---
_id: '1299'
abstract:
- lang: eng
text: Recent experiments have shown that motion detection in Drosophila starts with
splitting the visual input into two parallel channels encoding brightness increments
(ON) or decrements (OFF). This suggests the existence of either two (ON-ON, OFF-OFF)
or four (for all pairwise interactions) separate motion detectors. To decide between
these possibilities, we stimulated flies using sequences of ON and OFF brightness
pulses while recording from motion-sensitive tangential cells. We found direction-selective
responses to sequences of same sign (ON-ON, OFF-OFF), but not of opposite sign
(ON-OFF, OFF-ON), refuting the existence of four separate detectors. Based on
further measurements, we propose a model that reproduces a variety of additional
experimental data sets, including ones that were previously interpreted as support
for four separate detectors. Our experiments and the derived model mark an important
step in guiding further dissection of the fly motion detection circuit.
author:
- first_name: Hubert
full_name: Eichner, Hubert
last_name: Eichner
- first_name: Maximilian A
full_name: Maximilian Jösch
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Bettina
full_name: Schnell, Bettina
last_name: Schnell
- first_name: Dierk
full_name: Reiff, Dierk F
last_name: Reiff
- first_name: Alexander
full_name: Borst, Alexander
last_name: Borst
citation:
ama: Eichner H, Jösch MA, Schnell B, Reiff D, Borst A. Internal structure of the
fly elementary motion detector. Neuron. 2011;70(6):1155-1164. doi:10.1016/j.neuron.2011.03.028
apa: Eichner, H., Jösch, M. A., Schnell, B., Reiff, D., & Borst, A. (2011).
Internal structure of the fly elementary motion detector. Neuron. Elsevier.
https://doi.org/10.1016/j.neuron.2011.03.028
chicago: Eichner, Hubert, Maximilian A Jösch, Bettina Schnell, Dierk Reiff, and
Alexander Borst. “Internal Structure of the Fly Elementary Motion Detector.” Neuron.
Elsevier, 2011. https://doi.org/10.1016/j.neuron.2011.03.028.
ieee: H. Eichner, M. A. Jösch, B. Schnell, D. Reiff, and A. Borst, “Internal structure
of the fly elementary motion detector,” Neuron, vol. 70, no. 6. Elsevier,
pp. 1155–1164, 2011.
ista: Eichner H, Jösch MA, Schnell B, Reiff D, Borst A. 2011. Internal structure
of the fly elementary motion detector. Neuron. 70(6), 1155–1164.
mla: Eichner, Hubert, et al. “Internal Structure of the Fly Elementary Motion Detector.”
Neuron, vol. 70, no. 6, Elsevier, 2011, pp. 1155–64, doi:10.1016/j.neuron.2011.03.028.
short: H. Eichner, M.A. Jösch, B. Schnell, D. Reiff, A. Borst, Neuron 70 (2011)
1155–1164.
date_created: 2018-12-11T11:51:14Z
date_published: 2011-06-23T00:00:00Z
date_updated: 2021-01-12T06:49:43Z
day: '23'
doi: 10.1016/j.neuron.2011.03.028
extern: 1
intvolume: ' 70'
issue: '6'
month: '06'
page: 1155 - 1164
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '5969'
quality_controlled: 0
status: public
title: Internal structure of the fly elementary motion detector
type: journal_article
volume: 70
year: '2011'
...
---
_id: '1467'
abstract:
- lang: eng
text: We propose a general conjecture for the mixed Hodge polynomial of the generic
character varieties of representations of the fundamental group of a Riemann surface
of genus g to GLn(C) with fixed generic semisimple conjugacy classes at k punctures.
This conjecture generalizes the Cauchy identity for Macdonald polynomials and
is a common generalization of two formulas that we prove in this paper. The first
is a formula for the E-polynomial of these character varieties which we obtain
using the character table of GLn(Fq). We use this formula to compute the Euler
characteristic of character varieties. The second formula gives the Poincaré polynomial
of certain associated quiver varieties which we obtain using the character table
of gln(Fq). In the last main result we prove that the Poincaré polynomials of
the quiver varieties equal certain multiplicities in the tensor product of irreducible
characters of GLn(Fq). As a consequence we find a curious connection between Kac-Moody
algebras associated with comet-shaped, and typically wild, quivers and the representation
theory of GLn(Fq).
acknowledgement: |-
Hausel’s work was supported by National Science Foundation grants DMS-0305505 and DMS-0604775, by an Alfred Sloan Fellowship, and by a Royal Society University Research Fellowship. Letellier’s work supported by Agence Nationale de la Recherche grant ANR-09-JCJC-0102-01.
Rodriguez-Villegas’s work supported by National Science Foundation grant DMS-0200605, by an FRA from the University of Texas at Austin, by EPSRC grant EP/G027110/1, by visiting fellowships at All Souls and Wadham Colleges in Oxford, and by a Research Scholarship from the Clay Mathematical Institute.
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Emmanuel
full_name: Letellier, Emmanuel
last_name: Letellier
- first_name: Fernando
full_name: Rodríguez Villegas, Fernando
last_name: Rodríguez Villegas
citation:
ama: Hausel T, Letellier E, Rodríguez Villegas F. Arithmetic harmonic analysis on
character and quiver varieties. Duke Mathematical Journal. 2011;160(2):323-400.
doi:10.1215/00127094-1444258
apa: Hausel, T., Letellier, E., & Rodríguez Villegas, F. (2011). Arithmetic
harmonic analysis on character and quiver varieties. Duke Mathematical Journal.
Duke University Press. https://doi.org/10.1215/00127094-1444258
chicago: Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Arithmetic
Harmonic Analysis on Character and Quiver Varieties.” Duke Mathematical Journal.
Duke University Press, 2011. https://doi.org/10.1215/00127094-1444258.
ieee: T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Arithmetic harmonic analysis
on character and quiver varieties,” Duke Mathematical Journal, vol. 160,
no. 2. Duke University Press, pp. 323–400, 2011.
ista: Hausel T, Letellier E, Rodríguez Villegas F. 2011. Arithmetic harmonic analysis
on character and quiver varieties. Duke Mathematical Journal. 160(2), 323–400.
mla: Hausel, Tamás, et al. “Arithmetic Harmonic Analysis on Character and Quiver
Varieties.” Duke Mathematical Journal, vol. 160, no. 2, Duke University
Press, 2011, pp. 323–400, doi:10.1215/00127094-1444258.
short: T. Hausel, E. Letellier, F. Rodríguez Villegas, Duke Mathematical Journal
160 (2011) 323–400.
date_created: 2018-12-11T11:52:11Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:56Z
day: '01'
doi: 10.1215/00127094-1444258
extern: 1
intvolume: ' 160'
issue: '2'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0810.2076
month: '01'
oa: 1
page: 323 - 400
publication: Duke Mathematical Journal
publication_status: published
publisher: Duke University Press
publist_id: '5728'
quality_controlled: 0
status: public
title: Arithmetic harmonic analysis on character and quiver varieties
type: journal_article
volume: 160
year: '2011'
...
---
_id: '1723'
abstract:
- lang: eng
text: The emergence of differences in the arrangement of cells is the first step
towards the establishment of many organs. Understanding this process is limited
by the lack of systematic characterization of epithelial organisation. Here we
apply network theory at the scale of individual cells to uncover patterns in cell-to-cell
contacts that govern epithelial organisation. We provide an objective characterisation
of epithelia using network representation, where cells are nodes and cell contacts
are links. The features of individual cells, together with attributes of the cellular
network, produce a defining signature that distinguishes epithelia from different
organs, species, developmental stages and genetic conditions. The approach permits
characterization, quantification and classification of normal and perturbed epithelia,
and establishes a framework for understanding molecular mechanisms that underpin
the architecture of complex tissues.
acknowledgement: We acknowledge the MRC for funding, M.M.B. acknowledges Darwin College,
EMBO YIP and Schlumberger Ltd for support. L.M.E. is funded by the Marie Curie and
the EMBO fellowships. L.d.F.C. is grateful to FAPESP (05/00587-5) and CNPq (301303/06-1)
for financial support. Part of this work was performed during a Visiting Scholarship
to L.d.F.C. from St Catharine's College, University of Cambridge. J.B. is supported
by the MRC (UK) and A.K. by a FEBS fellowship
author:
- first_name: Luis
full_name: Escudero, Luis M
last_name: Escudero
- first_name: Luciano
full_name: Costa, Luciano
last_name: Costa
- first_name: Anna
full_name: Anna Kicheva
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: James
full_name: Briscoe, James
last_name: Briscoe
- first_name: Matthew
full_name: Freeman, Matthew
last_name: Freeman
- first_name: Madan
full_name: Babu, Madan M
last_name: Babu
citation:
ama: Escudero L, Costa L, Kicheva A, Briscoe J, Freeman M, Babu M. Epithelial organisation
revealed by a network of cellular contacts. Nature Communications. 2011;2(1).
doi:10.1038/ncomms1536
apa: Escudero, L., Costa, L., Kicheva, A., Briscoe, J., Freeman, M., & Babu,
M. (2011). Epithelial organisation revealed by a network of cellular contacts.
Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms1536
chicago: Escudero, Luis, Luciano Costa, Anna Kicheva, James Briscoe, Matthew Freeman,
and Madan Babu. “Epithelial Organisation Revealed by a Network of Cellular Contacts.”
Nature Communications. Nature Publishing Group, 2011. https://doi.org/10.1038/ncomms1536.
ieee: L. Escudero, L. Costa, A. Kicheva, J. Briscoe, M. Freeman, and M. Babu, “Epithelial
organisation revealed by a network of cellular contacts,” Nature Communications,
vol. 2, no. 1. Nature Publishing Group, 2011.
ista: Escudero L, Costa L, Kicheva A, Briscoe J, Freeman M, Babu M. 2011. Epithelial
organisation revealed by a network of cellular contacts. Nature Communications.
2(1).
mla: Escudero, Luis, et al. “Epithelial Organisation Revealed by a Network of Cellular
Contacts.” Nature Communications, vol. 2, no. 1, Nature Publishing Group,
2011, doi:10.1038/ncomms1536.
short: L. Escudero, L. Costa, A. Kicheva, J. Briscoe, M. Freeman, M. Babu, Nature
Communications 2 (2011).
date_created: 2018-12-11T11:53:40Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:46Z
day: '01'
doi: 10.1038/ncomms1536
extern: 1
intvolume: ' 2'
issue: '1'
month: '01'
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5405'
quality_controlled: 0
status: public
title: Epithelial organisation revealed by a network of cellular contacts
type: journal_article
volume: 2
year: '2011'
...
---
_id: '1724'
abstract:
- lang: eng
text: Morphogens, such as Decapentaplegic (Dpp) in the fly imaginal discs, form
graded concentration profiles that control patterning and growth of developing
organs. In the imaginal discs, proliferative growth is homogeneous in space, posing
the conundrum of how morphogen concentration gradients could control position-independent
growth. To understand the mechanism of proliferation control by the Dpp gradient,
we quantified Dpp concentration and signaling levels during wing disc growth.
Both Dpp concentration and signaling gradients scale with tissue size during development.
On average, cells divide when Dpp signaling levels have increased by 50%. Our
observations are consistent with a growth control mechanism based on temporal
changes of cellular morphogen signaling levels. For a scaling gradient, this mechanism
generates position-independent growth rates.
acknowledgement: P.M., T.B., and F.J. were supported by the Max-Planck-Gesellschaft.
O.W., A.K., C.S., and M.G.-G. were supported by Geneva University and by European
Research Council advanced investigator grant (SARA), SystemsX (LipidX), Swiss National
Science Foundation (SNF), National Centre of Competence in Research (NCCR) chemical
biology and Frontiers in Genetics and R'equip grants
author:
- first_name: Ortrud
full_name: Wartlick, Ortrud
last_name: Wartlick
- first_name: Peer
full_name: Mumcu, Peer
last_name: Mumcu
- first_name: Anna
full_name: Anna Kicheva
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Thomas
full_name: Bittig, Thomas
last_name: Bittig
- first_name: Carole
full_name: Seum, Carole
last_name: Seum
- first_name: Frank
full_name: Jülicher, Frank
last_name: Jülicher
- first_name: Marcos
full_name: González-Gaitán, Marcos A
last_name: González Gaitán
citation:
ama: Wartlick O, Mumcu P, Kicheva A, et al. Dynamics of Dpp signaling and proliferation
control. Science. 2011;331(6021):1154-1159. doi:10.1126/science.1200037
apa: Wartlick, O., Mumcu, P., Kicheva, A., Bittig, T., Seum, C., Jülicher, F., &
González Gaitán, M. (2011). Dynamics of Dpp signaling and proliferation control.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1200037
chicago: Wartlick, Ortrud, Peer Mumcu, Anna Kicheva, Thomas Bittig, Carole Seum,
Frank Jülicher, and Marcos González Gaitán. “Dynamics of Dpp Signaling and Proliferation
Control.” Science. American Association for the Advancement of Science,
2011. https://doi.org/10.1126/science.1200037.
ieee: O. Wartlick et al., “Dynamics of Dpp signaling and proliferation control,”
Science, vol. 331, no. 6021. American Association for the Advancement of
Science, pp. 1154–1159, 2011.
ista: Wartlick O, Mumcu P, Kicheva A, Bittig T, Seum C, Jülicher F, González Gaitán
M. 2011. Dynamics of Dpp signaling and proliferation control. Science. 331(6021),
1154–1159.
mla: Wartlick, Ortrud, et al. “Dynamics of Dpp Signaling and Proliferation Control.”
Science, vol. 331, no. 6021, American Association for the Advancement of
Science, 2011, pp. 1154–59, doi:10.1126/science.1200037.
short: O. Wartlick, P. Mumcu, A. Kicheva, T. Bittig, C. Seum, F. Jülicher, M. González
Gaitán, Science 331 (2011) 1154–1159.
date_created: 2018-12-11T11:53:40Z
date_published: 2011-03-04T00:00:00Z
date_updated: 2021-01-12T06:52:46Z
day: '04'
doi: 10.1126/science.1200037
extern: 1
intvolume: ' 331'
issue: '6021'
month: '03'
page: 1154 - 1159
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5406'
quality_controlled: 0
status: public
title: Dynamics of Dpp signaling and proliferation control
type: journal_article
volume: 331
year: '2011'
...
---
_id: '1754'
abstract:
- lang: eng
text: 'We report on a technique enabling electrical control of the contact silicidation
process in silicon nanowire devices. Undoped silicon nanowires were contacted
by pairs of nickel electrodes and each contact was selectively silicided by means
of the Joule effect. By a realtime monitoring of the nanowire electrical resistance
during the contact silicidation process we were able to fabricate nickel-silicide/silicon/nickel-
silicide devices with controlled silicon channel length down to 8 nm. '
acknowledgement: This work was supported by the Agence Nationale de la Recherche (ANR)
through the ACCESS and COHESION projects and by the European Commission through
the Chemtronics program MEST-CT-2005-020513
author:
- first_name: Massimo
full_name: Mongillo, Massimo
last_name: Mongillo
- first_name: Panayotis
full_name: Spathis, Panayotis
last_name: Spathis
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Pascal
full_name: Gentile, Pascal
last_name: Gentile
- first_name: Marc
full_name: Sanquer, Marc
last_name: Sanquer
- first_name: Silvano
full_name: De Franceschi, Silvano
last_name: De Franceschi
citation:
ama: Mongillo M, Spathis P, Katsaros G, Gentile P, Sanquer M, De Franceschi S. Joule-assisted
silicidation for short-channel silicon nanowire devices. ACS Nano. 2011;5(9):7117-7123.
doi:10.1021/nn202524j
apa: Mongillo, M., Spathis, P., Katsaros, G., Gentile, P., Sanquer, M., & De
Franceschi, S. (2011). Joule-assisted silicidation for short-channel silicon nanowire
devices. ACS Nano. American Chemical Society. https://doi.org/10.1021/nn202524j
chicago: Mongillo, Massimo, Panayotis Spathis, Georgios Katsaros, Pascal Gentile,
Marc Sanquer, and Silvano De Franceschi. “Joule-Assisted Silicidation for Short-Channel
Silicon Nanowire Devices.” ACS Nano. American Chemical Society, 2011. https://doi.org/10.1021/nn202524j.
ieee: M. Mongillo, P. Spathis, G. Katsaros, P. Gentile, M. Sanquer, and S. De Franceschi,
“Joule-assisted silicidation for short-channel silicon nanowire devices,” ACS
Nano, vol. 5, no. 9. American Chemical Society, pp. 7117–7123, 2011.
ista: Mongillo M, Spathis P, Katsaros G, Gentile P, Sanquer M, De Franceschi S.
2011. Joule-assisted silicidation for short-channel silicon nanowire devices.
ACS Nano. 5(9), 7117–7123.
mla: Mongillo, Massimo, et al. “Joule-Assisted Silicidation for Short-Channel Silicon
Nanowire Devices.” ACS Nano, vol. 5, no. 9, American Chemical Society,
2011, pp. 7117–23, doi:10.1021/nn202524j.
short: M. Mongillo, P. Spathis, G. Katsaros, P. Gentile, M. Sanquer, S. De Franceschi,
ACS Nano 5 (2011) 7117–7123.
date_created: 2018-12-11T11:53:50Z
date_published: 2011-09-27T00:00:00Z
date_updated: 2021-01-12T06:52:59Z
day: '27'
doi: 10.1021/nn202524j
extern: '1'
external_id:
arxiv:
- '1110.5668'
intvolume: ' 5'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1110.5668
month: '09'
oa: 1
oa_version: Preprint
page: 7117 - 7123
publication: ACS Nano
publication_status: published
publisher: American Chemical Society
publist_id: '5370'
quality_controlled: '1'
status: public
title: Joule-assisted silicidation for short-channel silicon nanowire devices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2011'
...
---
_id: '1755'
abstract:
- lang: eng
text: Spin-selective tunneling of holes in SiGe nanocrystals contacted by normal-metal
leads is reported. The spin selectivity arises from an interplay of the orbital
effect of the magnetic field with the strong spin-orbit interaction present in
the valence band of the semiconductor. We demonstrate both experimentally and
theoretically that spin-selective tunneling in semiconductor nanostructures can
be achieved without the use of ferromagnetic contacts. The reported effect, which
relies on mixing the light and heavy holes, should be observable in a broad class
of quantum-dot systems formed in semiconductors with a degenerate valence band.
acknowledgement: The work was supported by the Agence Nationale de la Recherche (through
the ACCESS and COHESION projects), U.S. DOE Contract No. DE-FG02-08ER46482 (Yale),
and the Nanosciences Foundation at Grenoble, France. G. K. acknowledges support
from the Deutsche Forschungsgemeinschaft
author:
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Vitaly
full_name: Golovach, Vitaly N
last_name: Golovach
- first_name: Panayotis
full_name: Spathis, Panayotis N
last_name: Spathis
- first_name: Natalia
full_name: Ares, Natalia
last_name: Ares
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Frank
full_name: Fournel, Frank
last_name: Fournel
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
- first_name: Leonid
full_name: Glazman, Leonid I
last_name: Glazman
- first_name: Silvano
full_name: De Franceschi, Silvano
last_name: De Franceschi
citation:
ama: Katsaros G, Golovach V, Spathis P, et al. Observation of spin-selective tunneling
in sige nanocrystals. Physical Review Letters. 2011;107(24). doi:10.1103/PhysRevLett.107.246601
apa: Katsaros, G., Golovach, V., Spathis, P., Ares, N., Stoffel, M., Fournel, F.,
… De Franceschi, S. (2011). Observation of spin-selective tunneling in sige nanocrystals.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.107.246601
chicago: Katsaros, Georgios, Vitaly Golovach, Panayotis Spathis, Natalia Ares, Mathieu
Stoffel, Frank Fournel, Oliver Schmidt, Leonid Glazman, and Silvano De Franceschi.
“Observation of Spin-Selective Tunneling in Sige Nanocrystals.” Physical Review
Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.246601.
ieee: G. Katsaros et al., “Observation of spin-selective tunneling in sige
nanocrystals,” Physical Review Letters, vol. 107, no. 24. American Physical
Society, 2011.
ista: Katsaros G, Golovach V, Spathis P, Ares N, Stoffel M, Fournel F, Schmidt O,
Glazman L, De Franceschi S. 2011. Observation of spin-selective tunneling in sige
nanocrystals. Physical Review Letters. 107(24).
mla: Katsaros, Georgios, et al. “Observation of Spin-Selective Tunneling in Sige
Nanocrystals.” Physical Review Letters, vol. 107, no. 24, American Physical
Society, 2011, doi:10.1103/PhysRevLett.107.246601.
short: G. Katsaros, V. Golovach, P. Spathis, N. Ares, M. Stoffel, F. Fournel, O.
Schmidt, L. Glazman, S. De Franceschi, Physical Review Letters 107 (2011).
date_created: 2018-12-11T11:53:50Z
date_published: 2011-12-07T00:00:00Z
date_updated: 2021-01-12T06:53:00Z
day: '07'
doi: 10.1103/PhysRevLett.107.246601
extern: 1
intvolume: ' 107'
issue: '24'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1107.3919
month: '12'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5369'
quality_controlled: 0
status: public
title: Observation of spin-selective tunneling in sige nanocrystals
type: journal_article
volume: 107
year: '2011'
...
---
_id: '1776'
abstract:
- lang: eng
text: Superconducting circuits have been successfully established as systems to
prepare and investigate microwave light fields at the quantum level. In contrast
to optical experiments where light is detected using photon counters, microwaves
are usually measured with well developed linear amplifiers. This makes measurements
of correlation functions - one of the important tools in optics - harder to achieve
because they traditionally rely on photon counters and beam splitters. Here, we
demonstrate a system where we can prepare on demand single microwave photons in
a cavity and detect them at the two outputs of the cavity using linear amplifiers.
Together with efficient data processing, this allows us to measure different observables
of the cavity photons, including the first-order correlation function. Using these
techniques we demonstrate cooling of a thermal background field in the cavity.
acknowledgement: Australian National University,Aust. Res. Counc. Cent. Excellence
Quantum-Atom Opt.,Griffith University,Ian Potter Foundation,International Union
of Pure and Applied Physics
alternative_title:
- 'Journal of Physics: Conference Series'
author:
- first_name: Deniz
full_name: Bozyigit, Deniz
last_name: Bozyigit
- first_name: C
full_name: Lang, C
last_name: Lang
- first_name: L.
full_name: Steffen, L. Kraig
last_name: Steffen
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Christopher
full_name: Eichler, Christopher
last_name: Eichler
- first_name: Matthias
full_name: Baur, Matthias P
last_name: Baur
- first_name: R
full_name: Bianchetti, R
last_name: Bianchetti
- first_name: Peter
full_name: Leek, Peter J
last_name: Leek
- first_name: Stefan
full_name: Filipp, Stefan
last_name: Filipp
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
- first_name: Marcus
full_name: Da Silva, Marcus P
last_name: Da Silva
- first_name: Alexandre
full_name: Blais, Alexandre
last_name: Blais
citation:
ama: 'Bozyigit D, Lang C, Steffen L, et al. Correlation measurements of individual
microwave photons emitted from a symmetric cavity. In: Vol 264. IOP Publishing
Ltd.; 2011. doi:10.1088/1742-6596/264/1/012024'
apa: Bozyigit, D., Lang, C., Steffen, L., Fink, J. M., Eichler, C., Baur, M., …
Blais, A. (2011). Correlation measurements of individual microwave photons emitted
from a symmetric cavity (Vol. 264). Presented at the International Conference
on Atomic Physics, IOP Publishing Ltd. https://doi.org/10.1088/1742-6596/264/1/012024
chicago: Bozyigit, Deniz, C Lang, L. Steffen, Johannes M Fink, Christopher Eichler,
Matthias Baur, R Bianchetti, et al. “Correlation Measurements of Individual Microwave
Photons Emitted from a Symmetric Cavity,” Vol. 264. IOP Publishing Ltd., 2011.
https://doi.org/10.1088/1742-6596/264/1/012024.
ieee: D. Bozyigit et al., “Correlation measurements of individual microwave
photons emitted from a symmetric cavity,” presented at the International Conference
on Atomic Physics, 2011, vol. 264, no. 1.
ista: 'Bozyigit D, Lang C, Steffen L, Fink JM, Eichler C, Baur M, Bianchetti R,
Leek P, Filipp S, Wallraff A, Da Silva M, Blais A. 2011. Correlation measurements
of individual microwave photons emitted from a symmetric cavity. International
Conference on Atomic Physics, Journal of Physics: Conference Series, vol. 264.'
mla: Bozyigit, Deniz, et al. Correlation Measurements of Individual Microwave
Photons Emitted from a Symmetric Cavity. Vol. 264, no. 1, IOP Publishing Ltd.,
2011, doi:10.1088/1742-6596/264/1/012024.
short: D. Bozyigit, C. Lang, L. Steffen, J.M. Fink, C. Eichler, M. Baur, R. Bianchetti,
P. Leek, S. Filipp, A. Wallraff, M. Da Silva, A. Blais, in:, IOP Publishing Ltd.,
2011.
conference:
name: International Conference on Atomic Physics
date_created: 2018-12-11T11:53:57Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2019-04-26T07:22:05Z
day: '01'
doi: 10.1088/1742-6596/264/1/012024
extern: 1
intvolume: ' 264'
issue: '1'
month: '01'
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '5339'
quality_controlled: 0
status: public
title: Correlation measurements of individual microwave photons emitted from a symmetric
cavity
type: conference
volume: 264
year: '2011'
...
---
_id: '1777'
abstract:
- lang: eng
text: A wide range of experiments studying microwave photons localized in superconducting
cavities have made important contributions to our understanding of the quantum
properties of radiation. Propagating microwave photons, however, have so far been
studied much less intensely. Here we present measurements in which we reconstruct
the quantum state of itinerant single photon Fock states and their superposition
with the vacuum by analyzing moments of the measured amplitude distribution up
to fourth order. Using linear amplifiers and quadrature amplitude detectors, we
have developed efficient methods to separate the detected single photon signal
from the noise added by the amplifier. From our measurement data we have also
reconstructed the corresponding Wigner function.
acknowledgement: This work was supported by the European Research Council (ERC) through
a Starting Grant and by ETHZ
article_processing_charge: No
author:
- first_name: Christopher
full_name: Eichler, Christopher
last_name: Eichler
- first_name: Deniz
full_name: Bozyigit, Deniz
last_name: Bozyigit
- first_name: C
full_name: Lang, C
last_name: Lang
- first_name: L.
full_name: Steffen, L.
last_name: Steffen
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Eichler C, Bozyigit D, Lang C, Steffen L, Fink JM, Wallraff A. Experimental
state tomography of itinerant single microwave photons. Physical Review Letters.
2011;106(22). doi:10.1103/PhysRevLett.106.220503
apa: Eichler, C., Bozyigit, D., Lang, C., Steffen, L., Fink, J. M., & Wallraff,
A. (2011). Experimental state tomography of itinerant single microwave photons.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.106.220503
chicago: Eichler, Christopher, Deniz Bozyigit, C Lang, L. Steffen, Johannes M Fink,
and Andreas Wallraff. “Experimental State Tomography of Itinerant Single Microwave
Photons.” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.106.220503.
ieee: C. Eichler, D. Bozyigit, C. Lang, L. Steffen, J. M. Fink, and A. Wallraff,
“Experimental state tomography of itinerant single microwave photons,” Physical
Review Letters, vol. 106, no. 22. American Physical Society, 2011.
ista: Eichler C, Bozyigit D, Lang C, Steffen L, Fink JM, Wallraff A. 2011. Experimental
state tomography of itinerant single microwave photons. Physical Review Letters.
106(22).
mla: Eichler, Christopher, et al. “Experimental State Tomography of Itinerant Single
Microwave Photons.” Physical Review Letters, vol. 106, no. 22, American
Physical Society, 2011, doi:10.1103/PhysRevLett.106.220503.
short: C. Eichler, D. Bozyigit, C. Lang, L. Steffen, J.M. Fink, A. Wallraff, Physical
Review Letters 106 (2011).
date_created: 2018-12-11T11:53:57Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2021-11-16T07:57:13Z
day: '01'
doi: 10.1103/PhysRevLett.106.220503
extern: '1'
intvolume: ' 106'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1011.6668
month: '06'
oa: 1
oa_version: None
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5338'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1103/PhysRevLett.106.249901
status: public
title: Experimental state tomography of itinerant single microwave photons
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 106
year: '2011'
...
---
_id: '1778'
abstract:
- lang: eng
text: Creating a train of single photons and monitoring its propagation and interaction
is challenging in most physical systems, as photons generally interact very weakly
with other systems. However, when confining microwave frequency photons in a transmission
line resonator, effective photon-photon interactions can be mediated by qubits
embedded in the resonator. Here, we observe the phenomenon of photon blockade
through second-order correlation function measurements. The experiments clearly
demonstrate antibunching in a continuously pumped source of single microwave photons
measured by using microwave beam splitters, linear amplifiers, and quadrature
amplitude detectors. We also investigate resonance fluorescence and Rayleigh scattering
in Mollow-triplet-like spectra.
acknowledgement: This work was supported by the European Research Council (ERC) through
a Starting Grant and by ETHZ. M. P. d. S. was supported by NSERC. A. B. was supported
by NSERC, CIFAR, and the Alfred P. Sloan Foundation
author:
- first_name: C
full_name: Lang, C
last_name: Lang
- first_name: Deniz
full_name: Bozyigit, Deniz
last_name: Bozyigit
- first_name: Christopher
full_name: Eichler, Christopher
last_name: Eichler
- first_name: L.
full_name: Steffen, L. Kraig
last_name: Steffen
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Abdufarrukh
full_name: Abdumalikov, Abdufarrukh A
last_name: Abdumalikov
- first_name: Matthias
full_name: Baur, Matthias P
last_name: Baur
- first_name: Stefan
full_name: Filipp, Stefan
last_name: Filipp
- first_name: Marcus
full_name: Da Silva, Marcus P
last_name: Da Silva
- first_name: Alexandre
full_name: Blais, Alexandre
last_name: Blais
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Lang C, Bozyigit D, Eichler C, et al. Observation of resonant photon blockade
at microwave frequencies using correlation function measurements. Physical
Review Letters. 2011;106(24). doi:10.1103/PhysRevLett.106.243601
apa: Lang, C., Bozyigit, D., Eichler, C., Steffen, L., Fink, J. M., Abdumalikov,
A., … Wallraff, A. (2011). Observation of resonant photon blockade at microwave
frequencies using correlation function measurements. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.106.243601
chicago: Lang, C, Deniz Bozyigit, Christopher Eichler, L. Steffen, Johannes M Fink,
Abdufarrukh Abdumalikov, Matthias Baur, et al. “Observation of Resonant Photon
Blockade at Microwave Frequencies Using Correlation Function Measurements.” Physical
Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.106.243601.
ieee: C. Lang et al., “Observation of resonant photon blockade at microwave
frequencies using correlation function measurements,” Physical Review Letters,
vol. 106, no. 24. American Physical Society, 2011.
ista: Lang C, Bozyigit D, Eichler C, Steffen L, Fink JM, Abdumalikov A, Baur M,
Filipp S, Da Silva M, Blais A, Wallraff A. 2011. Observation of resonant photon
blockade at microwave frequencies using correlation function measurements. Physical
Review Letters. 106(24).
mla: Lang, C., et al. “Observation of Resonant Photon Blockade at Microwave Frequencies
Using Correlation Function Measurements.” Physical Review Letters, vol.
106, no. 24, American Physical Society, 2011, doi:10.1103/PhysRevLett.106.243601.
short: C. Lang, D. Bozyigit, C. Eichler, L. Steffen, J.M. Fink, A. Abdumalikov,
M. Baur, S. Filipp, M. Da Silva, A. Blais, A. Wallraff, Physical Review Letters
106 (2011).
date_created: 2018-12-11T11:53:57Z
date_published: 2011-06-15T00:00:00Z
date_updated: 2021-01-12T06:53:08Z
day: '15'
doi: 10.1103/PhysRevLett.106.243601
extern: 1
intvolume: ' 106'
issue: '24'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1102.0461
month: '06'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5336'
quality_controlled: 0
status: public
title: Observation of resonant photon blockade at microwave frequencies using correlation
function measurements
type: journal_article
volume: 106
year: '2011'
...
---
_id: '1775'
abstract:
- lang: eng
text: At optical frequencies the radiation produced by a source, such as a laser,
a black body or a single-photon emitter, is frequently characterized by analysing
the temporal correlations of emitted photons using single-photon counters. At
microwave frequencies, however, there are no efficient single-photon counters
yet. Instead, well-developed linear amplifiers allow for efficient measurement
of the amplitude of an electromagnetic field. Here, we demonstrate first- and
second-order correlation function measurements of a pulsed microwave-frequency
single-photon source integrated on the same chip with a 50/50 beam splitter followed
by linear amplifiers and quadrature amplitude detectors. We clearly observe single-photon
coherence in first-order and photon antibunching in second-order correlation function
measurements of the propagating fields.
acknowledgement: This work was supported by the European Research Council (ERC) through
a Starting Grant and by ETHZ. M.P.d.S. was supported by a NSERC postdoctoral fellowship.
A.B. was supported by NSERC, CIFAR and the Alfred P. Sloan Foundation
author:
- first_name: Deniz
full_name: Bozyigit, Deniz
last_name: Bozyigit
- first_name: C
full_name: Lang, C
last_name: Lang
- first_name: L.
full_name: Steffen, L. Kraig
last_name: Steffen
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Christopher
full_name: Eichler, Christopher
last_name: Eichler
- first_name: Matthias
full_name: Baur, Matthias P
last_name: Baur
- first_name: R
full_name: Bianchetti, R
last_name: Bianchetti
- first_name: Peter
full_name: Leek, Peter J
last_name: Leek
- first_name: Stefan
full_name: Filipp, Stefan
last_name: Filipp
- first_name: Marcus
full_name: Da Silva, Marcus P
last_name: Da Silva
- first_name: Alexandre
full_name: Blais, Alexandre
last_name: Blais
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Bozyigit D, Lang C, Steffen L, et al. Antibunching of microwave-frequency photons
observed in correlation measurements using linear detectors. Nature Physics.
2011;7(2):154-158. doi:10.1038/nphys1845
apa: Bozyigit, D., Lang, C., Steffen, L., Fink, J. M., Eichler, C., Baur, M., …
Wallraff, A. (2011). Antibunching of microwave-frequency photons observed in correlation
measurements using linear detectors. Nature Physics. Nature Publishing
Group. https://doi.org/10.1038/nphys1845
chicago: Bozyigit, Deniz, C Lang, L. Steffen, Johannes M Fink, Christopher Eichler,
Matthias Baur, R Bianchetti, et al. “Antibunching of Microwave-Frequency Photons
Observed in Correlation Measurements Using Linear Detectors.” Nature Physics.
Nature Publishing Group, 2011. https://doi.org/10.1038/nphys1845.
ieee: D. Bozyigit et al., “Antibunching of microwave-frequency photons observed
in correlation measurements using linear detectors,” Nature Physics, vol.
7, no. 2. Nature Publishing Group, pp. 154–158, 2011.
ista: Bozyigit D, Lang C, Steffen L, Fink JM, Eichler C, Baur M, Bianchetti R, Leek
P, Filipp S, Da Silva M, Blais A, Wallraff A. 2011. Antibunching of microwave-frequency
photons observed in correlation measurements using linear detectors. Nature Physics.
7(2), 154–158.
mla: Bozyigit, Deniz, et al. “Antibunching of Microwave-Frequency Photons Observed
in Correlation Measurements Using Linear Detectors.” Nature Physics, vol.
7, no. 2, Nature Publishing Group, 2011, pp. 154–58, doi:10.1038/nphys1845.
short: D. Bozyigit, C. Lang, L. Steffen, J.M. Fink, C. Eichler, M. Baur, R. Bianchetti,
P. Leek, S. Filipp, M. Da Silva, A. Blais, A. Wallraff, Nature Physics 7 (2011)
154–158.
date_created: 2018-12-11T11:53:57Z
date_published: 2011-02-01T00:00:00Z
date_updated: 2021-01-12T06:53:07Z
day: '01'
doi: 10.1038/nphys1845
extern: 1
intvolume: ' 7'
issue: '2'
month: '02'
page: 154 - 158
publication: Nature Physics
publication_status: published
publisher: Nature Publishing Group
publist_id: '5340'
quality_controlled: 0
status: public
title: Antibunching of microwave-frequency photons observed in correlation measurements
using linear detectors
type: journal_article
volume: 7
year: '2011'
...
---
_id: '1781'
abstract:
- lang: eng
text: Microwave cavities with high quality factors enable coherent coupling of distant
quantum systems. Virtual photons lead to a transverse interaction between qubits
when they are nonresonant with the cavity but resonant with each other. We experimentally
investigate the inverse scaling of the interqubit coupling with the detuning from
a cavity mode and its proportionality to the qubit-cavity interaction strength.
We demonstrate that the enhanced coupling at higher frequencies is mediated by
multiple higher-harmonic cavity modes. Moreover, we observe dark states of the
coupled qubit-qubit system and analyze their relation to the symmetry of the applied
driving field at different frequencies.
acknowledgement: This work was supported by the Swiss National Science Foundation
(SNF), the Austrian Science Foundation (FWF), and ETH Zurich
author:
- first_name: Stefan
full_name: Filipp, Stefan
last_name: Filipp
- first_name: M
full_name: Göppl, M
last_name: Göppl
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Matthias
full_name: Baur, Matthias P
last_name: Baur
- first_name: R
full_name: Bianchetti, R
last_name: Bianchetti
- first_name: L.
full_name: Steffen, L. Kraig
last_name: Steffen
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Filipp S, Göppl M, Fink JM, et al. Multimode mediated qubit-qubit coupling
and dark-state symmetries in circuit quantum electrodynamics. Physical Review
A - Atomic, Molecular, and Optical Physics. 2011;83(6). doi:10.1103/PhysRevA.83.063827
apa: Filipp, S., Göppl, M., Fink, J. M., Baur, M., Bianchetti, R., Steffen, L.,
& Wallraff, A. (2011). Multimode mediated qubit-qubit coupling and dark-state
symmetries in circuit quantum electrodynamics. Physical Review A - Atomic,
Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.83.063827
chicago: Filipp, Stefan, M Göppl, Johannes M Fink, Matthias Baur, R Bianchetti,
L. Steffen, and Andreas Wallraff. “Multimode Mediated Qubit-Qubit Coupling and
Dark-State Symmetries in Circuit Quantum Electrodynamics.” Physical Review
A - Atomic, Molecular, and Optical Physics. American Physical Society, 2011.
https://doi.org/10.1103/PhysRevA.83.063827.
ieee: S. Filipp et al., “Multimode mediated qubit-qubit coupling and dark-state
symmetries in circuit quantum electrodynamics,” Physical Review A - Atomic,
Molecular, and Optical Physics, vol. 83, no. 6. American Physical Society,
2011.
ista: Filipp S, Göppl M, Fink JM, Baur M, Bianchetti R, Steffen L, Wallraff A. 2011.
Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum
electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. 83(6).
mla: Filipp, Stefan, et al. “Multimode Mediated Qubit-Qubit Coupling and Dark-State
Symmetries in Circuit Quantum Electrodynamics.” Physical Review A - Atomic,
Molecular, and Optical Physics, vol. 83, no. 6, American Physical Society,
2011, doi:10.1103/PhysRevA.83.063827.
short: S. Filipp, M. Göppl, J.M. Fink, M. Baur, R. Bianchetti, L. Steffen, A. Wallraff,
Physical Review A - Atomic, Molecular, and Optical Physics 83 (2011).
date_created: 2018-12-11T11:53:58Z
date_published: 2011-06-22T00:00:00Z
date_updated: 2021-01-12T06:53:09Z
day: '22'
doi: 10.1103/PhysRevA.83.063827
extern: 1
intvolume: ' 83'
issue: '6'
month: '06'
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '5335'
quality_controlled: 0
status: public
title: Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit
quantum electrodynamics
type: journal_article
volume: 83
year: '2011'
...
---
_id: '1780'
abstract:
- lang: eng
text: Continuous variable entanglement between two modes of a radiation field is
usually studied at optical frequencies. Here we demonstrate experiments that show
the entanglement between microwave photons of different energy in a broadband
squeezed beam. We use a Josephson parametric amplifier to generate the two-mode
correlated state and detect all four quadrature components simultaneously in a
two-channel heterodyne setup using amplitude detectors. Analyzing two-dimensional
phase space histograms for all possible pairs of quadratures allows us to determine
the full covariance matrix, which is in good agreement with the one expected for
a two-mode squeezed state.
acknowledgement: This work was supported by the European Research Council (ERC) through
a Starting grant and by ETHZ. S. F. acknowledges the Austrian Science Foundation
(FWF) for support
author:
- first_name: Christopher
full_name: Eichler, Christopher
last_name: Eichler
- first_name: Deniz
full_name: Bozyigit, Deniz
last_name: Bozyigit
- first_name: C
full_name: Lang, C
last_name: Lang
- first_name: Matthias
full_name: Baur, Matthias P
last_name: Baur
- first_name: L.
full_name: Steffen, L. Kraig
last_name: Steffen
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Stefan
full_name: Filipp, Stefan
last_name: Filipp
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Eichler C, Bozyigit D, Lang C, et al. Observation of two-mode squeezing in
the microwave frequency domain. Physical Review Letters. 2011;107(11).
doi:10.1103/PhysRevLett.107.113601
apa: Eichler, C., Bozyigit, D., Lang, C., Baur, M., Steffen, L., Fink, J. M., …
Wallraff, A. (2011). Observation of two-mode squeezing in the microwave frequency
domain. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.107.113601
chicago: Eichler, Christopher, Deniz Bozyigit, C Lang, Matthias Baur, L. Steffen,
Johannes M Fink, Stefan Filipp, and Andreas Wallraff. “Observation of Two-Mode
Squeezing in the Microwave Frequency Domain.” Physical Review Letters.
