---
_id: '3003'
abstract:
- lang: eng
text: 'Plant development displays an exceptional plasticity and adaptability that
involves the dynamic, asymmetric distribution of the phytohormone auxin. Polar
auxin flow, which requires polarly localized transport facilitators of the PIN
family, largely contributes to the establishment and maintenance of the auxin
gradients. Functionally overlapping action of PIN proteins mediates multiple developmental
processes, including embryo formation, organ development and tropisms. Here we
show that PIN proteins exhibit synergistic interactions, which involve cross-regulation
of PIN gene expression in pin mutants or plants with inhibited auxin transport.
Auxin itself positively feeds back on PIN gene expression in a tissue-specific
manner through an AUX/IAA-dependent signalling pathway. This regulatory switch
is indicative of a mechanism by which the loss of a specific PIN protein is compensated
for by auxin-dependent ectopic: expression of its homologues. The compensatory
properties of the PIN-dependent transport network might enable the stabilization
of auxin gradients and potentially contribute to the robustness of plant adaptive
development.'
author:
- first_name: Anne
full_name: Vieten, Anne
last_name: Vieten
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Justyna
full_name: Wiśniewska, Justyna
last_name: Wiśniewska
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: René
full_name: Benjamins, René
last_name: Benjamins
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Vieten A, Vanneste S, Wiśniewska J, et al. Functional redundancy of PIN proteins
is accompanied by auxin-dependent cross-regulation of PIN expression. Development.
2005;132(20):4521-4531. doi:10.1242/dev.02027
apa: Vieten, A., Vanneste, S., Wiśniewska, J., Benková, E., Benjamins, R., Beeckman,
T., … Friml, J. (2005). Functional redundancy of PIN proteins is accompanied by
auxin-dependent cross-regulation of PIN expression. Development. Company
of Biologists. https://doi.org/10.1242/dev.02027
chicago: Vieten, Anne, Steffen Vanneste, Justyna Wiśniewska, Eva Benková, René Benjamins,
Tom Beeckman, Christian Luschnig, and Jiří Friml. “Functional Redundancy of PIN
Proteins Is Accompanied by Auxin-Dependent Cross-Regulation of PIN Expression.”
Development. Company of Biologists, 2005. https://doi.org/10.1242/dev.02027.
ieee: A. Vieten et al., “Functional redundancy of PIN proteins is accompanied
by auxin-dependent cross-regulation of PIN expression,” Development, vol.
132, no. 20. Company of Biologists, pp. 4521–4531, 2005.
ista: Vieten A, Vanneste S, Wiśniewska J, Benková E, Benjamins R, Beeckman T, Luschnig
C, Friml J. 2005. Functional redundancy of PIN proteins is accompanied by auxin-dependent
cross-regulation of PIN expression. Development. 132(20), 4521–4531.
mla: Vieten, Anne, et al. “Functional Redundancy of PIN Proteins Is Accompanied
by Auxin-Dependent Cross-Regulation of PIN Expression.” Development, vol.
132, no. 20, Company of Biologists, 2005, pp. 4521–31, doi:10.1242/dev.02027.
short: A. Vieten, S. Vanneste, J. Wiśniewska, E. Benková, R. Benjamins, T. Beeckman,
C. Luschnig, J. Friml, Development 132 (2005) 4521–4531.
date_created: 2018-12-11T12:00:48Z
date_published: 2005-10-01T00:00:00Z
date_updated: 2021-01-12T07:40:23Z
day: '01'
doi: 10.1242/dev.02027
extern: 1
intvolume: ' 132'
issue: '20'
month: '10'
page: 4521 - 4531
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '3700'
quality_controlled: 0
status: public
title: Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation
of PIN expression
type: journal_article
volume: 132
year: '2005'
...
---
_id: '3004'
abstract:
- lang: eng
text: Molecular mechanisms of pattern formation in the plant embryo are not well
understood. Recent molecular and cellular studies, in conjunction with earlier
microsurgical, physiological, and genetic work, are now starting to define the
outlines of a model where gradients of the signaling molecule auxin play a central
role in embryo patterning. It is relatively clear how these gradients are established
and interpreted, but how they are maintained is still unresolved. Here, we have
studied the contributions of auxin biosynthesis, conjugation, and transport pathways
to the maintenance of embryonic auxin gradients. Auxin homeostasis in the embryo
was manipulated by region-specific conditional expression of indoleacetic acid-tryptophan
monooxygenase or indoleacetic acid-lysine synthetase, bacterial enzymes for auxin
biosynthesis or conjugation. Neither manipulation of auxin biosynthesis nor of
auxin conjugation interfered with auxin gradients and patterning in the embryo.
This result suggests a compensatory mechanism for buffering auxin gradients in
the embryo. Chemical and genetic inhibition revealed that auxin transport activity,
in particular that of the PIN-FORMED1 (PIN1) and PIN4 proteins, is a major factor
in the maintenance of these gradients.
author:
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Olivier
full_name: Meurette, Olivier
last_name: Meurette
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Göran
full_name: Sandberg, Göran
last_name: Sandberg
- first_name: Paul
full_name: Hooykaas, Paul
last_name: Hooykaas
- first_name: Remko
full_name: Offringa, Remko
last_name: Offringa
citation:
ama: Weijers D, Sauer M, Meurette O, et al. Maintenance of embryonic auxin distribution
for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis.
Plant Cell. 2005;17(9):2517-2526. doi:10.1105/tpc.105.034637
apa: Weijers, D., Sauer, M., Meurette, O., Friml, J., Ljung, K., Sandberg, G., …
Offringa, R. (2005). Maintenance of embryonic auxin distribution for apical basal
patterning by PIN FORMED dependent auxin transport in Arabidopsis. Plant Cell.
