---
OA_place: repository
OA_type: green
_id: '18031'
abstract:
- lang: eng
text: 'Molecular-scale components are expected to be central to the realization
of nanoscale electronic devices1,2,3. Although molecular-scale switching has been
reported in atomic quantum point contacts4,5,6, single-molecule junctions provide
the additional flexibility of tuning the on/off conductance states through molecular
design. To date, switching in single-molecule junctions has been attributed to
changes in the conformation or charge state of the molecule7,8,9,10,11,12. Here,
we demonstrate reversible binary switching in a single-molecule junction by mechanical
control of the metal–molecule contact geometry. We show that 4,4''-bipyridine–gold
single-molecule junctions can be reversibly switched between two conductance states
through repeated junction elongation and compression. Using first-principles calculations,
we attribute the different measured conductance states to distinct contact geometries
at the flexible but stable nitrogen–gold bond: conductance is low when the N–Au
bond is perpendicular to the conducting π-system, and high otherwise. This switching
mechanism, inherent to the pyridine–gold link, could form the basis of a new class
of mechanically activated single-molecule switches.'
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Su Ying
full_name: Quek, Su Ying
last_name: Quek
- first_name: Maria
full_name: Kamenetska, Maria
last_name: Kamenetska
- first_name: Michael L.
full_name: Steigerwald, Michael L.
last_name: Steigerwald
- first_name: Hyoung Joon
full_name: Choi, Hyoung Joon
last_name: Choi
- first_name: Steven G.
full_name: Louie, Steven G.
last_name: Louie
- first_name: Mark S.
full_name: Hybertsen, Mark S.
last_name: Hybertsen
- first_name: J. B.
full_name: Neaton, J. B.
last_name: Neaton
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
citation:
ama: Quek SY, Kamenetska M, Steigerwald ML, et al. Mechanically controlled binary
conductance switching of a single-molecule junction. Nature Nanotechnology.
2009;4(4):230-234. doi:10.1038/nnano.2009.10
apa: Quek, S. Y., Kamenetska, M., Steigerwald, M. L., Choi, H. J., Louie, S. G.,
Hybertsen, M. S., … Venkataraman, L. (2009). Mechanically controlled binary conductance
switching of a single-molecule junction. Nature Nanotechnology. Springer
Nature. https://doi.org/10.1038/nnano.2009.10
chicago: Quek, Su Ying, Maria Kamenetska, Michael L. Steigerwald, Hyoung Joon Choi,
Steven G. Louie, Mark S. Hybertsen, J. B. Neaton, and Latha Venkataraman. “Mechanically
Controlled Binary Conductance Switching of a Single-Molecule Junction.” Nature
Nanotechnology. Springer Nature, 2009. https://doi.org/10.1038/nnano.2009.10.
ieee: S. Y. Quek et al., “Mechanically controlled binary conductance switching
of a single-molecule junction,” Nature Nanotechnology, vol. 4, no. 4. Springer
Nature, pp. 230–234, 2009.
ista: Quek SY, Kamenetska M, Steigerwald ML, Choi HJ, Louie SG, Hybertsen MS, Neaton
JB, Venkataraman L. 2009. Mechanically controlled binary conductance switching
of a single-molecule junction. Nature Nanotechnology. 4(4), 230–234.
mla: Quek, Su Ying, et al. “Mechanically Controlled Binary Conductance Switching
of a Single-Molecule Junction.” Nature Nanotechnology, vol. 4, no. 4, Springer
Nature, 2009, pp. 230–34, doi:10.1038/nnano.2009.10.
short: S.Y. Quek, M. Kamenetska, M.L. Steigerwald, H.J. Choi, S.G. Louie, M.S. Hybertsen,
J.B. Neaton, L. Venkataraman, Nature Nanotechnology 4 (2009) 230–234.
date_created: 2024-09-09T13:53:36Z
date_published: 2009-04-01T00:00:00Z
date_updated: 2025-01-03T10:42:35Z
day: '01'
doi: 10.1038/nnano.2009.10
extern: '1'
external_id:
arxiv:
- '0901.1139'
pmid:
- '19350032'
intvolume: ' 4'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0901.1139
month: '04'
oa: 1
oa_version: Preprint
page: 230-234
pmid: 1
publication: Nature Nanotechnology
publication_identifier:
eissn:
- 1748-3395
issn:
- 1748-3387
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanically controlled binary conductance switching of a single-molecule junction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2009'
...
---
_id: '1825'
abstract:
- lang: eng
text: 'Many membrane channels and receptors exhibit adaptive, or desensitized, response
to a strong sustained input stimulus. A key mechanism that underlies this response
is the slow, activity-dependent removal of responding molecules to a pool which
is unavailable to respond immediately to the input. This mechanism is implemented
in different ways in various biological systems and has traditionally been studied
separately for each. Here we highlight the common aspects of this principle, shared
by many biological systems, and suggest a unifying theoretical framework. We study
theoretically a class of models which describes the general mechanism and allows
us to distinguish its universal from system-specific features. We show that under
general conditions, regardless of the details of kinetics, molecule availability
encodes an averaging over past activity and feeds back multiplicatively on the
system output. The kinetics of recovery from unavailability determines the effective
memory kernel inside the feedback branch, giving rise to a variety of system-specific
forms of adaptive response—precise or input-dependent, exponential or power-law—as
special cases of the same model. '
author:
- first_name: Tamar
full_name: Tamar Friedlander
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Naama
full_name: Brenner, Naama
last_name: Brenner
citation:
ama: Friedlander T, Brenner N. Adaptive response by state-dependent inactivation.
PNAS. 2009;106(52):22558-22563. doi:10.1073/pnas.0902146106
apa: Friedlander, T., & Brenner, N. (2009). Adaptive response by state-dependent
inactivation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0902146106
chicago: Friedlander, Tamar, and Naama Brenner. “Adaptive Response by State-Dependent
Inactivation.” PNAS. National Academy of Sciences, 2009. https://doi.org/10.1073/pnas.0902146106 .
ieee: T. Friedlander and N. Brenner, “Adaptive response by state-dependent inactivation,”
PNAS, vol. 106, no. 52. National Academy of Sciences, pp. 22558–22563,
2009.
ista: Friedlander T, Brenner N. 2009. Adaptive response by state-dependent inactivation.
PNAS. 106(52), 22558–22563.
mla: Friedlander, Tamar, and Naama Brenner. “Adaptive Response by State-Dependent
Inactivation.” PNAS, vol. 106, no. 52, National Academy of Sciences, 2009,
pp. 22558–63, doi:10.1073/pnas.0902146106
.
short: T. Friedlander, N. Brenner, PNAS 106 (2009) 22558–22563.
date_created: 2018-12-11T11:54:13Z
date_published: 2009-12-01T00:00:00Z
date_updated: 2021-01-12T06:53:26Z
day: '01'
doi: '10.1073/pnas.0902146106 '
extern: 1
intvolume: ' 106'
issue: '52'
main_file_link:
- open_access: '1'
url: http://www.pnas.org/content/106/52/22558.full.pdf
month: '12'
oa: 1
page: 22558 - 22563
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5281'
quality_controlled: 0
status: public
title: Adaptive response by state-dependent inactivation
type: journal_article
volume: 106
year: '2009'
...
---
OA_type: closed access
_id: '18356'
abstract:
- lang: eng
text: Similarity is one of the most important abstract concepts in human perception
of the world. In computer vision, numerous applications deal with comparing objects
observed in a scene with some a priori known patterns. Often, it happens that
while two objects are not similar, they have large similar parts, that is, they
are partially similar. Here, we present a novel approach to quantify partial similarity
using the notion of Pareto optimality. We exemplify our approach on the problems
of recognizing non-rigid geometric objects, images, and analyzing text sequences.
article_processing_charge: No
article_type: original
author:
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Michael M.
full_name: Bronstein, Michael M.
last_name: Bronstein
- first_name: Alfred M.
full_name: Bruckstein, Alfred M.
last_name: Bruckstein
- first_name: Ron
full_name: Kimmel, Ron
last_name: Kimmel
citation:
ama: Bronstein AM, Bronstein MM, Bruckstein AM, Kimmel R. Partial similarity of
objects, or how to compare a centaur to a horse. International Journal of Computer
Vision. 2009;84(2):163-183. doi:10.1007/s11263-008-0147-3
apa: Bronstein, A. M., Bronstein, M. M., Bruckstein, A. M., & Kimmel, R. (2009).
Partial similarity of objects, or how to compare a centaur to a horse. International
Journal of Computer Vision. Springer Nature. https://doi.org/10.1007/s11263-008-0147-3
chicago: Bronstein, Alex M., Michael M. Bronstein, Alfred M. Bruckstein, and Ron
Kimmel. “Partial Similarity of Objects, or How to Compare a Centaur to a Horse.”
