---
_id: '3183'
abstract:
- lang: eng
text: This paper describes two algorithms capable of real-time segmentation of foreground
from background layers in stereo video sequences. Automatic separation of layers
from colour/contrast or from stereo alone is known to be error-prone. Here, colour,
contrast and stereo matching information are fused to infer layers accurately
and efficiently. The first algorithm, Layered Dynamic Programming (LDP), solves
stereo in an extended 6-state space that represents both foreground/background
layers and occluded regions. The stereo-match likelihood is then fused with a
contrast-sensitive colour model that is learned on the fly, and stereo disparities
are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC),
does not directly solve stereo. Instead the stereo match likelihood is marginalised
over foreground and background hypotheses, and fused with a contrast-sensitive
colour model like the one used in LDP. Segmentation is solved efficiently by ternary
graph cut. Both algorithms are evaluated with respect to ground truth data and
found to have similar perfomance, substantially better than stereo or colour/contrast
alone. However, their characteristics with respect to computational efficiency
are rather different. The algorithms are demonstrated in the application of background
substitution and shown to give good quality composite video output.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Antonio
full_name: Criminisi, Antonio
last_name: Criminisi
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Geoffrey
full_name: Cross, Geoffrey
last_name: Cross
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: 'Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Bi-layer segmentation
of binocular stereo video. In: Vol 2. IEEE; 2005:407-414. doi:10.1109/CVPR.2005.91'
apa: 'Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., & Rother, C. (2005).
Bi-layer segmentation of binocular stereo video (Vol. 2, pp. 407–414). Presented
at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2005.91'
chicago: Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross,
and Carsten Rother. “Bi-Layer Segmentation of Binocular Stereo Video,” 2:407–14.
IEEE, 2005. https://doi.org/10.1109/CVPR.2005.91.
ieee: 'V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Bi-layer
segmentation of binocular stereo video,” presented at the CVPR: Computer Vision
and Pattern Recognition, 2005, vol. 2, pp. 407–414.'
ista: 'Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2005. Bi-layer segmentation
of binocular stereo video. CVPR: Computer Vision and Pattern Recognition vol.
2, 407–414.'
mla: Kolmogorov, Vladimir, et al. Bi-Layer Segmentation of Binocular Stereo Video.
Vol. 2, IEEE, 2005, pp. 407–14, doi:10.1109/CVPR.2005.91.
short: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, in:, IEEE, 2005,
pp. 407–414.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:52Z
date_published: 2005-07-25T00:00:00Z
date_updated: 2021-01-12T07:41:38Z
day: '25'
doi: 10.1109/CVPR.2005.91
extern: 1
intvolume: ' 2'
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67281/criminisi_cvpr2005.pdf
month: '07'
page: 407 - 414
publication_status: published
publisher: IEEE
publist_id: '3502'
quality_controlled: 0
status: public
title: Bi-layer segmentation of binocular stereo video
type: conference
volume: 2
year: '2005'
...
---
_id: '3182'
abstract:
- lang: eng
text: In the work of the authors (2003), we showed that graph cuts can find hypersurfaces
of globally minimal length (or area) under any Riemannian metric. Here we show
that graph cuts on directed regular grids can approximate a significantly more
general class of continuous non-symmetric metrics. Using submodularity condition
(Boros and Hammer, 2002 and Kolmogorov and Zabih, 2004), we obtain a tight characterization
of graph-representable metrics. Such "submodular" metrics have an elegant
geometric interpretation via hypersurface functionals combining length/area and
flux. Practically speaking, we attend 'geo-cuts' algorithm to a wider class of
geometrically motivated hypersurface functionals and show how to globally optimize
any combination of length/area and flux of a given vector field. The concept of
flux was recently introduced into computer vision by Vasilevskiy and Siddiqi (2002)
but it was mainly studied within variational framework so far. We are first to
show that flux can be integrated into graph cuts as well. Combining geometric
concepts of flux and length/area within the global optimization framework of graph
cuts allows principled discrete segmentation models and advances the slate of
the art for the graph cuts methods in vision. In particular we address the "shrinking"
problem of graph cuts, improve segmentation of long thin objects, and introduce
useful shape constraints.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Yuri
full_name: Boykov, Yuri
last_name: Boykov
citation:
ama: 'Kolmogorov V, Boykov Y. What metrics can be approximated by geo cuts or global
optimization of length area and flux. In: Vol 1. IEEE; 2005:564-571. doi:10.1109/ICCV.2005.252'
apa: 'Kolmogorov, V., & Boykov, Y. (2005). What metrics can be approximated
by geo cuts or global optimization of length area and flux (Vol. 1, pp. 564–571).
Presented at the ICCV: International Conference on Computer Vision, IEEE. https://doi.org/10.1109/ICCV.2005.252'
chicago: Kolmogorov, Vladimir, and Yuri Boykov. “What Metrics Can Be Approximated
by Geo Cuts or Global Optimization of Length Area and Flux,” 1:564–71. IEEE, 2005.
https://doi.org/10.1109/ICCV.2005.252.
ieee: 'V. Kolmogorov and Y. Boykov, “What metrics can be approximated by geo cuts
or global optimization of length area and flux,” presented at the ICCV: International
Conference on Computer Vision, 2005, vol. 1, pp. 564–571.'
ista: 'Kolmogorov V, Boykov Y. 2005. What metrics can be approximated by geo cuts
or global optimization of length area and flux. ICCV: International Conference
on Computer Vision vol. 1, 564–571.'
mla: Kolmogorov, Vladimir, and Yuri Boykov. What Metrics Can Be Approximated
by Geo Cuts or Global Optimization of Length Area and Flux. Vol. 1, IEEE,
2005, pp. 564–71, doi:10.1109/ICCV.2005.252.
short: V. Kolmogorov, Y. Boykov, in:, IEEE, 2005, pp. 564–571.
conference:
name: 'ICCV: International Conference on Computer Vision'
date_created: 2018-12-11T12:01:52Z
date_published: 2005-12-05T00:00:00Z
date_updated: 2021-01-12T07:41:38Z
day: '05'
doi: 10.1109/ICCV.2005.252
extern: 1
intvolume: ' 1'
month: '12'
page: 564 - 571
publication_status: published
publisher: IEEE
publist_id: '3501'
quality_controlled: 0
status: public
title: What metrics can be approximated by geo cuts or global optimization of length
area and flux
type: conference
volume: 1
year: '2005'
...
---
_id: '3181'
abstract:
- lang: eng
text: Tree-reweighted max-product (TRW) message passing [9] is a modified form of
the ordinary max-product algorithm for attempting to find minimal energy configurations
in Markov random field with cycles. For a TRW fixed point satisfying the strong
tree agreement condition, the algorithm outputs a configuration that is provably
optimal. In this paper, we focus on the case of binary variables with pairwise
couplings, and establish stronger properties of TRW fixed points that satisfy
only the milder condition of weak tree agreement (WTA). First, we demonstrate
how it is possible to identify part of the optimal solution - i.e., a provably
optimal solution for a subset of nodes - without knowing a complete solution.
