---
_id: '12657'
abstract:
- lang: eng
text: An enhanced temperature-index glacier melt model, incorporating incoming shortwave
radiation and albedo, is presented. The model is an attempt to combine the high
temporal resolution and accuracy of physically based melt models with the lower
data requirements and computational simplicity of empirical melt models, represented
by the ‘degree-day’ method and its variants. The model is run with both measured
and modelled radiation data, to test its applicability to glaciers with differing
data availability. Five automatic weather stations were established on Haut Glacier
d’Arolla, Switzerland, between May and September 2001. Reference surface melt
rates were calculated using a physically based energy-balance melt model. The
performance of the enhanced temperature-index model was tested at each of the
four validation stations by comparing predicted hourly melt rates with reference
melt rates. Predictions made with three other temperature-index models were evaluated
in the same way for comparison. The enhanced temperature-index model offers significant
improvements over the other temperature-index models, and accounts for 90–95%
of the variation in the reference melt rate. The improvement is lower, but still
significant, when the model is forced by modelled shortwave radiation data, thus
offering a better alternative to existing models that require only temperature
data input.
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: Ben
full_name: Brock, Ben
last_name: Brock
- first_name: Ulrich
full_name: Strasser, Ulrich
last_name: Strasser
- first_name: Paolo
full_name: Burlando, Paolo
last_name: Burlando
- first_name: Martin
full_name: Funk, Martin
last_name: Funk
- first_name: Javier
full_name: Corripio, Javier
last_name: Corripio
citation:
ama: 'Pellicciotti F, Brock B, Strasser U, Burlando P, Funk M, Corripio J. An enhanced
temperature-index glacier melt model including the shortwave radiation balance:
Development and testing for Haut Glacier d’Arolla, Switzerland. Journal of
Glaciology. 2005;51(175):573-587. doi:10.3189/172756505781829124'
apa: 'Pellicciotti, F., Brock, B., Strasser, U., Burlando, P., Funk, M., & Corripio,
J. (2005). An enhanced temperature-index glacier melt model including the shortwave
radiation balance: Development and testing for Haut Glacier d’Arolla, Switzerland.
Journal of Glaciology. Cambridge University Press. https://doi.org/10.3189/172756505781829124'
chicago: 'Pellicciotti, Francesca, Ben Brock, Ulrich Strasser, Paolo Burlando, Martin
Funk, and Javier Corripio. “An Enhanced Temperature-Index Glacier Melt Model Including
the Shortwave Radiation Balance: Development and Testing for Haut Glacier d’Arolla,
Switzerland.” Journal of Glaciology. Cambridge University Press, 2005.
https://doi.org/10.3189/172756505781829124.'
ieee: 'F. Pellicciotti, B. Brock, U. Strasser, P. Burlando, M. Funk, and J. Corripio,
“An enhanced temperature-index glacier melt model including the shortwave radiation
balance: Development and testing for Haut Glacier d’Arolla, Switzerland,” Journal
of Glaciology, vol. 51, no. 175. Cambridge University Press, pp. 573–587,
2005.'
ista: 'Pellicciotti F, Brock B, Strasser U, Burlando P, Funk M, Corripio J. 2005.
An enhanced temperature-index glacier melt model including the shortwave radiation
balance: Development and testing for Haut Glacier d’Arolla, Switzerland. Journal
of Glaciology. 51(175), 573–587.'
mla: 'Pellicciotti, Francesca, et al. “An Enhanced Temperature-Index Glacier Melt
Model Including the Shortwave Radiation Balance: Development and Testing for Haut
Glacier d’Arolla, Switzerland.” Journal of Glaciology, vol. 51, no. 175,
Cambridge University Press, 2005, pp. 573–87, doi:10.3189/172756505781829124.'
short: F. Pellicciotti, B. Brock, U. Strasser, P. Burlando, M. Funk, J. Corripio,
Journal of Glaciology 51 (2005) 573–587.
date_created: 2023-02-20T08:18:51Z
date_published: 2005-10-19T00:00:00Z
date_updated: 2023-02-20T08:45:37Z
day: '19'
doi: 10.3189/172756505781829124
extern: '1'
intvolume: ' 51'
issue: '175'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3189/172756505781829124
month: '10'
oa: 1
oa_version: Published Version
page: 573-587
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: 'An enhanced temperature-index glacier melt model including the shortwave radiation
balance: Development and testing for Haut Glacier d’Arolla, Switzerland'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2005'
...
---
_id: '1298'
abstract:
- lang: eng
text: Genetically encoded fluorescent probes of neural activity represent new promising
tools for systems neuroscience. Here, we present a comparative in vivo analysis
of 10 different genetically encoded calcium indicators, as well as the pH-sensitive
synapto-pHluorin. We analyzed their fluorescence changes in presynaptic boutons
of the Drosophila larval neuromuscular junction. Robust neural activity did not
result in any or noteworthy fluorescence changes when Flash-Pericam, Camgaroo-1,
and Camgaroo-2 were expressed. However, calculated on the raw data, fractional
fluorescence changes up to 18% were reported by synapto-pHluorin, Yellow Cameleon
2.0, 2.3, and 3.3, Inverse-Pericam, GCaMP1.3, GCaMP1.6, and the troponin C-based
calcium sensor TN-L15. The response characteristics of all of these indicators
differed considerably from each other, with GCaMP1.6 reporting high rates of neural
activity with the largest and fastest fluorescence changes. However, GCaMP1.6
suffered from photobleaching, whereas the fluorescence signals of the double-chromophore
indicators were in general smaller but more photostable and reproducible, with
TN-L15 showing the fastest rise of the signals at lower activity rates. We show
for GCaMP1.3 and YC3.3 that an expanded range of neural activity evoked fairly
linear fluorescence changes and a corresponding linear increase in the signal-to-noise
ratio (SNR). The expression level of the indicator biased the signal kinetics
and SNR, whereas the signal amplitude was independent. The presented data will
be useful for in vivo experiments with respect to the selection of an appropriate
indicator, as well as for the correct interpretation of the optical signals.
acknowledgement: This work was supported by the Max-Planck-Society.
author:
- first_name: Dierk
full_name: Reiff, Dierk F
last_name: Reiff
- first_name: Alexandra
full_name: Ihring, Alexandra
last_name: Ihring
- first_name: Giovanna
full_name: Guerrero, Giovanna
last_name: Guerrero
- first_name: Ehud
full_name: Isacoff, Ehud Y
last_name: Isacoff
- first_name: Maximilian A
full_name: Maximilian Jösch
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Junichi
full_name: Nakai, Junichi
last_name: Nakai
- first_name: Alexander
full_name: Borst, Alexander
last_name: Borst
citation:
ama: Reiff D, Ihring A, Guerrero G, et al. In vivo performance of genetically encoded
indicators of neural activity in flies. Journal of Neuroscience. 2005;25(19):4766-4778.
doi:10.1523/JNEUROSCI.4900-04.2005
apa: Reiff, D., Ihring, A., Guerrero, G., Isacoff, E., Jösch, M. A., Nakai, J.,
& Borst, A. (2005). In vivo performance of genetically encoded indicators
of neural activity in flies. Journal of Neuroscience. Society for Neuroscience.
https://doi.org/10.1523/JNEUROSCI.4900-04.2005
chicago: Reiff, Dierk, Alexandra Ihring, Giovanna Guerrero, Ehud Isacoff, Maximilian
A Jösch, Junichi Nakai, and Alexander Borst. “In Vivo Performance of Genetically
Encoded Indicators of Neural Activity in Flies.” Journal of Neuroscience.
Society for Neuroscience, 2005. https://doi.org/10.1523/JNEUROSCI.4900-04.2005.
ieee: D. Reiff et al., “In vivo performance of genetically encoded indicators
of neural activity in flies,” Journal of Neuroscience, vol. 25, no. 19.
Society for Neuroscience, pp. 4766–4778, 2005.
ista: Reiff D, Ihring A, Guerrero G, Isacoff E, Jösch MA, Nakai J, Borst A. 2005.
In vivo performance of genetically encoded indicators of neural activity in flies.
