---
_id: '8427'
abstract:
- lang: eng
text: We show that any sufficiently (finitely) smooth ℤ₂-symmetric strictly convex
domain sufficiently close to a circle is dynamically spectrally rigid; i.e., all
deformations among domains in the same class that preserve the length of all periodic
orbits of the associated billiard flow must necessarily be isometric deformations.
This gives a partial answer to a question of P. Sarnak.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jacopo
full_name: De Simoi, Jacopo
last_name: De Simoi
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Qiaoling
full_name: Wei, Qiaoling
last_name: Wei
citation:
ama: De Simoi J, Kaloshin V, Wei Q. Dynamical spectral rigidity among Z2-symmetric
strictly convex domains close to a circle. Annals of Mathematics. 2017;186(1):277-314.
doi:10.4007/annals.2017.186.1.7
apa: De Simoi, J., Kaloshin, V., & Wei, Q. (2017). Dynamical spectral rigidity
among Z2-symmetric strictly convex domains close to a circle. Annals of Mathematics.
Annals of Mathematics. https://doi.org/10.4007/annals.2017.186.1.7
chicago: De Simoi, Jacopo, Vadim Kaloshin, and Qiaoling Wei. “Dynamical Spectral
Rigidity among Z2-Symmetric Strictly Convex Domains Close to a Circle.” Annals
of Mathematics. Annals of Mathematics, 2017. https://doi.org/10.4007/annals.2017.186.1.7.
ieee: J. De Simoi, V. Kaloshin, and Q. Wei, “Dynamical spectral rigidity among Z2-symmetric
strictly convex domains close to a circle,” Annals of Mathematics, vol.
186, no. 1. Annals of Mathematics, pp. 277–314, 2017.
ista: De Simoi J, Kaloshin V, Wei Q. 2017. Dynamical spectral rigidity among Z2-symmetric
strictly convex domains close to a circle. Annals of Mathematics. 186(1), 277–314.
mla: De Simoi, Jacopo, et al. “Dynamical Spectral Rigidity among Z2-Symmetric Strictly
Convex Domains Close to a Circle.” Annals of Mathematics, vol. 186, no.
1, Annals of Mathematics, 2017, pp. 277–314, doi:10.4007/annals.2017.186.1.7.
short: J. De Simoi, V. Kaloshin, Q. Wei, Annals of Mathematics 186 (2017) 277–314.
date_created: 2020-09-17T10:46:42Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2021-01-12T08:19:12Z
day: '01'
doi: 10.4007/annals.2017.186.1.7
extern: '1'
external_id:
arxiv:
- '1606.00230'
fulldoi: https://doi.org/10.4007/annals.2017.186.1.7
intvolume: ' 186'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.00230
month: '07'
oa: 1
oa_version: Preprint
page: 277-314
publication: Annals of Mathematics
publication_identifier:
issn:
- 0003-486X
publication_status: published
publisher: Annals of Mathematics
quality_controlled: '1'
status: public
title: Dynamical spectral rigidity among Z2-symmetric strictly convex domains close
to a circle
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 186
year: '2017'
...
---
_id: '8444'
abstract:
- lang: eng
text: Biophysical investigation of membrane proteins generally requires their extraction
from native sources using detergents, a step that can lead, possibly irreversibly,
to protein denaturation. The propensity of dodecylphosphocholine (DPC), a detergent
widely utilized in NMR studies of membrane proteins, to distort their structure
has been the subject of much controversy. It has been recently proposed that the
binding specificity of the yeast mitochondrial ADP/ATP carrier (yAAC3) toward
cardiolipins is preserved in DPC, thereby suggesting that DPC is a suitable environment
in which to study membrane proteins. In this communication, we used all-atom molecular
dynamics simulations to investigate the specific binding of cardiolipins to yAAC3.
Our data demonstrate that the interaction interface observed in a native-like
environment differs markedly from that inferred from an NMR investigation in DPC,
implying that in this detergent, the protein structure is distorted. We further
investigated yAAC3 solubilized in DPC and in the milder dodecylmaltoside with
thermal-shift assays. The loss of thermal transition observed in DPC confirms
that the protein is no longer properly folded in this environment.
article_processing_charge: No
article_type: original
author:
- first_name: François
full_name: Dehez, François
last_name: Dehez
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Martin S.
full_name: King, Martin S.
last_name: King
- first_name: Edmund R.S.
full_name: Kunji, Edmund R.S.
last_name: Kunji
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
citation:
ama: Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. Mitochondrial ADP/ATP carrier
in dodecylphosphocholine binds cardiolipins with non-native affinity. Biophysical
Journal. 2017;113(11):2311-2315. doi:10.1016/j.bpj.2017.09.019
apa: Dehez, F., Schanda, P., King, M. S., Kunji, E. R. S., & Chipot, C. (2017).
Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with
non-native affinity. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2017.09.019
chicago: Dehez, François, Paul Schanda, Martin S. King, Edmund R.S. Kunji, and Christophe
Chipot. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins
with Non-Native Affinity.” Biophysical Journal. Elsevier, 2017. https://doi.org/10.1016/j.bpj.2017.09.019.
ieee: F. Dehez, P. Schanda, M. S. King, E. R. S. Kunji, and C. Chipot, “Mitochondrial
ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity,”
Biophysical Journal, vol. 113, no. 11. Elsevier, pp. 2311–2315, 2017.
ista: Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. 2017. Mitochondrial ADP/ATP
carrier in dodecylphosphocholine binds cardiolipins with non-native affinity.
Biophysical Journal. 113(11), 2311–2315.
mla: Dehez, François, et al. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine
Binds Cardiolipins with Non-Native Affinity.” Biophysical Journal, vol.
113, no. 11, Elsevier, 2017, pp. 2311–15, doi:10.1016/j.bpj.2017.09.019.
short: F. Dehez, P. Schanda, M.S. King, E.R.S. Kunji, C. Chipot, Biophysical Journal
113 (2017) 2311–2315.
date_created: 2020-09-18T10:05:54Z
date_published: 2017-12-05T00:00:00Z
date_updated: 2021-01-12T08:19:18Z
day: '05'
doi: 10.1016/j.bpj.2017.09.019
extern: '1'
fulldoi: https://doi.org/10.1016/j.bpj.2017.09.019
intvolume: ' 113'
issue: '11'
keyword:
- Biophysics
language:
- iso: eng
month: '12'
oa_version: None
page: 2311-2315
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with
non-native affinity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2017'
...
---
OA_place: publisher
OA_type: gold
_id: '8445'
abstract:
- lang: eng
text: Proteins perform their functions in solution but their structures are most
frequently studied inside crystals. Here we probe how the crystal packing alters
microsecond dynamics, using solid-state NMR measurements and multi-microsecond
MD simulations of different crystal forms of ubiquitin. In particular, near-rotary-resonance
relaxation dispersion (NERRD) experiments probe angular backbone motion, while
Bloch–McConnell relaxation dispersion data report on fluctuations of the local
electronic environment. These experiments and simulations reveal that the packing
of the protein can significantly alter the thermodynamics and kinetics of local
conformational exchange. Moreover, we report small-amplitude reorientational motion
of protein molecules in the crystal lattice with an ~3–5° amplitude on a tens-of-microseconds
time scale in one of the crystals, but not in others. An intriguing possibility
arises that overall motion is to some extent coupled to local dynamics. Our study
highlights the importance of considering the packing when analyzing dynamics of
crystalline proteins.
article_number: '145'
article_processing_charge: Yes
article_type: original
author:
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Sergei A.
full_name: Izmailov, Sergei A.
last_name: Izmailov
- first_name: Olga N.
full_name: Rogacheva, Olga N.
last_name: Rogacheva
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Joyce
full_name: Woodhouse, Joyce
last_name: Woodhouse
- first_name: Anastasya
full_name: Shilova, Anastasya
last_name: Shilova
- first_name: Yi
full_name: Xue, Yi
last_name: Xue
- first_name: Tairan
full_name: Yuwen, Tairan
last_name: Yuwen
- first_name: Nicolas
full_name: Coquelle, Nicolas
last_name: Coquelle
- first_name: Jacques-Philippe
full_name: Colletier, Jacques-Philippe
last_name: Colletier
- first_name: Nikolai R.
full_name: Skrynnikov, Nikolai R.
last_name: Skrynnikov
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Kurauskas V, Izmailov SA, Rogacheva ON, et al. Slow conformational exchange
and overall rocking motion in ubiquitin protein crystals. Nature Communications.
2017;8. doi:10.1038/s41467-017-00165-8
apa: Kurauskas, V., Izmailov, S. A., Rogacheva, O. N., Hessel, A., Ayala, I., Woodhouse,
J., … Schanda, P. (2017). Slow conformational exchange and overall rocking motion
in ubiquitin protein crystals. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-017-00165-8
chicago: Kurauskas, Vilius, Sergei A. Izmailov, Olga N. Rogacheva, Audrey Hessel,
Isabel Ayala, Joyce Woodhouse, Anastasya Shilova, et al. “Slow Conformational
Exchange and Overall Rocking Motion in Ubiquitin Protein Crystals.” Nature
Communications. Springer Nature, 2017. https://doi.org/10.1038/s41467-017-00165-8.
ieee: V. Kurauskas et al., “Slow conformational exchange and overall rocking
motion in ubiquitin protein crystals,” Nature Communications, vol. 8. Springer
Nature, 2017.
ista: Kurauskas V, Izmailov SA, Rogacheva ON, Hessel A, Ayala I, Woodhouse J, Shilova
A, Xue Y, Yuwen T, Coquelle N, Colletier J-P, Skrynnikov NR, Schanda P. 2017.
