---
_id: '9483'
abstract:
- lang: eng
text: Imprinted genes are expressed primarily or exclusively from either the maternal
or paternal allele, a phenomenon that occurs in flowering plants and mammals.
Flowering plant imprinted gene expression has been described primarily in endosperm,
a terminal nutritive tissue consumed by the embryo during seed development or
after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated
by differences in cytosine DNA methylation between the paternal and maternal genomes
as well as by Polycomb group proteins. Currently, only 11 imprinted A. thaliana
genes are known. Here, we use extensive sequencing of cDNA libraries to identify
9 paternally expressed and 34 maternally expressed imprinted genes in A. thaliana
endosperm that are regulated by the DNA-demethylating glycosylase DEMETER, the
DNA methyltransferase MET1, and/or the core Polycomb group protein FIE. These
genes encode transcription factors, proteins involved in hormone signaling, components
of the ubiquitin protein degradation pathway, regulators of histone and DNA methylation,
and small RNA pathway proteins. We also identify maternally expressed genes that
may be regulated by unknown mechanisms or deposited from maternal tissues. We
did not detect any imprinted genes in the embryo. Our results show that imprinted
gene expression is an extensive mechanistically complex phenomenon that likely
affects multiple aspects of seed development.
article_processing_charge: No
article_type: original
author:
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Juhyun
full_name: Shin, Juhyun
last_name: Shin
- first_name: Rie
full_name: Uzawa, Rie
last_name: Uzawa
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Stephanie
full_name: Cohen, Stephanie
last_name: Cohen
- first_name: Matthew J.
full_name: Bauer, Matthew J.
last_name: Bauer
- first_name: Meryl
full_name: Hashimoto, Meryl
last_name: Hashimoto
- first_name: Ryan C.
full_name: Kirkbride, Ryan C.
last_name: Kirkbride
- first_name: John J.
full_name: Harada, John J.
last_name: Harada
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Hsieh T-F, Shin J, Uzawa R, et al. Regulation of imprinted gene expression
in Arabidopsis endosperm. Proceedings of the National Academy of Sciences.
2011;108(5):1755-1762. doi:10.1073/pnas.1019273108
apa: Hsieh, T.-F., Shin, J., Uzawa, R., Silva, P., Cohen, S., Bauer, M. J., … Fischer,
R. L. (2011). Regulation of imprinted gene expression in Arabidopsis endosperm.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1019273108
chicago: Hsieh, Tzung-Fu, Juhyun Shin, Rie Uzawa, Pedro Silva, Stephanie Cohen,
Matthew J. Bauer, Meryl Hashimoto, et al. “Regulation of Imprinted Gene Expression
in Arabidopsis Endosperm.” Proceedings of the National Academy of Sciences.
National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1019273108.
ieee: T.-F. Hsieh et al., “Regulation of imprinted gene expression in Arabidopsis
endosperm,” Proceedings of the National Academy of Sciences, vol. 108,
no. 5. National Academy of Sciences, pp. 1755–1762, 2011.
ista: Hsieh T-F, Shin J, Uzawa R, Silva P, Cohen S, Bauer MJ, Hashimoto M, Kirkbride
RC, Harada JJ, Zilberman D, Fischer RL. 2011. Regulation of imprinted gene expression
in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 108(5),
1755–1762.
mla: Hsieh, Tzung-Fu, et al. “Regulation of Imprinted Gene Expression in Arabidopsis
Endosperm.” Proceedings of the National Academy of Sciences, vol. 108,
no. 5, National Academy of Sciences, 2011, pp. 1755–62, doi:10.1073/pnas.1019273108.
short: T.-F. Hsieh, J. Shin, R. Uzawa, P. Silva, S. Cohen, M.J. Bauer, M. Hashimoto,
R.C. Kirkbride, J.J. Harada, D. Zilberman, R.L. Fischer, Proceedings of the National
Academy of Sciences 108 (2011) 1755–1762.
date_created: 2021-06-07T07:40:38Z
date_published: 2011-02-01T00:00:00Z
date_updated: 2021-12-14T08:33:49Z
day: '01'
department:
- _id: DaZi
doi: 10.1073/pnas.1019273108
extern: '1'
external_id:
pmid:
- '21257907'
intvolume: ' 108'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1019273108
month: '02'
oa: 1
oa_version: Published Version
page: 1755-1762
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Regulation of imprinted gene expression in Arabidopsis endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 108
year: '2011'
...
---
_id: '967'
abstract:
- lang: eng
text: Motivated by recent experiments on the material Ba3NiSb 2O9, we consider a
spin-one quantum antiferromagnet on a triangular lattice with the Heisenberg bilinear
and biquadratic exchange interactions and a single-ion anisotropy. Using a fermionic
"triplon" representation for spins, we study the phase diagram within
mean-field theory. In addition to a fully gapped spin-liquid ground state, we
find a state where one gapless triplon mode with a Fermi surface coexists with
d+id topological pairing of the other triplons. Despite the existence of a Fermi
surface, this ground state has fully gapped bulk spin excitations. Such a state
has linear in-temperature specific heat and constant in-plane spin susceptibility,
with an unusually high Wilson ratio.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Todadri
full_name: Senthil, Todadri S
last_name: Senthil
- first_name: Patrick
full_name: Lee, Patrick
last_name: Lee
citation:
ama: Serbyn M, Senthil T, Lee P. Exotic S=1 spin-liquid state with fermionic excitations
on the triangular lattice. Physical Review B - Condensed Matter and Materials
Physics. 2011;84(18). doi:10.1103/PhysRevB.84.180403
apa: Serbyn, M., Senthil, T., & Lee, P. (2011). Exotic S=1 spin-liquid state
with fermionic excitations on the triangular lattice. Physical Review B - Condensed
Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.84.180403
chicago: Serbyn, Maksym, Todadri Senthil, and Patrick Lee. “Exotic S=1 Spin-Liquid
State with Fermionic Excitations on the Triangular Lattice.” Physical Review
B - Condensed Matter and Materials Physics. American Physical Society, 2011.
https://doi.org/10.1103/PhysRevB.84.180403.
ieee: M. Serbyn, T. Senthil, and P. Lee, “Exotic S=1 spin-liquid state with fermionic
excitations on the triangular lattice,” Physical Review B - Condensed Matter
and Materials Physics, vol. 84, no. 18. American Physical Society, 2011.
ista: Serbyn M, Senthil T, Lee P. 2011. Exotic S=1 spin-liquid state with fermionic
excitations on the triangular lattice. Physical Review B - Condensed Matter and
Materials Physics. 84(18).
mla: Serbyn, Maksym, et al. “Exotic S=1 Spin-Liquid State with Fermionic Excitations
on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials
Physics, vol. 84, no. 18, American Physical Society, 2011, doi:10.1103/PhysRevB.84.180403.
short: M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials
Physics 84 (2011).
date_created: 2018-12-11T11:49:27Z
date_published: 2011-11-03T00:00:00Z
date_updated: 2021-01-12T08:22:18Z
day: '03'
doi: 10.1103/PhysRevB.84.180403
extern: 1
intvolume: ' 84'
issue: '18'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1108.3070
month: '11'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6432'
quality_controlled: 0
status: public
title: Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice
type: journal_article
volume: 84
year: '2011'
...
---
_id: '969'
abstract:
- lang: eng
text: We investigate the isotope effect on the London penetration depth of a superconductor
which measures n S/m*, the ratio of superfluid density to effective mass. We use
a simplified model of electrons weakly coupled to a single phonon frequency ω
E, but assume that the energy gap Δ does not have any isotope effect. Nevertheless,
we find an isotope effect for n S/m* which is significant if Δ is sufficiently
large that it becomes comparable to ω E, a regime of interest to high-T c cuprate
superconductors and possibly other families of unconventional superconductors
with relatively high T c. Our model is too simple to describe the cuprates and
it gives the wrong sign of the isotope effect when compared with experiment, but
it is a proof of principle that the isotope effect exists for n S/m* in materials
where the pairing gap and T c are not of phonon origin and have no isotope effect.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Patrick
full_name: Lee, Patrick
last_name: Lee
citation:
ama: Serbyn M, Lee P. Isotope effect on the superfluid density in conventional and
high-temperature superconductors. Physical Review B - Condensed Matter and
Materials Physics. 2011;83(2). doi:10.1103/PhysRevB.83.024506
apa: Serbyn, M., & Lee, P. (2011). Isotope effect on the superfluid density
in conventional and high-temperature superconductors. Physical Review B - Condensed
Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.83.024506
chicago: Serbyn, Maksym, and Patrick Lee. “Isotope Effect on the Superfluid Density
in Conventional and High-Temperature Superconductors.” Physical Review B -
Condensed Matter and Materials Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevB.83.024506.
