---
_id: '843'
abstract:
- lang: eng
text: The impact of an amino acid replacement on the organism's fitness can vary
from lethal to selectively neutral and even, in rare cases, beneficial. Substantial
data are available on either pathogenic or acceptable replacements. However, the
whole distribution of coefficients of selection against individual replacements
is not known for any organism. To ascertain this distribution for human proteins,
we combined data on pathogenic missense mutations, on human non-synonymous SNPs
and on human-chimpanzee divergence of orthologous proteins. Fractions of amino
acid replacements which reduce fitness by >10-2, 10-2-10-4, 10-4-10-5 and <10-5
are 25, 49, 14 and 12%, respectively. On average, the strength of selection against
a replacement is substantially higher when chemically dissimilar amino acids are
involved, and the Grantham's index of a replacement explains 35% of variance in
the average logarithm of selection coefficients associated with different replacements.
Still, the impact of a replacement depends on its context within the protein more
than on its own nature. Reciprocal replacements are often associated with rather
different selection coefficients, in particular, replacements of non-polar amino
acids with polar ones are typically much more deleterious than replacements in
the opposite direction. However, differences between evolutionary fluxes of reciprocal
replacements are only weakly correlated with the differences between the corresponding
selection coefficients.
author:
- first_name: Lev
full_name: Yampolsky, Lev Y
last_name: Yampolsky
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
citation:
ama: Yampolsky L, Kondrashov F, Kondrashov A. Distribution of the strength of selection
against amino acid replacements in human proteins. Human Molecular Genetics.
2005;14(21):3191-3201. doi:10.1093/hmg/ddi350
apa: Yampolsky, L., Kondrashov, F., & Kondrashov, A. (2005). Distribution of
the strength of selection against amino acid replacements in human proteins. Human
Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/ddi350
chicago: Yampolsky, Lev, Fyodor Kondrashov, and Alexey Kondrashov. “Distribution
of the Strength of Selection against Amino Acid Replacements in Human Proteins.”
Human Molecular Genetics. Oxford University Press, 2005. https://doi.org/10.1093/hmg/ddi350.
ieee: L. Yampolsky, F. Kondrashov, and A. Kondrashov, “Distribution of the strength
of selection against amino acid replacements in human proteins,” Human Molecular
Genetics, vol. 14, no. 21. Oxford University Press, pp. 3191–3201, 2005.
ista: Yampolsky L, Kondrashov F, Kondrashov A. 2005. Distribution of the strength
of selection against amino acid replacements in human proteins. Human Molecular
Genetics. 14(21), 3191–3201.
mla: Yampolsky, Lev, et al. “Distribution of the Strength of Selection against Amino
Acid Replacements in Human Proteins.” Human Molecular Genetics, vol. 14,
no. 21, Oxford University Press, 2005, pp. 3191–201, doi:10.1093/hmg/ddi350.
short: L. Yampolsky, F. Kondrashov, A. Kondrashov, Human Molecular Genetics 14 (2005)
3191–3201.
date_created: 2018-12-11T11:48:48Z
date_published: 2005-11-01T00:00:00Z
date_updated: 2021-01-12T08:19:13Z
day: '01'
doi: 10.1093/hmg/ddi350
extern: 1
intvolume: ' 14'
issue: '21'
month: '11'
page: 3191 - 3201
publication: Human Molecular Genetics
publication_status: published
publisher: Oxford University Press
publist_id: '6807'
quality_controlled: 0
status: public
title: Distribution of the strength of selection against amino acid replacements in
human proteins
type: journal_article
volume: 14
year: '2005'
...
---
_id: '8491'
abstract:
- lang: eng
text: Fast multidimensional NMR with a time resolution of a few seconds provides
a new tool for high throughput screening and site-resolved real-time studies of
kinetic molecular processes by NMR. Recently we have demonstrated the feasibility
to record protein 1H–15N correlation spectra in a few seconds of acquisition time
using a new SOFAST-HMQC experiment (Schanda and Brutscher (2005) J. Am. Chem.
Soc. 127, 8014). Here, we investigate in detail the performance of SOFAST-HMQC
to record 1H–15N and 1H−13C correlation spectra of proteins of different size
and at different magnetic field strengths. Compared to standard 1H–15N correlation
experiments SOFAST-HMQC provides a significant gain in sensitivity, especially
for fast repetition rates. Guidelines are provided on how to set up SOFAST-HMQC
experiments for a given protein sample. In addition, an alternative pulse scheme,
IPAP-SOFAST-HMQC is presented that allows application on NMR spectrometers equipped
with cryogenic probes, and fast measurement of one-bond 1H–13C and 1H–15N scalar
and residual dipolar coupling constants.
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: Ēriks
full_name: Kupče, Ēriks
last_name: Kupče
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Schanda P, Kupče Ē, Brutscher B. SOFAST-HMQC experiments for recording two-dimensional
deteronuclear correlation spectra of proteins within a few seconds. Journal
of Biomolecular NMR. 2005;33(4):199-211. doi:10.1007/s10858-005-4425-x
apa: Schanda, P., Kupče, Ē., & Brutscher, B. (2005). SOFAST-HMQC experiments
for recording two-dimensional deteronuclear correlation spectra of proteins within
a few seconds. Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-005-4425-x
chicago: Schanda, Paul, Ēriks Kupče, and Bernhard Brutscher. “SOFAST-HMQC Experiments
for Recording Two-Dimensional Deteronuclear Correlation Spectra of Proteins within
a Few Seconds.” Journal of Biomolecular NMR. Springer Nature, 2005. https://doi.org/10.1007/s10858-005-4425-x.
ieee: P. Schanda, Ē. Kupče, and B. Brutscher, “SOFAST-HMQC experiments for recording
two-dimensional deteronuclear correlation spectra of proteins within a few seconds,”
Journal of Biomolecular NMR, vol. 33, no. 4. Springer Nature, pp. 199–211,
2005.
ista: Schanda P, Kupče Ē, Brutscher B. 2005. SOFAST-HMQC experiments for recording
two-dimensional deteronuclear correlation spectra of proteins within a few seconds.
Journal of Biomolecular NMR. 33(4), 199–211.
mla: Schanda, Paul, et al. “SOFAST-HMQC Experiments for Recording Two-Dimensional
Deteronuclear Correlation Spectra of Proteins within a Few Seconds.” Journal
of Biomolecular NMR, vol. 33, no. 4, Springer Nature, 2005, pp. 199–211, doi:10.1007/s10858-005-4425-x.
short: P. Schanda, Ē. Kupče, B. Brutscher, Journal of Biomolecular NMR 33 (2005)
199–211.
date_created: 2020-09-18T10:13:59Z
date_published: 2005-12-01T00:00:00Z
date_updated: 2021-01-12T08:19:38Z
day: '01'
doi: 10.1007/s10858-005-4425-x
extern: '1'
intvolume: ' 33'
issue: '4'
keyword:
- Spectroscopy
- Biochemistry
language:
- iso: eng
month: '12'
oa_version: None
page: 199-211
publication: Journal of Biomolecular NMR
publication_identifier:
issn:
- 0925-2738
- 1573-5001
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation
spectra of proteins within a few seconds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2005'
...
---
_id: '8492'
abstract:
- lang: eng
text: We demonstrate for different protein samples that 2D 1H−15N correlation NMR
spectra can be recorded in a few seconds of acquisition time using a new band-selective
optimized flip-angle short-transient heteronuclear multiple quantum coherence
experiment. This has enabled us to measure fast hydrogen−deuterium exchange rate
constants along the backbone of a small globular protein fragment by real-time
2D NMR.
