful suggestions
and the Koonin group members for helpful discussions.
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. Evolution of alternative splicing: Deletions, insertions
and origin of functional parts of proteins from intron sequences. Trends in
Genetics. 2003;19(3):115-119. doi:10.1016/S0168-9525(02)00029-X'
apa: 'Kondrashov, F., & Koonin, E. (2003). Evolution of alternative splicing:
Deletions, insertions and origin of functional parts of proteins from intron sequences.
Trends in Genetics. Elsevier. https://doi.org/10.1016/S0168-9525(02)00029-X'
chicago: 'Kondrashov, Fyodor, and Eugene Koonin. “Evolution of Alternative Splicing:
Deletions, Insertions and Origin of Functional Parts of Proteins from Intron Sequences.”
Trends in Genetics. Elsevier, 2003. https://doi.org/10.1016/S0168-9525(02)00029-X.'
ieee: 'F. Kondrashov and E. Koonin, “Evolution of alternative splicing: Deletions,
insertions and origin of functional parts of proteins from intron sequences,”
Trends in Genetics, vol. 19, no. 3. Elsevier, pp. 115–119, 2003.'
ista: 'Kondrashov F, Koonin E. 2003. Evolution of alternative splicing: Deletions,
insertions and origin of functional parts of proteins from intron sequences. Trends
in Genetics. 19(3), 115–119.'
mla: 'Kondrashov, Fyodor, and Eugene Koonin. “Evolution of Alternative Splicing:
Deletions, Insertions and Origin of Functional Parts of Proteins from Intron Sequences.”
Trends in Genetics, vol. 19, no. 3, Elsevier, 2003, pp. 115–19, doi:10.1016/S0168-9525(02)00029-X.'
short: F. Kondrashov, E. Koonin, Trends in Genetics 19 (2003) 115–119.
date_created: 2018-12-11T11:48:58Z
date_published: 2003-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:58Z
day: '01'
doi: 10.1016/S0168-9525(02)00029-X
extern: 1
intvolume: ' 19'
issue: '3'
month: '01'
page: 115 - 119
publication: Trends in Genetics
publication_status: published
publisher: Elsevier
publist_id: '6776'
quality_controlled: 0
status: public
title: 'Evolution of alternative splicing: Deletions, insertions and origin of functional
parts of proteins from intron sequences'
type: journal_article
volume: 19
year: '2003'
...
---
_id: '166'
abstract:
- lang: eng
text: For any number field k, upper bounds are established for the number of k-rational
points of bounded height on non-singular del Pezzo surfaces defined over k, which
are equipped with suitable conic bundle structures over k.
alternative_title:
- Bonner mathematische Schriften
arxiv: 1
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: M
full_name: Swarbick Jones, M
last_name: Swarbick Jones
citation:
ama: Browning TD, Swarbick Jones M. Counting rational points on del Pezzo surfaces
of degree 5. Proceedings of the Bonn session in analytic number theory and
diophantine equations. 2003;360.
apa: Browning, T. D., & Swarbick Jones, M. (2003). Counting rational points
on del Pezzo surfaces of degree 5. Proceedings of the Bonn Session in Analytic
Number Theory and Diophantine Equations. Mathematisches Institut der Universität
Bonn.
chicago: Browning, Timothy D, and M Swarbick Jones. “Counting Rational Points on
Del Pezzo Surfaces of Degree 5.” Proceedings of the Bonn Session in Analytic
Number Theory and Diophantine Equations. Mathematisches Institut der Universität
Bonn, 2003.
ieee: T. D. Browning and M. Swarbick Jones, “Counting rational points on del Pezzo
surfaces of degree 5,” Proceedings of the Bonn session in analytic number theory
and diophantine equations, vol. 360. Mathematisches Institut der Universität
Bonn, 2003.
ista: Browning TD, Swarbick Jones M. 2003. Counting rational points on del Pezzo
surfaces of degree 5. Proceedings of the Bonn session in analytic number theory
and diophantine equations. 360.
