---
_id: '2791'
abstract:
- lang: eng
text: Generally, the motion of fluids is smooth and laminar at low speeds but becomes
highly disordered and turbulent as the velocity increases. The transition from
laminar to turbulent flow can involve a sequence of instabilities in which the
system realizes progressively more complicated states, or it can occur suddenly.
Once the transition has taken place, it is generally assumed that, under steady
conditions, the turbulent state will persist indefinitely. The flow of a fluid
down a straight pipe provides a ubiquitous example of a shear flow undergoing
a sudden transition from laminar to turbulent motion. Extensive calculations and
experimental studies have shown that, at relatively low flow rates, turbulence
in pipes is transient, and is characterized by an exponential distribution of
lifetimes. They also suggest that for Reynolds numbers exceeding a critical value
the lifetime diverges (that is, becomes infinitely large), marking a change from
transient to persistent turbulence. Here we present experimental data and numerical
calculations covering more than two decades of lifetimes, showing that the lifetime
does not in fact diverge but rather increases exponentially with the Reynolds
number. This implies that turbulence in pipes is only a transient event (contrary
to the commonly accepted view), and that the turbulent and laminar states remain
dynamically connected, suggesting avenues for turbulence control.
author:
- first_name: Björn
full_name: Björn Hof
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Jerry
full_name: Westerweel, Jerry
last_name: Westerweel
- first_name: Tobias
full_name: Schneider, Tobias M
last_name: Schneider
- first_name: Bruno
full_name: Eckhardt, Bruno
last_name: Eckhardt
citation:
ama: Hof B, Westerweel J, Schneider T, Eckhardt B. Finite lifetime of turbulence
in shear flows. Nature. 2006;443(7107):59-62. doi:10.1038/nature05089
apa: Hof, B., Westerweel, J., Schneider, T., & Eckhardt, B. (2006). Finite lifetime
of turbulence in shear flows. Nature. Nature Publishing Group. https://doi.org/10.1038/nature05089
chicago: Hof, Björn, Jerry Westerweel, Tobias Schneider, and Bruno Eckhardt. “Finite
Lifetime of Turbulence in Shear Flows.” Nature. Nature Publishing Group,
2006. https://doi.org/10.1038/nature05089.
ieee: B. Hof, J. Westerweel, T. Schneider, and B. Eckhardt, “Finite lifetime of
turbulence in shear flows,” Nature, vol. 443, no. 7107. Nature Publishing
Group, pp. 59–62, 2006.
ista: Hof B, Westerweel J, Schneider T, Eckhardt B. 2006. Finite lifetime of turbulence
in shear flows. Nature. 443(7107), 59–62.
mla: Hof, Björn, et al. “Finite Lifetime of Turbulence in Shear Flows.” Nature,
vol. 443, no. 7107, Nature Publishing Group, 2006, pp. 59–62, doi:10.1038/nature05089.
short: B. Hof, J. Westerweel, T. Schneider, B. Eckhardt, Nature 443 (2006) 59–62.
date_created: 2018-12-11T11:59:37Z
date_published: 2006-09-07T00:00:00Z
date_updated: 2021-01-12T06:59:44Z
day: '07'
doi: 10.1038/nature05089
extern: 1
intvolume: ' 443'
issue: '7107'
month: '09'
page: 59 - 62
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '4098'
quality_controlled: 0
status: public
title: Finite lifetime of turbulence in shear flows
type: journal_article
volume: 443
year: '2006'
...
---
_id: '2792'
abstract:
- lang: eng
text: Transition to turbulence in pipe flow has posed a riddle in fluid dynamics
since the pioneering experiments of Reynolds[1]. Although the laminar flow is
linearly stable for all flow rates, practical pipe flows become turbulent at large
enough flow speeds. Turbulence arises suddenly and fully without distinct steps
and without a clear critical point. The complexity of this problem has puzzled
mathematicians, physicists and engineers for more than a century and no satisfactory
explanation of this problem has been given. In a very recent theoretical approach
it has been suggested that unstable solutions of the Navier Stokes equations may
hold the key to understanding this problem. In numerical studies such unstable
states have been identified as exact solutions for the idealized case of a pipe
with periodic boundary conditions[2, 3]. These solutions have the form of waves
extending through the entire pipe and travelling in the streamwise direction at
a phase speed close to the bulk velocity of the fluid. With the aid of a recently
developed high-speed stereoscopic Particle Image Velocimetry (PIV) system, we
were able to observe transients of such unstable solutions in turbulent pipe flow[4].