International Journal of Computer Vision. Springer Nature, 2009. https://doi.org/10.1007/s11263-008-0147-3.
ieee: A. M. Bronstein, M. M. Bronstein, A. M. Bruckstein, and R. Kimmel, “Partial
similarity of objects, or how to compare a centaur to a horse,” International
Journal of Computer Vision, vol. 84, no. 2. Springer Nature, pp. 163–183,
2009.
ista: Bronstein AM, Bronstein MM, Bruckstein AM, Kimmel R. 2009. Partial similarity
of objects, or how to compare a centaur to a horse. International Journal of Computer
Vision. 84(2), 163–183.
mla: Bronstein, Alex M., et al. “Partial Similarity of Objects, or How to Compare
a Centaur to a Horse.” International Journal of Computer Vision, vol. 84,
no. 2, Springer Nature, 2009, pp. 163–83, doi:10.1007/s11263-008-0147-3.
short: A.M. Bronstein, M.M. Bronstein, A.M. Bruckstein, R. Kimmel, International
Journal of Computer Vision 84 (2009) 163–183.
date_created: 2024-10-15T11:20:54Z
date_published: 2009-08-01T00:00:00Z
date_updated: 2024-10-22T07:55:59Z
day: '01'
doi: 10.1007/s11263-008-0147-3
extern: '1'
intvolume: ' 84'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
page: 163-183
publication: International Journal of Computer Vision
publication_identifier:
eissn:
- 1573-1405
issn:
- 0920-5691
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Partial similarity of objects, or how to compare a centaur to a horse
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 84
year: '2009'
...
---
OA_type: closed access
_id: '18357'
abstract:
- lang: eng
text: 'This paper explores the problem of similarity criteria between nonrigid shapes.
Broadly speaking, such criteria are divided into intrinsic and extrinsic, the
first referring to the metric structure of the object and the latter to how it
is laid out in the Euclidean space. Both criteria have their advantages and disadvantages:
extrinsic similarity is sensitive to nonrigid deformations, while intrinsic similarity
is sensitive to topological noise. In this paper, we approach the problem from
the perspective of metric geometry. We show that by unifying the extrinsic and
intrinsic similarity criteria, it is possible to obtain a stronger topology-invariant
similarity, suitable for comparing deformed shapes with different topology. We
construct this new joint criterion as a tradeoff between the extrinsic and intrinsic
similarity and use it as a set-valued distance. Numerical results demonstrate
the efficiency of our approach in cases where using either extrinsic or intrinsic
criteria alone would fail.'
article_processing_charge: No
article_type: original
author:
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Michael M.
full_name: Bronstein, Michael M.
last_name: Bronstein
- first_name: Ron
full_name: Kimmel, Ron
last_name: Kimmel
citation:
ama: Bronstein AM, Bronstein MM, Kimmel R. Topology-invariant similarity of nonrigid
shapes. International Journal of Computer Vision. 2009;81(3):281-301. doi:10.1007/s11263-008-0172-2
apa: Bronstein, A. M., Bronstein, M. M., & Kimmel, R. (2009). Topology-invariant
similarity of nonrigid shapes. International Journal of Computer Vision.
Springer Nature. https://doi.org/10.1007/s11263-008-0172-2
chicago: Bronstein, Alex M., Michael M. Bronstein, and Ron Kimmel. “Topology-Invariant
Similarity of Nonrigid Shapes.” International Journal of Computer Vision.
Springer Nature, 2009. https://doi.org/10.1007/s11263-008-0172-2.
ieee: A. M. Bronstein, M. M. Bronstein, and R. Kimmel, “Topology-invariant similarity
of nonrigid shapes,” International Journal of Computer Vision, vol. 81,
no. 3. Springer Nature, pp. 281–301, 2009.
ista: Bronstein AM, Bronstein MM, Kimmel R. 2009. Topology-invariant similarity
of nonrigid shapes. International Journal of Computer Vision. 81(3), 281–301.
mla: Bronstein, Alex M., et al. “Topology-Invariant Similarity of Nonrigid Shapes.”
International Journal of Computer Vision, vol. 81, no. 3, Springer Nature,
2009, pp. 281–301, doi:10.1007/s11263-008-0172-2.
short: A.M. Bronstein, M.M. Bronstein, R. Kimmel, International Journal of Computer
Vision 81 (2009) 281–301.
date_created: 2024-10-15T11:20:54Z
date_published: 2009-03-01T00:00:00Z
date_updated: 2024-10-22T07:27:15Z
day: '01'
doi: 10.1007/s11263-008-0172-2
extern: '1'
intvolume: ' 81'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 281-301
publication: International Journal of Computer Vision
publication_identifier:
eissn:
- 1573-1405
issn:
- 0920-5691
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Topology-invariant similarity of nonrigid shapes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 81
year: '2009'
...
---
OA_type: closed access
_id: '18391'
abstract:
- lang: eng
text: We introduce a design of a coded light-based 3D color video camera optimized
for build up cost as well as accuracy in depth reconstruction and acquisition
speed. The components of the system include a monochromatic camera and an off-the-shelf
LED projector synchronized by a miniature circuit. The projected patterns are
captured and processed at a rate of 200 fps and allow for real-time reconstruction
of both depth and color at video rates. The reconstruction and display are performed
at around 30 depth profiles and color texture per second using a graphics processing
unit (GPU).
article_processing_charge: No
author:
- first_name: O.
full_name: Rubinstein, O.
last_name: Rubinstein
- first_name: Y.
full_name: Honen, Y.
last_name: Honen
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: M. M.
full_name: Bronstein, M. M.
last_name: Bronstein
- first_name: R.
full_name: Kimmel, R.
last_name: Kimmel
citation:
ama: 'Rubinstein O, Honen Y, Bronstein AM, Bronstein MM, Kimmel R. 3D-color video
camera. In: 12th International Conference on Computer Vision Workshops.
IEEE; 2009. doi:10.1109/iccvw.2009.5457433'
apa: 'Rubinstein, O., Honen, Y., Bronstein, A. M., Bronstein, M. M., & Kimmel,
R. (2009). 3D-color video camera. In 12th International Conference on Computer
Vision Workshops. Kyoto, Japan: IEEE. https://doi.org/10.1109/iccvw.2009.5457433'
chicago: Rubinstein, O., Y. Honen, Alex M. Bronstein, M. M. Bronstein, and R. Kimmel.
“3D-Color Video Camera.” In 12th International Conference on Computer Vision
Workshops. IEEE, 2009. https://doi.org/10.1109/iccvw.2009.5457433.
ieee: O. Rubinstein, Y. Honen, A. M. Bronstein, M. M. Bronstein, and R. Kimmel,
“3D-color video camera,” in 12th International Conference on Computer Vision
Workshops, Kyoto, Japan, 2009.
ista: 'Rubinstein O, Honen Y, Bronstein AM, Bronstein MM, Kimmel R. 2009. 3D-color
video camera. 12th International Conference on Computer Vision Workshops. ICCV:
International Conference on Computer Vision.'
mla: Rubinstein, O., et al. “3D-Color Video Camera.” 12th International Conference
on Computer Vision Workshops, IEEE, 2009, doi:10.1109/iccvw.2009.5457433.
short: O. Rubinstein, Y. Honen, A.M. Bronstein, M.M. Bronstein, R. Kimmel, in:,
12th International Conference on Computer Vision Workshops, IEEE, 2009.
conference:
end_date: 2009-10-04
location: Kyoto, Japan
name: 'ICCV: International Conference on Computer Vision'
start_date: 2009-09-27
date_created: 2024-10-15T11:20:54Z
date_published: 2009-10-15T00:00:00Z
date_updated: 2024-11-19T13:00:24Z
day: '15'
doi: 10.1109/iccvw.2009.5457433
extern: '1'
language:
- iso: eng
month: '10'
oa_version: None
publication: 12th International Conference on Computer Vision Workshops
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 3D-color video camera
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2009'
...
---
_id: '18392'
abstract:
- lang: eng
text: Feature-based methods have recently gained popularity in computer vision and
pattern recognition communities, in applications such as object recognition and
image retrieval. In this paper, we explore analogous approaches in the 3D world
applied to the problem of non-rigid shape search and retrieval in large databases.
article_processing_charge: No
author:
- first_name: Maks
full_name: Ovsjanikov, Maks
last_name: Ovsjanikov
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Michael M.
full_name: Bronstein, Michael M.
last_name: Bronstein
- first_name: Leonidas J.
full_name: Guibas, Leonidas J.
last_name: Guibas
citation:
ama: 'Ovsjanikov M, Bronstein AM, Bronstein MM, Guibas LJ. Shape Google: A computer
vision approach to isometry invariant shape retrieval. In: 12th International
Conference on Computer Vision Workshops. IEEE; 2009. doi:10.1109/iccvw.2009.5457682'
apa: 'Ovsjanikov, M., Bronstein, A. M., Bronstein, M. M., & Guibas, L. J. (2009).
Shape Google: A computer vision approach to isometry invariant shape retrieval.
In 12th International Conference on Computer Vision Workshops. Kyoto, Japan:
IEEE. https://doi.org/10.1109/iccvw.2009.5457682'
chicago: 'Ovsjanikov, Maks, Alex M. Bronstein, Michael M. Bronstein, and Leonidas
J. Guibas. “Shape Google: A Computer Vision Approach to Isometry Invariant Shape
Retrieval.” In 12th International Conference on Computer Vision Workshops.