American Society of Plant Biologists. https://doi.org/10.1105/tpc.105.034637
chicago: Weijers, Dolf, Michael Sauer, Olivier Meurette, Jiří Friml, Karin Ljung,
Göran Sandberg, Paul Hooykaas, and Remko Offringa. “Maintenance of Embryonic Auxin
Distribution for Apical Basal Patterning by PIN FORMED Dependent Auxin Transport
in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2005.
https://doi.org/10.1105/tpc.105.034637.
ieee: D. Weijers et al., “Maintenance of embryonic auxin distribution for
apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis,”
Plant Cell, vol. 17, no. 9. American Society of Plant Biologists, pp. 2517–2526,
2005.
ista: Weijers D, Sauer M, Meurette O, Friml J, Ljung K, Sandberg G, Hooykaas P,
Offringa R. 2005. Maintenance of embryonic auxin distribution for apical basal
patterning by PIN FORMED dependent auxin transport in Arabidopsis. Plant Cell.
17(9), 2517–2526.
mla: Weijers, Dolf, et al. “Maintenance of Embryonic Auxin Distribution for Apical
Basal Patterning by PIN FORMED Dependent Auxin Transport in Arabidopsis.” Plant
Cell, vol. 17, no. 9, American Society of Plant Biologists, 2005, pp. 2517–26,
doi:10.1105/tpc.105.034637.
short: D. Weijers, M. Sauer, O. Meurette, J. Friml, K. Ljung, G. Sandberg, P. Hooykaas,
R. Offringa, Plant Cell 17 (2005) 2517–2526.
date_created: 2018-12-11T12:00:48Z
date_published: 2005-07-01T00:00:00Z
date_updated: 2021-01-12T07:40:24Z
day: '01'
doi: 10.1105/tpc.105.034637
extern: 1
intvolume: ' 17'
issue: '9'
month: '07'
page: 2517 - 2526
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3698'
quality_controlled: 0
status: public
title: Maintenance of embryonic auxin distribution for apical basal patterning by
PIN FORMED dependent auxin transport in Arabidopsis
type: journal_article
volume: 17
year: '2005'
...
---
_id: '3141'
abstract:
- lang: eng
text: The two actin-related subunits of the Arp2/3 complex, Arp2 and Arp3, are proposed
to form a pseudo actin dimer that nucleates actin polymerization. However, in
the crystal structure of the inactive complex, they are too far apart to form
such a nucleus. Here, we show using EM that yeast and bovine Arp2/3 complexes
exist in a distribution among open, intermediate and closed conformations. The
crystal structure docks well into the open conformation. The activator WASp binds
at the cleft between Arp2 and Arp3, and all WASp-bound complexes are closed. The
inhibitor coronin binds near the p35 subunit, and all coronin-bound complexes
are open. Activating and loss-of-function mutations in the p35 subunit skew conformational
distribution in opposite directions, closed and open, respectively. We conclude
that WASp stabilizes p35-dependent closure of the complex, holding Arp2 and Arp3
closer together to nucleate an actin filament.
author:
- first_name: Avital
full_name: Rodal, Avital A
last_name: Rodal
- first_name: Olga
full_name: Sokolova, Olga
last_name: Sokolova
- first_name: Deborah
full_name: Robins, Deborah B
last_name: Robins
- first_name: Karen
full_name: Daugherty, Karen M
last_name: Daugherty
- first_name: Simon
full_name: Simon Hippenmeyer
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Howard
full_name: Riezman, Howard
last_name: Riezman
- first_name: Nikolaus
full_name: Grigorieff, Nikolaus
last_name: Grigorieff
- first_name: Bruce
full_name: Goode, Bruce L
last_name: Goode
citation:
ama: Rodal A, Sokolova O, Robins D, et al. Conformational changes in the Arp2 3
complex leading to actin nucleation. Nature Structural and Molecular Biology.
2005;12(1):26-31. doi:10.1038/nsmb870
apa: Rodal, A., Sokolova, O., Robins, D., Daugherty, K., Hippenmeyer, S., Riezman,
H., … Goode, B. (2005). Conformational changes in the Arp2 3 complex leading to
actin nucleation. Nature Structural and Molecular Biology. Nature Publishing
Group. https://doi.org/10.1038/nsmb870
chicago: Rodal, Avital, Olga Sokolova, Deborah Robins, Karen Daugherty, Simon Hippenmeyer,
Howard Riezman, Nikolaus Grigorieff, and Bruce Goode. “Conformational Changes
in the Arp2 3 Complex Leading to Actin Nucleation.” Nature Structural and Molecular
Biology. Nature Publishing Group, 2005. https://doi.org/10.1038/nsmb870.
ieee: A. Rodal et al., “Conformational changes in the Arp2 3 complex leading
to actin nucleation,” Nature Structural and Molecular Biology, vol. 12,
no. 1. Nature Publishing Group, pp. 26–31, 2005.
ista: Rodal A, Sokolova O, Robins D, Daugherty K, Hippenmeyer S, Riezman H, Grigorieff
N, Goode B. 2005. Conformational changes in the Arp2 3 complex leading to actin
nucleation. Nature Structural and Molecular Biology. 12(1), 26–31.
mla: Rodal, Avital, et al. “Conformational Changes in the Arp2 3 Complex Leading
to Actin Nucleation.” Nature Structural and Molecular Biology, vol. 12,
no. 1, Nature Publishing Group, 2005, pp. 26–31, doi:10.1038/nsmb870.
short: A. Rodal, O. Sokolova, D. Robins, K. Daugherty, S. Hippenmeyer, H. Riezman,
N. Grigorieff, B. Goode, Nature Structural and Molecular Biology 12 (2005) 26–31.
date_created: 2018-12-11T12:01:38Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:21Z
day: '01'
doi: 10.1038/nsmb870
extern: 1
intvolume: ' 12'
issue: '1'
month: '01'
page: 26 - 31
publication: Nature Structural and Molecular Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3554'
quality_controlled: 0
status: public
title: Conformational changes in the Arp2 3 complex leading to actin nucleation
type: journal_article
volume: 12
year: '2005'
...