Slow conformational exchange and overall rocking motion in ubiquitin protein crystals.
Nature Communications. 8, 145.
mla: Kurauskas, Vilius, et al. “Slow Conformational Exchange and Overall Rocking
Motion in Ubiquitin Protein Crystals.” Nature Communications, vol. 8, 145,
Springer Nature, 2017, doi:10.1038/s41467-017-00165-8.
short: V. Kurauskas, S.A. Izmailov, O.N. Rogacheva, A. Hessel, I. Ayala, J. Woodhouse,
A. Shilova, Y. Xue, T. Yuwen, N. Coquelle, J.-P. Colletier, N.R. Skrynnikov, P.
Schanda, Nature Communications 8 (2017).
date_created: 2020-09-18T10:06:01Z
date_published: 2017-07-27T00:00:00Z
date_updated: 2025-01-22T14:32:38Z
day: '27'
doi: 10.1038/s41467-017-00165-8
extern: '1'
fulldoi: https://doi.org/10.1038/s41467-017-00165-8
intvolume: ' 8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-017-00165-8
month: '07'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Slow conformational exchange and overall rocking motion in ubiquitin protein
crystals
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '8446'
abstract:
- lang: eng
text: Solid‐state NMR spectroscopy can provide insight into protein structure and
dynamics at the atomic level without inherent protein size limitations. However,
a major hurdle to studying large proteins by solid‐state NMR spectroscopy is related
to spectral complexity and resonance overlap, which increase with molecular weight
and severely hamper the assignment process. Here the use of two sets of experiments
is shown to expand the tool kit of 1H‐detected assignment approaches, which correlate
a given amide pair either to the two adjacent CO–CA pairs (4D hCOCANH/hCOCAcoNH),
or to the amide 1H of the neighboring residue (3D HcocaNH/HcacoNH, which can be
extended to 5D). The experiments are based on efficient coherence transfers between
backbone atoms using INEPT transfers between carbons and cross‐polarization for
heteronuclear transfers. The utility of these experiments is exemplified with
application to assemblies of deuterated, fully amide‐protonated proteins from
approximately 20 to 60 kDa monomer, at magic‐angle spinning (MAS) frequencies
from approximately 40 to 55 kHz. These experiments will also be applicable to
protonated proteins at higher MAS frequencies. The resonance assignment of a domain
within the 50.4 kDa bacteriophage T5 tube protein pb6 is reported, and this is
compared to NMR assignments of the isolated domain in solution. This comparison
reveals contacts of this domain to the core of the polymeric tail tube assembly.
article_processing_charge: No
article_type: original
author:
- first_name: Hugo
full_name: Fraga, Hugo
last_name: Fraga
- first_name: Charles‐Adrien
full_name: Arnaud, Charles‐Adrien
last_name: Arnaud
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Maxime
full_name: Audin, Maxime
last_name: Audin
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Carsten
full_name: Krichel, Carsten
last_name: Krichel
- first_name: Jia‐Ying
full_name: Guan, Jia‐Ying
last_name: Guan
- first_name: Jerome
full_name: Boisbouvier, Jerome
last_name: Boisbouvier
- first_name: Remco
full_name: Sprangers, Remco
last_name: Sprangers
- first_name: Cécile
full_name: Breyton, Cécile
last_name: Breyton
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Fraga H, Arnaud C, Gauto DF, et al. Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D
correlation experiments for resonance assignment of large proteins. ChemPhysChem.
2017;18(19):2697-2703. doi:10.1002/cphc.201700572
apa: Fraga, H., Arnaud, C., Gauto, D. F., Audin, M., Kurauskas, V., Macek, P., …
Schanda, P. (2017). Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments
for resonance assignment of large proteins. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201700572
chicago: Fraga, Hugo, Charles‐Adrien Arnaud, Diego F. Gauto, Maxime Audin, Vilius
Kurauskas, Pavel Macek, Carsten Krichel, et al. “Solid‐state NMR H–N–(C)–H and
H–N–C–C 3D/4D Correlation Experiments for Resonance Assignment of Large Proteins.”
ChemPhysChem. Wiley, 2017. https://doi.org/10.1002/cphc.201700572.
ieee: H. Fraga et al., “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation
experiments for resonance assignment of large proteins,” ChemPhysChem,
vol. 18, no. 19. Wiley, pp. 2697–2703, 2017.
ista: Fraga H, Arnaud C, Gauto DF, Audin M, Kurauskas V, Macek P, Krichel C, Guan
J, Boisbouvier J, Sprangers R, Breyton C, Schanda P. 2017. Solid‐state NMR H–N–(C)–H
and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins.
ChemPhysChem. 18(19), 2697–2703.
mla: Fraga, Hugo, et al. “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D Correlation
Experiments for Resonance Assignment of Large Proteins.” ChemPhysChem,
vol. 18, no. 19, Wiley, 2017, pp. 2697–703, doi:10.1002/cphc.201700572.
short: H. Fraga, C. Arnaud, D.F. Gauto, M. Audin, V. Kurauskas, P. Macek, C. Krichel,
J. Guan, J. Boisbouvier, R. Sprangers, C. Breyton, P. Schanda, ChemPhysChem 18
(2017) 2697–2703.
date_created: 2020-09-18T10:06:09Z
date_published: 2017-08-09T00:00:00Z
date_updated: 2021-01-12T08:19:19Z
day: '09'
doi: 10.1002/cphc.201700572
extern: '1'
fulldoi: https://doi.org/10.1002/cphc.201700572
intvolume: ' 18'
issue: '19'
keyword:
- Physical and Theoretical Chemistry
- Atomic and Molecular Physics
- and Optics
language:
- iso: eng
month: '08'
oa_version: None
page: 2697-2703
publication: ChemPhysChem
publication_identifier:
issn:
- 1439-4235
- 1439-7641
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance
assignment of large proteins
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2017'
...
---
_id: '8447'
abstract:
- lang: eng
text: 'Solid-state NMR spectroscopy can provide site-resolved information about
protein dynamics over many time scales. Here we combine protein deuteration, fast
magic-angle spinning (~45–60 kHz) and proton detection to study dynamics of ubiquitin
in microcrystals, and in particular a mutant in a region that undergoes microsecond
motions in a β-turn region in the wild-type protein. We use 15N R1ρ relaxation
measurements as a function of the radio-frequency (RF) field strength, i.e. relaxation
dispersion, to probe how the G53A mutation alters these dynamics. We report a
population-inversion of conformational states: the conformation that in the wild-type
protein is populated only sparsely becomes the predominant state. We furthermore
explore the potential to use amide-1H R1ρ relaxation to obtain insight into dynamics.
We show that while quantitative interpretation of 1H relaxation remains beyond
reach under the experimental conditions, due to coherent contributions to decay,
one may extract qualitative information about flexibility.'
article_processing_charge: No
article_type: original
author:
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Petra
full_name: Rovó, Petra
last_name: Rovó
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Rasmus
full_name: Linser, Rasmus
last_name: Linser
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. Protein conformational
dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type
and G53A ubiquitin crystals. Solid State Nuclear Magnetic Resonance. 2017;87(10):86-95.
doi:10.1016/j.ssnmr.2017.04.002'
apa: 'Gauto, D. F., Hessel, A., Rovó, P., Kurauskas, V., Linser, R., & Schanda,
P. (2017). Protein conformational dynamics studied by 15N and 1HR1ρ relaxation
dispersion: Application to wild-type and G53A ubiquitin crystals. Solid State
Nuclear Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.ssnmr.2017.04.002'
chicago: 'Gauto, Diego F., Audrey Hessel, Petra Rovó, Vilius Kurauskas, Rasmus Linser,
and Paul Schanda. “Protein Conformational Dynamics Studied by 15N and 1HR1ρ Relaxation
Dispersion: Application to Wild-Type and G53A Ubiquitin Crystals.” Solid State
Nuclear Magnetic Resonance. Elsevier, 2017. https://doi.org/10.1016/j.ssnmr.2017.04.002.'
ieee: 'D. F. Gauto, A. Hessel, P. Rovó, V. Kurauskas, R. Linser, and P. Schanda,
“Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion:
Application to wild-type and G53A ubiquitin crystals,” Solid State Nuclear
Magnetic Resonance, vol. 87, no. 10. Elsevier, pp. 86–95, 2017.'
ista: 'Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. 2017. Protein
conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application
to wild-type and G53A ubiquitin crystals. Solid State Nuclear Magnetic Resonance.
87(10), 86–95.'
mla: 'Gauto, Diego F., et al. “Protein Conformational Dynamics Studied by 15N and
1HR1ρ Relaxation Dispersion: Application to Wild-Type and G53A Ubiquitin Crystals.”
