---
_id: '3005'
author:
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Philip
full_name: Benfey, Philip
last_name: Benfey
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Malcolm
full_name: Bennett, Malcolm
last_name: Bennett
- first_name: Thomas
full_name: Berleth, Thomas
last_name: Berleth
- first_name: Niko
full_name: Geldner, Niko
last_name: Geldner
- first_name: Markus
full_name: Grebe, Markus
last_name: Grebe
- first_name: Marcus
full_name: Heisler, Marcus
last_name: Heisler
- first_name: Jan
full_name: Hejátko, Jan
last_name: Hejátko
- first_name: Gerd
full_name: Jürgens, Gerd
last_name: Jürgens
- first_name: Thomas
full_name: Laux, Thomas
last_name: Laux
- first_name: Keith
full_name: Lindsey, Keith
last_name: Lindsey
- first_name: Wolfgang
full_name: Lukowitz, Wolfgang
last_name: Lukowitz
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
- first_name: Remko
full_name: Offringa, Remko
last_name: Offringa
- first_name: Ben
full_name: Scheres, Ben
last_name: Scheres
- first_name: Ranjan
full_name: Swarup, Ranjan
last_name: Swarup
- first_name: Ramón
full_name: Torres Ruiz, Ramón
last_name: Torres Ruiz
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
citation:
ama: 'Friml J, Benfey P, Benková E, et al. Apical-basal polarity: Why plant cells
don’t stand on their heads. Trends in Plant Science. 2006;11(1):12-14.
doi:10.1016/j.tplants.2005.11.010'
apa: 'Friml, J., Benfey, P., Benková, E., Bennett, M., Berleth, T., Geldner, N.,
… Zažímalová, E. (2006). Apical-basal polarity: Why plant cells don’t stand on
their heads. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2005.11.010'
chicago: 'Friml, Jiří, Philip Benfey, Eva Benková, Malcolm Bennett, Thomas Berleth,
Niko Geldner, Markus Grebe, et al. “Apical-Basal Polarity: Why Plant Cells Don’t
Stand on Their Heads.” Trends in Plant Science. Cell Press, 2006. https://doi.org/10.1016/j.tplants.2005.11.010.'
ieee: 'J. Friml et al., “Apical-basal polarity: Why plant cells don’t stand
on their heads,” Trends in Plant Science, vol. 11, no. 1. Cell Press, pp.
12–14, 2006.'
ista: 'Friml J, Benfey P, Benková E, Bennett M, Berleth T, Geldner N, Grebe M, Heisler
M, Hejátko J, Jürgens G, Laux T, Lindsey K, Lukowitz W, Luschnig C, Offringa R,
Scheres B, Swarup R, Torres Ruiz R, Weijers D, Zažímalová E. 2006. Apical-basal
polarity: Why plant cells don’t stand on their heads. Trends in Plant Science.
11(1), 12–14.'
mla: 'Friml, Jiří, et al. “Apical-Basal Polarity: Why Plant Cells Don’t Stand on
Their Heads.” Trends in Plant Science, vol. 11, no. 1, Cell Press, 2006,
pp. 12–14, doi:10.1016/j.tplants.2005.11.010.'
short: J. Friml, P. Benfey, E. Benková, M. Bennett, T. Berleth, N. Geldner, M. Grebe,
M. Heisler, J. Hejátko, G. Jürgens, T. Laux, K. Lindsey, W. Lukowitz, C. Luschnig,
R. Offringa, B. Scheres, R. Swarup, R. Torres Ruiz, D. Weijers, E. Zažímalová,
Trends in Plant Science 11 (2006) 12–14.
date_created: 2018-12-11T12:00:49Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:40:24Z
day: '01'
doi: 10.1016/j.tplants.2005.11.010
extern: '1'
intvolume: ' 11'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 12 - 14
publication: Trends in Plant Science
publication_status: published
publisher: Cell Press
publist_id: '3697'
status: public
title: 'Apical-basal polarity: Why plant cells don''t stand on their heads'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2006'
...
---
_id: '3008'
abstract:
- lang: eng
text: Plants and some animals have a profound capacity to regenerate organs from
adult tissues. Molecular mechanisms for regeneration have, however, been largely
unexplored. Here we investigate a local regeneration response in Arabidopsis roots.
Laser-induced wounding disrupts the flow of auxin-a cell-fate-instructive plant
hormone-in root tips, and we demonstrate that resulting cell-fate changes require
the PLETHORA, SHORTROOT, and SCARECROW transcription factors. These transcription
factors regulate the expression and polar position of PIN auxin efflux-facilitating
membrane proteins to reconstitute auxin transport in renewed root tips. Thus,
a regeneration mechanism using embryonic root stem-cell patterning factors first
responds to and subsequently stabilizes a new hormone distribution.
author:
- first_name: Jian
full_name: Xu, Jian
last_name: Xu
- first_name: Hugo
full_name: Hofhuis, Hugo
last_name: Hofhuis
- first_name: Renze
full_name: Heidstra, Renze
last_name: Heidstra
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Ben
full_name: Scheres, Ben
last_name: Scheres
citation:
ama: Xu J, Hofhuis H, Heidstra R, Sauer M, Friml J, Scheres B. A molecular framework
for plant regeneration. Science. 2006;311(5759):385-388. doi:10.1126/science.1121790
apa: Xu, J., Hofhuis, H., Heidstra, R., Sauer, M., Friml, J., & Scheres, B.
(2006). A molecular framework for plant regeneration. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.1121790
chicago: Xu, Jian, Hugo Hofhuis, Renze Heidstra, Michael Sauer, Jiří Friml, and
Ben Scheres. “A Molecular Framework for Plant Regeneration.” Science. American
Association for the Advancement of Science, 2006. https://doi.org/10.1126/science.1121790.
ieee: J. Xu, H. Hofhuis, R. Heidstra, M. Sauer, J. Friml, and B. Scheres, “A molecular
framework for plant regeneration,” Science, vol. 311, no. 5759. American
Association for the Advancement of Science, pp. 385–388, 2006.
ista: Xu J, Hofhuis H, Heidstra R, Sauer M, Friml J, Scheres B. 2006. A molecular
framework for plant regeneration. Science. 311(5759), 385–388.
mla: Xu, Jian, et al. “A Molecular Framework for Plant Regeneration.” Science,
vol. 311, no. 5759, American Association for the Advancement of Science, 2006,
pp. 385–88, doi:10.1126/science.1121790.
short: J. Xu, H. Hofhuis, R. Heidstra, M. Sauer, J. Friml, B. Scheres, Science 311
(2006) 385–388.
date_created: 2018-12-11T12:00:50Z
date_published: 2006-01-20T00:00:00Z
date_updated: 2021-01-12T07:40:25Z
day: '20'
doi: 10.1126/science.1121790
extern: 1
intvolume: ' 311'
issue: '5759'
month: '01'
page: 385 - 388
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '3695'
quality_controlled: 0
status: public
title: A molecular framework for plant regeneration
type: journal_article
volume: 311
year: '2006'
...
---
_id: '3009'
author:
- first_name: Tomasz
full_name: Paciorek, Tomasz
last_name: Paciorek
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Paciorek T, Friml J. Auxin signaling. Journal of Cell Science. 2006;119(7):1199-1202.
doi:10.1242/jcs.02910
apa: Paciorek, T., & Friml, J. (2006). Auxin signaling. Journal of Cell Science.
Company of Biologists. https://doi.org/10.1242/jcs.02910
chicago: Paciorek, Tomasz, and Jiří Friml. “Auxin Signaling.” Journal of Cell
Science. Company of Biologists, 2006. https://doi.org/10.1242/jcs.02910.
ieee: T. Paciorek and J. Friml, “Auxin signaling,” Journal of Cell Science,
vol. 119, no. 7. Company of Biologists, pp. 1199–1202, 2006.
ista: Paciorek T, Friml J. 2006. Auxin signaling. Journal of Cell Science. 119(7),
1199–1202.
mla: Paciorek, Tomasz, and Jiří Friml. “Auxin Signaling.” Journal of Cell Science,
vol. 119, no. 7, Company of Biologists, 2006, pp. 1199–202, doi:10.1242/jcs.02910.
short: T. Paciorek, J. Friml, Journal of Cell Science 119 (2006) 1199–1202.
date_created: 2018-12-11T12:00:50Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:40:25Z
day: '01'
doi: 10.1242/jcs.02910
extern: '1'
external_id:
pmid:
- ' 16554435'
intvolume: ' 119'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/16554435
month: '01'
oa: 1
oa_version: Published Version
page: 1199 - 1202
pmid: 1
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '3693'
quality_controlled: '1'
status: public
title: Auxin signaling
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2006'
...
---
_id: '3016'
abstract:
- lang: eng
text: Plant development is characterized by a profound ability to regenerate and
form tissues with new axes of polarity. An unsolved question concerns how the
position within a tissue and cues from neighboring cells are integrated to specify
the polarity of individual cells. The canalization hypothesis proposes a feedback
effect of the phytohormone auxin on the directionality of intercellular auxin
flow as a means to polarize tissues. Here we identify a cellular and molecular
mechanism for canalization. Local auxin application, wounding, or auxin accumulation
during de novo organ formation lead to rearrangements in the subcellular polar
localization of PIN auxin transport components. This auxin effect on PIN polarity
is cell-specific, does not depend on PIN transcription, and involves the Aux/IAA-ARF
(indole-3-acetic acid-auxin response factor) signaling pathway. Our data suggest
that auxin acts as polarizing cue, which links individual cell polarity with tissue
and organ polarity through control of PIN polar targeting. This feedback regulation
provides a conceptual framework for polarization during multiple regenerative
and patterning processes in plants.
article_processing_charge: No
author:
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Jozef
full_name: Balla, Jozef
last_name: Balla
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
- first_name: Justyna
full_name: Wiśniewska, Justyna
last_name: Wiśniewska
- first_name: Vilém
full_name: Reinöhl, Vilém
last_name: Reinöhl
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Sauer M, Balla J, Luschnig C, et al. Canalization of auxin flow by Aux/IAA-ARF-dependent
feedback regulation of PIN polarity. Genes and Development. 2006;20(20):2902-2911.
doi:10.1101/gad.390806
apa: Sauer, M., Balla, J., Luschnig, C., Wiśniewska, J., Reinöhl, V., Friml, J.,
& Benková, E. (2006). Canalization of auxin flow by Aux/IAA-ARF-dependent
feedback regulation of PIN polarity. Genes and Development. Cold Spring
Harbor Laboratory Press. https://doi.org/10.1101/gad.390806
chicago: Sauer, Michael, Jozef Balla, Christian Luschnig, Justyna Wiśniewska, Vilém
Reinöhl, Jiří Friml, and Eva Benková. “Canalization of Auxin Flow by Aux/IAA-ARF-Dependent
Feedback Regulation of PIN Polarity.” Genes and Development. Cold Spring
Harbor Laboratory Press, 2006. https://doi.org/10.1101/gad.390806.
ieee: M. Sauer et al., “Canalization of auxin flow by Aux/IAA-ARF-dependent
feedback regulation of PIN polarity,” Genes and Development, vol. 20, no.
20. Cold Spring Harbor Laboratory Press, pp. 2902–2911, 2006.
ista: Sauer M, Balla J, Luschnig C, Wiśniewska J, Reinöhl V, Friml J, Benková E.
2006. Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation
of PIN polarity. Genes and Development. 20(20), 2902–2911.
mla: Sauer, Michael, et al. “Canalization of Auxin Flow by Aux/IAA-ARF-Dependent
Feedback Regulation of PIN Polarity.” Genes and Development, vol. 20, no.
20, Cold Spring Harbor Laboratory Press, 2006, pp. 2902–11, doi:10.1101/gad.390806.
short: M. Sauer, J. Balla, C. Luschnig, J. Wiśniewska, V. Reinöhl, J. Friml, E.
Benková, Genes and Development 20 (2006) 2902–2911.
date_created: 2018-12-11T12:00:53Z
date_published: 2006-10-15T00:00:00Z
date_updated: 2021-11-16T07:53:09Z
day: '15'
doi: 10.1101/gad.390806
extern: '1'
intvolume: ' 20'
issue: '20'
language:
- iso: eng
month: '10'
oa_version: None
page: 2902 - 2911
publication: Genes and Development
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '3686'
related_material:
link:
- relation: erratum
url: http://genesdev.cshlp.org/content/21/11/1431.short
status: public
title: Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of
PIN polarity
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 20
year: '2006'
...
---
_id: '3017'
abstract:
- lang: eng
text: The plant hormone auxin plays crucial roles in regulating plant growth development,
including embryo and root patterning, organ formation, vascular tissue differentiation
and growth responses to environmental stimuli. Asymmetric auxin distribution patterns
have been observed within tissues, and these so-called auxin gradients change
dynamically during different developmental processes. Most auxin is synthesized
in the shoot and distributed directionally throughout the plant. This polar auxin
transport is mediated by auxin influx and efflux facilitators, whose subcellular
polar localizations guide the direction of auxin flow. The polar localization
of PIN auxin efflux carriers changes in response to developmental and external
cues in order to channel auxin flow in a regulated manner for organized growth.
Auxin itself modulates the expression and subcellular localization of PIN proteins,
contributing to a complex pattern of feedback regulation. Here we review the available
information mainly from studies of a model plant, Arabidopsis thaliana, on the
generation of auxin gradients, the regulation of polar auxin transport and further
downstream cellular events.
author:
- first_name: Hirokazu
full_name: Tanaka, Hirokazu
last_name: Tanaka
- first_name: Pankaj
full_name: Dhonukshe, Pankaj
last_name: Dhonukshe
- first_name: Philip
full_name: Brewer, Philip
last_name: Brewer
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Tanaka H, Dhonukshe P, Brewer P, Friml J. Spatiotemporal asymmetric auxin
distribution: A means to coordinate plant development. Cellular and Molecular
Life Sciences. 2006;63(23):2738-2754. doi:10.1007/s00018-006-6116-5'
apa: 'Tanaka, H., Dhonukshe, P., Brewer, P., & Friml, J. (2006). Spatiotemporal
asymmetric auxin distribution: A means to coordinate plant development. Cellular
and Molecular Life Sciences. Birkhäuser. https://doi.org/10.1007/s00018-006-6116-5'
chicago: 'Tanaka, Hirokazu, Pankaj Dhonukshe, Philip Brewer, and Jiří Friml. “Spatiotemporal
Asymmetric Auxin Distribution: A Means to Coordinate Plant Development.” Cellular
and Molecular Life Sciences. Birkhäuser, 2006. https://doi.org/10.1007/s00018-006-6116-5.'
ieee: 'H. Tanaka, P. Dhonukshe, P. Brewer, and J. Friml, “Spatiotemporal asymmetric
auxin distribution: A means to coordinate plant development,” Cellular and
Molecular Life Sciences, vol. 63, no. 23. Birkhäuser, pp. 2738–2754, 2006.'
ista: 'Tanaka H, Dhonukshe P, Brewer P, Friml J. 2006. Spatiotemporal asymmetric
auxin distribution: A means to coordinate plant development. Cellular and Molecular
Life Sciences. 63(23), 2738–2754.'
mla: 'Tanaka, Hirokazu, et al. “Spatiotemporal Asymmetric Auxin Distribution: A
Means to Coordinate Plant Development.” Cellular and Molecular Life Sciences,
vol. 63, no. 23, Birkhäuser, 2006, pp. 2738–54, doi:10.1007/s00018-006-6116-5.'
short: H. Tanaka, P. Dhonukshe, P. Brewer, J. Friml, Cellular and Molecular Life
Sciences 63 (2006) 2738–2754.
date_created: 2018-12-11T12:00:53Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2021-01-12T07:40:29Z
day: '01'
doi: 10.1007/s00018-006-6116-5
extern: '1'
intvolume: ' 63'
issue: '23'
language:
- iso: eng
month: '12'
oa_version: None
page: 2738 - 2754
publication: Cellular and Molecular Life Sciences
publication_status: published
publisher: Birkhäuser
publist_id: '3685'
quality_controlled: '1'
status: public
title: 'Spatiotemporal asymmetric auxin distribution: A means to coordinate plant
development'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 63
year: '2006'
...
---
_id: '3018'
abstract:
- lang: eng
text: The directional flow of the plant hormone auxin mediates multiple developmental
processes, including patterning and tropisms. Apical and basal plasma membrane
localization of AUXIN-RESISTANT1 (AUX1) and PIN-FORMED1 (PIN1) auxin transport
components underpins the directionality of intercellular auxin flow in Arabidopsis
thaliana roots. Here, we examined the mechanism of polar trafficking of AUX1.
Real-time live cell analysis along with subcellular markers revealed that AUX1
resides at the apical plasma membrane of protophloem cells and at highly dynamic
subpopulations of Golgi apparatus and endosomes in all cell types. Plasma membrane
and intracellular pools of AUX1 are interconnected by actin-dependent constitutive
trafficking, which is not sensitive to the vesicle trafficking inhibitor brefeldin
A. AUX1 subcellular dynamics are not influenced by the auxin influx inhibitor
NOA but are blocked by the auxin efflux inhibitors TIBA and PBA. Furthermore,
auxin transport inhibitors and interference with the sterol composition of membranes
disrupt polar AUX1 distribution at the plasma membrane. Compared with PIN1 trafficking,
AUX1 dynamics display different sensitivities to trafficking inhibitors and are
independent of the endosomal trafficking regulator ARF GEF GNOM. Hence, AUX1 uses
a novel trafficking pathway in plants that is distinct from PIN trafficking, providing
an additional mechanism for the fine regulation of auxin transport.
author:
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Pankaj
full_name: Dhonukshe, Pankaj
last_name: Dhonukshe
- first_name: Ranjan
full_name: Swarup, Ranjan
last_name: Swarup
- first_name: Malcolm
full_name: Bennett, Malcolm
last_name: Bennett
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Kleine Vehn J, Dhonukshe P, Swarup R, Bennett M, Friml J. Subcellular trafficking
of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from
PIN1. Plant Cell. 2006;18(11):3171-3181. doi:10.1105/tpc.106.042770
apa: Kleine Vehn, J., Dhonukshe, P., Swarup, R., Bennett, M., & Friml, J. (2006).
Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel
pathway distinct from PIN1. Plant Cell. American Society of Plant Biologists.
https://doi.org/10.1105/tpc.106.042770
chicago: Kleine Vehn, Jürgen, Pankaj Dhonukshe, Ranjan Swarup, Malcolm Bennett,
and Jiří Friml. “Subcellular Trafficking of the Arabidopsis Auxin Influx Carrier
AUX1 Uses a Novel Pathway Distinct from PIN1.” Plant Cell. American Society
of Plant Biologists, 2006. https://doi.org/10.1105/tpc.106.042770.
ieee: J. Kleine Vehn, P. Dhonukshe, R. Swarup, M. Bennett, and J. Friml, “Subcellular
trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway
distinct from PIN1,” Plant Cell, vol. 18, no. 11. American Society of Plant
Biologists, pp. 3171–3181, 2006.
ista: Kleine Vehn J, Dhonukshe P, Swarup R, Bennett M, Friml J. 2006. Subcellular
trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway
distinct from PIN1. Plant Cell. 18(11), 3171–3181.
mla: Kleine Vehn, Jürgen, et al. “Subcellular Trafficking of the Arabidopsis Auxin
Influx Carrier AUX1 Uses a Novel Pathway Distinct from PIN1.” Plant Cell,
vol. 18, no. 11, American Society of Plant Biologists, 2006, pp. 3171–81, doi:10.1105/tpc.106.042770.
short: J. Kleine Vehn, P. Dhonukshe, R. Swarup, M. Bennett, J. Friml, Plant Cell
18 (2006) 3171–3181.
date_created: 2018-12-11T12:00:53Z
date_published: 2006-11-01T00:00:00Z
date_updated: 2021-01-12T07:40:29Z
day: '01'
doi: 10.1105/tpc.106.042770
extern: 1
intvolume: ' 18'
issue: '11'
month: '11'
page: 3171 - 3181
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3684'
quality_controlled: 0
status: public
title: Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a
novel pathway distinct from PIN1
type: journal_article
volume: 18
year: '2006'
...
---
_id: '3020'
abstract:
- lang: eng
text: High throughput microarray transcription analyses provide us with the expression
profiles for large amounts of plant genes. However, their tissue and cellular
resolution is limited. Thus, for detailed functional analysis, it is still necessary
to examine the expression pattern of selected candidate genes at a cellular level.
Here, we present an in situ mRNA hybridization method that is routinely used for
the analysis of plant gene expression patterns. The protocol is optimized for
whole mount mRNA localizations in Arabidopsis seedling tissues including embryos,
roots, hypocotyls and young primary leaves. It can also be used for comparable
tissues in other species. Part of the protocol can also be automated and performed
by a liquid handling robot. Here we present a detailed protocol, recommended controls
and troubleshooting, along with examples of several applications. The total time
to carry out the entire procedure is ∼7 d, depending on the tissue used.
author:
- first_name: Jan
full_name: Hejátko, Jan
last_name: Hejátko
- first_name: Ikram
full_name: Blilou, Ikram
last_name: Blilou
- first_name: Philip
full_name: Brewer, Philip B
last_name: Brewer
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Ben
full_name: Scheres, Ben
last_name: Scheres
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Hejátko J, Blilou I, Brewer P, Friml J, Scheres B, Benková E. In situ hybridization
technique for mRNA detection in whole mount Arabidopsis samples. Nature Protocols.
2006;1(4):1939-1946. doi:10.1038/nprot.2006.333
apa: Hejátko, J., Blilou, I., Brewer, P., Friml, J., Scheres, B., & Benková,
E. (2006). In situ hybridization technique for mRNA detection in whole mount Arabidopsis
samples. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.333
chicago: Hejátko, Jan, Ikram Blilou, Philip Brewer, Jiří Friml, Ben Scheres, and
Eva Benková. “In Situ Hybridization Technique for MRNA Detection in Whole Mount
Arabidopsis Samples.” Nature Protocols. Nature Publishing Group, 2006.
https://doi.org/10.1038/nprot.2006.333.
ieee: J. Hejátko, I. Blilou, P. Brewer, J. Friml, B. Scheres, and E. Benková, “In
situ hybridization technique for mRNA detection in whole mount Arabidopsis samples,”
Nature Protocols, vol. 1, no. 4. Nature Publishing Group, pp. 1939–1946,
2006.
ista: Hejátko J, Blilou I, Brewer P, Friml J, Scheres B, Benková E. 2006. In situ
hybridization technique for mRNA detection in whole mount Arabidopsis samples.
Nature Protocols. 1(4), 1939–1946.
mla: Hejátko, Jan, et al. “In Situ Hybridization Technique for MRNA Detection in
Whole Mount Arabidopsis Samples.” Nature Protocols, vol. 1, no. 4, Nature
Publishing Group, 2006, pp. 1939–46, doi:10.1038/nprot.2006.333.
short: J. Hejátko, I. Blilou, P. Brewer, J. Friml, B. Scheres, E. Benková, Nature
Protocols 1 (2006) 1939–1946.
date_created: 2018-12-11T12:00:54Z
date_published: 2006-11-01T00:00:00Z
date_updated: 2021-01-12T07:40:30Z
day: '01'
doi: 10.1038/nprot.2006.333
extern: 1
intvolume: ' 1'
issue: '4'
month: '11'
page: 1939 - 1946
publication: Nature Protocols
publication_status: published
publisher: Nature Publishing Group
publist_id: '3683'
quality_controlled: 0
status: public
title: In situ hybridization technique for mRNA detection in whole mount Arabidopsis
samples
type: journal_article
volume: 1
year: '2006'
...
---
_id: '3015'
abstract:
- lang: eng
text: 'As the field of plant molecular biology is swiftly advancing, a need has
been created for methods that allow rapid and reliable in situ localization of
proteins in plant cells. Here we describe a whole-mount ''immunolocalization''
technique for various plant tissues, including roots, hypocotyls, cotyledons,
young primary leaves and embryos of Arabidopsis thaliana and other species. The
detailed protocol, recommended controls and troubleshooting are presented, along
with examples of applications. The protocol consists of five main procedures:
tissue fixation, tissue permeation, blocking, primary and secondary antibody incubation.
Notably, the first procedure (tissue fixation) includes several steps (4-12) that
are absolutely necessary for protein localization in hypocotyls, cotyledons and
young primary leaves but should be omitted for other tissues. The protocol is
usually done in 3 days, but could also be completed in 2 days.'
author:
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Tomasz
full_name: Paciorek, Tomasz
last_name: Paciorek
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Sauer M, Paciorek T, Benková E, Friml J. Immunocytochemical techniques for
whole mount in situ protein localization in plants. Nature Protocols. 2006;1(1):98-103.
doi:10.1038/nprot.2006.15
apa: Sauer, M., Paciorek, T., Benková, E., & Friml, J. (2006). Immunocytochemical
techniques for whole mount in situ protein localization in plants. Nature Protocols.
Nature Publishing Group. https://doi.org/10.1038/nprot.2006.15
chicago: Sauer, Michael, Tomasz Paciorek, Eva Benková, and Jiří Friml. “Immunocytochemical
Techniques for Whole Mount in Situ Protein Localization in Plants.” Nature
Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.15.
ieee: M. Sauer, T. Paciorek, E. Benková, and J. Friml, “Immunocytochemical techniques
for whole mount in situ protein localization in plants,” Nature Protocols,
vol. 1, no. 1. Nature Publishing Group, pp. 98–103, 2006.
ista: Sauer M, Paciorek T, Benková E, Friml J. 2006. Immunocytochemical techniques
for whole mount in situ protein localization in plants. Nature Protocols. 1(1),
98–103.
mla: Sauer, Michael, et al. “Immunocytochemical Techniques for Whole Mount in Situ
Protein Localization in Plants.” Nature Protocols, vol. 1, no. 1, Nature
Publishing Group, 2006, pp. 98–103, doi:10.1038/nprot.2006.15.
short: M. Sauer, T. Paciorek, E. Benková, J. Friml, Nature Protocols 1 (2006) 98–103.
date_created: 2018-12-11T12:00:52Z
date_published: 2006-06-01T00:00:00Z
date_updated: 2021-01-12T07:40:28Z
day: '01'
doi: 10.1038/nprot.2006.15
extern: 1
intvolume: ' 1'
issue: '1'
month: '06'
page: 98 - 103
publication: Nature Protocols
publication_status: published
publisher: Nature Publishing Group
publist_id: '3688'
quality_controlled: 0
status: public
title: Immunocytochemical techniques for whole mount in situ protein localization
in plants
type: journal_article
volume: 1
year: '2006'
...
---
_id: '3013'
abstract:
- lang: eng
text: 'There is a growing demand for methods that allow rapid and reliable in situ
localization of proteins in plant cells. The immunocytochemistry protocol presented
here can be used routinely to observe protein localization patterns in tissue
sections of various plant species. This protocol is especially suitable for plant
species with more-complex tissue architecture (such as maize, Zea mays), which
makes it difficult to use an easier whole-mount procedure for protein localization.
To facilitate the antibody-antigen reaction, it is necessary to include a wax-embedding
and tissue-sectioning step. The protocol consists of the following procedures:
chemical fixation of tissue, dehydration, wax embedding, sectioning, dewaxing,
rehydration, blocking and antibody incubation. The detailed protocol, recommended
controls and troubleshooting are presented here, along with examples of applications.'
author:
- first_name: Tomasz
full_name: Paciorek, Tomasz
last_name: Paciorek
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Jozef
full_name: Balla, Jozef
last_name: Balla
- first_name: Justyna
full_name: Wiśniewska, Justyna
last_name: Wiśniewska
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Paciorek T, Sauer M, Balla J, Wiśniewska J, Friml J. Immunocytochemical technique
for protein localization in sections of plant tissues. Nature Protocols.
2006;1(1):104-107. doi:10.1038/nprot.2006.16
apa: Paciorek, T., Sauer, M., Balla, J., Wiśniewska, J., & Friml, J. (2006).
Immunocytochemical technique for protein localization in sections of plant tissues.
Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.16
chicago: Paciorek, Tomasz, Michael Sauer, Jozef Balla, Justyna Wiśniewska, and Jiří
Friml. “Immunocytochemical Technique for Protein Localization in Sections of Plant
Tissues.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.16.
ieee: T. Paciorek, M. Sauer, J. Balla, J. Wiśniewska, and J. Friml, “Immunocytochemical
technique for protein localization in sections of plant tissues,” Nature Protocols,
vol. 1, no. 1. Nature Publishing Group, pp. 104–107, 2006.
ista: Paciorek T, Sauer M, Balla J, Wiśniewska J, Friml J. 2006. Immunocytochemical
technique for protein localization in sections of plant tissues. Nature Protocols.
1(1), 104–107.
mla: Paciorek, Tomasz, et al. “Immunocytochemical Technique for Protein Localization
in Sections of Plant Tissues.” Nature Protocols, vol. 1, no. 1, Nature
Publishing Group, 2006, pp. 104–07, doi:10.1038/nprot.2006.16.
short: T. Paciorek, M. Sauer, J. Balla, J. Wiśniewska, J. Friml, Nature Protocols
1 (2006) 104–107.
date_created: 2018-12-11T12:00:52Z
date_published: 2006-06-01T00:00:00Z
date_updated: 2021-01-12T07:40:27Z
day: '01'
doi: 10.1038/nprot.2006.16
extern: 1
intvolume: ' 1'
issue: '1'
month: '06'
page: 104 - 107
publication: Nature Protocols
publication_status: published
publisher: Nature Publishing Group
publist_id: '3689'
quality_controlled: 0
status: public
title: Immunocytochemical technique for protein localization in sections of plant
tissues
type: journal_article
volume: 1
year: '2006'
...
---
_id: '3014'
abstract:
- lang: eng
text: Plant biology is currently confronted with an overflow of expression profile
data provided by high-throughput microarray transcription analyses. However, the
tissue and cellular resolution of these techniques is limited. Thus, it is still
necessary to examine the expression pattern of selected candidate genes at a cellular
level. Here we present an in situ mRNA hybridization method that is routinely
used in the analysis of gene expression patterns. The protocol is optimized for
mRNA localizations in sectioned tissue of Arabidopsis seedlings including embryos,
roots, hypocotyls, young primary leaves and flowers. The detailed protocol, recommended
controls and troubleshooting are presented along with examples of application.
The total time for the process is 10 days.
author:
- first_name: Philip
full_name: Brewer, Philip B
last_name: Brewer
- first_name: Marcus
full_name: Heisler, Marcus G
last_name: Heisler
- first_name: Jan
full_name: Hejátko, Jan
last_name: Hejátko
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Brewer P, Heisler M, Hejátko J, Friml J, Benková E. In situ hybridization for
mRNA detection in Arabidopsis tissue sections. Nature Protocols. 2006;1(3):1462-1467.
doi:10.1038/nprot.2006.226
apa: Brewer, P., Heisler, M., Hejátko, J., Friml, J., & Benková, E. (2006).
In situ hybridization for mRNA detection in Arabidopsis tissue sections. Nature
Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.226
chicago: Brewer, Philip, Marcus Heisler, Jan Hejátko, Jiří Friml, and Eva Benková.
“In Situ Hybridization for MRNA Detection in Arabidopsis Tissue Sections.” Nature
Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.226.
ieee: P. Brewer, M. Heisler, J. Hejátko, J. Friml, and E. Benková, “In situ hybridization
for mRNA detection in Arabidopsis tissue sections,” Nature Protocols, vol.
1, no. 3. Nature Publishing Group, pp. 1462–1467, 2006.
ista: Brewer P, Heisler M, Hejátko J, Friml J, Benková E. 2006. In situ hybridization
for mRNA detection in Arabidopsis tissue sections. Nature Protocols. 1(3), 1462–1467.
mla: Brewer, Philip, et al. “In Situ Hybridization for MRNA Detection in Arabidopsis
Tissue Sections.” Nature Protocols, vol. 1, no. 3, Nature Publishing Group,
2006, pp. 1462–67, doi:10.1038/nprot.2006.226.
short: P. Brewer, M. Heisler, J. Hejátko, J. Friml, E. Benková, Nature Protocols
1 (2006) 1462–1467.
date_created: 2018-12-11T12:00:52Z
date_published: 2006-08-01T00:00:00Z
date_updated: 2021-01-12T07:40:28Z
day: '01'
doi: 10.1038/nprot.2006.226
extern: 1
intvolume: ' 1'
issue: '3'
month: '08'
page: 1462 - 1467
publication: Nature Protocols
publication_status: published
publisher: Nature Publishing Group
publist_id: '3687'
quality_controlled: 0
status: public
title: In situ hybridization for mRNA detection in Arabidopsis tissue sections
type: journal_article
volume: 1
year: '2006'
...
---
_id: '3152'
abstract:
- lang: eng
text: The basic concepts of the molecular machinery that mediates cell migration
have been gleaned from cell culture systems. However, the three-dimensional environment
within an organism presents migrating cells with a much greater challenge. They
must move between and among other cells while interpreting multiple attractive
and repulsive cues to choose their proper path. They must coordinate their cell
adhesion with their surroundings and know when to start and stop moving. New insights
into the control of these remaining mysteries have emerged from genetic dissection
and live imaging of germ cell migration in Drosophila, zebrafish, and mouse embryos.
In this review, we first describe germ cell migration in cellular and mechanistic
detail in these different model systems. We then compare these systems to highlight
the emerging principles. Finally, we contrast the migration of germ cells with
that of immune and cancer cells to outline the conserved and different mechanisms.
author:
- first_name: Prabhat
full_name: Kunwar, Prabhat S
last_name: Kunwar
- first_name: Daria E
full_name: Daria Siekhaus
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Ruth
full_name: Lehmann, Ruth
last_name: Lehmann
citation:
ama: Kunwar P, Siekhaus DE, Lehmann R. In vivo migration A germ cell perspective.
Annual Review of Cell and Developmental Biology. 2006;22:237-265. doi:10.1146/annurev.cellbio.22.010305.103337
apa: Kunwar, P., Siekhaus, D. E., & Lehmann, R. (2006). In vivo migration A
germ cell perspective. Annual Review of Cell and Developmental Biology.
Annual Reviews. https://doi.org/10.1146/annurev.cellbio.22.010305.103337
chicago: Kunwar, Prabhat, Daria E Siekhaus, and Ruth Lehmann. “In Vivo Migration
A Germ Cell Perspective.” Annual Review of Cell and Developmental Biology.
Annual Reviews, 2006. https://doi.org/10.1146/annurev.cellbio.22.010305.103337.
ieee: P. Kunwar, D. E. Siekhaus, and R. Lehmann, “In vivo migration A germ cell
perspective,” Annual Review of Cell and Developmental Biology, vol. 22.
Annual Reviews, pp. 237–265, 2006.
ista: Kunwar P, Siekhaus DE, Lehmann R. 2006. In vivo migration A germ cell perspective.
Annual Review of Cell and Developmental Biology. 22, 237–265.
mla: Kunwar, Prabhat, et al. “In Vivo Migration A Germ Cell Perspective.” Annual
Review of Cell and Developmental Biology, vol. 22, Annual Reviews, 2006, pp.
237–65, doi:10.1146/annurev.cellbio.22.010305.103337.
short: P. Kunwar, D.E. Siekhaus, R. Lehmann, Annual Review of Cell and Developmental
Biology 22 (2006) 237–265.
date_created: 2018-12-11T12:01:42Z
date_published: 2006-06-14T00:00:00Z
date_updated: 2021-01-12T07:41:25Z
day: '14'
doi: 10.1146/annurev.cellbio.22.010305.103337
extern: 1
intvolume: ' 22'
month: '06'
page: 237 - 265
publication: Annual Review of Cell and Developmental Biology
publication_status: published
publisher: Annual Reviews
publist_id: '3543'
quality_controlled: 0
status: public
title: In vivo migration A germ cell perspective
type: journal_article
volume: 22
year: '2006'
...
---
_id: '3189'
abstract:
- lang: eng
text: This paper presents an algorithm capable of real-time separation of foreground
from background in monocular video sequences. Automatic segmentation of layers
from colour/contrast or from motion alone is known to be error-prone. Here motion,
colour and contrast cues are probabilistically fused together with spatial and
temporal priors to infer layers accurately and efficiently. Central to our algorithm
is the fact that pixel velocities are not needed, thus removing the need for optical
flow estimation, with its tendency to error and computational expense. Instead,
an efficient motion vs non-motion classifier is trained to operate directly and
jointly on intensity-change and contrast. Its output is then fused with colour
information. The prior on segmentation is represented by a second order, temporal,
Hidden Markov Model, together with a spatial MRF favouring coherence except where
contrast is high. Finally, accurate layer segmentation and explicit occlusion
detection are efficiently achieved by binary graph cut. The segmentation accuracy
of the proposed algorithm is quantitatively evaluated with respect to existing
ground-truth data and found to be comparable to the accuracy of a state of the
art stereo segmentation algorithm. Fore-ground/background segmentation is demonstrated
in the application of live background substitution and shown to generate convincingly
good quality composite video.
author:
- first_name: Antonio
full_name: Criminisi, Antonio
last_name: Criminisi
- first_name: Geoffrey
full_name: Cross, Geoffrey
last_name: Cross
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Criminisi A, Cross G, Blake A, Kolmogorov V. Bilayer segmentation of live
video. In: Vol 1. IEEE; 2006:53-60. doi:10.1109/CVPR.2006.69'
apa: 'Criminisi, A., Cross, G., Blake, A., & Kolmogorov, V. (2006). Bilayer
segmentation of live video (Vol. 1, pp. 53–60). Presented at the CVPR: Computer
Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2006.69'
chicago: Criminisi, Antonio, Geoffrey Cross, Andrew Blake, and Vladimir Kolmogorov.
“Bilayer Segmentation of Live Video,” 1:53–60. IEEE, 2006. https://doi.org/10.1109/CVPR.2006.69.
ieee: 'A. Criminisi, G. Cross, A. Blake, and V. Kolmogorov, “Bilayer segmentation
of live video,” presented at the CVPR: Computer Vision and Pattern Recognition,
2006, vol. 1, pp. 53–60.'
ista: 'Criminisi A, Cross G, Blake A, Kolmogorov V. 2006. Bilayer segmentation of
live video. CVPR: Computer Vision and Pattern Recognition vol. 1, 53–60.'
mla: Criminisi, Antonio, et al. Bilayer Segmentation of Live Video. Vol.