Second, we show that for submodular functions, a WTA fixed point always yields
a globally optimal solution. We establish that for binary variables, any WTA fixed
point always achieves the global maximum of the linear programming relaxation
underlying the TRW method.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Martin
full_name: Wainwright, Martin J
last_name: Wainwright
citation:
ama: 'Kolmogorov V, Wainwright M. On the optimality of tree reweighted max product
message passing. In: AUAI Press; 2005:316-323.'
apa: 'Kolmogorov, V., & Wainwright, M. (2005). On the optimality of tree reweighted
max product message passing (pp. 316–323). Presented at the UAI: Uncertainty in
Artificial Intelligence, AUAI Press.'
chicago: Kolmogorov, Vladimir, and Martin Wainwright. “On the Optimality of Tree
Reweighted Max Product Message Passing,” 316–23. AUAI Press, 2005.
ieee: 'V. Kolmogorov and M. Wainwright, “On the optimality of tree reweighted max
product message passing,” presented at the UAI: Uncertainty in Artificial Intelligence,
2005, pp. 316–323.'
ista: 'Kolmogorov V, Wainwright M. 2005. On the optimality of tree reweighted max
product message passing. UAI: Uncertainty in Artificial Intelligence, 316–323.'
mla: Kolmogorov, Vladimir, and Martin Wainwright. On the Optimality of Tree Reweighted
Max Product Message Passing. AUAI Press, 2005, pp. 316–23.
short: V. Kolmogorov, M. Wainwright, in:, AUAI Press, 2005, pp. 316–323.
conference:
name: 'UAI: Uncertainty in Artificial Intelligence'
date_created: 2018-12-11T12:01:51Z
date_published: 2005-07-01T00:00:00Z
date_updated: 2021-01-12T07:41:38Z
day: '01'
extern: 1
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67405/trw_opt_uai05.pdf
month: '07'
page: 316 - 323
publication_status: published
publisher: AUAI Press
publist_id: '3500'
quality_controlled: 0
status: public
title: On the optimality of tree reweighted max product message passing
type: conference
year: '2005'
...
---
_id: '3417'
abstract:
- lang: eng
text: Recently, direct measurements of forces stabilizing single proteins or individual
receptor–ligand bonds became possible with ultra-sensitive force probe methods
like the atomic force microscope (AFM). In force spectroscopy experiments using
AFM, a single molecule or receptor–ligand pair is tethered between the tip of
a micromachined cantilever and a supporting surface. While the molecule is stretched,
forces are measured by the deflection of the cantilever and plotted against extension,
yielding a force spectrum characteristic for each biomolecular system. In order
to obtain statistically relevant results, several hundred to thousand single-molecule
experiments have to be performed, each resulting in a unique force spectrum. We
developed software and algorithms to analyse large numbers of force spectra. Our
algorithms include the fitting polymer extension models to force peaks as well
as the automatic alignment of spectra. The aligned spectra allowed recognition
of patterns of peaks across different spectra. We demonstrate the capabilities
of our software by analysing force spectra that were recorded by unfolding single
transmembrane proteins such as bacteriorhodopsin and NhaA. Different unfolding
pathways were detected by classifying peak patterns. Deviant spectra, e.g. those
with no attachment or erratic peaks, can be easily identified. The software is
based on the programming language C++, the GNU Scientific Library (GSL), the software
WaveMetrics IGOR Pro and available open-source at http://bioinformatics.org/fskit/.
author:
- first_name: Michael
full_name: Kuhn, Michael
last_name: Kuhn
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Maurice
full_name: Hubain, Maurice
last_name: Hubain
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Kuhn M, Janovjak HL, Hubain M, Mueller D. Automated alignment and pattern recognition
of single-molecule force spectroscopy data. Journal of Microscopy. 2005;218(2):125-132.
doi:10.1111/j.1365-2818.2005.01478.x
apa: Kuhn, M., Janovjak, H. L., Hubain, M., & Mueller, D. (2005). Automated
alignment and pattern recognition of single-molecule force spectroscopy data.
Journal of Microscopy. Wiley-Blackwell. https://doi.org/10.1111/j.1365-2818.2005.01478.x
chicago: Kuhn, Michael, Harald L Janovjak, Maurice Hubain, and Daniel Mueller. “Automated
Alignment and Pattern Recognition of Single-Molecule Force Spectroscopy Data.”
Journal of Microscopy. Wiley-Blackwell, 2005. https://doi.org/10.1111/j.1365-2818.2005.01478.x.
ieee: M. Kuhn, H. L. Janovjak, M. Hubain, and D. Mueller, “Automated alignment and
pattern recognition of single-molecule force spectroscopy data,” Journal of
Microscopy, vol. 218, no. 2. Wiley-Blackwell, pp. 125–132, 2005.
ista: Kuhn M, Janovjak HL, Hubain M, Mueller D. 2005. Automated alignment and pattern
recognition of single-molecule force spectroscopy data. Journal of Microscopy.
218(2), 125–132.
mla: Kuhn, Michael, et al. “Automated Alignment and Pattern Recognition of Single-Molecule
Force Spectroscopy Data.” Journal of Microscopy, vol. 218, no. 2, Wiley-Blackwell,
2005, pp. 125–32, doi:10.1111/j.1365-2818.2005.01478.x.
short: M. Kuhn, H.L. Janovjak, M. Hubain, D. Mueller, Journal of Microscopy 218
(2005) 125–132.
date_created: 2018-12-11T12:03:13Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T07:43:20Z
day: '01'
doi: 10.1111/j.1365-2818.2005.01478.x
extern: 1
intvolume: ' 218'
issue: '2'
month: '05'
page: 125 - 132
publication: Journal of Microscopy
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2984'
quality_controlled: 0
status: public
title: Automated alignment and pattern recognition of single-molecule force spectroscopy
data
type: journal_article
volume: 218
year: '2005'
...
---
_id: '3416'
abstract:
- lang: eng
text: In the last decade atomic force microscopy has been used to measure the mechanical
stability of single proteins. These force spectroscopy experiments have shown
that many water-soluble and membrane proteins unfold via one or more intermediates.
Recently, Li and co-workers found a linear correlation between the unfolding force
of the native state and the intermediate in fibronectin, which they suggested
indicated the presence of a molecular memory or multiple unfolding pathways (1).
Here, we apply two independent methods in combination with Monte Carlo simulations
to analyze the unfolding of α-helices E and D of bacteriorhodopsin (BR). We show
that correlation analysis of unfolding forces is very sensitive to errors in force
calibration of the instrument. In contrast, a comparison of relative forces provides
a robust measure for the stability of unfolding intermediates. The proposed approach
detects three energetically different states of α-helices E and D in trimeric
BR. These states are not observed for monomeric BR and indicate that substantial
information is hidden in forced unfolding experiments of single proteins.
author:
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Tanuj
full_name: Sapra, Tanuj K
last_name: Sapra
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Janovjak HL, Sapra T, Mueller D. Complex stability of single proteins explored
by forced unfolding experiments. Biophysical Journal. 2005;88(5):37-39.
doi:10.1529/biophysj.105.059774
apa: Janovjak, H. L., Sapra, T., & Mueller, D. (2005). Complex stability of
single proteins explored by forced unfolding experiments. Biophysical Journal.
Biophysical Society. https://doi.org/10.1529/biophysj.105.059774
chicago: Janovjak, Harald L, Tanuj Sapra, and Daniel Mueller. “Complex Stability
of Single Proteins Explored by Forced Unfolding Experiments.” Biophysical Journal.