---
_id: '3143'
abstract:
- lang: eng
text: Two ETS transcription factors of the Pea3 subfamily are induced in subpopulations
of dorsal root ganglion (DRG) sensory and spinal motor neurons by target-derived
factors. Their expression controls late aspects of neuronal differentiation such
as target invasion and branching. Here, we show that the late onset of ETS gene
expression is an essential requirement for normal sensory neuron differentiation.
We provide genetic evidence in the mouse that precocious ETS expression in DRG
sensory neurons perturbs axonal projections, the acquisition of terminal differentiation
markers, and their dependence on neurotrophic support. Together, our findings
indicate that DRG sensory neurons exhibit a temporal developmental switch that
can be revealed by distinct responses to ETS transcription factor signaling at
sequential steps of neuronal maturation.
author:
- first_name: Simon
full_name: Simon Hippenmeyer
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Eline
full_name: Vrieseling, Eline
last_name: Vrieseling
- first_name: Markus
full_name: Sigrist, Markus
last_name: Sigrist
- first_name: Thomas
full_name: Portmann, Thomas
last_name: Portmann
- first_name: Celia
full_name: Laengle, Celia
last_name: Laengle
- first_name: David
full_name: Ladle, David R
last_name: Ladle
- first_name: Silvia
full_name: Arber, Silvia
last_name: Arber
citation:
ama: Hippenmeyer S, Vrieseling E, Sigrist M, et al. A developmental switch in the
response of DRG neurons to ETS transcription factor signaling. PLoS Biology.
2005;3(5):0878-0890. doi:10.1371/journal.pbio.0030159
apa: Hippenmeyer, S., Vrieseling, E., Sigrist, M., Portmann, T., Laengle, C., Ladle,
D., & Arber, S. (2005). A developmental switch in the response of DRG neurons
to ETS transcription factor signaling. PLoS Biology. Public Library of
Science. https://doi.org/10.1371/journal.pbio.0030159
chicago: Hippenmeyer, Simon, Eline Vrieseling, Markus Sigrist, Thomas Portmann,
Celia Laengle, David Ladle, and Silvia Arber. “A Developmental Switch in the Response
of DRG Neurons to ETS Transcription Factor Signaling.” PLoS Biology. Public
Library of Science, 2005. https://doi.org/10.1371/journal.pbio.0030159.
ieee: S. Hippenmeyer et al., “A developmental switch in the response of DRG
neurons to ETS transcription factor signaling,” PLoS Biology, vol. 3, no.
5. Public Library of Science, pp. 0878–0890, 2005.
ista: Hippenmeyer S, Vrieseling E, Sigrist M, Portmann T, Laengle C, Ladle D, Arber
S. 2005. A developmental switch in the response of DRG neurons to ETS transcription
factor signaling. PLoS Biology. 3(5), 0878–0890.
mla: Hippenmeyer, Simon, et al. “A Developmental Switch in the Response of DRG Neurons
to ETS Transcription Factor Signaling.” PLoS Biology, vol. 3, no. 5, Public
Library of Science, 2005, pp. 0878–90, doi:10.1371/journal.pbio.0030159.
short: S. Hippenmeyer, E. Vrieseling, M. Sigrist, T. Portmann, C. Laengle, D. Ladle,
S. Arber, PLoS Biology 3 (2005) 0878–0890.
date_created: 2018-12-11T12:01:38Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T07:41:21Z
day: '01'
doi: 10.1371/journal.pbio.0030159
extern: 1
intvolume: ' 3'
issue: '5'
month: '05'
page: 0878 - 0890
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '3552'
quality_controlled: 0
status: public
title: A developmental switch in the response of DRG neurons to ETS transcription
factor signaling
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: '3175'
abstract:
- lang: eng
text: This paper addresses the novel problem of automatically synthesizing an output
image from a large collection of different input images. The synthesized image,
called a digital tapestry, can be viewed as a visual summary or a virtual 'thumbnail'
of all the images in the input collection. The problem of creating the tapestry
is cast as a multi-class labeling problem such that each region in the tapestry
is constructed from input image blocks that are salient and such that neighboring
blocks satisfy spatial compatibility. This is formulated using a Markov Random
Field and optimized via the graph cut based expansion move algorithm. The standard
expansion move algorithm can only handle energies with metric terms, while our
energy contains non-metric (soft and hard) constraints. Therefore we propose two
novel contributions. First, we extend the expansion move algorithm for energy
functions with non-metric hard constraints. Secondly, we modify it for functions
with "almost" metric soft terms, and show that it gives good results
in practice. The proposed framework was tested on several consumer photograph
collections, and the results are presented.
author:
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Sanjiv
full_name: Kumar, Sanjiv
last_name: Kumar
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
citation:
ama: 'Rother C, Kumar S, Kolmogorov V, Blake A. Digital tapestry. In: Vol 1. IEEE;
2005:589-596. doi:10.1109/CVPR.2005.130'
apa: 'Rother, C., Kumar, S., Kolmogorov, V., & Blake, A. (2005). Digital tapestry
(Vol. 1, pp. 589–596). Presented at the CVPR: Computer Vision and Pattern Recognition,
IEEE. https://doi.org/10.1109/CVPR.2005.130'
chicago: Rother, Carsten, Sanjiv Kumar, Vladimir Kolmogorov, and Andrew Blake. “Digital
Tapestry,” 1:589–96. IEEE, 2005. https://doi.org/10.1109/CVPR.2005.130.
