---
_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.
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.
date_created: 2018-12-11T11:57:51Z
date_published: 2013-07-22T00:00:00Z
date_updated: 2021-01-12T06:57:40Z
day: '22'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1016/j.cub.2013.06.019
external_id:
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'
issue: '14'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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: '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.'
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.
date_created: 2018-12-11T11:57:52Z
date_published: 2013-01-03T00:00:00Z
date_updated: 2021-01-12T06:57:42Z
day: '03'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2012.12.001
ec_funded: 1
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'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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: '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
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
date_created: 2018-12-11T11:58:08Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2023-02-23T10:35:42Z
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: '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.'
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: 2021-01-12T06:57:58Z
day: '30'
department:
- _id: ChLa
doi: 10.1109/TPAMI.2013.140
intvolume: ' 36'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
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: '2692'
abstract:
- lang: eng
text: The group III metabotropic glutamate (mGlu) receptors mGlu7 and mGlu8 are
receiving increased attention as potential novel therapeutic targets for anxiety
disorders. The effects mediated by these receptors appear to result from a complex
interplay of facilitatory and inhibitory actions at different brain sites in the
anxiety/fear circuits. To better understand the effect of mGlu7 and mGlu8 receptors
on extinction of contextual fear and their critical sites of action in the fear
networks, we focused on the amygdala. Direct injection into the basolateral complex
of the amygdala of the mGlu7 receptor agonist AMN082 facilitated extinction, whereas
the mGlu8 receptor agonist (S)-3,4-DCPG sustained freezing during the extinction
acquisition trial. We also determined at the ultrastructural level the synaptic
distribution of these receptors in the basal nucleus (BA) and intercalated cell
clusters (ITCs) of the amygdala. Both areas are thought to exert key roles in
fear extinction. We demonstrate that mGlu7 and mGlu8 receptors are located in
different presynaptic terminals forming both asymmetric and symmetric synapses,
and that they preferentially target neurons expressing mGlu1α receptors mostly
located around ITCs. In addition we show that mGlu7 and mGlu8 receptors were segregated
to different inputs to a significant extent. In particular, mGlu7a receptors were
primarily onto glutamatergic afferents arising from the BA or midline thalamic
nuclei, but not the medial prefrontal cortex (mPFC), as revealed by combined anterograde
tracing and pre-embedding electron microscopy. On the other hand, mGlu8a showed
a more restricted distribution in the BA and appeared absent from thalamic, mPFC
and intrinsic inputs. This segregation of mGlu7 and mGlu8 receptors in different
neuronal pathways of the fear circuit might explain the distinct effects on fear
extinction training observed with mGlu7 and mGlu8 receptor agonists.
author:
- first_name: Alice
full_name: Dobi, Alice
last_name: Dobi
- first_name: Simone
full_name: Sartori, Simone B
last_name: Sartori
- first_name: Daniela
full_name: Busti, Daniela
last_name: Busti
- first_name: Herman
full_name: Van Der Putten, Herman V
last_name: Van Der Putten
- first_name: Nicolas
full_name: Singewald, Nicolas
last_name: Singewald
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Francesco
full_name: Ferraguti, Francesco
last_name: Ferraguti
citation:
ama: Dobi A, Sartori S, Busti D, et al. Neural substrates for the distinct effects
of presynaptic group III metabotropic glutamate receptors on extinction of contextual
fear conditioning in mice. Neuropharmacology. 2013;66:274-289. doi:10.1016/j.neuropharm.2012.05.025
apa: Dobi, A., Sartori, S., Busti, D., Van Der Putten, H., Singewald, N., Shigemoto,
R., & Ferraguti, F. (2013). Neural substrates for the distinct effects of
presynaptic group III metabotropic glutamate receptors on extinction of contextual
fear conditioning in mice. Neuropharmacology. Elsevier. https://doi.org/10.1016/j.neuropharm.2012.05.025
chicago: Dobi, Alice, Simone Sartori, Daniela Busti, Herman Van Der Putten, Nicolas
Singewald, Ryuichi Shigemoto, and Francesco Ferraguti. “Neural Substrates for
the Distinct Effects of Presynaptic Group III Metabotropic Glutamate Receptors
on Extinction of Contextual Fear Conditioning in Mice.” Neuropharmacology.
Elsevier, 2013. https://doi.org/10.1016/j.neuropharm.2012.05.025.
ieee: A. Dobi et al., “Neural substrates for the distinct effects of presynaptic
group III metabotropic glutamate receptors on extinction of contextual fear conditioning
in mice,” Neuropharmacology, vol. 66. Elsevier, pp. 274–289, 2013.
ista: Dobi A, Sartori S, Busti D, Van Der Putten H, Singewald N, Shigemoto R, Ferraguti
F. 2013. Neural substrates for the distinct effects of presynaptic group III metabotropic
glutamate receptors on extinction of contextual fear conditioning in mice. Neuropharmacology.
66, 274–289.
mla: Dobi, Alice, et al. “Neural Substrates for the Distinct Effects of Presynaptic
Group III Metabotropic Glutamate Receptors on Extinction of Contextual Fear Conditioning
in Mice.” Neuropharmacology, vol. 66, Elsevier, 2013, pp. 274–89, doi:10.1016/j.neuropharm.2012.05.025.
short: A. Dobi, S. Sartori, D. Busti, H. Van Der Putten, N. Singewald, R. Shigemoto,
F. Ferraguti, Neuropharmacology 66 (2013) 274–289.
date_created: 2018-12-11T11:59:06Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2021-01-12T06:59:05Z
day: '01'
doi: 10.1016/j.neuropharm.2012.05.025
extern: 1
intvolume: ' 66'
month: '03'
page: 274 - 289
publication: Neuropharmacology
publication_status: published
publisher: Elsevier
publist_id: '4205'
quality_controlled: 0
status: public
title: Neural substrates for the distinct effects of presynaptic group III metabotropic
glutamate receptors on extinction of contextual fear conditioning in mice
type: journal_article
volume: 66
year: '2013'
...
---
_id: '2691'
abstract:
- lang: eng
text: P/Q-type voltage-dependent calcium channels play key roles in transmitter
release, integration of dendritic signals, generation of dendritic spikes, and
gene expression. High intracellular calcium concentration transient produced by
these channels is restricted to tens to hundreds of nanometers from the channels.
Therefore, precise localization of these channels along the plasma membrane was
long sought to decipher how each neuronal cell function is controlled. Here, we
analyzed the distribution of Cav2.1 subunit of the P/Q-type channel using highly
sensitive SDS-digested freeze-fracture replica labeling in the rat cerebellar
Purkinje cells. The labeling efficiency was such that the number of immunogold
particles in each parallel fiber active zone was comparable to that of functional
channels calculated from previous reports. Two distinct patterns of Cav2.1 distribution,
scattered and clustered, were found in Purkinje cells. The scattered Cav2.1 had
a somatodendritic gradient with the density of immunogold particles increasing
2.5-fold from soma to distal dendrites. The other population with 74-fold higher
density than the scattered particles was found within clusters of intramembrane
particles on the P-face of soma and primary dendrites. Both populations of Cav2.1
were found as early as P3 and increased in the second postnatal week to a mature
level. Using double immunogold labeling, we found that virtually all of the Cav2.1
clusters were colocalized with two types of calcium-activated potassium channels,
BK and SK2, with the nearest neighbor distance of 40∼nm. Calcium nanodomain created
by the opening of Cav2.1 channels likely activates the two channels that limit
the extent of depolarization.
author:
- first_name: Dwi
full_name: Indriati, Dwi Wahyu
last_name: Indriati
- first_name: Naomi
full_name: Kamasawa, Naomi
last_name: Kamasawa
- first_name: Ko
full_name: Matsui, Ko
last_name: Matsui
- first_name: Andrea
full_name: Meredith, Andrea L
last_name: Meredith
- first_name: Masahiko
full_name: Watanabe, Masahiko
last_name: Watanabe
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: 'Indriati D, Kamasawa N, Matsui K, Meredith A, Watanabe M, Shigemoto R. Quantitative
localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels in Purkinje
cells: Somatodendritic gradient and distinct somatic coclustering with calcium-activated
potassium channels. Journal of Neuroscience. 2013;33(8):3668-3678. doi:10.1523/JNEUROSCI.2921-12.2013'
apa: 'Indriati, D., Kamasawa, N., Matsui, K., Meredith, A., Watanabe, M., &
Shigemoto, R. (2013). Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent
calcium channels in Purkinje cells: Somatodendritic gradient and distinct somatic
coclustering with calcium-activated potassium channels. Journal of Neuroscience.
Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2921-12.2013'
chicago: 'Indriati, Dwi, Naomi Kamasawa, Ko Matsui, Andrea Meredith, Masahiko Watanabe,
and Ryuichi Shigemoto. “Quantitative Localization of Cav2.1 (P/Q-Type) Voltage-Dependent
Calcium Channels in Purkinje Cells: Somatodendritic Gradient and Distinct Somatic
Coclustering with Calcium-Activated Potassium Channels.” Journal of Neuroscience.
Society for Neuroscience, 2013. https://doi.org/10.1523/JNEUROSCI.2921-12.2013.'
ieee: 'D. Indriati, N. Kamasawa, K. Matsui, A. Meredith, M. Watanabe, and R. Shigemoto,
“Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels
in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering
with calcium-activated potassium channels,” Journal of Neuroscience, vol.
33, no. 8. Society for Neuroscience, pp. 3668–3678, 2013.'
ista: 'Indriati D, Kamasawa N, Matsui K, Meredith A, Watanabe M, Shigemoto R. 2013.
Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels
in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering
with calcium-activated potassium channels. Journal of Neuroscience. 33(8), 3668–3678.'
mla: 'Indriati, Dwi, et al. “Quantitative Localization of Cav2.1 (P/Q-Type) Voltage-Dependent
Calcium Channels in Purkinje Cells: Somatodendritic Gradient and Distinct Somatic
Coclustering with Calcium-Activated Potassium Channels.” Journal of Neuroscience,
vol. 33, no. 8, Society for Neuroscience, 2013, pp. 3668–78, doi:10.1523/JNEUROSCI.2921-12.2013.'
short: D. Indriati, N. Kamasawa, K. Matsui, A. Meredith, M. Watanabe, R. Shigemoto,
Journal of Neuroscience 33 (2013) 3668–3678.
date_created: 2018-12-11T11:59:05Z
date_published: 2013-02-20T00:00:00Z
date_updated: 2021-01-12T06:59:05Z
day: '20'
doi: 10.1523/JNEUROSCI.2921-12.2013
extern: 1
intvolume: ' 33'
issue: '8'
month: '02'
page: 3668 - 3678
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '4206'
quality_controlled: 0
status: public
title: 'Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels
in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering with
calcium-activated potassium channels'
type: journal_article
volume: 33
year: '2013'
...
---
_id: '2690'
abstract:
- lang: eng
text: Establishing the spatiotemporal concentration profile of neurotransmitter
following synaptic vesicular release is essential for our understanding of inter-neuronal
communication. Such profile is a determinant of synaptic strength, short-term
plasticity and inter-synaptic crosstalk. Synaptically released glutamate has been
suggested to reach a few millimolar in concentration and last for <1 ms. The
synaptic cleft is often conceived as a single concentration compartment, whereas
a huge gradient likely exists. Modelling studies have attempted to describe this
gradient, but two key parameters, the number of glutamate in a vesicle (NGlu)
and its diffusion coefficient (DGlu) in the extracellular space, remained unresolved.
To determine this profile, the rat calyx of Held synapse at postnatal day 12-16
was studied where diffusion of glutamate occurs two-dimensionally and where quantification
of AMPA receptor distribution on individual postsynaptic specialization on medial
nucleus of the trapezoid body principal cells is possible using SDS-digested freeze-fracture
replica labelling. To assess the performance of these receptors as glutamate sensors,
a kinetic model of the receptors was constructed from outside-out patch recordings.
From here, we simulated synaptic responses and compared them with the EPSC recordings.
Combinations of NGlu and DGlu with an optimum of 7000 and 0.3 μm2 ms-1 reproduced
the data, suggesting slow diffusion. Further simulations showed that a single
vesicle does not saturate the synaptic receptors, and that glutamate spillover
does not affect the conductance amplitude at this synapse. Using the estimated
profile, we also evaluated how the number of multiple vesicle releases at individual
active zones affects the amplitude of postsynaptic signals.
author:
- first_name: Timotheus
full_name: Budisantoso, Timotheus
last_name: Budisantoso
- first_name: Harumi
full_name: Harumi Harada
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Naomi
full_name: Kamasawa, Naomi
last_name: Kamasawa
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Ko
full_name: Matsui, Ko
last_name: Matsui
citation:
ama: Budisantoso T, Harada H, Kamasawa N, Fukazawa Y, Shigemoto R, Matsui K. Evaluation
of glutamate concentration transient in the synaptic cleft of the rat calyx of
Held. Journal of Physiology. 2013;591(1):219-239. doi:10.1113/jphysiol.2012.241398
apa: Budisantoso, T., Harada, H., Kamasawa, N., Fukazawa, Y., Shigemoto, R., &
Matsui, K. (2013). Evaluation of glutamate concentration transient in the synaptic
cleft of the rat calyx of Held. Journal of Physiology. Wiley-Blackwell.
https://doi.org/10.1113/jphysiol.2012.241398
chicago: Budisantoso, Timotheus, Harumi Harada, Naomi Kamasawa, Yugo Fukazawa, Ryuichi
Shigemoto, and Ko Matsui. “Evaluation of Glutamate Concentration Transient in
the Synaptic Cleft of the Rat Calyx of Held.” Journal of Physiology. Wiley-Blackwell,
2013. https://doi.org/10.1113/jphysiol.2012.241398.
ieee: T. Budisantoso, H. Harada, N. Kamasawa, Y. Fukazawa, R. Shigemoto, and K.
Matsui, “Evaluation of glutamate concentration transient in the synaptic cleft
of the rat calyx of Held,” Journal of Physiology, vol. 591, no. 1. Wiley-Blackwell,
pp. 219–239, 2013.
ista: Budisantoso T, Harada H, Kamasawa N, Fukazawa Y, Shigemoto R, Matsui K. 2013.
Evaluation of glutamate concentration transient in the synaptic cleft of the rat
calyx of Held. Journal of Physiology. 591(1), 219–239.
mla: Budisantoso, Timotheus, et al. “Evaluation of Glutamate Concentration Transient
in the Synaptic Cleft of the Rat Calyx of Held.” Journal of Physiology,
vol. 591, no. 1, Wiley-Blackwell, 2013, pp. 219–39, doi:10.1113/jphysiol.2012.241398.
short: T. Budisantoso, H. Harada, N. Kamasawa, Y. Fukazawa, R. Shigemoto, K. Matsui,
Journal of Physiology 591 (2013) 219–239.
date_created: 2018-12-11T11:59:05Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T06:59:04Z
day: '01'
doi: 10.1113/jphysiol.2012.241398
extern: 1
intvolume: ' 591'
issue: '1'
month: '01'
page: 219 - 239
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4207'
quality_controlled: 0
status: public
title: Evaluation of glutamate concentration transient in the synaptic cleft of the
rat calyx of Held
type: journal_article
volume: 591
year: '2013'
...
---
_id: '2693'
abstract:
- lang: eng
text: Inhibitory parvalbumin-containing interneurons (PVIs) control neuronal discharge
and support the generation of theta- and gammafrequency oscillations in cortical
networks. Fast GABAergic input onto PVIs is crucial for their synchronization
and oscillatory entrainment, but the role of metabotropic GABAB receptors (GABABRs)
in mediating slow presynaptic and postsynaptic inhibition remains unknown. In
this study, we have combined high-resolution immunoelectron microscopy, whole-cell
patch-clamp recording, and computational modeling to investigate the subcellular
distribution and effects of GABABRs and their postsynaptic effector Kir3 channels
in rat hippocampal PVIs. Pre-embedding immunogold labeling revealed that the receptors
and channels localize at high levels to the extrasynaptic membrane of parvalbumin-immunoreactive
dendrites. Immunoreactivity forGABABRs was also present at lower levels on PVI
axon terminals. Whole-cell recordings further showed that synaptically released
GABA in response to extracellular stimulation evokes large GABABR-mediated slow
IPSCs in perisomatic-targeting (PT) PVIs, but only small or no currents in dendrite-targeting
(DT) PVIs. In contrast, paired recordings demonstrated that GABABR activation
results in presynaptic inhibition at the output synapses of both PT and DT PVIs,
but more strongly in the latter. Finally, computational analysis indicated that
GABAB IPSCs can phasically modulate the discharge of PT interneurons at theta
frequencies. In summary, our results show that GABABRs differentially mediate
slow presynaptic and postsynaptic inhibition in PVIs and can contribute to the
dynamic modulation of their activity during oscillations. Furthermore, these data
provide evidence for a compartment-specific molecular divergence of hippocampal
PVI subtypes, suggesting that activation of GABABRs may shift the balance between
perisomatic and dendritic inhibition.
author:
- first_name: Sam
full_name: Booker, Sam A
last_name: Booker
- first_name: Anna
full_name: Gross, Anna
last_name: Gross
- first_name: Daniel
full_name: Althof, Daniel
last_name: Althof
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Bernhard
full_name: Bettler, Bernhard
last_name: Bettler
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Matthew
full_name: Hearing, Matthew C
last_name: Hearing
- first_name: Kevin
full_name: Wickman, Kevin D
last_name: Wickman
- first_name: Masahiko
full_name: Watanabe, Masahiko
last_name: Watanabe
- first_name: Ákos
full_name: Kulik, Ákos
last_name: Kulik
- first_name: Imre
full_name: Vida, Imre
last_name: Vida
citation:
ama: Booker S, Gross A, Althof D, et al. Differential GABAB-receptor-mediated effects
in perisomatic- and dendrite-targeting parvalbumin interneurons. Journal of
Neuroscience. 2013;33(18):7961-7974. doi:10.1523/JNEUROSCI.1186-12.2013
apa: Booker, S., Gross, A., Althof, D., Shigemoto, R., Bettler, B., Frotscher, M.,
… Vida, I. (2013). Differential GABAB-receptor-mediated effects in perisomatic-
and dendrite-targeting parvalbumin interneurons. Journal of Neuroscience.
Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1186-12.2013
chicago: Booker, Sam, Anna Gross, Daniel Althof, Ryuichi Shigemoto, Bernhard Bettler,
Michael Frotscher, Matthew Hearing, et al. “Differential GABAB-Receptor-Mediated
Effects in Perisomatic- and Dendrite-Targeting Parvalbumin Interneurons.” Journal
of Neuroscience. Society for Neuroscience, 2013. https://doi.org/10.1523/JNEUROSCI.1186-12.2013.
ieee: S. Booker et al., “Differential GABAB-receptor-mediated effects in
perisomatic- and dendrite-targeting parvalbumin interneurons,” Journal of Neuroscience,
vol. 33, no. 18. Society for Neuroscience, pp. 7961–7974, 2013.
ista: Booker S, Gross A, Althof D, Shigemoto R, Bettler B, Frotscher M, Hearing
M, Wickman K, Watanabe M, Kulik Á, Vida I. 2013. Differential GABAB-receptor-mediated
effects in perisomatic- and dendrite-targeting parvalbumin interneurons. Journal
of Neuroscience. 33(18), 7961–7974.
mla: Booker, Sam, et al. “Differential GABAB-Receptor-Mediated Effects in Perisomatic-
and Dendrite-Targeting Parvalbumin Interneurons.” Journal of Neuroscience,
vol. 33, no. 18, Society for Neuroscience, 2013, pp. 7961–74, doi:10.1523/JNEUROSCI.1186-12.2013.
short: S. Booker, A. Gross, D. Althof, R. Shigemoto, B. Bettler, M. Frotscher, M.
Hearing, K. Wickman, M. Watanabe, Á. Kulik, I. Vida, Journal of Neuroscience 33
(2013) 7961–7974.
date_created: 2018-12-11T11:59:06Z
date_published: 2013-05-01T00:00:00Z
date_updated: 2021-01-12T06:59:05Z
day: '01'
doi: 10.1523/JNEUROSCI.1186-12.2013
extern: 1
intvolume: ' 33'
issue: '18'
month: '05'
page: 7961 - 7974
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '4204'
quality_controlled: 0
status: public
title: Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting
parvalbumin interneurons
type: journal_article
volume: 33
year: '2013'
...
---
_id: '2698'
abstract:
- lang: eng
text: We consider non-interacting particles subject to a fixed external potential
V and a self-generated magnetic field B. The total energy includes the field energy
β∫B2 and we minimize over all particle states and magnetic fields. In the case
of spin-1/2 particles this minimization leads to the coupled Maxwell-Pauli system.
The parameter β tunes the coupling strength between the field and the particles
and it effectively determines the strength of the field. We investigate the stability
and the semiclassical asymptotics, h→0, of the total ground state energy E(β,h,V).
The relevant parameter measuring the field strength in the semiclassical limit
is κ=βh. We are not able to give the exact leading order semiclassical asymptotics
uniformly in κ or even for fixed κ. We do however give upper and lower bounds
on E with almost matching dependence on κ. In the simultaneous limit h→0 and κ→∞
we show that the standard non-magnetic Weyl asymptotics holds. The same result
also holds for the spinless case, i.e. where the Pauli operator is replaced by
the Schrödinger operator.
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Søren
full_name: Fournais, Søren
last_name: Fournais
- first_name: Jan
full_name: Solovej, Jan
last_name: Solovej
citation:
ama: Erdös L, Fournais S, Solovej J. Stability and semiclassics in self-generated
fields. Journal of the European Mathematical Society. 2013;15(6):2093-2113.
doi:10.4171/JEMS/416
apa: Erdös, L., Fournais, S., & Solovej, J. (2013). Stability and semiclassics
in self-generated fields. Journal of the European Mathematical Society.
European Mathematical Society. https://doi.org/10.4171/JEMS/416
chicago: Erdös, László, Søren Fournais, and Jan Solovej. “Stability and Semiclassics
in Self-Generated Fields.” Journal of the European Mathematical Society.
European Mathematical Society, 2013. https://doi.org/10.4171/JEMS/416.
ieee: L. Erdös, S. Fournais, and J. Solovej, “Stability and semiclassics in self-generated
fields,” Journal of the European Mathematical Society, vol. 15, no. 6.
European Mathematical Society, pp. 2093–2113, 2013.
ista: Erdös L, Fournais S, Solovej J. 2013. Stability and semiclassics in self-generated
fields. Journal of the European Mathematical Society. 15(6), 2093–2113.
mla: Erdös, László, et al. “Stability and Semiclassics in Self-Generated Fields.”
Journal of the European Mathematical Society, vol. 15, no. 6, European
Mathematical Society, 2013, pp. 2093–113, doi:10.4171/JEMS/416.
short: L. Erdös, S. Fournais, J. Solovej, Journal of the European Mathematical Society
15 (2013) 2093–2113.
date_created: 2018-12-11T11:59:07Z
date_published: 2013-10-16T00:00:00Z
date_updated: 2021-01-12T06:59:07Z
day: '16'
department:
- _id: LaEr
doi: 10.4171/JEMS/416
external_id:
arxiv:
- '1105.0506'
intvolume: ' 15'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1105.0506
month: '10'
oa: 1
oa_version: Preprint
page: 2093 - 2113
publication: Journal of the European Mathematical Society
publication_status: published
publisher: European Mathematical Society
publist_id: '4198'
quality_controlled: '1'
status: public
title: Stability and semiclassics in self-generated fields
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2013'
...
---
_id: '2697'
abstract:
- lang: eng
text: We consider Hermitian and symmetric random band matrices H = (h xy ) in d⩾1
d ⩾ 1 dimensions. The matrix entries h xy , indexed by x,y∈(Z/LZ)d x , y ∈ ( Z
/ L Z ) d , are independent, centred random variables with variances sxy=E|hxy|2
s x y = E | h x y | 2 . We assume that s xy is negligible if |x − y| exceeds the
band width W. In one dimension we prove that the eigenvectors of H are delocalized
if W≫L4/5 W ≫ L 4 / 5 . We also show that the magnitude of the matrix entries
|Gxy|2 | G x y | 2 of the resolvent G=G(z)=(H−z)−1 G = G ( z ) = ( H - z ) - 1
is self-averaging and we compute E|Gxy|2 E | G x y | 2 . We show that, as L→∞
L → ∞ and W≫L4/5 W ≫ L 4 / 5 , the behaviour of E|Gxy|2 E | G x y | 2 is governed
by a diffusion operator whose diffusion constant we compute. Similar results are
obtained in higher dimensions.
author:
- first_name: László
full_name: László Erdös
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Antti
full_name: Knowles, Antti
last_name: Knowles
- first_name: Horng
full_name: Yau, Horng-Tzer
last_name: Yau
- first_name: Jun
full_name: Yin, Jun
last_name: Yin
citation:
ama: Erdös L, Knowles A, Yau H, Yin J. Delocalization and diffusion profile for
random band matrices. Communications in Mathematical Physics. 2013;323(1):367-416.
doi:10.1007/s00220-013-1773-3
apa: Erdös, L., Knowles, A., Yau, H., & Yin, J. (2013). Delocalization and diffusion
profile for random band matrices. Communications in Mathematical Physics.
Springer. https://doi.org/10.1007/s00220-013-1773-3
chicago: Erdös, László, Antti Knowles, Horng Yau, and Jun Yin. “Delocalization and
Diffusion Profile for Random Band Matrices.” Communications in Mathematical
Physics. Springer, 2013. https://doi.org/10.1007/s00220-013-1773-3.
ieee: L. Erdös, A. Knowles, H. Yau, and J. Yin, “Delocalization and diffusion profile
for random band matrices,” Communications in Mathematical Physics, vol.
323, no. 1. Springer, pp. 367–416, 2013.
ista: Erdös L, Knowles A, Yau H, Yin J. 2013. Delocalization and diffusion profile
for random band matrices. Communications in Mathematical Physics. 323(1), 367–416.
mla: Erdös, László, et al. “Delocalization and Diffusion Profile for Random Band
Matrices.” Communications in Mathematical Physics, vol. 323, no. 1, Springer,
2013, pp. 367–416, doi:10.1007/s00220-013-1773-3.
short: L. Erdös, A. Knowles, H. Yau, J. Yin, Communications in Mathematical Physics
323 (2013) 367–416.
date_created: 2018-12-11T11:59:07Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2021-01-12T06:59:07Z
day: '01'
doi: 10.1007/s00220-013-1773-3
extern: 1
intvolume: ' 323'
issue: '1'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1205.5669
month: '10'
oa: 1
page: 367 - 416
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '4199'
quality_controlled: 0
status: public
title: Delocalization and diffusion profile for random band matrices
type: journal_article
volume: 323
year: '2013'
...
---
_id: '2718'
abstract:
- lang: eng
text: Even though both population and quantitative genetics, and evolutionary computation,
deal with the same questions, they have developed largely independently of each
other. I review key results from each field, emphasising those that apply independently
of the (usually unknown) relation between genotype and phenotype. The infinitesimal
model provides a simple framework for predicting the response of complex traits
to selection, which in biology has proved remarkably successful. This allows one
to choose the schedule of population sizes and selection intensities that will
maximise the response to selection, given that the total number of individuals
realised, C = ∑t Nt, is constrained. This argument shows that for an additive
trait (i.e., determined by the sum of effects of the genes), the optimum population
size and the maximum possible response (i.e., the total change in trait mean)
are both proportional to √C.
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: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: 'Barton NH, Paixao T. Can quantitative and population genetics help us understand
evolutionary computation? In: Proceedings of the 15th Annual Conference on
Genetic and Evolutionary Computation. ACM; 2013:1573-1580. doi:10.1145/2463372.2463568'
apa: 'Barton, N. H., & Paixao, T. (2013). Can quantitative and population genetics
help us understand evolutionary computation? In Proceedings of the 15th annual
conference on Genetic and evolutionary computation (pp. 1573–1580). Amsterdam,
Netherlands: ACM. https://doi.org/10.1145/2463372.2463568'
chicago: Barton, Nicholas H, and Tiago Paixao. “Can Quantitative and Population
Genetics Help Us Understand Evolutionary Computation?” In Proceedings of the
15th Annual Conference on Genetic and Evolutionary Computation, 1573–80. ACM,
2013. https://doi.org/10.1145/2463372.2463568.
ieee: N. H. Barton and T. Paixao, “Can quantitative and population genetics help
us understand evolutionary computation?,” in Proceedings of the 15th annual
conference on Genetic and evolutionary computation, Amsterdam, Netherlands,
2013, pp. 1573–1580.
ista: 'Barton NH, Paixao T. 2013. Can quantitative and population genetics help
us understand evolutionary computation? Proceedings of the 15th annual conference
on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation
conference, 1573–1580.'
mla: Barton, Nicholas H., and Tiago Paixao. “Can Quantitative and Population Genetics
Help Us Understand Evolutionary Computation?” Proceedings of the 15th Annual
Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–80,
doi:10.1145/2463372.2463568.
short: N.H. Barton, T. Paixao, in:, Proceedings of the 15th Annual Conference on
Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–1580.
conference:
end_date: 2013-07-10
location: Amsterdam, Netherlands
name: 'GECCO: Genetic and evolutionary computation conference'
start_date: 2013-07-06
date_created: 2018-12-11T11:59:14Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2021-01-12T06:59:15Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1145/2463372.2463568
ec_funded: 1
file:
- access_level: open_access
checksum: 9d9be9090ce5c20766e0eb076ace5b98
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:38Z
date_updated: 2020-07-14T12:45:45Z
file_id: '5159'
file_name: IST-2016-564-v1+1_NickGECCO_2013_1_-1.pdf
file_size: 475844
relation: main_file
file_date_updated: 2020-07-14T12:45:45Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 1573 - 1580
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Proceedings of the 15th annual conference on Genetic and evolutionary
computation
publication_status: published
publisher: ACM
publist_id: '4174'
pubrep_id: '564'
quality_controlled: '1'
scopus_import: 1
status: public
title: Can quantitative and population genetics help us understand evolutionary computation?
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2720'
abstract:
- lang: eng
text: 'Knowledge of the rate and fitness effects of mutations is essential for understanding
the process of evolution. Mutations are inherently difficult to study because
they are rare and are frequently eliminated by natural selection. In the ciliate
Tetrahymena thermophila, mutations can accumulate in the germline genome without
being exposed to selection. We have conducted a mutation accumulation (MA) experiment
in this species. Assuming that all mutations are deleterious and have the same
effect, we estimate that the deleterious mutation rate per haploid germline genome
per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that
germline mutations decrease fitness by s = 11% when expressed in a homozygous
state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially
recessive on average (h = 0.26; 95% CI: –0.022, 0.62) and that the rate of lethal
mutations is <10% of the deleterious mutation rate. Comparisons between the
observed evolutionary responses in the germline and somatic genomes and the results
from individual-based simulations of MA suggest that the two genomes have similar
mutational parameters. These are the first estimates of the deleterious mutation
rate and fitness effects from the eukaryotic supergroup Chromalveolata and are
within the range of those of other eukaryotes.'
article_processing_charge: No
author:
- first_name: Hongan
full_name: Long, Hongan
last_name: Long
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Ricardo
full_name: Azevedo, Ricardo
last_name: Azevedo
- first_name: Rebecca
full_name: Zufall, Rebecca
last_name: Zufall
citation:
ama: Long H, Paixao T, Azevedo R, Zufall R. Accumulation of spontaneous mutations
in the ciliate Tetrahymena thermophila. Genetics. 2013;195(2):527-540.
doi:10.1534/genetics.113.153536
apa: Long, H., Paixao, T., Azevedo, R., & Zufall, R. (2013). Accumulation of
spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics.
Genetics Society of America. https://doi.org/10.1534/genetics.113.153536
chicago: Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation
of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics.
Genetics Society of America, 2013. https://doi.org/10.1534/genetics.113.153536.
ieee: H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous
mutations in the ciliate Tetrahymena thermophila,” Genetics, vol. 195,
no. 2. Genetics Society of America, pp. 527–540, 2013.
ista: Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations
in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540.
mla: Long, Hongan, et al. “Accumulation of Spontaneous Mutations in the Ciliate
Tetrahymena Thermophila.” Genetics, vol. 195, no. 2, Genetics Society of
America, 2013, pp. 527–40, doi:10.1534/genetics.113.153536.
short: H. Long, T. Paixao, R. Azevedo, R. Zufall, Genetics 195 (2013) 527–540.
date_created: 2018-12-11T11:59:15Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2021-01-12T06:59:16Z
day: '01'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1534/genetics.113.153536
ec_funded: 1
external_id:
pmid:
- '23934880'
intvolume: ' 195'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781978/
month: '10'
oa: 1
oa_version: Submitted Version
page: 527-540
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '4172'
quality_controlled: '1'
scopus_import: 1
status: public
title: Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 195
year: '2013'
...
---
_id: '2719'
abstract:
- lang: eng
text: Prediction of the evolutionary process is a long standing problem both in
the theory of evolutionary biology and evolutionary computation (EC). It has long
been realized that heritable variation is crucial to both the response to selection
and the success of genetic algorithms. However, not all variation contributes
in the same way to the response. Quantitative genetics has developed a large body
of work trying to estimate and understand how different components of the variance
in fitness in the population contribute to the response to selection. We illustrate
how to apply some concepts of quantitative genetics to the analysis of genetic
algorithms. In particular, we derive estimates for the short term prediction of
the response to selection and we use variance decomposition to gain insight on
local aspects of the landscape. Finally, we propose a new population based genetic
algorithm that uses these methods to improve its operation.
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Paixao T, Barton NH. A variance decomposition approach to the analysis of
genetic algorithms. In: Proceedings of the 15th Annual Conference on Genetic
and Evolutionary Computation. ACM; 2013:845-852. doi:10.1145/2463372.2463470'
apa: 'Paixao, T., & Barton, N. H. (2013). A variance decomposition approach
to the analysis of genetic algorithms. In Proceedings of the 15th annual conference
on Genetic and evolutionary computation (pp. 845–852). Amsterdam, Netherlands:
ACM. https://doi.org/10.1145/2463372.2463470'
chicago: Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach
to the Analysis of Genetic Algorithms.” In Proceedings of the 15th Annual Conference
on Genetic and Evolutionary Computation, 845–52. ACM, 2013. https://doi.org/10.1145/2463372.2463470.
ieee: T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis
of genetic algorithms,” in Proceedings of the 15th annual conference on Genetic
and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 845–852.
ista: 'Paixao T, Barton NH. 2013. A variance decomposition approach to the analysis
of genetic algorithms. Proceedings of the 15th annual conference on Genetic and
evolutionary computation. GECCO: Genetic and evolutionary computation conference,
845–852.'
mla: Paixao, Tiago, and Nicholas H. Barton. “A Variance Decomposition Approach to
the Analysis of Genetic Algorithms.” Proceedings of the 15th Annual Conference
on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–52, doi:10.1145/2463372.2463470.
short: T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on
Genetic and Evolutionary Computation, ACM, 2013, pp. 845–852.
conference:
end_date: 2013-07-10
location: Amsterdam, Netherlands
name: 'GECCO: Genetic and evolutionary computation conference'
start_date: 2013-07-06
date_created: 2018-12-11T11:59:15Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2021-01-12T06:59:15Z
day: '01'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1145/2463372.2463470
ec_funded: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 845 - 852
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Proceedings of the 15th annual conference on Genetic and evolutionary
computation
publication_status: published
publisher: ACM
publist_id: '4173'
quality_controlled: '1'
scopus_import: 1
status: public
title: A variance decomposition approach to the analysis of genetic algorithms
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2782'
abstract:
- lang: eng
text: We consider random n×n matrices of the form (XX*+YY*)^{-1/2}YY*(XX*+YY*)^{-1/2},
where X and Y have independent entries with zero mean and variance one. These
matrices are the natural generalization of the Gaussian case, which are known
as MANOVA matrices and which have joint eigenvalue density given by the third
classical ensemble, the Jacobi ensemble. We show that, away from the spectral
edge, the eigenvalue density converges to the limiting density of the Jacobi ensemble
even on the shortest possible scales of order 1/n (up to log n factors). This
result is the analogue of the local Wigner semicircle law and the local Marchenko-Pastur
law for general MANOVA matrices.