Biophysical Society, 2005. https://doi.org/10.1529/biophysj.105.059774.
ieee: H. L. Janovjak, T. Sapra, and D. Mueller, “Complex stability of single proteins
explored by forced unfolding experiments,” Biophysical Journal, vol. 88,
no. 5. Biophysical Society, pp. 37–39, 2005.
ista: Janovjak HL, Sapra T, Mueller D. 2005. Complex stability of single proteins
explored by forced unfolding experiments. Biophysical Journal. 88(5), 37–39.
mla: Janovjak, Harald L., et al. “Complex Stability of Single Proteins Explored
by Forced Unfolding Experiments.” Biophysical Journal, vol. 88, no. 5,
Biophysical Society, 2005, pp. 37–39, doi:10.1529/biophysj.105.059774.
short: H.L. Janovjak, T. Sapra, D. Mueller, Biophysical Journal 88 (2005) 37–39.
date_created: 2018-12-11T12:03:13Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T07:43:19Z
day: '01'
doi: 10.1529/biophysj.105.059774
extern: 1
intvolume: ' 88'
issue: '5'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305525/
month: '05'
oa: 1
page: 37 - 39
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '2985'
quality_controlled: 0
status: public
title: Complex stability of single proteins explored by forced unfolding experiments
type: journal_article
volume: 88
year: '2005'
...
---
_id: '3418'
abstract:
- lang: eng
text: Atomic force microscopy (AFM) allows the critical forces that unfold single
proteins and rupture individual receptor–ligand bonds to be measured. To derive
the shape of the energy landscape, the dynamic strength of the system is probed
at different force loading rates. This is usually achieved by varying the pulling
speed between a few nm/s and a few mgrm/s, although for a more complete investigation
of the kinetic properties higher speeds are desirable. Above 10 mgrm/s, the hydrodynamic
drag force acting on the AFM cantilever reaches the same order of magnitude as
the molecular forces. This has limited the maximum pulling speed in AFM single-molecule
force spectroscopy experiments. Here, we present an approach for considering these
hydrodynamic effects, thereby allowing a correct evaluation of AFM force measurements
recorded over an extended range of pulling speeds (and thus loading rates). To
support and illustrate our theoretical considerations, we experimentally evaluated
the mechanical unfolding of a multi-domain protein recorded at 30 mgrm/s pulling
speed.
author:
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Jens
full_name: Struckmeier, Jens
last_name: Struckmeier
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Janovjak HL, Struckmeier J, Mueller D. Hydrodynamic effects in fast AFM single
molecule force measurements. European Biophysics Journal. 2005;34(1):91-96.
doi:10.1007/s00249-004-0430-3
apa: Janovjak, H. L., Struckmeier, J., & Mueller, D. (2005). Hydrodynamic effects
in fast AFM single molecule force measurements. European Biophysics Journal.
Springer. https://doi.org/10.1007/s00249-004-0430-3
chicago: Janovjak, Harald L, Jens Struckmeier, and Daniel Mueller. “Hydrodynamic
Effects in Fast AFM Single Molecule Force Measurements.” European Biophysics
Journal. Springer, 2005. https://doi.org/10.1007/s00249-004-0430-3.
ieee: H. L. Janovjak, J. Struckmeier, and D. Mueller, “Hydrodynamic effects in fast
AFM single molecule force measurements,” European Biophysics Journal, vol.
34, no. 1. Springer, pp. 91–96, 2005.
ista: Janovjak HL, Struckmeier J, Mueller D. 2005. Hydrodynamic effects in fast
AFM single molecule force measurements. European Biophysics Journal. 34(1), 91–96.
mla: Janovjak, Harald L., et al. “Hydrodynamic Effects in Fast AFM Single Molecule
Force Measurements.” European Biophysics Journal, vol. 34, no. 1, Springer,
2005, pp. 91–96, doi:10.1007/s00249-004-0430-3.
short: H.L. Janovjak, J. Struckmeier, D. Mueller, European Biophysics Journal 34
(2005) 91–96.
date_created: 2018-12-11T12:03:14Z
date_published: 2005-02-01T00:00:00Z
date_updated: 2021-01-12T07:43:20Z
day: '01'
doi: 10.1007/s00249-004-0430-3
extern: 1
intvolume: ' 34'
issue: '1'
month: '02'
page: 91 - 96
publication: European Biophysics Journal
publication_status: published
publisher: Springer
publist_id: '2983'
quality_controlled: 0
status: public
title: Hydrodynamic effects in fast AFM single molecule force measurements
type: journal_article
volume: 34
year: '2005'
...
---
_id: '3433'
author:
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: 'Bollback JP. Posterior mapping and posterior predictive distributions. In:
Nielsen R, ed. Statistical Methods in Molecular Evolution. Springer; 2005:439-462.
doi:10.1007/0-387-27733-1'
apa: Bollback, J. P. (2005). Posterior mapping and posterior predictive distributions.
In R. Nielsen (Ed.), Statistical methods in Molecular Evolution (pp. 439–462).
Springer. https://doi.org/10.1007/0-387-27733-1
chicago: Bollback, Jonathan P. “Posterior Mapping and Posterior Predictive Distributions.”
In Statistical Methods in Molecular Evolution, edited by Rasmus Nielsen,
439–62. Springer, 2005. https://doi.org/10.1007/0-387-27733-1.
ieee: J. P. Bollback, “Posterior mapping and posterior predictive distributions,”
in Statistical methods in Molecular Evolution, R. Nielsen, Ed. Springer,
2005, pp. 439–462.
ista: 'Bollback JP. 2005.Posterior mapping and posterior predictive distributions.
In: Statistical methods in Molecular Evolution. , 439–462.'
mla: Bollback, Jonathan P. “Posterior Mapping and Posterior Predictive Distributions.”
Statistical Methods in Molecular Evolution, edited by Rasmus Nielsen, Springer,
2005, pp. 439–62, doi:10.1007/0-387-27733-1.
short: J.P. Bollback, in:, R. Nielsen (Ed.), Statistical Methods in Molecular Evolution,
Springer, 2005, pp. 439–462.
date_created: 2018-12-11T12:03:18Z
date_published: 2005-04-21T00:00:00Z
date_updated: 2021-01-12T07:43:26Z
day: '21'
doi: 10.1007/0-387-27733-1
editor:
- first_name: Rasmus
full_name: Nielsen, Rasmus
last_name: Nielsen
extern: 1
month: '04'
page: 439 - 462
publication: Statistical methods in Molecular Evolution
publication_status: published
publisher: Springer
publist_id: '2967'
quality_controlled: 0
status: public
title: Posterior mapping and posterior predictive distributions
type: book_chapter
year: '2005'
...
