---
_id: '844'
abstract:
- lang: eng
text: Mutation rate varies greatly between nucleotide sites of the human genome
and depends both on the global genomic location and the local sequence context
of a site. In particular, CpG context elevates the mutation rate by an order of
magnitude. Mutations also vary widely in their effect on the molecular function,
phenotype, and fitness. Independence of the probability of occurrence of a new
mutation's effect has been a fundamental premise in genetics. However, highly
mutable contexts may be preserved by negative selection at important sites but
destroyed by mutation at sites under no selection. Thus, there may be a positive
correlation between the rate of mutations at a nucleotide site and the magnitude
of their effect on fitness. We studied the impact of CpG context on the rate of
human-chimpanzee divergence and on intrahuman nucleotide diversity at non-synonymous
coding sites. We compared nucleotides that occupy identical positions within codons
of identical amino acids and only differ by being within versus outside CpG context.
Nucleotides within CpG context are under a stronger negative selection, as revealed
by their lower, proportionally to the mutation rate, rate of evolution and nucleotide
diversity. In particular, the probability of fixation of a non-synonymous transition
at a CpG site is two times lower than at a CpG site. Thus, sites with different
mutation rates are not necessarily selectively equivalent. This suggests that
the mutation rate may complement sequence conservation as a characteristic predictive
of functional importance of nucleotide sites.
acknowledgement: This work was supported in part by NIH grants R01 GM078598 and U54
LM008748.
author:
- first_name: Steffen
full_name: Schmidt, Steffen
last_name: Schmidt
- first_name: Anna
full_name: Gerasimova, Anna
last_name: Gerasimova
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Ivan
full_name: Adzuhbei, Ivan A
last_name: Adzuhbei
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Shamil
full_name: Sunyaev, Shamil R
last_name: Sunyaev
citation:
ama: Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S.
Hypermutable non-synonymous sites are under stronger negative selection. PLoS
Genetics. 2008;4(11). doi:10.1371/journal.pgen.1000281
apa: Schmidt, S., Gerasimova, A., Kondrashov, F., Adzuhbei, I., Kondrashov, A.,
& Sunyaev, S. (2008). Hypermutable non-synonymous sites are under stronger
negative selection. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1000281
chicago: Schmidt, Steffen, Anna Gerasimova, Fyodor Kondrashov, Ivan Adzuhbei, Alexey
Kondrashov, and Shamil Sunyaev. “Hypermutable Non-Synonymous Sites Are under Stronger
Negative Selection.” PLoS Genetics. Public Library of Science, 2008. https://doi.org/10.1371/journal.pgen.1000281.
ieee: S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, and
S. Sunyaev, “Hypermutable non-synonymous sites are under stronger negative selection,”
PLoS Genetics, vol. 4, no. 11. Public Library of Science, 2008.
ista: Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S.
2008. Hypermutable non-synonymous sites are under stronger negative selection.
PLoS Genetics. 4(11).
mla: Schmidt, Steffen, et al. “Hypermutable Non-Synonymous Sites Are under Stronger
Negative Selection.” PLoS Genetics, vol. 4, no. 11, Public Library of Science,
2008, doi:10.1371/journal.pgen.1000281.
short: S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, S.
Sunyaev, PLoS Genetics 4 (2008).
date_created: 2018-12-11T11:48:48Z
date_published: 2008-11-01T00:00:00Z
date_updated: 2021-01-12T08:19:16Z
day: '01'
doi: 10.1371/journal.pgen.1000281
extern: 1
intvolume: ' 4'
issue: '11'
month: '11'
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '6800'
quality_controlled: 0
status: public
title: Hypermutable non-synonymous sites are under stronger negative selection
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: 4
year: '2008'
...
---
_id: '8480'
abstract:
- lang: eng
text: The KIX domain of the transcription co-activator CBP is a three-helix bundle
protein that folds via rapid accumulation of an intermediate state, followed by
a slower folding phase. Recent NMR relaxation dispersion studies revealed the
presence of a low-populated (excited) state of KIX that exists in equilibrium
with the natively folded form under non-denaturing conditions, and likely represents
the equilibrium analog of the folding intermediate. Here, we combine amide hydrogen/deuterium
exchange measurements using rapid NMR data acquisition techniques with backbone
15N and 13C relaxation dispersion experiments to further investigate the equilibrium
folding of the KIX domain. Residual structure within the folding intermediate
is detected by both methods, and their combination enables reliable quantification
of the amount of persistent residual structure. Three well-defined folding subunits
are found, which display variable stability and correspond closely to the individual
helices in the native state. While two of the three helices (α2 and α3) are partially
formed in the folding intermediate (to ∼ 50% and ∼ 80%, respectively, at 20 °C),
the third helix is disordered. The observed helical content within the excited
state exceeds the helical propensities predicted for the corresponding peptide
regions, suggesting that the two helices are weakly mutually stabilized, while
methyl 13C relaxation dispersion data indicate that a defined packing arrangement
is unlikely. Temperature-dependent experiments reveal that the largest enthalpy
and entropy changes along the folding reaction occur during the final transition
from the intermediate to the native state. Our experimental data are consistent
with a folding mechanism where helices α2 and α3 form rapidly, although to different
extents, while helix α1 consolidates only as folding proceeds to complete the
native state-structure.
article_processing_charge: No
article_type: original
author:
- 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
- first_name: Robert
full_name: Konrat, Robert
last_name: Konrat
- first_name: Martin
full_name: Tollinger, Martin
last_name: Tollinger
citation:
ama: 'Schanda P, Brutscher B, Konrat R, Tollinger M. Folding of the KIX domain:
Characterization of the equilibrium analog of a folding intermediate using 15N/13C
relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Journal
of Molecular Biology. 2008;380(4):726-741. doi:10.1016/j.jmb.2008.05.040'
apa: 'Schanda, P., Brutscher, B., Konrat, R., & Tollinger, M. (2008). Folding
of the KIX domain: Characterization of the equilibrium analog of a folding intermediate
using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy.
Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2008.05.040'
chicago: 'Schanda, Paul, Bernhard Brutscher, Robert Konrat, and Martin Tollinger.
“Folding of the KIX Domain: Characterization of the Equilibrium Analog of a Folding
Intermediate Using 15N/13C Relaxation Dispersion and Fast 1H/2H Amide Exchange
NMR Spectroscopy.” Journal of Molecular Biology. Elsevier, 2008. https://doi.org/10.1016/j.jmb.2008.05.040.'
ieee: 'P. Schanda, B. Brutscher, R. Konrat, and M. Tollinger, “Folding of the KIX
domain: Characterization of the equilibrium analog of a folding intermediate using
15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy,”
Journal of Molecular Biology, vol. 380, no. 4. Elsevier, pp. 726–741, 2008.'
ista: 'Schanda P, Brutscher B, Konrat R, Tollinger M. 2008. Folding of the KIX domain:
Characterization of the equilibrium analog of a folding intermediate using 15N/13C
relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Journal
of Molecular Biology. 380(4), 726–741.'
mla: 'Schanda, Paul, et al. “Folding of the KIX Domain: Characterization of the
Equilibrium Analog of a Folding Intermediate Using 15N/13C Relaxation Dispersion
and Fast 1H/2H Amide Exchange NMR Spectroscopy.” Journal of Molecular Biology,
vol. 380, no. 4, Elsevier, 2008, pp. 726–41, doi:10.1016/j.jmb.2008.05.040.'
short: P. Schanda, B. Brutscher, R. Konrat, M. Tollinger, Journal of Molecular Biology
380 (2008) 726–741.
date_created: 2020-09-18T10:12:29Z
date_published: 2008-07-18T00:00:00Z
date_updated: 2021-01-12T08:19:34Z
day: '18'
doi: 10.1016/j.jmb.2008.05.040
extern: '1'
intvolume: ' 380'
issue: '4'
keyword:
- Molecular Biology
language:
- iso: eng
month: '07'
oa_version: None
page: 726-741
publication: Journal of Molecular Biology
publication_identifier:
issn:
- 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Folding of the KIX domain: Characterization of the equilibrium analog of a
folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange
NMR spectroscopy'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 380
year: '2008'
...
---
_id: '8481'
abstract:
- lang: eng
text: 'The copK gene is localized on the pMOL30 plasmid of Cupriavidus metallidurans
CH34 within the complex cop cluster of genes, for which 21 genes have been identified.
The expression of the corresponding periplasmic CopK protein is strongly upregulated
in the presence of copper, leading to a high periplasmic accumulation. The structure
and metal-binding properties of CopK were investigated by NMR and mass spectrometry.
The protein is dimeric in the apo state with a dissociation constant in the range
of 10- 5 M estimated from analytical ultracentrifugation. Mass spectrometry revealed
that CopK has two high-affinity Cu(I)-binding sites per monomer with different
Cu(I) affinities. Binding of Cu(II) was observed but appeared to be non-specific.