American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.113601.
ieee: C. Eichler et al., “Observation of two-mode squeezing in the microwave
frequency domain,” Physical Review Letters, vol. 107, no. 11. American
Physical Society, 2011.
ista: Eichler C, Bozyigit D, Lang C, Baur M, Steffen L, Fink JM, Filipp S, Wallraff
A. 2011. Observation of two-mode squeezing in the microwave frequency domain.
Physical Review Letters. 107(11).
mla: Eichler, Christopher, et al. “Observation of Two-Mode Squeezing in the Microwave
Frequency Domain.” Physical Review Letters, vol. 107, no. 11, American
Physical Society, 2011, doi:10.1103/PhysRevLett.107.113601.
short: C. Eichler, D. Bozyigit, C. Lang, M. Baur, L. Steffen, J.M. Fink, S. Filipp,
A. Wallraff, Physical Review Letters 107 (2011).
date_created: 2018-12-11T11:53:58Z
date_published: 2011-09-06T00:00:00Z
date_updated: 2021-01-12T06:53:09Z
day: '06'
doi: 10.1103/PhysRevLett.107.113601
extern: 1
intvolume: ' 107'
issue: '11'
month: '09'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5334'
quality_controlled: 0
status: public
title: Observation of two-mode squeezing in the microwave frequency domain
type: journal_article
volume: 107
year: '2011'
...
---
_id: '1815'
abstract:
- lang: eng
text: Many membrane channels and receptors exhibit adaptive, or desensitized, response
to a strong sustained input stimulus, often supported by protein activity-dependent
inactivation. Adaptive response is thought to be related to various cellular functions
such as homeostasis and enlargement of dynamic range by background compensation.
Here we study the quantitative relation between adaptive response and background
compensation within a modeling framework. We show that any particular type of
adaptive response is neither sufficient nor necessary for adaptive enlargement
of dynamic range. In particular a precise adaptive response, where system activity
is maintained at a constant level at steady state, does not ensure a large dynamic
range neither in input signal nor in system output. A general mechanism for input
dynamic range enlargement can come about from the activity-dependent modulation
of protein responsiveness by multiple biochemical modification, regardless of
the type of adaptive response it induces. Therefore hierarchical biochemical processes
such as methylation and phosphorylation are natural candidates to induce this
property in signaling systems.
author:
- first_name: Tamar
full_name: Tamar Friedlander
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Naama
full_name: Brenner, Naama
last_name: Brenner
citation:
ama: Friedlander T, Brenner N. Adaptive response and enlargement of dynamic range.
Mathematical Biosciences and Engineering. 2011;8(2):515-526. doi:10.3934/mbe.2011.8.515
apa: Friedlander, T., & Brenner, N. (2011). Adaptive response and enlargement
of dynamic range. Mathematical Biosciences and Engineering. Arizona State
University. https://doi.org/10.3934/mbe.2011.8.515
chicago: Friedlander, Tamar, and Naama Brenner. “Adaptive Response and Enlargement
of Dynamic Range.” Mathematical Biosciences and Engineering. Arizona State
University, 2011. https://doi.org/10.3934/mbe.2011.8.515.
ieee: T. Friedlander and N. Brenner, “Adaptive response and enlargement of dynamic
range,” Mathematical Biosciences and Engineering, vol. 8, no. 2. Arizona
State University, pp. 515–526, 2011.
ista: Friedlander T, Brenner N. 2011. Adaptive response and enlargement of dynamic
range. Mathematical Biosciences and Engineering. 8(2), 515–526.
mla: Friedlander, Tamar, and Naama Brenner. “Adaptive Response and Enlargement of
Dynamic Range.” Mathematical Biosciences and Engineering, vol. 8, no. 2,
Arizona State University, 2011, pp. 515–26, doi:10.3934/mbe.2011.8.515.
short: T. Friedlander, N. Brenner, Mathematical Biosciences and Engineering 8 (2011)
515–526.
date_created: 2018-12-11T11:54:10Z
date_published: 2011-04-02T00:00:00Z
date_updated: 2021-01-12T06:53:23Z
day: '02'
doi: 10.3934/mbe.2011.8.515
extern: 1
intvolume: ' 8'
issue: '2'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1003.2791
month: '04'
oa: 1
page: 515 - 526
publication: Mathematical Biosciences and Engineering
publication_status: published
publisher: Arizona State University
publist_id: '5291'
quality_controlled: 0
status: public
title: Adaptive response and enlargement of dynamic range
type: journal_article
volume: 8
year: '2011'
...
---
_id: '1863'
abstract:
- lang: eng
text: The Levene model is the simplest mathematical model to describe the evolution
of gene frequencies in spatially subdivided populations. It provides insight into
how locally varying selection promotes a population’s genetic diversity. Despite
its simplicity, interesting problems have remained unsolved even in the diallelic
case. In this paper we answer an open problem by establishing that for two alleles
at one locus and J demes, up to 2J−1 polymorphic equilibria may coexist. We first
present a proof for the case of stable monomorphisms and then show that the result
also holds for protected alleles. These findings allow us to prove that any odd
number (up to 2J−1) of equilibria is possible, before we extend the proof to even
numbers. We conclude with some numerical results and show that for J>2, the
proportion of parameter space affording this maximum is extremely small.
acknowledgement: FWF 21305
author:
- first_name: Sebastian
full_name: Sebastian Novak
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
citation:
ama: Novak S. The number of equilibria in the diallelic Levene model with multiple
demes. Theoretical Population Biology. 2011;79(3):97-101. doi:10.1016/j.tpb.2010.12.002
apa: Novak, S. (2011). The number of equilibria in the diallelic Levene model with
multiple demes. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2010.12.002
chicago: Novak, Sebastian. “The Number of Equilibria in the Diallelic Levene Model
with Multiple Demes.” Theoretical Population Biology. Academic Press, 2011.
https://doi.org/10.1016/j.tpb.2010.12.002.
ieee: S. Novak, “The number of equilibria in the diallelic Levene model with multiple
demes,” Theoretical Population Biology, vol. 79, no. 3. Academic Press,
pp. 97–101, 2011.
ista: Novak S. 2011. The number of equilibria in the diallelic Levene model with
multiple demes. Theoretical Population Biology. 79(3), 97–101.
mla: Novak, Sebastian. “The Number of Equilibria in the Diallelic Levene Model with
Multiple Demes.” Theoretical Population Biology, vol. 79, no. 3, Academic
Press, 2011, pp. 97–101, doi:10.1016/j.tpb.2010.12.002.
short: S. Novak, Theoretical Population Biology 79 (2011) 97–101.
date_created: 2018-12-11T11:54:25Z
date_published: 2011-05-01T00:00:00Z
date_updated: 2021-01-12T06:53:42Z
day: '01'
doi: 10.1016/j.tpb.2010.12.002
extern: 1
intvolume: ' 79'
issue: '3'
month: '05'
page: 97 - 101
publication: Theoretical Population Biology
publication_status: published
publisher: Academic Press
publist_id: '5236'
quality_controlled: 0
status: public
title: The number of equilibria in the diallelic Levene model with multiple demes
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
volume: 79
year: '2011'
...
---
_id: '1975'
abstract:
- lang: eng
text: 'Modern α-proteobacteria are thought to be closely related to the ancient
symbiont of eukaryotes, an ancestor of mitochondria. Respiratory complex I from
α-proteobacteria and mitochondria is well conserved at the level of the 14 "core"
subunits, consistent with that notion. Mitochondrial complex I contains the core
subunits, present in all species, and up to 31 "supernumerary" subunits,
generally thought to have originated only within eukaryotic lineages. However,
the full protein composition of an α-proteobacterial complex I has not been established
previously. Here, we report the first purification and characterization of complex
I from the α-proteobacterium Paracoccus denitrificans. Single particle electron
microscopy shows that the complex has a well defined L-shape. Unexpectedly, in
addition to the 14 core subunits, the enzyme also contains homologues of three
supernumerary mitochondrial subunits as follows: B17.2, AQDQ/18, and 13 kDa (bovine
nomenclature). This finding suggests that evolution of complex I via addition
of supernumerary or "accessory" subunits started before the original
endosymbiotic event that led to the creation of the eukaryotic cell. It also provides
further confirmation that α-proteobacteria are the closest extant relatives of
mitochondria.'
acknowledgement: 'This work was supported by the Medical Research Council. '
author:
- first_name: Chui
full_name: Yip, Chui Y
last_name: Yip
- first_name: Michael
full_name: Harbour, Michael E
last_name: Harbour
- first_name: Kamburapola
full_name: Jayawardena, Kamburapola G
last_name: Jayawardena
- first_name: Ian
full_name: Fearnley, Ian M
last_name: Fearnley
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Yip C, Harbour M, Jayawardena K, Fearnley I, Sazanov LA. Evolution of respiratory
complex I "Supernumerary" subunits are present in the α-proteobacterial
enzyme. Journal of Biological Chemistry. 2011;286(7):5023-5033. doi:10.1074/jbc.M110.194993
apa: Yip, C., Harbour, M., Jayawardena, K., Fearnley, I., & Sazanov, L. A. (2011).
Evolution of respiratory complex I "Supernumerary" subunits
are present in the α-proteobacterial enzyme. Journal of Biological Chemistry.
American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M110.194993
chicago: Yip, Chui, Michael Harbour, Kamburapola Jayawardena, Ian Fearnley, and
Leonid A Sazanov. “Evolution of Respiratory Complex I "Supernumerary"
Subunits Are Present in the α-Proteobacterial Enzyme.” Journal of Biological
Chemistry. American Society for Biochemistry and Molecular Biology, 2011.
https://doi.org/10.1074/jbc.M110.194993.
ieee: C. Yip, M. Harbour, K. Jayawardena, I. Fearnley, and L. A. Sazanov, “Evolution
of respiratory complex I "Supernumerary" subunits are present
in the α-proteobacterial enzyme,” Journal of Biological Chemistry, vol.
286, no. 7. American Society for Biochemistry and Molecular Biology, pp. 5023–5033,
2011.
ista: Yip C, Harbour M, Jayawardena K, Fearnley I, Sazanov LA. 2011. Evolution of
respiratory complex I "Supernumerary" subunits are present in
the α-proteobacterial enzyme. Journal of Biological Chemistry. 286(7), 5023–5033.
mla: Yip, Chui, et al. “Evolution of Respiratory Complex I "Supernumerary"
Subunits Are Present in the α-Proteobacterial Enzyme.” Journal of Biological
Chemistry, vol. 286, no. 7, American Society for Biochemistry and Molecular
Biology, 2011, pp. 5023–33, doi:10.1074/jbc.M110.194993.
short: C. Yip, M. Harbour, K. Jayawardena, I. Fearnley, L.A. Sazanov, Journal of
Biological Chemistry 286 (2011) 5023–5033.
date_created: 2018-12-11T11:55:00Z
date_published: 2011-02-18T00:00:00Z
date_updated: 2021-01-12T06:54:27Z
day: '18'
doi: 10.1074/jbc.M110.194993
extern: 1
intvolume: ' 286'
issue: '7'
month: '02'
page: 5023 - 5033
publication: Journal of Biological Chemistry
publication_status: published
publisher: American Society for Biochemistry and Molecular Biology
publist_id: '5112'
quality_controlled: 0
status: public
title: Evolution of respiratory complex I "Supernumerary" subunits are present
in the α-proteobacterial enzyme
type: journal_article
volume: 286
year: '2011'
...
---
_id: '1973'
abstract:
- lang: eng
text: Complex I is the first and largest enzyme of the respiratory chain, coupling
electron transfer between NADH and ubiquinone to the translocation of four protons
across the membrane. It has a central role in cellular energy production and has
been implicated in many human neurodegenerative diseases. The L-shaped enzyme
consists of hydrophilic and membrane domains. Previously, we determined the structure
of the hydrophilic domain. Here we report the crystal structure of the Esherichia
coli complex I membrane domain at 3.0 Ã. resolution. It includes six subunits,
NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold
of the homologous antiporter-like subunits L, M and N is novel, with two inverted
structural repeats of five transmembrane helices arranged, unusually, face-to-back.
Each repeat includes a discontinuous transmembrane helix and forms half of a channel
across the membrane. A network of conserved polar residues connects the two half-channels,
completing the proton translocation pathway. Unexpectedly, lysines rather than
carboxylate residues act as the main elements of the proton pump in these subunits.
The fourth probable proton-translocation channel is at the interface of subunits
N, K, J and A. The structure indicates that proton translocation in complex I,
uniquely, involves coordinated conformational changes in six symmetrical structural
elements.
acknowledgement: This work was funded by the Medical Research Council.
author:
- first_name: Rouslan
full_name: Efremov, Rouslan G
last_name: Efremov
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Efremov R, Sazanov LA. Structure of the membrane domain of respiratory complex
i. Nature. 2011;476(7361):414-421. doi:10.1038/nature10330
apa: Efremov, R., & Sazanov, L. A. (2011). Structure of the membrane domain
of respiratory complex i. Nature. Nature Publishing Group. https://doi.org/10.1038/nature10330
chicago: Efremov, Rouslan, and Leonid A Sazanov. “Structure of the Membrane Domain
of Respiratory Complex I.” Nature. Nature Publishing Group, 2011. https://doi.org/10.1038/nature10330.
ieee: R. Efremov and L. A. Sazanov, “Structure of the membrane domain of respiratory
complex i,” Nature, vol. 476, no. 7361. Nature Publishing Group, pp. 414–421,
2011.
ista: Efremov R, Sazanov LA. 2011. Structure of the membrane domain of respiratory
complex i. Nature. 476(7361), 414–421.
mla: Efremov, Rouslan, and Leonid A. Sazanov. “Structure of the Membrane Domain
of Respiratory Complex I.” Nature, vol. 476, no. 7361, Nature Publishing
Group, 2011, pp. 414–21, doi:10.1038/nature10330.
short: R. Efremov, L.A. Sazanov, Nature 476 (2011) 414–421.
date_created: 2018-12-11T11:54:59Z
date_published: 2011-08-25T00:00:00Z
date_updated: 2021-01-12T06:54:26Z
day: '25'
doi: 10.1038/nature10330
extern: 1
intvolume: ' 476'
issue: '7361'
month: '08'
page: 414 - 421
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '5110'
quality_controlled: 0
status: public
title: Structure of the membrane domain of respiratory complex i
type: journal_article
volume: 476
year: '2011'
...
---
_id: '1974'
abstract:
- lang: eng
text: Complex I is the first enzyme of the respiratory chain and plays a central
role in cellular energy production. It has been implicated in many human neurodegenerative
diseases, as well as in ageing. One of the biggest membrane protein complexes,
it is an L-shaped assembly consisting of hydrophilic and membrane domains. Previously,
we have determined structures of the hydrophilic domain in several redox states.
Last year was marked by fascinating breakthroughs in the understanding of the
complete structure. We described the architecture of the membrane domain and of
the entire bacterial complex I. X-ray analysis of the larger mitochondrial enzyme
has also been published. The core subunits of the bacterial and mitochondrial
enzymes have remarkably similar structures. The proposed mechanism of coupling
between electron transfer and proton translocation involves long-range conformational
changes, coordinated in part by a long α-helix, akin to the coupling rod of a
steam engine.
acknowledgement: The work in authors’ laboratory was funded by the Medical Research
Council.
author:
- first_name: Rouslan
full_name: Efremov, Rouslan G
last_name: Efremov
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: 'Efremov R, Sazanov LA. Respiratory complex I: “steam engine” of the cell?
Current Opinion in Structural Biology. 2011;21(4):532-540. doi:10.1016/j.sbi.2011.07.002'
apa: 'Efremov, R., & Sazanov, L. A. (2011). Respiratory complex I: “steam engine”
of the cell? Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2011.07.002'
chicago: 'Efremov, Rouslan, and Leonid A Sazanov. “Respiratory Complex I: ‘steam
Engine’ of the Cell?” Current Opinion in Structural Biology. Elsevier,
2011. https://doi.org/10.1016/j.sbi.2011.07.002.'
ieee: 'R. Efremov and L. A. Sazanov, “Respiratory complex I: ‘steam engine’ of the
cell?,” Current Opinion in Structural Biology, vol. 21, no. 4. Elsevier,
pp. 532–540, 2011.'
ista: 'Efremov R, Sazanov LA. 2011. Respiratory complex I: ‘steam engine’ of the
cell? Current Opinion in Structural Biology. 21(4), 532–540.'
mla: 'Efremov, Rouslan, and Leonid A. Sazanov. “Respiratory Complex I: ‘steam Engine’
of the Cell?” Current Opinion in Structural Biology, vol. 21, no. 4, Elsevier,
2011, pp. 532–40, doi:10.1016/j.sbi.2011.07.002.'
short: R. Efremov, L.A. Sazanov, Current Opinion in Structural Biology 21 (2011)
532–540.
date_created: 2018-12-11T11:54:59Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2021-01-12T06:54:27Z
day: '01'
doi: 10.1016/j.sbi.2011.07.002
extern: 1
intvolume: ' 21'
issue: '4'
month: '08'
page: 532 - 540
publication: Current Opinion in Structural Biology
publication_status: published
publisher: Elsevier
publist_id: '5111'
quality_controlled: 0
status: public
title: 'Respiratory complex I: ''steam engine'' of the cell?'
type: journal_article
volume: 21
year: '2011'
...
---
_id: '1985'
abstract:
- lang: eng
text: |2-
In Escherichia coli, the pole-to-pole oscillation of the Min proteins directs septum formation to midcell, which is required for symmetric cell division. In vitro, protein waves emerge from the self-organization of MinD, a membrane-binding ATPase, and its activator MinE. For wave propagation, the proteins need to cycle through states of collective membrane binding and unbinding. Although MinD presumably undergoes cooperative membrane attachment, it is unclear how synchronous detachment is coordinated. We used confocal and single-molecule microscopy to elucidate the order of events during Min wave propagation. We propose that protein detachment at the rear of the wave, and the formation of the E-ring, are accomplished by two complementary processes: first, local accumulation of MinE due to rapid rebinding, leading to dynamic instability; and second, a structural change induced by membrane-interaction of MinE in an equimolar MinD-MinE (MinDE) complex, which supports the robustness of pattern formation.
acknowledgement: This work was also supported by the Max Planck Society (M.L., E.F.-F.,
P.S.).
author:
- first_name: Martin
full_name: Martin Loose
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Elisabeth
full_name: Fischer-Friedrich, Elisabeth
last_name: Fischer Friedrich
- first_name: Christoph
full_name: Herold, Christoph
last_name: Herold
- first_name: Karsten
full_name: Kruse, Karsten
last_name: Kruse
- first_name: Petra
full_name: 'Schwille, Petra '
last_name: Schwille
citation:
ama: Loose M, Fischer Friedrich E, Herold C, Kruse K, Schwille P. Min protein patterns
emerge from rapid rebinding and membrane interaction of MinE. Nature Structural
and Molecular Biology. 2011;18(5):577-583. doi:10.1038/nsmb.2037
apa: Loose, M., Fischer Friedrich, E., Herold, C., Kruse, K., & Schwille, P.
(2011). Min protein patterns emerge from rapid rebinding and membrane interaction
of MinE. Nature Structural and Molecular Biology. Nature Publishing Group.
https://doi.org/10.1038/nsmb.2037
chicago: Loose, Martin, Elisabeth Fischer Friedrich, Christoph Herold, Karsten Kruse,
and Petra Schwille. “Min Protein Patterns Emerge from Rapid Rebinding and Membrane
Interaction of MinE.” Nature Structural and Molecular Biology. Nature Publishing
Group, 2011. https://doi.org/10.1038/nsmb.2037.
ieee: M. Loose, E. Fischer Friedrich, C. Herold, K. Kruse, and P. Schwille, “Min
protein patterns emerge from rapid rebinding and membrane interaction of MinE,”
Nature Structural and Molecular Biology, vol. 18, no. 5. Nature Publishing
Group, pp. 577–583, 2011.
ista: Loose M, Fischer Friedrich E, Herold C, Kruse K, Schwille P. 2011. Min protein
patterns emerge from rapid rebinding and membrane interaction of MinE. Nature
Structural and Molecular Biology. 18(5), 577–583.
mla: Loose, Martin, et al. “Min Protein Patterns Emerge from Rapid Rebinding and
Membrane Interaction of MinE.” Nature Structural and Molecular Biology,
vol. 18, no. 5, Nature Publishing Group, 2011, pp. 577–83, doi:10.1038/nsmb.2037.
short: M. Loose, E. Fischer Friedrich, C. Herold, K. Kruse, P. Schwille, Nature
Structural and Molecular Biology 18 (2011) 577–583.
date_created: 2018-12-11T11:55:03Z
date_published: 2011-05-01T00:00:00Z
date_updated: 2021-01-12T06:54:31Z
day: '01'
doi: 10.1038/nsmb.2037
extern: 1
intvolume: ' 18'
issue: '5'
month: '05'
page: 577 - 583
publication: Nature Structural and Molecular Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '5098'
quality_controlled: 0
status: public
title: Min protein patterns emerge from rapid rebinding and membrane interaction of
MinE
type: journal_article
volume: 18
year: '2011'
...
---
_id: '1986'
abstract:
- lang: eng
text: One of the most fundamental features of biological systems is probably their
ability to self-organize in space and time on different scales. Despite many elaborate
theoretical models of how molecular self-organization can come about, only a few
experimental systems of biological origin have so far been rigorously described,
due mostly to their inherent complexity. The most promising strategy of modern
biophysics is thus to identify minimal biological systems showing self-organized
emergent behavior. One of the best-understood examples of protein self-organization,
which has recently been successfully reconstituted in vitro, is represented by
the oscillations of the Min proteins in Escherichia coli. In this review, we summarize
the current understanding of the mechanism of Min protein self-organization in
vivo and in vitro. We discuss the potential of the Min oscillations to sense the
geometry of the cell and suggest that spontaneous protein waves could be a general
means of intracellular organization. We hypothesize that cooperative membrane
binding and unbinding, e.g., as an energy-dependent switch, may act as an important
regulatory mechanism for protein oscillations and pattern formation in the cell.
author:
- first_name: Martin
full_name: Martin Loose
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Karsten
full_name: Kruse, Karsten
last_name: Kruse
- first_name: Petra
full_name: 'Schwille, Petra '
last_name: Schwille
citation:
ama: 'Loose M, Kruse K, Schwille P. Protein self-organization: Lessons from the
min system. Annual Review of Biophysics. 2011;40(1):315-336. doi:10.1146/annurev-biophys-042910-155332'
apa: 'Loose, M., Kruse, K., & Schwille, P. (2011). Protein self-organization:
Lessons from the min system. Annual Review of Biophysics. Annual Reviews.
https://doi.org/10.1146/annurev-biophys-042910-155332'
chicago: 'Loose, Martin, Karsten Kruse, and Petra Schwille. “Protein Self-Organization:
Lessons from the Min System.” Annual Review of Biophysics. Annual Reviews,
2011. https://doi.org/10.1146/annurev-biophys-042910-155332.'
ieee: 'M. Loose, K. Kruse, and P. Schwille, “Protein self-organization: Lessons
from the min system,” Annual Review of Biophysics, vol. 40, no. 1. Annual
Reviews, pp. 315–336, 2011.'
ista: 'Loose M, Kruse K, Schwille P. 2011. Protein self-organization: Lessons from
the min system. Annual Review of Biophysics. 40(1), 315–336.'
mla: 'Loose, Martin, et al. “Protein Self-Organization: Lessons from the Min System.”
Annual Review of Biophysics, vol. 40, no. 1, Annual Reviews, 2011, pp.
315–36, doi:10.1146/annurev-biophys-042910-155332.'
short: M. Loose, K. Kruse, P. Schwille, Annual Review of Biophysics 40 (2011) 315–336.
date_created: 2018-12-11T11:55:04Z
date_published: 2011-06-09T00:00:00Z
date_updated: 2021-01-12T06:54:31Z
day: '09'
doi: 10.1146/annurev-biophys-042910-155332
extern: 1
intvolume: ' 40'
issue: '1'
month: '06'
page: 315 - 336
publication: Annual Review of Biophysics
publication_status: published
publisher: Annual Reviews
publist_id: '5097'
quality_controlled: 0
status: public
title: 'Protein self-organization: Lessons from the min system'
type: journal_article
volume: 40
year: '2011'
...
---
_id: '2072'
abstract:
- lang: eng
text: Many species have morphologically and genetically differentiated sex chromosomes,
such as the XY pair of mammals. Y chromosomes are often highly degenerated and
carry few functional genes, so that XY males have only one copy of most Xlinked
genes (whereas females have two). As a result, chromosome-wide mechanisms of dosage
compensation, such as the mammalian X-inactivation, often evolve to reestablish
expression balance. A similar phenomenon is expected in femaleheterogametic species,
where ZW females should suffer from imbalances due to W-chromosome degeneration.
However, no global dosage compensation mechanisms have been detected in the two
independent ZW systems that have been studied systematically (birds and silkworm),
leading to the suggestion that lack of global dosage compensation may be a general
feature of female-heterogametic species. However, analyses of other independently
evolved ZW systems are required to test if this is the case. In this study, we
use published genomic and expression data to test for the presence of global dosage
compensation in Schistosoma mansoni, a trematode parasite that causes schistosomiasis
in humans. We find that Z-linked expression is reduced relative to autosomal expression
in females but not males, consistent with incomplete or localized dosage compensation.
This gives further support to the theory that female-heterogametic species may
not require global mechanisms of dosage compensation.
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Doris
full_name: Bachtrog, Doris
last_name: Bachtrog
citation:
ama: Vicoso B, Bachtrog D. Lack of global dosage compensation in Schistosoma mansoni,
a female-heterogametic parasite. Genome Biology and Evolution. 2011;3(1):230-235.
doi:10.1093/gbe/evr010
apa: Vicoso, B., & Bachtrog, D. (2011). Lack of global dosage compensation in
Schistosoma mansoni, a female-heterogametic parasite. Genome Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/gbe/evr010
chicago: Vicoso, Beatriz, and Doris Bachtrog. “Lack of Global Dosage Compensation
in Schistosoma Mansoni, a Female-Heterogametic Parasite.” Genome Biology and
Evolution. Oxford University Press, 2011. https://doi.org/10.1093/gbe/evr010.
ieee: B. Vicoso and D. Bachtrog, “Lack of global dosage compensation in Schistosoma
mansoni, a female-heterogametic parasite,” Genome Biology and Evolution,
vol. 3, no. 1. Oxford University Press, pp. 230–235, 2011.
ista: Vicoso B, Bachtrog D. 2011. Lack of global dosage compensation in Schistosoma
mansoni, a female-heterogametic parasite. Genome Biology and Evolution. 3(1),
230–235.
mla: Vicoso, Beatriz, and Doris Bachtrog. “Lack of Global Dosage Compensation in
Schistosoma Mansoni, a Female-Heterogametic Parasite.” Genome Biology and Evolution,
vol. 3, no. 1, Oxford University Press, 2011, pp. 230–35, doi:10.1093/gbe/evr010.
short: B. Vicoso, D. Bachtrog, Genome Biology and Evolution 3 (2011) 230–235.
date_created: 2018-12-11T11:55:33Z
date_published: 2011-02-11T00:00:00Z
date_updated: 2021-01-12T06:55:08Z
day: '11'
ddc:
- '570'
doi: 10.1093/gbe/evr010
extern: '1'
file:
- access_level: open_access
checksum: 7855c134436e4f6a13d63b6606d7e8dd
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T07:41:28Z
date_updated: 2020-07-14T12:45:27Z
file_id: '6395'
file_name: 2011_GBE_Vicoso.pdf
file_size: 212547
relation: main_file
file_date_updated: 2020-07-14T12:45:27Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 230 - 235
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '4966'
quality_controlled: '1'
status: public
title: Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic
parasite
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2011'
...
---
_id: '2099'
abstract:
- lang: eng
text: We present a new technique for passive and markerless facial performance capture
based on anchor frames. Our method starts with high resolution per-frame geometry
acquisition using state-of-theart stereo reconstruction, and proceeds to establish
a single triangle mesh that is propagated through the entire performance. Leveraging
the fact that facial performances often contain repetitive subsequences, we identify
anchor frames as those which contain similar facial expressions to a manually
chosen reference expression. Anchor frames are automatically computed over one
or even multiple performances. We introduce a robust image-space tracking method
that computes pixel matches directly from the reference frame to all anchor frames,
and thereby to the remaining frames in the sequence via sequential matching. This
allows us to propagate one reconstructed frame to an entire sequence in parallel,
in contrast to previous sequential methods. Our anchored reconstruction approach
also limits tracker drift and robustly handles occlusions and motion blur. The
parallel tracking and mesh propagation offer low computation times. Our technique
will even automatically match anchor frames across different sequences captured
on different occasions, propagating a single mesh to all performances.
author:
- first_name: Thabo
full_name: Beeler, Thabo
last_name: Beeler
- first_name: Fabian
full_name: Hahn, Fabian
last_name: Hahn
- first_name: Derek
full_name: Bradley, Derek J
last_name: Bradley
- first_name: Bernd
full_name: Bernd Bickel
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Paul
full_name: Beardsley, Paul A
last_name: Beardsley
- first_name: Craig
full_name: Gotsman, Craig
last_name: Gotsman
- first_name: Robert
full_name: Sumner, Robert W
last_name: Sumner
- first_name: Markus
full_name: Groß, Markus S
last_name: Groß
citation:
ama: Beeler T, Hahn F, Bradley D, et al. High-quality passive facial performance
capture using anchor frames. ACM Transactions on Graphics. 2011;30(4).
doi:10.1145/2010324.1964970
apa: Beeler, T., Hahn, F., Bradley, D., Bickel, B., Beardsley, P., Gotsman, C.,
… Groß, M. (2011). High-quality passive facial performance capture using anchor
frames. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2010324.1964970
chicago: Beeler, Thabo, Fabian Hahn, Derek Bradley, Bernd Bickel, Paul Beardsley,
Craig Gotsman, Robert Sumner, and Markus Groß. “High-Quality Passive Facial Performance
Capture Using Anchor Frames.” ACM Transactions on Graphics. ACM, 2011.
https://doi.org/10.1145/2010324.1964970.
ieee: T. Beeler et al., “High-quality passive facial performance capture
using anchor frames,” ACM Transactions on Graphics, vol. 30, no. 4. ACM,
2011.
ista: Beeler T, Hahn F, Bradley D, Bickel B, Beardsley P, Gotsman C, Sumner R, Groß
M. 2011. High-quality passive facial performance capture using anchor frames.
ACM Transactions on Graphics. 30(4).
mla: Beeler, Thabo, et al. “High-Quality Passive Facial Performance Capture Using
Anchor Frames.” ACM Transactions on Graphics, vol. 30, no. 4, ACM, 2011,
doi:10.1145/2010324.1964970.
short: T. Beeler, F. Hahn, D. Bradley, B. Bickel, P. Beardsley, C. Gotsman, R. Sumner,
M. Groß, ACM Transactions on Graphics 30 (2011).
date_created: 2018-12-11T11:55:42Z
date_published: 2011-07-01T00:00:00Z
date_updated: 2021-01-12T06:55:17Z
day: '01'
doi: 10.1145/2010324.1964970
extern: 1
intvolume: ' 30'
issue: '4'
month: '07'
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '4936'
quality_controlled: 0
status: public
title: High-quality passive facial performance capture using anchor frames
type: journal_article
volume: 30
year: '2011'
...
---
_id: '2098'
abstract:
- lang: eng
text: This chapter presents a method for real-time animation of highly detailed
facial expressions based on sparse motion captures data and a limited set of static
example poses. The method for real-time animation of highly detailed facial expressions
decomposes geometry into large-scale motion and fine-scale details, such as expression
wrinkles. Both large- and fine-scale deformation algorithms run entirely on the
GPU, and our implementation based on CUDA achieves an overall performance of about
30 fps. The face conveys the most relevant visual characteristics of human identity
and expression. Hence, realistic facial animations or interactions with virtual
avatars are important for storytelling and gameplay. However, current approaches
are either computationally expensive, require very specialized capture hardware,
or are extremely labor intensive. At runtime, given an arbitrary facial expression,
the algorithm computes the skin strain from the relative distance between marker
points and derives fine-scale corrections for the largescale deformation. During
gameplay only the sparse set of marker-point positions is transmitted to the GPU.
The face animation is entirely computed on the GPU where the resulting mesh can
directly be used as input for the rendering stages. This data can be easily obtained
by traditional capture hardware. The proposed in-game algorithm is fast. It also
is easy to implement and maps well onto programmable GPUs.
author:
- first_name: Bernd
full_name: Bernd Bickel
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Manuel
full_name: Lang, Manuel
last_name: Lang
citation:
ama: 'Bickel B, Lang M. From sparse mocap to highly detailed facial animation. In:
GPU Computing Gems Emerald Edition. Science Direct; 2011:413-426. doi:10.1016/B978-0-12-384988-5.00027-9'
apa: Bickel, B., & Lang, M. (2011). From sparse mocap to highly detailed facial
animation. In GPU Computing Gems Emerald Edition (pp. 413–426). Science
Direct. https://doi.org/10.1016/B978-0-12-384988-5.00027-9
chicago: Bickel, Bernd, and Manuel Lang. “From Sparse Mocap to Highly Detailed Facial
Animation.” In GPU Computing Gems Emerald Edition, 413–26. Science Direct,
2011. https://doi.org/10.1016/B978-0-12-384988-5.00027-9.
ieee: B. Bickel and M. Lang, “From sparse mocap to highly detailed facial animation,”
in GPU Computing Gems Emerald Edition, Science Direct, 2011, pp. 413–426.
ista: 'Bickel B, Lang M. 2011.From sparse mocap to highly detailed facial animation.
In: GPU Computing Gems Emerald Edition. , 413–426.'
mla: Bickel, Bernd, and Manuel Lang. “From Sparse Mocap to Highly Detailed Facial
Animation.” GPU Computing Gems Emerald Edition, Science Direct, 2011, pp.
413–26, doi:10.1016/B978-0-12-384988-5.00027-9.
short: B. Bickel, M. Lang, in:, GPU Computing Gems Emerald Edition, Science Direct,
2011, pp. 413–426.
date_created: 2018-12-11T11:55:42Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T06:55:17Z
day: '01'
doi: 10.1016/B978-0-12-384988-5.00027-9
extern: 1
month: '01'
page: 413 - 426
publication: GPU Computing Gems Emerald Edition
publication_status: published
publisher: Science Direct
publist_id: '4935'
quality_controlled: 0
status: public
title: From sparse mocap to highly detailed facial animation
type: book_chapter
year: '2011'
...
---
_id: '2100'
abstract:
- lang: eng
text: Acquiring panoramic images using stitching takes a lot of time and moving
objects may cause ghosting. It is also difficult to obtain a full spherical panorama,
because the downward picture cannot be captured while the camera is mounted on
the tripod.
author:
- first_name: Jonas
full_name: Pfeil, Jonas
last_name: Pfeil
- first_name: Kristian
full_name: Hildebrand, Kristian
last_name: Hildebrand
- first_name: Carsten
full_name: Gremzow, Carsten
last_name: Gremzow
- first_name: Bernd
full_name: Bernd Bickel
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Marc
full_name: Alexa, Marc
last_name: Alexa
citation:
ama: 'Pfeil J, Hildebrand K, Gremzow C, Bickel B, Alexa M. Throwable panoramic ball
camera. In: ACM; 2011. doi:10.1145/2073370.2073373'
apa: Pfeil, J., Hildebrand, K., Gremzow, C., Bickel, B., & Alexa, M. (2011).
Throwable panoramic ball camera. Presented at the SIGGRAPH Asia, ACM. https://doi.org/10.1145/2073370.2073373
chicago: Pfeil, Jonas, Kristian Hildebrand, Carsten Gremzow, Bernd Bickel, and Marc
Alexa. “Throwable Panoramic Ball Camera.” ACM, 2011. https://doi.org/10.1145/2073370.2073373.
ieee: J. Pfeil, K. Hildebrand, C. Gremzow, B. Bickel, and M. Alexa, “Throwable panoramic
ball camera,” presented at the SIGGRAPH Asia, 2011.
ista: Pfeil J, Hildebrand K, Gremzow C, Bickel B, Alexa M. 2011. Throwable panoramic
ball camera. SIGGRAPH Asia.
mla: Pfeil, Jonas, et al. Throwable Panoramic Ball Camera. ACM, 2011, doi:10.1145/2073370.2073373.
short: J. Pfeil, K. Hildebrand, C. Gremzow, B. Bickel, M. Alexa, in:, ACM, 2011.
conference:
name: SIGGRAPH Asia
date_created: 2018-12-11T11:55:43Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2021-01-12T06:55:19Z
day: '01'
doi: 10.1145/2073370.2073373
extern: 1
month: '12'
publication_status: published
publisher: ACM
publist_id: '4934'
quality_controlled: 0
status: public
title: Throwable panoramic ball camera
type: conference
year: '2011'
...
---
_id: '2116'
abstract:
- lang: eng
text: Let P be the Ornstein-Uhlenbeck semigroup associated with the stochastic Cauchy
problem dU(t)=AU(t)dt+dWH(t), where A is the generator of a C 0-semigroup S on
a Banach space E, H is a Hilbert subspace of E, and W H is an H-cylindrical Brownian
motion. Assuming that S restricts to a C 0-semigroup on H, we obtain L p -bounds
for D H P(t). We show that if P is analytic, then the invariance assumption is
fulfilled. As an application we determine the L p -domain of the generator of
P explicitly in the case where S restricts to a C 0-semigroup on H which is similar
to an analytic contraction semigroup. The results are applied to the 1D stochastic
heat equation driven by additive space-time white noise.
acknowledgement: 'The authors are supported by VIDI subsidy 639.032.201 (JM) and VICI
subsidy 639.033.604 (JvN) of the Netherlands Organisation for Scientific Research
(NWO). '
author:
- first_name: Jan
full_name: Jan Maas
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Jan
full_name: Van Neerven, Jan
last_name: Van Neerven
citation:
ama: 'Maas J, Van Neerven J. Gradient estimates and domain identification for analytic
Ornstein-Uhlenbeck operators. In: Parabolic Problems. Vol 80. Birkhäuser;
2011:463-477. doi:10.1007/978-3-0348-0075-4_24'
apa: Maas, J., & Van Neerven, J. (2011). Gradient estimates and domain identification
for analytic Ornstein-Uhlenbeck operators. In Parabolic Problems (Vol.
80, pp. 463–477). Birkhäuser. https://doi.org/10.1007/978-3-0348-0075-4_24
chicago: Maas, Jan, and Jan Van Neerven. “Gradient Estimates and Domain Identification
for Analytic Ornstein-Uhlenbeck Operators.” In Parabolic Problems, 80:463–77.
Birkhäuser, 2011. https://doi.org/10.1007/978-3-0348-0075-4_24.
ieee: J. Maas and J. Van Neerven, “Gradient estimates and domain identification
for analytic Ornstein-Uhlenbeck operators,” in Parabolic Problems, vol.
80, Birkhäuser, 2011, pp. 463–477.
ista: 'Maas J, Van Neerven J. 2011.Gradient estimates and domain identification
for analytic Ornstein-Uhlenbeck operators. In: Parabolic Problems. vol. 80, 463–477.'
mla: Maas, Jan, and Jan Van Neerven. “Gradient Estimates and Domain Identification
for Analytic Ornstein-Uhlenbeck Operators.” Parabolic Problems, vol. 80,
Birkhäuser, 2011, pp. 463–77, doi:10.1007/978-3-0348-0075-4_24.
short: J. Maas, J. Van Neerven, in:, Parabolic Problems, Birkhäuser, 2011, pp. 463–477.
date_created: 2018-12-11T11:55:48Z
date_published: 2011-06-10T00:00:00Z
date_updated: 2021-01-12T06:55:24Z
day: '10'
doi: 10.1007/978-3-0348-0075-4_24
extern: 1
intvolume: ' 80'
main_file_link:
- open_access: '1'
url: 'http://arxiv.org/abs/0911.4336 '
month: '06'
oa: 1
page: 463 - 477
publication: Parabolic Problems
publication_status: published
publisher: Birkhäuser
publist_id: '4918'
quality_controlled: 0
status: public
title: Gradient estimates and domain identification for analytic Ornstein-Uhlenbeck
operators
type: book_chapter
volume: 80
year: '2011'
...
---
_id: '2122'
abstract:
- lang: eng
text: We study, in L1(R̃n; γ) with respect to the gaussian measure, non- tangential
maximal functions and conical square functions associ- ated with the Ornstein-Uhlenbeck
operator by developing a set of techniques which allow us, to some extent, to
compensate for the non-doubling character of the gaussian measure. The main result
asserts that conical square functions can be controlled in L1-norm by non-tangential
maximal functions. Along the way we prove a change of aperture result for the
latter. This complements recent results on gaussian Hardy spaces due to Mauceri
and Meda.
acknowledgement: The first named author is supported by Rubicon subsidy 680-50-0901
of the Netherlands Organisation for Scientific Research (NWO). The second named
author is supported by VICI subsidy 639.033.604 of the Netherlands Organisation
for Scientific Research (NWO
author:
- first_name: Jan
full_name: Jan Maas
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Jan
full_name: van Neerven, Jan M
last_name: Van Neerven
- first_name: Pierre
full_name: Portal, Pierre
last_name: Portal
citation:
ama: Maas J, Van Neerven J, Portal P. Conical square functions and non-tangential
maximal functions with respect to the Gaussian measure. Publicacions Matemàtiques.