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
citation:
ama: Schanda P, Brutscher B. Very fast two-dimensional NMR spectroscopy for real-time
investigation of dynamic events in proteins on the time scale of seconds. Journal
of the American Chemical Society. 2005;127(22):8014-8015. doi:10.1021/ja051306e
apa: Schanda, P., & Brutscher, B. (2005). Very fast two-dimensional NMR spectroscopy
for real-time investigation of dynamic events in proteins on the time scale of
seconds. Journal of the American Chemical Society. American Chemical Society.
https://doi.org/10.1021/ja051306e
chicago: Schanda, Paul, and Bernhard Brutscher. “Very Fast Two-Dimensional NMR Spectroscopy
for Real-Time Investigation of Dynamic Events in Proteins on the Time Scale of
Seconds.” Journal of the American Chemical Society. American Chemical Society,
2005. https://doi.org/10.1021/ja051306e.
ieee: P. Schanda and B. Brutscher, “Very fast two-dimensional NMR spectroscopy for
real-time investigation of dynamic events in proteins on the time scale of seconds,”
Journal of the American Chemical Society, vol. 127, no. 22. American Chemical
Society, pp. 8014–8015, 2005.
ista: Schanda P, Brutscher B. 2005. Very fast two-dimensional NMR spectroscopy for
real-time investigation of dynamic events in proteins on the time scale of seconds.
Journal of the American Chemical Society. 127(22), 8014–8015.
mla: Schanda, Paul, and Bernhard Brutscher. “Very Fast Two-Dimensional NMR Spectroscopy
for Real-Time Investigation of Dynamic Events in Proteins on the Time Scale of
Seconds.” Journal of the American Chemical Society, vol. 127, no. 22, American
Chemical Society, 2005, pp. 8014–15, doi:10.1021/ja051306e.
short: P. Schanda, B. Brutscher, Journal of the American Chemical Society 127 (2005)
8014–8015.
date_created: 2020-09-18T10:14:05Z
date_published: 2005-05-14T00:00:00Z
date_updated: 2021-01-12T08:19:39Z
day: '14'
doi: 10.1021/ja051306e
extern: '1'
intvolume: ' 127'
issue: '22'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '05'
oa_version: None
page: 8014-8015
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic
events in proteins on the time scale of seconds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 127
year: '2005'
...
---
_id: '8516'
abstract:
- lang: eng
text: "The purpose of this paper is to construct examples of diffusion for E-Hamiltonian
perturbations\r\nof completely integrable Hamiltonian systems in 2d-dimensional
phase space, with d large.\r\nIn the first part of the paper, simple and explicit
examples are constructed illustrating absence\r\nof ‘long-time’ stability for
size E Hamiltonian perturbations of quasi-convex integrable systems\r\nalready
when the dimension 2d of phase space becomes as large as log 1/E . We first produce\r\nthe
example in Gevrey class and then a real analytic one, with some additional work.\r\nIn
the second part, we consider again E-Hamiltonian perturbations of completely integrable\r\nHamiltonian
system in 2d-dimensional space with E-small but not too small, |E| > exp(−d),
with\r\nd the number of degrees of freedom assumed large. It is shown that for
a class of analytic\r\ntime-periodic perturbations, there exist linearly diffusing
trajectories. The underlying idea for\r\nboth examples is similar and consists
in coupling a fixed degree of freedom with a large\r\nnumber of them. The procedure
and analytical details are however significantly different. As\r\nmentioned, the
construction in Part I is totally elementary while Part II is more involved, relying\r\nin
particular on the theory of normally hyperbolic invariant manifolds, methods of
generating\r\nfunctions, Aubry–Mather theory, and Mather’s variational methods."
article_processing_charge: No
article_type: original
author:
- first_name: Jean
full_name: Bourgain, Jean
last_name: Bourgain
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Bourgain J, Kaloshin V. On diffusion in high-dimensional Hamiltonian systems.
Journal of Functional Analysis. 2005;229(1):1-61. doi:10.1016/j.jfa.2004.09.006
apa: Bourgain, J., & Kaloshin, V. (2005). On diffusion in high-dimensional Hamiltonian
systems. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2004.09.006
chicago: Bourgain, Jean, and Vadim Kaloshin. “On Diffusion in High-Dimensional Hamiltonian
Systems.” Journal of Functional Analysis. Elsevier, 2005. https://doi.org/10.1016/j.jfa.2004.09.006.
ieee: J. Bourgain and V. Kaloshin, “On diffusion in high-dimensional Hamiltonian
systems,” Journal of Functional Analysis, vol. 229, no. 1. Elsevier, pp.
1–61, 2005.
ista: Bourgain J, Kaloshin V. 2005. On diffusion in high-dimensional Hamiltonian
systems. Journal of Functional Analysis. 229(1), 1–61.
mla: Bourgain, Jean, and Vadim Kaloshin. “On Diffusion in High-Dimensional Hamiltonian
Systems.” Journal of Functional Analysis, vol. 229, no. 1, Elsevier, 2005,
pp. 1–61, doi:10.1016/j.jfa.2004.09.006.
short: J. Bourgain, V. Kaloshin, Journal of Functional Analysis 229 (2005) 1–61.
date_created: 2020-09-18T10:49:06Z
date_published: 2005-12-01T00:00:00Z
date_updated: 2021-01-12T08:19:49Z
day: '01'
doi: 10.1016/j.jfa.2004.09.006
extern: '1'
intvolume: ' 229'
issue: '1'
keyword:
- Analysis
language:
- iso: eng
month: '12'
oa_version: None
page: 1-61
publication: Journal of Functional Analysis
publication_identifier:
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: On diffusion in high-dimensional Hamiltonian systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 229
year: '2005'
...
---
_id: '877'
abstract:
- lang: eng
text: "Sequence analysis of protein and mitochondrially encoded tRNA genes shows
that substitutions\r\nproducing pathogenic effects in humans are often found in
normal, healthy individuals from other species.\r\nAnalysis of stability of protein
and tRNA structures shows that the disease-causing effects of pathogenic\r\nmutations
can be neutralized by other, compensatory substitutions that restore the structural
stability of the\r\nmolecule. Further study of such substitutions will, hopefully,
lead to new methods for curing genetic dis-\r\neases that may be based on the
correction of molecule stability as a whole instead of reversing an individual\r\npathogenic
mutation."
article_processing_charge: No
article_type: original
author:
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov F. The analysis of monomer sequences in protein and tRNA and the
manifestation of the compensation of pathogenic deviations in their evolution.
Biofizika. 2005;50(3):389-395.
apa: Kondrashov, F. (2005). The analysis of monomer sequences in protein and tRNA
and the manifestation of the compensation of pathogenic deviations in their evolution.
Biofizika. Pleiades Publishing.
chicago: Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA
and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.”
Biofizika. Pleiades Publishing, 2005.
ieee: F. Kondrashov, “The analysis of monomer sequences in protein and tRNA and
the manifestation of the compensation of pathogenic deviations in their evolution,”
Biofizika, vol. 50, no. 3. Pleiades Publishing, pp. 389–395, 2005.
ista: Kondrashov F. 2005. The analysis of monomer sequences in protein and tRNA
and the manifestation of the compensation of pathogenic deviations in their evolution.
Biofizika. 50(3), 389–395.
mla: Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA
and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.”
