---
_id: '246'
abstract:
- lang: eng
text: Given an intersection of two quadrics X Pm1, with m > 9, the quantitative
arithmetic of the set X(Q) is investigated under the assumption that the singular
locus of X consists of a pair of conjugate singular points defined over Q(i).
acknowledgement: "EP/E053262/1\tEngineering and Physical Sciences Research Council"
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Ritabrata
full_name: Munshi, Ritabrata
last_name: Munshi
citation:
ama: Browning TD, Munshi R. Rational points on singular intersections of quadrics.
Compositio Mathematica. 2013;149(9):1457-1494. doi:10.1112/S0010437X13007185
apa: Browning, T. D., & Munshi, R. (2013). Rational points on singular intersections
of quadrics. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/S0010437X13007185
chicago: Browning, Timothy D, and Ritabrata Munshi. “Rational Points on Singular
Intersections of Quadrics.” Compositio Mathematica. Cambridge University
Press, 2013. https://doi.org/10.1112/S0010437X13007185.
ieee: T. D. Browning and R. Munshi, “Rational points on singular intersections of
quadrics,” Compositio Mathematica, vol. 149, no. 9. Cambridge University
Press, pp. 1457–1494, 2013.
ista: Browning TD, Munshi R. 2013. Rational points on singular intersections of
quadrics. Compositio Mathematica. 149(9), 1457–1494.
mla: Browning, Timothy D., and Ritabrata Munshi. “Rational Points on Singular Intersections
of Quadrics.” Compositio Mathematica, vol. 149, no. 9, Cambridge University
Press, 2013, pp. 1457–94, doi:10.1112/S0010437X13007185.
short: T.D. Browning, R. Munshi, Compositio Mathematica 149 (2013) 1457–1494.
date_created: 2018-12-11T11:45:25Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2021-01-12T06:57:37Z
day: '01'
doi: 10.1112/S0010437X13007185
extern: 1
intvolume: ' 149'
issue: '9'
month: '09'
page: 1457 - 1494
publication: Compositio Mathematica
publication_status: published
publisher: Cambridge University Press
publist_id: '7658'
quality_controlled: 0
status: public
title: Rational points on singular intersections of quadrics
type: journal_article
volume: 149
year: '2013'
...
---
_id: '2466'
abstract:
- lang: eng
text: 'We introduce a new method for efficiently simulating liquid with extreme
amounts of spatial adaptivity. Our method combines several key components to drastically
speed up the simulation of large-scale fluid phenomena: We leverage an alternative
Eulerian tetrahedral mesh discretization to significantly reduce the complexity
of the pressure solve while increasing the robustness with respect to element
quality and removing the possibility of locking. Next, we enable subtle free-surface
phenomena by deriving novel second-order boundary conditions consistent with our
discretization. We couple this discretization with a spatially adaptive Fluid-Implicit
Particle (FLIP) method, enabling efficient, robust, minimally-dissipative simulations
that can undergo sharp changes in spatial resolution while minimizing artifacts.
Along the way, we provide a new method for generating a smooth and detailed surface
from a set of particles with variable sizes. Finally, we explore several new sizing
functions for determining spatially adaptive simulation resolutions, and we show
how to couple them to our simulator. We combine each of these elements to produce
a simulation algorithm that is capable of creating animations at high maximum
resolutions while avoiding common pitfalls like inaccurate boundary conditions
and inefficient computation.'
article_number: '103'
article_processing_charge: No
author:
- first_name: Ryoichi
full_name: Ando, Ryoichi
last_name: Ando
- first_name: Nils
full_name: Thuerey, Nils
last_name: Thuerey
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Ando R, Thuerey N, Wojtan C. Highly adaptive liquid simulations on tetrahedral
meshes. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461982
apa: Ando, R., Thuerey, N., & Wojtan, C. (2013). Highly adaptive liquid simulations
on tetrahedral meshes. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461982
chicago: Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “Highly Adaptive Liquid
Simulations on Tetrahedral Meshes.” ACM Transactions on Graphics. ACM,
2013. https://doi.org/10.1145/2461912.2461982.
ieee: R. Ando, N. Thuerey, and C. Wojtan, “Highly adaptive liquid simulations on
tetrahedral meshes,” ACM Transactions on Graphics, vol. 32, no. 4. ACM,
2013.
ista: Ando R, Thuerey N, Wojtan C. 2013. Highly adaptive liquid simulations on tetrahedral
meshes. ACM Transactions on Graphics. 32(4), 103.
mla: Ando, Ryoichi, et al. “Highly Adaptive Liquid Simulations on Tetrahedral Meshes.”
ACM Transactions on Graphics, vol. 32, no. 4, 103, ACM, 2013, doi:10.1145/2461912.2461982.
short: R. Ando, N. Thuerey, C. Wojtan, ACM Transactions on Graphics 32 (2013).
date_created: 2018-12-11T11:57:50Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2025-09-29T14:13:52Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2461912.2461982
external_id:
isi:
- '000321840100072'
file:
- access_level: open_access
checksum: aeea6b0ff2b27c695aeb8408c7d2fc50
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:25Z
date_updated: 2020-07-14T12:45:41Z
file_id: '5279'
file_name: IST-2016-605-v1+1_tetflip_fixed.pdf
file_size: 8601561
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '4436'
pubrep_id: '605'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Highly adaptive liquid simulations on tetrahedral meshes
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 32
year: '2013'
...
---
_id: '2467'
abstract:
- lang: eng
text: This paper presents a method for computing topology changes for triangle meshes
in an interactive geometric modeling environment. Most triangle meshes in practice
do not exhibit desirable geometric properties, so we develop a solution that is
independent of standard assumptions and robust to geometric errors. Specifically,
we provide the first method for topology change applicable to arbitrary non-solid,
non-manifold, non-closed, self-intersecting surfaces. We prove that this new method
for topology change produces the expected conventional results when applied to
solid (closed, manifold, non-self-intersecting) surfaces---that is, we prove a
backwards-compatibility property relative to prior work. Beyond solid surfaces,
we present empirical evidence that our method remains tolerant to a variety of
surface aberrations through the incorporation of a novel error correction scheme.
Finally, we demonstrate how topology change applied to non-solid objects enables
wholly new and useful behaviors.
article_number: '34'
article_processing_charge: No
author:
- first_name: Gilbert
full_name: Bernstein, Gilbert
last_name: Bernstein
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Bernstein G, Wojtan C. Putting holes in holey geometry: Topology change for
arbitrary surfaces. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2462027'
apa: 'Bernstein, G., & Wojtan, C. (2013). Putting holes in holey geometry: Topology
change for arbitrary surfaces. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2462027'
chicago: 'Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry:
Topology Change for Arbitrary Surfaces.” ACM Transactions on Graphics.
ACM, 2013. https://doi.org/10.1145/2461912.2462027.'
ieee: 'G. Bernstein and C. Wojtan, “Putting holes in holey geometry: Topology change
for arbitrary surfaces,” ACM Transactions on Graphics, vol. 32, no. 4.
ACM, 2013.'
ista: 'Bernstein G, Wojtan C. 2013. Putting holes in holey geometry: Topology change
for arbitrary surfaces. ACM Transactions on Graphics. 32(4), 34.'
mla: 'Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology
Change for Arbitrary Surfaces.” ACM Transactions on Graphics, vol. 32,
no. 4, 34, ACM, 2013, doi:10.1145/2461912.2462027.'
short: G. Bernstein, C. Wojtan, ACM Transactions on Graphics 32 (2013).
date_created: 2018-12-11T11:57:50Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2025-09-29T14:13:25Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2461912.2462027
external_id:
isi:
- '000321840100003'
file:
- access_level: open_access
checksum: 9c8425d62246996ca632c5a01870515b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:43Z
date_updated: 2020-07-14T12:45:41Z
file_id: '4768'
file_name: IST-2016-604-v1+1_toptop2013.pdf
file_size: 3514674
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '4435'
pubrep_id: '604'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Putting holes in holey geometry: Topology change for arbitrary surfaces'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 32
year: '2013'
...