1, IEEE, 2006, pp. 53–60, doi:10.1109/CVPR.2006.69.
short: A. Criminisi, G. Cross, A. Blake, V. Kolmogorov, in:, IEEE, 2006, pp. 53–60.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:54Z
date_published: 2006-07-05T00:00:00Z
date_updated: 2021-01-12T07:41:40Z
day: '05'
doi: 10.1109/CVPR.2006.69
extern: 1
intvolume: ' 1'
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/en-us/um/people/ablake/papers/ablake/criminisi_cvpr06.pdf
month: '07'
page: 53 - 60
publication_status: published
publisher: IEEE
publist_id: '3494'
quality_controlled: 0
status: public
title: Bilayer segmentation of live video
type: conference
volume: 1
year: '2006'
...
---
_id: '3190'
abstract:
- lang: eng
text: Algorithms for discrete energy minimization are of fundamental importance
in computer vision. In this paper, we focus on the recent technique proposed by
Wainwright et al. (Nov. 2005)- tree-reweighted max-product message passing (TRW).
It was inspired by the problem of maximizing a lower bound on the energy. However,
the algorithm is not guaranteed to increase this bound - it may actually go down.
In addition, TRW does not always converge. We develop a modification of this algorithm
which we call sequential tree-reweighted message passing. Its main property is
that the bound is guaranteed not to decrease. We also give a weak tree agreement
condition which characterizes local maxima of the bound with respect to TRW algorithms.
We prove that our algorithm has a limit point that achieves weak tree agreement.
Finally, we show that, our algorithm requires half as much memory as traditional
message passing approaches. Experimental results demonstrate that on certain synthetic
and real problems, our algorithm outperforms both the ordinary belief propagation
and tree-reweighted algorithm in (M. J. Wainwright, et al., Nov. 2005). In addition,
on stereo problems with Potts interactions, we obtain a lower energy than graph
cuts.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: Kolmogorov V. Convergent tree reweighted message passing for energy minimization.
IEEE Transactions on Pattern Analysis and Machine Intelligence. 2006;28(10):1568-1583.
doi:10.1109/TPAMI.2006.200
apa: Kolmogorov, V. (2006). Convergent tree reweighted message passing for energy
minimization. IEEE Transactions on Pattern Analysis and Machine Intelligence.
IEEE. https://doi.org/10.1109/TPAMI.2006.200
chicago: Kolmogorov, Vladimir. “Convergent Tree Reweighted Message Passing for Energy
Minimization.” IEEE Transactions on Pattern Analysis and Machine Intelligence.
IEEE, 2006. https://doi.org/10.1109/TPAMI.2006.200.
ieee: V. Kolmogorov, “Convergent tree reweighted message passing for energy minimization,”
IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28,
no. 10. IEEE, pp. 1568–1583, 2006.
ista: Kolmogorov V. 2006. Convergent tree reweighted message passing for energy
minimization. IEEE Transactions on Pattern Analysis and Machine Intelligence.
28(10), 1568–1583.
mla: Kolmogorov, Vladimir. “Convergent Tree Reweighted Message Passing for Energy
Minimization.” IEEE Transactions on Pattern Analysis and Machine Intelligence,
vol. 28, no. 10, IEEE, 2006, pp. 1568–83, doi:10.1109/TPAMI.2006.200.
short: V. Kolmogorov, IEEE Transactions on Pattern Analysis and Machine Intelligence
28 (2006) 1568–1583.
date_created: 2018-12-11T12:01:55Z
date_published: 2006-08-21T00:00:00Z
date_updated: 2021-01-12T07:41:41Z
day: '21'
doi: 10.1109/TPAMI.2006.200
extern: 1
intvolume: ' 28'
issue: '10'
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67371/trw_maxproduct_aistats05.pdf
month: '08'
page: 1568 - 1583
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '3495'
quality_controlled: 0
status: public
title: Convergent tree reweighted message passing for energy minimization
type: journal_article
volume: 28
year: '2006'
...
---
_id: '3188'
abstract:
- lang: eng
text: 'We introduce the term cosegmentation which denotes the task of segmenting
simultaneously the common parts of an image pair. A generative model for cosegmentation
is presented. Inference in the model leads to minimizing an energy with an MRF
term encoding spatial coherency and a global constraint which attempts to match
the appearance histograms of the common parts. This energy has not been proposed
previously and its optimization is challenging and NP-hard. For this problem a
novel optimization scheme which we call trust region graph cuts is presented.
We demonstrate that this framework has the potential to improve a wide range of
research: Object driven image retrieval, video tracking and segmentation, and
interactive image editing. The power of the framework lies in its generality,
the common part can be a rigid/non-rigid object (or scene), observed from different
viewpoints or even similar objects of the same class.'
author:
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Thomas
full_name: Minka, Thomas P
last_name: Minka
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
citation:
ama: 'Rother C, Kolmogorov V, Minka T, Blake A. Cosegmentation of image pairs by
histogram matching - Incorporating a global constraint into MRFs. In: IEEE; 2006:993-1000.
doi:10.1109/CVPR.2006.91'
apa: 'Rother, C., Kolmogorov, V., Minka, T., & Blake, A. (2006). Cosegmentation
of image pairs by histogram matching - Incorporating a global constraint into
MRFs (pp. 993–1000). Presented at the CVPR: Computer Vision and Pattern Recognition,
IEEE. https://doi.org/10.1109/CVPR.2006.91'
chicago: Rother, Carsten, Vladimir Kolmogorov, Thomas Minka, and Andrew Blake. “Cosegmentation
of Image Pairs by Histogram Matching - Incorporating a Global Constraint into
MRFs,” 993–1000. IEEE, 2006. https://doi.org/10.1109/CVPR.2006.91.
ieee: 'C. Rother, V. Kolmogorov, T. Minka, and A. Blake, “Cosegmentation of image
pairs by histogram matching - Incorporating a global constraint into MRFs,” presented
at the CVPR: Computer Vision and Pattern Recognition, 2006, pp. 993–1000.'
ista: 'Rother C, Kolmogorov V, Minka T, Blake A. 2006. Cosegmentation of image pairs
by histogram matching - Incorporating a global constraint into MRFs. CVPR: Computer
Vision and Pattern Recognition, 993–1000.'
mla: Rother, Carsten, et al. Cosegmentation of Image Pairs by Histogram Matching
- Incorporating a Global Constraint into MRFs. IEEE, 2006, pp. 993–1000, doi:10.1109/CVPR.2006.91.
short: C. Rother, V. Kolmogorov, T. Minka, A. Blake, in:, IEEE, 2006, pp. 993–1000.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:54Z
date_published: 2006-07-05T00:00:00Z
date_updated: 2021-01-12T07:41:40Z
day: '05'
doi: 10.1109/CVPR.2006.91
extern: 1
month: '07'
page: 993 - 1000
publication_status: published
publisher: IEEE
publist_id: '3493'
quality_controlled: 0
status: public
title: Cosegmentation of image pairs by histogram matching - Incorporating a global
constraint into MRFs
type: conference
year: '2006'
...
---
_id: '3214'
abstract:
- lang: eng
text: |-
The Feistel-network is a popular structure underlying many block-ciphers where the cipher is constructed from many simpler rounds, each defined by some function which is derived from the secret key.
Luby and Rackoff showed that the three-round Feistel-network – each round instantiated with a pseudorandom function secure against adaptive chosen plaintext attacks (CPA) – is a CPA secure pseudorandom permutation, thus giving some confidence in the soundness of using a Feistel-network to design block-ciphers.
But the round functions used in actual block-ciphers are – for efficiency reasons – far from being pseudorandom. We investigate the security of the Feistel-network against CPA distinguishers when the only security guarantee we have for the round functions is that they are secure against non-adaptive chosen plaintext attacks (nCPA). We show that in the information-theoretic setting, four rounds with nCPA secure round functions are sufficient (and necessary) to get a CPA secure permutation. Unfortunately, this result does not translate into the more interesting pseudorandom setting. In fact, under the so-called Inverse Decisional Diffie-Hellman assumption the Feistel-network with four rounds, each instantiated with a nCPA secure pseudorandom function, is in general not a CPA secure pseudorandom permutation.
acknowledgement: Most of this work was done while the K. Pietrzak was a PhD student
at ETH where he was supported by the Swiss National Science Foundation, project
No. 200020- 103847/1. Currently he is partially supported by the Commission of the
European Communities through the IST program under contract IST-2002-507932 ECRYPT.
alternative_title:
- LNCS
author:
- first_name: Ueli
full_name: Maurer, Ueli M
last_name: Maurer
- first_name: Yvonne
full_name: Oswald, Yvonne A
last_name: Oswald
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Johan
full_name: Sjödin, Johan
last_name: Sjödin
citation:
ama: 'Maurer U, Oswald Y, Pietrzak KZ, Sjödin J. Luby Rackoff ciphers from weak
round functions . In: Vol 4004. Springer; 2006:391-408. doi:10.1007/11761679_24'
apa: 'Maurer, U., Oswald, Y., Pietrzak, K. Z., & Sjödin, J. (2006). Luby Rackoff
ciphers from weak round functions (Vol. 4004, pp. 391–408). Presented at the
EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/11761679_24'
chicago: Maurer, Ueli, Yvonne Oswald, Krzysztof Z Pietrzak, and Johan Sjödin. “Luby
Rackoff Ciphers from Weak Round Functions ,” 4004:391–408. Springer, 2006. https://doi.org/10.1007/11761679_24.
ieee: 'U. Maurer, Y. Oswald, K. Z. Pietrzak, and J. Sjödin, “Luby Rackoff ciphers
from weak round functions ,” presented at the EUROCRYPT: Theory and Applications
of Cryptographic Techniques, 2006, vol. 4004, pp. 391–408.'
ista: 'Maurer U, Oswald Y, Pietrzak KZ, Sjödin J. 2006. Luby Rackoff ciphers from
weak round functions . EUROCRYPT: Theory and Applications of Cryptographic Techniques,
LNCS, vol. 4004, 391–408.'
mla: Maurer, Ueli, et al. Luby Rackoff Ciphers from Weak Round Functions .
Vol. 4004, Springer, 2006, pp. 391–408, doi:10.1007/11761679_24.
short: U. Maurer, Y. Oswald, K.Z. Pietrzak, J. Sjödin, in:, Springer, 2006, pp.
391–408.
conference:
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
date_created: 2018-12-11T12:02:03Z
date_published: 2006-07-11T00:00:00Z
date_updated: 2021-01-12T07:41:51Z
day: '11'
doi: 10.1007/11761679_24
extern: 1
intvolume: ' 4004'
month: '07'
page: 391 - 408
publication_status: published
publisher: Springer
publist_id: '3465'
quality_controlled: 0
status: public
title: 'Luby Rackoff ciphers from weak round functions '
type: conference
volume: 4004
year: '2006'
...
---
_id: '3215'
abstract:
- lang: eng
text: 'Most cryptographic primitives such as encryption, authentication or secret
sharing require randomness. Usually one assumes that perfect randomness is available,
but those primitives might also be realized under weaker assumptions. In this
work we continue the study of building secure cryptographic primitives from imperfect
random sources initiated by Dodis and Spencer (FOCS’02). Their main result shows
that there exists a (high-entropy) source of randomness allowing for perfect encryption
of a bit, and yet from which one cannot extract even a single weakly random bit,
separating encryption from extraction. Our main result separates encryption from
2-out-2 secret sharing (both in the information-theoretic and in the computational
settings): any source which can be used to achieve one-bit encryption also can
be used for 2-out-2 secret sharing of one bit, but the converse is false, even
for high-entropy sources. Therefore, possibility of extraction strictly implies
encryption, which in turn strictly implies 2-out-2 secret sharing.'
acknowledgement: Supported in part by NSF career award CCR-0133806 and NSF grant 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: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Bartosz
full_name: Przydatek, Bartosz
last_name: Przydatek
citation:
ama: 'Dodis Y, Pietrzak KZ, Przydatek B. Separating sources for encryption and secret
sharing. In: Vol 3876. Springer; 2006:601-616. doi:10.1007/11681878_31'
apa: 'Dodis, Y., Pietrzak, K. Z., & Przydatek, B. (2006). Separating sources
for encryption and secret sharing (Vol. 3876, pp. 601–616). Presented at the TCC:
Theory of Cryptography Conference, Springer. https://doi.org/10.1007/11681878_31'
chicago: Dodis, Yevgeniy, Krzysztof Z Pietrzak, and Bartosz Przydatek. “Separating
Sources for Encryption and Secret Sharing,” 3876:601–16. Springer, 2006. https://doi.org/10.1007/11681878_31.
ieee: 'Y. Dodis, K. Z. Pietrzak, and B. Przydatek, “Separating sources for encryption
and secret sharing,” presented at the TCC: Theory of Cryptography Conference,
2006, vol. 3876, pp. 601–616.'
ista: 'Dodis Y, Pietrzak KZ, Przydatek B. 2006. Separating sources for encryption
and secret sharing. TCC: Theory of Cryptography Conference, LNCS, vol. 3876, 601–616.'
mla: Dodis, Yevgeniy, et al. Separating Sources for Encryption and Secret Sharing.
Vol. 3876, Springer, 2006, pp. 601–16, doi:10.1007/11681878_31.
short: Y. Dodis, K.Z. Pietrzak, B. Przydatek, in:, Springer, 2006, pp. 601–616.
conference:
name: 'TCC: Theory of Cryptography Conference'
date_created: 2018-12-11T12:02:04Z
date_published: 2006-04-11T00:00:00Z
date_updated: 2021-01-12T07:41:51Z
day: '11'
doi: 10.1007/11681878_31
extern: 1
intvolume: ' 3876'
month: '04'
page: 601 - 616
publication_status: published
publisher: Springer
publist_id: '3466'
quality_controlled: 0
status: public
title: Separating sources for encryption and secret sharing
type: conference
volume: 3876
year: '2006'
...
---
_id: '3217'
abstract:
- lang: eng
text: |-
To prove that a secure key-agreement protocol exists one must at least show P ≠NP. Moreover any proof that the sequential composition of two non-adaptively secure pseudorandom functions is secure against at least two adaptive queries must falsify the decisional Diffie-Hellman assumption, a standard assumption from public-key cryptography. Hence proving any of this two seemingly unrelated statements would require a significant breakthrough. We show that at least one of the two statements is true.
To our knowledge this gives the first positive cryptographic result (namely that composition implies some weak adaptive security) which holds in Minicrypt, but not in Cryptomania, i.e. under the assumption that one-way functions exist, but public-key cryptography does not.
acknowledgement: Author was supported during the writing of this work by the Swiss
National Science Foundation, project No. 200020-103847/1. Part of this work is supported
by the Commission of the European Communities through the IST program under contract
IST-2002-507932
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 implies adaptive security in minicrypt. In: Vol 4004.
Springer; 2006:328-338. doi:10.1007/11761679_20'
apa: 'Pietrzak, K. Z. (2006). Composition implies adaptive security in minicrypt
(Vol. 4004, pp. 328–338). Presented at the EUROCRYPT: Theory and Applications
of Cryptographic Techniques, Springer. https://doi.org/10.1007/11761679_20'
chicago: Pietrzak, Krzysztof Z. “Composition Implies Adaptive Security in Minicrypt,”
4004:328–38. Springer, 2006. https://doi.org/10.1007/11761679_20.
ieee: 'K. Z. Pietrzak, “Composition implies adaptive security in minicrypt,” presented
at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2006, vol.
4004, pp. 328–338.'
ista: 'Pietrzak KZ. 2006. Composition implies adaptive security in minicrypt. EUROCRYPT:
Theory and Applications of Cryptographic Techniques, LNCS, vol. 4004, 328–338.'
mla: Pietrzak, Krzysztof Z. Composition Implies Adaptive Security in Minicrypt.
Vol. 4004, Springer, 2006, pp. 328–38, doi:10.1007/11761679_20.
short: K.Z. Pietrzak, in:, Springer, 2006, pp. 328–338.
conference:
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
date_created: 2018-12-11T12:02:04Z
date_published: 2006-07-11T00:00:00Z
date_updated: 2021-01-12T07:41:52Z
day: '11'
doi: 10.1007/11761679_20
extern: 1
intvolume: ' 4004'
month: '07'
page: 328 - 338
publication_status: published
publisher: Springer
publist_id: '3464'
quality_controlled: 0
status: public
title: Composition implies adaptive security in minicrypt
type: conference
volume: 4004
year: '2006'
...
---
_id: '3216'
abstract:
- lang: eng
text: |-
We prove a new upper bound on the advantage of any adversary for distinguishing the encrypted CBC-MAC (EMAC) based on random permutations from a random function. Our proof uses techniques recently introduced in [BPR05], which again were inspired by [DGH + 04].
The bound we prove is tight — in the sense that it matches the advantage of known attacks up to a constant factor — for a wide range of the parameters: let n denote the block-size, q the number of queries the adversary is allowed to make and ℓ an upper bound on the length (i.e. number of blocks) of the messages, then for ℓ ≤ 2 n/8 and q≥ł2 the advantage is in the order of q 2/2 n (and in particular independent of ℓ). This improves on the previous bound of q 2ℓΘ(1/ln ln ℓ)/2 n from [BPR05] and matches the trivial attack (which thus is basically optimal) where one simply asks random queries until a collision is found.
acknowledgement: Part of this work is supported by the Commission of the European
Communities through the IST program under contract IST-2002-507932 ECRYPT.
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. A tight bound for EMAC. In: Vol 4052. Springer; 2006:168-179.
doi:10.1007/11787006_15'
apa: 'Pietrzak, K. Z. (2006). A tight bound for EMAC (Vol. 4052, pp. 168–179). Presented
at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/11787006_15'
chicago: Pietrzak, Krzysztof Z. “A Tight Bound for EMAC,” 4052:168–79. Springer,
2006. https://doi.org/10.1007/11787006_15.
ieee: 'K. Z. Pietrzak, “A tight bound for EMAC,” presented at the ICALP: Automata,
Languages and Programming, 2006, vol. 4052, pp. 168–179.'
ista: 'Pietrzak KZ. 2006. A tight bound for EMAC. ICALP: Automata, Languages and
Programming, LNCS, vol. 4052, 168–179.'
mla: Pietrzak, Krzysztof Z. A Tight Bound for EMAC. Vol. 4052, Springer,
2006, pp. 168–79, doi:10.1007/11787006_15.
short: K.Z. Pietrzak, in:, Springer, 2006, pp. 168–179.
conference:
name: 'ICALP: Automata, Languages and Programming'
date_created: 2018-12-11T12:02:04Z
date_published: 2006-07-28T00:00:00Z
date_updated: 2021-01-12T07:41:52Z
day: '28'
doi: 10.1007/11787006_15
extern: 1
intvolume: ' 4052'
month: '07'
page: 168 - 179
publication_status: published
publisher: Springer
publist_id: '3463'
quality_controlled: 0
status: public
title: A tight bound for EMAC
type: conference
volume: 4052
year: '2006'
...
---
_id: '3522'
abstract:
- lang: eng
text: We observed sharp wave/ripples (SWR) during exploration within brief (<
2.4 s) interruptions of or during theta oscillations. CA1 network responses of
SWRs occurring during exploration (eSWR) and SWRs detected in waking immobility
or sleep were similar. However, neuronal activity during eSWR was location dependent,
and eSWR-related firing was stronger inside the place field than outside. The
eSPW-related firing increase was stronger than the baseline increase inside compared
to outside, suggesting a “supralinear” summation of eSWR and place-selective inputs.
Pairs of cells with similar place fields and/or correlated firing during exploration
showed stronger coactivation during eSWRs and subsequent sleep-SWRs. Sequential
activation of place cells was not required for the reactivation of waking co-firing
patterns; cell pairs with symmetrical cross-correlations still showed reactivated
waking co-firing patterns during sleep-SWRs. We suggest that place-selective firing
during eSWRs facilitates initial associations between cells with similar place
fields that enable place-related ensemble patterns to recur during subsequent
sleep-SWRs.
author:
- first_name: Joseph
full_name: Joseph O'Neill
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Timothy
full_name: Senior,Timothy
last_name: Senior
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: O’Neill J, Senior T, Csicsvari JL. Place-selective firing of CA1 pyramidal
cells during sharp wave/ripple network patterns in exploratory behavior. Neuron.
2006;49(1):143-155. doi:10.1016/j.neuron.2005.10.037
apa: O’Neill, J., Senior, T., & Csicsvari, J. L. (2006). Place-selective firing
of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory
behavior. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2005.10.037
chicago: O’Neill, Joseph, Timothy Senior, and Jozsef L Csicsvari. “Place-Selective
Firing of CA1 Pyramidal Cells during Sharp Wave/Ripple Network Patterns in Exploratory
Behavior.” Neuron. Elsevier, 2006. https://doi.org/10.1016/j.neuron.2005.10.037.
ieee: J. O’Neill, T. Senior, and J. L. Csicsvari, “Place-selective firing of CA1
pyramidal cells during sharp wave/ripple network patterns in exploratory behavior,”
Neuron, vol. 49, no. 1. Elsevier, pp. 143–155, 2006.
ista: O’Neill J, Senior T, Csicsvari JL. 2006. Place-selective firing of CA1 pyramidal
cells during sharp wave/ripple network patterns in exploratory behavior. Neuron.
49(1), 143–155.
mla: O’Neill, Joseph, et al. “Place-Selective Firing of CA1 Pyramidal Cells during
Sharp Wave/Ripple Network Patterns in Exploratory Behavior.” Neuron, vol.
49, no. 1, Elsevier, 2006, pp. 143–55, doi:10.1016/j.neuron.2005.10.037.
short: J. O’Neill, T. Senior, J.L. Csicsvari, Neuron 49 (2006) 143–155.
date_created: 2018-12-11T12:03:46Z
date_published: 2006-01-05T00:00:00Z
date_updated: 2021-01-12T07:44:03Z
day: '05'
doi: 10.1016/j.neuron.2005.10.037
extern: 1
intvolume: ' 49'
issue: '1'
month: '01'
page: 143 - 155
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2863'
quality_controlled: 0
status: public
title: Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network
patterns in exploratory behavior
type: journal_article
volume: 49
year: '2006'
...
---
_id: '3607'
abstract:
- lang: eng
text: We apply new analytical methods to understand the consequences of population
bottlenecks for expected additive genetic variance. We analyze essentially all
models for multilocus epistasis that have been numerically simulated to demonstrate
increased additive variance. We conclude that for biologically plausible models,
large increases in expected additive variance–attributable to epistasis rather
than dominance–are unlikely. Naciri-Graven and Goudet (2003) found that as the
number of epistatically interacting loci increases, additive variance tends to
be inflated more after a bottleneck. We argue that this result reflects biologically
unrealistic aspects of their models. Specifically, as the number of loci increases,
higher-order epistatic interactions become increasingly important in these models,
with an increasing fraction of the genetic variance becoming nonadditive, contrary
to empirical observations. As shown by Barton and Turelli (2004), without dominance,
conversion of nonadditive to additive variance depends only on the variance components
and not on the number of loci per se. Numerical results indicating that more inbreeding
is needed to produce maximal release of additive variance with more loci follow
directly from our analytical results, which show that high levels of inbreeding
(F > 0.5) are needed for significant conversion of higher-order components.
We discuss alternative approaches to modeling multilocus epistasis and understanding
its consequences.
author:
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Turelli M, Barton NH. Will population bottlenecks and multilocus epistasis
increase additive genetic variance? Evolution; International Journal of Organic
Evolution. 2006;60(9):1763-1776. doi:10.1111/j.0014-3820.2006.tb00521.x
apa: Turelli, M., & Barton, N. H. (2006). Will population bottlenecks and multilocus
epistasis increase additive genetic variance? Evolution; International Journal
of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2006.tb00521.x
chicago: Turelli, Michael, and Nicholas H Barton. “Will Population Bottlenecks and
Multilocus Epistasis Increase Additive Genetic Variance?” Evolution; International
Journal of Organic Evolution. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.0014-3820.2006.tb00521.x.
ieee: M. Turelli and N. H. Barton, “Will population bottlenecks and multilocus epistasis
increase additive genetic variance?,” Evolution; International Journal of Organic
Evolution, vol. 60, no. 9. Wiley-Blackwell, pp. 1763–1776, 2006.
ista: Turelli M, Barton NH. 2006. Will population bottlenecks and multilocus epistasis
increase additive genetic variance? Evolution; International Journal of Organic
Evolution. 60(9), 1763–1776.
mla: Turelli, Michael, and Nicholas H. Barton. “Will Population Bottlenecks and
Multilocus Epistasis Increase Additive Genetic Variance?” Evolution; International
Journal of Organic Evolution, vol. 60, no. 9, Wiley-Blackwell, 2006, pp. 1763–76,
doi:10.1111/j.0014-3820.2006.tb00521.x.
short: M. Turelli, N.H. Barton, Evolution; International Journal of Organic Evolution
60 (2006) 1763–1776.
date_created: 2018-12-11T12:04:13Z
date_published: 2006-09-01T00:00:00Z
date_updated: 2021-01-12T07:44:37Z
day: '01'
doi: 10.1111/j.0014-3820.2006.tb00521.x
extern: 1
intvolume: ' 60'
issue: '9'
month: '09'
page: 1763 - 1776
publication: Evolution; International Journal of Organic Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2776'
quality_controlled: 0
status: public
title: Will population bottlenecks and multilocus epistasis increase additive genetic
variance?
type: journal_article
volume: 60
year: '2006'
...
---
_id: '3683'
abstract:
- lang: eng
text: Many algorithms to remove distortion from document images have be proposed
in recent years, but so far there is no reliable method for comparing their performance.
In this paper we propose a collection of methods to measure the quality of such
restoration algorithms for document image which show a non-linear distortion due
to perspective or page curl. For the result from these measurement to be meaningful,
a common data set of ground truth is required. We therefore started with the buildup
of a document image database that is meant to serve as a common data basis for
all kinds of restoration from images of 3D-shaped document. The long term goal
would be to establish this database and following extensions in the area of document
image dewarping as an as fruitful and indispensable tool as e.g. the NIST database
is for OCR, or the Caltech database is for object and face recognition.
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Thomas
full_name: Breuel,Thomas M
last_name: Breuel
citation:
ama: 'Lampert C, Breuel T. Objective quality measurement for geometric document
image restoration. In: Springer; 2006.'
apa: 'Lampert, C., & Breuel, T. (2006). Objective quality measurement for geometric
document image restoration. Presented at the DAS: Document Analysis Systems, Springer.'
chicago: Lampert, Christoph, and Thomas Breuel. “Objective Quality Measurement for
Geometric Document Image Restoration.” Springer, 2006.
ieee: 'C. Lampert and T. Breuel, “Objective quality measurement for geometric document
image restoration,” presented at the DAS: Document Analysis Systems, 2006.'
ista: 'Lampert C, Breuel T. 2006. Objective quality measurement for geometric document
image restoration. DAS: Document Analysis Systems.'
mla: Lampert, Christoph, and Thomas Breuel. Objective Quality Measurement for
Geometric Document Image Restoration. Springer, 2006.
short: C. Lampert, T. Breuel, in:, Springer, 2006.
conference:
name: 'DAS: Document Analysis Systems'
date_created: 2018-12-11T12:04:36Z
date_published: 2006-03-16T00:00:00Z
date_updated: 2021-01-12T07:45:07Z
day: '16'
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/~chl/papers/lampert-das2006.pdf
month: '03'
publication_status: published
publisher: Springer
publist_id: '2692'
quality_controlled: 0
status: public
title: Objective quality measurement for geometric document image restoration
type: conference
year: '2006'
...
---
_id: '3685'
abstract:
- lang: eng
text: 'Video compression currently is dominated by engineering and fine-tuned heuristic
methods. In this paper, we propose to instead apply the well-developed machinery
of machine learning in order to support the optimization of existing video encoders
and the creation of new ones. Exemplarily, we show how by machine learning we
can improve one encoding step that is crucial for the performance of all current
video standards: macroblock mode decision. By formulating the problem in a Bayesian
setup, we show that macroblock mode decision can be reduced to a classification
problem with a cost function for misclassification that is sample dependent. We
demonstrate how to apply different machine learning techniques to obtain suitable
classifiers and we show in detailed experiments that all of these perform better
than the state-of-the-art heuristic method'
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. Machine learning for video compression: Macroblock mode decision.
In: IEEE; 2006:936-940. doi:10.1109/ICPR.2006.778'
apa: 'Lampert, C. (2006). Machine learning for video compression: Macroblock mode
decision (pp. 936–940). Presented at the ICPR: International Conference on Pattern
Recognition, IEEE. https://doi.org/10.1109/ICPR.2006.778'
chicago: 'Lampert, Christoph. “Machine Learning for Video Compression: Macroblock
Mode Decision,” 936–40. IEEE, 2006. https://doi.org/10.1109/ICPR.2006.778.'
ieee: 'C. Lampert, “Machine learning for video compression: Macroblock mode decision,”
presented at the ICPR: International Conference on Pattern Recognition, 2006,
pp. 936–940.'
ista: 'Lampert C. 2006. Machine learning for video compression: Macroblock mode
decision. ICPR: International Conference on Pattern Recognition, 936–940.'
mla: 'Lampert, Christoph. Machine Learning for Video Compression: Macroblock
Mode Decision. IEEE, 2006, pp. 936–40, doi:10.1109/ICPR.2006.778.'
short: C. Lampert, in:, IEEE, 2006, pp. 936–940.
conference:
name: 'ICPR: International Conference on Pattern Recognition'
date_created: 2018-12-11T12:04:37Z
date_published: 2006-09-18T00:00:00Z
date_updated: 2021-01-12T07:45:08Z
day: '18'
doi: 10.1109/ICPR.2006.778
extern: 1
month: '09'
page: 936 - 940
publication_status: published
publisher: IEEE
publist_id: '2689'
quality_controlled: 0
status: public
title: 'Machine learning for video compression: Macroblock mode decision'
type: conference
year: '2006'
...
---
_id: '3750'
abstract:
- lang: eng
text: We applied a single-cell assay to characterize how transcription dynamics
affects protein expression levels of a tetracycline-inducible gene expression
system. Transcriptional activity of the tetracycline promoter in response to a
steady level of inducer is steady in ΔacrAB efflux mutant but pulsating in wildtype
Escherichia coli cells. We found that the expression level of the green fluorescent
protein is several folds higher in ΔacrAB efflux mutant than in wildtype cells.
author:
- first_name: Thuc
full_name: Le,Thuc T.
last_name: Le
- first_name: Calin C
full_name: Calin Guet
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Philippe
full_name: Cluzel,Philippe
last_name: Cluzel
citation:
ama: Le T, Guet CC, Cluzel P. Protein expression enhancement in efflux-deleted mutant
bacteria. Protein Expression and Purification. 2006;48(1):28-31.
apa: Le, T., Guet, C. C., & Cluzel, P. (2006). Protein expression enhancement
in efflux-deleted mutant bacteria. Protein Expression and Purification.
Elsevier.
chicago: Le, Thuc, Calin C Guet, and Philippe Cluzel. “Protein Expression Enhancement
in Efflux-Deleted Mutant Bacteria.” Protein Expression and Purification.
Elsevier, 2006.
ieee: T. Le, C. C. Guet, and P. Cluzel, “Protein expression enhancement in efflux-deleted
mutant bacteria,” Protein Expression and Purification, vol. 48, no. 1.
Elsevier, pp. 28–31, 2006.
ista: Le T, Guet CC, Cluzel P. 2006. Protein expression enhancement in efflux-deleted
mutant bacteria. Protein Expression and Purification. 48(1), 28–31.
mla: Le, Thuc, et al. “Protein Expression Enhancement in Efflux-Deleted Mutant Bacteria.”
Protein Expression and Purification, vol. 48, no. 1, Elsevier, 2006, pp.
28–31.
short: T. Le, C.C. Guet, P. Cluzel, Protein Expression and Purification 48 (2006)
28–31.
date_created: 2018-12-11T12:04:58Z
date_published: 2006-07-01T00:00:00Z
date_updated: 2021-01-12T07:51:56Z
day: '01'
extern: 1
intvolume: ' 48'
issue: '1'
month: '07'
page: 28 - 31
publication: Protein Expression and Purification
publication_status: published
publisher: Elsevier
publist_id: '2478'
quality_controlled: 0
status: public
title: Protein expression enhancement in efflux-deleted mutant bacteria
type: journal_article
volume: 48
year: '2006'
...
---
_id: '3767'
abstract:
- lang: eng
text: Models of RNA secondary structure folding are widely used to study evolution
in theory and simulation. However, systematic studies of the parameters involved
are rare. In this paper, we study by simulation how RNA evolution is influenced
by three different factors, namely the mutation rate, scaling of the fitness function,
and distance measure. We found that for low mutation rates the qualitative evolutionary
behavior is robust with respect to the scaling of the fitness function. For efficient
mutation rates, which are close to the error threshold, scaling and distance measure
have a strong influence on the evolutionary behavior. A global distance measure
that takes sequence information additively into account lowers the error threshold.
When using a local sequence-structure alignment for the distance, we observed
a smoother evolution of the fitness over time. Finally, in addition to the well
known error threshold, we identify another threshold of the mutation rate, called
divergence threshold, where the qualitative transient behavior changes from a
localized to an exploratory search.
author:
- first_name: Anne
full_name: Anne Kupczok
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Peter
full_name: Dittrich,Peter
last_name: Dittrich
citation:
ama: Kupczok A, Dittrich P. Determinants of simulated RNA evolution. Journal
of Theoretical Biology. 2006;238(3):726-735. doi:10.1016/j.jtbi.2005.06.019
apa: Kupczok, A., & Dittrich, P. (2006). Determinants of simulated RNA evolution.
Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2005.06.019
chicago: Kupczok, Anne, and Peter Dittrich. “Determinants of Simulated RNA Evolution.”
Journal of Theoretical Biology. Elsevier, 2006. https://doi.org/10.1016/j.jtbi.2005.06.019.
ieee: A. Kupczok and P. Dittrich, “Determinants of simulated RNA evolution.,” Journal
of Theoretical Biology, vol. 238, no. 3. Elsevier, pp. 726–35, 2006.
ista: Kupczok A, Dittrich P. 2006. Determinants of simulated RNA evolution. Journal
of Theoretical Biology. 238(3), 726–35.
mla: Kupczok, Anne, and Peter Dittrich. “Determinants of Simulated RNA Evolution.”
Journal of Theoretical Biology, vol. 238, no. 3, Elsevier, 2006, pp. 726–35,
doi:10.1016/j.jtbi.2005.06.019.
short: A. Kupczok, P. Dittrich, Journal of Theoretical Biology 238 (2006) 726–35.
date_created: 2018-12-11T12:05:03Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:03Z
day: '01'
doi: 10.1016/j.jtbi.2005.06.019
extern: 1
intvolume: ' 238'
issue: '3'
month: '01'
page: 726 - 35
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '2461'
quality_controlled: 0
status: public
title: Determinants of simulated RNA evolution.
type: journal_article
volume: 238
year: '2006'
...
---
_id: '3813'
abstract:
- lang: eng
text: Hyperpolarization-activated channels (Ih or HCN channels) are widely expressed
in principal neurons in the central nervous system. However, Ih in inhibitory
GABAergic interneurons is less well characterized. We examined the functional
properties of Ih in fast-spiking basket cells (BCs) of the dentate gyrus, using
hippocampal slices from 17- to 21-day-old rats. Bath application of the Ih channel
blocker ZD 7288 at a concentration of 30 microm induced a hyperpolarization of
5.7 +/- 1.5 mV, an increase in input resistance and a correlated increase in apparent
membrane time constant. ZD 7288 blocked a hyperpolarization-activated current
in a concentration-dependent manner (IC50, 1.4 microm). The effects of ZD 7288
were mimicked by external Cs+. The reversal potential of Ih was -27.4 mV, corresponding
to a Na+ to K+ permeability ratio (PNa/PK) of 0.36. The midpoint potential of
the activation curve of Ih was -83.9 mV, and the activation time constant at -120
mV was 190 ms. Single-cell expression analysis using reverse transcription followed
by quantitative polymerase chain reaction revealed that BCs coexpress HCN1 and
HCN2 subunit mRNA, suggesting the formation of heteromeric HCN1/2 channels. ZD
7288 increased the current threshold for evoking antidromic action potentials
by extracellular stimulation, consistent with the expression of Ih in BC axons.
Finally, ZD 7288 decreased the frequency of miniature inhibitory postsynaptic
currents (mIPSCs) in hippocampal granule cells, the main target cells of BCs,
to 70 +/- 4% of the control value. In contrast, the amplitude of mIPSCs was unchanged,
consistent with the presence of Ih in inhibitory terminals. In conclusion, our
results suggest that Ih channels are expressed in the somatodendritic region,
axon and presynaptic elements of fast-spiking BCs in the hippocampus.
author:
- first_name: Yexica
full_name: Aponte, Yexica
last_name: Aponte
- first_name: Cheng
full_name: Lien, Cheng-Chang
last_name: Lien
- first_name: Ellen
full_name: Reisinger, Ellen
last_name: Reisinger
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Aponte Y, Lien C, Reisinger E, Jonas PM. Hyperpolarization-activated cation
channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology.
2006;574(Pt 1):229-243. doi:10.1113/jphysiol.2005.104042
apa: Aponte, Y., Lien, C., Reisinger, E., & Jonas, P. M. (2006). Hyperpolarization-activated
cation channels in fast-spiking interneurons of rat hippocampus. Journal of
Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2005.104042
chicago: Aponte, Yexica, Cheng Lien, Ellen Reisinger, and Peter M Jonas. “Hyperpolarization-Activated
Cation Channels in Fast-Spiking Interneurons of Rat Hippocampus.” Journal of
Physiology. Wiley-Blackwell, 2006. https://doi.org/10.1113/jphysiol.2005.104042.
ieee: Y. Aponte, C. Lien, E. Reisinger, and P. M. Jonas, “Hyperpolarization-activated
cation channels in fast-spiking interneurons of rat hippocampus,” Journal of
Physiology, vol. 574, no. Pt 1. Wiley-Blackwell, pp. 229–43, 2006.
ista: Aponte Y, Lien C, Reisinger E, Jonas PM. 2006. Hyperpolarization-activated
cation channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology.
574(Pt 1), 229–43.
mla: Aponte, Yexica, et al. “Hyperpolarization-Activated Cation Channels in Fast-Spiking
Interneurons of Rat Hippocampus.” Journal of Physiology, vol. 574, no.