---
_id: '3509'
abstract:
- lang: eng
text: Methods, apparatus and computer program products can generate light weight
but highly realistic and accurate colored models of three-dimensional colored
objects. The colored model may be generated from a second plurality of points
that define a coarse digital representation of the surface and at least one texture
map containing information derived from a first plurality of colored points that
define a fine digital representation of the surface. This derivation is achieved
by mapping points within the texture map to the fine digital representation of
the three-dimensional surface. Colored scan data may be used to construct the
fine digital representation as a triangulated surface (i.e., triangulation) using
a wrapping operation.
applicant:
- Raindrop Geomagic, Inc.
article_processing_charge: No
author:
- first_name: Steven
full_name: Williams, Steven
last_name: Williams
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Ping
full_name: Fu, Ping
last_name: Fu
citation:
ama: Williams S, Edelsbrunner H, Fu P. Methods, apparatus and computer program products
for modeling three-dimensional colored objects. 2005.
apa: Williams, S., Edelsbrunner, H., & Fu, P. (2005). Methods, apparatus and
computer program products for modeling three-dimensional colored objects.
chicago: Williams, Steven, Herbert Edelsbrunner, and Ping Fu. “Methods, Apparatus
and Computer Program Products for Modeling Three-Dimensional Colored Objects,”
2005.
ieee: S. Williams, H. Edelsbrunner, and P. Fu, “Methods, apparatus and computer
program products for modeling three-dimensional colored objects.” 2005.
ista: Williams S, Edelsbrunner H, Fu P. 2005. Methods, apparatus and computer program
products for modeling three-dimensional colored objects.
mla: Williams, Steven, et al. Methods, Apparatus and Computer Program Products
for Modeling Three-Dimensional Colored Objects. 2005.
short: S. Williams, H. Edelsbrunner, P. Fu, (2005).
date_created: 2018-12-11T12:03:42Z
date_published: 2005-02-08T00:00:00Z
date_updated: 2022-01-05T13:59:09Z
day: '08'
extern: '1'
ipc: G06T17/20 ; G06T15/04
ipn: US6853373B2
main_file_link:
- open_access: '1'
url: https://patents.google.com/patent/US6853373B2/
month: '02'
oa: 1
oa_version: Published Version
publication_date: 2005-02-08
publist_id: '2878'
status: public
title: Methods, apparatus and computer program products for modeling three-dimensional
colored objects
type: patent
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2005'
...
---
_id: '3558'
abstract:
- lang: eng
text: The tandem algorithm combines the marching cube algorithm for surface extraction
and the edge contraction algorithm for surface simplification in lock-step to
avoid the costly intermediate step of storing the entire extracted surface triangulation.
Beyond this basic strategy, we introduce refinements to prevent artifacts in the
resulting triangulation, first, by carefully monitoring the amount of simplification
during the process and, second, by driving the simplification toward a compromise
between shape approximation and mesh quality. We have implemented the algorithm
and used extensive computational experiments to document the effects of various
design options and to further fine-tune the algorithm.
acknowledgement: 'Partially supported the generated triangulations. Two questions
arise: “how do by NSF grant CCR-00-86013 (BioGeometry).'
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: David
full_name: Cohen-Steiner, David
last_name: Cohen Steiner
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Attali D, Cohen Steiner D, Edelsbrunner H. Extraction and simplification of
iso-surfaces in tandem. In: ACM; 2005:139-148.'
apa: 'Attali, D., Cohen Steiner, D., & Edelsbrunner, H. (2005). Extraction and
simplification of iso-surfaces in tandem (pp. 139–148). Presented at the SGP:
Eurographics Symposium on Geometry processing, ACM.'
chicago: Attali, Dominique, David Cohen Steiner, and Herbert Edelsbrunner. “Extraction
and Simplification of Iso-Surfaces in Tandem,” 139–48. ACM, 2005.
ieee: 'D. Attali, D. Cohen Steiner, and H. Edelsbrunner, “Extraction and simplification
of iso-surfaces in tandem,” presented at the SGP: Eurographics Symposium on Geometry
processing, 2005, pp. 139–148.'
ista: 'Attali D, Cohen Steiner D, Edelsbrunner H. 2005. Extraction and simplification
of iso-surfaces in tandem. SGP: Eurographics Symposium on Geometry processing,
139–148.'
mla: Attali, Dominique, et al. Extraction and Simplification of Iso-Surfaces
in Tandem. ACM, 2005, pp. 139–48.
short: D. Attali, D. Cohen Steiner, H. Edelsbrunner, in:, ACM, 2005, pp. 139–148.
conference:
name: 'SGP: Eurographics Symposium on Geometry processing'
date_created: 2018-12-11T12:03:57Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T07:44:18Z
day: '01'
extern: 1
main_file_link:
- open_access: '0'
url: http://dl.acm.org/citation.cfm?id=1281943
month: '01'
page: 139 - 148
publication_status: published
publisher: ACM
publist_id: '2827'
quality_controlled: 0
status: public
title: Extraction and simplification of iso-surfaces in tandem
type: conference
year: '2005'
...
---
_id: '3576'
abstract:
- lang: eng
text: |-
ears of research in biology have established that all cellular functions are deeply connected to the shape and dynamics of their molec- ular actors. As a response, structural molecular biology has emerged as a new line of experimental research focused on revealing the structure of biomolecules. The analysis of these structures has led to the development of computational biology, whose aim is to predict from molecular simulation properties inaccessible to experimental probes.
Here we focus on the representation of biomolecules used in these sim- ulations, and in particular on the hard sphere models. We review how the geometry of the union of such spheres is used to model their interactions with their environment, and how it has been included in simulations of molecular dynamics.
In parallel, we review our own developments in mathematics and com- puter science on understanding the geometry of unions of balls, and their applications in molecular simulation.
alternative_title:
- Mathematical Sciences Research Institute Publications
author:
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Patrice
full_name: Koehl, Patrice
last_name: Koehl
citation:
ama: 'Edelsbrunner H, Koehl P. The geometry of biomolecular solvation. In: Combinatorial
and Computational Geometry. Vol 52. Cambridge University Press; 2005:243-275.'
apa: Edelsbrunner, H., & Koehl, P. (2005). The geometry of biomolecular solvation.
In Combinatorial and Computational Geometry (Vol. 52, pp. 243–275). Cambridge
University Press.
chicago: Edelsbrunner, Herbert, and Patrice Koehl. “The Geometry of Biomolecular
Solvation.” In Combinatorial and Computational Geometry, 52:243–75. Cambridge
University Press, 2005.
ieee: H. Edelsbrunner and P. Koehl, “The geometry of biomolecular solvation,” in
Combinatorial and Computational Geometry, vol. 52, Cambridge University
Press, 2005, pp. 243–275.
ista: 'Edelsbrunner H, Koehl P. 2005.The geometry of biomolecular solvation. In:
Combinatorial and Computational Geometry. Mathematical Sciences Research Institute
Publications, vol. 52, 243–275.'
mla: Edelsbrunner, Herbert, and Patrice Koehl. “The Geometry of Biomolecular Solvation.”
Combinatorial and Computational Geometry, vol. 52, Cambridge University
Press, 2005, pp. 243–75.
short: H. Edelsbrunner, P. Koehl, in:, Combinatorial and Computational Geometry,
Cambridge University Press, 2005, pp. 243–275.
date_created: 2018-12-11T12:04:03Z
date_published: 2005-08-08T00:00:00Z
date_updated: 2021-01-12T07:44:25Z
day: '08'
extern: 1
intvolume: ' 52'
main_file_link:
- open_access: '0'
url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.117.3732
month: '08'
page: 243 - 275
publication: Combinatorial and Computational Geometry
publication_status: published
publisher: Cambridge University Press
publist_id: '2809'
quality_controlled: 0
status: public
title: The geometry of biomolecular solvation
type: book_chapter
volume: 52
year: '2005'
...