Journal of Neuroscience. 25(19), 4766–4778.
mla: Reiff, Dierk, et al. “In Vivo Performance of Genetically Encoded Indicators
of Neural Activity in Flies.” Journal of Neuroscience, vol. 25, no. 19,
Society for Neuroscience, 2005, pp. 4766–78, doi:10.1523/JNEUROSCI.4900-04.2005.
short: D. Reiff, A. Ihring, G. Guerrero, E. Isacoff, M.A. Jösch, J. Nakai, A. Borst,
Journal of Neuroscience 25 (2005) 4766–4778.
date_created: 2018-12-11T11:51:13Z
date_published: 2005-03-11T00:00:00Z
date_updated: 2021-01-12T06:49:42Z
day: '11'
doi: 10.1523/JNEUROSCI.4900-04.2005
extern: 1
intvolume: ' 25'
issue: '19'
month: '03'
page: 4766 - 4778
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '5975'
quality_controlled: 0
status: public
title: In vivo performance of genetically encoded indicators of neural activity in
flies
type: journal_article
volume: 25
year: '2005'
...
---
_id: '3416'
abstract:
- lang: eng
text: In the last decade atomic force microscopy has been used to measure the mechanical
stability of single proteins. These force spectroscopy experiments have shown
that many water-soluble and membrane proteins unfold via one or more intermediates.
Recently, Li and co-workers found a linear correlation between the unfolding force
of the native state and the intermediate in fibronectin, which they suggested
indicated the presence of a molecular memory or multiple unfolding pathways (1).
Here, we apply two independent methods in combination with Monte Carlo simulations
to analyze the unfolding of α-helices E and D of bacteriorhodopsin (BR). We show
that correlation analysis of unfolding forces is very sensitive to errors in force
calibration of the instrument. In contrast, a comparison of relative forces provides
a robust measure for the stability of unfolding intermediates. The proposed approach
detects three energetically different states of α-helices E and D in trimeric
BR. These states are not observed for monomeric BR and indicate that substantial
information is hidden in forced unfolding experiments of single proteins.
author:
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Tanuj
full_name: Sapra, Tanuj K
last_name: Sapra
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Janovjak HL, Sapra T, Mueller D. Complex stability of single proteins explored
by forced unfolding experiments. Biophysical Journal. 2005;88(5):37-39.
doi:10.1529/biophysj.105.059774
apa: Janovjak, H. L., Sapra, T., & Mueller, D. (2005). Complex stability of
single proteins explored by forced unfolding experiments. Biophysical Journal.
Biophysical Society. https://doi.org/10.1529/biophysj.105.059774
chicago: Janovjak, Harald L, Tanuj Sapra, and Daniel Mueller. “Complex Stability
of Single Proteins Explored by Forced Unfolding Experiments.” Biophysical Journal.
Biophysical Society, 2005. https://doi.org/10.1529/biophysj.105.059774.
ieee: H. L. Janovjak, T. Sapra, and D. Mueller, “Complex stability of single proteins
explored by forced unfolding experiments,” Biophysical Journal, vol. 88,
no. 5. Biophysical Society, pp. 37–39, 2005.
ista: Janovjak HL, Sapra T, Mueller D. 2005. Complex stability of single proteins
explored by forced unfolding experiments. Biophysical Journal. 88(5), 37–39.
mla: Janovjak, Harald L., et al. “Complex Stability of Single Proteins Explored
by Forced Unfolding Experiments.” Biophysical Journal, vol. 88, no. 5,
Biophysical Society, 2005, pp. 37–39, doi:10.1529/biophysj.105.059774.
short: H.L. Janovjak, T. Sapra, D. Mueller, Biophysical Journal 88 (2005) 37–39.
date_created: 2018-12-11T12:03:13Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T07:43:19Z
day: '01'
doi: 10.1529/biophysj.105.059774
extern: 1
intvolume: ' 88'
issue: '5'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305525/
month: '05'
oa: 1
page: 37 - 39
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '2985'
quality_controlled: 0
status: public
title: Complex stability of single proteins explored by forced unfolding experiments
type: journal_article
volume: 88
year: '2005'
...
---
_id: '3417'
abstract:
- lang: eng
text: Recently, direct measurements of forces stabilizing single proteins or individual
receptor–ligand bonds became possible with ultra-sensitive force probe methods
like the atomic force microscope (AFM). In force spectroscopy experiments using
AFM, a single molecule or receptor–ligand pair is tethered between the tip of
a micromachined cantilever and a supporting surface. While the molecule is stretched,
forces are measured by the deflection of the cantilever and plotted against extension,
yielding a force spectrum characteristic for each biomolecular system. In order
to obtain statistically relevant results, several hundred to thousand single-molecule
experiments have to be performed, each resulting in a unique force spectrum. We
developed software and algorithms to analyse large numbers of force spectra. Our
algorithms include the fitting polymer extension models to force peaks as well
as the automatic alignment of spectra. The aligned spectra allowed recognition
of patterns of peaks across different spectra. We demonstrate the capabilities
of our software by analysing force spectra that were recorded by unfolding single
transmembrane proteins such as bacteriorhodopsin and NhaA. Different unfolding
pathways were detected by classifying peak patterns. Deviant spectra, e.g. those
with no attachment or erratic peaks, can be easily identified. The software is
based on the programming language C++, the GNU Scientific Library (GSL), the software
WaveMetrics IGOR Pro and available open-source at http://bioinformatics.org/fskit/.
author:
- first_name: Michael
full_name: Kuhn, Michael
last_name: Kuhn
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Maurice
full_name: Hubain, Maurice
last_name: Hubain
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Kuhn M, Janovjak HL, Hubain M, Mueller D. Automated alignment and pattern recognition
of single-molecule force spectroscopy data. Journal of Microscopy. 2005;218(2):125-132.
doi:10.1111/j.1365-2818.2005.01478.x
apa: Kuhn, M., Janovjak, H. L., Hubain, M., & Mueller, D. (2005). Automated
alignment and pattern recognition of single-molecule force spectroscopy data.
Journal of Microscopy. Wiley-Blackwell. https://doi.org/10.1111/j.1365-2818.2005.01478.x
chicago: Kuhn, Michael, Harald L Janovjak, Maurice Hubain, and Daniel Mueller. “Automated
Alignment and Pattern Recognition of Single-Molecule Force Spectroscopy Data.”
Journal of Microscopy. Wiley-Blackwell, 2005. https://doi.org/10.1111/j.1365-2818.2005.01478.x.
ieee: M. Kuhn, H. L. Janovjak, M. Hubain, and D. Mueller, “Automated alignment and
pattern recognition of single-molecule force spectroscopy data,” Journal of
Microscopy, vol. 218, no. 2. Wiley-Blackwell, pp. 125–132, 2005.
ista: Kuhn M, Janovjak HL, Hubain M, Mueller D. 2005. Automated alignment and pattern
recognition of single-molecule force spectroscopy data. Journal of Microscopy.
218(2), 125–132.
mla: Kuhn, Michael, et al. “Automated Alignment and Pattern Recognition of Single-Molecule
Force Spectroscopy Data.” Journal of Microscopy, vol. 218, no. 2, Wiley-Blackwell,
2005, pp. 125–32, doi:10.1111/j.1365-2818.2005.01478.x.
short: M. Kuhn, H.L. Janovjak, M. Hubain, D. Mueller, Journal of Microscopy 218
(2005) 125–132.
date_created: 2018-12-11T12:03:13Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T07:43:20Z
day: '01'
doi: 10.1111/j.1365-2818.2005.01478.x
extern: 1
intvolume: ' 218'
issue: '2'
month: '05'
page: 125 - 132
publication: Journal of Microscopy
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2984'
quality_controlled: 0
status: public
title: Automated alignment and pattern recognition of single-molecule force spectroscopy
data
type: journal_article
volume: 218
year: '2005'
...