ieee: 'C. Rother, S. Kumar, V. Kolmogorov, and A. Blake, “Digital tapestry,” presented
at the CVPR: Computer Vision and Pattern Recognition, 2005, vol. 1, pp. 589–596.'
ista: 'Rother C, Kumar S, Kolmogorov V, Blake A. 2005. Digital tapestry. CVPR: Computer
Vision and Pattern Recognition vol. 1, 589–596.'
mla: Rother, Carsten, et al. Digital Tapestry. Vol. 1, IEEE, 2005, pp. 589–96,
doi:10.1109/CVPR.2005.130.
short: C. Rother, S. Kumar, V. Kolmogorov, A. Blake, in:, IEEE, 2005, pp. 589–596.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:50Z
date_published: 2005-07-25T00:00:00Z
date_updated: 2021-01-12T07:41:35Z
day: '25'
doi: 10.1109/CVPR.2005.130
extern: 1
intvolume: ' 1'
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/en-us/um/people/ablake/papers/ablake/rother_cvpr05.pdf
month: '07'
page: 589 - 596
publication_status: published
publisher: IEEE
publist_id: '3503'
quality_controlled: 0
status: public
title: Digital tapestry
type: conference
volume: 1
year: '2005'
...
---
_id: '3176'
abstract:
- lang: eng
text: |
This paper demonstrates the high quality, real-time segmentation techniques. We achieve 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 performance, 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: IEEE; 2005:1186-1186. doi:10.1109/CVPR.2005.90'
apa: 'Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., & Rother, C. (2005).
Bi-layer segmentation of binocular stereo video (pp. 1186–1186). Presented at
the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2005.90'
chicago: Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross,
and Carsten Rother. “Bi-Layer Segmentation of Binocular Stereo Video,” 1186–1186.
IEEE, 2005. https://doi.org/10.1109/CVPR.2005.90.
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, pp. 1186–1186.'
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, 1186–1186.'
mla: Kolmogorov, Vladimir, et al. Bi-Layer Segmentation of Binocular Stereo Video.
IEEE, 2005, pp. 1186–1186, doi:10.1109/CVPR.2005.90.
short: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, in:, IEEE, 2005,
pp. 1186–1186.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:50Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:35Z
day: '01'
doi: 10.1109/CVPR.2005.90
extern: 1
month: '01'
page: 1186 - 1186
publication_status: published
publisher: IEEE
publist_id: '3504'
quality_controlled: 0
status: public
title: Bi-layer segmentation of binocular stereo video
type: conference
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: '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: '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: '3211'
abstract:
- lang: eng
text: We present an improved bound on the advantage of any q-query adversary at
distinguishing between the CBC MAC over a random n-bit permutation and a random
function outputting n bits. The result assumes that no message queried is a prefix
of any other, as is the case when all messages to be MACed have the same length.
We go on to give an improved analysis of the encrypted CBC MAC, where there is
no restriction on queried messages. Letting m be the block length of the longest
query, our bounds are about mq2/2n for the basic CBC MAC and mo(1)q2/2n for the
encrypted CBC MAC, improving prior bounds of m2q2/2n. The new bounds translate
into improved guarantees on the probability of forging these MACs.
acknowledgement: Pietrzak was supported by the Swiss National Science Foundation,
project No. 200020-103847/1.
alternative_title:
- LNCS
author:
- first_name: Mihir
full_name: Bellare, Mihir
last_name: Bellare
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Phillip
full_name: Rogaway, Phillip
last_name: Rogaway
citation:
ama: 'Bellare M, Pietrzak KZ, Rogaway P. Improved security analyses for CBC MACs.
In: Vol 3621. Springer; 2005:527-545. doi:10.1007/11535218_32'
apa: 'Bellare, M., Pietrzak, K. Z., & Rogaway, P. (2005). Improved security
analyses for CBC MACs (Vol. 3621, pp. 527–545). Presented at the CRYPTO: International
Cryptology Conference, Springer. https://doi.org/10.1007/11535218_32'
chicago: Bellare, Mihir, Krzysztof Z Pietrzak, and Phillip Rogaway. “Improved Security
Analyses for CBC MACs,” 3621:527–45. Springer, 2005. https://doi.org/10.1007/11535218_32.
ieee: 'M. Bellare, K. Z. Pietrzak, and P. Rogaway, “Improved security analyses for
CBC MACs,” presented at the CRYPTO: International Cryptology Conference, 2005,
vol. 3621, pp. 527–545.'
ista: 'Bellare M, Pietrzak KZ, Rogaway P. 2005. Improved security analyses for CBC
MACs. CRYPTO: International Cryptology Conference, LNCS, vol. 3621, 527–545.'
mla: Bellare, Mihir, et al. Improved Security Analyses for CBC MACs. Vol.
3621, Springer, 2005, pp. 527–45, doi:10.1007/11535218_32.
short: M. Bellare, K.Z. Pietrzak, P. Rogaway, in:, Springer, 2005, pp. 527–545.
conference:
name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:02Z
date_published: 2005-09-12T00:00:00Z
date_updated: 2021-01-12T07:41:50Z
day: '12'
doi: 10.1007/11535218_32
extern: 1
intvolume: ' 3621'
month: '09'
page: 527 - 545
publication_status: published
publisher: Springer
publist_id: '3469'
quality_controlled: 0
status: public
title: Improved security analyses for CBC MACs
type: conference
volume: 3621
year: '2005'
...
