---
_id: '12201'
abstract:
- lang: eng
text: The development of plant lateral organs is interesting because, although many
of the same genes seem to be involved in the early growth of primordia, completely
different gene combinations are required for the complete development of organs
such as leaves and stamens. Thus, the genes common to the development of most
organs, which generally form and polarize the primordial ‘envelope’, must at some
stage interact with those that ‘install’ the functional content of the organ –
in the case of the stamen, the four microsporangia. Although distinct genetic
pathways of organ initiation, polarity establishment and setting up the reproductive
cell line can readily be recognized, they do not occur sequentially. Rather, they
are activated early and run in parallel. There is evidence for continuing crosstalk
between these pathways.
acknowledgement: X.F. holds a Clarendon Scholarship from the University of Oxford.
We thank Angela Hay and Jill Harrison for helpful advice and discussion.
article_processing_charge: No
article_type: original
author:
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Hugh G.
full_name: Dickinson, Hugh G.
last_name: Dickinson
citation:
ama: Feng X, Dickinson HG. Packaging the male germline in plants. Trends in Genetics.
2007;23(10):503-510. doi:10.1016/j.tig.2007.08.005
apa: Feng, X., & Dickinson, H. G. (2007). Packaging the male germline in plants.
Trends in Genetics. Elsevier BV. https://doi.org/10.1016/j.tig.2007.08.005
chicago: Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.”
Trends in Genetics. Elsevier BV, 2007. https://doi.org/10.1016/j.tig.2007.08.005.
ieee: X. Feng and H. G. Dickinson, “Packaging the male germline in plants,” Trends
in Genetics, vol. 23, no. 10. Elsevier BV, pp. 503–510, 2007.
ista: Feng X, Dickinson HG. 2007. Packaging the male germline in plants. Trends
in Genetics. 23(10), 503–510.
mla: Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.”
Trends in Genetics, vol. 23, no. 10, Elsevier BV, 2007, pp. 503–10, doi:10.1016/j.tig.2007.08.005.
short: X. Feng, H.G. Dickinson, Trends in Genetics 23 (2007) 503–510.
date_created: 2023-01-16T09:22:44Z
date_published: 2007-10-01T00:00:00Z
date_updated: 2023-05-08T10:58:47Z
department:
- _id: XiFe
doi: 10.1016/j.tig.2007.08.005
extern: '1'
external_id:
pmid:
- '17825943'
intvolume: ' 23'
issue: '10'
keyword:
- Genetics
language:
- iso: eng
month: '10'
oa_version: None
page: 503-510
pmid: 1
publication: Trends in Genetics
publication_identifier:
issn:
- 0168-9525
publication_status: published
publisher: Elsevier BV
quality_controlled: '1'
scopus_import: '1'
status: public
title: Packaging the male germline in plants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2007'
...
---
_id: '128'
abstract:
- lang: eng
text: 'A 671 nm diode laser with a mode-hop-free tuning range of 40 GHz is described.
This long tuning range is achieved by simultaneously ramping the external cavity
length with the laser injection current. The laser output pointing remains fixed,
independent of its frequency because of the cover slip cavity design. This system
is simple, economical, robust, and easy to use for spectroscopy, as we demonstrate
with lithium vapor and lithium atom beam experiments. '
acknowledgement: "National Science Foundation\r\nThis work was supported with NSF
Grant No. PHY-0653623. We thank Dr. W. Bickel and Dr. J. Jones for diagnostic equipment,
K. Guerin for assistance with mechanical drawings, and M. Parker of Rincon Research
Inc. for optics components."
article_number: '106108'
arxiv: 1
author:
- first_name: Adra
full_name: Carr, Adra
last_name: Carr
- first_name: Yancey
full_name: Serchest, Yancey
last_name: Serchest
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: John
full_name: Perreault, John
last_name: Perreault
- first_name: Vincent
full_name: Lonij, Vincent
last_name: Lonij
- first_name: Alexander
full_name: Cronin, Alexander
last_name: Cronin
citation:
ama: Carr A, Serchest Y, Waitukaitis SR, Perreault J, Lonij V, Cronin A. Cover slip
external cavity diode laser. Review of Scientific Instruments. 2007;78(10).
doi:10.1063/1.2801006
apa: Carr, A., Serchest, Y., Waitukaitis, S. R., Perreault, J., Lonij, V., &
Cronin, A. (2007). Cover slip external cavity diode laser. Review of Scientific
Instruments. American Institute of Physics. https://doi.org/10.1063/1.2801006
chicago: Carr, Adra, Yancey Serchest, Scott R Waitukaitis, John Perreault, Vincent
Lonij, and Alexander Cronin. “Cover Slip External Cavity Diode Laser.” Review
of Scientific Instruments. American Institute of Physics, 2007. https://doi.org/10.1063/1.2801006.
ieee: A. Carr, Y. Serchest, S. R. Waitukaitis, J. Perreault, V. Lonij, and A. Cronin,
“Cover slip external cavity diode laser,” Review of Scientific Instruments,
vol. 78, no. 10. American Institute of Physics, 2007.
ista: Carr A, Serchest Y, Waitukaitis SR, Perreault J, Lonij V, Cronin A. 2007.
Cover slip external cavity diode laser. Review of Scientific Instruments. 78(10),
106108.
mla: Carr, Adra, et al. “Cover Slip External Cavity Diode Laser.” Review of Scientific
Instruments, vol. 78, no. 10, 106108, American Institute of Physics, 2007,
doi:10.1063/1.2801006.
short: A. Carr, Y. Serchest, S.R. Waitukaitis, J. Perreault, V. Lonij, A. Cronin,
Review of Scientific Instruments 78 (2007).
date_created: 2018-12-11T11:44:46Z
date_published: 2007-10-29T00:00:00Z
date_updated: 2021-01-12T06:49:35Z
day: '29'
doi: 10.1063/1.2801006
extern: '1'
external_id:
arxiv:
- '0708.0014'
intvolume: ' 78'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0708.0014
month: '10'
oa: 1
oa_version: Preprint
publication: Review of Scientific Instruments
publication_status: published
publisher: American Institute of Physics
publist_id: '7925'
quality_controlled: '1'
status: public
title: Cover slip external cavity diode laser
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 78
year: '2007'
...
---
_id: '1297'
abstract:
- lang: eng
text: In flies, the large tangential cells of the lobula plate represent an important
processing center for visual navigation based on optic flow. Although the visual
response properties of these cells have been well studied in blowflies, information
on their synaptic organization is mostly lacking. Here we study the distribution
of presynaptic release and postsynaptic inhibitory sites in the same set of cells
in Drosophila melanogaster. By making use of transgenic tools and immunohistochemistry,
our results suggest that HS and VS cells of Drosophila express γ-aminobutyric
acid (GABA) receptors in their dendritic region within the lobula plate, thus
being postsynaptic to inhibitory input there. At their axon terminals in the protocerebrum,
both cell types express synaptobrevin, suggesting the presence of presynaptic
specializations there. HS- and VS-cell terminals additionally show evidence for
postsynaptic GABAergic input, superimposed on this synaptic polarity. Our findings
are in line with the general circuit for visual motion detection and receptive
field properties as postulated from electrophysiological and optical recordings
in blowflies, suggesting a similar functional organization of lobula plate tangential
cells in the two species.
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: 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, Borst A, Reiff D. Synaptic organization of lobula plate
tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release
sites. Journal of Comparative Neurology. 2007;502(4):598-610. doi:10.1002/cne.21319'
apa: 'Raghu, S., Jösch, M. A., Borst, A., & Reiff, D. (2007). Synaptic organization
of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors
and chemical release sites. Journal of Comparative Neurology. Wiley-Blackwell.
https://doi.org/10.1002/cne.21319'
chicago: 'Raghu, Shamprasad, Maximilian A Jösch, Alexander Borst, and Dierk Reiff.
“Synaptic Organization of Lobula Plate Tangential Cells in Drosophila: γ-Aminobutyric
Acid Receptors and Chemical Release Sites.” Journal of Comparative Neurology.