---
_id: '2468'
abstract:
- lang: eng
text: Our work concerns the combination of an Eulerian liquid simulation with a
high-resolution surface tracker (e.g. the level set method or a Lagrangian triangle
mesh). The naive application of a high-resolution surface tracker to a low-resolution
velocity field can produce many visually disturbing physical and topological artifacts
that limit their use in practice. We address these problems by defining an error
function which compares the current state of the surface tracker to the set of
physically valid surface states. By reducing this error with a gradient descent
technique, we introduce a novel physics-based surface fairing method. Similarly,
by treating this error function as a potential energy, we derive a new surface
correction force that mimics the vortex sheet equations. We demonstrate our results
with both level set and mesh-based surface trackers.
article_number: '68'
article_processing_charge: No
author:
- first_name: Morten
full_name: Bojsen-Hansen, Morten
id: 439F0C8C-F248-11E8-B48F-1D18A9856A87
last_name: Bojsen-Hansen
orcid: 0000-0002-4417-3224
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Bojsen-Hansen M, Wojtan C. Liquid surface tracking with error compensation.
ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461991
apa: Bojsen-Hansen, M., & Wojtan, C. (2013). Liquid surface tracking with error
compensation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461991
chicago: Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with
Error Compensation.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2461991.
ieee: M. Bojsen-Hansen and C. Wojtan, “Liquid surface tracking with error compensation,”
ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013.
ista: Bojsen-Hansen M, Wojtan C. 2013. Liquid surface tracking with error compensation.
ACM Transactions on Graphics. 32(4), 68.
mla: Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error
Compensation.” ACM Transactions on Graphics, vol. 32, no. 4, 68, ACM, 2013,
doi:10.1145/2461912.2461991.
short: M. Bojsen-Hansen, C. Wojtan, ACM Transactions on Graphics 32 (2013).
corr_author: '1'
date_created: 2018-12-11T11:57:50Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2025-09-29T14:12:53Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2461912.2461991
external_id:
isi:
- '000321840100037'
file:
- access_level: open_access
checksum: 53d905e0180e23ef3e813b969ffed4e1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:37Z
date_updated: 2020-07-14T12:45:41Z
file_id: '4761'
file_name: IST-2016-603-v1+1_liquidError_web.pdf
file_size: 5813685
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '4434'
pubrep_id: '603'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Liquid surface tracking with error compensation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 32
year: '2013'
...
---
_id: '2469'
abstract:
- lang: eng
text: Cadherins are transmembrane proteins that mediate cell–cell adhesion in animals.
By regulating contact formation and stability, cadherins play a crucial role in
tissue morphogenesis and homeostasis. Here, we review the three major unctions
of cadherins in cell–cell contact formation and stability. Two of those functions
lead to a decrease in interfacial ension at the forming cell–cell contact, thereby
promoting contact expansion — first, by providing adhesion tension that lowers
interfacial tension at the cell–cell contact, and second, by signaling to the
actomyosin cytoskeleton in order to reduce cortex tension and thus interfacial
tension at the contact. The third function of cadherins in cell–cell contact formation
is to stabilize the contact by resisting mechanical forces that pull on the contact.
article_processing_charge: No
author:
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Maître J-L, Heisenberg C-PJ. Three functions of cadherins in cell adhesion.
Current Biology. 2013;23(14):R626-R633. doi:10.1016/j.cub.2013.06.019
apa: Maître, J.-L., & Heisenberg, C.-P. J. (2013). Three functions of cadherins
in cell adhesion. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.06.019
chicago: Maître, Jean-Léon, and Carl-Philipp J Heisenberg. “Three Functions of Cadherins
in Cell Adhesion.” Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.06.019.
ieee: J.-L. Maître and C.-P. J. Heisenberg, “Three functions of cadherins in cell
adhesion,” Current Biology, vol. 23, no. 14. Cell Press, pp. R626–R633,
2013.
ista: Maître J-L, Heisenberg C-PJ. 2013. Three functions of cadherins in cell adhesion.
Current Biology. 23(14), R626–R633.
mla: Maître, Jean-Léon, and Carl-Philipp J. Heisenberg. “Three Functions of Cadherins
in Cell Adhesion.” Current Biology, vol. 23, no. 14, Cell Press, 2013,
pp. R626–33, doi:10.1016/j.cub.2013.06.019.
short: J.-L. Maître, C.-P.J. Heisenberg, Current Biology 23 (2013) R626–R633.
corr_author: '1'
date_created: 2018-12-11T11:57:51Z
date_published: 2013-07-22T00:00:00Z
date_updated: 2025-09-29T14:12:25Z
day: '22'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1016/j.cub.2013.06.019
external_id:
isi:
- '000322414200018'
pmid:
- '23885883'
file:
- access_level: open_access
checksum: 6a424b2f007b41d4955a9135793b2162
content_type: application/pdf
creator: dernst
date_created: 2019-01-24T15:40:22Z
date_updated: 2020-07-14T12:45:41Z
file_id: '5881'
file_name: 2013_CurrentBiology_Maitre.pdf
file_size: 247320
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '14'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: R626 - R633
pmid: 1
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '4433'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Three functions of cadherins in cell adhesion
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 23
year: '2013'
...
---
_id: '247'
abstract:
- lang: eng
text: An improved estimate is provided for the number of Fq-rational points on a
geometrically irreducible, projective, cubic hypersurface that is not equal to
a cone.
acknowledgement: "EP/E053262/1\tEngineering and Physical Sciences Research Council"
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Browning TD. The Lang-Weil estimate for cubic hypersurfaces. Canadian Mathematical
Bulletin. 2013;56(3):500-502. doi:10.4153/CMB-2011-177-4
apa: Browning, T. D. (2013). The Lang-Weil estimate for cubic hypersurfaces. Canadian
Mathematical Bulletin. Unknown. https://doi.org/10.4153/CMB-2011-177-4
chicago: Browning, Timothy D. “The Lang-Weil Estimate for Cubic Hypersurfaces.”
Canadian Mathematical Bulletin. Unknown, 2013. https://doi.org/10.4153/CMB-2011-177-4.
ieee: T. D. Browning, “The Lang-Weil estimate for cubic hypersurfaces,” Canadian
Mathematical Bulletin, vol. 56, no. 3. Unknown, pp. 500–502, 2013.
ista: Browning TD. 2013. The Lang-Weil estimate for cubic hypersurfaces. Canadian
Mathematical Bulletin. 56(3), 500–502.
mla: Browning, Timothy D. “The Lang-Weil Estimate for Cubic Hypersurfaces.” Canadian
Mathematical Bulletin, vol. 56, no. 3, Unknown, 2013, pp. 500–02, doi:10.4153/CMB-2011-177-4.
short: T.D. Browning, Canadian Mathematical Bulletin 56 (2013) 500–502.
date_created: 2018-12-11T11:45:25Z
date_published: 2013-08-31T00:00:00Z
date_updated: 2021-01-12T06:57:40Z
day: '31'
doi: 10.4153/CMB-2011-177-4
extern: 1
intvolume: ' 56'
issue: '3'
month: '08'
page: 500 - 502
publication: Canadian Mathematical Bulletin
publication_status: published
publisher: Unknown
publist_id: '7657'
quality_controlled: 0
status: public
title: The Lang-Weil estimate for cubic hypersurfaces
type: journal_article
volume: 56
year: '2013'
...
---
_id: '2470'
abstract:
- lang: eng
text: Background:Auxin binding protein 1 (ABP1) is a putative auxin receptor and
its function is indispensable for plant growth and development. ABP1 has been
shown to be involved in auxin-dependent regulation of cell division and expansion,
in plasma-membrane-related processes such as changes in transmembrane potential,
and in the regulation of clathrin-dependent endocytosis. However, the ABP1-regulated
downstream pathway remains elusive.Methodology/Principal Findings:Using auxin
transport assays and quantitative analysis of cellular morphology we show that
ABP1 regulates auxin efflux from tobacco BY-2 cells. The overexpression of ABP1can
counterbalance increased auxin efflux and auxin starvation phenotypes caused by
the overexpression of PIN auxin efflux carrier. Relevant mechanism involves the
ABP1-controlled vesicle trafficking processes, including positive regulation of
endocytosis of PIN auxin efflux carriers, as indicated by fluorescence recovery
after photobleaching (FRAP) and pharmacological manipulations.Conclusions/Significance:The
findings indicate the involvement of ABP1 in control of rate of auxin transport
across plasma membrane emphasizing the role of ABP1 in regulation of PIN activity
at the plasma membrane, and highlighting the relevance of ABP1 for the formation
of developmentally important, PIN-dependent auxin gradients.
article_number: e70050
article_processing_charge: No
author:
- first_name: Milada
full_name: Čovanová, Milada
last_name: Čovanová
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Jan
full_name: Rychtář, Jan
last_name: Rychtář
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
citation:
ama: Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. Overexpression
of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco
cells. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070050
apa: Čovanová, M., Sauer, M., Rychtář, J., Friml, J., Petrášek, J., & Zažímalová,
E. (2013). Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent
auxin transport in tobacco cells. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0070050
chicago: Čovanová, Milada, Michael Sauer, Jan Rychtář, Jiří Friml, Jan Petrášek,
and Eva Zažímalová. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent
Auxin Transport in Tobacco Cells.” PLoS One. Public Library of Science,
2013. https://doi.org/10.1371/journal.pone.0070050.
ieee: M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, and E. Zažímalová,
“Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport
in tobacco cells,” PLoS One, vol. 8, no. 7. Public Library of Science,
2013.
ista: Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. 2013. Overexpression
of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco
cells. PLoS One. 8(7), e70050.
mla: Čovanová, Milada, et al. “Overexpression of the Auxin Binding PROTEIN1 Modulates
PIN-Dependent Auxin Transport in Tobacco Cells.” PLoS One, vol. 8, no.