ieee: M. Serbyn and P. Lee, “Isotope effect on the superfluid density in conventional
and high-temperature superconductors,” Physical Review B - Condensed Matter
and Materials Physics, vol. 83, no. 2. American Physical Society, 2011.
ista: Serbyn M, Lee P. 2011. Isotope effect on the superfluid density in conventional
and high-temperature superconductors. Physical Review B - Condensed Matter and
Materials Physics. 83(2).
mla: Serbyn, Maksym, and Patrick Lee. “Isotope Effect on the Superfluid Density
in Conventional and High-Temperature Superconductors.” Physical Review B -
Condensed Matter and Materials Physics, vol. 83, no. 2, American Physical
Society, 2011, doi:10.1103/PhysRevB.83.024506.
short: M. Serbyn, P. Lee, Physical Review B - Condensed Matter and Materials Physics
83 (2011).
date_created: 2018-12-11T11:49:28Z
date_published: 2011-01-19T00:00:00Z
date_updated: 2021-01-12T08:22:19Z
day: '19'
doi: 10.1103/PhysRevB.83.024506
extern: 1
intvolume: ' 83'
issue: '2'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1009.2429
month: '01'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6434'
quality_controlled: 0
status: public
title: Isotope effect on the superfluid density in conventional and high-temperature
superconductors
type: journal_article
volume: 83
year: '2011'
...
---
_id: '8471'
abstract:
- lang: eng
text: Despite the importance of protein fibrils in the context of conformational
diseases, information on their structure is still sparse. Hydrogen/deuterium exchange
measurements of backbone amide protons allow the identification hydrogen-bonding
patterns and reveal pertinent information on the amyloid β-sheet architecture.
However, they provide only little information on the identity of residues exposed
to solvent or buried inside the fibril core. NMR spectroscopy is a potent method
for identifying solvent-accessible residues in proteins via observation of polarization
transfer between chemically exchanging side-chain protons and water protons. We
show here that the combined use of highly deuterated samples and fast magic-angle
spinning greatly attenuates unwanted spin diffusion and allows identification
of polarization exchange with the solvent in a site-specific manner. We apply
this measurement protocol to HET-s(218–289) prion fibrils under different conditions
(including physiological pH, where protofibrils assemble together into thicker
fibrils) and demonstrate that each protofibril of HET-s(218–289), is surrounded
by water, thus excluding the existence of extended dry interfibril contacts. We
also show that exchangeable side-chain protons inside the hydrophobic core of
HET-s(218–289) do not exchange over time intervals of weeks to months. The experiments
proposed in this study can provide insight into the detailed structural features
of amyloid fibrils in general.
article_processing_charge: No
article_type: original
author:
- first_name: Hélène
full_name: Van Melckebeke, Hélène
last_name: Van Melckebeke
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Julia
full_name: Gath, Julia
last_name: Gath
- first_name: Christian
full_name: Wasmer, Christian
last_name: Wasmer
- first_name: René
full_name: Verel, René
last_name: Verel
- first_name: Adam
full_name: Lange, Adam
last_name: Lange
- first_name: Beat H.
full_name: Meier, Beat H.
last_name: Meier
- first_name: Anja
full_name: Böckmann, Anja
last_name: Böckmann
citation:
ama: Van Melckebeke H, Schanda P, Gath J, et al. Probing water accessibility in
HET-s(218–289) amyloid fibrils by solid-state NMR. Journal of Molecular Biology.
2011;405(3):765-772. doi:10.1016/j.jmb.2010.11.004
apa: Van Melckebeke, H., Schanda, P., Gath, J., Wasmer, C., Verel, R., Lange, A.,
… Böckmann, A. (2011). Probing water accessibility in HET-s(218–289) amyloid fibrils
by solid-state NMR. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2010.11.004
chicago: Van Melckebeke, Hélène, Paul Schanda, Julia Gath, Christian Wasmer, René
Verel, Adam Lange, Beat H. Meier, and Anja Böckmann. “Probing Water Accessibility
in HET-s(218–289) Amyloid Fibrils by Solid-State NMR.” Journal of Molecular
Biology. Elsevier, 2011. https://doi.org/10.1016/j.jmb.2010.11.004.
ieee: H. Van Melckebeke et al., “Probing water accessibility in HET-s(218–289)
amyloid fibrils by solid-state NMR,” Journal of Molecular Biology, vol.
405, no. 3. Elsevier, pp. 765–772, 2011.
ista: Van Melckebeke H, Schanda P, Gath J, Wasmer C, Verel R, Lange A, Meier BH,
Böckmann A. 2011. Probing water accessibility in HET-s(218–289) amyloid fibrils
by solid-state NMR. Journal of Molecular Biology. 405(3), 765–772.
mla: Van Melckebeke, Hélène, et al. “Probing Water Accessibility in HET-s(218–289)
Amyloid Fibrils by Solid-State NMR.” Journal of Molecular Biology, vol.
405, no. 3, Elsevier, 2011, pp. 765–72, doi:10.1016/j.jmb.2010.11.004.
short: H. Van Melckebeke, P. Schanda, J. Gath, C. Wasmer, R. Verel, A. Lange, B.H.
Meier, A. Böckmann, Journal of Molecular Biology 405 (2011) 765–772.
date_created: 2020-09-18T10:11:03Z
date_published: 2011-01-21T00:00:00Z
date_updated: 2021-01-12T08:19:30Z
day: '21'
doi: 10.1016/j.jmb.2010.11.004
extern: '1'
intvolume: ' 405'
issue: '3'
language:
- iso: eng
month: '01'
oa_version: None
page: 765-772
publication: Journal of Molecular Biology
publication_identifier:
issn:
- 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state
NMR
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 405
year: '2011'
...
---
_id: '8505'
abstract:
- lang: eng
text: The classical principle of least action says that orbits of mechanical systems
extremize action; an important subclass are those orbits that minimize action.
In this paper we utilize this principle along with Aubry-Mather theory to construct
(Birkhoff) regions of instability for a certain three-body problem, given by a
Hamiltonian system of 2 degrees of freedom. We believe that these methods can
be applied to construct instability regions for a variety of Hamiltonian systems
with 2 degrees of freedom. The Hamiltonian model we consider describes dynamics
of a Sun-Jupiter-comet system, and under some simplifying assumptions, we show
the existence of instabilities for the orbit of the comet. In particular, we show
that a comet which starts close to an orbit in the shape of an ellipse of eccentricity
e=0.66 can increase in eccentricity up to e=0.96. In the sequels to this paper,
we extend the result to beyond e=1 and show the existence of ejection orbits.
Such orbits are initially well within the range of our solar system. This might
give an indication of why most objects rotating around the Sun in our solar system
have relatively low eccentricity.
article_processing_charge: No
article_type: original
author:
- first_name: Joseph
full_name: Galante, Joseph
last_name: Galante
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Galante J, Kaloshin V. Destruction of invariant curves in the restricted circular
planar three-body problem by using comparison of action. Duke Mathematical
Journal. 2011;159(2):275-327. doi:10.1215/00127094-1415878
apa: Galante, J., & Kaloshin, V. (2011). Destruction of invariant curves in
the restricted circular planar three-body problem by using comparison of action.
Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-1415878
chicago: Galante, Joseph, and Vadim Kaloshin. “Destruction of Invariant Curves in
the Restricted Circular Planar Three-Body Problem by Using Comparison of Action.”
Duke Mathematical Journal. Duke University Press, 2011. https://doi.org/10.1215/00127094-1415878.
ieee: J. Galante and V. Kaloshin, “Destruction of invariant curves in the restricted
circular planar three-body problem by using comparison of action,” Duke Mathematical
Journal, vol. 159, no. 2. Duke University Press, pp. 275–327, 2011.
ista: Galante J, Kaloshin V. 2011. Destruction of invariant curves in the restricted
circular planar three-body problem by using comparison of action. Duke Mathematical
Journal. 159(2), 275–327.
mla: Galante, Joseph, and Vadim Kaloshin. “Destruction of Invariant Curves in the
Restricted Circular Planar Three-Body Problem by Using Comparison of Action.”