Wiley-Blackwell, 2007. https://doi.org/10.1002/cne.21319.'
ieee: 'S. Raghu, M. A. Jösch, A. Borst, and D. Reiff, “Synaptic organization of
lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and
chemical release sites,” Journal of Comparative Neurology, vol. 502, no.
4. Wiley-Blackwell, pp. 598–610, 2007.'
ista: 'Raghu S, Jösch MA, Borst A, Reiff D. 2007. Synaptic organization of lobula
plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical
release sites. Journal of Comparative Neurology. 502(4), 598–610.'
mla: 'Raghu, Shamprasad, et al. “Synaptic Organization of Lobula Plate Tangential
Cells in Drosophila: γ-Aminobutyric Acid Receptors and Chemical Release Sites.”
Journal of Comparative Neurology, vol. 502, no. 4, Wiley-Blackwell, 2007,
pp. 598–610, doi:10.1002/cne.21319.'
short: S. Raghu, M.A. Jösch, A. Borst, D. Reiff, Journal of Comparative Neurology
502 (2007) 598–610.
date_created: 2018-12-11T11:51:13Z
date_published: 2007-06-01T00:00:00Z
date_updated: 2021-01-12T06:49:42Z
day: '01'
doi: 10.1002/cne.21319
extern: 1
intvolume: ' 502'
issue: '4'
month: '06'
page: 598 - 610
publication: Journal of Comparative Neurology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5974'
quality_controlled: 0
status: public
title: 'Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric
acid receptors and chemical release sites'
type: journal_article
volume: 502
year: '2007'
...
---
_id: '3411'
abstract:
- lang: eng
text: Mechanical single-molecule techniques offer exciting possibilities to investigate
protein folding and stability in native environments at submolecular resolution.
By applying a free-energy reconstruction procedure developed by Hummer and Szabo,
which is based on a statistical theorem introduced by Jarzynski, we determined
the unfolding free energy of the membrane proteins bacteriorhodopsin (BR), halorhodopsin,
and the sodium-proton antiporter NhaA. The calculated energies ranged from 290.5kcal/mol
for BR to 485.5kcal/mol for NhaA. For the remarkably stable BR, the equilibrium
unfolding free energy was independent of pulling rate and temperature ranging
between 18 and 42°C. Our experiments also revealed heterogeneous energetic properties
in individual transmembrane helices. In halorhodopsin, the stabilization of a
short helical segment yielded a characteristic signature in the energy profile.
In NhaA, a pronounced peak was observed at a functionally important site in the
protein. Since a large variety of single- and multispan membrane proteins can
be tackled in mechanical unfolding experiments, our approach provides a basis
for systematically elucidating energetic properties of membrane proteins with
the resolution of individual secondary-structure elements.
author:
- first_name: Johannes
full_name: Preiner, Johannes
last_name: Preiner
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Christian
full_name: Rankl, Christian
last_name: Rankl
- first_name: Helene
full_name: Knaus, Helene
last_name: Knaus
- first_name: David
full_name: Cisneros, David A
last_name: Cisneros
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: Ferry
full_name: Kienberger, Ferry
last_name: Kienberger
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
- first_name: Peter
full_name: Hinterdorfer, Peter
last_name: Hinterdorfer
citation:
ama: Preiner J, Janovjak HL, Rankl C, et al. Free energy of membrane protein unfolding
derived from single-molecule force measurements. Biophysical Journal. 2007;93(3):930-937.
doi:10.1529/biophysj.106.096982
apa: Preiner, J., Janovjak, H. L., Rankl, C., Knaus, H., Cisneros, D., Kedrov, A.,
… Hinterdorfer, P. (2007). Free energy of membrane protein unfolding derived from
single-molecule force measurements. Biophysical Journal. Biophysical Society.
https://doi.org/10.1529/biophysj.106.096982
chicago: Preiner, Johannes, Harald L Janovjak, Christian Rankl, Helene Knaus, David
Cisneros, Alexej Kedrov, Ferry Kienberger, Daniel Mueller, and Peter Hinterdorfer.
“Free Energy of Membrane Protein Unfolding Derived from Single-Molecule Force
Measurements.” Biophysical Journal. Biophysical Society, 2007. https://doi.org/10.1529/biophysj.106.096982.
ieee: J. Preiner et al., “Free energy of membrane protein unfolding derived
from single-molecule force measurements,” Biophysical Journal, vol. 93,
no. 3. Biophysical Society, pp. 930–937, 2007.
ista: Preiner J, Janovjak HL, Rankl C, Knaus H, Cisneros D, Kedrov A, Kienberger
F, Mueller D, Hinterdorfer P. 2007. Free energy of membrane protein unfolding
derived from single-molecule force measurements. Biophysical Journal. 93(3), 930–937.
mla: Preiner, Johannes, et al. “Free Energy of Membrane Protein Unfolding Derived
from Single-Molecule Force Measurements.” Biophysical Journal, vol. 93,
no. 3, Biophysical Society, 2007, pp. 930–37, doi:10.1529/biophysj.106.096982.
short: J. Preiner, H.L. Janovjak, C. Rankl, H. Knaus, D. Cisneros, A. Kedrov, F.
Kienberger, D. Mueller, P. Hinterdorfer, Biophysical Journal 93 (2007) 930–937.
date_created: 2018-12-11T12:03:11Z
date_published: 2007-08-01T00:00:00Z
date_updated: 2021-01-12T07:43:18Z
day: '01'
doi: 10.1529/biophysj.106.096982
extern: 1
intvolume: ' 93'
issue: '3'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1913163/
month: '08'
oa: 1
page: 930 - 937
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '2990'
quality_controlled: 0
status: public
title: Free energy of membrane protein unfolding derived from single-molecule force
measurements
type: journal_article
volume: 93
year: '2007'
...
---
_id: '3412'
abstract:
- lang: eng
text: |-
Molecular interactions are the basic language of biological processes.
They establish the forces interacting between the building blocks of
proteins and other macromolecules, thus determining their functional
roles. Because molecular interactions trigger virtually every
biological process, approaches to decipher their language are needed.
Single-molecule force spectroscopy (SMFS) has been used to detect
and characterize different types of molecular interactions that occur
between and within native membrane proteins. The first experiments
detected and localized molecular interactions that stabilized
membrane proteins, including how these interactions were established
during folding of α-helical secondary structure elements into
the native protein and how they changed with oligomerization, temperature,
and mutations. SMFS also enables investigators to detect
and locate molecular interactions established during ligand and inhibitor
binding. These exciting applications provide opportunities
for studying the molecular forces of life. Further developments will
elucidate the origins of molecular interactions encoded in their lifetimes,
interaction ranges, interplay, and dynamics characteristic of biological systems.
author:
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- 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: Kedrov A, Janovjak HL, Sapra T, Mueller D. Deciphering molecular interactions
of native membrane proteins by single-molecule force spectroscopy. Annual Review
of Biophysics. 2007;36:233-260. doi:10.1146/annurev.biophys.36.040306.132640
apa: Kedrov, A., Janovjak, H. L., Sapra, T., & Mueller, D. (2007). Deciphering
molecular interactions of native membrane proteins by single-molecule force spectroscopy.
Annual Review of Biophysics. Annual Reviews. https://doi.org/10.1146/annurev.biophys.36.040306.132640
chicago: Kedrov, Alexej, Harald L Janovjak, Tanuj Sapra, and Daniel Mueller. “Deciphering
Molecular Interactions of Native Membrane Proteins by Single-Molecule Force Spectroscopy.”