Solid State Nuclear Magnetic Resonance, vol. 87, no. 10, Elsevier, 2017,
pp. 86–95, doi:10.1016/j.ssnmr.2017.04.002.'
short: D.F. Gauto, A. Hessel, P. Rovó, V. Kurauskas, R. Linser, P. Schanda, Solid
State Nuclear Magnetic Resonance 87 (2017) 86–95.
date_created: 2020-09-18T10:06:18Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2021-01-12T08:19:20Z
day: '01'
doi: 10.1016/j.ssnmr.2017.04.002
extern: '1'
fulldoi: https://doi.org/10.1016/j.ssnmr.2017.04.002
intvolume: ' 87'
issue: '10'
keyword:
- Nuclear and High Energy Physics
- Instrumentation
- General Chemistry
- Radiation
language:
- iso: eng
month: '10'
oa_version: None
page: 86-95
publication: Solid State Nuclear Magnetic Resonance
publication_identifier:
issn:
- 0926-2040
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion:
Application to wild-type and G53A ubiquitin crystals'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2017'
...
---
_id: '8448'
abstract:
- lang: eng
text: We present an improved fast mixing device based on the rapid mixing of two
solutions inside the NMR probe, as originally proposed by Hore and coworkers (J.
Am. Chem. Soc. 125 (2003) 12484–12492). Such a device is important for off-equilibrium
studies of molecular kinetics by multidimensional real-time NMR spectrsocopy.
The novelty of this device is that it allows removing the injector from the NMR
detection volume after mixing, and thus provides good magnetic field homogeneity
independently of the initial sample volume placed in the NMR probe. The apparatus
is simple to build, inexpensive, and can be used without any hardware modification
on any type of liquid-state NMR spectrometer. We demonstrate the performance of
our fast mixing device in terms of improved magnetic field homogeneity, and show
an application to the study of protein folding and the structural characterization
of transiently populated folding intermediates.
article_processing_charge: No
article_type: original
author:
- first_name: Rémi
full_name: Franco, Rémi
last_name: Franco
- first_name: Adrien
full_name: Favier, Adrien
last_name: Favier
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Franco R, Favier A, Schanda P, Brutscher B. Optimized fast mixing device for
real-time NMR applications. Journal of Magnetic Resonance. 2017;281(8):125-129.
doi:10.1016/j.jmr.2017.05.016
apa: Franco, R., Favier, A., Schanda, P., & Brutscher, B. (2017). Optimized
fast mixing device for real-time NMR applications. Journal of Magnetic Resonance.
Elsevier. https://doi.org/10.1016/j.jmr.2017.05.016
chicago: Franco, Rémi, Adrien Favier, Paul Schanda, and Bernhard Brutscher. “Optimized
Fast Mixing Device for Real-Time NMR Applications.” Journal of Magnetic Resonance.
Elsevier, 2017. https://doi.org/10.1016/j.jmr.2017.05.016.
ieee: R. Franco, A. Favier, P. Schanda, and B. Brutscher, “Optimized fast mixing
device for real-time NMR applications,” Journal of Magnetic Resonance,
vol. 281, no. 8. Elsevier, pp. 125–129, 2017.
ista: Franco R, Favier A, Schanda P, Brutscher B. 2017. Optimized fast mixing device
for real-time NMR applications. Journal of Magnetic Resonance. 281(8), 125–129.
mla: Franco, Rémi, et al. “Optimized Fast Mixing Device for Real-Time NMR Applications.”
Journal of Magnetic Resonance, vol. 281, no. 8, Elsevier, 2017, pp. 125–29,
doi:10.1016/j.jmr.2017.05.016.
short: R. Franco, A. Favier, P. Schanda, B. Brutscher, Journal of Magnetic Resonance
281 (2017) 125–129.
date_created: 2020-09-18T10:06:27Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:20Z
day: '01'
doi: 10.1016/j.jmr.2017.05.016
extern: '1'
fulldoi: https://doi.org/10.1016/j.jmr.2017.05.016
intvolume: ' 281'
issue: '8'
keyword:
- Nuclear and High Energy Physics
- Biophysics
- Biochemistry
- Condensed Matter Physics
language:
- iso: eng
month: '08'
oa_version: None
page: 125-129
publication: Journal of Magnetic Resonance
publication_identifier:
issn:
- 1090-7807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Optimized fast mixing device for real-time NMR applications
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 281
year: '2017'
...
---
_id: '8449'
abstract:
- lang: eng
text: Ensuring the correct folding of RNA molecules in the cell is of major importance
for a large variety of biological functions. Therefore, chaperone proteins that
assist RNA in adopting their functionally active states are abundant in all living
organisms. An important feature of RNA chaperone proteins is that they do not
require an external energy source to perform their activity, and that they interact
transiently and non-specifically with their RNA targets. So far, little is known
about the mechanistic details of the RNA chaperone activity of these proteins.
Prominent examples of RNA chaperones are bacterial cold shock proteins (Csp) that
have been reported to bind single-stranded RNA and DNA. Here, we have used advanced
NMR spectroscopy techniques to investigate at atomic resolution the RNA-melting
activity of CspA, the major cold shock protein of Escherichia coli, upon binding
to different RNA hairpins. Real-time NMR provides detailed information on the
folding kinetics and folding pathways. Finally, comparison of wild-type CspA with
single-point mutants and small peptides yields insights into the complementary
roles of aromatic and positively charged amino-acid side chains for the RNA chaperone
activity of the protein.
article_processing_charge: No
article_type: original
author:
- first_name: Enrico
full_name: Rennella, Enrico
last_name: Rennella
- first_name: Tomáš
full_name: Sára, Tomáš
last_name: Sára
- first_name: Michael
full_name: Juen, Michael
last_name: Juen
- first_name: Christoph
full_name: Wunderlich, Christoph
last_name: Wunderlich
- first_name: Lionel
full_name: Imbert, Lionel
last_name: Imbert
- first_name: Zsofia
full_name: Solyom, Zsofia
last_name: Solyom
- first_name: Adrien
full_name: Favier, Adrien
last_name: Favier
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Katharina
full_name: Weinhäupl, Katharina
last_name: Weinhäupl
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Robert
full_name: Konrat, Robert
last_name: Konrat
- first_name: Christoph
full_name: Kreutz, Christoph
last_name: Kreutz
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Rennella E, Sára T, Juen M, et al. RNA binding and chaperone activity of the
E.coli cold-shock protein CspA. Nucleic Acids Research. 2017;45(7):4255-4268.
doi:10.1093/nar/gkx044
apa: Rennella, E., Sára, T., Juen, M., Wunderlich, C., Imbert, L., Solyom, Z., …
Brutscher, B. (2017). RNA binding and chaperone activity of the E.coli cold-shock
protein CspA. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkx044
chicago: Rennella, Enrico, Tomáš Sára, Michael Juen, Christoph Wunderlich, Lionel
Imbert, Zsofia Solyom, Adrien Favier, et al. “RNA Binding and Chaperone Activity
of the E.Coli Cold-Shock Protein CspA.” Nucleic Acids Research. Oxford
University Press, 2017. https://doi.org/10.1093/nar/gkx044.
ieee: E. Rennella et al., “RNA binding and chaperone activity of the E.coli
cold-shock protein CspA,” Nucleic Acids Research, vol. 45, no. 7. Oxford
University Press, pp. 4255–4268, 2017.
ista: Rennella E, Sára T, Juen M, Wunderlich C, Imbert L, Solyom Z, Favier A, Ayala
I, Weinhäupl K, Schanda P, Konrat R, Kreutz C, Brutscher B. 2017. RNA binding
and chaperone activity of the E.coli cold-shock protein CspA. Nucleic Acids Research.
45(7), 4255–4268.
mla: Rennella, Enrico, et al. “RNA Binding and Chaperone Activity of the E.Coli
Cold-Shock Protein CspA.” Nucleic Acids Research, vol. 45, no. 7, Oxford
University Press, 2017, pp. 4255–68, doi:10.1093/nar/gkx044.
short: E. Rennella, T. Sára, M. Juen, C. Wunderlich, L. Imbert, Z. Solyom, A. Favier,
I. Ayala, K. Weinhäupl, P. Schanda, R. Konrat, C. Kreutz, B. Brutscher, Nucleic
Acids Research 45 (2017) 4255–4268.
date_created: 2020-09-18T10:06:34Z
date_published: 2017-04-20T00:00:00Z
date_updated: 2021-01-12T08:19:20Z
day: '20'
doi: 10.1093/nar/gkx044
extern: '1'
fulldoi: https://doi.org/10.1093/nar/gkx044
intvolume: ' 45'
issue: '7'
language:
- iso: eng
month: '04'
oa_version: None
page: 4255-4268
publication: Nucleic Acids Research
publication_identifier:
issn:
- 0305-1048
- 1362-4962
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: RNA binding and chaperone activity of the E.coli cold-shock protein CspA
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2017'
...