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Brendan
full_name: Farrell, Brendan
last_name: Farrell
citation:
ama: Erdös L, Farrell B. Local eigenvalue density for general MANOVA matrices. Journal
of Statistical Physics. 2013;152(6):1003-1032. doi:10.1007/s10955-013-0807-8
apa: Erdös, L., & Farrell, B. (2013). Local eigenvalue density for general MANOVA
matrices. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-013-0807-8
chicago: Erdös, László, and Brendan Farrell. “Local Eigenvalue Density for General
MANOVA Matrices.” Journal of Statistical Physics. Springer, 2013. https://doi.org/10.1007/s10955-013-0807-8.
ieee: L. Erdös and B. Farrell, “Local eigenvalue density for general MANOVA matrices,”
Journal of Statistical Physics, vol. 152, no. 6. Springer, pp. 1003–1032,
2013.
ista: Erdös L, Farrell B. 2013. Local eigenvalue density for general MANOVA matrices.
Journal of Statistical Physics. 152(6), 1003–1032.
mla: Erdös, László, and Brendan Farrell. “Local Eigenvalue Density for General MANOVA
Matrices.” Journal of Statistical Physics, vol. 152, no. 6, Springer, 2013,
pp. 1003–32, doi:10.1007/s10955-013-0807-8.
short: L. Erdös, B. Farrell, Journal of Statistical Physics 152 (2013) 1003–1032.
date_created: 2018-12-11T11:59:34Z
date_published: 2013-07-18T00:00:00Z
date_updated: 2021-01-12T06:59:41Z
day: '18'
department:
- _id: LaEr
doi: 10.1007/s10955-013-0807-8
external_id:
arxiv:
- '1207.0031'
intvolume: ' 152'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1207.0031
month: '07'
oa: 1
oa_version: Preprint
page: 1003 - 1032
publication: Journal of Statistical Physics
publication_status: published
publisher: Springer
publist_id: '4107'
quality_controlled: '1'
scopus_import: 1
status: public
title: Local eigenvalue density for general MANOVA matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 152
year: '2013'
...
---
_id: '2781'
abstract:
- lang: eng
text: 'We consider the ensemble of adjacency matrices of Erdős-Rényi random graphs,
that is, graphs on N vertices where every edge is chosen independently and with
probability p = p(N). We rescale the matrix so that its bulk eigenvalues are of
order one. We prove that, as long as pN→∞(with a speed at least logarithmic in
N), the density of eigenvalues of the Erdős-Rényi ensemble is given by the Wigner
semicircle law for spectral windows of length larger than N-1 (up to logarithmic
corrections). As a consequence, all eigenvectors are proved to be completely delocalized
in the sense that the ℓ∞-norms of the ℓ2-normalized eigenvectors are at most of
order N-1/2 with a very high probability. The estimates in this paper will be
used in the companion paper [Spectral statistics of Erdős-Rényi graphs II: Eigenvalue
spacing and the extreme eigenvalues (2011) Preprint] to prove the universality
of eigenvalue distributions both in the bulk and at the spectral edges under the
further restriction that pN »N2/3.'
author:
- first_name: László
full_name: László Erdös
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Antti
full_name: Knowles, Antti
last_name: Knowles
- first_name: Horng
full_name: Yau, Horng-Tzer
last_name: Yau
- first_name: Jun
full_name: Yin, Jun
last_name: Yin
citation:
ama: 'Erdös L, Knowles A, Yau H, Yin J. Spectral statistics of Erdős-Rényi graphs
I: Local semicircle law. Annals of Probability. 2013;41(3 B):2279-2375.
doi:10.1214/11-AOP734'
apa: 'Erdös, L., Knowles, A., Yau, H., & Yin, J. (2013). Spectral statistics
of Erdős-Rényi graphs I: Local semicircle law. Annals of Probability. Institute
of Mathematical Statistics. https://doi.org/10.1214/11-AOP734'
chicago: 'Erdös, László, Antti Knowles, Horng Yau, and Jun Yin. “Spectral Statistics
of Erdős-Rényi Graphs I: Local Semicircle Law.” Annals of Probability.
Institute of Mathematical Statistics, 2013. https://doi.org/10.1214/11-AOP734.'
ieee: 'L. Erdös, A. Knowles, H. Yau, and J. Yin, “Spectral statistics of Erdős-Rényi
graphs I: Local semicircle law,” Annals of Probability, vol. 41, no. 3
B. Institute of Mathematical Statistics, pp. 2279–2375, 2013.'
ista: 'Erdös L, Knowles A, Yau H, Yin J. 2013. Spectral statistics of Erdős-Rényi
graphs I: Local semicircle law. Annals of Probability. 41(3 B), 2279–2375.'
mla: 'Erdös, László, et al. “Spectral Statistics of Erdős-Rényi Graphs I: Local
Semicircle Law.” Annals of Probability, vol. 41, no. 3 B, Institute of
Mathematical Statistics, 2013, pp. 2279–375, doi:10.1214/11-AOP734.'
short: L. Erdös, A. Knowles, H. Yau, J. Yin, Annals of Probability 41 (2013) 2279–2375.
date_created: 2018-12-11T11:59:34Z
date_published: 2013-05-01T00:00:00Z
date_updated: 2021-01-12T06:59:41Z
day: '01'
doi: 10.1214/11-AOP734
extern: 1
intvolume: ' 41'
issue: 3 B
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1103.1919
month: '05'
oa: 1
page: 2279 - 2375
publication: Annals of Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '4109'
quality_controlled: 0
status: public
title: 'Spectral statistics of Erdős-Rényi graphs I: Local semicircle law'
type: journal_article
volume: 41
year: '2013'
...
---
_id: '2780'
abstract:
- lang: eng
text: We consider a general class of random matrices whose entries are centred random
variables, independent up to a symmetry constraint. We establish precise high-probability
bounds on the averages of arbitrary monomials in the resolvent matrix entries.
Our results generalize the previous results of Erdős et al. (Ann Probab, arXiv:1103.1919,
2013; Commun Math Phys, arXiv:1103.3869, 2013; J Combin 1(2):15-85, 2011) which
constituted a key step in the proof of the local semicircle law with optimal error
bound in mean-field random matrix models. Our bounds apply to random band matrices
and improve previous estimates from order 2 to order 4 in the cases relevant to
applications. In particular, they lead to a proof of the diffusion approximation
for the magnitude of the resolvent of random band matrices. This, in turn, implies
new delocalization bounds on the eigenvectors. The applications are presented
in a separate paper (Erdős et al., arXiv:1205.5669, 2013).
author:
- first_name: László
full_name: László Erdös
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Antti
full_name: Knowles, Antti
last_name: Knowles
- first_name: Horng
full_name: Yau, Horng-Tzer
last_name: Yau
citation:
ama: Erdös L, Knowles A, Yau H. Averaging fluctuations in resolvents of random band
matrices. Annales Henri Poincare. 2013;14(8):1837-1926. doi:10.1007/s00023-013-0235-y
apa: Erdös, L., Knowles, A., & Yau, H. (2013). Averaging fluctuations in resolvents
of random band matrices. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-013-0235-y
chicago: Erdös, László, Antti Knowles, and Horng Yau. “Averaging Fluctuations in
Resolvents of Random Band Matrices.” Annales Henri Poincare. Birkhäuser,
2013. https://doi.org/10.1007/s00023-013-0235-y.
ieee: L. Erdös, A. Knowles, and H. Yau, “Averaging fluctuations in resolvents of
random band matrices,” Annales Henri Poincare, vol. 14, no. 8. Birkhäuser,
pp. 1837–1926, 2013.
ista: Erdös L, Knowles A, Yau H. 2013. Averaging fluctuations in resolvents of random
band matrices. Annales Henri Poincare. 14(8), 1837–1926.
mla: Erdös, László, et al. “Averaging Fluctuations in Resolvents of Random Band
Matrices.” Annales Henri Poincare, vol. 14, no. 8, Birkhäuser, 2013, pp.
1837–926, doi:10.1007/s00023-013-0235-y.
short: L. Erdös, A. Knowles, H. Yau, Annales Henri Poincare 14 (2013) 1837–1926.
date_created: 2018-12-11T11:59:33Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2021-01-12T06:59:40Z
day: '01'
doi: 10.1007/s00023-013-0235-y
extern: 1
intvolume: ' 14'
issue: '8'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1205.5664
month: '12'
oa: 1
page: 1837 - 1926
publication: Annales Henri Poincare
publication_status: published
publisher: Birkhäuser
publist_id: '4110'
quality_controlled: 0
status: public
title: Averaging fluctuations in resolvents of random band matrices
type: journal_article
volume: 14
year: '2013'
...
---
_id: '2807'
abstract:
- lang: eng
text: 'We consider several basic problems of algebraic topology, with connections
to combinatorial and geometric questions, from the point of view of computational
complexity. The extension problem asks, given topological spaces X; Y , a subspace
A ⊆ X, and a (continuous) map f : A → Y , whether f can be extended to a map X
→ Y . For computational purposes, we assume that X and Y are represented as finite
simplicial complexes, A is a subcomplex of X, and f is given as a simplicial map.
In this generality the problem is undecidable, as follows from Novikov''s result
from the 1950s on uncomputability of the fundamental group π1(Y ). We thus study
the problem under the assumption that, for some k ≥ 2, Y is (k - 1)-connected;
informally, this means that Y has \no holes up to dimension k-1" (a basic
example of such a Y is the sphere Sk). We prove that, on the one hand, this problem
is still undecidable for dimX = 2k. On the other hand, for every fixed k ≥ 2,
we obtain an algorithm that solves the extension problem in polynomial time assuming
Y (k - 1)-connected and dimX ≤ 2k - 1. For dimX ≤ 2k - 2, the algorithm also provides
a classification of all extensions up to homotopy (continuous deformation). This
relies on results of our SODA 2012 paper, and the main new ingredient is a machinery
of objects with polynomial-time homology, which is a polynomial-time analog of
objects with effective homology developed earlier by Sergeraert et al. We also
consider the computation of the higher homotopy groups πk(Y ), k ≥ 2, for a 1-connected
Y . Their computability was established by Brown in 1957; we show that πk(Y )
can be computed in polynomial time for every fixed k ≥ 2. On the other hand, Anick
proved in 1989 that computing πk(Y ) is #P-hard if k is a part of input, where
Y is a cell complex with certain rather compact encoding. We strengthen his result
to #P-hardness for Y given as a simplicial complex. '
author:
- first_name: Martin
full_name: Čadek, Martin
last_name: Čadek
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
- first_name: Jiří
full_name: Matoušek, Jiří
last_name: Matoušek
- first_name: Lukáš
full_name: Vokřínek, Lukáš
last_name: Vokřínek
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. Extending continuous maps:
Polynomiality and undecidability. In: 45th Annual ACM Symposium on Theory of
Computing. ACM; 2013:595-604. doi:10.1145/2488608.2488683'
apa: 'Čadek, M., Krcál, M., Matoušek, J., Vokřínek, L., & Wagner, U. (2013).
Extending continuous maps: Polynomiality and undecidability. In 45th Annual
ACM Symposium on theory of computing (pp. 595–604). Palo Alto, CA, United
States: ACM. https://doi.org/10.1145/2488608.2488683'
chicago: 'Čadek, Martin, Marek Krcál, Jiří Matoušek, Lukáš Vokřínek, and Uli Wagner.
“Extending Continuous Maps: Polynomiality and Undecidability.” In 45th Annual
ACM Symposium on Theory of Computing, 595–604. ACM, 2013. https://doi.org/10.1145/2488608.2488683.'
ieee: 'M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, and U. Wagner, “Extending continuous
maps: Polynomiality and undecidability,” in 45th Annual ACM Symposium on theory
of computing, Palo Alto, CA, United States, 2013, pp. 595–604.'
ista: 'Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. 2013. Extending continuous
maps: Polynomiality and undecidability. 45th Annual ACM Symposium on theory of
computing. STOC: Symposium on the Theory of Computing, 595–604.'
mla: 'Čadek, Martin, et al. “Extending Continuous Maps: Polynomiality and Undecidability.”
45th Annual ACM Symposium on Theory of Computing, ACM, 2013, pp. 595–604,
doi:10.1145/2488608.2488683.'
short: M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, U. Wagner, in:, 45th Annual
ACM Symposium on Theory of Computing, ACM, 2013, pp. 595–604.
conference:
end_date: 2013-06-04
location: Palo Alto, CA, United States
name: 'STOC: Symposium on the Theory of Computing'
start_date: 2013-06-01
date_created: 2018-12-11T11:59:42Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2021-01-12T06:59:51Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
- _id: HeEd
doi: 10.1145/2488608.2488683
file:
- access_level: open_access
checksum: 06c2ce5c1135fbc1f71ca15eeb242dcf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:29Z
date_updated: 2020-07-14T12:45:48Z
file_id: '5081'
file_name: IST-2016-533-v1+1_Extending_continuous_maps_polynomiality_and_undecidability.pdf
file_size: 447945
relation: main_file
file_date_updated: 2020-07-14T12:45:48Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 595 - 604
publication: 45th Annual ACM Symposium on theory of computing
publication_status: published
publisher: ACM
publist_id: '4078'
pubrep_id: '533'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Extending continuous maps: Polynomiality and undecidability'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2808'
abstract:
- lang: eng
text: In order to establish a reference for analysis of the function of auxin and
the auxin biosynthesis regulators SHORT INTERNODE/ STYLISH (SHI/STY) during Physcomitrella
patens reproductive development, we have described male (antheridial) and female
(archegonial) development in detail, including temporal and positional information
of organ initiation. This has allowed us to define discrete stages of organ morphogenesis
and to show that reproductive organ development in P. patens is highly organized
and that organ phyllotaxis differs between vegetative and reproductive development.
Using the PpSHI1 and PpSHI2 reporter and knockout lines, the auxin reporters GmGH3pro:GUS
and PpPINApro:GFP-GUS, and the auxin-conjugating transgene PpSHI2pro:IAAL, we
could show that the PpSHI genes, and by inference also auxin, play important roles
for reproductive organ development in moss. The PpSHI genes are required for the
apical opening of the reproductive organs, the final differentiation of the egg
cell, and the progression of canal cells into a cell death program. The apical
cells of the archegonium, the canal cells, and the egg cell are also sites of
auxin responsiveness and are affected by reduced levels of active auxin, suggesting
that auxin mediates PpSHI function in the reproductive organs.
author:
- first_name: Katarina
full_name: Landberg, Katarina
last_name: Landberg
- first_name: Eric
full_name: Pederson, Eric
last_name: Pederson
- first_name: Tom
full_name: Viaene, Tom
last_name: Viaene
- first_name: Behruz
full_name: Bozorg, Behruz
last_name: Bozorg
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Henrik
full_name: Jönsson, Henrik
last_name: Jönsson
- first_name: Mattias
full_name: Thelander, Mattias
last_name: Thelander
- first_name: Eva
full_name: Sundberg, Eva
last_name: Sundberg
citation:
ama: Landberg K, Pederson E, Viaene T, et al. The moss physcomitrella patens reproductive
organ development is highly organized, affected by the two SHI/STY genes and by
the level of active auxin in the SHI/STY expression domain. Plant Physiology.
2013;162(3):1406-1419. doi:10.1104/pp.113.214023
apa: Landberg, K., Pederson, E., Viaene, T., Bozorg, B., Friml, J., Jönsson, H.,
… Sundberg, E. (2013). The moss physcomitrella patens reproductive organ development
is highly organized, affected by the two SHI/STY genes and by the level of active
auxin in the SHI/STY expression domain. Plant Physiology. American Society
of Plant Biologists. https://doi.org/10.1104/pp.113.214023
chicago: Landberg, Katarina, Eric Pederson, Tom Viaene, Behruz Bozorg, Jiří Friml,
Henrik Jönsson, Mattias Thelander, and Eva Sundberg. “The Moss Physcomitrella
Patens Reproductive Organ Development Is Highly Organized, Affected by the Two
SHI/STY Genes and by the Level of Active Auxin in the SHI/STY Expression Domain.”
Plant Physiology. American Society of Plant Biologists, 2013. https://doi.org/10.1104/pp.113.214023.
ieee: K. Landberg et al., “The moss physcomitrella patens reproductive organ
development is highly organized, affected by the two SHI/STY genes and by the
level of active auxin in the SHI/STY expression domain,” Plant Physiology,
vol. 162, no. 3. American Society of Plant Biologists, pp. 1406–1419, 2013.
ista: Landberg K, Pederson E, Viaene T, Bozorg B, Friml J, Jönsson H, Thelander
M, Sundberg E. 2013. The moss physcomitrella patens reproductive organ development
is highly organized, affected by the two SHI/STY genes and by the level of active
auxin in the SHI/STY expression domain. Plant Physiology. 162(3), 1406–1419.
mla: Landberg, Katarina, et al. “The Moss Physcomitrella Patens Reproductive Organ
Development Is Highly Organized, Affected by the Two SHI/STY Genes and by the
Level of Active Auxin in the SHI/STY Expression Domain.” Plant Physiology,
vol. 162, no. 3, American Society of Plant Biologists, 2013, pp. 1406–19, doi:10.1104/pp.113.214023.
short: K. Landberg, E. Pederson, T. Viaene, B. Bozorg, J. Friml, H. Jönsson, M.