Annual Review of Biophysics. Annual Reviews, 2007. https://doi.org/10.1146/annurev.biophys.36.040306.132640.
ieee: A. Kedrov, H. L. Janovjak, T. Sapra, and D. Mueller, “Deciphering molecular
interactions of native membrane proteins by single-molecule force spectroscopy,”
Annual Review of Biophysics, vol. 36. Annual Reviews, pp. 233–260, 2007.
ista: Kedrov A, Janovjak HL, Sapra T, Mueller D. 2007. Deciphering molecular interactions
of native membrane proteins by single-molecule force spectroscopy. Annual Review
of Biophysics. 36, 233–260.
mla: Kedrov, Alexej, et al. “Deciphering Molecular Interactions of Native Membrane
Proteins by Single-Molecule Force Spectroscopy.” Annual Review of Biophysics,
vol. 36, Annual Reviews, 2007, pp. 233–60, doi:10.1146/annurev.biophys.36.040306.132640.
short: A. Kedrov, H.L. Janovjak, T. Sapra, D. Mueller, Annual Review of Biophysics
36 (2007) 233–260.
date_created: 2018-12-11T12:03:11Z
date_published: 2007-06-01T00:00:00Z
date_updated: 2019-04-26T07:22:27Z
day: '01'
doi: 10.1146/annurev.biophys.36.040306.132640
extern: 1
intvolume: ' 36'
month: '06'
page: 233 - 260
publication: Annual Review of Biophysics
publication_status: published
publisher: Annual Reviews
publist_id: '2989'
quality_controlled: 0
status: public
title: Deciphering molecular interactions of native membrane proteins by single-molecule
force spectroscopy
type: review
volume: 36
year: '2007'
...
---
_id: '3427'
abstract:
- lang: eng
text: "We present a general theoretical framework to discuss mechanisms of morphogen
transport and gradient formation in a cell layer. Trafficking events on the cellular
scale lead to transport on larger scales. We discuss in particular the case of
transcytosis where morphogens undergo repeated rounds of internalization into
cells and recycling. Based on a description on the cellular scale, we derive effective
nonlinear transport equations in one and two dimensions which are valid on larger
scales. We derive analytic expressions for the concentration dependence of the
effective diffusion coefficient and the effective degradation rate. We discuss
the effects of a directional bias on morphogen transport and those of the coupling
of the morphogen and receptor kinetics. Furthermore, we discuss general properties
of cellular transport processes such as the robustness of gradients and relate
our results to recent experiments on the morphogen Decapentaplegic (Dpp) that
acts in the wing disk of the fruit fly Drosophila.\r\n© 2007 The American Physical
Society"
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: Gonzalez Gaitan, Marcos
last_name: Gonzalez Gaitan
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
citation:
ama: Bollenbach MT, Kruse K, Pantazis P, Gonzalez Gaitan M, Julicher F. Morphogen
transport in epithelia. Physical Review E Statistical Nonlinear and Soft Matter
Physics. 2007;75(1). doi:10.1103/PhysRevE.75.011901
apa: Bollenbach, M. T., Kruse, K., Pantazis, P., Gonzalez Gaitan, M., & Julicher,
F. (2007). Morphogen transport in epithelia. Physical Review E Statistical
Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.75.011901
chicago: Bollenbach, Mark Tobias, Karsten Kruse, Periklis Pantazis, Marcos Gonzalez
Gaitan, and Frank Julicher. “Morphogen Transport in Epithelia.” Physical Review
E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics,
2007. https://doi.org/10.1103/PhysRevE.75.011901.
ieee: M. T. Bollenbach, K. Kruse, P. Pantazis, M. Gonzalez Gaitan, and F. Julicher,
“Morphogen transport in epithelia,” Physical Review E Statistical Nonlinear
and Soft Matter Physics, vol. 75, no. 1. American Institute of Physics, 2007.
ista: Bollenbach MT, Kruse K, Pantazis P, Gonzalez Gaitan M, Julicher F. 2007. Morphogen
transport in epithelia. Physical Review E Statistical Nonlinear and Soft Matter
Physics. 75(1).
mla: Bollenbach, Mark Tobias, et al. “Morphogen Transport in Epithelia.” Physical
Review E Statistical Nonlinear and Soft Matter Physics, vol. 75, no. 1, American
Institute of Physics, 2007, doi:10.1103/PhysRevE.75.011901.
short: M.T. Bollenbach, K. Kruse, P. Pantazis, M. Gonzalez Gaitan, F. Julicher,
Physical Review E Statistical Nonlinear and Soft Matter Physics 75 (2007).
date_created: 2018-12-11T12:03:16Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:43:24Z
day: '01'
doi: 10.1103/PhysRevE.75.011901
extern: '1'
external_id:
arxiv:
- q-bio/0609011v1
intvolume: ' 75'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/q-bio/0609011v1
month: '01'
oa: 1
oa_version: Preprint
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '2974'
status: public
title: Morphogen transport in epithelia
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 75
year: '2007'
...
---
_id: '3432'
abstract:
- lang: eng
text: Evolution has left its signature on the molecules and morphology of living
organisms. Ancestral reconstruction offers an excellent tool for understanding
the process of evolution using comparative information. Methods for ancestral
reconstruction have generally focused on reconstructing the ancestral states at
the internal nodes of a phylogeny. Often, we are not interested in particular
nodes of the phylogeny but the whole history of a character. This chapter focuses
on a Bayesian method for estimating these histories, or mutational paths, on phylogenies.
Mutational path methods differ most notably from other approaches in their ability
to estimate not only the ancestral states at the internal nodes of a phylogeny,
but also the order and timing of mutational changes across the phylogeny. The
chapter provides a concise introduction to the statistical tools needed for sampling
mutational paths on a phylogeny.
author:
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Paul
full_name: Gardner, Paul P
last_name: Gardner
- first_name: Rasmus
full_name: Nielsen, Rasmus
last_name: Nielsen
citation:
ama: 'Bollback JP, Gardner P, Nielsen R. Estimating the history of mutations on
a phylogeny. In: Liberles D, ed. Ancestral Sequence Reconstruction. Oxford
University Press; 2007:69-79. doi:10.1093/acprof:oso/9780199299188.003.0006'
apa: Bollback, J. P., Gardner, P., & Nielsen, R. (2007). Estimating the history
of mutations on a phylogeny. In D. Liberles (Ed.), Ancestral Sequence Reconstruction
(pp. 69–79). Oxford University Press. https://doi.org/10.1093/acprof:oso/9780199299188.003.0006
chicago: Bollback, Jonathan P, Paul Gardner, and Rasmus Nielsen. “Estimating the
History of Mutations on a Phylogeny.” In Ancestral Sequence Reconstruction,
edited by David Liberles, 69–79. Oxford University Press, 2007. https://doi.org/10.1093/acprof:oso/9780199299188.003.0006.
ieee: J. P. Bollback, P. Gardner, and R. Nielsen, “Estimating the history of mutations
on a phylogeny,” in Ancestral Sequence Reconstruction, D. Liberles, Ed.
Oxford University Press, 2007, pp. 69–79.
ista: 'Bollback JP, Gardner P, Nielsen R. 2007.Estimating the history of mutations
on a phylogeny. In: Ancestral Sequence Reconstruction. , 69–79.'
mla: Bollback, Jonathan P., et al. “Estimating the History of Mutations on a Phylogeny.”
Ancestral Sequence Reconstruction, edited by David Liberles, Oxford University
Press, 2007, pp. 69–79, doi:10.1093/acprof:oso/9780199299188.003.0006.
short: J.P. Bollback, P. Gardner, R. Nielsen, in:, D. Liberles (Ed.), Ancestral
Sequence Reconstruction, Oxford University Press, 2007, pp. 69–79.
date_created: 2018-12-11T12:03:18Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:43:26Z
day: '01'
doi: 10.1093/acprof:oso/9780199299188.003.0006
editor:
- first_name: David
full_name: Liberles, David A
last_name: Liberles
extern: 1
month: '01'
page: 69 - 79
publication: Ancestral Sequence Reconstruction
publication_status: published
publisher: Oxford University Press
publist_id: '2968'
quality_controlled: 0
status: public
title: Estimating the history of mutations on a phylogeny
type: book_chapter
year: '2007'
...