---
_id: '3418'
abstract:
- lang: eng
text: Atomic force microscopy (AFM) allows the critical forces that unfold single
proteins and rupture individual receptor–ligand bonds to be measured. To derive
the shape of the energy landscape, the dynamic strength of the system is probed
at different force loading rates. This is usually achieved by varying the pulling
speed between a few nm/s and a few mgrm/s, although for a more complete investigation
of the kinetic properties higher speeds are desirable. Above 10 mgrm/s, the hydrodynamic
drag force acting on the AFM cantilever reaches the same order of magnitude as
the molecular forces. This has limited the maximum pulling speed in AFM single-molecule
force spectroscopy experiments. Here, we present an approach for considering these
hydrodynamic effects, thereby allowing a correct evaluation of AFM force measurements
recorded over an extended range of pulling speeds (and thus loading rates). To
support and illustrate our theoretical considerations, we experimentally evaluated
the mechanical unfolding of a multi-domain protein recorded at 30 mgrm/s pulling
speed.
author:
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Jens
full_name: Struckmeier, Jens
last_name: Struckmeier
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Janovjak HL, Struckmeier J, Mueller D. Hydrodynamic effects in fast AFM single
molecule force measurements. European Biophysics Journal. 2005;34(1):91-96.
doi:10.1007/s00249-004-0430-3
apa: Janovjak, H. L., Struckmeier, J., & Mueller, D. (2005). Hydrodynamic effects
in fast AFM single molecule force measurements. European Biophysics Journal.
Springer. https://doi.org/10.1007/s00249-004-0430-3
chicago: Janovjak, Harald L, Jens Struckmeier, and Daniel Mueller. “Hydrodynamic
Effects in Fast AFM Single Molecule Force Measurements.” European Biophysics
Journal. Springer, 2005. https://doi.org/10.1007/s00249-004-0430-3.
ieee: H. L. Janovjak, J. Struckmeier, and D. Mueller, “Hydrodynamic effects in fast
AFM single molecule force measurements,” European Biophysics Journal, vol.
34, no. 1. Springer, pp. 91–96, 2005.
ista: Janovjak HL, Struckmeier J, Mueller D. 2005. Hydrodynamic effects in fast
AFM single molecule force measurements. European Biophysics Journal. 34(1), 91–96.
mla: Janovjak, Harald L., et al. “Hydrodynamic Effects in Fast AFM Single Molecule
Force Measurements.” European Biophysics Journal, vol. 34, no. 1, Springer,
2005, pp. 91–96, doi:10.1007/s00249-004-0430-3.
short: H.L. Janovjak, J. Struckmeier, D. Mueller, European Biophysics Journal 34
(2005) 91–96.
date_created: 2018-12-11T12:03:14Z
date_published: 2005-02-01T00:00:00Z
date_updated: 2021-01-12T07:43:20Z
day: '01'
doi: 10.1007/s00249-004-0430-3
extern: 1
intvolume: ' 34'
issue: '1'
month: '02'
page: 91 - 96
publication: European Biophysics Journal
publication_status: published
publisher: Springer
publist_id: '2983'
quality_controlled: 0
status: public
title: Hydrodynamic effects in fast AFM single molecule force measurements
type: journal_article
volume: 34
year: '2005'
...
---
_id: '3426'
abstract:
- lang: eng
text: We discuss the formation of graded morphogen profiles in a cell layer by nonlinear
transport phenomena, important for patterning developing organisms. We focus on
a process termed transcytosis, where morphogen transport results from the binding
of ligands to receptors on the cell surface, incorporation into the cell, and
subsequent externalization. Starting from a microscopic model, we derive effective
transport equations. We show that, in contrast to morphogen transport by extracellular
diffusion, transcytosis leads to robust ligand profiles which are insensitive
to the rate of ligand production.
article_processing_charge: No
arxiv: 1
author:
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Karsten
full_name: Kruse, Karsten
last_name: Kruse
- first_name: Periklis
full_name: Pantazis, Periklis
last_name: Pantazis
- first_name: Marcos
full_name: González Gaitán, Marcos
last_name: González Gaitán
- first_name: Frank
full_name: Jülicher, Frank
last_name: Jülicher
citation:
ama: Bollenbach MT, Kruse K, Pantazis P, González Gaitán M, Jülicher F. Robust formation
of morphogen gradients. Physical Review Letters. 2005;94(1). doi:10.1103/PhysRevLett.94.018103
apa: Bollenbach, M. T., Kruse, K., Pantazis, P., González Gaitán, M., & Jülicher,
F. (2005). Robust formation of morphogen gradients. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.94.018103
chicago: Bollenbach, Mark Tobias, Karsten Kruse, Periklis Pantazis, Marcos González
Gaitán, and Frank Jülicher. “Robust Formation of Morphogen Gradients.” Physical
Review Letters. American Physical Society, 2005. https://doi.org/10.1103/PhysRevLett.94.018103.
ieee: M. T. Bollenbach, K. Kruse, P. Pantazis, M. González Gaitán, and F. Jülicher,
“Robust formation of morphogen gradients,” Physical Review Letters, vol.
94, no. 1. American Physical Society, 2005.
ista: Bollenbach MT, Kruse K, Pantazis P, González Gaitán M, Jülicher F. 2005. Robust
formation of morphogen gradients. Physical Review Letters. 94(1).
mla: Bollenbach, Mark Tobias, et al. “Robust Formation of Morphogen Gradients.”
Physical Review Letters, vol. 94, no. 1, American Physical Society, 2005,
doi:10.1103/PhysRevLett.94.018103.
short: M.T. Bollenbach, K. Kruse, P. Pantazis, M. González Gaitán, F. Jülicher,
Physical Review Letters 94 (2005).
date_created: 2018-12-11T12:03:16Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T07:43:23Z
day: '01'
doi: 10.1103/PhysRevLett.94.018103
extern: '1'
external_id:
arxiv:
- q-bio/0412014
intvolume: ' 94'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/q-bio/0412014
month: '01'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '2975'
status: public
title: Robust formation of morphogen gradients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 94
year: '2005'
...
---
_id: '3433'
author:
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: 'Bollback JP. Posterior mapping and posterior predictive distributions. In:
Nielsen R, ed. Statistical Methods in Molecular Evolution. Springer; 2005:439-462.
doi:10.1007/0-387-27733-1'
apa: Bollback, J. P. (2005). Posterior mapping and posterior predictive distributions.
In R. Nielsen (Ed.), Statistical methods in Molecular Evolution (pp. 439–462).
Springer. https://doi.org/10.1007/0-387-27733-1
chicago: Bollback, Jonathan P. “Posterior Mapping and Posterior Predictive Distributions.”
In Statistical Methods in Molecular Evolution, edited by Rasmus Nielsen,
439–62. Springer, 2005. https://doi.org/10.1007/0-387-27733-1.
ieee: J. P. Bollback, “Posterior mapping and posterior predictive distributions,”
in Statistical methods in Molecular Evolution, R. Nielsen, Ed. Springer,
2005, pp. 439–462.
ista: 'Bollback JP. 2005.Posterior mapping and posterior predictive distributions.
In: Statistical methods in Molecular Evolution. , 439–462.'
mla: Bollback, Jonathan P. “Posterior Mapping and Posterior Predictive Distributions.”
Statistical Methods in Molecular Evolution, edited by Rasmus Nielsen, Springer,
2005, pp. 439–62, doi:10.1007/0-387-27733-1.
short: J.P. Bollback, in:, R. Nielsen (Ed.), Statistical Methods in Molecular Evolution,
Springer, 2005, pp. 439–462.
date_created: 2018-12-11T12:03:18Z
date_published: 2005-04-21T00:00:00Z
date_updated: 2021-01-12T07:43:26Z
day: '21'
doi: 10.1007/0-387-27733-1
editor:
- first_name: Rasmus
full_name: Nielsen, Rasmus
last_name: Nielsen
extern: 1
month: '04'
page: 439 - 462
publication: Statistical methods in Molecular Evolution
publication_status: published
publisher: Springer
publist_id: '2967'
quality_controlled: 0
status: public
title: Posterior mapping and posterior predictive distributions
type: book_chapter
year: '2005'
...