author:
- first_name: Björn
full_name: Björn Hof
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Casimir
full_name: van Doorne, Casimir W
last_name: Van Doorne
- first_name: Jerry
full_name: Westerweel, Jerry
last_name: Westerweel
- first_name: Frans
full_name: Nieuwstadt, Frans T
last_name: Nieuwstadt
citation:
ama: Hof B, Van Doorne C, Westerweel J, Nieuwstadt F. Observation of nonlinear travelling
waves in turbulent pipe flow. Fluid Mechanics and its Applications. 2006;78:109-114.
doi:10.1007/1-4020-4159-4_11
apa: Hof, B., Van Doorne, C., Westerweel, J., & Nieuwstadt, F. (2006). Observation
of nonlinear travelling waves in turbulent pipe flow. Fluid Mechanics and Its
Applications. Springer. https://doi.org/10.1007/1-4020-4159-4_11
chicago: Hof, Björn, Casimir Van Doorne, Jerry Westerweel, and Frans Nieuwstadt.
“Observation of Nonlinear Travelling Waves in Turbulent Pipe Flow.” Fluid Mechanics
and Its Applications. Springer, 2006. https://doi.org/10.1007/1-4020-4159-4_11.
ieee: B. Hof, C. Van Doorne, J. Westerweel, and F. Nieuwstadt, “Observation of nonlinear
travelling waves in turbulent pipe flow,” Fluid Mechanics and its Applications,
vol. 78. Springer, pp. 109–114, 2006.
ista: Hof B, Van Doorne C, Westerweel J, Nieuwstadt F. 2006. Observation of nonlinear
travelling waves in turbulent pipe flow. Fluid Mechanics and its Applications.
78, 109–114.
mla: Hof, Björn, et al. “Observation of Nonlinear Travelling Waves in Turbulent
Pipe Flow.” Fluid Mechanics and Its Applications, vol. 78, Springer, 2006,
pp. 109–14, doi:10.1007/1-4020-4159-4_11.
short: B. Hof, C. Van Doorne, J. Westerweel, F. Nieuwstadt, Fluid Mechanics and
Its Applications 78 (2006) 109–114.
date_created: 2018-12-11T11:59:37Z
date_published: 2006-01-18T00:00:00Z
date_updated: 2021-01-12T06:59:45Z
day: '18'
doi: 10.1007/1-4020-4159-4_11
extern: 1
intvolume: ' 78'
month: '01'
page: 109 - 114
publication: Fluid Mechanics and its Applications
publication_status: published
publisher: Springer
publist_id: '4097'
quality_controlled: 0
status: public
title: Observation of nonlinear travelling waves in turbulent pipe flow
type: journal_article
volume: 78
year: '2006'
...
---
_id: '2894'
abstract:
- lang: eng
text: IL-10 is a potent anti-inflammatory and immunomodulatory cytokine, exerting
major effects in the degree and quality of the immune response. Using a newly
generated IL-10 reporter mouse model, which easily allows the study of IL-10 expression
from each allele in a single cell, we report here for the first time that IL-10
is predominantly monoallelic expressed in CD4+ T cells. Furthermore, we have compelling
evidence that this expression pattern is not due to parental imprinting, allelic
exclusion, or strong allelic bias. Instead, our results support a stochastic regulation
mechanism, in which the probability to initiate allelic transcription depends
on the strength of TCR signaling and subsequent capacity to overcome restrictions
imposed by chromatin hypoacetylation. In vivo Ag-experienced T cells show a higher
basal probability to transcribe IL-10 when compared with naive cells, yet still
show mostly monoallelic IL-10 expression. Finally, statistical analysis on allelic
expression data shows transcriptional independence between both alleles. We conclude
that CD4+ T cells have a low probability for IL-10 allelic activation resulting
in a predominantly monoallelic expression pattern, and that IL-10 expression appears
to be stochastically regulated by controlling the frequency of expressing cells,
rather than absolute protein levels per cell.
author:
- first_name: Dinis
full_name: Calado, Dinis P
last_name: Calado
- first_name: Tiago
full_name: Tiago Paixao
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Dan
full_name: Holmberg, Dan
last_name: Holmberg
- first_name: Matthias
full_name: Haury, Matthias
last_name: Haury
citation:
ama: Calado D, Paixao T, Holmberg D, Haury M. Stochastic Monoallelic Expression
of IL 10 in T Cells. Journal of Immunology. 2006;177(8):5358-5364. doi:10.4049/jimmunol.177.8.5358
apa: Calado, D., Paixao, T., Holmberg, D., & Haury, M. (2006). Stochastic Monoallelic
Expression of IL 10 in T Cells. Journal of Immunology. American Association
of Immunologists. https://doi.org/10.4049/jimmunol.177.8.5358
chicago: Calado, Dinis, Tiago Paixao, Dan Holmberg, and Matthias Haury. “Stochastic
Monoallelic Expression of IL 10 in T Cells.” Journal of Immunology. American
Association of Immunologists, 2006. https://doi.org/10.4049/jimmunol.177.8.5358 .