mla: Browning, Timothy D., and M. Swarbick Jones. “Counting Rational Points on Del
Pezzo Surfaces of Degree 5.” Proceedings of the Bonn Session in Analytic Number
Theory and Diophantine Equations, vol. 360, Mathematisches Institut der Universität
Bonn, 2003.
short: T.D. Browning, M. Swarbick Jones, Proceedings of the Bonn Session in Analytic
Number Theory and Diophantine Equations 360 (2003).
date_created: 2018-12-11T11:44:58Z
date_published: 2003-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:20Z
day: '01'
extern: '1'
external_id:
arxiv:
- '1311.1665'
intvolume: ' 360'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1311.1665
month: '01'
oa: 1
oa_version: None
publication: Proceedings of the Bonn session in analytic number theory and diophantine
equations
publication_status: published
publisher: Mathematisches Institut der Universität Bonn
publist_id: '7755'
status: public
title: Counting rational points on del Pezzo surfaces of degree 5
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 360
year: '2003'
...
---
_id: '1959'
abstract:
- lang: eng
text: 'The molecular organization of bacterial NADH: ubiquinone oxidoreductase (complex
I or NDH-1) is not established, apart from a rough separation into dehydrogenase,
connecting and membrane domains. In this work, complex I was purified from Escherichia
coli and fragmented by replacing dodecylmaltoside with other detergents. Exchange
into decyl maltoside led to the removal of the hydrophobic subunit NuoL from the
otherwise intact complex. Diheptanoyl phosphocholine led to the loss of NuoL and
NuoM subunits, whereas other subunits remained in the complex. The presence of
N,N-dimethyldodecylamine N-oxide or Triton X-100 led to further disruption of
the membrane domain into fragments containing NuoL/M/N, NuoA/K/N, and NuoH/J subunits.
Among the hydrophilic subunits, NuoCD was most readily dissociated from the complex,
whereas NuoB was partially dissociated from the peripheral arm assembly in N,N-dimethyldodecylamine
N-oxide. A model of subunit arrangement in bacterial complex I based on these
data is proposed. Subunits NuoL and NuoM, which are homologous to antiporters
and are implicated in proton pumping, are located at the distal end of the membrane
arm, spatially separated from the redox centers of the peripheral arm. This is
consistent with proposals that the mechanism of proton pumping by complex I is
likely to involve long range conformational changes.'
acknowledgement: his work was supported by the Medical Research Council.
author:
- first_name: Peter
full_name: Holt, Peter J
last_name: Holt
- first_name: David
full_name: Morgan, David J
last_name: Morgan
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: 'Holt P, Morgan D, Sazanov LA. The location of NuoL and NuoM subunits in the
membrane domain of the Escherichia coli Complex I: implications for the mechanism
of proton pumping. Journal of Biological Chemistry. 2003;278(44):43114-43120.
doi:10.1074/jbc.M308247200'
apa: 'Holt, P., Morgan, D., & Sazanov, L. A. (2003). The location of NuoL and
NuoM subunits in the membrane domain of the Escherichia coli Complex I: implications
for the mechanism of proton pumping. Journal of Biological Chemistry. American
Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M308247200'
chicago: 'Holt, Peter, David Morgan, and Leonid A Sazanov. “The Location of NuoL
and NuoM Subunits in the Membrane Domain of the Escherichia Coli Complex I: Implications
for the Mechanism of Proton Pumping.” Journal of Biological Chemistry.