---
_id: '8450'
abstract:
- lang: eng
text: Methyl groups are very useful probes of structure, dynamics, and interactions
in protein NMR spectroscopy. In particular, methyl-directed experiments provide
high sensitivity even in very large proteins, such as membrane proteins in a membrane-mimicking
environment. In this chapter, we discuss the approach for labeling methyl groups
in E. coli-based protein expression, as exemplified with the mitochondrial carrier
GGC.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Remy
full_name: Sounier, Remy
last_name: Sounier
citation:
ama: 'Kurauskas V, Schanda P, Sounier R. Methyl-specific isotope labeling strategies
for NMR studies of membrane proteins. In: Membrane Protein Structure and Function
Characterization. Vol 1635. Springer Nature; 2017:109-123. doi:10.1007/978-1-4939-7151-0_6'
apa: Kurauskas, V., Schanda, P., & Sounier, R. (2017). Methyl-specific isotope
labeling strategies for NMR studies of membrane proteins. In Membrane protein
structure and function characterization (Vol. 1635, pp. 109–123). Springer
Nature. https://doi.org/10.1007/978-1-4939-7151-0_6
chicago: Kurauskas, Vilius, Paul Schanda, and Remy Sounier. “Methyl-Specific Isotope
Labeling Strategies for NMR Studies of Membrane Proteins.” In Membrane Protein
Structure and Function Characterization, 1635:109–23. Springer Nature, 2017.
https://doi.org/10.1007/978-1-4939-7151-0_6.
ieee: V. Kurauskas, P. Schanda, and R. Sounier, “Methyl-specific isotope labeling
strategies for NMR studies of membrane proteins,” in Membrane protein structure
and function characterization, vol. 1635, Springer Nature, 2017, pp. 109–123.
ista: 'Kurauskas V, Schanda P, Sounier R. 2017.Methyl-specific isotope labeling
strategies for NMR studies of membrane proteins. In: Membrane protein structure
and function characterization. Methods in Molecular Biology, vol. 1635, 109–123.'
mla: Kurauskas, Vilius, et al. “Methyl-Specific Isotope Labeling Strategies for
NMR Studies of Membrane Proteins.” Membrane Protein Structure and Function
Characterization, vol. 1635, Springer Nature, 2017, pp. 109–23, doi:10.1007/978-1-4939-7151-0_6.
short: V. Kurauskas, P. Schanda, R. Sounier, in:, Membrane Protein Structure and
Function Characterization, Springer Nature, 2017, pp. 109–123.
date_created: 2020-09-18T10:06:44Z
date_published: 2017-07-29T00:00:00Z
date_updated: 2022-08-26T09:14:20Z
day: '29'
doi: 10.1007/978-1-4939-7151-0_6
extern: '1'
fulldoi: https://doi.org/10.1007/978-1-4939-7151-0_6
intvolume: ' 1635'
language:
- iso: eng
month: '07'
oa_version: None
page: 109-123
publication: Membrane protein structure and function characterization
publication_identifier:
isbn:
- '9781493971497'
- '9781493971510'
issn:
- 1064-3745
- 1940-6029
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Methyl-specific isotope labeling strategies for NMR studies of membrane proteins
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 1635
year: '2017'
...
---
_id: '8451'
abstract:
- lang: eng
text: The structure, dynamics, and function of membrane proteins are intimately
linked to the properties of the membrane environment in which the proteins are
embedded. For structural and biophysical characterization, membrane proteins generally
need to be extracted from the membrane and reconstituted in a suitable membrane‐mimicking
environment. Ensuring functional and structural integrity in these environments
is often a major concern. The styrene/maleic acid co‐polymer has recently been
shown to be able to extract lipid/membrane protein patches directly from native
membranes to form nanosize discoidal proteolipid particles, also referred to as
native nanodiscs. In this work, we show that high‐resolution solid‐state NMR spectra
can be obtained from an integral membrane protein in native nanodiscs, as exemplified
by the 2×34 kDa bacterial cation diffusion facilitator CzcD.
article_processing_charge: No
article_type: original
author:
- first_name: Beate
full_name: Bersch, Beate
last_name: Bersch
- first_name: Jonas M.
full_name: Dörr, Jonas M.
last_name: Dörr
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: J. Antoinette
full_name: Killian, J. Antoinette
last_name: Killian
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. Proton-detected solid-state
NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs.
Angewandte Chemie International Edition. 2017;56(9):2508-2512. doi:10.1002/anie.201610441
apa: Bersch, B., Dörr, J. M., Hessel, A., Killian, J. A., & Schanda, P. (2017).
Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein
in native nanodiscs. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201610441
chicago: Bersch, Beate, Jonas M. Dörr, Audrey Hessel, J. Antoinette Killian, and
Paul Schanda. “Proton-Detected Solid-State NMR Spectroscopy of a Zinc Diffusion
Facilitator Protein in Native Nanodiscs.” Angewandte Chemie International Edition.
Wiley, 2017. https://doi.org/10.1002/anie.201610441.
ieee: B. Bersch, J. M. Dörr, A. Hessel, J. A. Killian, and P. Schanda, “Proton-detected
solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native
nanodiscs,” Angewandte Chemie International Edition, vol. 56, no. 9. Wiley,
pp. 2508–2512, 2017.
ista: Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. 2017. Proton-detected
solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native
nanodiscs. Angewandte Chemie International Edition. 56(9), 2508–2512.
mla: Bersch, Beate, et al. “Proton-Detected Solid-State NMR Spectroscopy of a Zinc
Diffusion Facilitator Protein in Native Nanodiscs.” Angewandte Chemie International
Edition, vol. 56, no. 9, Wiley, 2017, pp. 2508–12, doi:10.1002/anie.201610441.
short: B. Bersch, J.M. Dörr, A. Hessel, J.A. Killian, P. Schanda, Angewandte Chemie
International Edition 56 (2017) 2508–2512.
date_created: 2020-09-18T10:06:50Z
date_published: 2017-01-27T00:00:00Z
date_updated: 2021-01-12T08:19:22Z
day: '27'
doi: 10.1002/anie.201610441
extern: '1'
fulldoi: https://doi.org/10.1002/anie.201610441
intvolume: ' 56'
issue: '9'
language:
- iso: eng
month: '01'
oa_version: None
page: 2508-2512
publication: Angewandte Chemie International Edition
publication_identifier:
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator
protein in native nanodiscs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 56
year: '2017'
...
---
_id: '9065'
abstract:
- lang: eng
text: Magnetic anisotropy in strontium iridate (Sr2IrO4) is found to be large because
of the strong spin-orbit interactions. In our work, we studied the in-plane magnetic
anisotropy of Sr2IrO4 and traced the anisotropic exchange interactions between
the isospins in the crystal. The magnetic-field-dependent torque τ(H) showed a
prominent transition from the canted antiferromagnetic state to the weak ferromagnetic
(WFM) state. A comprehensive analysis was conducted to examine the isotropic and
anisotropic regimes and probe the easy magnetization axis along the a b plane.
The angle-dependent torque τ(θ) revealed a deviation from the sinusoidal behavior,
and small differences in hysteresis were observed around 0° and 90° in the low-magnetic-field
regime. This indicates that the orientation of the easy axis of the FM component
is along the b axis, where the antiferromagnetic to WFM spin-flop transition occurs.
We compared the coefficients of the magnetic susceptibility tensors and captured
the anisotropy of the material. The in-plane τ(θ) revealed a tendency toward isotropic
behavior for fields with values above the field value of the WFM transition.
article_number: '155102'
article_processing_charge: No
article_type: original
author:
- first_name: Muhammad
full_name: Nauman, Muhammad
id: 32c21954-2022-11eb-9d5f-af9f93c24e71
last_name: Nauman
orcid: 0000-0002-2111-4846
- first_name: Yunjeong
full_name: Hong, Yunjeong
last_name: Hong
- first_name: Tayyaba
full_name: Hussain, Tayyaba
last_name: Hussain
- first_name: M. S.
full_name: Seo, M. S.
last_name: Seo
- first_name: S. Y.
full_name: Park, S. Y.
last_name: Park
- first_name: N.
full_name: Lee, N.
last_name: Lee
- first_name: Y. J.
full_name: Choi, Y. J.
last_name: Choi
- first_name: Woun
full_name: Kang, Woun
last_name: Kang
- first_name: Younjung
full_name: Jo, Younjung
last_name: Jo
citation:
ama: Nauman M, Hong Y, Hussain T, et al. In-plane magnetic anisotropy in strontium
iridate Sr2IrO4. Physical Review B. 2017;96(15). doi:10.1103/physrevb.96.155102
apa: Nauman, M., Hong, Y., Hussain, T., Seo, M. S., Park, S. Y., Lee, N., … Jo,
Y. (2017). In-plane magnetic anisotropy in strontium iridate Sr2IrO4. Physical
Review B. American Physical Society. https://doi.org/10.1103/physrevb.96.155102
chicago: Nauman, Muhammad, Yunjeong Hong, Tayyaba Hussain, M. S. Seo, S. Y. Park,
N. Lee, Y. J. Choi, Woun Kang, and Younjung Jo. “In-Plane Magnetic Anisotropy
in Strontium Iridate Sr2IrO4.” Physical Review B. American Physical Society,
2017. https://doi.org/10.1103/physrevb.96.155102.
ieee: M. Nauman et al., “In-plane magnetic anisotropy in strontium iridate
Sr2IrO4,” Physical Review B, vol. 96, no. 15. American Physical Society,
2017.
ista: Nauman M, Hong Y, Hussain T, Seo MS, Park SY, Lee N, Choi YJ, Kang W, Jo Y.