The solution structure of apo-CopK revealed an all-β fold formed of two β-sheets
in perpendicular orientation with an unstructured C-terminal tail. The dimer interface
is formed by the surface of the C-terminal β-sheet. Binding of the first Cu(I)-ion
induces a major structural modification involving dissociation of the dimeric
apo-protein. Backbone chemical shifts determined for the 1Cu(I)-bound form confirm
the conservation of the N-terminal β-sheet, while the last strand of the C-terminal
sheet appears in slow conformational exchange. We hypothesize that the partial
disruption of the C-terminal β-sheet is related to dimer dissociation. NH-exchange
data acquired on the apo-protein are consistent with a lower thermodynamic stability
of the C-terminal sheet. CopK contains seven methionine residues, five of which
appear highly conserved. Chemical shift data suggest implication of two or three
methionines (Met54, Met38, Met28) in the first Cu(I) site. Addition of a second
Cu(I) ion further increases protein plasticity. Comparison of the structural and
metal-binding properties of CopK with other periplasmic copper-binding proteins
reveals two conserved features within these functionally related proteins: the
all-β fold and the methionine-rich Cu(I)-binding site.'
article_processing_charge: No
article_type: original
author:
- first_name: Beate
full_name: Bersch, Beate
last_name: Bersch
- 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: Sébastien
full_name: van Aelst, Sébastien
last_name: van Aelst
- first_name: Tatiana
full_name: Vallaeys, Tatiana
last_name: Vallaeys
- first_name: Jacques
full_name: Covès, Jacques
last_name: Covès
- first_name: Max
full_name: Mergeay, Max
last_name: Mergeay
- first_name: Ruddy
full_name: Wattiez, Ruddy
last_name: Wattiez
citation:
ama: Bersch B, Favier A, Schanda P, et al. Molecular structure and metal-binding
properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans
CH34 during copper challenge. Journal of Molecular Biology. 2008;380(2):386-403.
doi:10.1016/j.jmb.2008.05.017
apa: Bersch, B., Favier, A., Schanda, P., van Aelst, S., Vallaeys, T., Covès, J.,
… Wattiez, R. (2008). Molecular structure and metal-binding properties of the
periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper
challenge. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2008.05.017
chicago: Bersch, Beate, Adrien Favier, Paul Schanda, Sébastien van Aelst, Tatiana
Vallaeys, Jacques Covès, Max Mergeay, and Ruddy Wattiez. “Molecular Structure
and Metal-Binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus
Metallidurans CH34 during Copper Challenge.” Journal of Molecular Biology.
Elsevier, 2008. https://doi.org/10.1016/j.jmb.2008.05.017.
ieee: B. Bersch et al., “Molecular structure and metal-binding properties
of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during
copper challenge,” Journal of Molecular Biology, vol. 380, no. 2. Elsevier,
pp. 386–403, 2008.
ista: Bersch B, Favier A, Schanda P, van Aelst S, Vallaeys T, Covès J, Mergeay M,
Wattiez R. 2008. Molecular structure and metal-binding properties of the periplasmic
CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge.
Journal of Molecular Biology. 380(2), 386–403.
mla: Bersch, Beate, et al. “Molecular Structure and Metal-Binding Properties of
the Periplasmic CopK Protein Expressed in Cupriavidus Metallidurans CH34 during
Copper Challenge.” Journal of Molecular Biology, vol. 380, no. 2, Elsevier,
2008, pp. 386–403, doi:10.1016/j.jmb.2008.05.017.
short: B. Bersch, A. Favier, P. Schanda, S. van Aelst, T. Vallaeys, J. Covès, M.
Mergeay, R. Wattiez, Journal of Molecular Biology 380 (2008) 386–403.
date_created: 2020-09-18T10:12:37Z
date_published: 2008-07-04T00:00:00Z
date_updated: 2021-01-12T08:19:34Z
day: '04'
doi: 10.1016/j.jmb.2008.05.017
extern: '1'
intvolume: ' 380'
issue: '2'
keyword:
- Molecular Biology
language:
- iso: eng
month: '07'
oa_version: None
page: 386-403
publication: Journal of Molecular Biology
publication_identifier:
issn:
- 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Molecular structure and metal-binding properties of the periplasmic CopK protein
expressed in Cupriavidus metallidurans CH34 during copper challenge
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 380
year: '2008'
...
---
_id: '8482'
abstract:
- lang: eng
text: The SOFAST-HMQC experiment [P. Schanda, B. Brutscher, Very fast two-dimensional
NMR spectroscopy for real-time investigation of dynamic events in proteins on
the time scale of seconds, J. Am. Chem. Soc. 127 (2005) 8014–8015] allows recording
two-dimensional correlation spectra of macromolecules such as proteins in only
a few seconds acquisition time. To achieve the highest possible sensitivity, SOFAST-HMQC
experiments are preferably performed on high-field NMR spectrometers equipped
with cryogenically cooled probes. The duty cycle of over 80% in fast-pulsing SOFAST-HMQC
experiments, however, may cause problems when using a cryogenic probe. Here we
introduce SE-IPAP-SOFAST-HMQC, a new pulse sequence that provides comparable sensitivity
to standard SOFAST-HMQC, while avoiding heteronuclear decoupling during 1H detection,
and thus significantly reducing the radiofrequency load of the probe during the
experiment. The experiment is also attractive for fast and sensitive measurement
of heteronuclear one-bond spin coupling constants.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Thomas
full_name: Kern, Thomas
last_name: Kern
- 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: Kern T, Schanda P, Brutscher B. Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing
2D NMR with reduced radiofrequency load. Journal of Magnetic Resonance.
2008;190(2):333-338. doi:10.1016/j.jmr.2007.11.015
apa: Kern, T., Schanda, P., & Brutscher, B. (2008). Sensitivity-enhanced IPAP-SOFAST-HMQC
for fast-pulsing 2D NMR with reduced radiofrequency load. Journal of Magnetic
Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2007.11.015
chicago: Kern, Thomas, Paul Schanda, and Bernhard Brutscher. “Sensitivity-Enhanced
IPAP-SOFAST-HMQC for Fast-Pulsing 2D NMR with Reduced Radiofrequency Load.” Journal
of Magnetic Resonance. Elsevier, 2008. https://doi.org/10.1016/j.jmr.2007.11.015.
ieee: T. Kern, P. Schanda, and B. Brutscher, “Sensitivity-enhanced IPAP-SOFAST-HMQC
for fast-pulsing 2D NMR with reduced radiofrequency load,” Journal of Magnetic
Resonance, vol. 190, no. 2. Elsevier, pp. 333–338, 2008.
ista: Kern T, Schanda P, Brutscher B. 2008. Sensitivity-enhanced IPAP-SOFAST-HMQC
for fast-pulsing 2D NMR with reduced radiofrequency load. Journal of Magnetic
Resonance. 190(2), 333–338.
mla: Kern, Thomas, et al. “Sensitivity-Enhanced IPAP-SOFAST-HMQC for Fast-Pulsing
2D NMR with Reduced Radiofrequency Load.” Journal of Magnetic Resonance,
vol. 190, no. 2, Elsevier, 2008, pp. 333–38, doi:10.1016/j.jmr.2007.11.015.
short: T. Kern, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 190 (2008)
333–338.
date_created: 2020-09-18T10:12:46Z
date_published: 2008-02-01T00:00:00Z
date_updated: 2021-01-12T08:19:35Z
day: '01'
doi: 10.1016/j.jmr.2007.11.015
extern: '1'
intvolume: ' 190'
issue: '2'
keyword:
- Nuclear and High Energy Physics
- Biophysics
- Biochemistry
- Condensed Matter Physics
language:
- iso: eng
month: '02'
oa_version: None
page: 333-338
publication: Journal of Magnetic Resonance
publication_identifier:
issn:
- 1090-7807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced
radiofrequency load
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 190
year: '2008'
...
---
_id: '8509'
abstract:
- lang: eng
text: The goal of this paper is to present to nonspecialists what is perhaps the
simplest possible geometrical picture explaining the mechanism of Arnold diffusion.
We choose to speak of a specific model—that of geometric rays in a periodic optical
medium. This model is equivalent to that of a particle in a periodic potential
in ${\mathbb R}^{n}$ with energy prescribed and to the geodesic flow in a Riemannian
metric on ${\mathbb R}^{n} $.
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Mark
full_name: Levi, Mark
last_name: Levi
citation:
ama: Kaloshin V, Levi M. Geometry of Arnold diffusion. SIAM Review. 2008;50(4):702-720.
doi:10.1137/070703235
apa: Kaloshin, V., & Levi, M. (2008). Geometry of Arnold diffusion. SIAM
Review. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/070703235
chicago: Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” SIAM
Review. Society for Industrial & Applied Mathematics, 2008. https://doi.org/10.1137/070703235.
ieee: V. Kaloshin and M. Levi, “Geometry of Arnold diffusion,” SIAM Review,
vol. 50, no. 4. Society for Industrial & Applied Mathematics, pp. 702–720,
2008.
ista: Kaloshin V, Levi M. 2008. Geometry of Arnold diffusion. SIAM Review. 50(4),
702–720.
mla: Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” SIAM Review,
vol. 50, no. 4, Society for Industrial & Applied Mathematics, 2008, pp. 702–20,
doi:10.1137/070703235.
short: V. Kaloshin, M. Levi, SIAM Review 50 (2008) 702–720.
date_created: 2020-09-18T10:48:12Z
date_published: 2008-11-05T00:00:00Z
date_updated: 2021-01-12T08:19:46Z
day: '05'
doi: 10.1137/070703235
extern: '1'
intvolume: ' 50'
issue: '4'
keyword:
- Theoretical Computer Science
- Applied Mathematics
- Computational Mathematics
language:
- iso: eng
month: '11'
oa_version: None
page: 702-720
publication: SIAM Review
publication_identifier:
issn:
- 0036-1445
- 1095-7200
publication_status: published
publisher: Society for Industrial & Applied Mathematics
quality_controlled: '1'
status: public
title: Geometry of Arnold diffusion
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2008'
...