---
_id: '3612'
abstract:
- lang: eng
text: Left-right asymmetry in snails is intriguing because individuals of opposite
chirality are either unable to mate or can only mate with difficulty, so could
be reproductively isolated from each other. We have therefore investigated chiral
evolution in the Japanese land snail genus Euhadra to understand whether changes
in chirality have promoted speciation. In particular, we aimed to understand the
effect of the maternal inheritance of chirality on reproductive isolation and
gene flow. We found that the mitochondrial DNA phylogeny of Euhadra is consistent
with a single, relatively ancient evolution of sinistral species and suggests
either recent “single-gene speciation” or gene flow between chiral morphs that
are unable to mate. To clarify the conditions under which new chiral morphs might
evolve and whether single-gene speciation can occur, we developed a mathematical
model that is relevant to any maternal-effect gene. The model shows that reproductive
character displacement can promote the evolution of new chiral morphs, tending
to counteract the positive frequency-dependent selection that would otherwise
drive the more common chiral morph to fixation. This therefore suggests a general
mechanism as to how chiral variation arises in snails. In populations that contain
both chiral morphs, two different situations are then possible. In the first,
gene flow is substantial between morphs even without interchiral mating, because
of the maternal inheritance of chirality. In the second, reproductive isolation
is possible but unstable, and will also lead to gene flow if intrachiral matings
occasionally produce offspring with the opposite chirality. Together, the results
imply that speciation by chiral reversal is only meaningful in the context of
a complex biogeographical process, and so must usually involve other factors.
In order to understand the roles of reproductive character displacement and gene
flow in the chiral evolution of Euhadra, it will be necessary to investigate populations
in which both chiral morphs coexist.
author:
- first_name: Angus
full_name: Davison, Angus
last_name: Davison
- first_name: Satoshi
full_name: Chiba, Satoshi
last_name: Chiba
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Bernard
full_name: Clarke, Bernard
last_name: Clarke
citation:
ama: Davison A, Chiba S, Barton NH, Clarke B. Speciation and gene flow between snails
of opposing chirality. PLoS Biology. 2005;3(9). doi:10.1371/journal.pbio.0030282
apa: Davison, A., Chiba, S., Barton, N. H., & Clarke, B. (2005). Speciation
and gene flow between snails of opposing chirality. PLoS Biology. Public
Library of Science. https://doi.org/10.1371/journal.pbio.0030282
chicago: Davison, Angus, Satoshi Chiba, Nicholas H Barton, and Bernard Clarke. “Speciation
and Gene Flow between Snails of Opposing Chirality.” PLoS Biology. Public
Library of Science, 2005. https://doi.org/10.1371/journal.pbio.0030282.
ieee: A. Davison, S. Chiba, N. H. Barton, and B. Clarke, “Speciation and gene flow
between snails of opposing chirality,” PLoS Biology, vol. 3, no. 9. Public
Library of Science, 2005.
ista: Davison A, Chiba S, Barton NH, Clarke B. 2005. Speciation and gene flow between
snails of opposing chirality. PLoS Biology. 3(9).
mla: Davison, Angus, et al. “Speciation and Gene Flow between Snails of Opposing
Chirality.” PLoS Biology, vol. 3, no. 9, Public Library of Science, 2005,
doi:10.1371/journal.pbio.0030282.
short: A. Davison, S. Chiba, N.H. Barton, B. Clarke, PLoS Biology 3 (2005).
date_created: 2018-12-11T12:04:14Z
date_published: 2005-08-09T00:00:00Z
date_updated: 2021-01-12T07:44:39Z
day: '09'
doi: 10.1371/journal.pbio.0030282
extern: 1
intvolume: ' 3'
issue: '9'
month: '08'
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '2771'
quality_controlled: 0
status: public
title: Speciation and gene flow between snails of opposing chirality
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 3
year: '2005'
...
---
_id: '3611'
abstract:
- lang: eng
text: 'We present two novel methods to infer mating patterns from genetic data.
They differ from existing statistical methods of parentage inference in that they
apply to populations that deviate from Hardy–Weinberg and linkage equilibrium,
and so are suited for the study of assortative mating in hybrid zones. The core
data set consists of genotypes at several loci for a number of full-sib clutches
of unknown parentage. Our inference is based throughout on estimates of allelic
associations within and across loci, such as heterozygote deficit and pairwise
linkage disequilibrium. In the first method, the most likely parents of a given
clutch are determined from the genotypic distribution of the associated adult
population, given an explicit model of nonrandom mating. This leads to estimates
of the strength of assortment. The second approach is based solely on the offspring
genotypes and relies on the fact that a linear relation exists between associations
among the offspring and those in the population of breeding pairs. We apply both
methods to a sample from the hybrid zone between the fire-bellied toads Bombina
bombina and B. variegata (Anura: Disco glossidae) in Croatia. Consistently, both
approaches provide no evidence for a departure from random mating, despite adequate
statistical power. Instead, B. variegata-like individuals among the adults contributed
disproportionately to the offspring cohort, consistent with their preference for
the type of breeding habitat in which this study was conducted.'
author:
- first_name: Beate
full_name: Nürnberger, Beate
last_name: Nürnberger
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Loeske
full_name: Kruuk, Loeske E
last_name: Kruuk
- first_name: Timothy
full_name: Vines, Timothy H
last_name: Vines
citation:
ama: 'Nürnberger B, Barton NH, Kruuk L, Vines T. Mating patterns in a Bombina hybrid
zone: Inferences from adult and full sib genotypes. Heredity. 2005;94(2):247-257.
doi:10.1038/sj.hdy.6800607'
apa: 'Nürnberger, B., Barton, N. H., Kruuk, L., & Vines, T. (2005). Mating patterns
in a Bombina hybrid zone: Inferences from adult and full sib genotypes. Heredity.
Nature Publishing Group. https://doi.org/10.1038/sj.hdy.6800607'
chicago: 'Nürnberger, Beate, Nicholas H Barton, Loeske Kruuk, and Timothy Vines.
“Mating Patterns in a Bombina Hybrid Zone: Inferences from Adult and Full Sib
Genotypes.” Heredity. Nature Publishing Group, 2005. https://doi.org/10.1038/sj.hdy.6800607.'
ieee: 'B. Nürnberger, N. H. Barton, L. Kruuk, and T. Vines, “Mating patterns in
a Bombina hybrid zone: Inferences from adult and full sib genotypes,” Heredity,
vol. 94, no. 2. Nature Publishing Group, pp. 247–257, 2005.'
ista: 'Nürnberger B, Barton NH, Kruuk L, Vines T. 2005. Mating patterns in a Bombina
hybrid zone: Inferences from adult and full sib genotypes. Heredity. 94(2), 247–257.'
mla: 'Nürnberger, Beate, et al. “Mating Patterns in a Bombina Hybrid Zone: Inferences
from Adult and Full Sib Genotypes.” Heredity, vol. 94, no. 2, Nature Publishing
Group, 2005, pp. 247–57, doi:10.1038/sj.hdy.6800607.'
short: B. Nürnberger, N.H. Barton, L. Kruuk, T. Vines, Heredity 94 (2005) 247–257.
date_created: 2018-12-11T12:04:14Z
date_published: 2005-02-01T00:00:00Z
date_updated: 2021-01-12T07:44:39Z
day: '01'
doi: 10.1038/sj.hdy.6800607
extern: 1
intvolume: ' 94'
issue: '2'
month: '02'
page: 247 - 257
publication: Heredity
publication_status: published
publisher: Nature Publishing Group
publist_id: '2772'
quality_controlled: 0
status: public
title: 'Mating patterns in a Bombina hybrid zone: Inferences from adult and full sib
genotypes'
type: journal_article
volume: 94
year: '2005'
...