ieee: D. Calado, T. Paixao, D. Holmberg, and M. Haury, “Stochastic Monoallelic Expression
of IL 10 in T Cells,” Journal of Immunology, vol. 177, no. 8. American
Association of Immunologists, pp. 5358–5364, 2006.
ista: Calado D, Paixao T, Holmberg D, Haury M. 2006. Stochastic Monoallelic Expression
of IL 10 in T Cells. Journal of Immunology. 177(8), 5358–5364.
mla: Calado, Dinis, et al. “Stochastic Monoallelic Expression of IL 10 in T Cells.”
Journal of Immunology, vol. 177, no. 8, American Association of Immunologists,
2006, pp. 5358–64, doi:10.4049/jimmunol.177.8.5358
.
short: D. Calado, T. Paixao, D. Holmberg, M. Haury, Journal of Immunology 177 (2006)
5358–5364.
date_created: 2018-12-11T12:00:11Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:32Z
day: '01'
doi: '10.4049/jimmunol.177.8.5358 '
extern: 1
intvolume: ' 177'
issue: '8'
month: '01'
page: 5358 - 5364
publication: Journal of Immunology
publication_status: published
publisher: American Association of Immunologists
publist_id: '3864'
quality_controlled: 0
status: public
title: Stochastic Monoallelic Expression of IL 10 in T Cells
type: journal_article
volume: 177
year: '2006'
...
---
_id: '2921'
abstract:
- lang: eng
text: Most binocular stereo algorithms assume that all scene elements are visible
from both cameras. Scene elements that are visible from only one camera, known
as occlusions, pose an important challenge for stereo. Occlusions are important
for segmentation, because they appear near discontinuities. However, stereo algorithms
tend to ignore occlusions because of their difficulty. One reason is that occlusions
require the input images to be treated symmetrically, which complicates the problem
formulation. Worse, certain depth maps imply physically impossible scene configurations,
and must be excluded from the output. In this chapter we approach the problem
of binocular stereo with occlusions from an energy minimization viewpoint. We
begin by reviewing traditional stereo methods that do not handle occlusions. If
occlusions are ignored, it is easy to formulate the stereo problem as a pixel
labeling problem, which leads to an energy function that is common in early vision.
This kind of energy function can he minimized using graph cuts, which is a combinatorial
optimization technique that has proven to be very effective for low-level vision
problems. Motivated by this, we have designed two graph cut stereo algorithms
that are designed to handle occlusions. These algorithms produce promising experimental
results on real data with ground truth.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Ramin
full_name: Zabih, Ramin
last_name: Zabih
citation:
ama: 'Kolmogorov V, Zabih R. Graph cut algorithms for binocular stereo with occlusions.
In: Handbook of Mathematical Models in Computer Vision. Springer; 2006:423-427.
doi:10.1007/0-387-28831-7_26'
apa: Kolmogorov, V., & Zabih, R. (2006). Graph cut algorithms for binocular
stereo with occlusions. In Handbook of Mathematical Models in Computer Vision
(pp. 423–427). Springer. https://doi.org/10.1007/0-387-28831-7_26
chicago: Kolmogorov, Vladimir, and Ramin Zabih. “Graph Cut Algorithms for Binocular
Stereo with Occlusions.” In Handbook of Mathematical Models in Computer Vision,
423–27. Springer, 2006. https://doi.org/10.1007/0-387-28831-7_26.
ieee: V. Kolmogorov and R. Zabih, “Graph cut algorithms for binocular stereo with
occlusions,” in Handbook of Mathematical Models in Computer Vision, Springer,
2006, pp. 423–427.
ista: 'Kolmogorov V, Zabih R. 2006.Graph cut algorithms for binocular stereo with
occlusions. In: Handbook of Mathematical Models in Computer Vision. , 423–427.'
mla: Kolmogorov, Vladimir, and Ramin Zabih. “Graph Cut Algorithms for Binocular
Stereo with Occlusions.” Handbook of Mathematical Models in Computer Vision,
Springer, 2006, pp. 423–27, doi:10.1007/0-387-28831-7_26.
short: V. Kolmogorov, R. Zabih, in:, Handbook of Mathematical Models in Computer
Vision, Springer, 2006, pp. 423–427.
date_created: 2018-12-11T12:00:21Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:42Z
day: '01'
doi: 10.1007/0-387-28831-7_26
extern: 1
month: '01'
page: 423 - 427
publication: Handbook of Mathematical Models in Computer Vision
publication_status: published
publisher: Springer
publist_id: '3816'
quality_controlled: 0
status: public
title: Graph cut algorithms for binocular stereo with occlusions
type: book_chapter
year: '2006'
...