Duke Mathematical Journal, vol. 159, no. 2, Duke University Press, 2011,
pp. 275–327, doi:10.1215/00127094-1415878.
short: J. Galante, V. Kaloshin, Duke Mathematical Journal 159 (2011) 275–327.
date_created: 2020-09-18T10:47:41Z
date_published: 2011-08-04T00:00:00Z
date_updated: 2021-01-12T08:19:45Z
day: '04'
doi: 10.1215/00127094-1415878
extern: '1'
intvolume: ' 159'
issue: '2'
keyword:
- General Mathematics
language:
- iso: eng
month: '08'
oa_version: None
page: 275-327
publication: Duke Mathematical Journal
publication_identifier:
issn:
- 0012-7094
publication_status: published
publisher: Duke University Press
quality_controlled: '1'
status: public
title: Destruction of invariant curves in the restricted circular planar three-body
problem by using comparison of action
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 159
year: '2011'
...
---
_id: '881'
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: 'Kondrashov F. Gene Dosage and Duplication. In: Evolution after Gene Duplication.
Wiley-Blackwell; 2011:57-76. doi:10.1002/9780470619902.ch4'
apa: Kondrashov, F. (2011). Gene Dosage and Duplication. In Evolution after Gene
Duplication (pp. 57–76). Wiley-Blackwell. https://doi.org/10.1002/9780470619902.ch4
chicago: Kondrashov, Fyodor. “Gene Dosage and Duplication.” In Evolution after
Gene Duplication, 57–76. Wiley-Blackwell, 2011. https://doi.org/10.1002/9780470619902.ch4.
ieee: F. Kondrashov, “Gene Dosage and Duplication,” in Evolution after Gene Duplication,
Wiley-Blackwell, 2011, pp. 57–76.
ista: 'Kondrashov F. 2011.Gene Dosage and Duplication. In: Evolution after Gene
Duplication. , 57–76.'
mla: Kondrashov, Fyodor. “Gene Dosage and Duplication.” Evolution after Gene
Duplication, Wiley-Blackwell, 2011, pp. 57–76, doi:10.1002/9780470619902.ch4.
short: F. Kondrashov, in:, Evolution after Gene Duplication, Wiley-Blackwell, 2011,
pp. 57–76.
date_created: 2018-12-11T11:49:00Z
date_published: 2011-03-14T00:00:00Z
date_updated: 2021-01-12T08:21:08Z
day: '14'
doi: 10.1002/9780470619902.ch4
extern: 1
month: '03'
page: 57 - 76
publication: Evolution after Gene Duplication
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6766'
quality_controlled: 0
status: public
title: Gene Dosage and Duplication
type: book_chapter
year: '2011'
...
---
_id: '919'
abstract:
- lang: eng
text: Collective cell migration in tissues occurs throughout embryonic development,
during wound healing, and in cancerous tumor invasion, yet most detailed knowledge
of cell migration comes from single-cell studies. As single cells migrate, the
shape of the cell body fluctuates dramatically through cyclic processes of extension,
adhesion, and retraction, accompanied by erratic changes in migration direction.
Within confluent cell layers, such subcellular motions must be coupled between
neighbors, yet the influence of these subcellular motions on collective migration
is not known. Here we study motion within a confluent epithelial cell sheet, simultaneously
measuring collective migration and subcellular motions, covering a broad range
of length scales, time scales, and cell densities. At large length scales and
time scales collective migration slows as cell density rises, yet the fastest
cells move in large, multicell groups whose scale grows with increasing cell density.
This behavior has an intriguing analogy to dynamic heterogeneities found in particulate
systems as they become more crowded and approach a glass transition. In addition
we find a diminishing self-diffusivity of short-wavelength motions within the
cell layer, and growing peaks in the vibrational density of states associated
with cooperative cell-shape fluctuations. Both of these observations are also
intriguingly reminiscent of a glass transition. Thus, these results provide a
broad and suggestive analogy between cell motion within a confluent layer and
the dynamics of supercooled colloidal and molecular fluids approaching a glass
transition.
author:
- first_name: Thomas
full_name: Angelini, Thomas
last_name: Angelini
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Xavier
full_name: Trepatc, Xavier
last_name: Trepatc
- first_name: Manuel
full_name: Marquez, Manuel
last_name: Marquez
- first_name: Jeffrey
full_name: Fredberg, Jeffrey
last_name: Fredberg
- first_name: David
full_name: Weitz, David
last_name: Weitz
citation:
ama: Angelini T, Hannezo EB, Trepatc X, Marquez M, Fredberg J, Weitz D. Glass-like
dynamics of collective cell migration. Proceedings of the National Academy
of Sciences of the United States of America. 2011;108(12):4714-4719. doi:10.1073/pnas.1010059108
apa: Angelini, T., Hannezo, E. B., Trepatc, X., Marquez, M., Fredberg, J., &
Weitz, D. (2011). Glass-like dynamics of collective cell migration. Proceedings
of the National Academy of Sciences of the United States of America. PNAS.
https://doi.org/10.1073/pnas.1010059108
chicago: Angelini, Thomas, Edouard B Hannezo, Xavier Trepatc, Manuel Marquez, Jeffrey
Fredberg, and David Weitz. “Glass-like Dynamics of Collective Cell Migration.”
Proceedings of the National Academy of Sciences of the United States of America.
PNAS, 2011. https://doi.org/10.1073/pnas.1010059108.
ieee: T. Angelini, E. B. Hannezo, X. Trepatc, M. Marquez, J. Fredberg, and D. Weitz,
“Glass-like dynamics of collective cell migration,” Proceedings of the National
Academy of Sciences of the United States of America, vol. 108, no. 12. PNAS,
pp. 4714–4719, 2011.
ista: Angelini T, Hannezo EB, Trepatc X, Marquez M, Fredberg J, Weitz D. 2011. Glass-like
dynamics of collective cell migration. Proceedings of the National Academy of
Sciences of the United States of America. 108(12), 4714–4719.
mla: Angelini, Thomas, et al. “Glass-like Dynamics of Collective Cell Migration.”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 108, no. 12, PNAS, 2011, pp. 4714–19, doi:10.1073/pnas.1010059108.
short: T. Angelini, E.B. Hannezo, X. Trepatc, M. Marquez, J. Fredberg, D. Weitz,
Proceedings of the National Academy of Sciences of the United States of America
108 (2011) 4714–4719.
date_created: 2018-12-11T11:49:12Z
date_published: 2011-03-22T00:00:00Z
date_updated: 2021-01-12T08:21:54Z
day: '22'
doi: 10.1073/pnas.1010059108
extern: '1'
intvolume: ' 108'
issue: '12'
language:
- iso: eng
month: '03'
oa_version: None
page: 4714 - 4719
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_status: published
publisher: PNAS
publist_id: '6522'
quality_controlled: '1'
status: public
title: Glass-like dynamics of collective cell migration
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2011'
...
---
_id: '918'
abstract:
- lang: eng
text: We study theoretically the shapes of a dividing epithelial monolayer of cells
lying on top of an elastic stroma. The negative tension created by cell division
provokes a buckling instability at a finite wave vector leading to the formation
of periodic arrays of villi and crypts. The instability is similar to the buckling
of a metallic plate under compression. We use the results to rationalize the various
structures of the intestinal lining observed in vivo. Taking into account the
coupling between cell division and local curvature, we obtain different patterns
of villi and crypts, which could explain the different morphologies of the small
intestine and the colon.
acknowledgement: We thank S. Fre and M. Huygue for discussion and for showing us in
vivo samples and A. Bergès for help with the manuscript.
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Jacques
full_name: Prost, Jacques
last_name: Prost
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
citation:
ama: Hannezo EB, Prost J, Joanny J. Instabilities of monolayered epithelia Shape
and structure of villi and crypts. Physical Review Letters. 2011;107(7).
doi:10.1103/PhysRevLett.107.078104
apa: Hannezo, E. B., Prost, J., & Joanny, J. (2011). Instabilities of monolayered
epithelia Shape and structure of villi and crypts. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.107.078104
chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Instabilities of Monolayered
Epithelia Shape and Structure of Villi and Crypts.” Physical Review Letters.
American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.078104.
ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Instabilities of monolayered epithelia
Shape and structure of villi and crypts,” Physical Review Letters, vol.
107, no. 7. American Physical Society, 2011.
ista: Hannezo EB, Prost J, Joanny J. 2011. Instabilities of monolayered epithelia
Shape and structure of villi and crypts. Physical Review Letters. 107(7).
mla: Hannezo, Edouard B., et al. “Instabilities of Monolayered Epithelia Shape and
Structure of Villi and Crypts.” Physical Review Letters, vol. 107, no.
7, American Physical Society, 2011, doi:10.1103/PhysRevLett.107.078104.
short: E.B. Hannezo, J. Prost, J. Joanny, Physical Review Letters 107 (2011).
date_created: 2018-12-11T11:49:11Z
date_published: 2011-08-11T00:00:00Z
date_updated: 2021-01-12T08:21:54Z
day: '11'
doi: 10.1103/PhysRevLett.107.078104
extern: '1'
intvolume: ' 107'
issue: '7'
language:
- iso: eng
month: '08'
oa_version: None
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6521'
status: public
title: Instabilities of monolayered epithelia Shape and structure of villi and crypts
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 107
year: '2011'
...