---
_id: '3613'
abstract:
- lang: eng
text: 'The extent of genetic variation in fitness is a crucial issue in evolutionary
biology and yet remains largely unresolved. In Drosophila melanogaster, we have
devised a method that allows the net effects on fitness of heterozygous wild-type
chromosomes to be measured, by competing them against two different “balancer”
chromosomes. We have applied the method to a large sample of 40 wild-type third
chromosomes and have measured fitnesses of nonlethal chromosomes as well as chromosomes
bearing recessive lethals. The measurements were made in the environment to which
the population was adapted and did not involve inbreeding. The results show an
extraordinary similarity in the behavior of replicates of the same chromosome,
indicating consistent genetic effects on total fitness. Some invading chromosomes
increased rapidly and some slowly, and some rose to appreciable frequency after
several months, but then declined again: in every case, the same pattern was seen
in each replicate. We estimated relative fitnesses, rates of change of fitness,
and relative viabilities, for each chromosome. There were significant fluctuations
around the fitted model, which were also highly replicable. Wild-type chromosomes
varied substantially in their effects on heterozygous fitness, and these effects
vary through time, most likely as a result of genotype × environment interactions.'
author:
- first_name: Michael
full_name: Gardner, Michael P
last_name: Gardner
- first_name: Kevin
full_name: Fowler, Kevin
last_name: Fowler
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Linda
full_name: Patridge, Linda
last_name: Patridge
citation:
ama: 'Gardner M, Fowler K, Barton NH, Patridge L. Genetic variation for total fitness
in Drosophila melanogaster: Complex yet replicable patterns. Genetics.
2005;169(3):1553-1571. doi:10.1534/genetics.104.032367'
apa: 'Gardner, M., Fowler, K., Barton, N. H., & Patridge, L. (2005). Genetic
variation for total fitness in Drosophila melanogaster: Complex yet replicable
patterns. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.104.032367'
chicago: 'Gardner, Michael, Kevin Fowler, Nicholas H Barton, and Linda Patridge.
“Genetic Variation for Total Fitness in Drosophila Melanogaster: Complex yet Replicable
Patterns.” Genetics. Genetics Society of America, 2005. https://doi.org/10.1534/genetics.104.032367.'
ieee: 'M. Gardner, K. Fowler, N. H. Barton, and L. Patridge, “Genetic variation
for total fitness in Drosophila melanogaster: Complex yet replicable patterns,”
Genetics, vol. 169, no. 3. Genetics Society of America, pp. 1553–1571,
2005.'
ista: 'Gardner M, Fowler K, Barton NH, Patridge L. 2005. Genetic variation for total
fitness in Drosophila melanogaster: Complex yet replicable patterns. Genetics.
169(3), 1553–1571.'
mla: 'Gardner, Michael, et al. “Genetic Variation for Total Fitness in Drosophila
Melanogaster: Complex yet Replicable Patterns.” Genetics, vol. 169, no.
3, Genetics Society of America, 2005, pp. 1553–71, doi:10.1534/genetics.104.032367.'
short: M. Gardner, K. Fowler, N.H. Barton, L. Patridge, Genetics 169 (2005) 1553–1571.
date_created: 2018-12-11T12:04:15Z
date_published: 2005-03-01T00:00:00Z
date_updated: 2021-01-12T07:44:40Z
day: '01'
doi: 10.1534/genetics.104.032367
extern: 1
intvolume: ' 169'
issue: '3'
month: '03'
page: 1553 - 1571
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '2770'
quality_controlled: 0
status: public
title: 'Genetic variation for total fitness in Drosophila melanogaster: Complex yet
replicable patterns'
type: journal_article
volume: 169
year: '2005'
...
---
_id: '3691'
abstract:
- lang: eng
text: In strictly pseudoconvex domains with smooth boundary, we prove a commutator
relationship between admissible integral operators, as introduced by Lieb and
Range, and smooth vector fields which are tangential at boundary points. This
makes it possible to gain estimates for admissible operators in function spaces
which involve tangential derivatives. Examples are given under with circumstances
these can be transformed into genuine Sobolev- and C k-estimates.
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Lampert C. Boundary regularity of admissible operators. Publicacions Matemàtiques.
2005;49(1):179-195. doi:10.5565/PUBLMAT_49105_08
apa: Lampert, C. (2005). Boundary regularity of admissible operators. Publicacions
Matemàtiques. Universitat Autònoma de Barcelona, Departament de Matemàtique.
https://doi.org/10.5565/PUBLMAT_49105_08
chicago: Lampert, Christoph. “Boundary Regularity of Admissible Operators.” Publicacions
Matemàtiques. Universitat Autònoma de Barcelona, Departament de Matemàtique,
2005. https://doi.org/10.5565/PUBLMAT_49105_08.
ieee: C. Lampert, “Boundary regularity of admissible operators,” Publicacions
Matemàtiques, vol. 49, no. 1. Universitat Autònoma de Barcelona, Departament
de Matemàtique, pp. 179–195, 2005.
ista: Lampert C. 2005. Boundary regularity of admissible operators. Publicacions
Matemàtiques. 49(1), 179–195.
mla: Lampert, Christoph. “Boundary Regularity of Admissible Operators.” Publicacions
Matemàtiques, vol. 49, no. 1, Universitat Autònoma de Barcelona, Departament
de Matemàtique, 2005, pp. 179–95, doi:10.5565/PUBLMAT_49105_08.
short: C. Lampert, Publicacions Matemàtiques 49 (2005) 179–195.
date_created: 2018-12-11T12:04:38Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T07:48:59Z
day: '01'
doi: 10.5565/PUBLMAT_49105_08
extern: 1
intvolume: ' 49'
issue: '1'
month: '01'
page: 179 - 195
publication: Publicacions Matemàtiques
publication_status: published
publisher: Universitat Autònoma de Barcelona, Departament de Matemàtique
publist_id: '2673'
quality_controlled: 0
status: public
title: Boundary regularity of admissible operators
type: journal_article
volume: 49
year: '2005'
...
---
_id: '3721'
abstract:
- lang: eng
text: Recent advances in atomic force microscopy allowed globular and membrane proteins
to be mechanically unfolded on a single-molecule level. Presented is an extension
to the existing force spectroscopy experiments. While unfolding single bacteriorhodopsins
from native purple membranes, small oscillation amplitudes (6–9nm) were supplied
to the vertical displacement of the cantilever at a frequency of 3kHz. The phase
and amplitude response of the cantilever-protein system was converted to reveal
the elastic (conservative) and viscous (dissipative) contributions to the unfolding
process. The elastic response (stiffness) of the extended parts of the protein
were in the range of a few tens pN/nm and could be well described by the derivative
of the wormlike chain model. Discrete events in the viscous response coincided
with the unfolding of single secondary structure elements and were in the range
of 1μNs/m. In addition, these force modulation spectroscopy experiments revealed
novel mechanical unfolding intermediates of bacteriorhodopsin. We found that kinks
result in a loss of unfolding cooperativity in transmembrane helices. Reconstructing
force-distance spectra by the integration of amplitude-distance spectra verified
their position, offering a novel approach to detect intermediates during the forced
unfolding of single proteins.
author:
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
- first_name: Andrew
full_name: Humphris, Andrew D
last_name: Humphris
citation:
ama: Janovjak HL, Mueller D, Humphris A. Molecular force modulation spectroscopy
revealing the dynamic response of single bacteriorhodopsins. Biophysical Journal.