---
_id: '8510'
abstract:
- lang: eng
text: In this paper, using the ideas of Bessi and Mather, we present a simple mechanical
system exhibiting Arnold diffusion. This system of a particle in a small periodic
potential can be also interpreted as ray propagation in a periodic optical medium
with a near-constant index of refraction. Arnold diffusion in this context manifests
itself as an arbitrary finite change of direction for nearly constant index of
refraction.
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Mark
full_name: Levi, Mark
last_name: Levi
citation:
ama: Kaloshin V, Levi M. An example of Arnold diffusion for near-integrable Hamiltonians.
Bulletin of the American Mathematical Society. 2008;45(3):409-427. doi:10.1090/s0273-0979-08-01211-1
apa: Kaloshin, V., & Levi, M. (2008). An example of Arnold diffusion for near-integrable
Hamiltonians. Bulletin of the American Mathematical Society. American Mathematical
Society. https://doi.org/10.1090/s0273-0979-08-01211-1
chicago: Kaloshin, Vadim, and Mark Levi. “An Example of Arnold Diffusion for Near-Integrable
Hamiltonians.” Bulletin of the American Mathematical Society. American
Mathematical Society, 2008. https://doi.org/10.1090/s0273-0979-08-01211-1.
ieee: V. Kaloshin and M. Levi, “An example of Arnold diffusion for near-integrable
Hamiltonians,” Bulletin of the American Mathematical Society, vol. 45,
no. 3. American Mathematical Society, pp. 409–427, 2008.
ista: Kaloshin V, Levi M. 2008. An example of Arnold diffusion for near-integrable
Hamiltonians. Bulletin of the American Mathematical Society. 45(3), 409–427.
mla: Kaloshin, Vadim, and Mark Levi. “An Example of Arnold Diffusion for Near-Integrable
Hamiltonians.” Bulletin of the American Mathematical Society, vol. 45,
no. 3, American Mathematical Society, 2008, pp. 409–27, doi:10.1090/s0273-0979-08-01211-1.
short: V. Kaloshin, M. Levi, Bulletin of the American Mathematical Society 45 (2008)
409–427.
date_created: 2020-09-18T10:48:20Z
date_published: 2008-07-01T00:00:00Z
date_updated: 2021-01-12T08:19:47Z
day: '01'
doi: 10.1090/s0273-0979-08-01211-1
extern: '1'
intvolume: ' 45'
issue: '3'
keyword:
- Applied Mathematics
- General Mathematics
language:
- iso: eng
month: '07'
oa_version: None
page: 409-427
publication: Bulletin of the American Mathematical Society
publication_identifier:
issn:
- 0273-0979
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
status: public
title: An example of Arnold diffusion for near-integrable Hamiltonians
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2008'
...
---
_id: '895'
abstract:
- lang: eng
text: Background. The arginine vasopressin V1a receptor (V1aR) modulates social
cognition and behavior in a wide variety of species. Variation in a repetitive
microsatellite element in the 5′ flanking region of the V1aR gene (AVPR1A) in
rodents has been associated with variation in brain V1aR expression and in social
behavior. In humans, the 5′ flanking region of AVPR1A contains a tandem duplication
of two ∼350 bp, microsatellite-containing elements located approximately 3.5 kb
upstream of the transcription start site. The first block, referred to as DupA,
contains a polymorphic (GT) 25microsatellite; the second block, DupB, has a complex
(CT) 4-(TT)-(CT)8-(GT)24polymorphic motif, known as RS3. Polymorphisms in RS3
have been associated with variation in sociobehavioral traits in humans, including
autism spectrum disorders. Thus, evolution of these regions may have contributed
to variation in social behavior in primates. We examined the structure of these
regions in six ape, six monkey, and one prosimian species. Results. Both tandem
repeat blocks are present upstream of the AVPR1A coding region in five of the
ape species we investigated, while monkeys have only one copy of this region.
As in humans, the microsatellites within DupA and DupB are polymorphic in many
primate species. Furthermore, both single (lacking DupB) and duplicated alleles
(containing both DupA and DupB) are present in chimpanzee (Pan troglodytes) populations
with allele frequencies of 0.795 and 0.205 for the single and duplicated alleles,
respectively, based on the analysis of 47 wild-caught individuals. Finally, a
phylogenetic reconstruction suggests two alternate evolutionary histories for
this locus. Conclusion. There is no obvious relationship between the presence
of the RS3 duplication and social organization in primates. However, polymorphisms
identified in some species may be useful in future genetic association studies.
In particular, the presence of both single and duplicated alleles in chimpanzees
provides a unique opportunity to assess the functional role of this duplication
in contributing to variation in social behavior in primates. While our initial
studies show no signs of directional selection on this locus in chimps, pharmacological
and genetic association studies support a potential role for this region in influencing
V1aR expression and social behavior.
acknowledgement: |
We thank the caretakers at Zoo Atlanta and Yerkes National Primate Center for help with procuring specimens. Additional DNA samples were supplied by Bill Hopkins, Emory University (chimpanzee), Allyson Bennet, Wake Forest University (chimpanzee, rhesus macaque, bonnet macaque), Mar Sanchez, Emory University (rhesus macaque), and Anne Yoder, Duke University (galago). Susan Lambeth, M.D. Anderson Cancer Center, and Katie Chace, Yerkes National Primate Center, helped provide records regarding the origins of wild born chimps at these centers. We would like to thank Dr Lisa McGraw and two anonymous reviewers for their com- ments on this manuscript. This work was supported by NSF IBN-9876754, NIH RR00165, NIMH56897 (LJY), MH64692 (LJY) and a Howard Hughes Predoctoral Fellowship (ZRD).
author:
- first_name: Zoe
full_name: Donaldson, Zoe R
last_name: Donaldson
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Andrea
full_name: Putnam, Andrea S
last_name: Putnam
- first_name: Yaohui
full_name: Bai, Yaohui
last_name: Bai
- first_name: Tara
full_name: Stoinski, Tara S
last_name: Stoinski
- first_name: Elizabeth
full_name: Hammock, Elizabeth A
last_name: Hammock
- first_name: Larry
full_name: Young, Larry
last_name: Young
citation:
ama: Donaldson Z, Kondrashov F, Putnam A, et al. Evolution of a behavior-linked
microsatellite-containing element in the 5′ flanking region of the primate AVPR1A
gene. BMC Evolutionary Biology. 2008;8(1). doi:10.1186/1471-2148-8-180
apa: Donaldson, Z., Kondrashov, F., Putnam, A., Bai, Y., Stoinski, T., Hammock,
E., & Young, L. (2008). Evolution of a behavior-linked microsatellite-containing
element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary
Biology. BioMed Central. https://doi.org/10.1186/1471-2148-8-180
chicago: Donaldson, Zoe, Fyodor Kondrashov, Andrea Putnam, Yaohui Bai, Tara Stoinski,
Elizabeth Hammock, and Larry Young. “Evolution of a Behavior-Linked Microsatellite-Containing
Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary
Biology. BioMed Central, 2008. https://doi.org/10.1186/1471-2148-8-180.
ieee: Z. Donaldson et al., “Evolution of a behavior-linked microsatellite-containing
element in the 5′ flanking region of the primate AVPR1A gene,” BMC Evolutionary
Biology, vol. 8, no. 1. BioMed Central, 2008.
ista: Donaldson Z, Kondrashov F, Putnam A, Bai Y, Stoinski T, Hammock E, Young L.
2008. Evolution of a behavior-linked microsatellite-containing element in the
5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. 8(1).
mla: Donaldson, Zoe, et al. “Evolution of a Behavior-Linked Microsatellite-Containing
Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary
Biology, vol. 8, no. 1, BioMed Central, 2008, doi:10.1186/1471-2148-8-180.
short: Z. Donaldson, F. Kondrashov, A. Putnam, Y. Bai, T. Stoinski, E. Hammock,
L. Young, BMC Evolutionary Biology 8 (2008).
date_created: 2018-12-11T11:49:04Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:29Z
day: '01'
doi: 10.1186/1471-2148-8-180
extern: 1
intvolume: ' 8'
issue: '1'
month: '01'
publication: BMC Evolutionary Biology
publication_status: published
publisher: BioMed Central
publist_id: '6753'
quality_controlled: 0
status: public
title: Evolution of a behavior-linked microsatellite-containing element in the 5′
flanking region of the primate AVPR1A gene
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: 8
year: '2008'
...