---
_id: '3002'
abstract:
- lang: eng
text: Arabidopsis thaliana is currently the most important model organism for basic
molecular plant research. It is also a favourable model for developmental biology,
as its embryogenesis follows a nearly invariant pattern of cell divisions and
cell type specifications. Study of embryogenesis can involve genetic, physiological
or biochemical approaches, but is always limited by the inaccessibility of the
embryos which develop deep inside maternal tissue. Thus, for developmental studies,
there is an increasing demand for methods which allow embryogenesis under artificial
conditions, providing better accessibility to experimental manipulation. In this
chapter, we address theoretical aspects of embryo culture, give some thoughts
on which embryo culture system is suited best for which application and finally
discuss three current methods which have been successfully used in Arabidopsis
embryo culture. © 2006 Springer-Verlag Berlin Heidelberg.
alternative_title:
- Plant Cell Monographs
author:
- 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
citation:
ama: 'Sauer M, Friml J. In vitro culture of Arabidopsis embryos. In: Mujib A, Šamaj
J, eds. Somatic Embryogenesis. Vol 2. Springer; 2006:343-354. doi:10.1007/7089_020'
apa: Sauer, M., & Friml, J. (2006). In vitro culture of Arabidopsis embryos.
In A. Mujib & J. Šamaj (Eds.), Somatic Embryogenesis (Vol. 2, pp. 343–354).
Springer. https://doi.org/10.1007/7089_020
chicago: Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos.”
In Somatic Embryogenesis, edited by Abdul Mujib and Jozef Šamaj, 2:343–54.
Springer, 2006. https://doi.org/10.1007/7089_020.
ieee: M. Sauer and J. Friml, “In vitro culture of Arabidopsis embryos,” in Somatic
Embryogenesis, vol. 2, A. Mujib and J. Šamaj, Eds. Springer, 2006, pp. 343–354.
ista: 'Sauer M, Friml J. 2006.In vitro culture of Arabidopsis embryos. In: Somatic
Embryogenesis. Plant Cell Monographs, vol. 2, 343–354.'
mla: Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos.”
Somatic Embryogenesis, edited by Abdul Mujib and Jozef Šamaj, vol. 2, Springer,
2006, pp. 343–54, doi:10.1007/7089_020.
short: M. Sauer, J. Friml, in:, A. Mujib, J. Šamaj (Eds.), Somatic Embryogenesis,
Springer, 2006, pp. 343–354.
date_created: 2018-12-11T12:00:48Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:40:23Z
day: '01'
doi: 10.1007/7089_020
editor:
- first_name: Abdul
full_name: Mujib, Abdul
last_name: Mujib
- first_name: Jozef
full_name: Šamaj, Jozef
last_name: Šamaj
extern: 1
intvolume: ' 2'
month: '01'
page: 343 - 354
publication: Somatic Embryogenesis
publication_status: published
publisher: Springer
publist_id: '3699'
quality_controlled: 0
status: public
title: In vitro culture of Arabidopsis embryos
type: book_chapter
volume: 2
year: '2006'
...
---
_id: '3012'
abstract:
- lang: eng
text: Intercellular flow of the phytohormone auxin underpins multiple developmental
processes in plants. Plant-specific pin-formed (PIN) proteins and several phosphoglycoprotein
(PGP) transporters are crucial factors in auxin transport-related development,
yet the molecular function of PINs remains unknown. Here, we show that PINs mediate
auxin efflux from mammalian and yeast cells without needing additional plant-specific
factors. Conditional gain-of-function alleles and quantitative measurements of
auxin accumulation in Arabidopsis and tobacco cultured cells revealed that the
action of PINs in auxin efflux is distinct from PGP, rate-limiting, specific to
auxins, and sensitive to auxin transport inhibitors. This suggests a direct involvement
of PINs in catalyzing cellular auxin efflux.