---
_id: '3443'
abstract:
- lang: eng
text: In the hippocampal CA1 area, a relatively homogenous population of pyramidal
cells is accompanied by a diversity of GABAergic interneurons. Previously, we
found that parvalbumin-expressing basket, axo-axonic, bistratified, and oriens-lacunosum
moleculare cells, innervating different domains of pyramidal cells, have distinct
firing patterns during network oscillations in vivo. A second family of interneurons,
expressing cholecystokinin but not parvalbumin, is known to target the same domains
of pyramidal cells as do the parvalbumin cells. To test the temporal activity
of these independent and parallel GABAergic inputs, we recorded the precise spike
timing of identified cholecystokinin interneurons during hippocampal network oscillations
in anesthetized rats and determined their molecular expression profiles and synaptic
targets. The cells were cannabinoid receptor type 1 immunopositive. Contrary to
the stereotyped firing of parvalbumin interneurons, cholecystokinin-expressing
basket and dendrite-innervating cells discharge, on average, with 1.7 ± 2.0 Hz
during high-frequency ripple oscillations in an episode-dependent manner. During
theta oscillations, cholecystokinin- expressing interneurons fire with 8.8 ± 3.3
Hz at a characteristic time on the ascending phase of theta waves (155 ± 81°),
when place cells start firing in freely moving animals. The firing patterns of
some interneurons recorded in drug-free behaving rats were similar to cholecystokinin
cells in anesthetized animals. Our results demonstrate that cholecystokinin- and
parvalbumin-expressing interneurons make different contributions to network oscillations
and play distinct roles in different brain states. We suggest that the specific
spike timing of cholecystokinin interneurons and their sensitivity to endocannabinoids
might contribute to differentiate subgroups of pyramidal cells forming neuronal
assemblies, whereas parvalbumin interneurons contribute to synchronizing the entire
network. Copyright © 2005 Society for Neuroscience.
author:
- first_name: Thomas
full_name: Klausberger,Thomas
last_name: Klausberger
- first_name: Laszlo
full_name: Marton,Laszlo F
last_name: Marton
- first_name: Joseph
full_name: Joseph O'Neill
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Jojanneke
full_name: Huck, Jojanneke H
last_name: Huck
- first_name: Yannis
full_name: Dalezios, Yannis
last_name: Dalezios
- first_name: Pablo
full_name: Fuentealba,Pablo
last_name: Fuentealba
- first_name: Wai
full_name: Suen, Wai Yee
last_name: Suen
- first_name: Edit
full_name: Papp, Edit Cs
last_name: Papp
- first_name: Takeshi
full_name: Kaneko, Takeshi
last_name: Kaneko
- first_name: Masahiko
full_name: Watanabe, Masahiko
last_name: Watanabe
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Péter
full_name: Somogyi, Péter
last_name: Somogyi
citation:
ama: Klausberger T, Marton L, O’Neill J, et al. Complementary roles of cholecystokinin-
and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations.
Journal of Neuroscience. 2005;25(42):9782-9793. doi:10.1523/JNEUROSCI.3269-05.2005
apa: Klausberger, T., Marton, L., O’Neill, J., Huck, J., Dalezios, Y., Fuentealba,
P., … Somogyi, P. (2005). Complementary roles of cholecystokinin- and parvalbumin-expressing
GABAergic neurons in hippocampal network oscillations. Journal of Neuroscience.
Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.3269-05.2005
chicago: Klausberger, Thomas, Laszlo Marton, Joseph O’Neill, Jojanneke Huck, Yannis
Dalezios, Pablo Fuentealba, Wai Suen, et al. “Complementary Roles of Cholecystokinin-
and Parvalbumin-Expressing GABAergic Neurons in Hippocampal Network Oscillations.”
Journal of Neuroscience. Society for Neuroscience, 2005. https://doi.org/10.1523/JNEUROSCI.3269-05.2005.
ieee: T. Klausberger et al., “Complementary roles of cholecystokinin- and
parvalbumin-expressing GABAergic neurons in hippocampal network oscillations,”
Journal of Neuroscience, vol. 25, no. 42. Society for Neuroscience, pp.
9782–9793, 2005.
ista: Klausberger T, Marton L, O’Neill J, Huck J, Dalezios Y, Fuentealba P, Suen
W, Papp E, Kaneko T, Watanabe M, Csicsvari JL, Somogyi P. 2005. Complementary
roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal
network oscillations. Journal of Neuroscience. 25(42), 9782–9793.
mla: Klausberger, Thomas, et al. “Complementary Roles of Cholecystokinin- and Parvalbumin-Expressing
GABAergic Neurons in Hippocampal Network Oscillations.” Journal of Neuroscience,
vol. 25, no. 42, Society for Neuroscience, 2005, pp. 9782–93, doi:10.1523/JNEUROSCI.3269-05.2005.
short: T. Klausberger, L. Marton, J. O’Neill, J. Huck, Y. Dalezios, P. Fuentealba,
W. Suen, E. Papp, T. Kaneko, M. Watanabe, J.L. Csicsvari, P. Somogyi, Journal
of Neuroscience 25 (2005) 9782–9793.
date_created: 2018-12-11T12:03:21Z
date_published: 2005-10-19T00:00:00Z
date_updated: 2021-01-12T07:43:30Z
day: '19'
doi: 10.1523/JNEUROSCI.3269-05.2005
extern: 1
intvolume: ' 25'
issue: '42'
month: '10'
page: 9782 - 9793
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '2944'
quality_controlled: 0
status: public
title: Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic
neurons in hippocampal network oscillations
type: journal_article
volume: 25
year: '2005'
...
---
_id: '3509'
abstract:
- lang: eng
text: Methods, apparatus and computer program products can generate light weight
but highly realistic and accurate colored models of three-dimensional colored
objects. The colored model may be generated from a second plurality of points
that define a coarse digital representation of the surface and at least one texture
map containing information derived from a first plurality of colored points that
define a fine digital representation of the surface. This derivation is achieved
by mapping points within the texture map to the fine digital representation of
the three-dimensional surface. Colored scan data may be used to construct the
fine digital representation as a triangulated surface (i.e., triangulation) using
a wrapping operation.
applicant:
- Raindrop Geomagic, Inc.
article_processing_charge: No
author:
- first_name: Steven
full_name: Williams, Steven
last_name: Williams
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Ping
full_name: Fu, Ping
last_name: Fu
citation:
ama: Williams S, Edelsbrunner H, Fu P. Methods, apparatus and computer program products
for modeling three-dimensional colored objects. 2005.
apa: Williams, S., Edelsbrunner, H., & Fu, P. (2005). Methods, apparatus and
computer program products for modeling three-dimensional colored objects.
chicago: Williams, Steven, Herbert Edelsbrunner, and Ping Fu. “Methods, Apparatus
and Computer Program Products for Modeling Three-Dimensional Colored Objects,”
2005.
ieee: S. Williams, H. Edelsbrunner, and P. Fu, “Methods, apparatus and computer
program products for modeling three-dimensional colored objects.” 2005.
ista: Williams S, Edelsbrunner H, Fu P. 2005. Methods, apparatus and computer program
products for modeling three-dimensional colored objects.
mla: Williams, Steven, et al. Methods, Apparatus and Computer Program Products
for Modeling Three-Dimensional Colored Objects. 2005.
short: S. Williams, H. Edelsbrunner, P. Fu, (2005).
date_created: 2018-12-11T12:03:42Z
date_published: 2005-02-08T00:00:00Z
date_updated: 2022-01-05T13:59:09Z
day: '08'
extern: '1'
ipc: G06T17/20 ; G06T15/04
ipn: US6853373B2
main_file_link:
- open_access: '1'
url: https://patents.google.com/patent/US6853373B2/
month: '02'
oa: 1
oa_version: Published Version
publication_date: 2005-02-08
publist_id: '2878'
status: public
title: Methods, apparatus and computer program products for modeling three-dimensional
colored objects
type: patent
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2005'
...
---
_id: '3557'
abstract:
- lang: eng
text: A challenging problem in computer-aided geometric design is the decomposition
of a surface into four-sided regions that are then represented by NURBS patches.