Biofizika, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 389–95.
short: F. Kondrashov, Biofizika 50 (2005) 389–395.
date_created: 2018-12-11T11:48:58Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T08:21:01Z
day: '01'
extern: '1'
external_id:
pmid:
- '15977826'
intvolume: ' 50'
issue: '3'
language:
- iso: eng
main_file_link:
- url: http://pleiades.online/abstract/biophys/5/biophys0349_abstract.pdf
month: '05'
oa_version: None
page: 389 - 395
pmid: 1
publication: Biofizika
publication_status: published
publisher: Pleiades Publishing
publist_id: '6769'
quality_controlled: '1'
status: public
title: The analysis of monomer sequences in protein and tRNA and the manifestation
of the compensation of pathogenic deviations in their evolution
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2005'
...
---
_id: '878'
abstract:
- lang: eng
text: |
Negative trade-offs are thought to be a pervasive phenomenon and to inhibit evolution at all levels. New evidence shows that at the molecular level, there may be no trade-offs preventing the emergence of an enzyme with multiple functions.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov F. In search of the limits of evolution. Nature Genetics.
2005;37(1):9-10. doi:10.1038/ng0105-9
apa: Kondrashov, F. (2005). In search of the limits of evolution. Nature Genetics.
Nature Publishing Group. https://doi.org/10.1038/ng0105-9
chicago: Kondrashov, Fyodor. “In Search of the Limits of Evolution.” Nature Genetics.
Nature Publishing Group, 2005. https://doi.org/10.1038/ng0105-9.
ieee: F. Kondrashov, “In search of the limits of evolution,” Nature Genetics,
vol. 37, no. 1. Nature Publishing Group, pp. 9–10, 2005.
ista: Kondrashov F. 2005. In search of the limits of evolution. Nature Genetics.
37(1), 9–10.
mla: Kondrashov, Fyodor. “In Search of the Limits of Evolution.” Nature Genetics,
vol. 37, no. 1, Nature Publishing Group, 2005, pp. 9–10, doi:10.1038/ng0105-9.
short: F. Kondrashov, Nature Genetics 37 (2005) 9–10.
date_created: 2018-12-11T11:48:59Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:02Z
day: '01'
doi: 10.1038/ng0105-9
extern: 1
intvolume: ' 37'
issue: '1'
month: '01'
page: 9 - 10
publication: Nature Genetics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6770'
quality_controlled: 0
status: public
title: In search of the limits of evolution
type: journal_article
volume: 37
year: '2005'
...
---
_id: '880'
abstract:
- lang: eng
text: Here, I describe a case of loss of the D-arm by mitochondrial cysteine tRNA
in the nine-banded armadillo (Dasypus novemcinctus) convergent with mt tRNASer(AGY).
Such evolution sheds light on the relationship between structure and function
of tRNA molecules and its impact on the patterns of molecular evolution.
article_processing_charge: No
author:
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov F. The convergent evolution of the secondary structure of mitochondrial
cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika.
2005;50(3):396-403.
apa: Kondrashov, F. (2005). The convergent evolution of the secondary structure
of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus.
Biofizika. Pleiades Publishing.
chicago: Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure
of Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.”
Biofizika. Pleiades Publishing, 2005.
ieee: F. Kondrashov, “The convergent evolution of the secondary structure of mitochondrial
cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus,” Biofizika,
vol. 50, no. 3. Pleiades Publishing, pp. 396–403, 2005.
ista: Kondrashov F. 2005. The convergent evolution of the secondary structure of
mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus.
Biofizika. 50(3), 396–403.
mla: Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure of
Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.”
Biofizika, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 396–403.
short: F. Kondrashov, Biofizika 50 (2005) 396–403.
date_created: 2018-12-11T11:48:59Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T08:21:07Z
day: '01'
extern: '1'
external_id:
pmid:
- '15977827'
intvolume: ' 50'
issue: '3'
language:
- iso: eng
main_file_link:
- url: http://pleiades.online/abstract/biophys/5/biophys0356_abstract.pdf
month: '05'
oa_version: None
page: 396 - 403
pmid: 1
publication: Biofizika
publication_status: published
publisher: Pleiades Publishing
publist_id: '6768'
quality_controlled: '1'
status: public
title: The convergent evolution of the secondary structure of mitochondrial cysteine
tRNA in the nine-banded armadillo Dasypus novemcinctus
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2005'
...
---
_id: '882'
abstract:
- lang: eng
text: Some mutations in human mitochondrial tRNAs are severely pathogenic. The available
computational methods have a poor record of predicting the impact of a tRNA mutation
on the phenotype and fitness. Here patterns of evolution at tRNA sites that harbor
pathogenic mutations and at sites that harbor phenotypically cryptic polymorphisms
were compared. Mutations that are pathogenic to humans occupy more conservative
sites, are only rarely fixed in closely related species, and, when located in
stem structures, often disrupt Watson-Crick pairing and display signs of compensatory
evolution. These observations make it possible to classify ∼90% of all known pathogenic
mutations as deleterious together with only ∼30% of polymorphisms. These polymorphisms
segregate at frequencies that are more than two times lower than frequencies of
polymorphisms classified as benign, indicating that at least ∼30% of known polymorphisms
in mitochondrial tRNAs affect fitness negatively.
acknowledgement: |
The author thanks P. Andolfatto, D. Bachtrog, N. Esipova, S. Makeev, A. Kondrashov, V. Ramensky, V. Tumanyan and P. Vlasov for a critical reading of the manuscript. The author is an NSF Graduate Research Fellow. This work was supported by a Contract of the Russian Ministry of Science and Education (02.434.11.1008) and a grant on Molecular and Cellular Biology from RAS.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov F. Prediction of pathogenic mutations in mitochondrially encoded
human tRNAs. Human Molecular Genetics. 2005;14(16):2415-2419. doi:10.1093/hmg/ddi243
apa: Kondrashov, F. (2005). Prediction of pathogenic mutations in mitochondrially
encoded human tRNAs. Human Molecular Genetics. Oxford University Press.
https://doi.org/10.1093/hmg/ddi243
chicago: Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially
Encoded Human TRNAs.” Human Molecular Genetics. Oxford University Press,
2005. https://doi.org/10.1093/hmg/ddi243.
ieee: F. Kondrashov, “Prediction of pathogenic mutations in mitochondrially encoded
human tRNAs,” Human Molecular Genetics, vol. 14, no. 16. Oxford University
Press, pp. 2415–2419, 2005.
ista: Kondrashov F. 2005. Prediction of pathogenic mutations in mitochondrially
encoded human tRNAs. Human Molecular Genetics. 14(16), 2415–2419.
mla: Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially
Encoded Human TRNAs.” Human Molecular Genetics, vol. 14, no. 16, Oxford
University Press, 2005, pp. 2415–19, doi:10.1093/hmg/ddi243.
short: F. Kondrashov, Human Molecular Genetics 14 (2005) 2415–2419.
date_created: 2018-12-11T11:49:00Z
date_published: 2005-08-15T00:00:00Z
date_updated: 2021-01-12T08:21:10Z
day: '15'
doi: 10.1093/hmg/ddi243
extern: 1
intvolume: ' 14'
issue: '16'
month: '08'
page: 2415 - 2419
publication: Human Molecular Genetics
publication_status: published
publisher: Oxford University Press
publist_id: '6767'
quality_controlled: 0
status: public
title: Prediction of pathogenic mutations in mitochondrially encoded human tRNAs
type: journal_article
volume: 14
year: '2005'
...
---
_id: '893'
abstract:
- lang: eng
text: Amino acid composition of proteins varies substantially between taxa and,
thus, can evolve. For example, proteins from organisms with (G+C)-rich (or (A+T)-rich)
genomes contain more (or fewer) amino acids encoded by (G+C)-rich codons. However,
no universal trends in ongoing changes of amino acid frequencies have been reported.
We compared sets of orthologous proteins encoded by triplets of closely related
genomes from 15 taxa representing all three domains of life (Bacteria, Archaea
and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys,
Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly
are consistently lost. The same nine amino acids are currently accrued or lost
in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms.