---
_id: '3436'
abstract:
- lang: eng
text: 'he potential for di? erences between genetic paternity and paternity inferred
from behavioral observation has long been recognized. These di? erences are associated
with the challenge for females of seeking both genetic and material bene? ts;
this challenge is less severe in species with polygynous, non-resource-based mating
systems (such as leks) than in those with resource-based systems. We pres- ent
the ? rst study of paternity patt erns in a non-resource-based species that does
not form true leks. We compared paternity inferred from observed mating behavior
to genetically assigned paternity in the Satin Bowerbird (Ptilonorhynchus violaceus)
using eight microsatellite markers. Mating behavior was observed and recorded
via automated video-cameras positioned at all bowers (29?34 bowers each year)
in the study site throughout each mating season. We obtained blood samples and
identi- ? ed mothers for 11 chicks in 9 nests. For all chicks, the most likely
genetic father had been observed to mate with the mother in the year the chick
was sampled. All most likely genetic fathers were assigned with high con? dence
and all were bower- holding males. These results demonstrate that genetic paternity
can be inferred from observed mating behavior with reasonable con? dence in Satin
Bowerbirds. Observed male mating-success is therefore a reliable predictor of
reproductive success, and this suggests that high skew in observed male mating-success
translates directly to high skew in reproductive success. '
author:
- first_name: Sheila
full_name: Reynolds, Sheila M
last_name: Reynolds
- first_name: Katie
full_name: Dryer, Katie
last_name: Dryer
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: J Albert
full_name: Uy, J Albert
last_name: Uy
- first_name: Gail
full_name: Patricelli, Gail L
last_name: Patricelli
- first_name: Timothy
full_name: Robson, Timothy
last_name: Robson
- first_name: Gerald
full_name: Borgia, Gerald
last_name: Borgia
- first_name: Michael
full_name: Braun, Michael J
last_name: Braun
citation:
ama: Reynolds S, Dryer K, Bollback JP, et al. Behavioral paternity predicts genetic
paternity in satin bowerbirds, a species with a non-resource-based mating system.
The Auk. 2007;124(3):857-867. doi:10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2
apa: Reynolds, S., Dryer, K., Bollback, J. P., Uy, J. A., Patricelli, G., Robson,
T., … Braun, M. (2007). Behavioral paternity predicts genetic paternity in satin
bowerbirds, a species with a non-resource-based mating system. The Auk.
University of California Press. https://doi.org/10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2
chicago: Reynolds, Sheila, Katie Dryer, Jonathan P Bollback, J Albert Uy, Gail Patricelli,
Timothy Robson, Gerald Borgia, and Michael Braun. “Behavioral Paternity Predicts
Genetic Paternity in Satin Bowerbirds, a Species with a Non-Resource-Based Mating
System.” The Auk. University of California Press, 2007. https://doi.org/10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2.
ieee: S. Reynolds et al., “Behavioral paternity predicts genetic paternity
in satin bowerbirds, a species with a non-resource-based mating system,” The
Auk, vol. 124, no. 3. University of California Press, pp. 857–867, 2007.
ista: Reynolds S, Dryer K, Bollback JP, Uy JA, Patricelli G, Robson T, Borgia G,
Braun M. 2007. Behavioral paternity predicts genetic paternity in satin bowerbirds,
a species with a non-resource-based mating system. The Auk. 124(3), 857–867.
mla: Reynolds, Sheila, et al. “Behavioral Paternity Predicts Genetic Paternity in
Satin Bowerbirds, a Species with a Non-Resource-Based Mating System.” The Auk,
vol. 124, no. 3, University of California Press, 2007, pp. 857–67, doi:10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2.
short: S. Reynolds, K. Dryer, J.P. Bollback, J.A. Uy, G. Patricelli, T. Robson,
G. Borgia, M. Braun, The Auk 124 (2007) 857–867.
date_created: 2018-12-11T12:03:19Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:43:27Z
day: '01'
doi: 10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2
extern: 1
intvolume: ' 124'
issue: '3'
month: '01'
page: 857 - 867
publication: The Auk
publication_status: published
publisher: University of California Press
publist_id: '2964'
quality_controlled: 0
status: public
title: Behavioral paternity predicts genetic paternity in satin bowerbirds, a species
with a non-resource-based mating system
type: journal_article
volume: 124
year: '2007'
...
---
_id: '3450'
author:
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: György
full_name: Buzsáki, György
last_name: Buzsáki
citation:
ama: Jonas PM, Buzsáki G. Neural inhibition. Scholarpedia. 2007;2. doi:10.4249/scholarpedia.3286
apa: Jonas, P. M., & Buzsáki, G. (2007). Neural inhibition. Scholarpedia.
Scholarpedia. https://doi.org/10.4249/scholarpedia.3286
chicago: Jonas, Peter M, and György Buzsáki. “Neural Inhibition.” Scholarpedia.
Scholarpedia, 2007. https://doi.org/10.4249/scholarpedia.3286.
ieee: P. M. Jonas and G. Buzsáki, “Neural inhibition,” Scholarpedia, vol.
2. Scholarpedia, 2007.
ista: Jonas PM, Buzsáki G. 2007. Neural inhibition. Scholarpedia. 2.
mla: Jonas, Peter M., and György Buzsáki. “Neural Inhibition.” Scholarpedia,
vol. 2, Scholarpedia, 2007, doi:10.4249/scholarpedia.3286.
short: P.M. Jonas, G. Buzsáki, Scholarpedia 2 (2007).
date_created: 2018-12-11T12:03:23Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:43:32Z
day: '01'
doi: 10.4249/scholarpedia.3286
extern: 1
intvolume: ' 2'
month: '01'
publication: Scholarpedia
publication_status: published
publisher: Scholarpedia
publist_id: '2937'
quality_controlled: 0
status: public
title: Neural inhibition
type: journal_article
volume: 2
year: '2007'
...
---
_id: '3523'
abstract:
- lang: eng
text: On the linear track, the recent firing sequences of CA1 place cells recur
during sharp wave/ripple patterns (SWRs) in a reverse temporal order [Foster &
Wilson (2006) Nature, 440, 680-683]. We have found similar reverse-order reactivation
during SWRs in open-field exploration where the firing sequence of cells varied
before each SWR. Both the onset times and the firing patterns of cells showed
a tendency for reversed sequences during SWRs. These effects were observed for
SWRs that occurred during exploration, but not for those during longer immobility
periods. Additionally, reverse reactivation was stronger when it was preceded
by higher speed (> 5 cm/s) run periods. The trend for reverse-order SWR reactivation
was not significantly different in familiar and novel environments, even though
SWR-associated firing rates of both pyramidal cells and interneurons were reduced
in novel environments as compared with familiar. During exploration-associated
SWRs (eSWR) place cells retain place-selective firing [O'Neill et al. (2006) Neuron,
49, 143-155]. Here, we have shown that each cell's firing onset was more delayed
and firing probability more reduced during eSWRs the further the rat was from
the middle of the cell's place field; that is, cells receiving less momentary
place-related excitatory drive fired later during SWR events. However, even controlling
for place field distance, the recent firing of cells was still significantly correlated
with SWR reactivation sequences. We therefore propose that both place-related
drive and the firing history of cells contribute to reverse reactivation during
eSWRs.
author:
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Joseph
full_name: Joseph O'Neill
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Kevin
full_name: Allen, Kevin
last_name: Allen
- first_name: Timothy
full_name: Senior,Timothy
last_name: Senior
citation:
ama: Csicsvari JL, O’Neill J, Allen K, Senior T. Place-selective firing contributes
to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in
open-field exploration. European Journal of Neuroscience. 2007;26(3):704-716.
doi:10.1111/j.1460-9568.2007.05684.x
apa: Csicsvari, J. L., O’Neill, J., Allen, K., & Senior, T. (2007). Place-selective
firing contributes to the reverse-order reactivation of CA1 pyramidal cells during
sharp waves in open-field exploration. European Journal of Neuroscience.
Wiley-Blackwell. https://doi.org/10.1111/j.1460-9568.2007.05684.x
chicago: Csicsvari, Jozsef L, Joseph O’Neill, Kevin Allen, and Timothy Senior. “Place-Selective
Firing Contributes to the Reverse-Order Reactivation of CA1 Pyramidal Cells during
Sharp Waves in Open-Field Exploration.” European Journal of Neuroscience.
Wiley-Blackwell, 2007. https://doi.org/10.1111/j.1460-9568.2007.05684.x.
ieee: J. L. Csicsvari, J. O’Neill, K. Allen, and T. Senior, “Place-selective firing
contributes to the reverse-order reactivation of CA1 pyramidal cells during sharp
waves in open-field exploration,” European Journal of Neuroscience, vol.