IEEE, 2009. https://doi.org/10.1109/iccvw.2009.5457682.'
ieee: 'M. Ovsjanikov, A. M. Bronstein, M. M. Bronstein, and L. J. Guibas, “Shape
Google: A computer vision approach to isometry invariant shape retrieval,” in
12th International Conference on Computer Vision Workshops, Kyoto, Japan,
2009.'
ista: 'Ovsjanikov M, Bronstein AM, Bronstein MM, Guibas LJ. 2009. Shape Google:
A computer vision approach to isometry invariant shape retrieval. 12th International
Conference on Computer Vision Workshops. ICCV: International Conference on Computer
Vision.'
mla: 'Ovsjanikov, Maks, et al. “Shape Google: A Computer Vision Approach to Isometry
Invariant Shape Retrieval.” 12th International Conference on Computer Vision
Workshops, IEEE, 2009, doi:10.1109/iccvw.2009.5457682.'
short: M. Ovsjanikov, A.M. Bronstein, M.M. Bronstein, L.J. Guibas, in:, 12th International
Conference on Computer Vision Workshops, IEEE, 2009.
conference:
end_date: 2009-10-04
location: Kyoto, Japan
name: 'ICCV: International Conference on Computer Vision'
start_date: 2009-10-27
date_created: 2024-10-15T11:20:54Z
date_published: 2009-11-01T00:00:00Z
date_updated: 2024-11-18T10:38:45Z
day: '01'
doi: 10.1109/iccvw.2009.5457682
extern: '1'
language:
- iso: eng
month: '11'
oa_version: None
publication: 12th International Conference on Computer Vision Workshops
publication_identifier:
isbn:
- '9781424444427'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Shape Google: A computer vision approach to isometry invariant shape retrieval'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2009'
...
---
_id: '18393'
abstract:
- lang: eng
text: Shape-from-X is a generic type of inverse problems in computer vision, in
which a shape is reconstructed from some measurements. A specially challenging
setting of this problem is the case in which the reconstructed shapes are non-rigid.
In this paper, we propose a framework for intrinsic regularization of such problems.
The assumption is that we have the geometric structure of a shape which is intrinsically
(up to bending) similar to the one we would like to reconstruct. For that goal,
we formulate a variation with respect to vertex coordinates of a triangulated
mesh approximating the continuous shape. The numerical core of the proposed method
is based on differentiating the fast marching update step for geodesic distance
computation.
article_processing_charge: No
author:
- first_name: Yohai S.
full_name: Devir, Yohai S.
last_name: Devir
- first_name: Guy
full_name: Rosman, Guy
last_name: Rosman
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Michael M.
full_name: Bronstein, Michael M.
last_name: Bronstein
- first_name: Ron
full_name: Kimmel, Ron
last_name: Kimmel
citation:
ama: 'Devir YS, Rosman G, Bronstein AM, Bronstein MM, Kimmel R. On reconstruction
of non-rigid shapes with intrinsic regularization. In: 12th International Conference
on Computer Vision Workshops. IEEE; 2009. doi:10.1109/iccvw.2009.5457688'
apa: 'Devir, Y. S., Rosman, G., Bronstein, A. M., Bronstein, M. M., & Kimmel,
R. (2009). On reconstruction of non-rigid shapes with intrinsic regularization.
In 12th International Conference on Computer Vision Workshops. Kyoto, Japan:
IEEE. https://doi.org/10.1109/iccvw.2009.5457688'
chicago: Devir, Yohai S., Guy Rosman, Alex M. Bronstein, Michael M. Bronstein, and
Ron Kimmel. “On Reconstruction of Non-Rigid Shapes with Intrinsic Regularization.”
In 12th International Conference on Computer Vision Workshops. IEEE, 2009.
https://doi.org/10.1109/iccvw.2009.5457688.
ieee: Y. S. Devir, G. Rosman, A. M. Bronstein, M. M. Bronstein, and R. Kimmel, “On
reconstruction of non-rigid shapes with intrinsic regularization,” in 12th
International Conference on Computer Vision Workshops, Kyoto, Japan, 2009.
ista: 'Devir YS, Rosman G, Bronstein AM, Bronstein MM, Kimmel R. 2009. On reconstruction
of non-rigid shapes with intrinsic regularization. 12th International Conference
on Computer Vision Workshops. ICCV: International Conference on Computer Vision.'
mla: Devir, Yohai S., et al. “On Reconstruction of Non-Rigid Shapes with Intrinsic
Regularization.” 12th International Conference on Computer Vision Workshops,
IEEE, 2009, doi:10.1109/iccvw.2009.5457688.
short: Y.S. Devir, G. Rosman, A.M. Bronstein, M.M. Bronstein, R. Kimmel, in:, 12th
International Conference on Computer Vision Workshops, IEEE, 2009.
conference:
end_date: 2009-10-04
location: Kyoto, Japan
name: 'ICCV: International Conference on Computer Vision'
start_date: 2009-09-27
date_created: 2024-10-15T11:20:54Z
date_published: 2009-11-01T00:00:00Z
date_updated: 2024-11-18T10:29:12Z
day: '01'
doi: 10.1109/iccvw.2009.5457688
extern: '1'
language:
- iso: eng
month: '11'
oa_version: None
publication: 12th International Conference on Computer Vision Workshops
publication_identifier:
isbn:
- '9781424444427'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: On reconstruction of non-rigid shapes with intrinsic regularization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2009'
...
---
_id: '18438'
abstract:
- lang: eng
text: 'Partial matching of geometric structures is important in computer vision,
pattern recognition and shape analysis applications. The problem consists of matching
similar parts of shapes that may be dissimilar as a whole. Recently, it was proposed
to consider partial similarity as a multi-criterion optimization problem trying
to simultaneously maximize the similarity and the significance of the matching
parts. A major challenge in that framework is providing a quantitative measure
of the significance of a part of an object. Here, we define the significance of
a part of a shape by its discriminative power with respect do a given shape database
— that is, the uniqueness of the part. We define a point-wise significance density
using a statistical weighting approach similar to the term frequency-inverse document
frequency (tf-idf) weighting employed in search engines. The significance measure
of a given part is obtained by integrating over this density. Numerical experiments
show that the proposed approach produces intuitive significant parts, and demonstrate
an improvement in the performance of partial matching between shapes. '
article_processing_charge: No
author:
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Michael M.
full_name: Bronstein, Michael M.
last_name: Bronstein
- first_name: Yair
full_name: Carmon, Yair
last_name: Carmon
- first_name: Ron
full_name: Kimmel, Ron
last_name: Kimmel
citation:
ama: Bronstein AM, Bronstein MM, Carmon Y, Kimmel R. Partial similarity of shapes
using a statistical significance measure. IPSJ Transactions on Computer Vision
and Applications. 2009;1:105-114. doi:10.2197/ipsjtcva.1.105
apa: Bronstein, A. M., Bronstein, M. M., Carmon, Y., & Kimmel, R. (2009). Partial
similarity of shapes using a statistical significance measure. IPSJ Transactions
on Computer Vision and Applications. Information Processing Society of Japan.
https://doi.org/10.2197/ipsjtcva.1.105
chicago: Bronstein, Alex M., Michael M. Bronstein, Yair Carmon, and Ron Kimmel.
“Partial Similarity of Shapes Using a Statistical Significance Measure.” IPSJ
Transactions on Computer Vision and Applications. Information Processing Society
of Japan, 2009. https://doi.org/10.2197/ipsjtcva.1.105.
ieee: A. M. Bronstein, M. M. Bronstein, Y. Carmon, and R. Kimmel, “Partial similarity
of shapes using a statistical significance measure,” IPSJ Transactions on Computer
Vision and Applications, vol. 1. Information Processing Society of Japan,
pp. 105–114, 2009.
ista: Bronstein AM, Bronstein MM, Carmon Y, Kimmel R. 2009. Partial similarity of
shapes using a statistical significance measure. IPSJ Transactions on Computer
Vision and Applications. 1, 105–114.
mla: Bronstein, Alex M., et al. “Partial Similarity of Shapes Using a Statistical
Significance Measure.” IPSJ Transactions on Computer Vision and Applications,
vol. 1, Information Processing Society of Japan, 2009, pp. 105–14, doi:10.2197/ipsjtcva.1.105.
short: A.M. Bronstein, M.M. Bronstein, Y. Carmon, R. Kimmel, IPSJ Transactions on
Computer Vision and Applications 1 (2009) 105–114.
date_created: 2024-10-15T11:20:55Z
date_published: 2009-03-31T00:00:00Z
date_updated: 2024-12-18T16:01:54Z
day: '31'
doi: 10.2197/ipsjtcva.1.105
extern: '1'
intvolume: ' 1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.2197/ipsjtcva.1.105
month: '03'
oa: 1
oa_version: Published Version
page: 105-114
publication: IPSJ Transactions on Computer Vision and Applications
publication_identifier:
eissn:
- 1882-6695
publication_status: published
publisher: Information Processing Society of Japan
quality_controlled: '1'
scopus_import: '1'
status: public
title: Partial similarity of shapes using a statistical significance measure
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2009'
...
---
_id: '7751'
abstract:
- lang: eng
text: "This work demonstrates that environmental conditions experienced by individuals
can shape their development and affect the stability of genetic associations.