---
_id: '9522'
abstract:
- lang: eng
text: Little is known about chromatin remodeling events immediately after fertilization.
A recent report by Autran et al. (2011) in Cell now shows that chromatin regulatory
pathways that silence transposable elements are responsible for global delayed
activation of gene expression in the early Arabidopsis embryo.
article_processing_charge: No
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zilberman D. Balancing Parental Contributions in Plant Embryonic Gene Activation.
Vol 20. Elsevier; 2011:735-736. doi:10.1016/j.devcel.2011.05.018
apa: Zilberman, D. (2011). Balancing parental contributions in plant embryonic
gene activation. Developmental Cell (Vol. 20, pp. 735–736). Elsevier.
https://doi.org/10.1016/j.devcel.2011.05.018
chicago: Zilberman, Daniel. Balancing Parental Contributions in Plant Embryonic
Gene Activation. Developmental Cell. Vol. 20. Elsevier, 2011. https://doi.org/10.1016/j.devcel.2011.05.018.
ieee: D. Zilberman, Balancing parental contributions in plant embryonic gene
activation, vol. 20, no. 6. Elsevier, 2011, pp. 735–736.
ista: Zilberman D. 2011. Balancing parental contributions in plant embryonic gene
activation, Elsevier,p.
mla: Zilberman, Daniel. “Balancing Parental Contributions in Plant Embryonic Gene
Activation.” Developmental Cell, vol. 20, no. 6, Elsevier, 2011, pp. 735–36,
doi:10.1016/j.devcel.2011.05.018.
short: D. Zilberman, Balancing Parental Contributions in Plant Embryonic Gene Activation,
Elsevier, 2011.
date_created: 2021-06-08T06:23:39Z
date_published: 2011-06-14T00:00:00Z
date_updated: 2021-12-14T08:34:37Z
day: '14'
department:
- _id: DaZi
doi: 10.1016/j.devcel.2011.05.018
extern: '1'
external_id:
pmid:
- '21664571'
intvolume: ' 20'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2011.05.018
month: '06'
oa: 1
oa_version: Published Version
page: 735-736
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Balancing parental contributions in plant embryonic gene activation
type: other_academic_publication
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 20
year: '2011'
...
---
_id: '9648'
abstract:
- lang: eng
text: In this paper, we establish a correspondence between the incremental algorithm
for computing AT-models [8,9] and the one for computing persistent homology [6,14,15].
We also present a decremental algorithm for computing AT-models that allows to
extend the persistence computation to a wider setting. Finally, we show how to
combine incremental and decremental techniques for persistent homology computation.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Rocio
full_name: Gonzalez-Diaz, Rocio
last_name: Gonzalez-Diaz
- first_name: Adrian
full_name: Ion, Adrian
id: 29F89302-F248-11E8-B48F-1D18A9856A87
last_name: Ion
- first_name: Maria Jose
full_name: Jimenez, Maria Jose
last_name: Jimenez
- first_name: Regina
full_name: Poyatos, Regina
last_name: Poyatos
citation:
ama: 'Gonzalez-Diaz R, Ion A, Jimenez MJ, Poyatos R. Incremental-decremental algorithm
for computing AT-models and persistent homology. In: Computer Analysis of Images
and Patterns. Vol 6854. Springer Nature; 2011:286-293. doi:10.1007/978-3-642-23672-3_35'
apa: 'Gonzalez-Diaz, R., Ion, A., Jimenez, M. J., & Poyatos, R. (2011). Incremental-decremental
algorithm for computing AT-models and persistent homology. In Computer Analysis
of Images and Patterns (Vol. 6854, pp. 286–293). Seville, Spain: Springer
Nature. https://doi.org/10.1007/978-3-642-23672-3_35'
chicago: Gonzalez-Diaz, Rocio, Adrian Ion, Maria Jose Jimenez, and Regina Poyatos.
“Incremental-Decremental Algorithm for Computing AT-Models and Persistent Homology.”
In Computer Analysis of Images and Patterns, 6854:286–93. Springer Nature,
2011. https://doi.org/10.1007/978-3-642-23672-3_35.
ieee: R. Gonzalez-Diaz, A. Ion, M. J. Jimenez, and R. Poyatos, “Incremental-decremental
algorithm for computing AT-models and persistent homology,” in Computer Analysis
of Images and Patterns, Seville, Spain, 2011, vol. 6854, pp. 286–293.
ista: 'Gonzalez-Diaz R, Ion A, Jimenez MJ, Poyatos R. 2011. Incremental-decremental
algorithm for computing AT-models and persistent homology. Computer Analysis of
Images and Patterns. CAIP: International Conference on Computer Analysis of Images
and Patterns, LNCS, vol. 6854, 286–293.'
mla: Gonzalez-Diaz, Rocio, et al. “Incremental-Decremental Algorithm for Computing
AT-Models and Persistent Homology.” Computer Analysis of Images and Patterns,
vol. 6854, Springer Nature, 2011, pp. 286–93, doi:10.1007/978-3-642-23672-3_35.
short: R. Gonzalez-Diaz, A. Ion, M.J. Jimenez, R. Poyatos, in:, Computer Analysis
of Images and Patterns, Springer Nature, 2011, pp. 286–293.
conference:
end_date: 2011-08-31
location: Seville, Spain
name: 'CAIP: International Conference on Computer Analysis of Images and Patterns'
start_date: 2011-08-29
date_created: 2021-07-11T22:01:19Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2021-08-12T13:53:17Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-642-23672-3_35
intvolume: ' 6854'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://hdl.handle.net/11441/30766
month: '08'
oa: 1
oa_version: Published Version
page: 286-293
publication: Computer Analysis of Images and Patterns
publication_identifier:
eissn:
- '16113349'
isbn:
- '9783642236716'
issn:
- '03029743'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Incremental-decremental algorithm for computing AT-models and persistent homology
type: conference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 6854
year: '2011'
...
---
_id: '968'
abstract:
- lang: eng
text: A Reply to the Comment by Andrei Sergeev, M. Reizer, and V. Mitin.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Mikhail
full_name: Skvortsov, Mikhail A
last_name: Skvortsov
- first_name: Andrei
full_name: Varlamov, Andrei A
last_name: Varlamov
- first_name: Victor
full_name: Galitski, Victor M
last_name: Galitski
citation:
ama: 'Serbyn M, Skvortsov M, Varlamov A, Galitski V. Serbyn et al. Reply: Physical
Review Letters. 2011;106(13). doi:10.1103/PhysRevLett.106.139702'
apa: 'Serbyn, M., Skvortsov, M., Varlamov, A., & Galitski, V. (2011). Serbyn
et al. Reply: Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.106.139702'
chicago: Serbyn, Maksym, Mikhail Skvortsov, Andrei Varlamov, and Victor Galitski.
“Serbyn et Al. Reply:” Physical Review Letters. American Physical Society,
2011. https://doi.org/10.1103/PhysRevLett.106.139702.
ieee: M. Serbyn, M. Skvortsov, A. Varlamov, and V. Galitski, “Serbyn et al. Reply:,”
Physical Review Letters, vol. 106, no. 13. American Physical Society, 2011.
ista: 'Serbyn M, Skvortsov M, Varlamov A, Galitski V. 2011. Serbyn et al. Reply:
Physical Review Letters. 106(13).'
mla: Serbyn, Maksym, et al. “Serbyn et Al. Reply:” Physical Review Letters,
vol. 106, no. 13, American Physical Society, 2011, doi:10.1103/PhysRevLett.106.139702.
short: M. Serbyn, M. Skvortsov, A. Varlamov, V. Galitski, Physical Review Letters
106 (2011).
date_created: 2018-12-11T11:49:27Z
date_published: 2011-04-01T00:00:00Z
date_updated: 2021-01-12T08:22:19Z
day: '01'
doi: 10.1103/PhysRevLett.106.139702
extern: 1
intvolume: ' 106'
issue: '13'
month: '04'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6433'
quality_controlled: 0
status: public
title: 'Serbyn et al. Reply:'
type: journal_article
volume: 106
year: '2011'
...