---
_id: '3212'
abstract:
- lang: eng
text: |-
The Full-Domain Hash (FDH) signature scheme [3] forms one the most basic usages of random oracles. It works with a family F of trapdoor permutations (TDP), where the signature of m is computed as f−1(h(m)) (here f ∈R F and h is modelled as a random oracle). It is known to be existentially unforgeable for any TDP family F [3], although a much tighter security reduction is known for a restrictive class of TDP’s [10,14] — namely, those induced by a family of claw-free permutations (CFP) pairs. The latter result was shown [11] to match the best possible “black-box” security reduction in the random oracle model, irrespective of the TDP family F (e.g., RSA) one might use.
In this work we investigate the question if it is possible to instantiate the random oracle h with a “real” family of hash functions H such that the corresponding schemes can be proven secure in the standard model, under some natural assumption on the family F. Our main result rules out the existence of such instantiations for any assumption on F which (1) is satisfied by a family of random permutations; and (2) does not allow the attacker to invert f ∈R F on an a-priori unbounded number of points. Moreover, this holds even if the choice of H can arbitrarily depend on f. As an immediate corollary, we rule out instantiating FDH based on general claw-free permutations, which shows that in order to prove the security of FDH in the standard model one must utilize significantly more structure on F than what is sufficient for the best proof of security in the random oracle model.
acknowledgement: Supported by NSF CAREER Award CCR-0133806 and TC Grant No.CCR-0311095.
Supported by the Swiss National Science Foundation, project No. 200020-103847/1
alternative_title:
- LNCS
author:
- first_name: Yevgeniy
full_name: Dodis, Yevgeniy
last_name: Dodis
- first_name: Roberto
full_name: Oliveira, Roberto
last_name: Oliveira
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Dodis Y, Oliveira R, Pietrzak KZ. On the generic insecurity of the full domain
hash. In: Vol 3621. Springer; 2005:449-466. doi:10.1007/11535218_27'
apa: 'Dodis, Y., Oliveira, R., & Pietrzak, K. Z. (2005). On the generic insecurity
of the full domain hash (Vol. 3621, pp. 449–466). Presented at the CRYPTO: International
Cryptology Conference, Springer. https://doi.org/10.1007/11535218_27'
chicago: Dodis, Yevgeniy, Roberto Oliveira, and Krzysztof Z Pietrzak. “On the Generic
Insecurity of the Full Domain Hash,” 3621:449–66. Springer, 2005. https://doi.org/10.1007/11535218_27.
ieee: 'Y. Dodis, R. Oliveira, and K. Z. Pietrzak, “On the generic insecurity of
the full domain hash,” presented at the CRYPTO: International Cryptology Conference,
2005, vol. 3621, pp. 449–466.'
ista: 'Dodis Y, Oliveira R, Pietrzak KZ. 2005. On the generic insecurity of the
full domain hash. CRYPTO: International Cryptology Conference, LNCS, vol. 3621,
449–466.'
mla: Dodis, Yevgeniy, et al. On the Generic Insecurity of the Full Domain Hash.
Vol. 3621, Springer, 2005, pp. 449–66, doi:10.1007/11535218_27.
short: Y. Dodis, R. Oliveira, K.Z. Pietrzak, in:, Springer, 2005, pp. 449–466.
conference:
name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:03Z
date_published: 2005-09-12T00:00:00Z
date_updated: 2021-01-12T07:41:50Z
day: '12'
doi: 10.1007/11535218_27
extern: 1
intvolume: ' 3621'
month: '09'
page: 449 - 466
publication_status: published
publisher: Springer
publist_id: '3470'
quality_controlled: 0
status: public
title: On the generic insecurity of the full domain hash
type: conference
volume: 3621
year: '2005'
...
---
_id: '3213'
abstract:
- lang: eng
text: |-
We study the question whether the sequential or parallel composition of two functions, each indistinguishable from a random function by non-adaptive distinguishers is secure against adaptive distinguishers. The sequential composition of F and G is the function G(F()), the parallel composition is F G where ⋆ is some group operation. It has been shown that composition indeed gives adaptive security in the information theoretic setting, but unfortunately the proof does not translate into the more interesting computational case.
In this work we show that in the computational setting composition does not imply adaptive security: If there is a prime order cyclic group where the decisional Diffie-Hellman assumption holds, then there are functions F and G which are indistinguishable by non-adaptive polynomially time-bounded adversaries, but whose parallel composition can be completely broken (i.e. we recover the key) with only three adaptive queries. We give a similar result for sequential composition. Interestingly, we need a standard assumption from the asymmetric (aka. public-key) world to prove a negative result for symmetric (aka. private-key) systems.
acknowledgement: Supported by the Swiss National Science Foundation, project No. 200020-103847/1.
alternative_title:
- LNCS
author:
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Pietrzak KZ. Composition does not imply adaptive security. In: Vol 3621. Springer;
2005:55-65. doi:10.1007/11535218_4'
apa: 'Pietrzak, K. Z. (2005). Composition does not imply adaptive security (Vol.
3621, pp. 55–65). Presented at the CRYPTO: International Cryptology Conference,
Springer. https://doi.org/10.1007/11535218_4'
chicago: Pietrzak, Krzysztof Z. “Composition Does Not Imply Adaptive Security,”
3621:55–65. Springer, 2005. https://doi.org/10.1007/11535218_4.
ieee: 'K. Z. Pietrzak, “Composition does not imply adaptive security,” presented
at the CRYPTO: International Cryptology Conference, 2005, vol. 3621, pp. 55–65.'
ista: 'Pietrzak KZ. 2005. Composition does not imply adaptive security. CRYPTO:
International Cryptology Conference, LNCS, vol. 3621, 55–65.'
mla: Pietrzak, Krzysztof Z. Composition Does Not Imply Adaptive Security.