2011;55(2):313-341. doi:10.5565/PUBLMAT_55211_03
apa: Maas, J., Van Neerven, J., & Portal, P. (2011). Conical square functions
and non-tangential maximal functions with respect to the Gaussian measure. Publicacions
Matemàtiques. Universitat Autònoma de Barcelona, Departament de Matemàtique.
https://doi.org/10.5565/PUBLMAT_55211_03
chicago: Maas, Jan, Jan Van Neerven, and Pierre Portal. “Conical Square Functions
and Non-Tangential Maximal Functions with Respect to the Gaussian Measure.” Publicacions
Matemàtiques. Universitat Autònoma de Barcelona, Departament de Matemàtique,
2011. https://doi.org/10.5565/PUBLMAT_55211_03
.
ieee: J. Maas, J. Van Neerven, and P. Portal, “Conical square functions and non-tangential
maximal functions with respect to the Gaussian measure,” Publicacions Matemàtiques,
vol. 55, no. 2. Universitat Autònoma de Barcelona, Departament de Matemàtique,
pp. 313–341, 2011.
ista: Maas J, Van Neerven J, Portal P. 2011. Conical square functions and non-tangential
maximal functions with respect to the Gaussian measure. Publicacions Matemàtiques.
55(2), 313–341.
mla: Maas, Jan, et al. “Conical Square Functions and Non-Tangential Maximal Functions
with Respect to the Gaussian Measure.” Publicacions Matemàtiques, vol.
55, no. 2, Universitat Autònoma de Barcelona, Departament de Matemàtique, 2011,
pp. 313–41, doi:10.5565/PUBLMAT_55211_03
.
short: J. Maas, J. Van Neerven, P. Portal, Publicacions Matemàtiques 55 (2011) 313–341.
date_created: 2018-12-11T11:55:50Z
date_published: 2011-07-01T00:00:00Z
date_updated: 2021-01-12T06:55:26Z
day: '01'
doi: "10.5565/PUBLMAT_55211_03\t "
extern: 1
intvolume: ' 55'
issue: '2'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1003.4092
month: '07'
oa: 1
page: 313 - 341
publication: Publicacions Matemàtiques
publication_status: published
publisher: Universitat Autònoma de Barcelona, Departament de Matemàtique
publist_id: '4910'
quality_controlled: 0
status: public
title: Conical square functions and non-tangential maximal functions with respect
to the Gaussian measure
type: journal_article
volume: 55
year: '2011'
...
---
_id: '2123'
abstract:
- lang: eng
text: We prove a Trotter product formula for gradient flows in metric spaces. This
result is applied to establish convergence in the L 2-Wasserstein metric of the
splitting method for some Fokker-Planck equations and porous medium type equations
perturbed by a potential.
acknowledgement: The second named author is supported by Rubicon subsidy 680-50-0901
of the Netherlands Organisation for Scientific Research (NWO).
article_processing_charge: No
author:
- first_name: Philippe
full_name: Clément, Philippe
last_name: Clément
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
citation:
ama: Clément P, Maas J. A Trotter product formula for gradient flows in metric spaces.
Journal of Evolution Equations. 2011;11(2):405-427. doi:10.1007/s00028-010-0096-5
apa: Clément, P., & Maas, J. (2011). A Trotter product formula for gradient
flows in metric spaces. Journal of Evolution Equations. Birkhäuser. https://doi.org/10.1007/s00028-010-0096-5
chicago: Clément, Philippe, and Jan Maas. “A Trotter Product Formula for Gradient
Flows in Metric Spaces.” Journal of Evolution Equations. Birkhäuser, 2011.
https://doi.org/10.1007/s00028-010-0096-5.
ieee: P. Clément and J. Maas, “A Trotter product formula for gradient flows in metric
spaces,” Journal of Evolution Equations, vol. 11, no. 2. Birkhäuser, pp.
405–427, 2011.
ista: Clément P, Maas J. 2011. A Trotter product formula for gradient flows in metric
spaces. Journal of Evolution Equations. 11(2), 405–427.
mla: Clément, Philippe, and Jan Maas. “A Trotter Product Formula for Gradient Flows
in Metric Spaces.” Journal of Evolution Equations, vol. 11, no. 2, Birkhäuser,
2011, pp. 405–27, doi:10.1007/s00028-010-0096-5.
short: P. Clément, J. Maas, Journal of Evolution Equations 11 (2011) 405–427.
date_created: 2018-12-11T11:55:51Z
date_published: 2011-01-21T00:00:00Z
date_updated: 2021-11-16T08:05:46Z
day: '21'
doi: 10.1007/s00028-010-0096-5
extern: '1'
intvolume: ' 11'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1005.0998
month: '01'
oa: 1
oa_version: None
page: 405 - 427
publication: Journal of Evolution Equations
publication_status: published
publisher: Birkhäuser
publist_id: '4911'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/s00028-012-0173-z
status: public
title: A Trotter product formula for gradient flows in metric spaces
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 11
year: '2011'
...
---
_id: '2126'
abstract:
- lang: eng
text: |
Let K be an irreducible and reversible Markov kernel on a finite set X. We construct a metric W on the set of probability measures on X and show that with respect to this metric, the law of the continuous time Markov chain evolves as the gradient flow of the entropy. This result is a discrete counterpart of the Wasserstein gradient flow interpretation of the heat flow in Rn by Jordan, Kinderlehrer and Otto (1998). The metric W is similar to, but different from, the L2-Wasserstein metric, and is defined via a discrete variant of the Benamou–Brenier formula.
acknowledgement: Supported by Rubicon subsidy 680-50-0901 of the Netherlands Organisation
for Scientific Research (NWO)
author:
- first_name: Jan
full_name: Jan Maas
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
citation:
ama: Maas J. Gradient flows of the entropy for finite Markov chains. Journal
of Functional Analysis. 2011;261(8):2250-2292. doi:10.1016/j.jfa.2011.06.009
apa: Maas, J. (2011). Gradient flows of the entropy for finite Markov chains. Journal
of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2011.06.009
chicago: Maas, Jan. “Gradient Flows of the Entropy for Finite Markov Chains.” Journal
of Functional Analysis. Academic Press, 2011. https://doi.org/10.1016/j.jfa.2011.06.009 .
ieee: J. Maas, “Gradient flows of the entropy for finite Markov chains,” Journal
of Functional Analysis, vol. 261, no. 8. Academic Press, pp. 2250–2292, 2011.
ista: Maas J. 2011. Gradient flows of the entropy for finite Markov chains. Journal
of Functional Analysis. 261(8), 2250–2292.
mla: Maas, Jan. “Gradient Flows of the Entropy for Finite Markov Chains.” Journal
of Functional Analysis, vol. 261, no. 8, Academic Press, 2011, pp. 2250–92,
doi:10.1016/j.jfa.2011.06.009
.
short: J. Maas, Journal of Functional Analysis 261 (2011) 2250–2292.
date_created: 2018-12-11T11:55:51Z
date_published: 2011-03-04T00:00:00Z
date_updated: 2021-01-12T06:55:28Z
day: '04'
doi: '10.1016/j.jfa.2011.06.009 '
extern: 1
intvolume: ' 261'
issue: '8'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1102.5238
month: '03'
oa: 1
page: 2250 - 2292
publication: Journal of Functional Analysis
publication_status: published
publisher: Academic Press
publist_id: '4909'
quality_controlled: 0
status: public
title: Gradient flows of the entropy for finite Markov chains
type: journal_article
volume: 261
year: '2011'
...
---
_id: '2138'
abstract:
- lang: eng
text: A (diatomic) shape resonance is a metastable state of a pair of colliding
atoms quasi-bound by the centrifugal barrier imposed by the angular momentum involved
in the collision. The temporary trapping of the atoms' scattering wavefunction
corresponds to an enhanced atom pair density at low interatomic separations. This
leads to larger overlap of the wavefunctions involved in a molecule formation
process such as photoassociation, rendering the process more efficient. However,
for an ensemble of atoms, the atom pair density will only be enhanced if the energy
of the resonance comes close to the temperature of the atomic ensemble. Herein
we explore the possibility of controlling the energy of a shape resonance by shifting
it toward the temperature of atoms confined in a trap. The shifts are imparted
by the interaction of non-resonant light with the anisotropic polarizability of
the atom pair, which affects both the centrifugal barrier and the pair's rotational
and vibrational levels. We find that at laser intensities of up to 5×109 W/cm2
the pair density is increased by one order of magnitude for 87Rb atoms at 100μK
and by two orders of magnitude for 88Sr atoms at 20μK.
acknowledgement: Financial support from the Deutsche Forschungsgemeinschaft (Grant
No. KO 2301/2), by the Spanish project FIS2008-02380 (MICINN) as well as the Grants
FQM-2445 and FQM-4643 (Junta de Andaluc´ıa), Campus de Excelencia Internacional
Proyecto GENIL CEB09-0010
author:
- first_name: Ruzin
full_name: Ağanoğlu, Ruzin
last_name: Ağanoğlu
- first_name: Mikhail
full_name: Mikhail Lemeshko
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Břetislav
full_name: Friedrich, Břetislav
last_name: Friedrich
- first_name: Rosario
full_name: González-Férez, Rosario
last_name: González Férez
- first_name: Christiane
full_name: Koch, Christiane P
last_name: Koch
citation:
ama: Ağanoğlu R, Lemeshko M, Friedrich B, González Férez R, Koch C. Controlling
a diatomic shape resonance with non-resonant light. Unknown. 2011.
apa: Ağanoğlu, R., Lemeshko, M., Friedrich, B., González Férez, R., & Koch,
C. (2011). Controlling a diatomic shape resonance with non-resonant light. Unknown.
ArXiv.
chicago: Ağanoğlu, Ruzin, Mikhail Lemeshko, Břetislav Friedrich, Rosario González
Férez, and Christiane Koch. “Controlling a Diatomic Shape Resonance with Non-Resonant
Light.” Unknown. ArXiv, 2011.
ieee: R. Ağanoğlu, M. Lemeshko, B. Friedrich, R. González Férez, and C. Koch, “Controlling
a diatomic shape resonance with non-resonant light,” Unknown. ArXiv, 2011.
ista: Ağanoğlu R, Lemeshko M, Friedrich B, González Férez R, Koch C. 2011. Controlling
a diatomic shape resonance with non-resonant light. Unknown, .
mla: Ağanoğlu, Ruzin, et al. “Controlling a Diatomic Shape Resonance with Non-Resonant
Light.” Unknown, ArXiv, 2011.
short: R. Ağanoğlu, M. Lemeshko, B. Friedrich, R. González Férez, C. Koch, Unknown
(2011).
date_created: 2018-12-11T11:55:55Z
date_published: 2011-05-04T00:00:00Z
date_updated: 2021-01-12T06:55:32Z
day: '04'
extern: 1
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1105.0761
month: '05'
oa: 1
publication: Unknown
publication_status: published
publisher: ArXiv
publist_id: '4886'
quality_controlled: 0
status: public
title: Controlling a diatomic shape resonance with non-resonant light
type: preprint
year: '2011'
...
---
_id: '2200'
abstract:
- lang: eng
text: We made use of supersymmetric (SUSY) quantum mechanics to find the condition
under which the Stark effect problem for a polar and polarizable closed-shell
diatomic molecule subjected to collinear electrostatic and nonresonant radiative
fields becomes exactly solvable. The condition Δω = ω2/4(m+1)2 connects values
of the dimensionless parameters ω and Δω that characterize the strengths of the
permanent and induced dipole interactions of the molecule with the respective
fields. The exact solutions are obtained for the \J̃ = m, m; ω, Δω) family of
'stretched' states. The field-free and strong-field limits of the combined-fields
problem were found to exhibit supersymmetry and shape invariance, which is indeed
the reason why they are analytically solvable. By making use of the analytic form
of the \J̃ = m,m; ω, Δω) wavefunctions, we obtained simple formulae for the expectation
values of the space-fixed electric dipole moment, the alignment cosine and the
angular momentum squared, and derived a 'sum rule' that combines the above expectation
values into a formula for the eigenenergy. The analytic expressions for the characteristics
of the strongly oriented and aligned states provide direct access to the values
of the interaction parameters required for creating such states in the laboratory.
acknowledgement: SK thanks the ARO for financial support
author:
- first_name: Mikhail
full_name: Mikhail Lemeshko
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Mustafa
full_name: Mustafa, Mustafa K
last_name: Mustafa
- first_name: Sabre
full_name: Kais, Sabre
last_name: Kais
- first_name: Břetislav
full_name: Friedrich, Břetislav
last_name: Friedrich
citation:
ama: Lemeshko M, Mustafa M, Kais S, Friedrich B. Supersymmetry identifies molecular
Stark states whose eigenproperties can be obtained analytically. New Journal
of Physics. 2011;13. doi:10.1088/1367-2630/13/6/063036
apa: Lemeshko, M., Mustafa, M., Kais, S., & Friedrich, B. (2011). Supersymmetry
identifies molecular Stark states whose eigenproperties can be obtained analytically.
New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/13/6/063036
chicago: Lemeshko, Mikhail, Mustafa Mustafa, Sabre Kais, and Břetislav Friedrich.
“Supersymmetry Identifies Molecular Stark States Whose Eigenproperties Can Be
Obtained Analytically.” New Journal of Physics. IOP Publishing Ltd., 2011.
https://doi.org/10.1088/1367-2630/13/6/063036.
ieee: M. Lemeshko, M. Mustafa, S. Kais, and B. Friedrich, “Supersymmetry identifies
molecular Stark states whose eigenproperties can be obtained analytically,” New
Journal of Physics, vol. 13. IOP Publishing Ltd., 2011.
ista: Lemeshko M, Mustafa M, Kais S, Friedrich B. 2011. Supersymmetry identifies
molecular Stark states whose eigenproperties can be obtained analytically. New
Journal of Physics. 13.
mla: Lemeshko, Mikhail, et al. “Supersymmetry Identifies Molecular Stark States
Whose Eigenproperties Can Be Obtained Analytically.” New Journal of Physics,
vol. 13, IOP Publishing Ltd., 2011, doi:10.1088/1367-2630/13/6/063036.
short: M. Lemeshko, M. Mustafa, S. Kais, B. Friedrich, New Journal of Physics 13
(2011).
date_created: 2018-12-11T11:56:17Z
date_published: 2011-06-20T00:00:00Z
date_updated: 2021-01-12T06:55:57Z
day: '20'
doi: 10.1088/1367-2630/13/6/063036
extern: 1
intvolume: ' 13'
main_file_link:
- open_access: '1'
url: 'http://arxiv.org/abs/1106.4402 '
month: '06'
oa: 1
publication: New Journal of Physics
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '4774'
quality_controlled: 0
status: public
title: Supersymmetry identifies molecular Stark states whose eigenproperties can be
obtained analytically
type: journal_article
volume: 13
year: '2011'
...
---
_id: '2199'
abstract:
- lang: eng
text: By invoking supersymmetry, we found a condition under which the Stark-effect
problem for a polar and polarizable molecule subject to nonresonant electric fields
becomes exactly solvable for the family of stretched states. The analytic expressions
for the wave function and eigenenergy and other expectation values allow one to
readily reverse-engineer the problem of finding the values of the interaction
parameters required for creating quantum states with preordained characteristics.
The method also allows the construction of families of isospectral potentials,
realizable with combined fields.
acknowledgement: 'ARO '
author:
- first_name: Mikhail
full_name: Mikhail Lemeshko
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Mustafa
full_name: Mustafa, Mustafa K
last_name: Mustafa
- first_name: Sabre
full_name: Kais, Sabre
last_name: Kais
- first_name: Břetislav
full_name: Friedrich, Břetislav
last_name: Friedrich
citation:
ama: Lemeshko M, Mustafa M, Kais S, Friedrich B. Supersymmetric factorization yields
exact solutions to the molecular Stark-effect problem for "stretched"
states. Physical Review A - Atomic, Molecular, and Optical Physics. 2011;83(4).
doi:10.1103/PhysRevA.83.043415
apa: Lemeshko, M., Mustafa, M., Kais, S., & Friedrich, B. (2011). Supersymmetric
factorization yields exact solutions to the molecular Stark-effect problem for
"stretched" states. Physical Review A - Atomic, Molecular,
and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.83.043415
chicago: Lemeshko, Mikhail, Mustafa Mustafa, Sabre Kais, and Břetislav Friedrich.
“Supersymmetric Factorization Yields Exact Solutions to the Molecular Stark-Effect
Problem for "Stretched" States.” Physical Review A - Atomic,
Molecular, and Optical Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevA.83.043415.
ieee: M. Lemeshko, M. Mustafa, S. Kais, and B. Friedrich, “Supersymmetric factorization
yields exact solutions to the molecular Stark-effect problem for "stretched"
states,” Physical Review A - Atomic, Molecular, and Optical Physics, vol.
83, no. 4. American Physical Society, 2011.
ista: Lemeshko M, Mustafa M, Kais S, Friedrich B. 2011. Supersymmetric factorization
yields exact solutions to the molecular Stark-effect problem for "stretched"
states. Physical Review A - Atomic, Molecular, and Optical Physics. 83(4).
mla: Lemeshko, Mikhail, et al. “Supersymmetric Factorization Yields Exact Solutions
to the Molecular Stark-Effect Problem for "Stretched" States.”
Physical Review A - Atomic, Molecular, and Optical Physics, vol. 83, no.
4, American Physical Society, 2011, doi:10.1103/PhysRevA.83.043415.
short: M. Lemeshko, M. Mustafa, S. Kais, B. Friedrich, Physical Review A - Atomic,
Molecular, and Optical Physics 83 (2011).
date_created: 2018-12-11T11:56:17Z
date_published: 2011-04-25T00:00:00Z
date_updated: 2021-01-12T06:55:56Z
day: '25'
doi: 10.1103/PhysRevA.83.043415
extern: 1
intvolume: ' 83'
issue: '4'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1105.5262
month: '04'
oa: 1
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '4776'
quality_controlled: 0
status: public
title: Supersymmetric factorization yields exact solutions to the molecular Stark-effect
problem for "stretched" states
type: journal_article
volume: 83
year: '2011'
...
---
_id: '2198'
abstract:
- lang: eng
text: We show that dressing polar molecules with a far-off-resonant optical field
leads to new types of intermolecular potentials, which undergo a crossover from
the inverse power to oscillating behavior depending on the intermolecular distance,
and whose parameters can be tuned by varying the laser intensity and wavelength.
We present analytic expressions for the potential energy surfaces, thereby providing
direct access to the parameters of an optical field required to design intermolecular
interactions experimentally.
author:
- first_name: Mikhail
full_name: Mikhail Lemeshko
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Lemeshko M. Shaping interactions between polar molecules with far-off-resonant
light. Physical Review A - Atomic, Molecular, and Optical Physics. 2011;83(5).
doi:10.1103/PhysRevA.83.051402
apa: Lemeshko, M. (2011). Shaping interactions between polar molecules with far-off-resonant
light. Physical Review A - Atomic, Molecular, and Optical Physics. American
Physical Society. https://doi.org/10.1103/PhysRevA.83.051402
chicago: Lemeshko, Mikhail. “Shaping Interactions between Polar Molecules with Far-off-Resonant
Light.” Physical Review A - Atomic, Molecular, and Optical Physics. American
Physical Society, 2011. https://doi.org/10.1103/PhysRevA.83.051402.
ieee: M. Lemeshko, “Shaping interactions between polar molecules with far-off-resonant
light,” Physical Review A - Atomic, Molecular, and Optical Physics, vol.
83, no. 5. American Physical Society, 2011.
ista: Lemeshko M. 2011. Shaping interactions between polar molecules with far-off-resonant
light. Physical Review A - Atomic, Molecular, and Optical Physics. 83(5).
mla: Lemeshko, Mikhail. “Shaping Interactions between Polar Molecules with Far-off-Resonant
Light.” Physical Review A - Atomic, Molecular, and Optical Physics, vol.
83, no. 5, American Physical Society, 2011, doi:10.1103/PhysRevA.83.051402.
short: M. Lemeshko, Physical Review A - Atomic, Molecular, and Optical Physics 83
(2011).
date_created: 2018-12-11T11:56:17Z
date_published: 2011-05-27T00:00:00Z
date_updated: 2021-01-12T06:55:55Z
day: '27'
doi: 10.1103/PhysRevA.83.051402
extern: 1
intvolume: ' 83'
issue: '5'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1104.1046
month: '05'
oa: 1
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '4775'
quality_controlled: 0
status: public
title: Shaping interactions between polar molecules with far-off-resonant light
type: journal_article
volume: 83
year: '2011'
...
---
_id: '2312'
abstract:
- lang: eng
text: Soon, the genetic basis of most human Mendelian diseases will be solved. The
next challenge will be to leverage this information to uncover basic mechanisms
of disease and develop new therapies. To understand how this transformation is
already beginning to unfold, we focus on the ciliopathies, a class of multi-organ
diseases caused by disruption of the primary cilium. Through a convergence of
data involving mutant gene discovery, proteomics, and cell biology, more than
a dozen phenotypically distinguishable conditions are now united as ciliopathies.
Sitting at the interface between simple and complex genetic conditions, these
diseases provide clues to the future direction of human genetics.
author:
- first_name: Gaia
full_name: Gaia Novarino
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Naiara
full_name: Akizu, Naiara
last_name: Akizu
- first_name: Joseph
full_name: Gleeson, Joseph G
last_name: Gleeson
citation:
ama: 'Novarino G, Akizu N, Gleeson J. Modeling human disease in humans: The ciliopathies.
Cell. 2011;147(1):70-79. doi:10.1016/j.cell.2011.09.014'
apa: 'Novarino, G., Akizu, N., & Gleeson, J. (2011). Modeling human disease
in humans: The ciliopathies. Cell. Cell Press. https://doi.org/10.1016/j.cell.2011.09.014'
chicago: 'Novarino, Gaia, Naiara Akizu, and Joseph Gleeson. “Modeling Human Disease
in Humans: The Ciliopathies.” Cell. Cell Press, 2011. https://doi.org/10.1016/j.cell.2011.09.014.'
ieee: 'G. Novarino, N. Akizu, and J. Gleeson, “Modeling human disease in humans:
The ciliopathies,” Cell, vol. 147, no. 1. Cell Press, pp. 70–79, 2011.'
ista: 'Novarino G, Akizu N, Gleeson J. 2011. Modeling human disease in humans: The
ciliopathies. Cell. 147(1), 70–79.'
mla: 'Novarino, Gaia, et al. “Modeling Human Disease in Humans: The Ciliopathies.”
Cell, vol. 147, no. 1, Cell Press, 2011, pp. 70–79, doi:10.1016/j.cell.2011.09.014.'
short: G. Novarino, N. Akizu, J. Gleeson, Cell 147 (2011) 70–79.
date_created: 2018-12-11T11:56:55Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2019-04-26T07:22:10Z
day: '01'
doi: 10.1016/j.cell.2011.09.014
extern: 1
intvolume: ' 147'
issue: '1'
month: '01'
page: 70 - 79
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '4615'
quality_controlled: 0
status: public
title: 'Modeling human disease in humans: The ciliopathies'
type: review
volume: 147
year: '2011'
...
---
_id: '2320'
abstract:
- lang: eng
text: The binding of polarons, or its absence, is an old and subtle topic. After
defining the model we state some recent theorems of ours. First, the transition
from many-body collapse to the existence of a thermodynamic limit for N polarons
occurs precisely at U = 2α, where U is the electronic Coulomb repulsion and α
is the polaron coupling constant. Second, if U is large enough, there is no multi-polaron
binding of any kind. We also discuss the Pekar-Tomasevich approximation to the
ground state energy, which is valid for large α. Finally, we derive exact results,
not reported before, about the one-dimensional toy model introduced by E. P. Gross.
author:
- first_name: Rupert
full_name: Frank, Rupert L
last_name: Frank
- first_name: Élliott
full_name: Lieb, Élliott H
last_name: Lieb
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Lawrence
full_name: Thomas, Lawrence E
last_name: Thomas
citation:
ama: 'Frank R, Lieb É, Seiringer R, Thomas L. Binding, stability, and non-binding
of multi-polaron systems. In: World Scientific Publishing; 2011:21-32. doi:10.1142/9789814350365_0002'
apa: 'Frank, R., Lieb, É., Seiringer, R., & Thomas, L. (2011). Binding, stability,
and non-binding of multi-polaron systems (pp. 21–32). Presented at the QMath:
Mathematical Results in Quantum Physics, World Scientific Publishing. https://doi.org/10.1142/9789814350365_0002'
chicago: Frank, Rupert, Élliott Lieb, Robert Seiringer, and Lawrence Thomas. “Binding,
Stability, and Non-Binding of Multi-Polaron Systems,” 21–32. World Scientific
Publishing, 2011. https://doi.org/10.1142/9789814350365_0002.
ieee: 'R. Frank, É. Lieb, R. Seiringer, and L. Thomas, “Binding, stability, and
non-binding of multi-polaron systems,” presented at the QMath: Mathematical Results
in Quantum Physics, 2011, pp. 21–32.'
ista: 'Frank R, Lieb É, Seiringer R, Thomas L. 2011. Binding, stability, and non-binding
of multi-polaron systems. QMath: Mathematical Results in Quantum Physics, 21–32.'
mla: Frank, Rupert, et al. Binding, Stability, and Non-Binding of Multi-Polaron
Systems. World Scientific Publishing, 2011, pp. 21–32, doi:10.1142/9789814350365_0002.
short: R. Frank, É. Lieb, R. Seiringer, L. Thomas, in:, World Scientific Publishing,
2011, pp. 21–32.
conference:
name: 'QMath: Mathematical Results in Quantum Physics'
date_created: 2018-12-11T11:56:58Z
date_published: 2011-05-26T00:00:00Z
date_updated: 2021-01-12T06:56:45Z
day: '26'
doi: 10.1142/9789814350365_0002
extern: 1
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1010.0737
month: '05'
oa: 1
page: 21 - 32
publication_status: published
publisher: World Scientific Publishing
publist_id: '4607'
quality_controlled: 0
status: public
title: Binding, stability, and non-binding of multi-polaron systems
type: conference
year: '2011'
...
---
_id: '2321'
abstract:
- lang: eng
text: We derive a sharp bound on the location of non-positive eigenvalues of Schrödinger
operators on the half-line with complex-valued potentials.
alternative_title:
- 'Operator Theory: Advances and Applications'
author:
- first_name: Rupert
full_name: Frank, Rupert L
last_name: Frank
- first_name: Ari
full_name: Laptev, Ari
last_name: Laptev
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Frank R, Laptev A, Seiringer R. A sharp bound on eigenvalues of Schrödinger
operators on the halfline with complex-valued potentials. In: Vol 214. Springer;
2011:39-44. doi:10.1007/978-3-7643-9994-8_3'
apa: 'Frank, R., Laptev, A., & Seiringer, R. (2011). A sharp bound on eigenvalues
of Schrödinger operators on the halfline with complex-valued potentials (Vol.
214, pp. 39–44). Presented at the OTAMP: Operator Theory, Analysis and Mathematical
Physics, Springer. https://doi.org/10.1007/978-3-7643-9994-8_3'
chicago: Frank, Rupert, Ari Laptev, and Robert Seiringer. “ A Sharp Bound on Eigenvalues
of Schrödinger Operators on the Halfline with Complex-Valued Potentials,” 214:39–44.
Springer, 2011. https://doi.org/10.1007/978-3-7643-9994-8_3.
ieee: 'R. Frank, A. Laptev, and R. Seiringer, “ A sharp bound on eigenvalues of
Schrödinger operators on the halfline with complex-valued potentials,” presented
at the OTAMP: Operator Theory, Analysis and Mathematical Physics, 2011, vol. 214,
pp. 39–44.'
ista: 'Frank R, Laptev A, Seiringer R. 2011. A sharp bound on eigenvalues of Schrödinger
operators on the halfline with complex-valued potentials. OTAMP: Operator Theory,
Analysis and Mathematical Physics, Operator Theory: Advances and Applications,
vol. 214, 39–44.'
mla: Frank, Rupert, et al. A Sharp Bound on Eigenvalues of Schrödinger Operators
on the Halfline with Complex-Valued Potentials. Vol. 214, Springer, 2011,
pp. 39–44, doi:10.1007/978-3-7643-9994-8_3.
short: R. Frank, A. Laptev, R. Seiringer, in:, Springer, 2011, pp. 39–44.
conference:
name: 'OTAMP: Operator Theory, Analysis and Mathematical Physics'
date_created: 2018-12-11T11:56:59Z
date_published: 2011-03-31T00:00:00Z
date_updated: 2021-01-12T06:56:46Z
day: '31'
doi: 10.1007/978-3-7643-9994-8_3
extern: 1
intvolume: ' 214'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0903.2053
month: '03'
oa: 1
page: 39 - 44
publication_status: published
publisher: Springer
publist_id: '4606'
quality_controlled: 0
status: public
title: ' A sharp bound on eigenvalues of Schrödinger operators on the halfline with
complex-valued potentials'
type: conference
volume: 214
year: '2011'
...
---
_id: '233'
abstract:
- lang: eng
text: 'For an irreducible polynomial in at most two variables the problem of representing
power-free integers is investigated. '
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. Power-free values of polynomials. Archiv der Mathematik.
2011;96(2):139-150. doi:10.1007/s00013-011-0224-7
apa: Browning, T. D. (2011). Power-free values of polynomials. Archiv Der Mathematik.
Birkhäuser. https://doi.org/10.1007/s00013-011-0224-7
chicago: Browning, Timothy D. “Power-Free Values of Polynomials.” Archiv Der
Mathematik. Birkhäuser, 2011. https://doi.org/10.1007/s00013-011-0224-7.
ieee: T. D. Browning, “Power-free values of polynomials,” Archiv der Mathematik,
vol. 96, no. 2. Birkhäuser, pp. 139–150, 2011.
ista: Browning TD. 2011. Power-free values of polynomials. Archiv der Mathematik.
96(2), 139–150.
mla: Browning, Timothy D. “Power-Free Values of Polynomials.” Archiv Der Mathematik,
vol. 96, no. 2, Birkhäuser, 2011, pp. 139–50, doi:10.1007/s00013-011-0224-7.
short: T.D. Browning, Archiv Der Mathematik 96 (2011) 139–150.
date_created: 2018-12-11T11:45:21Z
date_published: 2011-02-19T00:00:00Z
date_updated: 2021-01-12T06:56:49Z
day: '19'
doi: 10.1007/s00013-011-0224-7
extern: 1
intvolume: ' 96'
issue: '2'
month: '02'
page: 139 - 150
publication: Archiv der Mathematik
publication_status: published
publisher: Birkhäuser
publist_id: '7670'
quality_controlled: 0
status: public
title: Power-free values of polynomials
type: journal_article
volume: 96
year: '2011'
...
---
_id: '234'
abstract:
- lang: eng
text: We investigate the average order of the divisor function at values of binary
cubic forms that are reducible over Q and discuss some applications.
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 divisor problem for binary cubic forms. Journal de Theorie
des Nombres de Bordeaux. 2011;23(3):579-602. doi:10.5802/jtnb.778
apa: Browning, T. D. (2011). The divisor problem for binary cubic forms. Journal
de Theorie Des Nombres de Bordeaux. Universite de Bordeaux. https://doi.org/10.5802/jtnb.778
chicago: Browning, Timothy D. “The Divisor Problem for Binary Cubic Forms.” Journal
de Theorie Des Nombres de Bordeaux. Universite de Bordeaux, 2011. https://doi.org/10.5802/jtnb.778.
ieee: T. D. Browning, “The divisor problem for binary cubic forms,” Journal de
Theorie des Nombres de Bordeaux, vol. 23, no. 3. Universite de Bordeaux, pp.
579–602, 2011.
ista: Browning TD. 2011. The divisor problem for binary cubic forms. Journal de
Theorie des Nombres de Bordeaux. 23(3), 579–602.
mla: Browning, Timothy D. “The Divisor Problem for Binary Cubic Forms.” Journal
de Theorie Des Nombres de Bordeaux, vol. 23, no. 3, Universite de Bordeaux,
2011, pp. 579–602, doi:10.5802/jtnb.778.
short: T.D. Browning, Journal de Theorie Des Nombres de Bordeaux 23 (2011) 579–602.
date_created: 2018-12-11T11:45:21Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:53Z
day: '01'
doi: 10.5802/jtnb.778
extern: 1
intvolume: ' 23'
issue: '3'
month: '01'
page: 579 - 602
publication: Journal de Theorie des Nombres de Bordeaux
publication_status: published
publisher: Universite de Bordeaux
publist_id: '7671'
quality_controlled: 0
status: public
title: The divisor problem for binary cubic forms
type: journal_article
volume: 23
year: '2011'
...
---
_id: '235'
abstract:
- lang: eng
text: For given positive integers m and n, we consider the frequency of representations
of m/n as a sum of unit fractions.
article_processing_charge: No
article_type: original
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Christian
full_name: Elsholtz, Christian
last_name: Elsholtz
citation:
ama: Browning TD, Elsholtz C. The number of representations of rationals as a sum
of unit fractions. Illinois Journal of Mathematics. 2011;55(2):685-696.
apa: Browning, T. D., & Elsholtz, C. (2011). The number of representations of
rationals as a sum of unit fractions. Illinois Journal of Mathematics.
University of Illinois Press.
chicago: Browning, Timothy D, and Christian Elsholtz. “The Number of Representations
of Rationals as a Sum of Unit Fractions.” Illinois Journal of Mathematics.
University of Illinois Press, 2011.
ieee: T. D. Browning and C. Elsholtz, “The number of representations of rationals
as a sum of unit fractions,” Illinois Journal of Mathematics, vol. 55,
no. 2. University of Illinois Press, pp. 685–696, 2011.
ista: Browning TD, Elsholtz C. 2011. The number of representations of rationals
as a sum of unit fractions. Illinois Journal of Mathematics. 55(2), 685–696.
mla: Browning, Timothy D., and Christian Elsholtz. “The Number of Representations
of Rationals as a Sum of Unit Fractions.” Illinois Journal of Mathematics,
vol. 55, no. 2, University of Illinois Press, 2011, pp. 685–96.
short: T.D. Browning, C. Elsholtz, Illinois Journal of Mathematics 55 (2011) 685–696.
date_created: 2018-12-11T11:45:21Z
date_published: 2011-07-01T00:00:00Z
date_updated: 2021-01-12T06:56:57Z
day: '01'
extern: '1'
intvolume: ' 55'
issue: '2'
language:
- iso: eng
month: '07'
oa_version: None
page: 685 - 696
publication: Illinois Journal of Mathematics
publication_status: published
publisher: University of Illinois Press
publist_id: '7669'
quality_controlled: '1'
status: public
title: The number of representations of rationals as a sum of unit fractions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2011'
...
---
_id: '236'
abstract:
- lang: eng
text: An asymptotic formula is established for the number of Q-rational points of
bounded height on a nonsingular quartic Del Pezzo surface with a conic bundle
structure.
acknowledgement: "EP/E053262/1\tEngineering and Physical Sciences Research Council"
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. Manin’s conjecture for quartic Del Pezzo surfaces
with a conic fibration. Duke Mathematical Journal. 2011;160(1):1-69. doi:10.1215/00127094-1443466
apa: De La Bretèche, R., & Browning, T. D. (2011). Manin’s conjecture for quartic
Del Pezzo surfaces with a conic fibration. Duke Mathematical Journal. Duke
University Press. https://doi.org/10.1215/00127094-1443466
chicago: De La Bretèche, Régis, and Timothy D Browning. “Manin’s Conjecture for
Quartic Del Pezzo Surfaces with a Conic Fibration.” Duke Mathematical Journal.
Duke University Press, 2011. https://doi.org/10.1215/00127094-1443466.
ieee: R. De La Bretèche and T. D. Browning, “Manin’s conjecture for quartic Del
Pezzo surfaces with a conic fibration,” Duke Mathematical Journal, vol.
160, no. 1. Duke University Press, pp. 1–69, 2011.
ista: De La Bretèche R, Browning TD. 2011. Manin’s conjecture for quartic Del Pezzo
surfaces with a conic fibration. Duke Mathematical Journal. 160(1), 1–69.
mla: De La Bretèche, Régis, and Timothy D. Browning. “Manin’s Conjecture for Quartic
Del Pezzo Surfaces with a Conic Fibration.” Duke Mathematical Journal,
vol. 160, no. 1, Duke University Press, 2011, pp. 1–69, doi:10.1215/00127094-1443466.
short: R. De La Bretèche, T.D. Browning, Duke Mathematical Journal 160 (2011) 1–69.
date_created: 2018-12-11T11:45:21Z
date_published: 2011-09-27T00:00:00Z
date_updated: 2021-01-12T06:57:00Z
day: '27'
doi: 10.1215/00127094-1443466
extern: 1
intvolume: ' 160'
issue: '1'
month: '09'
page: 1 - 69
publication: Duke Mathematical Journal
publication_status: published
publisher: Duke University Press
publist_id: '7668'
quality_controlled: 0
status: public
title: Manin's conjecture for quartic Del Pezzo surfaces with a conic fibration
type: journal_article
volume: 160
year: '2011'
...
---
_id: '2390'
abstract:
- lang: eng
text: 'We resolve several longstanding problems concerning the stability and the
absence of multi-particle binding for N≥2 polarons. Fröhlich''s 1937 polaron model
describes non-relativistic particles interacting with a scalar quantized field
with coupling √α, and with each other by Coulomb repulsion of strength U. We prove
the following: (i) While there is a known thermodynamic instability for U<2α,
stability of matter does hold for U>2α, that is, the ground state energy per
particle has a finite limit as N→∞. (ii) There is no binding of any kind if U
exceeds a critical value that depends on α but not on N. The same results are
shown to hold for the Pekar-Tomasevich model.'
author:
- first_name: Rupert
full_name: Frank, Rupert L
last_name: Frank
- first_name: Élliott
full_name: Lieb, Élliott H
last_name: Lieb
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Lawrence
full_name: Thomas, Lawrence E
last_name: Thomas
citation:
ama: Frank R, Lieb É, Seiringer R, Thomas L. Stability and absence of binding for
multi-polaron systems. Publications Mathematiques de l Institut des Hautes
Etudes Scientifiques. 2011;113(1):39-67. doi:10.1007/s10240-011-0031-5
apa: Frank, R., Lieb, É., Seiringer, R., & Thomas, L. (2011). Stability and
absence of binding for multi-polaron systems. Publications Mathematiques de
l Institut Des Hautes Etudes Scientifiques. Springer. https://doi.org/10.1007/s10240-011-0031-5
chicago: Frank, Rupert, Élliott Lieb, Robert Seiringer, and Lawrence Thomas. “Stability
and Absence of Binding for Multi-Polaron Systems.” Publications Mathematiques
de l Institut Des Hautes Etudes Scientifiques. Springer, 2011. https://doi.org/10.1007/s10240-011-0031-5.
ieee: R. Frank, É. Lieb, R. Seiringer, and L. Thomas, “Stability and absence of
binding for multi-polaron systems,” Publications Mathematiques de l Institut
des Hautes Etudes Scientifiques, vol. 113, no. 1. Springer, pp. 39–67, 2011.
ista: Frank R, Lieb É, Seiringer R, Thomas L. 2011. Stability and absence of binding
for multi-polaron systems. Publications Mathematiques de l Institut des Hautes
Etudes Scientifiques. 113(1), 39–67.
mla: Frank, Rupert, et al. “Stability and Absence of Binding for Multi-Polaron Systems.”
Publications Mathematiques de l Institut Des Hautes Etudes Scientifiques,
vol. 113, no. 1, Springer, 2011, pp. 39–67, doi:10.1007/s10240-011-0031-5.
short: R. Frank, É. Lieb, R. Seiringer, L. Thomas, Publications Mathematiques de
l Institut Des Hautes Etudes Scientifiques 113 (2011) 39–67.
date_created: 2018-12-11T11:57:23Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2021-01-12T06:57:12Z
day: '01'
doi: 10.1007/s10240-011-0031-5
extern: 1
intvolume: ' 113'
issue: '1'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1004.4892
month: '06'
oa: 1
page: 39 - 67
publication: Publications Mathematiques de l Institut des Hautes Etudes Scientifiques
publication_status: published
publisher: Springer
publist_id: '4534'
quality_controlled: 0
status: public
title: Stability and absence of binding for multi-polaron systems
type: journal_article
volume: 113
year: '2011'
...