---
_id: '3395'
abstract:
- lang: eng
text: Defining population structure and genetic diversity levels is of the utmost
importance for developing efficient conservation strategies. Overfishing has caused
mean annual catches of the European spiny lobster (Palinurus elephas) to decrease
alarmingly along its distribution area. In this context, there is a need for comprehensive
studies aiming to evaluate the genetic health of the exploited populations. The
present study is based on a set of ten nuclear markers amplified in 331 individuals
from ten different localities covering most of P. elephas distribution area. Samples
from Atlantic and Mediterranean basins showed small but significant differences,
indicating that P. elephas populations do not behave as a single panmictic unit
but form two partially-overlapping groups. Despite intense overfishing, our dataset
did not recover a recent bottleneck signal, and instead showed a large and stable
historical effective size. This result could be accounted for by specific life-history
traits (reproduction and longevity) and the limitations of molecular markers in
covering recent timescales for nontemporal samples. The findings of the present
study emphasize the need to integrate information on effective population sizes
and life-history parameters when evaluating population connectivity levels from
genetic data.
acknowledgement: This work was supported by a pre-doctoral fellowship awarded by the
Autonomous Government of Catalonia to F.P. (2006FIC-00082). Research was funded
by projects FBBVA-BIOCON 08-187/09, CGL2006-13423, and CTM2007-66635. The authors
are part of the research group 2009SGR-636, 2009SGR-655, and 2009SGR-1364 of the
Generalitat de Catalunya. F.P. acknowledges EU-Synthesys grant (GB-TAF-4474).
article_processing_charge: No
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
- first_name: Enrique
full_name: Macpherson, Enrique
last_name: Macpherson
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
citation:
ama: Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Effect of oceanographic
barriers and overfishing on the population genetic structure of the European spiny
lobster Palinurus elephas. Biological Journal of the Linnean Society. 2011;104(2):407-418.
doi:10.1111/j.1095-8312.2011.01728.x
apa: Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011).
Effect of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster Palinurus elephas. Biological Journal of the
Linnean Society. Wiley-Blackwell. https://doi.org/10.1111/j.1095-8312.2011.01728.x
chicago: Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta
Pascual. “Effect of Oceanographic Barriers and Overfishing on the Population Genetic
Structure of the European Spiny Lobster Palinurus Elephas.” Biological Journal
of the Linnean Society. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1095-8312.2011.01728.x.
ieee: F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Effect
of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster Palinurus elephas,” Biological Journal of the
Linnean Society, vol. 104, no. 2. Wiley-Blackwell, pp. 407–418, 2011.
ista: Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Effect of oceanographic
barriers and overfishing on the population genetic structure of the European spiny
lobster Palinurus elephas. Biological Journal of the Linnean Society. 104(2),
407–418.
mla: Palero, Ferran, et al. “Effect of Oceanographic Barriers and Overfishing on
the Population Genetic Structure of the European Spiny Lobster Palinurus Elephas.”
Biological Journal of the Linnean Society, vol. 104, no. 2, Wiley-Blackwell,
2011, pp. 407–18, doi:10.1111/j.1095-8312.2011.01728.x.
short: F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, Biological
Journal of the Linnean Society 104 (2011) 407–418.
date_created: 2018-12-11T12:03:06Z
date_published: 2011-09-14T00:00:00Z
date_updated: 2023-02-23T14:07:31Z
day: '14'
department:
- _id: NiBa
doi: 10.1111/j.1095-8312.2011.01728.x
intvolume: ' 104'
issue: '2'
language:
- iso: eng
month: '09'
oa_version: None
page: 407 - 418
publication: Biological Journal of the Linnean Society
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3212'
quality_controlled: '1'
related_material:
record:
- id: '9762'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Effect of oceanographic barriers and overfishing on the population genetic
structure of the European spiny lobster Palinurus elephas
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 104
year: '2011'
...
---
_id: '9762'
abstract:
- lang: eng
text: Defining population structure and genetic diversity levels is of the utmost
importance for developing efficient conservation strategies. Overfishing has caused
mean annual catches of the European spiny lobster (Palinurus elephas) to decrease
alarmingly along its distribution area. In this context, there is a need for comprehensive
studies to evaluate the genetic health of the exploited populations. The present
work is based on a set of 10 nuclear markers amplified in 331 individuals from
10 different localities covering most of P. elephas distribution area. Samples
from Atlantic and Mediterranean basins showed small but significant differences,
indicating that P. elephas populations do not behave as a single panmictic unit
but form two partially-overlapping groups. Despite intense overfishing, our dataset
did not recover a recent bottleneck signal, and showed a large and stable historical
effective size instead. This result could be accounted for by specific life history
traits (reproduction and longevity) and the limitations of molecular markers in
covering very recent timescales for non temporal samples. Our study emphasizes
the necessity of integrating information on effective population sizes and life
history parameters when evaluating population connectivity levels from genetic
data.
article_processing_charge: No
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
- first_name: Enrique
full_name: Macpherson, Enrique
last_name: Macpherson
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
citation:
ama: 'Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Data from: Effect
of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster (Palinurus elephas). 2011. doi:10.5061/dryad.299h8'
apa: 'Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011).
Data from: Effect of oceanographic barriers and overfishing on the population
genetic structure of the European spiny lobster (Palinurus elephas). IST Austria.
https://doi.org/10.5061/dryad.299h8'
chicago: 'Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta
Pascual. “Data from: Effect of Oceanographic Barriers and Overfishing on the Population
Genetic Structure of the European Spiny Lobster (Palinurus Elephas).” IST Austria,
2011. https://doi.org/10.5061/dryad.299h8.'
ieee: 'F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Data from:
Effect of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster (Palinurus elephas).” IST Austria, 2011.'
ista: 'Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Data from:
Effect of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster (Palinurus elephas), IST Austria, 10.5061/dryad.299h8.'
mla: 'Palero, Ferran, et al. Data from: Effect of Oceanographic Barriers and
Overfishing on the Population Genetic Structure of the European Spiny Lobster
(Palinurus Elephas). IST Austria, 2011, doi:10.5061/dryad.299h8.'
short: F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, (2011).
date_created: 2021-08-02T07:11:19Z
date_published: 2011-05-12T00:00:00Z
date_updated: 2023-02-23T11:25:25Z
day: '12'
department:
- _id: NiBa
doi: 10.5061/dryad.299h8
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.299h8
month: '05'
oa: 1
oa_version: Published Version
publisher: IST Austria
related_material:
record:
- id: '3395'
relation: used_in_publication
status: public
status: public
title: 'Data from: Effect of oceanographic barriers and overfishing on the population
genetic structure of the European spiny lobster (Palinurus elephas)'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2011'
...
---
_id: '9943'
abstract:
- lang: eng
text: Segmentation is the process of partitioning digital images into meaningful
regions. The analysis of biological high content images often requires segmentation
as a first step. We propose ilastik as an easy-to-use tool which allows the user
without expertise in image processing to perform segmentation and classification
in a unified way. ilastik learns from labels provided by the user through a convenient
mouse interface. Based on these labels, ilastik infers a problem specific segmentation.
A random forest classifier is used in the learning step, in which each pixel's
neighborhood is characterized by a set of generic (nonlinear) features. ilastik
supports up to three spatial plus one spectral dimension and makes use of all
dimensions in the feature calculation. ilastik provides realtime feedback that
enables the user to interactively refine the segmentation result and hence further
fine-tune the classifier. An uncertainty measure guides the user to ambiguous
regions in the images. Real time performance is achieved by multi-threading which
fully exploits the capabilities of modern multi-core machines. Once a classifier
has been trained on a set of representative images, it can be exported and used
to automatically process a very large number of images (e.g. using the CellProfiler
pipeline). ilastik is an open source project and released under the BSD license
at www.ilastik.org.
article_processing_charge: No
author:
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Christoph
full_name: Straehle, Christoph
last_name: Straehle
- first_name: Ullrich
full_name: Köthe, Ullrich
last_name: Köthe
- first_name: Fred A.
full_name: Hamprecht, Fred A.
last_name: Hamprecht
citation:
ama: 'Sommer CM, Straehle C, Köthe U, Hamprecht FA. Ilastik: Interactive learning
and segmentation toolkit. In: 2011 IEEE International Symposium on Biomedical
Imaging: From Nano to Micro. Institute of Electrical and Electronics Engineers;
2011. doi:10.1109/isbi.2011.5872394'
apa: 'Sommer, C. M., Straehle, C., Köthe, U., & Hamprecht, F. A. (2011). Ilastik:
Interactive learning and segmentation toolkit. In 2011 IEEE International Symposium
on Biomedical Imaging: from Nano to Micro. Chicago, Illinois, USA: Institute
of Electrical and Electronics Engineers. https://doi.org/10.1109/isbi.2011.5872394'
chicago: 'Sommer, Christoph M, Christoph Straehle, Ullrich Köthe, and Fred A. Hamprecht.