All amino acids with declining frequencies are thought to be among the first incorporated
into the genetic code; conversely, all amino acids with increasing frequencies,
except Ser, were probably recruited late. Thus, expansion of initially under-represented
amino acids, which began over 3,400 million years ago, apparently continues to
this day.
acknowledgement: S.S. and I.A.A. were supported by the Genome Canada Foundation.
author:
- first_name: Ingo
full_name: Jordan, Ingo K
last_name: Jordan
- 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: Adzhubeǐ, Ivan A
last_name: Adzhubeǐ
- first_name: Yuri
full_name: Wolf, Yuri I
last_name: Wolf
- first_name: Eugene
full_name: Koonin, Eugene V
last_name: Koonin
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Shamil
full_name: Sunyaev, Shamil R
last_name: Sunyaev
citation:
ama: Jordan I, Kondrashov F, Adzhubeǐ I, et al. A universal trend of amino acid
gain and loss in protein evolution. Nature. 2005;433(7026):633-638. doi:10.1038/nature03306
apa: Jordan, I., Kondrashov, F., Adzhubeǐ, I., Wolf, Y., Koonin, E., Kondrashov,
A., & Sunyaev, S. (2005). A universal trend of amino acid gain and loss in
protein evolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature03306
chicago: Jordan, Ingo, Fyodor Kondrashov, Ivan Adzhubeǐ, Yuri Wolf, Eugene Koonin,
Alexey Kondrashov, and Shamil Sunyaev. “A Universal Trend of Amino Acid Gain and
Loss in Protein Evolution.” Nature. Nature Publishing Group, 2005. https://doi.org/10.1038/nature03306.
ieee: I. Jordan et al., “A universal trend of amino acid gain and loss in
protein evolution,” Nature, vol. 433, no. 7026. Nature Publishing Group,
pp. 633–638, 2005.
ista: Jordan I, Kondrashov F, Adzhubeǐ I, Wolf Y, Koonin E, Kondrashov A, Sunyaev
S. 2005. A universal trend of amino acid gain and loss in protein evolution. Nature.
433(7026), 633–638.
mla: Jordan, Ingo, et al. “A Universal Trend of Amino Acid Gain and Loss in Protein
Evolution.” Nature, vol. 433, no. 7026, Nature Publishing Group, 2005,
pp. 633–38, doi:10.1038/nature03306.
short: I. Jordan, F. Kondrashov, I. Adzhubeǐ, Y. Wolf, E. Koonin, A. Kondrashov,
S. Sunyaev, Nature 433 (2005) 633–638.
date_created: 2018-12-11T11:49:03Z
date_published: 2005-02-10T00:00:00Z
date_updated: 2021-01-12T08:21:23Z
day: '10'
doi: 10.1038/nature03306
extern: 1
intvolume: ' 433'
issue: '7026'
month: '02'
page: 633 - 638
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6757'
quality_controlled: 0
status: public
title: A universal trend of amino acid gain and loss in protein evolution
type: journal_article
volume: 433
year: '2005'
...
---
_id: '1740'
abstract:
- lang: eng
text: 'A systematic study of the morphology of self-organized islands in the InAs/GaAs(0
0 1) and Ge/Si(0 0 1) systems is presented, based on high-resolution scanning
tunneling microscopy measurements. We demonstrate that in both cases two main
island families coexist: smaller pyramids bound by one type of shallow facets
and larger multifaceted domes. Their structure and facet orientation are precisely
determined, thus solving a highly debated argument in the case of InAs/GaAs(0
0 1). The comparison between the two material systems reveals the existence of
striking similarities that extend even to the nature of island precursors and
to the islands that form when depositing InGaAs or GeSi alloys. The implications
of these observations on a possible universal description of the Stranski-Krastanow
growth mode are discussed with respect to recent theoretical results.'
author:
- first_name: Giovanni
full_name: Costantini, Giovanni
last_name: Costantini
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Carlos
full_name: Manzano, Carlos
last_name: Manzano
- first_name: P
full_name: Acosta-Diaz, P
last_name: Acosta Diaz
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Rudeeson
full_name: Songmuang, Rudeeson
last_name: Songmuang
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
- first_name: Hans
full_name: Von Känel, Hans
last_name: Von Känel
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
citation:
ama: Costantini G, Rastelli A, Manzano C, et al. Pyramids and domes in the InAs/GaAs
(0 0 1) and Ge/Si (0 0 1) systems. Journal of Crystal Growth. 2005;278(1-4):38-45.
doi:10.1016/j.jcrysgro.2004.12.047
apa: Costantini, G., Rastelli, A., Manzano, C., Acosta Diaz, P., Katsaros, G., Songmuang,
R., … Kern, K. (2005). Pyramids and domes in the InAs/GaAs (0 0 1) and Ge/Si (0
0 1) systems. Journal of Crystal Growth. Elsevier. https://doi.org/10.1016/j.jcrysgro.2004.12.047
chicago: Costantini, Giovanni, Armando Rastelli, Carlos Manzano, P Acosta Diaz,
Georgios Katsaros, Rudeeson Songmuang, Oliver Schmidt, Hans Von Känel, and Klaus
Kern. “Pyramids and Domes in the InAs/GaAs (0 0 1) and Ge/Si (0 0 1) Systems.”
Journal of Crystal Growth. Elsevier, 2005. https://doi.org/10.1016/j.jcrysgro.2004.12.047.
ieee: G. Costantini et al., “Pyramids and domes in the InAs/GaAs (0 0 1)
and Ge/Si (0 0 1) systems,” Journal of Crystal Growth, vol. 278, no. 1–4.
Elsevier, pp. 38–45, 2005.
ista: Costantini G, Rastelli A, Manzano C, Acosta Diaz P, Katsaros G, Songmuang
R, Schmidt O, Von Känel H, Kern K. 2005. Pyramids and domes in the InAs/GaAs (0
0 1) and Ge/Si (0 0 1) systems. Journal of Crystal Growth. 278(1–4), 38–45.
mla: Costantini, Giovanni, et al. “Pyramids and Domes in the InAs/GaAs (0 0 1) and
Ge/Si (0 0 1) Systems.” Journal of Crystal Growth, vol. 278, no. 1–4, Elsevier,
2005, pp. 38–45, doi:10.1016/j.jcrysgro.2004.12.047.
short: G. Costantini, A. Rastelli, C. Manzano, P. Acosta Diaz, G. Katsaros, R. Songmuang,
O. Schmidt, H. Von Känel, K. Kern, Journal of Crystal Growth 278 (2005) 38–45.
date_created: 2018-12-11T11:53:45Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T06:52:54Z
day: '01'
doi: 10.1016/j.jcrysgro.2004.12.047
extern: 1
intvolume: ' 278'
issue: 1-4
month: '05'
page: 38 - 45
publication: Journal of Crystal Growth
publication_status: published
publisher: Elsevier
publist_id: '5384'
quality_controlled: 0
status: public
title: Pyramids and domes in the InAs/GaAs (0 0 1) and Ge/Si (0 0 1) systems
type: journal_article
volume: 278
year: '2005'
...