author:
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Jozef
full_name: Mravec, Jozef
last_name: Mravec
- first_name: Rodolphe
full_name: Bouchard, Rodolphe
last_name: Bouchard
- first_name: Joshua
full_name: Blakeslee, Joshua
last_name: Blakeslee
- first_name: Melinda F
full_name: Melinda Abas
id: 3CFB3B1C-F248-11E8-B48F-1D18A9856A87
last_name: Abas
- first_name: Daniela
full_name: Seifertová, Daniela
last_name: Seifertová
- first_name: Justyna
full_name: Wiśniewska, Justyna
last_name: Wiśniewska
- first_name: Zerihun
full_name: Tadele, Zerihun
last_name: Tadele
- first_name: Martin
full_name: Kubeš, Martin
last_name: Kubeš
- first_name: Milada
full_name: Čovanová, Milada
last_name: Čovanová
- first_name: Pankaj
full_name: Dhonukshe, Pankaj
last_name: Dhonukshe
- first_name: Petr
full_name: Skůpa, Petr
last_name: Skůpa
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Lucie
full_name: Perry, Lucie
last_name: Perry
- first_name: Pavel
full_name: Křeček, Pavel
last_name: Křeček
- first_name: Ok
full_name: Lee, Ok Ran
last_name: Lee
- first_name: Gerald
full_name: Fink, Gerald R
last_name: Fink
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
- first_name: Angus
full_name: Murphy, Angus S
last_name: Murphy
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Petrášek J, Mravec J, Bouchard R, et al. PIN proteins perform a rate-limiting
function in cellular auxin efflux. Science. 2006;312(5775):914-918. doi:10.1126/science.1123542
apa: Petrášek, J., Mravec, J., Bouchard, R., Blakeslee, J., Abas, M. F., Seifertová,
D., … Friml, J. (2006). PIN proteins perform a rate-limiting function in cellular
auxin efflux. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.1123542
chicago: Petrášek, Jan, Jozef Mravec, Rodolphe Bouchard, Joshua Blakeslee, Melinda
F Abas, Daniela Seifertová, Justyna Wiśniewska, et al. “PIN Proteins Perform a
Rate-Limiting Function in Cellular Auxin Efflux.” Science. American Association
for the Advancement of Science, 2006. https://doi.org/10.1126/science.1123542.
ieee: J. Petrášek et al., “PIN proteins perform a rate-limiting function
in cellular auxin efflux,” Science, vol. 312, no. 5775. American Association
for the Advancement of Science, pp. 914–918, 2006.
ista: Petrášek J, Mravec J, Bouchard R, Blakeslee J, Abas MF, Seifertová D, Wiśniewska
J, Tadele Z, Kubeš M, Čovanová M, Dhonukshe P, Skůpa P, Benková E, Perry L, Křeček
P, Lee O, Fink G, Geisler M, Murphy A, Luschnig C, Zažímalová E, Friml J. 2006.
PIN proteins perform a rate-limiting function in cellular auxin efflux. Science.
312(5775), 914–918.
mla: Petrášek, Jan, et al. “PIN Proteins Perform a Rate-Limiting Function in Cellular
Auxin Efflux.” Science, vol. 312, no. 5775, American Association for the
Advancement of Science, 2006, pp. 914–18, doi:10.1126/science.1123542.
short: J. Petrášek, J. Mravec, R. Bouchard, J. Blakeslee, M.F. Abas, D. Seifertová,
J. Wiśniewska, Z. Tadele, M. Kubeš, M. Čovanová, P. Dhonukshe, P. Skůpa, E. Benková,
L. Perry, P. Křeček, O. Lee, G. Fink, M. Geisler, A. Murphy, C. Luschnig, E. Zažímalová,
J. Friml, Science 312 (2006) 914–918.
date_created: 2018-12-11T12:00:51Z
date_published: 2006-05-12T00:00:00Z
date_updated: 2021-01-12T07:40:27Z
day: '12'
doi: 10.1126/science.1123542
extern: 1
intvolume: ' 312'
issue: '5775'
month: '05'
page: 914 - 918
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '3690'
quality_controlled: 0
status: public
title: PIN proteins perform a rate-limiting function in cellular auxin efflux
type: journal_article
volume: 312
year: '2006'
...
---
_id: '3010'
abstract:
- lang: eng
text: The formation of the leaf vascular pattern has fascinated biologists for centuries.
In the early leaf primordium, complex networks of procambial cells emerge from
homogeneous subepidermal tissue. The molecular nature of the underlying positional
information is unknown, but various lines of evidence implicate gradually restricted
transport routes of the plant hormone auxin in defining sites of procambium formation.
Here we show that a crucial member of the AtPIN family of auxin-efflux-associated
proteins, AtPIN1, is expressed prior to pre-procambial and procambial cell fate
markers in domains that become restricted toward sites of procambium formation.
Subcellular AtPIN1 polarity indicates that auxin is directed to distinct "convergence
points" in the epidermis, from where it defines the positions of major veins.
