---
_id: '908'
abstract:
- lang: eng
text: Although some data link archaeal and eukaryotic translation, the overall mechanism
of protein synthesis in archaea remains largely obscure. Both archaeal (aRF1)
and eukaryotic (eRF1) single release factors recognize all three stop codons.
The archaeal genus Methanosarcinaceae contains two aRF1 homologs, and also uses
the UAG stop to encode the 22nd amino acid, pyrrolysine. Here we provide an analysis
of the last stage of archaeal translation in pyrrolysine-utilizing species. We
demonstrated that only one of two Methanosarcina barkeri aRF1 homologs possesses
activity and recognizes all three stop codons. The second aRF1 homolog may have
another unknown function. The mechanism of pyrrolysine incorporation in the Methanosarcinaceae
is discussed.
acknowledgement: We are grateful to Andrey Poltaraus and his colleagues for sequencing
a/eRF1 genes. We thank Tatyana Pestova and Chris Hellen for the gift of plasmids
encoding initiation factors eIF1, eIF1A, eIF4A, eIF4B, eIF4G, eIF5, eIF5B, and Anna
Yaremchuk and Michael Tukalo for M. jannaschii aRF1. This work was supported by
grants from the Presidium of the (Program Molecular and Cell Biology), the Russian
Foundation for Basic Research (08-04-01091-а to E.A. and 08-04-00375a to L.F.),
the National Institute for General Medical Sciences (to D.S.), the National Science
Foundation (to D.S.) and the Office of Basic Energy Sciences, DOE (to D.S.).
author:
- first_name: Elena
full_name: Alkalaeva, Elena Z
last_name: Alkalaeva
- first_name: Boris
full_name: Eliseev, Boris D
last_name: Eliseev
- first_name: Alexandre
full_name: Ambrogelly, Alexandre
last_name: Ambrogelly
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Sarath
full_name: Gundllapalli, Sarath B
last_name: Gundllapalli
- first_name: Ludmila
full_name: Frolova, Ludmila Y
last_name: Frolova
- first_name: Dieter
full_name: Söll, Dieter G
last_name: Söll
- first_name: Lev
full_name: Kisselev, Lev L
last_name: Kisselev
citation:
ama: Alkalaeva E, Eliseev B, Ambrogelly A, et al. Translation termination in pyrrolysine-utilizing
archaea. FEBS Letters. 2009;583(21):3455-3460. doi:10.1016/j.febslet.2009.09.044
apa: Alkalaeva, E., Eliseev, B., Ambrogelly, A., Vlasov, P., Kondrashov, F., Gundllapalli,
S., … Kisselev, L. (2009). Translation termination in pyrrolysine-utilizing archaea.
FEBS Letters. Elsevier. https://doi.org/10.1016/j.febslet.2009.09.044
chicago: Alkalaeva, Elena, Boris Eliseev, Alexandre Ambrogelly, Peter Vlasov, Fyodor
Kondrashov, Sarath Gundllapalli, Ludmila Frolova, Dieter Söll, and Lev Kisselev.
“Translation Termination in Pyrrolysine-Utilizing Archaea.” FEBS Letters.
Elsevier, 2009. https://doi.org/10.1016/j.febslet.2009.09.044.
ieee: E. Alkalaeva et al., “Translation termination in pyrrolysine-utilizing
archaea,” FEBS Letters, vol. 583, no. 21. Elsevier, pp. 3455–3460, 2009.
ista: Alkalaeva E, Eliseev B, Ambrogelly A, Vlasov P, Kondrashov F, Gundllapalli
S, Frolova L, Söll D, Kisselev L. 2009. Translation termination in pyrrolysine-utilizing
archaea. FEBS Letters. 583(21), 3455–3460.
mla: Alkalaeva, Elena, et al. “Translation Termination in Pyrrolysine-Utilizing
Archaea.” FEBS Letters, vol. 583, no. 21, Elsevier, 2009, pp. 3455–60,
doi:10.1016/j.febslet.2009.09.044.
short: E. Alkalaeva, B. Eliseev, A. Ambrogelly, P. Vlasov, F. Kondrashov, S. Gundllapalli,
L. Frolova, D. Söll, L. Kisselev, FEBS Letters 583 (2009) 3455–3460.
date_created: 2018-12-11T11:49:08Z
date_published: 2009-11-03T00:00:00Z
date_updated: 2021-01-12T08:21:49Z
day: '03'
doi: 10.1016/j.febslet.2009.09.044
extern: 1
intvolume: ' 583'
issue: '21'
month: '11'
page: 3455 - 3460
publication: FEBS Letters
publication_status: published
publisher: Elsevier
publist_id: '6740'
quality_controlled: 0
status: public
title: Translation termination in pyrrolysine-utilizing archaea
type: journal_article
volume: 583
year: '2009'
...
---
_id: '9147'
abstract:
- lang: eng
text: As part of an ongoing effort to develop a parameterization of wave-induced
abyssal mixing, the authors derive an heuristic model for nonlinear wave breaking
and energy dissipation associated with internal tides. Then the saturation and
dissipation of internal tides for idealized and observed topography samples are
investigated. One of the main results is that the wave-induced mixing could be
more intense and more confined to the bottom than previously assumed in numerical
models. Furthermore, in this model wave breaking and mixing clearly depend on
the small scales of the topography below 10 km or so, which is below the current
resolution of global bathymetry. This motivates the use of a statistical approach
to represent the unresolved topography when addressing the role of internal tides
in mixing the deep ocean.
article_processing_charge: No
article_type: original
author:
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Oliver
full_name: Bühler, Oliver
last_name: Bühler
citation:
ama: Muller CJ, Bühler O. Saturation of the internal tides and induced mixing in
the abyssal ocean. Journal of Physical Oceanography. 2009;39(9):2077-2096.
doi:10.1175/2009jpo4141.1
apa: Muller, C. J., & Bühler, O. (2009). Saturation of the internal tides and
induced mixing in the abyssal ocean. Journal of Physical Oceanography.
American Meteorological Society. https://doi.org/10.1175/2009jpo4141.1
chicago: Muller, Caroline J, and Oliver Bühler. “Saturation of the Internal Tides
and Induced Mixing in the Abyssal Ocean.” Journal of Physical Oceanography.
American Meteorological Society, 2009. https://doi.org/10.1175/2009jpo4141.1.
ieee: C. J. Muller and O. Bühler, “Saturation of the internal tides and induced
mixing in the abyssal ocean,” Journal of Physical Oceanography, vol. 39,
no. 9. American Meteorological Society, pp. 2077–2096, 2009.
ista: Muller CJ, Bühler O. 2009. Saturation of the internal tides and induced mixing
in the abyssal ocean. Journal of Physical Oceanography. 39(9), 2077–2096.
mla: Muller, Caroline J., and Oliver Bühler. “Saturation of the Internal Tides and
Induced Mixing in the Abyssal Ocean.” Journal of Physical Oceanography,
vol. 39, no. 9, American Meteorological Society, 2009, pp. 2077–96, doi:10.1175/2009jpo4141.1.
short: C.J. Muller, O. Bühler, Journal of Physical Oceanography 39 (2009) 2077–2096.
date_created: 2021-02-15T14:41:08Z
date_published: 2009-09-01T00:00:00Z
date_updated: 2022-01-24T13:50:37Z
day: '01'
doi: 10.1175/2009jpo4141.1
extern: '1'
intvolume: ' 39'
issue: '9'
keyword:
- Oceanography
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1175/2009JPO4141.1
month: '09'
oa: 1
oa_version: Published Version
page: 2077-2096
publication: Journal of Physical Oceanography
publication_identifier:
issn:
- 1520-0485
- 0022-3670
publication_status: published
publisher: American Meteorological Society
quality_controlled: '1'
status: public
title: Saturation of the internal tides and induced mixing in the abyssal ocean
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 39
year: '2009'
...
---
_id: '9148'
abstract:
- lang: eng
text: Several observational studies have shown a tight relationship between tropical
precipitation and column‐integrated water vapor. We show that the observed relationship
in the tropics between column‐integrated water vapor, precipitation, and its variance
can be qualitatively reproduced by a simple and physically motivated two‐layer
model. It has previously been argued that features of this relationship could
be explained by analogy with the theory of continuous phase transitions. Instead,
our model explicitly assumes that the onset of precipitation is governed by a
stability threshold involving boundary‐layer water vapor. This allows us to explain
the precipitation‐humidity relationship over a broader range of water vapor values,
and may explain the observed temperature dependence of the relationship.
article_number: L16804
article_processing_charge: No
article_type: original
author:
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Larissa E.
full_name: Back, Larissa E.
last_name: Back
- first_name: Paul A.
full_name: O'Gorman, Paul A.
last_name: O'Gorman
- first_name: Kerry A.
full_name: Emanuel, Kerry A.
last_name: Emanuel
citation:
ama: Muller CJ, Back LE, O’Gorman PA, Emanuel KA. A model for the relationship between
tropical precipitation and column water vapor. Geophysical Research Letters.
2009;36(16). doi:10.1029/2009gl039667
apa: Muller, C. J., Back, L. E., O’Gorman, P. A., & Emanuel, K. A. (2009). A
model for the relationship between tropical precipitation and column water vapor.
Geophysical Research Letters. American Geophysical Union. https://doi.org/10.1029/2009gl039667
chicago: Muller, Caroline J, Larissa E. Back, Paul A. O’Gorman, and Kerry A. Emanuel.