The implication of this observation is that the environmental response may influence
the evolution of traits in the wild. Here, we examined how the genetic architecture
of a suite of sexually dimorphic traits changed as a function of environmental
conditions in an unmanaged population of Soay sheep (Ovis aries) on the island
of Hirta, St. Kilda, northwest Scotland. We examined the stability of phenotypic,
genetic, and environmental (residual) covariance in males during the first year
of life between horn length, body weight, and parasite load in environments of
different quality. We then examined the same covariance structures across environments
within and between the adult sexes. We found significant genotype-by-environment
interactions for lamb male body weight and parasite load, leading to a change
in the genetic correlation among environments. Horn length was genetically correlated
with body weight in males but not females and the genetic correlation among traits
within and between the sexes was dependent upon the environmental conditions experienced
during adulthood. Genetic correlations were smaller in more favorable environmental
conditions, suggesting that in good environments, loci are expressed that have
sex-specific effects. The reduction in genetic correlation between the sexes may
allow independent evolutionary trajectories for each sex. This study demonstrates
that the genetic architecture of traits is not stable under temporally varying
environments and highlights the fact that evolutionary processes may depend largely
upon ecological conditions.\r\nENVIRONMENTAL heterogeneity has long been recognized
as an important factor influencing the evolution of fitness-related traits in
the wild (Roff 2002). The evolution of a trait depends upon the selection upon
it, underlying genetic variation, and to a large degree the genetic relationships
with other traits (Lynch and Walsh 1998). There is evidence that selection can
vary considerably from year to year (Price et al. 1984; Robinson et al. 2008)
and genetic variability in quantitative traits can change in response to environmental
conditions (Hoffmann and Merilä 1999; Charmantier and Garant 2005). However, we
know surprisingly little about the influence of environmental conditions on genetic
correlations between traits in wild populations. Laboratory evidence suggests
that the environment may influence genetic relationships between traits (Sgrò
and Hoffmann 2004), but estimates obtained in a controlled or in an arbitrary
range of conditions show a lack of concordance with those obtained in wild habitats
(Conner et al. 2003). As a result, laboratory and environment-specific estimates
of genetic correlations can make predictions for a trait's evolution, but these
are valid only for the environment in which they were measured. Therefore, at
present, it is difficult to generalize about the evolution of a trait that is
expressed in populations that experience variable environmental conditions (Steppan
et al. 2002).\r\nThe influence of changing environmental conditions on the G matrix
(the matrix of additive genetic variance and covariances corresponding to a set
of traits) has been the focus of theoretical quantitative genetic studies (e.g.,
Jones et al. 2003). There is evidence of genotype-by-environment interaction for
many traits expressed in wild populations (Charmantier and Garant 2005) and thus
we may also expect that associations between traits may depend upon the environmental
conditions encountered by an individual. Genetic correlations among traits may
arise from pleiotropy, where a given locus affects more than one trait (Cheverud
1988; Lynch and Walsh 1998), which may limit the potential for those traits to
evolve independently. There has recently been much interest in assessing genetic
correlations between the sexes (Rice and Chippindale 2001; Foerster et al. 2007;
Poissant et al. 2008), but all of these predictions have also been made in average
environmental conditions. For sexually dimorphic traits, expectations of between-sex
genetic correlations are unclear (Lande 1980; Badyaev 2002). We might expect that
the genetic determination of a trait and the patterns of genetic covariance between
traits may differ both within and between the sexes, producing the differences
in trait growth that are commonly observed (Lande 1980; Badyaev 2002; Roff 2002),
but so far evidence suggests that genetic expression in both sexes is influenced
by the same developmental pathway (Roff 2002; Jensen et al. 2003; Parker and Garant
2005). However, to our knowledge, no study has yet determined whether genetic
correlations, both within and between the sexes, vary across gradients of the
environmental conditions encountered by individuals in the wild (Garant et al.
2008).\r\nThis study aims to assess the stability of phenotypic, genetic, and
environmental (residual) associations between traits, within and between the sexes,
across a range of environmental conditions experienced by a wild population. We
focus on the traits of horn length, body weight, and parasite load in a feral
population of Soay sheep (Ovis aries) from the island of Hirta, St. Kilda, United
Kingdom. Weather conditions, population density, and consequently resource availability
fluctuate from year to year, providing substantial differences between individuals
in the environments they experience and thus their survival rates (Clutton-Brock
and Pemberton 2004). These varying conditions, combined with a large pedigree
and extensive repeated morphological measures, provide an excellent opportunity
to assess the potential effects of environmental heterogeneity on genetic architecture
of traits. Previous studies on this population have shown additive genetic variance
for many morphological traits (Milner et al. 2000; Coltman et al. 2001; Wilson
et al. 2005), genetic correlations between traits (Coltman et al. 2001), and genotype-by-environment
interactions for birth weight (Wilson et al. 2006). Here we apply a random regression
animal model approach to assess the extent to which quantitative genetic parameters
of a range of morphological traits measured during life vary as a function of
environmental conditions. We then extend this methodology to the multivariate
case, testing whether the phenotypic covariance structure, and the underlying
G matrix, depends on the environmental conditions experienced. Since the traits
considered here are known to be sexually dimorphic and there are differences in
trait growth and survival across ages, we look at sex-specific traits in lambs
and then across all ages."
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Alastair J.
full_name: Wilson, Alastair J.
last_name: Wilson
- first_name: Jill G.
full_name: Pilkington, Jill G.
last_name: Pilkington
- first_name: Tim H.
full_name: Clutton-Brock, Tim H.
last_name: Clutton-Brock
- first_name: Josephine M.
full_name: Pemberton, Josephine M.
last_name: Pemberton
- first_name: Loeske E. B.
full_name: Kruuk, Loeske E. B.
last_name: Kruuk
citation:
ama: Robinson MR, Wilson AJ, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk
LEB. The impact of environmental heterogeneity on genetic architecture in a wild
population of soay sheep. Genetics. 2009;181(4):1639-1648. doi:10.1534/genetics.108.086801
apa: Robinson, M. R., Wilson, A. J., Pilkington, J. G., Clutton-Brock, T. H., Pemberton,
J. M., & Kruuk, L. E. B. (2009). The impact of environmental heterogeneity
on genetic architecture in a wild population of soay sheep. Genetics. Genetics
Society of America. https://doi.org/10.1534/genetics.108.086801
chicago: Robinson, Matthew Richard, Alastair J. Wilson, Jill G. Pilkington, Tim
H. Clutton-Brock, Josephine M. Pemberton, and Loeske E. B. Kruuk. “The Impact
of Environmental Heterogeneity on Genetic Architecture in a Wild Population of
Soay Sheep.” Genetics. Genetics Society of America, 2009. https://doi.org/10.1534/genetics.108.086801.
ieee: M. R. Robinson, A. J. Wilson, J. G. Pilkington, T. H. Clutton-Brock, J. M.
Pemberton, and L. E. B. Kruuk, “The impact of environmental heterogeneity on genetic
architecture in a wild population of soay sheep,” Genetics, vol. 181, no.
4. Genetics Society of America, pp. 1639–1648, 2009.
ista: Robinson MR, Wilson AJ, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk
LEB. 2009. The impact of environmental heterogeneity on genetic architecture in
a wild population of soay sheep. Genetics. 181(4), 1639–1648.
mla: Robinson, Matthew Richard, et al. “The Impact of Environmental Heterogeneity
on Genetic Architecture in a Wild Population of Soay Sheep.” Genetics,
vol. 181, no. 4, Genetics Society of America, 2009, pp. 1639–48, doi:10.1534/genetics.108.086801.
short: M.R. Robinson, A.J. Wilson, J.G. Pilkington, T.H. Clutton-Brock, J.M. Pemberton,
L.E.B. Kruuk, Genetics 181 (2009) 1639–1648.
date_created: 2020-04-30T11:01:57Z
date_published: 2009-04-01T00:00:00Z
date_updated: 2021-01-12T08:15:17Z
day: '01'
doi: 10.1534/genetics.108.086801
extern: '1'
intvolume: ' 181'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 1639-1648
publication: Genetics
publication_identifier:
issn:
- 0016-6731
- 1943-2631
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
status: public
title: The impact of environmental heterogeneity on genetic architecture in a wild
population of soay sheep
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 181
year: '2009'
...
---
_id: '8026'
abstract:
- lang: eng
text: Recent theoretical work has provided a basic understanding of signal propagation
in networks of spiking neurons, but mechanisms for gating and controlling these
signals have not been investigated previously. Here we introduce an idea for the
gating of multiple signals in cortical networks that combines principles of signal
propagation with aspects of balanced networks. Specifically, we studied networks
in which incoming excitatory signals are normally cancelled by locally evoked
inhibition, leaving the targeted layer unresponsive. Transmission can be gated
'on' by modulating excitatory and inhibitory gains to upset this detailed balance.
We illustrate gating through detailed balance in large networks of integrate-and-fire
neurons. We show successful gating of multiple signals and study failure modes
that produce effects reminiscent of clinically observed pathologies. Provided
that the individual signals are detectable, detailed balance has a large capacity
for gating multiple signals.
article_processing_charge: No
article_type: original
author:
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: L F
full_name: Abbott, L F
last_name: Abbott
citation:
ama: Vogels TP, Abbott LF. Gating multiple signals through detailed balance of excitation
and inhibition in spiking networks. Nature Neuroscience. 2009;12(4):483-491.
doi:10.1038/nn.2276
apa: Vogels, T. P., & Abbott, L. F. (2009). Gating multiple signals through
detailed balance of excitation and inhibition in spiking networks. Nature Neuroscience.
Springer Nature. https://doi.org/10.1038/nn.2276
chicago: Vogels, Tim P, and L F Abbott. “Gating Multiple Signals through Detailed
Balance of Excitation and Inhibition in Spiking Networks.” Nature Neuroscience.