---
_id: '1741'
abstract:
- lang: eng
text: SiGe islands move laterally on a Si(001) substrate during in situ postgrowth
annealing. This surprising behavior is revealed by an analysis of the substrate
surface morphology after island removal using wet chemical etching. We explain
the island motion by asymmetric surface-mediated alloying. Material leaves one
side of the island by surface diffusion, and mixes with additional Si from the
surrounding surface as it redeposits on the other side. Thus the island moves
laterally while becoming larger and more dilute.
acknowledgement: The work was supported by the BMBF (03N8711)
author:
- first_name: Ulrich
full_name: Denker, Ulrich
last_name: Denker
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Jerry
full_name: Tersoff, Jerry
last_name: Tersoff
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Giovanni
full_name: Costantini, Giovanni
last_name: Costantini
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
- first_name: Neng
full_name: Jin-Phillipp, Neng Y
last_name: Jin Phillipp
- first_name: David
full_name: Jesson, David E
last_name: Jesson
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
citation:
ama: Denker U, Rastelli A, Stoffel M, et al. Lateral motion of SiGe islands driven
by surface-mediated alloying. Physical Review Letters. 2005;94(21). doi:10.1103/PhysRevLett.94.216103
apa: Denker, U., Rastelli, A., Stoffel, M., Tersoff, J., Katsaros, G., Costantini,
G., … Schmidt, O. (2005). Lateral motion of SiGe islands driven by surface-mediated
alloying. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.94.216103
chicago: Denker, Ulrich, Armando Rastelli, Mathieu Stoffel, Jerry Tersoff, Georgios
Katsaros, Giovanni Costantini, Klaus Kern, Neng Jin Phillipp, David Jesson, and
Oliver Schmidt. “Lateral Motion of SiGe Islands Driven by Surface-Mediated Alloying.”
Physical Review Letters. American Physical Society, 2005. https://doi.org/10.1103/PhysRevLett.94.216103.
ieee: U. Denker et al., “Lateral motion of SiGe islands driven by surface-mediated
alloying,” Physical Review Letters, vol. 94, no. 21. American Physical
Society, 2005.
ista: Denker U, Rastelli A, Stoffel M, Tersoff J, Katsaros G, Costantini G, Kern
K, Jin Phillipp N, Jesson D, Schmidt O. 2005. Lateral motion of SiGe islands driven
by surface-mediated alloying. Physical Review Letters. 94(21).
mla: Denker, Ulrich, et al. “Lateral Motion of SiGe Islands Driven by Surface-Mediated
Alloying.” Physical Review Letters, vol. 94, no. 21, American Physical
Society, 2005, doi:10.1103/PhysRevLett.94.216103.
short: U. Denker, A. Rastelli, M. Stoffel, J. Tersoff, G. Katsaros, G. Costantini,
K. Kern, N. Jin Phillipp, D. Jesson, O. Schmidt, Physical Review Letters 94 (2005).
date_created: 2018-12-11T11:53:46Z
date_published: 2005-06-03T00:00:00Z
date_updated: 2021-01-12T06:52:54Z
day: '03'
doi: 10.1103/PhysRevLett.94.216103
extern: 1
intvolume: ' 94'
issue: '21'
month: '06'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5383'
quality_controlled: 0
status: public
title: Lateral motion of SiGe islands driven by surface-mediated alloying
type: journal_article
volume: 94
year: '2005'
...
---
_id: '1742'
abstract:
- lang: eng
text: The effects of substrate temperature, growth rate, and postgrowth annealing
on the composition of Ge islands grown on Si(001) were investigated with a combination
of selective wet chemical etching and atomic force microscopy. A simple kinetic
model comprising only surface diffusion processes can explain all the experimentally
observed compositional profiles for pyramid and dome islands grown in the 560-620°C
range. From this model three-dimensional compositional maps were extracted. By
performing annealing experiments a change in the composition of the domes was
observed. This could be explained as the result of the islands' movement induced
by alloying-driven energy minimization. Also in this case kinetically hindered
bulk diffusion processes are not needed to explain the experimental observations.
acknowledgement: G. K. acknowledges the financial support of DAAD (Deutscher Akademischer
Austausch Dienst)
author:
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Giovanni
full_name: Costantini, Giovanni
last_name: Costantini
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Rubén
full_name: Esteban, Rubén
last_name: Esteban
- first_name: Alexander
full_name: Bittner, Alexander M
last_name: Bittner
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Ulrich
full_name: Denker, Ulrich
last_name: Denker
- 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, Costantini G, Stoffel M, et al. Kinetic origin of island intermixing
during the growth of Ge on Si (001). Physical Review B - Condensed Matter and
Materials Physics. 2005;72(19). doi:10.1103/PhysRevB.72.195320
apa: Katsaros, G., Costantini, G., Stoffel, M., Esteban, R., Bittner, A., Rastelli,
A., … Kern, K. (2005). Kinetic origin of island intermixing during the growth
of Ge on Si (001). Physical Review B - Condensed Matter and Materials Physics.
American Physical Society. https://doi.org/10.1103/PhysRevB.72.195320
chicago: Katsaros, Georgios, Giovanni Costantini, Mathieu Stoffel, Rubén Esteban,
Alexander Bittner, Armando Rastelli, Ulrich Denker, Oliver Schmidt, and Klaus
Kern. “Kinetic Origin of Island Intermixing during the Growth of Ge on Si (001).”
Physical Review B - Condensed Matter and Materials Physics. American Physical
Society, 2005. https://doi.org/10.1103/PhysRevB.72.195320.
ieee: G. Katsaros et al., “Kinetic origin of island intermixing during the
growth of Ge on Si (001),” Physical Review B - Condensed Matter and Materials
Physics, vol. 72, no. 19. American Physical Society, 2005.
ista: Katsaros G, Costantini G, Stoffel M, Esteban R, Bittner A, Rastelli A, Denker
U, Schmidt O, Kern K. 2005. Kinetic origin of island intermixing during the growth
of Ge on Si (001). Physical Review B - Condensed Matter and Materials Physics.
72(19).
mla: Katsaros, Georgios, et al. “Kinetic Origin of Island Intermixing during the
Growth of Ge on Si (001).” Physical Review B - Condensed Matter and Materials
Physics, vol. 72, no. 19, American Physical Society, 2005, doi:10.1103/PhysRevB.72.195320.
short: G. Katsaros, G. Costantini, M. Stoffel, R. Esteban, A. Bittner, A. Rastelli,
U. Denker, O. Schmidt, K. Kern, Physical Review B - Condensed Matter and Materials
Physics 72 (2005).
date_created: 2018-12-11T11:53:46Z
date_published: 2005-11-15T00:00:00Z
date_updated: 2021-01-12T06:52:55Z
day: '15'
doi: 10.1103/PhysRevB.72.195320
extern: 1
intvolume: ' 72'
issue: '19'
month: '11'
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '5382'
quality_controlled: 0
status: public
title: Kinetic origin of island intermixing during the growth of Ge on Si (001)
type: journal_article
volume: 72
year: '2005'
...
---
_id: '1743'
abstract:
- lang: eng
text: Laterally aligned multilayer GeSiSi islands grown on a patterned Si (001)
substrate are disclosed by selective etching of Si in a KOH solution. This procedure
allows us to visualize the vertical alignment of the islands in a three-dimensional
perspective. Our technique reveals that partly coalesced double islands in the
initial layer do not merge together, but instead gradually reproduce into well-separated
double islands in upper layers. We attribute this effect to very thin spacer layers,
which efficiently transfer the strain modulation of each island through the spacer
layer to the surface. The etching rate of Si is reduced in tensile strained regions,
which helps to preserve sufficient Si between the stacked islands to form a periodic
array of freestanding and vertically modulated heterostructure pillars.
acknowledgement: This work was supported by the BMBF (03N8711) and the EU NOE SANDiE
author:
- first_name: Zheyang
full_name: Zhong, Zheyang
last_name: Zhong
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Giovanni
full_name: Costantini, Giovanni
last_name: Costantini
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
- first_name: Neng
full_name: Jin-Phillipp, Neng Y
last_name: Jin Phillipp
- first_name: Günther
full_name: Bauer, Günther
last_name: Bauer
citation:
ama: Zhong Z, Katsaros G, Stoffel M, et al. Periodic pillar structures by Si etching
of multilayer GeSi/Si islands. Applied Physics Letters. 2005;87(26):1-3.
doi:10.1063/1.2150278
apa: Zhong, Z., Katsaros, G., Stoffel, M., Costantini, G., Kern, K., Schmidt, O.,
… Bauer, G. (2005). Periodic pillar structures by Si etching of multilayer GeSi/Si
islands. Applied Physics Letters. American Institute of Physics. https://doi.org/10.1063/1.2150278
chicago: Zhong, Zheyang, Georgios Katsaros, Mathieu Stoffel, Giovanni Costantini,
Klaus Kern, Oliver Schmidt, Neng Jin Phillipp, and Günther Bauer. “Periodic Pillar
Structures by Si Etching of Multilayer GeSi/Si Islands.” Applied Physics Letters.