There are various approaches published in the literature and implemented as commercially
available software, but all fall short in either automation or quality of the
result. At Raindrop Geomagic, we have recently taken a fresh approach based on
concepts from Morse theory. This by itself is not a new idea, but we have some
novel ingredients that make this work, one being a rational notion of hierarchy
that guides the construction of a simplified decomposition sensitive to only the
major critical points.
author:
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Edelsbrunner H. Surface tiling with differential topology. In: ACM; 2005:9-11.
doi:http://dx.doi.org/10.2312/SGP/SGP05/009-011'
apa: 'Edelsbrunner, H. (2005). Surface tiling with differential topology (pp. 9–11).
Presented at the SGP: Eurographics Symposium on Geometry processing, ACM. http://dx.doi.org/10.2312/SGP/SGP05/009-011'
chicago: Edelsbrunner, Herbert. “Surface Tiling with Differential Topology,” 9–11.
ACM, 2005. http://dx.doi.org/10.2312/SGP/SGP05/009-011.
ieee: 'H. Edelsbrunner, “Surface tiling with differential topology,” presented at
the SGP: Eurographics Symposium on Geometry processing, 2005, pp. 9–11.'
ista: 'Edelsbrunner H. 2005. Surface tiling with differential topology. SGP: Eurographics
Symposium on Geometry processing, 9–11.'
mla: Edelsbrunner, Herbert. Surface Tiling with Differential Topology. ACM,
2005, pp. 9–11, doi:http://dx.doi.org/10.2312/SGP/SGP05/009-011.
short: H. Edelsbrunner, in:, ACM, 2005, pp. 9–11.
conference:
name: 'SGP: Eurographics Symposium on Geometry processing'
date_created: 2018-12-11T12:03:57Z
date_published: 2005-07-01T00:00:00Z
date_updated: 2021-01-12T07:44:17Z
day: '01'
doi: http://dx.doi.org/10.2312/SGP/SGP05/009-011
extern: 1
main_file_link:
- open_access: '0'
url: http://www.cs.duke.edu/~edels/Papers/2005-P-03-SurfaceTiling.pdf
month: '07'
page: 9 - 11
publication_status: published
publisher: ACM
publist_id: '2828'
quality_controlled: 0
status: public
title: Surface tiling with differential topology
type: conference
year: '2005'
...
---
_id: '3558'
abstract:
- lang: eng
text: The tandem algorithm combines the marching cube algorithm for surface extraction
and the edge contraction algorithm for surface simplification in lock-step to
avoid the costly intermediate step of storing the entire extracted surface triangulation.
Beyond this basic strategy, we introduce refinements to prevent artifacts in the
resulting triangulation, first, by carefully monitoring the amount of simplification
during the process and, second, by driving the simplification toward a compromise
between shape approximation and mesh quality. We have implemented the algorithm
and used extensive computational experiments to document the effects of various
design options and to further fine-tune the algorithm.
acknowledgement: 'Partially supported the generated triangulations. Two questions
arise: “how do by NSF grant CCR-00-86013 (BioGeometry).'
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: David
full_name: Cohen-Steiner, David
last_name: Cohen Steiner
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Attali D, Cohen Steiner D, Edelsbrunner H. Extraction and simplification of
iso-surfaces in tandem. In: ACM; 2005:139-148.'
apa: 'Attali, D., Cohen Steiner, D., & Edelsbrunner, H. (2005). Extraction and
simplification of iso-surfaces in tandem (pp. 139–148). Presented at the SGP:
Eurographics Symposium on Geometry processing, ACM.'
chicago: Attali, Dominique, David Cohen Steiner, and Herbert Edelsbrunner. “Extraction
and Simplification of Iso-Surfaces in Tandem,” 139–48. ACM, 2005.
ieee: 'D. Attali, D. Cohen Steiner, and H. Edelsbrunner, “Extraction and simplification
of iso-surfaces in tandem,” presented at the SGP: Eurographics Symposium on Geometry
processing, 2005, pp. 139–148.'
ista: 'Attali D, Cohen Steiner D, Edelsbrunner H. 2005. Extraction and simplification
of iso-surfaces in tandem. SGP: Eurographics Symposium on Geometry processing,
139–148.'
mla: Attali, Dominique, et al. Extraction and Simplification of Iso-Surfaces
in Tandem. ACM, 2005, pp. 139–48.
short: D. Attali, D. Cohen Steiner, H. Edelsbrunner, in:, ACM, 2005, pp. 139–148.
conference:
name: 'SGP: Eurographics Symposium on Geometry processing'
date_created: 2018-12-11T12:03:57Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T07:44:18Z
day: '01'
extern: 1
main_file_link:
- open_access: '0'
url: http://dl.acm.org/citation.cfm?id=1281943
month: '01'
page: 139 - 148
publication_status: published
publisher: ACM
publist_id: '2827'
quality_controlled: 0
status: public
title: Extraction and simplification of iso-surfaces in tandem
type: conference
year: '2005'
...
---
_id: '3576'
abstract:
- lang: eng
text: |-
ears of research in biology have established that all cellular functions are deeply connected to the shape and dynamics of their molec- ular actors. As a response, structural molecular biology has emerged as a new line of experimental research focused on revealing the structure of biomolecules. The analysis of these structures has led to the development of computational biology, whose aim is to predict from molecular simulation properties inaccessible to experimental probes.
Here we focus on the representation of biomolecules used in these sim- ulations, and in particular on the hard sphere models. We review how the geometry of the union of such spheres is used to model their interactions with their environment, and how it has been included in simulations of molecular dynamics.
In parallel, we review our own developments in mathematics and com- puter science on understanding the geometry of unions of balls, and their applications in molecular simulation.
alternative_title:
- Mathematical Sciences Research Institute Publications
author:
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Patrice
full_name: Koehl, Patrice
last_name: Koehl
citation:
ama: 'Edelsbrunner H, Koehl P. The geometry of biomolecular solvation. In: Combinatorial
and Computational Geometry. Vol 52. Cambridge University Press; 2005:243-275.'
apa: Edelsbrunner, H., & Koehl, P. (2005). The geometry of biomolecular solvation.
In Combinatorial and Computational Geometry (Vol. 52, pp. 243–275). Cambridge
University Press.
chicago: Edelsbrunner, Herbert, and Patrice Koehl. “The Geometry of Biomolecular
Solvation.” In Combinatorial and Computational Geometry, 52:243–75. Cambridge
University Press, 2005.
ieee: H. Edelsbrunner and P. Koehl, “The geometry of biomolecular solvation,” in
Combinatorial and Computational Geometry, vol. 52, Cambridge University
Press, 2005, pp. 243–275.
ista: 'Edelsbrunner H, Koehl P. 2005.The geometry of biomolecular solvation. In:
Combinatorial and Computational Geometry. Mathematical Sciences Research Institute
Publications, vol. 52, 243–275.'
mla: Edelsbrunner, Herbert, and Patrice Koehl. “The Geometry of Biomolecular Solvation.”
Combinatorial and Computational Geometry, vol. 52, Cambridge University
Press, 2005, pp. 243–75.
short: H. Edelsbrunner, P. Koehl, in:, Combinatorial and Computational Geometry,
Cambridge University Press, 2005, pp. 243–275.
date_created: 2018-12-11T12:04:03Z
date_published: 2005-08-08T00:00:00Z
date_updated: 2021-01-12T07:44:25Z
day: '08'
extern: 1
intvolume: ' 52'
main_file_link:
- open_access: '0'
url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.117.3732
month: '08'
page: 243 - 275
publication: Combinatorial and Computational Geometry
publication_status: published
publisher: Cambridge University Press
publist_id: '2809'
quality_controlled: 0
status: public
title: The geometry of biomolecular solvation
type: book_chapter
volume: 52
year: '2005'
...
---
_id: '3588'
article_processing_charge: No
author:
- first_name: Irinka
full_name: Castanon Ortega, Irinka
last_name: Castanon Ortega
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: 'Castanon Ortega I, Heisenberg C-PJ. Cell migration during zebrafish gastrulation.