Vol. 3621, Springer, 2005, pp. 55–65, doi:10.1007/11535218_4.
short: K.Z. Pietrzak, in:, Springer, 2005, pp. 55–65.
conference:
name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:03Z
date_published: 2005-09-12T00:00:00Z
date_updated: 2021-01-12T07:41:50Z
day: '12'
doi: 10.1007/11535218_4
extern: 1
intvolume: ' 3621'
month: '09'
page: 55 - 65
publication_status: published
publisher: Springer
publist_id: '3468'
quality_controlled: 0
status: public
title: Composition does not imply adaptive security
type: conference
volume: 3621
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: '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: '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: '13431'
abstract:
- lang: eng
text: 'Hydrogel stamps can microstructure solid surfaces, i.e., modify the surface
topology of metals, glasses, and crystals. It is demonstrated that stamps soaked
in an appropriate etchant can remove material with micrometer-scale precision.
The Figure shows an array of concentric circles etched in glass using the immersion
wet stamping process described (scale bar: 500 μm).'
article_processing_charge: No
article_type: original
author:
- first_name: S. K.
full_name: Smoukov, S. K.
last_name: Smoukov
- first_name: K. J. M.
full_name: Bishop, K. J. M.
last_name: Bishop
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: C. J.
full_name: Campbell, C. J.
last_name: Campbell
- first_name: B. A.
full_name: Grzybowski, B. A.
last_name: Grzybowski
citation:
ama: Smoukov SK, Bishop KJM, Klajn R, Campbell CJ, Grzybowski BA. Cutting into solids
with micropatterned gels. Advanced Materials. 2005;17(11):1361-1365. doi:10.1002/adma.200402086
apa: Smoukov, S. K., Bishop, K. J. M., Klajn, R., Campbell, C. J., & Grzybowski,
B. A. (2005). Cutting into solids with micropatterned gels. Advanced Materials.
Wiley. https://doi.org/10.1002/adma.200402086
chicago: Smoukov, S. K., K. J. M. Bishop, Rafal Klajn, C. J. Campbell, and B. A.
Grzybowski. “Cutting into Solids with Micropatterned Gels.” Advanced Materials.
Wiley, 2005. https://doi.org/10.1002/adma.200402086.
ieee: S. K. Smoukov, K. J. M. Bishop, R. Klajn, C. J. Campbell, and B. A. Grzybowski,
“Cutting into solids with micropatterned gels,” Advanced Materials, vol.
17, no. 11. Wiley, pp. 1361–1365, 2005.
ista: Smoukov SK, Bishop KJM, Klajn R, Campbell CJ, Grzybowski BA. 2005. Cutting
into solids with micropatterned gels. Advanced Materials. 17(11), 1361–1365.
mla: Smoukov, S. K., et al. “Cutting into Solids with Micropatterned Gels.” Advanced
Materials, vol. 17, no. 11, Wiley, 2005, pp. 1361–65, doi:10.1002/adma.200402086.
short: S.K. Smoukov, K.J.M. Bishop, R. Klajn, C.J. Campbell, B.A. Grzybowski, Advanced
Materials 17 (2005) 1361–1365.
date_created: 2023-08-01T10:38:01Z
date_published: 2005-06-24T00:00:00Z
date_updated: 2023-08-08T11:53:16Z
day: '24'
doi: 10.1002/adma.200402086
extern: '1'
external_id:
pmid:
- '34412440'
intvolume: ' 17'
issue: '11'
keyword:
- Mechanical Engineering
- Mechanics of Materials
- General Materials Science
language:
- iso: eng
month: '06'
oa_version: None
page: 1361-1365
pmid: 1
publication: Advanced Materials
publication_identifier:
eissn:
- 1521-4095
issn:
- 0935-9648
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cutting into solids with micropatterned gels
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2005'
...
---
_id: '13432'
abstract:
- lang: eng
text: A new experimental technique is described that uses reaction−diffusion phenomena
as a means of one-step microfabrication of complex, multilevel surface reliefs.
Thin films of dry gelatin doped with potassium hexacyanoferrate are chemically
micropatterned with a solution of silver nitrate delivered from an agarose stamp.
Precipitation reaction between the two salts causes the surface to deform. The
mechanism of surface deformation is shown to involve a sequence of reactions,
diffusion, and gel swelling/contraction. This mechanism is established experimentally
and provides a basis of a theoretical lattice-gas model that allows prediction
surface topographies emerging from arbitrary geometries of the stamped features.
The usefulness of the technique is demonstrated by using it to rapidly prepare
two types of mold for passive microfluidic mixers.
article_processing_charge: No
article_type: original
author:
- first_name: Christopher J.
full_name: Campbell, Christopher J.
last_name: Campbell
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Marcin
full_name: Fialkowski, Marcin
last_name: Fialkowski
- first_name: Bartosz A.
full_name: Grzybowski, Bartosz A.
last_name: Grzybowski
citation:
ama: Campbell CJ, Klajn R, Fialkowski M, Grzybowski BA. One-step multilevel microfabrication
by reaction−diffusion. Langmuir. 2005;21(1):418-423. doi:10.1021/la0487747
apa: Campbell, C. J., Klajn, R., Fialkowski, M., & Grzybowski, B. A. (2005).
One-step multilevel microfabrication by reaction−diffusion. Langmuir. American
Chemical Society. https://doi.org/10.1021/la0487747
chicago: Campbell, Christopher J., Rafal Klajn, Marcin Fialkowski, and Bartosz A.
Grzybowski. “One-Step Multilevel Microfabrication by Reaction−diffusion.” Langmuir.