2017. In-plane magnetic anisotropy in strontium iridate Sr2IrO4. Physical Review
B. 96(15), 155102.
mla: Nauman, Muhammad, et al. “In-Plane Magnetic Anisotropy in Strontium Iridate
Sr2IrO4.” Physical Review B, vol. 96, no. 15, 155102, American Physical
Society, 2017, doi:10.1103/physrevb.96.155102.
short: M. Nauman, Y. Hong, T. Hussain, M.S. Seo, S.Y. Park, N. Lee, Y.J. Choi, W.
Kang, Y. Jo, Physical Review B 96 (2017).
date_created: 2021-02-02T15:49:21Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2021-02-03T12:53:00Z
day: '01'
doi: 10.1103/physrevb.96.155102
extern: '1'
fulldoi: https://doi.org/10.1103/physrevb.96.155102
intvolume: ' 96'
issue: '15'
language:
- iso: eng
month: '10'
oa_version: None
publication: Physical Review B
publication_identifier:
issn:
- 2469-9950
- 2469-9969
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: In-plane magnetic anisotropy in strontium iridate Sr2IrO4
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 96
year: '2017'
...
---
_id: '909'
abstract:
- lang: eng
text: We study the lengths of curves passing through a fixed number of points on
the boundary of a convex shape in the plane. We show that, for any convex shape
K, there exist four points on the boundary of K such that the length of any curve
passing through these points is at least half of the perimeter of K. It is also
shown that the same statement does not remain valid with the additional constraint
that the points are extreme points of K. Moreover, the factor ½ cannot
be achieved with any fixed number of extreme points. We conclude the paper with
a few other inequalities related to the perimeter of a convex shape.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Vladislav
full_name: Vysotsky, Vladislav
last_name: Vysotsky
citation:
ama: Akopyan A, Vysotsky V. On the lengths of curves passing through boundary points
of a planar convex shape. The American Mathematical Monthly. 2017;124(7):588-596.
doi:10.4169/amer.math.monthly.124.7.588
apa: Akopyan, A., & Vysotsky, V. (2017). On the lengths of curves passing through
boundary points of a planar convex shape. The American Mathematical Monthly.
Mathematical Association of America. https://doi.org/10.4169/amer.math.monthly.124.7.588
chicago: Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing
through Boundary Points of a Planar Convex Shape.” The American Mathematical
Monthly. Mathematical Association of America, 2017. https://doi.org/10.4169/amer.math.monthly.124.7.588.
ieee: A. Akopyan and V. Vysotsky, “On the lengths of curves passing through boundary
points of a planar convex shape,” The American Mathematical Monthly, vol.
124, no. 7. Mathematical Association of America, pp. 588–596, 2017.
ista: Akopyan A, Vysotsky V. 2017. On the lengths of curves passing through boundary
points of a planar convex shape. The American Mathematical Monthly. 124(7), 588–596.
mla: Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing
through Boundary Points of a Planar Convex Shape.” The American Mathematical
Monthly, vol. 124, no. 7, Mathematical Association of America, 2017, pp. 588–96,
doi:10.4169/amer.math.monthly.124.7.588.
short: A. Akopyan, V. Vysotsky, The American Mathematical Monthly 124 (2017) 588–596.
date_created: 2018-12-11T11:49:09Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2025-07-10T12:01:35Z
day: '01'
department:
- _id: HeEd
doi: 10.4169/amer.math.monthly.124.7.588
ec_funded: 1
external_id:
arxiv:
- '1605.07997'
isi:
- '000413947300002'
fulldoi: https://doi.org/10.4169/amer.math.monthly.124.7.588
intvolume: ' 124'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1605.07997
month: '01'
oa: 1
oa_version: Submitted Version
page: 588 - 596
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: The American Mathematical Monthly
publication_identifier:
issn:
- 0002-9890
publication_status: published
publisher: Mathematical Association of America
publist_id: '6534'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the lengths of curves passing through boundary points of a planar convex
shape
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 124
year: '2017'
...
---
_id: '910'
abstract:
- lang: eng
text: "Frequency-independent selection is generally considered as a force that acts
to reduce the genetic variation in evolving populations, yet rigorous arguments
for this idea are scarce. When selection fluctuates in time, it is unclear whether
frequency-independent selection may maintain genetic polymorphism without invoking
additional mechanisms. We show that constant frequency-independent selection with
arbitrary epistasis on a well-mixed haploid population eliminates genetic variation
if we assume linkage equilibrium between alleles. To this end, we introduce the
notion of frequency-independent selection at the level of alleles, which is sufficient
to prove our claim and contains the notion of frequency-independent selection
on haploids. When selection and recombination are weak but of the same order,
there may be strong linkage disequilibrium; numerical calculations show that stable
equilibria are highly unlikely. Using the example of a diallelic two-locus model,
we then demonstrate that frequency-independent selection that fluctuates in time
can maintain stable polymorphism if linkage disequilibrium changes its sign periodically.
We put our findings in the context of results from the existing literature and
point out those scenarios in which the possible role of frequency-independent
selection in maintaining genetic variation remains unclear.\r\n"
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Novak S, Barton NH. When does frequency-independent selection maintain genetic
variation? Genetics. 2017;207(2):653-668. doi:10.1534/genetics.117.300129
apa: Novak, S., & Barton, N. H. (2017). When does frequency-independent selection
maintain genetic variation? Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300129
chicago: Novak, Sebastian, and Nicholas H Barton. “When Does Frequency-Independent
Selection Maintain Genetic Variation?” Genetics. Genetics Society of America,
2017. https://doi.org/10.1534/genetics.117.300129.
ieee: S. Novak and N. H. Barton, “When does frequency-independent selection maintain
genetic variation?,” Genetics, vol. 207, no. 2. Genetics Society of America,
pp. 653–668, 2017.
ista: Novak S, Barton NH. 2017. When does frequency-independent selection maintain
genetic variation? Genetics. 207(2), 653–668.
mla: Novak, Sebastian, and Nicholas H. Barton. “When Does Frequency-Independent
Selection Maintain Genetic Variation?” Genetics, vol. 207, no. 2, Genetics
Society of America, 2017, pp. 653–68, doi:10.1534/genetics.117.300129.
short: S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.
corr_author: '1'
date_created: 2018-12-11T11:49:09Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2025-04-15T08:22:21Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1534/genetics.117.300129
ec_funded: 1
external_id:
isi:
- '000412232600019'
file:
- access_level: open_access
checksum: f7c32dabf52e6d9e709d9203761e39fd
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:12Z
date_updated: 2020-07-14T12:48:15Z
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file_name: IST-2018-974-v1+1_manuscript.pdf
file_size: 494268
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
fulldoi: https://doi.org/10.1534/genetics.117.300129
has_accepted_license: '1'
intvolume: ' 207'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 653 - 668
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '6533'
pubrep_id: '974'
quality_controlled: '1'
scopus_import: '1'
status: public
title: When does frequency-independent selection maintain genetic variation?
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 207
year: '2017'
...
---
_id: '911'
abstract:
- lang: eng
text: We develop a probabilistic technique for colorizing grayscale natural images.
In light of the intrinsic uncertainty of this task, the proposed probabilistic
framework has numerous desirable properties. In particular, our model is able
to produce multiple plausible and vivid colorizations for a given grayscale image
and is one of the first colorization models to provide a proper stochastic sampling
scheme. Moreover, our training procedure is supported by a rigorous theoretical
framework that does not require any ad hoc heuristics and allows for efficient
modeling and learning of the joint pixel color distribution.We demonstrate strong
quantitative and qualitative experimental results on the CIFAR-10 dataset and
the challenging ILSVRC 2012 dataset.
article_processing_charge: No
arxiv: 1
author:
- first_name: Amélie
full_name: Royer, Amélie
id: 3811D890-F248-11E8-B48F-1D18A9856A87
last_name: Royer
orcid: 0000-0002-8407-0705
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Royer A, Kolesnikov A, Lampert C. Probabilistic image colorization. In: BMVA
Press; 2017:85.1-85.12. doi:10.5244/c.31.85'
apa: 'Royer, A., Kolesnikov, A., & Lampert, C. (2017). Probabilistic image colorization
(p. 85.1-85.12). Presented at the BMVC: British Machine Vision Conference, London,
United Kingdom: BMVA Press. https://doi.org/10.5244/c.31.85'
chicago: Royer, Amélie, Alexander Kolesnikov, and Christoph Lampert. “Probabilistic
Image Colorization,” 85.1-85.12. BMVA Press, 2017. https://doi.org/10.5244/c.31.85.
ieee: 'A. Royer, A. Kolesnikov, and C. Lampert, “Probabilistic image colorization,”
presented at the BMVC: British Machine Vision Conference, London, United Kingdom,
2017, p. 85.1-85.12.'
ista: 'Royer A, Kolesnikov A, Lampert C. 2017. Probabilistic image colorization.