7, e70050, Public Library of Science, 2013, doi:10.1371/journal.pone.0070050.
short: M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, E. Zažímalová,
PLoS One 8 (2013).
date_created: 2018-12-11T11:57:51Z
date_published: 2013-07-23T00:00:00Z
date_updated: 2025-09-29T14:11:54Z
day: '23'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1371/journal.pone.0070050
external_id:
isi:
- '000325211000181'
file:
- access_level: open_access
checksum: 2d47ef47616ef4de1d517d146548184e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:21Z
date_updated: 2020-07-14T12:45:41Z
file_id: '4681'
file_name: IST-2016-413-v1+1_journal.pone.0070050.pdf
file_size: 2294955
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '4432'
pubrep_id: '413'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin
transport in tobacco cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
year: '2013'
...
---
_id: '2471'
abstract:
- lang: eng
text: The impact of disulfide bonds on protein stability goes beyond simple equilibrium
thermodynamics effects associated with the conformational entropy of the unfolded
state. Indeed, disulfide crosslinks may play a role in the prevention of dysfunctional
association and strongly affect the rates of irreversible enzyme inactivation,
highly relevant in biotechnological applications. While these kinetic-stability
effects remain poorly understood, by analogy with proposed mechanisms for processes
of protein aggregation and fibrillogenesis, we propose that they may be determined
by the properties of sparsely-populated, partially-unfolded intermediates. Here
we report the successful design, on the basis of high temperature molecular-dynamics
simulations, of six thermodynamically and kinetically stabilized variants of phytase
from Citrobacter braakii (a biotechnologically important enzyme) with one, two
or three engineered disulfides. Activity measurements and 3D crystal structure
determination demonstrate that the engineered crosslinks do not cause dramatic
alterations in the native structure. The inactivation kinetics for all the variants
displays a strongly non-Arrhenius temperature dependence, with the time-scale
for the irreversible denaturation process reaching a minimum at a given temperature
within the range of the denaturation transition. We show this striking feature
to be a signature of a key role played by a partially unfolded, intermediate state/ensemble.
Energetic and mutational analyses confirm that the intermediate is highly unfolded
(akin to a proposed critical intermediate in the misfolding of the prion protein),
a result that explains the observed kinetic stabilization. Our results provide
a rationale for the kinetic-stability consequences of disulfide-crosslink engineering
and an experimental methodology to arrive at energetic/structural descriptions
of the sparsely populated and elusive intermediates that play key roles in irreversible
protein denaturation.
article_number: e70013
article_processing_charge: No
author:
- first_name: Inmaculada
full_name: Sanchez Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez Romero
- first_name: Antonio
full_name: Ariza, Antonio
last_name: Ariza
- first_name: Keith
full_name: Wilson, Keith
last_name: Wilson
- first_name: Michael
full_name: Skjøt, Michael
last_name: Skjøt
- first_name: Jesper
full_name: Vind, Jesper
last_name: Vind
- first_name: Leonardo
full_name: De Maria, Leonardo
last_name: De Maria
- first_name: Lars
full_name: Skov, Lars
last_name: Skov
- first_name: Jose
full_name: Sánchez Ruiz, Jose
last_name: Sánchez Ruiz
citation:
ama: Sanchez-Romero I, Ariza A, Wilson K, et al. Mechanism of protein kinetic stabilization
by engineered disulfide crosslinks. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070013
apa: Sanchez-Romero, I., Ariza, A., Wilson, K., Skjøt, M., Vind, J., De Maria, L.,
… Sánchez Ruiz, J. (2013). Mechanism of protein kinetic stabilization by engineered
disulfide crosslinks. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0070013
chicago: Sanchez-Romero, Inmaculada, Antonio Ariza, Keith Wilson, Michael Skjøt,
Jesper Vind, Leonardo De Maria, Lars Skov, and Jose Sánchez Ruiz. “Mechanism of
Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” PLoS One.
Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070013.
ieee: I. Sanchez-Romero et al., “Mechanism of protein kinetic stabilization
by engineered disulfide crosslinks,” PLoS One, vol. 8, no. 7. Public Library
of Science, 2013.
ista: Sanchez-Romero I, Ariza A, Wilson K, Skjøt M, Vind J, De Maria L, Skov L,
Sánchez Ruiz J. 2013. Mechanism of protein kinetic stabilization by engineered
disulfide crosslinks. PLoS One. 8(7), e70013.
mla: Sanchez-Romero, Inmaculada, et al. “Mechanism of Protein Kinetic Stabilization
by Engineered Disulfide Crosslinks.” PLoS One, vol. 8, no. 7, e70013, Public
Library of Science, 2013, doi:10.1371/journal.pone.0070013.
short: I. Sanchez-Romero, A. Ariza, K. Wilson, M. Skjøt, J. Vind, L. De Maria, L.
Skov, J. Sánchez Ruiz, PLoS One 8 (2013).
date_created: 2018-12-11T11:57:51Z
date_published: 2013-07-30T00:00:00Z
date_updated: 2025-09-29T14:10:56Z
day: '30'
ddc:
- '570'
department:
- _id: HaJa
doi: 10.1371/journal.pone.0070013
external_id:
isi:
- '000323114200054'
file:
- access_level: open_access
checksum: c0c96cc76ed7ef0d036a31a7e33c9a37
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:07Z
date_updated: 2020-07-14T12:45:41Z
file_id: '5124'
file_name: IST-2016-414-v1+1_journal.pone.0070013.pdf
file_size: 1323666
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '4430'
pubrep_id: '414'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanism of protein kinetic stabilization by engineered disulfide crosslinks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
year: '2013'
...
---
_id: '2472'
abstract:
- lang: eng
text: Plant-specific PIN-formed (PIN) efflux transporters for the plant hormone
auxin are required for tissue-specific directional auxin transport and cellular
auxin homeostasis. The Arabidopsis PIN protein family has been shown to play important
roles in developmental processes such as embryogenesis, organogenesis, vascular
tissue differentiation, root meristem patterning and tropic growth. Here we analyzed
roles of the less characterised Arabidopsis PIN6 auxin transporter. PIN6 is auxin-inducible
and is expressed during multiple auxin-regulated developmental processes. Loss
of pin6 function interfered with primary root growth and lateral root development.
Misexpression of PIN6 affected auxin transport and interfered with auxin homeostasis
in other growth processes such as shoot apical dominance, lateral root primordia
development, adventitious root formation, root hair outgrowth and root waving.
These changes in auxin-regulated growth correlated with a reduction in total auxin
transport as well as with an altered activity of DR5-GUS auxin response reporter.