Pt 1, Wiley-Blackwell, 2006, pp. 229–43, doi:10.1113/jphysiol.2005.104042.
short: Y. Aponte, C. Lien, E. Reisinger, P.M. Jonas, Journal of Physiology 574 (2006)
229–43.
date_created: 2018-12-11T12:05:19Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:23Z
day: '01'
doi: 10.1113/jphysiol.2005.104042
extern: 1
intvolume: ' 574'
issue: Pt 1
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1817792/
month: '01'
oa: 1
page: 229 - 43
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2397'
quality_controlled: 0
status: public
title: Hyperpolarization-activated cation channels in fast-spiking interneurons of
rat hippocampus
type: journal_article
volume: 574
year: '2006'
...
---
_id: '3814'
abstract:
- lang: eng
text: The axon terminals (mossy fibers) of hippocampal dentate granule cells form
characteristic synaptic connections with large spines or excrescences of both
hilar mossy cells and CA3 pyramidal neurons. Interneurons of the hilar region
and area CA3 are also prominent targets of mossy fibers. The tracing of biocytin-filled
mossy fibers and immunolabeling of target cells with interneuron markers has revealed
that the majority of mossy fiber synapses project to gamma aminobutyric acid (GABA)-ergic
inhibitory interneurons rather than to excitatory principal cells, although the
functional implications of these quantitative differences are unclear. Following
a brief description of the "classical" mossy fiber synapse on excrescences
of CA3 pyramidal cells, the present review focuses on the contacts formed between
granule cells and GABAergic interneurons, both normally and after synaptic reorganization.
In response to deafferentation of mossy cell target cells, which include both
granule cells and interneurons, mossy fibers "sprout" new axon collaterals
that form a band of supragranular mossy fibers in the inner molecular layer of
the dentate gyrus. Although most newly formed recurrent mossy fibers establish
synapses with granule cells, there is an apparently convergent input of new mossy
fibers onto GABA-immunoreactive interneuron dendrites that traverse the inner
molecular layer. These mossy fiber-interneuron synapses in the dentate gyrus are
observed in chronically epileptic rats and may be the structural correlate of
the granule cell hyperinhibition observed in these animals in vivo. Together,
the findings reviewed here establish mossy fiber synapses as an important component
of inhibitory circuits in the hippocampus.
author:
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Robert
full_name: Sloviter, Robert S
last_name: Sloviter
citation:
ama: Frotscher M, Jonas PM, Sloviter R. Synapses formed by normal and abnormal hippocampal
mossy fibers (Review). Cell and Tissue Research. 2006;326(2):361-367. doi:10.1007/s00441-006-0269-2
apa: Frotscher, M., Jonas, P. M., & Sloviter, R. (2006). Synapses formed by
normal and abnormal hippocampal mossy fibers (Review). Cell and Tissue Research.
Springer. https://doi.org/10.1007/s00441-006-0269-2
chicago: Frotscher, Michael, Peter M Jonas, and Robert Sloviter. “Synapses Formed
by Normal and Abnormal Hippocampal Mossy Fibers (Review).” Cell and Tissue
Research. Springer, 2006. https://doi.org/10.1007/s00441-006-0269-2.
ieee: M. Frotscher, P. M. Jonas, and R. Sloviter, “Synapses formed by normal and
abnormal hippocampal mossy fibers (Review),” Cell and Tissue Research,
vol. 326, no. 2. Springer, pp. 361–7, 2006.
ista: Frotscher M, Jonas PM, Sloviter R. 2006. Synapses formed by normal and abnormal
hippocampal mossy fibers (Review). Cell and Tissue Research. 326(2), 361–7.
mla: Frotscher, Michael, et al. “Synapses Formed by Normal and Abnormal Hippocampal
Mossy Fibers (Review).” Cell and Tissue Research, vol. 326, no. 2, Springer,
2006, pp. 361–67, doi:10.1007/s00441-006-0269-2.
short: M. Frotscher, P.M. Jonas, R. Sloviter, Cell and Tissue Research 326 (2006)
361–7.
date_created: 2018-12-11T12:05:19Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2019-04-26T07:22:35Z
day: '01'
doi: 10.1007/s00441-006-0269-2
extern: 1
intvolume: ' 326'
issue: '2'
month: '01'
page: 361 - 7
publication: Cell and Tissue Research
publication_status: published
publisher: Springer
publist_id: '2395'
quality_controlled: 0
status: public
title: Synapses formed by normal and abnormal hippocampal mossy fibers (Review)
type: review
volume: 326
year: '2006'
...
---
_id: '3815'
abstract:
- lang: eng
text: It is widely accepted that the hippocampus plays a major role in learning
and memory. The mossy fiber synapse between granule cells in the dentate gyrus
and pyramidal neurons in the CA3 region is a key component of the hippocampal
trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp
recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms
of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+)
channel density in mossy fiber boutons leads to a large amplitude of the presynaptic
action potential. Together with the fast gating of presynaptic Ca(2+) channels,
this generates a large and brief presynaptic Ca(2+) influx, which can trigger
transmitter release with high efficiency and temporal precision. The large number
of release sites, the large size of the releasable pool of vesicles, and the huge
extent of presynaptic plasticity confer unique strength to this synapse, suggesting
a large impact onto the CA3 pyramidal cell network under specific behavioral conditions.
The characteristic properties of the hippocampal mossy fiber synapse may be important
for pattern separation and information storage in the dentate gyrus-CA3 cell network.
author:
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
- first_name: Dominique
full_name: Engel, Dominique
last_name: Engel
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. Timing and efficacy of transmitter
release at mossy fiber synapses in the hippocampal network. Pflugers Archiv :
European Journal of Physiology. 2006;453(3):361-372. doi:10.1007/s00424-006-0093-2'
apa: 'Bischofberger, J., Engel, D., Frotscher, M., & Jonas, P. M. (2006). Timing
and efficacy of transmitter release at mossy fiber synapses in the hippocampal
network. Pflugers Archiv : European Journal of Physiology. Springer. https://doi.org/10.1007/s00424-006-0093-2'
chicago: 'Bischofberger, Josef, Dominique Engel, Michael Frotscher, and Peter M
Jonas. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in
the Hippocampal Network.” Pflugers Archiv : European Journal of Physiology.
Springer, 2006. https://doi.org/10.1007/s00424-006-0093-2.'
ieee: 'J. Bischofberger, D. Engel, M. Frotscher, and P. M. Jonas, “Timing and efficacy
of transmitter release at mossy fiber synapses in the hippocampal network,” Pflugers
Archiv : European Journal of Physiology, vol. 453, no. 3. Springer, pp. 361–72,
2006.'
ista: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. 2006. Timing and efficacy
of transmitter release at mossy fiber synapses in the hippocampal network. Pflugers
Archiv : European Journal of Physiology. 453(3), 361–72.'
mla: 'Bischofberger, Josef, et al. “Timing and Efficacy of Transmitter Release at
Mossy Fiber Synapses in the Hippocampal Network.” Pflugers Archiv : European
Journal of Physiology, vol. 453, no. 3, Springer, 2006, pp. 361–72, doi:10.1007/s00424-006-0093-2.'
short: 'J. Bischofberger, D. Engel, M. Frotscher, P.M. Jonas, Pflugers Archiv :
European Journal of Physiology 453 (2006) 361–72.'
date_created: 2018-12-11T12:05:19Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:24Z
day: '01'
doi: 10.1007/s00424-006-0093-2
extern: 1
intvolume: ' 453'
issue: '3'
month: '01'
page: 361 - 72
publication: 'Pflugers Archiv : European Journal of Physiology'
publication_status: published
publisher: Springer
publist_id: '2396'
quality_controlled: 0
status: public
title: Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal
network
type: journal_article
volume: 453
year: '2006'
...
---
_id: '3811'
abstract:
- lang: eng
text: Networks of GABAergic neurons are key elements in the generation of gamma
oscillations in the brain. Computational studies suggested that the emergence
of coherent oscillations requires hyperpolarizing inhibition. Here, we show that
GABA(A) receptor-mediated inhibition in mature interneurons of the hippocampal
dentate gyrus is shunting rather than hyperpolarizing. Unexpectedly, when shunting
inhibition is incorporated into a structured interneuron network model with fast
and strong synapses, coherent oscillations emerge. In comparison to hyperpolarizing
inhibition, networks with shunting inhibition show several advantages. First,
oscillations are generated with smaller tonic excitatory drive. Second, network
frequencies are tuned to the gamma band. Finally, robustness against heterogeneity
in the excitatory drive is markedly improved. In single interneurons, shunting
inhibition shortens the interspike interval for low levels of drive but prolongs
it for high levels, leading to homogenization of neuronal firing rates. Thus,
shunting inhibition may confer increased robustness to gamma oscillations in the
brain.
author:
- first_name: Imre
full_name: Vida, Imre
last_name: Vida
- first_name: Marlene
full_name: Bartos, Marlene
last_name: Bartos
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Vida I, Bartos M, Jonas PM. Shunting inhibition improves robustness of gamma
oscillations in hippocampal interneuron networks by homogenizing firing rates.
Neuron. 2006;49(1):107-117. doi:10.1016/j.neuron.2005.11.036
apa: Vida, I., Bartos, M., & Jonas, P. M. (2006). Shunting inhibition improves
robustness of gamma oscillations in hippocampal interneuron networks by homogenizing
firing rates. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2005.11.036
chicago: Vida, Imre, Marlene Bartos, and Peter M Jonas. “Shunting Inhibition Improves
Robustness of Gamma Oscillations in Hippocampal Interneuron Networks by Homogenizing
Firing Rates.” Neuron. Elsevier, 2006. https://doi.org/10.1016/j.neuron.2005.11.036.
ieee: I. Vida, M. Bartos, and P. M. Jonas, “Shunting inhibition improves robustness
of gamma oscillations in hippocampal interneuron networks by homogenizing firing
rates,” Neuron, vol. 49, no. 1. Elsevier, pp. 107–17, 2006.
ista: Vida I, Bartos M, Jonas PM. 2006. Shunting inhibition improves robustness
of gamma oscillations in hippocampal interneuron networks by homogenizing firing
rates. Neuron. 49(1), 107–17.
mla: Vida, Imre, et al. “Shunting Inhibition Improves Robustness of Gamma Oscillations
in Hippocampal Interneuron Networks by Homogenizing Firing Rates.” Neuron,
vol. 49, no. 1, Elsevier, 2006, pp. 107–17, doi:10.1016/j.neuron.2005.11.036.
short: I. Vida, M. Bartos, P.M. Jonas, Neuron 49 (2006) 107–17.
date_created: 2018-12-11T12:05:18Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:22Z
day: '01'
doi: 10.1016/j.neuron.2005.11.036
extern: 1
intvolume: ' 49'
issue: '1'
month: '01'
page: 107 - 17
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2398'
quality_controlled: 0
status: public
title: Shunting inhibition improves robustness of gamma oscillations in hippocampal
interneuron networks by homogenizing firing rates
type: journal_article
volume: 49
year: '2006'
...
---
_id: '3817'
author:
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Eckart
full_name: Gundelfinger, Eckart
last_name: Gundelfinger
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Erwin
full_name: Neher, Erwin
last_name: Neher
- first_name: Peter
full_name: Seeburg, Peter
last_name: Seeburg
citation:
ama: Frotscher M, Gundelfinger E, Jonas PM, Neher E, Seeburg P. The most important
recent advances in synapse research from my point of view--and what remains to
be done. Cell and Tissue Research. 2006;326(2):203-204. doi:10.1007/s00441-006-0325-y
apa: Frotscher, M., Gundelfinger, E., Jonas, P. M., Neher, E., & Seeburg, P.
(2006). The most important recent advances in synapse research from my point of
view--and what remains to be done. Cell and Tissue Research. Springer.
https://doi.org/10.1007/s00441-006-0325-y
chicago: Frotscher, Michael, Eckart Gundelfinger, Peter M Jonas, Erwin Neher, and
Peter Seeburg. “The Most Important Recent Advances in Synapse Research from My
Point of View--and What Remains to Be Done.” Cell and Tissue Research.
Springer, 2006. https://doi.org/10.1007/s00441-006-0325-y.
ieee: M. Frotscher, E. Gundelfinger, P. M. Jonas, E. Neher, and P. Seeburg, “The
most important recent advances in synapse research from my point of view--and
what remains to be done,” Cell and Tissue Research, vol. 326, no. 2. Springer,
pp. 203–4, 2006.
ista: Frotscher M, Gundelfinger E, Jonas PM, Neher E, Seeburg P. 2006. The most
important recent advances in synapse research from my point of view--and what
remains to be done. Cell and Tissue Research. 326(2), 203–4.
mla: Frotscher, Michael, et al. “The Most Important Recent Advances in Synapse Research
from My Point of View--and What Remains to Be Done.” Cell and Tissue Research,
vol. 326, no. 2, Springer, 2006, pp. 203–04, doi:10.1007/s00441-006-0325-y.
short: M. Frotscher, E. Gundelfinger, P.M. Jonas, E. Neher, P. Seeburg, Cell and
Tissue Research 326 (2006) 203–4.
date_created: 2018-12-11T12:05:20Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:24Z
day: '01'
doi: 10.1007/s00441-006-0325-y
extern: 1
intvolume: ' 326'
issue: '2'
month: '01'
page: 203 - 4
publication: Cell and Tissue Research
publication_status: published
publisher: Springer
publist_id: '2394'
quality_controlled: 0
status: public
title: The most important recent advances in synapse research from my point of view--and
what remains to be done
type: journal_article
volume: 326
year: '2006'
...
---
_id: '3912'
abstract:
- lang: eng
text: Invasive species often dramatically change native species communities by directly
and indirectly out-competing native species. We studied the direct interference
abilities of the invasive garden ant, Lasius neglectus VAN LOON, BOOMSMA &
ANDRÁSFALVY, 1990, by performing one-to-one aggression tests of L. neglectus workers
towards three native Lasius ant species that occur at the edge of a L. neglectus
supercolony in Seva, Spain. Our results show that L. neglectus is highly aggressive
against all three native Lasius species tested (L. grandis FOREL, 1909, L. emarginatus
(OLIVIER, 1792), and L. cinereus SEIFERT, 1992), expressed as a higher attack
rate of L. neglectus and behavioural dominance throughout the aggressive encounters.
Attacks of L. neglectus were performed fastest and most frequent against L. grandis,
and also the highest antennation frequencies were observed in encounters between
these two species. This could be due to the largest difference in body size, or
due to a greater overlap in ecological niche between L. neglectus and L. grandis
compared to the other two native species. There was only weak support for L. neglectus
workers from the periphery of the supercolony to be more aggressive relative to
workers from the centre, even though the former encounter native ant species on
a daily basis at the edge of the supercolony.
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Suzanne
full_name: Lommen, Suzanne
last_name: Lommen
- first_name: Klaus
full_name: Petersen, Klaus
last_name: Petersen
- first_name: Jes
full_name: Pedersen, Jes
last_name: Pedersen
citation:
ama: 'Cremer S, Ugelvig LV, Lommen S, Petersen K, Pedersen J. Attack of the invasive
garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae)
against native Lasius species in Spain. Myrmecological News. 2006;9:13-19.'
apa: 'Cremer, S., Ugelvig, L. V., Lommen, S., Petersen, K., & Pedersen, J. (2006).
Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera:
Formicidae) against native Lasius species in Spain. Myrmecological News.
Österreichische Gesellschaft für Entomofaunistik.'
chicago: 'Cremer, Sylvia, Line V Ugelvig, Suzanne Lommen, Klaus Petersen, and Jes
Pedersen. “Attack of the Invasive Garden Ant: Aggression Behaviour of Lasius Neglectus
(Hymenoptera: Formicidae) against Native Lasius Species in Spain.” Myrmecological
News. Österreichische Gesellschaft für Entomofaunistik, 2006.'
ieee: 'S. Cremer, L. V. Ugelvig, S. Lommen, K. Petersen, and J. Pedersen, “Attack
of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera:
Formicidae) against native Lasius species in Spain,” Myrmecological News,
vol. 9. Österreichische Gesellschaft für Entomofaunistik, pp. 13–19, 2006.'
ista: 'Cremer S, Ugelvig LV, Lommen S, Petersen K, Pedersen J. 2006. Attack of the
invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae)
against native Lasius species in Spain. Myrmecological News. 9, 13–19.'
mla: 'Cremer, Sylvia, et al. “Attack of the Invasive Garden Ant: Aggression Behaviour
of Lasius Neglectus (Hymenoptera: Formicidae) against Native Lasius Species in
Spain.” Myrmecological News, vol. 9, Österreichische Gesellschaft für Entomofaunistik,
2006, pp. 13–19.'
short: S. Cremer, L.V. Ugelvig, S. Lommen, K. Petersen, J. Pedersen, Myrmecological
News 9 (2006) 13–19.
date_created: 2018-12-11T12:05:51Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2021-01-12T07:53:09Z
day: '01'
extern: '1'
intvolume: ' 9'
language:
- iso: eng
month: '12'
oa_version: None
page: 13 - 19
publication: Myrmecological News
publication_status: published
publisher: Österreichische Gesellschaft für Entomofaunistik
publist_id: '2239'
status: public
title: 'Attack of the invasive garden ant: aggression behaviour of Lasius neglectus
(Hymenoptera: Formicidae) against native Lasius species in Spain'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2006'
...
---
_id: '3914'
abstract:
- lang: eng
text: We compare the performances of established means of character selection for
discriminant analysis in species distinction with a combination procedure for
finding the optimal character combination (minimum classification error, minimum
number of required characters), using morphometric data sets from the ant genera
Cardiocondyla, Lasius and Tetramorium. The established methods are empirical character
selection as well as forward selection, backward elimination and stepwise selection
of discriminant analysis. The combination procedure is clearly superior to the
established methods of character selection, and is widely applicable.
author:
- first_name: Karl
full_name: Moder, Karl
last_name: Moder
- first_name: Birgit
full_name: Schlick Steiner, Birgit
last_name: Schlick Steiner
- first_name: Florian
full_name: Steiner, Florian
last_name: Steiner
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Erhard
full_name: Christian, Erhard
last_name: Christian
- first_name: Bernhard
full_name: Seifert, Bernhard
last_name: Seifert
citation:
ama: 'Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B. Optimal
species distinction by discriminant analysis: comparing established methods of
character selection with a combination procedure using ant morphometrics as a
case study. Journal of Zoological Systematics and Evolutionary Research.
2006;45(1):82-87. doi:10.1111/j.1439-0469.2006.00372.x'
apa: 'Moder, K., Schlick Steiner, B., Steiner, F., Cremer, S., Christian, E., &
Seifert, B. (2006). Optimal species distinction by discriminant analysis: comparing
established methods of character selection with a combination procedure using
ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary
Research. Wiley-Blackwell. https://doi.org/10.1111/j.1439-0469.2006.00372.x'
chicago: 'Moder, Karl, Birgit Schlick Steiner, Florian Steiner, Sylvia Cremer, Erhard
Christian, and Bernhard Seifert. “Optimal Species Distinction by Discriminant
Analysis: Comparing Established Methods of Character Selection with a Combination
Procedure Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics
and Evolutionary Research. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.1439-0469.2006.00372.x.'
ieee: 'K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, and B.
Seifert, “Optimal species distinction by discriminant analysis: comparing established
methods of character selection with a combination procedure using ant morphometrics
as a case study,” Journal of Zoological Systematics and Evolutionary Research,
vol. 45, no. 1. Wiley-Blackwell, pp. 82–87, 2006.'
ista: 'Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B.
2006. Optimal species distinction by discriminant analysis: comparing established
methods of character selection with a combination procedure using ant morphometrics
as a case study. Journal of Zoological Systematics and Evolutionary Research.
45(1), 82–87.'
mla: 'Moder, Karl, et al. “Optimal Species Distinction by Discriminant Analysis:
Comparing Established Methods of Character Selection with a Combination Procedure
Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics
and Evolutionary Research, vol. 45, no. 1, Wiley-Blackwell, 2006, pp. 82–87,
doi:10.1111/j.1439-0469.2006.00372.x.'
short: K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, B. Seifert,
Journal of Zoological Systematics and Evolutionary Research 45 (2006) 82–87.
date_created: 2018-12-11T12:05:52Z
date_published: 2006-08-29T00:00:00Z
date_updated: 2021-01-12T07:53:10Z
day: '29'
doi: 10.1111/j.1439-0469.2006.00372.x
extern: '1'
intvolume: ' 45'
issue: '1'
language:
- iso: eng
month: '08'
oa_version: None
page: 82 - 87
publication: Journal of Zoological Systematics and Evolutionary Research
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2241'
status: public
title: 'Optimal species distinction by discriminant analysis: comparing established
methods of character selection with a combination procedure using ant morphometrics
as a case study'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2006'
...
---
_id: '3913'
abstract:
- lang: eng
text: Many invasive ant species, such as the Argentine ant or the red imported fire
ant, have huge colonies with thousands of mass-foraging workers, which quickly
monopolise resources and therefore represent a considerable threat to the native
ant fauna. Cardiocondyla obscurior and several other species of this myrmicine
genus have similarly been transferred throughout the tropics by human activities.
However, because their colonies are tiny and workers forage solitarily, Cardiocondyla
are often not recognized as successful invaders. Here, we document that the life
history of Cardiocondyla closely resembles that of the more conspicuous tramp
species, with polygyny, intranidal mating, budding, worker sterility, low genetic
variability, and possibly also unicoloniality. Given that introduced Cardiocondyla
may locally reach a very high population density, the effects of these stealthy
invaders on the native arthropod fauna should receive more attention.
author:
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Norbert
full_name: Eckl, Norbert
last_name: Eckl
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
citation:
ama: 'Heinze J, Cremer S, Eckl N, Schrempf A. Stealthy invaders: the biology of
Cardiocondyla tramp ants. Insectes Sociaux. 2006;53(1):1-7. doi:10.1007/s00040-005-0847-4'
apa: 'Heinze, J., Cremer, S., Eckl, N., & Schrempf, A. (2006). Stealthy invaders:
the biology of Cardiocondyla tramp ants. Insectes Sociaux. Springer. https://doi.org/10.1007/s00040-005-0847-4'
chicago: 'Heinze, Jürgen, Sylvia Cremer, Norbert Eckl, and Alexandra Schrempf. “Stealthy
Invaders: The Biology of Cardiocondyla Tramp Ants.” Insectes Sociaux. Springer,
2006. https://doi.org/10.1007/s00040-005-0847-4.'
ieee: 'J. Heinze, S. Cremer, N. Eckl, and A. Schrempf, “Stealthy invaders: the biology
of Cardiocondyla tramp ants,” Insectes Sociaux, vol. 53, no. 1. Springer,
pp. 1–7, 2006.'
ista: 'Heinze J, Cremer S, Eckl N, Schrempf A. 2006. Stealthy invaders: the biology
of Cardiocondyla tramp ants. Insectes Sociaux. 53(1), 1–7.'
mla: 'Heinze, Jürgen, et al. “Stealthy Invaders: The Biology of Cardiocondyla Tramp
Ants.” Insectes Sociaux, vol. 53, no. 1, Springer, 2006, pp. 1–7, doi:10.1007/s00040-005-0847-4.'
short: J. Heinze, S. Cremer, N. Eckl, A. Schrempf, Insectes Sociaux 53 (2006) 1–7.
date_created: 2018-12-11T12:05:51Z
date_published: 2006-02-01T00:00:00Z
date_updated: 2021-01-12T07:53:09Z
day: '01'
doi: 10.1007/s00040-005-0847-4
extern: '1'
intvolume: ' 53'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 1 - 7
publication: Insectes Sociaux
publication_status: published
publisher: Springer
publist_id: '2240'
status: public
title: 'Stealthy invaders: the biology of Cardiocondyla tramp ants'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2006'
...
---
_id: '3932'
abstract:
- lang: eng
text: 'OBJECTIVES: The EGFR is expressed in malignant ovarian tumor tissue, and
tissue content of EGFR has been directly associated with poor prognosis in patients
with ovarian cancer. The uPA system plays a role in pericellular proteolysis,
cell migration, invasion, and is over-expressed in ovarian cancer. This study
explored the effects of EGF on uPAR expression in the ovarian cancer cell line
OVCAR-3. METHODS: We used OVCAR-3 cells and the following methods: cell migration
assay, time-lapse video microscopy, real-time PCR, assays for cellular binding
of 125I-uPA and cellular degradation of 125I-uPA:PAI-1 complex, biosynthetic labeling
using 35S-methionin, Western blot, Northern blot, and ELISAs for uPA, PAI-1, and
uPAR. RESULTS: EGF up-regulates both protein and mRNA not only for uPAR, but also
for the ligand uPA and its inhibitor PAI-1. Cell surface uPAR, in control as well
as EGF-stimulated cells, is present only in the intact, not the cleaved, form.
Ligand binding experiments showed an increase of endogenously occupied uPAR, whereas
non-occupied receptor sites were not increased. In addition, EGF treatment resulted
in decreased degradation of radiolabeled uPA:PAI-1 complex. This suggests decreased
internalization of uPAR, since the complex is internalized together with uPAR.
Like EGF, colchicine, which inhibits endocytosis, increased cell surface expression
of uPAR. In addition, we found an immediate increase of uPAR after exposing the
cells to EGF and this was accompanied by a transient increase of cell migration.
The increase of cell surface uPAR in response to EGF is accompanied by increased
release of the soluble form of uPAR (suPAR) to the medium as well as by increased
cell migration. Both uPAR and suPAR increased in cells treated with the endocytosis
inhibitor colchicine even though cell migration was inhibited, suggesting that
the mechanism of uPAR shedding is not related to cell migration. CONCLUSION: Increased
cell surface uPAR in response to EGF stimulation results from mobilization of
uPAR from detergent-resistant domains, increased expression of uPAR mRNA, and
decreased internalization and degradation of uPAR. Both the anti-uPAR antibody
R3, which inhibits binding of uPA, and the EGFR phosphorylation inhibitor Iressa
inhibited cell migration in response to uPA as well as to EGF, suggesting that
EGFR and uPAR are engaged in the same multiprotein assembly on the cell surface.'
author:
- first_name: Emir
full_name: Henic, Emir
last_name: Henic
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Stefan
full_name: Hansson, Stefan
last_name: Hansson
- first_name: Gunilla
full_name: Høyer-Hansen, Gunilla
last_name: Høyer Hansen
- first_name: Bertil
full_name: Casslén, Bertil
last_name: Casslén
citation:
ama: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. EGF-stimulated migration
in ovarian cancer cells is associated with decreased internalization, increased
surface expression, and increased shedding of the urokinase plasminogen activator
receptor. Gynecologic Oncology. 2006;101(1):28-39. doi:10.1016/j.ygyno.2005.09.038
apa: Henic, E., Sixt, M. K., Hansson, S., Høyer Hansen, G., & Casslén, B. (2006).
EGF-stimulated migration in ovarian cancer cells is associated with decreased
internalization, increased surface expression, and increased shedding of the urokinase
plasminogen activator receptor. Gynecologic Oncology. Elsevier. https://doi.org/10.1016/j.ygyno.2005.09.038
chicago: Henic, Emir, Michael K Sixt, Stefan Hansson, Gunilla Høyer Hansen, and
Bertil Casslén. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated
with Decreased Internalization, Increased Surface Expression, and Increased Shedding
of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology.
Elsevier, 2006. https://doi.org/10.1016/j.ygyno.2005.09.038.
ieee: E. Henic, M. K. Sixt, S. Hansson, G. Høyer Hansen, and B. Casslén, “EGF-stimulated
migration in ovarian cancer cells is associated with decreased internalization,
increased surface expression, and increased shedding of the urokinase plasminogen
activator receptor,” Gynecologic Oncology, vol. 101, no. 1. Elsevier, pp.
28–39, 2006.
ista: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. 2006. EGF-stimulated
migration in ovarian cancer cells is associated with decreased internalization,
increased surface expression, and increased shedding of the urokinase plasminogen
activator receptor. Gynecologic Oncology. 101(1), 28–39.
mla: Henic, Emir, et al. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated
with Decreased Internalization, Increased Surface Expression, and Increased Shedding
of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology,
vol. 101, no. 1, Elsevier, 2006, pp. 28–39, doi:10.1016/j.ygyno.2005.09.038.
short: E. Henic, M.K. Sixt, S. Hansson, G. Høyer Hansen, B. Casslén, Gynecologic
Oncology 101 (2006) 28–39.
date_created: 2018-12-11T12:05:57Z
date_published: 2006-04-01T00:00:00Z
date_updated: 2021-01-12T07:53:17Z
day: '01'
doi: 10.1016/j.ygyno.2005.09.038
extern: 1
intvolume: ' 101'
issue: '1'
month: '04'
page: 28 - 39
publication: Gynecologic Oncology
publication_status: published
publisher: Elsevier
publist_id: '2194'
quality_controlled: 0
status: public
title: EGF-stimulated migration in ovarian cancer cells is associated with decreased
internalization, increased surface expression, and increased shedding of the urokinase
plasminogen activator receptor
type: journal_article
volume: 101
year: '2006'
...
---
_id: '3978'
abstract:
- lang: eng
text: Evaluating the quality of experimentally determined protein structural models
is an essential step toward identifying potential errors and guiding further structural
refinement. Herein, we report the use of proton local density as a sensitive measure
to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256
high-resolution crystal structures with protons added and optimized, we show that
the local density of different proton types display distinct distributions. These
distributions can be characterized by statistical moments and are used to establish
local density Z-scores for evaluating both global and local packing for individual
protons. Analysis of 546 crystal structures at various resolutions shows that
the local density Z-scores increase as the structural resolution decreases and
correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733)
generated by all atom contact analysis. Local density Z-scores for NMR structures
exhibit a significantly wider range of values than for X-ray structures and demonstrate
a combination of potentially problematic inflation and compression. Water-refined
NMR structures show improved packing quality. Our analysis of a high-quality structural
ensemble of ubiquitin refined against order parameters shows proton density distributions
that correlate nearly perfectly with our standards derived from crystal structures,
further validating our approach. We present an automated analysis and visualization
tool for proton packing to evaluate the quality of NMR structures.
author:
- first_name: Yih
full_name: Ban, Yih-En Andrew
last_name: Ban
- first_name: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
- first_name: Pei
full_name: Zhou, Pei
last_name: Zhou
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. Evaluating the quality of NMR structures
by local density of protons. Proteins: Structure, Function and Bioinformatics.
2006;62(4):852-864. doi:10.1002/prot.20811'
apa: 'Ban, Y., Rudolph, J., Zhou, P., & Edelsbrunner, H. (2006). Evaluating
the quality of NMR structures by local density of protons. Proteins: Structure,
Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/prot.20811'
chicago: 'Ban, Yih, Johannes Rudolph, Pei Zhou, and Herbert Edelsbrunner. “Evaluating
the Quality of NMR Structures by Local Density of Protons.” Proteins: Structure,
Function and Bioinformatics. Wiley-Blackwell, 2006. https://doi.org/10.1002/prot.20811.'
ieee: 'Y. Ban, J. Rudolph, P. Zhou, and H. Edelsbrunner, “Evaluating the quality
of NMR structures by local density of protons,” Proteins: Structure, Function
and Bioinformatics, vol. 62, no. 4. Wiley-Blackwell, pp. 852–864, 2006.'
ista: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. 2006. Evaluating the quality of
NMR structures by local density of protons. Proteins: Structure, Function and
Bioinformatics. 62(4), 852–864.'
mla: 'Ban, Yih, et al. “Evaluating the Quality of NMR Structures by Local Density
of Protons.” Proteins: Structure, Function and Bioinformatics, vol. 62,
no. 4, Wiley-Blackwell, 2006, pp. 852–64, doi:10.1002/prot.20811.'
short: 'Y. Ban, J. Rudolph, P. Zhou, H. Edelsbrunner, Proteins: Structure, Function
and Bioinformatics 62 (2006) 852–864.'
date_created: 2018-12-11T12:06:14Z
date_published: 2006-03-01T00:00:00Z
date_updated: 2021-01-12T07:53:36Z
day: '01'
doi: 10.1002/prot.20811
extern: 1
intvolume: ' 62'
issue: '4'
month: '03'
page: 852 - 864
publication: 'Proteins: Structure, Function and Bioinformatics'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2146'
quality_controlled: 0
status: public
title: Evaluating the quality of NMR structures by local density of protons
type: journal_article
volume: 62
year: '2006'
...
---
_id: '3979'
abstract:
- lang: eng
text: Protein-protein interactions, which form the basis for most cellular processes,
result in the formation of protein interfaces. Believing that the local shape
of proteins is crucial, we take a geometric approach and present a definition
of an interface surface formed by two or more proteins as a subset of their Voronoi
diagram. The definition deals with the difficult and important problem of specifying
interface boundaries by invoking methods used in the alpha shape representation
of molecules, the discrete flow on Delaunay simplices to define pockets and reconstruct
surfaces, and the assessment of the importance of topological features. We present
an algorithm to construct the surface and define a hierarchy that distinguishes
core and peripheral regions. This hierarchy is shown to have correlation with
hot-spots in protein-protein interactions. Finally, we study the geometric and
topological properties of interface surfaces and show their high degree of contortion.
author:
- first_name: Yih
full_name: Ban, Yih-En Andrew
last_name: Ban
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
citation:
ama: Ban Y, Edelsbrunner H, Rudolph J. Interface surfaces for protein-protein complexes.
Journal of the ACM. 2006;53(3):361-378. doi:10.1145/1147954.1147957
apa: Ban, Y., Edelsbrunner, H., & Rudolph, J. (2006). Interface surfaces for
protein-protein complexes. Journal of the ACM. ACM. https://doi.org/10.1145/1147954.1147957
chicago: Ban, Yih, Herbert Edelsbrunner, and Johannes Rudolph. “Interface Surfaces
for Protein-Protein Complexes.” Journal of the ACM. ACM, 2006. https://doi.org/10.1145/1147954.1147957.
ieee: Y. Ban, H. Edelsbrunner, and J. Rudolph, “Interface surfaces for protein-protein
complexes,” Journal of the ACM, vol. 53, no. 3. ACM, pp. 361–378, 2006.
ista: Ban Y, Edelsbrunner H, Rudolph J. 2006. Interface surfaces for protein-protein
complexes. Journal of the ACM. 53(3), 361–378.
mla: Ban, Yih, et al. “Interface Surfaces for Protein-Protein Complexes.” Journal
of the ACM, vol. 53, no. 3, ACM, 2006, pp. 361–78, doi:10.1145/1147954.1147957.
short: Y. Ban, H. Edelsbrunner, J. Rudolph, Journal of the ACM 53 (2006) 361–378.
date_created: 2018-12-11T12:06:14Z
date_published: 2006-05-01T00:00:00Z
date_updated: 2021-01-12T07:53:37Z
day: '01'
doi: 10.1145/1147954.1147957
extern: 1
intvolume: ' 53'
issue: '3'
month: '05'
page: 361 - 378
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '2147'
quality_controlled: 0
status: public
title: Interface surfaces for protein-protein complexes
type: journal_article
volume: 53
year: '2006'
...
---
_id: '3980'
abstract:
- lang: eng
text: Given a smoothly embedded 2-manifold in R-3, we define the elevation of a
point as the height difference to a canonically defined second point on the same
manifold. Our definition is invariant under rigid motions and can be used to define
features such as lines of discontinuous or continuous but non-smooth elevation.
We give an algorithm for finding points of locally maximum elevation, which we
suggest mark cavities and protrusions and are useful in matching shapes as for
example in protein docking.
author:
- first_name: Pankaj
full_name: Agarwal, Pankaj K
last_name: Agarwal
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Yusu
full_name: Wang, Yusu
last_name: Wang
citation:
ama: Agarwal P, Edelsbrunner H, Harer J, Wang Y. Extreme elevation on a 2-manifold.
Discrete & Computational Geometry. 2006;36(4):553-572. doi:10.1007/s00454-006-1265-8
apa: Agarwal, P., Edelsbrunner, H., Harer, J., & Wang, Y. (2006). Extreme elevation
on a 2-manifold. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-006-1265-8
chicago: Agarwal, Pankaj, Herbert Edelsbrunner, John Harer, and Yusu Wang. “Extreme
Elevation on a 2-Manifold.” Discrete & Computational Geometry. Springer,
2006. https://doi.org/10.1007/s00454-006-1265-8.
ieee: P. Agarwal, H. Edelsbrunner, J. Harer, and Y. Wang, “Extreme elevation on
a 2-manifold,” Discrete & Computational Geometry, vol. 36, no. 4. Springer,
pp. 553–572, 2006.
ista: Agarwal P, Edelsbrunner H, Harer J, Wang Y. 2006. Extreme elevation on a 2-manifold.
Discrete & Computational Geometry. 36(4), 553–572.
mla: Agarwal, Pankaj, et al. “Extreme Elevation on a 2-Manifold.” Discrete &
Computational Geometry, vol. 36, no. 4, Springer, 2006, pp. 553–72, doi:10.1007/s00454-006-1265-8.
short: P. Agarwal, H. Edelsbrunner, J. Harer, Y. Wang, Discrete & Computational
Geometry 36 (2006) 553–572.
date_created: 2018-12-11T12:06:15Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2021-01-12T07:53:38Z
day: '01'
doi: 10.1007/s00454-006-1265-8
extern: 1
intvolume: ' 36'
issue: '4'
month: '12'
page: 553 - 572
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '2148'
quality_controlled: 0
status: public
title: Extreme elevation on a 2-manifold
type: journal_article
volume: 36
year: '2006'
...
---
_id: '4345'
abstract:
- lang: eng
text: Der Artikel beschäftigt sich mit dem Konzept der Bibliothek 2.0 (bzw. Library
2.0). Er skizziert anhand einiger Beispiele die Entwicklung zum Web 2.0 und beschreibt,
wie Web 2.0-Technologien und -Anwendungen in Bibliotheken eingesetzt werden. Im
Mittelpunkt stehen Social-Tagging-Systeme, benutzerorientierte Erweiterungen von
Bibliothekskatalogen und Dokumentenservern sowie der Einsatz von Weblogs an Bibliotheken.
Ferner werden neue Anforderungen an Bibliothekare diskutiert.
author:
- first_name: Patrick
full_name: Patrick Danowski
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
- first_name: Lambert
full_name: Heller,Lambert
last_name: Heller
citation:
ama: Danowski P, Heller L. Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst.