BMVC: British Machine Vision Conference, 85.1-85.12.'
mla: Royer, Amélie, et al. Probabilistic Image Colorization. BMVA Press,
2017, p. 85.1-85.12, doi:10.5244/c.31.85.
short: A. Royer, A. Kolesnikov, C. Lampert, in:, BMVA Press, 2017, p. 85.1-85.12.
conference:
end_date: 2017-09-07
location: London, United Kingdom
name: 'BMVC: British Machine Vision Conference'
start_date: 2017-09-04
corr_author: '1'
date_created: 2018-12-11T11:49:09Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2026-04-08T07:26:44Z
day: '01'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.5244/c.31.85
ec_funded: 1
external_id:
arxiv:
- '1705.04258'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-08-10T07:14:33Z
date_updated: 2020-08-10T07:14:33Z
file_id: '8224'
file_name: 2017_BMVC_Royer.pdf
file_size: 1625363
relation: main_file
success: 1
file_date_updated: 2020-08-10T07:14:33Z
fulldoi: https://doi.org/10.5244/c.31.85
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 85.1-85.12
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_identifier:
eisbn:
- 190172560X
publication_status: published
publisher: BMVA Press
publist_id: '6532'
quality_controlled: '1'
related_material:
record:
- id: '8390'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Probabilistic image colorization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '9137'
abstract:
- lang: eng
text: Pools of air cooled by partial rain evaporation span up to several hundreds
of kilometers in nature and typically last less than 1 day, ultimately losing
their identity to the large-scale flow. These fundamentally differ in character
from the radiatively-driven dry pools defining convective aggregation. Advancement
in remote sensing and in computer capabilities has promoted exploration of how
precipitation-induced cold pool processes modify the convective spectrum and life
cycle. This contribution surveys current understanding of such cold pools over
the tropical and subtropical oceans. In shallow convection with low rain rates,
the cold pools moisten, preserving the near-surface equivalent potential temperature
or increasing it if the surface moisture fluxes cannot ventilate beyond the new
surface layer; both conditions indicate downdraft origin air from within the boundary
layer. When rain rates exceed ∼ 2 mm h−1, convective-scale downdrafts can bring
down drier air of lower equivalent potential temperature from above the boundary
layer. The resulting density currents facilitate the lifting of locally thermodynamically
favorable air and can impose an arc-shaped mesoscale cloud organization. This
organization allows clouds capable of reaching 4–5 km within otherwise dry environments.
These are more commonly observed in the northern hemisphere trade wind regime,
where the flow to the intertropical convergence zone is unimpeded by the equator.
Their near-surface air properties share much with those shown from cold pools
sampled in the equatorial Indian Ocean. Cold pools are most effective at influencing
the mesoscale organization when the atmosphere is moist in the lower free troposphere
and dry above, suggesting an optimal range of water vapor paths. Outstanding questions
on the relationship between cold pools, their accompanying moisture distribution
and cloud cover are detailed further. Near-surface water vapor rings are documented
in one model inside but near the cold pool edge; these are not consistent with
observations, but do improve with smaller horizontal grid spacings.
article_processing_charge: No
article_type: original
author:
- first_name: Paquita
full_name: Zuidema, Paquita
last_name: Zuidema
- first_name: Giuseppe
full_name: Torri, Giuseppe
last_name: Torri
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Arunchandra
full_name: Chandra, Arunchandra
last_name: Chandra
citation:
ama: Zuidema P, Torri G, Muller CJ, Chandra A. A survey of precipitation-induced
atmospheric cold pools over oceans and their interactions with the larger-scale
environment. Surveys in Geophysics. 2017;38(6):1283-1305. doi:10.1007/s10712-017-9447-x
apa: Zuidema, P., Torri, G., Muller, C. J., & Chandra, A. (2017). A survey of
precipitation-induced atmospheric cold pools over oceans and their interactions
with the larger-scale environment. Surveys in Geophysics. Springer Nature.
https://doi.org/10.1007/s10712-017-9447-x
chicago: Zuidema, Paquita, Giuseppe Torri, Caroline J Muller, and Arunchandra Chandra.
“A Survey of Precipitation-Induced Atmospheric Cold Pools over Oceans and Their
Interactions with the Larger-Scale Environment.” Surveys in Geophysics.
Springer Nature, 2017. https://doi.org/10.1007/s10712-017-9447-x.
ieee: P. Zuidema, G. Torri, C. J. Muller, and A. Chandra, “A survey of precipitation-induced
atmospheric cold pools over oceans and their interactions with the larger-scale
environment,” Surveys in Geophysics, vol. 38, no. 6. Springer Nature, pp.
1283–1305, 2017.
ista: Zuidema P, Torri G, Muller CJ, Chandra A. 2017. A survey of precipitation-induced
atmospheric cold pools over oceans and their interactions with the larger-scale
environment. Surveys in Geophysics. 38(6), 1283–1305.
mla: Zuidema, Paquita, et al. “A Survey of Precipitation-Induced Atmospheric Cold
Pools over Oceans and Their Interactions with the Larger-Scale Environment.” Surveys
in Geophysics, vol. 38, no. 6, Springer Nature, 2017, pp. 1283–305, doi:10.1007/s10712-017-9447-x.
short: P. Zuidema, G. Torri, C.J. Muller, A. Chandra, Surveys in Geophysics 38 (2017)
1283–1305.
date_created: 2021-02-15T14:20:07Z
date_published: 2017-11-14T00:00:00Z
date_updated: 2022-01-24T12:41:45Z
day: '14'
doi: 10.1007/s10712-017-9447-x
extern: '1'
fulldoi: https://doi.org/10.1007/s10712-017-9447-x
intvolume: ' 38'
issue: '6'
keyword:
- Geochemistry and Petrology
- Geophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s10712-017-9447-x
month: '11'
oa: 1
oa_version: Published Version
page: 1283-1305
publication: Surveys in Geophysics
publication_identifier:
issn:
- 0169-3298
- 1573-0956
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: A survey of precipitation-induced atmospheric cold pools over oceans and their
interactions with the larger-scale environment
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 38
year: '2017'
...
---
_id: '9138'
abstract:
- lang: eng
text: Convective self-aggregation, the spontaneous organization of initially scattered
convection into isolated convective clusters despite spatially homogeneous boundary
conditions and forcing, was first recognized and studied in idealized numerical
simulations. While there is a rich history of observational work on convective
clustering and organization, there have been only a few studies that have analyzed
observations to look specifically for processes related to self-aggregation in
models. Here we review observational work in both of these categories and motivate
the need for more of this work. We acknowledge that self-aggregation may appear
to be far-removed from observed convective organization in terms of time scales,
initial conditions, initiation processes, and mean state extremes, but we argue
that these differences vary greatly across the diverse range of model simulations
in the literature and that these comparisons are already offering important insights
into real tropical phenomena. Some preliminary new findings are presented, including
results showing that a self-aggregation simulation with square geometry has too
broad distribution of humidity and is too dry in the driest regions when compared
with radiosonde records from Nauru, while an elongated channel simulation has
realistic representations of atmospheric humidity and its variability. We discuss
recent work increasing our understanding of how organized convection and climate
change may interact, and how model discrepancies related to this question are
prompting interest in observational comparisons. We also propose possible future
directions for observational work related to convective aggregation, including
novel satellite approaches and a ground-based observational network.
article_processing_charge: No
article_type: original
author:
- first_name: Christopher E.
full_name: Holloway, Christopher E.
last_name: Holloway
- first_name: Allison A.
full_name: Wing, Allison A.
last_name: Wing
- first_name: Sandrine
full_name: Bony, Sandrine
last_name: Bony
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Hirohiko
full_name: Masunaga, Hirohiko
last_name: Masunaga
- first_name: Tristan S.
full_name: L’Ecuyer, Tristan S.
last_name: L’Ecuyer
- first_name: David D.
full_name: Turner, David D.
last_name: Turner
- first_name: Paquita
full_name: Zuidema, Paquita
last_name: Zuidema
citation:
ama: Holloway CE, Wing AA, Bony S, et al. Observing convective aggregation. Surveys
in Geophysics. 2017;38(6):1199-1236. doi:10.1007/s10712-017-9419-1
apa: Holloway, C. E., Wing, A. A., Bony, S., Muller, C. J., Masunaga, H., L’Ecuyer,
T. S., … Zuidema, P. (2017). Observing convective aggregation. Surveys in Geophysics.
Springer Nature. https://doi.org/10.1007/s10712-017-9419-1
chicago: Holloway, Christopher E., Allison A. Wing, Sandrine Bony, Caroline J Muller,
Hirohiko Masunaga, Tristan S. L’Ecuyer, David D. Turner, and Paquita Zuidema.