---
_id: '1717'
abstract:
- lang: eng
text: 'Two key processes are in the basis of morphogenesis: the spatial allocation
of cell types in fields of naïve cells and the regulation of growth. Both are
controlled by morphogens, which activate target genes in the growing tissue in
a concentration-dependent manner. Thus the morphogen model is an intrinsically
quantitative concept. However, quantitative studies were performed only in recent
years on two morphogens: Bicoid and Decapentaplegic. This review covers quantitative
aspects of the formation and precision of the Decapentaplegic morphogen gradient.
The morphogen gradient concept is transitioning from a soft definition to a precise
idea of what the gradient could really do.'
acknowledgement: This work was supported by the University of Geneva, Max Planck Society,
VW, EU, SNF, and HFSP
author:
- first_name: Anna
full_name: Anna Kicheva
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Marcos
full_name: González-Gaitán, Marcos A
last_name: González Gaitán
citation:
ama: Kicheva A, González Gaitán M. The Decapentaplegic morphogen gradient a precise
definition. Current Opinion in Cell Biology. 2008;20(2):137-143. doi:10.1016/j.ceb.2008.01.008
apa: Kicheva, A., & González Gaitán, M. (2008). The Decapentaplegic morphogen
gradient a precise definition. Current Opinion in Cell Biology. Elsevier.
https://doi.org/10.1016/j.ceb.2008.01.008
chicago: Kicheva, Anna, and Marcos González Gaitán. “The Decapentaplegic Morphogen
Gradient a Precise Definition.” Current Opinion in Cell Biology. Elsevier,
2008. https://doi.org/10.1016/j.ceb.2008.01.008.
ieee: A. Kicheva and M. González Gaitán, “The Decapentaplegic morphogen gradient
a precise definition,” Current Opinion in Cell Biology, vol. 20, no. 2.
Elsevier, pp. 137–143, 2008.
ista: Kicheva A, González Gaitán M. 2008. The Decapentaplegic morphogen gradient
a precise definition. Current Opinion in Cell Biology. 20(2), 137–143.
mla: Kicheva, Anna, and Marcos González Gaitán. “The Decapentaplegic Morphogen Gradient
a Precise Definition.” Current Opinion in Cell Biology, vol. 20, no. 2,
Elsevier, 2008, pp. 137–43, doi:10.1016/j.ceb.2008.01.008.
short: A. Kicheva, M. González Gaitán, Current Opinion in Cell Biology 20 (2008)
137–143.
date_created: 2018-12-11T11:53:38Z
date_published: 2008-04-01T00:00:00Z
date_updated: 2021-01-12T06:52:44Z
day: '01'
doi: 10.1016/j.ceb.2008.01.008
extern: 1
intvolume: ' 20'
issue: '2'
month: '04'
page: 137 - 143
publication: Current Opinion in Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '5412'
quality_controlled: 0
status: public
title: The Decapentaplegic morphogen gradient a precise definition
type: journal_article
volume: 20
year: '2008'
...
---
_id: '1719'
abstract:
- lang: eng
text: We study the mechanics of tissue growth via cell division and cell death (apoptosis).
The rearrangements of cells can on large scales and times be captured by a continuum
theory which describes the tissue as an effective viscous material with active
stresses generated by cell division. We study the effects of anisotropies of cell
division on cell rearrangements and show that average cellular trajectories exhibit
anisotropic scaling behaviors. If cell division and apoptosis balance, there is
no net growth, but for anisotropic cell division the tissue undergoes spontaneous
shear deformations. Our description is relevant for the study of developing tissues
such as the imaginal disks of the fruit fly Drosophila melanogaster, which grow
anisotropically.
author:
- first_name: Thomas
full_name: Bittig, Thomas
last_name: Bittig
- first_name: Ortrud
full_name: Wartlick, Ortrud
last_name: Wartlick
- first_name: Anna
full_name: Anna Kicheva
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Marcos
full_name: González-Gaitárr, Marcos
last_name: González Gaitárr
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
citation:
ama: Bittig T, Wartlick O, Kicheva A, González Gaitárr M, Julicher F. Dynamics of
anisotropic tissue growth. New Journal of Physics. 2008;10. doi:10.1088/1367-2630/10/6/063001
apa: Bittig, T., Wartlick, O., Kicheva, A., González Gaitárr, M., & Julicher,
F. (2008). Dynamics of anisotropic tissue growth. New Journal of Physics.
IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/10/6/063001
chicago: Bittig, Thomas, Ortrud Wartlick, Anna Kicheva, Marcos González Gaitárr,
and Frank Julicher. “Dynamics of Anisotropic Tissue Growth.” New Journal of
Physics. IOP Publishing Ltd., 2008. https://doi.org/10.1088/1367-2630/10/6/063001.
ieee: T. Bittig, O. Wartlick, A. Kicheva, M. González Gaitárr, and F. Julicher,
“Dynamics of anisotropic tissue growth,” New Journal of Physics, vol. 10.
IOP Publishing Ltd., 2008.
ista: Bittig T, Wartlick O, Kicheva A, González Gaitárr M, Julicher F. 2008. Dynamics
of anisotropic tissue growth. New Journal of Physics. 10.
mla: Bittig, Thomas, et al. “Dynamics of Anisotropic Tissue Growth.” New Journal
of Physics, vol. 10, IOP Publishing Ltd., 2008, doi:10.1088/1367-2630/10/6/063001.
short: T. Bittig, O. Wartlick, A. Kicheva, M. González Gaitárr, F. Julicher, New
Journal of Physics 10 (2008).
date_created: 2018-12-11T11:53:39Z
date_published: 2008-06-03T00:00:00Z
date_updated: 2021-01-12T06:52:44Z
day: '03'
doi: 10.1088/1367-2630/10/6/063001
extern: 1
intvolume: ' 10'
month: '06'
publication: New Journal of Physics
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '5411'
quality_controlled: 0
status: public
title: Dynamics of anisotropic tissue growth
type: journal_article
volume: 10
year: '2008'
...
---
_id: '1749'
abstract:
- lang: eng
text: Scanning probe microscopy; Semiconductor quantum dots; Composition gradients;
Composition profiles; Nanotomography; Single quantum dots; Strained sige/si; Three-dimensional
(3D); Wet-chemical etchings; X-ray scattering measurements; quantum dot; methodology;
nanotechnology; optical tomography; scanning probe microscopy; three dimensional
imaging; Imaging, Three-Dimensional; Materials Testing; Microscopy, Scanning Probe;
Nanotechnology; Quantum Dots; Tomography,
acknowledgement: This work was supported by the BMBF (No. 03N8711) and the EU project
D-DotFET (No. 012150)
author:
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Ângelo
full_name: Malachias, Ângelo S
last_name: Malachias
- first_name: Tsvetelina
full_name: Merdzhanova, Tsvetelina
last_name: Merdzhanova
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
- first_name: Till
full_name: Metzger, Till H
last_name: Metzger
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
citation:
ama: Rastelli A, Stoffel M, Malachias Â, et al. Three-dimensional composition profiles
of single quantum dots determined by scanning-probe-microscopy-based nanotomography.
Nano Letters. 2008;8(5):1404-1409. doi:10.1021/nl080290y
apa: Rastelli, A., Stoffel, M., Malachias, Â., Merdzhanova, T., Katsaros, G., Kern,
K., … Schmidt, O. (2008). Three-dimensional composition profiles of single quantum
dots determined by scanning-probe-microscopy-based nanotomography. Nano Letters.
American Chemical Society. https://doi.org/10.1021/nl080290y
chicago: Rastelli, Armando, Mathieu Stoffel, Ângelo Malachias, Tsvetelina Merdzhanova,
Georgios Katsaros, Klaus Kern, Till Metzger, and Oliver Schmidt. “Three-Dimensional
Composition Profiles of Single Quantum Dots Determined by Scanning-Probe-Microscopy-Based
Nanotomography.” Nano Letters. American Chemical Society, 2008. https://doi.org/10.1021/nl080290y.
ieee: A. Rastelli et al., “Three-dimensional composition profiles of single
quantum dots determined by scanning-probe-microscopy-based nanotomography,” Nano
Letters, vol. 8, no. 5. American Chemical Society, pp. 1404–1409, 2008.
ista: Rastelli A, Stoffel M, Malachias Â, Merdzhanova T, Katsaros G, Kern K, Metzger
T, Schmidt O. 2008. Three-dimensional composition profiles of single quantum dots
determined by scanning-probe-microscopy-based nanotomography. Nano Letters. 8(5),
1404–1409.
mla: Rastelli, Armando, et al. “Three-Dimensional Composition Profiles of Single
Quantum Dots Determined by Scanning-Probe-Microscopy-Based Nanotomography.” Nano
Letters, vol. 8, no. 5, American Chemical Society, 2008, pp. 1404–09, doi:10.1021/nl080290y.
short: A. Rastelli, M. Stoffel, Â. Malachias, T. Merdzhanova, G. Katsaros, K. Kern,
T. Metzger, O. Schmidt, Nano Letters 8 (2008) 1404–1409.
date_created: 2018-12-11T11:53:48Z
date_published: 2008-05-01T00:00:00Z
date_updated: 2021-01-12T06:52:57Z
day: '01'
doi: 10.1021/nl080290y
extern: 1
intvolume: ' 8'
issue: '5'
month: '05'
page: 1404 - 1409
publication: Nano Letters
publication_status: published
publisher: American Chemical Society
publist_id: '5374'
quality_controlled: 0
status: public
title: Three-dimensional composition profiles of single quantum dots determined by
scanning-probe-microscopy-based nanotomography
type: journal_article
volume: 8
year: '2008'
...