American Society for Biochemistry and Molecular Biology, 2003. https://doi.org/10.1074/jbc.M308247200.'
ieee: 'P. Holt, D. Morgan, and L. A. Sazanov, “The location of NuoL and NuoM subunits
in the membrane domain of the Escherichia coli Complex I: implications for the
mechanism of proton pumping,” Journal of Biological Chemistry, vol. 278,
no. 44. American Society for Biochemistry and Molecular Biology, pp. 43114–43120,
2003.'
ista: 'Holt P, Morgan D, Sazanov LA. 2003. The location of NuoL and NuoM subunits
in the membrane domain of the Escherichia coli Complex I: implications for the
mechanism of proton pumping. Journal of Biological Chemistry. 278(44), 43114–43120.'
mla: 'Holt, Peter, et al. “The Location of NuoL and NuoM Subunits in the Membrane
Domain of the Escherichia Coli Complex I: Implications for the Mechanism of Proton
Pumping.” Journal of Biological Chemistry, vol. 278, no. 44, American Society
for Biochemistry and Molecular Biology, 2003, pp. 43114–20, doi:10.1074/jbc.M308247200.'
short: P. Holt, D. Morgan, L.A. Sazanov, Journal of Biological Chemistry 278 (2003)
43114–43120.
date_created: 2018-12-11T11:54:55Z
date_published: 2003-10-31T00:00:00Z
date_updated: 2021-01-12T06:54:21Z
day: '31'
doi: 10.1074/jbc.M308247200
extern: 1
intvolume: ' 278'
issue: '44'
month: '10'
page: 43114 - 43120
publication: Journal of Biological Chemistry
publication_status: published
publisher: American Society for Biochemistry and Molecular Biology
publist_id: '5124'
quality_controlled: 0
status: public
title: 'The location of NuoL and NuoM subunits in the membrane domain of the Escherichia
coli Complex I: implications for the mechanism of proton pumping'
type: journal_article
volume: 278
year: '2003'
...
---
_id: '1960'
abstract:
- lang: eng
text: NADH-ubiquinone oxidoreductase (complex I or NDH-1) was purified from the
BL21 strain of Escherichia coli using an improved procedure. The complex was effectively
stabilized by addition of divalent cations and lipids, making the preparation
suitable for structural studies. The ubiquinone reductase activity of the enzyme
was fully restored by addition of native E. coli lipids. Two different two-dimensional
crystal forms, with p2 and p3 symmetry, were obtained using lipids containing
native E. coli extracts. Analysis of the crystals showed that they are formed
by fully intact complex I in an L-shaped conformation. Activity assays and single
particle analysis indicated that complex I maintains this structure in detergent
solution and does not adopt a different conformation in the active state. Thus,
we provide the first experimental evidence that complex I from E. coli has an
L-shape in a lipid bilayer and confirm that this is also the case for the active
enzyme in solution. This suggests strongly that bacterial complex I exists in
an L-shaped conformation in vivo. Our results also indicate that native lipids
play an important role in the activation, stabilization and, as a consequence,
crystallization of purified complex I from E. coli.
author:
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Joe
full_name: Carroll, Joe D
last_name: Carroll
- first_name: Peter
full_name: Holt, Peter J
last_name: Holt
- first_name: Laurence
full_name: Toime, Laurence J
last_name: Toime
- first_name: Ian
full_name: Fearnley, Ian M
last_name: Fearnley
citation:
ama: Sazanov LA, Carroll J, Holt P, Toime L, Fearnley I. A role for native lipids
in the stabilization and two dimensional crystallization of the Escherichia coli
NADH ubiquinone oxidoreductase (complex I). Journal of Biological Chemistry.
2003;278(21):19483-19491. doi:10.1074/jbc.M208959200
apa: Sazanov, L. A., Carroll, J., Holt, P., Toime, L., & Fearnley, I. (2003).
A role for native lipids in the stabilization and two dimensional crystallization
of the Escherichia coli NADH ubiquinone oxidoreductase (complex I). Journal
of Biological Chemistry. American Society for Biochemistry and Molecular Biology.
https://doi.org/10.1074/jbc.M208959200
chicago: Sazanov, Leonid A, Joe Carroll, Peter Holt, Laurence Toime, and Ian Fearnley.