Overall, the data indicate that PIN6 regulates auxin homeostasis during plant
development.
article_number: e70069
article_processing_charge: No
author:
- first_name: Christopher
full_name: Cazzonelli, Christopher
last_name: Cazzonelli
- first_name: Marleen
full_name: Vanstraelen, Marleen
last_name: Vanstraelen
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Kuide
full_name: Yin, Kuide
last_name: Yin
- first_name: Ashley
full_name: Carron Arthur, Ashley
last_name: Carron Arthur
- first_name: Nazia
full_name: Nisar, Nazia
last_name: Nisar
- first_name: Gauri
full_name: Tarle, Gauri
last_name: Tarle
- first_name: Abby
full_name: Cuttriss, Abby
last_name: Cuttriss
- first_name: Iain
full_name: Searle, Iain
last_name: Searle
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Ulrike
full_name: Mathesius, Ulrike
last_name: Mathesius
- first_name: Josette
full_name: Masle, Josette
last_name: Masle
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Barry
full_name: Pogson, Barry
last_name: Pogson
citation:
ama: Cazzonelli C, Vanstraelen M, Simon S, et al. Role of the Arabidopsis PIN6 auxin
transporter in auxin homeostasis and auxin-mediated development. PLoS One.
2013;8(7). doi:10.1371/journal.pone.0070069
apa: Cazzonelli, C., Vanstraelen, M., Simon, S., Yin, K., Carron Arthur, A., Nisar,
N., … Pogson, B. (2013). Role of the Arabidopsis PIN6 auxin transporter in auxin
homeostasis and auxin-mediated development. PLoS One. Public Library of
Science. https://doi.org/10.1371/journal.pone.0070069
chicago: Cazzonelli, Christopher, Marleen Vanstraelen, Sibu Simon, Kuide Yin, Ashley
Carron Arthur, Nazia Nisar, Gauri Tarle, et al. “Role of the Arabidopsis PIN6
Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” PLoS
One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070069.
ieee: C. Cazzonelli et al., “Role of the Arabidopsis PIN6 auxin transporter
in auxin homeostasis and auxin-mediated development,” PLoS One, vol. 8,
no. 7. Public Library of Science, 2013.
ista: Cazzonelli C, Vanstraelen M, Simon S, Yin K, Carron Arthur A, Nisar N, Tarle
G, Cuttriss A, Searle I, Benková E, Mathesius U, Masle J, Friml J, Pogson B. 2013.
Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated
development. PLoS One. 8(7), e70069.
mla: Cazzonelli, Christopher, et al. “Role of the Arabidopsis PIN6 Auxin Transporter
in Auxin Homeostasis and Auxin-Mediated Development.” PLoS One, vol. 8,
no. 7, e70069, Public Library of Science, 2013, doi:10.1371/journal.pone.0070069.
short: C. Cazzonelli, M. Vanstraelen, S. Simon, K. Yin, A. Carron Arthur, N. Nisar,
G. Tarle, A. Cuttriss, I. Searle, E. Benková, U. Mathesius, J. Masle, J. Friml,
B. Pogson, PLoS One 8 (2013).
date_created: 2018-12-11T11:57:52Z
date_published: 2013-07-29T00:00:00Z
date_updated: 2025-09-29T14:11:25Z
day: '29'
ddc:
- '580'
- '570'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1371/journal.pone.0070069
ec_funded: 1
external_id:
isi:
- '000323369700128'
file:
- access_level: open_access
checksum: 3be71828b6c2ba9c90eb7056e3f7f57a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:34Z
date_updated: 2020-07-14T12:45:41Z
file_id: '5222'
file_name: IST-2015-393-v1+1_journal.pone.0070069.pdf
file_size: 9003465
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '4431'
pubrep_id: '393'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated
development
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
year: '2013'
...
---
_id: '2473'
abstract:
- lang: eng
text: 'When a mutation with selective advantage s spreads through a panmictic population,
it may cause two lineages at a linked locus to coalesce; the probability of coalescence
is exp(−2rT), where T∼log(2Ns)/s is the time to fixation, N is the number of haploid
individuals, and r is the recombination rate. Population structure delays fixation,
and so weakens the effect of a selective sweep. However, favourable alleles spread
through a spatially continuous population behind a narrow wavefront; ancestral
lineages are confined at the tip of this front, and so coalesce rapidly. In extremely
dense populations, coalescence is dominated by rare fluctuations ahead of the
front. However, we show that for moderate densities, a simple quasi-deterministic
approximation applies: the rate of coalescence within the front is λ∼2g(η)/(ρℓ),
where ρ is the population density and is the characteristic scale of the wavefront;
g(η) depends only on the strength of random drift, . The net effect of a sweep
on coalescence also depends crucially on whether two lineages are ever both within
the wavefront at the same time: even in the extreme case when coalescence within
the front is instantaneous, the net rate of coalescence may be lower than in a
single panmictic population. Sweeps can also have a substantial impact on the
rate of gene flow. A single lineage will jump to a new location when it is hit
by a sweep, with mean square displacement ; this can be substantial if the species’
range, L, is large, even if the species-wide rate of sweeps per map length, Λ/R,
is small. This effect is half as strong in two dimensions. In contrast, the rate
of coalescence between lineages, at random locations in space and on the genetic
map, is proportional to (c/L)(Λ/R), where c is the wavespeed: thus, on average,
one-dimensional structure is likely to reduce coalescence due to sweeps, relative
to panmixis. In two dimensions, genes must move along the front before they can
coalesce; this process is rapid, being dominated by rare fluctuations. This leads
to a dramatically higher rate of coalescence within the wavefront than if lineages
simply diffused along the front. Nevertheless, the net rate of coalescence due
to a sweep through a two-dimensional population is likely to be lower than it
would be with panmixis.'
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: Barton NH, Etheridge A, Kelleher J, Véber A. Genetic hitch-hiking in spatially
extended populations. Theoretical Population Biology. 2013;87(8):75-89.
doi:10.1016/j.tpb.2012.12.001
apa: Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Genetic
hitch-hiking in spatially extended populations. Theoretical Population Biology.
Elsevier. https://doi.org/10.1016/j.tpb.2012.12.001
chicago: Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber.
“Genetic Hitch-Hiking in Spatially Extended Populations.” Theoretical Population
Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2012.12.001.
ieee: N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Genetic hitch-hiking
in spatially extended populations,” Theoretical Population Biology, vol.
87, no. 8. Elsevier, pp. 75–89, 2013.
ista: Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Genetic hitch-hiking in
spatially extended populations. Theoretical Population Biology. 87(8), 75–89.
mla: Barton, Nicholas H., et al. “Genetic Hitch-Hiking in Spatially Extended Populations.”
Theoretical Population Biology, vol. 87, no. 8, Elsevier, 2013, pp. 75–89,
doi:10.1016/j.tpb.2012.12.001.
short: N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population
Biology 87 (2013) 75–89.
corr_author: '1'
date_created: 2018-12-11T11:57:52Z
date_published: 2013-01-03T00:00:00Z
date_updated: 2025-09-29T14:10:28Z
day: '03'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2012.12.001
ec_funded: 1
external_id:
isi:
- '000322688800008'
file:
- access_level: open_access
checksum: 4274ec1f433b838a7d5b941cc9684ca7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:54Z
date_updated: 2020-07-14T12:45:41Z
file_id: '5376'
file_name: IST-2013-118-v1+1_bartonetalRevision.pdf
file_size: 1706282
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 87'
isi: 1
issue: '8'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 75 - 89
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Theoretical Population Biology
publication_status: published
publisher: Elsevier
publist_id: '4428'
pubrep_id: '118'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic hitch-hiking in spatially extended populations
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 87
year: '2013'
...
---
_id: '2478'
abstract:
- lang: eng
text: Despite the pivotal functions of the NMDA receptor (NMDAR) for neural circuit
development and synaptic plasticity, the molecular mechanisms underlying the dynamics
of NMDAR trafficking are poorly understood. The cell adhesion molecule neuroligin-1
(NL1) modifies NMDAR-dependent synaptic transmission and synaptic plasticity,
but it is unclear whether NL1 controls synaptic accumulation or function of the
receptors. Here, we provide evidence that NL1 regulates the abundance of NMDARs
at postsynaptic sites. This function relies on extracellular, NL1 isoform-specific
sequences that facilitate biochemical interactions between NL1 and the NMDAR GluN1
subunit. Our work uncovers NL1 isoform-specific cisinteractions with ionotropic
glutamate receptors as a key mechanism for controlling synaptic properties.
author:
- first_name: Elaine
full_name: Budreck, Elaine C
last_name: Budreck
- first_name: Oh
full_name: Kwon, Oh-Bin
last_name: Kwon
- first_name: Jung
full_name: Jung, Jung-Hoon
last_name: Jung
- first_name: Stéphane
full_name: Baudouin, Stéphane J
last_name: Baudouin
- first_name: Albert
full_name: Thommen, Albert
last_name: Thommen
- first_name: Hye
full_name: Kim, Hye-Sun
last_name: Kim
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
- first_name: Harumi
full_name: Harumi Harada
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Katsuhiko
full_name: Tabuchi, Katsuhiko
last_name: Tabuchi
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Peter
full_name: Scheiffele, Peter
last_name: Scheiffele
- first_name: Joung
full_name: Kim, Joung-Hun
last_name: Kim
citation:
ama: Budreck E, Kwon O, Jung J, et al. Neuroligin-1 controls synaptic abundance
of NMDA-type glutamate receptors through extracellular coupling. PNAS.