2006;40(11):1250-1271. doi:424
apa: Danowski, P., & Heller, L. (2006). Bibliothek 2.0 - Die Bibliothek der
Zukunft? Bibliotheksdienst. Zentral- und Landesbibliothek Berlin. https://doi.org/424
chicago: Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 - Die Bibliothek
Der Zukunft?” Bibliotheksdienst. Zentral- und Landesbibliothek Berlin,
2006. https://doi.org/424.
ieee: P. Danowski and L. Heller, “Bibliothek 2.0 - Die Bibliothek der Zukunft?,”
Bibliotheksdienst, vol. 40, no. 11. Zentral- und Landesbibliothek Berlin,
pp. 1250–1271, 2006.
ista: Danowski P, Heller L. 2006. Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst.
40(11), 1250–1271.
mla: Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 - Die Bibliothek Der
Zukunft?” Bibliotheksdienst, vol. 40, no. 11, Zentral- und Landesbibliothek
Berlin, 2006, pp. 1250–71, doi:424.
short: P. Danowski, L. Heller, Bibliotheksdienst 40 (2006) 1250–1271.
date_created: 2018-12-11T12:08:23Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:17Z
day: '01'
doi: '424'
extern: 1
intvolume: ' 40'
issue: '11'
main_file_link:
- open_access: '0'
url: http://www.zlb.de/aktivitaeten/bd_neu/heftinhalte2006/DigitaleBib011106.pdf
month: '01'
page: 1250 - 1271
publication: Bibliotheksdienst
publication_status: published
publisher: Zentral- und Landesbibliothek Berlin
publist_id: '1229'
quality_controlled: 0
status: public
title: Bibliothek 2.0 - Die Bibliothek der Zukunft?
type: journal_article
volume: 40
year: '2006'
...
---
_id: '4352'
abstract:
- lang: eng
text: 'Anopheles darlingi is the primary malaria vector in Latin America, and is
especially important in Amazonian Brazil. Historically, control efforts have been
focused on indoor house spraying using a variety of insecticides, but since the
mid-1990s there has been a shift to patient treatment and focal insecticide fogging.
Anopheles darlingi was believed to have been significantly reduced in a gold-mining
community, Peixoto de Azevedo (in Mato Grosso State), in the early 1990s by insecticide
use during a severe malaria epidemic. In contrast, although An. darlingi was eradicated
from some districts of the city of Belem (the capital of Para State) in 1968 to
reduce malaria, populations around the water protection area in the eastern district
were treated only briefly. To investigate the population structure of An. darlingi
including evidence for a population bottleneck in Peixoto, we analyzed eight microsatellite
loci of 256 individuals from seven locations in Brazil: three in Amapa State,
three in Para State, and one in Mato Grosso State. Allelic diversity and mean
expected heterozygosity were high for all populations (mean number alleles/locus
and H(E) were 13.5 and 0.834, respectively) and did not differ significantly between
locations. Significant heterozygote deficits were associated with linkage disequilibrium,
most likely due to either the Wahlund effect or selection. We found no evidence
for a population bottleneck in Peixoto, possibly because the reduction was not
extreme enough to be detected. Overall estimates of long-term N(e) varied from
92.4 individuals under the linkage disequilibrium model to infinity under the
heterozygote excess model. Fixation indices and analysis of molecular variance
demonstrated significant differentiation between locations north and south of
the Amazon River, suggesting a degree of genetic isolation between them, attributed
to isolation by distance.'
author:
- first_name: Jan
full_name: Conn, Jan E
last_name: Conn
- first_name: Joseph
full_name: Vineis, Joseph H
last_name: Vineis
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: David
full_name: Onyabe, David Y
last_name: Onyabe
- first_name: Richard
full_name: Wilkerson, Richard C
last_name: Wilkerson
- first_name: Marinete
full_name: Povoa, Marinete M
last_name: Povoa
citation:
ama: Conn J, Vineis J, Bollback JP, Onyabe D, Wilkerson R, Povoa M. Population structure
of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern
Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene.
2006;74(5):798-806.
apa: Conn, J., Vineis, J., Bollback, J. P., Onyabe, D., Wilkerson, R., & Povoa,
M. (2006). Population structure of the malaria vector Anopheles darlingi in a
malaria-endemic region of eastern Amazonian Brazil. The American Journal of
Tropical Medicine and Hygiene. American Society of Tropical Medicine and Hygiene.
chicago: Conn, Jan, Joseph Vineis, Jonathan P Bollback, David Onyabe, Richard Wilkerson,
and Marinete Povoa. “Population Structure of the Malaria Vector Anopheles Darlingi
in a Malaria-Endemic Region of Eastern Amazonian Brazil.” The American Journal
of Tropical Medicine and Hygiene. American Society of Tropical Medicine and
Hygiene, 2006.
ieee: J. Conn, J. Vineis, J. P. Bollback, D. Onyabe, R. Wilkerson, and M. Povoa,
“Population structure of the malaria vector Anopheles darlingi in a malaria-endemic
region of eastern Amazonian Brazil,” The American Journal of Tropical Medicine
and Hygiene, vol. 74, no. 5. American Society of Tropical Medicine and Hygiene,
pp. 798–806, 2006.
ista: Conn J, Vineis J, Bollback JP, Onyabe D, Wilkerson R, Povoa M. 2006. Population
structure of the malaria vector Anopheles darlingi in a malaria-endemic region
of eastern Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene.
74(5), 798–806.
mla: Conn, Jan, et al. “Population Structure of the Malaria Vector Anopheles Darlingi
in a Malaria-Endemic Region of Eastern Amazonian Brazil.” The American Journal
of Tropical Medicine and Hygiene, vol. 74, no. 5, American Society of Tropical
Medicine and Hygiene, 2006, pp. 798–806.
short: J. Conn, J. Vineis, J.P. Bollback, D. Onyabe, R. Wilkerson, M. Povoa, The
American Journal of Tropical Medicine and Hygiene 74 (2006) 798–806.
date_created: 2018-12-11T12:08:25Z
date_published: 2006-05-01T00:00:00Z
date_updated: 2021-01-12T07:56:20Z
day: '01'
extern: 1
intvolume: ' 74'
issue: '5'
main_file_link:
- open_access: '0'
url: http://www.ajtmh.org/content/74/5/798.full
month: '05'
page: 798 - 806
publication: The American Journal of Tropical Medicine and Hygiene
publication_status: published
publisher: American Society of Tropical Medicine and Hygiene
publist_id: '1108'
quality_controlled: 0
status: public
title: Population structure of the malaria vector Anopheles darlingi in a malaria-endemic
region of eastern Amazonian Brazil
type: journal_article
volume: 74
year: '2006'
...
---
_id: '4351'
abstract:
- lang: eng
text: 'BACKGROUND: Character mapping on phylogenies has played an important, if
not critical role, in our understanding of molecular, morphological, and behavioral
evolution. Until very recently we have relied on parsimony to infer character
changes. Parsimony has a number of serious limitations that are drawbacks to our
understanding. Recent statistical methods have been developed that free us from
these limitations enabling us to overcome the problems of parsimony by accommodating
uncertainty in evolutionary time, ancestral states, and the phylogeny. RESULTS:
SIMMAP has been developed to implement stochastic character mapping that is useful
to both molecular evolutionists, systematists, and bioinformaticians. Researchers
can address questions about positive selection, patterns of amino acid substitution,
character association, and patterns of morphological evolution. CONCLUSION: Stochastic
character mapping, as implemented in the SIMMAP software, enables users to address
questions that require mapping characters onto phylogenies using a probabilistic
approach that does not rely on parsimony. Analyses can be performed using a fully
Bayesian approach that is not reliant on considering a single topology, set of
substitution model parameters, or reconstruction of ancestral states. Uncertainty
in these quantities is accommodated by using MCMC samples from their respective
posterior distributions.'
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. SIMMAP: stochastic character mapping of discrete traits on phylogenies.
BMC Bioinformatics. 2006;7. doi:10.1186/1471-2105-7-88'
apa: 'Bollback, J. P. (2006). SIMMAP: stochastic character mapping of discrete traits
on phylogenies. BMC Bioinformatics. BioMed Central. https://doi.org/10.1186/1471-2105-7-88'
chicago: 'Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete
Traits on Phylogenies.” BMC Bioinformatics. BioMed Central, 2006. https://doi.org/10.1186/1471-2105-7-88.'
ieee: 'J. P. Bollback, “SIMMAP: stochastic character mapping of discrete traits
on phylogenies,” BMC Bioinformatics, vol. 7. BioMed Central, 2006.'
ista: 'Bollback JP. 2006. SIMMAP: stochastic character mapping of discrete traits
on phylogenies. BMC Bioinformatics. 7.'
mla: 'Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete Traits
on Phylogenies.” BMC Bioinformatics, vol. 7, BioMed Central, 2006, doi:10.1186/1471-2105-7-88.'
short: J.P. Bollback, BMC Bioinformatics 7 (2006).
date_created: 2018-12-11T12:08:25Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:20Z
day: '01'
doi: 10.1186/1471-2105-7-88
extern: 1
intvolume: ' 7'
month: '01'
publication: BMC Bioinformatics
publication_status: published
publisher: BioMed Central
publist_id: '1109'
quality_controlled: 0
status: public
title: 'SIMMAP: stochastic character mapping of discrete traits on phylogenies'
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: 7
year: '2006'
...
---
_id: '3180'
abstract:
- lang: eng
text: 'One of the most exciting advances in early vision has been the development
of efficient energy minimization algorithms. Many early vision tasks require labeling
each pixel with some quantity such as depth or texture. While many such problems
can be elegantly expressed in the language of Markov Random Fields (MRF''s), the
resulting energy minimization problems were widely viewed as intractable. Recently,
algorithms such as graph cuts and loopy belief propagation (LBP) have proven to
be very powerful: for example, such methods form the basis for almost all the
top-performing stereo methods. Unfortunately, most papers define their own energy
function, which is minimized with a specific algorithm of their choice. As a result,
the tradeoffs among different energy minimization algorithms are not well understood.
In this paper we describe a set of energy minimization benchmarks, which we use
to compare the solution quality and running time of several common energy minimization
algorithms. We investigate three promising recent methods - graph cuts, LBP, and
tree-reweighted message passing - as well as the well-known older iterated conditional
modes (ICM) algorithm. Our benchmark problems are drawn from published energy
functions used for stereo, image stitching and interactive segmentation. We also
provide a general-purpose software interface that allows vision researchers to
easily switch between optimization methods with minimal overhead. We expect that
the availability of our benchmarks and interface will make it significantly easier
for vision researchers to adopt the best method for their specific problems. Benchmarks,
code, results and images are available at http://vision.middlebury.edu/MRF.'
author:
- first_name: Richard
full_name: Szeliski, Richard S
last_name: Szeliski
- first_name: Ramin
full_name: Zabih, Ramin
last_name: Zabih
- first_name: Daniel
full_name: Scharstein, Daniel
last_name: Scharstein
- first_name: Olga
full_name: Veksler, Olga
last_name: Veksler
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Aseem
full_name: Agarwala, Aseem
last_name: Agarwala
- first_name: Marshall
full_name: Tappen, Marshall F
last_name: Tappen
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: 'Szeliski R, Zabih R, Scharstein D, et al. A comparative study of energy minimization
methods for Markov random fields. In: Vol 3952. Springer; 2006:16-29. doi:10.1007/11744047_2'
apa: 'Szeliski, R., Zabih, R., Scharstein, D., Veksler, O., Kolmogorov, V., Agarwala,
A., … Rother, C. (2006). A comparative study of energy minimization methods for
Markov random fields (Vol. 3952, pp. 16–29). Presented at the ECCV: European Conference
on Computer Vision, Springer. https://doi.org/10.1007/11744047_2'
chicago: Szeliski, Richard, Ramin Zabih, Daniel Scharstein, Olga Veksler, Vladimir
Kolmogorov, Aseem Agarwala, Marshall Tappen, and Carsten Rother. “A Comparative
Study of Energy Minimization Methods for Markov Random Fields,” 3952:16–29. Springer,
2006. https://doi.org/10.1007/11744047_2.
ieee: 'R. Szeliski et al., “A comparative study of energy minimization methods
for Markov random fields,” presented at the ECCV: European Conference on Computer
Vision, 2006, vol. 3952, pp. 16–29.'
ista: 'Szeliski R, Zabih R, Scharstein D, Veksler O, Kolmogorov V, Agarwala A, Tappen
M, Rother C. 2006. A comparative study of energy minimization methods for Markov
random fields. ECCV: European Conference on Computer Vision vol. 3952, 16–29.'
mla: Szeliski, Richard, et al. A Comparative Study of Energy Minimization Methods
for Markov Random Fields. Vol. 3952, Springer, 2006, pp. 16–29, doi:10.1007/11744047_2.
short: R. Szeliski, R. Zabih, D. Scharstein, O. Veksler, V. Kolmogorov, A. Agarwala,
M. Tappen, C. Rother, in:, Springer, 2006, pp. 16–29.
conference:
name: 'ECCV: European Conference on Computer Vision'
date_created: 2018-12-11T12:01:51Z
date_published: 2006-05-03T00:00:00Z
date_updated: 2021-01-12T07:41:37Z
day: '03'
doi: 10.1007/11744047_2
extern: 1
intvolume: ' 3952'
main_file_link:
- open_access: '0'
url: http://research-srv.microsoft.com/pubs/67896/szsvkatr-eccv06.pdf
month: '05'
page: 16 - 29
publication_status: published
publisher: Springer
publist_id: '3499'
quality_controlled: 0
status: public
title: A comparative study of energy minimization methods for Markov random fields
type: conference
volume: 3952
year: '2006'
...
---
_id: '3184'
abstract:
- lang: eng
text: 'Algorithms for discrete energy minimization play a fundamental role for low-level
vision. Known techniques include graph cuts, belief propagation (BP) and recently
introduced tree-reweighted message passing (TRW). So far, the standard benchmark
for their comparison has been a 4-connected grid-graph arising in pixel-labelling
stereo. This minimization problem, however, has been largely solved: recent work
shows that for many scenes TRW finds the global optimum. Furthermore, it is known
that a 4-connecled grid-graph is a poor stereo model since it does not take occlusions
into account. We propose the problem of stereo with occlusions as a new test bed
for minimization algorithms. This is a more challenging graph since it has much
larger connectivity, and it also serves as a better stereo model. An attractive
feature of this problem is that increased connectivity does not result in increased
complexity of message passing algorithms. Indeed, one contribution of this paper
is to show that sophisticated implementations of BP and TRW have the same time
and memory complexity as that of 4-connecled grid-graph stereo. The main conclusion
of our experimental study is that for our problem graph cut outperforms both TRW
and BP considerably. TRW achieves consistently a lower energy than BP. However,
as connectivity increases the speed of convergence of TRW becomes slower. Unlike
4-connected grids, the difference between the energy of the best optimization
method and the lower bound of TRW appears significant. This shows the hardness
of the problem and motivates future research.'
alternative_title:
- LNCS
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: 'Kolmogorov V, Rother C. Comparison of energy minimization algorithms for highly
connected graphs. In: Vol 3952 LNCS. Springer; 2006:1-15. doi:10.1007/11744047_1'
apa: 'Kolmogorov, V., & Rother, C. (2006). Comparison of energy minimization
algorithms for highly connected graphs (Vol. 3952 LNCS, pp. 1–15). Presented at
the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744047_1'
chicago: Kolmogorov, Vladimir, and Carsten Rother. “Comparison of Energy Minimization
Algorithms for Highly Connected Graphs,” 3952 LNCS:1–15. Springer, 2006. https://doi.org/10.1007/11744047_1.
ieee: 'V. Kolmogorov and C. Rother, “Comparison of energy minimization algorithms
for highly connected graphs,” presented at the ECCV: European Conference on Computer
Vision, 2006, vol. 3952 LNCS, pp. 1–15.'
ista: 'Kolmogorov V, Rother C. 2006. Comparison of energy minimization algorithms
for highly connected graphs. ECCV: European Conference on Computer Vision, LNCS,
vol. 3952 LNCS, 1–15.'
mla: Kolmogorov, Vladimir, and Carsten Rother. Comparison of Energy Minimization
Algorithms for Highly Connected Graphs. Vol. 3952 LNCS, Springer, 2006, pp.
1–15, doi:10.1007/11744047_1.
short: V. Kolmogorov, C. Rother, in:, Springer, 2006, pp. 1–15.
conference:
name: 'ECCV: European Conference on Computer Vision'
date_created: 2018-12-11T12:01:52Z
date_published: 2006-05-03T00:00:00Z
date_updated: 2021-01-12T07:41:39Z
day: '03'
doi: 10.1007/11744047_1
extern: 1
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67889/paper_eccv06-trw.pdf
month: '05'
page: 1 - 15
publication_status: published
publisher: Springer
publist_id: '3498'
quality_controlled: 0
status: public
title: Comparison of energy minimization algorithms for highly connected graphs
type: conference
volume: 3952 LNCS
year: '2006'
...
---
_id: '3185'
abstract:
- lang: eng
text: This paper describes models and algorithms for the real-time segmentation
of foreground from background layers in stereo video sequences. Automatic separation
of layers from color/contrast or from stereo alone is known to be error-prone.
Here, color, 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 six-state space that represents both foreground/background
layers and occluded regions. The stereo-match likelihood is then fused with a
contrast-sensitive color 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 marginalized
over disparities to evaluate foreground and background hypotheses and then fused
with a contrast-sensitive color 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 either stereo or color/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. Probabilistic fusion
of stereo with color and contrast for bilayer segmentation. IEEE Transactions
on Pattern Analysis and Machine Intelligence. 2006;28(9):1480-1492. doi:10.1109/TPAMI.2006.193
apa: Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., & Rother, C. (2006).
Probabilistic fusion of stereo with color and contrast for bilayer segmentation.
IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2006.193
chicago: Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross,
and Carsten Rother. “Probabilistic Fusion of Stereo with Color and Contrast for
Bilayer Segmentation.” IEEE Transactions on Pattern Analysis and Machine Intelligence.
IEEE, 2006. https://doi.org/10.1109/TPAMI.2006.193.
ieee: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Probabilistic
fusion of stereo with color and contrast for bilayer segmentation,” IEEE Transactions
on Pattern Analysis and Machine Intelligence, vol. 28, no. 9. IEEE, pp. 1480–1492,
2006.
ista: Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2006. Probabilistic
fusion of stereo with color and contrast for bilayer segmentation. IEEE Transactions
on Pattern Analysis and Machine Intelligence. 28(9), 1480–1492.
mla: Kolmogorov, Vladimir, et al. “Probabilistic Fusion of Stereo with Color and
Contrast for Bilayer Segmentation.” IEEE Transactions on Pattern Analysis and
Machine Intelligence, vol. 28, no. 9, IEEE, 2006, pp. 1480–92, doi:10.1109/TPAMI.2006.193.
short: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, IEEE Transactions
on Pattern Analysis and Machine Intelligence 28 (2006) 1480–1492.
date_created: 2018-12-11T12:01:53Z
date_published: 2006-09-01T00:00:00Z
date_updated: 2021-01-12T07:41:39Z
day: '01'
doi: 10.1109/TPAMI.2006.193
extern: 1
intvolume: ' 28'
issue: '9'
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67414/criminisi_pami2006.pdf
month: '09'
page: 1480 - 1492
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '3496'
quality_controlled: 0
status: public
title: Probabilistic fusion of stereo with color and contrast for bilayer segmentation
type: journal_article
volume: 28
year: '2006'
...
---
_id: '3186'
abstract:
- lang: eng
text: We introduce a new approach to modelling gradient flows of contours and surfaces.
While standard variational methods (e.g. level sets) compute local interface motion
in a differential fashion by estimating local contour velocity via energy derivatives,
we propose to solve surface evolution PDEs by explicitly estimating integral motion
of the whole surface. We formulate an optimization problem directly based on an
integral characterization of gradient flow as an infinitesimal move of the (whole)
surface giving the largest energy decrease among all moves of equal size. We show
that this problem can be efficiently solved using recent advances in algorithms
for global hypersurface optimization [4, 2, 11]. In particular, we employ the
geo-cuts method [4] that uses ideas from integral geometry to represent continuous
surfaces as cuts on discrete graphs. The resulting interface evolution algorithm
is validated on some 2D and 3D examples similar to typical demonstrations of level-set
methods. Our method can compute gradient flows of hypersurfaces with respect to
a fairly general class of continuous functional and it is flexible with respect
to distance metrics on the space of contours/surfaces. Preliminary tests for standard
L2 distance metric demonstrate numerical stability, topological changes and an
absence of any oscillatory motion.
alternative_title:
- LNCS
author:
- first_name: Yuri
full_name: Boykov, Yuri
last_name: Boykov
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Daniel
full_name: Cremers, Daniel
last_name: Cremers
- first_name: Andrew
full_name: Delong, Andrew
last_name: Delong
citation:
ama: 'Boykov Y, Kolmogorov V, Cremers D, Delong A. An integral solution to surface
evolution PDEs via geo cuts. In: Vol 3953. Springer; 2006:409-422. doi:10.1007/11744078_32'
apa: 'Boykov, Y., Kolmogorov, V., Cremers, D., & Delong, A. (2006). An integral
solution to surface evolution PDEs via geo cuts (Vol. 3953, pp. 409–422). Presented
at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744078_32'
chicago: Boykov, Yuri, Vladimir Kolmogorov, Daniel Cremers, and Andrew Delong. “An
Integral Solution to Surface Evolution PDEs via Geo Cuts,” 3953:409–22. Springer,
2006. https://doi.org/10.1007/11744078_32.
ieee: 'Y. Boykov, V. Kolmogorov, D. Cremers, and A. Delong, “An integral solution
to surface evolution PDEs via geo cuts,” presented at the ECCV: European Conference
on Computer Vision, 2006, vol. 3953, pp. 409–422.'
ista: 'Boykov Y, Kolmogorov V, Cremers D, Delong A. 2006. An integral solution to
surface evolution PDEs via geo cuts. ECCV: European Conference on Computer Vision,
LNCS, vol. 3953, 409–422.'
mla: Boykov, Yuri, et al. An Integral Solution to Surface Evolution PDEs via
Geo Cuts. Vol. 3953, Springer, 2006, pp. 409–22, doi:10.1007/11744078_32.
short: Y. Boykov, V. Kolmogorov, D. Cremers, A. Delong, in:, Springer, 2006, pp.
409–422.
conference:
name: 'ECCV: European Conference on Computer Vision'
date_created: 2018-12-11T12:01:53Z
date_published: 2006-04-28T00:00:00Z
date_updated: 2021-01-12T07:41:39Z
day: '28'
doi: 10.1007/11744078_32
extern: 1
intvolume: ' 3953'
month: '04'
page: 409 - 422
publication_status: published
publisher: Springer
publist_id: '3497'
quality_controlled: 0
status: public
title: An integral solution to surface evolution PDEs via geo cuts
type: conference
volume: 3953
year: '2006'
...
---
_id: '3404'
alternative_title:
- Manuals in Biomedical Research
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: Ravi
full_name: Sawhney, Ravi K
last_name: Sawhney
- first_name: Martin
full_name: Stark, Martin
last_name: Stark
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: 'Janovjak HL, Sawhney R, Stark M, Mueller D. Atomic force microscopy. In: Techniques
in Microscopy for Biomedical Applications. Vol 2. World Scientific Publishing;
2006:213-284.'
apa: Janovjak, H. L., Sawhney, R., Stark, M., & Mueller, D. (2006). Atomic force
microscopy. In Techniques in Microscopy for Biomedical Applications (Vol.
2, pp. 213–284). World Scientific Publishing.
chicago: Janovjak, Harald L, Ravi Sawhney, Martin Stark, and Daniel Mueller. “Atomic
Force Microscopy.” In Techniques in Microscopy for Biomedical Applications,
2:213–84. World Scientific Publishing, 2006.
ieee: H. L. Janovjak, R. Sawhney, M. Stark, and D. Mueller, “Atomic force microscopy,”
in Techniques in Microscopy for Biomedical Applications, vol. 2, World
Scientific Publishing, 2006, pp. 213–284.
ista: 'Janovjak HL, Sawhney R, Stark M, Mueller D. 2006.Atomic force microscopy.
In: Techniques in Microscopy for Biomedical Applications. Manuals in Biomedical
Research, vol. 2, 213–284.'
mla: Janovjak, Harald L., et al. “Atomic Force Microscopy.” Techniques in Microscopy
for Biomedical Applications, vol. 2, World Scientific Publishing, 2006, pp.
213–84.
short: H.L. Janovjak, R. Sawhney, M. Stark, D. Mueller, in:, Techniques in Microscopy
for Biomedical Applications, World Scientific Publishing, 2006, pp. 213–284.
date_created: 2018-12-11T12:03:09Z
date_published: 2006-09-28T00:00:00Z
date_updated: 2021-01-12T07:43:15Z
day: '28'
extern: 1
intvolume: ' 2'
month: '09'
page: 213 - 284
publication: Techniques in Microscopy for Biomedical Applications
publication_status: published
publisher: World Scientific Publishing
publist_id: '2998'
quality_controlled: 0
status: public
title: Atomic force microscopy
type: book_chapter
volume: 2
year: '2006'
...
---
_id: '3413'
abstract:
- lang: eng
text: |-
Despite their crucial importance for cellular function, little is known about the folding mechanisms of membrane proteins. Recently details of the folding energy landscape were elucidated by atomic force microscope (AFM)-based single molecule force spectroscopy. Upon unfolding and extraction of individual membrane proteins energy barriers in structural elements such as loops and helices were mapped and quantified with the precision of a few amino acids.
Here we report on the next logical step: controlled refolding of single proteins into the membrane. First individual bacteriorhodopsin monomers were partially unfolded and extracted from the purple membrane by pulling at the C-terminal end with an AFM tip. Then by gradually lowering the tip, the protein was allowed to refold into the membrane while the folding force was recorded.
We discovered that upon refolding certain helices are pulled into the membraneagainst a sizable externalforce of several tens of picoNewton. From the mechanical work, which the helix performs on the AFM cantilever, we derive an upper limit for the Gibbs free folding energy. Subsequent unfolding allowed us to analyze the pattern of unfolding barriers and corroborate that the protein had refolded into the native state.
author:
- first_name: Max
full_name: Kessler, Max
last_name: Kessler
- first_name: Kay
full_name: Gottschalk, Kay E
last_name: Gottschalk
- 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: Hermann
full_name: Gaub, Hermann
last_name: Gaub
citation:
ama: Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. Bacteriorhodopsin
folds into the membrane against an external force. Journal of Molecular Biology.
2006;357(2):644-654. doi:10.1016/j.jmb.2005.12.065
apa: Kessler, M., Gottschalk, K., Janovjak, H. L., Mueller, D., & Gaub, H. (2006).
Bacteriorhodopsin folds into the membrane against an external force. Journal
of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2005.12.065
chicago: Kessler, Max, Kay Gottschalk, Harald L Janovjak, Daniel Mueller, and Hermann
Gaub. “Bacteriorhodopsin Folds into the Membrane against an External Force.” Journal
of Molecular Biology. Elsevier, 2006. https://doi.org/10.1016/j.jmb.2005.12.065.
ieee: M. Kessler, K. Gottschalk, H. L. Janovjak, D. Mueller, and H. Gaub, “Bacteriorhodopsin
folds into the membrane against an external force,” Journal of Molecular Biology,
vol. 357, no. 2. Elsevier, pp. 644–654, 2006.
ista: Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. 2006. Bacteriorhodopsin
folds into the membrane against an external force. Journal of Molecular Biology.
357(2), 644–654.
mla: Kessler, Max, et al. “Bacteriorhodopsin Folds into the Membrane against an
External Force.” Journal of Molecular Biology, vol. 357, no. 2, Elsevier,
2006, pp. 644–54, doi:10.1016/j.jmb.2005.12.065.
short: M. Kessler, K. Gottschalk, H.L. Janovjak, D. Mueller, H. Gaub, Journal of
Molecular Biology 357 (2006) 644–654.
date_created: 2018-12-11T12:03:12Z
date_published: 2006-03-24T00:00:00Z
date_updated: 2021-01-12T07:43:18Z
day: '24'
doi: 10.1016/j.jmb.2005.12.065
extern: 1
intvolume: ' 357'
issue: '2'
month: '03'
page: 644 - 654
publication: Journal of Molecular Biology
publication_status: published
publisher: Elsevier
publist_id: '2988'
quality_controlled: 0
status: public
title: Bacteriorhodopsin folds into the membrane against an external force
type: journal_article
volume: 357
year: '2006'
...
---
_id: '3414'
abstract:
- lang: eng
text: Mechanisms of folding and misfolding of membrane proteins are of interest
in cell biology. Recently, we have established single-molecule force spectroscopy
to observe directly the stepwise folding of the Na+/H+antiporter NhaA from Escherichia
coli in vitro. Here, we improved this approach significantly to track the folding
intermediates of asingle NhaA polypeptide forming structural segments such as
the Na+-binding site, transmembrane α-helices, and helical pairs. The folding
rates of structural segments ranged from 0.31 s−1 to 47 s−1, providing detailed
insight into a distinct folding hierarchy of an unfolded polypeptide into the
native membrane protein structure. In some cases, however, the folding chain formed
stable and kinetically trapped non-native structures, which could be assigned
to misfolding events of the antiporter.
author:
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Christine
full_name: Ziegler, Christine
last_name: Ziegler
- first_name: Werner
full_name: Kühlbrandt, Werner
last_name: Kühlbrandt
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. Observing folding
pathways and kinetics of a single sodium-proton antiporter from Escherichia coli.
Journal of Molecular Biology. 2006;355(1):2-8. doi:10.1016/j.jmb.2005.10.028
apa: Kedrov, A., Janovjak, H. L., Ziegler, C., Kühlbrandt, W., & Mueller, D.
(2006). Observing folding pathways and kinetics of a single sodium-proton antiporter
from Escherichia coli. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2005.10.028
chicago: Kedrov, Alexej, Harald L Janovjak, Christine Ziegler, Werner Kühlbrandt,
and Daniel Mueller. “Observing Folding Pathways and Kinetics of a Single Sodium-Proton
Antiporter from Escherichia Coli.” Journal of Molecular Biology. Elsevier,
2006. https://doi.org/10.1016/j.jmb.2005.10.028.
ieee: A. Kedrov, H. L. Janovjak, C. Ziegler, W. Kühlbrandt, and D. Mueller, “Observing
folding pathways and kinetics of a single sodium-proton antiporter from Escherichia
coli,” Journal of Molecular Biology, vol. 355, no. 1. Elsevier, pp. 2–8,
2006.
ista: Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. 2006. Observing
folding pathways and kinetics of a single sodium-proton antiporter from Escherichia
coli. Journal of Molecular Biology. 355(1), 2–8.
mla: Kedrov, Alexej, et al. “Observing Folding Pathways and Kinetics of a Single
Sodium-Proton Antiporter from Escherichia Coli.” Journal of Molecular Biology,
vol. 355, no. 1, Elsevier, 2006, pp. 2–8, doi:10.1016/j.jmb.2005.10.028.
short: A. Kedrov, H.L. Janovjak, C. Ziegler, W. Kühlbrandt, D. Mueller, Journal
of Molecular Biology 355 (2006) 2–8.
date_created: 2018-12-11T12:03:12Z
date_published: 2006-01-06T00:00:00Z
date_updated: 2021-01-12T07:43:19Z
day: '06'
doi: 10.1016/j.jmb.2005.10.028
extern: 1
intvolume: ' 355'
issue: '1'
month: '01'
page: 2 - 8
publication: Journal of Molecular Biology
publication_status: published
publisher: Elsevier
publist_id: '2987'
quality_controlled: 0
status: public
title: Observing folding pathways and kinetics of a single sodium-proton antiporter
from Escherichia coli
type: journal_article
volume: 355
year: '2006'
...
---
_id: '3415'
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: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: David
full_name: Cisneros, David
last_name: Cisneros
- first_name: Tanuj
full_name: Sapra, Tanuj K
last_name: Sapra
- 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, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. Imaging
and detecting molecular interactions of single membrane proteins. Neurobiology
of Aging. 2006;27:546-561. doi:10.1016/j.neurobiolaging.2005.03.031
apa: Janovjak, H. L., Kedrov, A., Cisneros, D., Sapra, T., Struckmeier, J., &
Mueller, D. (2006). Imaging and detecting molecular interactions of single membrane
proteins. Neurobiology of Aging. Elsevier. https://doi.org/10.1016/j.neurobiolaging.2005.03.031
chicago: Janovjak, Harald L, Alexej Kedrov, David Cisneros, Tanuj Sapra, Jens Struckmeier,
and Daniel Mueller. “Imaging and Detecting Molecular Interactions of Single Membrane
Proteins.” Neurobiology of Aging. Elsevier, 2006. https://doi.org/10.1016/j.neurobiolaging.2005.03.031.
ieee: H. L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, and D. Mueller,
“Imaging and detecting molecular interactions of single membrane proteins,” Neurobiology
of Aging, vol. 27. Elsevier, pp. 546–561, 2006.
ista: Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. 2006.
Imaging and detecting molecular interactions of single membrane proteins. Neurobiology
of Aging. 27, 546–561.
mla: Janovjak, Harald L., et al. “Imaging and Detecting Molecular Interactions of
Single Membrane Proteins.” Neurobiology of Aging, vol. 27, Elsevier, 2006,
pp. 546–61, doi:10.1016/j.neurobiolaging.2005.03.031.
short: H.L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, D. Mueller,
Neurobiology of Aging 27 (2006) 546–561.
date_created: 2018-12-11T12:03:12Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2019-04-26T07:22:27Z
day: '01'
doi: 10.1016/j.neurobiolaging.2005.03.031
extern: 1
intvolume: ' 27'
month: '01'
page: 546 - 561
publication: Neurobiology of Aging
publication_status: published
publisher: Elsevier
publist_id: '2986'
quality_controlled: 0
status: public
title: Imaging and detecting molecular interactions of single membrane proteins
type: review
volume: 27
year: '2006'
...
---
_id: '3437'
abstract:
- lang: eng
text: The mutational landscape model is a theoretical model describing sequence
evolution in natural populations. However, recent experimental work has begun
to test its predictions in laboratory populations of microbes. Several of these
studies have focused on testing the prediction that the effects of beneficial
mutations should be roughly exponentially distributed. The prediction appears
to be borne out by most of these studies, at least qualitatively. Another study
showed that a modified version of the model was able to predict, with reasonable
accuracy, which of a ranked set of beneficial alleles will be fixed next. Although
it remains to be seen whether the mutational landscape model adequately describes
adaptation in organisms other than microbes, together these studies suggest that
adaptive evolution has surprisingly general properties that can be successfully
captured by theoretical models.
author:
- first_name: Andrea
full_name: Betancourt, Andrea J
last_name: Betancourt
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: 'Betancourt A, Bollback JP. Fitness effects of beneficial mutations: the mutational
landscape model in experimental evolution. Current Opinion in Genetics &
Development. 2006;16(6):618-623. doi:10.1016/j.gde.2006.10.006'
apa: 'Betancourt, A., & Bollback, J. P. (2006). Fitness effects of beneficial
mutations: the mutational landscape model in experimental evolution. Current
Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2006.10.006'
chicago: 'Betancourt, Andrea, and Jonathan P Bollback. “Fitness Effects of Beneficial
Mutations: The Mutational Landscape Model in Experimental Evolution.” Current
Opinion in Genetics & Development. Elsevier, 2006. https://doi.org/10.1016/j.gde.2006.10.006.'
ieee: 'A. Betancourt and J. P. Bollback, “Fitness effects of beneficial mutations:
the mutational landscape model in experimental evolution,” Current Opinion
in Genetics & Development, vol. 16, no. 6. Elsevier, pp. 618–623, 2006.'
ista: 'Betancourt A, Bollback JP. 2006. Fitness effects of beneficial mutations:
the mutational landscape model in experimental evolution. Current Opinion in Genetics
& Development. 16(6), 618–623.'
mla: 'Betancourt, Andrea, and Jonathan P. Bollback. “Fitness Effects of Beneficial
Mutations: The Mutational Landscape Model in Experimental Evolution.” Current
Opinion in Genetics & Development, vol. 16, no. 6, Elsevier, 2006, pp.
618–23, doi:10.1016/j.gde.2006.10.006.'
short: A. Betancourt, J.P. Bollback, Current Opinion in Genetics & Development
16 (2006) 618–623.
date_created: 2018-12-11T12:03:19Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2021-01-12T07:43:27Z
day: '01'
doi: 10.1016/j.gde.2006.10.006
extern: 1
intvolume: ' 16'
issue: '6'
month: '12'
page: 618 - 623
publication: Current Opinion in Genetics & Development
publication_status: published
publisher: Elsevier
publist_id: '2963'
quality_controlled: 0
status: public
title: 'Fitness effects of beneficial mutations: the mutational landscape model in
experimental evolution'
type: journal_article
volume: 16
year: '2006'
...
---
_id: '3431'
abstract:
- lang: eng
text: Ising models with pairwise interactions are the least structured, or maximum-entropy,
probability distributions that exactly reproduce measured pairwise correlations
between spins. Here we use this equivalence to construct Ising models that describe
the correlated spiking activity of populations of 40 neurons in the retina, and
show that pairwise interactions account for observed higher-order correlations.
By first finding a representative ensemble for observed networks we can create
synthetic networks of 120 neurons, and find that with increasing size the networks
operate closer to a critical point and start exhibiting collective behaviors reminiscent
of spin glasses.
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: E.
full_name: Schneidman, E.
last_name: Schneidman
- first_name: M.
full_name: Berry, M. J.
last_name: Berry
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Tkačik G, Schneidman E, Berry M, Bialek W. Ising models for networks of real
neurons. ArXiv. 2006:1-4.
apa: Tkačik, G., Schneidman, E., Berry, M., & Bialek, W. (2006). Ising models
for networks of real neurons. ArXiv. ArXiv.
chicago: Tkačik, Gašper, E. Schneidman, M. Berry, and William Bialek. “Ising Models
for Networks of Real Neurons.” ArXiv. ArXiv, 2006.
ieee: G. Tkačik, E. Schneidman, M. Berry, and W. Bialek, “Ising models for networks
of real neurons,” ArXiv. ArXiv, pp. 1–4, 2006.
ista: Tkačik G, Schneidman E, Berry M, Bialek W. 2006. Ising models for networks
of real neurons. ArXiv, 1–4, .
mla: Tkačik, Gašper, et al. “Ising Models for Networks of Real Neurons.” ArXiv,
ArXiv, 2006, pp. 1–4.
short: G. Tkačik, E. Schneidman, M. Berry, W. Bialek, ArXiv (2006) 1–4.
date_created: 2018-12-11T12:03:18Z
date_published: 2006-11-22T00:00:00Z
date_updated: 2021-01-12T07:43:25Z
day: '22'
extern: 1
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/q-bio/0611072
month: '11'
oa: 1
page: 1 - 4
publication: ArXiv
publication_status: published
publisher: ArXiv
publist_id: '2969'
quality_controlled: 0
status: public
title: Ising models for networks of real neurons
type: preprint
year: '2006'
...