Thelander, E. Sundberg, Plant Physiology 162 (2013) 1406–1419.
date_created: 2018-12-11T11:59:42Z
date_published: 2013-07-03T00:00:00Z
date_updated: 2021-01-12T06:59:51Z
day: '03'
department:
- _id: JiFr
doi: 10.1104/pp.113.214023
external_id:
pmid:
- '23669745'
intvolume: ' 162'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707547/
month: '07'
oa: 1
oa_version: Submitted Version
page: 1406 - 1419
pmid: 1
publication: Plant Physiology
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '4079'
quality_controlled: '1'
scopus_import: 1
status: public
title: The moss physcomitrella patens reproductive organ development is highly organized,
affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY
expression domain
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 162
year: '2013'
...
---
_id: '2806'
abstract:
- lang: eng
text: A novel Taylor-Couette system has been constructed for investigations of transitional
as well as high Reynolds number turbulent flows in very large aspect ratios. The
flexibility of the setup enables studies of a variety of problems regarding hydrodynamic
instabilities and turbulence in rotating flows. The inner and outer cylinders
and the top and bottom endplates can be rotated independently with rotation rates
of up to 30 Hz, thereby covering five orders of magnitude in Reynolds numbers
(Re = 101-106). The radius ratio can be easily changed, the highest realized one
is η = 0.98 corresponding to an aspect ratio of 260 gap width in the vertical
and 300 in the azimuthal direction. For η < 0.98 the aspect ratio can be dynamically
changed during measurements and complete transparency in the radial direction
over the full length of the cylinders is provided by the usage of a precision
glass inner cylinder. The temperatures of both cylinders are controlled independently.
Overall this apparatus combines an unmatched variety in geometry, rotation rates,
and temperatures, which is provided by a sophisticated high-precision bearing
system. Possible applications are accurate studies of the onset of turbulence
and spatio-temporal intermittent flow patterns in very large domains, transport
processes of turbulence at high Re, the stability of Keplerian flows for different
boundary conditions, and studies of baroclinic instabilities.
article_number: '065106'
author:
- first_name: Kerstin
full_name: Avila, Kerstin
last_name: Avila
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Avila K, Hof B. High-precision Taylor-Couette experiment to study subcritical
transitions and the role of boundary conditions and size effects. Review of
Scientific Instruments. 2013;84(6). doi:10.1063/1.4807704
apa: Avila, K., & Hof, B. (2013). High-precision Taylor-Couette experiment to
study subcritical transitions and the role of boundary conditions and size effects.
Review of Scientific Instruments. American Institute of Physics. https://doi.org/10.1063/1.4807704
chicago: Avila, Kerstin, and Björn Hof. “High-Precision Taylor-Couette Experiment
to Study Subcritical Transitions and the Role of Boundary Conditions and Size
Effects.” Review of Scientific Instruments. American Institute of Physics,
2013. https://doi.org/10.1063/1.4807704.
ieee: K. Avila and B. Hof, “High-precision Taylor-Couette experiment to study subcritical
transitions and the role of boundary conditions and size effects,” Review of
Scientific Instruments, vol. 84, no. 6. American Institute of Physics, 2013.
ista: Avila K, Hof B. 2013. High-precision Taylor-Couette experiment to study subcritical
transitions and the role of boundary conditions and size effects. Review of Scientific
Instruments. 84(6), 065106.
mla: Avila, Kerstin, and Björn Hof. “High-Precision Taylor-Couette Experiment to
Study Subcritical Transitions and the Role of Boundary Conditions and Size Effects.”
Review of Scientific Instruments, vol. 84, no. 6, 065106, American Institute
of Physics, 2013, doi:10.1063/1.4807704.
short: K. Avila, B. Hof, Review of Scientific Instruments 84 (2013).
date_created: 2018-12-11T11:59:42Z
date_published: 2013-06-06T00:00:00Z
date_updated: 2021-01-12T06:59:50Z
day: '06'
department:
- _id: BjHo
doi: 10.1063/1.4807704
intvolume: ' 84'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
publication: Review of Scientific Instruments
publication_status: published
publisher: American Institute of Physics
publist_id: '4081'
quality_controlled: '1'
scopus_import: 1
status: public
title: High-precision Taylor-Couette experiment to study subcritical transitions and
the role of boundary conditions and size effects
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 84
year: '2013'
...
---
_id: '2805'
abstract:
- lang: eng
text: Transition in shear flows is characterized by localized turbulent regions
embedded in the surrounding laminar flow. These so-called turbulent spots or puffs
are observed in a variety of shear flows and in certain Reynolds-number regimes,
and they are advected by the flow while keeping their characteristic length. We
show here for the case of pipe flow that this seemingly passive advection of turbulent
puffs involves continuous entrainment and relaminarization of laminar and turbulent
fluid across strongly convoluted interfaces. Surprisingly, interface areas are
almost two orders of magnitude larger than the pipe cross-section, while local
entrainment velocities are much smaller than the mean speed. Even though these
velocities were shown to be small and proportional to the Kolmogorov velocity
scale (in agreement with a prediction by Corrsin) in a flow without mean shear
before, we find that, in pipe flow, local entrainment velocities are about an
order of magnitude smaller than this scale. The Lagrangian method used to study
the dynamics of the laminar-turbulent interfaces allows accurate determination
of the leading and trailing edge speeds. However, to resolve the highly complex
interface dynamics requires much higher numerical resolutions than for ordinary
turbulent flows. This method also reveals that the volume flux across the leading
edge has the same radial dependence but the opposite sign as that across the trailing
edge, and it is this symmetry that is responsible for the puff shape remaining
constant.
author:
- first_name: Markus
full_name: Holzner, Markus
last_name: Holzner
- first_name: Baofang
full_name: Song, Baofang
last_name: Song
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
- first_name: Björn
full_name: Björn Hof
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Holzner M, Song B, Avila M, Hof B. Lagrangian approach to laminar-turbulent
interfaces in transitional pipe flow. Journal of Fluid Mechanics. 2013;723:140-162.
doi:10.1017/jfm.2013.127
apa: Holzner, M., Song, B., Avila, M., & Hof, B. (2013). Lagrangian approach
to laminar-turbulent interfaces in transitional pipe flow. Journal of Fluid
Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2013.127
chicago: Holzner, Markus, Baofang Song, Marc Avila, and Björn Hof. “Lagrangian Approach
to Laminar-Turbulent Interfaces in Transitional Pipe Flow.” Journal of Fluid
Mechanics. Cambridge University Press, 2013. https://doi.org/10.1017/jfm.2013.127.
ieee: M. Holzner, B. Song, M. Avila, and B. Hof, “Lagrangian approach to laminar-turbulent
interfaces in transitional pipe flow,” Journal of Fluid Mechanics, vol.
723. Cambridge University Press, pp. 140–162, 2013.
ista: Holzner M, Song B, Avila M, Hof B. 2013. Lagrangian approach to laminar-turbulent
interfaces in transitional pipe flow. Journal of Fluid Mechanics. 723, 140–162.
mla: Holzner, Markus, et al. “Lagrangian Approach to Laminar-Turbulent Interfaces
in Transitional Pipe Flow.” Journal of Fluid Mechanics, vol. 723, Cambridge
University Press, 2013, pp. 140–62, doi:10.1017/jfm.2013.127.
short: M. Holzner, B. Song, M. Avila, B. Hof, Journal of Fluid Mechanics 723 (2013)
140–162.
date_created: 2018-12-11T11:59:41Z
date_published: 2013-05-01T00:00:00Z
date_updated: 2021-01-12T06:59:50Z
day: '01'
doi: 10.1017/jfm.2013.127
extern: 1
intvolume: ' 723'
month: '05'
page: 140 - 162
publication: Journal of Fluid Mechanics
publication_status: published
publisher: Cambridge University Press
publist_id: '4084'
quality_controlled: 0
status: public
title: Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow
type: journal_article
volume: 723
year: '2013'
...
---
_id: '2810'
abstract:
- lang: eng
text: The epistatic interactions that underlie evolutionary constraint have mainly
been studied for constant external conditions. However, environmental changes
may modulate epistasis and hence affect genetic constraints. Here we investigate
genetic constraints in the adaptive evolution of a novel regulatory function in
variable environments, using the lac repressor, LacI, as a model system. We have
systematically reconstructed mutational trajectories from wild type LacI to three
different variants that each exhibit an inverse response to the inducing ligand
IPTG, and analyzed the higher-order interactions between genetic and environmental
changes. We find epistasis to depend strongly on the environment. As a result,
mutational steps essential to inversion but inaccessible by positive selection
in one environment, become accessible in another. We present a graphical method
to analyze the observed complex higher-order interactions between multiple mutations
and environmental change, and show how the interactions can be explained by a
combination of mutational effects on allostery and thermodynamic stability. This
dependency of genetic constraint on the environment should fundamentally affect
evolutionary dynamics and affects the interpretation of phylogenetic data.
article_number: e1003580
author:
- first_name: Marjon
full_name: De Vos, Marjon
id: 3111FFAC-F248-11E8-B48F-1D18A9856A87
last_name: De Vos
- first_name: Frank
full_name: Poelwijk, Frank
last_name: Poelwijk
- first_name: Nico
full_name: Battich, Nico
last_name: Battich
- first_name: Joseph
full_name: Ndika, Joseph
last_name: Ndika
- first_name: Sander
full_name: Tans, Sander
last_name: Tans
citation:
ama: de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. Environmental dependence
of genetic constraint. PLoS Genetics. 2013;9(6). doi:10.1371/journal.pgen.1003580
apa: de Vos, M., Poelwijk, F., Battich, N., Ndika, J., & Tans, S. (2013). Environmental
dependence of genetic constraint. PLoS Genetics. Public Library of Science.
https://doi.org/10.1371/journal.pgen.1003580
chicago: Vos, Marjon de, Frank Poelwijk, Nico Battich, Joseph Ndika, and Sander
Tans. “Environmental Dependence of Genetic Constraint.” PLoS Genetics.
Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003580.
ieee: M. de Vos, F. Poelwijk, N. Battich, J. Ndika, and S. Tans, “Environmental
dependence of genetic constraint,” PLoS Genetics, vol. 9, no. 6. Public
Library of Science, 2013.
ista: de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. 2013. Environmental dependence
of genetic constraint. PLoS Genetics. 9(6), e1003580.
mla: de Vos, Marjon, et al. “Environmental Dependence of Genetic Constraint.” PLoS
Genetics, vol. 9, no. 6, e1003580, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003580.
short: M. de Vos, F. Poelwijk, N. Battich, J. Ndika, S. Tans, PLoS Genetics 9 (2013).
date_created: 2018-12-11T11:59:43Z
date_published: 2013-06-27T00:00:00Z
date_updated: 2021-01-12T06:59:52Z
day: '27'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1371/journal.pgen.1003580
file:
- access_level: open_access
checksum: 7a4736dd80496d29ff6908b6f2329b4e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:51Z
date_updated: 2020-07-14T12:45:48Z
file_id: '4713'
file_name: IST-2016-412-v1+1_journal.pgen.1003580.pdf
file_size: 474655
relation: main_file
file_date_updated: 2020-07-14T12:45:48Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '4075'
pubrep_id: '412'
quality_controlled: '1'
scopus_import: 1
status: public
title: Environmental dependence of genetic constraint
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '2814'
abstract:
- lang: eng
text: We study the problem of generating a test sequence that achieves maximal coverage
for a reactive system under test. We formulate the problem as a repeated game
between the tester and the system, where the system state space is partitioned
according to some coverage criterion and the objective of the tester is to maximize
the set of partitions (or coverage goals) visited during the game. We show the
complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete,
but is NP-complete for deterministic systems. For the special case of non-deterministic
systems with a re-initializing "reset" action, which represent running
a new test input on a re-initialized system, we show that the complexity is coNP-complete.
Our proof technique for reset games uses randomized testing strategies that circumvent
the exponentially large memory requirement of deterministic testing strategies.
We also discuss the memory requirement for deterministic strategies and extensions
of our results to other models, such as pushdown systems and timed systems.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Luca
full_name: Alfaro, Luca
last_name: Alfaro
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
citation:
ama: Chatterjee K, Alfaro L, Majumdar R. The complexity of coverage. International
Journal of Foundations of Computer Science. 2013;24(2):165-185. doi:10.1142/S0129054113400066
apa: Chatterjee, K., Alfaro, L., & Majumdar, R. (2013). The complexity of coverage.
International Journal of Foundations of Computer Science. World Scientific
Publishing. https://doi.org/10.1142/S0129054113400066
chicago: Chatterjee, Krishnendu, Luca Alfaro, and Ritankar Majumdar. “The Complexity
of Coverage.” International Journal of Foundations of Computer Science.
World Scientific Publishing, 2013. https://doi.org/10.1142/S0129054113400066.
ieee: K. Chatterjee, L. Alfaro, and R. Majumdar, “The complexity of coverage,” International
Journal of Foundations of Computer Science, vol. 24, no. 2. World Scientific
Publishing, pp. 165–185, 2013.
ista: Chatterjee K, Alfaro L, Majumdar R. 2013. The complexity of coverage. International
Journal of Foundations of Computer Science. 24(2), 165–185.
mla: Chatterjee, Krishnendu, et al. “The Complexity of Coverage.” International
Journal of Foundations of Computer Science, vol. 24, no. 2, World Scientific
Publishing, 2013, pp. 165–85, doi:10.1142/S0129054113400066.
short: K. Chatterjee, L. Alfaro, R. Majumdar, International Journal of Foundations
of Computer Science 24 (2013) 165–185.
date_created: 2018-12-11T11:59:44Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2021-01-12T06:59:54Z
day: '01'
department:
- _id: KrCh
doi: 10.1142/S0129054113400066
ec_funded: 1
external_id:
arxiv:
- '0804.4525'
intvolume: ' 24'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0804.4525
month: '02'
oa: 1
oa_version: Preprint
page: 165 - 185
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: International Journal of Foundations of Computer Science
publication_status: published
publisher: World Scientific Publishing
publist_id: '4070'
quality_controlled: '1'
scopus_import: 1
status: public
title: The complexity of coverage
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2013'
...
---
_id: '2811'
abstract:
- lang: eng
text: 'In pipe, channel, and boundary layer flows turbulence first occurs intermittently
in space and time: at moderate Reynolds numbers domains of disordered turbulent
motion are separated by quiescent laminar regions. Based on direct numerical simulations
of pipe flow we argue here that the spatial intermittency has its origin in a
nearest neighbor interaction between turbulent regions. We further show that in
this regime turbulent flows are intrinsically intermittent with a well-defined
equilibrium turbulent fraction but without ever assuming a steady pattern. This
transition scenario is analogous to that found in simple models such as coupled
map lattices. The scaling observed implies that laminar intermissions of the turbulent
flow will persist to arbitrarily large Reynolds numbers.'
article_number: '063012'
author:
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Avila M, Hof B. Nature of laminar-turbulence intermittency in shear flows.
Physical Review E. 2013;87(6). doi:10.1103/PhysRevE.87.063012
apa: Avila, M., & Hof, B. (2013). Nature of laminar-turbulence intermittency
in shear flows. Physical Review E. American Institute of Physics. https://doi.org/10.1103/PhysRevE.87.063012
chicago: Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency
in Shear Flows.” Physical Review E. American Institute of Physics, 2013.
https://doi.org/10.1103/PhysRevE.87.063012.
ieee: M. Avila and B. Hof, “Nature of laminar-turbulence intermittency in shear
flows,” Physical Review E, vol. 87, no. 6. American Institute of Physics,
2013.
ista: Avila M, Hof B. 2013. Nature of laminar-turbulence intermittency in shear
flows. Physical Review E. 87(6), 063012.
mla: Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in
Shear Flows.” Physical Review E, vol. 87, no. 6, 063012, American Institute
of Physics, 2013, doi:10.1103/PhysRevE.87.063012.
short: M. Avila, B. Hof, Physical Review E 87 (2013).
date_created: 2018-12-11T11:59:43Z
date_published: 2013-06-18T00:00:00Z
date_updated: 2021-01-12T06:59:53Z
day: '18'
department:
- _id: BjHo
doi: 10.1103/PhysRevE.87.063012
ec_funded: 1
external_id:
arxiv:
- '1306.5890'
intvolume: ' 87'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1306.5890
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Physical Review E
publication_status: published
publisher: American Institute of Physics
publist_id: '4074'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nature of laminar-turbulence intermittency in shear flows
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2013'
...
---
_id: '2813'
abstract:
- lang: eng
text: Turbulence is ubiquitous in nature, yet even for the case of ordinary Newtonian
fluids like water, our understanding of this phenomenon is limited. Many liquids
of practical importance are more complicated (e.g., blood, polymer melts, paints),
however; they exhibit elastic as well as viscous characteristics, and the relation
between stress and strain is nonlinear. We demonstrate here for a model system
of such complex fluids that at high shear rates, turbulence is not simply modified
as previously believed but is suppressed and replaced by a different type of disordered
motion, elasto-inertial turbulence. Elasto-inertial turbulence is found to occur
at much lower Reynolds numbers than Newtonian turbulence, and the dynamical properties
differ significantly. The friction scaling observed coincides with the so-called
"maximum drag reduction" asymptote, which is exhibited by a wide range
of viscoelastic fluids.
author:
- first_name: Devranjan
full_name: Samanta, Devranjan
last_name: Samanta
- first_name: Yves
full_name: Dubief, Yves
last_name: Dubief
- first_name: Markus
full_name: Holzner, Markus
last_name: Holzner
- first_name: Christof
full_name: Schäfer, Christof
last_name: Schäfer
- first_name: Alexander
full_name: Morozov, Alexander
last_name: Morozov
- first_name: Christian
full_name: Wagner, Christian
last_name: Wagner
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Samanta D, Dubief Y, Holzner M, et al. Elasto-inertial turbulence. PNAS.