---
_id: '1751'
abstract:
- lang: eng
text: When strained Stranski-Krastanow islands are used as "self-assembled
quantum dots," a key goal is to control the island position. Here we show
that nanoscale grooves can control the nucleation of epitaxial Ge islands on Si(001),
and can drive lateral motion of existing islands onto the grooves, even when the
grooves are very narrow and shallow compared to the islands. A position centered
on the groove minimizes energy. We use as prototype grooves the trenches which
form naturally around islands. During coarsening, the shrinking islands move laterally
to sit directly astride that trench. In subsequent growth, we demonstrate that
islands nucleate on the "empty trenches" which remain on the surface
after complete dissolution of the original islands.
author:
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Jerry
full_name: Tersoff, Jerry
last_name: Tersoff
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: P
full_name: Acosta-Diaz, P
last_name: Acosta Diaz
- first_name: Gouranga
full_name: Kar, Gouranga S
last_name: Kar
- first_name: Giovanni
full_name: Costantini, Giovanni
last_name: Costantini
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
citation:
ama: Katsaros G, Tersoff J, Stoffel M, et al. Positioning of strained islands by
interaction with surface nanogrooves. Physical Review Letters. 2008;101(9).
doi:10.1103/PhysRevLett.101.096103
apa: Katsaros, G., Tersoff, J., Stoffel, M., Rastelli, A., Acosta Diaz, P., Kar,
G., … Kern, K. (2008). Positioning of strained islands by interaction with surface
nanogrooves. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.101.096103
chicago: Katsaros, Georgios, Jerry Tersoff, Mathieu Stoffel, Armando Rastelli, P
Acosta Diaz, Gouranga Kar, Giovanni Costantini, Oliver Schmidt, and Klaus Kern.
“Positioning of Strained Islands by Interaction with Surface Nanogrooves.” Physical
Review Letters. American Physical Society, 2008. https://doi.org/10.1103/PhysRevLett.101.096103.
ieee: G. Katsaros et al., “Positioning of strained islands by interaction
with surface nanogrooves,” Physical Review Letters, vol. 101, no. 9. American
Physical Society, 2008.
ista: Katsaros G, Tersoff J, Stoffel M, Rastelli A, Acosta Diaz P, Kar G, Costantini
G, Schmidt O, Kern K. 2008. Positioning of strained islands by interaction with
surface nanogrooves. Physical Review Letters. 101(9).
mla: Katsaros, Georgios, et al. “Positioning of Strained Islands by Interaction
with Surface Nanogrooves.” Physical Review Letters, vol. 101, no. 9, American
Physical Society, 2008, doi:10.1103/PhysRevLett.101.096103.
short: G. Katsaros, J. Tersoff, M. Stoffel, A. Rastelli, P. Acosta Diaz, G. Kar,
G. Costantini, O. Schmidt, K. Kern, Physical Review Letters 101 (2008).
date_created: 2018-12-11T11:53:49Z
date_published: 2008-08-29T00:00:00Z
date_updated: 2021-01-12T06:52:58Z
day: '29'
doi: 10.1103/PhysRevLett.101.096103
extern: 1
intvolume: ' 101'
issue: '9'
month: '08'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5373'
quality_controlled: 0
status: public
title: Positioning of strained islands by interaction with surface nanogrooves
type: journal_article
volume: 101
year: '2008'
...
---
_id: '1763'
abstract:
- lang: eng
text: The field of cavity quantum electrodynamics (QED), traditionally studied in
atomic systems, has gained new momentum by recent reports of quantum optical experiments
with solid-state semiconducting and superconducting systems. In cavity QED, the
observation of the vacuum Rabi mode splitting is used to investigate the nature
of matter-light interaction at a quantum-mechanical level. However, this effect
can, at least in principle, be explained classically as the normal mode splitting
of two coupled linear oscillators. It has been suggested that an observation of
the scaling of the resonant atom-photon coupling strength in the Jaynes-Cummings
energy ladder with the square root of photon number n is sufficient to prove that
the system is quantum mechanical in nature. Here we report a direct spectroscopic
observation of this characteristic quantum nonlinearity. Measuring the photonic
degree of freedom of the coupled system, our measurements provide unambiguous
spectroscopic evidence for the quantum nature of the resonant atom-field interaction
in cavity QED. We explore atom-photon superposition states involving up to two
photons, using a spectroscopic pump and probe technique. The experiments have
been performed in a circuit QED set-up, in which very strong coupling is realized
by the large dipole coupling strength and the long coherence time of a superconducting
qubit embedded in a high-quality on-chip microwave cavity. Circuit QED systems
also provide a natural quantum interface between flying qubits (photons) and stationary
qubits for applications in quantum information processing and communication.
acknowledgement: This work was supported by SNF and ETHZ. P.J.L. was supported by
the EU with an MC-EIF. A.B. was supported by NSERC, CIFAR and FQRNT
author:
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: M
full_name: Göppl, M
last_name: Göppl
- 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: Alexandre
full_name: Blais, Alexandre
last_name: Blais
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Fink JM, Göppl M, Baur M, et al. Climbing the Jaynes-Cummings ladder and observing
its √n nonlinearity in a cavity QED system. Nature. 2008;454(7202):315-318.
doi:10.1038/nature07112
apa: Fink, J. M., Göppl, M., Baur, M., Bianchetti, R., Leek, P., Blais, A., &
Wallraff, A. (2008). Climbing the Jaynes-Cummings ladder and observing its √n
nonlinearity in a cavity QED system. Nature. Nature Publishing Group. https://doi.org/10.1038/nature07112
chicago: Fink, Johannes M, M Göppl, Matthias Baur, R Bianchetti, Peter Leek, Alexandre
Blais, and Andreas Wallraff. “Climbing the Jaynes-Cummings Ladder and Observing
Its √n Nonlinearity in a Cavity QED System.” Nature. Nature Publishing
Group, 2008. https://doi.org/10.1038/nature07112.
ieee: J. M. Fink et al., “Climbing the Jaynes-Cummings ladder and observing
its √n nonlinearity in a cavity QED system,” Nature, vol. 454, no. 7202.
Nature Publishing Group, pp. 315–318, 2008.
ista: Fink JM, Göppl M, Baur M, Bianchetti R, Leek P, Blais A, Wallraff A. 2008.
Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity
QED system. Nature. 454(7202), 315–318.
mla: Fink, Johannes M., et al. “Climbing the Jaynes-Cummings Ladder and Observing
Its √n Nonlinearity in a Cavity QED System.” Nature, vol. 454, no. 7202,
Nature Publishing Group, 2008, pp. 315–18, doi:10.1038/nature07112.
short: J.M. Fink, M. Göppl, M. Baur, R. Bianchetti, P. Leek, A. Blais, A. Wallraff,
Nature 454 (2008) 315–318.
date_created: 2018-12-11T11:53:53Z
date_published: 2008-07-17T00:00:00Z
date_updated: 2021-01-12T06:53:03Z
day: '17'
doi: 10.1038/nature07112
extern: 1
intvolume: ' 454'
issue: '7202'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0902.1827
month: '07'
oa: 1
page: 315 - 318
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '5358'
quality_controlled: 0
status: public
title: Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a
cavity QED system
type: journal_article
volume: 454
year: '2008'
...