“Ilastik: Interactive Learning and Segmentation Toolkit.” In 2011 IEEE International
Symposium on Biomedical Imaging: From Nano to Micro. Institute of Electrical
and Electronics Engineers, 2011. https://doi.org/10.1109/isbi.2011.5872394.'
ieee: 'C. M. Sommer, C. Straehle, U. Köthe, and F. A. Hamprecht, “Ilastik: Interactive
learning and segmentation toolkit,” in 2011 IEEE International Symposium on
Biomedical Imaging: from Nano to Micro, Chicago, Illinois, USA, 2011.'
ista: 'Sommer CM, Straehle C, Köthe U, Hamprecht FA. 2011. Ilastik: Interactive
learning and segmentation toolkit. 2011 IEEE International Symposium on Biomedical
Imaging: from Nano to Micro. ISBI: International Symposium on Biomedical Imaging.'
mla: 'Sommer, Christoph M., et al. “Ilastik: Interactive Learning and Segmentation
Toolkit.” 2011 IEEE International Symposium on Biomedical Imaging: From Nano
to Micro, Institute of Electrical and Electronics Engineers, 2011, doi:10.1109/isbi.2011.5872394.'
short: 'C.M. Sommer, C. Straehle, U. Köthe, F.A. Hamprecht, in:, 2011 IEEE International
Symposium on Biomedical Imaging: From Nano to Micro, Institute of Electrical and
Electronics Engineers, 2011.'
conference:
end_date: 2011-04-02
location: Chicago, Illinois, USA
name: 'ISBI: International Symposium on Biomedical Imaging'
start_date: 2011-03-30
date_created: 2021-08-19T11:49:58Z
date_published: 2011-06-09T00:00:00Z
date_updated: 2023-02-23T14:13:38Z
day: '09'
department:
- _id: Bio
doi: 10.1109/isbi.2011.5872394
extern: '1'
keyword:
- image segmentation
- biomedical imaging
- three dimensional displays
- neurons
- retina
- observers
- image color analysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.researchgate.net/publication/224241106_Ilastik_Interactive_learning_and_segmentation_toolkit
month: '06'
oa: 1
oa_version: Preprint
publication: '2011 IEEE International Symposium on Biomedical Imaging: from Nano to
Micro'
publication_identifier:
eissn:
- 1945-8452
isbn:
- 978-1-4244-4127-3
issn:
- 1945-7928
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
status: public
title: 'Ilastik: Interactive learning and segmentation toolkit'
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2011'
...
---
_id: '10907'
abstract:
- lang: eng
text: This paper presents a method to create a model of an articulated object using
the planar motion in an initialization video. The model consists of rigid parts
connected by points of articulation. The rigid parts are described by the positions
of salient feature-points tracked throughout the video. Following a filtering
step that identifies points that belong to different objects, rigid parts are
found by a grouping process in a graph pyramid. Valid articulation points are
selected by verifying multiple hypotheses for each pair of parts.
acknowledgement: This work has been partially supported by the Austrian Science Fund
under grants S9103-N13 and P18716-N13.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Nicole M.
full_name: Artner, Nicole M.
last_name: Artner
- first_name: Adrian
full_name: Ion, Adrian
id: 29F89302-F248-11E8-B48F-1D18A9856A87
last_name: Ion
- first_name: Walter G.
full_name: Kropatsch, Walter G.
last_name: Kropatsch
citation:
ama: 'Artner NM, Ion A, Kropatsch WG. Spatio-temporal extraction of articulated
models in a graph pyramid. In: Jiang X, Ferrer M, Torsello A, eds. Graph-Based
Representations in Pattern Recognition. Vol 6658. LNIP. Berlin, Heidelberg:
Springer; 2011:215-224. doi:10.1007/978-3-642-20844-7_22'
apa: 'Artner, N. M., Ion, A., & Kropatsch, W. G. (2011). Spatio-temporal extraction
of articulated models in a graph pyramid. In X. Jiang, M. Ferrer, & A. Torsello
(Eds.), Graph-Based Representations in Pattern Recognition (Vol. 6658,
pp. 215–224). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-20844-7_22'
chicago: 'Artner, Nicole M., Adrian Ion, and Walter G. Kropatsch. “Spatio-Temporal
Extraction of Articulated Models in a Graph Pyramid.” In Graph-Based Representations
in Pattern Recognition, edited by Xiaoyi Jiang, Miquel Ferrer, and Andrea
Torsello, 6658:215–24. LNIP. Berlin, Heidelberg: Springer, 2011. https://doi.org/10.1007/978-3-642-20844-7_22.'
ieee: N. M. Artner, A. Ion, and W. G. Kropatsch, “Spatio-temporal extraction of
articulated models in a graph pyramid,” in Graph-Based Representations in Pattern
Recognition, Münster, Germany, 2011, vol. 6658, pp. 215–224.
ista: 'Artner NM, Ion A, Kropatsch WG. 2011. Spatio-temporal extraction of articulated
models in a graph pyramid. Graph-Based Representations in Pattern Recognition.
GbRPR: Graph-based Representations in Pattern RecognitionLNIP, LNCS, vol. 6658,
215–224.'
mla: Artner, Nicole M., et al. “Spatio-Temporal Extraction of Articulated Models
in a Graph Pyramid.” Graph-Based Representations in Pattern Recognition,
edited by Xiaoyi Jiang et al., vol. 6658, Springer, 2011, pp. 215–24, doi:10.1007/978-3-642-20844-7_22.
short: N.M. Artner, A. Ion, W.G. Kropatsch, in:, X. Jiang, M. Ferrer, A. Torsello
(Eds.), Graph-Based Representations in Pattern Recognition, Springer, Berlin,
Heidelberg, 2011, pp. 215–224.
conference:
end_date: 2011-05-20
location: Münster, Germany
name: 'GbRPR: Graph-based Representations in Pattern Recognition'
start_date: 2011-05-18
date_created: 2022-03-21T08:08:35Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2023-09-05T14:10:15Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-642-20844-7_22
editor:
- first_name: Xiaoyi
full_name: Jiang, Xiaoyi
last_name: Jiang
- first_name: Miquel
full_name: Ferrer, Miquel
last_name: Ferrer
- first_name: Andrea
full_name: Torsello, Andrea
last_name: Torsello
intvolume: ' 6658'
language:
- iso: eng
month: '06'
oa_version: None
page: 215-224
place: Berlin, Heidelberg
publication: Graph-Based Representations in Pattern Recognition
publication_identifier:
eisbn:
- '9783642208447'
eissn:
- 1611-3349
isbn:
- '9783642208430'
issn:
- 0302-9743
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
series_title: LNIP
status: public
title: Spatio-temporal extraction of articulated models in a graph pyramid
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 6658
year: '2011'
...
---
_id: '3275'
abstract:
- lang: eng
text: 'Chemokines organize immune cell trafficking by inducing either directed (tactic)
or random (kinetic) migration and by activating integrins in order to support
surface adhesion (haptic). Beyond that the same chemokines can establish clearly
defined functional areas in secondary lymphoid organs. Until now it is unclear
how chemokines can fulfill such diverse functions. One decisive prerequisite to
explain these capacities is to know how chemokines are presented in tissue. In
theory chemokines could occur either soluble or immobilized, and could be distributed
either homogenously or as a concentration gradient. To dissect if and how the
presenting mode of chemokines influences immune cells, I tested the response of
dendritic cells (DCs) to differentially displayed chemokines. DCs are antigen
presenting cells that reside in the periphery and migrate into draining lymph
nodes (LNs) once exposed to inflammatory stimuli to activate naïve T cells. DCs
are guided to and within the LN by the chemokine receptor CCR7, which has two
ligands, the chemokines CCL19 and CCL21. Both CCR7 ligands are expressed by fibroblastic
reticular cells in the LN, but differ in their ability to bind to heparan sulfate
residues. CCL21 has a highly charged C-terminal extension, which mediates binding
to anionic surfaces, whereas CCL19 is lacking such residues and likely distributes
as a soluble molecule. This study shows that surface-bound CCL21 causes random,
haptokinetic DC motility, which is confined to the chemokine coated area by insideout
activation of β2 integrins that mediate cell binding to the surface. CCL19 on
the other hand forms concentration gradients which trigger directional, chemotactic
movement, but no surface adhesion. In addition DCs can actively manipulate this
system by recruiting and activating serine proteases on their surfaces, which
create - by proteolytically removing the adhesive C-terminus - a solubilized variant
of CCL21 that functionally resembles CCL19. By generating a CCL21 concentration
gradient DCs establish a positive feedback loop to recruit further DCs from the
periphery to the CCL21 coated region. In addition DCs can sense chemotactic gradients
as well as immobilized haptokinetic fields at the same time and integrate these
signals. The result is chemotactically biased haptokinesis - directional migration
confined to a chemokine coated track or area - which could explain the dynamic
but spatially tightly controlled swarming leukocyte locomotion patterns that have
been observed in lymphatic organs by intravital microscopists. The finding that
DCs can approach soluble cues in a non-adhesive manner while they attach to surfaces
coated with immobilized cues raises the question how these cells transmit intracellular
forces to the environment, especially in the non-adherent migration mode. In order
to migrate, cells have to generate and transmit force to the extracellular substrate.