In: Wedlich D, ed. Cell Migration in Development and Disease. Wiley-VCH;
2005:71-105. doi:10.1002/3527604669'
apa: Castanon Ortega, I., & Heisenberg, C.-P. J. (2005). Cell migration during
zebrafish gastrulation. In D. Wedlich (Ed.), Cell Migration in Development
and Disease (pp. 71–105). Wiley-VCH. https://doi.org/10.1002/3527604669
chicago: Castanon Ortega, Irinka, and Carl-Philipp J Heisenberg. “Cell Migration
during Zebrafish Gastrulation.” In Cell Migration in Development and Disease,
edited by Doris Wedlich, 71–105. Wiley-VCH, 2005. https://doi.org/10.1002/3527604669.
ieee: I. Castanon Ortega and C.-P. J. Heisenberg, “Cell migration during zebrafish
gastrulation,” in Cell Migration in Development and Disease, D. Wedlich,
Ed. Wiley-VCH, 2005, pp. 71–105.
ista: 'Castanon Ortega I, Heisenberg C-PJ. 2005.Cell migration during zebrafish
gastrulation. In: Cell Migration in Development and Disease. , 71–105.'
mla: Castanon Ortega, Irinka, and Carl-Philipp J. Heisenberg. “Cell Migration during
Zebrafish Gastrulation.” Cell Migration in Development and Disease, edited
by Doris Wedlich, Wiley-VCH, 2005, pp. 71–105, doi:10.1002/3527604669.
short: I. Castanon Ortega, C.-P.J. Heisenberg, in:, D. Wedlich (Ed.), Cell Migration
in Development and Disease, Wiley-VCH, 2005, pp. 71–105.
date_created: 2018-12-11T12:04:07Z
date_published: 2005-03-14T00:00:00Z
date_updated: 2021-01-12T07:44:29Z
day: '14'
doi: 10.1002/3527604669
editor:
- first_name: Doris
full_name: Wedlich, Doris
last_name: Wedlich
extern: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 71 - 105
publication: Cell Migration in Development and Disease
publication_status: published
publisher: Wiley-VCH
publist_id: '2795'
status: public
title: Cell migration during zebrafish gastrulation
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2005'
...
---
_id: '3589'
abstract:
- lang: eng
text: During zebrafish gastrulation, the interplay between patterning events and
morphogenesis creates an embryo out of a seemingly unstructured blastula stage
embryo, an embryo with distinct polarities along its anterior–posterior, dorsoventral
and left–right axes at the end of gastrulation.
article_processing_charge: No
author:
- first_name: Mathias
full_name: Köppen, Mathias
last_name: Köppen
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: 'Köppen M, Heisenberg C-PJ. Cleavage and gastrulation in zebrafish embryos.
In: Encyclopedia of Life Sciences. Wiley-Blackwell; 2005. doi:10.1038/npg.els.0001072'
apa: Köppen, M., & Heisenberg, C.-P. J. (2005). Cleavage and gastrulation in
zebrafish embryos. In Encyclopedia of Life Sciences. Wiley-Blackwell. https://doi.org/10.1038/npg.els.0001072
chicago: Köppen, Mathias, and Carl-Philipp J Heisenberg. “Cleavage and Gastrulation
in Zebrafish Embryos.” In Encyclopedia of Life Sciences. Wiley-Blackwell,
2005. https://doi.org/10.1038/npg.els.0001072.
ieee: M. Köppen and C.-P. J. Heisenberg, “Cleavage and gastrulation in zebrafish
embryos,” in Encyclopedia of Life Sciences, Wiley-Blackwell, 2005.
ista: 'Köppen M, Heisenberg C-PJ. 2005.Cleavage and gastrulation in zebrafish embryos.
In: Encyclopedia of Life Sciences. .'
mla: Köppen, Mathias, and Carl-Philipp J. Heisenberg. “Cleavage and Gastrulation
in Zebrafish Embryos.” Encyclopedia of Life Sciences, Wiley-Blackwell,
2005, doi:10.1038/npg.els.0001072.
short: M. Köppen, C.-P.J. Heisenberg, in:, Encyclopedia of Life Sciences, Wiley-Blackwell,
2005.
date_created: 2018-12-11T12:04:07Z
date_published: 2005-09-23T00:00:00Z
date_updated: 2021-01-12T07:44:30Z
day: '23'
doi: 10.1038/npg.els.0001072
extern: '1'
language:
- iso: eng
month: '09'
oa_version: None
publication: Encyclopedia of Life Sciences
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2794'
status: public
title: Cleavage and gastrulation in zebrafish embryos
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2005'
...
---
_id: '3590'
acknowledgement: 'BOOK REVIEWED - Gastrulation: From Cells to Embryo, Edited by Claudio
Stern. Published by Cold Spring Harbor Laboratory Press: 2004. '
article_processing_charge: No
author:
- first_name: Irinka
full_name: Castanon Ortega, Irinka
last_name: Castanon Ortega
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Castanon Ortega I, Heisenberg C-PJ. A stern view of gastrulation. Nature
Cell Biology. 2005;7(1):19-19. doi:10.1038/ncb0105-19
apa: Castanon Ortega, I., & Heisenberg, C.-P. J. (2005). A stern view of gastrulation.
Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb0105-19
chicago: Castanon Ortega, Irinka, and Carl-Philipp J Heisenberg. “A Stern View of
Gastrulation.” Nature Cell Biology. Nature Publishing Group, 2005. https://doi.org/10.1038/ncb0105-19.
ieee: I. Castanon Ortega and C.-P. J. Heisenberg, “A stern view of gastrulation,”
Nature Cell Biology, vol. 7, no. 1. Nature Publishing Group, pp. 19–19,
2005.
ista: Castanon Ortega I, Heisenberg C-PJ. 2005. A stern view of gastrulation. Nature
Cell Biology. 7(1), 19–19.
mla: Castanon Ortega, Irinka, and Carl-Philipp J. Heisenberg. “A Stern View of Gastrulation.”
Nature Cell Biology, vol. 7, no. 1, Nature Publishing Group, 2005, pp.
19–19, doi:10.1038/ncb0105-19.
short: I. Castanon Ortega, C.-P.J. Heisenberg, Nature Cell Biology 7 (2005) 19–19.
date_created: 2018-12-11T12:04:07Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2020-10-07T06:26:47Z
day: '01'
doi: 10.1038/ncb0105-19
extern: '1'
intvolume: ' 7'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 19 - 19
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '2793'
status: public
title: A stern view of gastrulation
type: review
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2005'
...
---
_id: '3611'
abstract:
- lang: eng
text: 'We present two novel methods to infer mating patterns from genetic data.
They differ from existing statistical methods of parentage inference in that they
apply to populations that deviate from Hardy–Weinberg and linkage equilibrium,
and so are suited for the study of assortative mating in hybrid zones. The core
data set consists of genotypes at several loci for a number of full-sib clutches
of unknown parentage. Our inference is based throughout on estimates of allelic
associations within and across loci, such as heterozygote deficit and pairwise
linkage disequilibrium. In the first method, the most likely parents of a given
clutch are determined from the genotypic distribution of the associated adult
population, given an explicit model of nonrandom mating. This leads to estimates
of the strength of assortment. The second approach is based solely on the offspring
genotypes and relies on the fact that a linear relation exists between associations
among the offspring and those in the population of breeding pairs. We apply both
methods to a sample from the hybrid zone between the fire-bellied toads Bombina
bombina and B. variegata (Anura: Disco glossidae) in Croatia. Consistently, both
approaches provide no evidence for a departure from random mating, despite adequate
statistical power. Instead, B. variegata-like individuals among the adults contributed
disproportionately to the offspring cohort, consistent with their preference for
the type of breeding habitat in which this study was conducted.'
author:
- first_name: Beate
full_name: Nürnberger, Beate
last_name: Nürnberger
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Loeske
full_name: Kruuk, Loeske E
last_name: Kruuk
- first_name: Timothy
full_name: Vines, Timothy H
last_name: Vines
citation:
ama: 'Nürnberger B, Barton NH, Kruuk L, Vines T. Mating patterns in a Bombina hybrid
zone: Inferences from adult and full sib genotypes. Heredity. 2005;94(2):247-257.
doi:10.1038/sj.hdy.6800607'
apa: 'Nürnberger, B., Barton, N. H., Kruuk, L., & Vines, T. (2005). Mating patterns
in a Bombina hybrid zone: Inferences from adult and full sib genotypes. Heredity.