American Chemical Society, 2005. https://doi.org/10.1021/la0487747.
ieee: C. J. Campbell, R. Klajn, M. Fialkowski, and B. A. Grzybowski, “One-step multilevel
microfabrication by reaction−diffusion,” Langmuir, vol. 21, no. 1. American
Chemical Society, pp. 418–423, 2005.
ista: Campbell CJ, Klajn R, Fialkowski M, Grzybowski BA. 2005. One-step multilevel
microfabrication by reaction−diffusion. Langmuir. 21(1), 418–423.
mla: Campbell, Christopher J., et al. “One-Step Multilevel Microfabrication by Reaction−diffusion.”
Langmuir, vol. 21, no. 1, American Chemical Society, 2005, pp. 418–23,
doi:10.1021/la0487747.
short: C.J. Campbell, R. Klajn, M. Fialkowski, B.A. Grzybowski, Langmuir 21 (2005)
418–423.
date_created: 2023-08-01T10:38:29Z
date_published: 2005-01-21T00:00:00Z
date_updated: 2023-08-08T12:15:48Z
day: '21'
doi: 10.1021/la0487747
extern: '1'
external_id:
pmid:
- '15620333'
intvolume: ' 21'
issue: '1'
keyword:
- Electrochemistry
- Spectroscopy
- Surfaces and Interfaces
- Condensed Matter Physics
- General Materials Science
language:
- iso: eng
month: '01'
oa_version: None
page: 418-423
pmid: 1
publication: Langmuir
publication_identifier:
eissn:
- 1520-5827
issn:
- 0743-7463
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: One-step multilevel microfabrication by reaction−diffusion
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2005'
...
---
_id: '13433'
abstract:
- lang: eng
text: Self-assembled monolayers (SAMs) of alkane thiols on gold and other metals
are versatile constructs with which to study interfacial phenomena and reactions
at surfaces. Surface properties of SAMs - e.g., wettability, stability in diverse
environments, propensity to interact with or to resist adsorption of macromolecules
-- depend on and can be controlled flexibly by the properties of the functional
(head) groups in the w position of the alkyl chain. SAMs provide a basis for many
important scientific and technological applications, ranging from micropatterning
methods, through sensing, to biological recognition. Despite their importance,
the literature on SAMs and the synthesis of molecules that constitute them remains
scattered and often conflicting. The purpose of this Review is (i) to summarize
the applications and physical properties of SAMs and (ii) to systematize the strategies
of synthesis of ω-functionalized alkane thiols. Generic retrosynthetic scheme
is developed that allows efficient synthetic planning. Issues related to the selection
of appropriate protecting groups and the ways of introduction of the thiol functionality
are discussed in detail, and illustrated with examples of syntheses of several
complex alkane thiols.
article_processing_charge: No
article_type: original
author:
- first_name: Dariusz
full_name: Witt, Dariusz
last_name: Witt
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Piotr
full_name: Barski, Piotr
last_name: Barski
- first_name: Bartosz
full_name: Grzybowski, Bartosz
last_name: Grzybowski
citation:
ama: Witt D, Klajn R, Barski P, Grzybowski B. Applications, properties and synthesis
of w-functionalized n-alkanethiols and disulfides - the building blocks of self-assembled
monolayers. Current Organic Chemistry. 2005;8(18):1763-1797. doi:10.2174/1385272043369421
apa: Witt, D., Klajn, R., Barski, P., & Grzybowski, B. (2005). Applications,
properties and synthesis of w-functionalized n-alkanethiols and disulfides - the
building blocks of self-assembled monolayers. Current Organic Chemistry.
Bentham Science. https://doi.org/10.2174/1385272043369421
chicago: Witt, Dariusz, Rafal Klajn, Piotr Barski, and Bartosz Grzybowski. “Applications,
Properties and Synthesis of w-Functionalized n-Alkanethiols and Disulfides - the
Building Blocks of Self-Assembled Monolayers.” Current Organic Chemistry.
Bentham Science, 2005. https://doi.org/10.2174/1385272043369421.
ieee: D. Witt, R. Klajn, P. Barski, and B. Grzybowski, “Applications, properties
and synthesis of w-functionalized n-alkanethiols and disulfides - the building
blocks of self-assembled monolayers,” Current Organic Chemistry, vol. 8,
no. 18. Bentham Science, pp. 1763–1797, 2005.
ista: Witt D, Klajn R, Barski P, Grzybowski B. 2005. Applications, properties and
synthesis of w-functionalized n-alkanethiols and disulfides - the building blocks
of self-assembled monolayers. Current Organic Chemistry. 8(18), 1763–1797.
mla: Witt, Dariusz, et al. “Applications, Properties and Synthesis of w-Functionalized
n-Alkanethiols and Disulfides - the Building Blocks of Self-Assembled Monolayers.”
Current Organic Chemistry, vol. 8, no. 18, Bentham Science, 2005, pp. 1763–97,
doi:10.2174/1385272043369421.
short: D. Witt, R. Klajn, P. Barski, B. Grzybowski, Current Organic Chemistry 8
(2005) 1763–1797.
date_created: 2023-08-01T10:38:58Z
date_published: 2005-12-01T00:00:00Z
date_updated: 2023-08-08T12:39:52Z
day: '01'
doi: 10.2174/1385272043369421
extern: '1'
intvolume: ' 8'
issue: '18'
keyword:
- Organic Chemistry
language:
- iso: eng
month: '12'
oa_version: None
page: 1763-1797
publication: Current Organic Chemistry
publication_identifier:
eissn:
- 1875-5348
issn:
- 1385-2728
publication_status: published
publisher: Bentham Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Applications, properties and synthesis of w-functionalized n-alkanethiols and
disulfides - the building blocks of self-assembled monolayers
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2005'
...