---
_id: '2391'
abstract:
- lang: eng
text: The change in energy of an ideal Fermi gas when a local one-body potential
is inserted into the system, or when the density is changed locally, are important
quantities in condensed matter physics. We show that they can be rigorously bounded
from below by a universal constant times the value given by the semiclassical
approximation.
author:
- first_name: Rupert
full_name: Frank, Rupert L
last_name: Frank
- first_name: Mathieu
full_name: Lewin, Mathieu
last_name: Lewin
- first_name: Élliott
full_name: Lieb, Élliott H
last_name: Lieb
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Frank R, Lewin M, Lieb É, Seiringer R. Energy cost to make a hole in the fermi
sea. Physical Review Letters. 2011;106(15). doi:10.1103/PhysRevLett.106.150402
apa: Frank, R., Lewin, M., Lieb, É., & Seiringer, R. (2011). Energy cost to
make a hole in the fermi sea. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/PhysRevLett.106.150402
chicago: Frank, Rupert, Mathieu Lewin, Élliott Lieb, and Robert Seiringer. “Energy
Cost to Make a Hole in the Fermi Sea.” Physical Review Letters. American
Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.106.150402.
ieee: R. Frank, M. Lewin, É. Lieb, and R. Seiringer, “Energy cost to make a hole
in the fermi sea,” Physical Review Letters, vol. 106, no. 15. American
Physical Society, 2011.
ista: Frank R, Lewin M, Lieb É, Seiringer R. 2011. Energy cost to make a hole in
the fermi sea. Physical Review Letters. 106(15).
mla: Frank, Rupert, et al. “Energy Cost to Make a Hole in the Fermi Sea.” Physical
Review Letters, vol. 106, no. 15, American Physical Society, 2011, doi:10.1103/PhysRevLett.106.150402.
short: R. Frank, M. Lewin, É. Lieb, R. Seiringer, Physical Review Letters 106 (2011).
date_created: 2018-12-11T11:57:24Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T06:57:12Z
day: '01'
doi: 10.1103/PhysRevLett.106.150402
extern: 1
intvolume: ' 106'
issue: '15'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1102.1414
month: '01'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '4535'
quality_controlled: 0
status: public
title: Energy cost to make a hole in the fermi sea
type: journal_article
volume: 106
year: '2011'
...
---
_id: '239'
abstract:
- lang: eng
text: An effective search bound is established for the least non-trivial integer
zero of an arbitrary cubic form C ε ℤ[X 1,...,X n], provided that n ≥ 17.
acknowledgement: "EP/E053262/1\tEngineering and Physical Sciences Research Council"
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Rainer
full_name: Dietmann, Rainer
last_name: Dietmann
- first_name: Peter
full_name: Elliott, Peter
last_name: Elliott
citation:
ama: Browning TD, Dietmann R, Elliott P. Least zero of a cubic form. Mathematische
Annalen. 2011;352(3):745-778. doi:10.1007/s00208-011-0651-6
apa: Browning, T. D., Dietmann, R., & Elliott, P. (2011). Least zero of a cubic
form. Mathematische Annalen. Springer. https://doi.org/10.1007/s00208-011-0651-6
chicago: Browning, Timothy D, Rainer Dietmann, and Peter Elliott. “Least Zero of
a Cubic Form.” Mathematische Annalen. Springer, 2011. https://doi.org/10.1007/s00208-011-0651-6.
ieee: T. D. Browning, R. Dietmann, and P. Elliott, “Least zero of a cubic form,”
Mathematische Annalen, vol. 352, no. 3. Springer, pp. 745–778, 2011.
ista: Browning TD, Dietmann R, Elliott P. 2011. Least zero of a cubic form. Mathematische
Annalen. 352(3), 745–778.
mla: Browning, Timothy D., et al. “Least Zero of a Cubic Form.” Mathematische
Annalen, vol. 352, no. 3, Springer, 2011, pp. 745–78, doi:10.1007/s00208-011-0651-6.
short: T.D. Browning, R. Dietmann, P. Elliott, Mathematische Annalen 352 (2011)
745–778.
date_created: 2018-12-11T11:45:22Z
date_published: 2011-03-06T00:00:00Z
date_updated: 2021-01-12T06:57:11Z
day: '06'
doi: 10.1007/s00208-011-0651-6
extern: 1
intvolume: ' 352'
issue: '3'
month: '03'
page: 745 - 778
publication: Mathematische Annalen
publication_status: published
publisher: Springer
publist_id: '7665'
quality_controlled: 0
status: public
title: Least zero of a cubic form
type: journal_article
volume: 352
year: '2011'
...
---
_id: '2393'
abstract:
- lang: eng
text: We investigate the low energy excitation spectrum of a Bose gas with weak,
long range repulsive interactions. In particular, we prove that the Bogoliubov
spectrum of elementary excitations with linear dispersion relation for small momentum
becomes exact in the mean-field limit.
author:
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Seiringer R. The excitation spectrum for weakly interacting Bosons. Communications
in Mathematical Physics. 2011;306(2):565-578. doi:10.1007/s00220-011-1261-6
apa: Seiringer, R. (2011). The excitation spectrum for weakly interacting Bosons.
Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-011-1261-6
chicago: Seiringer, Robert. “The Excitation Spectrum for Weakly Interacting Bosons.”
Communications in Mathematical Physics. Springer, 2011. https://doi.org/10.1007/s00220-011-1261-6.
ieee: R. Seiringer, “The excitation spectrum for weakly interacting Bosons,” Communications
in Mathematical Physics, vol. 306, no. 2. Springer, pp. 565–578, 2011.
ista: Seiringer R. 2011. The excitation spectrum for weakly interacting Bosons.
Communications in Mathematical Physics. 306(2), 565–578.
mla: Seiringer, Robert. “The Excitation Spectrum for Weakly Interacting Bosons.”
Communications in Mathematical Physics, vol. 306, no. 2, Springer, 2011,
pp. 565–78, doi:10.1007/s00220-011-1261-6.
short: R. Seiringer, Communications in Mathematical Physics 306 (2011) 565–578.
date_created: 2018-12-11T11:57:24Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2021-01-12T06:57:13Z
day: '01'
doi: 10.1007/s00220-011-1261-6
extern: 1
intvolume: ' 306'
issue: '2'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1008.5349
month: '09'
oa: 1
page: 565 - 578
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '4533'
quality_controlled: 0
status: public
title: The excitation spectrum for weakly interacting Bosons
type: journal_article
volume: 306
year: '2011'
...
---
_id: '2436'
abstract:
- lang: eng
text: 'Let EMBEDk→d be the following algorithmic problem: Given a finite simplicial
complex K of dimension at most k, does there exist a (piecewise linear) embedding
of K into Rd? Known results easily imply the polynomiality of EMBEDk→2 (k = 1;
2; the case k = 1, d = 2 is graph planarity) and of EMBEDk→2k for all k ≥ 3. We
show that the celebrated result of Novikov on the algorithmic unsolvability of
recognizing the 5-sphere implies that EMBEDd→d and EMBED (d-1)→d are undecidable
for each d ≥ 5. Our main result is the NP-hardness of EMBED2→4 and, more generally,
of EMBED k→d for all k; d with d ≥ 4 and d ≥ k ≥ (2d - 2)/3. These dimensions
fall outside the metastable range of a theorem of Haefliger and Weber, which characterizes
embeddability using the deleted product obstruction. Our reductions are based
on examples, due to Segal, Spież, Freedman, Krushkal, Teichner, and Skopenkov,
showing that outside the metastable range the deleted product obstruction is not
sufficient to characterize embeddability. '
acknowledgement: |-
We would like to thank Colin Rourke for explanations concerning PL topology and for examples showing the difference between PL embeddability and topological embeddability
mentioned in Section 2. We also thank Michael Joswig, Gil Kalai, Frank Lutz, Alexander Nabutovsky, and Robin Thomas for kindly answering our questions. The second author would also like to thank Sergio Cabello for helpful discussions regarding linear-time algorithms for EMBED2!2.
Finally, we are grateful to two anonymous referees for careful reading and valuable suggestions.
Research of U.Wagner was supported by the Swiss National Science Foundation (SNF Projects
200021-116741 and 200021-125309).
author:
- first_name: Jiří
full_name: Matoušek, Jiří
last_name: Matoušek
- first_name: Martin
full_name: Martin Tancer
id: 38AC689C-F248-11E8-B48F-1D18A9856A87
last_name: Tancer
orcid: 0000-0002-1191-6714
- first_name: Uli
full_name: Uli Wagner
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Matoušek J, Tancer M, Wagner U. Hardness of embedding simplicial complexes
in Rd. Journal of the European Mathematical Society. 2011;13(2):259-295.
doi:10.4171/JEMS/252
apa: Matoušek, J., Tancer, M., & Wagner, U. (2011). Hardness of embedding simplicial
complexes in Rd. Journal of the European Mathematical Society. European
Mathematical Society. https://doi.org/10.4171/JEMS/252
chicago: Matoušek, Jiří, Martin Tancer, and Uli Wagner. “Hardness of Embedding Simplicial
Complexes in Rd.” Journal of the European Mathematical Society. European
Mathematical Society, 2011. https://doi.org/10.4171/JEMS/252.
ieee: J. Matoušek, M. Tancer, and U. Wagner, “Hardness of embedding simplicial complexes
in Rd,” Journal of the European Mathematical Society, vol. 13, no. 2. European
Mathematical Society, pp. 259–295, 2011.
ista: Matoušek J, Tancer M, Wagner U. 2011. Hardness of embedding simplicial complexes
in Rd. Journal of the European Mathematical Society. 13(2), 259–295.
mla: Matoušek, Jiří, et al. “Hardness of Embedding Simplicial Complexes in Rd.”
Journal of the European Mathematical Society, vol. 13, no. 2, European
Mathematical Society, 2011, pp. 259–95, doi:10.4171/JEMS/252.
short: J. Matoušek, M. Tancer, U. Wagner, Journal of the European Mathematical Society
13 (2011) 259–295.
date_created: 2018-12-11T11:57:39Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T06:57:28Z
day: '01'
doi: 10.4171/JEMS/252
extern: 1
intvolume: ' 13'
issue: '2'
month: '01'
page: 259 - 295
publication: Journal of the European Mathematical Society
publication_status: published
publisher: European Mathematical Society
publist_id: '4470'
quality_controlled: 0
status: public
title: Hardness of embedding simplicial complexes in Rd
type: journal_article
volume: 13
year: '2011'
...
---
_id: '2437'
abstract:
- lang: eng
text: We introduce a new notion of minors for simplicial complexes (hypergraphs),
so-called homological minors. Our motivation is to propose a general approach
to attack certain extremal problems for sparse simplicial complexes and the corresponding
threshold problems for random complexes. In this paper, we focus on threshold
problems. The basic model for random complexes is the Linial-Meshulam model Xk(n,
p). By definition, such a complex has n vertices, a complete (k -1)-dimensional
skeleton, and every possible k-dimensional simplex is chosen independently with
probability p. We show that for every k, t≥ 1, there is a constant C = C(k, t)
such that for p≥ C/n, the random complex Xk(n, p) asymptotically almost surely
contains K tk (the complete k-dimensional complex on t vertices) as a homological
minor. As corollary, the threshold for (topological) embeddability of Xk(n, p)
into R2k is at p = θ(1/n). The method can be extended to other models of random
complexes (for which the lower skeleta are not necessarily complete) and also
to more general Tverberg-type problems, where instead of continuous maps without
doubly covered image points (embeddings), we consider maps without qfold covered
image points.
author:
- first_name: Uli
full_name: Uli Wagner
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Wagner U. Minors in random and expanding hypergraphs. In: ACM; 2011:351-360.
doi:10.1145/1998196.1998256'
apa: 'Wagner, U. (2011). Minors in random and expanding hypergraphs (pp. 351–360).
Presented at the SGC: Symposuim on Computational Geometry, ACM. https://doi.org/10.1145/1998196.1998256'
chicago: Wagner, Uli. “Minors in Random and Expanding Hypergraphs,” 351–60. ACM,
2011. https://doi.org/10.1145/1998196.1998256.
ieee: 'U. Wagner, “Minors in random and expanding hypergraphs,” presented at the
SGC: Symposuim on Computational Geometry, 2011, pp. 351–360.'
ista: 'Wagner U. 2011. Minors in random and expanding hypergraphs. SGC: Symposuim
on Computational Geometry, 351–360.'
mla: Wagner, Uli. Minors in Random and Expanding Hypergraphs. ACM, 2011,
pp. 351–60, doi:10.1145/1998196.1998256.
short: U. Wagner, in:, ACM, 2011, pp. 351–360.
conference:
name: 'SGC: Symposuim on Computational Geometry'
date_created: 2018-12-11T11:57:39Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T06:57:29Z
day: '01'
doi: 10.1145/1998196.1998256
extern: 1
month: '01'
page: 351 - 360
publication_status: published
publisher: ACM
publist_id: '4469'
quality_controlled: 0
status: public
title: Minors in random and expanding hypergraphs
type: conference
year: '2011'
...
---
_id: '2454'
abstract:
- lang: eng
text: Within a multicellular tissue cells may coordinately form a singular or multiple
polar axes, but it is unclear whether a common mechanism governs different types
of polar axis formation. The phosphorylation status of PIN proteins, which is
directly affected by the PINOID (PID) protein kinase and the PP2A protein phosphatase,
is known to regulate the apical-basal polarity of PIN localization in bipolar
cells of roots and shoot apices. Here, we provide evidence that the phosphorylation
status-mediated PIN polarity switch is widely used to modulate cellular processes
in Arabidopsis including multipolar pavement cells (PC) with interdigitated lobes
and indentations. The degree of PC interdigitation was greatly reduced either
when the FYPP1 gene, which encodes a PP2A called phytochrome-associated serine/threonine
protein phosphatase, was knocked out or when the PID gene was overexpressed (35S:PID).
These genetic modifications caused PIN1 localization to switch from lobe to indentation
regions. The PP2A and PID mediated switching of PIN1 localization is strikingly
similar to their regulation of the apical-basal polarity switch of PIN proteins
in other cells. Our findings suggest a common mechanism for the regulation of
PIN1 polarity formation, a fundamental cellular process that is crucial for pattern
formation both at the tissue/organ and cellular levels.
author:
- first_name: Hongjiang
full_name: Hongjiang Li
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Deshu
full_name: Lin, Deshu
last_name: Lin
- first_name: Pankaj
full_name: Dhonukshe, Pankaj B
last_name: Dhonukshe
- first_name: Shingo
full_name: Nagawa, Shingo
last_name: Nagawa
- first_name: Dandan
full_name: Chen, Dandan
last_name: Chen
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Ben
full_name: Scheres, Ben
last_name: Scheres
- first_name: Hongwei
full_name: Guo, Hongwei
last_name: Guo
- first_name: Zhenbiao
full_name: Yang, Zhenbiao
last_name: Yang
citation:
ama: Li H, Lin D, Dhonukshe P, et al. Phosphorylation switch modulates the interdigitated
pattern of PIN1 localization and cell expansion in Arabidopsis leaf epidermis.
Cell Research. 2011;21(6):970-978. doi:10.1038/cr.2011.49
apa: Li, H., Lin, D., Dhonukshe, P., Nagawa, S., Chen, D., Friml, J., … Yang, Z.
(2011). Phosphorylation switch modulates the interdigitated pattern of PIN1 localization
and cell expansion in Arabidopsis leaf epidermis. Cell Research. Nature
Publishing Group. https://doi.org/10.1038/cr.2011.49
chicago: Li, Hongjiang, Deshu Lin, Pankaj Dhonukshe, Shingo Nagawa, Dandan Chen,
Jiří Friml, Ben Scheres, Hongwei Guo, and Zhenbiao Yang. “Phosphorylation Switch
Modulates the Interdigitated Pattern of PIN1 Localization and Cell Expansion in
Arabidopsis Leaf Epidermis.” Cell Research. Nature Publishing Group, 2011.
https://doi.org/10.1038/cr.2011.49.
ieee: H. Li et al., “Phosphorylation switch modulates the interdigitated
pattern of PIN1 localization and cell expansion in Arabidopsis leaf epidermis,”
Cell Research, vol. 21, no. 6. Nature Publishing Group, pp. 970–978, 2011.
ista: Li H, Lin D, Dhonukshe P, Nagawa S, Chen D, Friml J, Scheres B, Guo H, Yang
Z. 2011. Phosphorylation switch modulates the interdigitated pattern of PIN1 localization
and cell expansion in Arabidopsis leaf epidermis. Cell Research. 21(6), 970–978.
mla: Li, Hongjiang, et al. “Phosphorylation Switch Modulates the Interdigitated
Pattern of PIN1 Localization and Cell Expansion in Arabidopsis Leaf Epidermis.”
Cell Research, vol. 21, no. 6, Nature Publishing Group, 2011, pp. 970–78,
doi:10.1038/cr.2011.49.
short: H. Li, D. Lin, P. Dhonukshe, S. Nagawa, D. Chen, J. Friml, B. Scheres, H.
Guo, Z. Yang, Cell Research 21 (2011) 970–978.
date_created: 2018-12-11T11:57:45Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2021-01-12T06:57:35Z
day: '01'
doi: 10.1038/cr.2011.49
extern: 1
intvolume: ' 21'
issue: '6'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203702/
month: '06'
oa: 1
page: 970 - 978
publication: Cell Research
publication_status: published
publisher: Nature Publishing Group
publist_id: '4449'
quality_controlled: 0
status: public
title: Phosphorylation switch modulates the interdigitated pattern of PIN1 localization
and cell expansion in Arabidopsis leaf epidermis
type: journal_article
volume: 21
year: '2011'
...
---
_id: '2460'
abstract:
- lang: eng
text: In unicellular and multicellular organisms, cell polarity is essential for
a wide range of biological processes. An important feature of cell polarity is
the asymmetric distribution of proteins in or at the plasma membrane. In plants
such polar localized proteins play various specific roles ranging from organizing
cell morphogenesis, asymmetric cell division, pathogen defense, nutrient transport
and establishment of hormone gradients for developmental patterning. Moreover,
flexible respecification of cell polarities enables plants to adjust their physiology
and development to environmental changes. Having evolved multicellularity independently
and lacking major cell polarity mechanisms of animal cells, plants came up with
alternative solutions to generate and respecify cell polarity as well as to regulate
polar domains at the plasma membrane.
author:
- first_name: Jan
full_name: Dettmer, Jan
last_name: Dettmer
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Dettmer J, Friml J. Cell polarity in plants: When two do the same, it is not
the same... Current Opinion in Cell Biology. 2011;23(6):686-696. doi:10.1016/j.ceb.2011.09.006'
apa: 'Dettmer, J., & Friml, J. (2011). Cell polarity in plants: When two do
the same, it is not the same... Current Opinion in Cell Biology. Elsevier.
https://doi.org/10.1016/j.ceb.2011.09.006'
chicago: 'Dettmer, Jan, and Jiří Friml. “Cell Polarity in Plants: When Two Do the
Same, It Is Not the Same...” Current Opinion in Cell Biology. Elsevier,
2011. https://doi.org/10.1016/j.ceb.2011.09.006.'
ieee: 'J. Dettmer and J. Friml, “Cell polarity in plants: When two do the same,
it is not the same...,” Current Opinion in Cell Biology, vol. 23, no. 6.
Elsevier, pp. 686–696, 2011.'
ista: 'Dettmer J, Friml J. 2011. Cell polarity in plants: When two do the same,
it is not the same... Current Opinion in Cell Biology. 23(6), 686–696.'
mla: 'Dettmer, Jan, and Jiří Friml. “Cell Polarity in Plants: When Two Do the Same,
It Is Not the Same...” Current Opinion in Cell Biology, vol. 23, no. 6,
Elsevier, 2011, pp. 686–96, doi:10.1016/j.ceb.2011.09.006.'
short: J. Dettmer, J. Friml, Current Opinion in Cell Biology 23 (2011) 686–696.
date_created: 2018-12-11T11:57:47Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2021-01-12T06:57:37Z
day: '01'
doi: 10.1016/j.ceb.2011.09.006
extern: '1'
intvolume: ' 23'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 686 - 696
publication: Current Opinion in Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '4443'
quality_controlled: '1'
status: public
title: 'Cell polarity in plants: When two do the same, it is not the same...'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2011'
...
---
_id: '2511'
abstract:
- lang: eng
text: Parkinson's disease is a common neurodegenerative disorder characterized by
a profound motor disability that is traceable to the emergence of synchronous,
rhythmic spiking in neurons of the external segment of the globus pallidus (GPe).
The origins of this pathophysiology are poorly defined for the generation of pacemaking.
After the induction of a parkinsonian state in mice, there was a progressive decline
in autonomous GPe pacemaking, which normally serves to desynchronize activity.
The loss was attributable to the downregulation of an ion channel that is essential
in pacemaking, the hyperpolarization and cyclic nucleotide-gated (HCN) channel.
Viral delivery of HCN2 subunits restored pacemaking and reduced burst spiking
in GPe neurons. However, the motor disability induced by dopamine (DA) depletion
was not reversed, suggesting that the loss of pacemaking was a consequence, rather
than a cause, of key network pathophysiology, a conclusion that is consistent
with the ability of L-type channel antagonists to attenuate silencing after DA
depletion.
author:
- first_name: Savio
full_name: Chan, Savio
last_name: Chan
- first_name: Kelly
full_name: Glajch, Kelly E
last_name: Glajch
- first_name: Tracy
full_name: Gertler, Tracy S
last_name: Gertler
- first_name: Jaime
full_name: Guzmán, Jaime N
last_name: Guzmán
- first_name: Jeff
full_name: Mercer, Jeff N
last_name: Mercer
- first_name: Alan
full_name: Lewis, Alan S
last_name: Lewis
- first_name: Alan
full_name: Goldberg, Alan B
last_name: Goldberg
- first_name: Tatiana
full_name: Tkatch, Tatiana
last_name: Tkatch
- first_name: Ryuichi
full_name: Ryuichi Shigemoto
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Sheila
full_name: Fleming, Sheila M
last_name: Fleming
- first_name: Dane
full_name: Chetkovich, Dane M
last_name: Chetkovich
- first_name: Pavel
full_name: Osten, Pavel
last_name: Osten
- first_name: Hitoshi
full_name: Kita, Hitoshi
last_name: Kita
- first_name: James
full_name: Surmeier, James D
last_name: Surmeier
citation:
ama: Chan S, Glajch K, Gertler T, et al. HCN channelopathy in external globus pallidus
neurons in models of Parkinson s disease. Nature Neuroscience. 2011;14(1):85-94.
doi:10.1038/nn.2692
apa: Chan, S., Glajch, K., Gertler, T., Guzmán, J., Mercer, J., Lewis, A., … Surmeier,
J. (2011). HCN channelopathy in external globus pallidus neurons in models of
Parkinson s disease. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.2692
chicago: Chan, Savio, Kelly Glajch, Tracy Gertler, Jaime Guzmán, Jeff Mercer, Alan
Lewis, Alan Goldberg, et al. “HCN Channelopathy in External Globus Pallidus Neurons
in Models of Parkinson s Disease.” Nature Neuroscience. Nature Publishing
Group, 2011. https://doi.org/10.1038/nn.2692.
ieee: S. Chan et al., “HCN channelopathy in external globus pallidus neurons
in models of Parkinson s disease,” Nature Neuroscience, vol. 14, no. 1.
Nature Publishing Group, pp. 85–94, 2011.
ista: Chan S, Glajch K, Gertler T, Guzmán J, Mercer J, Lewis A, Goldberg A, Tkatch
T, Shigemoto R, Fleming S, Chetkovich D, Osten P, Kita H, Surmeier J. 2011. HCN
channelopathy in external globus pallidus neurons in models of Parkinson s disease.
Nature Neuroscience. 14(1), 85–94.
mla: Chan, Savio, et al. “HCN Channelopathy in External Globus Pallidus Neurons
in Models of Parkinson s Disease.” Nature Neuroscience, vol. 14, no. 1,
Nature Publishing Group, 2011, pp. 85–94, doi:10.1038/nn.2692.
short: S. Chan, K. Glajch, T. Gertler, J. Guzmán, J. Mercer, A. Lewis, A. Goldberg,
T. Tkatch, R. Shigemoto, S. Fleming, D. Chetkovich, P. Osten, H. Kita, J. Surmeier,
Nature Neuroscience 14 (2011) 85–94.
date_created: 2018-12-11T11:58:06Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T06:57:56Z
day: '01'
doi: 10.1038/nn.2692
extern: 1
intvolume: ' 14'
issue: '1'
month: '01'
page: 85 - 94
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '4390'
quality_controlled: 0
status: public
title: HCN channelopathy in external globus pallidus neurons in models of Parkinson
s disease
type: journal_article
volume: 14
year: '2011'
...
---
_id: '2512'
abstract:
- lang: eng
text: GABAergic inhibition plays a central role in the control of pyramidal cell
ensemble activities; thus, any signaling mechanism that regulates inhibition is
able to fine-tune network patterns. Here, we provide evidence that the retrograde
nitric oxide (NO)- cGMP cascade triggered by NMDA receptor (NMDAR) activation
plays a role in the control of hippocampal GABAergic transmission in mice. GABAergic
synapses express neuronal nitric oxide synthase (nNOS) postsynaptically and NO
receptors (NO-sensitive guanylyl cyclase) in the presynaptic terminals. We hypothesized
that-similar to glutamatergic synapses-the Ca 2+ transients required to activate
nNOS were provided by NMDA receptor activation. Indeed, administration of 5 μm
NMDA induced a robust nNOS-dependent cGMP production in GABAergic terminals, selectively
in the CA1 and CA3c areas. Furthermore, using preembedding, postembedding, and
SDS-digested freeze-fracture replica immunogold labeling, we provided quantitative
immunocytochemical evidence that NMDAR subunits GluN1, GluN2A, and GluN2B were
present in most somatic GABAergic synapses postsynaptically. These data indicate
that NMDARs can modulate hippocampal GABAergic inhibition via NO- cGMP signaling
in an activity-dependent manner and that this effect is subregion specific in
the mouse hippocampus.
author:
- first_name: Eszter
full_name: Szabadits, Eszter
last_name: Szabadits
- first_name: Csaba
full_name: Cserép, Csaba
last_name: Cserép
- first_name: András
full_name: Szonyi, András
last_name: Szonyi
- 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: Masahiko
full_name: Watanabe, Masahiko
last_name: Watanabe
- first_name: Shigeyoshi
full_name: Itohara, Shigeyoshi
last_name: Itohara
- first_name: Tamás
full_name: Freund, Tamás F
last_name: Freund
- first_name: Gábor
full_name: Nyíri, Gábor
last_name: Nyíri
citation:
ama: Szabadits E, Cserép C, Szonyi A, et al. NMDA receptors in hippocampal GABAergic
synapses and their role in nitric oxide signaling. Journal of Neuroscience.
2011;31(16):5893-5904. doi:10.1523/JNEUROSCI.5938-10.2011
apa: Szabadits, E., Cserép, C., Szonyi, A., Fukazawa, Y., Shigemoto, R., Watanabe,
M., … Nyíri, G. (2011). NMDA receptors in hippocampal GABAergic synapses and their
role in nitric oxide signaling. Journal of Neuroscience. Society for Neuroscience.
https://doi.org/10.1523/JNEUROSCI.5938-10.2011
chicago: Szabadits, Eszter, Csaba Cserép, András Szonyi, Yugo Fukazawa, Ryuichi
Shigemoto, Masahiko Watanabe, Shigeyoshi Itohara, Tamás Freund, and Gábor Nyíri.
“NMDA Receptors in Hippocampal GABAergic Synapses and Their Role in Nitric Oxide
Signaling.” Journal of Neuroscience. Society for Neuroscience, 2011. https://doi.org/10.1523/JNEUROSCI.5938-10.2011.
ieee: E. Szabadits et al., “NMDA receptors in hippocampal GABAergic synapses
and their role in nitric oxide signaling,” Journal of Neuroscience, vol.
31, no. 16. Society for Neuroscience, pp. 5893–5904, 2011.
ista: Szabadits E, Cserép C, Szonyi A, Fukazawa Y, Shigemoto R, Watanabe M, Itohara
S, Freund T, Nyíri G. 2011. NMDA receptors in hippocampal GABAergic synapses and
their role in nitric oxide signaling. Journal of Neuroscience. 31(16), 5893–5904.
mla: Szabadits, Eszter, et al. “NMDA Receptors in Hippocampal GABAergic Synapses
and Their Role in Nitric Oxide Signaling.” Journal of Neuroscience, vol.
31, no. 16, Society for Neuroscience, 2011, pp. 5893–904, doi:10.1523/JNEUROSCI.5938-10.2011.
short: E. Szabadits, C. Cserép, A. Szonyi, Y. Fukazawa, R. Shigemoto, M. Watanabe,
S. Itohara, T. Freund, G. Nyíri, Journal of Neuroscience 31 (2011) 5893–5904.
date_created: 2018-12-11T11:58:06Z
date_published: 2011-04-20T00:00:00Z
date_updated: 2021-01-12T06:57:56Z
day: '20'
doi: 10.1523/JNEUROSCI.5938-10.2011
extern: 1
intvolume: ' 31'
issue: '16'
month: '04'
page: 5893 - 5904
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '4389'
quality_controlled: 0
status: public
title: NMDA receptors in hippocampal GABAergic synapses and their role in nitric oxide
signaling
type: journal_article
volume: 31
year: '2011'
...
---
_id: '2513'
abstract:
- lang: eng
text: 'SK2-containing channels are expressed in the postsynaptic density (PSD) of
dendritic spines on mouse hippocampal area CA1 pyramidal neurons and influence
synaptic responses, plasticity and learning. The Sk2 gene (also known as Kcnn2)
encodes two isoforms that differ only in the length of their N-terminal domains.
SK2-long (SK2-L) and SK2-short (SK2-S) are coexpressed in CA1 pyramidal neurons
and likely form heteromeric channels. In mice lacking SK2-L (SK2-S only mice),
SK2-S-containing channels were expressed in the extrasynaptic membrane, but were
excluded from the PSD. The SK channel contribution to excitatory postsynaptic
potentials was absent in SK2-S only mice and was restored by SK2-L re-expression.
Blocking SK channels increased the amount of long-term potentiation induced in
area CA1 in slices from wild-type mice but had no effect in slices from SK2-S
only mice. Furthermore, SK2-S only mice outperformed wild-type mice in the novel
object recognition task. These results indicate that SK2-L directs synaptic SK2-containing
channel expression and is important for normal synaptic signaling, plasticity
and learning. '
author:
- first_name: Duane
full_name: Allen, Duane H
last_name: Allen
- first_name: Chris
full_name: Bond, Chris T
last_name: Bond
- first_name: Rafael
full_name: Luján, Rafael
last_name: Luján
- first_name: Carmen
full_name: Ballesteros-Merino, Carmen
last_name: Ballesteros Merino
- first_name: Michael
full_name: Lin, Michael T
last_name: Lin
- first_name: Kang
full_name: Wang, Kang
last_name: Wang
- first_name: Nathan
full_name: Klett, Nathan
last_name: Klett
- 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
- first_name: Robert
full_name: Stackman, Robert W
last_name: Stackman
- first_name: James
full_name: Maylie, James G
last_name: Maylie
- first_name: John
full_name: Adelman, John P
last_name: Adelman
citation:
ama: Allen D, Bond C, Luján R, et al. The SK2-long isoform directs synaptic localization
and function of SK2-containing channels. Nature Neuroscience. 2011;14(6):744-749.
doi:10.1038/nn.2832
apa: Allen, D., Bond, C., Luján, R., Ballesteros Merino, C., Lin, M., Wang, K.,
… Adelman, J. (2011). The SK2-long isoform directs synaptic localization and function
of SK2-containing channels. Nature Neuroscience. Nature Publishing Group.
https://doi.org/10.1038/nn.2832
chicago: Allen, Duane, Chris Bond, Rafael Luján, Carmen Ballesteros Merino, Michael
Lin, Kang Wang, Nathan Klett, et al. “The SK2-Long Isoform Directs Synaptic Localization
and Function of SK2-Containing Channels.” Nature Neuroscience. Nature Publishing
Group, 2011. https://doi.org/10.1038/nn.2832.
ieee: D. Allen et al., “The SK2-long isoform directs synaptic localization
and function of SK2-containing channels,” Nature Neuroscience, vol. 14,
no. 6. Nature Publishing Group, pp. 744–749, 2011.
ista: Allen D, Bond C, Luján R, Ballesteros Merino C, Lin M, Wang K, Klett N, Watanabe
M, Shigemoto R, Stackman R, Maylie J, Adelman J. 2011. The SK2-long isoform directs
synaptic localization and function of SK2-containing channels. Nature Neuroscience.
14(6), 744–749.
mla: Allen, Duane, et al. “The SK2-Long Isoform Directs Synaptic Localization and
Function of SK2-Containing Channels.” Nature Neuroscience, vol. 14, no.
6, Nature Publishing Group, 2011, pp. 744–49, doi:10.1038/nn.2832.
short: D. Allen, C. Bond, R. Luján, C. Ballesteros Merino, M. Lin, K. Wang, N. Klett,
M. Watanabe, R. Shigemoto, R. Stackman, J. Maylie, J. Adelman, Nature Neuroscience
14 (2011) 744–749.
date_created: 2018-12-11T11:58:07Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2021-01-12T06:57:56Z
day: '01'
doi: 10.1038/nn.2832
extern: 1
intvolume: ' 14'
issue: '6'
month: '06'
page: 744 - 749
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '4388'
quality_controlled: 0
status: public
title: The SK2-long isoform directs synaptic localization and function of SK2-containing
channels
type: journal_article
volume: 14
year: '2011'
...
---
_id: '2717'
abstract:
- lang: eng
text: 'We consider Hermitian and symmetric random band matrices H in d ≥ 1 dimensions.
The matrix elements H xy, indexed by, are independent, uniformly distributed random
variables if {pipe}x-y{pipe} is less than the band width W, and zero otherwise.
We prove that the time evolution of a quantum particle subject to the Hamiltonian
H is diffusive on time scales. We also show that the localization length of the
eigenvectors of H is larger than a factor W d/6 times the band width. All results
are uniform in the size of the matrix. '
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
citation:
ama: Erdös L, Knowles A. Quantum diffusion and eigenfunction delocalization in a
random band matrix model. Communications in Mathematical Physics. 2011;303(2):509-554.
doi:10.1007/s00220-011-1204-2
apa: Erdös, L., & Knowles, A. (2011). Quantum diffusion and eigenfunction delocalization
in a random band matrix model. Communications in Mathematical Physics.
Springer. https://doi.org/10.1007/s00220-011-1204-2
chicago: Erdös, László, and Antti Knowles. “Quantum Diffusion and Eigenfunction
Delocalization in a Random Band Matrix Model.” Communications in Mathematical
Physics. Springer, 2011. https://doi.org/10.1007/s00220-011-1204-2.
ieee: L. Erdös and A. Knowles, “Quantum diffusion and eigenfunction delocalization
in a random band matrix model,” Communications in Mathematical Physics,
vol. 303, no. 2. Springer, pp. 509–554, 2011.
ista: Erdös L, Knowles A. 2011. Quantum diffusion and eigenfunction delocalization
in a random band matrix model. Communications in Mathematical Physics. 303(2),
509–554.
mla: Erdös, László, and Antti Knowles. “Quantum Diffusion and Eigenfunction Delocalization
in a Random Band Matrix Model.” Communications in Mathematical Physics,
vol. 303, no. 2, Springer, 2011, pp. 509–54, doi:10.1007/s00220-011-1204-2.
short: L. Erdös, A. Knowles, Communications in Mathematical Physics 303 (2011) 509–554.
date_created: 2018-12-11T11:59:14Z
date_published: 2011-04-01T00:00:00Z
date_updated: 2021-01-12T06:59:15Z
day: '01'
doi: 10.1007/s00220-011-1204-2
extern: 1
intvolume: ' 303'
issue: '2'
month: '04'
page: 509 - 554
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '4175'
quality_controlled: 0
status: public
title: Quantum diffusion and eigenfunction delocalization in a random band matrix
model
type: journal_article
volume: 303
year: '2011'
...
---
_id: '2765'
abstract:
- lang: eng
text: 'This is a study of the universality of spectral statistics for large random
matrices. Considered are N×N symmetric, Hermitian, or quaternion self-dual random
matrices with independent identically distributed entries (Wigner matrices), where
the probability distribution of each matrix element is given by a measure v with
zero expectation and with subexponential decay. The main result is that the correlation
functions of the local eigenvalue statistics in the bulk of the spectrum coincide
with those of the Gaussian Orthogonal Ensemble (GOE), the Gaussian Unitary Ensemble
(GUE), and the Gaussian Symplectic Ensemble (GSE), respectively, in the limit
as N → ∞. This approach is based on a study of the Dyson Brownian motion via a
related new dynamics, the local relaxation flow. As a main input, it is established
that the density of the eigenvalues converges to the Wigner semicircle law, and
this holds even down to the smallest possible scale. Moreover, it is shown that
the eigenvectors are completely delocalized. These results hold even without the
condition that the matrix elements are identically distributed: only independence
is used. In fact, for the matrix elements of the Green function strong estimates
are given that imply that the local statistics of any two ensembles in the bulk
are identical if the first four moments of the matrix elements match. Universality
at the spectral edges requires matching only two moments. A Wigner-type estimate
is also proved, and it is shown that the eigenvalues repel each other on arbitrarily
small scales.'
author:
- first_name: László
full_name: László Erdös
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
citation:
ama: 'Erdös L. Universality of Wigner random matrices: A survey of recent results.
Russian Mathematical Surveys. 2011;66(3):507-626. doi:10.1070/RM2011v066n03ABEH004749'
apa: 'Erdös, L. (2011). Universality of Wigner random matrices: A survey of recent
results. Russian Mathematical Surveys. IOP Publishing Ltd. https://doi.org/10.1070/RM2011v066n03ABEH004749'
chicago: 'Erdös, László. “Universality of Wigner Random Matrices: A Survey of Recent
Results.” Russian Mathematical Surveys. IOP Publishing Ltd., 2011. https://doi.org/10.1070/RM2011v066n03ABEH004749.'
ieee: 'L. Erdös, “Universality of Wigner random matrices: A survey of recent results,”
Russian Mathematical Surveys, vol. 66, no. 3. IOP Publishing Ltd., pp.
507–626, 2011.'
ista: 'Erdös L. 2011. Universality of Wigner random matrices: A survey of recent
results. Russian Mathematical Surveys. 66(3), 507–626.'
mla: 'Erdös, László. “Universality of Wigner Random Matrices: A Survey of Recent
Results.” Russian Mathematical Surveys, vol. 66, no. 3, IOP Publishing
Ltd., 2011, pp. 507–626, doi:10.1070/RM2011v066n03ABEH004749.'
short: L. Erdös, Russian Mathematical Surveys 66 (2011) 507–626.
date_created: 2018-12-11T11:59:29Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2019-04-26T07:22:20Z
day: '01'
doi: 10.1070/RM2011v066n03ABEH004749
extern: 1
intvolume: ' 66'
issue: '3'
main_file_link:
- open_access: '0'
url: http://arxiv.org/abs/1004.0861
month: '01'
page: 507 - 626
publication: Russian Mathematical Surveys
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '4125'
quality_controlled: 0
status: public
title: 'Universality of Wigner random matrices: A survey of recent results'
type: review
volume: 66
year: '2011'
...
---
_id: '2766'
abstract:
- lang: eng
text: We consider Hermitian and symmetric random band matrices H in d ≥ dimensions.
The matrix elements Hxy, indexed by x,y ∈ Λ ⊂ ℤd are independent and their variances
satisfy σ2xy:= E{pipe}Hxy{pipe}2 = W-d f((x-y)/W for some probability density
f. We assume that the law of each matrix element Hxy is symmetric and exhibits
subexponential decay. We prove that the time evolution of a quantum particle subject
to the Hamiltonian H is diffusive on time scales ≪ Wd/3. We also show that the
localization length of the eigenvectors of H is larger than a factor Wd/6 times
the band width W. All results are uniform in the size {pipe}Λ{pipe} of the matrix.
This extends our recent result (Erdo{double acute}s and Knowles in Commun. Math.
Phys., 2011) to general band matrices. As another consequence of our proof we
show that, for a larger class of random matrices satisfying Σx σ2xy for all y,
the largest eigenvalue of H is bounded with high probability by 2+M-2/3+e{open}
for any e{open} > 0, where M:= 1/(maxx,y σ2xy).
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
citation:
ama: Erdös L, Knowles A. Quantum diffusion and delocalization for band matrices
with general distribution. Annales Henri Poincare. 2011;12(7):1227-1319.
doi:10.1007/s00023-011-0104-5
apa: Erdös, L., & Knowles, A. (2011). Quantum diffusion and delocalization for
band matrices with general distribution. Annales Henri Poincare. Birkhäuser.
https://doi.org/10.1007/s00023-011-0104-5
chicago: Erdös, László, and Antti Knowles. “Quantum Diffusion and Delocalization
for Band Matrices with General Distribution.” Annales Henri Poincare. Birkhäuser,
2011. https://doi.org/10.1007/s00023-011-0104-5.
ieee: L. Erdös and A. Knowles, “Quantum diffusion and delocalization for band matrices
with general distribution,” Annales Henri Poincare, vol. 12, no. 7. Birkhäuser,
pp. 1227–1319, 2011.
ista: Erdös L, Knowles A. 2011. Quantum diffusion and delocalization for band matrices
with general distribution. Annales Henri Poincare. 12(7), 1227–1319.
mla: Erdös, László, and Antti Knowles. “Quantum Diffusion and Delocalization for
Band Matrices with General Distribution.” Annales Henri Poincare, vol.
12, no. 7, Birkhäuser, 2011, pp. 1227–319, doi:10.1007/s00023-011-0104-5.
short: L. Erdös, A. Knowles, Annales Henri Poincare 12 (2011) 1227–1319.
date_created: 2018-12-11T11:59:29Z
date_published: 2011-11-01T00:00:00Z
date_updated: 2021-01-12T06:59:33Z
day: '01'
doi: 10.1007/s00023-011-0104-5
extern: 1
intvolume: ' 12'
issue: '7'
month: '11'
page: 1227 - 1319
publication: Annales Henri Poincare
publication_status: published
publisher: Birkhäuser
publist_id: '4124'
quality_controlled: 0
status: public
title: Quantum diffusion and delocalization for band matrices with general distribution
type: journal_article
volume: 12
year: '2011'
...