2013;110(26):10557-10562. doi:10.1073/pnas.1219666110
apa: Samanta, D., Dubief, Y., Holzner, M., Schäfer, C., Morozov, A., Wagner, C.,
& Hof, B. (2013). Elasto-inertial turbulence. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.1219666110
chicago: Samanta, Devranjan, Yves Dubief, Markus Holzner, Christof Schäfer, Alexander
Morozov, Christian Wagner, and Björn Hof. “Elasto-Inertial Turbulence.” PNAS.
National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1219666110.
ieee: D. Samanta et al., “Elasto-inertial turbulence,” PNAS, vol.
110, no. 26. National Academy of Sciences, pp. 10557–10562, 2013.
ista: Samanta D, Dubief Y, Holzner M, Schäfer C, Morozov A, Wagner C, Hof B. 2013.
Elasto-inertial turbulence. PNAS. 110(26), 10557–10562.
mla: Samanta, Devranjan, et al. “Elasto-Inertial Turbulence.” PNAS, vol.
110, no. 26, National Academy of Sciences, 2013, pp. 10557–62, doi:10.1073/pnas.1219666110.
short: D. Samanta, Y. Dubief, M. Holzner, C. Schäfer, A. Morozov, C. Wagner, B.
Hof, PNAS 110 (2013) 10557–10562.
date_created: 2018-12-11T11:59:44Z
date_published: 2013-06-25T00:00:00Z
date_updated: 2021-01-12T06:59:54Z
day: '25'
department:
- _id: BjHo
doi: 10.1073/pnas.1219666110
external_id:
pmid:
- '23757498'
intvolume: ' 110'
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696777/
month: '06'
oa: 1
oa_version: Submitted Version
page: 10557 - 10562
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '4073'
quality_controlled: '1'
scopus_import: 1
status: public
title: Elasto-inertial turbulence
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2812'
abstract:
- lang: eng
text: 'We consider the problem of deciding whether the persistent homology group
of a simplicial pair (K, L) can be realized as the homology H* (X) of some complex
X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded
in ℝ3. As a consequence, we show that it is NP-hard to simplify level and sublevel
sets of scalar functions on S3 within a given tolerance constraint. This problem
has relevance to the visualization of medical images by isosurfaces. We also show
an implication to the theory of well groups of scalar functions: not every well
group can be realized by some level set, and deciding whether a well group can
be realized is NP-hard.'
acknowledgement: Some of the authors were partially supported by the GIGA ANR grant
(contract ANR-09-BLAN-0331-01) and the European project CG-Learning (contract 255827).
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
- first_name: Olivier
full_name: Devillers, Olivier
last_name: Devillers
- first_name: Marc
full_name: Glisse, Marc
last_name: Glisse
- first_name: André
full_name: Lieutier, André
last_name: Lieutier
citation:
ama: 'Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction
and simplification in R3. In: Proceedings of the 29th Annual Symposium on Computational
Geometry. ACM; 2013:117-125. doi:10.1145/2462356.2462373'
apa: 'Attali, D., Bauer, U., Devillers, O., Glisse, M., & Lieutier, A. (2013).
Homological reconstruction and simplification in R3. In Proceedings of the
29th annual symposium on Computational Geometry (pp. 117–125). Rio de Janeiro,
Brazil: ACM. https://doi.org/10.1145/2462356.2462373'
chicago: Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André
Lieutier. “Homological Reconstruction and Simplification in R3.” In Proceedings
of the 29th Annual Symposium on Computational Geometry, 117–25. ACM, 2013.
https://doi.org/10.1145/2462356.2462373.
ieee: D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological
reconstruction and simplification in R3,” in Proceedings of the 29th annual
symposium on Computational Geometry, Rio de Janeiro, Brazil, 2013, pp. 117–125.
ista: 'Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2013. Homological reconstruction
and simplification in R3. Proceedings of the 29th annual symposium on Computational
Geometry. SoCG: Symposium on Computational Geometry, 117–125.'
mla: Attali, Dominique, et al. “Homological Reconstruction and Simplification in
R3.” Proceedings of the 29th Annual Symposium on Computational Geometry,
ACM, 2013, pp. 117–25, doi:10.1145/2462356.2462373.
short: D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, in:, Proceedings
of the 29th Annual Symposium on Computational Geometry, ACM, 2013, pp. 117–125.
conference:
end_date: 2013-06-20
location: Rio de Janeiro, Brazil
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2013-06-17
date_created: 2018-12-11T11:59:44Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2023-02-23T10:15:15Z
day: '01'
department:
- _id: HeEd
doi: 10.1145/2462356.2462373
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://hal.archives-ouvertes.fr/hal-00833791/
month: '06'
oa: 1
oa_version: Submitted Version
page: 117 - 125
publication: Proceedings of the 29th annual symposium on Computational Geometry
publication_status: published
publisher: ACM
publist_id: '4072'
quality_controlled: '1'
related_material:
record:
- id: '1805'
relation: later_version
status: public
scopus_import: 1
status: public
title: Homological reconstruction and simplification in R3
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2817'
abstract:
- lang: eng
text: The basic idea of evolutionary game theory is that payoff determines reproductive
rate. Successful individuals have a higher payoff and produce more offspring.
But in evolutionary and ecological situations there is not only reproductive rate
but also carrying capacity. Individuals may differ in their exposure to density
limiting effects. Here we explore an alternative approach to evolutionary game
theory by assuming that the payoff from the game determines the carrying capacity
of individual phenotypes. Successful strategies are less affected by density limitation
(crowding) and reach higher equilibrium abundance. We demonstrate similarities
and differences between our framework and the standard replicator equation. Our
equation is defined on the positive orthant, instead of the simplex, but has the
same equilibrium points as the replicator equation. Linear stability analysis
produces the classical conditions for asymptotic stability of pure strategies,
but the stability properties of internal equilibria can differ in the two frameworks.
For example, in a two-strategy game with an internal equilibrium that is always
stable under the replicator equation, the corresponding equilibrium can be unstable
in the new framework resulting in a limit cycle.
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Novak S, Chatterjee K, Nowak M. Density games. Journal of Theoretical Biology.
2013;334:26-34. doi:10.1016/j.jtbi.2013.05.029
apa: Novak, S., Chatterjee, K., & Nowak, M. (2013). Density games. Journal
of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2013.05.029
chicago: Novak, Sebastian, Krishnendu Chatterjee, and Martin Nowak. “Density Games.”
Journal of Theoretical Biology. Elsevier, 2013. https://doi.org/10.1016/j.jtbi.2013.05.029.
ieee: S. Novak, K. Chatterjee, and M. Nowak, “Density games,” Journal of Theoretical
Biology, vol. 334. Elsevier, pp. 26–34, 2013.
ista: Novak S, Chatterjee K, Nowak M. 2013. Density games. Journal of Theoretical
Biology. 334, 26–34.
mla: Novak, Sebastian, et al. “Density Games.” Journal of Theoretical Biology,
vol. 334, Elsevier, 2013, pp. 26–34, doi:10.1016/j.jtbi.2013.05.029.
short: S. Novak, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 334 (2013)
26–34.
date_created: 2018-12-11T11:59:45Z
date_published: 2013-10-07T00:00:00Z
date_updated: 2021-01-12T06:59:55Z
day: '07'
ddc:
- '000'
department:
- _id: NiBa
- _id: KrCh
doi: 10.1016/j.jtbi.2013.05.029
ec_funded: 1
file:
- access_level: open_access
checksum: 3c29059ab03a4b8f97a07646b817ddbb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:54Z
date_updated: 2020-07-14T12:45:49Z
file_id: '5110'
file_name: IST-2016-400-v1+1_1-s2.0-S0022519313002609-main.pdf
file_size: 834604
relation: main_file
file_date_updated: 2020-07-14T12:45:49Z
has_accepted_license: '1'
intvolume: ' 334'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 26 - 34
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '3984'
pubrep_id: '400'
quality_controlled: '1'
scopus_import: 1
status: public
title: Density games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 334
year: '2013'
...
---
_id: '2819'
abstract:
- lang: eng
text: 'We introduce quantatitive timed refinement metrics and quantitative timed
simulation functions, incorporating zenoness checks, for timed systems. These
functions assign positive real numbers between zero and infinity which quantify
the timing mismatches between two timed systems, amongst non-zeno runs. We quantify
timing mismatches in three ways: (1) the maximum timing mismatch that can arise,
(2) the "steady-state" maximum timing mismatches, where initial transient
timing mismatches are ignored; and (3) the (long-run) average timing mismatches
amongst two systems. These three kinds of mismatches constitute three important
types of timing differences. Our event times are the global times, measured from
the start of the system execution, not just the time durations of individual steps.
We present algorithms over timed automata for computing the three quantitative
simulation functions to within any desired degree of accuracy. In order to compute
the values of the quantitative simulation functions, we use a game theoretic formulation.
We introduce two new kinds of objectives for two player games on finite state
game graphs: (1) eventual debit-sum level objectives, and (2) average debit-sum
level objectives. We present algorithms for computing the optimal values for these
objectives for player 1, and then use these algorithms to compute the values of
the quantitative timed simulation functions. '
acknowledgement: 'This work has been financially supported in part by the European
Commission FP7-ICT Cognitive Systems, Interaction, and Robotics under the contract
# 270180 (NOP-TILUS); by Fundacao para Ciencia e Tecnologia under project PTDC/EEA-CRO/104901/2008
(Modeling and control of Networked vehicle systems in persistent autonomous operations);
by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic
Techniques in Formal Verification; FWF NFN Grant No S11407-N23 (RiSE); ERC Start
grant (279307: Graph Games); and the Microsoft faculty fellows award'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Vinayak
full_name: Prabhu, Vinayak
last_name: Prabhu
citation:
ama: 'Chatterjee K, Prabhu V. Quantitative timed simulation functions and refinement
metrics for real-time systems. In: Proceedings of the 16th International Conference
on Hybrid Systems: Computation and Control. Vol 1. Springer; 2013:273-282.
doi:10.1145/2461328.2461370'
apa: 'Chatterjee, K., & Prabhu, V. (2013). Quantitative timed simulation functions
and refinement metrics for real-time systems. In Proceedings of the 16th International
Conference on Hybrid Systems: Computation and Control (Vol. 1, pp. 273–282).
Philadelphia, PA USA: Springer. https://doi.org/10.1145/2461328.2461370'
chicago: 'Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation
Functions and Refinement Metrics for Real-Time Systems.” In Proceedings of
the 16th International Conference on Hybrid Systems: Computation and Control,
1:273–82. Springer, 2013. https://doi.org/10.1145/2461328.2461370.'
ieee: 'K. Chatterjee and V. Prabhu, “Quantitative timed simulation functions and
refinement metrics for real-time systems,” in Proceedings of the 16th International
Conference on Hybrid Systems: Computation and Control, Philadelphia, PA USA,
2013, vol. 1, pp. 273–282.'
ista: 'Chatterjee K, Prabhu V. 2013. Quantitative timed simulation functions and
refinement metrics for real-time systems. Proceedings of the 16th International
Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems -
Computation and Control vol. 1, 273–282.'
mla: 'Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation
Functions and Refinement Metrics for Real-Time Systems.” Proceedings of the
16th International Conference on Hybrid Systems: Computation and Control,
vol. 1, Springer, 2013, pp. 273–82, doi:10.1145/2461328.2461370.'
short: 'K. Chatterjee, V. Prabhu, in:, Proceedings of the 16th International Conference
on Hybrid Systems: Computation and Control, Springer, 2013, pp. 273–282.'
conference:
end_date: 2013-04-11
location: Philadelphia, PA USA
name: 'HSCC: Hybrid Systems - Computation and Control'
start_date: 2013-04-08
date_created: 2018-12-11T11:59:46Z
date_published: 2013-04-01T00:00:00Z
date_updated: 2021-01-12T06:59:56Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/2461328.2461370
ec_funded: 1
intvolume: ' 1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1212.6556
month: '04'
oa: 1
oa_version: Preprint
page: 273 - 282
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: 'Proceedings of the 16th International Conference on Hybrid Systems:
Computation and Control'
publication_status: published
publisher: Springer
publist_id: '3982'
quality_controlled: '1'
scopus_import: 1
status: public
title: Quantitative timed simulation functions and refinement metrics for real-time
systems
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2013'
...
---
_id: '2818'
abstract:
- lang: eng
text: Models of neural responses to stimuli with complex spatiotemporal correlation
structure often assume that neurons are selective for only a small number of linear
projections of a potentially high-dimensional input. In this review, we explore
recent modeling approaches where the neural response depends on the quadratic
form of the input rather than on its linear projection, that is, the neuron is
sensitive to the local covariance structure of the signal preceding the spike.
To infer this quadratic dependence in the presence of arbitrary (e.g., naturalistic)
stimulus distribution, we review several inference methods, focusing in particular
on two information theory–based approaches (maximization of stimulus energy and
of noise entropy) and two likelihood-based approaches (Bayesian spike-triggered
covariance and extensions of generalized linear models). We analyze the formal
relationship between the likelihood-based and information-based approaches to
demonstrate how they lead to consistent inference. We demonstrate the practical
feasibility of these procedures by using model neurons responding to a flickering
variance stimulus.
author:
- first_name: Kanaka
full_name: Rajan, Kanaka
last_name: Rajan
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Rajan K, Marre O, Tkačik G. Learning quadratic receptive fields from neural
responses to natural stimuli. Neural Computation. 2013;25(7):1661-1692.
doi:10.1162/NECO_a_00463
apa: Rajan, K., Marre, O., & Tkačik, G. (2013). Learning quadratic receptive
fields from neural responses to natural stimuli. Neural Computation. MIT
Press . https://doi.org/10.1162/NECO_a_00463
chicago: Rajan, Kanaka, Olivier Marre, and Gašper Tkačik. “Learning Quadratic Receptive
Fields from Neural Responses to Natural Stimuli.” Neural Computation. MIT
Press , 2013. https://doi.org/10.1162/NECO_a_00463.
ieee: K. Rajan, O. Marre, and G. Tkačik, “Learning quadratic receptive fields from
neural responses to natural stimuli,” Neural Computation, vol. 25, no.
7. MIT Press , pp. 1661–1692, 2013.
ista: Rajan K, Marre O, Tkačik G. 2013. Learning quadratic receptive fields from
neural responses to natural stimuli. Neural Computation. 25(7), 1661–1692.
mla: Rajan, Kanaka, et al. “Learning Quadratic Receptive Fields from Neural Responses
to Natural Stimuli.” Neural Computation, vol. 25, no. 7, MIT Press , 2013,
pp. 1661–92, doi:10.1162/NECO_a_00463.
short: K. Rajan, O. Marre, G. Tkačik, Neural Computation 25 (2013) 1661–1692.
date_created: 2018-12-11T11:59:45Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2021-01-12T06:59:56Z
day: '01'
department:
- _id: GaTk
doi: 10.1162/NECO_a_00463
external_id:
arxiv:
- '1209.0121'
intvolume: ' 25'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1209.0121
month: '07'
oa: 1
oa_version: Preprint
page: 1661 - 1692
publication: Neural Computation
publication_status: published
publisher: 'MIT Press '
publist_id: '3983'
quality_controlled: '1'
scopus_import: 1
status: public
title: Learning quadratic receptive fields from neural responses to natural stimuli
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2013'
...
---
_id: '2826'
abstract:
- lang: eng
text: Myopia, or near-sightedness, is an ocular refractive error of unfocused image
quality in front of the retinal plane. Individuals with high-grade myopia (dioptric
power greater than -6.00) are predisposed to ocular morbidities such as glaucoma,
retinal detachment, and myopic maculopathy. Nonsyndromic, high-grade myopia is
highly heritable, and to date multiple gene loci have been reported. We performed
exome sequencing in 4 individuals from an 11-member family of European descent
from the United States. Affected individuals had a mean dioptric spherical equivalent
of -22.00 sphere. A premature stop codon mutation c.157C>T (p.Gln53*) cosegregating
with disease was discovered within SCO2 that maps to chromosome 22q13.33. Subsequent
analyses identified three additional mutations in three highly myopic unrelated
individuals (c.341G>A, c.418G>A, and c.776C>T). To determine differential
gene expression in a developmental mouse model, we induced myopia by applying
a -15.00D lens over one eye. Messenger RNA levels of SCO2 were significantly downregulated
in myopic mouse retinae. Immunohistochemistry in mouse eyes confirmed SCO2 protein
localization in retina, retinal pigment epithelium, and sclera. SCO2 encodes for
a copper homeostasis protein influential in mitochondrial cytochrome c oxidase
activity. Copper deficiencies have been linked with photoreceptor loss and myopia
with increased scleral wall elasticity. Retinal thinning has been reported with
an SC02 variant. Human mutation identification with support from an induced myopic
animal provides biological insights of myopic development.
author:
- first_name: Khanh
full_name: Tran Viet, Khanh
last_name: Tran Viet
- first_name: Caldwell
full_name: Powell, Caldwell
last_name: Powell
- first_name: Veluchamy
full_name: Barathi, Veluchamy
last_name: Barathi
- first_name: Thomas
full_name: Klemm, Thomas
last_name: Klemm
- first_name: Sebastian
full_name: Maurer Stroh, Sebastian
last_name: Maurer Stroh
- first_name: Vachiranee
full_name: Limviphuvadh, Vachiranee
last_name: Limviphuvadh
- first_name: Vincent
full_name: Soler, Vincent
last_name: Soler
- first_name: Candice
full_name: Ho, Candice
last_name: Ho
- first_name: Tammy
full_name: Yanovitch, Tammy
last_name: Yanovitch
- first_name: Georg
full_name: Schneider, Georg
id: 329095A0-F248-11E8-B48F-1D18A9856A87
last_name: Schneider
- first_name: Yi
full_name: Li, Yi
last_name: Li
- first_name: Erica
full_name: Nading, Erica
last_name: Nading
- first_name: Ravikanth
full_name: Metlapally, Ravikanth
last_name: Metlapally
- first_name: Seang
full_name: Saw, Seang
last_name: Saw
- first_name: Liang
full_name: Goh, Liang
last_name: Goh
- first_name: Steve
full_name: Rozen, Steve
last_name: Rozen
- first_name: Terri
full_name: Young, Terri
last_name: Young
citation:
ama: Tran Viet K, Powell C, Barathi V, et al. Mutations in SCO2 are associated with
autosomal-dominant high-grade myopia. American Journal of Human Genetics.