Springer Nature, 2009. https://doi.org/10.1038/nn.2276.
ieee: T. P. Vogels and L. F. Abbott, “Gating multiple signals through detailed balance
of excitation and inhibition in spiking networks,” Nature Neuroscience,
vol. 12, no. 4. Springer Nature, pp. 483–491, 2009.
ista: Vogels TP, Abbott LF. 2009. Gating multiple signals through detailed balance
of excitation and inhibition in spiking networks. Nature Neuroscience. 12(4),
483–491.
mla: Vogels, Tim P., and L. F. Abbott. “Gating Multiple Signals through Detailed
Balance of Excitation and Inhibition in Spiking Networks.” Nature Neuroscience,
vol. 12, no. 4, Springer Nature, 2009, pp. 483–91, doi:10.1038/nn.2276.
short: T.P. Vogels, L.F. Abbott, Nature Neuroscience 12 (2009) 483–491.
date_created: 2020-06-25T13:10:55Z
date_published: 2009-04-01T00:00:00Z
date_updated: 2021-01-12T08:16:36Z
day: '01'
doi: 10.1038/nn.2276
extern: '1'
external_id:
pmid:
- '19305402'
intvolume: ' 12'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2693069/
month: '04'
oa: 1
oa_version: Submitted Version
page: 483-491
pmid: 1
publication: Nature Neuroscience
publication_identifier:
issn:
- 1097-6256
- 1546-1726
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Gating multiple signals through detailed balance of excitation and inhibition
in spiking networks
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 12
year: '2009'
...
---
_id: '8474'
abstract:
- lang: eng
text: Hydrogen bonds are ubiquitous interactions in proteins, and are important
for their folding and functionality. Scalar coupling constants across hydrogen
bonds in the protein backbone, some as small as 0.5 Hz, can be directly measured
in the solid state by NMR spectroscopy (see figure). The nuclei on both sides
of the hydrogen bond can be identified and the size of the coupling constant can
be measured accurately.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Matthias
full_name: Huber, Matthias
last_name: Huber
- first_name: René
full_name: Verel, René
last_name: Verel
- first_name: Matthias
full_name: Ernst, Matthias
last_name: Ernst
- first_name: "Beatâ\x80\NH."
full_name: "Meier, Beatâ\x80\NH."
last_name: Meier
citation:
ama: Schanda P, Huber M, Verel R, Ernst M, Meier B. Direct detection of 3hJN’ hydrogen-bond
scalar couplings in proteins by solid-state NMR spectroscopy. Angewandte Chemie
International Edition. 2009;48(49):9322-9325. doi:10.1002/anie.200904411
apa: Schanda, P., Huber, M., Verel, R., Ernst, M., & Meier, B. (2009). Direct
detection of 3hJN’ hydrogen-bond scalar couplings in proteins by solid-state NMR
spectroscopy. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.200904411
chicago: "Schanda, Paul, Matthias Huber, René Verel, Matthias Ernst, and Beatâ\x80\NH.
Meier. “Direct Detection of 3hJN’ Hydrogen-Bond Scalar Couplings in Proteins by
Solid-State NMR Spectroscopy.” Angewandte Chemie International Edition.
Wiley, 2009. https://doi.org/10.1002/anie.200904411."
ieee: P. Schanda, M. Huber, R. Verel, M. Ernst, and B. Meier, “Direct detection
of 3hJN’ hydrogen-bond scalar couplings in proteins by solid-state NMR spectroscopy,”
Angewandte Chemie International Edition, vol. 48, no. 49. Wiley, pp. 9322–9325,
2009.
ista: Schanda P, Huber M, Verel R, Ernst M, Meier B. 2009. Direct detection of 3hJN’
hydrogen-bond scalar couplings in proteins by solid-state NMR spectroscopy. Angewandte
Chemie International Edition. 48(49), 9322–9325.
mla: Schanda, Paul, et al. “Direct Detection of 3hJN’ Hydrogen-Bond Scalar Couplings
in Proteins by Solid-State NMR Spectroscopy.” Angewandte Chemie International
Edition, vol. 48, no. 49, Wiley, 2009, pp. 9322–25, doi:10.1002/anie.200904411.
short: P. Schanda, M. Huber, R. Verel, M. Ernst, B. Meier, Angewandte Chemie International
Edition 48 (2009) 9322–9325.
date_created: 2020-09-18T10:11:33Z
date_published: 2009-11-17T00:00:00Z
date_updated: 2021-01-12T08:19:31Z
day: '17'
doi: 10.1002/anie.200904411
extern: '1'
intvolume: ' 48'
issue: '49'
keyword:
- General Chemistry
- Catalysis
language:
- iso: eng
month: '11'
oa_version: None
page: 9322-9325
publication: Angewandte Chemie International Edition
publication_identifier:
issn:
- 1433-7851
- 1521-3773
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Direct detection of 3hJN' hydrogen-bond scalar couplings in proteins by solid-state
NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2009'
...
---
_id: '8475'
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Schanda P. Fast-pulsing longitudinal relaxation optimized techniques: Enriching
the toolbox of fast biomolecular NMR spectroscopy. Progress in Nuclear Magnetic
Resonance Spectroscopy. 2009;55(3):238-265. doi:10.1016/j.pnmrs.2009.05.002'
apa: 'Schanda, P. (2009). Fast-pulsing longitudinal relaxation optimized techniques:
Enriching the toolbox of fast biomolecular NMR spectroscopy. Progress in Nuclear
Magnetic Resonance Spectroscopy. Elsevier. https://doi.org/10.1016/j.pnmrs.2009.05.002'
chicago: 'Schanda, Paul. “Fast-Pulsing Longitudinal Relaxation Optimized Techniques:
Enriching the Toolbox of Fast Biomolecular NMR Spectroscopy.” Progress in Nuclear
Magnetic Resonance Spectroscopy. Elsevier, 2009. https://doi.org/10.1016/j.pnmrs.2009.05.002.'
ieee: 'P. Schanda, “Fast-pulsing longitudinal relaxation optimized techniques: Enriching
the toolbox of fast biomolecular NMR spectroscopy,” Progress in Nuclear Magnetic
Resonance Spectroscopy, vol. 55, no. 3. Elsevier, pp. 238–265, 2009.'
ista: 'Schanda P. 2009. Fast-pulsing longitudinal relaxation optimized techniques:
Enriching the toolbox of fast biomolecular NMR spectroscopy. Progress in Nuclear
Magnetic Resonance Spectroscopy. 55(3), 238–265.'
mla: 'Schanda, Paul. “Fast-Pulsing Longitudinal Relaxation Optimized Techniques:
Enriching the Toolbox of Fast Biomolecular NMR Spectroscopy.” Progress in Nuclear
Magnetic Resonance Spectroscopy, vol. 55, no. 3, Elsevier, 2009, pp. 238–65,
doi:10.1016/j.pnmrs.2009.05.002.'
short: P. Schanda, Progress in Nuclear Magnetic Resonance Spectroscopy 55 (2009)
238–265.
date_created: 2020-09-18T10:11:42Z
date_published: 2009-10-01T00:00:00Z
date_updated: 2021-01-12T08:19:32Z
day: '01'
doi: 10.1016/j.pnmrs.2009.05.002
extern: '1'
intvolume: ' 55'
issue: '3'
language:
- iso: eng
month: '10'
oa_version: None
page: 238-265
publication: Progress in Nuclear Magnetic Resonance Spectroscopy
publication_identifier:
issn:
- 0079-6565
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Fast-pulsing longitudinal relaxation optimized techniques: Enriching the toolbox
of fast biomolecular NMR spectroscopy'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2009'
...
---
_id: '8476'
abstract:
- lang: eng
text: Atomic-resolution information on the structure and dynamics of nucleic acids
is essential for a better understanding of the mechanistic basis of many cellular
processes. NMR spectroscopy is a powerful method for studying the structure and
dynamics of nucleic acids; however, solution NMR studies are currently limited
to relatively small nucleic acids at high concentrations. Thus, technological
and methodological improvements that increase the experimental sensitivity and
spectral resolution of NMR spectroscopy are required for studies of larger nucleic
acids or protein−nucleic acid complexes. Here we introduce a series of imino-proton-detected
NMR experiments that yield an over 2-fold increase in sensitivity compared to
conventional pulse schemes. These methods can be applied to the detection of base
pair interactions, RNA−ligand titration experiments, measurement of residual dipolar
15N−1H couplings, and direct measurements of conformational transitions. These
NMR experiments employ longitudinal spin relaxation enhancement techniques that
have proven useful in protein NMR spectroscopy. The performance of these new experiments
is demonstrated for a 10 kDa TAR-TAR*GA RNA kissing complex and a 26 kDa tRNA.
article_processing_charge: No
article_type: original
author:
- first_name: Jonathan
full_name: Farjon, Jonathan
last_name: Farjon
- first_name: Jérôme
full_name: Boisbouvier, Jérôme
last_name: Boisbouvier
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Arthur
full_name: Pardi, Arthur
last_name: Pardi
- first_name: Jean-Pierre
full_name: Simorre, Jean-Pierre
last_name: Simorre
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Farjon J, Boisbouvier J, Schanda P, Pardi A, Simorre J-P, Brutscher B. Longitudinal-relaxation-enhanced
NMR experiments for the study of nucleic acids in solution. Journal of the
American Chemical Society. 2009;131(24):8571-8577. doi:10.1021/ja901633y
apa: Farjon, J., Boisbouvier, J., Schanda, P., Pardi, A., Simorre, J.-P., &
Brutscher, B. (2009). Longitudinal-relaxation-enhanced NMR experiments for the
study of nucleic acids in solution. Journal of the American Chemical Society.
American Chemical Society. https://doi.org/10.1021/ja901633y
chicago: Farjon, Jonathan, Jérôme Boisbouvier, Paul Schanda, Arthur Pardi, Jean-Pierre
Simorre, and Bernhard Brutscher. “Longitudinal-Relaxation-Enhanced NMR Experiments
for the Study of Nucleic Acids in Solution.” Journal of the American Chemical
Society. American Chemical Society, 2009. https://doi.org/10.1021/ja901633y.
ieee: J. Farjon, J. Boisbouvier, P. Schanda, A. Pardi, J.-P. Simorre, and B. Brutscher,
“Longitudinal-relaxation-enhanced NMR experiments for the study of nucleic acids
in solution,” Journal of the American Chemical Society, vol. 131, no. 24.