---
_id: '2764'
abstract:
- lang: eng
text: Consider the Dyson Brownian motion with parameter β, where β=1,2,4 corresponds
to the eigenvalue flows for the eigenvalues of symmetric, hermitian and quaternion
self-dual ensembles. For any β≥1, we prove that the relaxation time to local equilibrium
for the Dyson Brownian motion is bounded above by N -ζ for some ζ> 0. The proof
is based on an estimate of the entropy flow of the Dyson Brownian motion w. r.
t. a "pseudo equilibrium measure". As an application of this estimate,
we prove that the eigenvalue spacing statistics in the bulk of the spectrum for
N×N symmetric Wigner ensemble is the same as that of the Gaussian Orthogonal Ensemble
(GOE) in the limit N→∞. The assumptions on the probability distribution of the
matrix elements of the Wigner ensemble are a subexponential decay and some minor
restriction on the support.
author:
- first_name: László
full_name: László Erdös
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
- first_name: Horng
full_name: Yau, Horng-Tzer
last_name: Yau
citation:
ama: Erdös L, Schlein B, Yau H. Universality of random matrices and local relaxation
flow. Inventiones Mathematicae. 2011;185(1):75-119. doi:10.1007/s00222-010-0302-7
apa: Erdös, L., Schlein, B., & Yau, H. (2011). Universality of random matrices
and local relaxation flow. Inventiones Mathematicae. Springer. https://doi.org/10.1007/s00222-010-0302-7
chicago: Erdös, László, Benjamin Schlein, and Horng Yau. “Universality of Random
Matrices and Local Relaxation Flow.” Inventiones Mathematicae. Springer,
2011. https://doi.org/10.1007/s00222-010-0302-7.
ieee: L. Erdös, B. Schlein, and H. Yau, “Universality of random matrices and local
relaxation flow,” Inventiones Mathematicae, vol. 185, no. 1. Springer,
pp. 75–119, 2011.
ista: Erdös L, Schlein B, Yau H. 2011. Universality of random matrices and local
relaxation flow. Inventiones Mathematicae. 185(1), 75–119.
mla: Erdös, László, et al. “Universality of Random Matrices and Local Relaxation
Flow.” Inventiones Mathematicae, vol. 185, no. 1, Springer, 2011, pp. 75–119,
doi:10.1007/s00222-010-0302-7.
short: L. Erdös, B. Schlein, H. Yau, Inventiones Mathematicae 185 (2011) 75–119.
date_created: 2018-12-11T11:59:29Z
date_published: 2011-07-01T00:00:00Z
date_updated: 2021-01-12T06:59:32Z
day: '01'
doi: 10.1007/s00222-010-0302-7
extern: 1
intvolume: ' 185'
issue: '1'
month: '07'
page: 75 - 119
publication: Inventiones Mathematicae
publication_status: published
publisher: Springer
publist_id: '4126'
quality_controlled: 0
status: public
title: Universality of random matrices and local relaxation flow
type: journal_article
volume: 185
year: '2011'
...
---
_id: '2799'
abstract:
- lang: eng
text: Shear flows undergo a sudden transition from laminar to turbulent motion as
the velocity increases, and the onset of turbulence radically changes transport
efficiency and mixing properties. Even for the well-studied case of pipe flow,
it has not been possible to determine at what Reynolds number the motion will
be either persistently turbulent or ultimately laminar. We show that in pipes,
turbulence that is transient at low Reynolds numbers becomes sustained at a distinct
critical point. Through extensive experiments and computer simulations, we were
able to identify and characterize the processes ultimately responsible for sustaining
turbulence. In contrast to the classical Landau-Ruelle-Takens view that turbulence
arises from an increase in the temporal complexity of fluid motion, here, spatial
proliferation of chaotic domains is the decisive process and intrinsic to the
nature of fluid turbulence.
author:
- first_name: Kerstin
full_name: Avila, Kerstin
last_name: Avila
- first_name: David
full_name: Moxey, David
last_name: Moxey
- first_name: Alberto
full_name: de Lózar, Alberto
last_name: De Lózar
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
- first_name: Dwight
full_name: Barkley, Dwight
last_name: Barkley
- first_name: Björn
full_name: Björn Hof
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Avila K, Moxey D, De Lózar A, Avila M, Barkley D, Hof B. The onset of turbulence
in pipe flow. Science. 2011;333(6039):192-196. doi:10.1126/science.1203223
apa: Avila, K., Moxey, D., De Lózar, A., Avila, M., Barkley, D., & Hof, B. (2011).
The onset of turbulence in pipe flow. Science. American Association for
the Advancement of Science. https://doi.org/10.1126/science.1203223
chicago: Avila, Kerstin, David Moxey, Alberto De Lózar, Marc Avila, Dwight Barkley,
and Björn Hof. “The Onset of Turbulence in Pipe Flow.” Science. American
Association for the Advancement of Science, 2011. https://doi.org/10.1126/science.1203223.
ieee: K. Avila, D. Moxey, A. De Lózar, M. Avila, D. Barkley, and B. Hof, “The onset
of turbulence in pipe flow,” Science, vol. 333, no. 6039. American Association
for the Advancement of Science, pp. 192–196, 2011.
ista: Avila K, Moxey D, De Lózar A, Avila M, Barkley D, Hof B. 2011. The onset of
turbulence in pipe flow. Science. 333(6039), 192–196.
mla: Avila, Kerstin, et al. “The Onset of Turbulence in Pipe Flow.” Science,
vol. 333, no. 6039, American Association for the Advancement of Science, 2011,
pp. 192–96, doi:10.1126/science.1203223.
short: K. Avila, D. Moxey, A. De Lózar, M. Avila, D. Barkley, B. Hof, Science 333
(2011) 192–196.
date_created: 2018-12-11T11:59:39Z
date_published: 2011-07-08T00:00:00Z
date_updated: 2021-01-12T06:59:47Z
day: '08'
doi: 10.1126/science.1203223
extern: 1
intvolume: ' 333'
issue: '6039'
month: '07'
page: 192 - 196
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '4090'
quality_controlled: 0
status: public
title: The onset of turbulence in pipe flow
type: journal_article
volume: 333
year: '2011'
...
---
_id: '2800'
abstract:
- lang: eng
text: In shear flows, turbulence first occurs in the form of localized structures
(puffs/spots) surrounded by laminar fluid. We here investigate such spatially
intermittent flows in a pipe experiment showing that turbulent puffs have a well-defined
interaction distance, which sets their minimum spacing as well as the maximum
observable turbulent fraction. Two methodologies are employed. Starting from a
laminar flow, puffs are first created by locally injecting a jet of fluid through
the pipe wall. When the perturbation is applied periodically at low frequencies,
as expected, a regular sequence of puffs is observed where the puff spacing is
given by the ratio of the mean flow speed to the perturbation frequency. At large
frequencies however puffs are found to interact and annihilate each other. Varying
the perturbation frequency, an interaction distance is determined which sets the
highest possible turbulence fraction. This enables us to establish an upper bound
for the friction factor in the transitional regime, which provides a well-defined
link between the Blasius and the Hagen-Poiseuille friction laws. In the second
set of experiments, the Reynolds number is reduced suddenly from fully turbulent
to the intermittent regime. The resulting flow reorganizes itself to a sequence
of constant size puffs which, unlike in Couette and Taylor–Couette flow are randomly
spaced. The minimum distance between the turbulent patches is identical to the
puff interaction length. The puff interaction length is found to be in agreement
with the wavelength of regular stripe and spiral patterns in plane Couette and
Taylor–Couette flow.
author:
- first_name: Devranjan
full_name: Samanta, Devranjan
last_name: Samanta
- first_name: Alberto
full_name: de Lózar, Alberto
last_name: De Lózar
- first_name: Björn
full_name: Björn Hof
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Samanta D, De Lózar A, Hof B. Experimental investigation of laminar turbulent
intermittency in pipe flow. Journal of Fluid Mechanics. 2011;681:193-204.
doi:10.1017/jfm.2011.189
apa: Samanta, D., De Lózar, A., & Hof, B. (2011). Experimental investigation
of laminar turbulent intermittency in pipe flow. Journal of Fluid Mechanics.
Cambridge University Press. https://doi.org/10.1017/jfm.2011.189
chicago: Samanta, Devranjan, Alberto De Lózar, and Björn Hof. “Experimental Investigation
of Laminar Turbulent Intermittency in Pipe Flow.” Journal of Fluid Mechanics.
Cambridge University Press, 2011. https://doi.org/10.1017/jfm.2011.189.
ieee: D. Samanta, A. De Lózar, and B. Hof, “Experimental investigation of laminar
turbulent intermittency in pipe flow,” Journal of Fluid Mechanics, vol.
681. Cambridge University Press, pp. 193–204, 2011.
ista: Samanta D, De Lózar A, Hof B. 2011. Experimental investigation of laminar
turbulent intermittency in pipe flow. Journal of Fluid Mechanics. 681, 193–204.
mla: Samanta, Devranjan, et al. “Experimental Investigation of Laminar Turbulent
Intermittency in Pipe Flow.” Journal of Fluid Mechanics, vol. 681, Cambridge
University Press, 2011, pp. 193–204, doi:10.1017/jfm.2011.189.
short: D. Samanta, A. De Lózar, B. Hof, Journal of Fluid Mechanics 681 (2011) 193–204.
date_created: 2018-12-11T11:59:40Z
date_published: 2011-08-25T00:00:00Z
date_updated: 2021-01-12T06:59:48Z
day: '25'
doi: 10.1017/jfm.2011.189
extern: 1
intvolume: ' 681'
month: '08'
page: 193 - 204
publication: Journal of Fluid Mechanics
publication_status: published
publisher: Cambridge University Press
publist_id: '4089'
quality_controlled: 0
status: public
title: Experimental investigation of laminar turbulent intermittency in pipe flow
type: journal_article
volume: 681
year: '2011'
...
---
_id: '2801'
abstract:
- lang: eng
text: Turbulent puffs in pipe flow are characterized by a sharp laminar-turbulent
interface at the trailing edge and a more diffused leading interface. It is known
that these laminar-turbulent interfaces propagate at a speed that is approximately
equal to the flow rate. Our results from direct numerical simulation show that,
locally, the interface velocity relative to the fluid (i) counteracts the advection
due to the laminar velocity profile so that the puff can preserve its characteristic
overall shape, (ii) is very small in magnitude, but involves a large interface
area so that the global propagation velocity relative to the mean flow can be
large and (iii) is determined by both inertial and viscous effects. The analysis
provides some new insights into the mechanisms that sustain or expand localized
turbulence and might be relevant for the design of new control strategies.
alternative_title:
- 'Journal of Physics: Conference Series'
author:
- first_name: Markus
full_name: Holzner, Markus
last_name: Holzner
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
- first_name: Alberto
full_name: de Lózar, Alberto
last_name: De Lózar
- 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, Avila M, De Lózar A, Hof B. A Lagrangian approach to the interface
velocity of turbulent puffs in pipe flow. In: Vol 318. IOP Publishing Ltd.; 2011.
doi:10.1088/1742-6596/318/5/052031'
apa: 'Holzner, M., Avila, M., De Lózar, A., & Hof, B. (2011). A Lagrangian approach
to the interface velocity of turbulent puffs in pipe flow (Vol. 318). Presented
at the ETC13: European Turbulence Conference, IOP Publishing Ltd. https://doi.org/10.1088/1742-6596/318/5/052031'
chicago: Holzner, Markus, Marc Avila, Alberto De Lózar, and Björn Hof. “A Lagrangian
Approach to the Interface Velocity of Turbulent Puffs in Pipe Flow,” Vol. 318.
IOP Publishing Ltd., 2011. https://doi.org/10.1088/1742-6596/318/5/052031.
ieee: 'M. Holzner, M. Avila, A. De Lózar, and B. Hof, “A Lagrangian approach to
the interface velocity of turbulent puffs in pipe flow,” presented at the ETC13:
European Turbulence Conference, 2011, vol. 318, no. 5.'
ista: 'Holzner M, Avila M, De Lózar A, Hof B. 2011. A Lagrangian approach to the
interface velocity of turbulent puffs in pipe flow. ETC13: European Turbulence
Conference, Journal of Physics: Conference Series, vol. 318.'
mla: Holzner, Markus, et al. A Lagrangian Approach to the Interface Velocity
of Turbulent Puffs in Pipe Flow. Vol. 318, no. 5, IOP Publishing Ltd., 2011,
doi:10.1088/1742-6596/318/5/052031.
short: M. Holzner, M. Avila, A. De Lózar, B. Hof, in:, IOP Publishing Ltd., 2011.
conference:
name: 'ETC13: European Turbulence Conference'
date_created: 2018-12-11T11:59:40Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2019-04-26T07:22:20Z
day: '01'
doi: 10.1088/1742-6596/318/5/052031
extern: 1
intvolume: ' 318'
issue: '5'
month: '09'
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '4088'
quality_controlled: 0
status: public
title: A Lagrangian approach to the interface velocity of turbulent puffs in pipe
flow
type: conference
volume: 318
year: '2011'
...
---
_id: '2874'
abstract:
- lang: eng
text: The apical hook develops in the upper part of the hypocotyl when seeds buried
in the soil germinate, and serves to protect cotyledons and the shoot apical meristem
from possible damage caused by pushing through the soil. The curvature is formed
through differential cell growth that occurs at the two opposite sides of the
hypocotyl, and it is established by a gradient of auxin activity and refined by
the coordinated action of auxin and ethylene. Here we show that gibberellins (GAs)
promote hook development through the transcriptional regulation of several genes
of the ethylene and auxin pathways in Arabidopsis. The level of GA activity determines
the speed of hook formation and the extent of the curvature during the formation
phase independently of ethylene, probably by modulating auxin transport and response
through HLS1, PIN3, and PIN7. Moreover, GAs cooperate with ethylene in preventing
hook opening, in part through the induction of ethylene production mediated by
ACS5/ETO2 and ACS8.
author:
- first_name: Javier
full_name: Gallego-Bartolomé, Javier
last_name: Gallego Bartolomé
- first_name: María
full_name: Arana, María V
last_name: Arana
- first_name: Filip
full_name: Vandenbussche, Filip
last_name: Vandenbussche
- first_name: Petra
full_name: Žádníková, Petra
last_name: Žádníková
- first_name: Eugenio
full_name: Minguet, Eugenio G
last_name: Minguet
- first_name: Vicente
full_name: Guardiola, Vicente
last_name: Guardiola
- first_name: Dominique
full_name: Van Der Straeten, Dominique
last_name: Van Der Straeten
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: David
full_name: Alabadí, David
last_name: Alabadí
- first_name: Miguel
full_name: Blázquez, Miguel A
last_name: Blázquez
citation:
ama: Gallego Bartolomé J, Arana M, Vandenbussche F, et al. Hierarchy of hormone
action controlling apical hook development in Arabidopsis. Plant Journal.
2011;67(4):622-634. doi:10.1111/j.1365-313X.2011.04621.x
apa: Gallego Bartolomé, J., Arana, M., Vandenbussche, F., Žádníková, P., Minguet,
E., Guardiola, V., … Blázquez, M. (2011). Hierarchy of hormone action controlling
apical hook development in Arabidopsis. Plant Journal. Wiley-Blackwell.
https://doi.org/10.1111/j.1365-313X.2011.04621.x
chicago: Gallego Bartolomé, Javier, María Arana, Filip Vandenbussche, Petra Žádníková,
Eugenio Minguet, Vicente Guardiola, Dominique Van Der Straeten, Eva Benková, David
Alabadí, and Miguel Blázquez. “Hierarchy of Hormone Action Controlling Apical
Hook Development in Arabidopsis.” Plant Journal. Wiley-Blackwell, 2011.
https://doi.org/10.1111/j.1365-313X.2011.04621.x.
ieee: J. Gallego Bartolomé et al., “Hierarchy of hormone action controlling
apical hook development in Arabidopsis,” Plant Journal, vol. 67, no. 4.
Wiley-Blackwell, pp. 622–634, 2011.
ista: Gallego Bartolomé J, Arana M, Vandenbussche F, Žádníková P, Minguet E, Guardiola
V, Van Der Straeten D, Benková E, Alabadí D, Blázquez M. 2011. Hierarchy of hormone
action controlling apical hook development in Arabidopsis. Plant Journal. 67(4),
622–634.
mla: Gallego Bartolomé, Javier, et al. “Hierarchy of Hormone Action Controlling
Apical Hook Development in Arabidopsis.” Plant Journal, vol. 67, no. 4,
Wiley-Blackwell, 2011, pp. 622–34, doi:10.1111/j.1365-313X.2011.04621.x.
short: J. Gallego Bartolomé, M. Arana, F. Vandenbussche, P. Žádníková, E. Minguet,
V. Guardiola, D. Van Der Straeten, E. Benková, D. Alabadí, M. Blázquez, Plant
Journal 67 (2011) 622–634.
date_created: 2018-12-11T12:00:04Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2021-01-12T07:00:24Z
day: '01'
doi: 10.1111/j.1365-313X.2011.04621.x
extern: 1
intvolume: ' 67'
issue: '4'
month: '08'
page: 622 - 634
publication: Plant Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3891'
quality_controlled: 0
status: public
title: Hierarchy of hormone action controlling apical hook development in Arabidopsis
type: journal_article
volume: 67
year: '2011'
...
---
_id: '2871'
abstract:
- lang: eng
text: Despite their relatively simple appearance, roots are incredibly complex organs
that are highly adapted to differing environments. Many aspects of root development
are co-ordinated by subtle spatial differences in the concentrations of the phytohormones
auxin and cytokinin. Events from the formation of a root during embryogenesis
to the determination of the network of lateral roots are controlled by interactions
between these hormones. Recently, interactions have been defined where auxin signaling
promotes the expression of cytokinin signaling inhibitors, cytokinin signaling
promotes the expression of auxin signaling inhibitors and finally where cytokinin
signaling regulates the complex network of auxin transport proteins to position
zones of high auxin signaling. We are witnessing a period of discovery in which
we are beginning to understand how these hormonal pathways communicate to regulate
root formation.
author:
- first_name: Anthony
full_name: Bishopp, Anthony
last_name: Bishopp
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Ykä
full_name: Helariutta, Ykä
last_name: Helariutta
citation:
ama: 'Bishopp A, Benková E, Helariutta Y. Sending mixed messages: Auxin-cytokinin
crosstalk in roots. Current Opinion in Plant Biology. 2011;14(1):10-16.
doi:10.1016/j.pbi.2010.08.014'
apa: 'Bishopp, A., Benková, E., & Helariutta, Y. (2011). Sending mixed messages:
Auxin-cytokinin crosstalk in roots. Current Opinion in Plant Biology. Elsevier.
https://doi.org/10.1016/j.pbi.2010.08.014'
chicago: 'Bishopp, Anthony, Eva Benková, and Ykä Helariutta. “Sending Mixed Messages:
Auxin-Cytokinin Crosstalk in Roots.” Current Opinion in Plant Biology.
Elsevier, 2011. https://doi.org/10.1016/j.pbi.2010.08.014.'
ieee: 'A. Bishopp, E. Benková, and Y. Helariutta, “Sending mixed messages: Auxin-cytokinin
crosstalk in roots,” Current Opinion in Plant Biology, vol. 14, no. 1.
Elsevier, pp. 10–16, 2011.'
ista: 'Bishopp A, Benková E, Helariutta Y. 2011. Sending mixed messages: Auxin-cytokinin
crosstalk in roots. Current Opinion in Plant Biology. 14(1), 10–16.'
mla: 'Bishopp, Anthony, et al. “Sending Mixed Messages: Auxin-Cytokinin Crosstalk
in Roots.” Current Opinion in Plant Biology, vol. 14, no. 1, Elsevier,
2011, pp. 10–16, doi:10.1016/j.pbi.2010.08.014.'
short: A. Bishopp, E. Benková, Y. Helariutta, Current Opinion in Plant Biology 14
(2011) 10–16.
date_created: 2018-12-11T12:00:03Z
date_published: 2011-02-01T00:00:00Z
date_updated: 2021-01-12T07:00:23Z
day: '01'
doi: 10.1016/j.pbi.2010.08.014
extern: 1
intvolume: ' 14'
issue: '1'
month: '02'
page: 10 - 16
publication: Current Opinion in Plant Biology
publication_status: published
publisher: Elsevier
publist_id: '3894'
quality_controlled: 0
status: public
title: 'Sending mixed messages: Auxin-cytokinin crosstalk in roots'
type: journal_article
volume: 14
year: '2011'
...
---
_id: '2898'
abstract:
- lang: eng
text: Sex allocation theory has been remarkably successful at explaining the prevalence
of even sex ratios in natural populations and at identifying specific conditions
that can result in biased sex ratios. Much of this theory focuses on parental
sex determination (SD) strategies. Here, we consider instead the evolutionary
causes and consequences of mixed offspring SD strategies, in which the genotype
of an individual determines not its sex, but the probability of developing one
of multiple sexes. We find that alleles specifying mixed offspring SD strategies
can generally outcompete alleles that specify pure strategies, but generate constraints
that may prevent a population from reaching an even sex ratio. We use our model
to analyze sex ratios in natural populations of Tetrahymena thermophila, a ciliate
with seven sexes determined by mixed SD alleles. We show that probabilistic SD
is sufficient to account for the occurrence of skewed sex ratios in natural populations
of T. thermophila, provided that their effective population sizes are small. Our
results highlight the importance of genetic drift in sex ratio evolution and suggest
that mixed offspring SD strategies should be more common than currently thought.
author:
- first_name: Tiago
full_name: Tiago Paixao
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Sujal
full_name: Phadke, Sujal S
last_name: Phadke
- first_name: Ricardo
full_name: Azevedo, Ricardo B
last_name: Azevedo
- first_name: Rebecca
full_name: Zufall, Rebecca A
last_name: Zufall
citation:
ama: Paixao T, Phadke S, Azevedo R, Zufall R. Sex ratio evolution under probabilistic
sex determination. Evolution; International Journal of Organic Evolution.
2011;65(7):2050-2060. doi:10.1111/j.1558-5646.2011.01266.x
apa: Paixao, T., Phadke, S., Azevedo, R., & Zufall, R. (2011). Sex ratio evolution
under probabilistic sex determination. Evolution; International Journal of
Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.1558-5646.2011.01266.x
chicago: Paixao, Tiago, Sujal Phadke, Ricardo Azevedo, and Rebecca Zufall. “Sex
Ratio Evolution under Probabilistic Sex Determination.” Evolution; International
Journal of Organic Evolution. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1558-5646.2011.01266.x.
ieee: T. Paixao, S. Phadke, R. Azevedo, and R. Zufall, “Sex ratio evolution under
probabilistic sex determination,” Evolution; International Journal of Organic
Evolution, vol. 65, no. 7. Wiley-Blackwell, pp. 2050–2060, 2011.
ista: Paixao T, Phadke S, Azevedo R, Zufall R. 2011. Sex ratio evolution under probabilistic
sex determination. Evolution; International Journal of Organic Evolution. 65(7),
2050–2060.
mla: Paixao, Tiago, et al. “Sex Ratio Evolution under Probabilistic Sex Determination.”
Evolution; International Journal of Organic Evolution, vol. 65, no. 7,
Wiley-Blackwell, 2011, pp. 2050–60, doi:10.1111/j.1558-5646.2011.01266.x.
short: T. Paixao, S. Phadke, R. Azevedo, R. Zufall, Evolution; International Journal
of Organic Evolution 65 (2011) 2050–2060.
date_created: 2018-12-11T12:00:13Z
date_published: 2011-03-01T00:00:00Z
date_updated: 2021-01-12T07:00:33Z
day: '01'
doi: 10.1111/j.1558-5646.2011.01266.x
extern: 1
intvolume: ' 65'
issue: '7'
month: '03'
page: 2050 - 2060
publication: Evolution; International Journal of Organic Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3860'
quality_controlled: 0
status: public
title: Sex ratio evolution under probabilistic sex determination
type: journal_article
volume: 65
year: '2011'
...
---
_id: '2897'
acknowledgement: TFs regulate gene expression by binding to specific sequences in
the promoter regions of their target genes. Promoters often contain multiple copies
of the same TF binding sites. How does this multiplicity evolve? One possibility
is that individuals with multiple, redundant binding sites have higher fitness.
However, nonadaptive processes are also likely to be important. Here, we develop
a mathematical model of the evolution of TF binding sites to help us disentangle
how different evolutionary mechanisms contribute to the evolution of binding site
redundancy and multiplicity. We show that recombination is expected to promote the
evolution of multiple binding sites. This prediction is corroborated by genome-wide
data from yeast. Another important factor in the evolution of multiplicity predicted
in our analysis is TF promiscuity, that is, the ability of a TF to bind to multiple
sequences. In addition, our analysis indicated that direct selection can have large
effects on the evolution of redundancy and multiplicity. Data from yeast identified
selection for changes in expression level as a candidate mechanism for the evolution
of multiple binding sites. We conclude that, although selection may play a major
role in the evolution of multiplicity in regulatory regions, nonadaptive forces
can also lead to high levels of multiplicity.
author:
- first_name: Tiago
full_name: Tiago Paixao
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Ricardo
full_name: Azevedo, Ricardo B
last_name: Azevedo
citation:
ama: Paixao T, Azevedo R. Redundancy and the Evolution of Cis Regulatory Element
Multiplicity. PLoS Computational Biology. 2011;6(7). doi:10.1371/journal.pcbi.1000848
apa: Paixao, T., & Azevedo, R. (2011). Redundancy and the Evolution of Cis Regulatory
Element Multiplicity. PLoS Computational Biology. Public Library of Science.
https://doi.org/10.1371/journal.pcbi.1000848
chicago: Paixao, Tiago, and Ricardo Azevedo. “Redundancy and the Evolution of Cis
Regulatory Element Multiplicity.” PLoS Computational Biology. Public Library
of Science, 2011. https://doi.org/10.1371/journal.pcbi.1000848.
ieee: T. Paixao and R. Azevedo, “Redundancy and the Evolution of Cis Regulatory
Element Multiplicity,” PLoS Computational Biology, vol. 6, no. 7. Public
Library of Science, 2011.
ista: Paixao T, Azevedo R. 2011. Redundancy and the Evolution of Cis Regulatory
Element Multiplicity. PLoS Computational Biology. 6(7).
mla: Paixao, Tiago, and Ricardo Azevedo. “Redundancy and the Evolution of Cis Regulatory
Element Multiplicity.” PLoS Computational Biology, vol. 6, no. 7, Public
Library of Science, 2011, doi:10.1371/journal.pcbi.1000848.
short: T. Paixao, R. Azevedo, PLoS Computational Biology 6 (2011).
date_created: 2018-12-11T12:00:13Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:33Z
day: '01'
doi: 10.1371/journal.pcbi.1000848
extern: 1
intvolume: ' 6'
issue: '7'
month: '01'
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '3861'
quality_controlled: 0
status: public
title: Redundancy and the Evolution of Cis Regulatory Element Multiplicity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 6
year: '2011'
...
---
_id: '2922'
author:
- first_name: Sara
full_name: Vicente, Sara
last_name: Vicente
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: 'Vicente S, Kolmogorov V, Rother C. Graph-cut Based Image Segmentation with
Connectivity Priors. In: Blake A, Kohli P, Rother C, eds. Markov Random Fields
for Vision and Image Processing. Massachusetts Institute of Technology Press;
2011.'
apa: Vicente, S., Kolmogorov, V., & Rother, C. (2011). Graph-cut Based Image
Segmentation with Connectivity Priors. In A. Blake, P. Kohli, & C. Rother
(Eds.), Markov Random Fields for Vision and Image Processing. Massachusetts
Institute of Technology Press.
chicago: Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Graph-Cut Based
Image Segmentation with Connectivity Priors.” In Markov Random Fields for Vision
and Image Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten
Rother. Massachusetts Institute of Technology Press, 2011.
ieee: S. Vicente, V. Kolmogorov, and C. Rother, “Graph-cut Based Image Segmentation
with Connectivity Priors,” in Markov Random Fields for Vision and Image Processing,
A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology
Press, 2011.
ista: 'Vicente S, Kolmogorov V, Rother C. 2011.Graph-cut Based Image Segmentation
with Connectivity Priors. In: Markov Random Fields for Vision and Image Processing.
.'
mla: Vicente, Sara, et al. “Graph-Cut Based Image Segmentation with Connectivity
Priors.” Markov Random Fields for Vision and Image Processing, edited by
Andrew Blake et al., Massachusetts Institute of Technology Press, 2011.
short: S. Vicente, V. Kolmogorov, C. Rother, in:, A. Blake, P. Kohli, C. Rother
(Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts Institute
of Technology Press, 2011.
date_created: 2018-12-11T12:00:21Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:43Z
day: '01'
editor:
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Pushmeet
full_name: Kohli, Pushmeet
last_name: Kohli
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
extern: 1
month: '01'
publication: Markov Random Fields for Vision and Image Processing
publication_status: published
publisher: Massachusetts Institute of Technology Press
publist_id: '3815'
quality_controlled: 0
status: public
title: Graph-cut Based Image Segmentation with Connectivity Priors
type: book_chapter
year: '2011'
...
---
_id: '2923'
author:
- first_name: M Pawan
full_name: Kumar, M Pawan
last_name: Kumar
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Philip
full_name: Torr, Philip H
last_name: Torr
citation:
ama: 'Kumar MP, Kolmogorov V, Torr P. Analyzing Convex Relaxations for MAP Estimation.
In: Blake A, Kohli P, Rother C, eds. Markov Random Fields for Vision and Image
Processing. Massachusetts Institute of Technology Press; 2011.'
apa: Kumar, M. P., Kolmogorov, V., & Torr, P. (2011). Analyzing Convex Relaxations
for MAP Estimation. In A. Blake, P. Kohli, & C. Rother (Eds.), Markov Random
Fields for Vision and Image Processing. Massachusetts Institute of Technology
Press.
chicago: Kumar, M Pawan, Vladimir Kolmogorov, and Philip Torr. “Analyzing Convex
Relaxations for MAP Estimation.” In Markov Random Fields for Vision and Image
Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother. Massachusetts
Institute of Technology Press, 2011.
ieee: M. P. Kumar, V. Kolmogorov, and P. Torr, “Analyzing Convex Relaxations for
MAP Estimation,” in Markov Random Fields for Vision and Image Processing,
A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology
Press, 2011.
ista: 'Kumar MP, Kolmogorov V, Torr P. 2011.Analyzing Convex Relaxations for MAP
Estimation. In: Markov Random Fields for Vision and Image Processing. .'
mla: Kumar, M. Pawan, et al. “Analyzing Convex Relaxations for MAP Estimation.”
Markov Random Fields for Vision and Image Processing, edited by Andrew
Blake et al., Massachusetts Institute of Technology Press, 2011.
short: M.P. Kumar, V. Kolmogorov, P. Torr, in:, A. Blake, P. Kohli, C. Rother (Eds.),
Markov Random Fields for Vision and Image Processing, Massachusetts Institute
of Technology Press, 2011.
date_created: 2018-12-11T12:00:21Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:43Z
day: '01'
editor:
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Pushmeet
full_name: Kohli, Pushmeet
last_name: Kohli
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
extern: 1
month: '01'
publication: Markov Random Fields for Vision and Image Processing
publication_status: published
publisher: Massachusetts Institute of Technology Press
publist_id: '3814'
quality_controlled: 0
status: public
title: Analyzing Convex Relaxations for MAP Estimation
type: book_chapter
year: '2011'
...
---
_id: '2924'
author:
- first_name: Antonio
full_name: Criminisi, Antonio
last_name: Criminisi
- first_name: Geoffrey
full_name: Cross, Geoffrey
last_name: Cross
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Criminisi A, Cross G, Blake A, Kolmogorov V. Bilayer Segmentation of Video.
In: Blake A, Kohli P, Rother C, eds. Markov Random Fields for Vision and Image
Processing. Massachusetts Institute of Technology Press; 2011.'
apa: Criminisi, A., Cross, G., Blake, A., & Kolmogorov, V. (2011). Bilayer Segmentation
of Video. In A. Blake, P. Kohli, & C. Rother (Eds.), Markov Random Fields
for Vision and Image Processing. Massachusetts Institute of Technology Press.
chicago: Criminisi, Antonio, Geoffrey Cross, Andrew Blake, and Vladimir Kolmogorov.
“Bilayer Segmentation of Video.” In Markov Random Fields for Vision and Image
Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother. Massachusetts
Institute of Technology Press, 2011.
ieee: A. Criminisi, G. Cross, A. Blake, and V. Kolmogorov, “Bilayer Segmentation
of Video,” in Markov Random Fields for Vision and Image Processing, A.
Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology Press,
2011.
ista: 'Criminisi A, Cross G, Blake A, Kolmogorov V. 2011.Bilayer Segmentation of
Video. In: Markov Random Fields for Vision and Image Processing. .'
mla: Criminisi, Antonio, et al. “Bilayer Segmentation of Video.” Markov Random
Fields for Vision and Image Processing, edited by Andrew Blake et al., Massachusetts
Institute of Technology Press, 2011.
short: A. Criminisi, G. Cross, A. Blake, V. Kolmogorov, in:, A. Blake, P. Kohli,
C. Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts
Institute of Technology Press, 2011.
date_created: 2018-12-11T12:00:22Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:43Z
day: '01'
editor:
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Pushmeet
full_name: Kohli, Pushmeet
last_name: Kohli
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
extern: 1
month: '01'
publication: Markov Random Fields for Vision and Image Processing
publication_status: published
publisher: Massachusetts Institute of Technology Press
publist_id: '3813'
quality_controlled: 0
status: public
title: Bilayer Segmentation of Video
type: book_chapter
year: '2011'
...
---
_id: '2925'
author:
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Yuri
full_name: Boykov, Yuri
last_name: Boykov
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
citation:
ama: 'Rother C, Kolmogorov V, Boykov Y, Blake A. Interactive Foreground Extraction
using graph cut. In: Blake A, Kohli P, Rother C, eds. Markov Random Fields
for Vision and Image Processing. Massachusetts Institute of Technology Press;
2011.'
apa: Rother, C., Kolmogorov, V., Boykov, Y., & Blake, A. (2011). Interactive
Foreground Extraction using graph cut. In A. Blake, P. Kohli, & C. Rother
(Eds.), Markov Random Fields for Vision and Image Processing. Massachusetts
Institute of Technology Press.
chicago: Rother, Carsten, Vladimir Kolmogorov, Yuri Boykov, and Andrew Blake. “Interactive
Foreground Extraction Using Graph Cut.” In Markov Random Fields for Vision
and Image Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten
Rother. Massachusetts Institute of Technology Press, 2011.
ieee: C. Rother, V. Kolmogorov, Y. Boykov, and A. Blake, “Interactive Foreground
Extraction using graph cut,” in Markov Random Fields for Vision and Image Processing,
A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology
Press, 2011.
ista: 'Rother C, Kolmogorov V, Boykov Y, Blake A. 2011.Interactive Foreground Extraction
using graph cut. In: Markov Random Fields for Vision and Image Processing. .'
mla: Rother, Carsten, et al. “Interactive Foreground Extraction Using Graph Cut.”
Markov Random Fields for Vision and Image Processing, edited by Andrew
Blake et al., Massachusetts Institute of Technology Press, 2011.
short: C. Rother, V. Kolmogorov, Y. Boykov, A. Blake, in:, A. Blake, P. Kohli, C.
Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts
Institute of Technology Press, 2011.
date_created: 2018-12-11T12:00:22Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:44Z
day: '01'
editor:
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Pushmeet
full_name: Kohli, Pushmeet
last_name: Kohli
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
extern: 1
month: '01'
publication: Markov Random Fields for Vision and Image Processing
publication_status: published
publisher: Massachusetts Institute of Technology Press
publist_id: '3812'
quality_controlled: 0
status: public
title: Interactive Foreground Extraction using graph cut
type: book_chapter
year: '2011'
...
---
_id: '2935'
author:
- first_name: Yuri
full_name: Boykov, Yuri
last_name: Boykov
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Boykov Y, Kolmogorov V. Basic graph cut algorithms. In: Blake A, Kohli P,
Rother C, eds. Markov Random Fields for Vision and Image Processing. Massachusetts
Institute of Technology Press; 2011:31-50.'
apa: Boykov, Y., & Kolmogorov, V. (2011). Basic graph cut algorithms. In A.
Blake, P. Kohli, & C. Rother (Eds.), Markov Random Fields for Vision and
Image Processing (pp. 31–50). Massachusetts Institute of Technology Press.
chicago: Boykov, Yuri, and Vladimir Kolmogorov. “Basic Graph Cut Algorithms.” In
Markov Random Fields for Vision and Image Processing, edited by Andrew
Blake, Pushmeet Kohli, and Carsten Rother, 31–50. Massachusetts Institute of Technology
Press, 2011.
ieee: Y. Boykov and V. Kolmogorov, “Basic graph cut algorithms,” in Markov Random
Fields for Vision and Image Processing, A. Blake, P. Kohli, and C. Rother,
Eds. Massachusetts Institute of Technology Press, 2011, pp. 31–50.
ista: 'Boykov Y, Kolmogorov V. 2011.Basic graph cut algorithms. In: Markov Random
Fields for Vision and Image Processing. , 31–50.'
mla: Boykov, Yuri, and Vladimir Kolmogorov. “Basic Graph Cut Algorithms.” Markov
Random Fields for Vision and Image Processing, edited by Andrew Blake et al.,
Massachusetts Institute of Technology Press, 2011, pp. 31–50.
short: Y. Boykov, V. Kolmogorov, in:, A. Blake, P. Kohli, C. Rother (Eds.), Markov
Random Fields for Vision and Image Processing, Massachusetts Institute of Technology
Press, 2011, pp. 31–50.
date_created: 2018-12-11T12:00:26Z
date_published: 2011-07-22T00:00:00Z
date_updated: 2021-01-12T07:39:53Z
day: '22'
editor:
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Pushmeet
full_name: Kohli, Pushmeet
last_name: Kohli
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
extern: 1
month: '07'
page: 31 - 50
publication: Markov Random Fields for Vision and Image Processing
publication_status: published
publisher: Massachusetts Institute of Technology Press
publist_id: '3801'
quality_controlled: 0
status: public
title: Basic graph cut algorithms
type: book_chapter
year: '2011'
...
---
_id: '2961'
abstract:
- lang: eng
text: |-
Rapid research progress in genotyping techniques have allowed large genome-wide association studies. Existing methods often focus on determining associations between single loci and a specic phenotype. However, a particular phenotype is usually the result of complex relationships between multiple loci and the environment. In this paper, we describe a two-stage method for detecting epistasis by combining the traditionally used single-locus search with a search for multiway interactions. Our method is based on an extended version of Fisher's exact test. To
perform this test, a Markov chain is constructed on the space of multidimensional contingency tables using the elements of a Markov basis as moves. We test our method on simulated data and compare it to a two-stage logistic regression method and to a fully Bayesian method, showing that we are able to detect the interacting loci when other methods fail to do so. Finally, we apply our method to a genome-wide data set consisting of 685 dogs and identify epistasis associated with canine hair length for four pairs of single nucleotide polymorphisms (SNPs).
acknowledgement: Anna-Sapfo Malaspinas is supported by a Janggen-Poehn Fellowship.
Caroline Uhler is supported by an International Fulbright Science and Technology
Fellowship.
author:
- first_name: Anna
full_name: 'Malaspinas, Anna-Sapfo '
last_name: Malaspinas
- first_name: Caroline
full_name: Caroline Uhler
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: Malaspinas A, Uhler C. Detecting epistasis via Markov bases. Journal of
Algebraic Statistics. 2011;2(1):36-53. doi:http://dx.doi.org/10.18409/jas.v2i1.27
apa: Malaspinas, A., & Uhler, C. (2011). Detecting epistasis via Markov bases.
Journal of Algebraic Statistics. Public Knowledge Project. http://dx.doi.org/10.18409/jas.v2i1.27
chicago: Malaspinas, Anna, and Caroline Uhler. “Detecting Epistasis via Markov Bases.”
Journal of Algebraic Statistics. Public Knowledge Project, 2011. http://dx.doi.org/10.18409/jas.v2i1.27.
ieee: A. Malaspinas and C. Uhler, “Detecting epistasis via Markov bases,” Journal
of Algebraic Statistics, vol. 2, no. 1. Public Knowledge Project, pp. 36–53,
2011.
ista: Malaspinas A, Uhler C. 2011. Detecting epistasis via Markov bases. Journal
of Algebraic Statistics. 2(1), 36–53.
mla: Malaspinas, Anna, and Caroline Uhler. “Detecting Epistasis via Markov Bases.”
Journal of Algebraic Statistics, vol. 2, no. 1, Public Knowledge Project,
2011, pp. 36–53, doi:http://dx.doi.org/10.18409/jas.v2i1.27.
short: A. Malaspinas, C. Uhler, Journal of Algebraic Statistics 2 (2011) 36–53.
date_created: 2018-12-11T12:00:34Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:40:05Z
day: '01'
doi: http://dx.doi.org/10.18409/jas.v2i1.27
extern: 1
intvolume: ' 2'
issue: '1'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1006.4929
month: '01'
oa: 1
page: 36 - 53
publication: Journal of Algebraic Statistics
publication_status: published
publisher: Public Knowledge Project
publist_id: '3764'
quality_controlled: 0
status: public
title: Detecting epistasis via Markov bases
type: journal_article
volume: 2
year: '2011'
...