“A Model for the Relationship between Tropical Precipitation and Column Water
Vapor.” Geophysical Research Letters. American Geophysical Union, 2009.
https://doi.org/10.1029/2009gl039667.
ieee: C. J. Muller, L. E. Back, P. A. O’Gorman, and K. A. Emanuel, “A model for
the relationship between tropical precipitation and column water vapor,” Geophysical
Research Letters, vol. 36, no. 16. American Geophysical Union, 2009.
ista: Muller CJ, Back LE, O’Gorman PA, Emanuel KA. 2009. A model for the relationship
between tropical precipitation and column water vapor. Geophysical Research Letters.
36(16), L16804.
mla: Muller, Caroline J., et al. “A Model for the Relationship between Tropical
Precipitation and Column Water Vapor.” Geophysical Research Letters, vol.
36, no. 16, L16804, American Geophysical Union, 2009, doi:10.1029/2009gl039667.
short: C.J. Muller, L.E. Back, P.A. O’Gorman, K.A. Emanuel, Geophysical Research
Letters 36 (2009).
date_created: 2021-02-15T14:41:28Z
date_published: 2009-08-25T00:00:00Z
date_updated: 2022-01-24T13:50:15Z
day: '25'
doi: 10.1029/2009gl039667
extern: '1'
intvolume: ' 36'
issue: '16'
keyword:
- General Earth and Planetary Sciences
- Geophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1029/2009GL039667
month: '08'
oa: 1
oa_version: Published Version
publication: Geophysical Research Letters
publication_identifier:
issn:
- 0094-8276
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
status: public
title: A model for the relationship between tropical precipitation and column water
vapor
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 36
year: '2009'
...
---
_id: '9453'
abstract:
- lang: eng
text: Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis
thaliana endosperm by cytosine demethylation of the maternal genome mediated by
the DNA glycosylase DEMETER, but the extent of the methylation changes is not
known. Here, we show that virtually the entire endosperm genome is demethylated,
coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted
sequences. Mutation of DEMETER partially restores endosperm CG methylation to
levels found in other tissues, indicating that CG demethylation is specific to
maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation
of embryo transposable elements. Our findings demonstrate extensive reconfiguration
of the endosperm methylation landscape that likely reinforces transposon silencing
in the embryo.
article_processing_charge: No
article_type: original
author:
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Christian A.
full_name: Ibarra, Christian A.
last_name: Ibarra
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: Leor
full_name: Eshed-Williams, Leor
last_name: Eshed-Williams
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Hsieh T-F, Ibarra CA, Silva P, et al. Genome-wide demethylation of Arabidopsis
endosperm. Science. 2009;324(5933):1451-1454. doi:10.1126/science.1172417
apa: Hsieh, T.-F., Ibarra, C. A., Silva, P., Zemach, A., Eshed-Williams, L., Fischer,
R. L., & Zilberman, D. (2009). Genome-wide demethylation of Arabidopsis endosperm.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1172417
chicago: Hsieh, Tzung-Fu, Christian A. Ibarra, Pedro Silva, Assaf Zemach, Leor Eshed-Williams,
Robert L. Fischer, and Daniel Zilberman. “Genome-Wide Demethylation of Arabidopsis
Endosperm.” Science. American Association for the Advancement of Science,
2009. https://doi.org/10.1126/science.1172417.
ieee: T.-F. Hsieh et al., “Genome-wide demethylation of Arabidopsis endosperm,”
Science, vol. 324, no. 5933. American Association for the Advancement of
Science, pp. 1451–1454, 2009.
ista: Hsieh T-F, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman
D. 2009. Genome-wide demethylation of Arabidopsis endosperm. Science. 324(5933),
1451–1454.
mla: Hsieh, Tzung-Fu, et al. “Genome-Wide Demethylation of Arabidopsis Endosperm.”
Science, vol. 324, no. 5933, American Association for the Advancement of
Science, 2009, pp. 1451–54, doi:10.1126/science.1172417.
short: T.-F. Hsieh, C.A. Ibarra, P. Silva, A. Zemach, L. Eshed-Williams, R.L. Fischer,
D. Zilberman, Science 324 (2009) 1451–1454.
date_created: 2021-06-04T08:55:41Z
date_published: 2009-06-12T00:00:00Z
date_updated: 2021-12-14T08:53:26Z
day: '12'
department:
- _id: DaZi
doi: 10.1126/science.1172417
extern: '1'
external_id:
pmid:
- '19520962'
intvolume: ' 324'
issue: '5933'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4044190/
month: '06'
oa: 1
oa_version: Submitted Version
page: 1451-1454
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome-wide demethylation of Arabidopsis endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 324
year: '2009'
...
---
_id: '964'
abstract:
- lang: eng
text: A theory of the fluctuation-induced Nernst efl'ect is developed for a two-dimensional
superconductor in a perpendicular magnetic field. First, we derive a simple phenomenological
formula for the Nernst coefficient, which naturally explains the giant Nernst
signal due to fluctuating Cooper pairs. The latter signal is shown to be large
even far from the transition and may exceed by orders of magnitude the Fermi liquid
terms. We also present a complete microscopic calculation of the Nernst coefficient
for arbitrary magnetic fields and temperatures, which is based on the standard
definition of heat current vertices. It is shown that the magnitude and the behavior
of the Nernst signal observed experimentally in disordered superconducting films
can be well understood on the basis of superconducting fluctuation theory.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Mikhail
full_name: Skvortsov, Mikhail A
last_name: Skvortsov
- first_name: Andrei
full_name: Varlamov, Andrei A
last_name: Varlamov
- first_name: Victor
full_name: Galitski, Victor M
last_name: Galitski
citation:
ama: 'Serbyn M, Skvortsov M, Varlamov A, Galitski V. Giant nernst effect due to
fluctuating cooper Pairs in superconductors. In: Vol 1134. American Institute
of Physics; 2009:140-145. doi:10.1063/1.3149485'
apa: Serbyn, M., Skvortsov, M., Varlamov, A., & Galitski, V. (2009). Giant nernst
effect due to fluctuating cooper Pairs in superconductors (Vol. 1134, pp. 140–145).
Presented at the Landau Memorial Conference on Advances in Theoretical Physics,
American Institute of Physics. https://doi.org/10.1063/1.3149485
chicago: Serbyn, Maksym, Mikhail Skvortsov, Andrei Varlamov, and Victor Galitski.
“Giant Nernst Effect Due to Fluctuating Cooper Pairs in Superconductors,” 1134:140–45.
American Institute of Physics, 2009. https://doi.org/10.1063/1.3149485.
ieee: M. Serbyn, M. Skvortsov, A. Varlamov, and V. Galitski, “Giant nernst effect
due to fluctuating cooper Pairs in superconductors,” presented at the Landau Memorial
Conference on Advances in Theoretical Physics, 2009, vol. 1134, pp. 140–145.
ista: Serbyn M, Skvortsov M, Varlamov A, Galitski V. 2009. Giant nernst effect due
to fluctuating cooper Pairs in superconductors. Landau Memorial Conference on
Advances in Theoretical Physics vol. 1134, 140–145.
mla: Serbyn, Maksym, et al. Giant Nernst Effect Due to Fluctuating Cooper Pairs
in Superconductors. Vol. 1134, American Institute of Physics, 2009, pp. 140–45,
doi:10.1063/1.3149485.
short: M. Serbyn, M. Skvortsov, A. Varlamov, V. Galitski, in:, American Institute
of Physics, 2009, pp. 140–145.
conference:
name: Landau Memorial Conference on Advances in Theoretical Physics
date_created: 2018-12-11T11:49:26Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T08:22:17Z
day: '01'
doi: 10.1063/1.3149485
extern: 1
intvolume: ' 1134'
month: '01'
page: 140 - 145
publication_status: published
publisher: American Institute of Physics
publist_id: '6435'
quality_controlled: 0
status: public
title: Giant nernst effect due to fluctuating cooper Pairs in superconductors
type: conference
volume: 1134
year: '2009'
...
---
_id: '1038'
abstract:
- lang: eng
text: One possible way to produce ultra-cold, high-phase-space-density quantum gases
of molecules in the rovibronic ground state is given by molecule association from
quantum-degenerate atomic gases on a Feshbach resonance and subsequent coherent
optical multi-photon transfer into the rovibronic ground state. In ultra-cold
samples of Cs2 molecules, we observe two-photon dark resonances that connect the
intermediate rovibrational level |v=73,J=2 with the rovibrational ground state
|v=0,J=0 of the singlet X 1 ∑ g + ground-state potential. For precise dark resonance
spectroscopy we exploit the fact that it is possible to efficiently populate the
level |v=73,J=2 by two-photon transfer from the dissociation threshold with the
stimulated Raman adiabatic passage (STIRAP) technique. We find that at least one
of the two-photon resonances is sufficiently strong to allow future implementation
of coherent STIRAP transfer of a molecular quantum gas to the rovibrational ground
state |v=0,J=0.
acknowledgement: "We are indebted to R. Grimm for generous support and we thank E.