American Chemical Society, pp. 8571–8577, 2009.
ista: Farjon J, Boisbouvier J, Schanda P, Pardi A, Simorre J-P, Brutscher B. 2009.
Longitudinal-relaxation-enhanced NMR experiments for the study of nucleic acids
in solution. Journal of the American Chemical Society. 131(24), 8571–8577.
mla: Farjon, Jonathan, et al. “Longitudinal-Relaxation-Enhanced NMR Experiments
for the Study of Nucleic Acids in Solution.” Journal of the American Chemical
Society, vol. 131, no. 24, American Chemical Society, 2009, pp. 8571–77, doi:10.1021/ja901633y.
short: J. Farjon, J. Boisbouvier, P. Schanda, A. Pardi, J.-P. Simorre, B. Brutscher,
Journal of the American Chemical Society 131 (2009) 8571–8577.
date_created: 2020-09-18T10:11:49Z
date_published: 2009-06-01T00:00:00Z
date_updated: 2021-01-12T08:19:32Z
day: '01'
doi: 10.1021/ja901633y
extern: '1'
intvolume: ' 131'
issue: '24'
language:
- iso: eng
month: '06'
oa_version: None
page: 8571-8577
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Longitudinal-relaxation-enhanced NMR experiments for the study of nucleic acids
in solution
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2009'
...
---
_id: '8477'
abstract:
- lang: eng
text: An optimized NMR experiment that combines the advantages of methyl-TROSY and
SOFAST-HMQC has been developed. It allows the recording of high quality methyl
1H−13C correlation spectra of protein assemblies of several hundreds of kDa in
a few seconds. The SOFAST-methyl-TROSY-based experiment offers completely new
opportunities for the study of structural and dynamic changes occurring in molecular
nanomachines while they perform their biological function in vitro.
article_processing_charge: No
article_type: original
author:
- first_name: Carlos
full_name: Amero, Carlos
last_name: Amero
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: M. Asunción
full_name: Durá, M. Asunción
last_name: Durá
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Dominique
full_name: Marion, Dominique
last_name: Marion
- first_name: Bruno
full_name: Franzetti, Bruno
last_name: Franzetti
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
- first_name: Jérôme
full_name: Boisbouvier, Jérôme
last_name: Boisbouvier
citation:
ama: Amero C, Schanda P, Durá MA, et al. Fast two-dimensional NMR spectroscopy
of high molecular weight protein assemblies. Journal of the American Chemical
Society. 2009;131(10):3448-3449. doi:10.1021/ja809880p
apa: Amero, C., Schanda, P., Durá, M. A., Ayala, I., Marion, D., Franzetti, B.,
… Boisbouvier, J. (2009). Fast two-dimensional NMR spectroscopy of high molecular
weight protein assemblies. Journal of the American Chemical Society. American
Chemical Society. https://doi.org/10.1021/ja809880p
chicago: Amero, Carlos, Paul Schanda, M. Asunción Durá, Isabel Ayala, Dominique
Marion, Bruno Franzetti, Bernhard Brutscher, and Jérôme Boisbouvier. “Fast Two-Dimensional
NMR Spectroscopy of High Molecular Weight Protein Assemblies.” Journal of the
American Chemical Society. American Chemical Society, 2009. https://doi.org/10.1021/ja809880p.
ieee: C. Amero et al., “Fast two-dimensional NMR spectroscopy of high molecular
weight protein assemblies,” Journal of the American Chemical Society, vol.
131, no. 10. American Chemical Society, pp. 3448–3449, 2009.
ista: Amero C, Schanda P, Durá MA, Ayala I, Marion D, Franzetti B, Brutscher B,
Boisbouvier J. 2009. Fast two-dimensional NMR spectroscopy of high molecular weight
protein assemblies. Journal of the American Chemical Society. 131(10), 3448–3449.
mla: Amero, Carlos, et al. “Fast Two-Dimensional NMR Spectroscopy of High Molecular
Weight Protein Assemblies.” Journal of the American Chemical Society, vol.
131, no. 10, American Chemical Society, 2009, pp. 3448–49, doi:10.1021/ja809880p.
short: C. Amero, P. Schanda, M.A. Durá, I. Ayala, D. Marion, B. Franzetti, B. Brutscher,
J. Boisbouvier, Journal of the American Chemical Society 131 (2009) 3448–3449.
date_created: 2020-09-18T10:12:01Z
date_published: 2009-02-25T00:00:00Z
date_updated: 2021-01-12T08:19:32Z
day: '25'
doi: 10.1021/ja809880p
extern: '1'
intvolume: ' 131'
issue: '10'
language:
- iso: eng
month: '02'
oa_version: None
page: 3448-3449
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Fast two-dimensional NMR spectroscopy of high molecular weight protein assemblies
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2009'
...
---
_id: '8478'
abstract:
- lang: eng
text: Allosteric regulation is an effective mechanism of control in biological processes.
In allosteric proteins a signal originating at one site in the molecule is communicated
through the protein structure to trigger a specific response at a remote site.
Using NMR relaxation dispersion techniques we directly observe the dynamic process
through which the KIX domain of CREB binding protein communicates allosteric information
between binding sites. KIX mediates cooperativity between pairs of transcription
factors through binding to two distinct interaction surfaces in an allosteric
manner. We show that binding the activation domain of the mixed lineage leukemia
(MLL) transcription factor to KIX induces a redistribution of the relative populations
of KIX conformations toward a high-energy state in which the allosterically activated
second binding site is already preformed, consistent with the Monod−Wyman−Changeux
(WMC) model of allostery. The structural rearrangement process that links the
two conformers and by which allosteric information is communicated occurs with
a time constant of 3 ms at 27 °C. Our dynamic NMR data reveal that an evolutionarily
conserved network of hydrophobic amino acids constitutes the pathway through which
information is transmitted.
article_processing_charge: No
article_type: original
author:
- first_name: Sven
full_name: Brüschweiler, Sven
last_name: Brüschweiler
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Karin
full_name: Kloiber, Karin
last_name: Kloiber
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
- first_name: Georg
full_name: Kontaxis, Georg
last_name: Kontaxis
- first_name: Robert
full_name: Konrat, Robert
last_name: Konrat
- first_name: Martin
full_name: Tollinger, Martin
last_name: Tollinger
citation:
ama: Brüschweiler S, Schanda P, Kloiber K, et al. Direct observation of the dynamic
process underlying allosteric signal transmission. Journal of the American
Chemical Society. 2009;131(8):3063-3068. doi:10.1021/ja809947w
apa: Brüschweiler, S., Schanda, P., Kloiber, K., Brutscher, B., Kontaxis, G., Konrat,
R., & Tollinger, M. (2009). Direct observation of the dynamic process underlying
allosteric signal transmission. Journal of the American Chemical Society.
American Chemical Society. https://doi.org/10.1021/ja809947w
chicago: Brüschweiler, Sven, Paul Schanda, Karin Kloiber, Bernhard Brutscher, Georg
Kontaxis, Robert Konrat, and Martin Tollinger. “Direct Observation of the Dynamic
Process Underlying Allosteric Signal Transmission.” Journal of the American
Chemical Society. American Chemical Society, 2009. https://doi.org/10.1021/ja809947w.
ieee: S. Brüschweiler et al., “Direct observation of the dynamic process
underlying allosteric signal transmission,” Journal of the American Chemical
Society, vol. 131, no. 8. American Chemical Society, pp. 3063–3068, 2009.
ista: Brüschweiler S, Schanda P, Kloiber K, Brutscher B, Kontaxis G, Konrat R,
Tollinger M. 2009. Direct observation of the dynamic process underlying allosteric
signal transmission. Journal of the American Chemical Society. 131(8), 3063–3068.
mla: Brüschweiler, Sven, et al. “Direct Observation of the Dynamic Process Underlying
Allosteric Signal Transmission.” Journal of the American Chemical Society,
vol. 131, no. 8, American Chemical Society, 2009, pp. 3063–68, doi:10.1021/ja809947w.
short: S. Brüschweiler, P. Schanda, K. Kloiber, B. Brutscher, G. Kontaxis, R. Konrat,
M. Tollinger, Journal of the American Chemical Society 131 (2009) 3063–3068.
date_created: 2020-09-18T10:12:14Z
date_published: 2009-02-09T00:00:00Z
date_updated: 2021-01-12T08:19:33Z
day: '09'
doi: 10.1021/ja809947w
extern: '1'
intvolume: ' 131'
issue: '8'
language:
- iso: eng
month: '02'
oa_version: None
page: 3063-3068
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Direct observation of the dynamic process underlying allosteric signal transmission
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2009'
...