Nature Publishing Group. https://doi.org/10.1038/sj.hdy.6800607'
chicago: 'Nürnberger, Beate, Nicholas H Barton, Loeske Kruuk, and Timothy Vines.
“Mating Patterns in a Bombina Hybrid Zone: Inferences from Adult and Full Sib
Genotypes.” Heredity. Nature Publishing Group, 2005. https://doi.org/10.1038/sj.hdy.6800607.'
ieee: 'B. Nürnberger, N. H. Barton, L. Kruuk, and T. Vines, “Mating patterns in
a Bombina hybrid zone: Inferences from adult and full sib genotypes,” Heredity,
vol. 94, no. 2. Nature Publishing Group, pp. 247–257, 2005.'
ista: 'Nürnberger B, Barton NH, Kruuk L, Vines T. 2005. Mating patterns in a Bombina
hybrid zone: Inferences from adult and full sib genotypes. Heredity. 94(2), 247–257.'
mla: 'Nürnberger, Beate, et al. “Mating Patterns in a Bombina Hybrid Zone: Inferences
from Adult and Full Sib Genotypes.” Heredity, vol. 94, no. 2, Nature Publishing
Group, 2005, pp. 247–57, doi:10.1038/sj.hdy.6800607.'
short: B. Nürnberger, N.H. Barton, L. Kruuk, T. Vines, Heredity 94 (2005) 247–257.
date_created: 2018-12-11T12:04:14Z
date_published: 2005-02-01T00:00:00Z
date_updated: 2021-01-12T07:44:39Z
day: '01'
doi: 10.1038/sj.hdy.6800607
extern: 1
intvolume: ' 94'
issue: '2'
month: '02'
page: 247 - 257
publication: Heredity
publication_status: published
publisher: Nature Publishing Group
publist_id: '2772'
quality_controlled: 0
status: public
title: 'Mating patterns in a Bombina hybrid zone: Inferences from adult and full sib
genotypes'
type: journal_article
volume: 94
year: '2005'
...
---
_id: '3612'
abstract:
- lang: eng
text: Left-right asymmetry in snails is intriguing because individuals of opposite
chirality are either unable to mate or can only mate with difficulty, so could
be reproductively isolated from each other. We have therefore investigated chiral
evolution in the Japanese land snail genus Euhadra to understand whether changes
in chirality have promoted speciation. In particular, we aimed to understand the
effect of the maternal inheritance of chirality on reproductive isolation and
gene flow. We found that the mitochondrial DNA phylogeny of Euhadra is consistent
with a single, relatively ancient evolution of sinistral species and suggests
either recent “single-gene speciation” or gene flow between chiral morphs that
are unable to mate. To clarify the conditions under which new chiral morphs might
evolve and whether single-gene speciation can occur, we developed a mathematical
model that is relevant to any maternal-effect gene. The model shows that reproductive
character displacement can promote the evolution of new chiral morphs, tending
to counteract the positive frequency-dependent selection that would otherwise
drive the more common chiral morph to fixation. This therefore suggests a general
mechanism as to how chiral variation arises in snails. In populations that contain
both chiral morphs, two different situations are then possible. In the first,
gene flow is substantial between morphs even without interchiral mating, because
of the maternal inheritance of chirality. In the second, reproductive isolation
is possible but unstable, and will also lead to gene flow if intrachiral matings
occasionally produce offspring with the opposite chirality. Together, the results
imply that speciation by chiral reversal is only meaningful in the context of
a complex biogeographical process, and so must usually involve other factors.
In order to understand the roles of reproductive character displacement and gene
flow in the chiral evolution of Euhadra, it will be necessary to investigate populations
in which both chiral morphs coexist.
author:
- first_name: Angus
full_name: Davison, Angus
last_name: Davison
- first_name: Satoshi
full_name: Chiba, Satoshi
last_name: Chiba
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Bernard
full_name: Clarke, Bernard
last_name: Clarke
citation:
ama: Davison A, Chiba S, Barton NH, Clarke B. Speciation and gene flow between snails
of opposing chirality. PLoS Biology. 2005;3(9). doi:10.1371/journal.pbio.0030282
apa: Davison, A., Chiba, S., Barton, N. H., & Clarke, B. (2005). Speciation
and gene flow between snails of opposing chirality. PLoS Biology. Public
Library of Science. https://doi.org/10.1371/journal.pbio.0030282
chicago: Davison, Angus, Satoshi Chiba, Nicholas H Barton, and Bernard Clarke. “Speciation
and Gene Flow between Snails of Opposing Chirality.” PLoS Biology. Public
Library of Science, 2005. https://doi.org/10.1371/journal.pbio.0030282.
ieee: A. Davison, S. Chiba, N. H. Barton, and B. Clarke, “Speciation and gene flow
between snails of opposing chirality,” PLoS Biology, vol. 3, no. 9. Public
Library of Science, 2005.
ista: Davison A, Chiba S, Barton NH, Clarke B. 2005. Speciation and gene flow between
snails of opposing chirality. PLoS Biology. 3(9).
mla: Davison, Angus, et al. “Speciation and Gene Flow between Snails of Opposing
Chirality.” PLoS Biology, vol. 3, no. 9, Public Library of Science, 2005,
doi:10.1371/journal.pbio.0030282.
short: A. Davison, S. Chiba, N.H. Barton, B. Clarke, PLoS Biology 3 (2005).
date_created: 2018-12-11T12:04:14Z
date_published: 2005-08-09T00:00:00Z
date_updated: 2021-01-12T07:44:39Z
day: '09'
doi: 10.1371/journal.pbio.0030282
extern: 1
intvolume: ' 3'
issue: '9'
license: https://creativecommons.org/licenses/by/4.0/
month: '08'
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '2771'
quality_controlled: 0
status: public
title: Speciation and gene flow between snails of opposing chirality
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 3
year: '2005'
...
---
_id: '3613'
abstract:
- lang: eng
text: 'The extent of genetic variation in fitness is a crucial issue in evolutionary
biology and yet remains largely unresolved. In Drosophila melanogaster, we have
devised a method that allows the net effects on fitness of heterozygous wild-type
chromosomes to be measured, by competing them against two different “balancer”
chromosomes. We have applied the method to a large sample of 40 wild-type third
chromosomes and have measured fitnesses of nonlethal chromosomes as well as chromosomes
bearing recessive lethals. The measurements were made in the environment to which
the population was adapted and did not involve inbreeding. The results show an
extraordinary similarity in the behavior of replicates of the same chromosome,
indicating consistent genetic effects on total fitness. Some invading chromosomes
increased rapidly and some slowly, and some rose to appreciable frequency after
several months, but then declined again: in every case, the same pattern was seen
in each replicate. We estimated relative fitnesses, rates of change of fitness,
and relative viabilities, for each chromosome. There were significant fluctuations
around the fitted model, which were also highly replicable. Wild-type chromosomes
varied substantially in their effects on heterozygous fitness, and these effects
vary through time, most likely as a result of genotype × environment interactions.'
author:
- first_name: Michael
full_name: Gardner, Michael P
last_name: Gardner
- first_name: Kevin
full_name: Fowler, Kevin
last_name: Fowler
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Linda
full_name: Patridge, Linda
last_name: Patridge
citation:
ama: 'Gardner M, Fowler K, Barton NH, Patridge L. Genetic variation for total fitness
in Drosophila melanogaster: Complex yet replicable patterns. Genetics.
2005;169(3):1553-1571. doi:10.1534/genetics.104.032367'
apa: 'Gardner, M., Fowler, K., Barton, N. H., & Patridge, L. (2005). Genetic
variation for total fitness in Drosophila melanogaster: Complex yet replicable
patterns. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.104.032367'
chicago: 'Gardner, Michael, Kevin Fowler, Nicholas H Barton, and Linda Patridge.