---
_id: '3449'
abstract:
- lang: eng
text: We argue that games are expressive enough to encompass (history-based) access
control, (resource) usage control (e.g., dynamic adaptive access control of reputation
systems), accountability based controls (e.g., insurance), controls derived from
rationality assumptions on participants (e.g., network mechanisms), and their
composition. Building on the extensive research into games, we demonstrate that
this expressive power coexists with a formal analysis framework comparable to
that available for access control.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rhada
full_name: Jagadeesan, Rhada
last_name: Jagadeesan
- first_name: Corin
full_name: Pitcher, Corin
last_name: Pitcher
citation:
ama: 'Chatterjee K, Jagadeesan R, Pitcher C. Games for controls. In: IEEE; 2006:70-82.
doi:10.1109/CSFW.2006.14'
apa: 'Chatterjee, K., Jagadeesan, R., & Pitcher, C. (2006). Games for controls
(pp. 70–82). Presented at the CSF: Computer Security Foundations, IEEE. https://doi.org/10.1109/CSFW.2006.14'
chicago: Chatterjee, Krishnendu, Rhada Jagadeesan, and Corin Pitcher. “Games for
Controls,” 70–82. IEEE, 2006. https://doi.org/10.1109/CSFW.2006.14.
ieee: 'K. Chatterjee, R. Jagadeesan, and C. Pitcher, “Games for controls,” presented
at the CSF: Computer Security Foundations, 2006, pp. 70–82.'
ista: 'Chatterjee K, Jagadeesan R, Pitcher C. 2006. Games for controls. CSF: Computer
Security Foundations, 70–82.'
mla: Chatterjee, Krishnendu, et al. Games for Controls. IEEE, 2006, pp. 70–82,
doi:10.1109/CSFW.2006.14.
short: K. Chatterjee, R. Jagadeesan, C. Pitcher, in:, IEEE, 2006, pp. 70–82.
conference:
name: 'CSF: Computer Security Foundations'
date_created: 2018-12-11T12:03:23Z
date_published: 2006-07-31T00:00:00Z
date_updated: 2021-01-12T07:43:32Z
day: '31'
doi: 10.1109/CSFW.2006.14
extern: 1
month: '07'
page: 70 - 82
publication_status: published
publisher: IEEE
publist_id: '2938'
quality_controlled: 0
status: public
title: Games for controls
type: conference
year: '2006'
...
---
_id: '3463'
abstract:
- lang: eng
text: It is widely accepted that the hippocampus plays a major role in learning
and memory. The mossy fiber synapse between granule cells in the dentate gyrus
and pyramidal neurons in the CA3 region is a key component of the hippocampal
trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp
recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms
of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+)
channel density in mossy fiber boutons leads to a large amplitude of the presynaptic
action potential. Together with the fast gating of presynaptic Ca(2+) channels,
this generates a large and brief presynaptic Ca(2+) influx, which can trigger
transmitter release with high efficiency and temporal precision. The large number
of release sites, the large size of the releasable pool of vesicles, and the huge
extent of presynaptic plasticity confer unique strength to this synapse, suggesting
a large impact onto the CA3 pyramidal cell network under specific behavioral conditions.
The characteristic properties of the hippocampal mossy fiber synapse may be important
for pattern separation and information storage in the dentate gyrus-CA3 cell network.
author:
- first_name: Joseph
full_name: Bischofberger, Joseph
last_name: Bischofberger
- first_name: Dominique
full_name: Engel, Dominique
last_name: Engel
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. Timing and efficacy of transmitter
release at mossy fiber synapses in the hippocampal network. (Review). Pflugers
Archiv : European Journal of Physiology. 2006;453(3):361-372. doi:10.1007/s00424-006-0093-2'
apa: 'Bischofberger, J., Engel, D., Frotscher, M., & Jonas, P. M. (2006). Timing
and efficacy of transmitter release at mossy fiber synapses in the hippocampal
network. (Review). Pflugers Archiv : European Journal of Physiology. Springer.
https://doi.org/10.1007/s00424-006-0093-2'
chicago: 'Bischofberger, Joseph, Dominique Engel, Michael Frotscher, and Peter M
Jonas. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in
the Hippocampal Network. (Review).” Pflugers Archiv : European Journal of Physiology.
Springer, 2006. https://doi.org/10.1007/s00424-006-0093-2.'
ieee: 'J. Bischofberger, D. Engel, M. Frotscher, and P. M. Jonas, “Timing and efficacy
of transmitter release at mossy fiber synapses in the hippocampal network. (Review),”
Pflugers Archiv : European Journal of Physiology, vol. 453, no. 3. Springer,
pp. 361–372, 2006.'
ista: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. 2006. Timing and efficacy
of transmitter release at mossy fiber synapses in the hippocampal network. (Review).
Pflugers Archiv : European Journal of Physiology. 453(3), 361–372.'
mla: 'Bischofberger, Joseph, et al. “Timing and Efficacy of Transmitter Release
at Mossy Fiber Synapses in the Hippocampal Network. (Review).” Pflugers Archiv :
European Journal of Physiology, vol. 453, no. 3, Springer, 2006, pp. 361–72,
doi:10.1007/s00424-006-0093-2.'
short: 'J. Bischofberger, D. Engel, M. Frotscher, P.M. Jonas, Pflugers Archiv :
European Journal of Physiology 453 (2006) 361–372.'
date_created: 2018-12-11T12:03:28Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2019-04-26T07:22:28Z
day: '01'
doi: 10.1007/s00424-006-0093-2
extern: 1
intvolume: ' 453'
issue: '3'
month: '12'
page: 361 - 372
publication: 'Pflugers Archiv : European Journal of Physiology'
publication_status: published
publisher: Springer
publist_id: '2924'
quality_controlled: 0
status: public
title: Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal
network. (Review)
type: review
volume: 453
year: '2006'
...
---
_id: '3499'
abstract:
- lang: eng
text: 'We study infinite stochastic games played by n-players on a finite graph
with goals specified by sets of infinite traces. The games are concurrent (each
player simultaneously and independently chooses an action at each round), stochastic
(the next state is determined by a probability distribution depending on the current
state and the chosen actions), infinite (the game continues for an infinite number
of rounds), nonzero-sum (the players’ goals are not necessarily conflicting),
and undiscounted. We show that if each player has an upward-closed objective,
then there exists an ε-Nash equilibrium in memoryless strategies, for every ε>0;
and exact Nash equilibria need not exist. Upward-closure of an objective means
that if a set Z of infinitely repeating states is winning, then all supersets
of Z of infinitely repeating states are also winning. Memoryless strategies are
strategies that are independent of history of plays and depend only on the current
state. We also study the complexity of finding values (payoff profile) of an ε-Nash
equilibrium. We show that the values of an ε-Nash equilibrium in nonzero-sum concurrent
games with upward-closed objectives for all players can be computed by computing
ε-Nash equilibrium values of nonzero-sum concurrent games with reachability objectives
for all players and a polynomial procedure. As a consequence we establish that
values of an ε-Nash equilibrium can be computed in TFNP (total functional NP),
and hence in EXPTIME. '
acknowledgement: This research was supported in part by the NSF grants CCR-0225610
and CCR- 0234690, and by the SNSF under the Indo-Swiss Joint Research Programme.
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
citation:
ama: 'Chatterjee K. Nash equilibrium for upward-closed objectives. In: Vol 4207.
Springer; 2006:271-286. doi:10.1007/11874683_18'
apa: 'Chatterjee, K. (2006). Nash equilibrium for upward-closed objectives (Vol.
4207, pp. 271–286). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_18'
chicago: Chatterjee, Krishnendu. “Nash Equilibrium for Upward-Closed Objectives,”
4207:271–86. Springer, 2006. https://doi.org/10.1007/11874683_18.
ieee: 'K. Chatterjee, “Nash equilibrium for upward-closed objectives,” presented
at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 271–286.'
ista: 'Chatterjee K. 2006. Nash equilibrium for upward-closed objectives. CSL: Computer
Science Logic, LNCS , vol. 4207, 271–286.'
mla: Chatterjee, Krishnendu. Nash Equilibrium for Upward-Closed Objectives.
Vol. 4207, Springer, 2006, pp. 271–86, doi:10.1007/11874683_18.
short: K. Chatterjee, in:, Springer, 2006, pp. 271–286.
conference:
name: 'CSL: Computer Science Logic'
date_created: 2018-12-11T12:03:39Z
date_published: 2006-09-28T00:00:00Z
date_updated: 2021-01-12T07:43:52Z
day: '28'
doi: 10.1007/11874683_18
extern: 1
intvolume: ' 4207'
month: '09'
page: 271 - 286
publication_status: published
publisher: Springer
publist_id: '2888'
quality_controlled: 0
status: public
title: Nash equilibrium for upward-closed objectives
type: conference
volume: 4207
year: '2006'
...
---
_id: '3500'
abstract:
- lang: eng
text: The classical algorithm for solving Bu ̈chi games requires time O(n · m) for
game graphs with n states and m edges. For game graphs with constant outdegree,
the best known algorithm has running time O(n2/logn). We present two new algorithms
for Bu ̈chi games. First, we give an algorithm that performs at most O(m) more
work than the classical algorithm, but runs in time O(n) on infinitely many graphs
of constant outdegree on which the classical algorithm requires time O(n2). Second,
we give an algorithm with running time O(n · m · log δ(n)/ log n), where 1 ≤ δ(n)
≤ n is the outdegree of the game graph. Note that this algorithm performs asymptotically
better than the classical algorithm if δ(n) = O(log n).
acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327
and the NSF ITR grant CCR-0225610 and the SNSF under the Indo-Swiss Joint Research
Programme.
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: Nir
full_name: Piterman, Nir
last_name: Piterman
citation:
ama: 'Chatterjee K, Henzinger TA, Piterman N. Algorithms for Büchi Games. In: ACM;
2006.'
apa: 'Chatterjee, K., Henzinger, T. A., & Piterman, N. (2006). Algorithms for
Büchi Games. Presented at the GDV: Games in Design and Verification, ACM.'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Nir Piterman. “Algorithms
for Büchi Games.” ACM, 2006.
ieee: 'K. Chatterjee, T. A. Henzinger, and N. Piterman, “Algorithms for Büchi Games,”
presented at the GDV: Games in Design and Verification, 2006.'
ista: 'Chatterjee K, Henzinger TA, Piterman N. 2006. Algorithms for Büchi Games.
GDV: Games in Design and Verification.'
mla: Chatterjee, Krishnendu, et al. Algorithms for Büchi Games. ACM, 2006.
short: K. Chatterjee, T.A. Henzinger, N. Piterman, in:, ACM, 2006.
conference:
name: 'GDV: Games in Design and Verification'
date_created: 2018-12-11T12:03:39Z
date_published: 2006-08-21T00:00:00Z
date_updated: 2021-01-12T07:43:53Z
day: '21'
extern: 1
main_file_link:
- open_access: '0'
url: http://www.cs.le.ac.uk/people/np183/publications/2006/CHP06.pdf
month: '08'
publication_status: published
publisher: ACM
publist_id: '2887'
quality_controlled: 0
status: public
title: Algorithms for Büchi Games
type: conference
year: '2006'
...
---
_id: '3510'
abstract:
- lang: eng
text: Embodiments automatically generate an accurate network of watertight NURBS
patches from polygonal models of objects while automatically detecting and preserving
character lines thereon. These embodiments generate from an initial triangulation
of the surface, a hierarchy of progressively coarser triangulations of the surface
by performing a sequence of edge contractions using a greedy algorithm that selects
edge contractions by their numerical properties. Operations are also performed
to connect the triangulations in the hierarchy using homeomorphisms that preserve
the topology of the initial triangulation in the coarsest triangulation. A desired
quadrangulation of the surface can then be generated by homeomorphically mapping
edges of a coarsest triangulation in the hierarchy back to the initial triangulation.
This quadrangulation is topologically consistent with the initial triangulation
and is defined by a plurality of quadrangular patches. These quadrangular patches
are linked together by a (U, V) mesh that is guaranteed to be continuous at patch
boundaries. A grid is then preferably fit to each of the quadrangles in the resulting
quadrangulation by decomposing each of the quadrangles into k.sup.2 smaller quadrangles.
A watertight NURBS model may be generated from the resulting quadrangulation.
applicant:
- Raindrop Geomagic, Inc.
article_processing_charge: No
author:
- 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
- first_name: Dmitry
full_name: Nekhayev, Dmitry
last_name: Nekhayev
- first_name: Michael
full_name: Facello, Michael
last_name: Facello
- first_name: Steven
full_name: Williams, Steven
last_name: Williams
citation:
ama: Edelsbrunner H, Fu P, Nekhayev D, Facello M, Williams S. Method, apparatus
and computer program products for automatically generating NURBS models of triangulated
surfaces using homeomorphism. 2006.
apa: Edelsbrunner, H., Fu, P., Nekhayev, D., Facello, M., & Williams, S. (2006).
Method, apparatus and computer program products for automatically generating NURBS
models of triangulated surfaces using homeomorphism.
chicago: Edelsbrunner, Herbert, Ping Fu, Dmitry Nekhayev, Michael Facello, and Steven
Williams. “Method, Apparatus and Computer Program Products for Automatically Generating
NURBS Models of Triangulated Surfaces Using Homeomorphism,” 2006.
ieee: H. Edelsbrunner, P. Fu, D. Nekhayev, M. Facello, and S. Williams, “Method,
apparatus and computer program products for automatically generating NURBS models
of triangulated surfaces using homeomorphism.” 2006.
ista: Edelsbrunner H, Fu P, Nekhayev D, Facello M, Williams S. 2006. Method, apparatus
and computer program products for automatically generating NURBS models of triangulated
surfaces using homeomorphism.
mla: Edelsbrunner, Herbert, et al. Method, Apparatus and Computer Program Products
for Automatically Generating NURBS Models of Triangulated Surfaces Using Homeomorphism.
2006.
short: H. Edelsbrunner, P. Fu, D. Nekhayev, M. Facello, S. Williams, (2006).
date_created: 2018-12-11T12:03:42Z
date_published: 2006-02-07T00:00:00Z
date_updated: 2022-01-05T12:58:26Z
day: '07'
extern: '1'
ipc: G06F 7/60 ; G06F 17/10 ; G06F 101/00
ipn: US6996505B1
main_file_link:
- open_access: '1'
url: https://patents.google.com/patent/US6996505
month: '02'
oa: 1
oa_version: Published Version
publication_date: 2006-02-07
publist_id: '2877'
status: public
title: Method, apparatus and computer program products for automatically generating
NURBS models of triangulated surfaces using homeomorphism
type: patent
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2006'
...
---
_id: '3511'
abstract:
- lang: eng
text: 'Methods, apparatus and computer program products provide efficient techniques
for designing and printing shells of hearing-aid devices with a high degree of
quality assurance and reliability and with a reduced number of manual and time
consuming production steps and operations. These techniques also preferably provide
hearing-aid shells having internal volumes that can approach a maximum allowable
ratio of internal volume relative to external volume. These high internal volumes
facilitate the inclusion of hearing-aid electrical components having higher degrees
of functionality and/or the use of smaller and less conspicuous hearing-aid shells.
A preferred method includes operations to generate a watertight digital model
of a hearing-aid shell by thickening a three-dimensional digital model of a shell
surface in a manner that eliminates self-intersections and results in a thickened
model having an internal volume that is a high percentage of an external volume
of the model. '
acknowledgement: sold to Siemens and Phonak
applicant:
- Phonak AG
article_processing_charge: No
author:
- first_name: Ping
full_name: Fu, Ping
last_name: Fu
- first_name: Dmitry
full_name: Nekhayev, Dmitry
last_name: Nekhayev
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Fu P, Nekhayev D, Edelsbrunner H. Manufacturing methods and systems for rapid
production of hearing-aid shells. 2006.
apa: Fu, P., Nekhayev, D., & Edelsbrunner, H. (2006). Manufacturing methods
and systems for rapid production of hearing-aid shells.
chicago: Fu, Ping, Dmitry Nekhayev, and Herbert Edelsbrunner. “Manufacturing Methods
and Systems for Rapid Production of Hearing-Aid Shells,” 2006.
ieee: P. Fu, D. Nekhayev, and H. Edelsbrunner, “Manufacturing methods and systems
for rapid production of hearing-aid shells.” 2006.
ista: Fu P, Nekhayev D, Edelsbrunner H. 2006. Manufacturing methods and systems
for rapid production of hearing-aid shells.
mla: Fu, Ping, et al. Manufacturing Methods and Systems for Rapid Production
of Hearing-Aid Shells. 2006.
short: P. Fu, D. Nekhayev, H. Edelsbrunner, (2006).
date_created: 2018-12-11T12:03:43Z
date_published: 2006-05-23T00:00:00Z
date_updated: 2022-01-05T13:03:56Z
day: '23'
extern: '1'
ipc: G06F 9/00
ipn: US7050876B1
main_file_link:
- open_access: '1'
url: https://patents.google.com/patent/US7050876B1
month: '05'
oa: 1
oa_version: Published Version
publication_date: 2006-05-23
publist_id: '2876'
status: public
title: Manufacturing methods and systems for rapid production of hearing-aid shells
type: patent
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2006'
...
---
_id: '3512'
abstract:
- lang: eng
text: Methods, apparatus and computer program products provide efficient techniques
for reconstructing surfaces from data point sets. These techniques include reconstructing
surfaces from sets of scanned data points that have preferably undergone preprocessing
operations to improve their quality by, for example, reducing noise and removing
outliers. These techniques include reconstructing a dense and locally two-dimensionally
distributed 3D point set (e.g., point cloud) by merging stars in two-dimensional
weighted Delaunay triangulations within estimated tangent planes. The techniques
include determining a plurality of stars from a plurality of points p.sub.i in
a 3D point set S that at least partially describes the 3D surface, by projecting
the plurality of points p.sub.i onto planes T.sub.i that are each estimated to
be tangent about a respective one of the plurality of points p.sub.i. The plurality
of stars are then merged into a digital model of the 3D surface.
applicant:
- Geomagic Inc.
article_processing_charge: No
author:
- first_name: Yates
full_name: Fletcher, Yates
last_name: Fletcher
- first_name: Tobias
full_name: Gloth, Tobias
last_name: Gloth
- 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: Fletcher Y, Gloth T, Edelsbrunner H, Fu P. Method, apparatus and computer products
that reconstruct surfaces from data points. 2006.
apa: Fletcher, Y., Gloth, T., Edelsbrunner, H., & Fu, P. (2006). Method, apparatus
and computer products that reconstruct surfaces from data points.
chicago: Fletcher, Yates, Tobias Gloth, Herbert Edelsbrunner, and Ping Fu. “Method,
Apparatus and Computer Products That Reconstruct Surfaces from Data Points,” 2006.
ieee: Y. Fletcher, T. Gloth, H. Edelsbrunner, and P. Fu, “Method, apparatus and
computer products that reconstruct surfaces from data points.” 2006.
ista: Fletcher Y, Gloth T, Edelsbrunner H, Fu P. 2006. Method, apparatus and computer
products that reconstruct surfaces from data points.
mla: Fletcher, Yates, et al. Method, Apparatus and Computer Products That Reconstruct
Surfaces from Data Points. 2006.
short: Y. Fletcher, T. Gloth, H. Edelsbrunner, P. Fu, (2006).
date_created: 2018-12-11T12:03:43Z
date_published: 2006-04-04T00:00:00Z
date_updated: 2022-01-05T14:00:00Z
day: '04'
extern: '1'
ipc: ' G06T17/20 ; B33Y50/00'
ipn: US7023432B2
main_file_link:
- open_access: '1'
url: https://patents.google.com/patent/US7023432B2
month: '04'
oa: 1
oa_version: Published Version
publication_date: 2006-04-04
publist_id: '2875'
status: public
title: Method, apparatus and computer products that reconstruct surfaces from data
points
type: patent
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2006'
...
---
_id: '3545'
abstract:
- lang: eng
text: The functional organization of the basal ganglia ( BG) is often defined according
to one of two opposing schemes. The first proposes multiple, essentially independent
channels of information processing. The second posits convergence and lateral
integration of striatal channels at the level of the globus pallidus ( GP). We
tested the hypothesis that these proposed aspects of functional connectivity within
the striatopallidal axis are dynamic and related to brain state. Local field potentials
( LFPs) were simultaneously recorded from multiple sites in striatum and GP in
anesthetized rats during slow-wave activity( SWA) and during global activation
evoked by sensory stimulation. Functional connectivity was inferred from comparative
analyses of the internuclear and intranuclear coherence between bipolar derivations
of LFPs. During prominent SWA, as shown in the electrocorticogram and local field
potentials in the basal ganglia, intranuclear coherence, and, thus, lateral functional
connectivity within striatum or globus pallidus was relatively weak. Furthermore,
the temporal coupling of LFPs recorded across these two nuclei involved functional
convergence at the level of GP. Global activation, indicated by a loss of SWA,
was accompanied by a rapid functional reorganization of the striatopallidal axis.
Prominent lateral functional connectivity developed within GP and, to a significantly
more constrained spatial extent, striatum. Additionally, functional convergence
on GP was no longer apparent, despite increased internuclear coherence. These
data demonstrate that functional connectivity within the BG is highly dynamic
and suggest that the relative expression of organizational principles, such as
parallel, independent processing channels, striatopallidal convergence, and lateral
integration within BG nuclei, is dependent on brain state.
author:
- first_name: Peter
full_name: Magill,Peter J
last_name: Magill
- first_name: Alek
full_name: Pogosyan,Alek
last_name: Pogosyan
- first_name: Andrew
full_name: Sharott,Andrew
last_name: Sharott
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: John
full_name: Bolam, John Paul
last_name: Bolam
- first_name: Peter
full_name: Brown,Peter
last_name: Brown
citation:
ama: Magill P, Pogosyan A, Sharott A, Csicsvari JL, Bolam J, Brown P. Changes in
functional connectivity within the rat striatopallidal axis during global brain
activation in vivo. Journal of Neuroscience. 2006;26(23):6318-6329. doi:10.1523/JNEUROSCI.0620-06.2006
apa: Magill, P., Pogosyan, A., Sharott, A., Csicsvari, J. L., Bolam, J., & Brown,
P. (2006). Changes in functional connectivity within the rat striatopallidal axis
during global brain activation in vivo. Journal of Neuroscience. Society
for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0620-06.2006
chicago: Magill, Peter, Alek Pogosyan, Andrew Sharott, Jozsef L Csicsvari, John
Bolam, and Peter Brown. “Changes in Functional Connectivity within the Rat Striatopallidal
Axis during Global Brain Activation in Vivo.” Journal of Neuroscience.
Society for Neuroscience, 2006. https://doi.org/10.1523/JNEUROSCI.0620-06.2006.
ieee: P. Magill, A. Pogosyan, A. Sharott, J. L. Csicsvari, J. Bolam, and P. Brown,
“Changes in functional connectivity within the rat striatopallidal axis during
global brain activation in vivo,” Journal of Neuroscience, vol. 26, no.
23. Society for Neuroscience, pp. 6318–6329, 2006.
ista: Magill P, Pogosyan A, Sharott A, Csicsvari JL, Bolam J, Brown P. 2006. Changes
in functional connectivity within the rat striatopallidal axis during global brain
activation in vivo. Journal of Neuroscience. 26(23), 6318–6329.
mla: Magill, Peter, et al. “Changes in Functional Connectivity within the Rat Striatopallidal
Axis during Global Brain Activation in Vivo.” Journal of Neuroscience,
vol. 26, no. 23, Society for Neuroscience, 2006, pp. 6318–29, doi:10.1523/JNEUROSCI.0620-06.2006.
short: P. Magill, A. Pogosyan, A. Sharott, J.L. Csicsvari, J. Bolam, P. Brown, Journal
of Neuroscience 26 (2006) 6318–6329.
date_created: 2018-12-11T12:03:53Z
date_published: 2006-06-07T00:00:00Z
date_updated: 2021-01-12T07:44:13Z
day: '07'
doi: 10.1523/JNEUROSCI.0620-06.2006
extern: 1
intvolume: ' 26'
issue: '23'
month: '06'
page: 6318 - 6329
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '2840'
quality_controlled: 0
status: public
title: Changes in functional connectivity within the rat striatopallidal axis during
global brain activation in vivo
type: journal_article
volume: 26
year: '2006'
...
---
_id: '3559'
abstract:
- lang: eng
text: Persistent homology is the mathematical core of recent work on shape, including
reconstruction, recognition, and matching. Its per- tinent information is encapsulated
by a pairing of the critical values of a function, visualized by points forming
a diagram in the plane. The original algorithm in [10] computes the pairs from
an ordering of the simplices in a triangulation and takes worst-case time cubic
in the number of simplices. The main result of this paper is an algorithm that
maintains the pairing in worst-case linear time per transposition in the ordering.
A side-effect of the algorithm’s anal- ysis is an elementary proof of the stability
of persistence diagrams [7] in the special case of piecewise-linear functions.
We use the algorithm to compute 1-parameter families of diagrams which we apply
to the study of protein folding trajectories.
acknowledgement: Partially supported by NSF under grant CCR- 00-86013, by DARPA under
grant HR0011-05-1-0007, and by the Lawrence Livermore National Laboratory under
grant B543154.
author:
- 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
- first_name: Dmitriy
full_name: Morozov, Dmitriy
last_name: Morozov
citation:
ama: 'Cohen Steiner D, Edelsbrunner H, Morozov D. Vines and vineyards by updating
persistence in linear time. In: ACM; 2006:119-126. doi:10.1145/1137856.1137877'
apa: 'Cohen Steiner, D., Edelsbrunner, H., & Morozov, D. (2006). Vines and vineyards
by updating persistence in linear time (pp. 119–126). Presented at the SCG: Symposium
on Computational Geometry, ACM. https://doi.org/10.1145/1137856.1137877'
chicago: Cohen Steiner, David, Herbert Edelsbrunner, and Dmitriy Morozov. “Vines
and Vineyards by Updating Persistence in Linear Time,” 119–26. ACM, 2006. https://doi.org/10.1145/1137856.1137877.
ieee: 'D. Cohen Steiner, H. Edelsbrunner, and D. Morozov, “Vines and vineyards by
updating persistence in linear time,” presented at the SCG: Symposium on Computational
Geometry, 2006, pp. 119–126.'
ista: 'Cohen Steiner D, Edelsbrunner H, Morozov D. 2006. Vines and vineyards by
updating persistence in linear time. SCG: Symposium on Computational Geometry,
119–126.'
mla: Cohen Steiner, David, et al. Vines and Vineyards by Updating Persistence
in Linear Time. ACM, 2006, pp. 119–26, doi:10.1145/1137856.1137877.
short: D. Cohen Steiner, H. Edelsbrunner, D. Morozov, in:, ACM, 2006, pp. 119–126.
conference:
name: 'SCG: Symposium on Computational Geometry'
date_created: 2018-12-11T12:03:58Z
date_published: 2006-06-01T00:00:00Z
date_updated: 2021-01-12T07:44:18Z
day: '01'
doi: 10.1145/1137856.1137877
extern: 1
month: '06'
page: 119 - 126
publication_status: published
publisher: ACM
publist_id: '2826'
quality_controlled: 0
status: public
title: Vines and vineyards by updating persistence in linear time
type: conference
year: '2006'
...
---
_id: '3560'
abstract:
- lang: eng
text: We continue the study of topological persistence [5] by investigat- ing the
problem of simplifying a function f in a way that removes topological noise as
determined by its persistence diagram [2]. To state our results, we call a function
g an ε-simplification of another function f if ∥f − g∥∞ ≤ ε, and the persistence
diagrams of g are the same as those of f except all points within L1-distance
at most ε from the diagonal have been removed. We prove that for func- tions f
on a 2-manifold such ε-simplification exists, and we give an algorithm to construct
them in the piecewise linear case.
acknowledgement: Partially supported by NSF under grant CCR-00-86013, by DARPA under
grant HR0011-05-1-0007, and by the Lawrence Livermore National Laboratory under
grant B543154.
author:
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Dmitriy
full_name: Morozov, Dmitriy
last_name: Morozov
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
citation:
ama: 'Edelsbrunner H, Morozov D, Pascucci V. Persistence-sensitive simplification
of functions on 2-manifolds. In: ACM; 2006:127-134. doi:10.1145/1137856.1137878'
apa: 'Edelsbrunner, H., Morozov, D., & Pascucci, V. (2006). Persistence-sensitive
simplification of functions on 2-manifolds (pp. 127–134). Presented at the SCG:
Symposium on Computational Geometry, ACM. https://doi.org/10.1145/1137856.1137878'
chicago: Edelsbrunner, Herbert, Dmitriy Morozov, and Valerio Pascucci. “Persistence-Sensitive
Simplification of Functions on 2-Manifolds,” 127–34. ACM, 2006. https://doi.org/10.1145/1137856.1137878.
ieee: 'H. Edelsbrunner, D. Morozov, and V. Pascucci, “Persistence-sensitive simplification
of functions on 2-manifolds,” presented at the SCG: Symposium on Computational
Geometry, 2006, pp. 127–134.'
ista: 'Edelsbrunner H, Morozov D, Pascucci V. 2006. Persistence-sensitive simplification
of functions on 2-manifolds. SCG: Symposium on Computational Geometry, 127–134.'
mla: Edelsbrunner, Herbert, et al. Persistence-Sensitive Simplification of Functions
on 2-Manifolds. ACM, 2006, pp. 127–34, doi:10.1145/1137856.1137878.
short: H. Edelsbrunner, D. Morozov, V. Pascucci, in:, ACM, 2006, pp. 127–134.
conference:
name: 'SCG: Symposium on Computational Geometry'
date_created: 2018-12-11T12:03:58Z
date_published: 2006-06-01T00:00:00Z
date_updated: 2021-01-12T07:44:19Z
day: '01'
doi: 10.1145/1137856.1137878
extern: 1
main_file_link:
- open_access: '0'
url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.132.4465
month: '06'
page: 127 - 134
publication_status: published
publisher: ACM
publist_id: '2825'
quality_controlled: 0
status: public
title: Persistence-sensitive simplification of functions on 2-manifolds
type: conference
year: '2006'
...
---
_id: '3594'
author:
- first_name: Josephine
full_name: Pemberton, Josephine M
last_name: Pemberton
- first_name: Graeme
full_name: Swanson, Graeme M
last_name: Swanson
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Suzanne
full_name: Livingstone, Suzanne R
last_name: Livingstone
- first_name: Helen
full_name: Senn, Helen V
last_name: Senn
citation:
ama: Pemberton J, Swanson G, Barton NH, Livingstone S, Senn H. Hybridisation between
red and sika deer in Scotland. Deer. 2006;13(9):22-26.
apa: Pemberton, J., Swanson, G., Barton, N. H., Livingstone, S., & Senn, H.
(2006). Hybridisation between red and sika deer in Scotland. Deer. BDS
.
chicago: Pemberton, Josephine, Graeme Swanson, Nicholas H Barton, Suzanne Livingstone,
and Helen Senn. “Hybridisation between Red and Sika Deer in Scotland.” Deer.
BDS , 2006.
ieee: J. Pemberton, G. Swanson, N. H. Barton, S. Livingstone, and H. Senn, “Hybridisation
between red and sika deer in Scotland,” Deer, vol. 13, no. 9. BDS , pp.
22–26, 2006.
ista: Pemberton J, Swanson G, Barton NH, Livingstone S, Senn H. 2006. Hybridisation
between red and sika deer in Scotland. Deer. 13(9), 22–26.
mla: Pemberton, Josephine, et al. “Hybridisation between Red and Sika Deer in Scotland.”
Deer, vol. 13, no. 9, BDS , 2006, pp. 22–26.
short: J. Pemberton, G. Swanson, N.H. Barton, S. Livingstone, H. Senn, Deer 13 (2006)
22–26.
date_created: 2018-12-11T12:04:08Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2019-04-26T07:22:31Z
day: '01'
extern: 1
intvolume: ' 13'
issue: '9'
month: '01'
page: 22 - 26
publication: Deer
publication_status: published
publisher: 'BDS '
publist_id: '2789'
quality_controlled: 0
status: public
title: Hybridisation between red and sika deer in Scotland
type: review
volume: 13
year: '2006'
...
---
_id: '3609'
abstract:
- lang: eng
text: Bombina bombina and B. variegata are two anciently diverged toad taxa that
have adapted to different breeding habitats yet hybridize freely in zones of overlap
where their parapatric distributions meet. Here, we report on a joint genetic
and ecological analysis of a hybrid zone in the vicinity of Stryi in western Ukraine.
We used five unlinked allozyme loci, two nuclear single nucleotide polymorphisms
and a mitochondrial DNA haplotype as genetic markers. Parallel allele frequency
clines with a sharp central step occur across a sharp ecotone, where transitions
in aquatic habitat, elevation, and terrestrial vegetation coincide. The width
of the hybrid zone, estimated as the inverse of the maximum gradient in allele
frequency, is 2.3 km. This is the smallest of four estimates derived from different
clinal transects across Europe. We argue that the narrow cline near Stryi is mainly
due to a combination of habitat distribution and habitat preference. Adult toads
show a preference for either ponds (B. bombina) or puddles (B. variegata), which
is known to affect the distribution of genotypes within the hybrid zones. At Stryi,
it should cause a reduction of the dispersal rate across the ecotone and thus
narrow the cline. A detailed comparison of all five intensively studied Bombina
transects lends support to the hypothesis that habitat distribution plus habitat
preference can jointly affect the structure of hybrid zones and, ultimately, the
resulting barriers to gene flow between differentiated gene pools. This study
also represents a resampling of an area that was last studied more than 70 years
ago. Our allele-frequency clines largely coincide with those that were described
then on the basis of morphological variation. However, we found asymmetrical introgression
of B. variegata genes into B. bombina territory along the bank of a river.
author:
- first_name: Alexey
full_name: Yanchukov, Alexey
last_name: Yanchukov
- first_name: Sebastian
full_name: Hofman, Sebastian
last_name: Hofman
- first_name: Jacek
full_name: Szymura, Jacek M
last_name: Szymura
- first_name: Sergey
full_name: Mezhzherin, Sergey V
last_name: Mezhzherin
- first_name: Sviatoslav
full_name: Morozov-Leonov, Sviatoslav
last_name: Morozov Leonov
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Beate
full_name: Nürnberger, Beate
last_name: Nürnberger
citation:
ama: 'Yanchukov A, Hofman S, Szymura J, et al. Hybridization of Bombina bombina
and B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine:
comparisons across transects and over time. Evolution; International Journal
of Organic Evolution. 2006;60(3):583-600. doi:10.1111/j.0014-3820.2006.tb01139.x'
apa: 'Yanchukov, A., Hofman, S., Szymura, J., Mezhzherin, S., Morozov Leonov, S.,
Barton, N. H., & Nürnberger, B. (2006). Hybridization of Bombina bombina and
B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons
across transects and over time. Evolution; International Journal of Organic
Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2006.tb01139.x'
chicago: 'Yanchukov, Alexey, Sebastian Hofman, Jacek Szymura, Sergey Mezhzherin,
Sviatoslav Morozov Leonov, Nicholas H Barton, and Beate Nürnberger. “Hybridization
of Bombina Bombina and B. Variegata (Anura, Discoglossidae) at a Sharp Ecotone
in Western Ukraine: Comparisons across Transects and over Time.” Evolution;
International Journal of Organic Evolution. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.0014-3820.2006.tb01139.x.'
ieee: 'A. Yanchukov et al., “Hybridization of Bombina bombina and B. variegata
(Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across
transects and over time,” Evolution; International Journal of Organic Evolution,
vol. 60, no. 3. Wiley-Blackwell, pp. 583–600, 2006.'
ista: 'Yanchukov A, Hofman S, Szymura J, Mezhzherin S, Morozov Leonov S, Barton
NH, Nürnberger B. 2006. Hybridization of Bombina bombina and B. variegata (Anura,
Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across transects
and over time. Evolution; International Journal of Organic Evolution. 60(3), 583–600.'
mla: 'Yanchukov, Alexey, et al. “Hybridization of Bombina Bombina and B. Variegata
(Anura, Discoglossidae) at a Sharp Ecotone in Western Ukraine: Comparisons across
Transects and over Time.” Evolution; International Journal of Organic Evolution,
vol. 60, no. 3, Wiley-Blackwell, 2006, pp. 583–600, doi:10.1111/j.0014-3820.2006.tb01139.x.'
short: A. Yanchukov, S. Hofman, J. Szymura, S. Mezhzherin, S. Morozov Leonov, N.H.
Barton, B. Nürnberger, Evolution; International Journal of Organic Evolution 60
(2006) 583–600.
date_created: 2018-12-11T12:04:13Z
date_published: 2006-03-01T00:00:00Z
date_updated: 2021-01-12T07:44:38Z
day: '01'
doi: 10.1111/j.0014-3820.2006.tb01139.x
extern: 1
intvolume: ' 60'
issue: '3'
month: '03'
page: 583 - 600
publication: Evolution; International Journal of Organic Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2774'
quality_controlled: 0
status: public
title: 'Hybridization of Bombina bombina and B. variegata (Anura, Discoglossidae)
at a sharp ecotone in western Ukraine: comparisons across transects and over time'
type: journal_article
volume: 60
year: '2006'
...
---
_id: '3608'
abstract:
- lang: eng
text: 'We study the evolution of inversions that capture locally adapted alleles
when two populations are exchanging migrants or hybridizing. By suppressing recombination
between the loci, a new inversion can spread. Neither drift nor coadaptation between
the alleles (epistasis) is needed, so this local adaptation mechanism may apply
to a broader range of genetic and demographic situations than alternative hypotheses
that have been widely discussed. The mechanism can explain many features observed
in inversion systems. It will drive an inversion to high frequency if there is
no countervailing force, which could explain fixed differences observed between
populations and species. An inversion can be stabilized at an intermediate frequency
if it also happens to capture one or more deleterious recessive mutations, which
could explain polymorphisms that are common in some species. This polymorphism
can cycle in frequency with the changing selective advantage of the locally favored
alleles. The mechanism can establish underdominant inversions that decrease heterokaryotype
fitness by several percent if the cause of fitness loss is structural, while if
the cause is genic there is no limit to the strength of underdominance that can
result. The mechanism is expected to cause loci responsible for adaptive species-specific
differences to map to inversions, as seen in recent QTL studies. We discuss data
that support the hypothesis, review other mechanisms for inversion evolution,
and suggest possible tests. '
author:
- first_name: Mark
full_name: Kirkpatrick, Mark
last_name: Kirkpatrick
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Kirkpatrick M, Barton NH. Chromosome inversions, local adaptation, and speciation.