---
_id: '1764'
abstract:
- lang: eng
text: Quantum theory predicts that empty space is not truly empty. Even in the absence
of any particles or radiation, in pure vacuum, virtual particles are constantly
created and annihilated. In an electromagnetic field, the presence of virtual
photons manifests itself as a small renormalization of the energy of a quantum
system, known as the Lamb shift. We present an experimental observation of the
Lamb shift in a solid-state system. The strong dispersive coupling of a superconducting
electronic circuit acting as a quantum bit (qubit) to the vacuum field in a transmission-line
resonator leads to measurable Lamb shifts of up to 1.4% of the qubit transition
frequency. The qubit is also observed to couple more strongly to the vacuum field
than to a single photon inside the cavity, an effect that is explained by taking
into account the limited anharmonicity of the higher excited qubit states.
acknowledgement: This work was supported by the Swiss National Science Foundation
and ETHZ. P.J.L. was supported by the European Commission with a Marie Curie Intra-European
Fellowship. A.B. was supported by the Natural Sciences and Engineering Research
Council of Canada, Canadian Institute for Advanced Research, and Fonds Québécois
de la Recherche sur la Nature et les Technologies
author:
- first_name: A
full_name: Fragner, A
last_name: Fragner
- 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: Peter
full_name: Leek, Peter J
last_name: Leek
- first_name: Alexandre
full_name: Blais, Alexandre
last_name: Blais
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Fragner A, Göppl M, Fink JM, et al. Resolving vacuum fluctuations in an electrical
circuit by measuring the lamb shift. Science. 2008;322(5906):1357-1360.
doi:10.1126/science.1164482
apa: Fragner, A., Göppl, M., Fink, J. M., Baur, M., Bianchetti, R., Leek, P., …
Wallraff, A. (2008). Resolving vacuum fluctuations in an electrical circuit by
measuring the lamb shift. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.1164482
chicago: Fragner, A, M Göppl, Johannes M Fink, Matthias Baur, R Bianchetti, Peter
Leek, Alexandre Blais, and Andreas Wallraff. “Resolving Vacuum Fluctuations in
an Electrical Circuit by Measuring the Lamb Shift.” Science. American Association
for the Advancement of Science, 2008. https://doi.org/10.1126/science.1164482.
ieee: A. Fragner et al., “Resolving vacuum fluctuations in an electrical
circuit by measuring the lamb shift,” Science, vol. 322, no. 5906. American
Association for the Advancement of Science, pp. 1357–1360, 2008.
ista: Fragner A, Göppl M, Fink JM, Baur M, Bianchetti R, Leek P, Blais A, Wallraff
A. 2008. Resolving vacuum fluctuations in an electrical circuit by measuring the
lamb shift. Science. 322(5906), 1357–1360.
mla: Fragner, A., et al. “Resolving Vacuum Fluctuations in an Electrical Circuit
by Measuring the Lamb Shift.” Science, vol. 322, no. 5906, American Association
for the Advancement of Science, 2008, pp. 1357–60, doi:10.1126/science.1164482.
short: A. Fragner, M. Göppl, J.M. Fink, M. Baur, R. Bianchetti, P. Leek, A. Blais,
A. Wallraff, Science 322 (2008) 1357–1360.
date_created: 2018-12-11T11:53:53Z
date_published: 2008-11-28T00:00:00Z
date_updated: 2021-01-12T06:53:03Z
day: '28'
doi: 10.1126/science.1164482
extern: 1
intvolume: ' 322'
issue: '5906'
month: '11'
page: 1357 - 1360
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5357'
quality_controlled: 0
status: public
title: Resolving vacuum fluctuations in an electrical circuit by measuring the lamb
shift
type: journal_article
volume: 322
year: '2008'
...
---
_id: '1765'
abstract:
- lang: eng
text: High quality on-chip microwave resonators have recently found prominent new
applications in quantum optics and quantum information processing experiments
with superconducting electronic circuits, a field now known as circuit quantum
electrodynamics (QED). They are also used as single photon detectors and parametric
amplifiers. Here we analyze the physical properties of coplanar waveguide resonators
and their relation to the materials properties for use in circuit QED. We have
designed and fabricated resonators with fundamental frequencies from 2 to 9 GHz
and quality factors ranging from a few hundreds to a several hundred thousands
controlled by appropriately designed input and output coupling capacitors. The
microwave transmission spectra measured at temperatures of 20 mK are shown to
be in good agreement with theoretical lumped element and distributed element transmission
matrix models. In particular, the experimentally determined resonance frequencies,
quality factors, and insertion losses are fully and consistently explained by
the two models for all measured devices. The high level of control and flexibility
in design renders these resonators ideal for storing and manipulating quantum
electromagnetic fields in integrated superconducting electronic circuits.
acknowledgement: This work was supported by Swiss National Fund (SNF) and ETH Zürich.
P.J.L. was supported by the EC with a MC-EIF
author:
- first_name: M
full_name: Göppl, M
last_name: Göppl
- first_name: A
full_name: Fragner, A
last_name: Fragner
- first_name: Matthias
full_name: Baur, Matthias P
last_name: Baur
- first_name: R
full_name: Bianchetti, R
last_name: Bianchetti
- first_name: Stefan
full_name: Filipp, Stefan
last_name: Filipp
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Peter
full_name: Leek, Peter J
last_name: Leek
- first_name: G
full_name: Puebla, G
last_name: Puebla
- first_name: L.
full_name: Steffen, L. Kraig
last_name: Steffen
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Göppl M, Fragner A, Baur M, et al. Coplanar waveguide resonators for circuit
quantum electrodynamics. Journal of Applied Physics. 2008;104(11). doi:10.1063/1.3010859
apa: Göppl, M., Fragner, A., Baur, M., Bianchetti, R., Filipp, S., Fink, J. M.,
… Wallraff, A. (2008). Coplanar waveguide resonators for circuit quantum electrodynamics.
Journal of Applied Physics. American Institute of Physics. https://doi.org/10.1063/1.3010859
chicago: Göppl, M, A Fragner, Matthias Baur, R Bianchetti, Stefan Filipp, Johannes
M Fink, Peter Leek, G Puebla, L. Steffen, and Andreas Wallraff. “Coplanar Waveguide
Resonators for Circuit Quantum Electrodynamics.” Journal of Applied Physics.
American Institute of Physics, 2008. https://doi.org/10.1063/1.3010859.
ieee: M. Göppl et al., “Coplanar waveguide resonators for circuit quantum
electrodynamics,” Journal of Applied Physics, vol. 104, no. 11. American
Institute of Physics, 2008.
ista: Göppl M, Fragner A, Baur M, Bianchetti R, Filipp S, Fink JM, Leek P, Puebla
G, Steffen L, Wallraff A. 2008. Coplanar waveguide resonators for circuit quantum
electrodynamics. Journal of Applied Physics. 104(11).
mla: Göppl, M., et al. “Coplanar Waveguide Resonators for Circuit Quantum Electrodynamics.”
Journal of Applied Physics, vol. 104, no. 11, American Institute of Physics,
2008, doi:10.1063/1.3010859.
short: M. Göppl, A. Fragner, M. Baur, R. Bianchetti, S. Filipp, J.M. Fink, P. Leek,
G. Puebla, L. Steffen, A. Wallraff, Journal of Applied Physics 104 (2008).
date_created: 2018-12-11T11:53:53Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:03Z
day: '01'
doi: 10.1063/1.3010859
extern: 1
intvolume: ' 104'
issue: '11'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0807.4094
month: '01'
oa: 1
publication: Journal of Applied Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5355'
quality_controlled: 0
status: public
title: Coplanar waveguide resonators for circuit quantum electrodynamics
type: journal_article
volume: 104
year: '2008'
...
---
_id: '1826'
abstract:
- lang: eng
text: Proliferating cell populations at steady-state growth often exhibit broad
protein distributions with exponential tails. The sources of this variation and
its universality are of much theoretical interest. Here we address the problem
by asymptotic analysis of the population balance equation. We show that the steady-state
distribution tail is determined by a combination of protein production and cell
division and is insensitive to other model details. Under general conditions this
tail is exponential with a dependence on parameters consistent with experiment.
We discuss the conditions for this effect to be dominant over other sources of
variation and the relation to experiments.
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. Cellular properties and population asymptotics in
the population balance equation. Physical Review Letters. 2008;101(1).
doi:10.1103/PhysRevLett.101.018104
apa: Friedlander, T., & Brenner, N. (2008). Cellular properties and population
asymptotics in the population balance equation. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.101.018104
chicago: Friedlander, Tamar, and Naama Brenner. “Cellular Properties and Population
Asymptotics in the Population Balance Equation.” Physical Review Letters.
American Physical Society, 2008. https://doi.org/10.1103/PhysRevLett.101.018104.
ieee: T. Friedlander and N. Brenner, “Cellular properties and population asymptotics
in the population balance equation,” Physical Review Letters, vol. 101,
no. 1. American Physical Society, 2008.
ista: Friedlander T, Brenner N. 2008. Cellular properties and population asymptotics
in the population balance equation. Physical Review Letters. 101(1).
mla: Friedlander, Tamar, and Naama Brenner. “Cellular Properties and Population
Asymptotics in the Population Balance Equation.” Physical Review Letters,
vol. 101, no. 1, American Physical Society, 2008, doi:10.1103/PhysRevLett.101.018104.
short: T. Friedlander, N. Brenner, Physical Review Letters 101 (2008).
date_created: 2018-12-11T11:54:13Z
date_published: 2008-07-01T00:00:00Z
date_updated: 2021-01-12T06:53:27Z
day: '01'
doi: 10.1103/PhysRevLett.101.018104
extern: 1
intvolume: ' 101'
issue: '1'
main_file_link:
- open_access: '0'
url: http://arxiv.org/abs/0804.4804
month: '07'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5280'
quality_controlled: 0
status: public
title: Cellular properties and population asymptotics in the population balance equation
type: journal_article
volume: 101
year: '2008'
...