Force transmission is the prerequisite to procure an expansion of the leading
edge and a forward motion of the whole cell body. In the current conceptions actin
polymerization at the leading edge is coupled to extracellular ligands via the
integrin family of transmembrane receptors, which allows the transmission of intracellular
force. Against the paradigm of force transmission during migration, leukocytes,
like DCs, are able to migrate in threedimensional environments without using integrin
transmembrane receptors (Lämmermann et al., 2008). This reflects the biological
function of leukocytes, as they can invade almost all tissues, whereby their migration
has to be independent from the extracellular environment. How the cells can achieve
this is unclear. For this study I examined DC migration in a defined threedimensional
environment and highlighted actin-dynamics with the probe Lifeact-GFP. The result
was that chemotactic DCs can switch between integrin-dependent and integrin- independent
locomotion and can thereby adapt to the adhesive properties of their environment.
If the cells are able to couple their actin cytoskeleton to the substrate, actin
polymerization is entirely converted into protrusion. Without coupling the actin
cortex undergoes slippage and retrograde actin flow can be observed. But retrograde
actin flow can be completely compensated by higher actin polymerization rate keeping
the migration velocity and the shape of the cells unaltered. Mesenchymal cells
like fibroblast cannot balance the loss of adhesive interaction, cannot protrude
into open space and, therefore, strictly depend on integrinmediated force coupling.
This leukocyte specific phenomenon of “adaptive force transmission” endows these
cells with the unique ability to transit and invade almost every type of tissue. '
acknowledgement: "I would like to express my sincere gratitude to the following people
who made with their continuous support and encouragement this thesis possible: First,
I want to thank Prof. Dr. Michael Sixt for his excellent supervision and mentoring,
especially for the nice, relaxed working atmosphere, a lot of brilliant ideas and
the freedom to work in my own way.\r\n\r\nProf. Dr. Reinhard Fässler for his constant
support of the Sixt lab and for providing excellent working conditions. \r\n\r\nProf.
Dr. Sanjiv Luther and Prof. Dr. Tobias Bollenbach for agreeing to be member of my
thesis committee and to evaluate my work.\r\n\r\nDr. Walther Göhring, Carmen Schmitz,
the Recombinant Protein Production core facility and the animal care takers for
providing the “infrastructure” for this thesis. \r\n\r\nProf. Dr. Daniel Legler,
Markus Bruckner and Dr. Julien Polleux for very fruitful collaborations and discussions.\r\n\r\nMy
labmates for their help, a lot of discussions and to make the Sixt lab to a convenient
place to work : Karin Hirsch, Tim Lämmeramnn, Holger Pflicke, Jörg Renkawitz, Michele
Weber and Alexander Eichner All members of the Department of Molecular Medicine
for their help. Especially I want to thank Sarah Schmidt, Karin Hirsch and Raphael
Ruppert for their friendship, nice chats and their uncensored point of view. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Kathrin
full_name: Schumann, Kathrin
id: F44D762E-4F9D-11E9-B64C-9EB26CEFFB5F
last_name: Schumann
citation:
ama: Schumann K. The role of chemotactic gradients in dendritic cell migration.
2011.
apa: Schumann, K. (2011). The role of chemotactic gradients in dendritic cell
migration. Institute of Science and Technology Austria.
chicago: Schumann, Kathrin. “The Role of Chemotactic Gradients in Dendritic Cell
Migration.” Institute of Science and Technology Austria, 2011.
ieee: K. Schumann, “The role of chemotactic gradients in dendritic cell migration,”
Institute of Science and Technology Austria, 2011.
ista: Schumann K. 2011. The role of chemotactic gradients in dendritic cell migration.
Institute of Science and Technology Austria.
mla: Schumann, Kathrin. The Role of Chemotactic Gradients in Dendritic Cell Migration.
Institute of Science and Technology Austria, 2011.
short: K. Schumann, The Role of Chemotactic Gradients in Dendritic Cell Migration,
Institute of Science and Technology Austria, 2011.
date_created: 2018-12-11T12:02:24Z
date_published: 2011-03-01T00:00:00Z
date_updated: 2023-09-07T11:31:48Z
day: '01'
ddc:
- '570'
- '579'
degree_awarded: PhD
department:
- _id: MiSi
file:
- access_level: closed
checksum: e69eee6252660f0b694a2ea8923ddc72
content_type: application/pdf
creator: dernst
date_created: 2019-03-26T08:12:21Z
date_updated: 2020-07-14T12:46:06Z
file_id: '6177'
file_name: 2011_Thesis_Kathrin_Schumann.pdf
file_size: 4487708
relation: main_file
- access_level: open_access
checksum: 71727d63f424b5b446f68f4b87ecadc0
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:24:30Z
date_updated: 2021-02-22T11:24:30Z
file_id: '9175'
file_name: 2011_Thesis_Schumann_noS.pdf
file_size: 4313127
relation: main_file
success: 1
file_date_updated: 2021-02-22T11:24:30Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '141'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '3371'
pubrep_id: '11'
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
title: The role of chemotactic gradients in dendritic cell migration
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2011'
...
---
_id: '3273'
alternative_title:
- ISTA Thesis
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
citation:
ama: Maître J-L. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors.
2011.
apa: Maître, J.-L. (2011). Mechanics of adhesion and de‐adhesion in zebrafish
germ layer progenitors. Institute of Science and Technology Austria.
chicago: Maître, Jean-Léon. “Mechanics of Adhesion and De‐adhesion in Zebrafish
Germ Layer Progenitors.” Institute of Science and Technology Austria, 2011.
ieee: J.-L. Maître, “Mechanics of adhesion and de‐adhesion in zebrafish germ layer
progenitors,” Institute of Science and Technology Austria, 2011.
ista: Maître J-L. 2011. Mechanics of adhesion and de‐adhesion in zebrafish germ
layer progenitors. Institute of Science and Technology Austria.
mla: Maître, Jean-Léon. Mechanics of Adhesion and De‐adhesion in Zebrafish Germ
Layer Progenitors. Institute of Science and Technology Austria, 2011.
short: J.-L. Maître, Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer
Progenitors, Institute of Science and Technology Austria, 2011.
date_created: 2018-12-11T12:02:23Z
date_published: 2011-12-12T00:00:00Z
date_updated: 2023-09-07T11:30:16Z
day: '12'
degree_awarded: PhD
department:
- _id: CaHe
language:
- iso: eng
month: '12'
oa_version: None
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '3373'
status: public
supervisor:
- 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
title: Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2011'
...
---
_id: '3238'
abstract:
- lang: eng
text: We construct efficient authentication protocols and message-authentication
codes (MACs) whose security can be reduced to the learning parity with noise (LPN)
problem. Despite a large body of work - starting with the HB protocol of Hopper
and Blum in 2001 - until now it was not even known how to construct an efficient
authentication protocol from LPN which is secure against man-in-the-middle (MIM)
attacks. A MAC implies such a (two-round) protocol. © 2011 International Association
for Cryptologic Research
acknowledgement: The European Regional Development Fund (ERDF),Guardtime,Qualcomm,Swedbank
alternative_title:
- LNCS
author:
- first_name: Eike
full_name: Kiltz, Eike
last_name: Kiltz
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: David
full_name: Cash, David
last_name: Cash
- first_name: Abhishek
full_name: Jain, Abhishek
last_name: Jain
- first_name: Daniele
full_name: Venturi, Daniele
last_name: Venturi
citation:
ama: 'Kiltz E, Pietrzak KZ, Cash D, Jain A, Venturi D. Efficient authentication
from hard learning problems. In: Vol 6632. Springer; 2011:7-26. doi:10.1007/978-3-642-20465-4_3'
apa: 'Kiltz, E., Pietrzak, K. Z., Cash, D., Jain, A., & Venturi, D. (2011).