American Institute of Physics, 2005. https://doi.org/10.1063/1.2150278.
ieee: Z. Zhong et al., “Periodic pillar structures by Si etching of multilayer
GeSi/Si islands,” Applied Physics Letters, vol. 87, no. 26. American Institute
of Physics, pp. 1–3, 2005.
ista: Zhong Z, Katsaros G, Stoffel M, Costantini G, Kern K, Schmidt O, Jin Phillipp
N, Bauer G. 2005. Periodic pillar structures by Si etching of multilayer GeSi/Si
islands. Applied Physics Letters. 87(26), 1–3.
mla: Zhong, Zheyang, et al. “Periodic Pillar Structures by Si Etching of Multilayer
GeSi/Si Islands.” Applied Physics Letters, vol. 87, no. 26, American Institute
of Physics, 2005, pp. 1–3, doi:10.1063/1.2150278.
short: Z. Zhong, G. Katsaros, M. Stoffel, G. Costantini, K. Kern, O. Schmidt, N.
Jin Phillipp, G. Bauer, Applied Physics Letters 87 (2005) 1–3.
date_created: 2018-12-11T11:53:46Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:55Z
day: '01'
doi: 10.1063/1.2150278
extern: 1
intvolume: ' 87'
issue: '26'
month: '01'
page: 1 - 3
publication: Applied Physics Letters
publication_status: published
publisher: American Institute of Physics
publist_id: '5381'
quality_controlled: 0
status: public
title: Periodic pillar structures by Si etching of multilayer GeSi/Si islands
type: journal_article
volume: 87
year: '2005'
...
---
_id: '1744'
abstract:
- lang: eng
text: This paper presents optical duobinary and dicode signalling, as alternatives
to the binary format, in order to improve the transmission performance in the
presense of non-linear effects in a dense wavelength division multiplex (WDM)
optical system. Duobinary signalling is applied to an optical system to explore
the reduction of stimulated Brillouin scattering (SBS) effects. Duobinary signalling
suppresses the SBS effects, and an eye-opening improvement of 0.25 to 1.2 dB is
achieved relative to binary transmission over a range of input power levels. An
experimental study demonstrates that duobinary modulation suppresses the four
wave mixing (FWM) products of a dense WDM system by a maximum of 3 dB. The suppression
is maintained over a range of channel spacings. An investigation of the impact
of fibre dispersion on FWM products under binary, duobinary and dicode modulation
in a dense WDM system is then performed, with interchannel spacing and optical
power variation. This leads to the development of a set of guidelines for the
application areas, in which it is appropriate to use duobinary or dicode modulation
in WDM systems as a means of mitigating the impact of FWM.
acknowledgement: IET
author:
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Izzat
full_name: Darwazeh, Izzat Z
last_name: Darwazeh
- first_name: Phil
full_name: Lane, Phil M
last_name: Lane
citation:
ama: Katsaros G, Darwazeh I, Lane P. Non linear transmission effects in duobinary
and dicode optical systems. IEE Proceedings - Optoelectronics. 2005;152(6):344-352.
doi:10.1049/ip-opt:20045067
apa: Katsaros, G., Darwazeh, I., & Lane, P. (2005). Non linear transmission
effects in duobinary and dicode optical systems. IEE Proceedings - Optoelectronics.
Institute of Electrical Engineers. https://doi.org/10.1049/ip-opt:20045067
chicago: Katsaros, Georgios, Izzat Darwazeh, and Phil Lane. “Non Linear Transmission
Effects in Duobinary and Dicode Optical Systems.” IEE Proceedings - Optoelectronics.
Institute of Electrical Engineers, 2005. https://doi.org/10.1049/ip-opt:20045067.
ieee: G. Katsaros, I. Darwazeh, and P. Lane, “Non linear transmission effects in
duobinary and dicode optical systems,” IEE Proceedings - Optoelectronics,
vol. 152, no. 6. Institute of Electrical Engineers, pp. 344–352, 2005.
ista: Katsaros G, Darwazeh I, Lane P. 2005. Non linear transmission effects in duobinary
and dicode optical systems. IEE Proceedings - Optoelectronics. 152(6), 344–352.
mla: Katsaros, Georgios, et al. “Non Linear Transmission Effects in Duobinary and
Dicode Optical Systems.” IEE Proceedings - Optoelectronics, vol. 152, no.
6, Institute of Electrical Engineers, 2005, pp. 344–52, doi:10.1049/ip-opt:20045067.
short: G. Katsaros, I. Darwazeh, P. Lane, IEE Proceedings - Optoelectronics 152
(2005) 344–352.
date_created: 2018-12-11T11:53:46Z
date_published: 2005-12-01T00:00:00Z
date_updated: 2021-01-12T06:52:55Z
day: '01'
doi: 10.1049/ip-opt:20045067
extern: 1
intvolume: ' 152'
issue: '6'
month: '12'
page: 344 - 352
publication: IEE Proceedings - Optoelectronics
publication_status: published
publisher: Institute of Electrical Engineers
publist_id: '5380'
quality_controlled: 0
status: public
title: Non linear transmission effects in duobinary and dicode optical systems
type: journal_article
volume: 152
year: '2005'
...
---
_id: '1795'
abstract:
- lang: eng
text: 'Background: Murine leukemia virus (MLV) vector particles can be pseudotyped
with a truncated variant of the human immunodeficiency virus type 1 (HIV-1) envelope
protein (Env) and selectively target gene transfer to human cells expressing both
CD4 and an appropriate co-receptor. Vector transduction mimics the HIV-1 entry
process and is therefore a safe tool to study HIV-1 entry. Results: Using FLY
cells, which express the MLV gag and pol genes, we generated stable producer cell
lines that express the HIV-1 envelope gene and a retroviral vector genome encoding
the green fluorescent protein (GFP). The BH10 or 89.6 P HIV-1 Env was expressed
from a bicistronic vector which allowed the rapid selection of stable cell lines.