Tiemann for valuable discussions and C. Amiot for providing the FTS data of LAC
on Cs2. We gratefully acknowledge funding by the Austrian Ministry of Science and
Research (BMWF)\r\nand the Austrian Science Fund (FWF) in the form of a START prize
grant and by the European Science Foundation (ESF) in the framework of the EuroQUAM
collective research project QuDipMol. R.H. acknowledges support by the European
Union in the form of a Marie Curie International Incoming Fellowship (IIF). The
work at Stony Brook was supported by the US NSF, under grant PHY0652459."
article_processing_charge: No
arxiv: 1
author:
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Mattias
full_name: Gustavsson, Mattias
last_name: Gustavsson
- first_name: Nadia
full_name: Bouloufa, Nadia
last_name: Bouloufa
- first_name: Olivier
full_name: Dulieu, Olivier
last_name: Dulieu
- first_name: Houssam
full_name: Salami, Houssam
last_name: Salami
- first_name: Thomas
full_name: Bergeman, Thomas
last_name: Bergeman
- first_name: Helmut
full_name: Ritsch, Helmut
last_name: Ritsch
- first_name: Russell
full_name: Hart, Russell
last_name: Hart
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: 'Mark M, Danzl JG, Haller E, et al. Dark resonances for ground-state transfer
of molecular quantum gases. Applied Physics B: Lasers and Optics. 2009;95(2):219-225.
doi:10.1007/s00340-009-3407-1'
apa: 'Mark, M., Danzl, J. G., Haller, E., Gustavsson, M., Bouloufa, N., Dulieu,
O., … Nägerl, H. (2009). Dark resonances for ground-state transfer of molecular
quantum gases. Applied Physics B: Lasers and Optics. Springer. https://doi.org/10.1007/s00340-009-3407-1'
chicago: 'Mark, Manfred, Johann G Danzl, Elmar Haller, Mattias Gustavsson, Nadia
Bouloufa, Olivier Dulieu, Houssam Salami, et al. “Dark Resonances for Ground-State
Transfer of Molecular Quantum Gases.” Applied Physics B: Lasers and Optics.
Springer, 2009. https://doi.org/10.1007/s00340-009-3407-1.'
ieee: 'M. Mark et al., “Dark resonances for ground-state transfer of molecular
quantum gases,” Applied Physics B: Lasers and Optics, vol. 95, no. 2. Springer,
pp. 219–225, 2009.'
ista: 'Mark M, Danzl JG, Haller E, Gustavsson M, Bouloufa N, Dulieu O, Salami H,
Bergeman T, Ritsch H, Hart R, Nägerl H. 2009. Dark resonances for ground-state
transfer of molecular quantum gases. Applied Physics B: Lasers and Optics. 95(2),
219–225.'
mla: 'Mark, Manfred, et al. “Dark Resonances for Ground-State Transfer of Molecular
Quantum Gases.” Applied Physics B: Lasers and Optics, vol. 95, no. 2, Springer,
2009, pp. 219–25, doi:10.1007/s00340-009-3407-1.'
short: 'M. Mark, J.G. Danzl, E. Haller, M. Gustavsson, N. Bouloufa, O. Dulieu, H.
Salami, T. Bergeman, H. Ritsch, R. Hart, H. Nägerl, Applied Physics B: Lasers
and Optics 95 (2009) 219–225.'
date_created: 2018-12-11T11:49:49Z
date_published: 2009-05-01T00:00:00Z
date_updated: 2021-01-12T06:47:50Z
day: '01'
doi: 10.1007/s00340-009-3407-1
extern: '1'
external_id:
arxiv:
- '0811.0695'
intvolume: ' 95'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0811.0695
month: '05'
oa: 1
oa_version: None
page: 219 - 225
publication: 'Applied Physics B: Lasers and Optics'
publication_status: published
publisher: Springer
publist_id: '6350'
status: public
title: Dark resonances for ground-state transfer of molecular quantum gases
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 95
year: '2009'
...
---
_id: '1040'
abstract:
- lang: eng
text: Ultracold atomic physics offers myriad possibilities to study strongly correlated
many-body systems in lower dimensions. Typically, only ground-state phases are
accessible. Using a tunable quantum gas of bosonic cesium atoms, we realized and
controlled in one-dimensional geometry a highly excited quantum phase that is
stabilized in the presence of attractive interactions by maintaining and strengthening
quantum correlations across a confinement-induced resonance. We diagnosed the
crossover from repulsive to attractive interactions in terms of the stiffness
and energy of the system. Our results open up the experimental study of metastable,
excited, many-body phases with strong correlations and their dynamical properties.
acknowledgement: We thank S. Giorgini and C. Menotti for helpful discussions and for
providing the theory curves shown in Fig. 3A. We are indebted to R. Grimm for generous
support and to H. Häffner and his group for the loan of a charge-coupled device
camera. We gratefully acknowledge funding by the Austrian Ministry of Science and
Research (Bundesministerium für Wissenschaft und Forschung) and the Austrian Science
Fund (Fonds zur Förderung der wissenschaftlichen Forschung) in the form of a START
prize grant and by the European Union through the Specific Targeted Research Project
FP7-ICT-2007-C project NAME-QUAM (Nanodesigning of Atomic and Molecular Quantum
Matter) and within the framework of the EuroQUASAR collective research project Quantum-Degenerate
Gases for Precision Measurements. R.H. is supported by a Marie Curie International
Incoming Fellowship within the 7th European Community Framework Programme.
article_processing_charge: No
arxiv: 1
author:
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Mattias
full_name: Gustavsson, Mattias
last_name: Gustavsson
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Russell
full_name: Hart, Russell
last_name: Hart
- first_name: Guido
full_name: Pupillo, Guido
last_name: Pupillo
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: Haller E, Gustavsson M, Mark M, et al. Realization of an excited, strongly
correlated quantum gas Phase. Science. 2009;325(5945):1224-1227. doi:10.1126/science.1175850
apa: Haller, E., Gustavsson, M., Mark, M., Danzl, J. G., Hart, R., Pupillo, G.,
& Nägerl, H. (2009). Realization of an excited, strongly correlated quantum
gas Phase. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.1175850
chicago: Haller, Elmar, Mattias Gustavsson, Manfred Mark, Johann G Danzl, Russell
Hart, Guido Pupillo, and Hanns Nägerl. “Realization of an Excited, Strongly Correlated
Quantum Gas Phase.” Science. American Association for the Advancement of
Science, 2009. https://doi.org/10.1126/science.1175850.
ieee: E. Haller et al., “Realization of an excited, strongly correlated quantum
gas Phase,” Science, vol. 325, no. 5945. American Association for the Advancement
of Science, pp. 1224–1227, 2009.
ista: Haller E, Gustavsson M, Mark M, Danzl JG, Hart R, Pupillo G, Nägerl H. 2009.
Realization of an excited, strongly correlated quantum gas Phase. Science. 325(5945),
1224–1227.
mla: Haller, Elmar, et al. “Realization of an Excited, Strongly Correlated Quantum
Gas Phase.” Science, vol. 325, no. 5945, American Association for the Advancement
of Science, 2009, pp. 1224–27, doi:10.1126/science.1175850.
short: E. Haller, M. Gustavsson, M. Mark, J.G. Danzl, R. Hart, G. Pupillo, H. Nägerl,
Science 325 (2009) 1224–1227.
date_created: 2018-12-11T11:49:50Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T06:47:51Z
day: '01'
doi: 10.1126/science.1175850
extern: '1'
external_id:
arxiv:
- '1006.0739'
intvolume: ' 325'
issue: '5945'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1006.0739
month: '01'
oa: 1
oa_version: None
page: 1224 - 1227
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6348'
status: public
title: Realization of an excited, strongly correlated quantum gas Phase
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 325
year: '2009'
...
---
_id: '1041'
abstract:
- lang: eng
text: We demonstrate efficient transfer of ultracold molecules into a deeply bound
rovibrational level of the singlet ground state potential in the presence of an
optical lattice. The overall molecule creation efficiency is 25%, and the transfer
efficiency to the rovibrational level |v = 73, J = 2) is above 80%. We find that
the molecules in |v = 73, J = 2) are trapped in the optical lattice, and that
the lifetime in the lattice is limited by optical excitation by the lattice light.
The molecule trapping time for a lattice depth of 15 atomic recoil energies is
about 20 ms. We determine the trapping frequency by the lattice phase and amplitude
modulation technique. It will now be possible to transfer the molecules to the
rovibrational ground state |v = 0, J = 0) in the presence of the optical lattice.
acknowledgement: We are indebted to R Grimm for generous support and we thank S Knoop,
N Boloufa, and O Dulieu for valuable discussions. We gratefully acknowledge funding
by the Austrian Ministry of Science and Research (BMWF) and the Austrian Science
Fund (FWF) in the form of a START prize grant. RH acknowledges support by the European
Union in the form of a Marie-Curie International Incoming Fellowship (IIF).
article_processing_charge: No
arxiv: 1
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Mattias
full_name: Gustavsson, Mattias
last_name: Gustavsson
- first_name: Russell
full_name: Hart, Russell
last_name: Hart
- first_name: Andreas
full_name: Liem, Andreas
last_name: Liem
- first_name: Holger
full_name: Zellmer, Holger
last_name: Zellmer
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: Danzl JG, Mark M, Haller E, et al. Deeply bound ultracold molecules in an optical
lattice. New Journal of Physics. 2009;11. doi:10.1088/1367-2630/11/5/055036
apa: Danzl, J. G., Mark, M., Haller, E., Gustavsson, M., Hart, R., Liem, A., … Nägerl,
H. (2009). Deeply bound ultracold molecules in an optical lattice. New Journal
of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/11/5/055036
chicago: Danzl, Johann G, Manfred Mark, Elmar Haller, Mattias Gustavsson, Russell
Hart, Andreas Liem, Holger Zellmer, and Hanns Nägerl. “Deeply Bound Ultracold
Molecules in an Optical Lattice.” New Journal of Physics. IOP Publishing
Ltd., 2009. https://doi.org/10.1088/1367-2630/11/5/055036.
ieee: J. G. Danzl et al., “Deeply bound ultracold molecules in an optical
lattice,” New Journal of Physics, vol. 11. IOP Publishing Ltd., 2009.
ista: Danzl JG, Mark M, Haller E, Gustavsson M, Hart R, Liem A, Zellmer H, Nägerl
H. 2009. Deeply bound ultracold molecules in an optical lattice. New Journal of
Physics. 11.
mla: Danzl, Johann G., et al. “Deeply Bound Ultracold Molecules in an Optical Lattice.”