26, no. 3. Wiley-Blackwell, pp. 704–716, 2007.
ista: Csicsvari JL, O’Neill J, Allen K, Senior T. 2007. Place-selective firing contributes
to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in
open-field exploration. European Journal of Neuroscience. 26(3), 704–716.
mla: Csicsvari, Jozsef L., et al. “Place-Selective Firing Contributes to the Reverse-Order
Reactivation of CA1 Pyramidal Cells during Sharp Waves in Open-Field Exploration.”
European Journal of Neuroscience, vol. 26, no. 3, Wiley-Blackwell, 2007,
pp. 704–16, doi:10.1111/j.1460-9568.2007.05684.x.
short: J.L. Csicsvari, J. O’Neill, K. Allen, T. Senior, European Journal of Neuroscience
26 (2007) 704–716.
date_created: 2018-12-11T12:03:46Z
date_published: 2007-08-01T00:00:00Z
date_updated: 2021-01-12T07:44:03Z
day: '01'
doi: 10.1111/j.1460-9568.2007.05684.x
extern: 1
intvolume: ' 26'
issue: '3'
month: '08'
page: 704 - 716
publication: European Journal of Neuroscience
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2862'
quality_controlled: 0
status: public
title: Place-selective firing contributes to the reverse-order reactivation of CA1
pyramidal cells during sharp waves in open-field exploration
type: journal_article
volume: 26
year: '2007'
...
---
_id: '3561'
abstract:
- lang: eng
text: The main result of this paper is an extension of de Silva's Weak Delaunay
Theorem to smoothly embedded curves and surfaces in Euclidean space. Assuming
a sufficiently fine sampling, we prove that i + 1 points in the sample span an
i-simplex in the restricted Delaunay triangulation iff every subset of the i +
1 points has a weak witness.
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Yuriy
full_name: Mileyko, Yuriy
last_name: Mileyko
citation:
ama: 'Attali D, Edelsbrunner H, Mileyko Y. Weak witnesses for Delaunay triangulations
of submanifolds. In: ACM; 2007:143-150. doi:10.1145/1236246.1236267'
apa: 'Attali, D., Edelsbrunner, H., & Mileyko, Y. (2007). Weak witnesses for
Delaunay triangulations of submanifolds (pp. 143–150). Presented at the SPM: Symposium
on Solid and Physical Modeling, ACM. https://doi.org/10.1145/1236246.1236267'
chicago: Attali, Dominique, Herbert Edelsbrunner, and Yuriy Mileyko. “Weak Witnesses
for Delaunay Triangulations of Submanifolds,” 143–50. ACM, 2007. https://doi.org/10.1145/1236246.1236267.
ieee: 'D. Attali, H. Edelsbrunner, and Y. Mileyko, “Weak witnesses for Delaunay
triangulations of submanifolds,” presented at the SPM: Symposium on Solid and
Physical Modeling, 2007, pp. 143–150.'
ista: 'Attali D, Edelsbrunner H, Mileyko Y. 2007. Weak witnesses for Delaunay triangulations
of submanifolds. SPM: Symposium on Solid and Physical Modeling, 143–150.'
mla: Attali, Dominique, et al. Weak Witnesses for Delaunay Triangulations of
Submanifolds. ACM, 2007, pp. 143–50, doi:10.1145/1236246.1236267.
short: D. Attali, H. Edelsbrunner, Y. Mileyko, in:, ACM, 2007, pp. 143–150.
conference:
name: 'SPM: Symposium on Solid and Physical Modeling'
date_created: 2018-12-11T12:03:58Z
date_published: 2007-06-01T00:00:00Z
date_updated: 2021-01-12T07:44:19Z
day: '01'
doi: 10.1145/1236246.1236267
extern: 1
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-00201055
month: '06'
oa: 1
page: 143 - 150
publication_status: published
publisher: ACM
publist_id: '2824'
quality_controlled: 0
status: public
title: Weak witnesses for Delaunay triangulations of submanifolds
type: conference
year: '2007'
...
---
_id: '3601'
abstract:
- lang: eng
text: In this paper, the multiobjective optimal design of space-based reconfigurable
sensor networks with novel adaptive MEMS antennas is investigated by using multiobjective
evolutionary algorithms. The non-dominated sorting genetic algorithm II (NSGA-II)
is employed to obtain multi-criteria Pareto-optimal solutions, which allows system
designers to easily make a reasonable trade-off choice from the set of non-dominated
solutions according to their preferences and system requirements. As a case study,
a cluster-based satellite sensing network is simulated under multiple objectives.
Most importantly, this paper also presents the application of our newly designed
adaptive MEMS antennas together with the NSGA-II to the multiobjective optimal
design of space-based reconfigurable sensor networks.
author:
- first_name: Erfu
full_name: Yang, Erfu
last_name: Yang
- first_name: Nakul
full_name: Haridas, Nakul
last_name: Haridas
- first_name: Ahmed
full_name: El-Rayis, Ahmed O
last_name: El Rayis
- first_name: Ahmet
full_name: Erdogan, Ahmet T
last_name: Erdogan
- first_name: Tughrul
full_name: Arslan, Tughrul
last_name: Arslan
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Yang E, Haridas N, El Rayis A, Erdogan A, Arslan T, Barton NH. Multiobjective
optimal design of MEMS-based reconfigurable and evolvable sensor networks for
space applications. In: IEEE; 2007:27-34. doi:10.1109/AHS.2007.76'
apa: 'Yang, E., Haridas, N., El Rayis, A., Erdogan, A., Arslan, T., & Barton,
N. H. (2007). Multiobjective optimal design of MEMS-based reconfigurable and evolvable
sensor networks for space applications (pp. 27–34). Presented at the AHS: NASA/ESA
Conference on Adaptive Hardware and Systems, IEEE. https://doi.org/10.1109/AHS.2007.76'
chicago: Yang, Erfu, Nakul Haridas, Ahmed El Rayis, Ahmet Erdogan, Tughrul Arslan,
and Nicholas H Barton. “Multiobjective Optimal Design of MEMS-Based Reconfigurable
and Evolvable Sensor Networks for Space Applications,” 27–34. IEEE, 2007. https://doi.org/10.1109/AHS.2007.76.
ieee: 'E. Yang, N. Haridas, A. El Rayis, A. Erdogan, T. Arslan, and N. H. Barton,
“Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor
networks for space applications,” presented at the AHS: NASA/ESA Conference on
Adaptive Hardware and Systems, 2007, pp. 27–34.'
ista: 'Yang E, Haridas N, El Rayis A, Erdogan A, Arslan T, Barton NH. 2007. Multiobjective
optimal design of MEMS-based reconfigurable and evolvable sensor networks for
space applications. AHS: NASA/ESA Conference on Adaptive Hardware and Systems,
27–34.'
mla: Yang, Erfu, et al. Multiobjective Optimal Design of MEMS-Based Reconfigurable
and Evolvable Sensor Networks for Space Applications. IEEE, 2007, pp. 27–34,
doi:10.1109/AHS.2007.76.
short: E. Yang, N. Haridas, A. El Rayis, A. Erdogan, T. Arslan, N.H. Barton, in:,
IEEE, 2007, pp. 27–34.
conference:
name: 'AHS: NASA/ESA Conference on Adaptive Hardware and Systems'
date_created: 2018-12-11T12:04:11Z
date_published: 2007-08-20T00:00:00Z
date_updated: 2021-01-12T07:44:35Z
day: '20'
doi: 10.1109/AHS.2007.76
extern: 1
month: '08'
page: 27 - 34
publication_status: published
publisher: IEEE
publist_id: '2782'
quality_controlled: 0
status: public
title: Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor
networks for space applications
type: conference
year: '2007'
...
---
_id: '3674'
abstract:
- lang: eng
text: "Evolution permeates all of biology. But researchers in molecular and cellular
biology, genetics, developmental biology, microbiology, and neuroscience have
only recently begun to think seriously in terms of evolution. The chief reasons
for this shift are the growing list of organisms with sequenced genomes; the increasingly
sophisticated ways of interpreting those sequences; and the ever more powerful
experimental techniques (and wider range of model organisms) with which to ask
questions about evolution as well as mechanism.\r\n\r\nEvolution serves as a primary
text for undergraduate and graduate courses in evolution. It is also a text working
scientists can use to educate themselves on how evolution affects their fields.