A codon-usage-optimized synthetic env gene permitted high, Rev-independent Env
expression. Vectors generated by these producer cells displayed different sensitivity
to entry inhibitors. Conclusion: These data illustrate that MLV/HIV-1 vectors
are a valuable screening system for entry inhibitors or neutralizing antisera
generated by vaccines.'
author:
- first_name: Sandra
full_name: Sandra Siegert
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
- first_name: Sonja
full_name: Thaler, Sonja
last_name: Thaler
- first_name: Ralf
full_name: Wagner, Ralf
last_name: Wagner
- first_name: Barbara
full_name: Schnierle, Barbara S
last_name: Schnierle
citation:
ama: Siegert S, Thaler S, Wagner R, Schnierle B. Assessment of HIV-1 entry inhibitors
by MLV/HIV-1 pseudotyped vectors. AIDS Research and Therapy. 2005;2(1).
doi:10.1186/1742-6405-2-7
apa: Siegert, S., Thaler, S., Wagner, R., & Schnierle, B. (2005). Assessment
of HIV-1 entry inhibitors by MLV/HIV-1 pseudotyped vectors. AIDS Research and
Therapy. BioMed Central. https://doi.org/10.1186/1742-6405-2-7
chicago: Siegert, Sandra, Sonja Thaler, Ralf Wagner, and Barbara Schnierle. “Assessment
of HIV-1 Entry Inhibitors by MLV/HIV-1 Pseudotyped Vectors.” AIDS Research
and Therapy. BioMed Central, 2005. https://doi.org/10.1186/1742-6405-2-7.
ieee: S. Siegert, S. Thaler, R. Wagner, and B. Schnierle, “Assessment of HIV-1 entry
inhibitors by MLV/HIV-1 pseudotyped vectors,” AIDS Research and Therapy,
vol. 2, no. 1. BioMed Central, 2005.
ista: Siegert S, Thaler S, Wagner R, Schnierle B. 2005. Assessment of HIV-1 entry
inhibitors by MLV/HIV-1 pseudotyped vectors. AIDS Research and Therapy. 2(1).
mla: Siegert, Sandra, et al. “Assessment of HIV-1 Entry Inhibitors by MLV/HIV-1
Pseudotyped Vectors.” AIDS Research and Therapy, vol. 2, no. 1, BioMed
Central, 2005, doi:10.1186/1742-6405-2-7.
short: S. Siegert, S. Thaler, R. Wagner, B. Schnierle, AIDS Research and Therapy
2 (2005).
date_created: 2018-12-11T11:54:03Z
date_published: 2005-09-12T00:00:00Z
date_updated: 2021-01-12T06:53:15Z
day: '12'
doi: 10.1186/1742-6405-2-7
extern: 1
intvolume: ' 2'
issue: '1'
month: '09'
publication: AIDS Research and Therapy
publication_status: published
publisher: BioMed Central
publist_id: '5315'
quality_controlled: 0
status: public
title: Assessment of HIV-1 entry inhibitors by MLV/HIV-1 pseudotyped vectors
type: journal_article
volume: 2
year: '2005'
...
---
_id: '1962'
abstract:
- lang: eng
text: |2-
Complex I of respiratory chains plays a central role in bioenergetics and is implicated in many human neurodegenerative diseases. An understanding of its mechanism requires a knowledge of the organization of redox centers. The arrangement of iron-sulfur clusters in the hydrophilic domain of complex I from Thermus thermophilus has been determined with the use of x-ray crystallography. One binuclear and six tetranuclear clusters are arranged, maximally 14 angstroms apart, in an 84-angstrom-long electron transfer chain. The binuclear cluster N1a and the tetranuclear cluster N7 are not in this pathway. Cluster N1a may play a role in the prevention of oxidative damage. The structure provides a framework for the interpretation of the large amounts of data accumulated on complex I.
acknowledgement: This work was funded by the Medical Research Council.
author:
- first_name: Philip
full_name: 'Hinchliffe, Philip '
last_name: Hinchliffe
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: 'Hinchliffe P, Sazanov LA. Biochemistry: Organization of iron-sulfur clusters
in respiratory complex I. Science. 2005;309(5735):771-774. doi:10.1126/science.1113988'
apa: 'Hinchliffe, P., & Sazanov, L. A. (2005). Biochemistry: Organization of
iron-sulfur clusters in respiratory complex I. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.1113988'
chicago: 'Hinchliffe, Philip, and Leonid A Sazanov. “Biochemistry: Organization
of Iron-Sulfur Clusters in Respiratory Complex I.” Science. American Association
for the Advancement of Science, 2005. https://doi.org/10.1126/science.1113988.'
ieee: 'P. Hinchliffe and L. A. Sazanov, “Biochemistry: Organization of iron-sulfur
clusters in respiratory complex I,” Science, vol. 309, no. 5735. American
Association for the Advancement of Science, pp. 771–774, 2005.'
ista: 'Hinchliffe P, Sazanov LA. 2005. Biochemistry: Organization of iron-sulfur
clusters in respiratory complex I. Science. 309(5735), 771–774.'
mla: 'Hinchliffe, Philip, and Leonid A. Sazanov. “Biochemistry: Organization of
Iron-Sulfur Clusters in Respiratory Complex I.” Science, vol. 309, no.
5735, American Association for the Advancement of Science, 2005, pp. 771–74, doi:10.1126/science.1113988.'
short: P. Hinchliffe, L.A. Sazanov, Science 309 (2005) 771–774.
date_created: 2018-12-11T11:54:56Z
date_published: 2005-07-29T00:00:00Z
date_updated: 2021-01-12T06:54:22Z
day: '29'
doi: 10.1126/science.1113988
extern: 1
intvolume: ' 309'
issue: '5735'
month: '07'
page: 771 - 774
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5122'
quality_controlled: 0
status: public
title: 'Biochemistry: Organization of iron-sulfur clusters in respiratory complex
I'
type: journal_article
volume: 309
year: '2005'
...
---
_id: '210'
abstract:
- lang: eng
text: Harold Davenport was one of the truly great mathematicians of the twentieth
century. Based on lectures he gave at the University of Michigan in the early
1960s, this book is concerned with the use of analytic methods in the study of
integer solutions to Diophantine equations and Diophantine inequalities. It provides
an excellent introduction to a timeless area of number theory that is still as
widely researched today as it was when the book originally appeared. The three
main themes of the book are Waring's problem and the representation of integers
by diagonal forms, the solubility in integers of systems of forms in many variables,
and the solubility in integers of diagonal inequalities. For the second edition
of the book a comprehensive foreword has been added in which three prominent authorities
describe the modern context and recent developments. A thorough bibliography has
also been added.
alternative_title:
- Cambridge Mathematical Library
article_processing_charge: No
author:
- first_name: Harold
full_name: Davenport, Harold
last_name: Davenport
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Davenport H, Browning TD. Analytic Methods for Diophantine Equations and
Diophantine Inequalities. Cambridge University Press; 2005. doi:10.1017/CBO9780511542893
apa: Davenport, H., & Browning, T. D. (2005). Analytic Methods for Diophantine
Equations and Diophantine Inequalities. Cambridge University Press. https://doi.org/10.1017/CBO9780511542893
chicago: Davenport, Harold, and Timothy D Browning. Analytic Methods for Diophantine
Equations and Diophantine Inequalities. Cambridge University Press, 2005.
https://doi.org/10.1017/CBO9780511542893.
ieee: H. Davenport and T. D. Browning, Analytic Methods for Diophantine Equations
and Diophantine Inequalities. Cambridge University Press, 2005.
ista: Davenport H, Browning TD. 2005. Analytic Methods for Diophantine Equations
and Diophantine Inequalities, Cambridge University Press, 140p.
mla: Davenport, Harold, and Timothy D. Browning. Analytic Methods for Diophantine
Equations and Diophantine Inequalities. Cambridge University Press, 2005,
doi:10.1017/CBO9780511542893.
short: H. Davenport, T.D. Browning, Analytic Methods for Diophantine Equations and
Diophantine Inequalities, Cambridge University Press, 2005.
date_created: 2018-12-11T11:45:13Z
date_published: 2005-03-03T00:00:00Z
date_updated: 2021-12-21T11:02:25Z
day: '03'
doi: 10.1017/CBO9780511542893
extern: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: '140'
publication_identifier:
eisbn:
- 9-780-5115-4289-3
publication_status: published
publisher: Cambridge University Press
publist_id: '7702'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Analytic Methods for Diophantine Equations and Diophantine Inequalities
type: book
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2005'
...