New Journal of Physics, vol. 11, IOP Publishing Ltd., 2009, doi:10.1088/1367-2630/11/5/055036.
short: J.G. Danzl, M. Mark, E. Haller, M. Gustavsson, R. Hart, A. Liem, H. Zellmer,
H. Nägerl, New Journal of Physics 11 (2009).
date_created: 2018-12-11T11:49:50Z
date_published: 2009-03-14T00:00:00Z
date_updated: 2021-01-12T06:47:51Z
day: '14'
doi: 10.1088/1367-2630/11/5/055036
extern: '1'
external_id:
arxiv:
- '0812.5070'
intvolume: ' 11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0812.5070
month: '03'
oa: 1
oa_version: None
publication: New Journal of Physics
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '6349'
status: public
title: Deeply bound ultracold molecules in an optical lattice
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2009'
...
---
_id: '1043'
abstract:
- lang: eng
text: One possibility for the creation of ultracold, high phase space density quantum
gases of molecules in the rovibronic ground state relies on first associating
weakly-bound molecules from quantum-degenerate atomic gases on a Feshbach resonance
and then transferring the molecules via several steps of coherent two-photon stimulated
Raman adiabatic passage (STIRAP) into the rovibronic ground state. Here, in ultracold
samples of Cs2 Feshbach molecules produced out of ultracold samples of Cs atoms,
we observe several optical transitions to deeply-bound rovibrational levels of
the excited 0 u+ molecular potentials with high resolution. At least one of these
transitions, although rather weak, allows efficient STIRAP transfer into the deeply-bound
vibrational level v = 73> of the singlet X 1Σg+ ground state potential, as
recently demonstrated (J. G. Danzl, E. Haller, M. Gustavsson, M. J. Mark, R. Hart,
N. Bouloufa, O. Dulieu, H. Ritsch, and H.-C. Nägerl, Science, 2008, 321, 1062).
From this level, the rovibrational ground state v = 0, J = 0> can be reached
with one more transfer step. In total, our results show that coherent ground state
transfer for Cs2 is possible using a maximum of two successive two-photon STIRAP
processes or one single four-photon STIRAP process.
acknowledgement: "We are indebted to R. Grimm for generous support and we thank T.
Bergeman, H.\r\nSalami, J. Hutson, J. Aldegunde, and E. Tiemann for valuable discussions.
We\r\ngratefully acknowledge funding by the Austrian Ministry of Science and Research\r\n(BMWF)
and the Austrian Science Fund (FWF) in the form of a START prize grant\r\nand by
the European Science Foundation (ESF) in the framework of the EuroQUAM collective
research project QuDipMol. R. H. acknowledges support by\r\nthe European Union in
form of a Marie Curie International Incoming Fellowship\r\n(IIF)."
article_processing_charge: No
arxiv: 1
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Mattias
full_name: Gustavsson, Mattias
last_name: Gustavsson
- first_name: Nadia
full_name: Bouloufa, Nadia
last_name: Bouloufa
- first_name: Olivier
full_name: Dulieu, Olivier
last_name: Dulieu
- first_name: Helmut
full_name: Ritsch, Helmut
last_name: Ritsch
- first_name: Russell
full_name: Hart, Russell
last_name: Hart
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: Danzl JG, Mark M, Haller E, et al. Precision molecular spectroscopy for ground
state transfer of molecular quantum gases. Faraday Discussions. 2009;142:283-295.
doi:10.1039/b820542f
apa: Danzl, J. G., Mark, M., Haller, E., Gustavsson, M., Bouloufa, N., Dulieu, O.,
… Nägerl, H. (2009). Precision molecular spectroscopy for ground state transfer
of molecular quantum gases. Faraday Discussions. Royal Society of Chemistry.
https://doi.org/10.1039/b820542f
chicago: Danzl, Johann G, Manfred Mark, Elmar Haller, Mattias Gustavsson, Nadia
Bouloufa, Olivier Dulieu, Helmut Ritsch, Russell Hart, and Hanns Nägerl. “Precision
Molecular Spectroscopy for Ground State Transfer of Molecular Quantum Gases.”
Faraday Discussions. Royal Society of Chemistry, 2009. https://doi.org/10.1039/b820542f.
ieee: J. G. Danzl et al., “Precision molecular spectroscopy for ground state
transfer of molecular quantum gases,” Faraday Discussions, vol. 142. Royal
Society of Chemistry, pp. 283–295, 2009.
ista: Danzl JG, Mark M, Haller E, Gustavsson M, Bouloufa N, Dulieu O, Ritsch H,
Hart R, Nägerl H. 2009. Precision molecular spectroscopy for ground state transfer
of molecular quantum gases. Faraday Discussions. 142, 283–295.
mla: Danzl, Johann G., et al. “Precision Molecular Spectroscopy for Ground State
Transfer of Molecular Quantum Gases.” Faraday Discussions, vol. 142, Royal
Society of Chemistry, 2009, pp. 283–95, doi:10.1039/b820542f.
short: J.G. Danzl, M. Mark, E. Haller, M. Gustavsson, N. Bouloufa, O. Dulieu, H.
Ritsch, R. Hart, H. Nägerl, Faraday Discussions 142 (2009) 283–295.
date_created: 2018-12-11T11:49:51Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T06:47:52Z
day: '01'
doi: 10.1039/b820542f
extern: '1'
external_id:
arxiv:
- '0811.2374'
intvolume: ' 142'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0811.2374
month: '01'
oa: 1
oa_version: Preprint
page: 283 - 295
publication: Faraday Discussions
publication_status: published
publisher: Royal Society of Chemistry
publist_id: '6347'
status: public
title: Precision molecular spectroscopy for ground state transfer of molecular quantum
gases
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 142
year: '2009'
...
---
_id: '11799'
abstract:
- lang: eng
text: We study the problem of matching bidders to items where each bidder i has
general, strictly monotonic utility functions u i,j (p j ) expressing her utility
of being matched to item j at price p j . For this setting we prove that a bidder
optimal outcome always exists, even when the utility functions are non-linear
and non-continuous. Furthermore, we give an algorithm to find such a solution.
Although the running time of this algorithm is exponential in the number of items,
it is polynomial in the number of bidders.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Paul
full_name: Dütting, Paul
last_name: Dütting
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Ingmar
full_name: Weber, Ingmar
last_name: Weber
citation:
ama: 'Dütting P, Henzinger MH, Weber I. Bidder optimal assignments for general utilities.
In: 5th International Workshop on Internet and Network Economics. Vol 5929.
Springer Nature; 2009:575-582. doi:10.1007/978-3-642-10841-9_58'
apa: 'Dütting, P., Henzinger, M. H., & Weber, I. (2009). Bidder optimal assignments
for general utilities. In 5th International Workshop on Internet and Network
Economics (Vol. 5929, pp. 575–582). Rome, Italy: Springer Nature. https://doi.org/10.1007/978-3-642-10841-9_58'
chicago: Dütting, Paul, Monika H Henzinger, and Ingmar Weber. “Bidder Optimal Assignments
for General Utilities.” In 5th International Workshop on Internet and Network
Economics, 5929:575–82. Springer Nature, 2009. https://doi.org/10.1007/978-3-642-10841-9_58.
ieee: P. Dütting, M. H. Henzinger, and I. Weber, “Bidder optimal assignments for
general utilities,” in 5th International Workshop on Internet and Network Economics,
Rome, Italy, 2009, vol. 5929, pp. 575–582.
ista: 'Dütting P, Henzinger MH, Weber I. 2009. Bidder optimal assignments for general
utilities. 5th International Workshop on Internet and Network Economics. WINE:
International Conference on Web and Internet Economics, LNCS, vol. 5929, 575–582.'
mla: Dütting, Paul, et al. “Bidder Optimal Assignments for General Utilities.” 5th
International Workshop on Internet and Network Economics, vol. 5929, Springer
Nature, 2009, pp. 575–82, doi:10.1007/978-3-642-10841-9_58.
short: P. Dütting, M.H. Henzinger, I. Weber, in:, 5th International Workshop on
Internet and Network Economics, Springer Nature, 2009, pp. 575–582.
conference:
end_date: 2009-12-18
location: Rome, Italy
name: 'WINE: International Conference on Web and Internet Economics'
start_date: 2009-12-14
date_created: 2022-08-11T12:33:38Z
date_published: 2009-12-01T00:00:00Z
date_updated: 2023-02-21T16:32:35Z
day: '01'
doi: 10.1007/978-3-642-10841-9_58
extern: '1'
intvolume: ' 5929'
language:
- iso: eng
month: '12'
oa_version: None
page: 575-582
publication: 5th International Workshop on Internet and Network Economics
publication_identifier:
isbn:
- '9783642108402'
issn:
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '11902'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Bidder optimal assignments for general utilities
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5929
year: '2009'
...