It differs from currently available alternatives in containing more molecular
biology than is traditionally the case. But this is not at the expense of traditional
evolutionary theory. Indeed, a glance at the Table of Contents and the authors'
interests reveals the range of material covered in this book. The authors are
world-renowned in population genetics, bacterial genomics, paleontology, human
genetics, and developmental biology. The integration of molecular biology and
evolutionary biology reflects the current direction of much research among evolutionary
scientists."
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Derek
full_name: Briggs, Derek
last_name: Briggs
- first_name: Jonathan
full_name: Eisen, Jonathan
last_name: Eisen
- first_name: David
full_name: Goldstein, David
last_name: Goldstein
- first_name: Nipam
full_name: Patel, Nipam
last_name: Patel
citation:
ama: Barton NH, Briggs D, Eisen J, Goldstein D, Patel N. Evolution. Cold
Spring Harbor Laboratory Press; 2007.
apa: Barton, N. H., Briggs, D., Eisen, J., Goldstein, D., & Patel, N. (2007).
Evolution. Cold Spring Harbor Laboratory Press.
chicago: Barton, Nicholas H, Derek Briggs, Jonathan Eisen, David Goldstein, and
Nipam Patel. Evolution. Cold Spring Harbor Laboratory Press, 2007.
ieee: N. H. Barton, D. Briggs, J. Eisen, D. Goldstein, and N. Patel, Evolution.
Cold Spring Harbor Laboratory Press, 2007.
ista: Barton NH, Briggs D, Eisen J, Goldstein D, Patel N. 2007. Evolution, Cold
Spring Harbor Laboratory Press, XIV, 833p.
mla: Barton, Nicholas H., et al. Evolution. Cold Spring Harbor Laboratory
Press, 2007.
short: N.H. Barton, D. Briggs, J. Eisen, D. Goldstein, N. Patel, Evolution, Cold
Spring Harbor Laboratory Press, 2007.
date_created: 2018-12-11T12:04:33Z
date_published: 2007-06-30T00:00:00Z
date_updated: 2021-12-21T15:55:28Z
day: '30'
extern: '1'
language:
- iso: eng
month: '06'
oa_version: None
page: XIV, 833
publication_identifier:
isbn:
- 978-087969684-9
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '2709'
quality_controlled: '1'
related_material:
link:
- description: available via catalog IST BookList
relation: other
url: https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=3251&query_desc=au%2Cwrdl%3A%20nicholas%20barton
- relation: supplementary_material
url: http://www.evolution-textbook.org/
status: public
title: Evolution
type: book
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2007'
...
---
_id: '3681'
abstract:
- lang: eng
text: |-
The extraction of a parametric global motion from a motion field is a task with several applications in video processing. We present two probabilistic formulations of the problem and carry out optimization using the RAST algorithm, a geometric matching method novel to motion estimation in video. RAST uses an exhaustive and adaptive search of transformation space and thus gives – in contrast to local sampling optimization techniques used in the past – a globally optimal solution. Among other applications, our framework can thus be used as a source of ground truth for benchmarking motion estimation algorithms.
Our main contributions are: first, the novel combination of a state-of-the-art MAP criterion for dominant motion estimation with a search procedure that guarantees global optimality. Second, experimental results that illustrate the superior performance of our approach on synthetic flow fields as well as real-world video streams. Third, a significant speedup of the search achieved by extending the model with an additional smoothness prior.
alternative_title:
- LCNS
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: Daniel
full_name: Keysers,Daniel
last_name: Keysers
- first_name: Thomas
full_name: Breuel,Thomas M
last_name: Breuel
citation:
ama: 'Ulges A, Lampert C, Keysers D, Breuel T. Optimal dominant motion estimation
using adaptive search of transformation space. In: Vol 4713. Springer; 2007:204-213.
doi:10.1007/978-3-540-74936-3_21'
apa: 'Ulges, A., Lampert, C., Keysers, D., & Breuel, T. (2007). Optimal dominant
motion estimation using adaptive search of transformation space (Vol. 4713, pp.
204–213). Presented at the DAGM: German Association For Pattern Recognition, Springer.
https://doi.org/10.1007/978-3-540-74936-3_21'
chicago: Ulges, Adrian, Christoph Lampert, Daniel Keysers, and Thomas Breuel. “Optimal
Dominant Motion Estimation Using Adaptive Search of Transformation Space,” 4713:204–13.
Springer, 2007. https://doi.org/10.1007/978-3-540-74936-3_21.
ieee: 'A. Ulges, C. Lampert, D. Keysers, and T. Breuel, “Optimal dominant motion
estimation using adaptive search of transformation space,” presented at the DAGM:
German Association For Pattern Recognition, 2007, vol. 4713, pp. 204–213.'
ista: 'Ulges A, Lampert C, Keysers D, Breuel T. 2007. Optimal dominant motion estimation
using adaptive search of transformation space. DAGM: German Association For Pattern
Recognition, LCNS, vol. 4713, 204–213.'
mla: Ulges, Adrian, et al. Optimal Dominant Motion Estimation Using Adaptive
Search of Transformation Space. Vol. 4713, Springer, 2007, pp. 204–13, doi:10.1007/978-3-540-74936-3_21.
short: A. Ulges, C. Lampert, D. Keysers, T. Breuel, in:, Springer, 2007, pp. 204–213.
conference:
name: 'DAGM: German Association For Pattern Recognition'
date_created: 2018-12-11T12:04:35Z
date_published: 2007-11-09T00:00:00Z
date_updated: 2021-01-12T07:45:06Z
day: '09'
doi: 10.1007/978-3-540-74936-3_21
extern: 1
intvolume: ' 4713'
month: '11'
page: 204 - 213
publication_status: published
publisher: Springer
publist_id: '2695'
quality_controlled: 0
status: public
title: Optimal dominant motion estimation using adaptive search of transformation
space
type: conference
volume: 4713
year: '2007'
...
---
_id: '3687'
abstract:
- lang: eng
text: |-
Recent years have seen huge advances in object recognition from images. Recognition rates beyond 95% are the rule rather than the exception on many datasets. However, most state-of-the-art methods can only decide if an object is present or not. They are not able to provide information on the object location or extent within in the image.
We report on a simple yet powerful scheme that extends many existing recognition methods to also perform localization of object bounding boxes. This is achieved by maximizing the classification score over all possible subrectangles in the image. Despite the impression that this would be computationally intractable, we show that in many situations efficient algorithms exist which solve a generalized maximum subrectangle problem.
We show how our method is applicable to a variety object detection frameworks and demonstrate its performance by applying it to the popular bag of visual words model, achieving competitive results on the PASCAL VOC 2006 dataset.
author:
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
- first_name: Thomas
full_name: Hofmann,Thomas
last_name: Hofmann
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Blaschko M, Hofmann T, Lampert C. Efficient Subwindow Search for Object
Localization. Max-Planck-Institute for Biological Cybernetics; 2007.
apa: Blaschko, M., Hofmann, T., & Lampert, C. (2007). Efficient subwindow
search for object localization. Unknown. Max-Planck-Institute for Biological
Cybernetics.
chicago: Blaschko, Matthew, Thomas Hofmann, and Christoph Lampert. Efficient
Subwindow Search for Object Localization. Unknown. Max-Planck-Institute
for Biological Cybernetics, 2007.
ieee: M. Blaschko, T. Hofmann, and C. Lampert, Efficient subwindow search for
object localization, no. 164. Max-Planck-Institute for Biological Cybernetics,
2007.
ista: Blaschko M, Hofmann T, Lampert C. 2007. Efficient subwindow search for object
localization, Max-Planck-Institute for Biological Cybernetics,p.
mla: Blaschko, Matthew, et al. “Efficient Subwindow Search for Object Localization.”