---
_id: '211'
abstract:
- lang: eng
text: Let f ∈ ℤ[x] be a polynomial of degree d. The paucity of non-trivial positive
integer solutions to the equation f(x1)+f(x 2)=f(x3)+f(x4) is established, provided
that d ≤ 7$. Also the corresponding situation is investigated for equal sums of
three like polynomials.
acknowledgement: grant number GR/R93155/01
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Browning TD. Equal sums of like polynomials. Bulletin of the London Mathematical
Society. 2005;37(6):801-808. doi:10.1112/S0024609305004741
apa: Browning, T. D. (2005). Equal sums of like polynomials. Bulletin of the
London Mathematical Society. John Wiley and Sons Ltd. https://doi.org/10.1112/S0024609305004741
chicago: Browning, Timothy D. “Equal Sums of like Polynomials.” Bulletin of the
London Mathematical Society. John Wiley and Sons Ltd, 2005. https://doi.org/10.1112/S0024609305004741.
ieee: T. D. Browning, “Equal sums of like polynomials,” Bulletin of the London
Mathematical Society, vol. 37, no. 6. John Wiley and Sons Ltd, pp. 801–808,
2005.
ista: Browning TD. 2005. Equal sums of like polynomials. Bulletin of the London
Mathematical Society. 37(6), 801–808.
mla: Browning, Timothy D. “Equal Sums of like Polynomials.” Bulletin of the London
Mathematical Society, vol. 37, no. 6, John Wiley and Sons Ltd, 2005, pp. 801–08,
doi:10.1112/S0024609305004741.
short: T.D. Browning, Bulletin of the London Mathematical Society 37 (2005) 801–808.
date_created: 2018-12-11T11:45:14Z
date_published: 2005-12-01T00:00:00Z
date_updated: 2021-01-12T06:55:22Z
day: '01'
doi: 10.1112/S0024609305004741
extern: 1
intvolume: ' 37'
issue: '6'
month: '12'
page: 801 - 808
publication: Bulletin of the London Mathematical Society
publication_status: published
publisher: John Wiley and Sons Ltd
publist_id: '7700'
quality_controlled: 0
status: public
title: Equal sums of like polynomials
type: journal_article
volume: 37
year: '2005'
...
---
_id: '212'
abstract:
- lang: eng
text: For any n ≧ 2, let F ∈ ℤ [ x 1, … , xn ] be a form of degree d≧ 2, which produces
a geometrically irreducible hypersurface in ℙn–1. This paper is concerned with
the number N(F;B) of rational points on F = 0 which have height at most B. For
any ε > 0 we establish the estimate N(F; B) = O(B n− 2+ ε ), whenever either
n ≦ 5 or the hypersurface is not a union of lines. Here the implied constant depends
at most upon d, n and ε.
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Roger
full_name: Heath-Brown, Roger
last_name: Heath Brown
citation:
ama: Browning TD, Heath Brown R. Counting rational points on hypersurfaces. Journal
fur die Reine und Angewandte Mathematik. 2005;(584):83-115. doi:https://doi.org/10.1515/crll.2005.2005.584.83
apa: Browning, T. D., & Heath Brown, R. (2005). Counting rational points on
hypersurfaces. Journal Fur Die Reine Und Angewandte Mathematik. Walter
de Gruyter and Co . https://doi.org/10.1515/crll.2005.2005.584.83
chicago: Browning, Timothy D, and Roger Heath Brown. “Counting Rational Points on
Hypersurfaces.” Journal Fur Die Reine Und Angewandte Mathematik. Walter
de Gruyter and Co , 2005. https://doi.org/10.1515/crll.2005.2005.584.83.
ieee: T. D. Browning and R. Heath Brown, “Counting rational points on hypersurfaces,”
Journal fur die Reine und Angewandte Mathematik, no. 584. Walter de Gruyter
and Co , pp. 83–115, 2005.
ista: Browning TD, Heath Brown R. 2005. Counting rational points on hypersurfaces.
Journal fur die Reine und Angewandte Mathematik. (584), 83–115.
mla: Browning, Timothy D., and Roger Heath Brown. “Counting Rational Points on Hypersurfaces.”
Journal Fur Die Reine Und Angewandte Mathematik, no. 584, Walter de Gruyter
and Co , 2005, pp. 83–115, doi:https://doi.org/10.1515/crll.2005.2005.584.83.
short: T.D. Browning, R. Heath Brown, Journal Fur Die Reine Und Angewandte Mathematik
(2005) 83–115.
date_created: 2018-12-11T11:45:14Z
date_published: 2005-11-26T00:00:00Z
date_updated: 2021-01-12T06:55:25Z
day: '26'
doi: https://doi.org/10.1515/crll.2005.2005.584.83
extern: 1
issue: '584'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0707.2296
month: '11'
oa: 1
page: 83 - 115
publication: Journal fur die Reine und Angewandte Mathematik
publication_status: published
publisher: 'Walter de Gruyter and Co '
publist_id: '7701'
quality_controlled: 0
status: public
title: Counting rational points on hypersurfaces
type: journal_article
year: '2005'
...
---
_id: '214'
abstract:
- lang: eng
text: Given an absolutely irreducible ternary form F, the purpose of this paper
is to produce better upper bounds for the number of integer solutions to the equation
F=0, that are restricted to lie in very lopsided boxes. As an application of the
main result, a new paucity estimate is obtained for equal sums of two like powers.
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Roger
full_name: Heath-Brown, Roger
last_name: Heath Brown
citation:
ama: Browning TD, Heath Brown R. Plane curves in boxes and equal sums of two powers.
Mathematische Zeitschrift. 2005;251(2):233-247. doi:10.1007/s00209-004-0719-z
apa: Browning, T. D., & Heath Brown, R. (2005). Plane curves in boxes and equal
sums of two powers. Mathematische Zeitschrift. Unknown. https://doi.org/10.1007/s00209-004-0719-z
chicago: Browning, Timothy D, and Roger Heath Brown. “Plane Curves in Boxes and
Equal Sums of Two Powers.” Mathematische Zeitschrift. Unknown, 2005. https://doi.org/10.1007/s00209-004-0719-z.
ieee: T. D. Browning and R. Heath Brown, “Plane curves in boxes and equal sums of
two powers,” Mathematische Zeitschrift, vol. 251, no. 2. Unknown, pp. 233–247,
2005.
ista: Browning TD, Heath Brown R. 2005. Plane curves in boxes and equal sums of
two powers. Mathematische Zeitschrift. 251(2), 233–247.
mla: Browning, Timothy D., and Roger Heath Brown. “Plane Curves in Boxes and Equal
Sums of Two Powers.” Mathematische Zeitschrift, vol. 251, no. 2, Unknown,
2005, pp. 233–47, doi:10.1007/s00209-004-0719-z.
short: T.D. Browning, R. Heath Brown, Mathematische Zeitschrift 251 (2005) 233–247.
date_created: 2018-12-11T11:45:15Z
date_published: 2005-09-01T00:00:00Z
date_updated: 2021-01-12T06:55:33Z
day: '01'
doi: 10.1007/s00209-004-0719-z
extern: 1
intvolume: ' 251'
issue: '2'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/math/0506497
month: '09'
oa: 1
page: 233 - 247
publication: Mathematische Zeitschrift
publication_status: published
publisher: Unknown
publist_id: '7699'
quality_controlled: 0
status: public
title: Plane curves in boxes and equal sums of two powers
type: journal_article
volume: 251
year: '2005'
...