Integrated polarities in all emerging veins indicate auxin drainage toward pre-existing
veins, but veins display divergent polarities as they become connected at both
ends. Auxin application and transport inhibition reveal that convergence point
positioning and AtPIN1 expression domain dynamics are self-organizing, auxin-transport-dependent
processes. We derive a model for self-regulated, reiterative patterning of all
vein orders and postulate at its onset a common epidermal auxin-focusing mechanism
for major-vein positioning and phyllotactic patterning.
author:
- first_name: Enrico
full_name: Scarpella, Enrico
last_name: Scarpella
- first_name: Danielle
full_name: Marcos, Danielle
last_name: Marcos
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Thomas
full_name: Berleth, Thomas
last_name: Berleth
citation:
ama: Scarpella E, Marcos D, Friml J, Berleth T. Control of leaf vascular patterning
by polar auxin transport. Genes and Development. 2006;20(8):1015-1027.
doi:10.1101/gad.1402406
apa: Scarpella, E., Marcos, D., Friml, J., & Berleth, T. (2006). Control of
leaf vascular patterning by polar auxin transport. Genes and Development.
Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.1402406
chicago: Scarpella, Enrico, Danielle Marcos, Jiří Friml, and Thomas Berleth. “Control
of Leaf Vascular Patterning by Polar Auxin Transport.” Genes and Development.
Cold Spring Harbor Laboratory Press, 2006. https://doi.org/10.1101/gad.1402406.
ieee: E. Scarpella, D. Marcos, J. Friml, and T. Berleth, “Control of leaf vascular
patterning by polar auxin transport,” Genes and Development, vol. 20, no.
8. Cold Spring Harbor Laboratory Press, pp. 1015–1027, 2006.
ista: Scarpella E, Marcos D, Friml J, Berleth T. 2006. Control of leaf vascular
patterning by polar auxin transport. Genes and Development. 20(8), 1015–1027.
mla: Scarpella, Enrico, et al. “Control of Leaf Vascular Patterning by Polar Auxin
Transport.” Genes and Development, vol. 20, no. 8, Cold Spring Harbor Laboratory
Press, 2006, pp. 1015–27, doi:10.1101/gad.1402406.
short: E. Scarpella, D. Marcos, J. Friml, T. Berleth, Genes and Development 20 (2006)
1015–1027.
date_created: 2018-12-11T12:00:51Z
date_published: 2006-04-15T00:00:00Z
date_updated: 2021-01-12T07:40:26Z
day: '15'
doi: 10.1101/gad.1402406
extern: 1
intvolume: ' 20'
issue: '8'
month: '04'
page: 1015 - 1027
publication: Genes and Development
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '3692'
quality_controlled: 0
status: public
title: Control of leaf vascular patterning by polar auxin transport
type: journal_article
volume: 20
year: '2006'
...
---
_id: '3007'
abstract:
- lang: eng
text: Root gravitropism describes the orientation of root growth along the gravity
vector and is mediated by differential cell elongation in the root meristem. This
response requires the coordinated, asymmetric distribution of the phytohormone
auxin within the root meristem, and depends on the concerted activities of PIN
proteins and AUX1 - members of the auxin transport pathway. Here, we show that
intracellular trafficking and proteasome activity combine to control PIN2 degradation
during root gravitropism. Following gravi-stimulation, proteasome-dependent variations
in PIN2 localization and degradation at the upper and lower sides of the root
result in asymmetric distribution of PIN2. Ubiquitination of PIN2 occurs in a
proteasome-dependent manner, indicating that the proteasome is involved in the
control of PIN2 turnover. Stabilization of PIN2 affects its abundance and distribution,
and leads to defects in auxin distribution and gravitropic responses. We describe
the effects of auxin on PIN2 localization and protein levels, indicating that
redistribution of auxin during the gravitropic response may be involved in the
regulation of PIN2 protein.
author:
- first_name: Lindy
full_name: Abas, Lindy
last_name: Abas
- first_name: René
full_name: Benjamins, René
last_name: Benjamins
- first_name: Nenad
full_name: Malenica, Nenad
last_name: Malenica
- first_name: Tomasz
full_name: Paciorek, Tomasz
last_name: Paciorek
- first_name: Justyna
full_name: Wiśniewska, Justyna
last_name: Wiśniewska
- first_name: Jeanette
full_name: Moulinier-Anzola, Jeanette C
last_name: Moulinier Anzola
- first_name: Tobias
full_name: Sieberer, Tobias
last_name: Sieberer
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
citation:
ama: Abas L, Benjamins R, Malenica N, et al. Intracellular trafficking and proteolysis
of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism.
Nature Cell Biology. 2006;8(3):249-256. doi:10.1038/ncb1369
apa: Abas, L., Benjamins, R., Malenica, N., Paciorek, T., Wiśniewska, J., Moulinier
Anzola, J., … Luschnig, C. (2006). Intracellular trafficking and proteolysis of
the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism.
Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb1369
chicago: Abas, Lindy, René Benjamins, Nenad Malenica, Tomasz Paciorek, Justyna Wiśniewska,
Jeanette Moulinier Anzola, Tobias Sieberer, Jiří Friml, and Christian Luschnig.
“Intracellular Trafficking and Proteolysis of the Arabidopsis Auxin-Efflux Facilitator
PIN2 Are Involved in Root Gravitropism.” Nature Cell Biology. Nature Publishing
Group, 2006. https://doi.org/10.1038/ncb1369.
ieee: L. Abas et al., “Intracellular trafficking and proteolysis of the Arabidopsis
auxin-efflux facilitator PIN2 are involved in root gravitropism,” Nature Cell
Biology, vol. 8, no. 3. Nature Publishing Group, pp. 249–256, 2006.
ista: Abas L, Benjamins R, Malenica N, Paciorek T, Wiśniewska J, Moulinier Anzola
J, Sieberer T, Friml J, Luschnig C. 2006. Intracellular trafficking and proteolysis
of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism.
Nature Cell Biology. 8(3), 249–256.
mla: Abas, Lindy, et al. “Intracellular Trafficking and Proteolysis of the Arabidopsis
Auxin-Efflux Facilitator PIN2 Are Involved in Root Gravitropism.” Nature Cell
Biology, vol. 8, no. 3, Nature Publishing Group, 2006, pp. 249–56, doi:10.1038/ncb1369.
short: L. Abas, R. Benjamins, N. Malenica, T. Paciorek, J. Wiśniewska, J. Moulinier
Anzola, T. Sieberer, J. Friml, C. Luschnig, Nature Cell Biology 8 (2006) 249–256.
date_created: 2018-12-11T12:00:50Z
date_published: 2006-03-01T00:00:00Z
date_updated: 2021-01-12T07:40:25Z
day: '01'
doi: 10.1038/ncb1369
extern: 1
intvolume: ' 8'
issue: '3'
month: '03'
page: 249 - 256
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3694'
quality_controlled: 0
status: public
title: Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator
PIN2 are involved in root gravitropism
type: journal_article
volume: 8
year: '2006'
...
---
_id: '3006'
abstract:
- lang: eng
text: 'Dividing plant cells perform a remarkable task of building a new cell wall
within the cytoplasm in a few minutes. A long-standing paradigm claims that this
primordial cell wall, known as the cell plate, is generated by delivery of newly
synthesized material from Golgi apparatus-originated secretory vesicles. Here,
we show that, in diverse plant species, cell surface material, including plasma
membrane proteins, cell wall components, and exogenously applied endocytic tracers,
is rapidly delivered to the forming cell plate. Importantly, this occurs even
when de novo protein synthesis is blocked. In addition, cytokinesis-specific syntaxin
KNOLLE as well as plasma membrane (PM) resident proteins localize to endosomes
that fuse to initiate the cell plate. The rate of endocytosis is strongly enhanced
during cell plate formation, and its genetic or pharmacological inhibition leads
to cytokinesis defects. Our results reveal that endocytic delivery of cell surface
material significantly contributes to cell plate formation during plant cytokinesis. '
author:
- first_name: Pankaj
full_name: Dhonukshe, Pankaj
last_name: Dhonukshe
- first_name: František
full_name: Baluška, František
last_name: Baluška
- first_name: Markus
full_name: Schlicht, Markus
last_name: Schlicht
- first_name: Andrej
full_name: Hlavacka, Andrej
last_name: Hlavacka
- first_name: Jozef
full_name: Šamaj, Jozef
last_name: Šamaj
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Theodorus
full_name: Gadella, Theodorus W
last_name: Gadella
citation:
ama: Dhonukshe P, Baluška F, Schlicht M, et al. Endocytosis of cell surface material
mediates cell plate formation during plant cytokinesis. Developmental Cell.
2006;10(1):137-150. doi:10.1016/j.devcel.2005.11.015
apa: Dhonukshe, P., Baluška, F., Schlicht, M., Hlavacka, A., Šamaj, J., Friml, J.,
& Gadella, T. (2006). Endocytosis of cell surface material mediates cell plate
formation during plant cytokinesis. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2005.11.015
chicago: Dhonukshe, Pankaj, František Baluška, Markus Schlicht, Andrej Hlavacka,
Jozef Šamaj, Jiří Friml, and Theodorus Gadella. “Endocytosis of Cell Surface Material
Mediates Cell Plate Formation during Plant Cytokinesis.” Developmental Cell.
Cell Press, 2006. https://doi.org/10.1016/j.devcel.2005.11.015.
ieee: P. Dhonukshe et al., “Endocytosis of cell surface material mediates
cell plate formation during plant cytokinesis,” Developmental Cell, vol.