2013;92(5):820-826. doi:10.1016/j.ajhg.2013.04.005
apa: Tran Viet, K., Powell, C., Barathi, V., Klemm, T., Maurer Stroh, S., Limviphuvadh,
V., … Young, T. (2013). Mutations in SCO2 are associated with autosomal-dominant
high-grade myopia. American Journal of Human Genetics. Cell Press. https://doi.org/10.1016/j.ajhg.2013.04.005
chicago: Tran Viet, Khanh, Caldwell Powell, Veluchamy Barathi, Thomas Klemm, Sebastian
Maurer Stroh, Vachiranee Limviphuvadh, Vincent Soler, et al. “Mutations in SCO2
Are Associated with Autosomal-Dominant High-Grade Myopia.” American Journal
of Human Genetics. Cell Press, 2013. https://doi.org/10.1016/j.ajhg.2013.04.005.
ieee: K. Tran Viet et al., “Mutations in SCO2 are associated with autosomal-dominant
high-grade myopia,” American Journal of Human Genetics, vol. 92, no. 5.
Cell Press, pp. 820–826, 2013.
ista: Tran Viet K, Powell C, Barathi V, Klemm T, Maurer Stroh S, Limviphuvadh V,
Soler V, Ho C, Yanovitch T, Schneider G, Li Y, Nading E, Metlapally R, Saw S,
Goh L, Rozen S, Young T. 2013. Mutations in SCO2 are associated with autosomal-dominant
high-grade myopia. American Journal of Human Genetics. 92(5), 820–826.
mla: Tran Viet, Khanh, et al. “Mutations in SCO2 Are Associated with Autosomal-Dominant
High-Grade Myopia.” American Journal of Human Genetics, vol. 92, no. 5,
Cell Press, 2013, pp. 820–26, doi:10.1016/j.ajhg.2013.04.005.
short: K. Tran Viet, C. Powell, V. Barathi, T. Klemm, S. Maurer Stroh, V. Limviphuvadh,
V. Soler, C. Ho, T. Yanovitch, G. Schneider, Y. Li, E. Nading, R. Metlapally,
S. Saw, L. Goh, S. Rozen, T. Young, American Journal of Human Genetics 92 (2013)
820–826.
date_created: 2018-12-11T11:59:48Z
date_published: 2013-05-02T00:00:00Z
date_updated: 2021-01-12T06:59:59Z
day: '02'
department:
- _id: MD
doi: 10.1016/j.ajhg.2013.04.005
external_id:
pmid:
- '23643385'
intvolume: ' 92'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644634/
month: '05'
oa: 1
oa_version: Submitted Version
page: 820 - 826
pmid: 1
publication: American Journal of Human Genetics
publication_status: published
publisher: Cell Press
publist_id: '3974'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mutations in SCO2 are associated with autosomal-dominant high-grade myopia
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 92
year: '2013'
...
---
_id: '2822'
abstract:
- lang: eng
text: Identification of genes that control root system architecture in crop plants
requires innovations that enable high-throughput and accurate measurements of
root system architecture through time. We demonstrate the ability of a semiautomated
3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative
genetic basis of root system growth in a rice biparental mapping population, Bala
x Azucena. We phenotyped >1,400 3D root models and >57,000 2D images for
a suite of 25 traits that quantified the distribution, shape, extent of exploration,
and the intrinsic size of root networks at days 12, 14, and 16 of growth in a
gellan gum medium. From these data we identified 89 quantitative trait loci, some
of which correspond to those found previously in soil-grown plants, and provide
evidence for genetic tradeoffs in root growth allocations, such as between the
extent and thoroughness of exploration. We also developed a multivariate method
for generating and mapping central root architecture phenotypes and used it to
identify five major quantitative trait loci (r2 = 24-37%), two of which were not
identified by our univariate analysis. Our imaging and analytical platform provides
a means to identify genes with high potential for improving root traits and agronomic
qualities of crops.
author:
- first_name: Christopher
full_name: Topp, Christopher
last_name: Topp
- first_name: Anjali
full_name: Iyer Pascuzzi, Anjali
last_name: Iyer Pascuzzi
- first_name: Jill
full_name: Anderson, Jill
last_name: Anderson
- first_name: Cheng
full_name: Lee, Cheng
last_name: Lee
- first_name: Paul
full_name: Zurek, Paul
last_name: Zurek
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
- first_name: Ying
full_name: Zheng, Ying
last_name: Zheng
- first_name: Alexander
full_name: Bucksch, Alexander
last_name: Bucksch
- first_name: Yuriy
full_name: Mileyko, Yuriy
last_name: Mileyko
- first_name: Taras
full_name: Galkovskyi, Taras
last_name: Galkovskyi
- first_name: Brad
full_name: Moore, Brad
last_name: Moore
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Thomas
full_name: Mitchell Olds, Thomas
last_name: Mitchell Olds
- first_name: Joshua
full_name: Weitz, Joshua
last_name: Weitz
- first_name: Philip
full_name: Benfey, Philip
last_name: Benfey
citation:
ama: Topp C, Iyer Pascuzzi A, Anderson J, et al. 3D phenotyping and quantitative
trait locus mapping identify core regions of the rice genome controlling root
architecture. PNAS. 2013;110(18):E1695-E1704. doi:10.1073/pnas.1304354110
apa: Topp, C., Iyer Pascuzzi, A., Anderson, J., Lee, C., Zurek, P., Symonova, O.,
… Benfey, P. (2013). 3D phenotyping and quantitative trait locus mapping identify
core regions of the rice genome controlling root architecture. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1304354110
chicago: Topp, Christopher, Anjali Iyer Pascuzzi, Jill Anderson, Cheng Lee, Paul
Zurek, Olga Symonova, Ying Zheng, et al. “3D Phenotyping and Quantitative Trait
Locus Mapping Identify Core Regions of the Rice Genome Controlling Root Architecture.”
PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1304354110.
ieee: C. Topp et al., “3D phenotyping and quantitative trait locus mapping
identify core regions of the rice genome controlling root architecture,” PNAS,
vol. 110, no. 18. National Academy of Sciences, pp. E1695–E1704, 2013.
ista: Topp C, Iyer Pascuzzi A, Anderson J, Lee C, Zurek P, Symonova O, Zheng Y,
Bucksch A, Mileyko Y, Galkovskyi T, Moore B, Harer J, Edelsbrunner H, Mitchell
Olds T, Weitz J, Benfey P. 2013. 3D phenotyping and quantitative trait locus mapping
identify core regions of the rice genome controlling root architecture. PNAS.
110(18), E1695–E1704.
mla: Topp, Christopher, et al. “3D Phenotyping and Quantitative Trait Locus Mapping
Identify Core Regions of the Rice Genome Controlling Root Architecture.” PNAS,
vol. 110, no. 18, National Academy of Sciences, 2013, pp. E1695–704, doi:10.1073/pnas.1304354110.
short: C. Topp, A. Iyer Pascuzzi, J. Anderson, C. Lee, P. Zurek, O. Symonova, Y.
Zheng, A. Bucksch, Y. Mileyko, T. Galkovskyi, B. Moore, J. Harer, H. Edelsbrunner,
T. Mitchell Olds, J. Weitz, P. Benfey, PNAS 110 (2013) E1695–E1704.
date_created: 2018-12-11T11:59:47Z
date_published: 2013-04-30T00:00:00Z
date_updated: 2021-01-12T06:59:58Z
day: '30'
department:
- _id: MaJö
- _id: HeEd
doi: 10.1073/pnas.1304354110
external_id:
pmid:
- '25673779'
intvolume: ' 110'
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378147/
month: '04'
oa: 1
oa_version: Submitted Version
page: E1695 - E1704
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3979'
quality_controlled: '1'
scopus_import: 1
status: public
title: 3D phenotyping and quantitative trait locus mapping identify core regions of
the rice genome controlling root architecture
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2821'
abstract:
- lang: eng
text: Many key aspects of plant development are regulated by the polarized transport
of the phytohormone auxin. Cellular auxin efflux, the rate-limiting step in this
process, has been shown to rely on the coordinated action of PIN-formed (PIN)
and B-type ATP binding cassette (ABCB) carriers. Here, we report that polar auxin
transport in the Arabidopsis thaliana root also requires the action of a Major
Facilitator Superfamily (MFS) transporter, Zinc-Induced Facilitator-Like 1 (ZIFL1).
Sequencing, promoter-reporter, and fluorescent protein fusion experiments indicate
that the full-length ZIFL1.1 protein and a truncated splice isoform, ZIFL1.3,
localize to the tonoplast of root cells and the plasma membrane of leaf stomatal
guard cells, respectively. Using reverse genetics, we show that the ZIFL1.1 transporter
regulates various root auxin-related processes, while the ZIFL1.3 isoform mediates
drought tolerance by regulating stomatal closure. Auxin transport and immunolocalization
assays demonstrate that ZIFL1.1 indirectly modulates cellular auxin efflux during
shootward auxin transport at the root tip, likely by regulating plasma membrane
PIN2 abundance. Finally, heterologous expression in yeast revealed that ZIFL1.1
and ZIFL1.3 share H+-coupled K+ transport activity. Thus, by determining the subcellular
and tissue distribution of two isoforms, alternative splicing dictates a dual
function for the ZIFL1 transporter. We propose that this MFS carrier regulates
stomatal movements and polar auxin transport by modulating potassium and proton
fluxes in Arabidopsis cells.
author:
- first_name: Estelle
full_name: Remy, Estelle
last_name: Remy
- first_name: Tânia
full_name: Cabrito, Tânia
last_name: Cabrito
- first_name: Pawel
full_name: Baster, Pawel
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Rita
full_name: Batista, Rita
last_name: Batista
- first_name: Miguel
full_name: Teixeira, Miguel
last_name: Teixeira
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Isabel
full_name: Sá Correia, Isabel
last_name: Sá Correia
- first_name: Paula
full_name: Duque, Paula
last_name: Duque
citation:
ama: Remy E, Cabrito T, Baster P, et al. A major facilitator superfamily transporter
plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis.
Plant Cell. 2013;25(3):901-926. doi:10.1105/tpc.113.110353
apa: Remy, E., Cabrito, T., Baster, P., Batista, R., Teixeira, M., Friml, J., …
Duque, P. (2013). A major facilitator superfamily transporter plays a dual role
in polar auxin transport and drought stress tolerance in Arabidopsis. Plant
Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.110353
chicago: Remy, Estelle, Tânia Cabrito, Pawel Baster, Rita Batista, Miguel Teixeira,
Jiří Friml, Isabel Sá Correia, and Paula Duque. “A Major Facilitator Superfamily
Transporter Plays a Dual Role in Polar Auxin Transport and Drought Stress Tolerance
in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2013.
https://doi.org/10.1105/tpc.113.110353.
ieee: E. Remy et al., “A major facilitator superfamily transporter plays
a dual role in polar auxin transport and drought stress tolerance in Arabidopsis,”
Plant Cell, vol. 25, no. 3. American Society of Plant Biologists, pp. 901–926,
2013.
ista: Remy E, Cabrito T, Baster P, Batista R, Teixeira M, Friml J, Sá Correia I,
Duque P. 2013. A major facilitator superfamily transporter plays a dual role in
polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell.
25(3), 901–926.
mla: Remy, Estelle, et al. “A Major Facilitator Superfamily Transporter Plays a
Dual Role in Polar Auxin Transport and Drought Stress Tolerance in Arabidopsis.”
Plant Cell, vol. 25, no. 3, American Society of Plant Biologists, 2013,
pp. 901–26, doi:10.1105/tpc.113.110353.
short: E. Remy, T. Cabrito, P. Baster, R. Batista, M. Teixeira, J. Friml, I. Sá
Correia, P. Duque, Plant Cell 25 (2013) 901–926.
date_created: 2018-12-11T11:59:46Z
date_published: 2013-04-24T00:00:00Z
date_updated: 2021-01-12T06:59:57Z
day: '24'
department:
- _id: JiFr
doi: 10.1105/tpc.113.110353
external_id:
pmid:
- '23524662'
intvolume: ' 25'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634696/
month: '04'
oa: 1
oa_version: Submitted Version
page: 901 - 926
pmid: 1
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3980'
quality_controlled: '1'
scopus_import: 1
status: public
title: A major facilitator superfamily transporter plays a dual role in polar auxin
transport and drought stress tolerance in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2013'
...
---
_id: '2827'
abstract:
- lang: eng
text: Removal of cargos from the cell surface via endocytosis is an efficient mechanism
to regulate activities of plasma membrane (PM)-resident proteins, such as receptors
or transporters. Salicylic acid (SA) is an important plant hormone that is traditionally
associated with pathogen defense. Here, we describe an unanticipated effect of
SA on subcellular endocytic cycling of proteins. Both exogenous treatments and
endogenously enhanced SA levels repressed endocytosis of different PM proteins.
The SA effect on endocytosis did not involve transcription or known components
of the SA signaling pathway for transcriptional regulation. SA likely targets
an endocytic mechanism that involves the coat protein clathrin, because SA interfered
with the clathrin incidence at the PM and clathrin-deficient mutants were less
sensitive to the impact of SA on the auxin distribution and root bending during
the gravitropic response. By contrast, SA did not affect the ligand-induced endocytosis
of the FLAGELLIN SENSING2 (FLS2) receptor during pathogen responses. Our data
suggest that the established SA impact on transcription in plant immunity and
the nontranscriptional effect of SA on clathrin-mediated endocytosis are independent
mechanisms by which SA regulates distinct aspects of plant physiology.
author:
- first_name: Yunlong
full_name: Du, Yunlong
last_name: Du
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Martina
full_name: Beck, Martina
last_name: Beck
- first_name: Ellie
full_name: Himschoot, Ellie
last_name: Himschoot
- first_name: Hongjiang
full_name: Li, Hongjiang
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Silke
full_name: Robatzek, Silke
last_name: Robatzek
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Du Y, Tejos R, Beck M, et al. Salicylic acid interferes with clathrin-mediated
endocytic protein trafficking. PNAS. 2013;110(19):7946-7951. doi:10.1073/pnas.1220205110
apa: Du, Y., Tejos, R., Beck, M., Himschoot, E., Li, H., Robatzek, S., … Friml,
J. (2013). Salicylic acid interferes with clathrin-mediated endocytic protein
trafficking. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1220205110
chicago: Du, Yunlong, Ricardo Tejos, Martina Beck, Ellie Himschoot, Hongjiang Li,
Silke Robatzek, Steffen Vanneste, and Jiří Friml. “Salicylic Acid Interferes with
Clathrin-Mediated Endocytic Protein Trafficking.” PNAS. National Academy
of Sciences, 2013. https://doi.org/10.1073/pnas.1220205110.
ieee: Y. Du et al., “Salicylic acid interferes with clathrin-mediated endocytic
protein trafficking,” PNAS, vol. 110, no. 19. National Academy of Sciences,
pp. 7946–7951, 2013.
ista: Du Y, Tejos R, Beck M, Himschoot E, Li H, Robatzek S, Vanneste S, Friml J.
2013. Salicylic acid interferes with clathrin-mediated endocytic protein trafficking.
PNAS. 110(19), 7946–7951.
mla: Du, Yunlong, et al. “Salicylic Acid Interferes with Clathrin-Mediated Endocytic
Protein Trafficking.” PNAS, vol. 110, no. 19, National Academy of Sciences,
2013, pp. 7946–51, doi:10.1073/pnas.1220205110.
short: Y. Du, R. Tejos, M. Beck, E. Himschoot, H. Li, S. Robatzek, S. Vanneste,
J. Friml, PNAS 110 (2013) 7946–7951.
date_created: 2018-12-11T11:59:48Z
date_published: 2013-05-07T00:00:00Z
date_updated: 2021-01-12T06:59:59Z
day: '07'
department:
- _id: JiFr
doi: 10.1073/pnas.1220205110
external_id:
pmid:
- '23613581'
intvolume: ' 110'
issue: '19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3651428/
month: '05'
oa: 1
oa_version: Submitted Version
page: 7946 - 7951
pmid: 1
project:
- _id: 2574781E-B435-11E9-9278-68D0E5697425
name: Koerber Prize 2010
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3972'
quality_controlled: '1'
scopus_import: 1
status: public
title: Salicylic acid interferes with clathrin-mediated endocytic protein trafficking
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2823'
abstract:
- lang: eng
text: The primary goal of restoration is to create self-sustaining ecological communities
that are resilient to periodic disturbance. Currently, little is known about how
restored communities respond to disturbance events such as fire and how this response
compares to remnant vegetation. Following the 2003 fires in south-eastern Australia
we examined the post-fire response of revegetation plantings and compared this
to remnant vegetation. Ten burnt and 10 unburnt (control) sites were assessed
for each of three types of vegetation (direct seeding revegetation, revegetation
using nursery seedlings (tubestock) and remnant woodland). Sixty sampling sites
were surveyed 6months after fire to quantify the initial survival of mid- and
overstorey plant species in each type of vegetation. Three and 5years after fire
all sites were resurveyed to assess vegetation structure, species diversity and
vigour, as well as indicators of soil function. Overall, revegetation showed high
(>60%) post-fire survival, but this varied among species depending on regeneration
strategy (obligate seeder or resprouter). The native ground cover, mid- and overstorey
in both types of plantings showed rapid recovery of vegetation structure and cover
within 3years of fire. This recovery was similar to the burnt remnant woodlands.