---
_id: '11905'
abstract:
- lang: eng
text: Given only the URL of a web page, can we identify its topic? This is the question
that we examine in this paper. Usually, web pages are classified using their content,
but a URL-only classifier is preferable, (i) when speed is crucial, (ii) to enable
content filtering before an (objection-able) web page is downloaded, (iii) when
a page's content is hidden in images, (iv) to annotate hyperlinks in a personalized
web browser, without fetching the target page, and (v) when a focused crawler
wants to infer the topic of a target page before devoting bandwidth to download
it. We apply a machine learning approach to the topic identification task and
evaluate its performance in extensive experiments on categorized web pages from
the Open Directory Project (ODP). When training separate binary classifiers for
each topic, we achieve typical F-measure values between 80 and 85, and a typical
precision of around 85. We also ran experiments on a small data set of university
web pages. For the task of classifying these pages into faculty, student, course
and project pages, our methods improve over previous approaches by 13.8 points
of F-measure.
article_processing_charge: No
author:
- first_name: Eda
full_name: Baykan, Eda
last_name: Baykan
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Ludmila
full_name: Marian, Ludmila
last_name: Marian
- first_name: Ingmar
full_name: Weber, Ingmar
last_name: Weber
citation:
ama: 'Baykan E, Henzinger MH, Marian L, Weber I. Purely URL-based topic classification.
In: 18th International World Wide Web Conference. Association for Computing
Machinery; 2009:1109-1110. doi:10.1145/1526709.1526880'
apa: 'Baykan, E., Henzinger, M. H., Marian, L., & Weber, I. (2009). Purely URL-based
topic classification. In 18th International World Wide Web Conference (pp.
1109–1110). New York, NY, United States: Association for Computing Machinery.
https://doi.org/10.1145/1526709.1526880'
chicago: Baykan, Eda, Monika H Henzinger, Ludmila Marian, and Ingmar Weber. “Purely
URL-Based Topic Classification.” In 18th International World Wide Web Conference,
1109–10. Association for Computing Machinery, 2009. https://doi.org/10.1145/1526709.1526880.
ieee: E. Baykan, M. H. Henzinger, L. Marian, and I. Weber, “Purely URL-based topic
classification,” in 18th International World Wide Web Conference, New York,
NY, United States, 2009, pp. 1109–1110.
ista: 'Baykan E, Henzinger MH, Marian L, Weber I. 2009. Purely URL-based topic classification.
18th International World Wide Web Conference. WWW: Conference on World Wide Web,
1109–1110.'
mla: Baykan, Eda, et al. “Purely URL-Based Topic Classification.” 18th International
World Wide Web Conference, Association for Computing Machinery, 2009, pp.
1109–10, doi:10.1145/1526709.1526880.
short: E. Baykan, M.H. Henzinger, L. Marian, I. Weber, in:, 18th International World
Wide Web Conference, Association for Computing Machinery, 2009, pp. 1109–1110.
conference:
end_date: 2009-04-24
location: New York, NY, United States
name: 'WWW: Conference on World Wide Web'
start_date: 2009-04-20
date_created: 2022-08-17T11:49:53Z
date_published: 2009-04-01T00:00:00Z
date_updated: 2023-02-17T14:54:56Z
day: '01'
doi: 10.1145/1526709.1526880
extern: '1'
language:
- iso: eng
month: '04'
oa_version: None
page: 1109-1110
publication: 18th International World Wide Web Conference
publication_identifier:
isbn:
- 978-1-60558-487-4
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Purely URL-based topic classification
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2009'
...
---
_id: '11906'
abstract:
- lang: eng
text: In the origin detection problem an algorithm is given a set S of documents,
ordered by creation time, and a query document D. It needs to output for every
consecutive sequence of k alphanumeric terms in D the earliest document in $S$
in which the sequence appeared (if such a document exists). Algorithms for the
origin detection problem can, for example, be used to detect the "origin" of text
segments in D and thus to detect novel content in D. They can also find the document
from which the author of D has copied the most (or show that D is mostly original.)
We concentrate on solutions that use only a fixed amount of memory. We propose
novel algorithms for this problem and evaluate them together with a large number
of previously published algorithms. Our results show that (1) detecting the origin
of text segments efficiently can be done with very high accuracy even when the
space used is less than 1% of the size of the documents in $S$, (2) the precision
degrades smoothly with the amount of available space, (3) various estimation techniques
can be used to increase the performance of the algorithms.
article_processing_charge: No
author:
- first_name: Ossama
full_name: Abdel Hamid, Ossama
last_name: Abdel Hamid
- first_name: Behshad
full_name: Behzadi, Behshad
last_name: Behzadi
- first_name: Stefan
full_name: Christoph, Stefan
last_name: Christoph
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: 'Abdel Hamid O, Behzadi B, Christoph S, Henzinger MH. Detecting the origin
of text segments efficiently. In: 18th International World Wide Web Conference.
Association for Computing Machinery; 2009:61-70. doi:10.1145/1526709.1526719'
apa: 'Abdel Hamid, O., Behzadi, B., Christoph, S., & Henzinger, M. H. (2009).
Detecting the origin of text segments efficiently. In 18th International World
Wide Web Conference (pp. 61–70). Madrid, Spain: Association for Computing
Machinery. https://doi.org/10.1145/1526709.1526719'
chicago: Abdel Hamid, Ossama, Behshad Behzadi, Stefan Christoph, and Monika H Henzinger.
“Detecting the Origin of Text Segments Efficiently.” In 18th International
World Wide Web Conference, 61–70. Association for Computing Machinery, 2009.
https://doi.org/10.1145/1526709.1526719.
ieee: O. Abdel Hamid, B. Behzadi, S. Christoph, and M. H. Henzinger, “Detecting
the origin of text segments efficiently,” in 18th International World Wide
Web Conference, Madrid, Spain, 2009, pp. 61–70.
ista: 'Abdel Hamid O, Behzadi B, Christoph S, Henzinger MH. 2009. Detecting the
origin of text segments efficiently. 18th International World Wide Web Conference.
WWW: International Conference on World Wide Web, 61–70.'
mla: Abdel Hamid, Ossama, et al. “Detecting the Origin of Text Segments Efficiently.”
18th International World Wide Web Conference, Association for Computing
Machinery, 2009, pp. 61–70, doi:10.1145/1526709.1526719.
short: O. Abdel Hamid, B. Behzadi, S. Christoph, M.H. Henzinger, in:, 18th International
World Wide Web Conference, Association for Computing Machinery, 2009, pp. 61–70.
conference:
end_date: 2009-04-24
location: Madrid, Spain
name: 'WWW: International Conference on World Wide Web'
start_date: 2009-04-20
date_created: 2022-08-17T11:54:30Z
date_published: 2009-04-01T00:00:00Z
date_updated: 2023-02-17T14:56:47Z
day: '01'
doi: 10.1145/1526709.1526719
extern: '1'
language:
- iso: eng
month: '04'
oa_version: None
page: 61-70
publication: 18th International World Wide Web Conference
publication_identifier:
isbn:
- 978-160558487-4
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Detecting the origin of text segments efficiently
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2009'
...
---
_id: '11912'
abstract:
- lang: eng
text: As the World Wide Web is growing rapidly, it is getting increasingly challenging
to gather representative information about it. Instead of crawling the web exhaustively
one has to resort to other techniques like sampling to determine the properties
of the web. A uniform random sample of the web would be useful to determine the
percentage of web pages in a specific language, on a topic or in a top level domain.
Unfortunately, no approach has been shown to sample the web pages in an unbiased
way. Three promising web sampling algorithms are based on random walks. They each
have been evaluated individually, but making a comparison on different data sets
is not possible. We directly compare these algorithms in this paper. We performed
three random walks on the web under the same conditions and analyzed their outcomes
in detail. We discuss the strengths and the weaknesses of each algorithm and propose
improvements based on experimental results.
alternative_title:
- LIPIcs
article_processing_charge: No
arxiv: 1
author:
- first_name: ' Eda'
full_name: Baykan, Eda
last_name: Baykan
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Stefan F.
full_name: Keller, Stefan F.
last_name: Keller
- first_name: Sebastian
full_name: de Castelberg, Sebastian
last_name: de Castelberg
- first_name: Markus
full_name: Kinzler, Markus
last_name: Kinzler
citation:
ama: 'Baykan Eda, Henzinger MH, Keller SF, de Castelberg S, Kinzler M. A comparison
of techniques for sampling web pages. In: 26th International Symposium on Theoretical
Aspects of Computer Science. Vol 3. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2009:13-30. doi:10.4230/LIPICS.STACS.2009.1809'
apa: 'Baykan, Eda, Henzinger, M. H., Keller, S. F., de Castelberg, S., & Kinzler,
M. (2009). A comparison of techniques for sampling web pages. In 26th International
Symposium on Theoretical Aspects of Computer Science (Vol. 3, pp. 13–30).
Freiburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.STACS.2009.1809'
chicago: Baykan, Eda, Monika H Henzinger, Stefan F. Keller, Sebastian de Castelberg,
and Markus Kinzler. “A Comparison of Techniques for Sampling Web Pages.” In 26th
International Symposium on Theoretical Aspects of Computer Science, 3:13–30.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2009. https://doi.org/10.4230/LIPICS.STACS.2009.1809.
ieee: Eda Baykan, M. H. Henzinger, S. F. Keller, S. de Castelberg, and M. Kinzler,
“A comparison of techniques for sampling web pages,” in 26th International
Symposium on Theoretical Aspects of Computer Science, Freiburg, Germany, 2009,
vol. 3, pp. 13–30.
ista: 'Baykan Eda, Henzinger MH, Keller SF, de Castelberg S, Kinzler M. 2009. A
comparison of techniques for sampling web pages. 26th International Symposium
on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects
of Computer Science, LIPIcs, vol. 3, 13–30.'
mla: Baykan, Eda, et al. “A Comparison of Techniques for Sampling Web Pages.” 26th
International Symposium on Theoretical Aspects of Computer Science, vol. 3,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2009, pp. 13–30, doi:10.4230/LIPICS.STACS.2009.1809.
short: Eda Baykan, M.H. Henzinger, S.F. Keller, S. de Castelberg, M. Kinzler, in:,
26th International Symposium on Theoretical Aspects of Computer Science, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2009, pp. 13–30.
conference:
end_date: 2009-02-28
location: Freiburg, Germany
name: 'STACS: Symposium on Theoretical Aspects of Computer Science'
start_date: 2009-02-26
date_created: 2022-08-18T06:57:25Z
date_published: 2009-02-01T00:00:00Z
date_updated: 2023-02-17T08:57:16Z
day: '01'
doi: 10.4230/LIPICS.STACS.2009.1809
extern: '1'
external_id:
arxiv:
- '0902.1604'
intvolume: ' 3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPIcs.STACS.2009.1809
month: '02'
oa: 1
oa_version: Published Version
page: 13-30
publication: 26th International Symposium on Theoretical Aspects of Computer Science
publication_identifier:
isbn:
- 978-3-939897-09-5
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: A comparison of techniques for sampling web pages
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2009'
...
---
_id: '12654'
abstract:
- lang: eng
text: 'We investigate the transferability of an enhanced temperature-index melt
model that was developed and tested on Haut Glacier d’Arolla, Switzerland, in
the 2001 season. The model’s empirical parameters (temperature factor, TF, and
shortwave radiation factor, SRF) are recalibrated for: (1) other locations on
Haut Glacier d’Arolla; (2) subperiods of distinct meteorological conditions; (3)
different years on Haut Glacier d’Arolla; and (4) other glaciers in different
years. The model parameters are optimized against simulations of an energy-balance
model validated against ablation observations. Results are compared with those
obtained with the original parameters. The model works very well when applied
to other sites, seasons and glaciers, with the exception of overcast conditions.
Differences are due to underestimation of high melt rates. The parameter values
are associated with the prevailing energy-balance conditions, showing that high
SRF are obtained on clear-sky days, whereas higher TF are typical of locations
where glacier winds prevail and turbulent fluxes are high. We also provide a range
of parameters clearly associated with the site’s location and its meteorological
characteristics that could help to assign parameter values to sites where few
data are available.'
article_processing_charge: No
article_type: original
author:
- first_name: Marco
full_name: Carenzo, Marco
last_name: Carenzo
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Stefan
full_name: Rimkus, Stefan
last_name: Rimkus
- first_name: Paolo
full_name: Burlando, Paolo
last_name: Burlando
citation:
ama: Carenzo M, Pellicciotti F, Rimkus S, Burlando P. Assessing the transferability
and robustness of an enhanced temperature-index glacier-melt model. Journal
of Glaciology. 2009;55(190):258-274. doi:10.3189/002214309788608804
apa: Carenzo, M., Pellicciotti, F., Rimkus, S., & Burlando, P. (2009). Assessing
the transferability and robustness of an enhanced temperature-index glacier-melt
model. Journal of Glaciology. Cambridge University Press. https://doi.org/10.3189/002214309788608804
chicago: Carenzo, Marco, Francesca Pellicciotti, Stefan Rimkus, and Paolo Burlando.
“Assessing the Transferability and Robustness of an Enhanced Temperature-Index
Glacier-Melt Model.” Journal of Glaciology. Cambridge University Press,
2009. https://doi.org/10.3189/002214309788608804.
ieee: M. Carenzo, F. Pellicciotti, S. Rimkus, and P. Burlando, “Assessing the transferability
and robustness of an enhanced temperature-index glacier-melt model,” Journal
of Glaciology, vol. 55, no. 190. Cambridge University Press, pp. 258–274,
2009.
ista: Carenzo M, Pellicciotti F, Rimkus S, Burlando P. 2009. Assessing the transferability
and robustness of an enhanced temperature-index glacier-melt model. Journal of
Glaciology. 55(190), 258–274.
mla: Carenzo, Marco, et al. “Assessing the Transferability and Robustness of an
Enhanced Temperature-Index Glacier-Melt Model.” Journal of Glaciology,
vol. 55, no. 190, Cambridge University Press, 2009, pp. 258–74, doi:10.3189/002214309788608804.
short: M. Carenzo, F. Pellicciotti, S. Rimkus, P. Burlando, Journal of Glaciology
55 (2009) 258–274.
date_created: 2023-02-20T08:18:34Z
date_published: 2009-03-01T00:00:00Z
date_updated: 2023-02-20T09:06:27Z
day: '01'
doi: 10.3189/002214309788608804
extern: '1'
intvolume: ' 55'
issue: '190'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3189/002214309788608804
month: '03'
oa: 1
oa_version: Published Version
page: 258-274
publication: Journal of Glaciology
publication_identifier:
eissn:
- 1727-5652
issn:
- 0022-1430
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Assessing the transferability and robustness of an enhanced temperature-index
glacier-melt model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2009'
...
---
_id: '12655'
abstract:
- lang: eng
text: We discuss the inclusion of the subsurface heat-conduction flux into the calculation
of the energy balance and ablation at the glacier–atmosphere interface. Data from
automatic weather stations are used to force an energy-balance model at several
locations on alpine glaciers and at one site in the dry Andes of central Chile.
The heat-conduction flux is computed using a two-layer scheme, assuming that 36%
of the net shortwave radiation is absorbed by the surface layer and that the rest
penetrates into the snowpack. We compare simulations conducted with and without
subsurface heat flux. Results show that assuming a surface temperature of zero
degrees leads to a larger overestimation of melt at the sites in the accumulation
area (10.4–13.3%) than in the ablation area (0.5–2.8%), due to lower air temperatures
and the presence of snow. The difference between simulations with and without
heat conduction is also high at the beginning and end of the ablation season (up
to 29% for the first 15 days of the season), when air temperatures are lower and
snow covers the glacier surface, while they are of little importance during periods
of sustained melt at all the locations investigated.
article_processing_charge: No
article_type: original
author:
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Marco
full_name: Carenzo, Marco
last_name: Carenzo
- first_name: Jakob
full_name: Helbing, Jakob
last_name: Helbing
- first_name: Stefan
full_name: Rimkus, Stefan
last_name: Rimkus
- first_name: Paolo
full_name: Burlando, Paolo
last_name: Burlando
citation:
ama: Pellicciotti F, Carenzo M, Helbing J, Rimkus S, Burlando P. On the role of
subsurface heat conduction in glacier energy-balance modelling. Annals of Glaciology.
2009;50(50):16-24. doi:10.3189/172756409787769555
apa: Pellicciotti, F., Carenzo, M., Helbing, J., Rimkus, S., & Burlando, P.
(2009). On the role of subsurface heat conduction in glacier energy-balance modelling.
Annals of Glaciology. International Glaciological Society. https://doi.org/10.3189/172756409787769555
chicago: Pellicciotti, Francesca, Marco Carenzo, Jakob Helbing, Stefan Rimkus, and
Paolo Burlando. “On the Role of Subsurface Heat Conduction in Glacier Energy-Balance
Modelling.” Annals of Glaciology. International Glaciological Society,
2009. https://doi.org/10.3189/172756409787769555.
ieee: F. Pellicciotti, M. Carenzo, J. Helbing, S. Rimkus, and P. Burlando, “On the
role of subsurface heat conduction in glacier energy-balance modelling,” Annals
of Glaciology, vol. 50, no. 50. International Glaciological Society, pp. 16–24,
2009.
ista: Pellicciotti F, Carenzo M, Helbing J, Rimkus S, Burlando P. 2009. On the role
of subsurface heat conduction in glacier energy-balance modelling. Annals of Glaciology.
50(50), 16–24.
mla: Pellicciotti, Francesca, et al. “On the Role of Subsurface Heat Conduction
in Glacier Energy-Balance Modelling.” Annals of Glaciology, vol. 50, no.
50, International Glaciological Society, 2009, pp. 16–24, doi:10.3189/172756409787769555.
short: F. Pellicciotti, M. Carenzo, J. Helbing, S. Rimkus, P. Burlando, Annals of
Glaciology 50 (2009) 16–24.
date_created: 2023-02-20T08:18:40Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2023-02-20T09:00:53Z
day: '01'
doi: 10.3189/172756409787769555
extern: '1'
intvolume: ' 50'
issue: '50'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3189/172756409787769555
month: '01'
oa: 1
oa_version: Published Version
page: 16-24
publication: Annals of Glaciology
publication_identifier:
eissn:
- 1727-5644
issn:
- 0260-3055
publication_status: published
publisher: International Glaciological Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the role of subsurface heat conduction in glacier energy-balance modelling
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2009'
...