2013;110(2):725-730. doi:10.1073/pnas.1214718110
apa: Budreck, E., Kwon, O., Jung, J., Baudouin, S., Thommen, A., Kim, H., … Kim,
J. (2013). Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors
through extracellular coupling. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1214718110
chicago: Budreck, Elaine, Oh Kwon, Jung Jung, Stéphane Baudouin, Albert Thommen,
Hye Kim, Yugo Fukazawa, et al. “Neuroligin-1 Controls Synaptic Abundance of NMDA-Type
Glutamate Receptors through Extracellular Coupling.” PNAS. National Academy
of Sciences, 2013. https://doi.org/10.1073/pnas.1214718110.
ieee: E. Budreck et al., “Neuroligin-1 controls synaptic abundance of NMDA-type
glutamate receptors through extracellular coupling,” PNAS, vol. 110, no.
2. National Academy of Sciences, pp. 725–730, 2013.
ista: Budreck E, Kwon O, Jung J, Baudouin S, Thommen A, Kim H, Fukazawa Y, Harada
H, Tabuchi K, Shigemoto R, Scheiffele P, Kim J. 2013. Neuroligin-1 controls synaptic
abundance of NMDA-type glutamate receptors through extracellular coupling. PNAS.
110(2), 725–730.
mla: Budreck, Elaine, et al. “Neuroligin-1 Controls Synaptic Abundance of NMDA-Type
Glutamate Receptors through Extracellular Coupling.” PNAS, vol. 110, no.
2, National Academy of Sciences, 2013, pp. 725–30, doi:10.1073/pnas.1214718110.
short: E. Budreck, O. Kwon, J. Jung, S. Baudouin, A. Thommen, H. Kim, Y. Fukazawa,
H. Harada, K. Tabuchi, R. Shigemoto, P. Scheiffele, J. Kim, PNAS 110 (2013) 725–730.
date_created: 2018-12-11T11:57:54Z
date_published: 2013-01-08T00:00:00Z
date_updated: 2021-01-12T06:57:43Z
day: '08'
doi: 10.1073/pnas.1214718110
extern: 1
intvolume: ' 110'
issue: '2'
month: '01'
page: 725 - 730
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '4423'
quality_controlled: 0
status: public
title: Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through
extracellular coupling
type: journal_article
volume: 110
year: '2013'
...
---
_id: '250'
abstract:
- lang: eng
text: Châtelet surfaces provide a rich source of geometrically rational surfaces
that do not always satisfy the Hasse principle. Restricting attention to a special
class of Châtelet surfaces, we investigate the frequency that such counter-examples
arise over the rational numbers.
acknowledgement: While working on this paper, the first author was supported by an
IUF Junior and ANR while the second author was supported by ERC grant 306457.
author:
- first_name: Régis
full_name: de la Bretèche, Régis
last_name: De La Bretèche
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: De La Bretèche R, Browning TD. Density of Châtelet surfaces failing the Hasse
principle. Proceedings of the London Mathematical Society. 2013;108(4):1030-1078.
doi:10.1112/plms/pdt060
apa: De La Bretèche, R., & Browning, T. D. (2013). Density of Châtelet surfaces
failing the Hasse principle. Proceedings of the London Mathematical Society.
Oxford University Press. https://doi.org/10.1112/plms/pdt060
chicago: De La Bretèche, Régis, and Timothy D Browning. “Density of Châtelet Surfaces
Failing the Hasse Principle.” Proceedings of the London Mathematical Society.
Oxford University Press, 2013. https://doi.org/10.1112/plms/pdt060.
ieee: R. De La Bretèche and T. D. Browning, “Density of Châtelet surfaces failing
the Hasse principle,” Proceedings of the London Mathematical Society, vol.
108, no. 4. Oxford University Press, pp. 1030–1078, 2013.
ista: De La Bretèche R, Browning TD. 2013. Density of Châtelet surfaces failing
the Hasse principle. Proceedings of the London Mathematical Society. 108(4), 1030–1078.
mla: De La Bretèche, Régis, and Timothy D. Browning. “Density of Châtelet Surfaces
Failing the Hasse Principle.” Proceedings of the London Mathematical Society,
vol. 108, no. 4, Oxford University Press, 2013, pp. 1030–78, doi:10.1112/plms/pdt060.
short: R. De La Bretèche, T.D. Browning, Proceedings of the London Mathematical
Society 108 (2013) 1030–1078.
date_created: 2018-12-11T11:45:26Z
date_published: 2013-11-29T00:00:00Z
date_updated: 2021-01-12T06:57:51Z
day: '29'
doi: 10.1112/plms/pdt060
extern: 1
intvolume: ' 108'
issue: '4'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1210.4010
month: '11'
oa: 1
page: 1030 - 1078
publication: Proceedings of the London Mathematical Society
publication_status: published
publisher: Oxford University Press
publist_id: '7652'
quality_controlled: 0
status: public
title: Density of Châtelet surfaces failing the Hasse principle
type: journal_article
volume: 108
year: '2013'
...
---
_id: '251'
abstract:
- lang: eng
text: We study the density of varieties in a certain family which do not satisfy
the Hasse principle. This work relies on results recently obtained by Colliot-Thélène
[3].
author:
- first_name: Régis
full_name: de la Bretèche, Régis
last_name: De La Bretèche
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: De La Bretèche R, Browning TD. Counter examples to the Hasse principle among
certain coflasque tori. Journal de Theorie des Nombres de Bordeaux. 2013;26(1):25-44.
doi:10.5802/jtnb.857
apa: De La Bretèche, R., & Browning, T. D. (2013). Counter examples to the Hasse
principle among certain coflasque tori. Journal de Theorie Des Nombres de Bordeaux.
Universite de Bordeaux I. https://doi.org/10.5802/jtnb.857
chicago: De La Bretèche, Régis, and Timothy D Browning. “Counter Examples to the
Hasse Principle among Certain Coflasque Tori.” Journal de Theorie Des Nombres
de Bordeaux. Universite de Bordeaux I, 2013. https://doi.org/10.5802/jtnb.857.
ieee: R. De La Bretèche and T. D. Browning, “Counter examples to the Hasse principle
among certain coflasque tori,” Journal de Theorie des Nombres de Bordeaux,
vol. 26, no. 1. Universite de Bordeaux I, pp. 25–44, 2013.
ista: De La Bretèche R, Browning TD. 2013. Counter examples to the Hasse principle
among certain coflasque tori. Journal de Theorie des Nombres de Bordeaux. 26(1),
25–44.
mla: De La Bretèche, Régis, and Timothy D. Browning. “Counter Examples to the Hasse
Principle among Certain Coflasque Tori.” Journal de Theorie Des Nombres de
Bordeaux, vol. 26, no. 1, Universite de Bordeaux I, 2013, pp. 25–44, doi:10.5802/jtnb.857.
short: R. De La Bretèche, T.D. Browning, Journal de Theorie Des Nombres de Bordeaux
26 (2013) 25–44.
date_created: 2018-12-11T11:45:26Z
date_published: 2013-05-14T00:00:00Z
date_updated: 2021-01-12T06:57:55Z
day: '14'
doi: 10.5802/jtnb.857
extern: 1
intvolume: ' 26'
issue: '1'
month: '05'
page: 25 - 44
publication: Journal de Theorie des Nombres de Bordeaux
publication_status: published
publisher: Universite de Bordeaux I
publist_id: '7651'
quality_controlled: 0
status: public
title: Counter examples to the Hasse principle among certain coflasque tori
type: journal_article
volume: 26
year: '2013'
...