Efficient authentication from hard learning problems (Vol. 6632, pp. 7–26). Presented
at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Tallinn,
Estonia: Springer. https://doi.org/10.1007/978-3-642-20465-4_3'
chicago: Kiltz, Eike, Krzysztof Z Pietrzak, David Cash, Abhishek Jain, and Daniele
Venturi. “Efficient Authentication from Hard Learning Problems,” 6632:7–26. Springer,
2011. https://doi.org/10.1007/978-3-642-20465-4_3.
ieee: 'E. Kiltz, K. Z. Pietrzak, D. Cash, A. Jain, and D. Venturi, “Efficient authentication
from hard learning problems,” presented at the EUROCRYPT: Theory and Applications
of Cryptographic Techniques, Tallinn, Estonia, 2011, vol. 6632, pp. 7–26.'
ista: 'Kiltz E, Pietrzak KZ, Cash D, Jain A, Venturi D. 2011. Efficient authentication
from hard learning problems. EUROCRYPT: Theory and Applications of Cryptographic
Techniques, LNCS, vol. 6632, 7–26.'
mla: Kiltz, Eike, et al. Efficient Authentication from Hard Learning Problems.
Vol. 6632, Springer, 2011, pp. 7–26, doi:10.1007/978-3-642-20465-4_3.
short: E. Kiltz, K.Z. Pietrzak, D. Cash, A. Jain, D. Venturi, in:, Springer, 2011,
pp. 7–26.
conference:
end_date: 2011-05-19
location: Tallinn, Estonia
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
start_date: 2011-05-15
date_created: 2018-12-11T12:02:11Z
date_published: 2011-05-01T00:00:00Z
date_updated: 2023-09-20T11:20:57Z
day: '01'
doi: 10.1007/978-3-642-20465-4_3
extern: '1'
intvolume: ' 6632'
language:
- iso: eng
month: '05'
oa_version: None
page: 7 - 26
publication_status: published
publisher: Springer
publist_id: '3442'
quality_controlled: '1'
related_material:
record:
- id: '1187'
relation: later_version
status: public
status: public
title: Efficient authentication from hard learning problems
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6632
year: '2011'
...
---
_id: '3392'
abstract:
- lang: eng
text: Migrating lymphocytes acquire a polarized phenotype with a leading and a trailing
edge, or uropod. Although in vitro experiments in cell lines or activated primary
cell cultures have established that Rho-p160 coiled-coil kinase (ROCK)-myosin
II-mediated uropod contractility is required for integrin de-adhesion on two-dimensional
surfaces and nuclear propulsion through narrow pores in three-dimensional matrices,
less is known about the role of these two events during the recirculation of primary,
nonactivated lymphocytes. Using pharmacological antagonists of ROCK and myosin
II, we report that inhibition of uropod contractility blocked integrin-independent
mouse T cell migration through narrow, but not large, pores in vitro. T cell crawling
on chemokine-coated endothelial cells under shear was severely impaired by ROCK
inhibition, whereas transendothelial migration was only reduced through endothelial
cells with high, but not low, barrier properties. Using three-dimensional thick-tissue
imaging and dynamic two-photon microscopy of T cell motility in lymphoid tissue,
we demonstrated a significant role for uropod contractility in intraluminal crawling
and transendothelial migration through lymph node, but not bone marrow, endothelial
cells. Finally, we demonstrated that ICAM-1, but not anatomical constraints or
integrin-independent interactions, reduced parenchymal motility of inhibitor-treated
T cells within the dense lymphoid microenvironment, thus assigning context-dependent
roles for uropod contraction during lymphocyte recirculation.
article_processing_charge: No
article_type: original
author:
- first_name: Silvia
full_name: Soriano, Silvia
last_name: Soriano
- first_name: Miroslav
full_name: Hons, Miroslav
last_name: Hons
orcid: 0000-0002-6625-3348
- first_name: Kathrin
full_name: Schumann, Kathrin
last_name: Schumann
- first_name: Varsha
full_name: Kumar, Varsha
last_name: Kumar
- first_name: Timo
full_name: Dennier, Timo
last_name: Dennier
- first_name: Ruth
full_name: Lyck, Ruth
last_name: Lyck
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Jens
full_name: Stein, Jens
last_name: Stein
citation:
ama: Soriano S, Hons M, Schumann K, et al. In vivo analysis of uropod function during
physiological T cell trafficking. Journal of Immunology. 2011;187(5):2356-2364.
doi:10.4049/jimmunol.1100935
apa: Soriano, S., Hons, M., Schumann, K., Kumar, V., Dennier, T., Lyck, R., … Stein,
J. (2011). In vivo analysis of uropod function during physiological T cell trafficking.
Journal of Immunology. American Association of Immunologists. https://doi.org/10.4049/jimmunol.1100935
chicago: Soriano, Silvia, Miroslav Hons, Kathrin Schumann, Varsha Kumar, Timo Dennier,
Ruth Lyck, Michael K Sixt, and Jens Stein. “In Vivo Analysis of Uropod Function
during Physiological T Cell Trafficking.” Journal of Immunology. American
Association of Immunologists, 2011. https://doi.org/10.4049/jimmunol.1100935.
ieee: S. Soriano et al., “In vivo analysis of uropod function during physiological
T cell trafficking,” Journal of Immunology, vol. 187, no. 5. American Association
of Immunologists, pp. 2356–2364, 2011.
ista: Soriano S, Hons M, Schumann K, Kumar V, Dennier T, Lyck R, Sixt MK, Stein
J. 2011. In vivo analysis of uropod function during physiological T cell trafficking.
Journal of Immunology. 187(5), 2356–2364.
mla: Soriano, Silvia, et al. “In Vivo Analysis of Uropod Function during Physiological
T Cell Trafficking.” Journal of Immunology, vol. 187, no. 5, American Association
of Immunologists, 2011, pp. 2356–64, doi:10.4049/jimmunol.1100935.
short: S. Soriano, M. Hons, K. Schumann, V. Kumar, T. Dennier, R. Lyck, M.K. Sixt,
J. Stein, Journal of Immunology 187 (2011) 2356–2364.
date_created: 2018-12-11T12:03:04Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2023-10-10T13:14:59Z
day: '01'
department:
- _id: MiSi
doi: 10.4049/jimmunol.1100935
intvolume: ' 187'
issue: '5'
language:
- iso: eng
month: '09'
oa_version: None
page: 2356 - 2364
publication: Journal of Immunology
publication_identifier:
eissn:
- 1550-6606
issn:
- 0022-1767
publication_status: published
publisher: American Association of Immunologists
publist_id: '3215'
quality_controlled: '1'
scopus_import: '1'
status: public
title: In vivo analysis of uropod function during physiological T cell trafficking
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 187
year: '2011'
...
---
_id: '3163'
abstract:
- lang: eng
text: We study multi-label prediction for structured output sets, a problem that
occurs, for example, in object detection in images, secondary structure prediction
in computational biology, and graph matching with symmetries. Conventional multilabel
classification techniques are typically not applicable in this situation, because
they require explicit enumeration of the label set, which is infeasible in case
of structured outputs. Relying on techniques originally designed for single-label
structured prediction, in particular structured support vector machines, results
in reduced prediction accuracy, or leads to infeasible optimization problems.
In this work we derive a maximum-margin training formulation for multi-label structured
prediction that remains computationally tractable while achieving high prediction
accuracy. It also shares most beneficial properties with single-label maximum-margin
approaches, in particular formulation as a convex optimization problem, efficient
working set training, and PAC-Bayesian generalization bounds.
author:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Lampert C. Maximum margin multi-label structured prediction. In: Neural Information
Processing Systems; 2011.'
apa: 'Lampert, C. (2011). Maximum margin multi-label structured prediction. Presented
at the NIPS: Neural Information Processing Systems, Granada, Spain: Neural Information
Processing Systems.'
chicago: Lampert, Christoph. “Maximum Margin Multi-Label Structured Prediction.”
Neural Information Processing Systems, 2011.
ieee: 'C. Lampert, “Maximum margin multi-label structured prediction,” presented
at the NIPS: Neural Information Processing Systems, Granada, Spain, 2011.'
ista: 'Lampert C. 2011. Maximum margin multi-label structured prediction. NIPS:
Neural Information Processing Systems.'
mla: Lampert, Christoph. Maximum Margin Multi-Label Structured Prediction.
Neural Information Processing Systems, 2011.
short: C. Lampert, in:, Neural Information Processing Systems, 2011.
conference:
end_date: 2011-12-14
location: Granada, Spain
name: 'NIPS: Neural Information Processing Systems'
start_date: 2011-12-12
date_created: 2018-12-11T12:01:45Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2023-10-17T11:47:35Z
day: '01'
department:
- _id: ChLa
language:
- iso: eng
month: '12'
oa_version: None
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '3522'
quality_controlled: '1'
related_material:
record:
- id: '3322'
relation: later_version
status: public
scopus_import: 1
status: public
title: Maximum margin multi-label structured prediction
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...