---
_id: '1302'
abstract:
- lang: eng
text: 'The nervous system of seeing animals derives information about optic flow
in two subsequent steps. First, local motion vectors are calculated from moving
retinal images, and second, the spatial distribution of these vectors is analyzed
on the dendrites of large downstream neurons. In dipteran flies, this second step
relies on a set of motion-sensitive lobula plate tangential cells (LPTCs), which
have been studied in great detail in large fly species. Yet, studies on neurons
that convey information to LPTCs and neuroanatomical investigations that enable
a mechanistic understanding of the underlying dendritic computations in LPTCs
are rare. We investigated the subcellular distribution of nicotinic acetylcholine
receptors (nAChRs) on two sets of LPTCs: vertical system (VS) and horizontal system
(HS) cells in Drosophila melanogaster. In this paper, we describe that both cell
types express Dα7-type nAChR subunits specifically on higher order dendritic branches,
similar to the expression of gamma aminobutyric acid (GABA) receptors. These findings
support a model in which directional selectivity of LPTCs is achieved by the dendritic
integration of excitatory, cholinergic, and inhibitory GABA-ergic input from local
motion detectors with opposite preferred direction. Nonetheless, whole-cell recordings
in mutant flies without Dα7 nAChRs revealed that direction selectivity of VS and
HS cells is largely retained. In addition, mutant LPTCs were responsive to acetylcholine
and remaining nAChR receptors were labeled by α-bungarotoxin. These results in
LPTCs with genetically manipulated excitatory input synapses suggest a robust
cellular implementation of dendritic processing that warrants direction selectivity.
The underlying mechanism that ensures appropriate nAChR-mediated synaptic currents
and the functional implications of separate sets or heteromultimeric nAChRs can
now be addressed in this system.'
author:
- first_name: Shamprasad
full_name: Raghu, Shamprasad V
last_name: Raghu
- first_name: Maximilian A
full_name: Maximilian Jösch
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Stephan
full_name: Sigrist, Stephan J
last_name: Sigrist
- first_name: Alexander
full_name: Borst, Alexander
last_name: Borst
- first_name: Dierk
full_name: Reiff, Dierk F
last_name: Reiff
citation:
ama: 'Raghu S, Jösch MA, Sigrist S, Borst A, Reiff D. Synaptic organization of lobula
plate tangential cells in Drosophila: Dα7 cholinergic receptors. Journal of
Neurogenetics. 2009;23(1-2):200-209. doi:10.1080/01677060802471684'
apa: 'Raghu, S., Jösch, M. A., Sigrist, S., Borst, A., & Reiff, D. (2009). Synaptic
organization of lobula plate tangential cells in Drosophila: Dα7 cholinergic receptors.
Journal of Neurogenetics. Informa Healthcare. https://doi.org/10.1080/01677060802471684'
chicago: 'Raghu, Shamprasad, Maximilian A Jösch, Stephan Sigrist, Alexander Borst,
and Dierk Reiff. “Synaptic Organization of Lobula Plate Tangential Cells in Drosophila:
Dα7 Cholinergic Receptors.” Journal of Neurogenetics. Informa Healthcare,
2009. https://doi.org/10.1080/01677060802471684.'
ieee: 'S. Raghu, M. A. Jösch, S. Sigrist, A. Borst, and D. Reiff, “Synaptic organization
of lobula plate tangential cells in Drosophila: Dα7 cholinergic receptors,” Journal
of Neurogenetics, vol. 23, no. 1–2. Informa Healthcare, pp. 200–209, 2009.'
ista: 'Raghu S, Jösch MA, Sigrist S, Borst A, Reiff D. 2009. Synaptic organization
of lobula plate tangential cells in Drosophila: Dα7 cholinergic receptors. Journal
of Neurogenetics. 23(1–2), 200–209.'
mla: 'Raghu, Shamprasad, et al. “Synaptic Organization of Lobula Plate Tangential
Cells in Drosophila: Dα7 Cholinergic Receptors.” Journal of Neurogenetics,
vol. 23, no. 1–2, Informa Healthcare, 2009, pp. 200–09, doi:10.1080/01677060802471684.'
short: S. Raghu, M.A. Jösch, S. Sigrist, A. Borst, D. Reiff, Journal of Neurogenetics
23 (2009) 200–209.
date_created: 2018-12-11T11:51:15Z
date_published: 2009-03-01T00:00:00Z
date_updated: 2021-01-12T06:49:44Z
day: '01'
doi: 10.1080/01677060802471684
extern: 1
intvolume: ' 23'
issue: 1-2
month: '03'
page: 200 - 209
publication: Journal of Neurogenetics
publication_status: published
publisher: Informa Healthcare
publist_id: '5972'
quality_controlled: 0
status: public
title: 'Synaptic organization of lobula plate tangential cells in Drosophila: Dα7
cholinergic receptors'
type: journal_article
volume: 23
year: '2009'
...
---
_id: '337'
abstract:
- lang: eng
text: 'The formation of hollow vs solid particles by means of the oxidation reaction
of solid metal particles depends on the differential self-diffusivities of the
reactants through the composite shell, the reaction probabilities at each interface,
and the concentration and diffusivity of the element in solution. By means of
a kinetic model of the oxidation process, we determine the phase diagrams for
the geometry of the oxidized particles and propose four shell growth regimes.
We experimentally illustrate the different growth scenarios by changing the conditions
of oxidation of cadmium spherical crystals using different chalcogen precursors. '
article_processing_charge: No
article_type: original
author:
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Pablo
full_name: Guardia, Pablo
last_name: Guardia
- first_name: Paul
full_name: Alivisatos, Paul
last_name: Alivisatos
citation:
ama: Cabot A, Ibáñez M, Guardia P, Alivisatos P. Reaction regimes on the synthesis
of hollow particles by the Kirkendall effect. Journal of the American Chemical
Society. 2009;131(32):11326-11328. doi:10.1021/ja903751p
apa: Cabot, A., Ibáñez, M., Guardia, P., & Alivisatos, P. (2009). Reaction regimes
on the synthesis of hollow particles by the Kirkendall effect. Journal of the
American Chemical Society. ACS. https://doi.org/10.1021/ja903751p
chicago: Cabot, Andreu, Maria Ibáñez, Pablo Guardia, and Paul Alivisatos. “Reaction
Regimes on the Synthesis of Hollow Particles by the Kirkendall Effect.” Journal
of the American Chemical Society. ACS, 2009. https://doi.org/10.1021/ja903751p.
ieee: A. Cabot, M. Ibáñez, P. Guardia, and P. Alivisatos, “Reaction regimes on the
synthesis of hollow particles by the Kirkendall effect,” Journal of the American
Chemical Society, vol. 131, no. 32. ACS, pp. 11326–11328, 2009.
ista: Cabot A, Ibáñez M, Guardia P, Alivisatos P. 2009. Reaction regimes on the
synthesis of hollow particles by the Kirkendall effect. Journal of the American
Chemical Society. 131(32), 11326–11328.
mla: Cabot, Andreu, et al. “Reaction Regimes on the Synthesis of Hollow Particles
by the Kirkendall Effect.” Journal of the American Chemical Society, vol.
131, no. 32, ACS, 2009, pp. 11326–28, doi:10.1021/ja903751p.
short: A. Cabot, M. Ibáñez, P. Guardia, P. Alivisatos, Journal of the American Chemical
Society 131 (2009) 11326–11328.
date_created: 2018-12-11T11:45:53Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:43:00Z
day: '01'
doi: 10.1021/ja903751p
extern: '1'
intvolume: ' 131'
issue: '32'
language:
- iso: eng
month: '01'
oa_version: None
page: 11326 - 11328
publication: Journal of the American Chemical Society
publication_status: published
publisher: ACS
publist_id: '7494'
quality_controlled: '1'
status: public
title: Reaction regimes on the synthesis of hollow particles by the Kirkendall effect
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2009'
...
---
_id: '3398'
abstract:
- lang: eng
text: Why is a particular architecture for a pathway chosen over seemingly equivalent
alternatives? Çağatay et al. (2009) use a synthetic biology approach to show that
fluctuations—or noise—in protein levels may play a key role in determining which
network design is selected during evolution.
article_processing_charge: No
author:
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Roy
full_name: Kishony, Roy
last_name: Kishony
citation:
ama: Bollenbach MT, Kishony R. Quiet gene circuit more fragile than its noisy peer.
Cell. 2009;139(3):460-461. doi:10.1016/j.cell.2009.10.005
apa: Bollenbach, M. T., & Kishony, R. (2009). Quiet gene circuit more fragile
than its noisy peer. Cell. Cell Press. https://doi.org/10.1016/j.cell.2009.10.005
chicago: Bollenbach, Mark Tobias, and Roy Kishony. “Quiet Gene Circuit More Fragile
than Its Noisy Peer.” Cell. Cell Press, 2009. https://doi.org/10.1016/j.cell.2009.10.005.
ieee: M. T. Bollenbach and R. Kishony, “Quiet gene circuit more fragile than its
noisy peer,” Cell, vol. 139, no. 3. Cell Press, pp. 460–461, 2009.
ista: Bollenbach MT, Kishony R. 2009. Quiet gene circuit more fragile than its noisy
peer. Cell. 139(3), 460–461.
mla: Bollenbach, Mark Tobias, and Roy Kishony. “Quiet Gene Circuit More Fragile
than Its Noisy Peer.” Cell, vol. 139, no. 3, Cell Press, 2009, pp. 460–61,
doi:10.1016/j.cell.2009.10.005.
short: M.T. Bollenbach, R. Kishony, Cell 139 (2009) 460–461.
date_created: 2018-12-11T12:03:07Z
date_published: 2009-10-30T00:00:00Z
date_updated: 2021-01-12T07:43:12Z
day: '30'
doi: 10.1016/j.cell.2009.10.005
extern: '1'
intvolume: ' 139'
issue: '3'
language:
- iso: eng
month: '10'
oa_version: None
page: 460 - 461
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3061'
status: public
title: Quiet gene circuit more fragile than its noisy peer
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 139
year: '2009'
...