Genetics. 2006;173(1):419-434. doi:10.1534/genetics.105.047985
apa: Kirkpatrick, M., & Barton, N. H. (2006). Chromosome inversions, local adaptation,
and speciation. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.105.047985
chicago: Kirkpatrick, Mark, and Nicholas H Barton. “Chromosome Inversions, Local
Adaptation, and Speciation.” Genetics. Genetics Society of America, 2006.
https://doi.org/10.1534/genetics.105.047985.
ieee: M. Kirkpatrick and N. H. Barton, “Chromosome inversions, local adaptation,
and speciation,” Genetics, vol. 173, no. 1. Genetics Society of America,
pp. 419–434, 2006.
ista: Kirkpatrick M, Barton NH. 2006. Chromosome inversions, local adaptation, and
speciation. Genetics. 173(1), 419–434.
mla: Kirkpatrick, Mark, and Nicholas H. Barton. “Chromosome Inversions, Local Adaptation,
and Speciation.” Genetics, vol. 173, no. 1, Genetics Society of America,
2006, pp. 419–34, doi:10.1534/genetics.105.047985.
short: M. Kirkpatrick, N.H. Barton, Genetics 173 (2006) 419–434.
date_created: 2018-12-11T12:04:13Z
date_published: 2006-05-01T00:00:00Z
date_updated: 2021-01-12T07:44:37Z
day: '01'
doi: 10.1534/genetics.105.047985
extern: 1
intvolume: ' 173'
issue: '1'
month: '05'
page: 419 - 434
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '2775'
quality_controlled: 0
status: public
title: Chromosome inversions, local adaptation, and speciation
type: journal_article
volume: 173
year: '2006'
...
---
_id: '3610'
abstract:
- lang: eng
text: For a model of diallelic loci with arbitrary epistasis, Barton and Turelli
[2004. Effects of genetic drift on variance components under a general model of
epistasis. Evolution 58, 2111–2132] gave results for variances among and within
replicate lines obtained by inbreeding without selection. Here, we discuss the
relation between their population genetic methods and classical quantitative genetic
arguments. In particular, we consider the case of no dominance using classical
identity by descent arguments, which generalizes their results from two alleles
to multiple alleles. To clarify the connections between the alternative methods,
we obtain the same results using an intermediate method, which explicitly identifies
the statistical effects of sets of loci. We also discuss the effects of population
bottlenecks on covariances among relatives.
author:
- first_name: William
full_name: Hill, William G
last_name: Hill
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: Hill W, Barton NH, Turelli M. Prediction of effects of genetic drift on variance
components under a general model of epistasis. Theoretical Population Biology.
2006;70(1):56-62. doi:10.1016/j.tpb.2005.10.001
apa: Hill, W., Barton, N. H., & Turelli, M. (2006). Prediction of effects of
genetic drift on variance components under a general model of epistasis. Theoretical
Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2005.10.001
chicago: Hill, William, Nicholas H Barton, and Michael Turelli. “Prediction of Effects
of Genetic Drift on Variance Components under a General Model of Epistasis.” Theoretical
Population Biology. Academic Press, 2006. https://doi.org/10.1016/j.tpb.2005.10.001.
ieee: W. Hill, N. H. Barton, and M. Turelli, “Prediction of effects of genetic drift
on variance components under a general model of epistasis,” Theoretical Population
Biology, vol. 70, no. 1. Academic Press, pp. 56–62, 2006.
ista: Hill W, Barton NH, Turelli M. 2006. Prediction of effects of genetic drift
on variance components under a general model of epistasis. Theoretical Population
Biology. 70(1), 56–62.
mla: Hill, William, et al. “Prediction of Effects of Genetic Drift on Variance Components
under a General Model of Epistasis.” Theoretical Population Biology, vol.
70, no. 1, Academic Press, 2006, pp. 56–62, doi:10.1016/j.tpb.2005.10.001.
short: W. Hill, N.H. Barton, M. Turelli, Theoretical Population Biology 70 (2006)
56–62.
date_created: 2018-12-11T12:04:14Z
date_published: 2006-08-01T00:00:00Z
date_updated: 2021-01-12T07:44:39Z
day: '01'
doi: 10.1016/j.tpb.2005.10.001
extern: 1
intvolume: ' 70'
issue: '1'
month: '08'
page: 56 - 62
publication: Theoretical Population Biology
publication_status: published
publisher: Academic Press
publist_id: '2773'
quality_controlled: 0
status: public
title: Prediction of effects of genetic drift on variance components under a general
model of epistasis
type: journal_article
volume: 70
year: '2006'
...
---
_id: '3679'
abstract:
- lang: eng
text: This paper describes a new system for "Finding Satellite Tracks” in astronomical
images based on the modern geometric approach. There is an increasing need of
using methods with solid mathematical and statistical foundation in astronomical
image processing. Where the computational methods are serving in all disciplines
of science, they are becoming popular in the field of astronomy as well. Currently
different computational systems are required to be numerically optimized before
to get applied on astronomical images. So at present there is no single system
which solves the problems of astronomers using computational methods based on
modern approaches. The system "Finding Satellite Tracks” is based on geometric
matching method "Recognition by Adaptive Subdivision of Transformation Space
(RAST)".
alternative_title:
- LNCS
author:
- first_name: Haider
full_name: Ali,Haider
last_name: Ali
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Thomas
full_name: Breuel,Thomas M
last_name: Breuel
citation:
ama: 'Ali H, Lampert C, Breuel T. Satellite tracks removal in astronomical images.
In: Vol 4225. Springer; 2006:892-901. doi:10.1007/11892755_92'
apa: 'Ali, H., Lampert, C., & Breuel, T. (2006). Satellite tracks removal in
astronomical images (Vol. 4225, pp. 892–901). Presented at the CIARP: Iberoamerican
Congress in Pattern Recognition, Springer. https://doi.org/10.1007/11892755_92'
chicago: Ali, Haider, Christoph Lampert, and Thomas Breuel. “Satellite Tracks Removal
in Astronomical Images,” 4225:892–901. Springer, 2006. https://doi.org/10.1007/11892755_92.
ieee: 'H. Ali, C. Lampert, and T. Breuel, “Satellite tracks removal in astronomical
images,” presented at the CIARP: Iberoamerican Congress in Pattern Recognition,
2006, vol. 4225, pp. 892–901.'
ista: 'Ali H, Lampert C, Breuel T. 2006. Satellite tracks removal in astronomical
images. CIARP: Iberoamerican Congress in Pattern Recognition, LNCS, vol. 4225,
892–901.'
mla: Ali, Haider, et al. Satellite Tracks Removal in Astronomical Images.
Vol. 4225, Springer, 2006, pp. 892–901, doi:10.1007/11892755_92.
short: H. Ali, C. Lampert, T. Breuel, in:, Springer, 2006, pp. 892–901.
conference:
name: 'CIARP: Iberoamerican Congress in Pattern Recognition'
date_created: 2018-12-11T12:04:35Z
date_published: 2006-10-31T00:00:00Z
date_updated: 2021-01-12T07:45:05Z
day: '31'
doi: 10.1007/11892755_92
extern: 1
intvolume: ' 4225'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/~chl/papers/ali-ciarp2006.pdf
month: '10'
page: 892 - 901
publication_status: published
publisher: Springer
publist_id: '2700'
quality_controlled: 0
status: public
title: Satellite tracks removal in astronomical images
type: conference
volume: 4225
year: '2006'
...
---
_id: '3677'
abstract:
- lang: eng
text: We propose a video retrieval framework based on a novel combination of spatiograms
and the Jensen-Shannon divergence, and validate its performance in two quantitative
experiments on TRECVID BBC Rushes data. In the first experiment, color-based methods
are tested by grouping redundant shots in an unsupervised clustering. Results
of the second experiment show that motion-based spatiograms make a promising fast,
compressed-domain descriptor for the detection of interview scenes.
alternative_title:
- TRECVID Notebook Papers and Slides
author:
- first_name: Adrian
full_name: Ulges, Adrian
last_name: Ulges
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Daniel
full_name: Keysers,Daniel
last_name: Keysers
citation:
ama: 'Ulges A, Lampert C, Keysers D. Spatiogram-based shot distances for video retrieval.
In: NIST (National Institute of Standards and Technology, US Department of Commerce);
2006:1-10.'
apa: Ulges, A., Lampert, C., & Keysers, D. (2006). Spatiogram-based shot distances
for video retrieval (pp. 1–10). Presented at the TRECVID Workshop, NIST (National
Institute of Standards and Technology, US Department of Commerce).
chicago: Ulges, Adrian, Christoph Lampert, and Daniel Keysers. “Spatiogram-Based
Shot Distances for Video Retrieval,” 1–10. NIST (National Institute of Standards
and Technology, US Department of Commerce), 2006.
ieee: A. Ulges, C. Lampert, and D. Keysers, “Spatiogram-based shot distances for
video retrieval,” presented at the TRECVID Workshop, 2006, pp. 1–10.
ista: Ulges A, Lampert C, Keysers D. 2006. Spatiogram-based shot distances for video
retrieval. TRECVID Workshop, TRECVID Notebook Papers and Slides, , 1–10.
mla: Ulges, Adrian, et al. Spatiogram-Based Shot Distances for Video Retrieval.
NIST (National Institute of Standards and Technology, US Department of Commerce),
2006, pp. 1–10.
short: A. Ulges, C. Lampert, D. Keysers, in:, NIST (National Institute of Standards
and Technology, US Department of Commerce), 2006, pp. 1–10.
conference:
name: TRECVID Workshop
date_created: 2018-12-11T12:04:34Z
date_published: 2006-11-14T00:00:00Z
date_updated: 2021-01-12T07:45:04Z
day: '14'
extern: 1
main_file_link:
- open_access: '0'
url: http://www-nlpir.nist.gov/projects/tvpubs/tv6.papers/dfki.pdf
month: '11'
page: 1 - 10
publication_status: published
publisher: NIST (National Institute of Standards and Technology, US Department of
Commerce)
publist_id: '2702'
quality_controlled: 0
status: public
title: Spatiogram-based shot distances for video retrieval
type: conference
year: '2006'
...
---
_id: '3680'
abstract:
- lang: eng
text: The detection of counterfeit in printed documents is currently based mainly
on built-in security features or on human expertise. We propose a classification
system that supports non-expert users to distinguish original documents from PC-made
forgeries by analyzing the printing technique used. Each letter in a document
is classified using a support vector machine that has been trained to distinguish
laser from inkjet printouts. A color-coded visualization helps the user to interpret
the per-letter classification results
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Lin
full_name: Mei,Lin
last_name: Mei
- first_name: Thomas
full_name: Breuel,Thomas M
last_name: Breuel
citation:
ama: 'Lampert C, Mei L, Breuel T. Printing technique classification for document
counterfeit detection. In: Vol 1. IEEE; 2006:639-634. doi:10.1109/ICCIAS.2006.294214'
apa: 'Lampert, C., Mei, L., & Breuel, T. (2006). Printing technique classification
for document counterfeit detection (Vol. 1, pp. 639–634). Presented at the CIS:
Computational Intelligence and Security, IEEE. https://doi.org/10.1109/ICCIAS.2006.294214'
chicago: Lampert, Christoph, Lin Mei, and Thomas Breuel. “Printing Technique Classification
for Document Counterfeit Detection,” 1:639–634. IEEE, 2006. https://doi.org/10.1109/ICCIAS.2006.294214.
ieee: 'C. Lampert, L. Mei, and T. Breuel, “Printing technique classification for
document counterfeit detection,” presented at the CIS: Computational Intelligence
and Security, 2006, vol. 1, pp. 639–634.'
ista: 'Lampert C, Mei L, Breuel T. 2006. Printing technique classification for document
counterfeit detection. CIS: Computational Intelligence and Security vol. 1, 639–634.'
mla: Lampert, Christoph, et al. Printing Technique Classification for Document
Counterfeit Detection. Vol. 1, IEEE, 2006, pp. 639–634, doi:10.1109/ICCIAS.2006.294214.
short: C. Lampert, L. Mei, T. Breuel, in:, IEEE, 2006, pp. 639–634.
conference:
name: 'CIS: Computational Intelligence and Security'
date_created: 2018-12-11T12:04:35Z
date_published: 2006-11-03T00:00:00Z
date_updated: 2021-01-12T07:45:06Z
day: '03'
doi: 10.1109/ICCIAS.2006.294214
extern: 1
intvolume: ' 1'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/~chl/papers/lampert-cis2006.pdf
month: '11'
page: 639 - 634
publication_status: published
publisher: IEEE
publist_id: '2698'
quality_controlled: 0
status: public
title: Printing technique classification for document counterfeit detection
type: conference
volume: 1
year: '2006'
...
---
_id: '3695'
abstract:
- lang: eng
text: We give an analytical and geometrical treatment of what it means to separate
a Gaussian kernel along arbitrary axes in Ropfn, and we present a separation scheme
that allows us to efficiently implement anisotropic Gaussian convolution filters
for data of arbitrary dimensionality. Based on our previous analysis we show that
this scheme is optimal with regard to the number of memory accesses and interpolation
operations needed. The proposed method relies on nonorthogonal convolution axes
and works completely in image space. Thus, it avoids the need for a fast Fourier
transform (FFT)-subroutine. Depending on the accuracy and speed requirements,
different interpolation schemes and methods to implement the one-dimensional Gaussian
(finite impulse response and infinite impulse response) can be integrated. Special
emphasis is put on analyzing the performance and accuracy of the new method. In
particular, we show that without any special optimization of the source code,
it can perform anisotropic Gaussian filtering faster than methods relying on the
FFT.
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Oliver
full_name: Wirjadi,Oliver
last_name: Wirjadi
citation:
ama: Lampert C, Wirjadi O. An optimal non-orthogonal separation of the anisotropic
Gaussian convolution filter. IEEE Transactions on Image Processing (TIP).
2006;15(11):3501-3513. doi:
10.1109/TIP.2006.877501
apa: Lampert, C., & Wirjadi, O. (2006). An optimal non-orthogonal separation
of the anisotropic Gaussian convolution filter. IEEE Transactions on Image
Processing (TIP). IEEE. https://doi.org/ 10.1109/TIP.2006.877501
chicago: Lampert, Christoph, and Oliver Wirjadi. “An Optimal Non-Orthogonal Separation
of the Anisotropic Gaussian Convolution Filter.” IEEE Transactions on Image
Processing (TIP). IEEE, 2006. https://doi.org/ 10.1109/TIP.2006.877501 .
ieee: C. Lampert and O. Wirjadi, “An optimal non-orthogonal separation of the anisotropic
Gaussian convolution filter,” IEEE Transactions on Image Processing (TIP),
vol. 15, no. 11. IEEE, pp. 3501–3513, 2006.
ista: Lampert C, Wirjadi O. 2006. An optimal non-orthogonal separation of the anisotropic
Gaussian convolution filter. IEEE Transactions on Image Processing (TIP). 15(11),
3501–3513.
mla: Lampert, Christoph, and Oliver Wirjadi. “An Optimal Non-Orthogonal Separation
of the Anisotropic Gaussian Convolution Filter.” IEEE Transactions on Image
Processing (TIP), vol. 15, no. 11, IEEE, 2006, pp. 3501–13, doi: 10.1109/TIP.2006.877501 .
short: C. Lampert, O. Wirjadi, IEEE Transactions on Image Processing (TIP) 15 (2006)
3501–3513.
date_created: 2018-12-11T12:04:40Z
date_published: 2006-11-01T00:00:00Z
date_updated: 2021-01-12T07:49:01Z
day: '01'
doi: ' 10.1109/TIP.2006.877501 '
extern: 1
intvolume: ' 15'
issue: '11'
main_file_link:
- open_access: '1'
url: http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:hbz:386-kluedo-14003
month: '11'
oa: 1
page: 3501 - 3513
publication: IEEE Transactions on Image Processing (TIP)
publication_status: published
publisher: IEEE
publist_id: '2669'
quality_controlled: 0
status: public
title: An optimal non-orthogonal separation of the anisotropic Gaussian convolution
filter
type: journal_article
volume: 15
year: '2006'
...
---
_id: '3693'
abstract:
- lang: eng
text: Gaussian filtering in one, two or three dimensions is among the most commonly
needed tasks in signal and image processing. Finite impulse response filters in
the time domain with Gaussian masks are easy to implement in either floating or
fixed point arithmetic, because Gaussian kernels are strictly positive and bounded.
But these implementations are slow for large images or kernels. With the recursive
IIR-filters and FFT-based methods, there are at least two alternative methods
to perform Gaussian filtering in a faster way, but so far they are only applicable
when floating-point hardware is available. In this paper, a fixed-point implementation
of recursive Gaussian filtering is discussed and applied to isotropic and anisotropic
image filtering by making use of a non-orthogonal separation scheme of the Gaussian
filter.
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Oliver
full_name: Wirjadi,Oliver
last_name: Wirjadi
citation:
ama: 'Lampert C, Wirjadi O. Anisotropic Gaussian filtering using fixed point arithmetic.
In: IEEE; 2006:1565-1568. doi:10.1109/ICIP.2006.312606'
apa: 'Lampert, C., & Wirjadi, O. (2006). Anisotropic Gaussian filtering using
fixed point arithmetic (pp. 1565–1568). Presented at the ICIP: IEEE International
Conference on Image Processing, IEEE. https://doi.org/10.1109/ICIP.2006.312606'
chicago: Lampert, Christoph, and Oliver Wirjadi. “Anisotropic Gaussian Filtering
Using Fixed Point Arithmetic,” 1565–68. IEEE, 2006. https://doi.org/10.1109/ICIP.2006.312606.
ieee: 'C. Lampert and O. Wirjadi, “Anisotropic Gaussian filtering using fixed point
arithmetic,” presented at the ICIP: IEEE International Conference on Image Processing,
2006, pp. 1565–1568.'
ista: 'Lampert C, Wirjadi O. 2006. Anisotropic Gaussian filtering using fixed point
arithmetic. ICIP: IEEE International Conference on Image Processing, 1565–1568.'
mla: Lampert, Christoph, and Oliver Wirjadi. Anisotropic Gaussian Filtering Using
Fixed Point Arithmetic. IEEE, 2006, pp. 1565–68, doi:10.1109/ICIP.2006.312606.
short: C. Lampert, O. Wirjadi, in:, IEEE, 2006, pp. 1565–1568.
conference:
name: 'ICIP: IEEE International Conference on Image Processing'
date_created: 2018-12-11T12:04:39Z
date_published: 2006-10-08T00:00:00Z
date_updated: 2021-01-12T07:49:00Z
day: '08'
doi: 10.1109/ICIP.2006.312606
extern: 1
month: '10'
page: 1565 - 1568
publication_status: published
publisher: IEEE
publist_id: '2670'
quality_controlled: 0
status: public
title: Anisotropic Gaussian filtering using fixed point arithmetic
type: conference
year: '2006'
...
---
_id: '3692'
author:
- first_name: Daniel
full_name: Keysers,Daniel
last_name: Keysers
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Thomas
full_name: Breuel,Thomas M
last_name: Breuel
citation:
ama: 'Keysers D, Lampert C, Breuel T. Color image dequantization by constrained
diffusion. In: Vol 6058. SPIE; 2006. doi:10.1117/12.648713'
apa: Keysers, D., Lampert, C., & Breuel, T. (2006). Color image dequantization
by constrained diffusion (Vol. 6058). Presented at the SPIE Electronic Imaging,
SPIE. https://doi.org/10.1117/12.648713
chicago: Keysers, Daniel, Christoph Lampert, and Thomas Breuel. “Color Image Dequantization
by Constrained Diffusion,” Vol. 6058. SPIE, 2006. https://doi.org/10.1117/12.648713.
ieee: D. Keysers, C. Lampert, and T. Breuel, “Color image dequantization by constrained
diffusion,” presented at the SPIE Electronic Imaging, 2006, vol. 6058.
ista: Keysers D, Lampert C, Breuel T. 2006. Color image dequantization by constrained
diffusion. SPIE Electronic Imaging vol. 6058.
mla: Keysers, Daniel, et al. Color Image Dequantization by Constrained Diffusion.
Vol. 6058, SPIE, 2006, doi:10.1117/12.648713.
short: D. Keysers, C. Lampert, T. Breuel, in:, SPIE, 2006.
conference:
name: SPIE Electronic Imaging
date_created: 2018-12-11T12:04:39Z
date_published: 2006-01-15T00:00:00Z
date_updated: 2019-05-10T12:19:52Z
day: '15'
doi: 10.1117/12.648713
extern: 1
intvolume: ' 6058'
month: '01'
publication_status: published
publisher: SPIE
publist_id: '2674'
quality_controlled: 0
status: public
title: Color image dequantization by constrained diffusion
type: conference
volume: 6058
year: '2006'
...
---
_id: '3729'
abstract:
- lang: eng
text: Measuring the visco-elastic properties of biological macromolecules constitutes
an important step towards the understanding of dynamic biological processes, such
as cell adhesion, muscle function, or plant cell wall stability. Force spectroscopy
techniques based on the atomic force microscope (AFM) are increasingly used to
study the complex visco-elastic response of (bio-)molecules on a single-molecule
level. These experiments either require that the AFM cantilever is actively oscillated
or that the molecule is clamped at constant force to monitor thermal cantilever
motion. Here we demonstrate that the visco-elasticity of single bio-molecules
can readily be extracted from the Brownian cantilever motion during conventional
force-extension measurements. It is shown that the characteristics of the cantilever
determine the signal-to-noise (S/N) ratio and time resolution. Using a small cantilever,
the visco-elastic properties of single dextran molecules were resolved with a
time resolution of 8.3 ms. The presented approach can be directly applied to probe
the dynamic response of complex bio-molecular systems or proteins in force-extension
experiments.
author:
- first_name: Christian
full_name: Bippes, Christian A
last_name: Bippes
- first_name: Andrew
full_name: Humphris, Andrew D
last_name: Humphris
- first_name: Martin
full_name: Stark, Martin
last_name: Stark
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Bippes C, Humphris A, Stark M, Mueller D, Janovjak HL. Direct measurement of
single-molecule visco-elasticity in atomic force microscope force-extension experiments.
European Biophysics Journal. 2006;35(3):287-292. doi:10.1007/s00249-005-0023-9
apa: Bippes, C., Humphris, A., Stark, M., Mueller, D., & Janovjak, H. L. (2006).
Direct measurement of single-molecule visco-elasticity in atomic force microscope
force-extension experiments. European Biophysics Journal. Springer. https://doi.org/10.1007/s00249-005-0023-9
chicago: Bippes, Christian, Andrew Humphris, Martin Stark, Daniel Mueller, and Harald
L Janovjak. “Direct Measurement of Single-Molecule Visco-Elasticity in Atomic
Force Microscope Force-Extension Experiments.” European Biophysics Journal.
Springer, 2006. https://doi.org/10.1007/s00249-005-0023-9.
ieee: C. Bippes, A. Humphris, M. Stark, D. Mueller, and H. L. Janovjak, “Direct
measurement of single-molecule visco-elasticity in atomic force microscope force-extension
experiments,” European Biophysics Journal, vol. 35, no. 3. Springer, pp.
287–292, 2006.
ista: Bippes C, Humphris A, Stark M, Mueller D, Janovjak HL. 2006. Direct measurement
of single-molecule visco-elasticity in atomic force microscope force-extension
experiments. European Biophysics Journal. 35(3), 287–292.
mla: Bippes, Christian, et al. “Direct Measurement of Single-Molecule Visco-Elasticity
in Atomic Force Microscope Force-Extension Experiments.” European Biophysics
Journal, vol. 35, no. 3, Springer, 2006, pp. 287–92, doi:10.1007/s00249-005-0023-9.
short: C. Bippes, A. Humphris, M. Stark, D. Mueller, H.L. Janovjak, European Biophysics
Journal 35 (2006) 287–292.
date_created: 2018-12-11T12:04:51Z
date_published: 2006-02-01T00:00:00Z
date_updated: 2021-01-12T07:51:46Z
day: '01'
doi: 10.1007/s00249-005-0023-9
extern: 1
intvolume: ' 35'
issue: '3'
month: '02'
page: 287 - 292
publication: European Biophysics Journal
publication_status: published
publisher: Springer
publist_id: '2500'
quality_controlled: 0
status: public
title: Direct measurement of single-molecule visco-elasticity in atomic force microscope
force-extension experiments
type: journal_article
volume: 35
year: '2006'
...
---
_id: '3728'
abstract:
- lang: eng
text: Mechanical unfolding of single bacteriorhodopsins from a membrane bilayer
is studied using molecular dynamics simulations. The initial conformation of the
lipid membrane is determined through all-atom simulations and then its coarse-grained
representation is used in the studies of stretching. A Go-like model with a realistic
contact map and with Lennard–Jones contact interactions is applied to model the
protein–membrane system. The model qualitatively reproduces the experimentally
observed differences between force-extension patterns obtained on bacteriorhodopsin
at different temperatures and predicts a lack of symmetry in the choice of the
terminus to pull by. It also illustrates the decisive role of the interactions
of the protein with the membrane in determining the force pattern and thus the
stability of transmembrane proteins.
author:
- first_name: Marek
full_name: Cieplak, Marek
last_name: Cieplak
- first_name: Sławomir
full_name: Filipek, Sławomir
last_name: Filipek
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Krystiana
full_name: Krzysko, Krystiana A
last_name: Krzysko
citation:
ama: 'Cieplak M, Filipek S, Janovjak HL, Krzysko K. Pulling single bacteriorhodopsin
out of a membrane: Comparison of simulation and experiment. Biochimica et Biophysica
Acta (BBA) - Biomembranes. 2006;1758(4):537-544. doi:10.1016/j.bbamem.2006.03.028'
apa: 'Cieplak, M., Filipek, S., Janovjak, H. L., & Krzysko, K. (2006). Pulling
single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment.
Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier. https://doi.org/10.1016/j.bbamem.2006.03.028'
chicago: 'Cieplak, Marek, Sławomir Filipek, Harald L Janovjak, and Krystiana Krzysko.
“Pulling Single Bacteriorhodopsin out of a Membrane: Comparison of Simulation
and Experiment.” Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier,
2006. https://doi.org/10.1016/j.bbamem.2006.03.028.'
ieee: 'M. Cieplak, S. Filipek, H. L. Janovjak, and K. Krzysko, “Pulling single bacteriorhodopsin
out of a membrane: Comparison of simulation and experiment,” Biochimica et
Biophysica Acta (BBA) - Biomembranes, vol. 1758, no. 4. Elsevier, pp. 537–544,
2006.'
ista: 'Cieplak M, Filipek S, Janovjak HL, Krzysko K. 2006. Pulling single bacteriorhodopsin
out of a membrane: Comparison of simulation and experiment. Biochimica et Biophysica
Acta (BBA) - Biomembranes. 1758(4), 537–544.'
mla: 'Cieplak, Marek, et al. “Pulling Single Bacteriorhodopsin out of a Membrane:
Comparison of Simulation and Experiment.” Biochimica et Biophysica Acta (BBA)
- Biomembranes, vol. 1758, no. 4, Elsevier, 2006, pp. 537–44, doi:10.1016/j.bbamem.2006.03.028.'
short: M. Cieplak, S. Filipek, H.L. Janovjak, K. Krzysko, Biochimica et Biophysica
Acta (BBA) - Biomembranes 1758 (2006) 537–544.
date_created: 2018-12-11T12:04:50Z
date_published: 2006-04-01T00:00:00Z
date_updated: 2021-01-12T07:51:46Z
day: '01'
doi: 10.1016/j.bbamem.2006.03.028
extern: 1
intvolume: ' 1758'
issue: '4'
month: '04'
page: 537 - 544
publication: Biochimica et Biophysica Acta (BBA) - Biomembranes
publication_status: published
publisher: Elsevier
publist_id: '2502'
quality_controlled: 0
status: public
title: 'Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation
and experiment'
type: journal_article
volume: 1758
year: '2006'
...
---
_id: '3722'
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
citation:
ama: 'Janovjak HL, Mueller D. Rastersondenmikroskopie. In: Bioanalytik. Spektrum
Akademischer Verlag; 2006.'
apa: Janovjak, H. L., & Mueller, D. (2006). Rastersondenmikroskopie. In Bioanalytik.
Spektrum Akademischer Verlag.
chicago: Janovjak, Harald L, and Daniel Mueller. “Rastersondenmikroskopie.” In Bioanalytik.
Spektrum Akademischer Verlag, 2006.
ieee: H. L. Janovjak and D. Mueller, “Rastersondenmikroskopie,” in Bioanalytik,
Spektrum Akademischer Verlag, 2006.
ista: 'Janovjak HL, Mueller D. 2006.Rastersondenmikroskopie. In: Bioanalytik. .'
mla: Janovjak, Harald L., and Daniel Mueller. “Rastersondenmikroskopie.” Bioanalytik,
Spektrum Akademischer Verlag, 2006.
short: H.L. Janovjak, D. Mueller, in:, Bioanalytik, Spektrum Akademischer Verlag,
2006.
date_created: 2018-12-11T12:04:48Z
date_published: 2006-06-16T00:00:00Z
date_updated: 2021-01-12T07:51:44Z
day: '16'
extern: 1
month: '06'
publication: Bioanalytik
publication_status: published
publisher: Spektrum Akademischer Verlag
publist_id: '2508'
quality_controlled: 0
status: public
title: Rastersondenmikroskopie
type: book_chapter
year: '2006'
...
---
_id: '3755'
abstract:
- lang: eng
text: A primitive example of adaptation in gene expression is the balance between
the rate of synthesis and degradation of cellular RNA, which allows rapid responses
to environmental signals. Here, we investigate how multidrug efflux pump systems
mediate the dynamics of a simple drug-inducible system in response to a steady
level of inducer. Using fluorescence correlation spectroscopy, we measured in
real time within a single bacterium the transcription activity at the RNA level
of the acrAB-TolC multidrug efflux pump system. When cells are exposed to constant
level of anhydrotetracycline inducer and are adsorbed onto a poly-L-lysine-coated
surface, we found that the acrAB-TolC promoter is steadily active. We also monitored
the activity of the tet promoter to characterize the effect of this efflux system
on the dynamics of drug-inducible transcription. We found that the transcriptional
response of the tet promoter to a steady level of aTc rises and then falls back
to its preinduction level. The rate of RNA degradation was constant throughout
the transcriptional pulse, indicating that the modulation of intracellular inducer
concentration alone can produce this pulsating response. Single-cell experiments
together with numerical simulations suggest that such pulsating response in drug-inducible
genetic systems is a property emerging from the dependence of drug-inducible transcription
on multidrug efflux systems.
author:
- first_name: Thuc
full_name: Le,Thuc T.
last_name: Le
- first_name: Thierry
full_name: Emonet,Thierry
last_name: Emonet
- first_name: Sébastien
full_name: Harlepp, Sébastien
last_name: Harlepp
- first_name: Calin C
full_name: Calin Guet
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Philippe
full_name: Cluzel,Philippe
last_name: Cluzel
citation:
ama: Le T, Emonet T, Harlepp S, Guet CC, Cluzel P. Dynamical determinants of drug-inducible
gene expression in a single bacterium. Biophysical Journal. 2006;90(9):3315-3321.
doi:10.1529/biophysj.105.073353
apa: Le, T., Emonet, T., Harlepp, S., Guet, C. C., & Cluzel, P. (2006). Dynamical
determinants of drug-inducible gene expression in a single bacterium. Biophysical
Journal. Biophysical Society. https://doi.org/10.1529/biophysj.105.073353
chicago: Le, Thuc, Thierry Emonet, Sébastien Harlepp, Calin C Guet, and Philippe
Cluzel. “Dynamical Determinants of Drug-Inducible Gene Expression in a Single
Bacterium.” Biophysical Journal. Biophysical Society, 2006. https://doi.org/10.1529/biophysj.105.073353.
ieee: T. Le, T. Emonet, S. Harlepp, C. C. Guet, and P. Cluzel, “Dynamical determinants
of drug-inducible gene expression in a single bacterium,” Biophysical Journal,
vol. 90, no. 9. Biophysical Society, pp. 3315–3321, 2006.
ista: Le T, Emonet T, Harlepp S, Guet CC, Cluzel P. 2006. Dynamical determinants
of drug-inducible gene expression in a single bacterium. Biophysical Journal.
90(9), 3315–3321.
mla: Le, Thuc, et al. “Dynamical Determinants of Drug-Inducible Gene Expression
in a Single Bacterium.” Biophysical Journal, vol. 90, no. 9, Biophysical
Society, 2006, pp. 3315–21, doi:10.1529/biophysj.105.073353.
short: T. Le, T. Emonet, S. Harlepp, C.C. Guet, P. Cluzel, Biophysical Journal 90
(2006) 3315–3321.
date_created: 2018-12-11T12:04:59Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:51:58Z
day: '01'
doi: 10.1529/biophysj.105.073353
extern: 1
intvolume: ' 90'
issue: '9'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1432126/
month: '01'
oa: 1
page: 3315 - 3321
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '2472'
quality_controlled: 0
status: public
title: Dynamical determinants of drug-inducible gene expression in a single bacterium
type: journal_article
volume: 90
year: '2006'
...
---
_id: '3758'
abstract:
- lang: eng
text: Control of physical simulation has become a popular topic in the field of
computer graphics. Keyframe control has been applied to simulations of rigid bodies,
smoke, liquid, flocks, and finite element-based elastic bodies. In this paper,
we create a framework for controlling systems of interacting particles -- paying
special attention to simulations of cloth and flocking behavior. We introduce
a novel integrator-swapping approximation in order to apply the adjoint method
to linearized implicit schemes appropriate for cloth simulation. This allows the
control of cloth while avoiding computationally infeasible derivative calculations.
Meanwhile, flocking control using the adjoint method is significantly more efficient
than currently-used methods for constraining group behaviors, allowing the controlled
simulation of greater numbers of agents in fewer optimization iterations.
article_processing_charge: No
author:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Peter
full_name: Mucha, Peter
last_name: Mucha
- first_name: Greg
full_name: Turk, Greg
last_name: Turk
citation:
ama: 'Wojtan C, Mucha P, Turk G. Keyframe control of complex particle systems using
the adjoint method. In: ACM; 2006:15-23.'
apa: 'Wojtan, C., Mucha, P., & Turk, G. (2006). Keyframe control of complex
particle systems using the adjoint method (pp. 15–23). Presented at the SCA: ACM
SIGGRAPH/Eurographics Symposium on Computer animation, ACM.'
chicago: Wojtan, Chris, Peter Mucha, and Greg Turk. “Keyframe Control of Complex
Particle Systems Using the Adjoint Method,” 15–23. ACM, 2006.
ieee: 'C. Wojtan, P. Mucha, and G. Turk, “Keyframe control of complex particle systems
using the adjoint method,” presented at the SCA: ACM SIGGRAPH/Eurographics Symposium
on Computer animation, 2006, pp. 15–23.'
ista: 'Wojtan C, Mucha P, Turk G. 2006. Keyframe control of complex particle systems
using the adjoint method. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer
animation, 15–23.'
mla: Wojtan, Chris, et al. Keyframe Control of Complex Particle Systems Using
the Adjoint Method. ACM, 2006, pp. 15–23.
short: C. Wojtan, P. Mucha, G. Turk, in:, ACM, 2006, pp. 15–23.
conference:
name: 'SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation'
date_created: 2018-12-11T12:05:00Z
date_published: 2006-09-01T00:00:00Z
date_updated: 2023-02-23T11:41:22Z
day: '01'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://www.amath.unc.edu/Faculty/mucha/Reprints/SCAclothcontrolpreprint.pdf
month: '09'
oa_version: None
page: 15 - 23
publication_status: published
publisher: ACM
publist_id: '2469'
status: public
title: Keyframe control of complex particle systems using the adjoint method
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2006'
...
---
_id: '3818'
abstract:
- lang: eng
text: Rigorous analysis of synaptic transmission in the central nervous system requires
access to presynaptic terminals. However, cortical terminals have been largely
inaccessible to presynaptic patch-clamp recording, due to their small size. Using
improved patch-clamp techniques in brain slices, we recorded from mossy fiber
terminals in the CA3 region of the hippocampus, which have a diameter of 2-5 microm.
The major steps of improvement were the enhanced visibility provided by high-numerical
aperture objectives and infrared illumination, the development of vibratomes with
minimal vertical blade vibrations and the use of sucrose-based solutions for storage
and cutting. Based on these improvements, we describe a protocol that allows us
to routinely record from hippocampal mossy fiber boutons. Presynaptic recordings
can be obtained in slices from both rats and mice. Presynaptic recordings can
be also obtained in slices from transgenic mice in which terminals are labeled
with enhanced green fluorescent protein.
author:
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
- first_name: Dominique
full_name: Engel, Dominique
last_name: Engel
- first_name: Liyi
full_name: Li, Liyi
last_name: Li
- first_name: Jörg
full_name: Geiger, Jörg R
last_name: Geiger
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Bischofberger J, Engel D, Li L, Geiger J, Jonas PM. Patch-clamp recording from
mossy fiber terminals in hippocampal slices. Nature Protocols. 2006;1(4):2075-2081.
doi:10.1038/nprot.2006.312
apa: Bischofberger, J., Engel, D., Li, L., Geiger, J., & Jonas, P. M. (2006).
Patch-clamp recording from mossy fiber terminals in hippocampal slices. Nature
Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.312
chicago: Bischofberger, Josef, Dominique Engel, Liyi Li, Jörg Geiger, and Peter
M Jonas. “Patch-Clamp Recording from Mossy Fiber Terminals in Hippocampal Slices.”
Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.312 .
ieee: J. Bischofberger, D. Engel, L. Li, J. Geiger, and P. M. Jonas, “Patch-clamp
recording from mossy fiber terminals in hippocampal slices,” Nature Protocols,
vol. 1, no. 4. Nature Publishing Group, pp. 2075–81, 2006.
ista: Bischofberger J, Engel D, Li L, Geiger J, Jonas PM. 2006. Patch-clamp recording
from mossy fiber terminals in hippocampal slices. Nature Protocols. 1(4), 2075–81.
mla: Bischofberger, Josef, et al. “Patch-Clamp Recording from Mossy Fiber Terminals
in Hippocampal Slices.” Nature Protocols, vol. 1, no. 4, Nature Publishing
Group, 2006, pp. 2075–81, doi:10.1038/nprot.2006.312 .
short: J. Bischofberger, D. Engel, L. Li, J. Geiger, P.M. Jonas, Nature Protocols
1 (2006) 2075–81.
date_created: 2018-12-11T12:05:20Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:25Z
day: '01'
doi: '10.1038/nprot.2006.312 '
extern: 1
intvolume: ' 1'
issue: '4'
month: '01'
page: 2075 - 81
publication: Nature Protocols
publication_status: published
publisher: Nature Publishing Group
publist_id: '2392'
quality_controlled: 0
status: public
title: Patch-clamp recording from mossy fiber terminals in hippocampal slices
type: journal_article
volume: 1
year: '2006'
...
---
_id: '3890'
abstract:
- lang: eng
text: We consider two-player infinite games played on graphs. The games are concurrent,
in that at each state the players choose their moves simultaneously and independently,
and stochastic, in that the moves determine a probability distribution for the
successor state. The value of a game is the maximal probability with which a player
can guarantee the satisfaction of her objective. We show that the values of concurrent
games with w-regular objectives expressed as parity conditions can be decided
in NP boolean AND coNP. This result substantially improves the best known previous
bound of 3EXPTIME. It also shows that the full class of concurrent parity games
is no harder than the special case of turn-based stochastic reachability games,
for which NP boolean AND coNP is the best known bound. While the previous, more
restricted NP boolean AND coNP results for graph games relied on the existence
of particularly simple (pure memoryless) optimal strategies, in concurrent games
with parity objectives optimal strategies may not exist, and epsilon-optimal strategies
(which achieve the value of the game within a parameter epsilon > 0) require
in general both randomization and infinite memory. Hence our proof must rely on
a more detailed analysis of strategies and, in addition to the main result, yields
two results that are interesting on their own. First, we show that there exist
epsilon-optimal strategies that in the limit coincide with memoryless strategies;
this parallels the celebrated result of Mertens-Neyman for concurrent games with
limit-average objectives. Second, we complete the characterization of the memory
requirements for epsilon-optimal strategies for concurrent games with parity conditions,
by showing that memoryless strategies suffice for epsilon-optimality for coBachi
conditions.
acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327
and the NSF ITR grant CCR-0225610.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Luca
full_name: de Alfaro, Luca
last_name: De Alfaro
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Chatterjee K, De Alfaro L, Henzinger TA. The complexity of quantitative concurrent
parity games. In: SIAM; 2006:678-687. doi:10.1145/1109557.1109631'
apa: 'Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2006). The complexity
of quantitative concurrent parity games (pp. 678–687). Presented at the SODA:
Symposium on Discrete Algorithms, SIAM. https://doi.org/10.1145/1109557.1109631'
chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “The Complexity
of Quantitative Concurrent Parity Games,” 678–87. SIAM, 2006. https://doi.org/10.1145/1109557.1109631.
ieee: 'K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “The complexity of quantitative
concurrent parity games,” presented at the SODA: Symposium on Discrete Algorithms,
2006, pp. 678–687.'
ista: 'Chatterjee K, De Alfaro L, Henzinger TA. 2006. The complexity of quantitative
concurrent parity games. SODA: Symposium on Discrete Algorithms, 678–687.'
mla: Chatterjee, Krishnendu, et al. The Complexity of Quantitative Concurrent
Parity Games. SIAM, 2006, pp. 678–87, doi:10.1145/1109557.1109631.
short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, SIAM, 2006, pp. 678–687.
conference:
name: 'SODA: Symposium on Discrete Algorithms'
date_created: 2018-12-11T12:05:43Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:59Z
day: '01'
doi: 10.1145/1109557.1109631
extern: 1
month: '01'
page: 678 - 687
publication_status: published
publisher: SIAM
publist_id: '2273'
quality_controlled: 0
status: public
title: The complexity of quantitative concurrent parity games
type: conference
year: '2006'
...
---
_id: '3889'
abstract:
- lang: eng
text: We study observation-based strategies for two-player turn-based games on graphs
with omega-regular objectives. An observation-based strategy relies on imperfect
information about the history of a play, namely, on the past sequence of observations.
Such games occur in the synthesis of a controller that does not see the private
state of the plant. Our main results are twofold. First, we give a fixed-point
algorithm for computing the set of states from which a player can win with a deterministic
observation-based strategy for any omega-regular objective. The fixed point is
computed in the lattice of antichains of state sets. This algorithm has the advantages
of being directed by the objective and of avoiding an explicit subset construction
on the game graph. Second, we give an algorithm for computing the set of states
from which a player can win with probability 1 with a randomized observation-based
strategy for a Buchi objective. This set is of interest because in the absence
of perfect information, randomized strategies are more powerful than deterministic
ones. We show that our algorithms are optimal by proving matching lower bounds.
acknowledgement: This research was supported in part by the NSF grants CCR-0225610
and CCR-0234690, by the SNSF under the Indo-Swiss Joint Research Programme, and
by the FRFC project “Centre Fédéré en Vérification” funded by the FNRS under grant
2.4530.02.
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: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jean
full_name: Raskin, Jean-François
last_name: Raskin
citation:
ama: 'Chatterjee K, Doyen L, Henzinger TA, Raskin J. Algorithms for omega-regular
games with imperfect information. In: Vol 4207. Springer; 2006:287-302. doi:10.1007/11874683_19'
apa: 'Chatterjee, K., Doyen, L., Henzinger, T. A., & Raskin, J. (2006). Algorithms
for omega-regular games with imperfect information (Vol. 4207, pp. 287–302). Presented
at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_19'
chicago: Chatterjee, Krishnendu, Laurent Doyen, Thomas A Henzinger, and Jean Raskin.
“Algorithms for Omega-Regular Games with Imperfect Information,” 4207:287–302.
Springer, 2006. https://doi.org/10.1007/11874683_19.
ieee: 'K. Chatterjee, L. Doyen, T. A. Henzinger, and J. Raskin, “Algorithms for
omega-regular games with imperfect information,” presented at the CSL: Computer
Science Logic, 2006, vol. 4207, pp. 287–302.'
ista: 'Chatterjee K, Doyen L, Henzinger TA, Raskin J. 2006. Algorithms for omega-regular
games with imperfect information. CSL: Computer Science Logic, LNCS, vol. 4207,
287–302.'
mla: Chatterjee, Krishnendu, et al. Algorithms for Omega-Regular Games with Imperfect
Information. Vol. 4207, Springer, 2006, pp. 287–302, doi:10.1007/11874683_19.
short: K. Chatterjee, L. Doyen, T.A. Henzinger, J. Raskin, in:, Springer, 2006,
pp. 287–302.
conference:
name: 'CSL: Computer Science Logic'
date_created: 2018-12-11T12:05:43Z
date_published: 2006-11-13T00:00:00Z
date_updated: 2021-01-12T07:52:59Z
day: '13'
doi: 10.1007/11874683_19
extern: 1
intvolume: ' 4207'
month: '11'
page: 287 - 302
publication_status: published
publisher: Springer
publist_id: '2276'
quality_controlled: 0
status: public
title: Algorithms for omega-regular games with imperfect information
type: conference
volume: 4207
year: '2006'
...
---
_id: '3891'
abstract:
- lang: eng
text: 'We study infinite stochastic games played by two-players over a finite state
space, with objectives specified by sets of infinite traces. The games are concurrent
(players make moves simultaneously and independently), stochastic (the next state
is determined by a probability distribution that depends on the current state
and chosen moves of the players) and infinite (proceeds for infinite number of
rounds). The analysis of concurrent stochastic games can be classified into: quantitative
analysis, analyzing the optimum value of the game; and qualitative analysis, analyzing
the set of states with optimum value 1. We consider concurrent games with tail
objectives, i.e., objectives that are independent of the finite-prefix of traces,
and show that the class of tail objectives are strictly richer than the omega-regular
objectives. We develop new proof techniques to extend several properties of concurrent
games with omega-regular objectives to concurrent games with tail objectives.
We prove the positive limit-one property for tail objectives, that states for
all concurrent games if the optimum value for a player is positive for a tail
objective Phi at some state, then there is a state where the optimum value is
1 for Phi, for the player. We also show that the optimum values of zero-sum (strictly
conflicting objectives) games with tail objectives can be related to equilibrium
values of nonzero-sum (not strictly conflicting objectives) games with simpler
reachability objectives. A consequence of our analysis presents a polynomial time
reduction of the quantitative analysis of tail objectives to the qualitative analysis
for the sub-class of one-player stochastic games (Markov decision processes).'
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
citation:
ama: 'Chatterjee K. Concurrent games with tail objectives. In: Vol 4207. Springer;
2006:256-270. doi:10.1007/11874683_17'
apa: 'Chatterjee, K. (2006). Concurrent games with tail objectives (Vol. 4207, pp.
256–270). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_17'
chicago: Chatterjee, Krishnendu. “Concurrent Games with Tail Objectives,” 4207:256–70.
Springer, 2006. https://doi.org/10.1007/11874683_17.
ieee: 'K. Chatterjee, “Concurrent games with tail objectives,” presented at the
CSL: Computer Science Logic, 2006, vol. 4207, pp. 256–270.'
ista: 'Chatterjee K. 2006. Concurrent games with tail objectives. CSL: Computer
Science Logic, LNCS , vol. 4207, 256–270.'
mla: Chatterjee, Krishnendu. Concurrent Games with Tail Objectives. Vol.
4207, Springer, 2006, pp. 256–70, doi:10.1007/11874683_17.
short: K. Chatterjee, in:, Springer, 2006, pp. 256–270.
conference:
name: 'CSL: Computer Science Logic'
date_created: 2018-12-11T12:05:44Z
date_published: 2006-09-28T00:00:00Z
date_updated: 2021-01-12T07:53:00Z
day: '28'
doi: 10.1007/11874683_17
extern: 1
intvolume: ' 4207'
month: '09'
page: 256 - 270
publication_status: published
publisher: Springer
publist_id: '2272'
quality_controlled: 0
status: public
title: Concurrent games with tail objectives
type: conference
volume: 4207
year: '2006'
...
---
_id: '3888'
abstract:
- lang: eng
text: A stochastic graph game is played by two players on a game graph with probabilistic
transitions. We consider stochastic graph games with omega-regular winning conditions
specified as Rabin or Streett objectives. These games are NP-complete and coNP-complete,
respectively. The value of the game for a player at a state s given an objective
Phi is the maximal probability with which the player can guarantee the satisfaction
of Phi from s. We present a strategy-improvement algorithm to compute values in
stochastic Rabin games, where an improvement step involves solving Markov decision
processes (MDPs) and nonstochastic Rabin games. The algorithm also computes values
for stochastic Streett games but does not directly yield an optimal strategy for
Streett objectives. We then show how to obtain an optimal strategy for Streett
objectives by solving certain nonstochastic Streett games.
acknowledgement: This research was supported in part by the NSF grants CCR-0225610
and CCR-0234690, and by the SNSF under the Indo-Swiss Joint Research Programme.
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
citation:
ama: 'Chatterjee K, Henzinger TA. Strategy improvement for stochastic Rabin and
Streett games. In: Vol 4137. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2006:375-389. doi:10.1007/11817949_25'
apa: 'Chatterjee, K., & Henzinger, T. A. (2006). Strategy improvement for stochastic
Rabin and Streett games (Vol. 4137, pp. 375–389). Presented at the CONCUR: Concurrency
Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/11817949_25'
chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Strategy Improvement for
Stochastic Rabin and Streett Games,” 4137:375–89. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2006. https://doi.org/10.1007/11817949_25.
ieee: 'K. Chatterjee and T. A. Henzinger, “Strategy improvement for stochastic Rabin
and Streett games,” presented at the CONCUR: Concurrency Theory, 2006, vol. 4137,
pp. 375–389.'
ista: 'Chatterjee K, Henzinger TA. 2006. Strategy improvement for stochastic Rabin
and Streett games. CONCUR: Concurrency Theory, LNCS, vol. 4137, 375–389.'
mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. Strategy Improvement for
Stochastic Rabin and Streett Games. Vol. 4137, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2006, pp. 375–89, doi:10.1007/11817949_25.
short: K. Chatterjee, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2006, pp. 375–389.
conference:
name: 'CONCUR: Concurrency Theory'
date_created: 2018-12-11T12:05:43Z
date_published: 2006-08-10T00:00:00Z
date_updated: 2021-01-12T07:52:58Z
day: '10'
doi: 10.1007/11817949_25
extern: 1
intvolume: ' 4137'
month: '08'
page: 375 - 389
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '2278'
quality_controlled: 0
status: public
title: Strategy improvement for stochastic Rabin and Streett games
type: conference
volume: 4137
year: '2006'
...
---
_id: '3908'
abstract:
- lang: eng
text: 'It is commonly believed that both the average length and the frequency of
microsatellites correlate with genome size. We have estimated the frequency and
the average length for 69 perfect dinucleotide microsatellites in an insect with
an exceptionally large genome: Chorthippus biguttulus (Orthoptera, Acrididae).
Dinucleotide microsatellites are not more frequent in C. biguttulus, but repeat
arrays are 1.4 to 2 times longer than in other insect species. The average repeat
number in C. biguttulus lies in the range of higher vertebrates. Natural populations
are highly variable. At least 30 alleles per locus were found and the expected
heterozygosity is above 0.95 at all three loci studied. In contrast, the observed
heterozygosity is much lower (≤0.51), which could be caused by long null alleles.'
author:
- first_name: Jana
full_name: Ustinova, Jana
last_name: Ustinova
- first_name: Roland
full_name: Achmann, Roland
last_name: Achmann
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Frieder
full_name: Mayer, Frieder
last_name: Mayer
citation:
ama: 'Ustinova J, Achmann R, Cremer S, Mayer F. Long repeats in a huge gemome: microsatellite
loci in the grasshopper Chorthippus biguttulus. Journal of Molecular Evolution.
2006;62(2):158-167. doi:10.1007/s00239-005-0022-6'
apa: 'Ustinova, J., Achmann, R., Cremer, S., & Mayer, F. (2006). Long repeats
in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus.
Journal of Molecular Evolution. Springer. https://doi.org/10.1007/s00239-005-0022-6'
chicago: 'Ustinova, Jana, Roland Achmann, Sylvia Cremer, and Frieder Mayer. “Long
Repeats in a Huge Gemome: Microsatellite Loci in the Grasshopper Chorthippus Biguttulus.”
Journal of Molecular Evolution. Springer, 2006. https://doi.org/10.1007/s00239-005-0022-6.'
ieee: 'J. Ustinova, R. Achmann, S. Cremer, and F. Mayer, “Long repeats in a huge
gemome: microsatellite loci in the grasshopper Chorthippus biguttulus,” Journal
of Molecular Evolution, vol. 62, no. 2. Springer, pp. 158–167, 2006.'
ista: 'Ustinova J, Achmann R, Cremer S, Mayer F. 2006. Long repeats in a huge gemome:
microsatellite loci in the grasshopper Chorthippus biguttulus. Journal of Molecular
Evolution. 62(2), 158–167.'
mla: 'Ustinova, Jana, et al. “Long Repeats in a Huge Gemome: Microsatellite Loci
in the Grasshopper Chorthippus Biguttulus.” Journal of Molecular Evolution,
vol. 62, no. 2, Springer, 2006, pp. 158–67, doi:10.1007/s00239-005-0022-6.'
short: J. Ustinova, R. Achmann, S. Cremer, F. Mayer, Journal of Molecular Evolution
62 (2006) 158–167.
date_created: 2018-12-11T12:05:49Z
date_published: 2006-02-01T00:00:00Z
date_updated: 2021-01-12T07:53:07Z
day: '01'
doi: 10.1007/s00239-005-0022-6
extern: '1'
intvolume: ' 62'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 158 - 167
publication: Journal of Molecular Evolution
publication_status: published
publisher: Springer
publist_id: '2242'
status: public
title: 'Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus
biguttulus'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 62
year: '2006'
...
---
_id: '3934'
abstract:
- lang: eng
text: T cells develop in the thymus in a highly specialized cellular and extracellular
microenvironment. The basement membrane molecule, laminin-5 (LN-5), is predominantly
found in the medulla of the human thymic lobules. Using high-resolution light
microscopy, we show here that LN-5 is localized in a bi-membranous conduit-like
structure, together with other typical basement membrane components including
collagen type IV, nidogen and perlecan. Other interstitial matrix components,
such as fibrillin-1 or -2, tenascin-C or fibrillar collagen types, were also associated
with these structures. Three-dimensional (3D) confocal microscopy suggested a
tubular structure, whereas immunoelectron and transmission electron microscopy
showed that the core of these tubes contained fibrillar collagens enwrapped by
the LN-5-containing membrane. These medullary conduits are surrounded by thymic
epithelial cells, which in vitro were found to bind LN-5, but also fibrillin and
tenascin-C. Dendritic cells were also detected in close vicinity to the conduits.
Both of these stromal cell types express major histocompatibility complex (MHC)
class II molecules capable of antigen presentation. The conduits are connected
to blood vessels but, with an average diameter of 2 mum, they are too small to
transport cells. However, evidence is provided that smaller molecules such as
a 10 kDa dextran, but not large molecules (>500 kDa), can be transported in
the conduits. These results clearly demonstrate that a conduit system, which is
also known from secondary lymphatic organs such as lymph nodes and spleen, is
present in the medulla of the human thymus, and that it might serve to transport
small blood-borne molecules or chemokines to defined locations within the medulla.
author:
- first_name: Mihaela
full_name: Drumea-Mirancea, Mihaela
last_name: Drumea Mirancea
- first_name: Johannes
full_name: Wessels, Johannes T
last_name: Wessels
- first_name: Claudia
full_name: Müller, Claudia A
last_name: Müller
- first_name: Mike
full_name: Essl, Mike
last_name: Essl
- first_name: Johannes
full_name: Eble, Johannes A
last_name: Eble
- first_name: Eva
full_name: Tolosa, Eva
last_name: Tolosa
- first_name: Manuel
full_name: Koch, Manuel
last_name: Koch
- first_name: Dieter
full_name: Reinhardt, Dieter P
last_name: Reinhardt
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Lydia
full_name: Sorokin, Lydia
last_name: Sorokin
- first_name: York
full_name: Stierhof, York-Dieter
last_name: Stierhof
- first_name: Heinz
full_name: Schwarz, Heinz
last_name: Schwarz
- first_name: Gerd
full_name: Klein, Gerd
last_name: Klein
citation:
ama: 'Drumea Mirancea M, Wessels J, Müller C, et al. Characterization of a conduit
system containing laminin-5 in the human thymus: a potential transport system
for small molecules. Journal of Cell Science. 2006;119(Pt 7):1396-1405.
doi:10.1242/jcs.02840'
apa: 'Drumea Mirancea, M., Wessels, J., Müller, C., Essl, M., Eble, J., Tolosa,
E., … Klein, G. (2006). Characterization of a conduit system containing laminin-5
in the human thymus: a potential transport system for small molecules. Journal
of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.02840'
chicago: 'Drumea Mirancea, Mihaela, Johannes Wessels, Claudia Müller, Mike Essl,
Johannes Eble, Eva Tolosa, Manuel Koch, et al. “Characterization of a Conduit
System Containing Laminin-5 in the Human Thymus: A Potential Transport System
for Small Molecules.” Journal of Cell Science. Company of Biologists, 2006.
https://doi.org/10.1242/jcs.02840.'
ieee: 'M. Drumea Mirancea et al., “Characterization of a conduit system containing
laminin-5 in the human thymus: a potential transport system for small molecules,”
Journal of Cell Science, vol. 119, no. Pt 7. Company of Biologists, pp.
1396–1405, 2006.'
ista: 'Drumea Mirancea M, Wessels J, Müller C, Essl M, Eble J, Tolosa E, Koch M,
Reinhardt D, Sixt MK, Sorokin L, Stierhof Y, Schwarz H, Klein G. 2006. Characterization
of a conduit system containing laminin-5 in the human thymus: a potential transport
system for small molecules. Journal of Cell Science. 119(Pt 7), 1396–1405.'
mla: 'Drumea Mirancea, Mihaela, et al. “Characterization of a Conduit System Containing
Laminin-5 in the Human Thymus: A Potential Transport System for Small Molecules.”
Journal of Cell Science, vol. 119, no. Pt 7, Company of Biologists, 2006,
pp. 1396–405, doi:10.1242/jcs.02840.'
short: M. Drumea Mirancea, J. Wessels, C. Müller, M. Essl, J. Eble, E. Tolosa, M.
Koch, D. Reinhardt, M.K. Sixt, L. Sorokin, Y. Stierhof, H. Schwarz, G. Klein,
Journal of Cell Science 119 (2006) 1396–1405.
date_created: 2018-12-11T12:05:58Z
date_published: 2006-04-01T00:00:00Z
date_updated: 2021-01-12T07:53:18Z
day: '01'
doi: 10.1242/jcs.02840
extern: 1
intvolume: ' 119'
issue: Pt 7
month: '04'
page: 1396 - 1405
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '2192'
quality_controlled: 0
status: public
title: 'Characterization of a conduit system containing laminin-5 in the human thymus:
a potential transport system for small molecules'
type: journal_article
volume: 119
year: '2006'
...
---
_id: '3935'
abstract:
- lang: eng
text: Integrins regulate cell behavior through the assembly of multiprotein complexes
at the site of cell adhesion. Parvins are components of such a multiprotein complex.
They consist of three members (alpha-, beta-, and gamma-parvin), form a functional
complex with integrin-linked kinase (ILK) and PINCH, and link integrins to the
actin cytoskeleton. Whereas alpha- and beta-parvins are widely expressed, gamma-parvin
has been reported to be expressed in hematopoietic organs. In the present study,
we report the expression pattern of the parvins in hematopoietic cells and the
phenotypic analysis of gamma-parvin-deficient mice. Whereas alpha-parvin is not
expressed in hematopoietic cells, beta-parvin is only found in myeloid cells and
gamma-parvin is present in both cells of the myeloid and lymphoid lineages, where
it binds ILK. Surprisingly, loss of gamma-parvin expression had no effect on blood
cell differentiation, proliferation, and survival and no consequence for the T-cell-dependent
antibody response and lymphocyte and dendritic cell migration. These data indicate
that despite the high expression of gamma-parvin in hematopoietic cells it must
play a more subtle role for blood cell homeostasis.
author:
- first_name: Haiyan
full_name: Chu, Haiyan
last_name: Chu
- first_name: Ingo
full_name: Thievessen, Ingo
last_name: Thievessen
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Ari
full_name: Waisman, Ari
last_name: Waisman
- first_name: Attila
full_name: Braun, Attila
last_name: Braun
- first_name: Angelika
full_name: Noegel, Angelika A
last_name: Noegel
- first_name: Reinhard
full_name: Fässler, Reinhard
last_name: Fässler
citation:
ama: Chu H, Thievessen I, Sixt MK, et al. γ-Parvin is dispensable for hematopoiesis,
leukocyte trafficking, and T-cell-dependent antibody response. Molecular and
Cellular Biology. 2006;26(5):1817-1825. doi:10.1128/MCB.26.5.1817-1825.2006
apa: Chu, H., Thievessen, I., Sixt, M. K., Lämmermann, T., Waisman, A., Braun, A.,
… Fässler, R. (2006). γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking,
and T-cell-dependent antibody response. Molecular and Cellular Biology.
American Society for Microbiology. https://doi.org/10.1128/MCB.26.5.1817-1825.2006
chicago: Chu, Haiyan, Ingo Thievessen, Michael K Sixt, Tim Lämmermann, Ari Waisman,
Attila Braun, Angelika Noegel, and Reinhard Fässler. “γ-Parvin Is Dispensable
for Hematopoiesis, Leukocyte Trafficking, and T-Cell-Dependent Antibody Response.”
Molecular and Cellular Biology. American Society for Microbiology, 2006.
https://doi.org/10.1128/MCB.26.5.1817-1825.2006.
ieee: H. Chu et al., “γ-Parvin is dispensable for hematopoiesis, leukocyte
trafficking, and T-cell-dependent antibody response,” Molecular and Cellular
Biology, vol. 26, no. 5. American Society for Microbiology, pp. 1817–1825,
2006.
ista: Chu H, Thievessen I, Sixt MK, Lämmermann T, Waisman A, Braun A, Noegel A,
Fässler R. 2006. γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking,
and T-cell-dependent antibody response. Molecular and Cellular Biology. 26(5),
1817–1825.
mla: Chu, Haiyan, et al. “γ-Parvin Is Dispensable for Hematopoiesis, Leukocyte Trafficking,
and T-Cell-Dependent Antibody Response.” Molecular and Cellular Biology,
vol. 26, no. 5, American Society for Microbiology, 2006, pp. 1817–25, doi:10.1128/MCB.26.5.1817-1825.2006.
short: H. Chu, I. Thievessen, M.K. Sixt, T. Lämmermann, A. Waisman, A. Braun, A.
Noegel, R. Fässler, Molecular and Cellular Biology 26 (2006) 1817–1825.
date_created: 2018-12-11T12:05:58Z
date_published: 2006-03-01T00:00:00Z
date_updated: 2021-01-12T07:53:18Z
day: '01'
doi: 10.1128/MCB.26.5.1817-1825.2006
extern: 1
intvolume: ' 26'
issue: '5'
month: '03'
page: 1817 - 1825
publication: Molecular and Cellular Biology
publication_status: published
publisher: American Society for Microbiology
publist_id: '2193'
quality_controlled: 0
status: public
title: γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent
antibody response
type: journal_article
volume: 26
year: '2006'
...
---
_id: '3936'
abstract:
- lang: eng
text: At least eight of the twelve known members of the beta1 integrin family are
expressed on hematopoietic cells. Among these, the VCAM-1 receptor alpha4beta1
has received most attention as a main factor mediating firm adhesion to the endothelium
during blood cell extravasation. Therapeutic trials are ongoing into the use of
antibodies and small molecule inhibitors to target this interaction and hence
obtain anti-inflammatory effects. However, extravasation is only one possible
process that is mediated by beta1 integrins and there is evidence that they also
mediate leukocyte retention and positioning in the tissue, lymphocyte activation
and possibly migration within the interstitium. Genetic mouse models where integrins
are selectively deleted on blood cells have been used to investigate these functions
and further studies will be invaluable to critically evaluate therapeutic trials.
author:
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Martina
full_name: Bauer, Martina
last_name: Bauer
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Reinhard
full_name: Fässler, Reinhard
last_name: Fässler
citation:
ama: 'Sixt MK, Bauer M, Lämmermann T, Fässler R. β1 integrins: zip codes and signaling
relay for blood cells. Current Opinion in Cell Biology. 2006;18(5):482-490.
doi:10.1016/j.ceb.2006.08.007'
apa: 'Sixt, M. K., Bauer, M., Lämmermann, T., & Fässler, R. (2006). β1 integrins:
zip codes and signaling relay for blood cells. Current Opinion in Cell Biology.
Elsevier. https://doi.org/10.1016/j.ceb.2006.08.007'
chicago: 'Sixt, Michael K, Martina Bauer, Tim Lämmermann, and Reinhard Fässler.
“Β1 Integrins: Zip Codes and Signaling Relay for Blood Cells.” Current Opinion
in Cell Biology. Elsevier, 2006. https://doi.org/10.1016/j.ceb.2006.08.007.'
ieee: 'M. K. Sixt, M. Bauer, T. Lämmermann, and R. Fässler, “β1 integrins: zip codes
and signaling relay for blood cells,” Current Opinion in Cell Biology,
vol. 18, no. 5. Elsevier, pp. 482–490, 2006.'
ista: 'Sixt MK, Bauer M, Lämmermann T, Fässler R. 2006. β1 integrins: zip codes
and signaling relay for blood cells. Current Opinion in Cell Biology. 18(5), 482–490.'
mla: 'Sixt, Michael K., et al. “Β1 Integrins: Zip Codes and Signaling Relay for
Blood Cells.” Current Opinion in Cell Biology, vol. 18, no. 5, Elsevier,
2006, pp. 482–90, doi:10.1016/j.ceb.2006.08.007.'
short: M.K. Sixt, M. Bauer, T. Lämmermann, R. Fässler, Current Opinion in Cell Biology
18 (2006) 482–490.
date_created: 2018-12-11T12:05:59Z
date_published: 2006-10-01T00:00:00Z
date_updated: 2021-01-12T07:53:19Z
day: '01'
doi: 10.1016/j.ceb.2006.08.007
extern: 1
intvolume: ' 18'
issue: '5'
month: '10'
page: 482 - 490
publication: Current Opinion in Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '2191'
quality_controlled: 0
status: public
title: 'β1 integrins: zip codes and signaling relay for blood cells'
type: journal_article
volume: 18
year: '2006'
...
---
_id: '4140'
abstract:
- lang: eng
text: Wnt11 is a key signal, determining cell polarization and migration during
vertebrate gastrulation. It is known that Wnt11 functionally interacts with several
signaling components, the homologues of which control planar cell polarity in
Drosophila melanogaster. Although in D. melanogaster these components are thought
to polarize cells by asymmetrically localizing at the plasma membrane, it is not
yet clear whether their subcellular localization plays a similarly important role
in vertebrates. We show that in zebrafish embryonic cells, Wnt11 locally functions
at the plasma membrane by accumulating its receptor, Frizzled 7, on adjacent sites
of cell contacts. Wnt11-induced Frizzled 7 accumulations recruit the intracellular
Wnt signaling mediator Dishevelled, as well as Wnt11 itself, and locally increase
cell contact persistence. This increase in cell contact persistence is mediated
by the local interaction of Wnt11, Frizzled 7, and the atypical cadherin Flamingo
at the plasma membrane, and it does not require the activity of further downstream
effectors of Wnt11 signaling, such as RhoA and Rok2. We propose that Wnt11, by
interacting with Frizzled 7 and Flamingo, modulates local cell contact persistence
to coordinate cell movements during gastrulation.
article_processing_charge: No
author:
- first_name: Sabine
full_name: Witzel, Sabine
last_name: Witzel
- first_name: Vitaly
full_name: Zimyanin, Vitaly
last_name: Zimyanin
- first_name: Filipa
full_name: Carreira Barbosa, Filipa
last_name: Carreira Barbosa
- first_name: Masazumi
full_name: Tada, Masazumi
last_name: Tada
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Witzel S, Zimyanin V, Carreira Barbosa F, Tada M, Heisenberg C-PJ. Wnt11 controls
cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane.
Journal of Cell Biology. 2006;175(5):791-802. doi:10.1083/jcb.200606017
apa: Witzel, S., Zimyanin, V., Carreira Barbosa, F., Tada, M., & Heisenberg,
C.-P. J. (2006). Wnt11 controls cell contact persistence by local accumulation
of Frizzled 7 at the plasma membrane. Journal of Cell Biology. Rockefeller
University Press. https://doi.org/10.1083/jcb.200606017
chicago: Witzel, Sabine, Vitaly Zimyanin, Filipa Carreira Barbosa, Masazumi Tada,
and Carl-Philipp J Heisenberg. “Wnt11 Controls Cell Contact Persistence by Local
Accumulation of Frizzled 7 at the Plasma Membrane.” Journal of Cell Biology.
Rockefeller University Press, 2006. https://doi.org/10.1083/jcb.200606017.
ieee: S. Witzel, V. Zimyanin, F. Carreira Barbosa, M. Tada, and C.-P. J. Heisenberg,
“Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at
the plasma membrane,” Journal of Cell Biology, vol. 175, no. 5. Rockefeller
University Press, pp. 791–802, 2006.
ista: Witzel S, Zimyanin V, Carreira Barbosa F, Tada M, Heisenberg C-PJ. 2006. Wnt11
controls cell contact persistence by local accumulation of Frizzled 7 at the plasma
membrane. Journal of Cell Biology. 175(5), 791–802.
mla: Witzel, Sabine, et al. “Wnt11 Controls Cell Contact Persistence by Local Accumulation
of Frizzled 7 at the Plasma Membrane.” Journal of Cell Biology, vol. 175,
no. 5, Rockefeller University Press, 2006, pp. 791–802, doi:10.1083/jcb.200606017.
short: S. Witzel, V. Zimyanin, F. Carreira Barbosa, M. Tada, C.-P.J. Heisenberg,
Journal of Cell Biology 175 (2006) 791–802.
date_created: 2018-12-11T12:07:11Z
date_published: 2006-12-04T00:00:00Z
date_updated: 2021-01-12T07:54:48Z
day: '04'
doi: 10.1083/jcb.200606017
extern: '1'
intvolume: ' 175'
issue: '5'
language:
- iso: eng
month: '12'
oa_version: None
page: 791 - 802
publication: Journal of Cell Biology
publication_status: published
publisher: Rockefeller University Press
publist_id: '1980'
status: public
title: Wnt11 controls cell contact persistence by local accumulation of Frizzled 7
at the plasma membrane
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 175
year: '2006'
...
---
_id: '4145'
abstract:
- lang: eng
text: The detection of microRNAs (miRNAs) at single-cell resolution is important
for studying the role of these posttranscriptional regulators. Here, we use a
dual-fluorescent green fluorescent protein (GFP)-reporter/monomeric red fluorescent
protein (mRFP)-sensor (DFRS) plasmid, injected into zebrafish blastomeres or electroporated
into defined tissues of mouse embryos in utero or ex utero, to monitor the dynamics
of specific miRNAs in individual live cells. This approach reveals, for example,
that in the developing mouse central nervous system,, miR-124a is expressed not
only in postmitotic neurons but also in neuronal progenitor cells. Collectively,
our results demonstrate that acute administration of DFRS plasmids.offers an alternative
to previous in situ hybridization and transgenic approaches and allows the monitoring
of miRNA appearance and disappearance in defined cell lineages during vertebrate
development.
article_processing_charge: No
author:
- first_name: Davide
full_name: Tonelli, Davide
last_name: Tonelli
- first_name: Frederico
full_name: Calegari, Frederico
last_name: Calegari
- first_name: Ji
full_name: Fei, Ji
last_name: Fei
- first_name: Tadashi
full_name: Nomura, Tadashi
last_name: Nomura
- first_name: Noriko
full_name: Osumi, Noriko
last_name: Osumi
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Wieland
full_name: Huttner, Wieland
last_name: Huttner
citation:
ama: Tonelli D, Calegari F, Fei J, et al. Single-cell detection of microRNAs in
developing vertebrate embryos after acute administration of a dual-fluorescence
reporter/sensor plasmid. Biotechniques. 2006;41(6):727-732. doi:10.2144/000112296
apa: Tonelli, D., Calegari, F., Fei, J., Nomura, T., Osumi, N., Heisenberg, C.-P.
J., & Huttner, W. (2006). Single-cell detection of microRNAs in developing
vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor
plasmid. Biotechniques. Informa Healthcare. https://doi.org/10.2144/000112296
chicago: Tonelli, Davide, Frederico Calegari, Ji Fei, Tadashi Nomura, Noriko Osumi,
Carl-Philipp J Heisenberg, and Wieland Huttner. “Single-Cell Detection of MicroRNAs
in Developing Vertebrate Embryos after Acute Administration of a Dual-Fluorescence
Reporter/Sensor Plasmid.” Biotechniques. Informa Healthcare, 2006. https://doi.org/10.2144/000112296.
ieee: D. Tonelli et al., “Single-cell detection of microRNAs in developing
vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor
plasmid,” Biotechniques, vol. 41, no. 6. Informa Healthcare, pp. 727–732,
2006.
ista: Tonelli D, Calegari F, Fei J, Nomura T, Osumi N, Heisenberg C-PJ, Huttner
W. 2006. Single-cell detection of microRNAs in developing vertebrate embryos after
acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques.
41(6), 727–732.
mla: Tonelli, Davide, et al. “Single-Cell Detection of MicroRNAs in Developing Vertebrate
Embryos after Acute Administration of a Dual-Fluorescence Reporter/Sensor Plasmid.”
Biotechniques, vol. 41, no. 6, Informa Healthcare, 2006, pp. 727–32, doi:10.2144/000112296.
short: D. Tonelli, F. Calegari, J. Fei, T. Nomura, N. Osumi, C.-P.J. Heisenberg,
W. Huttner, Biotechniques 41 (2006) 727–732.
date_created: 2018-12-11T12:07:12Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2021-01-12T07:54:50Z
day: '01'
doi: 10.2144/000112296
extern: '1'
intvolume: ' 41'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 727 - 732
publication: Biotechniques
publication_status: published
publisher: Informa Healthcare
publist_id: '1974'
status: public
title: Single-cell detection of microRNAs in developing vertebrate embryos after acute
administration of a dual-fluorescence reporter/sensor plasmid
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 41
year: '2006'
...
---
_id: '4176'
abstract:
- lang: eng
text: 'During vertebrate gastrulation, a well-orchestrated series of morphogenetic
changes leads to the formation of the three germ layers: the ectoderm, mesoderm
and endoderm. The analysis of gene expression patterns during gastrulation has
been central to the identification of genes involved in germ layer formation.
However, many proteins are regulated on a translational or post-translational
level and are thus undetectable by gene expression analysis. Therefore, we developed
a 2D-gel-based comparative proteomic approach to target proteins involved in germ
layer morphogenesis during zebrafish gastrulation. Proteomes of ectodermal and
mesendodermal progenitor cells were compared and 35 significantly regulated proteins
were identified by mass spectrometry, including several proteins with predicted
functions in cytoskeletal organization. A comparison of our proteomic results
with data obtained in an accompanying microarray-based gene expression analysis
revealed no significant overlap, confirming the complementary nature of proteomics
and transcriptomics. The regulation of ezrin2, which was identified based on a
reduction in spot intensity in mesendodermal cells, was independently validated.
Furthermore, we show that ezrin2 is activated by phosphorylation in mesendodermal
cells and is required for proper germ layer morphogenesis. We demonstrate the
feasibility of proteomics in zebrafish, concluding that proteomics is a valuable
tool for analysis of early development.'
article_processing_charge: No
author:
- first_name: Vinzenz
full_name: Link, Vinzenz
last_name: Link
- first_name: Lara
full_name: Carvalho, Lara
last_name: Carvalho
- first_name: Irinka
full_name: Castanon, Irinka
last_name: Castanon
- first_name: Petra
full_name: Stockinger, Petra
last_name: Stockinger
- first_name: Andrej
full_name: Shevchenko, Andrej
last_name: Shevchenko
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Link V, Carvalho L, Castanon I, Stockinger P, Shevchenko A, Heisenberg C-PJ.