---
_id: '8479'
abstract:
- lang: eng
text: Multidimensional NMR spectroscopy is a well-established technique for the
characterization of structure and fast-time-scale dynamics of highly populated
ground states of biological macromolecules. The investigation of short-lived excited
states that are important for molecular folding, misfolding and function, however,
remains a challenge for modern biomolecular NMR techniques. Off-equilibrium real-time
kinetic NMR methods allow direct observation of conformational or chemical changes
by following peak positions and intensities in a series of spectra recorded during
a kinetic event. Because standard multidimensional NMR methods required to yield
sufficient atom-resolution are intrinsically time-consuming, many interesting
phenomena are excluded from real-time NMR analysis. Recently, spatially encoded
ultrafast 2D NMR techniques have been proposed that allow one to acquire a 2D
NMR experiment within a single transient. In addition, when combined with the
SOFAST technique, such ultrafast experiments can be repeated at high rates. One
of the problems detected for such ultrafast protein NMR experiments is related
to the heteronuclear decoupling during detection with interferences between the
pulses and the oscillatory magnetic field gradients arising in this scheme. Here
we present a method for improved ultrafast data acquisition yielding higher signal
to noise and sharper lines in single-scan 2D NMR spectra. In combination with
a fast-mixing device, the recording of 1H–15N correlation spectra with repetition
rates of up to a few Hertz becomes feasible, enabling real-time studies of protein
kinetics occurring on time scales down to a few seconds.
article_processing_charge: No
article_type: original
author:
- first_name: Maayan
full_name: Gal, Maayan
last_name: Gal
- first_name: Thomas
full_name: Kern, Thomas
last_name: Kern
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Lucio
full_name: Frydman, Lucio
last_name: Frydman
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: 'Gal M, Kern T, Schanda P, Frydman L, Brutscher B. An improved ultrafast 2D
NMR experiment: Towards atom-resolved real-time studies of protein kinetics at
multi-Hz rates. Journal of Biomolecular NMR. 2009;43:1-10. doi:10.1007/s10858-008-9284-9'
apa: 'Gal, M., Kern, T., Schanda, P., Frydman, L., & Brutscher, B. (2009). An
improved ultrafast 2D NMR experiment: Towards atom-resolved real-time studies
of protein kinetics at multi-Hz rates. Journal of Biomolecular NMR. Springer
Nature. https://doi.org/10.1007/s10858-008-9284-9'
chicago: 'Gal, Maayan, Thomas Kern, Paul Schanda, Lucio Frydman, and Bernhard Brutscher.
“An Improved Ultrafast 2D NMR Experiment: Towards Atom-Resolved Real-Time Studies
of Protein Kinetics at Multi-Hz Rates.” Journal of Biomolecular NMR. Springer
Nature, 2009. https://doi.org/10.1007/s10858-008-9284-9.'
ieee: 'M. Gal, T. Kern, P. Schanda, L. Frydman, and B. Brutscher, “An improved ultrafast
2D NMR experiment: Towards atom-resolved real-time studies of protein kinetics
at multi-Hz rates,” Journal of Biomolecular NMR, vol. 43. Springer Nature,
pp. 1–10, 2009.'
ista: 'Gal M, Kern T, Schanda P, Frydman L, Brutscher B. 2009. An improved ultrafast
2D NMR experiment: Towards atom-resolved real-time studies of protein kinetics
at multi-Hz rates. Journal of Biomolecular NMR. 43, 1–10.'
mla: 'Gal, Maayan, et al. “An Improved Ultrafast 2D NMR Experiment: Towards Atom-Resolved
Real-Time Studies of Protein Kinetics at Multi-Hz Rates.” Journal of Biomolecular
NMR, vol. 43, Springer Nature, 2009, pp. 1–10, doi:10.1007/s10858-008-9284-9.'
short: M. Gal, T. Kern, P. Schanda, L. Frydman, B. Brutscher, Journal of Biomolecular
NMR 43 (2009) 1–10.
date_created: 2020-09-18T10:12:20Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T08:19:33Z
day: '01'
doi: 10.1007/s10858-008-9284-9
extern: '1'
intvolume: ' 43'
keyword:
- Spectroscopy
- Biochemistry
language:
- iso: eng
month: '01'
oa_version: None
page: 1-10
publication: Journal of Biomolecular NMR
publication_identifier:
issn:
- 0925-2738
- 1573-5001
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'An improved ultrafast 2D NMR experiment: Towards atom-resolved real-time studies
of protein kinetics at multi-Hz rates'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2009'
...
---
_id: '8508'
abstract:
- lang: eng
text: We study generic unfoldings of homoclinic tangencies of two-dimensional area-preserving
diffeomorphisms (conservative New house phenomena) and show that they give rise
to invariant hyperbolic sets of arbitrarily large Hausdorff dimension. As applications,
we discuss the size of the stochastic layer of a standard map and the Hausdorff
dimension of invariant hyperbolic sets for certain restricted three-body problems.
We avoid involved technical details and only concentrate on the ideas of the proof
of the presented results.
article_processing_charge: No
article_type: original
author:
- first_name: Anton
full_name: Gorodetski, Anton
last_name: Gorodetski
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Gorodetski A, Kaloshin V. Conservative homoclinic bifurcations and some applications.
Proceedings of the Steklov Institute of Mathematics. 2009;267(1):76-90.
doi:10.1134/s0081543809040063
apa: Gorodetski, A., & Kaloshin, V. (2009). Conservative homoclinic bifurcations
and some applications. Proceedings of the Steklov Institute of Mathematics.
Springer Nature. https://doi.org/10.1134/s0081543809040063
chicago: Gorodetski, Anton, and Vadim Kaloshin. “Conservative Homoclinic Bifurcations
and Some Applications.” Proceedings of the Steklov Institute of Mathematics.
Springer Nature, 2009. https://doi.org/10.1134/s0081543809040063.
ieee: A. Gorodetski and V. Kaloshin, “Conservative homoclinic bifurcations and some
applications,” Proceedings of the Steklov Institute of Mathematics, vol.
267, no. 1. Springer Nature, pp. 76–90, 2009.
ista: Gorodetski A, Kaloshin V. 2009. Conservative homoclinic bifurcations and some
applications. Proceedings of the Steklov Institute of Mathematics. 267(1), 76–90.
mla: Gorodetski, Anton, and Vadim Kaloshin. “Conservative Homoclinic Bifurcations
and Some Applications.” Proceedings of the Steklov Institute of Mathematics,
vol. 267, no. 1, Springer Nature, 2009, pp. 76–90, doi:10.1134/s0081543809040063.
short: A. Gorodetski, V. Kaloshin, Proceedings of the Steklov Institute of Mathematics
267 (2009) 76–90.
date_created: 2020-09-18T10:48:03Z
date_published: 2009-12-01T00:00:00Z
date_updated: 2021-01-12T08:19:46Z
day: '01'
doi: 10.1134/s0081543809040063
extern: '1'
intvolume: ' 267'
issue: '1'
keyword:
- Mathematics (miscellaneous)
language:
- iso: eng
month: '12'
oa_version: None
page: 76-90
publication: Proceedings of the Steklov Institute of Mathematics
publication_identifier:
issn:
- 0081-5438
- 1531-8605
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Conservative homoclinic bifurcations and some applications
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 267
year: '2009'
...
---
_id: '88'
abstract:
- lang: eng
text: 'We have developed a tunable source of Mie scale microdroplet aerosols that
can be used for the generation of energetic ions. To demonstrate this potential,
a terawatt Ti: Al2 O3 laser focused to 2×10 19 W/cm2 was used to irradiate heavy
water (D2 O) aerosols composed of micron-scale droplets. Energetic deuterium ions,
which were generated in the laser-droplet interaction, produced deuterium-deuterium
fusion with approximately 2×10^3 fusion neutrons measured per joule of incident
laser energy. '
acknowledgement: This work was supported by the National Science Foundation under
Grant Nos. PHY-0456898, PHY-0757989, and PHY-0456870 and the National Nuclear Security
Administration under Cooperative Agreement No. DE-FC52-03NA00156. Acknowledgment
is made to the Donors of the Petroleum Research Fund administered by the American
Chemical Society for partial support of this research.
article_number: '063503'
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Octavi
full_name: Semonin, Octavi
last_name: Semonin
- first_name: S
full_name: Bruce, S
last_name: Bruce
- first_name: C
full_name: Chan, C
last_name: Chan
- first_name: M
full_name: Maindi, M
last_name: Maindi
- first_name: Tom
full_name: Donnelly, Tom
last_name: Donnelly
- first_name: M
full_name: Maurer, M
last_name: Maurer
- first_name: Woosuk
full_name: Bang, Woosuk
last_name: Bang
- first_name: I.V
full_name: Churina, I.V
last_name: Churina
- first_name: Jens
full_name: Osterholz, Jens
last_name: Osterholz
- first_name: I
full_name: Kim, I
last_name: Kim
- first_name: Aaron
full_name: Bernstein, Aaron
last_name: Bernstein
- first_name: Todd
full_name: Ditmire, Todd
last_name: Ditmire
citation:
ama: Higginbotham AP, Semonin O, Bruce S, et al. Generation of Mie size microdroplet
aerosols with applications in laser-driven fusion experiments. Review of Scientific
Instruments. 2009;80(6). doi:10.1063/1.3155302
apa: Higginbotham, A. P., Semonin, O., Bruce, S., Chan, C., Maindi, M., Donnelly,
T., … Ditmire, T. (2009). Generation of Mie size microdroplet aerosols with applications
in laser-driven fusion experiments. Review of Scientific Instruments. American
Institute of Physics. https://doi.org/10.1063/1.3155302
chicago: Higginbotham, Andrew P, Octavi Semonin, S Bruce, C Chan, M Maindi, Tom
Donnelly, M Maurer, et al. “Generation of Mie Size Microdroplet Aerosols with
Applications in Laser-Driven Fusion Experiments.” Review of Scientific Instruments.