Unknown, no. 164, Max-Planck-Institute for Biological Cybernetics, 2007.
short: M. Blaschko, T. Hofmann, C. Lampert, Efficient Subwindow Search for Object
Localization, Max-Planck-Institute for Biological Cybernetics, 2007.
date_created: 2018-12-11T12:04:37Z
date_published: 2007-08-01T00:00:00Z
date_updated: 2019-04-26T07:22:33Z
day: '01'
extern: 1
issue: '164'
main_file_link:
- open_access: '0'
url: http://www.kyb.tuebingen.mpg.de/fileadmin/user_upload/files/publications/TR-164_[0].pdf
month: '08'
publication: Unknown
publication_status: published
publisher: Max-Planck-Institute for Biological Cybernetics
publist_id: '2681'
quality_controlled: 0
status: public
title: Efficient subwindow search for object localization
type: report
year: '2007'
...
---
_id: '3701'
abstract:
- lang: eng
text: |-
The extraction of a parametric global motion from a motion field is a task with several applications in video processing. We present two probabilistic formulations of the problem and carry out optimization using the RAST algorithm, a geometric matching method novel to motion estimation in video. RAST uses an exhaustive and adaptive search of transformation space and thus gives – in contrast to local sampling optimization techniques used in the past – a globally optimal solution. Among other applications, our framework can thus be used as a source of ground truth for benchmarking motion estimation algorithms.
Our main contributions are: first, the novel combination of a state-of-the-art MAP criterion for dominant motion estimation with a search procedure that guarantees global optimality. Second, experimental results that illustrate the superior performance of our approach on synthetic flow fields as well as real-world video streams. Third, a significant speedup of the search achieved by extending the model with an additional smoothness prior.
alternative_title:
- LNCS
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: Daniel
full_name: Keysers,Daniel
last_name: Keysers
- first_name: Thomas
full_name: Breuel,Thomas M
last_name: Breuel
citation:
ama: 'Ulges A, Lampert C, Keysers D, Breuel T. Optimal dominant motion estimation
using adaptive search of transformation space. In: Vol 4713. Springer; 2007:204-213.
doi:10.1007/978-3-540-74936-3_21'
apa: 'Ulges, A., Lampert, C., Keysers, D., & Breuel, T. (2007). Optimal dominant
motion estimation using adaptive search of transformation space (Vol. 4713, pp.
204–213). Presented at the DAGM: German Association For Pattern Recognition, Springer.
https://doi.org/10.1007/978-3-540-74936-3_21'
chicago: Ulges, Adrian, Christoph Lampert, Daniel Keysers, and Thomas Breuel. “Optimal
Dominant Motion Estimation Using Adaptive Search of Transformation Space,” 4713:204–13.
Springer, 2007. https://doi.org/10.1007/978-3-540-74936-3_21.
ieee: 'A. Ulges, C. Lampert, D. Keysers, and T. Breuel, “Optimal dominant motion
estimation using adaptive search of transformation space,” presented at the DAGM:
German Association For Pattern Recognition, 2007, vol. 4713, pp. 204–213.'
ista: 'Ulges A, Lampert C, Keysers D, Breuel T. 2007. Optimal dominant motion estimation
using adaptive search of transformation space. DAGM: German Association For Pattern
Recognition, LNCS, vol. 4713, 204–213.'
mla: Ulges, Adrian, et al. Optimal Dominant Motion Estimation Using Adaptive
Search of Transformation Space. Vol. 4713, Springer, 2007, pp. 204–13, doi:10.1007/978-3-540-74936-3_21.
short: A. Ulges, C. Lampert, D. Keysers, T. Breuel, in:, Springer, 2007, pp. 204–213.
conference:
name: 'DAGM: German Association For Pattern Recognition'
date_created: 2018-12-11T12:04:42Z
date_published: 2007-11-09T00:00:00Z
date_updated: 2021-01-12T07:51:35Z
day: '09'
doi: 10.1007/978-3-540-74936-3_21
extern: 1
intvolume: ' 4713'
month: '11'
page: 204 - 213
publication_status: published
publisher: Springer
publist_id: '2656'
quality_controlled: 0
status: public
title: Optimal dominant motion estimation using adaptive search of transformation
space
type: conference
volume: 4713
year: '2007'
...
---
_id: '3723'
abstract:
- lang: eng
text: 'The folding and function of proteins is guided by their multidimensional
energy landscapes. Local corrugations on rugged energy surfaces determine the
dynamics of functionally related conformational changes and molecular flexibilities.
By varying the temperature during the force-induced unfolding of the membrane
protein bacteriorhodopsin, we directly determined the energy roughness of individual
transmembrane α-helices. All helices have rugged energy surfaces with an overall
roughness scale of 4−6 kBT, in line with the vital roles of transmembrane helices
as functional and structural building blocks. Interestingly, the mechanical unfolding
of misfolded membrane proteins in vivo is likely to occur on similarly energy
rugged surfaces, which may also provide an energetic framework for small vertical
motions of functionally relevant helices. Finally, our results also indicate that
transmembrane protein structures can have rough energy surfaces despite their
highly restricted conformational spaces in confining lipid bilayer environments. '
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: Helene
full_name: Knaus, Helene
last_name: Knaus
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Janovjak HL, Knaus H, Mueller D. Transmembrane helices have rough energy surfaces.
Journal of the American Chemical Society. 2007;129(2):246-247. doi:10.1021/ja065684a
apa: Janovjak, H. L., Knaus, H., & Mueller, D. (2007). Transmembrane helices
have rough energy surfaces. Journal of the American Chemical Society. ACS.
https://doi.org/10.1021/ja065684a
chicago: Janovjak, Harald L, Helene Knaus, and Daniel Mueller. “Transmembrane Helices
Have Rough Energy Surfaces.” Journal of the American Chemical Society.
ACS, 2007. https://doi.org/10.1021/ja065684a.
ieee: H. L. Janovjak, H. Knaus, and D. Mueller, “Transmembrane helices have rough
energy surfaces,” Journal of the American Chemical Society, vol. 129, no.
2. ACS, pp. 246–247, 2007.
ista: Janovjak HL, Knaus H, Mueller D. 2007. Transmembrane helices have rough energy
surfaces. Journal of the American Chemical Society. 129(2), 246–247.
mla: Janovjak, Harald L., et al. “Transmembrane Helices Have Rough Energy Surfaces.”
Journal of the American Chemical Society, vol. 129, no. 2, ACS, 2007, pp.
246–47, doi:10.1021/ja065684a.
short: H.L. Janovjak, H. Knaus, D. Mueller, Journal of the American Chemical Society
129 (2007) 246–247.
date_created: 2018-12-11T12:04:49Z
date_published: 2007-01-17T00:00:00Z
date_updated: 2021-01-12T07:51:44Z
day: '17'
doi: 10.1021/ja065684a
extern: 1
intvolume: ' 129'
issue: '2'
month: '01'
page: 246 - 247
publication: Journal of the American Chemical Society
publication_status: published
publisher: ACS
publist_id: '2507'
quality_controlled: 0
status: public
title: Transmembrane helices have rough energy surfaces
type: journal_article
volume: 129
year: '2007'
...
---
_id: '3727'
abstract:
- lang: eng
text: Since its invention in the 1990s single-molecule force spectroscopy has been
increasingly applied to study protein (un-)folding, cell adhesion, and ligand–receptor
interactions. In most force spectroscopy studies, the cantilever of an atomic
force microscope (AFM) is separated from a surface at a constant velocity, thus
applying an increasing force to folded bio-molecules or bio-molecular bonds. Recently,
Fernandez and co-workers introduced the so-called force-clamp technique. Single
proteins were subjected to a defined constant force allowing their life times
and life time distributions to be directly measured. Up to now, the force-clamping
was performed by analogue PID controllers, which require complex additional hardware
and might make it difficult to combine the force-feedback with other modes such
as constant velocity. These points may be limiting the applicability and versatility
of this technique. Here we present a simple, fast, and all-digital (software-based)
PID controller that yields response times of a few milliseconds in combination
with a commercial AFM. We demonstrate the performance of our feedback loop by
force-clamp unfolding of single Ig27 domains of titin and the membrane proteins
bacteriorhodopsin (BR) and the sodium/proton antiporter NhaA.
author:
- first_name: Christian
full_name: Bippes, Christian A
last_name: Bippes
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Bippes C, Janovjak HL, Kedrov A, Mueller D. Digital force-feedback for protein
unfolding experiments using atomic force microscopy. Nanotechnology. 2007;18(4).
doi:10.1088/0957-4484/18/4/044022
apa: Bippes, C., Janovjak, H. L., Kedrov, A., & Mueller, D. (2007). Digital
force-feedback for protein unfolding experiments using atomic force microscopy.