---
_id: '2516'
abstract:
- lang: eng
text: 'We study the problem of object recognition for categories for which we have
no training examples, a task also called zero-data or zero-shot learning. This
situation has hardly been studied in computer vision research, even though it
occurs frequently: the world contains tens of thousands of different object classes
and for only few of them image collections have been formed and suitably annotated.
To tackle the problem we introduce attribute-based classification: objects are
identified based on a high-level description that is phrased in terms of semantic
attributes, such as the object''s color or shape. Because the identification of
each such property transcends the specific learning task at hand, the attribute
classifiers can be pre-learned independently, e.g. from existing image datasets
unrelated to the current task. Afterwards, new classes can be detected based on
their attribute representation, without the need for a new training phase. In
this paper we also introduce a new dataset, Animals with Attributes, of over 30,000
images of 50 animal classes, annotated with 85 semantic attributes. Extensive
experiments on this and two more datasets show that attribute-based classification
indeed is able to categorize images without access to any training images of the
target classes.'
article_processing_charge: No
author:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Hannes
full_name: Nickisch, Hannes
last_name: Nickisch
- first_name: Stefan
full_name: Harmeling, Stefan
last_name: Harmeling
citation:
ama: Lampert C, Nickisch H, Harmeling S. Attribute-based classification for zero-shot
learning of object categories. IEEE Transactions on Pattern Analysis and Machine
Intelligence. 2013;36(3):453-465. doi:10.1109/TPAMI.2013.140
apa: Lampert, C., Nickisch, H., & Harmeling, S. (2013). Attribute-based classification
for zero-shot learning of object categories. IEEE Transactions on Pattern Analysis
and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2013.140
chicago: Lampert, Christoph, Hannes Nickisch, and Stefan Harmeling. “Attribute-Based
Classification for Zero-Shot Learning of Object Categories.” IEEE Transactions
on Pattern Analysis and Machine Intelligence. IEEE, 2013. https://doi.org/10.1109/TPAMI.2013.140.
ieee: C. Lampert, H. Nickisch, and S. Harmeling, “Attribute-based classification
for zero-shot learning of object categories,” IEEE Transactions on Pattern
Analysis and Machine Intelligence, vol. 36, no. 3. IEEE, pp. 453–465, 2013.
ista: Lampert C, Nickisch H, Harmeling S. 2013. Attribute-based classification for
zero-shot learning of object categories. IEEE Transactions on Pattern Analysis
and Machine Intelligence. 36(3), 453–465.
mla: Lampert, Christoph, et al. “Attribute-Based Classification for Zero-Shot Learning
of Object Categories.” IEEE Transactions on Pattern Analysis and Machine Intelligence,
vol. 36, no. 3, IEEE, 2013, pp. 453–65, doi:10.1109/TPAMI.2013.140.
short: C. Lampert, H. Nickisch, S. Harmeling, IEEE Transactions on Pattern Analysis
and Machine Intelligence 36 (2013) 453–465.
date_created: 2018-12-11T11:58:08Z
date_published: 2013-07-30T00:00:00Z
date_updated: 2025-09-29T14:09:57Z
day: '30'
department:
- _id: ChLa
doi: 10.1109/TPAMI.2013.140
external_id:
isi:
- '000331450100005'
intvolume: ' 36'
isi: 1
issue: '3'
language:
- iso: eng
month: '07'
oa_version: None
page: 453 - 465
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '4385'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Attribute-based classification for zero-shot learning of object categories
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 36
year: '2013'
...
---
_id: '2517'
abstract:
- lang: eng
text: 'Traditional formal methods are based on a Boolean satisfaction notion: a
reactive system satisfies, or not, a given specification. We generalize formal
methods to also address the quality of systems. As an adequate specification formalism
we introduce the linear temporal logic LTL[F]. The satisfaction value of an LTL[F]
formula is a number between 0 and 1, describing the quality of the satisfaction.
The logic generalizes traditional LTL by augmenting it with a (parameterized)
set F of arbitrary functions over the interval [0,1]. For example, F may contain
the maximum or minimum between the satisfaction values of subformulas, their product,
and their average. The classical decision problems in formal methods, such as
satisfiability, model checking, and synthesis, are generalized to search and optimization
problems in the quantitative setting. For example, model checking asks for the
quality in which a specification is satisfied, and synthesis returns a system
satisfying the specification with the highest quality. Reasoning about quality
gives rise to other natural questions, like the distance between specifications.
We formalize these basic questions and study them for LTL[F]. By extending the
automata-theoretic approach for LTL to a setting that takes quality into an account,
we are able to solve the above problems and show that reasoning about LTL[F] has
roughly the same complexity as reasoning about traditional LTL.'
acknowledgement: 'ERC Grant QUALITY. '
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Shaull
full_name: Almagor, Shaull
last_name: Almagor
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: Almagor S, Boker U, Kupferman O. Formalizing and reasoning about quality. 2013;7966(Part
2):15-27. doi:10.1007/978-3-642-39212-2_3
apa: 'Almagor, S., Boker, U., & Kupferman, O. (2013). Formalizing and reasoning
about quality. Presented at the ICALP: Automata, Languages and Programming, Riga,
Latvia: Springer. https://doi.org/10.1007/978-3-642-39212-2_3'
chicago: Almagor, Shaull, Udi Boker, and Orna Kupferman. “Formalizing and Reasoning
about Quality.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39212-2_3.
ieee: S. Almagor, U. Boker, and O. Kupferman, “Formalizing and reasoning about quality,”
vol. 7966, no. Part 2. Springer, pp. 15–27, 2013.
ista: Almagor S, Boker U, Kupferman O. 2013. Formalizing and reasoning about quality.
7966(Part 2), 15–27.
mla: Almagor, Shaull, et al. Formalizing and Reasoning about Quality. Vol.
7966, no. Part 2, Springer, 2013, pp. 15–27, doi:10.1007/978-3-642-39212-2_3.
short: S. Almagor, U. Boker, O. Kupferman, 7966 (2013) 15–27.
conference:
end_date: 2013-07-12
location: Riga, Latvia
name: 'ICALP: Automata, Languages and Programming'
start_date: 2013-07-08
date_created: 2018-12-11T11:58:08Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2020-08-11T10:09:47Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-642-39212-2_3
ec_funded: 1
file:
- access_level: open_access
checksum: 85afbf6c18a2c7e377c52c9410e2d824
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T11:16:12Z
date_updated: 2020-07-14T12:45:42Z
file_id: '7860'
file_name: 2013_ICALP_Almagor.pdf
file_size: 363031
relation: main_file
file_date_updated: 2020-07-14T12:45:42Z
has_accepted_license: '1'
intvolume: ' 7966'
issue: Part 2
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 15 - 27
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: Springer
publist_id: '4384'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Formalizing and reasoning about quality
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7966
year: '2013'
...
---
_id: '2518'
abstract:
- lang: eng
text: A class of valued constraint satisfaction problems (VCSPs) is characterised
by a valued constraint language, a fixed set of cost functions on a finite domain.
An instance of the problem is specified by a sum of cost functions from the language
with the goal to minimise the sum. We study which classes of finite-valued languages
can be solved exactly by the basic linear programming relaxation (BLP). Thapper
and Živný showed [20] that if BLP solves the language then the language admits
a binary commutative fractional polymorphism. We prove that the converse is also
true. This leads to a necessary and a sufficient condition which can be checked
in polynomial time for a given language. In contrast, the previous necessary and
sufficient condition due to [20] involved infinitely many inequalities. More recently,
Thapper and Živný [21] showed (using, in particular, a technique introduced in
this paper) that core languages that do not satisfy our condition are NP-hard.
Taken together, these results imply that a finite-valued language can either be
solved using Linear Programming or is NP-hard.
alternative_title:
- LNCS
arxiv: 1
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Kolmogorov V. The power of linear programming for finite-valued CSPs: A constructive
characterization. In: Vol 7965. Springer; 2013:625-636. doi:10.1007/978-3-642-39206-1_53'
apa: 'Kolmogorov, V. (2013). The power of linear programming for finite-valued CSPs:
A constructive characterization (Vol. 7965, pp. 625–636). Presented at the ICALP:
Automata, Languages and Programming, Riga, Latvia: Springer. https://doi.org/10.1007/978-3-642-39206-1_53'
chicago: 'Kolmogorov, Vladimir. “The Power of Linear Programming for Finite-Valued
CSPs: A Constructive Characterization,” 7965:625–36. Springer, 2013. https://doi.org/10.1007/978-3-642-39206-1_53.'
ieee: 'V. Kolmogorov, “The power of linear programming for finite-valued CSPs: A
constructive characterization,” presented at the ICALP: Automata, Languages and
Programming, Riga, Latvia, 2013, vol. 7965, no. 1, pp. 625–636.'
ista: 'Kolmogorov V. 2013. The power of linear programming for finite-valued CSPs:
A constructive characterization. ICALP: Automata, Languages and Programming, LNCS,
vol. 7965, 625–636.'
mla: 'Kolmogorov, Vladimir. The Power of Linear Programming for Finite-Valued
CSPs: A Constructive Characterization. Vol. 7965, no. 1, Springer, 2013, pp.