2005;88(2):1423-1431. doi:10.1529/biophysj.104.052746
apa: Janovjak, H. L., Mueller, D., & Humphris, A. (2005). Molecular force modulation
spectroscopy revealing the dynamic response of single bacteriorhodopsins. Biophysical
Journal. Biophysical Society. https://doi.org/10.1529/biophysj.104.052746
chicago: Janovjak, Harald L, Daniel Mueller, and Andrew Humphris. “Molecular Force
Modulation Spectroscopy Revealing the Dynamic Response of Single Bacteriorhodopsins.”
Biophysical Journal. Biophysical Society, 2005. https://doi.org/10.1529/biophysj.104.052746.
ieee: H. L. Janovjak, D. Mueller, and A. Humphris, “Molecular force modulation spectroscopy
revealing the dynamic response of single bacteriorhodopsins,” Biophysical Journal,
vol. 88, no. 2. Biophysical Society, pp. 1423–1431, 2005.
ista: Janovjak HL, Mueller D, Humphris A. 2005. Molecular force modulation spectroscopy
revealing the dynamic response of single bacteriorhodopsins. Biophysical Journal.
88(2), 1423–1431.
mla: Janovjak, Harald L., et al. “Molecular Force Modulation Spectroscopy Revealing
the Dynamic Response of Single Bacteriorhodopsins.” Biophysical Journal,
vol. 88, no. 2, Biophysical Society, 2005, pp. 1423–31, doi:10.1529/biophysj.104.052746.
short: H.L. Janovjak, D. Mueller, A. Humphris, Biophysical Journal 88 (2005) 1423–1431.
date_created: 2018-12-11T12:04:48Z
date_published: 2005-02-01T00:00:00Z
date_updated: 2021-01-12T07:51:43Z
day: '01'
doi: 10.1529/biophysj.104.052746
extern: 1
intvolume: ' 88'
issue: '2'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305144/
month: '02'
oa: 1
page: 1423 - 1431
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '2509'
quality_controlled: 0
status: public
title: Molecular force modulation spectroscopy revealing the dynamic response of single
bacteriorhodopsins
type: journal_article
volume: 88
year: '2005'
...
---
_id: '3741'
abstract:
- lang: eng
text: In an age of increasingly large data sets, investigators in many different
disciplines have turned to clustering as a tool for data analysis and exploration.
Existing clustering methods, however, typically depend on several nontrivial assumptions
about the structure of data. Here, we reformulate the clustering problem from
an information theoretic perspective that avoids many of these assumptions. In
particular, our formulation obviates the need for defining a cluster "prototype,"
does not require an a priori similarity metric, is invariant to changes in the
representation of the data, and naturally captures nonlinear relations. We apply
this approach to different domains and find that it consistently produces clusters
that are more coherent than those extracted by existing algorithms. Finally, our
approach provides a way of clustering based on collective notions of similarity
rather than the traditional pairwise measures.
author:
- first_name: N.
full_name: Slonim,N.
last_name: Slonim
- first_name: G.
full_name: Atwal,G.
last_name: Atwal
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Slonim N, Atwal G, Tkačik G, Bialek W. Information-based clustering. PNAS.
2005;102(51):18297-18302. doi:10.1073/pnas.0507432102
apa: Slonim, N., Atwal, G., Tkačik, G., & Bialek, W. (2005). Information-based
clustering. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0507432102
chicago: Slonim, N., G. Atwal, Gašper Tkačik, and William Bialek. “Information-Based
Clustering.” PNAS. National Academy of Sciences, 2005. https://doi.org/10.1073/pnas.0507432102.
ieee: N. Slonim, G. Atwal, G. Tkačik, and W. Bialek, “Information-based clustering,”
PNAS, vol. 102, no. 51. National Academy of Sciences, pp. 18297–18302,
2005.
ista: Slonim N, Atwal G, Tkačik G, Bialek W. 2005. Information-based clustering.
PNAS. 102(51), 18297–18302.
mla: Slonim, N., et al. “Information-Based Clustering.” PNAS, vol. 102, no.
51, National Academy of Sciences, 2005, pp. 18297–302, doi:10.1073/pnas.0507432102.
short: N. Slonim, G. Atwal, G. Tkačik, W. Bialek, PNAS 102 (2005) 18297–18302.
date_created: 2018-12-11T12:04:55Z
date_published: 2005-12-20T00:00:00Z
date_updated: 2021-01-12T07:51:52Z
day: '20'
doi: 10.1073/pnas.0507432102
extern: 1
intvolume: ' 102'
issue: '51'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1317937
month: '12'
oa: 1
page: 18297 - 18302
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2490'
quality_controlled: 0
status: public
title: Information-based clustering
type: journal_article
volume: 102
year: '2005'
...
---
_id: '3746'
abstract:
- lang: eng
text: We address the practical problems of estimating the information relations
that characterize large networks. Building on methods developed for analysis of
the neural code, we show that reliable estimates of mutual information can be
obtained with manageable computational effort. The same methods allow estimation
of higher order, multi-information terms. These ideas are illustrated by analyses
of gene expression, financial markets, and consumer preferences. In each case,
information theoretic measures correlate with independent, intuitive measures
of the underlying structures in the system.
author:
- first_name: Noam
full_name: Slonim,Noam
last_name: Slonim
- first_name: Gurinder
full_name: Atwal,Gurinder S
last_name: Atwal
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Slonim N, Atwal G, Tkačik G, Bialek W. Estimating mutual information and multi-information
in large networks. ArXiv. 2005:1-11.
apa: Slonim, N., Atwal, G., Tkačik, G., & Bialek, W. (2005). Estimating mutual
information and multi-information in large networks. ArXiv. ArXiv.
chicago: Slonim, Noam, Gurinder Atwal, Gašper Tkačik, and William Bialek. “Estimating
Mutual Information and Multi-Information in Large Networks.” ArXiv. ArXiv,
2005.
ieee: N. Slonim, G. Atwal, G. Tkačik, and W. Bialek, “Estimating mutual information
and multi-information in large networks,” ArXiv. ArXiv, pp. 1–11, 2005.
ista: Slonim N, Atwal G, Tkačik G, Bialek W. 2005. Estimating mutual information
and multi-information in large networks. ArXiv, 1–11, .
mla: Slonim, Noam, et al. “Estimating Mutual Information and Multi-Information in
Large Networks.” ArXiv, ArXiv, 2005, pp. 1–11.
short: N. Slonim, G. Atwal, G. Tkačik, W. Bialek, ArXiv (2005) 1–11.
date_created: 2018-12-11T12:04:56Z
date_published: 2005-02-03T00:00:00Z
date_updated: 2021-01-12T07:51:54Z
day: '03'
extern: 1
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/cs/0502017v1
month: '02'
oa: 1
page: 1 - 11
publication: ArXiv
publication_status: published
publisher: ArXiv
publist_id: '2484'
quality_controlled: 0
status: public
title: Estimating mutual information and multi-information in large networks
type: preprint
year: '2005'
...
---
_id: '3808'
abstract:
- lang: eng
text: Action potentials in central neurons are initiated near the axon initial segment,
propagate into the axon, and finally invade the presynaptic terminals, where they
trigger transmitter release. Voltage-gated Na(+) channels are key determinants
of excitability, but Na(+) channel density and properties in axons and presynaptic
terminals of cortical neurons have not been examined yet. In hippocampal mossy
fiber boutons, which emerge from parent axons en passant, Na(+) channels are very
abundant, with an estimated number of approximately 2000 channels per bouton.