---
_id: '1444'
abstract:
- lang: eng
text: The paper surveys the mirror symmetry conjectures of Hausel-Thaddeus and Hausel-Rodriguez-Villegas
concerning the equality of certain Hodge numbers of SL(n, ℂ) vs. PGL(n, ℂ) flat
connections and character varieties for curves, respectively. Several new results
and conjectures and their relations to works of Hitchin, Gothen, Garsia-Haiman
and Earl-Kirwan are explained. These use the representation theory of finite groups
of Lie-type via the arithmetic of character varieties and lead to an unexpected
conjecture for a Hard Lefschetz theorem for their cohomology.
alternative_title:
- Progress in Mathematics
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
citation:
ama: 'Hausel T. Mirror symmetry and Langlands duality in the non-Abelian Hodge theory
of a curve. In: Geometric Methods in Algebra and Number Theory. Vol 235.
Springer; 2005:193-217. doi:10.1007/0-8176-4417-2_9'
apa: Hausel, T. (2005). Mirror symmetry and Langlands duality in the non-Abelian
Hodge theory of a curve. In Geometric Methods in Algebra and Number Theory
(Vol. 235, pp. 193–217). Springer. https://doi.org/10.1007/0-8176-4417-2_9
chicago: Hausel, Tamás. “Mirror Symmetry and Langlands Duality in the Non-Abelian
Hodge Theory of a Curve.” In Geometric Methods in Algebra and Number Theory,
235:193–217. Springer, 2005. https://doi.org/10.1007/0-8176-4417-2_9.
ieee: T. Hausel, “Mirror symmetry and Langlands duality in the non-Abelian Hodge
theory of a curve,” in Geometric Methods in Algebra and Number Theory,
vol. 235, Springer, 2005, pp. 193–217.
ista: 'Hausel T. 2005.Mirror symmetry and Langlands duality in the non-Abelian Hodge
theory of a curve. In: Geometric Methods in Algebra and Number Theory. Progress
in Mathematics, vol. 235, 193–217.'
mla: Hausel, Tamás. “Mirror Symmetry and Langlands Duality in the Non-Abelian Hodge
Theory of a Curve.” Geometric Methods in Algebra and Number Theory, vol.
235, Springer, 2005, pp. 193–217, doi:10.1007/0-8176-4417-2_9.
short: T. Hausel, in:, Geometric Methods in Algebra and Number Theory, Springer,
2005, pp. 193–217.
date_created: 2018-12-11T11:52:03Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:47Z
day: '01'
doi: 10.1007/0-8176-4417-2_9
extern: 1
intvolume: ' 235'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math/0406380
month: '01'
oa: 1
page: 193 - 217
publication: Geometric Methods in Algebra and Number Theory
publication_status: published
publisher: Springer
publist_id: '5752'
quality_controlled: 0
status: public
title: Mirror symmetry and Langlands duality in the non-Abelian Hodge theory of a
curve
type: book_chapter
volume: 235
year: '2005'
...
---
_id: '1447'
abstract:
- lang: eng
text: Building on a recent paper [8], here we argue that the combinatorics of matroids
are intimately related to the geometry and topology of toric hyperkähler varieties.
We show that just like toric varieties occupy a central role in Stanley’s proof
for the necessity of McMullen’s conjecture (or g-inequalities) about the classification
of face vectors of simplicial polytopes, the topology of toric hyperkähler varieties
leads to new restrictions on face vectors of matroid complexes. Namely in this
paper we will give two proofs that the injectivity part of the Hard Lefschetz
theorem survives for toric hyperkähler varieties. We explain how this implies
the g-inequalities for rationally representable matroids. We show how the geometrical
intuition in the first proof, coupled with results of Chari [3], leads to a proof
of the g-inequalities for general matroid complexes, which is a recent result
of Swartz [20]. The geometrical idea in the second proof will show that a pure
O-sequence should satisfy the g-inequalities, thus showing that our result is
in fact a consequence of a long-standing conjecture of Stanley.
acknowledgement: Financial support wa s provided by a Miller Research Fellowship at
the University of California at Berkeley , and by NSF grants DMS- 0072675 and DMS-0305505.
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
citation:
ama: Hausel T. Quaternionic geometry of matroids. Open Mathematics. 2005;3(1):26-38.
doi:10.2478/BF02475653
apa: Hausel, T. (2005). Quaternionic geometry of matroids. Open Mathematics.
Central European Science Journals. https://doi.org/10.2478/BF02475653
chicago: Hausel, Tamás. “Quaternionic Geometry of Matroids.” Open Mathematics.
Central European Science Journals, 2005. https://doi.org/10.2478/BF02475653.
ieee: T. Hausel, “Quaternionic geometry of matroids,” Open Mathematics, vol.
3, no. 1. Central European Science Journals, pp. 26–38, 2005.
ista: Hausel T. 2005. Quaternionic geometry of matroids. Open Mathematics. 3(1),
26–38.
mla: Hausel, Tamás. “Quaternionic Geometry of Matroids.” Open Mathematics,
vol. 3, no. 1, Central European Science Journals, 2005, pp. 26–38, doi:10.2478/BF02475653.
short: T. Hausel, Open Mathematics 3 (2005) 26–38.
date_created: 2018-12-11T11:52:05Z
date_published: 2005-03-01T00:00:00Z
date_updated: 2021-01-12T06:50:49Z
day: '01'
doi: 10.2478/BF02475653
extern: 1
intvolume: ' 3'
issue: '1'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math/0308146
month: '03'
oa: 1
page: 26 - 38
publication: Open Mathematics
publication_status: published
publisher: Central European Science Journals
publist_id: '5749'
quality_controlled: 0
status: public
title: Quaternionic geometry of matroids
type: journal_article
volume: 3
year: '2005'
...