625–36, doi:10.1007/978-3-642-39206-1_53.'
short: V. Kolmogorov, in:, Springer, 2013, pp. 625–636.
conference:
end_date: 2013-07-12
location: Riga, Latvia
name: 'ICALP: Automata, Languages and Programming'
start_date: 2013-07-08
corr_author: '1'
date_created: 2018-12-11T11:58:08Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2025-09-23T14:14:56Z
day: '01'
department:
- _id: VlKo
doi: 10.1007/978-3-642-39206-1_53
external_id:
arxiv:
- '1207.7213'
intvolume: ' 7965'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1207.7213
month: '07'
oa: 1
oa_version: Preprint
page: 625 - 636
publication_status: published
publisher: Springer
publist_id: '4383'
quality_controlled: '1'
related_material:
record:
- id: '2271'
relation: later_version
status: public
scopus_import: 1
status: public
title: 'The power of linear programming for finite-valued CSPs: A constructive characterization'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7965
year: '2013'
...
---
_id: '2520'
abstract:
- lang: eng
text: "We propose a probabilistic model to infer supervised latent variables in\r\nthe
Hamming space from observed data. Our model allows simultaneous\r\ninference of
the number of binary latent variables, and their values. The\r\nlatent variables
preserve neighbourhood structure of the data in a sense\r\nthat objects in the
same semantic concept have similar latent values, and\r\nobjects in different
concepts have dissimilar latent values. We formulate\r\nthe supervised infinite
latent variable problem based on an intuitive\r\nprinciple of pulling objects
together if they are of the same type, and\r\npushing them apart if they are not.
We then combine this principle with a\r\nflexible Indian Buffet Process prior
on the latent variables. We show that\r\nthe inferred supervised latent variables
can be directly used to perform a\r\nnearest neighbour search for the purpose
of retrieval. We introduce a new\r\napplication of dynamically extending hash
codes, and show how to\r\neffectively couple the structure of the hash codes with
continuously\r\ngrowing structure of the neighbourhood preserving infinite latent
feature\r\nspace."
author:
- first_name: Novi
full_name: Quadrianto, Novi
last_name: Quadrianto
- first_name: Viktoriia
full_name: Sharmanska, Viktoriia
id: 2EA6D09E-F248-11E8-B48F-1D18A9856A87
last_name: Sharmanska
orcid: 0000-0003-0192-9308
- first_name: David
full_name: Knowles, David
last_name: Knowles
- first_name: Zoubin
full_name: Ghahramani, Zoubin
last_name: Ghahramani
citation:
ama: 'Quadrianto N, Sharmanska V, Knowles D, Ghahramani Z. The supervised IBP: Neighbourhood
preserving infinite latent feature models. In: Proceedings of the 29th Conference
Uncertainty in Artificial Intelligence. AUAI Press; 2013:527-536.'
apa: 'Quadrianto, N., Sharmanska, V., Knowles, D., & Ghahramani, Z. (2013).
The supervised IBP: Neighbourhood preserving infinite latent feature models. In
Proceedings of the 29th conference uncertainty in Artificial Intelligence
(pp. 527–536). Bellevue, WA, United States: AUAI Press.'
chicago: 'Quadrianto, Novi, Viktoriia Sharmanska, David Knowles, and Zoubin Ghahramani.
“The Supervised IBP: Neighbourhood Preserving Infinite Latent Feature Models.”
In Proceedings of the 29th Conference Uncertainty in Artificial Intelligence,
527–36. AUAI Press, 2013.'
ieee: 'N. Quadrianto, V. Sharmanska, D. Knowles, and Z. Ghahramani, “The supervised
IBP: Neighbourhood preserving infinite latent feature models,” in Proceedings
of the 29th conference uncertainty in Artificial Intelligence, Bellevue, WA,
United States, 2013, pp. 527–536.'
ista: 'Quadrianto N, Sharmanska V, Knowles D, Ghahramani Z. 2013. The supervised
IBP: Neighbourhood preserving infinite latent feature models. Proceedings of the
29th conference uncertainty in Artificial Intelligence. UAI: Uncertainty in Artificial
Intelligence, 527–536.'
mla: 'Quadrianto, Novi, et al. “The Supervised IBP: Neighbourhood Preserving Infinite
Latent Feature Models.” Proceedings of the 29th Conference Uncertainty in Artificial
Intelligence, AUAI Press, 2013, pp. 527–36.'
short: N. Quadrianto, V. Sharmanska, D. Knowles, Z. Ghahramani, in:, Proceedings
of the 29th Conference Uncertainty in Artificial Intelligence, AUAI Press, 2013,
pp. 527–536.
conference:
end_date: 2013-07-15
location: Bellevue, WA, United States
name: 'UAI: Uncertainty in Artificial Intelligence'
start_date: 2013-07-11
date_created: 2018-12-11T11:58:09Z
date_published: 2013-07-11T00:00:00Z
date_updated: 2023-02-23T10:46:36Z
day: '11'
ddc:
- '000'
department:
- _id: ChLa
file:
- access_level: open_access
checksum: 325f20c4b926bd74d39006b97df572bd
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:16Z
date_updated: 2020-07-14T12:45:42Z
file_id: '5134'
file_name: IST-2013-137-v1+1_QuaShaKnoGha13.pdf
file_size: 1117100
relation: main_file
file_date_updated: 2020-07-14T12:45:42Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 527 - 536
publication: Proceedings of the 29th conference uncertainty in Artificial Intelligence
publication_identifier:
isbn:
- '9780974903996'
publication_status: published
publisher: AUAI Press
publist_id: '4381'
pubrep_id: '137'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The supervised IBP: Neighbourhood preserving infinite latent feature models'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '253'
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: 'Browning TD. Counting rational points on cubic hypersurfaces: Corrigendum.
Mathematika. 2013;60(1):101-107. doi:10.1112/S0025579313000132'
apa: 'Browning, T. D. (2013). Counting rational points on cubic hypersurfaces: Corrigendum.
Mathematika. Unknown. https://doi.org/10.1112/S0025579313000132'
chicago: 'Browning, Timothy D. “Counting Rational Points on Cubic Hypersurfaces:
Corrigendum.” Mathematika. Unknown, 2013. https://doi.org/10.1112/S0025579313000132.'
ieee: 'T. D. Browning, “Counting rational points on cubic hypersurfaces: Corrigendum,”
Mathematika, vol. 60, no. 1. Unknown, pp. 101–107, 2013.'
ista: 'Browning TD. 2013. Counting rational points on cubic hypersurfaces: Corrigendum.
Mathematika. 60(1), 101–107.'
mla: 'Browning, Timothy D. “Counting Rational Points on Cubic Hypersurfaces: Corrigendum.”
Mathematika, vol. 60, no. 1, Unknown, 2013, pp. 101–07, doi:10.1112/S0025579313000132.'
short: T.D. Browning, Mathematika 60 (2013) 101–107.
date_created: 2018-12-11T11:45:27Z
date_published: 2013-09-06T00:00:00Z
date_updated: 2021-01-12T06:58:03Z
day: '06'
doi: 10.1112/S0025579313000132
extern: 1
intvolume: ' 60'
issue: '1'
month: '09'
page: 101 - 107
publication: Mathematika
publication_status: published
publisher: Unknown
publist_id: '7649'
quality_controlled: 0
status: public
title: 'Counting rational points on cubic hypersurfaces: Corrigendum'
type: journal_article
volume: 60
year: '2013'
...