Presynaptic Na(+) channels show faster inactivation kinetics than somatic channels,
suggesting differences between subcellular compartments of the same cell. Computational
analysis of action potential propagation in axon-multibouton structures reveals
that Na(+) channels in boutons preferentially amplify the presynaptic action potential
and enhance Ca(2+) inflow, whereas Na(+) channels in axons control the reliability
and speed of propagation. Thus, presynaptic and axonal Na(+) channels contribute
differentially to mossy fiber synaptic transmission.
author:
- first_name: Dominique
full_name: Engel, Dominique
last_name: Engel
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Engel D, Jonas PM. Presynaptic action potential amplification by voltage-gated
Na+ channels in hippocampal mossy fiber boutons. Neuron. 2005;45(3):405-417.
doi:10.1016/j.neuron.2004.12.048
apa: Engel, D., & Jonas, P. M. (2005). Presynaptic action potential amplification
by voltage-gated Na+ channels in hippocampal mossy fiber boutons. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2004.12.048
chicago: Engel, Dominique, and Peter M Jonas. “Presynaptic Action Potential Amplification
by Voltage-Gated Na+ Channels in Hippocampal Mossy Fiber Boutons.” Neuron.
Elsevier, 2005. https://doi.org/10.1016/j.neuron.2004.12.048
.
ieee: D. Engel and P. M. Jonas, “Presynaptic action potential amplification by voltage-gated
Na+ channels in hippocampal mossy fiber boutons,” Neuron, vol. 45, no.
3. Elsevier, pp. 405–17, 2005.
ista: Engel D, Jonas PM. 2005. Presynaptic action potential amplification by voltage-gated
Na+ channels in hippocampal mossy fiber boutons. Neuron. 45(3), 405–17.
mla: Engel, Dominique, and Peter M. Jonas. “Presynaptic Action Potential Amplification
by Voltage-Gated Na+ Channels in Hippocampal Mossy Fiber Boutons.” Neuron,
vol. 45, no. 3, Elsevier, 2005, pp. 405–17, doi:10.1016/j.neuron.2004.12.048 .
short: D. Engel, P.M. Jonas, Neuron 45 (2005) 405–17.
date_created: 2018-12-11T12:05:17Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:21Z
day: '01'
doi: '10.1016/j.neuron.2004.12.048 '
extern: 1
intvolume: ' 45'
issue: '3'
month: '01'
page: 405 - 17
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2400'
quality_controlled: 0
status: public
title: Presynaptic action potential amplification by voltage-gated Na+ channels in
hippocampal mossy fiber boutons
type: journal_article
volume: 45
year: '2005'
...
---
_id: '3892'
abstract:
- lang: eng
text: 'In 2-player non-zero-sum games, Nash equilibria capture the options for rational
behavior if each player attempts to maximize her payoff. In contrast to classical
game theory, we consider lexicographic objectives: first, each player tries to
maximize her own payoff, and then, the player tries to minimize the opponent''s
payoff. Such objectives arise naturally in the verification of systems with multiple
components. There, instead of proving that each component satisfies its specification
no matter how the other components behave, it often suffices to prove that each
component satisfies its specification provided that the other components satisfy
their specifications. We say that a Nash equilibrium is secure if it is an equilibrium
with respect to the lexicographic objectives of both players. We prove that in
graph games with Borel winning conditions, which include the games that arise
in verification, there may be several Nash equilibria, but there is always a unique
maximal payoff profile of a secure equilibrium. We show how this equilibrium can
be computed in the case of omega-regular winning conditions, and we characterize
the memory requirements of strategies that achieve the equilibrium.'
acknowledgement: |-
This research was supported in part by the ONR grant N00014-02-1-0671, the AFOSR MURI grant F49620-00-1-0327, and the NSF grant CCR-0225610.
This is an extended version of the paper “Games with Secure Equilibria” that appeared in the proceedings of Logic in Computer Science (LICS), 2004.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Marcin
full_name: Jurdziński, Marcin
last_name: Jurdziński
citation:
ama: 'Chatterjee K, Henzinger TA, Jurdziński M. Games with secure equilibria. In:
Vol 3657. Springer; 2005:141-161. doi:10.1007/11561163_7'
apa: 'Chatterjee, K., Henzinger, T. A., & Jurdziński, M. (2005). Games with
secure equilibria (Vol. 3657, pp. 141–161). Presented at the FMCO: Formal Methods
for Components and Objects, Springer. https://doi.org/10.1007/11561163_7'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Marcin Jurdziński. “Games
with Secure Equilibria,” 3657:141–61. Springer, 2005. https://doi.org/10.1007/11561163_7.
ieee: 'K. Chatterjee, T. A. Henzinger, and M. Jurdziński, “Games with secure equilibria,”
presented at the FMCO: Formal Methods for Components and Objects, 2005, vol. 3657,
pp. 141–161.'
ista: 'Chatterjee K, Henzinger TA, Jurdziński M. 2005. Games with secure equilibria.
FMCO: Formal Methods for Components and Objects, LNCS, vol. 3657, 141–161.'
mla: Chatterjee, Krishnendu, et al. Games with Secure Equilibria. Vol. 3657,
Springer, 2005, pp. 141–61, doi:10.1007/11561163_7.
short: K. Chatterjee, T.A. Henzinger, M. Jurdziński, in:, Springer, 2005, pp. 141–161.
conference:
name: 'FMCO: Formal Methods for Components and Objects'
date_created: 2018-12-11T12:05:44Z
date_published: 2005-09-19T00:00:00Z
date_updated: 2021-01-12T07:53:00Z
day: '19'
doi: 10.1007/11561163_7
extern: 1
intvolume: ' 3657'
month: '09'
page: 141 - 161
publication_status: published
publisher: Springer
publist_id: '2269'
quality_controlled: 0
status: public
title: Games with secure equilibria
type: conference
volume: 3657
year: '2005'
...
---
_id: '3902'
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Jacobus
full_name: Boomsma, Jacobus
last_name: Boomsma
citation:
ama: 'Cremer S, Boomsma J. The drawback of mobility: invasive species in a globalised
world. In: Elsevier; 2005.'
apa: 'Cremer, S., & Boomsma, J. (2005). The drawback of mobility: invasive species
in a globalised world. Presented at the Marie Curie Conference, Elsevier.'
chicago: 'Cremer, Sylvia, and Jacobus Boomsma. “The Drawback of Mobility: Invasive
Species in a Globalised World.” Elsevier, 2005.'
ieee: 'S. Cremer and J. Boomsma, “The drawback of mobility: invasive species in
a globalised world,” presented at the Marie Curie Conference, 2005.'
ista: 'Cremer S, Boomsma J. 2005. The drawback of mobility: invasive species in
a globalised world. Marie Curie Conference.'
mla: 'Cremer, Sylvia, and Jacobus Boomsma. The Drawback of Mobility: Invasive
Species in a Globalised World. Elsevier, 2005.'
short: S. Cremer, J. Boomsma, in:, Elsevier, 2005.
conference:
name: Marie Curie Conference
date_created: 2018-12-11T12:05:47Z
date_published: 2005-09-01T00:00:00Z
date_updated: 2021-01-12T07:53:05Z
day: '01'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://www.docstoc.com/docs/15327566/1-The-drawback-of-mobility-invasive-species-in-a-globalised-world
month: '09'
oa_version: None
publication_status: published
publisher: Elsevier
publist_id: '2252'
status: public
title: 'The drawback of mobility: invasive species in a globalised world'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2005'
...