“A Role for Native Lipids in the Stabilization and Two Dimensional Crystallization
of the Escherichia Coli NADH Ubiquinone Oxidoreductase (Complex I).” Journal
of Biological Chemistry. American Society for Biochemistry and Molecular Biology,
2003. https://doi.org/10.1074/jbc.M208959200.
ieee: L. A. Sazanov, J. Carroll, P. Holt, L. Toime, and I. Fearnley, “A role for
native lipids in the stabilization and two dimensional crystallization of the
Escherichia coli NADH ubiquinone oxidoreductase (complex I),” Journal of Biological
Chemistry, vol. 278, no. 21. American Society for Biochemistry and Molecular
Biology, pp. 19483–19491, 2003.
ista: Sazanov LA, Carroll J, Holt P, Toime L, Fearnley I. 2003. A role for native
lipids in the stabilization and two dimensional crystallization of the Escherichia
coli NADH ubiquinone oxidoreductase (complex I). Journal of Biological Chemistry.
278(21), 19483–19491.
mla: Sazanov, Leonid A., et al. “A Role for Native Lipids in the Stabilization and
Two Dimensional Crystallization of the Escherichia Coli NADH Ubiquinone Oxidoreductase
(Complex I).” Journal of Biological Chemistry, vol. 278, no. 21, American
Society for Biochemistry and Molecular Biology, 2003, pp. 19483–91, doi:10.1074/jbc.M208959200.
short: L.A. Sazanov, J. Carroll, P. Holt, L. Toime, I. Fearnley, Journal of Biological
Chemistry 278 (2003) 19483–19491.
date_created: 2018-12-11T11:54:55Z
date_published: 2003-05-23T00:00:00Z
date_updated: 2021-01-12T06:54:21Z
day: '23'
doi: 10.1074/jbc.M208959200
extern: 1
intvolume: ' 278'
issue: '21'
month: '05'
page: 19483 - 19491
publication: Journal of Biological Chemistry
publication_status: published
publisher: American Society for Biochemistry and Molecular Biology
publist_id: '5125'
quality_controlled: 0
status: public
title: A role for native lipids in the stabilization and two dimensional crystallization
of the Escherichia coli NADH ubiquinone oxidoreductase (complex I)
type: journal_article
volume: 278
year: '2003'
...
---
_id: '205'
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Browning TD. Counting rational points on cubic and quartic surfaces. Acta
Arithmetica. 2003;108(3):275-295. doi:10.4064/aa108-3-7
apa: Browning, T. D. (2003). Counting rational points on cubic and quartic surfaces.
Acta Arithmetica. Instytut Matematyczny. https://doi.org/10.4064/aa108-3-7
chicago: Browning, Timothy D. “Counting Rational Points on Cubic and Quartic Surfaces.”
Acta Arithmetica. Instytut Matematyczny, 2003. https://doi.org/10.4064/aa108-3-7.
ieee: T. D. Browning, “Counting rational points on cubic and quartic surfaces,”
Acta Arithmetica, vol. 108, no. 3. Instytut Matematyczny, pp. 275–295,
2003.
ista: Browning TD. 2003. Counting rational points on cubic and quartic surfaces.
Acta Arithmetica. 108(3), 275–295.
mla: Browning, Timothy D. “Counting Rational Points on Cubic and Quartic Surfaces.”
Acta Arithmetica, vol. 108, no. 3, Instytut Matematyczny, 2003, pp. 275–95,
doi:10.4064/aa108-3-7.
short: T.D. Browning, Acta Arithmetica 108 (2003) 275–295.
date_created: 2018-12-11T11:45:12Z
date_published: 2003-01-01T00:00:00Z
date_updated: 2021-01-12T06:54:58Z
day: '01'
doi: 10.4064/aa108-3-7
extern: 1
intvolume: ' 108'
issue: '3'
month: '01'
page: 275 - 295
publication: Acta Arithmetica
publication_status: published
publisher: Instytut Matematyczny
publist_id: '7707'
quality_controlled: 0
status: public
title: Counting rational points on cubic and quartic surfaces
type: journal_article
volume: 108
year: '2003'
...