“Observing Convective Aggregation.” Surveys in Geophysics. Springer Nature,
2017. https://doi.org/10.1007/s10712-017-9419-1.
ieee: C. E. Holloway et al., “Observing convective aggregation,” Surveys
in Geophysics, vol. 38, no. 6. Springer Nature, pp. 1199–1236, 2017.
ista: Holloway CE, Wing AA, Bony S, Muller CJ, Masunaga H, L’Ecuyer TS, Turner DD,
Zuidema P. 2017. Observing convective aggregation. Surveys in Geophysics. 38(6),
1199–1236.
mla: Holloway, Christopher E., et al. “Observing Convective Aggregation.” Surveys
in Geophysics, vol. 38, no. 6, Springer Nature, 2017, pp. 1199–236, doi:10.1007/s10712-017-9419-1.
short: C.E. Holloway, A.A. Wing, S. Bony, C.J. Muller, H. Masunaga, T.S. L’Ecuyer,
D.D. Turner, P. Zuidema, Surveys in Geophysics 38 (2017) 1199–1236.
date_created: 2021-02-15T14:20:38Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2022-01-24T12:43:13Z
day: '01'
doi: 10.1007/s10712-017-9419-1
extern: '1'
fulldoi: https://doi.org/10.1007/s10712-017-9419-1
intvolume: ' 38'
issue: '6'
keyword:
- Geochemistry and Petrology
- Geophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s10712-017-9419-1
month: '11'
oa: 1
oa_version: Published Version
page: 1199-1236
publication: Surveys in Geophysics
publication_identifier:
issn:
- 0169-3298
- 1573-0956
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Observing convective aggregation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 38
year: '2017'
...
---
_id: '9139'
abstract:
- lang: eng
text: Organized convection in the tropics occurs across a range of spatial and temporal
scales and strongly influences cloud cover and humidity. One mode of organization
found is “self-aggregation,” in which moist convection spontaneously organizes
into one or several isolated clusters despite spatially homogeneous boundary conditions
and forcing. Self-aggregation is driven by interactions between clouds, moisture,
radiation, surface fluxes, and circulation, and occurs in a wide variety of idealized
simulations of radiative–convective equilibrium. Here we provide a review of convective
self-aggregation in numerical simulations, including its character, causes, and
effects. We describe the evolution of self-aggregation including its time and
length scales and the physical mechanisms leading to its triggering and maintenance,
and we also discuss possible links to climate and climate change.
article_processing_charge: No
article_type: original
author:
- first_name: Allison A.
full_name: Wing, Allison A.
last_name: Wing
- first_name: Kerry
full_name: Emanuel, Kerry
last_name: Emanuel
- first_name: Christopher E.
full_name: Holloway, Christopher E.
last_name: Holloway
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
citation:
ama: 'Wing AA, Emanuel K, Holloway CE, Muller CJ. Convective self-aggregation in
numerical simulations: A review. Surveys in Geophysics. 2017;38(6):1173-1197.
doi:10.1007/s10712-017-9408-4'
apa: 'Wing, A. A., Emanuel, K., Holloway, C. E., & Muller, C. J. (2017). Convective
self-aggregation in numerical simulations: A review. Surveys in Geophysics.
Springer Nature. https://doi.org/10.1007/s10712-017-9408-4'
chicago: 'Wing, Allison A., Kerry Emanuel, Christopher E. Holloway, and Caroline
J Muller. “Convective Self-Aggregation in Numerical Simulations: A Review.” Surveys
in Geophysics. Springer Nature, 2017. https://doi.org/10.1007/s10712-017-9408-4.'
ieee: 'A. A. Wing, K. Emanuel, C. E. Holloway, and C. J. Muller, “Convective self-aggregation
in numerical simulations: A review,” Surveys in Geophysics, vol. 38, no.
6. Springer Nature, pp. 1173–1197, 2017.'
ista: 'Wing AA, Emanuel K, Holloway CE, Muller CJ. 2017. Convective self-aggregation
in numerical simulations: A review. Surveys in Geophysics. 38(6), 1173–1197.'
mla: 'Wing, Allison A., et al. “Convective Self-Aggregation in Numerical Simulations:
A Review.” Surveys in Geophysics, vol. 38, no. 6, Springer Nature, 2017,
pp. 1173–97, doi:10.1007/s10712-017-9408-4.'
short: A.A. Wing, K. Emanuel, C.E. Holloway, C.J. Muller, Surveys in Geophysics
38 (2017) 1173–1197.
date_created: 2021-02-15T14:20:56Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2022-01-24T12:42:36Z
day: '01'
doi: 10.1007/s10712-017-9408-4
extern: '1'
fulldoi: https://doi.org/10.1007/s10712-017-9408-4
intvolume: ' 38'
issue: '6'
keyword:
- Geochemistry and Petrology
- Geophysics
language:
- iso: eng
month: '11'
oa_version: None
page: 1173-1197
publication: Surveys in Geophysics
publication_identifier:
issn:
- 0169-3298
- 1573-0956
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Convective self-aggregation in numerical simulations: A review'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 38
year: '2017'
...
---
_id: '915'
abstract:
- lang: eng
text: We propose a dual decomposition and linear program relaxation of the NP-hard
minimum cost multicut problem. Unlike other polyhedral relaxations of the multicut
polytope, it is amenable to efficient optimization by message passing. Like other
polyhedral relaxations, it can be tightened efficiently by cutting planes. We
define an algorithm that alternates between message passing and efficient separation
of cycle- and odd-wheel inequalities. This algorithm is more efficient than state-of-the-art
algorithms based on linear programming, including algorithms written in the framework
of leading commercial software, as we show in experiments with large instances
of the problem from applications in computer vision, biomedical image analysis
and data mining.
article_processing_charge: No
author:
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
- first_name: Bjoern
full_name: Andres, Bjoern
last_name: Andres
citation:
ama: 'Swoboda P, Andres B. A message passing algorithm for the minimum cost multicut
problem. In: Vol 2017. IEEE; 2017:4990-4999. doi:10.1109/CVPR.2017.530'
apa: 'Swoboda, P., & Andres, B. (2017). A message passing algorithm for the
minimum cost multicut problem (Vol. 2017, pp. 4990–4999). Presented at the CVPR:
Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.530'
chicago: Swoboda, Paul, and Bjoern Andres. “A Message Passing Algorithm for the
Minimum Cost Multicut Problem,” 2017:4990–99. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.530.
ieee: 'P. Swoboda and B. Andres, “A message passing algorithm for the minimum cost
multicut problem,” presented at the CVPR: Computer Vision and Pattern Recognition,
Honolulu, HA, United States, 2017, vol. 2017, pp. 4990–4999.'
ista: 'Swoboda P, Andres B. 2017. A message passing algorithm for the minimum cost
multicut problem. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4990–4999.'
mla: Swoboda, Paul, and Bjoern Andres. A Message Passing Algorithm for the Minimum
Cost Multicut Problem. Vol. 2017, IEEE, 2017, pp. 4990–99, doi:10.1109/CVPR.2017.530.
short: P. Swoboda, B. Andres, in:, IEEE, 2017, pp. 4990–4999.
conference:
end_date: 2017-07-26
location: Honolulu, HA, United States
name: 'CVPR: Computer Vision and Pattern Recognition'
start_date: 2017-07-21
corr_author: '1'
date_created: 2018-12-11T11:49:11Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2024-11-04T13:52:34Z
day: '01'
ddc:
- '000'
department:
- _id: VlKo
doi: 10.1109/CVPR.2017.530
ec_funded: 1
external_id:
isi:
- '000418371405009'
file:
- access_level: open_access
checksum: 7e51dacefa693574581a32da3eff63dc
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T12:52:46Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5849'
file_name: Swoboda_A_Message_Passing_CVPR_2017_paper.pdf
file_size: 883264
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
fulldoi: https://doi.org/10.1109/CVPR.2017.530
has_accepted_license: '1'
intvolume: ' 2017'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 4990-4999
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_identifier:
isbn:
- 978-153860457-1
publication_status: published
publisher: IEEE
publist_id: '6526'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A message passing algorithm for the minimum cost multicut problem
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '9152'
abstract:
- lang: eng
text: Previous numerical studies of the dissipation of internal tides in idealized
settings suggest the existence of a critical latitude (~29°) where dissipation
is enhanced. But observations only indicate a modest enhancement at this latitude.
To resolve this difference between observational and numerical results, the authors
study the latitudinal dependence of internal tides’ dissipation in more realistic
conditions. In particular, the ocean is not a quiescent medium; the presence of
large-scale currents or mesoscale eddies can impact the propagation and dissipation
of internal tides. This paper investigates the impact of a weak background mean
current in numerical simulations. The authors focus on the local dissipation of
high spatial mode internal waves near their generation site. The vertical profile
of dissipation and its variation with latitude without the mean current are consistent
with earlier studies. But adding a weak mean current has a major impact on the
latitudinal distribution of dissipation. The peak at the critical latitude disappears,
and the dissipation is closer to a constant, albeit with two weak peaks at ~25°
and ~35° latitude. This disappearance results from the Doppler shift of the internal
tides’ frequency, which hinders the nonlinear transfer of energy to small-scale
secondary waves via the parametric subharmonic instability (PSI). The new two
weak peaks correspond to the Doppler-shifted critical latitudes of the left- and
right-propagating waves. The results are confirmed in simulations with simple
sinusoidal topography. Thus, although nonlinear transfers via PSI are efficient
at dissipating internal tides, the exact location of the dissipation is sensitive
to large-scale oceanic conditions.
article_processing_charge: No
article_type: original
author:
- first_name: O.
full_name: Richet, O.
last_name: Richet
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: J.-M.
full_name: Chomaz, J.-M.
last_name: Chomaz
citation:
ama: Richet O, Muller CJ, Chomaz J-M. Impact of a mean current on the internal tide
energy dissipation at the critical latitude. Journal of Physical Oceanography.