---
_id: '3400'
abstract:
- lang: eng
text: |-
Invasive fungal infections pose a serious threat to immunocompromised people. Most of these infections are caused by either Candida or Aspergillus species, with A. fumigatus being the predominant causative agent of Invasive Aspergillosis. Affected people comprise mainly haematopoietic stem cell or solid organ transplant patients who receive either high-dose corticosteroids or immunosuppressants. These risk factors predispose to the development of Invasive
Aspergillosis which is lethal in 20 to 80 % of the cases, largely due to insufficient efficacy of current antifungal therapy. Thus one major aim in current mycological research is the identification of new drug targets.
The polysaccharide-based fungal cell wall is both essential to fungi and absent from human cells which makes it appear an attractive new target. Notably, many components of the A. fumigatus cell wall, including the polysaccharide galactomannan, glycoproteins, and glycolipids, contain the unusual sugar galactofuranose (Galf). In contrast to the other cell wall monosaccharides, Galf does not occur on human cells but is known as component of cell surface molecules of many pathogenic bacteria and protozoa, such as Mycobacterium tuberculosis or Leishmania major. These molecules are often essential for virulence or viability of these organisms which suggested a possible role of Galf in the pathogenicity of A. fumigatus.
To address the importance of Galf in A. fumigatus, the key biosynthesis gene glfA, encoding UDPgalactopyranose mutase (UGM), was deleted. In different experimental approaches it was demonstrated that the absence of the glfA gene led to a complete loss of Galf-containing glycans.
Analysis of the DeltaglfA phenotype revealed growth and sporulation defects, reduced thermotolerance and an increased susceptibility to antifungal drugs. Electron Microscopy indicated a cell wall defect as a likely cause for the observed impairments. Furthermore, the virulence of the DeltaglfA mutant was found to be severely attenuated in a murine model of Invasive Aspergillosis.
The second focus of this study was laid on further elucidation of the galactofuranosylation pathway in A. fumigatus. In eukaryotes, a UDP-Galf transporter is likely required to transport UDP-Galf from the
cytosol into the organelles of the secretory pathway, but no such activity had been described. Sixteen candidate genes were identified in the A. fumigatus genome of which one, glfB, was found in close proximity to the glfA gene. In vitro transport assays revealed specificity of GlfB for UDP-Galf suggesting that glfB encoded indeed a UDP-Galf transporter. The influence of glfB on
galactofuranosylation was determined by a DeltaglfB deletion mutant, which closely recapitulated the DeltaglfA phenotype and was likewise found to be completely devoid of Galf. It could be concluded that all galactofuranosylation processes in A. fumigatus occur in the secretory pathway, including the biosynthesis of the cell wall polysaccharide galactomannan whose subcellular origin was previously disputed.
Thus in the course of this study the first UDP-Galf specific nucleotide sugar transporter was identified and its requirement for galactofuranosylation in A. fumigatus demonstrated. Moreover, it was shown that blocking the galactofuranosylation pathway impaired virulence of A. fumigatus which suggests the UDP-Galf biosynthesis enzyme UGM as a target for new antifungal drugs.
author:
- first_name: Philipp S
full_name: Philipp Schmalhorst
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
citation:
ama: Schmalhorst PS. Biosynthesis of Galactofuranose Containing Glycans and Their
Relevance for the Pathogenic Fungus Aspergillus fumigatus. 2009:1-72.
apa: Schmalhorst, P. S. (2009). Biosynthesis of Galactofuranose Containing Glycans
and Their Relevance for the Pathogenic Fungus Aspergillus fumigatus. Gottfried
Wilhelm Leibniz Universität Hannover.
chicago: Schmalhorst, Philipp S. “Biosynthesis of Galactofuranose Containing Glycans
and Their Relevance for the Pathogenic Fungus Aspergillus Fumigatus.” Gottfried
Wilhelm Leibniz Universität Hannover, 2009.
ieee: P. S. Schmalhorst, “Biosynthesis of Galactofuranose Containing Glycans and
Their Relevance for the Pathogenic Fungus Aspergillus fumigatus,” Gottfried Wilhelm
Leibniz Universität Hannover, 2009.
ista: Schmalhorst PS. 2009. Biosynthesis of Galactofuranose Containing Glycans and
Their Relevance for the Pathogenic Fungus Aspergillus fumigatus. Gottfried Wilhelm
Leibniz Universität Hannover.
mla: Schmalhorst, Philipp S. Biosynthesis of Galactofuranose Containing Glycans
and Their Relevance for the Pathogenic Fungus Aspergillus Fumigatus. Gottfried
Wilhelm Leibniz Universität Hannover, 2009, pp. 1–72.
short: P.S. Schmalhorst, Biosynthesis of Galactofuranose Containing Glycans and
Their Relevance for the Pathogenic Fungus Aspergillus Fumigatus, Gottfried Wilhelm
Leibniz Universität Hannover, 2009.
date_created: 2018-12-11T12:03:07Z
date_published: 2009-08-13T00:00:00Z
date_updated: 2021-01-12T07:43:13Z
day: '13'
extern: 1
main_file_link:
- open_access: '0'
url: http://edok01.tib.uni-hannover.de/edoks/e01dh09/609861891.pdf
month: '08'
page: 1 - 72
publication_status: published
publisher: Gottfried Wilhelm Leibniz Universität Hannover
publist_id: '3058'
quality_controlled: 0
status: public
title: Biosynthesis of Galactofuranose Containing Glycans and Their Relevance for
the Pathogenic Fungus Aspergillus fumigatus
type: dissertation
year: '2009'
...
---
_id: '3408'
abstract:
- lang: eng
text: Mechanical forces govern physiological processes in all living organisms.
Many cellular forces, for example, those generated in cyclic conformational changes
of biological machines, have repetitive components. In apparent contrast, little
is known about how dynamic protein structures respond to periodic mechanical information.
Ubiquitin is a small protein found in all eukaryotes. We developed molecular dynamics
simulations to unfold single and multimeric ubiquitins with periodic forces. By
using a coarse-grained representation, we were able to model forces with periods
about 2 orders of magnitude longer than the protein's relaxation time. We found
that even a moderate periodic force weakened the protein and shifted its unfolding
pathways in a frequency- and amplitude-dependent manner. A complex dynamic response
with secondary structure refolding and an increasing importance of local interactions
was revealed. Importantly, repetitive forces with broadly distributed frequencies
elicited very similar molecular responses compared to fixed-frequency forces.
When testing the influence of pulling geometry on ubiquitin's mechanical stability,
it was found that the linkage involved in the mechanical degradation of cellular
proteins renders the protein remarkably insensitive to periodic forces. We also
devised a complementary kinetic energy landscape model that traces these observations
and explains periodic-force, single-molecule measurements. In turn, this analytical
model is capable of predicting dynamic protein responses. These results provide
new insights into ubiquitin mechanics and a potential mechanical role during protein
degradation, as well as first frameworks for dynamic protein stability and the
modeling of repetitive mechanical processes.
author:
- first_name: Piotr
full_name: Szymczak, Piotr
last_name: Szymczak
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Szymczak P, Janovjak HL. Periodic forces trigger a complex mechanical response
in ubiquitin. Journal of Molecular Biology. 2009;390(3):443-456. doi:10.1016/j.jmb.2009.04.071
apa: Szymczak, P., & Janovjak, H. L. (2009). Periodic forces trigger a complex
mechanical response in ubiquitin. Journal of Molecular Biology. Elsevier.
https://doi.org/10.1016/j.jmb.2009.04.071
chicago: Szymczak, Piotr, and Harald L Janovjak. “Periodic Forces Trigger a Complex
Mechanical Response in Ubiquitin.” Journal of Molecular Biology. Elsevier,
2009. https://doi.org/10.1016/j.jmb.2009.04.071.
ieee: P. Szymczak and H. L. Janovjak, “Periodic forces trigger a complex mechanical
response in ubiquitin,” Journal of Molecular Biology, vol. 390, no. 3.
Elsevier, pp. 443–456, 2009.
ista: Szymczak P, Janovjak HL. 2009. Periodic forces trigger a complex mechanical
response in ubiquitin. Journal of Molecular Biology. 390(3), 443–456.
mla: Szymczak, Piotr, and Harald L. Janovjak. “Periodic Forces Trigger a Complex
Mechanical Response in Ubiquitin.” Journal of Molecular Biology, vol. 390,
no. 3, Elsevier, 2009, pp. 443–56, doi:10.1016/j.jmb.2009.04.071.
short: P. Szymczak, H.L. Janovjak, Journal of Molecular Biology 390 (2009) 443–456.
date_created: 2018-12-11T12:03:10Z
date_published: 2009-07-17T00:00:00Z
date_updated: 2021-01-12T07:43:16Z
day: '17'
doi: 10.1016/j.jmb.2009.04.071
extern: 1
intvolume: ' 390'
issue: '3'
month: '07'
page: 443 - 456
publication: Journal of Molecular Biology
publication_status: published
publisher: Elsevier
publist_id: '2994'
quality_controlled: 0
status: public
title: Periodic forces trigger a complex mechanical response in ubiquitin
type: journal_article
volume: 390
year: '2009'
...