---
_id: '206'
abstract:
- lang: eng
text: Let T ⊂ ℙ 4 be a non-singular threefold of degree at least four. Then we show
that the number of points in T(ℚ), with height at most B, is o(B 3) or B → ∞.
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Browning TD. A note on the distribution of rational points on threefolds. Quarterly
Journal of Mathematics. 2003;54(1):33-39. doi:10.1093/qjmath/54.1.33
apa: Browning, T. D. (2003). A note on the distribution of rational points on threefolds.
Quarterly Journal of Mathematics. Unknown. https://doi.org/10.1093/qjmath/54.1.33
chicago: Browning, Timothy D. “A Note on the Distribution of Rational Points on
Threefolds.” Quarterly Journal of Mathematics. Unknown, 2003. https://doi.org/10.1093/qjmath/54.1.33.
ieee: T. D. Browning, “A note on the distribution of rational points on threefolds,”
Quarterly Journal of Mathematics, vol. 54, no. 1. Unknown, pp. 33–39, 2003.
ista: Browning TD. 2003. A note on the distribution of rational points on threefolds.
Quarterly Journal of Mathematics. 54(1), 33–39.
mla: Browning, Timothy D. “A Note on the Distribution of Rational Points on Threefolds.”
Quarterly Journal of Mathematics, vol. 54, no. 1, Unknown, 2003, pp. 33–39,
doi:10.1093/qjmath/54.1.33.
short: T.D. Browning, Quarterly Journal of Mathematics 54 (2003) 33–39.
date_created: 2018-12-11T11:45:12Z
date_published: 2003-03-01T00:00:00Z
date_updated: 2021-01-12T06:55:02Z
day: '01'
doi: 10.1093/qjmath/54.1.33
extern: 1
intvolume: ' 54'
issue: '1'
month: '03'
page: 33 - 39
publication: Quarterly Journal of Mathematics
publication_status: published
publisher: Unknown
publist_id: '7706'
quality_controlled: 0
status: public
title: A note on the distribution of rational points on threefolds
type: journal_article
volume: 54
year: '2003'
...
---
_id: '207'
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Browning TD. Sums of four biquadrates. Mathematical Proceedings of the Cambridge
Philosophical Society. 2003;134(3):385-395. doi:10.1017/S0305004102006382
apa: Browning, T. D. (2003). Sums of four biquadrates. Mathematical Proceedings
of the Cambridge Philosophical Society. Cambridge University Press. https://doi.org/10.1017/S0305004102006382
chicago: Browning, Timothy D. “Sums of Four Biquadrates.” Mathematical Proceedings
of the Cambridge Philosophical Society. Cambridge University Press, 2003.
https://doi.org/10.1017/S0305004102006382.
ieee: T. D. Browning, “Sums of four biquadrates,” Mathematical Proceedings of
the Cambridge Philosophical Society, vol. 134, no. 3. Cambridge University
Press, pp. 385–395, 2003.
ista: Browning TD. 2003. Sums of four biquadrates. Mathematical Proceedings of the
Cambridge Philosophical Society. 134(3), 385–395.
mla: Browning, Timothy D. “Sums of Four Biquadrates.” Mathematical Proceedings
of the Cambridge Philosophical Society, vol. 134, no. 3, Cambridge University
Press, 2003, pp. 385–95, doi:10.1017/S0305004102006382.
short: T.D. Browning, Mathematical Proceedings of the Cambridge Philosophical Society
134 (2003) 385–395.
date_created: 2018-12-11T11:45:12Z
date_published: 2003-05-01T00:00:00Z
date_updated: 2021-01-12T06:55:07Z
day: '01'
doi: 10.1017/S0305004102006382
extern: '1'
intvolume: ' 134'
issue: '3'
language:
- iso: eng
month: '05'
oa_version: None
page: 385 - 395
publication: Mathematical Proceedings of the Cambridge Philosophical Society
publication_status: published
publisher: Cambridge University Press
publist_id: '7704'
quality_controlled: '1'
status: public
title: Sums of four biquadrates
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 134
year: '2003'
...