10, no. 1. Cell Press, pp. 137–150, 2006.
ista: Dhonukshe P, Baluška F, Schlicht M, Hlavacka A, Šamaj J, Friml J, Gadella
T. 2006. Endocytosis of cell surface material mediates cell plate formation during
plant cytokinesis. Developmental Cell. 10(1), 137–150.
mla: Dhonukshe, Pankaj, et al. “Endocytosis of Cell Surface Material Mediates Cell
Plate Formation during Plant Cytokinesis.” Developmental Cell, vol. 10,
no. 1, Cell Press, 2006, pp. 137–50, doi:10.1016/j.devcel.2005.11.015.
short: P. Dhonukshe, F. Baluška, M. Schlicht, A. Hlavacka, J. Šamaj, J. Friml, T.
Gadella, Developmental Cell 10 (2006) 137–150.
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.devcel.2005.11.015
extern: 1
intvolume: ' 10'
issue: '1'
month: '01'
page: 137 - 150
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '3696'
quality_controlled: 0
status: public
title: Endocytosis of cell surface material mediates cell plate formation during plant
cytokinesis
type: journal_article
volume: 10
year: '2006'
...
---
_id: '3011'
abstract:
- lang: eng
text: Polar flow of the phytohormone auxin requires plasma membrane‐associated PIN
proteins and underlies multiple developmental processes in plants. Here we address
the importance of the polarity of subcellular PIN localization for the directionality
of auxin transport in Arabidopsis thaliana. Expression of different PINs in the
root epidermis revealed the importance of PIN polar positions for directional
auxin flow and root gravitropic growth. Interfering with sequence-embedded polarity
signals directly demonstrates that PIN polarity is a primary factor in determining
the direction of auxin flow in meristematic tissues. This finding provides a crucial
piece in the puzzle of how auxin flow can be redirected via rapid changes in PIN
polarity.
author:
- first_name: Justyna
full_name: Wiśniewska, Justyna
last_name: Wiśniewska
- first_name: Jian
full_name: Xu, Jian
last_name: Xu
- first_name: Daniela
full_name: Seifertová, Daniela
last_name: Seifertová
- first_name: Philip
full_name: Brewer, Philip B
last_name: Brewer
- first_name: Kamil
full_name: Růžička, Kamil
last_name: Růžička
- first_name: Ikram
full_name: Blilou, Ikram
last_name: Blilou
- first_name: David
full_name: Rouquié, David
last_name: Rouquié
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Ben
full_name: Scheres, Ben
last_name: Scheres
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Wiśniewska J, Xu J, Seifertová D, et al. Polar PIN localization directs auxin
flow in plants. Science. 2006;312(5775). doi:10.1126/science.1121356
apa: Wiśniewska, J., Xu, J., Seifertová, D., Brewer, P., Růžička, K., Blilou, I.,
… Friml, J. (2006). Polar PIN localization directs auxin flow in plants. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.1121356
chicago: Wiśniewska, Justyna, Jian Xu, Daniela Seifertová, Philip Brewer, Kamil
Růžička, Ikram Blilou, David Rouquié, Eva Benková, Ben Scheres, and Jiří Friml.
“Polar PIN Localization Directs Auxin Flow in Plants.” Science. American
Association for the Advancement of Science, 2006. https://doi.org/10.1126/science.1121356.
ieee: J. Wiśniewska et al., “Polar PIN localization directs auxin flow in
plants,” Science, vol. 312, no. 5775. American Association for the Advancement
of Science, 2006.
ista: Wiśniewska J, Xu J, Seifertová D, Brewer P, Růžička K, Blilou I, Rouquié D,
Benková E, Scheres B, Friml J. 2006. Polar PIN localization directs auxin flow
in plants. Science. 312(5775).
mla: Wiśniewska, Justyna, et al. “Polar PIN Localization Directs Auxin Flow in Plants.”
Science, vol. 312, no. 5775, American Association for the Advancement of
Science, 2006, doi:10.1126/science.1121356.
short: J. Wiśniewska, J. Xu, D. Seifertová, P. Brewer, K. Růžička, I. Blilou, D.
Rouquié, E. Benková, B. Scheres, J. Friml, Science 312 (2006).
date_created: 2018-12-11T12:00:51Z
date_published: 2006-05-12T00:00:00Z
date_updated: 2021-01-12T07:40:27Z
day: '12'
doi: 10.1126/science.1121356
extern: 1
intvolume: ' 312'
issue: '5775'
month: '05'
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '3691'
quality_controlled: 0
status: public
title: Polar PIN localization directs auxin flow in plants
type: journal_article
volume: 312
year: '2006'
...
---
_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'
license: https://creativecommons.org/licenses/by/4.0/
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'
...