2017;47(6):1457-1472. doi:10.1175/jpo-d-16-0197.1
apa: Richet, O., Muller, C. J., & Chomaz, J.-M. (2017). Impact of a mean current
on the internal tide energy dissipation at the critical latitude. Journal of
Physical Oceanography. American Meteorological Society. https://doi.org/10.1175/jpo-d-16-0197.1
chicago: Richet, O., Caroline J Muller, and J.-M. Chomaz. “Impact of a Mean Current
on the Internal Tide Energy Dissipation at the Critical Latitude.” Journal
of Physical Oceanography. American Meteorological Society, 2017. https://doi.org/10.1175/jpo-d-16-0197.1.
ieee: O. Richet, C. J. Muller, and J.-M. Chomaz, “Impact of a mean current on the
internal tide energy dissipation at the critical latitude,” Journal of Physical
Oceanography, vol. 47, no. 6. American Meteorological Society, pp. 1457–1472,
2017.
ista: Richet O, Muller CJ, Chomaz J-M. 2017. Impact of a mean current on the internal
tide energy dissipation at the critical latitude. Journal of Physical Oceanography.
47(6), 1457–1472.
mla: Richet, O., et al. “Impact of a Mean Current on the Internal Tide Energy Dissipation
at the Critical Latitude.” Journal of Physical Oceanography, vol. 47, no.
6, American Meteorological Society, 2017, pp. 1457–72, doi:10.1175/jpo-d-16-0197.1.
short: O. Richet, C.J. Muller, J.-M. Chomaz, Journal of Physical Oceanography 47
(2017) 1457–1472.
date_created: 2021-02-15T15:11:04Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2022-01-24T13:36:31Z
day: '01'
doi: 10.1175/jpo-d-16-0197.1
extern: '1'
fulldoi: https://doi.org/10.1175/jpo-d-16-0197.1
intvolume: ' 47'
issue: '6'
keyword:
- Oceanography
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1175/JPO-D-16-0197.1
month: '06'
oa: 1
oa_version: Published Version
page: 1457-1472
publication: Journal of Physical Oceanography
publication_identifier:
issn:
- 0022-3670
- 1520-0485
publication_status: published
publisher: American Meteorological Society
quality_controlled: '1'
status: public
title: Impact of a mean current on the internal tide energy dissipation at the critical
latitude
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 47
year: '2017'
...
---
_id: '916'
abstract:
- lang: eng
text: We study the quadratic assignment problem, in computer vision also known as
graph matching. Two leading solvers for this problem optimize the Lagrange decomposition
duals with sub-gradient and dual ascent (also known as message passing) updates.
We explore this direction further and propose several additional Lagrangean relaxations
of the graph matching problem along with corresponding algorithms, which are all
based on a common dual ascent framework. Our extensive empirical evaluation gives
several theoretical insights and suggests a new state-of-the-art anytime solver
for the considered problem. Our improvement over state-of-the-art is particularly
visible on a new dataset with large-scale sparse problem instances containing
more than 500 graph nodes each.
article_processing_charge: No
author:
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Carsten
full_name: Abu Alhaija, Carsten
last_name: Abu Alhaija
- first_name: Dagmar
full_name: Kainmueller, Dagmar
last_name: Kainmueller
- first_name: Bogdan
full_name: Savchynskyy, Bogdan
last_name: Savchynskyy
citation:
ama: 'Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. A study
of lagrangean decompositions and dual ascent solvers for graph matching. In: Vol
2017. IEEE; 2017:7062-7071. doi:10.1109/CVPR.2017.747'
apa: 'Swoboda, P., Rother, C., Abu Alhaija, C., Kainmueller, D., & Savchynskyy,
B. (2017). A study of lagrangean decompositions and dual ascent solvers for graph
matching (Vol. 2017, pp. 7062–7071). Presented at the CVPR: Computer Vision and
Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.747'
chicago: Swoboda, Paul, Carsten Rother, Carsten Abu Alhaija, Dagmar Kainmueller,
and Bogdan Savchynskyy. “A Study of Lagrangean Decompositions and Dual Ascent
Solvers for Graph Matching,” 2017:7062–71. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.747.
ieee: 'P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, and B. Savchynskyy,
“A study of lagrangean decompositions and dual ascent solvers for graph matching,”
presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA,
United States, 2017, vol. 2017, pp. 7062–7071.'
ista: 'Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. 2017. A
study of lagrangean decompositions and dual ascent solvers for graph matching.
CVPR: Computer Vision and Pattern Recognition vol. 2017, 7062–7071.'
mla: Swoboda, Paul, et al. A Study of Lagrangean Decompositions and Dual Ascent
Solvers for Graph Matching. Vol. 2017, IEEE, 2017, pp. 7062–71, doi:10.1109/CVPR.2017.747.
short: P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, B. Savchynskyy, in:,
IEEE, 2017, pp. 7062–7071.
conference:
end_date: 2017-07-26
location: Honolulu, HA, United States
name: 'CVPR: Computer Vision and Pattern Recognition'
start_date: 2017-07-21
corr_author: '1'
date_created: 2018-12-11T11:49:11Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2024-11-04T13:52:34Z
day: '01'
ddc:
- '000'
department:
- _id: VlKo
doi: 10.1109/CVPR.2017.747
ec_funded: 1
external_id:
isi:
- '000418371407018'
file:
- access_level: open_access
checksum: e38a2740daad1ea178465843b5072906
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T12:49:38Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5848'
file_name: 2017_CVPR_Swoboda2.pdf
file_size: 944332
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
fulldoi: https://doi.org/10.1109/CVPR.2017.747
has_accepted_license: '1'
intvolume: ' 2017'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 7062-7071
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_identifier:
isbn:
- 978-153860457-1
publication_status: published
publisher: IEEE
publist_id: '6525'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A study of lagrangean decompositions and dual ascent solvers for graph matching
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '9165'
abstract:
- lang: eng
text: Advances in colloidal synthesis allow for the design of particles with controlled
patches. This article reviews routes towards colloidal locomotion, where energy
is consumed and converted into motion, and its implementation with active patchy
particles. A special emphasis is given to phoretic swimmers, where the self-propulsion
originates from an interfacial phenomenon, raising experimental challenges and
opening up opportunities for particles with controlled anisotropic surface chemistry
and novel behaviors.
article_processing_charge: No
article_type: original
author:
- first_name: A.
full_name: Aubret, A.
last_name: Aubret
- first_name: S.
full_name: Ramananarivo, S.
last_name: Ramananarivo
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: 'Aubret A, Ramananarivo S, Palacci JA. Eppur si muove, and yet it moves: Patchy
(phoretic) swimmers. Current Opinion in Colloid & Interface Science.
2017;30:81-89. doi:10.1016/j.cocis.2017.05.007'
apa: 'Aubret, A., Ramananarivo, S., & Palacci, J. A. (2017). Eppur si muove,
and yet it moves: Patchy (phoretic) swimmers. Current Opinion in Colloid &
Interface Science. Elsevier. https://doi.org/10.1016/j.cocis.2017.05.007'
chicago: 'Aubret, A., S. Ramananarivo, and Jérémie A Palacci. “Eppur Si Muove, and
yet It Moves: Patchy (Phoretic) Swimmers.” Current Opinion in Colloid &
Interface Science. Elsevier, 2017. https://doi.org/10.1016/j.cocis.2017.05.007.'
ieee: 'A. Aubret, S. Ramananarivo, and J. A. Palacci, “Eppur si muove, and yet it
moves: Patchy (phoretic) swimmers,” Current Opinion in Colloid & Interface
Science, vol. 30. Elsevier, pp. 81–89, 2017.'
ista: 'Aubret A, Ramananarivo S, Palacci JA. 2017. Eppur si muove, and yet it moves:
Patchy (phoretic) swimmers. Current Opinion in Colloid & Interface Science.
30, 81–89.'
mla: 'Aubret, A., et al. “Eppur Si Muove, and yet It Moves: Patchy (Phoretic) Swimmers.”
Current Opinion in Colloid & Interface Science, vol. 30, Elsevier,
2017, pp. 81–89, doi:10.1016/j.cocis.2017.05.007.'
short: A. Aubret, S. Ramananarivo, J.A. Palacci, Current Opinion in Colloid &
Interface Science 30 (2017) 81–89.
date_created: 2021-02-18T14:29:42Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2021-02-22T09:32:11Z
day: '01'
doi: 10.1016/j.cocis.2017.05.007
extern: '1'
fulldoi: https://doi.org/10.1016/j.cocis.2017.05.007
intvolume: ' 30'
language:
- iso: eng
month: '07'
oa_version: None
page: 81-89
publication: Current Opinion in Colloid & Interface Science
publication_identifier:
issn:
- 1359-0294
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Eppur si muove, and yet it moves: Patchy (phoretic) swimmers'
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 30
year: '2017'
...