Identification of regulators of germ layer morphogenesis using proteomics in zebrafish.
Journal of Cell Science. 2006;119(10):2073-2083. doi:10.1242/jcs.02928
apa: Link, V., Carvalho, L., Castanon, I., Stockinger, P., Shevchenko, A., &
Heisenberg, C.-P. J. (2006). Identification of regulators of germ layer morphogenesis
using proteomics in zebrafish. Journal of Cell Science. Company of Biologists.
https://doi.org/10.1242/jcs.02928
chicago: Link, Vinzenz, Lara Carvalho, Irinka Castanon, Petra Stockinger, Andrej
Shevchenko, and Carl-Philipp J Heisenberg. “Identification of Regulators of Germ
Layer Morphogenesis Using Proteomics in Zebrafish.” Journal of Cell Science.
Company of Biologists, 2006. https://doi.org/10.1242/jcs.02928.
ieee: V. Link, L. Carvalho, I. Castanon, P. Stockinger, A. Shevchenko, and C.-P.
J. Heisenberg, “Identification of regulators of germ layer morphogenesis using
proteomics in zebrafish,” Journal of Cell Science, vol. 119, no. 10. Company
of Biologists, pp. 2073–2083, 2006.
ista: Link V, Carvalho L, Castanon I, Stockinger P, Shevchenko A, Heisenberg C-PJ.
2006. Identification of regulators of germ layer morphogenesis using proteomics
in zebrafish. Journal of Cell Science. 119(10), 2073–2083.
mla: Link, Vinzenz, et al. “Identification of Regulators of Germ Layer Morphogenesis
Using Proteomics in Zebrafish.” Journal of Cell Science, vol. 119, no.
10, Company of Biologists, 2006, pp. 2073–83, doi:10.1242/jcs.02928.
short: V. Link, L. Carvalho, I. Castanon, P. Stockinger, A. Shevchenko, C.-P.J.
Heisenberg, Journal of Cell Science 119 (2006) 2073–2083.
date_created: 2018-12-11T12:07:24Z
date_published: 2006-05-15T00:00:00Z
date_updated: 2021-01-12T07:55:04Z
day: '15'
doi: 10.1242/jcs.02928
extern: '1'
intvolume: ' 119'
issue: '10'
language:
- iso: eng
month: '05'
oa_version: None
page: 2073 - 2083
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '1944'
status: public
title: Identification of regulators of germ layer morphogenesis using proteomics in
zebrafish
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2006'
...
---
_id: '4173'
abstract:
- lang: eng
text: 'Background: Zebrafish (D. rerio) has become a powerful and widely used model
system for the analysis of vertebrate embryogenesis and organ development. While
genetic methods are readily available in zebrafish, protocols for two dimensional
(2D) gel electrophoresis and proteomics have yet to be developed. Results: As
a prerequisite to carry out proteomic experiments with early zebrafish embryos,
we developed a method to efficiently remove the yolk from large batches of embryos.
This method enabled high resolution 2D gel electrophoresis and improved Western
blotting considerably. Here, we provide detailed protocols for proteomics in zebrafish
from sample preparation to mass spectrometry (MS), including a comparison of databases
for MS identification of zebrafish proteins. Conclusion: The provided protocols
for proteomic analysis of early embryos enable research to be taken in novel directions
in embryogenesis.'
article_processing_charge: No
author:
- first_name: Vinzenz
full_name: Link, Vinzenz
last_name: Link
- first_name: Andrej
full_name: Shevchenko, Andrej
last_name: Shevchenko
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Link V, Shevchenko A, Heisenberg C-PJ. Proteomics of early zebrafish embryos.
BMC Developmental Biology. 2006;6:1-9. doi:10.1186/1471-213X-6-1
apa: Link, V., Shevchenko, A., & Heisenberg, C.-P. J. (2006). Proteomics of
early zebrafish embryos. BMC Developmental Biology. BioMed Central. https://doi.org/10.1186/1471-213X-6-1
chicago: Link, Vinzenz, Andrej Shevchenko, and Carl-Philipp J Heisenberg. “Proteomics
of Early Zebrafish Embryos.” BMC Developmental Biology. BioMed Central,
2006. https://doi.org/10.1186/1471-213X-6-1.
ieee: V. Link, A. Shevchenko, and C.-P. J. Heisenberg, “Proteomics of early zebrafish
embryos,” BMC Developmental Biology, vol. 6. BioMed Central, pp. 1–9, 2006.
ista: Link V, Shevchenko A, Heisenberg C-PJ. 2006. Proteomics of early zebrafish
embryos. BMC Developmental Biology. 6, 1–9.
mla: Link, Vinzenz, et al. “Proteomics of Early Zebrafish Embryos.” BMC Developmental
Biology, vol. 6, BioMed Central, 2006, pp. 1–9, doi:10.1186/1471-213X-6-1.
short: V. Link, A. Shevchenko, C.-P.J. Heisenberg, BMC Developmental Biology 6 (2006)
1–9.
date_created: 2018-12-11T12:07:23Z
date_published: 2006-01-13T00:00:00Z
date_updated: 2021-01-12T07:55:02Z
day: '13'
doi: 10.1186/1471-213X-6-1
extern: '1'
intvolume: ' 6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.biomedcentral.com/1471-213X/6/1
month: '01'
oa: 1
oa_version: None
page: 1 - 9
publication: BMC Developmental Biology
publication_status: published
publisher: BioMed Central
publist_id: '1945'
status: public
title: Proteomics of early zebrafish embryos
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
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2006'
...
---
_id: '4178'
abstract:
- lang: eng
text: Detailed reconstruction of the spatiotemporal history of embryonic cells is
key to understanding tissue formation processes but is often complicated by the
large number of cells involved, particularly so in vertebrates. Through a combination
of high-resolution time-lapse lineage tracing and antibody staining, we have analyzed
the movement of mesencephalic and metencephalic cell populations in the early
zebrafish embryo. To facilitate the analysis of our cell tracking data, we have
created TracePilot, a software tool that allows interactive manipulation and visualization
of tracking data. We demonstrate its utility by showing novel visualizations of
cell movement in the developing zebrafish brain. TracePilot (http://www.mpi-cbg.de/tracepilot)
is Java-based, available free of charge, and has a program structure that allows
the incorporation of additional analysis tools.
article_processing_charge: No
author:
- first_name: Tobias
full_name: Langenberg, Tobias
last_name: Langenberg
- first_name: Tadeusz
full_name: Dracz, Tadeusz
last_name: Dracz
- first_name: Andrew
full_name: Oates, Andrew
last_name: Oates
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Michael
full_name: Brand, Michael
last_name: Brand
citation:
ama: Langenberg T, Dracz T, Oates A, Heisenberg C-PJ, Brand M. Analysis and visualization
of cell movement in the developing zebrafish brain. Developmental Dynamics.
2006;235(4):928-933. doi:10.1002/dvdy.20692
apa: Langenberg, T., Dracz, T., Oates, A., Heisenberg, C.-P. J., & Brand, M.
(2006). Analysis and visualization of cell movement in the developing zebrafish
brain. Developmental Dynamics. Wiley-Blackwell. https://doi.org/10.1002/dvdy.20692
chicago: Langenberg, Tobias, Tadeusz Dracz, Andrew Oates, Carl-Philipp J Heisenberg,
and Michael Brand. “Analysis and Visualization of Cell Movement in the Developing
Zebrafish Brain.” Developmental Dynamics. Wiley-Blackwell, 2006. https://doi.org/10.1002/dvdy.20692.
ieee: T. Langenberg, T. Dracz, A. Oates, C.-P. J. Heisenberg, and M. Brand, “Analysis
and visualization of cell movement in the developing zebrafish brain,” Developmental
Dynamics, vol. 235, no. 4. Wiley-Blackwell, pp. 928–933, 2006.
ista: Langenberg T, Dracz T, Oates A, Heisenberg C-PJ, Brand M. 2006. Analysis and
visualization of cell movement in the developing zebrafish brain. Developmental
Dynamics. 235(4), 928–933.
mla: Langenberg, Tobias, et al. “Analysis and Visualization of Cell Movement in
the Developing Zebrafish Brain.” Developmental Dynamics, vol. 235, no.
4, Wiley-Blackwell, 2006, pp. 928–33, doi:10.1002/dvdy.20692.
short: T. Langenberg, T. Dracz, A. Oates, C.-P.J. Heisenberg, M. Brand, Developmental
Dynamics 235 (2006) 928–933.
date_created: 2018-12-11T12:07:25Z
date_published: 2006-04-01T00:00:00Z
date_updated: 2021-01-12T07:55:04Z
day: '01'
doi: 10.1002/dvdy.20692
extern: '1'
intvolume: ' 235'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 928 - 933
publication: Developmental Dynamics
publication_status: published
publisher: Wiley-Blackwell
publist_id: '1940'
status: public
title: Analysis and visualization of cell movement in the developing zebrafish brain
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 235
year: '2006'
...
---
_id: '4184'
abstract:
- lang: eng
text: Epithelial morphogenesis depends on coordinated changes in cell shape, a process
that is still poorly understood. During zebrafish epiboly and Drosophila dorsal
closure, cell-shape changes at the epithelial margin are of critical importance.
Here evidence is provided for a conserved mechanism of local actin and myosin
2 recruitment during theses events. It was found that during epiboly of the zebrafish
embryo, the movement of the outer epithelium (enveloping layer) over the yolk
cell surface involves the constriction of marginal cells. This process depends
on the recruitment of actin and myosin 2 within the yolk cytoplasm along the margin
of the enveloping layer. Actin and myosin 2 recruitment within the yolk cytoplasm
requires the Ste20-like kinase Msn1, an orthologue of Drosophila Misshapen. Similarly,
in Drosophila, actin and myosin 2 localization and cell constriction at the margin
of the epidermis mediate dorsal closure and are controlled by Misshapen. Thus,
this study has characterized a conserved mechanism underlying coordinated cell-shape
changes during epithelial morphogenesis.
article_processing_charge: No
author:
- first_name: Mathias
full_name: Köppen, Mathias
last_name: Köppen
- first_name: Beatriz
full_name: Fernández, Beatriz
last_name: Fernández
- first_name: Lara
full_name: Carvalho, Lara
last_name: Carvalho
- first_name: António
full_name: Jacinto, António
last_name: Jacinto
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: 'Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. Coordinated
cell-shape changes control epithelial movement in zebrafish and Drosophila. Development.
2006;133(14):2671-2681. doi:doi:
10.1242/dev.02439'
apa: 'Köppen, M., Fernández, B., Carvalho, L., Jacinto, A., & Heisenberg, C.-P.
J. (2006). Coordinated cell-shape changes control epithelial movement in zebrafish
and Drosophila. Development. Company of Biologists. https://doi.org/doi: 10.1242/dev.02439'
chicago: 'Köppen, Mathias, Beatriz Fernández, Lara Carvalho, António Jacinto, and
Carl-Philipp J Heisenberg. “Coordinated Cell-Shape Changes Control Epithelial
Movement in Zebrafish and Drosophila.” Development. Company of Biologists,
2006. https://doi.org/doi: 10.1242/dev.02439.'
ieee: M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, and C.-P. J. Heisenberg,
“Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila,”
Development, vol. 133, no. 14. Company of Biologists, pp. 2671–2681, 2006.
ista: Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. 2006. Coordinated
cell-shape changes control epithelial movement in zebrafish and Drosophila. Development.
133(14), 2671–2681.
mla: 'Köppen, Mathias, et al. “Coordinated Cell-Shape Changes Control Epithelial
Movement in Zebrafish and Drosophila.” Development, vol. 133, no. 14, Company
of Biologists, 2006, pp. 2671–81, doi:doi:
10.1242/dev.02439.'
short: M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, C.-P.J. Heisenberg, Development
133 (2006) 2671–2681.
date_created: 2018-12-11T12:07:27Z
date_published: 2006-07-15T00:00:00Z
date_updated: 2021-01-12T07:55:08Z
day: '15'
doi: 'doi: 10.1242/dev.02439'
extern: '1'
intvolume: ' 133'
issue: '14'
language:
- iso: eng
month: '07'
oa_version: None
page: 2671 - 2681
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '1935'
status: public
title: Coordinated cell-shape changes control epithelial movement in zebrafish and
Drosophila
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 133
year: '2006'
...
---
_id: '4218'
abstract:
- lang: eng
text: The molecular and cellular mechanisms governing cell motility and directed
migration in response to the chemokine SDF-1 are largely unknown. Here, we demonstrate
that zebrafish primordial germ cells whose migration is guided by SDF-1 generate
bleb-like protrusions that are powered by cytoplasmic flow. Protrusions are formed
at sites of higher levels of free calcium where activation of myosin contraction
occurs. Separation of the acto-myosin cortex from the plasma membrane at these
sites is followed by a flow of cytoplasm into the forming bleb. We propose that
polarized activation of the receptor CXCR4 leads to a rise in free calcium that
in turn activates myosin contraction in the part of the cell responding to higher
levels of the ligand SDF-1. The biased formation of new protrusions in a particular
region of the cell in response to SDF-1 defines the leading edge and the direction
of cell migration.
article_processing_charge: No
author:
- first_name: Heiko
full_name: Blaser, Heiko
last_name: Blaser
- first_name: Michal
full_name: Reichman Fried, Michal
last_name: Reichman Fried
- first_name: Irinka
full_name: Castanon, Irinka
last_name: Castanon
- first_name: Karin
full_name: Dumstrei, Karin
last_name: Dumstrei
- first_name: Florence
full_name: Marlow, Florence
last_name: Marlow
- first_name: Koichi
full_name: Kawakami, Koichi
last_name: Kawakami
- first_name: Lilianna
full_name: Solnica Krezel, Lilianna
last_name: Solnica Krezel
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Erez
full_name: Raz, Erez
last_name: Raz
citation:
ama: 'Blaser H, Reichman Fried M, Castanon I, et al. Migration of zebrafish primordial
germ cells: A role for myosin contraction and cytoplasmic flow. Developmental
Cell. 2006;11(5):613-627. doi:10.1016/j.devcel.2006.09.023'
apa: 'Blaser, H., Reichman Fried, M., Castanon, I., Dumstrei, K., Marlow, F., Kawakami,
K., … Raz, E. (2006). Migration of zebrafish primordial germ cells: A role for
myosin contraction and cytoplasmic flow. Developmental Cell. Cell Press.
https://doi.org/10.1016/j.devcel.2006.09.023'
chicago: 'Blaser, Heiko, Michal Reichman Fried, Irinka Castanon, Karin Dumstrei,
Florence Marlow, Koichi Kawakami, Lilianna Solnica Krezel, Carl-Philipp J Heisenberg,
and Erez Raz. “Migration of Zebrafish Primordial Germ Cells: A Role for Myosin
Contraction and Cytoplasmic Flow.” Developmental Cell. Cell Press, 2006.
https://doi.org/10.1016/j.devcel.2006.09.023.'
ieee: 'H. Blaser et al., “Migration of zebrafish primordial germ cells: A
role for myosin contraction and cytoplasmic flow,” Developmental Cell,
vol. 11, no. 5. Cell Press, pp. 613–627, 2006.'
ista: 'Blaser H, Reichman Fried M, Castanon I, Dumstrei K, Marlow F, Kawakami K,
Solnica Krezel L, Heisenberg C-PJ, Raz E. 2006. Migration of zebrafish primordial
germ cells: A role for myosin contraction and cytoplasmic flow. Developmental
Cell. 11(5), 613–627.'
mla: 'Blaser, Heiko, et al. “Migration of Zebrafish Primordial Germ Cells: A Role
for Myosin Contraction and Cytoplasmic Flow.” Developmental Cell, vol.
11, no. 5, Cell Press, 2006, pp. 613–27, doi:10.1016/j.devcel.2006.09.023.'
short: H. Blaser, M. Reichman Fried, I. Castanon, K. Dumstrei, F. Marlow, K. Kawakami,
L. Solnica Krezel, C.-P.J. Heisenberg, E. Raz, Developmental Cell 11 (2006) 613–627.
date_created: 2018-12-11T12:07:39Z
date_published: 2006-11-06T00:00:00Z
date_updated: 2021-01-12T07:55:23Z
day: '06'
doi: 10.1016/j.devcel.2006.09.023
extern: '1'
intvolume: ' 11'
issue: '5'
language:
- iso: eng
month: '11'
oa_version: None
page: 613 - 627
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '1898'
status: public
title: 'Migration of zebrafish primordial germ cells: A role for myosin contraction
and cytoplasmic flow'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2006'
...
---
_id: '4237'
abstract:
- lang: eng
text: The growth function of populations is central in biomathematics. The main
dogma is the existence of density-dependence mechanisms, which can be modelled
with distinct functional forms that depend on the size of the Population. One
important class of regulatory functions is the theta-logistic, which generalizes
the logistic equation. Using this model as a motivation, this paper introduces
a simple dynamical reformulation that generalizes many growth functions. The reformulation
consists of two equations, one for population size, and one for the growth rate.
Furthermore, the model shows that although population is density-dependent, the
dynamics of the growth rate does not depend either on population size, nor on
the carrying capacity. Actually, the growth equation is uncoupled from the population
size equation, and the model has only two parameters, a Malthusian parameter rho
and a competition coefficient theta. Distinct sign combinations of these parameters
reproduce not only the family of theta-logistics, but also the van Bertalanffy,
Gompertz and Potential Growth equations, among other possibilities. It is also
shown that, except for two critical points, there is a general size-scaling relation
that includes those appearing in the most important allometric theories, including
the recently proposed Metabolic Theory of Ecology. With this model, several issues
of general interest are discussed such as the growth of animal population, extinctions,
cell growth and allometry, and the effect of environment over a population. (c)
2005 Elsevier Ltd. All rights reserved.
article_processing_charge: No
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
citation:
ama: de Vladar H. Density-dependence as a size-independent regulatory mechanism.
Journal of Theoretical Biology. 2006;238(2):245-256. doi:3802
apa: de Vladar, H. (2006). Density-dependence as a size-independent regulatory mechanism.
Journal of Theoretical Biology. Elsevier. https://doi.org/3802
chicago: Vladar, Harold de. “Density-Dependence as a Size-Independent Regulatory
Mechanism.” Journal of Theoretical Biology. Elsevier, 2006. https://doi.org/3802.
ieee: H. de Vladar, “Density-dependence as a size-independent regulatory mechanism,”
Journal of Theoretical Biology, vol. 238, no. 2. Elsevier, pp. 245–256,
2006.
ista: de Vladar H. 2006. Density-dependence as a size-independent regulatory mechanism.
Journal of Theoretical Biology. 238(2), 245–256.
mla: de Vladar, Harold. “Density-Dependence as a Size-Independent Regulatory Mechanism.”
Journal of Theoretical Biology, vol. 238, no. 2, Elsevier, 2006, pp. 245–56,
doi:3802.
short: H. de Vladar, Journal of Theoretical Biology 238 (2006) 245–256.
date_created: 2018-12-11T12:07:46Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:31Z
day: '01'
doi: '3802'
extern: '1'
intvolume: ' 238'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 245 - 256
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '1878'
status: public
title: Density-dependence as a size-independent regulatory mechanism
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 238
year: '2006'
...
---
_id: '4235'
author:
- first_name: Harold
full_name: Harold Vladar
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
- first_name: J.
full_name: González,J. A
last_name: González
citation:
ama: de Vladar H, González J. Dynamic response of cancer under the influence of
immunological activity and therapy. Journal of Theoretical Biology. 2006:91-109.
apa: de Vladar, H., & González, J. (2006). Dynamic response of cancer under
the influence of immunological activity and therapy. Journal of Theoretical
Biology. Elsevier.
chicago: Vladar, Harold de, and J. González. “Dynamic Response of Cancer under the
Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology.
Elsevier, 2006.
ieee: H. de Vladar and J. González, “Dynamic response of cancer under the influence
of immunological activity and therapy,” Journal of Theoretical Biology.
Elsevier, pp. 91–109, 2006.
ista: de Vladar H, González J. 2006. Dynamic response of cancer under the influence
of immunological activity and therapy. Journal of Theoretical Biology., 91–109.
mla: de Vladar, Harold, and J. González. “Dynamic Response of Cancer under the Influence
of Immunological Activity and Therapy.” Journal of Theoretical Biology,
Elsevier, 2006, pp. 91–109.
short: H. de Vladar, J. González, Journal of Theoretical Biology (2006) 91–109.
date_created: 2018-12-11T12:07:45Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:30Z
day: '01'
extern: 1
month: '01'
page: 91 - 109
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '1879'
quality_controlled: 0
status: public
title: Dynamic response of cancer under the influence of immunological activity and
therapy
type: journal_article
year: '2006'
...
---
_id: '4248'
abstract:
- lang: eng
text: 'In finite populations, genetic drift generates interference between selected
loci, causing advantageous alleles to be found more often on different chromosomes
than on the same chromosome, which reduces the rate of adaptation. This “Hill–Robertson
effect” generates indirect selection to increase recombination rates. We present
a new method to quantify the strength of this selection. Our model represents
a new beneficial allele (A) entering a population as a single copy, while another
beneficial allele (B) is sweeping at another locus. A third locus affects the
recombination rate between selected loci. Using a branching process model, we
calculate the probability distribution of the number of copies of A on the different
genetic backgrounds, after it is established but while it is still rare. Then,
we use a deterministic model to express the change in frequency of the recombination
modifier, due to hitchhiking, as A goes to fixation. We show that this method
can give good estimates of selection for recombination. Moreover, it shows that
recombination is selected through two different effects: it increases the fixation
probability of new alleles, and it accelerates selective sweeps. The relative
importance of these two effects depends on the relative times of occurrence of
the beneficial alleles.'
author:
- first_name: Denis
full_name: Roze, Denis
last_name: Roze
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Roze D, Barton NH. The Hill-Robertson effect and the evolution of recombination.
Genetics. 2006;173(3):1793-1811. doi:10.1534/genetics.106.058586
apa: Roze, D., & Barton, N. H. (2006). The Hill-Robertson effect and the evolution
of recombination. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.106.058586
chicago: Roze, Denis, and Nicholas H Barton. “The Hill-Robertson Effect and the
Evolution of Recombination.” Genetics. Genetics Society of America, 2006.
https://doi.org/10.1534/genetics.106.058586
.
ieee: D. Roze and N. H. Barton, “The Hill-Robertson effect and the evolution of
recombination,” Genetics, vol. 173, no. 3. Genetics Society of America,
pp. 1793–1811, 2006.
ista: Roze D, Barton NH. 2006. The Hill-Robertson effect and the evolution of recombination.
Genetics. 173(3), 1793–1811.
mla: Roze, Denis, and Nicholas H. Barton. “The Hill-Robertson Effect and the Evolution
of Recombination.” Genetics, vol. 173, no. 3, Genetics Society of America,
2006, pp. 1793–811, doi:10.1534/genetics.106.058586
.
short: D. Roze, N.H. Barton, Genetics 173 (2006) 1793–1811.
date_created: 2018-12-11T12:07:50Z
date_published: 2006-07-01T00:00:00Z
date_updated: 2021-01-12T07:55:36Z
day: '01'
doi: '10.1534/genetics.106.058586 '
extern: 1
intvolume: ' 173'
issue: '3'
month: '07'
page: 1793 - 1811
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '1854'
quality_controlled: 0
status: public
title: The Hill-Robertson effect and the evolution of recombination
type: journal_article
volume: 173
year: '2006'
...
---
_id: '4250'
abstract:
- lang: eng
text: A recent analysis has shown that divergence between human and chimpanzee varies
greatly across the genome. Although this is consistent with ‘hybridisation’ between
the diverging human and chimp lineages, such observations can be explained more
simply by the null model of allopatric speciation.
author:
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Evolutionary Biology: How did the human species form? Current
Biology. 2006;16(16):647-650. doi:10.1016/j.cub.2006.07.032'
apa: 'Barton, N. H. (2006). Evolutionary Biology: How did the human species form?
Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2006.07.032'
chicago: 'Barton, Nicholas H. “Evolutionary Biology: How Did the Human Species Form?”
Current Biology. Cell Press, 2006. https://doi.org/10.1016/j.cub.2006.07.032.'
ieee: 'N. H. Barton, “Evolutionary Biology: How did the human species form?,” Current
Biology, vol. 16, no. 16. Cell Press, pp. 647–650, 2006.'
ista: 'Barton NH. 2006. Evolutionary Biology: How did the human species form? Current
Biology. 16(16), 647–650.'
mla: 'Barton, Nicholas H. “Evolutionary Biology: How Did the Human Species Form?”
Current Biology, vol. 16, no. 16, Cell Press, 2006, pp. 647–50, doi:10.1016/j.cub.2006.07.032.'
short: N.H. Barton, Current Biology 16 (2006) 647–650.
date_created: 2018-12-11T12:07:51Z
date_published: 2006-08-22T00:00:00Z
date_updated: 2019-04-26T07:22:41Z
day: '22'
doi: 10.1016/j.cub.2006.07.032
extern: 1
intvolume: ' 16'
issue: '16'
month: '08'
page: 647 - 650
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '1850'
quality_controlled: 0
status: public
title: 'Evolutionary Biology: How did the human species form?'
type: review
volume: 16
year: '2006'
...
---
_id: '4359'
alternative_title:
- LNCS 3855
author:
- first_name: Thomas
full_name: Thomas Wies
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
- first_name: Viktor
full_name: Kuncak, Viktor
last_name: Kuncak
- first_name: Patrick
full_name: Lam,Patrick
last_name: Lam
- first_name: Andreas
full_name: Podelski,Andreas
last_name: Podelski
- first_name: Martin
full_name: Rinard,Martin
last_name: Rinard
citation:
ama: 'Wies T, Kuncak V, Lam P, Podelski A, Rinard M. Field Constraint Analysis.
In: Springer; 2006:157-173. doi:1551'
apa: 'Wies, T., Kuncak, V., Lam, P., Podelski, A., & Rinard, M. (2006). Field
Constraint Analysis (pp. 157–173). Presented at the VMCAI: Verification, Model
Checking and Abstract Interpretation, Springer. https://doi.org/1551'
chicago: Wies, Thomas, Viktor Kuncak, Patrick Lam, Andreas Podelski, and Martin
Rinard. “Field Constraint Analysis,” 157–73. Springer, 2006. https://doi.org/1551.
ieee: 'T. Wies, V. Kuncak, P. Lam, A. Podelski, and M. Rinard, “Field Constraint
Analysis,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation,
2006, pp. 157–173.'
ista: 'Wies T, Kuncak V, Lam P, Podelski A, Rinard M. 2006. Field Constraint Analysis.
VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS 3855, ,
157–173.'
mla: Wies, Thomas, et al. Field Constraint Analysis. Springer, 2006, pp.
157–73, doi:1551.
short: T. Wies, V. Kuncak, P. Lam, A. Podelski, M. Rinard, in:, Springer, 2006,
pp. 157–173.
conference:
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
date_created: 2018-12-11T12:08:27Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:23Z
day: '01'
doi: '1551'
extern: 1
month: '01'
page: 157 - 173
publication_status: published
publisher: Springer
publist_id: '1097'
quality_controlled: 0
status: public
title: Field Constraint Analysis
type: conference
year: '2006'
...
---
_id: '4373'
alternative_title:
- LNCS
author:
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dejan
full_name: Dejan Nickovic
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Amir
full_name: Pnueli,Amir
last_name: Pnueli
citation:
ama: 'Maler O, Nickovic D, Pnueli A. Real Time Temporal Logic: Past, Present, Future.
In: Springer; 2006:2-16. doi:1571'
apa: 'Maler, O., Nickovic, D., & Pnueli, A. (2006). Real Time Temporal Logic:
Past, Present, Future (pp. 2–16). Presented at the FORMATS: Formal Modeling and
Analysis of Timed Systems, Springer. https://doi.org/1571'
chicago: 'Maler, Oded, Dejan Nickovic, and Amir Pnueli. “Real Time Temporal Logic:
Past, Present, Future,” 2–16. Springer, 2006. https://doi.org/1571.'
ieee: 'O. Maler, D. Nickovic, and A. Pnueli, “Real Time Temporal Logic: Past, Present,
Future,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems,
2006, pp. 2–16.'
ista: 'Maler O, Nickovic D, Pnueli A. 2006. Real Time Temporal Logic: Past, Present,
Future. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, , 2–16.'
mla: 'Maler, Oded, et al. Real Time Temporal Logic: Past, Present, Future.
Springer, 2006, pp. 2–16, doi:1571.'
short: O. Maler, D. Nickovic, A. Pnueli, in:, Springer, 2006, pp. 2–16.
conference:
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
date_created: 2018-12-11T12:08:31Z
date_published: 2006-01-23T00:00:00Z
date_updated: 2021-01-12T07:56:29Z
day: '23'
doi: '1571'
extern: 1
month: '01'
page: 2 - 16
publication_status: published
publisher: Springer
publist_id: '1084'
quality_controlled: 0
status: public
title: 'Real Time Temporal Logic: Past, Present, Future'
type: conference
year: '2006'
...
---
_id: '4374'
alternative_title:
- LNCS
author:
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dejan
full_name: Dejan Nickovic
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Amir
full_name: Pnueli,Amir
last_name: Pnueli
citation:
ama: 'Maler O, Nickovic D, Pnueli A. From MITL to Timed Automata. In: Springer;
2006:274-289. doi:1570'
apa: 'Maler, O., Nickovic, D., & Pnueli, A. (2006). From MITL to Timed Automata
(pp. 274–289). Presented at the FORMATS: Formal Modeling and Analysis of Timed
Systems, Springer. https://doi.org/1570'
chicago: Maler, Oded, Dejan Nickovic, and Amir Pnueli. “From MITL to Timed Automata,”
274–89. Springer, 2006. https://doi.org/1570.
ieee: 'O. Maler, D. Nickovic, and A. Pnueli, “From MITL to Timed Automata,” presented
at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2006, pp. 274–289.'
ista: 'Maler O, Nickovic D, Pnueli A. 2006. From MITL to Timed Automata. FORMATS:
Formal Modeling and Analysis of Timed Systems, LNCS, , 274–289.'
mla: Maler, Oded, et al. From MITL to Timed Automata. Springer, 2006, pp.
274–89, doi:1570.
short: O. Maler, D. Nickovic, A. Pnueli, in:, Springer, 2006, pp. 274–289.
conference:
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
date_created: 2018-12-11T12:08:31Z
date_published: 2006-10-19T00:00:00Z
date_updated: 2021-01-12T07:56:30Z
day: '19'
doi: '1570'
extern: 1
month: '10'
page: 274 - 289
publication_status: published
publisher: Springer
publist_id: '1085'
quality_controlled: 0
status: public
title: From MITL to Timed Automata
type: conference
year: '2006'
...
---
_id: '4406'
abstract:
- lang: eng
text: We propose and evaluate a new algorithm for checking the universality of nondeterministic
finite automata. In contrast to the standard algorithm, which uses the subset
construction to explicitly determinize the automaton, we keep the determinization
step implicit. Our algorithm computes the least fixed point of a monotone function
on the lattice of antichains of state sets. We evaluate the performance of our
algorithm experimentally using the random automaton model recently proposed by
Tabakov and Vardi. We show that on the difficult instances of this probabilistic
model, the antichain algorithm outperforms the standard one by several orders
of magnitude. We also show how variations of the antichain method can be used
for solving the language-inclusion problem for nondeterministic finite automata,
and the emptiness problem for alternating finite automata.
acknowledgement: This research was supported in part by the NSF grants CCR-0234690
and CCR-0225610, and the Belgian FNRS grant 2.4530.02 of the FRFC project “Centre
Fédéré en Vérification.”
alternative_title:
- LNCS
author:
- first_name: Martin
full_name: De Wulf, Martin
last_name: De Wulf
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jean
full_name: Raskin, Jean-François
last_name: Raskin
citation:
ama: 'De Wulf M, Doyen L, Henzinger TA, Raskin J. Antichains: A new algorithm for
checking universality of finite automata. In: Vol 4144. Springer; 2006:17-30.
doi:10.1007/11817963_5'
apa: 'De Wulf, M., Doyen, L., Henzinger, T. A., & Raskin, J. (2006). Antichains:
A new algorithm for checking universality of finite automata (Vol. 4144, pp. 17–30).
Presented at the CAV: Computer Aided Verification, Springer. https://doi.org/10.1007/11817963_5'
chicago: 'De Wulf, Martin, Laurent Doyen, Thomas A Henzinger, and Jean Raskin. “Antichains:
A New Algorithm for Checking Universality of Finite Automata,” 4144:17–30. Springer,
2006. https://doi.org/10.1007/11817963_5.'
ieee: 'M. De Wulf, L. Doyen, T. A. Henzinger, and J. Raskin, “Antichains: A new
algorithm for checking universality of finite automata,” presented at the CAV:
Computer Aided Verification, 2006, vol. 4144, pp. 17–30.'
ista: 'De Wulf M, Doyen L, Henzinger TA, Raskin J. 2006. Antichains: A new algorithm
for checking universality of finite automata. CAV: Computer Aided Verification,
LNCS, vol. 4144, 17–30.'
mla: 'De Wulf, Martin, et al. Antichains: A New Algorithm for Checking Universality
of Finite Automata. Vol. 4144, Springer, 2006, pp. 17–30, doi:10.1007/11817963_5.'
short: M. De Wulf, L. Doyen, T.A. Henzinger, J. Raskin, in:, Springer, 2006, pp.
17–30.
conference:
name: 'CAV: Computer Aided Verification'
date_created: 2018-12-11T12:08:41Z
date_published: 2006-08-08T00:00:00Z
date_updated: 2021-01-12T07:56:45Z
day: '08'
doi: 10.1007/11817963_5
extern: 1
intvolume: ' 4144'
month: '08'
page: 17 - 30
publication_status: published
publisher: Springer
publist_id: '326'
quality_controlled: 0
status: public
title: 'Antichains: A new algorithm for checking universality of finite automata'
type: conference
volume: 4144
year: '2006'
...
---
_id: '4401'
alternative_title:
- LNCS
author:
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
- first_name: Pavol
full_name: Pavol Cerny
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Steve
full_name: Zdancewic,Steve
last_name: Zdancewic
citation:
ama: 'Alur R, Cerny P, Zdancewic S. Preserving Secrecy Under Refinement. In: Springer;
2006:107-118. doi:1543'
apa: 'Alur, R., Cerny, P., & Zdancewic, S. (2006). Preserving Secrecy Under
Refinement (pp. 107–118). Presented at the ICALP: Automata, Languages and Programming,
Springer. https://doi.org/1543'
chicago: Alur, Rajeev, Pavol Cerny, and Steve Zdancewic. “Preserving Secrecy Under
Refinement,” 107–18. Springer, 2006. https://doi.org/1543.
ieee: 'R. Alur, P. Cerny, and S. Zdancewic, “Preserving Secrecy Under Refinement,”
presented at the ICALP: Automata, Languages and Programming, 2006, pp. 107–118.'
ista: 'Alur R, Cerny P, Zdancewic S. 2006. Preserving Secrecy Under Refinement.
ICALP: Automata, Languages and Programming, LNCS, , 107–118.'
mla: Alur, Rajeev, et al. Preserving Secrecy Under Refinement. Springer,
2006, pp. 107–18, doi:1543.
short: R. Alur, P. Cerny, S. Zdancewic, in:, Springer, 2006, pp. 107–118.
conference:
name: 'ICALP: Automata, Languages and Programming'
date_created: 2018-12-11T12:08:40Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:42Z
day: '01'
doi: '1543'
extern: 1
month: '01'
page: 107 - 118
publication_status: published
publisher: Springer
publist_id: '1054'
quality_controlled: 0
status: public
title: Preserving Secrecy Under Refinement
type: conference
year: '2006'
...
---
_id: '4437'
abstract:
- lang: eng
text: The synthesis of reactive systems requires the solution of two-player games
on graphs with ω-regular objectives. When the objective is specified by a linear
temporal logic formula or nondeterministic Büchi automaton, then previous algorithms
for solving the game require the construction of an equivalent deterministic automaton.
However, determinization for automata on infinite words is extremely complicated,
and current implementations fail to produce deterministic automata even for relatively
small inputs. We show how to construct, from a given nondeterministic Büchi automaton,
an equivalent nondeterministic parity automaton that is good for solving games
with objective . The main insight is that a nondeterministic automaton is good
for solving games if it fairly simulates the equivalent deterministic automaton.
In this way, we omit the determinization step in game solving and reactive synthesis.
The fact that our automata are nondeterministic makes them surprisingly simple,
amenable to symbolic implementation, and allows an incremental search for winning
strategies.
acknowledgement: This research was supported in part by the Swiss National Science
Foundation.
alternative_title:
- LNCS
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Nir
full_name: Piterman, Nir
last_name: Piterman
citation:
ama: 'Henzinger TA, Piterman N. Solving games without determinization. In: Vol 4207.
Springer; 2006:395-410. doi:10.1007/11874683_26'
apa: 'Henzinger, T. A., & Piterman, N. (2006). Solving games without determinization
(Vol. 4207, pp. 395–410). Presented at the CSL: Computer Science Logic, Springer.
https://doi.org/10.1007/11874683_26'
chicago: Henzinger, Thomas A, and Nir Piterman. “Solving Games without Determinization,”
4207:395–410. Springer, 2006. https://doi.org/10.1007/11874683_26.
ieee: 'T. A. Henzinger and N. Piterman, “Solving games without determinization,”
presented at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 395–410.'
ista: 'Henzinger TA, Piterman N. 2006. Solving games without determinization. CSL:
Computer Science Logic, LNCS, vol. 4207, 395–410.'
mla: Henzinger, Thomas A., and Nir Piterman. Solving Games without Determinization.
Vol. 4207, Springer, 2006, pp. 395–410, doi:10.1007/11874683_26.
short: T.A. Henzinger, N. Piterman, in:, Springer, 2006, pp. 395–410.
conference:
name: 'CSL: Computer Science Logic'
date_created: 2018-12-11T12:08:51Z
date_published: 2006-09-20T00:00:00Z
date_updated: 2021-01-12T07:56:58Z
day: '20'
doi: 10.1007/11874683_26
extern: 1
intvolume: ' 4207'
month: '09'
page: 395 - 410
publication_status: published
publisher: Springer
publist_id: '295'
quality_controlled: 0
status: public
title: Solving games without determinization
type: conference
volume: 4207
year: '2006'
...