Non-native (exotic) ground cover initially increased after fire, but was no different
in burnt and unburnt sites 5years after fire. Fire had no effect on species richness,
but burnt direct seeding sites had reduced species diversity (Simpson's Diversity
Index) while diversity was higher in burnt remnant woodlands. Indices of soil
function in all types of vegetation had recovered to levels found in unburnt sites
5years after fire. These results indicate that even young revegetation (stands
<10years old) showed substantial recovery from disturbance by fire. This suggests
that revegetation can provide an important basis for restoring woodland communities
in the fire-prone Australian environment.
author:
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: Susie
full_name: Wilson, Susie
last_name: Wilson
- first_name: David
full_name: Freudenberger, David
last_name: Freudenberger
- first_name: Nick
full_name: Nicholls, Nick
last_name: Nicholls
- first_name: Lori
full_name: Gould, Lori
last_name: Gould
- first_name: Sarah
full_name: Hnatiuk, Sarah
last_name: Hnatiuk
- first_name: Jeni
full_name: Delandre, Jeni
last_name: Delandre
citation:
ama: Pickup M, Wilson S, Freudenberger D, et al. Post-fire recovery of revegetated
woodland communities in south-eastern Australia. Austral Ecology. 2013;38(3):300-312.
doi:10.1111/j.1442-9993.2012.02404.x
apa: Pickup, M., Wilson, S., Freudenberger, D., Nicholls, N., Gould, L., Hnatiuk,
S., & Delandre, J. (2013). Post-fire recovery of revegetated woodland communities
in south-eastern Australia. Austral Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1442-9993.2012.02404.x
chicago: Pickup, Melinda, Susie Wilson, David Freudenberger, Nick Nicholls, Lori
Gould, Sarah Hnatiuk, and Jeni Delandre. “Post-Fire Recovery of Revegetated Woodland
Communities in South-Eastern Australia.” Austral Ecology. Wiley-Blackwell,
2013. https://doi.org/10.1111/j.1442-9993.2012.02404.x.
ieee: M. Pickup et al., “Post-fire recovery of revegetated woodland communities
in south-eastern Australia,” Austral Ecology, vol. 38, no. 3. Wiley-Blackwell,
pp. 300–312, 2013.
ista: Pickup M, Wilson S, Freudenberger D, Nicholls N, Gould L, Hnatiuk S, Delandre
J. 2013. Post-fire recovery of revegetated woodland communities in south-eastern
Australia. Austral Ecology. 38(3), 300–312.
mla: Pickup, Melinda, et al. “Post-Fire Recovery of Revegetated Woodland Communities
in South-Eastern Australia.” Austral Ecology, vol. 38, no. 3, Wiley-Blackwell,
2013, pp. 300–12, doi:10.1111/j.1442-9993.2012.02404.x.
short: M. Pickup, S. Wilson, D. Freudenberger, N. Nicholls, L. Gould, S. Hnatiuk,
J. Delandre, Austral Ecology 38 (2013) 300–312.
date_created: 2018-12-11T11:59:47Z
date_published: 2013-05-01T00:00:00Z
date_updated: 2021-01-12T06:59:58Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1442-9993.2012.02404.x
intvolume: ' 38'
issue: '3'
language:
- iso: eng
month: '05'
oa_version: None
page: 300 - 312
publication: Austral Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3978'
quality_controlled: '1'
scopus_import: 1
status: public
title: Post-fire recovery of revegetated woodland communities in south-eastern Australia
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2013'
...
---
_id: '2824'
abstract:
- lang: eng
text: We study synthesis of controllers for real-time systems, where the objective
is to stay in a given safe set. The problem is solved by obtaining winning strategies
in the setting of concurrent two player timed automaton games with safety objectives.
To prevent a player from winning by blocking time, we restrict each player to
strategies that ensure that the player cannot be responsible for causing a Zeno
run. We construct winning strategies for the controller which require access only
to (1) the system clocks (thus, controllers which require their own internal infinitely
precise clocks are not necessary), and (2) a logarithmic (in the number of clocks)
number of memory bits (i.e. a linear number of memory states). Precisely, we show
that for safety objectives, a memory of size (3 + lg (| C | + 1)) bits suffices
for winning controller strategies, where C is the set of clocks of the timed automaton
game, significantly improving the previous known exponential memory states bound.
We also settle the open question of whether winning region-based strategies require
memory for safety objectives by showing with an example the necessity of memory
for such strategies to win for safety objectives. Finally, we show that the decision
problem of determining if there exists a receptive player-1 winning strategy for
safety objectives is EXPTIME-complete over timed automaton games.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Vinayak
full_name: Prabhu, Vinayak
last_name: Prabhu
citation:
ama: Chatterjee K, Prabhu V. Synthesis of memory-efficient, clock-memory free, and
non-Zeno safety controllers for timed systems. Information and Computation.
2013;228-229:83-119. doi:10.1016/j.ic.2013.04.003
apa: Chatterjee, K., & Prabhu, V. (2013). Synthesis of memory-efficient, clock-memory
free, and non-Zeno safety controllers for timed systems. Information and Computation.
Elsevier. https://doi.org/10.1016/j.ic.2013.04.003
chicago: Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory-Efficient,
Clock-Memory Free, and Non-Zeno Safety Controllers for Timed Systems.” Information
and Computation. Elsevier, 2013. https://doi.org/10.1016/j.ic.2013.04.003.
ieee: K. Chatterjee and V. Prabhu, “Synthesis of memory-efficient, clock-memory
free, and non-Zeno safety controllers for timed systems,” Information and Computation,
vol. 228–229. Elsevier, pp. 83–119, 2013.
ista: Chatterjee K, Prabhu V. 2013. Synthesis of memory-efficient, clock-memory
free, and non-Zeno safety controllers for timed systems. Information and Computation.
228–229, 83–119.
mla: Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory-Efficient,
Clock-Memory Free, and Non-Zeno Safety Controllers for Timed Systems.” Information
and Computation, vol. 228–229, Elsevier, 2013, pp. 83–119, doi:10.1016/j.ic.2013.04.003.
short: K. Chatterjee, V. Prabhu, Information and Computation 228–229 (2013) 83–119.
date_created: 2018-12-11T11:59:47Z
date_published: 2013-04-24T00:00:00Z
date_updated: 2021-01-12T06:59:58Z
day: '24'
department:
- _id: KrCh
doi: 10.1016/j.ic.2013.04.003
ec_funded: 1
language:
- iso: eng
month: '04'
oa_version: None
page: 83-119
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Information and Computation
publication_status: published
publisher: Elsevier
publist_id: '3977'
quality_controlled: '1'
scopus_import: 1
status: public
title: Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers
for timed systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 228-229
year: '2013'
...
---
_id: '2832'
abstract:
- lang: eng
text: PIN-FORMED (PIN) proteins localize asymmetrically at the plasma membrane and
mediate intercellular polar transport of the plant hormone auxin that is crucial
for a multitude of developmental processes in plants. PIN localization is under
extensive control by environmental or developmental cues, but mechanisms regulating
PIN localization are not fully understood. Here we show that early endosomal components
ARF GEF BEN1 and newly identified Sec1/Munc18 family protein BEN2 are involved
in distinct steps of early endosomal trafficking. BEN1 and BEN2 are collectively
required for polar PIN localization, for their dynamic repolarization, and consequently
for auxin activity gradient formation and auxin-related developmental processes
including embryonic patterning, organogenesis, and vasculature venation patterning.
These results show that early endosomal trafficking is crucial for cell polarity
and auxin-dependent regulation of plant architecture.
article_number: e1003540
author:
- first_name: Hirokazu
full_name: Tanaka, Hirokazu
last_name: Tanaka
- first_name: Saeko
full_name: Kitakura, Saeko
last_name: Kitakura
- first_name: Hana
full_name: Rakusová, Hana
last_name: Rakusová
- first_name: Tomohiro
full_name: Uemura, Tomohiro
last_name: Uemura
- first_name: Mugurel
full_name: Feraru, Mugurel
last_name: Feraru
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Tatsuo
full_name: Kakimoto, Tatsuo
last_name: Kakimoto
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Tanaka H, Kitakura S, Rakusová H, et al. Cell polarity and patterning by PIN
trafficking through early endosomal compartments in arabidopsis thaliana. PLoS
Genetics. 2013;9(5). doi:10.1371/journal.pgen.1003540
apa: Tanaka, H., Kitakura, S., Rakusová, H., Uemura, T., Feraru, M., De Rycke, R.,
… Friml, J. (2013). Cell polarity and patterning by PIN trafficking through early
endosomal compartments in arabidopsis thaliana. PLoS Genetics. Public Library
of Science. https://doi.org/10.1371/journal.pgen.1003540
chicago: Tanaka, Hirokazu, Saeko Kitakura, Hana Rakusová, Tomohiro Uemura, Mugurel
Feraru, Riet De Rycke, Stéphanie Robert, Tatsuo Kakimoto, and Jiří Friml. “Cell
Polarity and Patterning by PIN Trafficking through Early Endosomal Compartments
in Arabidopsis Thaliana.” PLoS Genetics. Public Library of Science, 2013.
https://doi.org/10.1371/journal.pgen.1003540.
ieee: H. Tanaka et al., “Cell polarity and patterning by PIN trafficking
through early endosomal compartments in arabidopsis thaliana,” PLoS Genetics,
vol. 9, no. 5. Public Library of Science, 2013.
ista: Tanaka H, Kitakura S, Rakusová H, Uemura T, Feraru M, De Rycke R, Robert S,
Kakimoto T, Friml J. 2013. Cell polarity and patterning by PIN trafficking through
early endosomal compartments in arabidopsis thaliana. PLoS Genetics. 9(5), e1003540.
mla: Tanaka, Hirokazu, et al. “Cell Polarity and Patterning by PIN Trafficking through
Early Endosomal Compartments in Arabidopsis Thaliana.” PLoS Genetics, vol.
9, no. 5, e1003540, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003540.
short: H. Tanaka, S. Kitakura, H. Rakusová, T. Uemura, M. Feraru, R. De Rycke, S.
Robert, T. Kakimoto, J. Friml, PLoS Genetics 9 (2013).
date_created: 2018-12-11T11:59:50Z
date_published: 2013-05-05T00:00:00Z
date_updated: 2021-01-12T07:00:03Z
day: '05'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1371/journal.pgen.1003540
ec_funded: 1
file:
- access_level: open_access
checksum: 050237d6c53e8d1601b26808ee1dd6d8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:39Z
date_updated: 2020-07-14T12:45:50Z
file_id: '4957'
file_name: IST-2016-411-v1+1_journal.pgen.1003540.pdf
file_size: 3813091
relation: main_file
file_date_updated: 2020-07-14T12:45:50Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '3967'
pubrep_id: '411'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cell polarity and patterning by PIN trafficking through early endosomal compartments
in arabidopsis thaliana
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '2828'
abstract:
- lang: eng
text: 'We study the complexity of valued constraint satisfaction problems (VCSPs)
parametrized by a constraint language, a fixed set of cost functions over a finite
domain. An instance of the problem is specified by a sum of cost functions from
the language and the goal is to minimize the sum. Under the unique games conjecture,
the approximability of finite-valued VCSPs is well understood, see Raghavendra
[2008]. However, there is no characterization of finite-valued VCSPs, let alone
general-valued VCSPs, that can be solved exactly in polynomial time, thus giving
insights from a combinatorial optimization perspective. We consider the case of
languages containing all possible unary cost functions. In the case of languages
consisting of only {0, ∞}-valued cost functions (i.e., relations), such languages
have been called conservative and studied by Bulatov [2003, 2011] and recently
by Barto [2011]. Since we study valued languages, we call a language conservative
if it contains all finite-valued unary cost functions. The computational complexity
of conservative valued languages has been studied by Cohen et al. [2006] for languages
over Boolean domains, by Deineko et al. [2008] for {0, 1}-valued languages (a.k.a
Max-CSP), and by Takhanov [2010a] for {0, ∞}-valued languages containing all finite-valued
unary cost functions (a.k.a. Min-Cost-Hom). We prove a Schaefer-like dichotomy
theorem for conservative valued languages: if all cost functions in the language
satisfy a certain condition (specified by a complementary combination of STP and
MJN multimor-phisms), then any instance can be solved in polynomial time (via
a new algorithm developed in this article), otherwise the language is NP-hard.
This is the first complete complexity classification of general-valued constraint
languages over non-Boolean domains. It is a common phenomenon that complexity
classifications of problems over non-Boolean domains are significantly harder
than the Boolean cases. The polynomial-time algorithm we present for the tractable
cases is a generalization of the submodular minimization problem and a result
of Cohen et al. [2008]. Our results generalize previous results by Takhanov [2010a]
and (a subset of results) by Cohen et al. [2006] and Deineko et al. [2008]. Moreover,
our results do not rely on any computer-assisted search as in Deineko et al. [2008],
and provide a powerful tool for proving hardness of finite-valued and general-valued
languages.'
article_number: '10'
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Stanislav
full_name: Živný, Stanislav
last_name: Živný
citation:
ama: Kolmogorov V, Živný S. The complexity of conservative valued CSPs. Journal
of the ACM. 2013;60(2). doi:10.1145/2450142.2450146
apa: Kolmogorov, V., & Živný, S. (2013). The complexity of conservative valued
CSPs. Journal of the ACM. ACM. https://doi.org/10.1145/2450142.2450146
chicago: Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative
Valued CSPs.” Journal of the ACM. ACM, 2013. https://doi.org/10.1145/2450142.2450146.
ieee: V. Kolmogorov and S. Živný, “The complexity of conservative valued CSPs,”
Journal of the ACM, vol. 60, no. 2. ACM, 2013.
ista: Kolmogorov V, Živný S. 2013. The complexity of conservative valued CSPs. Journal
of the ACM. 60(2), 10.
mla: Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative
Valued CSPs.” Journal of the ACM, vol. 60, no. 2, 10, ACM, 2013, doi:10.1145/2450142.2450146.
short: V. Kolmogorov, S. Živný, Journal of the ACM 60 (2013).
date_created: 2018-12-11T11:59:48Z
date_published: 2013-04-02T00:00:00Z
date_updated: 2021-01-12T07:00:00Z
day: '02'
department:
- _id: VlKo
doi: 10.1145/2450142.2450146
external_id:
arxiv:
- '1110.2809'
intvolume: ' 60'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1110.2809
month: '04'
oa: 1
oa_version: Preprint
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '3971'
quality_controlled: '1'
scopus_import: 1
status: public
title: The complexity of conservative valued CSPs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2013'
...
---
_id: '2829'
abstract:
- lang: eng
text: Laminar-turbulent intermittency is intrinsic to the transitional regime of
a wide range of fluid flows including pipe, channel, boundary layer, and Couette
flow. In the latter turbulent spots can grow and form continuous stripes, yet
in the stripe-normal direction they remain interspersed by laminar fluid. We carry
out direct numerical simulations in a long narrow domain and observe that individual
turbulent stripes are transient. In agreement with recent observations in pipe
flow, we find that turbulence becomes sustained at a distinct critical point once
the spatial proliferation outweighs the inherent decaying process. By resolving
the asymptotic size distributions close to criticality we can for the first time
demonstrate scale invariance at the onset of turbulence.
article_number: '204502'
author:
- first_name: Liang
full_name: Shi, Liang
id: 374A3F1A-F248-11E8-B48F-1D18A9856A87
last_name: Shi
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Shi L, Avila M, Hof B. Scale invariance at the onset of turbulence in couette
flow. Physical Review Letters. 2013;110(20). doi:10.1103/PhysRevLett.110.204502
apa: Shi, L., Avila, M., & Hof, B. (2013). Scale invariance at the onset of
turbulence in couette flow. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/PhysRevLett.110.204502
chicago: Shi, Liang, Marc Avila, and Björn Hof. “Scale Invariance at the Onset of
Turbulence in Couette Flow.” Physical Review Letters. American Physical
Society, 2013. https://doi.org/10.1103/PhysRevLett.110.204502.
ieee: L. Shi, M. Avila, and B. Hof, “Scale invariance at the onset of turbulence
in couette flow,” Physical Review Letters, vol. 110, no. 20. American Physical
Society, 2013.
ista: Shi L, Avila M, Hof B. 2013. Scale invariance at the onset of turbulence in
couette flow. Physical Review Letters. 110(20), 204502.
mla: Shi, Liang, et al. “Scale Invariance at the Onset of Turbulence in Couette
Flow.” Physical Review Letters, vol. 110, no. 20, 204502, American Physical
Society, 2013, doi:10.1103/PhysRevLett.110.204502.
short: L. Shi, M. Avila, B. Hof, Physical Review Letters 110 (2013).
date_created: 2018-12-11T11:59:49Z
date_published: 2013-05-13T00:00:00Z
date_updated: 2021-01-12T07:00:00Z
day: '13'
department:
- _id: BjHo
doi: 10.1103/PhysRevLett.110.204502
ec_funded: 1
external_id:
arxiv:
- '1304.5446'
intvolume: ' 110'
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1304.5446
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
- _id: 2511D90C-B435-11E9-9278-68D0E5697425
grant_number: SFB 963 TP A8
name: Astrophysical instability of currents and turbulences
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '3970'
quality_controlled: '1'
scopus_import: 1
status: public
title: Scale invariance at the onset of turbulence in couette flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2834'
abstract:
- lang: eng
text: Although the equations governing fluid flow are well known, there are no analytical
expressions that describe the complexity of turbulent motion. A recent proposition
is that in analogy to low dimensional chaotic systems, turbulence is organized
around unstable solutions of the governing equations which provide the building
blocks of the disordered dynamics. We report the discovery of periodic solutions
which just like intermittent turbulence are spatially localized and show that
turbulent transients arise from one such solution branch.
article_number: '224502'
author:
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
- first_name: Fernando
full_name: Mellibovsky, Fernando
last_name: Mellibovsky
- first_name: Nicolas
full_name: Roland, Nicolas
last_name: Roland
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Avila M, Mellibovsky F, Roland N, Hof B. Streamwise-localized solutions at
the onset of turbulence in pipe flow. Physical Review Letters. 2013;110(22).
doi:10.1103/PhysRevLett.110.224502
apa: Avila, M., Mellibovsky, F., Roland, N., & Hof, B. (2013). Streamwise-localized
solutions at the onset of turbulence in pipe flow. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.110.224502
chicago: Avila, Marc, Fernando Mellibovsky, Nicolas Roland, and Björn Hof. “Streamwise-Localized
Solutions at the Onset of Turbulence in Pipe Flow.” Physical Review Letters.