Nanotechnology. IOP Publishing Ltd. https://doi.org/10.1088/0957-4484/18/4/044022
chicago: Bippes, Christian, Harald L Janovjak, Alexej Kedrov, and Daniel Mueller.
“Digital Force-Feedback for Protein Unfolding Experiments Using Atomic Force Microscopy.”
Nanotechnology. IOP Publishing Ltd., 2007. https://doi.org/10.1088/0957-4484/18/4/044022.
ieee: C. Bippes, H. L. Janovjak, A. Kedrov, and D. Mueller, “Digital force-feedback
for protein unfolding experiments using atomic force microscopy,” Nanotechnology,
vol. 18, no. 4. IOP Publishing Ltd., 2007.
ista: Bippes C, Janovjak HL, Kedrov A, Mueller D. 2007. Digital force-feedback for
protein unfolding experiments using atomic force microscopy. Nanotechnology. 18(4).
mla: Bippes, Christian, et al. “Digital Force-Feedback for Protein Unfolding Experiments
Using Atomic Force Microscopy.” Nanotechnology, vol. 18, no. 4, IOP Publishing
Ltd., 2007, doi:10.1088/0957-4484/18/4/044022.
short: C. Bippes, H.L. Janovjak, A. Kedrov, D. Mueller, Nanotechnology 18 (2007).
date_created: 2018-12-11T12:04:50Z
date_published: 2007-01-31T00:00:00Z
date_updated: 2021-01-12T07:51:46Z
day: '31'
doi: 10.1088/0957-4484/18/4/044022
extern: 1
intvolume: ' 18'
issue: '4'
month: '01'
publication: Nanotechnology
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '2501'
quality_controlled: 0
status: public
title: Digital force-feedback for protein unfolding experiments using atomic force
microscopy
type: journal_article
volume: 18
year: '2007'
...
---
_id: '3731'
abstract:
- lang: eng
text: A cell's ability to regulate gene transcription depends in large part on the
energy with which transcription factors (TFs) bind their DNA regulatory sites.
Obtaining accurate models of this binding energy is therefore an important goal
for quantitative biology. In this article, we present a principled likelihood-based
approach for inferring physical models of TF-DNA binding energy from the data
produced by modern high-throughput binding assays. Central to our analysis is
the ability to assess the relative likelihood of different model parameters given
experimental observations. We take a unique approach to this problem and show
how to compute likelihood without any explicit assumptions about the noise that
inevitably corrupts such measurements. Sampling possible choices for model parameters
according to this likelihood function, we can then make probabilistic predictions
for the identities of binding sites and their physical binding energies. Applying
this procedure to previously published data on the Saccharomyces cerevisiae TF
Abf1p, we find models of TF binding whose parameters are determined with remarkable
precision. Evidence for the accuracy of these models is provided by an astonishing
level of phylogenetic conservation in the predicted energies of putative binding
sites. Results from in vivo and in vitro experiments also provide highly consistent
characterizations of Abf1p, a result that contrasts with a previous analysis of
the same data.
author:
- first_name: Justin
full_name: Kinney,Justin B
last_name: Kinney
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Curtis
full_name: Callan,Curtis G
last_name: Callan
citation:
ama: Kinney J, Tkačik G, Callan C. Precise physical models of protein-DNA interaction
from high-throughput data. PNAS. 2007;104(2):501-506. doi:10.1073/pnas.0609908104
apa: Kinney, J., Tkačik, G., & Callan, C. (2007). Precise physical models of
protein-DNA interaction from high-throughput data. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.0609908104
chicago: Kinney, Justin, Gašper Tkačik, and Curtis Callan. “Precise Physical Models
of Protein-DNA Interaction from High-Throughput Data.” PNAS. National Academy
of Sciences, 2007. https://doi.org/10.1073/pnas.0609908104.
ieee: J. Kinney, G. Tkačik, and C. Callan, “Precise physical models of protein-DNA
interaction from high-throughput data,” PNAS, vol. 104, no. 2. National
Academy of Sciences, pp. 501–506, 2007.
ista: Kinney J, Tkačik G, Callan C. 2007. Precise physical models of protein-DNA
interaction from high-throughput data. PNAS. 104(2), 501–506.
mla: Kinney, Justin, et al. “Precise Physical Models of Protein-DNA Interaction
from High-Throughput Data.” PNAS, vol. 104, no. 2, National Academy of
Sciences, 2007, pp. 501–06, doi:10.1073/pnas.0609908104.
short: J. Kinney, G. Tkačik, C. Callan, PNAS 104 (2007) 501–506.
date_created: 2018-12-11T12:04:51Z
date_published: 2007-01-09T00:00:00Z
date_updated: 2021-01-12T07:51:48Z
day: '09'
doi: 10.1073/pnas.0609908104
extern: 1
intvolume: ' 104'
issue: '2'
main_file_link:
- open_access: '0'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1766414
month: '01'
page: 501 - 506
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2495'
quality_controlled: 0
status: public
title: Precise physical models of protein-DNA interaction from high-throughput data
type: journal_article
volume: 104
year: '2007'
...
---
_id: '3742'
abstract:
- lang: eng
text: 'Recent work has shown that probabilistic models based on pairwise interactions-in
the simplest case, the Ising model-provide surprisingly accurate descriptions
of experiments on real biological networks ranging from neurons to genes. Finding
these models requires us to solve an inverse problem: given experimentally measured
expectation values, what are the parameters of the underlying Hamiltonian? This
problem sits at the intersection of statistical physics and machine learning,
and we suggest that more efficient solutions are possible by merging ideas from
the two fields. We use a combination of recent coordinate descent algorithms with
an adaptation of the histogram Monte Carlo method, and implement these techniques
to take advantage of the sparseness found in data on real neurons. The resulting
algorithm learns the parameters of an Ising model describing a network of forty
neurons within a few minutes. This opens the possibility of analyzing much larger
data sets now emerging, and thus testing hypotheses about the collective behaviors
of these networks.'
author:
- first_name: Tamara
full_name: Broderick,Tamara
last_name: Broderick
- first_name: Miroslav
full_name: Dudik,Miroslav
last_name: Dudik
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Robert
full_name: Schapire,Robert E
last_name: Schapire
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Broderick T, Dudik M, Tkačik G, Schapire R, Bialek W. Faster solutions of the
inverse pairwise Ising problem. ArXiv. 2007;q-QM.
apa: Broderick, T., Dudik, M., Tkačik, G., Schapire, R., & Bialek, W. (2007).
Faster solutions of the inverse pairwise Ising problem. ArXiv. ArXiv.
chicago: Broderick, Tamara, Miroslav Dudik, Gašper Tkačik, Robert Schapire, and
William Bialek. “Faster Solutions of the Inverse Pairwise Ising Problem.” ArXiv.
ArXiv, 2007.
ieee: T. Broderick, M. Dudik, G. Tkačik, R. Schapire, and W. Bialek, “Faster solutions
of the inverse pairwise Ising problem,” ArXiv, vol. q-QM. ArXiv, 2007.
ista: Broderick T, Dudik M, Tkačik G, Schapire R, Bialek W. 2007. Faster solutions
of the inverse pairwise Ising problem. ArXiv, q-QM, .
mla: Broderick, Tamara, et al. “Faster Solutions of the Inverse Pairwise Ising Problem.”
ArXiv, vol. q-QM, ArXiv, 2007.
short: T. Broderick, M. Dudik, G. Tkačik, R. Schapire, W. Bialek, ArXiv q-QM (2007).
date_created: 2018-12-11T12:04:55Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:51:52Z
day: '01'
extern: 1
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0712.2437v2
month: '01'
oa: 1
publication: ArXiv
publication_status: published
publisher: ArXiv
publist_id: '2486'
quality_controlled: 0
status: public
title: Faster solutions of the inverse pairwise Ising problem
type: preprint
volume: q-bio.QM
year: '2007'
...