“Genetic Variation for Total Fitness in Drosophila Melanogaster: Complex yet Replicable
Patterns.” Genetics. Genetics Society of America, 2005. https://doi.org/10.1534/genetics.104.032367.'
ieee: 'M. Gardner, K. Fowler, N. H. Barton, and L. Patridge, “Genetic variation
for total fitness in Drosophila melanogaster: Complex yet replicable patterns,”
Genetics, vol. 169, no. 3. Genetics Society of America, pp. 1553–1571,
2005.'
ista: 'Gardner M, Fowler K, Barton NH, Patridge L. 2005. Genetic variation for total
fitness in Drosophila melanogaster: Complex yet replicable patterns. Genetics.
169(3), 1553–1571.'
mla: 'Gardner, Michael, et al. “Genetic Variation for Total Fitness in Drosophila
Melanogaster: Complex yet Replicable Patterns.” Genetics, vol. 169, no.
3, Genetics Society of America, 2005, pp. 1553–71, doi:10.1534/genetics.104.032367.'
short: M. Gardner, K. Fowler, N.H. Barton, L. Patridge, Genetics 169 (2005) 1553–1571.
date_created: 2018-12-11T12:04:15Z
date_published: 2005-03-01T00:00:00Z
date_updated: 2021-01-12T07:44:40Z
day: '01'
doi: 10.1534/genetics.104.032367
extern: 1
intvolume: ' 169'
issue: '3'
month: '03'
page: 1553 - 1571
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '2770'
quality_controlled: 0
status: public
title: 'Genetic variation for total fitness in Drosophila melanogaster: Complex yet
replicable patterns'
type: journal_article
volume: 169
year: '2005'
...
---
_id: '3684'
abstract:
- lang: eng
text: |-
Ever since text processors became popular, users have
dreamt of handling documents printed on paper as comfortably
as electronic ones, with full text search typically
appearing very close to the top of the wish list.
This paper presents the design of a prototype system that
takes a step into this direction. The user’s desktop is continuously
monitored and of each detected document a high
resolution snapshot is taken using a digital camera. The
resulting image is processed using specially designed dewarping
and OCR algorithms, making a digital and fully
searchable version of the document available to the user in
real-time. These steps are performed without any user interaction.
This enables the system to run as a background
task without disturbing the user in her work, while at the
same time offering electronic access to all paper documents
that have been present on the desktop during the uptime of
the system.
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Tim
full_name: Braun,Tim
last_name: Braun
- first_name: Adrian
full_name: Ulges, Adrian
last_name: Ulges
- first_name: Daniel
full_name: Keysers,Daniel
last_name: Keysers
- first_name: Thomas
full_name: Breuel,Thomas M
last_name: Breuel
citation:
ama: 'Lampert C, Braun T, Ulges A, Keysers D, Breuel T. Oblivious document capture
and real-time retrieval. In: CBDAR; 2005:79-86.'
apa: 'Lampert, C., Braun, T., Ulges, A., Keysers, D., & Breuel, T. (2005). Oblivious
document capture and real-time retrieval (pp. 79–86). Presented at the CBDAR:
Camera Based Document Analysis and Recognition , CBDAR.'
chicago: Lampert, Christoph, Tim Braun, Adrian Ulges, Daniel Keysers, and Thomas
Breuel. “Oblivious Document Capture and Real-Time Retrieval,” 79–86. CBDAR, 2005.
ieee: 'C. Lampert, T. Braun, A. Ulges, D. Keysers, and T. Breuel, “Oblivious document
capture and real-time retrieval,” presented at the CBDAR: Camera Based Document
Analysis and Recognition , 2005, pp. 79–86.'
ista: 'Lampert C, Braun T, Ulges A, Keysers D, Breuel T. 2005. Oblivious document
capture and real-time retrieval. CBDAR: Camera Based Document Analysis and Recognition
, 79–86.'
mla: Lampert, Christoph, et al. Oblivious Document Capture and Real-Time Retrieval.
CBDAR, 2005, pp. 79–86.
short: C. Lampert, T. Braun, A. Ulges, D. Keysers, T. Breuel, in:, CBDAR, 2005,
pp. 79–86.
conference:
name: 'CBDAR: Camera Based Document Analysis and Recognition '
date_created: 2018-12-11T12:04:36Z
date_published: 2005-08-29T00:00:00Z
date_updated: 2021-01-12T07:45:07Z
day: '29'
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/~chl/papers/lampert-cbdar2005.pdf
month: '08'
page: 79 - 86
publication_status: published
publisher: CBDAR
publist_id: '2693'
quality_controlled: 0
status: public
title: Oblivious document capture and real-time retrieval
type: conference
year: '2005'
...
---
_id: '3689'
abstract:
- lang: eng
text: Digital cameras have become almost ubiquitous and their use for fast and casual
capturing of natural images is unchallenged. For making images of documents, however,
they have not caught up to flatbed scanners yet, mainly because camera images
tend to suffer from distortion due to the perspective and are therefore limited
in their further use for archival or OCR. For images of non-planar paper surfaces
like books, page curl causes additional distortion, which poses an even greater
problem due to its nonlinearity. This paper presents a new algorithm for removing
both perspective and page curl distortion. It requires only a single camera image
as input and relies on a priori layout information instead of additional hardware.
Therefore, it is much more user friendly than most previous approaches, and allows
for flexible ad hoc document capture. Results are presented showing that the algorithm
produces visually pleasing output and increases OCR accuracy, thus having the
potential to become a general purpose preprocessing tool for camera based document
capture.
alternative_title:
- Document Analysis and Recognition
author:
- first_name: Adrian
full_name: Ulges, Adrian
last_name: Ulges
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Thomas
full_name: Breuel,Thomas M
last_name: Breuel
citation:
ama: 'Ulges A, Lampert C, Breuel T. Document image dewarping using robust estimation
of curled text lines. In: Vol 2. IEEE; 2005:1001-1005. doi: 10.1109/ICDAR.2005.90'
apa: 'Ulges, A., Lampert, C., & Breuel, T. (2005). Document image dewarping
using robust estimation of curled text lines (Vol. 2, pp. 1001–1005). Presented
at the ICDAR: International Conference on Document Analysis and Recognition, IEEE.
https://doi.org/ 10.1109/ICDAR.2005.90'
chicago: Ulges, Adrian, Christoph Lampert, and Thomas Breuel. “Document Image Dewarping
Using Robust Estimation of Curled Text Lines,” 2:1001–5. IEEE, 2005. https://doi.org/ 10.1109/ICDAR.2005.90.
ieee: 'A. Ulges, C. Lampert, and T. Breuel, “Document image dewarping using robust
estimation of curled text lines,” presented at the ICDAR: International Conference
on Document Analysis and Recognition, 2005, vol. 2, pp. 1001–1005.'
ista: 'Ulges A, Lampert C, Breuel T. 2005. Document image dewarping using robust
estimation of curled text lines. ICDAR: International Conference on Document Analysis
and Recognition, Document Analysis and Recognition, vol. 2, 1001–1005.'
mla: Ulges, Adrian, et al. Document Image Dewarping Using Robust Estimation of
Curled Text Lines. Vol. 2, IEEE, 2005, pp. 1001–05, doi: 10.1109/ICDAR.2005.90.
short: A. Ulges, C. Lampert, T. Breuel, in:, IEEE, 2005, pp. 1001–1005.
conference:
name: 'ICDAR: International Conference on Document Analysis and Recognition'
date_created: 2018-12-11T12:04:38Z
date_published: 2005-09-01T00:00:00Z
date_updated: 2021-01-12T07:48:58Z
day: '01'
doi: ' 10.1109/ICDAR.2005.90'
extern: 1
intvolume: ' 2'
main_file_link:
- open_access: '0'
url: http:/pub.ist.ac.at/~chl/papers/ulges-icdar2004.pdf
month: '09'
page: 1001 - 1005
publication_status: published
publisher: IEEE
publist_id: '2680'
quality_controlled: 0
status: public
title: Document image dewarping using robust estimation of curled text lines
type: conference
volume: 2
year: '2005'
...