---
_id: '1967'
abstract:
- lang: eng
text: Complex I of respiratory chains transfers electrons from NADH to ubiquinone,
coupled to the translocation of protons across the membrane. Two alternative coupling
mechanisms are being discussed, redox-driven or conformation-driven. Using "zero-length"
cross-linking reagent and isolated hydrophilic domains of complex I from Escherichia
coli and Thermus thermophilus, we show that the pattern of cross-links between
subunits changes significantly in the presence of NADH. Similar observations were
made previously with intact purified E. coli and bovine complex I. This indicates
that, upon reduction with NADH, similar conformational changes are likely to occur
in the intact enzyme and in the isolated hydrophilic domain (which can be used
for crystallographic studies). Within intact E. coli complex I, the cross-link
between the hydrophobic subunits NuoA and NuoJ was abolished in the presence of
NADH, indicating that conformational changes extend into the membrane domain,
possibly as part of a coupling mechanism. Unexpectedly, in the absence of any
chemical cross-linker, incubation of complex I with NADH resulted in covalent
cross-links between subunits Nqo4 (NuoCD) and Nqo6 (NuoB), as well as between
Nqo6 and Nqo9. Their formation depends on the presence of oxygen and so is likely
a result of oxidative damage via reactive oxygen species (ROS) induced cross-linking.
In addition, ROS- and metal ion-dependent proteolysis of these subunits (as well
as Nqo3) is observed. Fe-S cluster N2 is coordinated between subunits Nqo4 and
Nqo6 and could be involved in these processes. Our observations suggest that oxidative
damage to complex I in vivo may include not only side-chain modifications but
also protein cross-linking and degradation.
acknowledgement: This research was funded by the Medical Research Council.
author:
- first_name: John
full_name: Berrisford, John M
last_name: Berrisford
- first_name: Christopher
full_name: Thompson, Christopher J
last_name: Thompson
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Berrisford J, Thompson C, Sazanov LA. Chemical and NADH-induced, ROS-dependent,
cross-linking between sublimits of complex I from Escherichia coli and Thermus
thermophilus. Biochemistry. 2008;47(39):10262-10270. doi:10.1021/bi801160u
apa: Berrisford, J., Thompson, C., & Sazanov, L. A. (2008). Chemical and NADH-induced,
ROS-dependent, cross-linking between sublimits of complex I from Escherichia coli
and Thermus thermophilus. Biochemistry. ACS. https://doi.org/10.1021/bi801160u
chicago: Berrisford, John, Christopher Thompson, and Leonid A Sazanov. “Chemical
and NADH-Induced, ROS-Dependent, Cross-Linking between Sublimits of Complex I
from Escherichia Coli and Thermus Thermophilus.” Biochemistry. ACS, 2008.
https://doi.org/10.1021/bi801160u.
ieee: J. Berrisford, C. Thompson, and L. A. Sazanov, “Chemical and NADH-induced,
ROS-dependent, cross-linking between sublimits of complex I from Escherichia coli
and Thermus thermophilus,” Biochemistry, vol. 47, no. 39. ACS, pp. 10262–10270,
2008.
ista: Berrisford J, Thompson C, Sazanov LA. 2008. Chemical and NADH-induced, ROS-dependent,
cross-linking between sublimits of complex I from Escherichia coli and Thermus
thermophilus. Biochemistry. 47(39), 10262–10270.
mla: Berrisford, John, et al. “Chemical and NADH-Induced, ROS-Dependent, Cross-Linking
between Sublimits of Complex I from Escherichia Coli and Thermus Thermophilus.”
Biochemistry, vol. 47, no. 39, ACS, 2008, pp. 10262–70, doi:10.1021/bi801160u.
short: J. Berrisford, C. Thompson, L.A. Sazanov, Biochemistry 47 (2008) 10262–10270.
date_created: 2018-12-11T11:54:57Z
date_published: 2008-09-30T00:00:00Z
date_updated: 2021-01-12T06:54:24Z
day: '30'
doi: 10.1021/bi801160u
extern: 1
intvolume: ' 47'
issue: '39'
month: '09'
page: 10262 - 10270
publication: Biochemistry
publication_status: published
publisher: ACS
publist_id: '5115'
quality_controlled: 0
status: public
title: Chemical and NADH-induced, ROS-dependent, cross-linking between sublimits of
complex I from Escherichia coli and Thermus thermophilus
type: journal_article
volume: 47
year: '2008'
...
---
_id: '1968'
abstract:
- lang: eng
text: |2-
Complex I (NADH:ubiquinone oxidoreductase) is the largest protein complex of bacterial and mitochondrial respiratory chains. The first three-dimensional structure of bacterial complex I in vitrified ice was determined by electron cryo-microscopy and single particle analysis. The structure of the Escherichia coli enzyme incubated with either NAD+ (as a reference) or NADH was calculated to 35 and 39 Å resolution, respectively. The X-ray structure of the peripheral arm of Thermus thermophilus complex I was docked into the reference EM structure. The model obtained indicates that Fe-S cluster N2 is close to the membrane domain interface, allowing for effective electron transfer to membrane-embedded quinone. At the current resolution, the structures in the presence of NAD+ or NADH are similar. Additionally, side-view class averages were calculated for the negatively stained bovine enzyme. The structures of bovine complex I in the presence of either NAD+ or NADH also appeared to be similar. These observations indicate that conformational changes upon reduction with NADH, suggested to occur by a range of studies, are smaller than had been thought previously. The model of the entire bacterial complex I could be built from the crystal structures of subcomplexes using the EM envelope described here.
acknowledgement: This work was supported by the Medical Research Council.
author:
- first_name: David
full_name: Morgan, David J
last_name: Morgan
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Morgan D, Sazanov LA. Three-dimensional structure of respiratory complex I
from Escherichia coli in ice in the presence of nucleotides. Biochimica et
Biophysica Acta - Bioenergetics. 2008;1777(7-8):711-718. doi:10.1016/j.bbabio.2008.03.023
apa: Morgan, D., & Sazanov, L. A. (2008). Three-dimensional structure of respiratory
complex I from Escherichia coli in ice in the presence of nucleotides. Biochimica
et Biophysica Acta - Bioenergetics. Elsevier. https://doi.org/10.1016/j.bbabio.2008.03.023
chicago: Morgan, David, and Leonid A Sazanov. “Three-Dimensional Structure of Respiratory
Complex I from Escherichia Coli in Ice in the Presence of Nucleotides.” Biochimica
et Biophysica Acta - Bioenergetics. Elsevier, 2008. https://doi.org/10.1016/j.bbabio.2008.03.023.
ieee: D. Morgan and L. A. Sazanov, “Three-dimensional structure of respiratory complex
I from Escherichia coli in ice in the presence of nucleotides,” Biochimica
et Biophysica Acta - Bioenergetics, vol. 1777, no. 7–8. Elsevier, pp. 711–718,
2008.
ista: Morgan D, Sazanov LA. 2008. Three-dimensional structure of respiratory complex
I from Escherichia coli in ice in the presence of nucleotides. Biochimica et Biophysica
Acta - Bioenergetics. 1777(7–8), 711–718.
mla: Morgan, David, and Leonid A. Sazanov. “Three-Dimensional Structure of Respiratory
Complex I from Escherichia Coli in Ice in the Presence of Nucleotides.” Biochimica
et Biophysica Acta - Bioenergetics, vol. 1777, no. 7–8, Elsevier, 2008, pp.
711–18, doi:10.1016/j.bbabio.2008.03.023.
short: D. Morgan, L.A. Sazanov, Biochimica et Biophysica Acta - Bioenergetics 1777
(2008) 711–718.
date_created: 2018-12-11T11:54:58Z
date_published: 2008-07-01T00:00:00Z
date_updated: 2021-01-12T06:54:24Z
day: '01'
doi: 10.1016/j.bbabio.2008.03.023
extern: 1
intvolume: ' 1777'
issue: 7-8
month: '07'
page: 711 - 718
publication: Biochimica et Biophysica Acta - Bioenergetics
publication_status: published
publisher: Elsevier
publist_id: '5116'
quality_controlled: 0
status: public
title: Three-dimensional structure of respiratory complex I from Escherichia coli
in ice in the presence of nucleotides
type: journal_article
volume: 1777
year: '2008'
...
---
_id: '1982'
abstract:
- lang: eng
text: In the bacterium Escherichia coli, the Min proteins oscillate between the
cell poles to select the cell center as division site. This dynamic pattern has
been proposed to arise by self-organization of these proteins, and several models
have suggested a reaction-diffusion type mechanism. Here, we found that the Min
proteins spontaneously formed planar surface waves on a flat membrane in vitro.
The formation and maintenance of these patterns, which extended for hundreds of
micrometers, required adenosine 5′-triphosphate (ATP), and they persisted for
hours. We present a reaction-diffusion model of the MinD and MinE dynamics that
accounts for our experimental observations and also captures the in vivo oscillations.
acknowledgement: 'This work was supported by the Max-Planck-Society (M.L., P.S., E.F.). '
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: Jonas
full_name: 'Ries, Jonas '
last_name: Ries
- 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, Ries J, Kruse K, Schwille P. Spatial regulators
for bacterial cell division self-organize into surface waves in vitro. Science.