---
_id: '1726'
abstract:
- lang: eng
text: The development of a functional tissue requires coordination of the amplification
of progenitors and their differentiation into specific cell types. The molecular
basis for this coordination during myotome ontogeny is not well understood. Dermomytome
progenitors that colonize the myotome first acquire myocyte identity and subsequently
proliferate as Pax7-expressing progenitors before undergoing terminal differentiation.
We show that the dynamics of sonic hedgehog (Shh) signaling is crucial for this
transition in both avian and mouse embryos. Initially, Shh ligand emanating from
notochord/floor plate reaches the dermomyotome, where it both maintains the proliferation
of dermomyotome cells and promotes myogenic differentiation of progenitors that
colonized the myotome. Interfering with Shh signaling at this stage produces small
myotomes and accumulation of Pax7-expressing progenitors. An in vivo reporter
of Shh activity combined with mouse genetics revealed the existence of both activator
and repressor Shh activities operating on distinct subsets of cells during the
epaxial myotomal maturation. In contrast to observations in mice, in avians Shh
promotes the differentiation of both epaxial and hypaxial myotome domains. Subsequently,
myogenic progenitors become refractory to Shh; this is likely to occur at the
level of, or upstream of, smoothened signaling. The end of responsiveness to Shh
coincides with, and is thus likely to enable, the transition into the growth phase
of the myotome.
acknowledgement: This study was supported by grants from the Israel Science Foundation
(ISF) [11/09 to C.K.]; the Association Francaise contre les Myopathies (AFM) [15642
to C.K.]; the German Research Foundation (DFG) [UN 34/27-1 to C.K.]; the UK Medical
Research Council (MRC) [U117560541 to J.B. and A.K.]; Fondation Pour la Recherche
Médicale (FRM) (post-doctoral fellowship to V.R.). Deposited in PMC for release
after 6 months
author:
- first_name: Nitza
full_name: Kahane, Nitza
last_name: Kahane
- first_name: Vanessa
full_name: Ribes, Vanessa
last_name: Ribes
- first_name: Anna
full_name: Anna Kicheva
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: James
full_name: Briscoe, James
last_name: Briscoe
- first_name: Chaya
full_name: Kalcheim, Chaya
last_name: Kalcheim
citation:
ama: Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. The transition from differentiation
to growth during dermomyotome-derived myogenesis depends on temporally restricted
hedgehog signaling. Development. 2013;140(8):1740-1750. doi:10.1242/dev.092726
apa: Kahane, N., Ribes, V., Kicheva, A., Briscoe, J., & Kalcheim, C. (2013).
The transition from differentiation to growth during dermomyotome-derived myogenesis
depends on temporally restricted hedgehog signaling. Development. Company
of Biologists. https://doi.org/10.1242/dev.092726
chicago: Kahane, Nitza, Vanessa Ribes, Anna Kicheva, James Briscoe, and Chaya Kalcheim.
“The Transition from Differentiation to Growth during Dermomyotome-Derived Myogenesis
Depends on Temporally Restricted Hedgehog Signaling.” Development. Company
of Biologists, 2013. https://doi.org/10.1242/dev.092726.
ieee: N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, and C. Kalcheim, “The transition
from differentiation to growth during dermomyotome-derived myogenesis depends
on temporally restricted hedgehog signaling,” Development, vol. 140, no.
8. Company of Biologists, pp. 1740–1750, 2013.
ista: Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. 2013. The transition
from differentiation to growth during dermomyotome-derived myogenesis depends
on temporally restricted hedgehog signaling. Development. 140(8), 1740–1750.
mla: Kahane, Nitza, et al. “The Transition from Differentiation to Growth during
Dermomyotome-Derived Myogenesis Depends on Temporally Restricted Hedgehog Signaling.”
Development, vol. 140, no. 8, Company of Biologists, 2013, pp. 1740–50,
doi:10.1242/dev.092726.
short: N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, C. Kalcheim, Development 140
(2013) 1740–1750.
date_created: 2018-12-11T11:53:41Z
date_published: 2013-04-18T00:00:00Z
date_updated: 2021-01-12T06:52:47Z
day: '18'
doi: 10.1242/dev.092726
extern: 1
intvolume: ' 140'
issue: '8'
month: '04'
page: 1740 - 1750
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '5402'
quality_controlled: 0
status: public
title: The transition from differentiation to growth during dermomyotome-derived myogenesis
depends on temporally restricted hedgehog signaling
type: journal_article
volume: 140
year: '2013'
...
---
_id: '1727'
abstract:
- lang: eng
text: 'Cells at different positions in a developing tissue receive different concentrations
of signaling molecules, called morphogens, and this influences their cell fate.
Morphogen concentration gradients have been proposed to control patterning as
well as growth in many developing tissues. Some outstanding questions about tissue
patterning by morphogen gradients are the following: What are the mechanisms that
regulate gradient formation and shape? Is the positional information encoded in
the gradient sufficiently precise to determine the positions of target gene domain
boundaries? What are the temporal dynamics of gradients and how do they relate
to patterning and growth? These questions are inherently quantitative in nature
and addressing them requires measuring morphogen concentrations in cells, levels
of downstream signaling activity, and kinetics of morphogen transport. Here we
first present methods for quantifying morphogen gradient shape in which the measurements
can be calibrated to reflect actual morphogen concentrations. We then discuss
using fluorescence recovery after photobleaching to study the kinetics of morphogen
transport at the tissue level. Finally, we present particle tracking as a method
to study morphogen intracellular trafficking.'
author:
- first_name: Anna
full_name: Anna Kicheva
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Laurent
full_name: Holtzer, Laurent
last_name: Holtzer
- first_name: Ortrud
full_name: Wartlick, Ortrud
last_name: Wartlick
- first_name: Thomas
full_name: Schmidt, Thomas S
last_name: Schmidt
- first_name: Marcos
full_name: González-Gaitán, Marcos A
last_name: González Gaitán
citation:
ama: Kicheva A, Holtzer L, Wartlick O, Schmidt T, González Gaitán M. Quantitative
imaging of morphogen gradients in drosophila imaginal discs. Cold Spring Harbor
Protocols. 2013;8(5):387-403. doi:10.1101/pdb.top074237
apa: Kicheva, A., Holtzer, L., Wartlick, O., Schmidt, T., & González Gaitán,
M. (2013). Quantitative imaging of morphogen gradients in drosophila imaginal
discs. Cold Spring Harbor Protocols. Cold Spring Harbor Laboratory Press.
https://doi.org/10.1101/pdb.top074237
chicago: Kicheva, Anna, Laurent Holtzer, Ortrud Wartlick, Thomas Schmidt, and Marcos
González Gaitán. “Quantitative Imaging of Morphogen Gradients in Drosophila Imaginal
Discs.” Cold Spring Harbor Protocols. Cold Spring Harbor Laboratory Press,
2013. https://doi.org/10.1101/pdb.top074237.
ieee: A. Kicheva, L. Holtzer, O. Wartlick, T. Schmidt, and M. González Gaitán, “Quantitative
imaging of morphogen gradients in drosophila imaginal discs,” Cold Spring Harbor
Protocols, vol. 8, no. 5. Cold Spring Harbor Laboratory Press, pp. 387–403,
2013.
ista: Kicheva A, Holtzer L, Wartlick O, Schmidt T, González Gaitán M. 2013. Quantitative
imaging of morphogen gradients in drosophila imaginal discs. Cold Spring Harbor
Protocols. 8(5), 387–403.
mla: Kicheva, Anna, et al. “Quantitative Imaging of Morphogen Gradients in Drosophila
Imaginal Discs.” Cold Spring Harbor Protocols, vol. 8, no. 5, Cold Spring
Harbor Laboratory Press, 2013, pp. 387–403, doi:10.1101/pdb.top074237.
short: A. Kicheva, L. Holtzer, O. Wartlick, T. Schmidt, M. González Gaitán, Cold
Spring Harbor Protocols 8 (2013) 387–403.
date_created: 2018-12-11T11:53:41Z
date_published: 2013-05-01T00:00:00Z
date_updated: 2021-01-12T06:52:47Z
day: '01'
doi: 10.1101/pdb.top074237
extern: 1
intvolume: ' 8'
issue: '5'
month: '05'
page: 387 - 403
publication: Cold Spring Harbor Protocols
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '5401'
quality_controlled: 0
status: public
title: Quantitative imaging of morphogen gradients in drosophila imaginal discs
type: journal_article
volume: 8
year: '2013'
...