---
_id: '2960'
abstract:
- lang: eng
text: Traditional statistical methods for the confidentiality protection for statistical
databases do not scale well to deal with GWAS (genome-wide association studies)
databases and external information on them. The more recent concept of differential
privacy, introduced by the cryptographic community, is an approach which provides
a rigorous definition of privacy with meaningful privacy guarantees in the presence
of arbitrary external information. Building on such notions, we propose new methods
to release aggregate GWAS data without compromising an individual's privacy. We
present methods for releasing differentially private minor allele frequencies,
chi-square statistics and p-values. We compare these approaches on simulated data
and on a GWAS study of canine hair length involving 685 dogs. We also propose
a privacy-preserving method for finding genome-wide associations based on a differentially
private approach to penalized logistic regression.
author:
- first_name: Stephen
full_name: Fienberg, Stephen E
last_name: Fienberg
- first_name: Aleksandra
full_name: Slavkovic, Aleksandra
last_name: Slavkovic
- first_name: Caroline
full_name: Caroline Uhler
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: 'Fienberg S, Slavkovic A, Uhler C. Privacy Preserving GWAS Data Sharing. In:
IEEE; 2011. doi:10.1109/ICDMW.2011.140'
apa: Fienberg, S., Slavkovic, A., & Uhler, C. (2011). Privacy Preserving GWAS
Data Sharing. Presented at the Proceedings of the 11th IEEE International Conference
on Data Mining, IEEE. https://doi.org/10.1109/ICDMW.2011.140
chicago: Fienberg, Stephen, Aleksandra Slavkovic, and Caroline Uhler. “Privacy Preserving
GWAS Data Sharing.” IEEE, 2011. https://doi.org/10.1109/ICDMW.2011.140.
ieee: S. Fienberg, A. Slavkovic, and C. Uhler, “Privacy Preserving GWAS Data Sharing,”
presented at the Proceedings of the 11th IEEE International Conference on Data
Mining, 2011.
ista: Fienberg S, Slavkovic A, Uhler C. 2011. Privacy Preserving GWAS Data Sharing.
Proceedings of the 11th IEEE International Conference on Data Mining.
mla: Fienberg, Stephen, et al. Privacy Preserving GWAS Data Sharing. IEEE,
2011, doi:10.1109/ICDMW.2011.140.
short: S. Fienberg, A. Slavkovic, C. Uhler, in:, IEEE, 2011.
conference:
name: Proceedings of the 11th IEEE International Conference on Data Mining
date_created: 2018-12-11T12:00:34Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:40:05Z
day: '01'
doi: 10.1109/ICDMW.2011.140
extern: 1
month: '01'
publication_status: published
publisher: IEEE
publist_id: '3766'
quality_controlled: 0
status: public
title: Privacy Preserving GWAS Data Sharing
type: conference
year: '2011'
...
---
_id: '2975'
abstract:
- lang: eng
text: "Zero-knowledge proofs of knowledge (ZK-PoK) for discrete logarithms and related
problems are indispensable for practical cryptographic protocols. Recently, Camenisch,
Kiayias, and Yung provided a specification language (the CKY-language) for such
protocols which allows for a modular design and protocol analysis: for every zero-knowledge
proof specified in this language, protocol designers are ensured that there exists
an efficient protocol which indeed proves the specified statement.\n\nHowever,
the protocols resulting from their compilation techniques only satisfy the classical
notion of ZK-PoK, which is not retained are when they used as building blocks
for higher-level applications or composed with other protocols.\nThis problem
can be tackled by moving to the Universal Composability (UC) framework, which
guarantees retention of security when composing protocols in arbitrary ways. \nWhile
there exist generic transformations from $\\Sigma$-protocols to UC-secure protocols,
these transformation are often too inefficient for practice.\n \nIn this paper
we introduce a specification language akin to the CKY-language and a compiler
such that the resulting protocols are UC-secure and efficient. \nTo this end,
we propose an extension of the UC-framework addressing the \nissue that UC-secure
zero-knowledge proofs are by definition proofs of knowledge, and state a special
composition theorem which allows one to use the weaker -- but more efficient and
often sufficient -- notion of proofs of membership in the UC-framework. \nWe
believe that our contributions enable the design of practically efficient protocols
that are UC-secure and thus themselves can be used as building blocks."
acknowledgement: This work was in part funded by the Swiss Hasler Foundation, and
the EU FP7 grants 216483 and 216499, as well as by the NSF grant CNS-0716690.
alternative_title:
- LNCS
author:
- first_name: Jan
full_name: Camenisch, Jan
last_name: Camenisch
- first_name: Stephan
full_name: Stephan Krenn
id: 329FCCF0-F248-11E8-B48F-1D18A9856A87
last_name: Krenn
orcid: 0000-0003-2835-9093
- first_name: Victor
full_name: Shoup, Victor
last_name: Shoup
citation:
ama: 'Camenisch J, Krenn S, Shoup V. A Framework for Practical Universally Composable
Zero-Knowledge Protocols. In: Lee D, Wang X, eds. Vol 7073. Springer; 2011:449-467.
doi:10.1007/978-3-642-25385-0'
apa: 'Camenisch, J., Krenn, S., & Shoup, V. (2011). A Framework for Practical
Universally Composable Zero-Knowledge Protocols. In D. Lee & X. Wang (Eds.)
(Vol. 7073, pp. 449–467). Presented at the ASIACRYPT: Theory and Application of
Cryptology and Information Security, Springer. https://doi.org/10.1007/978-3-642-25385-0'
chicago: Camenisch, Jan, Stephan Krenn, and Victor Shoup. “A Framework for Practical
Universally Composable Zero-Knowledge Protocols.” edited by Dong Lee and Xiaoyun
Wang, 7073:449–67. Springer, 2011. https://doi.org/10.1007/978-3-642-25385-0.
ieee: 'J. Camenisch, S. Krenn, and V. Shoup, “A Framework for Practical Universally
Composable Zero-Knowledge Protocols,” presented at the ASIACRYPT: Theory and Application
of Cryptology and Information Security, 2011, vol. 7073, pp. 449–467.'
ista: 'Camenisch J, Krenn S, Shoup V. 2011. A Framework for Practical Universally
Composable Zero-Knowledge Protocols. ASIACRYPT: Theory and Application of Cryptology
and Information Security, LNCS, vol. 7073, 449–467.'
mla: Camenisch, Jan, et al. A Framework for Practical Universally Composable
Zero-Knowledge Protocols. Edited by Dong Lee and Xiaoyun Wang, vol. 7073,
Springer, 2011, pp. 449–67, doi:10.1007/978-3-642-25385-0.
short: J. Camenisch, S. Krenn, V. Shoup, in:, D. Lee, X. Wang (Eds.), Springer,
2011, pp. 449–467.
conference:
name: 'ASIACRYPT: Theory and Application of Cryptology and Information Security'
date_created: 2018-12-11T12:00:39Z
date_published: 2011-11-21T00:00:00Z
date_updated: 2021-01-12T07:40:11Z
day: '21'
doi: 10.1007/978-3-642-25385-0
editor:
- first_name: Dong
full_name: Lee, Dong Hoon
last_name: Lee
- first_name: Xiaoyun
full_name: Wang, Xiaoyun
last_name: Wang
extern: 1
intvolume: ' 7073'
main_file_link:
- open_access: '0'
url: http://eprint.iacr.org/2011/228.pdf
month: '11'
page: 449 - 467
publication_status: published
publisher: Springer
publist_id: '3728'
quality_controlled: 0
status: public
title: A Framework for Practical Universally Composable Zero-Knowledge Protocols
type: conference
volume: 7073
year: '2011'
...
---
_id: '2977'
abstract:
- lang: eng
text: "Cryptographic two-party protocols are used ubiquitously in\n everyday
life. While some of these protocols are easy to\n understand and implement
(e.g., key exchange or transmission of\n encrypted data), many of them are
much more complex (e.g.,\n e-banking and e-voting applications, or anonymous
authentication\n and credential systems).\n\n For a software engineer without
appropriate cryptographic skills\n the implementation of such protocols is
often difficult, time\n consuming and error-prone. For this reason, a number
of compilers\n supporting programmers have been published in recent\n years.
However, they are either designed for very specific\n cryptographic primitives
(e.g., zero-knowledge proofs of\n knowledge), or they only offer a very low
level of abstraction and\n thus again demand substantial mathematical and cryptographic\n
\ skills from the programmer. Finally, some of the existing\n compilers do
not produce executable code, but only metacode which\n has to be instantiated
with mathematical libraries, encryption\n routines, etc. before it can actually
be used.\n \n In this paper we present a cryptographically aware compiler
which\n is equally useful to cryptographers who want to benchmark\n protocols
designed on paper, and to programmers who want to\n implement complex security
sensitive protocols without having to\n understand all subtleties. Our tool
offers a high level of\n abstraction and outputs well-structured and documented
Java\n code. We believe that our compiler can contribute to shortening\n the
development cycles of cryptographic applications and to\n reducing their error-proneness."
acknowledgement: This work was in part funded by the European Community’s Seventh
Framework Programme (FP7) under grant agreement no. 216499 and the Swiss Hasler
Foundation under projects no. 09037 and 10069.
author:
- first_name: Endre
full_name: Bangerter, Endre
last_name: Bangerter
- first_name: Stephan
full_name: Stephan Krenn
id: 329FCCF0-F248-11E8-B48F-1D18A9856A87
last_name: Krenn
orcid: 0000-0003-2835-9093
- first_name: Martial
full_name: Seifriz, Martial
last_name: Seifriz
- first_name: Ulrich
full_name: Ultes-Nitsche, Ulrich
last_name: Ultes Nitsche
citation:
ama: 'Bangerter E, Krenn S, Seifriz M, Ultes Nitsche U. cPLC - A Cryptographic Programming
Language and Compiler. In: Venter H, Coetzee M, Loock M, eds. IEEE; 2011. doi:10.1109/ISSA.2011.6027533'
apa: 'Bangerter, E., Krenn, S., Seifriz, M., & Ultes Nitsche, U. (2011). cPLC
- A Cryptographic Programming Language and Compiler. In H. Venter, M. Coetzee,
& M. Loock (Eds.). Presented at the ISSA: Information Security South Africa,
IEEE. https://doi.org/10.1109/ISSA.2011.6027533'
chicago: Bangerter, Endre, Stephan Krenn, Martial Seifriz, and Ulrich Ultes Nitsche.
“CPLC - A Cryptographic Programming Language and Compiler.” edited by Hein Venter,
Marijke Coetzee, and Marianne Loock. IEEE, 2011. https://doi.org/10.1109/ISSA.2011.6027533.
ieee: 'E. Bangerter, S. Krenn, M. Seifriz, and U. Ultes Nitsche, “cPLC - A Cryptographic
Programming Language and Compiler,” presented at the ISSA: Information Security
South Africa, 2011.'
ista: 'Bangerter E, Krenn S, Seifriz M, Ultes Nitsche U. 2011. cPLC - A Cryptographic
Programming Language and Compiler. ISSA: Information Security South Africa.'
mla: Bangerter, Endre, et al. CPLC - A Cryptographic Programming Language and
Compiler. Edited by Hein Venter et al., IEEE, 2011, doi:10.1109/ISSA.2011.6027533.
short: E. Bangerter, S. Krenn, M. Seifriz, U. Ultes Nitsche, in:, H. Venter, M.
Coetzee, M. Loock (Eds.), IEEE, 2011.
conference:
name: 'ISSA: Information Security South Africa'
date_created: 2018-12-11T12:00:39Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2021-01-12T07:40:12Z
day: '01'
doi: 10.1109/ISSA.2011.6027533
editor:
- first_name: Hein
full_name: Venter, Hein S.
last_name: Venter
- first_name: Marijke
full_name: Coetzee, Marijke
last_name: Coetzee
- first_name: Marianne
full_name: Loock, Marianne
last_name: Loock
extern: 1
month: '08'
publication_status: published
publisher: IEEE
publist_id: '3726'
quality_controlled: 0
status: public
title: cPLC - A Cryptographic Programming Language and Compiler
type: conference
year: '2011'
...
---
_id: '2976'
abstract:
- lang: eng
text: |-
Side channel attacks on cryptographic systems exploit information
gained from physical implementations rather than theoretical
weaknesses of a scheme. In recent years, major achievements were made
for the class of so called access-driven cache attacks. Such attacks
exploit the leakage of the memory locations accessed by a victim
process.
In this paper we consider the AES block cipher and present an attack
which is capable of recovering the full secret key in almost realtime
for AES-128, requiring only a very limited number of observed
encryptions. Unlike previous attacks, we do not require any
information about the plaintext (such as its distribution, etc.).
Moreover, for the first time, we also show how the plaintext can be
recovered without having access to the ciphertext at all. It is the
first working attack on AES implementations using compressed
tables. There, no efficient techniques to identify the beginning
of AES rounds is known, which is the fundamental assumption underlying previous
attacks.
We have a fully working implementation of our attack which is able to
recover AES keys after observing as little as 100 encryptions. It
works against the OpenSSL 0.9.8n implementation of AES on Linux
systems. Our spy process does not require any special privileges
beyond those of a standard Linux user. A contribution of probably
independent interest is a denial of service attack on the task scheduler of
current Linux systems (CFS), which allows one to observe (on average)
every single memory access of a victim process.
acknowledgement: |-
This work was in part funded by the European Community’s Seventh Framework Programme (FP7) under grant agreement no. 216499 and the Swiss Hasler Foundation.
An extended abstract was also accepted for COSADE 2011.
author:
- first_name: David
full_name: Gullasch, David
last_name: Gullasch
- first_name: Endre
full_name: Bangerter, Endre
last_name: Bangerter
- first_name: Stephan
full_name: Stephan Krenn
id: 329FCCF0-F248-11E8-B48F-1D18A9856A87
last_name: Krenn
orcid: 0000-0003-2835-9093
citation:
ama: 'Gullasch D, Bangerter E, Krenn S. Cache Games - Bringing Access-Based Cache
Attacks on AES to Practice. In: IEEE; 2011:490-505. doi:10.1109/SP.2011.22'
apa: 'Gullasch, D., Bangerter, E., & Krenn, S. (2011). Cache Games - Bringing
Access-Based Cache Attacks on AES to Practice (pp. 490–505). Presented at the
S&P: IEEE Symposium on Security and Privacy, IEEE. https://doi.org/10.1109/SP.2011.22'
chicago: Gullasch, David, Endre Bangerter, and Stephan Krenn. “Cache Games - Bringing
Access-Based Cache Attacks on AES to Practice,” 490–505. IEEE, 2011. https://doi.org/10.1109/SP.2011.22.
ieee: 'D. Gullasch, E. Bangerter, and S. Krenn, “Cache Games - Bringing Access-Based
Cache Attacks on AES to Practice,” presented at the S&P: IEEE Symposium on
Security and Privacy, 2011, pp. 490–505.'
ista: 'Gullasch D, Bangerter E, Krenn S. 2011. Cache Games - Bringing Access-Based
Cache Attacks on AES to Practice. S&P: IEEE Symposium on Security and Privacy,
490–505.'
mla: Gullasch, David, et al. Cache Games - Bringing Access-Based Cache Attacks
on AES to Practice. IEEE, 2011, pp. 490–505, doi:10.1109/SP.2011.22.
short: D. Gullasch, E. Bangerter, S. Krenn, in:, IEEE, 2011, pp. 490–505.
conference:
name: 'S&P: IEEE Symposium on Security and Privacy'
date_created: 2018-12-11T12:00:39Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:40:11Z
day: '01'
doi: 10.1109/SP.2011.22
extern: 1
main_file_link:
- open_access: '0'
url: http://eprint.iacr.org/2010/594.pdf
month: '01'
page: 490 - 505
publication_status: published
publisher: IEEE
publist_id: '3727'
quality_controlled: 0
status: public
title: Cache Games - Bringing Access-Based Cache Attacks on AES to Practice
type: conference
year: '2011'
...
---
_id: '3092'
abstract:
- lang: eng
text: The phytohormone auxin is vital to plant growth and development. A unique
property of auxin among all other plant hormones is its cell-to-cell polar transport
that requires activity of polarly localized PIN-FORMED (PIN) auxin efflux transporters.
Despite the substantial molecular insight into the cellular PIN polarization,
the mechanistic understanding for developmentally and environmentally regulated
PIN polarization is scarce. The long-standing belief that auxin modulates its
own transport by means of a positive feedback mechanism has inspired both experimentalists
and theoreticians for more than two decades. Recently, theoretical models for
auxin-dependent patterning in plants include the feedback between auxin transport
and the PIN protein localization. These computer models aid to assess the complexity
of plant development by testing and predicting plausible scenarios for various
developmental processes that occur in planta. Although the majority of these models
rely on purely heuristic principles, the most recent mechanistic models tentatively
integrate biologically testable components into known cellular processes that
underlie the PIN polarity regulation. The existing and emerging computational
approaches to describe PIN polarization are presented and discussed in the light
of recent experimental data on the PIN polar targeting.
author:
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Willy
full_name: Govaerts, Willy
last_name: Govaerts
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jürgen
full_name: Kleine Vehn, Jürgen
last_name: Kleine Vehn
citation:
ama: 'Wabnik KT, Govaerts W, Friml J, Kleine Vehn J. Feedback models for polarized
auxin transport: An emerging trend. Molecular BioSystems. 2011;7(8):2352-2359.
doi:10.1039/c1mb05109a'
apa: 'Wabnik, K. T., Govaerts, W., Friml, J., & Kleine Vehn, J. (2011). Feedback
models for polarized auxin transport: An emerging trend. Molecular BioSystems.
Royal Society of Chemistry. https://doi.org/10.1039/c1mb05109a'
chicago: 'Wabnik, Krzysztof T, Willy Govaerts, Jiří Friml, and Jürgen Kleine Vehn.
“Feedback Models for Polarized Auxin Transport: An Emerging Trend.” Molecular
BioSystems. Royal Society of Chemistry, 2011. https://doi.org/10.1039/c1mb05109a.'
ieee: 'K. T. Wabnik, W. Govaerts, J. Friml, and J. Kleine Vehn, “Feedback models
for polarized auxin transport: An emerging trend,” Molecular BioSystems,
vol. 7, no. 8. Royal Society of Chemistry, pp. 2352–2359, 2011.'
ista: 'Wabnik KT, Govaerts W, Friml J, Kleine Vehn J. 2011. Feedback models for
polarized auxin transport: An emerging trend. Molecular BioSystems. 7(8), 2352–2359.'
mla: 'Wabnik, Krzysztof T., et al. “Feedback Models for Polarized Auxin Transport:
An Emerging Trend.” Molecular BioSystems, vol. 7, no. 8, Royal Society
of Chemistry, 2011, pp. 2352–59, doi:10.1039/c1mb05109a.'
short: K.T. Wabnik, W. Govaerts, J. Friml, J. Kleine Vehn, Molecular BioSystems
7 (2011) 2352–2359.
date_created: 2018-12-11T12:01:20Z
date_published: 2011-06-10T00:00:00Z
date_updated: 2021-01-12T07:41:00Z
day: '10'
doi: 10.1039/c1mb05109a
extern: '1'
external_id:
pmid:
- '21660355'
intvolume: ' 7'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/21660355
month: '06'
oa: 1
oa_version: Published Version
page: 2352 - 2359
pmid: 1
publication: Molecular BioSystems
publication_status: published
publisher: Royal Society of Chemistry
publist_id: '3608'
quality_controlled: '1'
status: public
title: 'Feedback models for polarized auxin transport: An emerging trend'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2011'
...
---
_id: '3089'
abstract:
- lang: eng
text: The phytohormone auxin is an important determinant of plant development. Directional
auxin flow within tissues depends on polar localization of PIN auxin transporters.
To explore regulation of PIN-mediated auxin transport, we screened for suppressors
of PIN1 overexpression (supo) and identified an inositol polyphosphate 1-phosphatase
mutant (supo1), with elevated inositol trisphosphate (InsP 3) and cytosolic Ca
2+ levels. Pharmacological and genetic increases in InsP 3 or Ca 2+ levels also
suppressed the PIN1 gain-of-function phenotypes and caused defects in basal PIN
localization, auxin transport and auxin-mediated development. In contrast, the
reductions in InsP 3 levels and Ca 2+ signaling antagonized the effects of the
supo1 mutation and disrupted preferentially apical PIN localization. InsP 3 and
Ca 2+ are evolutionarily conserved second messengers involved in various cellular
functions, particularly stress responses. Our findings implicate them as modifiers
of cell polarity and polar auxin transport, and highlight a potential integration
point through which Ca 2+ signaling-related stimuli could influence auxin-mediated
development.
author:
- first_name: Jing
full_name: Zhang, Jing
last_name: Zhang
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Philip
full_name: Brewer, Philip B
last_name: Brewer
- first_name: Marta
full_name: Michniewicz, Marta
last_name: Michniewicz
- first_name: Peter
full_name: Peter Grones
id: 399876EC-F248-11E8-B48F-1D18A9856A87
last_name: Grones
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Christian
full_name: Löfke, Christian
last_name: Löfke
- first_name: Thomas
full_name: Teichmann, Thomas
last_name: Teichmann
- first_name: Agnieszka
full_name: Bielach, Agnieszka
last_name: Bielach
- first_name: Bernard
full_name: Cannoot, Bernard
last_name: Cannoot
- first_name: Klára
full_name: Hoyerová, Klára
last_name: Hoyerová
- first_name: Xu
full_name: Xu Chen
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Hong
full_name: Xue, Hong-Wei
last_name: Xue
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Zhang J, Vanneste S, Brewer P, et al. Inositol trisphosphate-induced ca^2+
signaling modulates auxin transport and pin polarity. Developmental Cell.
2011;20(6):855-866. doi:10.1016/j.devcel.2011.05.013
apa: Zhang, J., Vanneste, S., Brewer, P., Michniewicz, M., Grones, P., Kleine Vehn,
J., … Friml, J. (2011). Inositol trisphosphate-induced ca^2+ signaling modulates
auxin transport and pin polarity. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2011.05.013
chicago: Zhang, Jing, Steffen Vanneste, Philip Brewer, Marta Michniewicz, Peter
Grones, Jürgen Kleine Vehn, Christian Löfke, et al. “Inositol Trisphosphate-Induced
Ca^2+ Signaling Modulates Auxin Transport and Pin Polarity.” Developmental
Cell. Cell Press, 2011. https://doi.org/10.1016/j.devcel.2011.05.013.
ieee: J. Zhang et al., “Inositol trisphosphate-induced ca^2+ signaling modulates
auxin transport and pin polarity,” Developmental Cell, vol. 20, no. 6.
Cell Press, pp. 855–866, 2011.
ista: Zhang J, Vanneste S, Brewer P, Michniewicz M, Grones P, Kleine Vehn J, Löfke
C, Teichmann T, Bielach A, Cannoot B, Hoyerová K, Chen X, Xue H, Benková E, Zažímalová
E, Friml J. 2011. Inositol trisphosphate-induced ca^2+ signaling modulates auxin
transport and pin polarity. Developmental Cell. 20(6), 855–866.
mla: Zhang, Jing, et al. “Inositol Trisphosphate-Induced Ca^2+ Signaling Modulates
Auxin Transport and Pin Polarity.” Developmental Cell, vol. 20, no. 6,
Cell Press, 2011, pp. 855–66, doi:10.1016/j.devcel.2011.05.013.
short: J. Zhang, S. Vanneste, P. Brewer, M. Michniewicz, P. Grones, J. Kleine Vehn,
C. Löfke, T. Teichmann, A. Bielach, B. Cannoot, K. Hoyerová, X. Chen, H. Xue,
E. Benková, E. Zažímalová, J. Friml, Developmental Cell 20 (2011) 855–866.
date_created: 2018-12-11T12:01:18Z
date_published: 2011-06-14T00:00:00Z
date_updated: 2021-01-12T07:40:58Z
day: '14'
doi: 10.1016/j.devcel.2011.05.013
extern: 1
intvolume: ' 20'
issue: '6'
month: '06'
page: 855 - 866
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '3612'
quality_controlled: 0
status: public
title: Inositol trisphosphate-induced ca^2+ signaling modulates auxin transport and
pin polarity
type: journal_article
volume: 20
year: '2011'
...
---
_id: '3090'
abstract:
- lang: eng
text: The polarized transport of the phytohormone auxin [1], which is crucial for
the regulation of different stages of plant development [2, 3], depends on the
asymmetric plasma membrane distribution of the PIN-FORMED (PIN) auxin efflux carriers
[4, 5]. The PIN polar localization results from clathrin-mediated endocytosis
(CME) from the plasma membrane and subsequent polar recycling [6]. The Arabidopsis
genome encodes two groups of dynamin-related proteins (DRPs) that show homology
to mammalian dynamin - a protein required for fission of endocytic vesicles during
CME [7, 8]. Here we show by coimmunoprecipitation (coIP), bimolecular fluorescence
complementation (BiFC), and Förster resonance energy transfer (FRET) that members
of the DRP1 group closely associate with PIN proteins at the cell plate. Localization
and phenotypic analysis of novel drp1 mutants revealed a requirement for DRP1
function in correct PIN distribution and in auxin-mediated development. We propose
that rapid and specific internalization of PIN proteins mediated by the DRP1 proteins
and the associated CME machinery from the cell plate membranes during cytokinesis
is an important mechanism for proper polar PIN positioning in interphase cells.
author:
- first_name: Jozef
full_name: Mravec, Jozef
last_name: Mravec
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Na
full_name: Li, Na
last_name: Li
- first_name: Sjef
full_name: Boeren, Sjef
last_name: Boeren
- first_name: Rumyana
full_name: Karlova, Rumyana
last_name: Karlova
- first_name: Saeko
full_name: Kitakura, Saeko
last_name: Kitakura
- first_name: Markéta
full_name: Pařezová, Markéta
last_name: Pařezová
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Thomasz
full_name: Nodzyński, Thomasz
last_name: Nodzyński
- first_name: Pankaj
full_name: Dhonukshe, Pankaj
last_name: Dhonukshe
- first_name: Sebastian
full_name: Bednarek, Sebastian Y
last_name: Bednarek
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Sacco
full_name: De Vries, Sacco
last_name: De Vries
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Mravec J, Petrášek J, Li N, et al. Cell plate restricted association of DRP1A
and PIN proteins is required for cell polarity establishment in arabidopsis. Current
Biology. 2011;21(12):1055-1060. doi:10.1016/j.cub.2011.05.018
apa: Mravec, J., Petrášek, J., Li, N., Boeren, S., Karlova, R., Kitakura, S., …
Friml, J. (2011). Cell plate restricted association of DRP1A and PIN proteins
is required for cell polarity establishment in arabidopsis. Current Biology.
Cell Press. https://doi.org/10.1016/j.cub.2011.05.018
chicago: Mravec, Jozef, Jan Petrášek, Na Li, Sjef Boeren, Rumyana Karlova, Saeko
Kitakura, Markéta Pařezová, et al. “Cell Plate Restricted Association of DRP1A
and PIN Proteins Is Required for Cell Polarity Establishment in Arabidopsis.”
Current Biology. Cell Press, 2011. https://doi.org/10.1016/j.cub.2011.05.018.
ieee: J. Mravec et al., “Cell plate restricted association of DRP1A and PIN
proteins is required for cell polarity establishment in arabidopsis,” Current
Biology, vol. 21, no. 12. Cell Press, pp. 1055–1060, 2011.
ista: Mravec J, Petrášek J, Li N, Boeren S, Karlova R, Kitakura S, Pařezová M, Naramoto
S, Nodzyński T, Dhonukshe P, Bednarek S, Zažímalová E, De Vries S, Friml J. 2011.
Cell plate restricted association of DRP1A and PIN proteins is required for cell
polarity establishment in arabidopsis. Current Biology. 21(12), 1055–1060.
mla: Mravec, Jozef, et al. “Cell Plate Restricted Association of DRP1A and PIN Proteins
Is Required for Cell Polarity Establishment in Arabidopsis.” Current Biology,
vol. 21, no. 12, Cell Press, 2011, pp. 1055–60, doi:10.1016/j.cub.2011.05.018.
short: J. Mravec, J. Petrášek, N. Li, S. Boeren, R. Karlova, S. Kitakura, M. Pařezová,
S. Naramoto, T. Nodzyński, P. Dhonukshe, S. Bednarek, E. Zažímalová, S. De Vries,
J. Friml, Current Biology 21 (2011) 1055–1060.
date_created: 2018-12-11T12:01:19Z
date_published: 2011-06-21T00:00:00Z
date_updated: 2021-01-12T07:40:59Z
day: '21'
doi: 10.1016/j.cub.2011.05.018
extern: 1
intvolume: ' 21'
issue: '12'
month: '06'
page: 1055 - 1060
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '3611'
quality_controlled: 0
status: public
title: Cell plate restricted association of DRP1A and PIN proteins is required for
cell polarity establishment in arabidopsis
type: journal_article
volume: 21
year: '2011'
...
---
_id: '3088'
abstract:
- lang: eng
text: 'Background: Whereas the majority of animals develop toward a predetermined
body plan, plants show iterative growth and continually produce new organs and
structures from actively dividing meristems. This raises an intriguing question:
How are these newly developed organs patterned? In Arabidopsis embryos, radial
symmetry is broken by the bisymmetric specification of the cotyledons in the apical
domain. Subsequently, this bisymmetry is propagated to the root promeristem. Results:
Here we present a mutually inhibitory feedback loop between auxin and cytokinin
that sets distinct boundaries of hormonal output. Cytokinins promote the bisymmetric
distribution of the PIN-FORMED (PIN) auxin efflux proteins, which channel auxin
toward a central domain. High auxin promotes transcription of the cytokinin signaling
inhibitor AHP6, which closes the interaction loop. This bisymmetric auxin response
domain specifies the differentiation of protoxylem in a bisymmetric pattern. In
embryonic roots, cytokinin is required to translate a bisymmetric auxin response
in the cotyledons to a bisymmetric vascular pattern in the root promeristem. Conclusions:
Our results present an interactive feedback loop between hormonal signaling and
transport by which small biases in hormonal input are propagated into distinct
signaling domains to specify the vascular pattern in the root meristem. It is
an intriguing possibility that such a mechanism could transform radial patterns
and allow continuous vascular connections between other newly emerging organs.'
author:
- first_name: Anthony
full_name: Bishopp, Anthony
last_name: Bishopp
- first_name: Hanna
full_name: Help, Hanna
last_name: Help
- first_name: Sedeer
full_name: El-Showk, Sedeer
last_name: El Showk
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Ben
full_name: Scheres, Ben
last_name: Scheres
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Ari
full_name: Mähönen, Ari Pekka
last_name: Mähönen
- first_name: Ykä
full_name: Helariutta, Ykä
last_name: Helariutta
citation:
ama: Bishopp A, Help H, El Showk S, et al. A mutually inhibitory interaction between
auxin and cytokinin specifies vascular pattern in roots. Current Biology.
2011;21(11):917-926. doi:10.1016/j.cub.2011.04.017
apa: Bishopp, A., Help, H., El Showk, S., Weijers, D., Scheres, B., Friml, J., …
Helariutta, Y. (2011). A mutually inhibitory interaction between auxin and cytokinin
specifies vascular pattern in roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2011.04.017
chicago: Bishopp, Anthony, Hanna Help, Sedeer El Showk, Dolf Weijers, Ben Scheres,
Jiří Friml, Eva Benková, Ari Mähönen, and Ykä Helariutta. “A Mutually Inhibitory
Interaction between Auxin and Cytokinin Specifies Vascular Pattern in Roots.”
Current Biology. Cell Press, 2011. https://doi.org/10.1016/j.cub.2011.04.017.
ieee: A. Bishopp et al., “A mutually inhibitory interaction between auxin
and cytokinin specifies vascular pattern in roots,” Current Biology, vol.
21, no. 11. Cell Press, pp. 917–926, 2011.
ista: Bishopp A, Help H, El Showk S, Weijers D, Scheres B, Friml J, Benková E, Mähönen
A, Helariutta Y. 2011. A mutually inhibitory interaction between auxin and cytokinin
specifies vascular pattern in roots. Current Biology. 21(11), 917–926.
mla: Bishopp, Anthony, et al. “A Mutually Inhibitory Interaction between Auxin and
Cytokinin Specifies Vascular Pattern in Roots.” Current Biology, vol. 21,
no. 11, Cell Press, 2011, pp. 917–26, doi:10.1016/j.cub.2011.04.017.
short: A. Bishopp, H. Help, S. El Showk, D. Weijers, B. Scheres, J. Friml, E. Benková,
A. Mähönen, Y. Helariutta, Current Biology 21 (2011) 917–926.
date_created: 2018-12-11T12:01:18Z
date_published: 2011-06-07T00:00:00Z
date_updated: 2021-01-12T07:40:58Z
day: '07'
doi: 10.1016/j.cub.2011.04.017
extern: 1
intvolume: ' 21'
issue: '11'
month: '06'
page: 917 - 926
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '3613'
quality_controlled: 0
status: public
title: A mutually inhibitory interaction between auxin and cytokinin specifies vascular
pattern in roots
type: journal_article
volume: 21
year: '2011'
...
---
_id: '3093'
abstract:
- lang: eng
text: |2-
Plants take up iron from the soil using the IRON-REGULATED TRANSPORTER 1 (IRT1) high-affinity iron transporter at the root surface. Sophisticated regulatory mechanisms allow plants to tightly control the levels of IRT1, ensuring optimal absorption of essential but toxic iron. Here, we demonstrate that overexpression of Arabidopsis thaliana IRT1 leads to constitutive IRT1 protein accumulation, metal overload, and oxidative stress. IRT1 is unexpectedly found in trans-Golgi network/early endosomes of root hair cells, and its levels and localization are unaffected by iron nutrition. Using pharmacological approaches, we show that IRT1 cycles to the plasma membrane to perform iron and metal uptake at the cell surface and is sent to the vacuole for proper turnover. We also prove that IRT1 is monoubiquitinated on several cytosol-exposed residues in vivo and that mutation of two putative monoubiquitination target residues in IRT1 triggers stabilization at the plasma membrane and leads to extreme lethality. Together, these data suggest a model in which monoubiquitin-dependent internalization/sorting and turnover keep the plasma membrane pool of IRT1 low to ensure proper iron uptake and to prevent metal toxicity. More generally, our work demonstrates the existence of monoubiquitin-dependent trafficking to lytic vacuoles in plants and points to proteasome-independent turnover of plasma membrane proteins.
author:
- first_name: Marie
full_name: Barberon, Marie
last_name: Barberon
- first_name: Enric
full_name: Zelazny, Enric
last_name: Zelazny
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Geneviève
full_name: Conéjéro, Geneviève
last_name: Conéjéro
- first_name: Cathy
full_name: Curie, Cathy
last_name: Curie
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Grégory
full_name: Vert, Grégory
last_name: Vert
citation:
ama: Barberon M, Zelazny E, Robert S, et al. Monoubiquitin dependent endocytosis
of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants.
PNAS. 2011;108(32):E450-E458. doi:10.1073/pnas.1100659108
apa: Barberon, M., Zelazny, E., Robert, S., Conéjéro, G., Curie, C., Friml, J.,
& Vert, G. (2011). Monoubiquitin dependent endocytosis of the Iron Regulated
Transporter 1 IRT1 transporter controls iron uptake in plants. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1100659108
chicago: Barberon, Marie, Enric Zelazny, Stéphanie Robert, Geneviève Conéjéro, Cathy
Curie, Jiří Friml, and Grégory Vert. “Monoubiquitin Dependent Endocytosis of the
Iron Regulated Transporter 1 IRT1 Transporter Controls Iron Uptake in Plants.”
PNAS. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1100659108.
ieee: M. Barberon et al., “Monoubiquitin dependent endocytosis of the Iron
Regulated Transporter 1 IRT1 transporter controls iron uptake in plants,” PNAS,
vol. 108, no. 32. National Academy of Sciences, pp. E450–E458, 2011.
ista: Barberon M, Zelazny E, Robert S, Conéjéro G, Curie C, Friml J, Vert G. 2011.
Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter
controls iron uptake in plants. PNAS. 108(32), E450–E458.
mla: Barberon, Marie, et al. “Monoubiquitin Dependent Endocytosis of the Iron Regulated
Transporter 1 IRT1 Transporter Controls Iron Uptake in Plants.” PNAS, vol.
108, no. 32, National Academy of Sciences, 2011, pp. E450–58, doi:10.1073/pnas.1100659108.
short: M. Barberon, E. Zelazny, S. Robert, G. Conéjéro, C. Curie, J. Friml, G. Vert,
PNAS 108 (2011) E450–E458.
date_created: 2018-12-11T12:01:20Z
date_published: 2011-08-09T00:00:00Z
date_updated: 2021-01-12T07:41:00Z
day: '09'
doi: 10.1073/pnas.1100659108
extern: 1
intvolume: ' 108'
issue: '32'
month: '08'
page: E450 - E458
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3607'
quality_controlled: 0
status: public
title: Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1
transporter controls iron uptake in plants
type: journal_article
volume: 108
year: '2011'
...
---
_id: '3094'
abstract:
- lang: eng
text: Summary Gravitropism aligns plant growth with gravity. It involves gravity
perception and the asymmetric distribution of the phytohormone auxin. Here we
provide insights into the mechanism for hypocotyl gravitropic growth. We show
that the Arabidopsis thaliana PIN3 auxin transporter is required for the asymmetric
auxin distribution for the gravitropic response. Gravistimulation polarizes PIN3
to the bottom side of hypocotyl endodermal cells, which correlates with an increased
auxin response at the lower hypocotyl side. Both PIN3 polarization and hypocotyl
bending require the activity of the trafficking regulator GNOM and the protein
kinase PINOID. Our data suggest that gravity-induced PIN3 polarization diverts
the auxin flow to mediate the asymmetric distribution of auxin for gravitropic
shoot bending.
author:
- first_name: Hana
full_name: Rakusová, Hana
last_name: Rakusová
- first_name: Javier
full_name: Gallego-Bartolomé, Javier
last_name: Gallego Bartolomé
- first_name: Marleen
full_name: Vanstraelen, Marleen
last_name: Vanstraelen
- first_name: Hélène
full_name: Robert, Hélène S
last_name: Robert
- first_name: David
full_name: Alabadí, David
last_name: Alabadí
- first_name: Miguel
full_name: Blázquez, Miguel A
last_name: Blázquez
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Rakusová H, Gallego Bartolomé J, Vanstraelen M, et al. Polarization of PIN3
dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana.
Plant Journal. 2011;67(5):817-826. doi:10.1111/j.1365-313X.2011.04636.x
apa: Rakusová, H., Gallego Bartolomé, J., Vanstraelen, M., Robert, H., Alabadí,
D., Blázquez, M., … Friml, J. (2011). Polarization of PIN3 dependent auxin transport
for hypocotyl gravitropic response in Arabidopsis thaliana. Plant Journal.
Wiley-Blackwell. https://doi.org/10.1111/j.1365-313X.2011.04636.x
chicago: Rakusová, Hana, Javier Gallego Bartolomé, Marleen Vanstraelen, Hélène Robert,
David Alabadí, Miguel Blázquez, Eva Benková, and Jiří Friml. “Polarization of
PIN3 Dependent Auxin Transport for Hypocotyl Gravitropic Response in Arabidopsis
Thaliana.” Plant Journal. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1365-313X.2011.04636.x.
ieee: H. Rakusová et al., “Polarization of PIN3 dependent auxin transport
for hypocotyl gravitropic response in Arabidopsis thaliana,” Plant Journal,
vol. 67, no. 5. Wiley-Blackwell, pp. 817–826, 2011.
ista: Rakusová H, Gallego Bartolomé J, Vanstraelen M, Robert H, Alabadí D, Blázquez
M, Benková E, Friml J. 2011. Polarization of PIN3 dependent auxin transport for
hypocotyl gravitropic response in Arabidopsis thaliana. Plant Journal. 67(5),
817–826.
mla: Rakusová, Hana, et al. “Polarization of PIN3 Dependent Auxin Transport for
Hypocotyl Gravitropic Response in Arabidopsis Thaliana.” Plant Journal,
vol. 67, no. 5, Wiley-Blackwell, 2011, pp. 817–26, doi:10.1111/j.1365-313X.2011.04636.x.
short: H. Rakusová, J. Gallego Bartolomé, M. Vanstraelen, H. Robert, D. Alabadí,
M. Blázquez, E. Benková, J. Friml, Plant Journal 67 (2011) 817–826.
date_created: 2018-12-11T12:01:21Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2021-01-12T07:41:01Z
day: '01'
doi: 10.1111/j.1365-313X.2011.04636.x
extern: 1
intvolume: ' 67'
issue: '5'
month: '09'
page: 817 - 826
publication: Plant Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3606'
quality_controlled: 0
status: public
title: Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response
in Arabidopsis thaliana
type: journal_article
volume: 67
year: '2011'
...
---
_id: '3091'
author:
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Sauer M, Friml J. Fleeting hormone cues get stabilized for plant organogenesis.
Molecular Systems Biology. 2011;7. doi:10.1038/msb.2011.45
apa: Sauer, M., & Friml, J. (2011). Fleeting hormone cues get stabilized for
plant organogenesis. Molecular Systems Biology. Nature Publishing Group.
https://doi.org/10.1038/msb.2011.45
chicago: Sauer, Michael, and Jiří Friml. “Fleeting Hormone Cues Get Stabilized for
Plant Organogenesis.” Molecular Systems Biology. Nature Publishing Group,
2011. https://doi.org/10.1038/msb.2011.45.
ieee: M. Sauer and J. Friml, “Fleeting hormone cues get stabilized for plant organogenesis,”
Molecular Systems Biology, vol. 7. Nature Publishing Group, 2011.
ista: Sauer M, Friml J. 2011. Fleeting hormone cues get stabilized for plant organogenesis.