2008;320(5877):789-792. doi:10.1126/science.1154413
apa: Loose, M., Fischer Friedrich, E., Ries, J., Kruse, K., & Schwille, P. (2008).
Spatial regulators for bacterial cell division self-organize into surface waves
in vitro. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.1154413
chicago: Loose, Martin, Elisabeth Fischer Friedrich, Jonas Ries, Karsten Kruse,
and Petra Schwille. “Spatial Regulators for Bacterial Cell Division Self-Organize
into Surface Waves in Vitro.” Science. American Association for the Advancement
of Science, 2008. https://doi.org/10.1126/science.1154413.
ieee: M. Loose, E. Fischer Friedrich, J. Ries, K. Kruse, and P. Schwille, “Spatial
regulators for bacterial cell division self-organize into surface waves in vitro,”
Science, vol. 320, no. 5877. American Association for the Advancement of
Science, pp. 789–792, 2008.
ista: Loose M, Fischer Friedrich E, Ries J, Kruse K, Schwille P. 2008. Spatial regulators
for bacterial cell division self-organize into surface waves in vitro. Science.
320(5877), 789–792.
mla: Loose, Martin, et al. “Spatial Regulators for Bacterial Cell Division Self-Organize
into Surface Waves in Vitro.” Science, vol. 320, no. 5877, American Association
for the Advancement of Science, 2008, pp. 789–92, doi:10.1126/science.1154413.
short: M. Loose, E. Fischer Friedrich, J. Ries, K. Kruse, P. Schwille, Science 320
(2008) 789–792.
date_created: 2018-12-11T11:55:02Z
date_published: 2008-05-09T00:00:00Z
date_updated: 2021-01-12T06:54:30Z
day: '09'
doi: 10.1126/science.1154413
extern: 1
intvolume: ' 320'
issue: '5877'
month: '05'
page: 789 - 792
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5101'
quality_controlled: 0
status: public
title: Spatial regulators for bacterial cell division self-organize into surface waves
in vitro
type: journal_article
volume: 320
year: '2008'
...
---
_id: '2065'
abstract:
- lang: eng
text: 'Population genetics models show that, under certain conditions, the X chromosome
is expected to be under more efficient selection than the autosomes. This could
lead to ''faster-X evolution'', if a large proportion of mutations are fixed by
positive selection, as suggested by recent studies in Drosophila. We used a multispecies
approach to test this: Muller''s element D, an autosomal arm, is fused to the
ancestral X chromosome in Drosophila pseudoobscura and its sister species, Drosophila
affinis. We tested whether the same set of genes had higher rates of non-synonymous
evolution when they were X-linked (in the D. pseudoobscura/D. affinis comparison)
than when they were autosomal (in Drosophila melanogaster/Drosophila yakuba).
Although not significant, our results suggest this may be the case, but only for
genes under particularly strong positive selection/weak purifying selection. They
also suggest that genes that have become X-linked have higher levels of codon
bias and slower synonymous site evolution, consistent with more effective selection
on codon usage at X-linked sites.'
acknowledgement: B.V. was supported by the Portuguese Foundation for Science and Technology,
P.R.H. is supported by the Natural Environmental Research Council (UK) and B.C.
was supported by the Royal Society (UK)
author:
- first_name: Beatriz
full_name: Beatriz Vicoso
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Penelope
full_name: Haddrill, Penelope R
last_name: Haddrill
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
citation:
ama: Vicoso B, Haddrill P, Charlesworth B. A multispecies approach for comparing
sequence evolution of X-linked and autosomal sites in Drosophila. Genetical
Research. 2008;90(5):421-431. doi:10.1017/S0016672308009804
apa: Vicoso, B., Haddrill, P., & Charlesworth, B. (2008). A multispecies approach
for comparing sequence evolution of X-linked and autosomal sites in Drosophila.
Genetical Research. Cambridge University Press. https://doi.org/10.1017/S0016672308009804
chicago: Vicoso, Beatriz, Penelope Haddrill, and Brian Charlesworth. “A Multispecies
Approach for Comparing Sequence Evolution of X-Linked and Autosomal Sites in Drosophila.”
Genetical Research. Cambridge University Press, 2008. https://doi.org/10.1017/S0016672308009804.
ieee: B. Vicoso, P. Haddrill, and B. Charlesworth, “A multispecies approach for
comparing sequence evolution of X-linked and autosomal sites in Drosophila,” Genetical
Research, vol. 90, no. 5. Cambridge University Press, pp. 421–431, 2008.
ista: Vicoso B, Haddrill P, Charlesworth B. 2008. A multispecies approach for comparing
sequence evolution of X-linked and autosomal sites in Drosophila. Genetical Research.
90(5), 421–431.
mla: Vicoso, Beatriz, et al. “A Multispecies Approach for Comparing Sequence Evolution
of X-Linked and Autosomal Sites in Drosophila.” Genetical Research, vol.
90, no. 5, Cambridge University Press, 2008, pp. 421–31, doi:10.1017/S0016672308009804.
short: B. Vicoso, P. Haddrill, B. Charlesworth, Genetical Research 90 (2008) 421–431.
date_created: 2018-12-11T11:55:30Z
date_published: 2008-10-01T00:00:00Z
date_updated: 2021-01-12T06:55:05Z
day: '01'
doi: 10.1017/S0016672308009804
extern: 1
intvolume: ' 90'
issue: '5'
month: '10'
page: 421 - 431
publication: Genetical Research
publication_status: published
publisher: Cambridge University Press
publist_id: '4972'
quality_controlled: 0
status: public
title: A multispecies approach for comparing sequence evolution of X-linked and autosomal
sites in Drosophila
type: journal_article
volume: 90
year: '2008'
...
---
_id: '2078'
abstract:
- lang: eng
text: 'This paper presents a novel method for real-time animation of highly-detailed
facial expressions based on a multi-scale decomposition of facial geometry into
large-scale motion and fine-scale details, such as expression wrinkles. Our hybrid
animation is tailored to the specific characteristics of large- and fine-scale
facial deformations: Large-scale deformations are computed with a fast linear
shell model, which is intuitively and accurately controlled through a sparse set
of motion-capture markers or user-defined handle points. Fine-scale facial details
are incorporated using a novel pose-space deformation technique, which learns
the correspondence of sparse measurements of skin strain to wrinkle formation
from a small set of example poses. Our hybrid method features real-time animation
of highly-detailed faces with realistic wrinkle formation, and allows both large-scale
deformations and fine-scale wrinkles to be edited intuitively. Furthermore, our
pose-space representation enables the transfer of facial details to novel expressions
or other facial models.'
acknowledgement: This research was supported by the NCCR Co-Me of the Swiss National
Science Foundation.
author:
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Manuel
full_name: Lang, Manuel
last_name: Lang
- first_name: Mario
full_name: Botsch, Mario
last_name: Botsch
- first_name: Miguel
full_name: Otaduy, Miguel
last_name: Otaduy
- first_name: Markus
full_name: Gross, Markus
last_name: Gross
citation:
ama: 'Bickel B, Lang M, Botsch M, Otaduy M, Gross M. Pose-space animation and transfer
of facial details. In: ACM; 2008:57-66. doi:10.2312/SCA/SCA08/057-066'
apa: 'Bickel, B., Lang, M., Botsch, M., Otaduy, M., & Gross, M. (2008). Pose-space
animation and transfer of facial details (pp. 57–66). Presented at the SIGGRAPH:
Eurographics Symposium on Computer Animation, ACM. https://doi.org/10.2312/SCA/SCA08/057-066'
chicago: Bickel, Bernd, Manuel Lang, Mario Botsch, Miguel Otaduy, and Markus Gross.
“Pose-Space Animation and Transfer of Facial Details,” 57–66. ACM, 2008. https://doi.org/10.2312/SCA/SCA08/057-066.
ieee: 'B. Bickel, M. Lang, M. Botsch, M. Otaduy, and M. Gross, “Pose-space animation
and transfer of facial details,” presented at the SIGGRAPH: Eurographics Symposium
on Computer Animation, 2008, pp. 57–66.'
ista: 'Bickel B, Lang M, Botsch M, Otaduy M, Gross M. 2008. Pose-space animation
and transfer of facial details. SIGGRAPH: Eurographics Symposium on Computer Animation,
57–66.'
mla: Bickel, Bernd, et al. Pose-Space Animation and Transfer of Facial Details.
ACM, 2008, pp. 57–66, doi:10.2312/SCA/SCA08/057-066.
short: B. Bickel, M. Lang, M. Botsch, M. Otaduy, M. Gross, in:, ACM, 2008, pp. 57–66.
conference:
name: 'SIGGRAPH: Eurographics Symposium on Computer Animation'
date_created: 2018-12-11T11:55:35Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T06:55:10Z
doi: 10.2312/SCA/SCA08/057-066
extern: '1'
language:
- iso: eng
oa_version: None
page: 57 - 66
publication_status: published
publisher: ACM
publist_id: '4960'
status: public
title: Pose-space animation and transfer of facial details
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2008'
...