American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.224502.
ieee: M. Avila, F. Mellibovsky, N. Roland, and B. Hof, “Streamwise-localized solutions
at the onset of turbulence in pipe flow,” Physical Review Letters, vol.
110, no. 22. American Physical Society, 2013.
ista: Avila M, Mellibovsky F, Roland N, Hof B. 2013. Streamwise-localized solutions
at the onset of turbulence in pipe flow. Physical Review Letters. 110(22), 224502.
mla: Avila, Marc, et al. “Streamwise-Localized Solutions at the Onset of Turbulence
in Pipe Flow.” Physical Review Letters, vol. 110, no. 22, 224502, American
Physical Society, 2013, doi:10.1103/PhysRevLett.110.224502.
short: M. Avila, F. Mellibovsky, N. Roland, B. Hof, Physical Review Letters 110
(2013).
date_created: 2018-12-11T11:59:50Z
date_published: 2013-05-29T00:00:00Z
date_updated: 2021-01-12T07:00:05Z
day: '29'
department:
- _id: BjHo
doi: 10.1103/PhysRevLett.110.224502
ec_funded: 1
external_id:
arxiv:
- '1212.0230'
intvolume: ' 110'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1212.0230
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '3965'
quality_controlled: '1'
scopus_import: 1
status: public
title: Streamwise-localized solutions at the onset of turbulence in pipe flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2833'
abstract:
- lang: eng
text: During development, mechanical forces cause changes in size, shape, number,
position, and gene expression of cells. They are therefore integral to any morphogenetic
processes. Force generation by actin-myosin networks and force transmission through
adhesive complexes are two self-organizing phenomena driving tissue morphogenesis.
Coordination and integration of forces by long-range force transmission and mechanosensing
of cells within tissues produce large-scale tissue shape changes. Extrinsic mechanical
forces also control tissue patterning by modulating cell fate specification and
differentiation. Thus, the interplay between tissue mechanics and biochemical
signaling orchestrates tissue morphogenesis and patterning in development.
acknowledgement: C.-P.H. is supported by the Institute of Science and Technology Austria
and grants from the Deutsche Forschungsgemeinschaft (DFG) and Fonds zur Förderung
der wissenschaftlichen Forschung (FWF).
author:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Yohanns
full_name: Bellaïche, Yohanns
last_name: Bellaïche
citation:
ama: Heisenberg C-PJ, Bellaïche Y. Forces in tissue morphogenesis and patterning.
Cell. 2013;153(5):948-962. doi:10.1016/j.cell.2013.05.008
apa: Heisenberg, C.-P. J., & Bellaïche, Y. (2013). Forces in tissue morphogenesis
and patterning. Cell. Cell Press. https://doi.org/10.1016/j.cell.2013.05.008
chicago: Heisenberg, Carl-Philipp J, and Yohanns Bellaïche. “Forces in Tissue Morphogenesis
and Patterning.” Cell. Cell Press, 2013. https://doi.org/10.1016/j.cell.2013.05.008.
ieee: C.-P. J. Heisenberg and Y. Bellaïche, “Forces in tissue morphogenesis and
patterning,” Cell, vol. 153, no. 5. Cell Press, pp. 948–962, 2013.
ista: Heisenberg C-PJ, Bellaïche Y. 2013. Forces in tissue morphogenesis and patterning.
Cell. 153(5), 948–962.
mla: Heisenberg, Carl-Philipp J., and Yohanns Bellaïche. “Forces in Tissue Morphogenesis
and Patterning.” Cell, vol. 153, no. 5, Cell Press, 2013, pp. 948–62, doi:10.1016/j.cell.2013.05.008.
short: C.-P.J. Heisenberg, Y. Bellaïche, Cell 153 (2013) 948–962.
date_created: 2018-12-11T11:59:50Z
date_published: 2013-05-23T00:00:00Z
date_updated: 2021-01-12T07:00:04Z
day: '23'
department:
- _id: CaHe
doi: 10.1016/j.cell.2013.05.008
intvolume: ' 153'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 948 - 962
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3966'
quality_controlled: '1'
scopus_import: 1
status: public
title: Forces in tissue morphogenesis and patterning
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 153
year: '2013'
...
---
_id: '2830'
author:
- first_name: Christine
full_name: Moussion, Christine
id: 3356F664-F248-11E8-B48F-1D18A9856A87
last_name: Moussion
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Moussion C, Sixt MK. A conduit to amplify innate immunity. Immunity.
2013;38(5):853-854. doi:10.1016/j.immuni.2013.05.005
apa: Moussion, C., & Sixt, M. K. (2013). A conduit to amplify innate immunity.
Immunity. Cell Press. https://doi.org/10.1016/j.immuni.2013.05.005
chicago: Moussion, Christine, and Michael K Sixt. “A Conduit to Amplify Innate Immunity.”
Immunity. Cell Press, 2013. https://doi.org/10.1016/j.immuni.2013.05.005.
ieee: C. Moussion and M. K. Sixt, “A conduit to amplify innate immunity,” Immunity,
vol. 38, no. 5. Cell Press, pp. 853–854, 2013.
ista: Moussion C, Sixt MK. 2013. A conduit to amplify innate immunity. Immunity.
38(5), 853–854.
mla: Moussion, Christine, and Michael K. Sixt. “A Conduit to Amplify Innate Immunity.”
Immunity, vol. 38, no. 5, Cell Press, 2013, pp. 853–54, doi:10.1016/j.immuni.2013.05.005.
short: C. Moussion, M.K. Sixt, Immunity 38 (2013) 853–854.
date_created: 2018-12-11T11:59:49Z
date_published: 2013-05-23T00:00:00Z
date_updated: 2021-01-12T07:00:01Z
day: '23'
department:
- _id: MiSi
doi: 10.1016/j.immuni.2013.05.005
intvolume: ' 38'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 853 - 854
publication: Immunity
publication_status: published
publisher: Cell Press
publist_id: '3969'
quality_controlled: '1'
scopus_import: 1
status: public
title: A conduit to amplify innate immunity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2013'
...
---
_id: '2842'
abstract:
- lang: eng
text: 'We outline two approaches to inference of neighbourhood size, N, and dispersal
rate, σ2, based on either allele frequencies or on the lengths of sequence blocks
that are shared between genomes. Over intermediate timescales (10-100 generations,
say), populations that live in two dimensions approach a quasi-equilibrium that
is independent of both their local structure and their deeper history. Over such
scales, the standardised covariance of allele frequencies (i.e. pairwise FS T)
falls with the logarithm of distance, and depends only on neighbourhood size,
N, and a ''local scale'', κ; the rate of gene flow, σ2, cannot be inferred. We
show how spatial correlations can be accounted for, assuming a Gaussian distribution
of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively,
inferences can be based on the distribution of the lengths of sequence that are
identical between blocks of genomes: long blocks (>0.1 cM, say) tell us about
intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood
size, the distribution of long blocks is given directly by the classical Wright-Malécot
formula; this relationship can be used to infer both N and σ2. With small neighbourhood
size, there is an appreciable chance that recombinant lineages will coalesce back
before escaping into the distant past. For this case, we show that if genomes
are sampled from some distance apart, then the distribution of lengths of blocks
that are identical in state is geometric, with a mean that depends on N and σ2.'
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. Inference in two dimensions:
Allele frequencies versus lengths of shared sequence blocks. Theoretical Population
Biology. 2013;87(1):105-119. doi:10.1016/j.tpb.2013.03.001'
apa: 'Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Inference
in two dimensions: Allele frequencies versus lengths of shared sequence blocks.
Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2013.03.001'
chicago: 'Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber.
“Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence
Blocks.” Theoretical Population Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2013.03.001.'
ieee: 'N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Inference in two
dimensions: Allele frequencies versus lengths of shared sequence blocks,” Theoretical
Population Biology, vol. 87, no. 1. Elsevier, pp. 105–119, 2013.'
ista: 'Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Inference in two dimensions:
Allele frequencies versus lengths of shared sequence blocks. Theoretical Population
Biology. 87(1), 105–119.'
mla: 'Barton, Nicholas H., et al. “Inference in Two Dimensions: Allele Frequencies
versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology,
vol. 87, no. 1, Elsevier, 2013, pp. 105–19, doi:10.1016/j.tpb.2013.03.001.'
short: N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population
Biology 87 (2013) 105–119.
date_created: 2018-12-11T11:59:53Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T07:00:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2013.03.001
ec_funded: 1
file:
- access_level: open_access
checksum: 9bf9d9a6fd03dd9df50906891f393bf8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:33Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5288'
file_name: IST-2016-558-v1+1_inference_revised3101NB.pdf
file_size: 1554712
relation: main_file
- access_level: open_access
checksum: 2bceddb76edacd0cd5fad73051e2a928
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:34Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5289'
file_name: IST-2016-558-v1+2_inference_revised3101NBApp.pdf
file_size: 822964
relation: main_file
file_date_updated: 2020-07-14T12:45:50Z
has_accepted_license: '1'
intvolume: ' 87'
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 105 - 119
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: '3953'
pubrep_id: '558'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Inference in two dimensions: Allele frequencies versus lengths of shared sequence
blocks'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2013'
...
---
_id: '2838'
abstract:
- lang: eng
text: Individuals with Down syndrome (DS) present important motor deficits that
derive from altered motor development of infants and young children. DYRK1A, a
candidate gene for DS abnormalities has been implicated in motor function due
to its expression in motor nuclei in the adult brain, and its overexpression in
DS mouse models leads to hyperactivity and altered motor learning. However, its
precise role in the adult motor system, or its possible involvement in postnatal
locomotor development has not yet been clarified. During the postnatal period
we observed time-specific expression of Dyrk1A in discrete subsets of brainstem
nuclei and spinal cord motor neurons. Interestingly, we describe for the first
time the presence of Dyrk1A in the presynaptic terminal of the neuromuscular junctions
and its axonal transport from the facial nucleus, suggesting a function for Dyrk1A
in these structures. Relevant to DS, Dyrk1A overexpression in transgenic mice
(TgDyrk1A) produces motor developmental alterations possibly contributing to DS
motor phenotypes and modifies the numbers of motor cholinergic neurons, suggesting
that the kinase may have a role in the development of the brainstem and spinal
cord motor system.
article_number: e54285
author:
- first_name: Gloria
full_name: Arquè Fuste, Gloria
id: 3CF33908-F248-11E8-B48F-1D18A9856A87
last_name: Arquè Fuste
- first_name: Anna
full_name: Casanovas, Anna
last_name: Casanovas
- first_name: Mara
full_name: Dierssen, Mara
last_name: Dierssen
citation:
ama: 'Arquè Fuste G, Casanovas A, Dierssen M. Dyrk1A is dynamically expressed on
subsets of motor neurons and in the neuromuscular junction: Possible role in Down
syndrome. PLoS One. 2013;8(1). doi:10.1371/journal.pone.0054285'
apa: 'Arquè Fuste, G., Casanovas, A., & Dierssen, M. (2013). Dyrk1A is dynamically
expressed on subsets of motor neurons and in the neuromuscular junction: Possible
role in Down syndrome. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0054285'
chicago: 'Arquè Fuste, Gloria, Anna Casanovas, and Mara Dierssen. “Dyrk1A Is Dynamically
Expressed on Subsets of Motor Neurons and in the Neuromuscular Junction: Possible
Role in Down Syndrome.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0054285.'
ieee: 'G. Arquè Fuste, A. Casanovas, and M. Dierssen, “Dyrk1A is dynamically expressed
on subsets of motor neurons and in the neuromuscular junction: Possible role in
Down syndrome,” PLoS One, vol. 8, no. 1. Public Library of Science, 2013.'
ista: 'Arquè Fuste G, Casanovas A, Dierssen M. 2013. Dyrk1A is dynamically expressed
on subsets of motor neurons and in the neuromuscular junction: Possible role in
Down syndrome. PLoS One. 8(1), e54285.'
mla: 'Arquè Fuste, Gloria, et al. “Dyrk1A Is Dynamically Expressed on Subsets of
Motor Neurons and in the Neuromuscular Junction: Possible Role in Down Syndrome.”
PLoS One, vol. 8, no. 1, e54285, Public Library of Science, 2013, doi:10.1371/journal.pone.0054285.'
short: G. Arquè Fuste, A. Casanovas, M. Dierssen, PLoS One 8 (2013).
date_created: 2018-12-11T11:59:52Z
date_published: 2013-01-16T00:00:00Z
date_updated: 2021-01-12T07:00:07Z
day: '16'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1371/journal.pone.0054285
file:
- access_level: open_access
checksum: 512733b21419574a45f10cabef3d7f81
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:38Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5160'
file_name: IST-2016-407-v1+1_journal.pone.0054285.pdf
file_size: 4795977
relation: main_file
file_date_updated: 2020-07-14T12:45:50Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3960'
pubrep_id: '407'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular
junction: Possible role in Down syndrome'
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2013'
...
---
_id: '2839'
abstract:
- lang: eng
text: Directional guidance of cells via gradients of chemokines is considered crucial
for embryonic development, cancer dissemination, and immune responses. Nevertheless,
the concept still lacks direct experimental confirmation in vivo. Here, we identify
endogenous gradients of the chemokine CCL21 within mouse skin and show that they
guide dendritic cells toward lymphatic vessels. Quantitative imaging reveals depots
of CCL21 within lymphatic endothelial cells and steeply decaying gradients within
the perilymphatic interstitium. These gradients match the migratory patterns of
the dendritic cells, which directionally approach vessels from a distance of up
to 90-micrometers. Interstitial CCL21 is immobilized to heparan sulfates, and
its experimental delocalization or swamping the endogenous gradients abolishes
directed migration. These findings functionally establish the concept of haptotaxis,
directed migration along immobilized gradients, in tissues.
acknowledgement: We thank M. Frank for technical assistance and S. Cremer, P. Schmalhorst,
and E. Kiermaier for critical reading of the manuscript. This work was supported
by a Humboldt Foundation postdoctoral fellowship (to M.W.), the German Research
Foundation (Si1323 1,2 to M.S.), the Human Frontier Science Program (HFSP RGP0058/2011
to M.S.), the European Research Council (ERC StG 281556 to M.S.), and the Swiss
National Science Foundation (31003A 127474 to D.F.L., 130488 to S.A.L.).
article_processing_charge: No
article_type: original
author:
- first_name: Michele
full_name: Weber, Michele
id: 3A3FC708-F248-11E8-B48F-1D18A9856A87
last_name: Weber
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Christine
full_name: Moussion, Christine
id: 3356F664-F248-11E8-B48F-1D18A9856A87
last_name: Moussion
- first_name: Ingrid
full_name: De Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: De Vries
- first_name: Daniel
full_name: Legler, Daniel
last_name: Legler
- first_name: Sanjiv
full_name: Luther, Sanjiv
last_name: Luther
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Weber M, Hauschild R, Schwarz J, et al. Interstitial dendritic cell guidance
by haptotactic chemokine gradients. Science. 2013;339(6117):328-332. doi:10.1126/science.1228456
apa: Weber, M., Hauschild, R., Schwarz, J., Moussion, C., de Vries, I., Legler,
D., … Sixt, M. K. (2013). Interstitial dendritic cell guidance by haptotactic
chemokine gradients. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.1228456
chicago: Weber, Michele, Robert Hauschild, Jan Schwarz, Christine Moussion, Ingrid
de Vries, Daniel Legler, Sanjiv Luther, Mark Tobias Bollenbach, and Michael K
Sixt. “Interstitial Dendritic Cell Guidance by Haptotactic Chemokine Gradients.”
Science. American Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1228456.
ieee: M. Weber et al., “Interstitial dendritic cell guidance by haptotactic
chemokine gradients,” Science, vol. 339, no. 6117. American Association
for the Advancement of Science, pp. 328–332, 2013.
ista: Weber M, Hauschild R, Schwarz J, Moussion C, de Vries I, Legler D, Luther
S, Bollenbach MT, Sixt MK. 2013. Interstitial dendritic cell guidance by haptotactic
chemokine gradients. Science. 339(6117), 328–332.
mla: Weber, Michele, et al. “Interstitial Dendritic Cell Guidance by Haptotactic
Chemokine Gradients.” Science, vol. 339, no. 6117, American Association
for the Advancement of Science, 2013, pp. 328–32, doi:10.1126/science.1228456.
short: M. Weber, R. Hauschild, J. Schwarz, C. Moussion, I. de Vries, D. Legler,
S. Luther, M.T. Bollenbach, M.K. Sixt, Science 339 (2013) 328–332.
date_created: 2018-12-11T11:59:52Z
date_published: 2013-01-18T00:00:00Z
date_updated: 2022-06-10T10:21:40Z
day: '18'
department:
- _id: MiSi
- _id: Bio
doi: 10.1126/science.1228456
ec_funded: 1
intvolume: ' 339'
issue: '6117'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://kops.uni-konstanz.de/bitstream/123456789/26341/2/Weber_263418.pdf
month: '01'
oa: 1
oa_version: Published Version
page: 328 - 332
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
- _id: 25ABD200-B435-11E9-9278-68D0E5697425
grant_number: RGP0058/2011
name: 'Cell migration in complex environments: from in vivo experiments to theoretical
models'
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '3959'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interstitial dendritic cell guidance by haptotactic chemokine gradients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 339
year: '2013'
...