American Institute of Physics, 2009. https://doi.org/10.1063/1.3155302.
ieee: A. P. Higginbotham et al., “Generation of Mie size microdroplet aerosols
with applications in laser-driven fusion experiments,” Review of Scientific
Instruments, vol. 80, no. 6. American Institute of Physics, 2009.
ista: Higginbotham AP, Semonin O, Bruce S, Chan C, Maindi M, Donnelly T, Maurer
M, Bang W, Churina I., Osterholz J, Kim I, Bernstein A, Ditmire T. 2009. Generation
of Mie size microdroplet aerosols with applications in laser-driven fusion experiments.
Review of Scientific Instruments. 80(6), 063503.
mla: Higginbotham, Andrew P., et al. “Generation of Mie Size Microdroplet Aerosols
with Applications in Laser-Driven Fusion Experiments.” Review of Scientific
Instruments, vol. 80, no. 6, 063503, American Institute of Physics, 2009,
doi:10.1063/1.3155302.
short: A.P. Higginbotham, O. Semonin, S. Bruce, C. Chan, M. Maindi, T. Donnelly,
M. Maurer, W. Bang, I.. Churina, J. Osterholz, I. Kim, A. Bernstein, T. Ditmire,
Review of Scientific Instruments 80 (2009).
date_created: 2018-12-11T11:44:34Z
date_published: 2009-06-25T00:00:00Z
date_updated: 2021-01-12T08:21:06Z
day: '25'
doi: 10.1063/1.3155302
extern: '1'
external_id:
pmid:
- ' 19566203'
intvolume: ' 80'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.osti.gov/biblio/22053583
month: '06'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Review of Scientific Instruments
publication_status: published
publisher: American Institute of Physics
publist_id: '7966'
quality_controlled: '1'
status: public
title: Generation of Mie size microdroplet aerosols with applications in laser-driven
fusion experiments
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 80
year: '2009'
...
---
_id: '908'
abstract:
- lang: eng
text: Although some data link archaeal and eukaryotic translation, the overall mechanism
of protein synthesis in archaea remains largely obscure. Both archaeal (aRF1)
and eukaryotic (eRF1) single release factors recognize all three stop codons.
The archaeal genus Methanosarcinaceae contains two aRF1 homologs, and also uses
the UAG stop to encode the 22nd amino acid, pyrrolysine. Here we provide an analysis
of the last stage of archaeal translation in pyrrolysine-utilizing species. We
demonstrated that only one of two Methanosarcina barkeri aRF1 homologs possesses
activity and recognizes all three stop codons. The second aRF1 homolog may have
another unknown function. The mechanism of pyrrolysine incorporation in the Methanosarcinaceae
is discussed.
acknowledgement: We are grateful to Andrey Poltaraus and his colleagues for sequencing
a/eRF1 genes. We thank Tatyana Pestova and Chris Hellen for the gift of plasmids
encoding initiation factors eIF1, eIF1A, eIF4A, eIF4B, eIF4G, eIF5, eIF5B, and Anna
Yaremchuk and Michael Tukalo for M. jannaschii aRF1. This work was supported by
grants from the Presidium of the (Program Molecular and Cell Biology), the Russian
Foundation for Basic Research (08-04-01091-а to E.A. and 08-04-00375a to L.F.),
the National Institute for General Medical Sciences (to D.S.), the National Science
Foundation (to D.S.) and the Office of Basic Energy Sciences, DOE (to D.S.).
author:
- first_name: Elena
full_name: Alkalaeva, Elena Z
last_name: Alkalaeva
- first_name: Boris
full_name: Eliseev, Boris D
last_name: Eliseev
- first_name: Alexandre
full_name: Ambrogelly, Alexandre
last_name: Ambrogelly
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Sarath
full_name: Gundllapalli, Sarath B
last_name: Gundllapalli
- first_name: Ludmila
full_name: Frolova, Ludmila Y
last_name: Frolova
- first_name: Dieter
full_name: Söll, Dieter G
last_name: Söll
- first_name: Lev
full_name: Kisselev, Lev L
last_name: Kisselev
citation:
ama: Alkalaeva E, Eliseev B, Ambrogelly A, et al. Translation termination in pyrrolysine-utilizing
archaea. FEBS Letters. 2009;583(21):3455-3460. doi:10.1016/j.febslet.2009.09.044
apa: Alkalaeva, E., Eliseev, B., Ambrogelly, A., Vlasov, P., Kondrashov, F., Gundllapalli,
S., … Kisselev, L. (2009). Translation termination in pyrrolysine-utilizing archaea.
FEBS Letters. Elsevier. https://doi.org/10.1016/j.febslet.2009.09.044
chicago: Alkalaeva, Elena, Boris Eliseev, Alexandre Ambrogelly, Peter Vlasov, Fyodor
Kondrashov, Sarath Gundllapalli, Ludmila Frolova, Dieter Söll, and Lev Kisselev.
“Translation Termination in Pyrrolysine-Utilizing Archaea.” FEBS Letters.
Elsevier, 2009. https://doi.org/10.1016/j.febslet.2009.09.044.
ieee: E. Alkalaeva et al., “Translation termination in pyrrolysine-utilizing
archaea,” FEBS Letters, vol. 583, no. 21. Elsevier, pp. 3455–3460, 2009.
ista: Alkalaeva E, Eliseev B, Ambrogelly A, Vlasov P, Kondrashov F, Gundllapalli
S, Frolova L, Söll D, Kisselev L. 2009. Translation termination in pyrrolysine-utilizing
archaea. FEBS Letters. 583(21), 3455–3460.
mla: Alkalaeva, Elena, et al. “Translation Termination in Pyrrolysine-Utilizing
Archaea.” FEBS Letters, vol. 583, no. 21, Elsevier, 2009, pp. 3455–60,
doi:10.1016/j.febslet.2009.09.044.
short: E. Alkalaeva, B. Eliseev, A. Ambrogelly, P. Vlasov, F. Kondrashov, S. Gundllapalli,
L. Frolova, D. Söll, L. Kisselev, FEBS Letters 583 (2009) 3455–3460.
date_created: 2018-12-11T11:49:08Z
date_published: 2009-11-03T00:00:00Z
date_updated: 2021-01-12T08:21:49Z
day: '03'
doi: 10.1016/j.febslet.2009.09.044
extern: 1
intvolume: ' 583'
issue: '21'
month: '11'
page: 3455 - 3460
publication: FEBS Letters
publication_status: published
publisher: Elsevier
publist_id: '6740'
quality_controlled: 0
status: public
title: Translation termination in pyrrolysine-utilizing archaea
type: journal_article
volume: 583
year: '2009'
...
---
_id: '9147'
abstract:
- lang: eng
text: As part of an ongoing effort to develop a parameterization of wave-induced
abyssal mixing, the authors derive an heuristic model for nonlinear wave breaking
and energy dissipation associated with internal tides. Then the saturation and
dissipation of internal tides for idealized and observed topography samples are
investigated. One of the main results is that the wave-induced mixing could be
more intense and more confined to the bottom than previously assumed in numerical
models. Furthermore, in this model wave breaking and mixing clearly depend on
the small scales of the topography below 10 km or so, which is below the current
resolution of global bathymetry. This motivates the use of a statistical approach
to represent the unresolved topography when addressing the role of internal tides
in mixing the deep ocean.
article_processing_charge: No
article_type: original
author:
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Oliver
full_name: Bühler, Oliver
last_name: Bühler
citation:
ama: Muller CJ, Bühler O. Saturation of the internal tides and induced mixing in
the abyssal ocean. Journal of Physical Oceanography. 2009;39(9):2077-2096.
doi:10.1175/2009jpo4141.1
apa: Muller, C. J., & Bühler, O. (2009). Saturation of the internal tides and
induced mixing in the abyssal ocean. Journal of Physical Oceanography.
American Meteorological Society. https://doi.org/10.1175/2009jpo4141.1
chicago: Muller, Caroline J, and Oliver Bühler. “Saturation of the Internal Tides
and Induced Mixing in the Abyssal Ocean.” Journal of Physical Oceanography.
American Meteorological Society, 2009. https://doi.org/10.1175/2009jpo4141.1.
ieee: C. J. Muller and O. Bühler, “Saturation of the internal tides and induced
mixing in the abyssal ocean,” Journal of Physical Oceanography, vol. 39,
no. 9. American Meteorological Society, pp. 2077–2096, 2009.
ista: Muller CJ, Bühler O. 2009. Saturation of the internal tides and induced mixing
in the abyssal ocean. Journal of Physical Oceanography. 39(9), 2077–2096.
mla: Muller, Caroline J., and Oliver Bühler. “Saturation of the Internal Tides and
Induced Mixing in the Abyssal Ocean.” Journal of Physical Oceanography,
vol. 39, no. 9, American Meteorological Society, 2009, pp. 2077–96, doi:10.1175/2009jpo4141.1.
short: C.J. Muller, O. Bühler, Journal of Physical Oceanography 39 (2009) 2077–2096.
date_created: 2021-02-15T14:41:08Z
date_published: 2009-09-01T00:00:00Z
date_updated: 2022-01-24T13:50:37Z
day: '01'
doi: 10.1175/2009jpo4141.1
extern: '1'
intvolume: ' 39'
issue: '9'
keyword:
- Oceanography
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1175/2009JPO4141.1
month: '09'
oa: 1
oa_version: Published Version
page: 2077-2096
publication: Journal of Physical Oceanography
publication_identifier:
issn:
- 1520-0485
- 0022-3670
publication_status: published
publisher: American Meteorological Society
quality_controlled: '1'
status: public
title: Saturation of the internal tides and induced mixing in the abyssal ocean
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 39
year: '2009'
...