Molecular Systems Biology. 7.
mla: Sauer, Michael, and Jiří Friml. “Fleeting Hormone Cues Get Stabilized for Plant
Organogenesis.” Molecular Systems Biology, vol. 7, Nature Publishing Group,
2011, doi:10.1038/msb.2011.45.
short: M. Sauer, J. Friml, Molecular Systems Biology 7 (2011).
date_created: 2018-12-11T12:01:19Z
date_published: 2011-07-05T00:00:00Z
date_updated: 2021-01-12T07:41:00Z
day: '05'
doi: 10.1038/msb.2011.45
extern: '1'
external_id:
pmid:
- '21734646'
intvolume: ' 7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159970/
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Systems Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3610'
quality_controlled: '1'
status: public
title: Fleeting hormone cues get stabilized for plant organogenesis
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2011'
...
---
_id: '3102'
abstract:
- lang: eng
text: 'Multicellular organisms depend on cell production, cell fate specification,
and correct patterning to shape their adult body. In plants, auxin plays a prominent
role in the timely coordination of these different cellular processes. A well-studied
example is lateral root initiation, in which auxin triggers founder cell specification
and cell cycle activation of xylem pole–positioned pericycle cells. Here, we report
that the E2Fa transcription factor of Arabidopsis thaliana is an essential component
that regulates the asymmetric cell division marking lateral root initiation. Moreover,
we demonstrate that E2Fa expression is regulated by the LATERAL ORGAN BOUNDARY
DOMAIN18/LATERAL ORGAN BOUNDARY DOMAIN33 (LBD18/LBD33) dimer that is, in turn,
regulated by the auxin signaling pathway. LBD18/LBD33 mediates lateral root organogenesis
through E2Fa transcriptional activation, whereas E2Fa expression under control
of the LBD18 promoter eliminates the need for LBD18. Besides lateral root initiation,
vascular patterning is disrupted in E2Fa knockout plants, similarly as it is affected
in auxin signaling and lbd mutants, indicating that the transcriptional induction
of E2Fa through LBDs represents a general mechanism for auxin-dependent cell cycle
activation. Our data illustrate how a conserved mechanism driving cell cycle entry
has been adapted evolutionarily to connect auxin signaling with control of processes
determining plant architecture. '
author:
- first_name: Barbara
full_name: Berckmans, Barbara
last_name: Berckmans
- first_name: Valya
full_name: Vassileva, Valya
last_name: Vassileva
- first_name: Stephan
full_name: Schmid, Stephan P
last_name: Schmid
- first_name: Sara
full_name: Maes, Sara
last_name: Maes
- first_name: Boris
full_name: Parizot, Boris
last_name: Parizot
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Zoltan
full_name: Magyar, Zoltan
last_name: Magyar
- first_name: Claire
full_name: Lessa Alvim Kamei, Claire
last_name: Lessa Alvim Kamei
- first_name: Csaba
full_name: Koncz, Csaba
last_name: Koncz
- first_name: Laszlo
full_name: Bögre, Laszlo
last_name: Bögre
- first_name: Geert
full_name: Persiau, Geert
last_name: Persiau
- first_name: Geert
full_name: De Jaeger, Geert
last_name: De Jaeger
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Rüdiger
full_name: Simon, Rüdiger
last_name: Simon
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Lieven
full_name: de Veyldera, Lieven
last_name: De Veyldera
citation:
ama: Berckmans B, Vassileva V, Schmid S, et al. Auxin Dependent cell cycle reactivation
through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary
proteins. Plant Cell. 2011;23(10):3671-3683. doi:10.1105/tpc.111.088377
apa: Berckmans, B., Vassileva, V., Schmid, S., Maes, S., Parizot, B., Naramoto,
S., … De Veyldera, L. (2011). Auxin Dependent cell cycle reactivation through
transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins.
Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.111.088377
chicago: Berckmans, Barbara, Valya Vassileva, Stephan Schmid, Sara Maes, Boris Parizot,
Satoshi Naramoto, Zoltan Magyar, et al. “Auxin Dependent Cell Cycle Reactivation
through Transcriptional Regulation of Arabidopsis E2Fa by Lateral Organ Boundary
Proteins.” Plant Cell. American Society of Plant Biologists, 2011. https://doi.org/10.1105/tpc.111.088377.
ieee: B. Berckmans et al., “Auxin Dependent cell cycle reactivation through
transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins,”
Plant Cell, vol. 23, no. 10. American Society of Plant Biologists, pp.
3671–3683, 2011.
ista: Berckmans B, Vassileva V, Schmid S, Maes S, Parizot B, Naramoto S, Magyar
Z, Lessa Alvim Kamei C, Koncz C, Bögre L, Persiau G, De Jaeger G, Friml J, Simon
R, Beeckman T, De Veyldera L. 2011. Auxin Dependent cell cycle reactivation through
transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins.
Plant Cell. 23(10), 3671–3683.
mla: Berckmans, Barbara, et al. “Auxin Dependent Cell Cycle Reactivation through
Transcriptional Regulation of Arabidopsis E2Fa by Lateral Organ Boundary Proteins.”
Plant Cell, vol. 23, no. 10, American Society of Plant Biologists, 2011,
pp. 3671–83, doi:10.1105/tpc.111.088377.
short: B. Berckmans, V. Vassileva, S. Schmid, S. Maes, B. Parizot, S. Naramoto,
Z. Magyar, C. Lessa Alvim Kamei, C. Koncz, L. Bögre, G. Persiau, G. De Jaeger,
J. Friml, R. Simon, T. Beeckman, L. De Veyldera, Plant Cell 23 (2011) 3671–3683.
date_created: 2018-12-11T12:01:24Z
date_published: 2011-10-14T00:00:00Z
date_updated: 2021-01-12T07:41:04Z
day: '14'
doi: 10.1105/tpc.111.088377
extern: 1
intvolume: ' 23'
issue: '10'
month: '10'
page: 3671 - 3683
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3598'
quality_controlled: 0
status: public
title: Auxin Dependent cell cycle reactivation through transcriptional regulation
of arabidopsis E2Fa by lateral organ boundary proteins
type: journal_article
volume: 23
year: '2011'
...
---
_id: '3103'
abstract:
- lang: eng
text: Endocytosis in plants has an essential role not only for basic cellular functions
but also for growth and development, hormonal signaling and communication with
the environment including nutrient delivery, toxin avoidance, and pathogen defense.
The major endocytic mechanism in plants depends on the coat protein clathrin.
It starts by clathrin-coated vesicle formation at the plasma membrane, where specific
cargoes are recognized and packaged for internalization. Recently, genetic, biochemical
and advanced microscopy studies provided initial insights into mechanisms and
roles of clathrin-mediated endocytosis in plants. Here we summarize the present
state of knowledge and compare mechanisms of clathrin-mediated endocytosis in
plants with animal and yeast paradigms as well as review plant-specific regulations
and roles of this process.
author:
- first_name: Xu
full_name: Chen, Xu
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Niloufer
full_name: Irani, Niloufer
last_name: Irani
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Chen X, Irani N, Friml J. Clathrin-mediated endocytosis: The gateway into
plant cells. Current Opinion in Plant Biology. 2011;14(6):674-682. doi:10.1016/j.pbi.2011.08.006'
apa: 'Chen, X., Irani, N., & Friml, J. (2011). Clathrin-mediated endocytosis:
The gateway into plant cells. Current Opinion in Plant Biology. Elsevier.
https://doi.org/10.1016/j.pbi.2011.08.006'
chicago: 'Chen, Xu, Niloufer Irani, and Jiří Friml. “Clathrin-Mediated Endocytosis:
The Gateway into Plant Cells.” Current Opinion in Plant Biology. Elsevier,
2011. https://doi.org/10.1016/j.pbi.2011.08.006.'
ieee: 'X. Chen, N. Irani, and J. Friml, “Clathrin-mediated endocytosis: The gateway
into plant cells,” Current Opinion in Plant Biology, vol. 14, no. 6. Elsevier,
pp. 674–682, 2011.'
ista: 'Chen X, Irani N, Friml J. 2011. Clathrin-mediated endocytosis: The gateway
into plant cells. Current Opinion in Plant Biology. 14(6), 674–682.'
mla: 'Chen, Xu, et al. “Clathrin-Mediated Endocytosis: The Gateway into Plant Cells.”
Current Opinion in Plant Biology, vol. 14, no. 6, Elsevier, 2011, pp. 674–82,
doi:10.1016/j.pbi.2011.08.006.'
short: X. Chen, N. Irani, J. Friml, Current Opinion in Plant Biology 14 (2011) 674–682.
date_created: 2018-12-11T12:01:24Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2021-01-12T07:41:05Z
day: '01'
doi: 10.1016/j.pbi.2011.08.006
extern: '1'
intvolume: ' 14'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 674 - 682
publication: Current Opinion in Plant Biology
publication_status: published
publisher: Elsevier
publist_id: '3596'
quality_controlled: '1'
status: public
title: 'Clathrin-mediated endocytosis: The gateway into plant cells'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2011'
...
---
_id: '3147'
abstract:
- lang: eng
text: Cancer cell of origin is difficult to identify by analyzing cells within terminal
stage tumors, whose identity could be concealed by the acquired plasticity. Thus,
an ideal approach to identify the cell of origin is to analyze proliferative abnormalities
in distinct lineages prior to malignancy. Here, we use mosaic analysis with double
markers (MADM) in mice to model gliomagenesis by initiating concurrent p53/Nf1
mutations sporadically in neural stem cells (NSCs). Surprisingly, MADM-based lineage
tracing revealed significant aberrant growth prior to malignancy only in oligodendrocyte
precursor cells (OPCs), but not in any other NSC-derived lineages or NSCs themselves.
Upon tumor formation, phenotypic and transcriptome analyses of tumor cells revealed
salient OPC features. Finally, introducing the same p53/Nf1 mutations directly
into OPCs consistently led to gliomagenesis. Our findings suggest OPCs as the
cell of origin in this model, even when initial mutations occur in NSCs, and highlight
the importance of analyzing premalignant stages to identify the cancer cell of
origin.
author:
- first_name: Chong
full_name: Liu, Chong
last_name: Liu
- first_name: Jonathan
full_name: Sage, Jonathan C
last_name: Sage
- first_name: Michael
full_name: Miller, Michael R
last_name: Miller
- first_name: Roel
full_name: Verhaak, Roel G
last_name: Verhaak
- first_name: Simon
full_name: Simon Hippenmeyer
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Hannes
full_name: Vogel, Hannes
last_name: Vogel
- first_name: Oded
full_name: Foreman, Oded
last_name: Foreman
- first_name: Roderick
full_name: Bronson, Roderick T
last_name: Bronson
- first_name: Akiko
full_name: Nishiyama, Akiko
last_name: Nishiyama
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
- first_name: Hui
full_name: Zong, Hui
last_name: Zong
citation:
ama: Liu C, Sage J, Miller M, et al. Mosaic analysis with double markers reveals
tumor cell of origin in glioma. Cell. 2011;146(2):209-221. doi:10.1016/j.cell.2011.06.014
apa: Liu, C., Sage, J., Miller, M., Verhaak, R., Hippenmeyer, S., Vogel, H., … Zong,
H. (2011). Mosaic analysis with double markers reveals tumor cell of origin in
glioma. Cell. Cell Press. https://doi.org/10.1016/j.cell.2011.06.014
chicago: Liu, Chong, Jonathan Sage, Michael Miller, Roel Verhaak, Simon Hippenmeyer,
Hannes Vogel, Oded Foreman, et al. “Mosaic Analysis with Double Markers Reveals
Tumor Cell of Origin in Glioma.” Cell. Cell Press, 2011. https://doi.org/10.1016/j.cell.2011.06.014.
ieee: C. Liu et al., “Mosaic analysis with double markers reveals tumor cell
of origin in glioma,” Cell, vol. 146, no. 2. Cell Press, pp. 209–221, 2011.
ista: Liu C, Sage J, Miller M, Verhaak R, Hippenmeyer S, Vogel H, Foreman O, Bronson
R, Nishiyama A, Luo L, Zong H. 2011. Mosaic analysis with double markers reveals
tumor cell of origin in glioma. Cell. 146(2), 209–221.
mla: Liu, Chong, et al. “Mosaic Analysis with Double Markers Reveals Tumor Cell
of Origin in Glioma.” Cell, vol. 146, no. 2, Cell Press, 2011, pp. 209–21,
doi:10.1016/j.cell.2011.06.014.
short: C. Liu, J. Sage, M. Miller, R. Verhaak, S. Hippenmeyer, H. Vogel, O. Foreman,
R. Bronson, A. Nishiyama, L. Luo, H. Zong, Cell 146 (2011) 209–221.
date_created: 2018-12-11T12:01:40Z
date_published: 2011-07-22T00:00:00Z
date_updated: 2021-01-12T07:41:23Z
day: '22'
doi: 10.1016/j.cell.2011.06.014
extern: 1
intvolume: ' 146'
issue: '2'
month: '07'
page: 209 - 221
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3548'
quality_controlled: 0
status: public
title: Mosaic analysis with double markers reveals tumor cell of origin in glioma
type: journal_article
volume: 146
year: '2011'
...
---
_id: '3204'
abstract:
- lang: eng
text: 'We introduce a new class of functions that can be minimized in polynomial
time in the value oracle model. These are functions f satisfying f(x) + f(y) ≥
f(x ∏ y) + f(x ∐ y) where the domain of each variable x i corresponds to nodes
of a rooted binary tree, and operations ∏,∐ are defined with respect to this tree.
Special cases include previously studied L-convex and bisubmodular functions,
which can be obtained with particular choices of trees. We present a polynomial-time
algorithm for minimizing functions in the new class. It combines Murota''s steepest
descent algorithm for L-convex functions with bisubmodular minimization algorithms. '
alternative_title:
- LNCS
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Kolmogorov V. Submodularity on a tree: Unifying Submodularity on a tree: Unifying
L-convex and bisubmodular functions convex and bisubmodular functions. In: Vol
6907. Springer; 2011:400-411. doi:10.1007/978-3-642-22993-0_37'
apa: 'Kolmogorov, V. (2011). Submodularity on a tree: Unifying Submodularity on
a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions
(Vol. 6907, pp. 400–411). Presented at the MFCS: Mathematical Foundations of Computer
Science, Springer. https://doi.org/10.1007/978-3-642-22993-0_37'
chicago: 'Kolmogorov, Vladimir. “Submodularity on a Tree: Unifying Submodularity
on a Tree: Unifying L-Convex and Bisubmodular Functions Convex and Bisubmodular
Functions,” 6907:400–411. Springer, 2011. https://doi.org/10.1007/978-3-642-22993-0_37.'
ieee: 'V. Kolmogorov, “Submodularity on a tree: Unifying Submodularity on a tree:
Unifying L-convex and bisubmodular functions convex and bisubmodular functions,”
presented at the MFCS: Mathematical Foundations of Computer Science, 2011, vol.
6907, pp. 400–411.'
ista: 'Kolmogorov V. 2011. Submodularity on a tree: Unifying Submodularity on a
tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions.
MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 6907, 400–411.'
mla: 'Kolmogorov, Vladimir. Submodularity on a Tree: Unifying Submodularity on
a Tree: Unifying L-Convex and Bisubmodular Functions Convex and Bisubmodular Functions.
Vol. 6907, Springer, 2011, pp. 400–11, doi:10.1007/978-3-642-22993-0_37.'
short: V. Kolmogorov, in:, Springer, 2011, pp. 400–411.
conference:
name: 'MFCS: Mathematical Foundations of Computer Science'
date_created: 2018-12-11T12:02:00Z
date_published: 2011-08-09T00:00:00Z
date_updated: 2021-01-12T07:41:47Z
day: '09'
doi: 10.1007/978-3-642-22993-0_37
extern: 1
intvolume: ' 6907'
main_file_link:
- open_access: '0'
url: http://arxiv.org/pdf/1007.1229v3
month: '08'
page: 400 - 411
publication_status: published
publisher: Springer
publist_id: '3478'
quality_controlled: 0
status: public
title: 'Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex
and bisubmodular functions convex and bisubmodular functions'
type: conference
volume: 6907
year: '2011'
...
---
_id: '3206'
abstract:
- lang: eng
text: In this paper we address the problem of finding the most probable state of
discrete Markov random field (MRF) with associative pairwise terms. Although of
practical importance, this problem is known to be NP-hard in general. We propose
a new type of MRF decomposition, submod-ular decomposition (SMD). Unlike existing
decomposition approaches SMD decomposes the initial problem into sub-problems
corresponding to a specific class label while preserving the graph structure of
each subproblem. Such decomposition enables us to take into account several types
of global constraints in an efficient manner. We study theoretical properties
of the proposed approach and demonstrate its applicability on a number of problems.
author:
- first_name: Anton
full_name: Osokin, Anton
last_name: Osokin
- first_name: Dmitry
full_name: Vetrov, Dmitry
last_name: Vetrov
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Osokin A, Vetrov D, Kolmogorov V. Submodular decomposition framework for inference
in associative Markov networks with global constraints. In: IEEE; 2011:1889-1896.
doi:10.1109/CVPR.2011.5995361'
apa: 'Osokin, A., Vetrov, D., & Kolmogorov, V. (2011). Submodular decomposition
framework for inference in associative Markov networks with global constraints
(pp. 1889–1896). Presented at the CVPR: Computer Vision and Pattern Recognition,
IEEE. https://doi.org/10.1109/CVPR.2011.5995361'
chicago: Osokin, Anton, Dmitry Vetrov, and Vladimir Kolmogorov. “Submodular Decomposition
Framework for Inference in Associative Markov Networks with Global Constraints,”
1889–96. IEEE, 2011. https://doi.org/10.1109/CVPR.2011.5995361.
ieee: 'A. Osokin, D. Vetrov, and V. Kolmogorov, “Submodular decomposition framework
for inference in associative Markov networks with global constraints,” presented
at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 1889–1896.'
ista: 'Osokin A, Vetrov D, Kolmogorov V. 2011. Submodular decomposition framework
for inference in associative Markov networks with global constraints. CVPR: Computer
Vision and Pattern Recognition, 1889–1896.'
mla: Osokin, Anton, et al. Submodular Decomposition Framework for Inference in
Associative Markov Networks with Global Constraints. IEEE, 2011, pp. 1889–96,
doi:10.1109/CVPR.2011.5995361.
short: A. Osokin, D. Vetrov, V. Kolmogorov, in:, IEEE, 2011, pp. 1889–1896.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:02:00Z
date_published: 2011-08-22T00:00:00Z
date_updated: 2021-01-12T07:41:47Z
day: '22'
doi: 10.1109/CVPR.2011.5995361
extern: 1
main_file_link:
- open_access: '0'
url: http://arxiv.org/pdf/1103.1077v1
month: '08'
page: 1889 - 1896
publication_status: published
publisher: IEEE
publist_id: '3476'
quality_controlled: 0
status: public
title: Submodular decomposition framework for inference in associative Markov networks
with global constraints
type: conference
year: '2011'
...
---
_id: '3205'
abstract:
- lang: eng
text: This paper proposes a novel Linear Programming (LP) based algorithm, called
Dynamic Tree-Block Coordinate Ascent (DT-BCA), for performing maximum a posteriori
(MAP) inference in probabilistic graphical models. Unlike traditional message
passing algorithms, which operate uniformly on the whole factor graph, our method
dynamically chooses regions of the factor graph on which to focus message-passing
efforts. We propose two criteria for selecting regions, including an efficiently
computable upper-bound on the increase in the objective possible by passing messages
in any particular region. This bound is derived from the theory of primal-dual
methods from combinatorial optimization, and the forest that maximizes the bounds
can be chosen efficiently using a maximum-spanning-tree-like algorithm. Experimental
results show that our dynamic schedules significantly speed up state-of-the-art
LP-based message-passing algorithms on a wide variety of real-world problems.
author:
- first_name: Daniel
full_name: Tarlow, Daniel
last_name: Tarlow
- first_name: Druv
full_name: Batra, Druv
last_name: Batra
- first_name: Pushmeet
full_name: Kohli, Pushmeet
last_name: Kohli
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Tarlow D, Batra D, Kohli P, Kolmogorov V. Dynamic tree block coordinate ascent.
In: Omnipress; 2011:113-120.'
apa: 'Tarlow, D., Batra, D., Kohli, P., & Kolmogorov, V. (2011). Dynamic tree
block coordinate ascent (pp. 113–120). Presented at the ICML: International Conference
on Machine Learning, Omnipress.'
chicago: Tarlow, Daniel, Druv Batra, Pushmeet Kohli, and Vladimir Kolmogorov. “Dynamic
Tree Block Coordinate Ascent,” 113–20. Omnipress, 2011.
ieee: 'D. Tarlow, D. Batra, P. Kohli, and V. Kolmogorov, “Dynamic tree block coordinate
ascent,” presented at the ICML: International Conference on Machine Learning,
2011, pp. 113–120.'
ista: 'Tarlow D, Batra D, Kohli P, Kolmogorov V. 2011. Dynamic tree block coordinate
ascent. ICML: International Conference on Machine Learning, 113–120.'
mla: Tarlow, Daniel, et al. Dynamic Tree Block Coordinate Ascent. Omnipress,
2011, pp. 113–20.
short: D. Tarlow, D. Batra, P. Kohli, V. Kolmogorov, in:, Omnipress, 2011, pp. 113–120.
conference:
name: 'ICML: International Conference on Machine Learning'
date_created: 2018-12-11T12:02:00Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:47Z
day: '01'
extern: 1
main_file_link:
- open_access: '0'
url: http://ttic.uchicago.edu/~dbatra/publications/assets/tbkk_icml11.pdf
month: '01'
page: 113 - 120
publication_status: published
publisher: Omnipress
publist_id: '3475'
quality_controlled: 0
status: public
title: Dynamic tree block coordinate ascent
type: conference
year: '2011'
...
---
_id: '3207'
abstract:
- lang: eng
text: 'Cosegmentation is typically defined as the task of jointly segmenting something
similar in a given set of images. Existing methods are too generic and so far
have not demonstrated competitive results for any specific task. In this paper
we overcome this limitation by adding two new aspects to cosegmentation: (1) the
"something" has to be an object, and (2) the "similarity"
measure is learned. In this way, we are able to achieve excellent results on the
recently introduced iCoseg dataset, which contains small sets of images of either
the same object instance or similar objects of the same class. The challenge of
this dataset lies in the extreme changes in viewpoint, lighting, and object deformations
within each set. We are able to considerably outperform several competitors. To
achieve this performance, we borrow recent ideas from object recognition: the
use of powerful features extracted from a pool of candidate object-like segmentations.
We believe that our work will be beneficial to several application areas, such
as image retrieval.'
author:
- first_name: Sara
full_name: Vicente, Sara
last_name: Vicente
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Vicente S, Rother C, Kolmogorov V. Object cosegmentation. In: IEEE; 2011:2217-2224.
doi:10.1109/CVPR.2011.5995530'
apa: 'Vicente, S., Rother, C., & Kolmogorov, V. (2011). Object cosegmentation
(pp. 2217–2224). Presented at the CVPR: Computer Vision and Pattern Recognition,
IEEE. https://doi.org/10.1109/CVPR.2011.5995530'
chicago: Vicente, Sara, Carsten Rother, and Vladimir Kolmogorov. “Object Cosegmentation,”
2217–24. IEEE, 2011. https://doi.org/10.1109/CVPR.2011.5995530.
ieee: 'S. Vicente, C. Rother, and V. Kolmogorov, “Object cosegmentation,” presented
at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 2217–2224.'
ista: 'Vicente S, Rother C, Kolmogorov V. 2011. Object cosegmentation. CVPR: Computer
Vision and Pattern Recognition, 2217–2224.'
mla: Vicente, Sara, et al. Object Cosegmentation. IEEE, 2011, pp. 2217–24,
doi:10.1109/CVPR.2011.5995530.
short: S. Vicente, C. Rother, V. Kolmogorov, in:, IEEE, 2011, pp. 2217–2224.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:02:01Z
date_published: 2011-08-22T00:00:00Z
date_updated: 2021-01-12T07:41:48Z
day: '22'
doi: 10.1109/CVPR.2011.5995530
extern: 1
month: '08'
page: 2217 - 2224
publication_status: published
publisher: IEEE
publist_id: '3477'
quality_controlled: 0
status: public
title: Object cosegmentation
type: conference
year: '2011'
...
---
_id: '3240'
abstract:
- lang: eng
text: 'The famous Leftover Hash Lemma (LHL) states that (almost) universal hash
functions are good randomness extractors. Despite its numerous applications, LHL-based
extractors suffer from the following two limitations: - Large Entropy Loss: to
extract v bits from distribution X of min-entropy m which are ε-close to uniform,
one must set v ≤ m - 2log(1/ε), meaning that the entropy loss L = def m - v ≥
2 log(1/ε). For many applications, such entropy loss is too large. - Large Seed
Length: the seed length n of (almost) universal hash function required by the
LHL must be at least n ≥ min (u - v, v + 2log(1/ε)) - O(1), where u is the length
of the source, and must grow with the number of extracted bits. Quite surprisingly,
we show that both limitations of the LHL - large entropy loss and large seed -
can be overcome (or, at least, mitigated) in various important scenarios. First,
we show that entropy loss could be reduced to L = log(1/ε) for the setting of
deriving secret keys for a wide range of cryptographic applications. Specifically,
the security of these schemes with an LHL-derived key gracefully degrades from
ε to at most ε + √ε2-L. (Notice that, unlike standard LHL, this bound is meaningful
even when one extracts more bits than the min-entropy we have!) Based on these
results we build a general computational extractor that enjoys low entropy loss
and can be used to instantiate a generic key derivation function for any cryptographic
application. Second, we study the soundness of the natural expand-then-extract
approach, where one uses a pseudorandom generator (PRG) to expand a short "input
seed" S into a longer "output seed" S′, and then use the resulting
S′ as the seed required by the LHL (or, more generally, by any randomness extractor).
We show that, in general, the expand-then-extract approach is not sound if the
Decisional Diffie-Hellman assumption is true. Despite that, we show that it is
sound either: (1) when extracting a "small" (logarithmic in the security
of the PRG) number of bits; or (2) in minicrypt. Implication (2) suggests that
the expand-then-extract approach is likely secure when used with "practical"
PRGs, despite lacking a reductionist proof of security! © 2011 International Association
for Cryptologic Research.'
alternative_title:
- LNCS
author:
- first_name: Boaz
full_name: Barak, Boaz
last_name: Barak
- first_name: Yevgeniy
full_name: Dodis, Yevgeniy
last_name: Dodis
- first_name: Hugo
full_name: Krawczyk, Hugo
last_name: Krawczyk
- first_name: Olivier
full_name: Pereira, Olivier
last_name: Pereira
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: François
full_name: Standaert, François-Xavier
last_name: Standaert
- first_name: Yu
full_name: Yu, Yu
last_name: Yu
citation:
ama: 'Barak B, Dodis Y, Krawczyk H, et al. Leftover hash lemma revisited. In: Vol
6841. Springer; 2011:1-20. doi:
10.1007/978-3-642-22792-9_1'
apa: 'Barak, B., Dodis, Y., Krawczyk, H., Pereira, O., Pietrzak, K. Z., Standaert,
F., & Yu, Y. (2011). Leftover hash lemma revisited (Vol. 6841, pp. 1–20).
Presented at the CRYPTO: International Cryptology Conference, Springer. https://doi.org/ 10.1007/978-3-642-22792-9_1'
chicago: Barak, Boaz, Yevgeniy Dodis, Hugo Krawczyk, Olivier Pereira, Krzysztof
Z Pietrzak, François Standaert, and Yu Yu. “Leftover Hash Lemma Revisited,” 6841:1–20.
Springer, 2011. https://doi.org/
10.1007/978-3-642-22792-9_1.
ieee: 'B. Barak et al., “Leftover hash lemma revisited,” presented at the
CRYPTO: International Cryptology Conference, 2011, vol. 6841, pp. 1–20.'
ista: 'Barak B, Dodis Y, Krawczyk H, Pereira O, Pietrzak KZ, Standaert F, Yu Y.
2011. Leftover hash lemma revisited. CRYPTO: International Cryptology Conference,
LNCS, vol. 6841, 1–20.'
mla: Barak, Boaz, et al. Leftover Hash Lemma Revisited. Vol. 6841, Springer,
2011, pp. 1–20, doi: 10.1007/978-3-642-22792-9_1.
short: B. Barak, Y. Dodis, H. Krawczyk, O. Pereira, K.Z. Pietrzak, F. Standaert,
Y. Yu, in:, Springer, 2011, pp. 1–20.
conference:
name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:12Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:03Z
day: '01'
doi: ' 10.1007/978-3-642-22792-9_1'
extern: 1
intvolume: ' 6841'
month: '01'
page: 1 - 20
publication_status: published
publisher: Springer
publist_id: '3440'
quality_controlled: 0
status: public
title: Leftover hash lemma revisited
type: conference
volume: 6841
year: '2011'
...
---
_id: '3264'
abstract:
- lang: eng
text: Verification of programs with procedures, multi-threaded programs, and higher-order
functional programs can be effectively au- tomated using abstraction and refinement
schemes that rely on spurious counterexamples for abstraction discovery. The analysis
of counterexam- ples can be automated by a series of interpolation queries, or,
alterna- tively, as a constraint solving query expressed by a set of recursion
free Horn clauses. (A set of interpolation queries can be formulated as a single
constraint over Horn clauses with linear dependency structure between the unknown
relations.) In this paper we present an algorithm for solving recursion free Horn
clauses over a combined theory of linear real/rational arithmetic and uninterpreted
functions. Our algorithm performs resolu- tion to deal with the clausal structure
and relies on partial solutions to deal with (non-local) instances of functionality
axioms.
alternative_title:
- LNCS
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Corneliu
full_name: Popeea, Corneliu
last_name: Popeea
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
citation:
ama: 'Gupta A, Popeea C, Rybalchenko A. Solving recursion-free Horn clauses over
LI+UIF. In: Yang H, ed. Vol 7078. Springer; 2011:188-203. doi:10.1007/978-3-642-25318-8_16'
apa: 'Gupta, A., Popeea, C., & Rybalchenko, A. (2011). Solving recursion-free
Horn clauses over LI+UIF. In H. Yang (Ed.) (Vol. 7078, pp. 188–203). Presented
at the APLAS: Asian Symposium on Programming Languages and Systems, Kenting, Taiwan:
Springer. https://doi.org/10.1007/978-3-642-25318-8_16'
chicago: Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Solving Recursion-Free
Horn Clauses over LI+UIF.” edited by Hongseok Yang, 7078:188–203. Springer, 2011.
https://doi.org/10.1007/978-3-642-25318-8_16.
ieee: 'A. Gupta, C. Popeea, and A. Rybalchenko, “Solving recursion-free Horn clauses
over LI+UIF,” presented at the APLAS: Asian Symposium on Programming Languages
and Systems, Kenting, Taiwan, 2011, vol. 7078, pp. 188–203.'
ista: 'Gupta A, Popeea C, Rybalchenko A. 2011. Solving recursion-free Horn clauses
over LI+UIF. APLAS: Asian Symposium on Programming Languages and Systems, LNCS,
vol. 7078, 188–203.'
mla: Gupta, Ashutosh, et al. Solving Recursion-Free Horn Clauses over LI+UIF.
Edited by Hongseok Yang, vol. 7078, Springer, 2011, pp. 188–203, doi:10.1007/978-3-642-25318-8_16.
short: A. Gupta, C. Popeea, A. Rybalchenko, in:, H. Yang (Ed.), Springer, 2011,
pp. 188–203.
conference:
end_date: 2011-12-07
location: Kenting, Taiwan
name: 'APLAS: Asian Symposium on Programming Languages and Systems'
start_date: 2011-12-05
date_created: 2018-12-11T12:02:20Z
date_published: 2011-12-05T00:00:00Z
date_updated: 2021-01-12T07:42:15Z
day: '05'
department:
- _id: ToHe
doi: 10.1007/978-3-642-25318-8_16
ec_funded: 1
editor:
- first_name: Hongseok
full_name: Yang, Hongseok
last_name: Yang
intvolume: ' 7078'
language:
- iso: eng
month: '12'
oa_version: None
page: 188 - 203
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: '3383'
quality_controlled: '1'
status: public
title: Solving recursion-free Horn clauses over LI+UIF
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 7078
year: '2011'
...
---
_id: '3266'
abstract:
- lang: eng
text: We present a joint image segmentation and labeling model (JSL) which, given
a bag of figure-ground segment hypotheses extracted at multiple image locations
and scales, constructs a joint probability distribution over both the compatible
image interpretations (tilings or image segmentations) composed from those segments,
and over their labeling into categories. The process of drawing samples from the
joint distribution can be interpreted as first sampling tilings, modeled as maximal
cliques, from a graph connecting spatially non-overlapping segments in the bag
[1], followed by sampling labels for those segments, conditioned on the choice
of a particular tiling. We learn the segmentation and labeling parameters jointly,
based on Maximum Likelihood with a novel Incremental Saddle Point estimation procedure.
The partition function over tilings and labelings is increasingly more accurately
approximated by including incorrect configurations that a not-yet-competent model
rates probable during learning. We show that the proposed methodologymatches the
current state of the art in the Stanford dataset [2], as well as in VOC2010, where
41.7% accuracy on the test set is achieved.
author:
- first_name: Adrian
full_name: Ion, Adrian
id: 29F89302-F248-11E8-B48F-1D18A9856A87
last_name: Ion
- first_name: Joao
full_name: Carreira, Joao
last_name: Carreira
- first_name: Cristian
full_name: Sminchisescu, Cristian
last_name: Sminchisescu
citation:
ama: 'Ion A, Carreira J, Sminchisescu C. Probabilistic joint image segmentation
and labeling. In: NIPS Proceedings. Vol 24. Neural Information Processing
Systems Foundation; 2011:1827-1835.'
apa: 'Ion, A., Carreira, J., & Sminchisescu, C. (2011). Probabilistic joint
image segmentation and labeling. In NIPS Proceedings (Vol. 24, pp. 1827–1835).
Granada, Spain: Neural Information Processing Systems Foundation.'
chicago: Ion, Adrian, Joao Carreira, and Cristian Sminchisescu. “Probabilistic Joint
Image Segmentation and Labeling.” In NIPS Proceedings, 24:1827–35. Neural
Information Processing Systems Foundation, 2011.
ieee: A. Ion, J. Carreira, and C. Sminchisescu, “Probabilistic joint image segmentation
and labeling,” in NIPS Proceedings, Granada, Spain, 2011, vol. 24, pp.
1827–1835.
ista: 'Ion A, Carreira J, Sminchisescu C. 2011. Probabilistic joint image segmentation
and labeling. NIPS Proceedings. NIPS: Neural Information Processing Systems vol.
24, 1827–1835.'
mla: Ion, Adrian, et al. “Probabilistic Joint Image Segmentation and Labeling.”
NIPS Proceedings, vol. 24, Neural Information Processing Systems Foundation,
2011, pp. 1827–35.
short: A. Ion, J. Carreira, C. Sminchisescu, in:, NIPS Proceedings, Neural Information
Processing Systems Foundation, 2011, pp. 1827–1835.
conference:
end_date: 2011-12-14
location: Granada, Spain
name: 'NIPS: Neural Information Processing Systems'
start_date: 2011-12-12
date_created: 2018-12-11T12:02:21Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2021-01-12T07:42:15Z
day: '01'
department:
- _id: HeEd
intvolume: ' 24'
language:
- iso: eng
month: '12'
oa_version: None
page: 1827 - 1835
publication: NIPS Proceedings
publication_status: published
publisher: Neural Information Processing Systems Foundation
publist_id: '3381'
quality_controlled: '1'
scopus_import: 1
status: public
title: Probabilistic joint image segmentation and labeling
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2011'
...
---
_id: '3269'
abstract:
- lang: eng
text: The unintentional scattering of light between neighboring surfaces in complex
projection environments increases the brightness and decreases the contrast, disrupting
the appearance of the desired imagery. To achieve satisfactory projection results,
the inverse problem of global illumination must be solved to cancel this secondary
scattering. In this paper, we propose a global illumination cancellation method
that minimizes the perceptual difference between the desired imagery and the actual
total illumination in the resulting physical environment. Using Gauss-Newton and
active set methods, we design a fast solver for the bound constrained nonlinear
least squares problem raised by the perceptual error metrics. Our solver is further
accelerated with a CUDA implementation and multi-resolution method to achieve
1–2 fps for problems with approximately 3000 variables. We demonstrate the global
illumination cancellation algorithm with our multi-projector system. Results show
that our method preserves the color fidelity of the desired imagery significantly
better than previous methods.
article_processing_charge: No
article_type: original
author:
- first_name: Yu
full_name: Sheng, Yu
last_name: Sheng
- first_name: Barbara
full_name: Cutler, Barbara
last_name: Cutler
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Joshua
full_name: Nasman, Joshua
last_name: Nasman
citation:
ama: Sheng Y, Cutler B, Chen C, Nasman J. Perceptual global illumination cancellation
in complex projection environments. Computer Graphics Forum. 2011;30(4):1261-1268.
doi:10.1111/j.1467-8659.2011.01985.x
apa: Sheng, Y., Cutler, B., Chen, C., & Nasman, J. (2011). Perceptual global
illumination cancellation in complex projection environments. Computer Graphics
Forum. Wiley-Blackwell. https://doi.org/10.1111/j.1467-8659.2011.01985.x
chicago: Sheng, Yu, Barbara Cutler, Chao Chen, and Joshua Nasman. “Perceptual Global
Illumination Cancellation in Complex Projection Environments.” Computer Graphics
Forum. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1467-8659.2011.01985.x.
ieee: Y. Sheng, B. Cutler, C. Chen, and J. Nasman, “Perceptual global illumination
cancellation in complex projection environments,” Computer Graphics Forum,
vol. 30, no. 4. Wiley-Blackwell, pp. 1261–1268, 2011.
ista: Sheng Y, Cutler B, Chen C, Nasman J. 2011. Perceptual global illumination
cancellation in complex projection environments. Computer Graphics Forum. 30(4),
1261–1268.
mla: Sheng, Yu, et al. “Perceptual Global Illumination Cancellation in Complex Projection
Environments.” Computer Graphics Forum, vol. 30, no. 4, Wiley-Blackwell,
2011, pp. 1261–68, doi:10.1111/j.1467-8659.2011.01985.x.
short: Y. Sheng, B. Cutler, C. Chen, J. Nasman, Computer Graphics Forum 30 (2011)
1261–1268.
date_created: 2018-12-11T12:02:22Z
date_published: 2011-07-19T00:00:00Z
date_updated: 2021-01-12T07:42:16Z
day: '19'
department:
- _id: HeEd
doi: 10.1111/j.1467-8659.2011.01985.x
intvolume: ' 30'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.cs.cmu.edu/%7Eshengyu/download/egsr2011_paper.pdf
month: '07'
oa: 1
oa_version: Published Version
page: 1261 - 1268
publication: Computer Graphics Forum
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3377'
quality_controlled: '1'
scopus_import: 1
status: public
title: Perceptual global illumination cancellation in complex projection environments
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2011'
...
---
_id: '3267'
abstract:
- lang: eng
text: 'We address the problem of localizing homology classes, namely, finding the
cycle representing a given class with the most concise geometric measure. We study
the problem with different measures: volume, diameter and radius. For volume,
that is, the 1-norm of a cycle, two main results are presented. First, we prove
that the problem is NP-hard to approximate within any constant factor. Second,
we prove that for homology of dimension two or higher, the problem is NP-hard
to approximate even when the Betti number is O(1). The latter result leads to
the inapproximability of the problem of computing the nonbounding cycle with the
smallest volume and computing cycles representing a homology basis with the minimal
total volume. As for the other two measures defined by pairwise geodesic distance,
diameter and radius, we show that the localization problem is NP-hard for diameter
but is polynomial for radius. Our work is restricted to homology over the ℤ2 field.'
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Daniel
full_name: Freedman, Daniel
last_name: Freedman
citation:
ama: Chen C, Freedman D. Hardness results for homology localization. Discrete
& Computational Geometry. 2011;45(3):425-448. doi:10.1007/s00454-010-9322-8
apa: Chen, C., & Freedman, D. (2011). Hardness results for homology localization.
Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-010-9322-8
chicago: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.”
Discrete & Computational Geometry. Springer, 2011. https://doi.org/10.1007/s00454-010-9322-8.
ieee: C. Chen and D. Freedman, “Hardness results for homology localization,” Discrete
& Computational Geometry, vol. 45, no. 3. Springer, pp. 425–448, 2011.
ista: Chen C, Freedman D. 2011. Hardness results for homology localization. Discrete
& Computational Geometry. 45(3), 425–448.
mla: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.”
Discrete & Computational Geometry, vol. 45, no. 3, Springer, 2011,
pp. 425–48, doi:10.1007/s00454-010-9322-8.
short: C. Chen, D. Freedman, Discrete & Computational Geometry 45 (2011) 425–448.
date_created: 2018-12-11T12:02:21Z
date_published: 2011-01-14T00:00:00Z
date_updated: 2023-02-21T16:07:10Z
day: '14'
department:
- _id: HeEd
doi: 10.1007/s00454-010-9322-8
intvolume: ' 45'
issue: '3'
language:
- iso: eng
month: '01'
oa_version: None
page: 425 - 448
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '3379'
quality_controlled: '1'
related_material:
record:
- id: '10909'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Hardness results for homology localization
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2011'
...
---
_id: '3268'
abstract:
- lang: eng
text: 'Algebraic topology is generally considered one of the purest subfield of
mathematics. However, over the last decade two interesting new lines of research
have emerged, one focusing on algorithms for algebraic topology, and the other
on applications of algebraic topology in engineering and science. Amongst the
new areas in which the techniques have been applied are computer vision and image
processing. In this paper, we survey the results of these endeavours. Because
algebraic topology is an area of mathematics with which most computer vision practitioners
have no experience, we review the machinery behind the theories of homology and
persistent homology; our review emphasizes intuitive explanations. In terms of
applications to computer vision, we focus on four illustrative problems: shape
signatures, natural image statistics, image denoising, and segmentation. Our hope
is that this review will stimulate interest on the part of computer vision researchers
to both use and extend the tools of this new field. '
alternative_title:
- Computer Science, Technology and Applications
author:
- first_name: Daniel
full_name: Freedman, Daniel
last_name: Freedman
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
citation:
ama: 'Freedman D, Chen C. Algebraic topology for computer vision. In: Computer
Vision. Nova Science Publishers; 2011:239-268.'
apa: Freedman, D., & Chen, C. (2011). Algebraic topology for computer vision.
In Computer Vision (pp. 239–268). Nova Science Publishers.
chicago: Freedman, Daniel, and Chao Chen. “Algebraic Topology for Computer Vision.”
In Computer Vision, 239–68. Nova Science Publishers, 2011.
ieee: D. Freedman and C. Chen, “Algebraic topology for computer vision,” in Computer
Vision, Nova Science Publishers, 2011, pp. 239–268.
ista: 'Freedman D, Chen C. 2011.Algebraic topology for computer vision. In: Computer
Vision. Computer Science, Technology and Applications, , 239–268.'
mla: Freedman, Daniel, and Chao Chen. “Algebraic Topology for Computer Vision.”
Computer Vision, Nova Science Publishers, 2011, pp. 239–68.
short: D. Freedman, C. Chen, in:, Computer Vision, Nova Science Publishers, 2011,
pp. 239–268.
date_created: 2018-12-11T12:02:22Z
date_published: 2011-11-30T00:00:00Z
date_updated: 2021-01-12T07:42:16Z
day: '30'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://www.hpl.hp.com/techreports/2009/HPL-2009-375.pdf
month: '11'
oa_version: None
page: 239 - 268
publication: Computer Vision
publication_status: published
publisher: Nova Science Publishers
publist_id: '3378'
quality_controlled: '1'
status: public
title: Algebraic topology for computer vision
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3288'
abstract:
- lang: eng
text: 'The zonula adherens (ZA) of epithelial cells is a site of cell-cell adhesion
where cellular forces are exerted and resisted. Increasing evidence indicates
that E-cadherin adhesion molecules at the ZA serve to sense force applied on the
junctions and coordinate cytoskeletal responses to those forces. Efforts to understand
the role that cadherins play in mechanotransduction have been limited by the lack
of assays to measure the impact of forces on the ZA. In this study we used 4D
imaging of GFP-tagged E-cadherin to analyse the movement of the ZA. Junctions
in confluent epithelial monolayers displayed prominent movements oriented orthogonal
(perpendicular) to the ZA itself. Two components were identified in these movements:
a relatively slow unidirectional (translational) component that could be readily
fitted by least-squares regression analysis, upon which were superimposed more
rapid oscillatory movements. Myosin IIB was a dominant factor responsible for
driving the unilateral translational movements. In contrast, frequency spectrum
analysis revealed that depletion of Myosin IIA increased the power of the oscillatory
movements. This implies that Myosin IIA may serve to dampen oscillatory movements
of the ZA. This extends our recent analysis of Myosin II at the ZA to demonstrate
that Myosin IIA and Myosin IIB make distinct contributions to junctional movement
at the ZA.'
acknowledgement: his work was funded by the National Health and Medical Research Council
(NHMRC) of Australia. M.S. was an Erwin Schroedinger postdoctoral fellow of the
Austrian Science Fund (FWF), S.K.W. is supported by a UQ International Research
Tuition Award and Research Scholarship, S.M .by an ANZ Trustees PhD Scholarship.
A.S.Y. is a Research Fellow of the NHMRC. Confocal imaging was performed at the
Australian Cancer Research Foundation (ACRF) Cancer Biology Imaging Centre at the
Institute for Molecular Bioscience, established with the generous support of the
ACRF.
author:
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Selwin
full_name: Wu, Selwin
last_name: Wu
- first_name: Guillermo
full_name: Gomez, Guillermo
last_name: Gomez
- first_name: Sabine
full_name: Mangold, Sabine
last_name: Mangold
- first_name: Alpha
full_name: Yap, Alpha
last_name: Yap
- first_name: Nicholas
full_name: Hamilton, Nicholas
last_name: Hamilton
citation:
ama: Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. Multicomponent analysis
of junctional movements regulated by Myosin II isoforms at the epithelial zonula
adherens. PLoS One. 2011;6(7). doi:10.1371/journal.pone.0022458
apa: Smutny, M., Wu, S., Gomez, G., Mangold, S., Yap, A., & Hamilton, N. (2011).
Multicomponent analysis of junctional movements regulated by Myosin II isoforms
at the epithelial zonula adherens. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0022458
chicago: Smutny, Michael, Selwin Wu, Guillermo Gomez, Sabine Mangold, Alpha Yap,
and Nicholas Hamilton. “Multicomponent Analysis of Junctional Movements Regulated
by Myosin II Isoforms at the Epithelial Zonula Adherens.” PLoS One. Public
Library of Science, 2011. https://doi.org/10.1371/journal.pone.0022458.
ieee: M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, and N. Hamilton, “Multicomponent
analysis of junctional movements regulated by Myosin II isoforms at the epithelial
zonula adherens,” PLoS One, vol. 6, no. 7. Public Library of Science, 2011.
ista: Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. 2011. Multicomponent
analysis of junctional movements regulated by Myosin II isoforms at the epithelial
zonula adherens. PLoS One. 6(7).
mla: Smutny, Michael, et al. “Multicomponent Analysis of Junctional Movements Regulated
by Myosin II Isoforms at the Epithelial Zonula Adherens.” PLoS One, vol.
6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pone.0022458.
short: M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, N. Hamilton, PLoS One 6 (2011).
date_created: 2018-12-11T12:02:28Z
date_published: 2011-07-22T00:00:00Z
date_updated: 2021-01-12T07:42:25Z
day: '22'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1371/journal.pone.0022458
file:
- access_level: open_access
checksum: 57a5eb11dd05241c48c44f492b3ec3ac
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T10:51:43Z
date_updated: 2020-07-14T12:46:06Z
file_id: '6399'
file_name: 2011_PLOS_Smutny.PDF
file_size: 1984567
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3357'
quality_controlled: '1'
status: public
title: Multicomponent analysis of junctional movements regulated by Myosin II isoforms
at the epithelial zonula adherens
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2011'
...
---
_id: '3286'
abstract:
- lang: eng
text: Cationic antimicrobial peptides (CAMPs) selectively target bacterial membranes
by electrostatic interactions with negatively charged lipids. It turned out that
for inhibition of microbial growth a high CAMP membrane concentration is required,
which can be realized by the incorporation of hydrophobic groups within the peptide.
Increasing hydrophobicity, however, reduces the CAMP selectivity for bacterial
over eukaryotic host membranes, thereby causing the risk of detrimental side-effects.
In this study we addressed how cationic amphipathic peptides—in particular a CAMP
with Lysine–Leucine–Lysine repeats (termed KLK)—affect the localization and dynamics
of molecules in eukaryotic membranes. We found KLK to selectively inhibit the
endocytosis of a subgroup of membrane proteins and lipids by electrostatically
interacting with negatively charged sialic acid moieties. Ultrastructural characterization
revealed the formation of membrane invaginations representing fission or fusion
intermediates, in which the sialylated proteins and lipids were immobilized. Experiments
on structurally different cationic amphipathic peptides (KLK, 6-MO-LF11-322 and
NK14-2) indicated a cooperation of electrostatic and hydrophobic forces that selectively
arrest sialylated membrane constituents.
acknowledgement: "This work was funded by the GEN-AU project of the Austrian Research
Promotion Agency, the Austrian Science Fund (FWF; project Y250-B03) and Intercell
AG.\nWe thank the following colleagues for providing plasmids and cells: Daniel
Legler (University of Konstanz, Switzerland), Jennifer Lippincott-Schwartz (NIH,
Bethesda, USA), Hannes Stockinger (Medical University Vienna, Austria), Katharina
Strub (University of Geneva, Switzerland), Lawrence Rajendran (ETH Zurich, Switzerland),
Eileen M. Lafer (UTHSC San Antonio, Texas, USA), Mark McNiven (Mayo Clinic, Minnesota,
USA), John Silvius (McGill University, Montreal, Canada), Christoph Romanin (JKU
Linz, Austria), Herbert Stangl (Medical University Vienna, Austria) and Anton van
der Merwe (Oxford University, Oxford, UK). We thank Harald Kotisch (MFPL, Vienna)
for excellent technical assistance in the processing of samples for electron microscopy
and Sergio Grinstein (Hospital for Sick Children Research Institute, Toronto) for
fruitful discussions. "
author:
- first_name: Julian
full_name: Weghuber, Julian
last_name: Weghuber
- first_name: Michael
full_name: Aichinger, Michael C.
last_name: Aichinger
- first_name: Mario
full_name: Brameshuber, Mario
last_name: Brameshuber
- first_name: Stefan
full_name: Stefan Wieser
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Verena
full_name: Verena Ruprecht
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Birgit
full_name: Plochberger, Birgit
last_name: Plochberger
- first_name: Josef
full_name: Madl, Josef
last_name: Madl
- first_name: Andreas
full_name: Horner, Andreas
last_name: Horner
- first_name: Siegfried
full_name: Reipert, Siegfried
last_name: Reipert
- first_name: Karl
full_name: Lohner, Karl
last_name: Lohner
- first_name: Tamas
full_name: Henics, Tamas
last_name: Henics
- first_name: Gerhard
full_name: Schuetz, Gerhard J
last_name: Schuetz
citation:
ama: Weghuber J, Aichinger M, Brameshuber M, et al. Cationic amphipathic peptides
accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic
host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes. 2011;1808(10):2581-2590.
doi:10.1016/j.bbamem.2011.06.007
apa: Weghuber, J., Aichinger, M., Brameshuber, M., Wieser, S., Ruprecht, V., Plochberger,
B., … Schuetz, G. (2011). Cationic amphipathic peptides accumulate sialylated
proteins and lipids in the plasma membrane of eukaryotic host cells. Biochimica
et Biophysica Acta (BBA) - Biomembranes. Elsevier. https://doi.org/10.1016/j.bbamem.2011.06.007
chicago: Weghuber, Julian, Michael Aichinger, Mario Brameshuber, Stefan Wieser,
Verena Ruprecht, Birgit Plochberger, Josef Madl, et al. “Cationic Amphipathic
Peptides Accumulate Sialylated Proteins and Lipids in the Plasma Membrane of Eukaryotic
Host Cells.” Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier,
2011. https://doi.org/10.1016/j.bbamem.2011.06.007.
ieee: J. Weghuber et al., “Cationic amphipathic peptides accumulate sialylated
proteins and lipids in the plasma membrane of eukaryotic host cells,” Biochimica
et Biophysica Acta (BBA) - Biomembranes, vol. 1808, no. 10. Elsevier, pp.
2581–2590, 2011.
ista: Weghuber J, Aichinger M, Brameshuber M, Wieser S, Ruprecht V, Plochberger
B, Madl J, Horner A, Reipert S, Lohner K, Henics T, Schuetz G. 2011. Cationic
amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane
of eukaryotic host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes.
1808(10), 2581–2590.
mla: Weghuber, Julian, et al. “Cationic Amphipathic Peptides Accumulate Sialylated
Proteins and Lipids in the Plasma Membrane of Eukaryotic Host Cells.” Biochimica
et Biophysica Acta (BBA) - Biomembranes, vol. 1808, no. 10, Elsevier, 2011,
pp. 2581–90, doi:10.1016/j.bbamem.2011.06.007.
short: J. Weghuber, M. Aichinger, M. Brameshuber, S. Wieser, V. Ruprecht, B. Plochberger,
J. Madl, A. Horner, S. Reipert, K. Lohner, T. Henics, G. Schuetz, Biochimica et
Biophysica Acta (BBA) - Biomembranes 1808 (2011) 2581–2590.
date_created: 2018-12-11T12:02:28Z
date_published: 2011-10-01T00:00:00Z
date_updated: 2021-01-12T07:42:24Z
day: '01'
doi: 10.1016/j.bbamem.2011.06.007
extern: 1
intvolume: ' 1808'
issue: '10'
month: '10'
page: 2581 - 2590
publication: Biochimica et Biophysica Acta (BBA) - Biomembranes
publication_status: published
publisher: Elsevier
publist_id: '3359'
quality_controlled: 0
status: public
title: Cationic amphipathic peptides accumulate sialylated proteins and lipids in
the plasma membrane of eukaryotic host cells
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
volume: 1808
year: '2011'
...
---
_id: '3287'
abstract:
- lang: eng
text: 'Diffusing membrane constituents are constantly exposed to a variety of forces
that influence their stochastic path. Single molecule experiments allow for resolving
trajectories at extremely high spatial and temporal accuracy, thereby offering
insights into en route interactions of the tracer. In this review we discuss approaches
to derive information about the underlying processes, based on single molecule
tracking experiments. In particular, we focus on a new versatile way to analyze
single molecule diffusion in the absence of a full analytical treatment. The method
is based on comprehensive comparison of an experimental data set against the hypothetical
outcome of multiple experiments performed on the computer. Since Monte Carlo simulations
can be easily and rapidly performed even on state-of-the-art PCs, our method provides
a simple way for testing various - even complicated - diffusion models. We describe
the new method in detail, and show the applicability on two specific examples:
firstly, kinetic rate constants can be derived for the transient interaction of
mobile membrane proteins; secondly, residence time and corral size can be extracted
for confined diffusion.'
author:
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Markus
full_name: Axmann, Markus
last_name: Axmann
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Gerhard
full_name: Schuetz, Gerhard
last_name: Schuetz
citation:
ama: Ruprecht V, Axmann M, Wieser S, Schuetz G. What can we learn from single molecule
trajectories? Current Protein & Peptide Science. 2011;12(8):714-724.
doi:10.2174/138920311798841753
apa: Ruprecht, V., Axmann, M., Wieser, S., & Schuetz, G. (2011). What can we
learn from single molecule trajectories? Current Protein & Peptide Science.
Bentham Science Publishers. https://doi.org/10.2174/138920311798841753
chicago: Ruprecht, Verena, Markus Axmann, Stefan Wieser, and Gerhard Schuetz. “What
Can We Learn from Single Molecule Trajectories?” Current Protein & Peptide
Science. Bentham Science Publishers, 2011. https://doi.org/10.2174/138920311798841753.
ieee: V. Ruprecht, M. Axmann, S. Wieser, and G. Schuetz, “What can we learn from
single molecule trajectories?,” Current Protein & Peptide Science,
vol. 12, no. 8. Bentham Science Publishers, pp. 714–724, 2011.
ista: Ruprecht V, Axmann M, Wieser S, Schuetz G. 2011. What can we learn from single
molecule trajectories? Current Protein & Peptide Science. 12(8), 714–724.
mla: Ruprecht, Verena, et al. “What Can We Learn from Single Molecule Trajectories?”
Current Protein & Peptide Science, vol. 12, no. 8, Bentham Science
Publishers, 2011, pp. 714–24, doi:10.2174/138920311798841753.
short: V. Ruprecht, M. Axmann, S. Wieser, G. Schuetz, Current Protein & Peptide
Science 12 (2011) 714–724.
date_created: 2018-12-11T12:02:28Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2021-01-12T07:42:24Z
day: '01'
department:
- _id: CaHe
- _id: MiSi
doi: 10.2174/138920311798841753
intvolume: ' 12'
issue: '8'
language:
- iso: eng
month: '12'
oa_version: None
page: 714 - 724
publication: Current Protein & Peptide Science
publication_status: published
publisher: Bentham Science Publishers
publist_id: '3358'
quality_controlled: '1'
scopus_import: 1
status: public
title: What can we learn from single molecule trajectories?
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2011'
...
---
_id: '3285'
abstract:
- lang: eng
text: Resolving the dynamical interplay of proteins and lipids in the live-cell
plasma membrane represents a central goal in current cell biology. Superresolution
concepts have introduced a means of capturing spatial heterogeneity at a nanoscopic
length scale. Similar concepts for detecting dynamical transitions (superresolution
chronoscopy) are still lacking. Here, we show that recently introduced spot-variation
fluorescence correlation spectroscopy allows for sensing transient confinement
times of membrane constituents at dramatically improved resolution. Using standard
diffraction-limited optics, spot-variation fluorescence correlation spectroscopy
captures signatures of single retardation events far below the transit time of
the tracer through the focal spot. We provide an analytical description of special
cases of transient binding of a tracer to pointlike traps, or association of a
tracer with nanodomains. The influence of trap mobility and the underlying binding
kinetics are quantified. Experimental approaches are suggested that allow for
gaining quantitative mechanistic insights into the interaction processes of membrane
constituents.
acknowledgement: Y 250-B03/Austrian Science Fund FWF/Austria
author:
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Didier
full_name: Marguet, Didier
last_name: Marguet
- first_name: Gerhard
full_name: Schuetz, Gerhard
last_name: Schuetz
citation:
ama: Ruprecht V, Wieser S, Marguet D, Schuetz G. Spot variation fluorescence correlation
spectroscopy allows for superresolution chronoscopy of confinement times in membranes.
Biophysical Journal. 2011;100(11):2839-2845. doi:10.1016/j.bpj.2011.04.035
apa: Ruprecht, V., Wieser, S., Marguet, D., & Schuetz, G. (2011). Spot variation
fluorescence correlation spectroscopy allows for superresolution chronoscopy of
confinement times in membranes. Biophysical Journal. Biophysical Society.
https://doi.org/10.1016/j.bpj.2011.04.035
chicago: Ruprecht, Verena, Stefan Wieser, Didier Marguet, and Gerhard Schuetz. “Spot
Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy
of Confinement Times in Membranes.” Biophysical Journal. Biophysical Society,
2011. https://doi.org/10.1016/j.bpj.2011.04.035.
ieee: V. Ruprecht, S. Wieser, D. Marguet, and G. Schuetz, “Spot variation fluorescence
correlation spectroscopy allows for superresolution chronoscopy of confinement
times in membranes,” Biophysical Journal, vol. 100, no. 11. Biophysical
Society, pp. 2839–2845, 2011.
ista: Ruprecht V, Wieser S, Marguet D, Schuetz G. 2011. Spot variation fluorescence
correlation spectroscopy allows for superresolution chronoscopy of confinement
times in membranes. Biophysical Journal. 100(11), 2839–2845.
mla: Ruprecht, Verena, et al. “Spot Variation Fluorescence Correlation Spectroscopy
Allows for Superresolution Chronoscopy of Confinement Times in Membranes.” Biophysical
Journal, vol. 100, no. 11, Biophysical Society, 2011, pp. 2839–45, doi:10.1016/j.bpj.2011.04.035.
short: V. Ruprecht, S. Wieser, D. Marguet, G. Schuetz, Biophysical Journal 100 (2011)
2839–2845.
date_created: 2018-12-11T12:02:27Z
date_published: 2011-06-08T00:00:00Z
date_updated: 2021-01-12T07:42:23Z
day: '08'
doi: 10.1016/j.bpj.2011.04.035
extern: '1'
intvolume: ' 100'
issue: '11'
language:
- iso: eng
month: '06'
oa_version: None
page: 2839 - 2845
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '3360'
status: public
title: Spot variation fluorescence correlation spectroscopy allows for superresolution
chronoscopy of confinement times in membranes
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2011'
...
---
_id: '3302'
abstract:
- lang: eng
text: Cloud computing aims to give users virtually unlimited pay-per-use computing
resources without the burden of managing the underlying infrastructure. We present
a new job execution environment Flextic that exploits scal- able static scheduling
techniques to provide the user with a flexible pricing model, such as a tradeoff
between dif- ferent degrees of execution speed and execution price, and at the
same time, reduce scheduling overhead for the cloud provider. We have evaluated
a prototype of Flextic on Amazon EC2 and compared it against Hadoop. For various
data parallel jobs from machine learning, im- age processing, and gene sequencing
that we considered, Flextic has low scheduling overhead and reduces job du- ration
by up to 15% compared to Hadoop, a dynamic cloud scheduler.
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Anmol
full_name: Singh, Anmol
id: 72A86902-E99F-11E9-9F62-915534D1B916
last_name: Singh
- first_name: Vasu
full_name: Singh, Vasu
id: 4DAE2708-F248-11E8-B48F-1D18A9856A87
last_name: Singh
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: 'Henzinger TA, Singh A, Singh V, Wies T, Zufferey D. Static scheduling in clouds.
In: USENIX; 2011:1-6.'
apa: 'Henzinger, T. A., Singh, A., Singh, V., Wies, T., & Zufferey, D. (2011).
Static scheduling in clouds (pp. 1–6). Presented at the HotCloud: Workshop on
Hot Topics in Cloud Computing, USENIX.'
chicago: Henzinger, Thomas A, Anmol Singh, Vasu Singh, Thomas Wies, and Damien Zufferey.
“Static Scheduling in Clouds,” 1–6. USENIX, 2011.
ieee: 'T. A. Henzinger, A. Singh, V. Singh, T. Wies, and D. Zufferey, “Static scheduling
in clouds,” presented at the HotCloud: Workshop on Hot Topics in Cloud Computing,
2011, pp. 1–6.'
ista: 'Henzinger TA, Singh A, Singh V, Wies T, Zufferey D. 2011. Static scheduling
in clouds. HotCloud: Workshop on Hot Topics in Cloud Computing, 1–6.'
mla: Henzinger, Thomas A., et al. Static Scheduling in Clouds. USENIX, 2011,
pp. 1–6.
short: T.A. Henzinger, A. Singh, V. Singh, T. Wies, D. Zufferey, in:, USENIX, 2011,
pp. 1–6.
conference:
end_date: 2011-06-15
name: 'HotCloud: Workshop on Hot Topics in Cloud Computing'
start_date: 2011-06-14
date_created: 2018-12-11T12:02:33Z
date_published: 2011-06-14T00:00:00Z
date_updated: 2021-01-12T07:42:31Z
day: '14'
ddc:
- '000'
- '005'
department:
- _id: ToHe
file:
- access_level: open_access
checksum: 21a461ac004bb535c83320fe79b30375
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:14Z
date_updated: 2020-07-14T12:46:06Z
file_id: '5333'
file_name: IST-2012-90-v1+1_Static_scheduling_in_clouds.pdf
file_size: 232770
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 1 - 6
publication_status: published
publisher: USENIX
publist_id: '3338'
pubrep_id: '90'
quality_controlled: '1'
status: public
title: Static scheduling in clouds
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3301'
abstract:
- lang: eng
text: The chemical master equation is a differential equation describing the time
evolution of the probability distribution over the possible “states” of a biochemical
system. The solution of this equation is of interest within the systems biology
field ever since the importance of the molec- ular noise has been acknowledged.
Unfortunately, most of the systems do not have analytical solutions, and numerical
solutions suffer from the course of dimensionality and therefore need to be approximated.
Here, we introduce the concept of tail approximation, which retrieves an approximation
of the probabilities in the tail of a distribution from the total probability
of the tail and its conditional expectation. This approximation method can then
be used to numerically compute the solution of the chemical master equation on
a subset of the state space, thus fighting the explosion of the state space, for
which this problem is renowned.
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Maria
full_name: Mateescu, Maria
last_name: Mateescu
citation:
ama: 'Henzinger TA, Mateescu M. Tail approximation for the chemical master equation.
In: Tampere International Center for Signal Processing; 2011.'
apa: 'Henzinger, T. A., & Mateescu, M. (2011). Tail approximation for the chemical
master equation. Presented at the WCSB: Workshop on Computational Systems Biology
(TICSP), Tampere International Center for Signal Processing.'
chicago: Henzinger, Thomas A, and Maria Mateescu. “Tail Approximation for the Chemical
Master Equation.” Tampere International Center for Signal Processing, 2011.
ieee: 'T. A. Henzinger and M. Mateescu, “Tail approximation for the chemical master
equation,” presented at the WCSB: Workshop on Computational Systems Biology (TICSP),
2011.'
ista: 'Henzinger TA, Mateescu M. 2011. Tail approximation for the chemical master
equation. WCSB: Workshop on Computational Systems Biology (TICSP).'
mla: Henzinger, Thomas A., and Maria Mateescu. Tail Approximation for the Chemical
Master Equation. Tampere International Center for Signal Processing, 2011.
short: T.A. Henzinger, M. Mateescu, in:, Tampere International Center for Signal
Processing, 2011.
conference:
name: 'WCSB: Workshop on Computational Systems Biology (TICSP)'
date_created: 2018-12-11T12:02:33Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:30Z
day: '01'
ddc:
- '005'
- '570'
department:
- _id: ToHe
file:
- access_level: open_access
checksum: aa4d7a832a5419e6c0090650ebff2b9a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:12Z
date_updated: 2020-07-14T12:46:06Z
file_id: '5331'
file_name: IST-2012-91-v1+1_Tail_approximation_for_the_chemical_master_equation.pdf
file_size: 240820
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
publication_status: published
publisher: Tampere International Center for Signal Processing
publist_id: '3339'
pubrep_id: '91'
quality_controlled: '1'
status: public
title: Tail approximation for the chemical master equation
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3299'
abstract:
- lang: eng
text: 'We introduce propagation models, a formalism designed to support general
and efficient data structures for the transient analysis of biochemical reaction
networks. We give two use cases for propagation abstract data types: the uniformization
method and numerical integration. We also sketch an implementation of a propagation
abstract data type, which uses abstraction to approximate states.'
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Maria
full_name: Mateescu, Maria
last_name: Mateescu
citation:
ama: 'Henzinger TA, Mateescu M. Propagation models for computing biochemical reaction
networks. In: Springer; 2011:1-3. doi:10.1145/2037509.2037510'
apa: 'Henzinger, T. A., & Mateescu, M. (2011). Propagation models for computing
biochemical reaction networks (pp. 1–3). Presented at the CMSB: Computational
Methods in Systems Biology, Paris, France: Springer. https://doi.org/10.1145/2037509.2037510'
chicago: Henzinger, Thomas A, and Maria Mateescu. “Propagation Models for Computing
Biochemical Reaction Networks,” 1–3. Springer, 2011. https://doi.org/10.1145/2037509.2037510.
ieee: 'T. A. Henzinger and M. Mateescu, “Propagation models for computing biochemical
reaction networks,” presented at the CMSB: Computational Methods in Systems Biology,
Paris, France, 2011, pp. 1–3.'
ista: 'Henzinger TA, Mateescu M. 2011. Propagation models for computing biochemical
reaction networks. CMSB: Computational Methods in Systems Biology, 1–3.'
mla: Henzinger, Thomas A., and Maria Mateescu. Propagation Models for Computing
Biochemical Reaction Networks. Springer, 2011, pp. 1–3, doi:10.1145/2037509.2037510.
short: T.A. Henzinger, M. Mateescu, in:, Springer, 2011, pp. 1–3.
conference:
end_date: 2011-09-23
location: Paris, France
name: 'CMSB: Computational Methods in Systems Biology'
start_date: 2011-09-21
date_created: 2018-12-11T12:02:32Z
date_published: 2011-09-21T00:00:00Z
date_updated: 2021-01-12T07:42:29Z
day: '21'
ddc:
- '000'
- '004'
department:
- _id: ToHe
doi: 10.1145/2037509.2037510
file:
- access_level: open_access
checksum: 7f5c65509db1a9fb049abedd9663ed06
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:50Z
date_updated: 2020-07-14T12:46:06Z
file_id: '4649'
file_name: IST-2012-92-v1+1_Propagation_models_for_computing_biochemical_reaction_networks.pdf
file_size: 255780
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 1 - 3
publication_status: published
publisher: Springer
publist_id: '3341'
pubrep_id: '92'
quality_controlled: '1'
scopus_import: 1
status: public
title: Propagation models for computing biochemical reaction networks
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3316'
abstract:
- lang: eng
text: In addition to being correct, a system should be robust, that is, it should
behave reasonably even after receiving unexpected inputs. In this paper, we summarize
two formal notions of robustness that we have introduced previously for reactive
systems. One of the notions is based on assigning costs for failures on a user-provided
notion of incorrect transitions in a specification. Here, we define a system to
be robust if a finite number of incorrect inputs does not lead to an infinite
number of incorrect outputs. We also give a more refined notion of robustness
that aims to minimize the ratio of output failures to input failures. The second
notion is aimed at liveness. In contrast to the previous notion, it has no concept
of recovery from an error. Instead, it compares the ratio of the number of liveness
constraints that the system violates to the number of liveness constraints that
the environment violates.
article_processing_charge: No
author:
- first_name: Roderick
full_name: Bloem, Roderick
last_name: Bloem
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Karin
full_name: Greimel, Karin
last_name: Greimel
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
citation:
ama: 'Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. Specification-centered
robustness. In: 6th IEEE International Symposium on Industrial and Embedded
Systems. IEEE; 2011:176-185. doi:10.1109/SIES.2011.5953660'
apa: 'Bloem, R., Chatterjee, K., Greimel, K., Henzinger, T. A., & Jobstmann,
B. (2011). Specification-centered robustness. In 6th IEEE International Symposium
on Industrial and Embedded Systems (pp. 176–185). Vasteras, Sweden: IEEE.
https://doi.org/10.1109/SIES.2011.5953660'
chicago: Bloem, Roderick, Krishnendu Chatterjee, Karin Greimel, Thomas A Henzinger,
and Barbara Jobstmann. “Specification-Centered Robustness.” In 6th IEEE International
Symposium on Industrial and Embedded Systems, 176–85. IEEE, 2011. https://doi.org/10.1109/SIES.2011.5953660.
ieee: R. Bloem, K. Chatterjee, K. Greimel, T. A. Henzinger, and B. Jobstmann, “Specification-centered
robustness,” in 6th IEEE International Symposium on Industrial and Embedded
Systems, Vasteras, Sweden, 2011, pp. 176–185.
ista: 'Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. 2011. Specification-centered
robustness. 6th IEEE International Symposium on Industrial and Embedded Systems. SIES:
International Symposium on Industrial Embedded Systems, 176–185.'
mla: Bloem, Roderick, et al. “Specification-Centered Robustness.” 6th IEEE International
Symposium on Industrial and Embedded Systems, IEEE, 2011, pp. 176–85, doi:10.1109/SIES.2011.5953660.
short: R. Bloem, K. Chatterjee, K. Greimel, T.A. Henzinger, B. Jobstmann, in:, 6th
IEEE International Symposium on Industrial and Embedded Systems, IEEE, 2011, pp.
176–185.
conference:
end_date: 2011-06-17
location: Vasteras, Sweden
name: ' SIES: International Symposium on Industrial Embedded Systems'
start_date: 2011-06-15
date_created: 2018-12-11T12:02:38Z
date_published: 2011-07-14T00:00:00Z
date_updated: 2021-01-12T07:42:36Z
day: '14'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1109/SIES.2011.5953660
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://openlib.tugraz.at/download.php?id=5cb57c8a49344&location=browse
month: '07'
oa: 1
oa_version: Published Version
page: 176 - 185
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: 6th IEEE International Symposium on Industrial and Embedded Systems
publication_status: published
publisher: IEEE
publist_id: '3323'
quality_controlled: '1'
scopus_import: 1
status: public
title: Specification-centered robustness
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3318'
abstract:
- lang: eng
text: Parvalbumin is thought to act in a manner similar to EGTA, but how a slow
Ca2+ buffer affects nanodomain-coupling regimes at GABAergic synapses is unclear.
Direct measurements of parvalbumin concentration and paired recordings in rodent
hippocampus and cerebellum revealed that parvalbumin affects synaptic dynamics
only when expressed at high levels. Modeling suggests that, in high concentrations,
parvalbumin may exert BAPTA-like effects, modulating nanodomain coupling via competition
with local saturation of endogenous fixed buffers.
author:
- first_name: Emmanuel
full_name: Eggermann, Emmanuel
last_name: Eggermann
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Eggermann E, Jonas PM. How the “slow” Ca(2+) buffer parvalbumin affects transmitter
release in nanodomain coupling regimes at GABAergic synapses. Nature Neuroscience.
2011;15:20-22. doi:10.1038/nn.3002
apa: Eggermann, E., & Jonas, P. M. (2011). How the “slow” Ca(2+) buffer parvalbumin
affects transmitter release in nanodomain coupling regimes at GABAergic synapses.
Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3002
chicago: Eggermann, Emmanuel, and Peter M Jonas. “How the ‘Slow’ Ca(2+) Buffer Parvalbumin
Affects Transmitter Release in Nanodomain Coupling Regimes at GABAergic Synapses.”
Nature Neuroscience. Nature Publishing Group, 2011. https://doi.org/10.1038/nn.3002.
ieee: E. Eggermann and P. M. Jonas, “How the ‘slow’ Ca(2+) buffer parvalbumin affects
transmitter release in nanodomain coupling regimes at GABAergic synapses,” Nature
Neuroscience, vol. 15. Nature Publishing Group, pp. 20–22, 2011.
ista: Eggermann E, Jonas PM. 2011. How the “slow” Ca(2+) buffer parvalbumin affects
transmitter release in nanodomain coupling regimes at GABAergic synapses. Nature
Neuroscience. 15, 20–22.
mla: Eggermann, Emmanuel, and Peter M. Jonas. “How the ‘Slow’ Ca(2+) Buffer Parvalbumin
Affects Transmitter Release in Nanodomain Coupling Regimes at GABAergic Synapses.”
Nature Neuroscience, vol. 15, Nature Publishing Group, 2011, pp. 20–22,
doi:10.1038/nn.3002.
short: E. Eggermann, P.M. Jonas, Nature Neuroscience 15 (2011) 20–22.
date_created: 2018-12-11T12:02:38Z
date_published: 2011-12-04T00:00:00Z
date_updated: 2021-01-12T07:42:37Z
day: '04'
department:
- _id: PeJo
doi: 10.1038/nn.3002
intvolume: ' 15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631701/
month: '12'
oa: 1
oa_version: Submitted Version
page: 20 - 22
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '3321'
quality_controlled: '1'
scopus_import: 1
status: public
title: How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain
coupling regimes at GABAergic synapses
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2011'
...
---
_id: '3335'
abstract:
- lang: eng
text: We study the topology of the Megaparsec Cosmic Web in terms of the scale-dependent
Betti numbers, which formalize the topological information content of the cosmic
mass distribution. While the Betti numbers do not fully quantify topology, they
extend the information beyond conventional cosmological studies of topology in
terms of genus and Euler characteristic. The richer information content of Betti
numbers goes along the availability of fast algorithms to compute them. For continuous
density fields, we determine the scale-dependence of Betti numbers by invoking
the cosmologically familiar filtration of sublevel or superlevel sets defined
by density thresholds. For the discrete galaxy distribution, however, the analysis
is based on the alpha shapes of the particles. These simplicial complexes constitute
an ordered sequence of nested subsets of the Delaunay tessellation, a filtration
defined by the scale parameter, α. As they are homotopy equivalent to the sublevel
sets of the distance field, they are an excellent tool for assessing the topological
structure of a discrete point distribution. In order to develop an intuitive understanding
for the behavior of Betti numbers as a function of α, and their relation to the
morphological patterns in the Cosmic Web, we first study them within the context
of simple heuristic Voronoi clustering models. These can be tuned to consist of
specific morphological elements of the Cosmic Web, i.e. clusters, filaments, or
sheets. To elucidate the relative prominence of the various Betti numbers in different
stages of morphological evolution, we introduce the concept of alpha tracks. Subsequently,
we address the topology of structures emerging in the standard LCDM scenario and
in cosmological scenarios with alternative dark energy content. The evolution
of the Betti numbers is shown to reflect the hierarchical evolution of the Cosmic
Web. We also demonstrate that the scale-dependence of the Betti numbers yields
a promising measure of cosmological parameters, with a potential to help in determining
the nature of dark energy and to probe primordial non-Gaussianities. We also discuss
the expected Betti numbers as a function of the density threshold for superlevel
sets of a Gaussian random field. Finally, we introduce the concept of persistent
homology. It measures scale levels of the mass distribution and allows us to separate
small from large scale features. Within the context of the hierarchical cosmic
structure formation, persistence provides a natural formalism for a multiscale
topology study of the Cosmic Web.
alternative_title:
- LNCS
author:
- first_name: Rien
full_name: Van De Weygaert, Rien
last_name: Van De Weygaert
- first_name: Gert
full_name: Vegter, Gert
last_name: Vegter
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Bernard
full_name: Jones, Bernard
last_name: Jones
- first_name: Pratyush
full_name: Pranav, Pratyush
last_name: Pranav
- first_name: Changbom
full_name: Park, Changbom
last_name: Park
- first_name: Wojciech
full_name: Hellwing, Wojciech
last_name: Hellwing
- first_name: Bob
full_name: Eldering, Bob
last_name: Eldering
- first_name: Nico
full_name: Kruithof, Nico
last_name: Kruithof
- first_name: Patrick
full_name: Bos, Patrick
last_name: Bos
- first_name: Johan
full_name: Hidding, Johan
last_name: Hidding
- first_name: Job
full_name: Feldbrugge, Job
last_name: Feldbrugge
- first_name: Eline
full_name: Ten Have, Eline
last_name: Ten Have
- first_name: Matti
full_name: Van Engelen, Matti
last_name: Van Engelen
- first_name: Manuel
full_name: Caroli, Manuel
last_name: Caroli
- first_name: Monique
full_name: Teillaud, Monique
last_name: Teillaud
citation:
ama: 'Van De Weygaert R, Vegter G, Edelsbrunner H, et al. Alpha, Betti and the Megaparsec
Universe: On the topology of the Cosmic Web. In: Gavrilova M, Tan K, Mostafavi
M, eds. Transactions on Computational Science XIV. Vol 6970. Special Issue
on Voronoi Diagrams and Delaunay Triangulation. Springer; 2011:60-101. doi:10.1007/978-3-642-25249-5_3'
apa: 'Van De Weygaert, R., Vegter, G., Edelsbrunner, H., Jones, B., Pranav, P.,
Park, C., … Teillaud, M. (2011). Alpha, Betti and the Megaparsec Universe: On
the topology of the Cosmic Web. In M. Gavrilova, K. Tan, & M. Mostafavi (Eds.),
Transactions on Computational Science XIV (Vol. 6970, pp. 60–101). Springer.
https://doi.org/10.1007/978-3-642-25249-5_3'
chicago: 'Van De Weygaert, Rien, Gert Vegter, Herbert Edelsbrunner, Bernard Jones,
Pratyush Pranav, Changbom Park, Wojciech Hellwing, et al. “Alpha, Betti and the
Megaparsec Universe: On the Topology of the Cosmic Web.” In Transactions on
Computational Science XIV, edited by Marina Gavrilova, Kenneth Tan, and Mir
Mostafavi, 6970:60–101. Special Issue on Voronoi Diagrams and Delaunay Triangulation.
Springer, 2011. https://doi.org/10.1007/978-3-642-25249-5_3.'
ieee: 'R. Van De Weygaert et al., “Alpha, Betti and the Megaparsec Universe:
On the topology of the Cosmic Web,” in Transactions on Computational Science
XIV, vol. 6970, M. Gavrilova, K. Tan, and M. Mostafavi, Eds. Springer, 2011,
pp. 60–101.'
ista: 'Van De Weygaert R, Vegter G, Edelsbrunner H, Jones B, Pranav P, Park C, Hellwing
W, Eldering B, Kruithof N, Bos P, Hidding J, Feldbrugge J, Ten Have E, Van Engelen
M, Caroli M, Teillaud M. 2011.Alpha, Betti and the Megaparsec Universe: On the
topology of the Cosmic Web. In: Transactions on Computational Science XIV. LNCS,
vol. 6970, 60–101.'
mla: 'Van De Weygaert, Rien, et al. “Alpha, Betti and the Megaparsec Universe: On
the Topology of the Cosmic Web.” Transactions on Computational Science XIV,
edited by Marina Gavrilova et al., vol. 6970, Springer, 2011, pp. 60–101, doi:10.1007/978-3-642-25249-5_3.'
short: R. Van De Weygaert, G. Vegter, H. Edelsbrunner, B. Jones, P. Pranav, C. Park,
W. Hellwing, B. Eldering, N. Kruithof, P. Bos, J. Hidding, J. Feldbrugge, E. Ten
Have, M. Van Engelen, M. Caroli, M. Teillaud, in:, M. Gavrilova, K. Tan, M. Mostafavi
(Eds.), Transactions on Computational Science XIV, Springer, 2011, pp. 60–101.
date_created: 2018-12-11T12:02:44Z
date_published: 2011-11-09T00:00:00Z
date_updated: 2021-01-12T07:42:44Z
day: '09'
department:
- _id: HeEd
doi: 10.1007/978-3-642-25249-5_3
editor:
- first_name: Marina
full_name: Gavrilova, Marina
last_name: Gavrilova
- first_name: Kenneth
full_name: Tan, Kenneth
last_name: Tan
- first_name: Mir
full_name: Mostafavi, Mir
last_name: Mostafavi
external_id:
arxiv:
- '1306.3640'
intvolume: ' 6970'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1306.3640
month: '11'
oa: 1
oa_version: Preprint
page: 60 - 101
publication: Transactions on Computational Science XIV
publication_status: published
publisher: Springer
publist_id: '3295'
quality_controlled: '1'
scopus_import: 1
series_title: Special Issue on Voronoi Diagrams and Delaunay Triangulation
status: public
title: 'Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web'
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6970
year: '2011'
...